The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
A thymus-dependent nonapeptide found in normal blood. Stimulates the formation of E rosettes and is believed to be involved in T-cell differentiation.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Negative test results in subjects who possess the attribute for which the test is conducted. The labeling of diseased persons as healthy when screening in the detection of disease. (Last, A Dictionary of Epidemiology, 2d ed)
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
A cell line derived from cultured tumor cells.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.
Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Histochemical localization of immunoreactive substances using labeled antibodies as reagents.
Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Established cell cultures that have the potential to propagate indefinitely.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
All of the processes involved in increasing CELL NUMBER including CELL DIVISION.
Research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
RNA present in neoplastic tissue.
The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements.
Tumors or cancer of the human BREAST.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Databases devoted to knowledge about specific genes and gene products.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
The study of existing genetic knowledge, and the generation of new genetic data, to understand and thus avoid DRUG TOXICITY and adverse effects from toxic substances from the environment.
Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Elements of limited time intervals, contributing to particular results or situations.
The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.
An optical source that emits photons in a coherent beam. Light Amplification by Stimulated Emission of Radiation (LASER) is brought about using devices that transform light of varying frequencies into a single intense, nearly nondivergent beam of monochromatic radiation. Lasers operate in the infrared, visible, ultraviolet, or X-ray regions of the spectrum.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
The functional hereditary units of PLANTS.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Techniques using a laser to cut away and harvest a specific cell or cluster of cells from a tissue section while viewing it under the microscope.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
Cell changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm, and other attributes conferring the ability to invade, metastasize, and kill.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips.
Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation.
Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc.
A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
A malignancy of mature PLASMA CELLS engaging in monoclonal immunoglobulin production. It is characterized by hyperglobulinemia, excess Bence-Jones proteins (free monoclonal IMMUNOGLOBULIN LIGHT CHAINS) in the urine, skeletal destruction, bone pain, and fractures. Other features include ANEMIA; HYPERCALCEMIA; and RENAL INSUFFICIENCY.
The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.
Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Sequential operating programs and data which instruct the functioning of a digital computer.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The protein complement of an organism coded for by its genome.
The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Intracellular signaling protein kinases that play a signaling role in the regulation of cellular energy metabolism. Their activity largely depends upon the concentration of cellular AMP which is increased under conditions of low energy or metabolic stress. AMP-activated protein kinases modify enzymes involved in LIPID METABOLISM, which in turn provide substrates needed to convert AMP into ATP.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
In screening and diagnostic tests, the probability that a person with a positive test is a true positive (i.e., has the disease), is referred to as the predictive value of a positive test; whereas, the predictive value of a negative test is the probability that the person with a negative test does not have the disease. Predictive value is related to the sensitivity and specificity of the test.
The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.
Any method used for determining the location of and relative distances between genes on a chromosome.
A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.
The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.
Removal and pathologic examination of specimens in the form of small pieces of tissue from the living body.
The worsening of a disease over time. This concept is most often used for chronic and incurable diseases where the stage of the disease is an important determinant of therapy and prognosis.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Tumors or cancer of the PROSTATE.
The seventh planet in order from the sun. It is one of the five outer planets of the solar system. It has five known natural satellites.
A basis of value established for the measure of quantity, weight, extent or quality, e.g. weight standards, standard solutions, methods, techniques, and procedures used in diagnosis and therapy.
Neoplasms associated with a proliferation of a single clone of PLASMA CELLS and characterized by the secretion of PARAPROTEINS.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Genes that determine the fate of a cell or CELLS in a region of the embryo during EMBRYONIC DEVELOPMENT.
Measurable biological parameters that serve for drug development, safety and dosing (DRUG MONITORING).
A malignant epithelial tumor with a glandular organization.
Substances that inhibit or prevent the proliferation of NEOPLASMS.
Wnt proteins are a large family of secreted glycoproteins that play essential roles in EMBRYONIC AND FETAL DEVELOPMENT, and tissue maintenance. They bind to FRIZZLED RECEPTORS and act as PARACRINE PROTEIN FACTORS to initiate a variety of SIGNAL TRANSDUCTION PATHWAYS. The canonical Wnt signaling pathway stabilizes the transcriptional coactivator BETA CATENIN.
A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
Mature LYMPHOCYTES and MONOCYTES transported by the blood to the body's extravascular space. They are morphologically distinguishable from mature granulocytic leukocytes by their large, non-lobed nuclei and lack of coarse, heavily stained cytoplasmic granules.
Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.
Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.
Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.
Ability of neoplasms to infiltrate and actively destroy surrounding tissue.
The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.
Tumors or cancer of the LUNG.
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
Genetic loci associated with a QUANTITATIVE TRAIT.
Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.
Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
Transport proteins that carry specific substances in the blood or across cell membranes.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
A suborder of FUNGI in the phylum MICROSPORIDIA, commonly lacking a pansporoblastic membrane. The sporoblast is usually dinucleate.
Physiological changes that occur in bodies after death.
Proteins found in any species of bacterium.
Resistance or diminished response of a neoplasm to an antineoplastic agent in humans, animals, or cell or tissue cultures.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A disturbance in the prooxidant-antioxidant balance in favor of the former, leading to potential damage. Indicators of oxidative stress include damaged DNA bases, protein oxidation products, and lipid peroxidation products (Sies, Oxidative Stress, 1991, pxv-xvi).
An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.
A group of heterogeneous lymphoid tumors generally expressing one or more B-cell antigens or representing malignant transformations of B-lymphocytes.
A mixture of solid hydrocarbons obtained from petroleum. It has a wide range of uses including as a stiffening agent in ointments, as a lubricant, and as a topical anti-inflammatory. It is also commonly used as an embedding material in histology.
A starch found in the tubers and roots of many plants. Since it is hydrolyzable to FRUCTOSE, it is classified as a fructosan. It has been used in physiologic investigation for determination of the rate of glomerular function.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.
The relationships of groups of organisms as reflected by their genetic makeup.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.
Tumors or cancer of the LIVER.
Morphological and physiological development of EMBRYOS.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
Thinly cut sections of frozen tissue specimens prepared with a cryostat or freezing microtome.
Neoplasms composed of cells from the deepest layer of the epidermis. The concept does not refer to neoplasms located in the stratum basale.
Methods for maintaining or growing CELLS in vitro.
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.
A primary malignant neoplasm of epithelial liver cells. It ranges from a well-differentiated tumor with EPITHELIAL CELLS indistinguishable from normal HEPATOCYTES to a poorly differentiated neoplasm. The cells may be uniform or markedly pleomorphic, or form GIANT CELLS. Several classification schemes have been suggested.
Specialized forms of antibody-producing B-LYMPHOCYTES. They synthesize and secrete immunoglobulin. They are found only in lymphoid organs and at sites of immune responses and normally do not circulate in the blood or lymph. (Rosen et al., Dictionary of Immunology, 1989, p169 & Abbas et al., Cellular and Molecular Immunology, 2d ed, p20)
A factor synthesized in a wide variety of tissues. It acts synergistically with TGF-alpha in inducing phenotypic transformation and can also act as a negative autocrine growth factor. TGF-beta has a potential role in embryonal development, cellular differentiation, hormone secretion, and immune function. TGF-beta is found mostly as homodimer forms of separate gene products TGF-beta1, TGF-beta2 or TGF-beta3. Heterodimers composed of TGF-beta1 and 2 (TGF-beta1.2) or of TGF-beta2 and 3 (TGF-beta2.3) have been isolated. The TGF-beta proteins are synthesized as precursor proteins.
The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM of a cell.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.

Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. (1/41147)

DNA or oligonucleotide arrays are widely used for large-scale expression measurements, using various implementations: macroarrays in which DNA is spotted onto nylon membranes of relatively large dimensions (with radioactive detection) on the one hand; microarrays on glass slides and oligonucleotide chips, both used with fluorescent probes, on the other hand. Nylon micro-arrays with colourimetric detection have also been described recently. The small physical dimensions of miniaturized systems allow small hybridization volumes (2-100 microl) and provide high probe concentrations, in contrast to macroarrays. We show, however, that actual sensitivity (defined as the amount of sample necessary for detection of a given mRNA species) is in fact similar for all these systems and that this is mostly due to the very different amounts of target material present on the respective arrays. We then demonstrate that the combination of nylon microarrays with(33)P-labelled radioactive probes provides 100-fold better sensitivity, making it possible to perform expression profiling experiments using submicrogram amounts of unamplified total RNA from small biological samples. This has important implications in basic and clinical research and makes this alternative approach particularly suitable for groups operating in an academic context.  (+info)

On-line monitoring of gene expression. (2/41147)

Gene expression in cultures of Escherichia coli has been determined in situ and on-line by the use of an electrochemical sensor. Intact bacteria were used to monitor the induction of the lacZ gene; the onset of stationary phase was also monitored, using a reporter gene fused to the RpoS-dependent promoter of the osmY gene. The technique described can in principle be used to determine the activity of any promoter, with a variety of reporter genes. This technology is non-intrusive, allows real-time monitoring of gene expression, and will be useful in the study of growth regulation and development.  (+info)

Computational methods for the identification of differential and coordinated gene expression. (3/41147)

With the first complete 'draft' of the human genome sequence expected for Spring 2000, the three basic challenges for today's bioinformatics are more than ever: (i) finding the genes; (ii) locating their coding regions; and (iii) predicting their functions. However, our capacity for interpreting vertebrate genomic and transcript (cDNA) sequences using experimental or computational means very much lags behind our raw sequencing power. If the performances of current programs in identifying internal coding exons are good, the precise 5'-->3' delineation of transcription units (and promoters) still requires additional experiments. Similarly, functional predictions made with reference to previously characterized homologues are leaving >50% of human genes unannotated or classified in uninformative categories ('kinase', 'ATP-binding', etc.). In the context of functional genomics, large-scale gene expression studies using massive cDNA tag sequencing, two-dimensional gel proteome analysis or microarray technologies are the only approaches providing genome-scale experimental information at a pace consistent with the progress of sequencing. Given the difficulty and cost of characterizing genes one by one, academic and industrial researchers are increasingly relying on those methods to prioritize their studies and choose their targets. The study of expression patterns can also provide some insight into the function, reveal regulatory pathways, indicate side effects of drugs or serve as a diagnostic tool. In this article, I review the theoretical and computational approaches used to: (i) identify genes differentially expressed (across cell types, developmental stages, pathological conditions, etc.); (ii) identify genes expressed in a coordinated manner across a set of conditions; and (iii) delineate clusters of genes sharing coherent expression features, eventually defining global biological pathways.  (+info)

Genome-wide expression profiling in Escherichia coli K-12. (4/41147)

We have established high resolution methods for global monitoring of gene expression in Escherichia coli. Hybridization of radiolabeled cDNA to spot blots on nylon membranes was compared to hybridization of fluorescently-labeled cDNA to glass microarrays for efficiency and reproducibility. A complete set of PCR primers was created for all 4290 annotated open reading frames (ORFs) from the complete genome sequence of E.coli K-12 (MG1655). Glass- and nylon-based arrays of PCR products were prepared and used to assess global changes in gene expression. Full-length coding sequences for array printing were generated by two-step PCR amplification. In this study we measured changes in RNA levels after exposure to heat shock and following treatment with isopropyl-beta-D-thiogalactopyranoside (IPTG). Both radioactive and fluorescence-based methods showed comparable results. Treatment with IPTG resulted in high level induction of the lacZYA and melAB operons. Following heat shock treatment 119 genes were shown to have significantly altered expression levels, including 35 previously uncharacterized ORFs and most genes of the heat shock stimulon. Analysis of spot intensities from hybridization to replicate arrays identified sets of genes with signals consistently above background suggesting that at least 25% of genes were expressed at detectable levels during growth in rich media.  (+info)

Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. (5/41147)

mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF(+) strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.  (+info)

NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae. (6/41147)

Analysis of global gene expression in Saccharomyces cerevisiae by the serial analysis of gene expression technique has permitted the identification of at least 302 previously unidentified transcripts from nonannotated open reading frames (NORFs). Transcription of one of these, NORF5/HUG1 (hydroxyurea and UV and gamma radiation induced), is induced by DNA damage, and this induction requires MEC1, a homolog of the ataxia telangiectasia mutated (ATM) gene. DNA damage-specific induction of HUG1, which is independent of the cell cycle stage, is due to the alleviation of repression by the Crt1p-Ssn6p-Tup1p complex. Overexpression of HUG1 is lethal in combination with a mec1 mutation in the presence of DNA damage or replication arrest, whereas a deletion of HUG1 rescues the lethality due to a mec1 null allele. HUG1 is the first example of a NORF with important biological functional properties and defines a novel component of the MEC1 checkpoint pathway.  (+info)

Microarray analysis of replicative senescence. (7/41147)

BACKGROUND: Limited replicative capacity is a defining characteristic of most normal human cells and culminates in senescence, an arrested state in which cells remain viable but display an altered pattern of gene and protein expression. To survey widely the alterations in gene expression, we have developed a DNA microarray analysis system that contains genes previously reported to be involved in aging, as well as those involved in many of the major biochemical signaling pathways. RESULTS: Senescence-associated gene expression was assessed in three cell types: dermal fibroblasts, retinal pigment epithelial cells, and vascular endothelial cells. Fibroblasts demonstrated a strong inflammatory-type response, but shared limited overlap in senescent gene expression patterns with the other two cell types. The characteristics of the senescence response were highly cell-type specific. A comparison of early- and late-passage cells stimulated with serum showed specific deficits in the early and mid G1 response of senescent cells. Several genes that are constitutively overexpressed in senescent fibroblasts are regulated during the cell cycle in early-passage cells, suggesting that senescent cells are locked in an activated state that mimics the early remodeling phase of wound repair. CONCLUSIONS: Replicative senescence triggers mRNA expression patterns that vary widely and cell lineage strongly influences these patterns. In fibroblasts, the senescent state mimics inflammatory wound repair processes and, as such, senescent cells may contribute to chronic wound pathologies.  (+info)

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. (8/41147)

DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290 E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated under this growth condition, consistent with known patterns of growth rate-dependent regulation and increased rate of protein synthesis in rapidly growing cells. The cells grown on minimal medium showed significantly elevated expression of many genes involved in biosynthesis of building blocks, most notably the amino acid biosynthetic pathways. Nearly half of the known RpoS-dependent genes were expressed at significantly higher levels in minimal medium than in rich medium, and rpoS expression was similarly elevated. The role of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark features of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protection of the cells from acid stress. A hypothesis invoking RpoS and UspA (universal stress protein, also significantly elevated in minimal glucose medium) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.  (+info)

Abstract Background Conventional differential gene expression analysis by methods such as students t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i.e., protein-protein interactions) for biological network inference. We propose a novel differentially weighted graphical LASSO (dwgLASSO) algorithm that builds group-specific networks and perform network-based differential gene expression analysis to select biomarker candidates by considering their topological differences between the groups. Results Through simulation, we showed that wgLASSO can achieve better performance in building biologically relevant networks than ...
Gene Expression Profiling Analysis of Bisphenol A-Induced Perturbation in Biological Processes in ER-Negative HEK293 Cells. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The heterogeneity of prostate cancers extends within clinical states and across states. At the extreme ends of the clinical spectrum are prognostically favorable localized tumors with a low biological potential for metastasis and tumors with a high propensity for early dissemination that are invariably lethal. These clinical phenotypes are related in part to the intrinsic biology of tumor cells and are reflected in the pattern of expression of specific genes. Using comprehensive gene expression analysis of tumor samples representing the nonmetastatic and metastatic phenotypes, we identified genes that were consistently and strongly differentially expressed and represent common and valid biological differences underlying clinical heterogeneity.. Few prior studies have used high-throughput gene expression analysis to study prostate cancer metastases. One reason is that well-preserved surgical tissue samples of metastatic prostate cancer are rare, which limits the availability of appropriate ...
Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n = 101) and/or poor quality control criteria (n = 10) (test set). With 10-marker classifiers, all training set samples as well as 97 of the 101 test
Osteoarthritis (OA) is characterized by alterations to subchondral bone as well as articular cartilage. Changes to bone in OA have also been identified at sites distal to the affected joint, which include increased bone volume fraction and reduced bone mineralization. Altered bone remodelling has been proposed to underlie these bone changes in OA. To investigate the molecular basis for these changes, we performed microarray gene expression profiling of bone obtained at autopsy from individuals with no evidence of joint disease (control) and from individuals undergoing joint replacement surgery for either degenerative hip OA, or fractured neck of femur (osteoporosis [OP]). The OP sample set was included because an inverse association, with respect to bone density, has been observed between OA and the low bone density disease OP. Compugen human 19K-oligo microarray slides were used to compare the gene expression profiles of OA, control and OP bone samples. Four sets of samples were analyzed, comprising 10
Since their first use nearly fifteen years ago [1], microarray gene expression profiling experiments have become a ubiquitous tool in the study of disease. The vast number of gene transcripts assayed by modern microarrays (105-106) has driven forward our understanding of biological processes tremendously, elucidating the genes and regulatory mechanisms that drive specific phenotypes. However, the high-dimensional data produced in these experiments--often comprising many more variables than samples and subject to noise--also presents analytical challenges.. The analysis of gene expression data can be broadly grouped into two categories: the identification of differentially expressed genes (or gene-sets) between two or more known conditions, and the unsupervised identification (clustering) of samples or genes that exhibit similar profiles across the data set. In the former case, each gene is tested individually for association with the phenotype of interest, adjusting at the end for the vast ...
A peripheral blood gene expression score is associated with plaque volume and phenotype by intravascular ultrasound with radiofrequency backscatter analysis: results from the ATLANTA study
TY - JOUR. T1 - Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma. T2 - A report from the International DLBCL Rituximab-CHOP Consortium Program Study. AU - Visco, C.. AU - Li, Y.. AU - Xu-Monette, Z. Y.. AU - Miranda, R. N.. AU - Green, T. M.. AU - Li, Y.. AU - Tzankov, A.. AU - Wen, W.. AU - Liu, W. M.. AU - Kahl, B. S.. AU - DAmore, E. S.G.. AU - Montes-Moreno, S.. AU - Dybkær, K.. AU - Chiu, A.. AU - Tam, W.. AU - Orazi, A.. AU - Zu, Y.. AU - Bhagat, G.. AU - Winter, J. N.. AU - Wang, H. Y.. AU - ONeill, S.. AU - Dunphy, C. H.. AU - Hsi, E. D.. AU - Zhao, X. F.. AU - Go, R. S.. AU - Choi, W. W.L.. AU - Zhou, F.. AU - Czader, M.. AU - Tong, J.. AU - Zhao, X.. AU - Van Krieken, J. H.. AU - Huang, Q.. AU - Ai, W.. AU - Etzell, J.. AU - Ponzoni, M.. AU - Ferreri, A. J.M.. AU - Piris, M. A.. AU - Møller, M. B.. AU - Bueso-Ramos, C. E.. AU - Medeiros, L. ...
Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma: a report from the International DLBCL Rituximab-CHOP Consortium Program Study.
Abstract: Association rules mining methods have been recently applied to gene expression data analysis to reveal relationships between genes and different conditions and features. However, not much effort has focused on detecting the relation between gene expression maps and related gene functions. Here we describe such an approach to mine association rules among gene functions in clusters of similar gene expression maps on mouse brain. The experimental results show that the detected association rules make sense biologically. By inspecting the obtained clusters and the genes having the gene functions of frequent itemsets, interesting clues were discovered that provide valuable insight to biological scientists. Moreover, discovered association rules can be potentially used to predict gene functions based on similarity of gene expression maps.. ...
TY - JOUR. T1 - Functional clustering of time series gene expression data by Granger causality. AU - Fujita, André. AU - Severino, Patricia. AU - Kojima, Kaname. AU - Sato, João R.. AU - Patriota, Alexandre G.. AU - Miyano, Satoru. PY - 2012/10/30. Y1 - 2012/10/30. N2 - Background: A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes.Results: In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its ...
Tahira, A. C., Kubrusly, M. S., Faria, M. F., Verjovski-Almeida, S., Reis, E. M., & Machado, M. C. C. (2010). Gene expression profiling reveals long intronic non-coding RNAs differentially expressed in pancreatic cancer and metastasis. Pancreas. Philadelphia ...
Purpose: Retinopathy of prematurity (ROP) is a common blinding disease caused by the abnormal growth of blood vessels in the retina of premature babies with low birth weight and low gestation period. However, the mechanisms and factors contributing to the progression of ROP are still unknown. The present study aimed to identify gene(s) responsible for ROP progression by a global gene expression profiling.. Methods: From a cohort of 600 subjects comprising ROP babies (n=350) and controls (n=250), 15 ROP babies at any stage (gestational age [GA] ≤ 35 weeks and/or birth weight [BW] ≤ 1700 g) and premature babies with no ROP (n=6) (GA ≤ 35 weeks and/or BW ≤ 1700 g) and full term babies of the same age and no ROP (n=3), were screened. RNA was isolated from 0.5-1 ml of blood using RNeasy mini kit from Qiagen and the purity and integrity of RNA was checked with Bioanalyzer 2100 (Agilent). Global gene expression profiling was performed by using Illumina bead Chip array having ~47,000 ...
TY - JOUR. T1 - Self-organizing latent lattice models for temporal gene expression profiling. AU - Zhang, Byoung Tak. AU - Yang, Jinsan. AU - Chi, Sung Wook. N1 - Funding Information: This work was supported by the Korean Government through BK21-IT, BrainTech, IMT2000 Bioinformatics and NRL Programs.. PY - 2003/7. Y1 - 2003/7. N2 - DNA microarrays are a high-throughput technology useful for functional genomics and gene expression analysis. While many microarray data are generated in sequence, most expression analysis tools are not utilizing the temporal information. Temporal expression profiling is important in many applications, including developmental studies, pathway analysis, and disease prognosis. In this paper, we develop a learning method designed for temporal gene expression profiling from massive DNA-microarray data. It attempts to learn probabilistic lattice maps of the gene expressions, which are then used for profiling the trajectories of temporal expressions of co-regulated genes. ...
Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks
Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish.
The increased use of microarray expression profiling to study both the molecular biology of cancer and the cellular physiology of difficult-to-isolate cell types has led to a growing need for methods that allow the use of limiting quantities of RNA. This limitation has prompted the development of amplification methods that produce the quantities of RNA required for microarray analysis. Efforts have become increasingly focused upon developing a protocol that minimizes amplification bias, provides versatility, and reduces technical complexity. We evaluated the new protocol Transplex™ Whole Transcriptome Amplification (WTA) produced by Rubicon Genomics. The kit was tested on Human Reference RNA (Stratagene) and on RNA extracted from a renal tumor cell line. Reproducibility, sensitivity and reliability in calling differentially expressed genes were evaluated by both Real-Time PCR and GeneChip® technology (Affymetrix). We tested reproducibility by comparing the expression profiles provided by U133 ...
Association rules mining methods have been recently applied to gene expression data analysis to reveal relationships between genes and different conditions and features. However, not much effort has focused on detecting the relation between gene expression maps and related gene functions. Here we describe such an approach to mine association rules among gene functions in clusters of similar gene expression maps on mouse brain. The experimental results show that the detected association rules make sense biologically.
Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement
Seker, H. (2004) A Multi-Fuzzy Filtering Approach to Reliable Gene Expression Profile Analysis. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, October 2004, pp. 37-40 ...
APC (Adenomatous polyposis coli) plays an important role in the pathogenesis of both familial and sporadic colorectal cancer. Patients carrying germline APC mutations develop multiple colonic adenomas at younger age and higher frequency than non-carrier cases which indicates that silencing of one APC allele may be sufficient to initiate the transformation process. To elucidate the biological dysregulation underlying adenoma formation we examined global gene expression profiles of adenomas and corresponding normal mucosa from an FAP patient. Differential expression of the most significant gene identified in this study was further validated by mRNA in situ hybridization, reverse transcriptase PCR and Northern blotting in different sets of adenomas, tumours and cancer cell lines. Eighty four genes were differentially expressed between all adenomas and corresponding normal mucosa, while only seven genes showed differential expression within the adenomas. The first group included pregnancy specific β-1
Background: Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Methods: Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Results: Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the ...
With the genomic revolution and the era of targeted therapy, prognostic and predictive gene signatures are becoming increasingly important in clinical research. They are expected to assist prognosis assessment and therapeutic decision making. Notwithstanding, an evidence-based approach is needed to bring gene signatures from the laboratory to clinical practice. In early breast cancer, multiple prognostic gene signatures are commercially available without having formally reached the highest levels of evidence-based criteria. We discuss specific concepts for developing and validating a prognostic signature and illustrate them with contemporary examples in breast cancer. When a prognostic signature has not been developed for predicting the magnitude of relative treatment benefit through an interaction effect, it may be wishful thinking to test its predictive value. We propose that new gene signatures be built specifically for predicting treatment effects for future patients and outline an approach for this
Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA. In the field of virology, when analyzing the host cells reaction to infection, the often high representation of viral RNA (vRNA) within total RNA preparations from infected cells is likely to interfere with microarray analysis. Yet, this effect has not been investigated despite the many reports that describe gene expression profiling of virus-infected cells using microarrays. In this study we used coronaviruses as a model to show that vRNA indeed interferes with microarray analysis, decreasing both sensitivity and accuracy. We also demonstrate that the removal of vRNA from total RNA samples, by means of virus-specific oligonucleotide capturing, significantly reduced the number of false-positive hits and increased the sensitivity of the method as tested on different array platforms. We therefore
Purpose This article provides a review of the transcriptomic expression profiling studies that have been performed on meningiomas so far. We discuss some future prospects and challenges ahead in the field of gene expression profiling. Methods We performed a systematic search in the PubMed and EMBASE databases in May 2010 using the following search terms alone or in combination: meningioma, microarray analysis, oligonucleotide array sequence analysis, or gene expression profiling. Only original research articles in English that had used RNA hybridized to high-resolution microarray chips to generate gene expression profiles were included. Results We identified 13 articles matching the inclusion criteria. All studies had been performed during the last decade. Conclusions The main results of the studies can be grouped in three categories: (1) several groups have identified meningioma-specific genes and genes associated with the three WHO grades, and the main histological subtypes of grade I ...
Observation of gene expression changes implying gene regulations using a repetitive experiment in time course has become more and more important. However, there is no effective method which can handle such kind of data. For instance, in a clinical/biological progression like inflammatory response or cancer formation, a great number of differentially expressed genes at different time points could be identified through a large-scale microarray approach. For each repetitive experiment with different samples, converting the microarray datasets into transactional databases with significant singleton genes at each time point would allow sequential patterns implying gene regulations to be identified. Although traditional sequential pattern mining methods have been successfully proposed and widely used in different interesting topics, like mining customer purchasing sequences from a transactional database, to our knowledge, the methods are not suitable for such biological dataset because every transaction in
Background Parkinsons disease (PD) is affecting 5 million people worldwide, but the response mechanisms of the striatum are still unclear. Therefore, identification of gene expression alterations in...
Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the transition phase 170 genes were differentially expressed, and 717 genes were differentially expressed between the transition and the
TY - JOUR. T1 - Mining cancer gene expression databases for latent information on intronic microRNAs. AU - Monterisi, Simona. AU - DArio, Giovanni. AU - Dama, Elisa. AU - Rotmensz, Nicole. AU - Confalonieri, Stefano. AU - Tordonato, Chiara. AU - Troglio, Flavia. AU - Bertalot, Giovanni. AU - Maisonneuve, Patrick. AU - Viale, Giuseppe. AU - Nicassio, Francesco. AU - Vecchi, Manuela. AU - Di Fiore, Pier Paolo. AU - Bianchi, Fabrizio. PY - 2015/2/1. Y1 - 2015/2/1. N2 - Around 50% of all human microRNAs reside within introns of coding genes and are usually co-transcribed. Gene expression datasets, therefore, should contain a wealth of miRNA-relevant latent information, exploitable for many basic and translational research aims. The present study was undertaken to investigate this possibility. We developed an in silico approach to identify intronic-miRNAs relevant to breast cancer, using public gene expression datasets. This led to the identification of a miRNA signature for aggressive breast ...
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BACKGROUND: Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at ...
The identification of a prognostic gene expression signature in breast cancer that is valid across multiple independent data sets and different microarray platforms is a challenging problem [1]. Recently, there have been reports of molecular prognostic and predictive signatures that were also valid in external independent cohorts [2-7]. One of these studies derived the prognostic signature from genes correlating with histological grade [4], while in [5] it was derived directly from correlations with clinical outcome data and was validated in estrogen receptor positive lymph node negative (ER+LN-) breast cancer. Another study validated a predictive score, based on 21 genes, for ER+LN-tamoxifen treated breast cancer [2]. These results are encouraging, yet, as explained recently in [8, 9], much larger cohort sizes may be needed before a consensus prognostic signature emerges. While the intrinsic subtype classification does appear to constitute a set of consensus signatures [7], it is also clear ...
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EpiRegNet aims to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields ...
1. Chockalingm A, Campbell NR, Fodor JG. Worldwide epidemic of hypertension. Can J Cardio. 2006;22:553-555 2. Tomson J, Lip GYH. Blood Pressure demographic: nature or nurture…… genes or environment?. BMC Med. 2005;3:3 3. WHO. World Health Report 2002: Reducing Risks, Promoting Healthy life. Geneva: World Health Organization. 2002 4. Heller RA. et al. Discovery and analysis of inflammatory disease related genes using cDNA microarrays. Proc Nat Acad Sci. 1997;94:2150- 2155 5. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996;14:1675-80 6. Tzouvelekis A, Patlakas G, Bouros D. Application of Microarray Technology in pulmonary diseases. Respir Res. 2004;5:26 7. King HC, Sinha AA. Gene expression profile analysis by DNA microarrays: promise and pitfalls. JAMA. 2001;286:2280-2288 8. LI JJ. Inflammation in hypertension: primary ...
Microarray gene expression data sets are jointly analyzed to increase statistical power. They could either be merged together or analyzed by meta-analysis. For a given ensemble of data sets, it cannot be foreseen which of these paradigms, merging or meta-analysis, works better. In this article, three joint analysis methods, Z-score normalization, ComBat and the inverse normal method (meta-analysis) were selected for survival prognosis and risk assessment of breast cancer patients. The methods were applied to eight microarray gene expression data sets, totaling 1324 patients with two clinical endpoints, overall survival and relapse-free survival. The performance derived from the joint analysis methods was evaluated using Cox regression for survival analysis and independent validation used as bias estimation. Overall, Z-score normalization had a better performance than ComBat and meta-analysis. Higher Area Under the Receiver Operating Characteristic curve and hazard ratio were also obtained when ...
This project is an investigation of whether analysing subsets of time series gene expression data can give additional information about putatively co-regulated genes, compared to only using the whole time series. The original gene expression data set was partitioned into subsets and similarity was computed for both the whole timed series and subsets. Pearson correlation was used as similarity measure between gene expression profiles. The results indicate that analysing co-expression in subsets of gene expression data derives true-positive connections, with respect to co-regulation, that are not detected by only using the whole time series data. Unfortunately, with the actual data set, chosen similarity measure and partitioning of the data, randomly generated connections have the same amount of true-positives as the ones derived by the applied analysis. However, it is worth to continue further analysis of the subsets of gene expression data, which is based on the multi-factorial nature of gene ...
Preface. Acknowledgments.. 1 Introduction.. 1.1 Basic Terminology.. 1.1.1 The Central Dogma of Molecular Biology.. 1.1.2 Genome.. 1.1.3 Proteome.. 1.1.4 DNA (Deoxyribonucleic Acid).. 1.1.5 RNA (Ribonucleic Acid).. 1.1.6 mRNA (messenger RNA).. 1.1.7 Genetic Code.. 1.1.8 Gene.. 1.1.9 Gene Expression and the Gene Expression Level.. 1.1.10 Protein.. 1.2 Overlapping Areas of Research.. 1.2.1 Genomics.. 1.2.2 Proteomics.. 1.2.3 Bioinformatics.. 1.2.4 Transcriptomics and Other -omics.. 1.2.5 Data Mining.. 2 Basic Analysis of Gene Expression Microarray Data.. 2.1 Introduction.. 2.2 Microarray Technology.. 2.2.1 Spotted Microarrays.. 2.2.2 Affymetrix GeneChip® Microarrays.. 2.2.3 Bead-Based Microarrays.. 2.3 Low-Level Preprocessing of Assymetrix Microarrays.. 2.3.1 MAS5.. 2.3.2 RMA.. 2.3.3 GCRMA.. 2.3.4 PLIER.. 2.4 Public Repositories of Microarray Data.. 2.4.1 Microarray Gene Expression Data Society (MGED) Standards.. 2.4.2 Public Databases.. Gene Expression Omnibus (GEO).. ...
Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
CG000170_TechNote_BiologicalandTechnicalVariationinSingleCell3GeneExpressionExperiments_RevA_.pdf. Technical Note - Biological & Technical Variation in Single Cell Gene Expression Experiments. The Chromium Single Cell 3′ v2 Reagent Kits protocol (Document CG00052) produces Single Cell 3′ short-read sequencer compatible libraries. Technical and biological variation may be present in the experiment design, and may impact data interpretation. Potential sources of technical variation include running a sample on two separate microfluidic chips or at different well positions on the same chip, and or technical variation introduced by sequencing libraries on separate Illumina flowcells or sequencing lanes. This Technical Note examines the potential sources of technical and biological variation and their effects on single cell gene expression. These factors need to be considered when designing an experiment to minimize bias and generate reliable single cell gene expression data.. FOR USE WITH. ...
Background & objective: Microarray and next generation sequencing (NGS) data are the important sources to find helpful molecular patterns. Also, the great number of gene expression data increases the challenge of how to identify the biomarkers associated with cancer. The random forest (RF) is used to effectively analyze the problems of large-p and small-n. Therefore, RF can be used to select and rank the genes for the diagnosis and effective treatment of cancer. Methods: The microarray gene expression data of colon, leukemia, and prostate cancers were collected from public databases. Primary preprocessing was done on them using limma package, and then, the RF classification method was implemented on datasets separately in R software. Finally, the selected genes in each of the cancers were evaluated and compared with those of previous experimental studies and their functionalities were assessed in molecular cancer processes. Result: The RF method extracted very small sets of genes while it retained its
Breast cancer is the most common malignancy among women in the United States with the second highest incidence of cancer-related death following lung cancer. The decision-making process regarding adjuvant therapy is a time intensive dialogue between the patient and her oncologist. There are multiple tools that help individualize the treatment options for a patient. Population-based analysis with Adjuvant! Online and genomic profiling with Oncotype DX are two commonly used tools in patients with early stage, node-negative breast cancer. This case report illustrates a situation in which the population-based prognostic and predictive information differed dramatically from that obtained from genomic profiling and affected the patients decision. In light of this case, we discuss the benefits and limitations of these tools.
Gene set analysis methods use prior biological knowledge to analyze gene expression data. This prior knowledge takes the form of predefined groups of genes, linked through their biological function. Gene set analysis methods have been successfully applied in transversal studies, their results being more sensitive and interpretable than those of methods investigating genomic data one gene at a time. The time-course gene set analysis (TcGSA) introduced here is an extension of such gene set analysis to longitudinal data. This method identifies a priori defined groups of genes whose expression is not stable over time, taking into account the potential heterogeneity between patients and between genes. When biological conditions are compared, it identifies the gene sets that have different expression dynamics according to these conditions. Data from 2 studies are analyzed: data from an HIV therapeutic vaccine trial, and data from a recent study on influenza and pneumococcal vaccines. In both cases, TcGSA
For more than a decade, global gene expression profiling has been extensively used to elucidate the biology of human papillomaviruses (HPV) and their role in cervical- and head-and-neck cancers. Since 2008, the expression profiling of miRNAs has been reported in multiple HPV studies. Two major strategies have been employed in the gene and miRNA profiling studies: In the first approach, HPV positive tumors were compared to normal tissues or to HPV negative tumors. The second strategy relied on analysis of cell cultures transfected with single HPV oncogenes or with HPV genomes compared to untransfected cells considered as models for the development of premalignant and malignant transformations.. In this review, we summarize what we have learned from a decade of global expression profiling studies. We performed comprehensive analysis of the overlap of the lists of differentially expressed genes and microRNAs, in both tissue samples and cell culture based studies. The review focuses mainly on HPV16, ...
A meta-analysis was performed across six public microarray datasets for human small cell lung cancer (SCLC) comprising 365 samples across eight different platforms. Genes were ranked according to effect size and p-value for tumor versus control samples, and false discovery rates were calculated. The top scoring 48 genes that were significant by both methods, along with the 48 highest rated surface antigen genes, were used to populate a gene list for subsequent single cell evaluation. High throughput gene expression analysis was performed for 400 individual cells from one SCLC line (H446) using the Fluidigm microfluidic platform. Supervised machine learning was applied to identify transcriptionally-defined subgroups among these cells. The non-parametric Kolmogorov-Smirnov test was then used to determine those surface markers best able to distinguish each cluster. Individual cells from each group were then FACS-isolated, and clonogenicity was evaluated after 14 days in culture. Using these surface ...
Title: Definition of Genes and Paths Involved in Alzheimers Disease: Using Gene Expression Profiles and Chemical Genetics at the Mouse Brain Level. VOLUME: 7 ISSUE: 5. Author(s):Pu Wu and Yinghe Hu. Affiliation:Key Lab of Brain Functional GenomicsMOE STCSM; Shanghai Institute of Brain Functional Ge-nomics, East China Normal University, 3663 Zhongshan Road N. Shanghai, 200062, China.. Keywords:cDKO mice, SNAP-25, hypothalamus, neuronal plasticity, NMDA receptor. Abstract: Gene expression profiling of a number of distinct brain regions under different behavioral and biological states was analyzed using DNA microarray technology. These included hippocampal development, aging process, environ-mental enrichment, fear conditioning, and calorie restriction. Our results identified numerous genes and signal pathways that may play critical roles in learning and memory, brain aging and longevity. Furthermore, chemical genetic approach combined with gene expression profiling analysis was applied to study ...
Gene expression profiling classifies individual tumors by their gene expression patterns and may also describe and predict therapeutic resistance and sensitivity patterns. Profiling in several cancers, such as breast cancer, colon cancer, lymphoma, leukemia, and melanoma [3], has already identified molecular subclasses of tumors. Identification of tumor subtypes may be predictive for prognosis or response to drug therapy [6, 7, 28-31].. The potential of routine gene expression profiling to predict clinical outcomes for cancer patients has yet to be determined. The Evaluation of Genomic Applications in Practice and Prevention Working Group stated in 2009 that there was insufficient evidence to make a recommendation for or against the use of tumor gene expression profiles to improve outcomes in defined populations of women with breast cancer [32]. Clearly, more work needs to be done to translate promising research findings into clinically relevant results.. Comparison of FFPET sample-derived ...
Gene co-expression network analysis of transcriptome data has enabled the identification of key genes and important networks underlying complex production and disease traits. This study used weighted gene co-expression network analysis (WGCNA) approach to (1) detect modules or clusters of differentially expressed genes (DEG) with similar expression patterns in calf rumen transcriptome during pre- and post-weaning periods and (2) identify regulatory mechanisms linking gene modules to relevant phenotypes during the pre-weaning period (day 33 [d33]): weight gain (BWT_d33), average daily gain (ADG_d33), blood glucose (Glucose_d33) and β-hydroxybutyrate (BHB_d33) concentrations and post-weaning period (d96): weight gain (BWT_d96), average daily gain (ADG_d96), blood glucose (Glucose_d96) and β-hydroxybutyrate (BHB_d96) concentrations, dry matter intake (DMI_d96) and feed efficiency (FE_d96). Rumen tissues were collected from 16 calves on d33 and another 16 on d96 for whole transcriptome sequencing ...
TY - JOUR. T1 - Gene expression profiling on lung cancer outcome prediction. T2 - Present clinical value and future premise. AU - Sun, Zhifu. AU - Yang, Ping. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2006/11. Y1 - 2006/11. N2 - DNA microarray has been widely used in cancer research to better predict clinical outcomes and potentially improve patient management. The new approach provides accurate tumor classification and outcome predictions, such as tumor stage, metastatic status, and patient survival, and offers some hope for individualized medicine. However, growing evidence suggests that gene-based prediction is not stable and little is known about the prediction power of gene expression profiles compared with well-known clinical and pathologic predictors. This review summarized up-to-date publications in microarray-based lung cancer clinical outcome prediction and conducted secondary analyses for those with sufficient sample sizes and associated clinical ...
Cervical cancer is the most common gynecologic malignant tumor, with a high incidence in 50-55-year-olds. This study aims to investigate the potential molecular mechanism of RRM2 for promoting the development of cervical cancer based on The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). RRM2 was found to be significant upregulated in cervical tissue (P,0.05) by extracting the expression of RRM2 from TCGA, GSE63514, GSE7410, GSE7803 and GSE9750. Survival analysis indicated that the overall survival was significantly worse in the patients with high-expression of RRM2 (P,0.05). The top 1000 positively/negatively correlated genes with RRM2 by Pearson Correlation test were extracted. The gene co-expression network by Weighted Gene Co-Expression Network Analysis (WGCNA) with these genes and the clinical characteristics (lymphocyte infiltration, monocyte infiltration, necrosis, neutrophil infiltration, the number of normal/stromal/tumor cells and the number of tumor nuclei) was ...
TY - JOUR. T1 - Single-cell gene expression profiling using FACS and qPCR with internal standards. AU - Porter, Joshua R.. AU - Telford, William G.. AU - Batchelor, Eric. N1 - Funding Information: We would like to thank V. Kapoor in the CCR ETIB Flow Cytometry Core for her aid in performing the cell sorting during the development of this protocol. We also thank M. Raffeld and the CCR LP Molecular Diagnostics Unit and J. Zhu and the NHLBI DNA Sequencing and Genomics Core for their aid in performing the qPCR during the development of this protocol. This research was supported by the Intramural Program of the NIH.. PY - 2017/2/25. Y1 - 2017/2/25. N2 - Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those populations. Single-cell gene expression measurements can help assess the role of noise in gene expression, identify correlations in the expression of pairs of genes, and reveal subpopulations of cells that ...
Background: Soft tissue sarcomas are heterogeneous and a major complication in their management is that the existing classification scheme is not definitive and is still evolving. Leiomyosarcomas, a major histologic category of soft tissue sarcomas, are malignant tumours displaying smooth muscle differentiation. Although defined as a single group, they exhibit a wide range of clinical behaviour. We aimed to carry out molecular classification to identify new molecular subgroups with clinical relevance. Methods: We used gene expression profiling on 20 extra-uterine leiomyosarcomas and cross-study analyses for molecular classification of leiomyosarcomas. Clinical significance of the subgroupings was investigated. Results: We have identified two distinct molecular subgroups of leiomyosarcomas. One group was characterised by high expression of 26 genes that included many genes from the sub-classification gene cluster proposed by Nielsen et al. These sub-classification genes include genes that have ...
A DNA microarray is a solid support such as a glass slide, silicon chip or nylon membrane on which DNA molecules are attached at precise locations. Using DNA microarrays, the expression of tens of thousands of genes in a biological sample can be detected in one experiment. Emerging data suggests that the use of DNA microarrays can aid the differentiation of tumors with similar morphological appearance, predict patient outcome independently of conventional prognostic factors and select for response or resistance to specific anti-cancer therapies. DNA microarray technology thus has the potential to supplement standard diagnostic procedures in oncology and permit a more individualized approach to patient management. Prior to clinical application, however, this methodology must be simplified, standardized, evaluated in external quality assessment schemes and made available at relatively low costs. Most importantly, the preliminary, but promising, early findings must be validated by high-level ...
TY - JOUR. T1 - Homogeneous datasets of triple negative breast cancers enable the identification of novel prognostic and predictive signatures. AU - Karn, Thomas. AU - Pusztai, Lajos. AU - Holtrich, Uwe. AU - Iwamoto, Takayuki. AU - Shiang, Christine Y.. AU - Schmidt, Marcus. AU - Müller, Volkmar. AU - Solbach, Christine. AU - Gaetje, Regine. AU - Hanker, Lars. AU - Ahr, Andre. AU - Liedtke, Cornelia. AU - Ruckhäberle, Eugen. AU - Kaufmann, Manfred. AU - Rody, Achim. PY - 2011/12/29. Y1 - 2011/12/29. N2 - Background: Current prognostic gene signatures for breast cancer mainly reflect proliferation status and have limited value in triple-negative (TNBC) cancers. The identification of prognostic signatures from TNBC cohorts was limited in the past due to small sample sizes. Methodology/Principal Findings: We assembled all currently publically available TNBC gene expression datasets generated on Affymetrix gene chips. Inter-laboratory variation was minimized by filtering methods for both samples ...
Combining congenic mapping with microarray expression profiling offers an opportunity to establish functional links between genotype and phenotype for complex traits such as type 1 diabetes (T1D). We used high-density oligonucleotide arrays to measure the relative expression levels of |39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes-resistant congenic strains, and two nondiabetic control strains. We developed a simple, yet general, method for measuring differential expression that provides an objective assessment of significance and used it to identify |400 gene expression differences and eight new candidates for the Idd9.1 locus. We also discovered a potential early biomarker for autoimmune hemolytic anemia that is based on different levels of erythrocyte-specific transcripts in the spleen. Overall, however, our results suggest that the dramatic disease protection conferred by six Idd loci (Idd3, Idd5.1, Idd5.2, Idd9.1, Idd9.2,
Table_6_Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum.XLSX
RNA Transcription Detected on Chromosomes 21 and 22 Using High Density Oligonucleotide Arrays. Thomas R. Gingeras, Affymetrix Inc., Santa Clara, CA. The first drafts of complete human genome sequence have brought with them the opportunities to map the RNA transcription patterns that are characteristic of each differentiated and undifferentiated cell type and characterize the sequence variations that underlie the phenotypic differences observed in the human population. By using the very high information content inherent in high-density oligonucleotide arrays it will be possible to map the locations of RNA transcription along the length of the entire human genome. Such a transcriptome map will provide information concerning: 1) the identification of novel transcription domains of the genome, 2) the predominant utilization of exon sequences during differentially spliced gene expression and 3) a empirically derived set of results which can be compared to the sequence annotation now being assembled ...
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation - Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time series gene expression following system perturbation: 1) Conditional, Tamoxifen dependent, activation of the cMyc proto-oncogene in rat fibroblast; 2) Genomic response to nutrition changes in D. melanogaster; 3) Patterns of gene activity as a consequence of ageing occurring over a life-span time series (25y-90y) sampled from T-cells of human donors. We show that the three datasets undergo similar transitions from an uncorrelated regime to a positively or negatively correlated one that is symptomatic of a shift from a ground or basal state to a polarized state. In
Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method. Two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. Although all methods tested here provided similar global results and biological conclusions, the new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and thus increased ability to find statistically significant differentially
An award for difficult RNA samples. Gene expression profiling using Next Generation Sequencing (NGS) is empowering an ever-increasing range of researchers to answer highly relevant biological and medical questions. At Lexogen, we are dedicated to developing innovative technologies for NGS and making these accessible for all scientists. With the Lexogen Research Award we wish to provide a chance for researchers to utilize more NGS. We ask you to submit a description of the project where you would use NGS and Lexogens RNA-Seq sample prep. The winners shall be given a product of Lexogen together with a free sequencing run and data analysis. The topic of this Research Award is High quality from low quality: Accurate gene expression profiling of low quality or FFPE samples. RNA sequencing is rapidly becoming the platform of choice for gene expression profiling projects. However, not all samples are created equal, and not all researchers have the luxury of working with high quality RNA for NGS library
Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M. lutarioriparius with an emphasis to identify putative genes involved in rhizome development. Approximately 66 gigabase (GB) paired-end clean reads were obtained and assembled into 169,064 unigenes with an average length of 759 bp. Among these unigenes, 103,899 (61.5%) were annotated in seven public protein databases. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218 and 1,077 genes were predominantly expressed in root, leaf, stem, lateral bud, and rhizome bud, respectively. Their expression patterns were further classified into 12 distinct
The aims of the present study were to identify key genes and pathways associated with hepatocellular carcinoma (HCC) progression and predict compounds potentially associated with this type of carcinogenesis. The gene expression profile data of the GSE49515 dataset was obtained from the Gene Expression Omnibus database. The limma software package was used to identify the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Biological Networks Gene Ontology tool and the Database for Annotation, Visualization and Integrated Discovery, respectively. The Michigan Molecular Interactions database plugin within the Cytoscape software platform was used to perform protein‑protein interaction (PPI) network analysis. Chemical‑gene interaction data for HCC were obtained from the Comparative Toxicogenomics Database to evaluate the associations between drugs and specific genes. A total of 302 DEGs, including ...
TY - JOUR. T1 - Co-expression network analysis of peripheral blood transcriptome identifies dysregulated protein processing in endoplasmic reticulum and immune response in recurrent MDD in older adults. AU - Ciobanu, Liliana G.. AU - Sachdev, Perminder S.. AU - Trollor, Julian N.. AU - Reppermund, Simone. AU - Thalamuthu, Anbupalam. AU - Mather, Karen A.. AU - Cohen-Woods, Sarah Louise. AU - Stacey, David. AU - Toben, Catherine. AU - Schubert, Klaus Oliver. AU - Baune, Bernhard T.. PY - 2018/12. Y1 - 2018/12. N2 - The molecular factors involved in the pathophysiology of major depressive disorder (MDD) remain poorly understood. One approach to examine the molecular basis of MDD is co-expression network analysis, which facilitates the examination of complex interactions between expression levels of individual genes and how they influence biological pathways affected in MDD. Here, we applied an unsupervised gene-network based approach to a prospective experimental design using microarray ...
TY - JOUR. T1 - The effect of a single, temperature-sensitive mutation on global gene expression in Escherichia coli. AU - Li, Yong. AU - Cole, Kyle. AU - Altman, Sidney. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2003/5/1. Y1 - 2003/5/1. N2 - High-density DNA microarrays have been used to explore the genomic profiling of gene expression of a defective Escherichia coli strain with a temperature-sensitive mutation in the protein component of RNase P. A novel gene cluster was discovered in which two of the genes are known substrates of RNase P. The expression pattern of essential genes and gene discovery from intergenic regions, for which other new transcripts are found, are also discussed.. AB - High-density DNA microarrays have been used to explore the genomic profiling of gene expression of a defective Escherichia coli strain with a temperature-sensitive mutation in the protein component of RNase P. A novel gene cluster was discovered in which two of the genes are ...
Gene expression in multiple individual cells from a tissue or culture sample varies according to cell-cycle, genetic, epigenetic and stochastic differences between the cells. However, single-cell differences have been largely neglected in the analysis of the functional consequences of genetic variation. Here we measure the expression of 92 genes affected by Wnt signaling in 1,440 single cells from 15 individuals to associate single-nucleotide polymorphisms (SNPs) with gene-expression phenotypes, while accounting for stochastic and cell-cycle differences between cells. We provide evidence that many heritable variations in gene function--such as burst size, burst frequency, cell cycle-specific expression and expression correlation/noise between cells--are masked when expression is averaged over many cells. Our results demonstrate how single-cell analyses provide insights into the mechanistic and network effects of genetic variability, with improved statistical power to model these effects on gene
The transcription factor c-Myb is required for modulation of progenitor cells in several tissues, including skeletal muscle and its upregulation is observed in many human being malignancies. in RMS sufferers. c-Myb could, therefore, lead to the growth phenotype by performing its inhibitory function in skeletal muscles difference. We also demonstrated that c-Myb proteins is normally abundant in migratory C2C12 myoblasts and its ectopic reflection potentiates cell motility. In overview, our outcomes implicate that metastatic properties of some RMS subtypes might end up being linked to c-Myb function. The transcription aspect c-Myb is normally needed for the regulations of progenitor cells in many tissue, including the hematopoietic program1,2, the adult human brain3, and colonic crypts4. It has a function in progenitor creation, keeping their expansion, migration, or family tree dedication. c-Myb appearance generally diminishes as progenitor cells differentiate. In truth, constitutive ...
Osaka-Dental-University-Susceptible rats (ODUS/Odu) are a useful animal model for human periodontal disease. Through comprehensive gene expression profiling, we aimed to evaluate the utility of ODUS/Odu-derived cells as an alternative to animal models for biomedical research into human periodontal disease. Using a GeneChip Rat Expression Array containing 15923 probes, the gene expression profiles of embryonic fibroblasts obtained from 13.5-day-old embryos of ODUS/Odu or control rats were comprehensively analyzed. This profiling revealed alterations in some genes that are likely to be related to periodontal disease in ODUS/Odu, based on a comparison with genes found in databases. Osteopontin (OPN), which is involved in immune defense reactions, bone metabolism and chronic inflammation, was among the genes whose expressions were significantly altered. Realtime RT-PCR analysis showed that the OPN mRNA level was increased by more than 5.8-fold in ODUS/Odu. Moreover, the expression of CD44, a ...
Autologous hematopoietic stem cell transplantation (aHSCT) has been used as a therapeutic approach in multiple sclerosis (MS). However, it is still unclear if the immune system that emerges from autologous CD34+ hematopoietic progenitor cells (HPC) of MS patients is pre-conditioned to re-develop the proinflammatory phenotype. The objective of this article is to compare the whole genome gene and microRNA expression signature in CD34+ HPC of MS patients and healthy donors (HD). CD34+ HPC were isolated from peripheral blood of eight MS patients and five HD and analyzed by whole genome gene expression and microRNA expression microarray. Among the differentially expressed genes (DEGs) only TNNT1 reached statistical significance (logFC=3.1, p,0.01). The microRNA expression was not significantly different between MS patients and HD. We did not find significant alterations of gene expression or microRNA profiles in CD34+ HPCs of MS patients. Our results support the use of aHSCT for treatment of MS. ...
The epithelial to mesenchymal transition (EMT) plays a key role in lung cancer progression and drug resistance. The dynamics and stability of gene expression patterns as cancer cells transition from E to M at a systems level and relevance to patient outcomes are unknown. Using comparative network and clustering analysis, we systematically analyzed time-series gene expression data from lung cancer cell lines H358 and A549 that were induced to undergo EMT. We also predicted the putative regulatory networks controlling EMT expression dynamics, especially for the EMT-dynamic genes and related these patterns to patient outcomes using data from TCGA. Example EMT hub regulatory genes were validated using RNAi. We identified several novel genes distinct from the static states of E or M that exhibited temporal expression patterns or periods during the EMT process that were shared in different lung cancer cell lines. For example, cell cycle and metabolic genes were found to be similarly down-regulated where
TY - JOUR. T1 - A Sequence Based Validation of Gene Expression Microarray Data. AU - Thallinger, Gerhard. AU - Obermayr, Eva. AU - Charoentong, Pornpimol. AU - Tong, Dan. AU - Trajanoski, Zlatko. AU - Zeillinger, Robert. PY - 2012. Y1 - 2012. UR - U2 - 10.3844/ajbsp.2012.1.9. DO - 10.3844/ajbsp.2012.1.9. M3 - Article. VL - 1. SP - 1. EP - 9. JO - American journal of bioinformatics. JF - American journal of bioinformatics. SN - 1948-9862. IS - 1. ER - ...
Early detection of breast cancer is key to successful treatment and patient survival. We have previously reported the potential use of gene expression profiling of peripheral blood cells for early detection of breast cancer. The aim of the present study was to refine these findings using a larger sample size and a commercially available microarray platform. Blood samples were collected from 121 females referred for diagnostic mammography following an initial suspicious screening mammogram. Diagnostic work-up revealed that 67 of these women had breast cancer while 54 had no malignant disease. Additionally, nine samples from six healthy female controls were included. Gene expression analyses were conducted using high density oligonucleotide microarrays. Partial Least Squares Regression (PLSR) was used for model building while a leave-one-out (LOO) double cross validation approach was used to identify predictors and estimate their prediction efficiency. A set of 738 probes that discriminated breast cancer
Temperature adaptation is one of the most important determinants of distribution and population size of organisms in nature. Recently, quantitative trait loci (QTL) mapping and gene expression profiling approaches have been used for detecting candidate genes for heat resistance. However, the resolution of QTL mapping is not high enough to examine the individual effects of various genes in each QTL. Heat stress-responsive genes, characterized by gene expression profiling studies, are not necessarily responsible for heat resistance. Some of these genes may be regulated in association with the heat stress response of other genes. To evaluate which heat-responsive genes are potential candidates for heat resistance with higher resolution than previous QTL mapping studies, we performed genome-wide deficiency screen for QTL for heat resistance. We screened 439 isogenic deficiency strains from the DrosDel project, covering 65.6% of the Drosophila melanogaster genome in order to map QTL for thermal resistance.
Developmental Anatomic Gene Expression Atlas (AGEA) The Allen Gene Expression Atlas (AGEA) for the Developing Mouse Brain is used to understand how voxels of the brain are related by gene expression (Correlation), and to find genes expressed at a particul
PubMed Central Canada (PMC Canada) provides free access to a stable and permanent online digital archive of full-text, peer-reviewed health and life sciences research publications. It builds on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature and is a member of the broader PMC International (PMCI) network of e-repositories.
TY - JOUR. T1 - Predicting response to docetaxel neoadjuvant chemotherapy for advanced breast cancers through genome-wide gene expression profiling. AU - Zembutsu, Hitoshi. AU - Suzuki, Yasuyo. AU - Sasaki, Aya. AU - Tsunoda, Tatsuhiko. AU - Okazaki, Minoru. AU - Yoshimoto, Masataka. AU - Hasegawa, Tadashi. AU - Hirata, Koichi. AU - Nakamura, Yusuke. PY - 2009. Y1 - 2009. N2 - Neoadjuvant chemotherapy with docetaxel for advanced breast cancer can improve the radicality for a subset of patients, but some patients suffer from severe adverse drug reactions without any benefit. To establish a method for predicting responses to docetaxel, we analyzed gene expression profiles of biopsy materials from 29 advanced breast cancers using a cDNA microarray consisting of 36,864 genes or ESTs, after enrichment of cancer cell population by laser microbeam microdissection. Analyzing eight PR (partial response) patients and twelve patients with SD (stable disease) or PD (progressive disease) response, we ...
Array-based comparative genomic hybridization (CGH) and gene expression profiling have become vital techniques for identifying molecular defects underlying genetic diseases. Regardless of the microarray platform, cyanine dyes (Cy3 and Cy5) are one of the most widely used fluorescent dye pairs for microarray analysis owing to their brightness and ease of incorporation, enabling high level of assay sensitivity. However, combining both dyes on arrays can become problematic during summer months when ozone levels rise to near 25 parts per billion (ppb). Under such conditions, Cy5 is known to rapidly degrade leading to loss of signal from either homebrew or commercial arrays. Cy5 can also suffer disproportionately from dye photobleaching resulting in distortion of (Cy5/Cy3) ratios used in copy number analysis. Our laboratory has been active in fluorescent dye research to find a suitable alternative to Cy5 that is stable to ozone and resistant to photo-bleaching. Here, we report on the development of such a
Purpose. human TM cells morphologically and started to specific many guns of TM cells while ceasing to specific pluripotency guns such as Nanog, April4, and Sox2. Functionally, the ability was created by these cells to phagocytose particles. Finally, publicity to dexamethasone or phorbol 12-myristate acetate triggered a specific boost in the creation and release of myocilin and matrix metalloproteinase-3, respectively, behavior quality of TM cells. Results. Our data show that iPSCs can be induced to assume a phenotype that resembles native TM cells in many important aspects. Not only do these cells represent a valuable research tool, but transplantation into glaucomatous eyes with elevated IOP may also restore function to the TM, resulting in re-establishment of IOP. … In order to induce iPSCs to differentiate into TM-like cells, iPSCs were cocultured with the human cell line hTM530 for up to 21 days. This immortalized cell line was used here since it grows at a very consistent rate and ...
Objective: To determine whether peripheral blood gene expression of patients with systemic lupus erythaematosus (SLE) correlates with disease activity measured using the SLE Disease Activity Index 2000 (SLEDAI-2K).. Methods: RNA was isolated from peripheral blood of 269 patients with SLE and profiled on a custom microarray. Hierarchical clustering and a heat map were used to categorise samples into major clusters based on gene expression pattern. Correlates, including demographic and disease-related characteristics such as SLEDAI-2K score, of the major sample clusters were compared using multivariate regression models.. Results: A set of 31 interferon (IFN)-regulated genes were seen to be driving the separations of samples into two clusters, one characterised by a relatively high IFN-regulated gene signature (n = 150) and the other by a relatively low IFN-regulated gene signature (n = 119). Disease activity measured using the SLEDAI-2K was significantly correlated with the high IFN gene ...
Gene expression network analysis and applications to immunology - We address the problem of using expression data and prior biological knowledge to identify differentially expressed pathways or groups of genes. Following an idea of Ideker et al. (2002), we construct a gene interaction network and search for high-scoring subnetworks. We make several improvements in terms of scoring functions and algorithms, resulting in higher speed and accuracy and easier biological interpretation. We also assign significance levels to our results, adjusted for multiple testing. Our methods are succesfully applied to three human microarray data sets, related to cancer and the immune system, retrieving several known and potential pathways. The method, denoted by the acronym GXNA (Gene eXpression Network Analysis) is implemented in software that is publicly available and can be used on virtually any microarray data set.
contribute to the vascular remodeling process associated with hypertension and atherosclerosis, the aims of this study were to assess the impact of 2-ME on pathophysiological pathways regulating SMC growth using transcriptional profiling. High-density oligonucleotide microarrays (Affymetrix Human Genome U_133 Plus 2.0 GeneChips) were used to identify differentially expressed genes in cultured human aortic SMCs treated with 2-ME (acutely, for 4 hrs, n=3; and chronically, for 48 hrs, n=3) and vehicle-treated time-matched controls (n=3 for each time point). Both single gene analysis (performed using Significance Analysis of Microarrays) as well as Gene Set Enrichment Analysis (GSEA, a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states) indicated downregulation of genes critically involved in mitotic spindle assembly and function in SMCs chronically treated with 2-ME when compared to ...
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.. Availability: Genoscape is an open-source software freely available from the Genoscape webpage ( Installation instructions and tutorial can also be found at this URL.. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.. ...
Purpose: To identify the novel gene signatures and molecular markers of nasopharyngeal carcinoma (NPC) by integrated bioinformatics analysis of multiple gene expression profiling datasets. Experimental Design: Seven published gene expression profiling studies and one of our unpublished works were reanalyzed to identify the common significantly dysregulated (CSD) genes in NPC. Overrepresentation analysis of cytogenetic bands, Gene Ontology (GO) categories, pathways were used to explore CSD genes functionally associated with carcinogenesis. The protein expressions of selected CSD genes were examined by immunohistochemistry on tissue microarrays, and the correlations of their expressions with clinical outcomes were evaluated. Results: Using the criteria (genes reported deregulated in more than one study), a total of 962 genes were identified as the CSD genes in NPC. Four up-regulated (BUB1B, CCND2, CENPF and MAD2L1) and two down-regulated (LTF and SLPI) genes were markedly reported in six studies. ...
Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages. We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes
TY - JOUR. T1 - MicroRNA expression profiling and Notch1 and Notch2 expression in minimal deviation adenocarcinoma of uterine cervix. AU - The Gynecological Pathology Study Group of the Korean Society of Pathologists. AU - Lee, Heejeong. AU - Kim, Kyu Rae. AU - Cho, Nam Hoon. AU - Hong, Sung Ran. AU - Jeong, Hoiseon. AU - Kwon, Sun Young. AU - Park, Kwang Hwa. AU - An, Hee Jung. AU - Kim, Tae Heon. AU - Kim, Insun. AU - Yoon, Hye Kyoung. AU - Suh, Kwang Sun. AU - Min, Ki Ouk. AU - Choi, Hyun Joo. AU - Park, Ji Young. AU - Yoo, Chong Woo. AU - Lee, Youn Soo. AU - Lee, Hee Jin. AU - Lee, Weon Sun. AU - Park, Chul Soo. AU - Lee, Yonghee. PY - 2014. Y1 - 2014. N2 - Background: MicroRNA (miRNA) expression is known to be deregulated in cervical carcinomas. However, no data is available about the miRNA expression pattern for the minimal deviation adenocarcinoma (MDA) of uterine cervix. We sought to detect deregulated miRNAs in MDA in an attempt to find the most dependable miRNA or their combinations to ...
TY - JOUR. T1 - Application of high-density DNA microarray to study smoke- and hydrogen peroxide-induced injury and repair in human bronchial epithelial cells. AU - Yoneda, Ken Y. AU - Mann-Jong Chang, Mary. AU - Chmiel, Ken. AU - Chen, Yin. AU - Wu, Reen. PY - 2003/8/1. Y1 - 2003/8/1. N2 - Recent advances in high-density DNA microarray technique allow the possibility to analyze thousands of genes simultaneously for their differential gene expression patterns in various biologic processes. Through clustering analysis and pattern recognition, the significance of these differentially expressed genes can be recognized and correlated with the biologic events that may take place inside the cell and tissue. High-density DNA microarray nylon membranes were used to explore gene expression and regulation associated with smoke-and hydrogen peroxide-induced injury and repair in differentiated human bronchial epithelial cells in vitro. At least three phases of change in gene expression could be recognized. ...
"Gene expression profiling in organ transplantation". Int J Nephrol. 2011: 180201. doi:10.4061/2011/180201. PMC 3154482. PMID ... Gene therapy[edit]. Gene therapy is another method that can be used. In this method, the genes that cause the body to reject ... of immune cells radiolabeled in vivo might-similarly to Gene Expression Profiling (GEP)-offer noninvasive testing.[24][25] ... Research is still being conducted, and no gene therapies are being used to date to treat patients.[27][28][29][30] Current ...
Leach, Martin (2004). "Gene Expression Informatics". Gene Expression Profiling. Methods in Molecular Biology. 258. pp. 153-166 ... GeneSweep or Gene Sweepstake was a sweepstake and scientific wager for scientists to bet on the total number of genes in the ... Wade, Nicholas (2003). "Gene Sweepstakes Ends, but Winner May Well Be Wrong". The New York Times. ISSN 0362-4331. ... Birney noted that, though the exact number was still unknown, there was no doubt that the number of human genes was much less ...
Gene expression profiling analysis. Medicine: Clinical decision support in ophthalmology and oncology Computational ... "A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in ...
Fan HC, Fu GK, Fodor SP (February 2015). "Expression profiling. Combinatorial labeling of single cells for gene expression ... September 2018). "Joint profiling of chromatin accessibility and gene expression in thousands of single cells". Science. 361 ( ... Cao J, Zhou W, Steemers F, Trapnell C, Shendure J (June 11, 2019). "Characterizing the temporal dynamics of gene expression in ... Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM (June 2018). "Single-cell mapping of gene expression ...
"Analysis of microarray experiments of gene expression profiling". American Journal of Obstetrics and Gynecology. 195 (2): 373- ... Genetics attempts to predict how mutations, individual genes and genetic interactions can affect the expression of a phenotype ... The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is ... A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified ( ...
"Expression profiling reveals off-target gene regulation by RNAi". Nature Biotechnology. 21 (6): 635-637. doi:10.1038/nbt831. ... Toxic effects due to over-expression of shRNAs: High level expression of shRNAs has been shown to be toxic. Strategies to ... Woods, N. B.; Bottero, V.; Schmidt, M.; Von Kalle, C.; Verma, I. M. (2006). "Gene therapy: Therapeutic gene causing lymphoma". ... or diseases associated with altered expression of endogenous genes such as drug-resistant lung cancer, neuropathic pain, ...
Although these gene-expression profiles look at different individual genes, they seem to classify a given tumor into similar ... October 2005). "Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with ... When specific DNA mutations or gene expression profiles are identified in the cancer cells this may guide the selection of ... This remains the most common method of testing for receptor status, but DNA multi-gene expression profiles can categorize ...
Gene expression profiling of Arabidopsis meiocytes. Plant Biology 13, 784-793. Roig, I., Brieno-Enriquez, M. A., Caldes, M. G ... Genes 2, 152-168. Yang, X., Makaroff, C. A., and Ma, H. (2003). The Arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-finger ...
"Global functional profiling of gene expression☆☆This work was funded in part by a Sun Microsystems grant awarded to S.D., NIH ... "Profiling Gene Expression Using Onto-Express". Genomics. 79 (2): 266-270. doi:10.1006/geno.2002.6698. Drǎghici, Sorin; Khatri, ... "Down-weighting overlapping genes improves gene set analysis". BMC Bioinformatics. 13 (1): 136. doi:10.1186/1471-2105-13-136. ... "A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures". Frontiers in Genetics. 10: ...
Cheang MC, van de Rijn M, Nielsen TO (2008). "Gene expression profiling of breast cancer". Annual Review of Pathology. 3: 67-97 ... Lersch R, Stellmach V, Stocks C, Giudice G, Fuchs E (Sep 1989). "Isolation, sequence, and expression of a human keratin K5 gene ... and cell-type-specific expression of a lacZ gene in the adult and during development". Differentiation; Research in Biological ... Keratin 5, also known as KRT5, K5, or CK5, is a protein that is encoded in humans by the KRT5 gene. It dimerizes with keratin ...
Expression profiling and novel gene discovery". J. Biol. Chem. 276 (36): 34131-41. doi:10.1074/jbc.M104271200. PMID 11427537. ... E3 ubiquitin-protein ligase ZNRF1 is an enzyme that in humans is encoded by the ZNRF1 gene. In a study identifying genes in rat ... The protein encoded by this human gene is highly similar in sequence to that encoded by the rat gene. GRCh38: Ensembl release ... "Entrez Gene: ZNRF1 zinc and ring finger 1". Hartley JL, Temple GF, Brasch MA (2001). "DNA cloning using in vitro site-specific ...
... expression profiling of stress responsive genes. Currently, he is a Professor Emeritus, School of Life Sciences, University of ... His research interests are: capturing differentially expressed genes during drought stress, cloning and functional analysis of ... promoter regions of target genes of drought response; isolation and characterization of family of drought responsive ...
Gheith OA (2011). "Gene expression profiling in organ transplantation". International Journal of Nephrology. 2011: 180201. doi: ... Cellular magnetic resonance imaging (MRI) of immune cells radiolabeled in vivo might-similarly to Gene Expression Profiling ( ... Gene Therapy Progress and Prospects: Gene therapy in organ transplantation Gene therapy in transplantation The John Iacomini ... Gene therapy is another method that can be used. In this method, the genes that cause the body to reject transplants would be ...
Gene Expression Omnibus. Retrieved 4 Apr 2015. "NHLRC2". UniGene EST Profiles. Retrieved 4 Apr 2015. "BLAST". NCBI BLAST. "BLAT ... NCBI GEO Profiles detailed several conditions under which NHLRC2 expression is increase in comparison to base expression levels ... According to NCBI GEO microarray expression patterns, as well as UniGene's Expressed Sequence Tag (EST) profiles, NHLRC2 is ... The full gene spans 62,533 base pairs (bp). Eleven exons are transcribe in the protein-coding mRNA.[failed verification] There ...
February 2002). "Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling ... Torres, TT; Metta, M; Ottenwälder, B; Schlötterer, C (January 2008). "Gene expression profiling by massively parallel ... The level of unique gene expression is represented by the count of transcripts present per million molecules, similar to SAGE ... 2000). "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays". Nature Biotechnology. ...
Hall PA, Jung K, Hillan KJ, Russell SE (July 2005). "Expression profiling the human septin gene family". The Journal of ... Septin 12 is a protein that in humans is encoded by the SEPT12 gene. This gene encodes a guanine-nucleotide binding protein and ... "Entrez Gene: Septin 12". Kuo PL, Chiang HS, Wang YY, Kuo YC, Chen MF, Yu IS, Teng YN, Lin SW, Lin YH (2013). "SEPT12- ... Lin YH, Lin YM, Wang YY, Yu IS, Lin YW, Wang YH, Wu CM, Pan HA, Chao SC, Yen PH, Lin SW, Kuo PL (May 2009). "The expression ...
"Gene expression profiling of avian macrophage activation." Veterinary Immunology and Immunopathology 105.3-4:289-99. 2006. ... "Gene expression modulation in chicken macrophages exposed to Mycoplasma synoviae or Escherichia coli." Veterinary Microbiology ... "Cloning and characterization of a putative cytadhesin gene (mgc1) from Mycoplasma gallisepticum." Infection and immunity 64.5: ...
"NCBI Gene KIAA1107". Retrieved 2016-05-08. "NCBI EST Profile KIAA1107". Retrieved 2016-05-08. "BioGPS KIAA1107 Gene Expression ... KIAA1107 is a protein that in humans is encoded by the KIAA1107 gene. KIAA1107 is a Serine-rich protein, whose expression was ... while in the diseased sample it was expressed higher than almost any other gene (95th-98th percentile of expression). Orthologs ... Expression of KIAA1107 does not appear to be ubiquitous in Homo sapiens. KIAA1107 is found to be expressed mostly in the brain ...
"High glucose-altered gene expression in mesangial cells. Actin-regulatory protein gene expression is triggered by oxidative ... ". "NCBI PRR12 Gene". "Genomatix Tools: El Dorado". "NCBI GeoProfiles db; QSER1 GDS596". "NCBI EST Profile db; QSER1". Clarkson ... This condition was studied as differential expression of genes involved in cell cycle regulation had been noted in these cells ... "ExPASy SUMOplot". Dombroski BA, Nayak RR, Ewens KG, Ankener W, Cheung VG, Spielman RS (May 2010). "Gene expression and genetic ...
Fan, Jinhong; Ngai, John (2001). "Onset of Odorant Receptor Gene Expression during Olfactory Sensory Neuron Regeneration". ... The difference in affinities causes differences in activation patterns resulting in unique odorant profiles.[7][8] The ... There are approximately 1000 different genes that code for the ORs, making them the largest gene family. An odorant will ... Bieri, S.; Monastyrskaia, K; Schilling, B (2004). "Olfactory Receptor Neuron Profiling using Sandalwood Odorants". Chemical ...
February 2001). "Differential gene expression profiling in human brain tumors". Physiological Genomics. 5 (1): 21-33. doi: ... In major depressive disorder, the expressions of GABAA subunit genes were altered, and the expression of GABRB2 was ... September 2005). "Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism ... Zhao J, Bao AM, Qi XR, Kamphuis W, Luchetti S, Lou JS, Swaab DF (May 2012). "Gene expression of GABA and glutamate pathway ...
Purcell M, Kruger A, Tainsky MA (2014-12-15). "Gene expression profiling of replicative and induced senescence". Cell Cycle. 13 ... G2: Fission yeast expressing some mutant forms of CDC2 unable to arrest in G2 in response to DNA damage, indicating the gene ... Genetic engineering of cells with specific gene knockouts can also result in cells that arrest at different phases of the cell ... M: A mutant screen of budding yeasts with mitotic arrest identified CDC16, CDC23, and CDC27 as key genes that, when mutated, ...
Forward and reverse suppression subtractive hybridization were used to generate profiles of gene over and under expression, and ... This allows for significantly expanded gene expression profiling. Arrays may be purchased from commercial suppliers tailored to ... Protocol for differential display, reverse northern and qPCR analysis of expression screening of gene expression difference ... Gene expression Northern blot RNA Seq Southern blot Primrose, Sandy B.; Twyman, Richard (2009-04-01). Principles of Genome ...
"Gene Expression Omnibus (GEO) Profile For GDS3834". National Center For Biotechnology Information (NCBI). Retrieved 9 May 2016 ... "Gene Expression Omnibus (GEO) Profile". National Center For Biotechnology Information. Retrieved 6 May 2016. "c10orf35". The ... This gene is located at locus 10q22.1. The physical properties of the c10orf35 protein were analyzed, and the molecular weight ... Chromosome 10 open reading frame 35 (c10orf35) is a gene that in humans, encodes for a protein-binding, transmembrane protein. ...
Clerk A, Kemp TJ, Zoumpoulidou G, Sugden PH (April 2007). "Cardiac myocyte gene expression profiling during H2O2-induced ... characterization and expression of a gene with a remarkable promoter". EMBO J. 4 (2): 437-43. doi:10.1002/j.1460-2075.1985. ... C20orf111 gene has no clear paralogs in the human genome. However, it has many orthologs in other organisms, and is conserved ... A few of the known genes near C20orf111 are given in the box below with their known function. Genomic DNA Length:14,968 base ...
Glinsky GV, Glinskii AB, Stephenson AJ, Hoffman RM, Gerald WL (Mar 2004). "Gene expression profiling predicts clinical outcome ... Krueppel-like factor 6 is a protein that in humans is encoded by the KLF6 gene. It is a tumor suppressor gene. This gene ... and/or maintenance of the basal expression of pregnancy-specific glycoprotein genes and possibly other TATA box-less genes. Two ... "Entrez Gene: KLF6 Kruppel-like factor 6". Botella LM, Sánchez-Elsner T, Sanz-Rodriguez F, Kojima S, Shimada J, Guerrero-Esteo M ...
June 2003). "Expression profiling reveals off-target gene regulation by RNAi". Nature Biotechnology. 21 (6): 635-7. doi:10.1038 ... Herndon MK, Quirk CC, Nilson JH (January 2016). "Chapter 2 - Control of Hormone Gene Expression". In Jameson JL, De Groot LJ, ... If siRNA is able to successfully reach its target, it has the potential to therapeutically regulate gene expression through its ... So far, applications of antisense RNAs in antivirus and anticancer treatments and in regulating the expression of related genes ...
Gene Expression and Profiling: gene arrays, real-time PCR. Mass Spectrometry: qualitative, quantitative, and structural ... Flow Cytometry Fluorescence Activating Cell Sorting Protein Expression, Identification, and Profiling: differential ... 2011 Sir Alec John Jeffreys: Developed techniques for DNA fingerprinting and DNA profiling 2010 Pat Brown: Pioneering work in ... Eugene A.; Lam, Henry H. N.; McDonald, W. Hayes; Neubert, Thomas A.; Sun, Rui-Xiang (2014). "Proteome informatics research ...
Glinsky GV, Glinskii AB, Stephenson AJ, Hoffman RM, Gerald WL (2004). "Gene expression profiling predicts clinical outcome of ... "Genomic sequence and expression analyses of human chromatin assembly factor 1 p150 gene". Gene. 264 (2): 187-96. doi:10.1016/ ... CHAF1A human gene location in the UCSC Genome Browser. CHAF1A human gene details in the UCSC Genome Browser. v t e. ... "Entrez Gene: CHAF1A chromatin assembly factor 1, subunit A (p150)". Mello JA, Silljé HH, Roche DM, Kirschner DB, Nigg EA, ...
"Conjugated bile acid-activated S1P receptor 2 is a key regulator of sphingosine kinase 2 and hepatic gene expression". ... "Efficacy, patient-reported outcomes and safety profile of ATX-101 (deoxycholic acid), an injectable drug for the reduction of ... also known by its gene name NR1H4.[15][16][17] Another bile acid receptor is the cell membrane receptor known as G protein- ...
... appearance-observable traits caused by the expression of a condition's genes. The features of craniosynostosis' particular ... defining a syndrome-specific risk profile". Journal of Plastic, Reconstructive & Aesthetic Surgery. 63 (10): 1635-41. doi: ... in FGFR genes) and mutations that lead to loss of function (in TWIST genes).[38][39] Craniosynostosis is therefore likely the ... Gene Loeys-Dietz syndrome wide-set eyes • split uvula or cleft palate • arterial tortuosity • aortic root dilatation • ...
... classical QTL analyses were combined with gene expression profiling i.e. by DNA microarrays. Such expression QTLs (eQTLs) ... Several genes factor into determining a person's natural skin color, so modifying only one of those genes can change skin color ... The DNA sequence of any genes in this region can then be compared to a database of DNA for genes whose function is already ... It may indicate that plant height is controlled by many genes of small effect, or by a few genes of large effect. ...
2009). «Fibulin-4 regulates expression of the tropoelastin gene and consequent elastic-fibre formation by human fibroblasts». ... 2009). «Association of genetic variants with chronic kidney disease in individuals with different lipid profiles». Int. J. Mol ... Ontologia do gene. Função molecular. •extracellular matrix structural constituent. •protein binding. •extracellular matrix ... Rosenbloom J (1984). «Elastin: relation of protein and gene structure to disease». Lab. Invest. 51 (6): 605-23. PMID 6150137. ...
Early examples of artistic expression, such as the Venus of Tan-Tan and the patterns found on elephant bones from Bilzingsleben ... It is thought that wild foods can have a significantly different nutritional profile than cultivated foods.[117] The greater ... "Chimps, Humans 96 Percent the Same, Gene Study Finds". Retrieved 23 December 2013 ...
The video exploits Tilton's facial expressions and preaching style. The original video contained no title screen and was ... Some of Tilton's fundraising letters were written by Gene Ewing, who heads a multimillion-dollar marketing empire writing ... to the Trinity Foundation for help told him they had lost all of their money making donations to some of the higher profile ...
"Expression profile of active genes in human periodontal ligament and isolation of PLAP-1, a novel SLRP family gene". Gene. 275 ... "Expression pattern and gene characterization of asporin. a newly discovered member of the leucine-rich repeat protein family". ... "Entrez Gene: ASPN asporin". مؤرشف من الأصل في 05 ديسمبر 2010. الوسيط ,مسار أرشيف=. تم تجاهله (مساعدة); الوسيط ,تاريخ أرشيف=. تم ... Yamada S، Ozawa Y، Tomoeda M، Matoba R، Matsubara K، Murakami S (May 2006). "Regulation of PLAP-1 expression in periodontal ...
2002). "Regulated expression of the apolipoprotein E/C-I/C-IV/C-II gene cluster in murine and human macrophages. A critical ... "DNA sequence variation in human apolipoprotein C4 gene and its effect on plasma lipid profile". Atherosclerosis. 152 (1): 193- ... Apolipoprotein (apo)C4 gene is a member of the apolipoprotein C gene family. It is expressed in the liver and has a predicted ... Apo C4 is a 3.3-kb gene consisting of 3 exons and 2 introns; it is located 0.5 kb 5' to the APOC2 gene.[5] ...
Rush J، Moritz A، Lee KA، Guo A، Goss VL، Spek EJ، Zhang H، Zha XM، Polakiewicz RD، Comb MJ (2005). "Immunoaffinity profiling ... Miehe U، Kadyrov M، Neumaier-Wagner P، Bartz C، Rath W، Huppertz B (2007). "Expression of the actin stress fiber-associated ... Gene. 165 (2): 267-71. PMID 8522188. doi:10.1016/0378-1119(95)00542-E. .mw-parser-output cite.citation{font-style:inherit}.mw- ... Brill LM، Salomon AR، Ficarro SB، Mukherji M، Stettler-Gill M، Peters EC (2004). "Robust phosphoproteomic profiling of tyrosine ...
Such a gene that exhibits multiple phenotypic expression is called a pleiotropic gene . Therefore mutation in a pleiotropic ... "Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and ... One basic model of pleiotropy's origin describes a single gene locus to the expression of a certain trait. The locus affects ... Sickle cell anemia is a pleiotropic disease because the expression of a single mutated HBB gene produces numerous consequences ...
"Control of Gene Expression". The Medical Biochemistry Page (en inglés). Consultado o 19 de setembro de 2008.. ... "Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles" (PDF). Proceedings of the National ... Serial Analysis of Gene Expression, Análise en serie da expresión xénica), MPSS (Massively Parallel Signature Sequencing, ... "Anatomy of a Comparative Gene Expression Study" (en inglés). Washington University in St. Louis - Dpt. of Computer Science & ...
For example, increased maternal licking and grooming has been shown to alter expression of the glutocorticoid receptor gene ... Stressors that are uncontrollable, threaten physical integrity, or involve trauma tend to have a high, flat diurnal profile of ... de Kloet ER, Sibug RM, Helmerhorst FM, Schmidt MV, Schmidt M (April 2005). "Stress, genes and the mechanism of programming the ... Kim JE, Cho BK, Cho DH, Park HJ (July 2013). "Expression of hypothalamic-pituitary-adrenal axis in common skin diseases: ...
de Kloet, RS; de Kloet SR (2005). "The evolution of the spindlin gene in birds: Sequence analysis of an intron of the spindlin ... The verb "parrot" in the dictionary means "to repeat by rote". Also clichés such as the British expression "sick as a parrot" ... Measures taken to conserve the habitats of some high-profile charismatic species have also protected many of the less ... Conservation measures to conserve the habitats of some of the high-profile charismatic parrot species has also protected many ...
In budding yeast, the candidate gene for activation of histone gene expression is SBF. SBF is a transcription factor that is ... Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (May 2007). "High-resolution profiling of ... This affects their function of gene regulation. In general, genes that are active have less bound histone, while inactive genes ... NPAT activates histone gene expression only after it has been phosphorylated by the G1/S-Cdk cyclin E-Cdk2 in early S phase.[ ...
In 1988 Ed Harlow demonstrates that cancer-causing and cancer-preventing genes (oncogenes and tumor-suppressor genes) interact; ... 21] See the classic paper McClintock B 1951 "Chromosome Organization and Genic Expression" (Cold Spring Harbor Symp. Quant. ... In 2011, Wigler, James Hicks and Nick Navin perform the first genomic profile of single cancer cells from a patient's tumor;[42 ... The program began as an initiative of Eugene G. Blackford and Franklin Hooper, director of the Brooklyn Institute of Arts and ...
Their subsequent work shows how the SREBP pathway regulates expression of many genes that control lipid formation and ... sample taken after fasting is taken by a doctor or a home cholesterol monitoring device to determine a lipoprotein profile. ... of a number of genes to stimulate their transcription. Among the genes transcribed are the LDL receptor and HMG-CoA reductase. ...
Mohamed Adhikari (2004). "'Not Black Enough': Changing Expressions of Coloured Identity in Post-Apartheid South Africa" (PDF). ... a number of high-profile cases highlighted the legal and community attitude that identifying as Aboriginal or Torres Strait ... "Sex-biased gene flow in African Americans but not in American Caucasians", GMR, 2007, Vol. 12, No. 6. ...
2006). "Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma". Int. J. Cancer. 118 (5): 1165-72. doi: ... Güre AO, Wei IJ, Old LJ, Chen YT (2002). "The SSX gene family: characterization of 9 complete genes". Int. J. Cancer. 101 (5): ... 2003). "A novel fusion gene, SS18L1/SSX1, in synovial sarcoma". Genes Chromosomes Cancer. 37 (2): 195-200. doi:10.1002/gcc. ... This article on a gene on the human X chromosome and/or its associated protein is a stub. You can help Wikipedia by expanding ...
The genes expressions are mapped in a control sample to formulate a developmental chart of the gene expression at certain time ... Gene expression studies[edit]. Although physical characteristics and sizes at various instars have been used to estimate fly ... This is done by breaking the stages down into smaller units separated by predictable changed in gene expression.[33] Three ... This chart can then be compared to the measured values of gene expression to accurately predict the age of an egg to within two ...
profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. Search. ... "Gastric and intestinal phenotypes of gastric carcinoma with reference to expression of brain (fetal)-type glycogen ... More than 65 mutations in the PYGM gene that lead to McArdle disease have been identified to date.[15][16] Symptoms of McArdle ... in the glycogen phosphorylase gene in a patient with hepatic glycogen storage disease and residual enzyme activity". Molecular ...
"Interactive Drug Analysis Profile - Isotretinoin". Medicines & Healthcare Products Regulatory Agency. 31 March ... Isotretinoin is also thought to affect the serotonergic system - it increases expression of 5-HT1A receptors in the pre- ... schizophrenia and the retinoid cascade have been linked to the same gene loci;[47] and retinoid dysfunction causes congenital ... "Thyroid hormones and retinoids: a possible link between genes and environment in schizophrenia" (PDF). Brain Research Reviews ...
profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. Search. ... "SOD1 mRNA expression in sporadic amyotrophic lateral sclerosis". Neurobiology of Disease. 39 (2): 198-203. doi:10.1016/j.nbd. ... The genes are located on chromosomes 21, 6, and 4, respectively (21q22.1, 6q25.3 and 4p15.3-p15.1). ... but more than 5-fold in mutants deleted for either the SOD1 or SOD2 genes.[31] Reactive oxygen species levels increase with age ...
Gene expression profiling revealed the prevalence of specific fibroblast growth factors (FGFs) and FGF receptors in NSCLC cell ... Recent research revealed that IL-6 secretion induced by HER2 overexpression activated STAT3 and altered gene expression, ... In addition, expression of PDGFRα and -β correlated with invasive behavior in human mammary carcinomas. This indicates the ... It has been shown that phosphorylation of STAT3 and RANTES expression are increased in response to tamoxifen in human breast ...
... a potential biomarker identified by laser-capture microdissection-micro serial analysis of gene expression of human prostate ... Over-expression and ectopic expression of the protein may be associated with prostate adenocarcinoma.[3] ... Dicarbonyl/L-xylulose reductase, also known as carbonyl reductase II, is an enzyme that in human is encoded by the DCXR gene ... The DCXR gene encodes a membrane protein that is approximately 34 kDa in size and composed of 224 amino acids. The protein is ...
... mutations in other genes are rare.[1] People who have one abnormal copy (are heterozygous) of the LDLR gene may develop ... Class II: LDLR is not properly transported from the endoplasmic reticulum to the Golgi apparatus for expression on the cell ... and each are classified from both the altered lipid profile and by the genetic abnormality. For example, high LDL (often due to ... Abnormalities in the ARH gene, also known as LDLRAP1, were first reported in a family in 1973.[14] In contrast to the other ...
Palladino, Paolo (June 2002). "Review of The Century of the Gene by Evelyn Fox Keller". The British Journal for the History of ... "Photoinactivation and the Expression of Genetic Information in Bacteriophage-Lambda"[2] (1963). ... "Community of Scholars Profile". Institute for Advanced Study website. Institute for Advanced Study. Retrieved 16 February 2013. ... "Review of The Century of the Gene by Evelyn Fox Keller". Kirkus Reviews. 1 October 200.. ...
Eugene Paul Wigner; Andrew Szanton (1992). Andrew Szanton, ed. The Recollections of Eugene P. Wigner As Told to Andrew Szanton ... nor even with an expression of emotional antipathy, for he loved to use religious expressions and metaphors, but simply by ... Horgan, J. (1992) Profile: Hans A. Bethe - Illuminator of the Stars, Scientific American 267(4), 32-40. ... Eugene Dynkin (1924-2014): Soviet and American mathematician. He has made contributions to the fields of probability and ...
A high-profile recall in 2009-2010 involving Toyota vehicles with throttles that became stuck in the open position may have ... Homi J. Bhabha derived an expression for the probability of scattering positrons by electrons, a process now known as Bhabha ... Shielding Space Travelers by Eugene Parker.. *Anomalous cosmic ray hydrogen spectra from Voyager 1 and 2 ...
"Profile Books. Retrieved 6 December 2015.. *^ Hello Igor... Daniel Radcliffe gets into character on the set of the brand new ... Gene Wilder portrayed the descendant of Dr. Frankenstein (who insists on pronouncing it "Fronkonsteen"), with Peter Boyle as ... "the author's original genius and happy power of expression" (620), although he is less convinced about the way in which the ... 2012: An interactive ebook app created by Inkle and Profile Books that retells the story with added interactive elements.[69] ...
"Profiles in Science. United States National Library of Medicine. Archived from the original on May 5, 2009.. ... l-gulonolactone oxidase coding gene.[185] In 2008, researchers at the University of Montpellier discovered that in humans and ... so that enzyme expression peaks in the morning to support biosynthesis later on when mid-day sunlight intensity demands high ... Lachapelle, MY; Drouin, G (2010). "Inactivation dates of the human and guinea pig vitamin C genes". Genetica. 139 (2): 199-207 ...
... gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global ... Categorizing regulated genes[edit]. Having identified some set of regulated genes, the next step in expression profiling ... is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global ... Gene set analysis demonstrated several major advantages over individual gene differential expression analysis.[17][18] Gene ...
Gene expression (GE) analyses by use of microarrays (MAs) have become an important part of biomedical and clinical research and ... Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of ... Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med. 2004;350:1617-1628.CrossRefPubMedGoogle ... Gene expression profiling of pediatric acute myelogenous leukemia. Blood. 2004;104:3679-3687.CrossRefPubMedGoogle Scholar ...
Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Measurement of gene expression profiles in toxicity determination. US6479235. 25 Nov 1998. 12 Nov 2002. Promega Corporation. ... Methods and systems for dynamic gene expression profiling. WO2004048528A2. 21 Nov 2003. 10 Jun 2004. Primera Biosystems. ...
At the facility, researchers will use image analysis technology and molecular biology processes to generate gene expression ... Rosetta Inpharmatics inaugurated Thursday a new gene expression profiling facility in Bothell, Wash. ... NEW YORK, December 14 - Rosetta Inpharmatics inaugurated Thursday a new gene. expression profiling facility in Bothell, Wash.. ... Our new facility in Bothell will help us further our efforts in gene. expression research, and will advance our goal to develop ...
The phenotypic expression of these genes, through the synthesis of specific proteins, involves interaction with envi ... The genetic basis for disease is determined by the inheritance of genes containing specific sequences of deoxyribonucleic acid ... changes in gene expression take place that result in the expression of hundreds of gene products and the suppression of others ... Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U ...
A novel technique for carrying out gene-expression profiling is set to challenge the market dominance of the current, widely ... Some scientists believe that digital gene-expression profiling, a fully quantitative approach for gene-expression analysis, ... A novel technique for carrying out gene-expression profiling is set to challenge the market dominance of the current, widely ... Tags: Biotechnology, Gene, Gene Expression, Genetic, Genetic Engineering, Genetics, Genome, Illumina, Life science, Microarray ...
Elucidation of β-Oxidation Pathways in Ralstonia eutropha H16 by Examination of Global Gene Expression Christopher J. Brigham, ... A Systems Biology Approach To Modeling Vibrio cholerae Gene Expression under Virulence-Inducing Conditions Sanjat Kanjilal, ... Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity Melanie J. ... GENE REGULATION. Transcriptomic and Phenotypic Characterization of a Bacillus subtilis Strain without Extracytoplasmic Function ...
Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. ... Expression profiling reveals off-target gene regulation by RNAi.. Jackson AL1, Bartz SR, Schelter J, Kobayashi SV, Burchard J, ... Transcript profiles revealed siRNA-specific rather than target-specific signatures, including direct silencing of nontargeted ... genes containing as few as eleven contiguous nucleotides of identity to the siRNA. These results demonstrate that siRNAs may ...
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... might be captured by profiling gene expression using DNA microarrays. Indeed, microarray profiling studies have identified ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer Message Subject (Your Name) has sent you a ...
... of phthalate toxicity in normal human cells and to provide information concerning inter-individual variation and gene- ... Gwinn MR, Whipkey DL, Tennant LB, Weston A [2007]. Gene expression profiling of di-n-butyl phthalate in normal human mammary ... Gene Expression Profiles of Di-n-butyl Phthalate in Normal Human Mammary Epithelial Cells. ... Data Mining Tool software (Affymetrix) was used to separate genes in clusters based on their expression patterns over time. ...
Our study provides a comprehensive picture of the gene expression landscape in hepatocytes grown on different substrate ... 1370 genes that were up-regulated and 2677 down-regulated genes on stiff substrate. Functional enrichment analysis indicated ... Differentially expressed gene Hepatocyte RNA-sequencing Substrate stiffness Tingting Xia and Runze Zhao contributed equally to ... Email authorView authors OrcID profile. *1.Key Laboratory of Biorheological Science and Technology, Ministry of Education, ...
Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, and ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis Message Subject (Your Name) has sent you a ...
A gene expression-based recurrence predictor algorithm was informative in predicting the outcome in patients with early-stage ... We analyzed expression profiles of 12,625 transcripts in prostate tumors from patients with distinct clinical outcomes after ... Prostate tumor samples were taken from the patients at the time of surgery and subjected to a microarray gene expression ... PAIs defined by the expression profile of the prostate cancer recurrence predictor signature 1 for 21 prostate carcinoma ...
Flagellar-associated genes:. We profiled expression of several less well-characterized genes recently shown to be present in ... Evaluation of the gene expression profiles identified ,100 clones showing at least a twofold change in expression during ... qRT-PCR expression profiling of selected genes:. We selected several genes from various categories that demonstrated ... Our genomic expression profiling uncovered differential expression of several genes involved in the cellular response to ...
Tumor Gene Expression Profiling To Predict Risk of Breast Cancer Recurrence: EGAPP™ Recommendation.  alert icon ... Several gene expression profiles (GEPs) are clinically available that provide variations on "recurrence risk scores" intended ... The EGAPP™ Working Group examined the scientific evidence to see whether gene expression profiling is valid and useful for this ... Summary of Findings on Gene Expression Profiling To Predict Risk for Breast Cancer Recurrence. In 2009, the independent ...
Through gene expression profiling, UC Davis neuroscientists are discovering ways to monitor brain health and predict strokes, ... Gene Expression Profiling. Through gene expression profiling, researchers are working to find ways to monitor brain health and ... Using the latest microarray technology, researchers are creating gene expression profiles of people who have suffered strokes ... and other cerebrovascular disorders and comparing those to the gene expression profiles of healthy subjects and those who have ...
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Gene expression data (GSE29801: NCBI, Geo) of macular and extramacular specimens of the retinas and retinal pigment epithelium ... Gene lists defined by cladogram nodes showed that the AMD-related deregulations occurring in the neural retina were different ... Gene lists from cladograms nodes were processed in Genomatix GePS to reveal the affected signaling pathway networks. ... Our analysis suggests a more complex transcriptional profile of the phenotypes than expected. Evaluation of the disease in much ...
... and gene expression profiling can be particularly helpful.. Several gene expression profiling tests exist, and many are being ... Gene expression profiling tests (Oncotype DX, MammaPrint, others) analyze a number of different genes within your cancer cells ... Ive heard that a gene expression profiling test might help in planning my treatment. What is it?. Answer From Sandhya Pruthi, ... The results of gene expression profiling tests help doctors determine who may benefit from additional (adjuvant) treatment ...
DNA Microarray-Based Gene Expression Profiling in Cancer: Aiding Cancer Diagnosis, Assessing Prognosis and Predicting Response ... Using DNA microarrays, the expression of tens of thousands of genes in a biological sample can be detected in one experiment. ...
Gene expression profile/profiling (GEP): The individual pattern of expression of a panel of genes that is regarded as a " ... Gene expression was examined using high-density oligonucleotide arrays. An analysis showed that gene expression profiling of ... class 2 gene expression profile signature and a negative SLNB result and individuals with a class 2 gene expression profile ... "gene expression profile class assignment of different sign for the tumor cells obtained from the two sites or a failed gene ...
Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR ... DNA databases and DNA profiling posted by the @ 3/12/2007 07:25:00 PM DNA databases and DNA profiling ...
QIAGEN offers a range of solutions for profiling pathogen gene expression. Our tools provide efficient mechanical disruption of ... For fast, one-step qRT-PCR using sequence-specific probes for gene expression analysis Show details ... Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ... Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ...
Isolation of specific neurons from C. elegans larvae for gene expression profiling.. Spencer WC1, McWhirter R1, Miller T2, ... Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of ... Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling ... Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling ...
Other articles related to gene, gene expression, expression, expression profiling, gene expression profiling, genes:. ... Gene expression profiling In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are ... Gene Expression Profiling. In the field of molecular biology, gene expression profiling is the measurement of the activity (the ... Gene Expression Profiling - Conclusions. ... Expression profiling provides new information about what genes do under various ...
... Julie Anne Côté,1,2,3 Frédéric Guénard,3 ... To characterize changes in gene expression profile during human mature adipocyte dedifferentiation in ceiling culture. Methods ... Gene expression analysis at days 0, 4, 7, and 12 of the cultures was performed using Affymetrix Human Gene 2.0 STvi arrays. ... Four clusters gathered genes with similar expression between day 4 to day 7 but decreasing expression from day 7 to day 12. ...
... solutions for high-quality gene expression and transcriptome analysis and profiling studies. ... and high confidence mapping of alternate transcripts and gene fusions. Discover novel gene isoforms, profile gene expression ... Analyze Gene Expression in Single Cells. Highly sensitive RNA-Seq methods enable gene expression analysis of very low-input ... RNA-Seq for Gene Expression Analysis. Illumina offers a complete, accessible RNA-Seq workflow solution for gene expression and ...
This review highlights the gene expression profile of androgen independent prostate cancer and the possible mechanisms that ... M. Omabe, J. C. Onyeanusi, N. Amos, M. Ezeani and S. Imakwu Okekpa, "Gene Expression Profile, Androgen Independence and ... This review highlights the gene expression profile of androgen independent prostate cancer and the possible mechanisms that ... "Genome-Wide Expression Profiling Reveals Transcriptomic Variation and Perturbed Gene Networks in Androgen-Dependent and ...
Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles ... The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously ... The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously ... Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles ...
  • DNA microarrays [1] measure the relative activity of previously identified target genes. (
  • Gene expression (GE) analyses by use of microarrays (MAs) have become an important part of biomedical and clinical research and the resulting data may provide important information regarding pathogenesis and be extrapolated for use in diagnosing/prognosticating lymphomas and leukemias. (
  • DNA microarrays forcomparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers. (
  • Some scientists believe that digital gene-expression profiling, a fully quantitative approach for gene-expression analysis, will eventually rival microarrays in this application area, according to the April 1 issue of GEN . (
  • To explore potential molecular variation underlying this clinical heterogeneity, we profiled gene expression in 62 primary prostate tumors, as well as 41 normal prostate specimens and nine lymph node metastases, using cDNA microarrays containing ≈26,000 genes. (
  • To further characterize the clinical relevance of tumor subtypes, we evaluated as surrogate markers two genes differentially expressed among tumor subgroups by using immunohistochemistry on tissue microarrays representing an independent set of 225 prostate tumors. (
  • The observed clinical heterogeneity of prostate cancer is likely to reflect underlying molecular heterogeneity among tumors, which, although largely invisible under the light microscope, might be captured by profiling gene expression using DNA microarrays. (
  • Gene transcription in each of 4 cell strains was analyzed using high-density oligonucleotide DNA microarrays (U133A, Affymetrix™) and changes in the expression of selected genes were verified by real-time polymerase chain reaction. (
  • The application of DNA microarrays allows the expression of hundreds to many thousands of genes to be monitored simultaneously, providing a broad and integrated picture of the way an organism responds to a changing environment ( 4 ). (
  • Using DNA microarrays, the expression of tens of thousands of genes in a biological sample can be detected in one experiment. (
  • 17.5K cDNA microarrays were utilized to profile the biopsy material. (
  • The advent of next-generation sequencing has made sequence based expression analysis an increasingly popular, "digital" alternative to microarrays called RNA-Seq. (
  • Current cancer research makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides known as probes are covalently attached to a solid surface such as glass, forming what is known as a gene chip. (
  • To determine whether abnormal expression of genes encoding proteins involved in cellular metabolism contributes to this dysfunction, we used cDNA microarrays to perform gene expression profiling of all major metabolic pathways in postmortem samples of PFC area 9 from 10 subjects with schizophrenia and 10 matched control subjects. (
  • Using Affymetrix microarrays, 1707 transcripts were identified with a more than twofold increase in expression in O4 + oligodendrocytes. (
  • Microarrays used in combination with fluorescence-activated cell sorting (FACS), is a particularly powerful strategy, because a large number of known and novel genes can be simultaneously assayed in purified populations of cells prospectively isolated from their native microenvironment within the developing brain. (
  • In this study, we used Affymetrix rat microarrays to compare gene expression profiles during the transition from A2B5 + oligodendrocyte progenitors to O4 + oligodendrocytes. (
  • Microarrays, also known as gene chips, are glass slides that have been coated with thousands of spots of DNA, each representing a different gene. (
  • Expression profiling using DNA microarrays has been very helpful to improve our knowledge of the pathobiology of many tumour types, including lymphomas. (
  • However, microarrays are being a helpful tool in the initial task of dissecting the PTCL expression profile. (
  • Writing in the May 18 issue of the journal Cancer Cell, Perou, also a member of the UNC Lineberger Comprehensive Cancer Center, and colleagues from UNC and Vanderbilt University presented their findings based on the gene expression patterns of 60 head and neck tumor samples that were assayed using DNA microarrays, a technology Perou pioneered. (
  • Expression profiling of blood by microarrays has been historically difficult due to the heterogeneous cellular nature of blood samples and the extremely high concentration of globin transcript present in whole blood total RNA. (
  • Researchers use DNA microarrays, or gene chips, to distinguish among different types of tissues based on the expression patterns of thousands of genes. (
  • The recommendations in this document are applicable to RNA expression assays used for cancer prognosis, such as reverse-transcriptase polymerase chain reaction (RT-PCR) and gene expression microarrays. (
  • We measured genome-wide gene expression in individual dissected brains from nurses and foragers using a total of 72 microarrays ( 17 ). (
  • Comparative analysis of gene expression profiles was performed using the dCHIP software and Significance Analysis of Microarrays (SAM) The sorting and classification of significant genes into different biological processes was conducted using PANTHER. (
  • The purpose of the current study was to investigate the expression of various groups of genes at different stages of aneurysm age in elastase-induced saccular aneurysms in rabbits through the use of deoxyribonucleic acid (DNA) microarrays. (
  • The development of gene-chip complementary deoxyribonucleic acid (DNA) microarrays has been made it possible to examine simultaneous expression of thousands of gene products in the same experiment. (
  • Here, we use adenoviral vectors and oligonucleotide microarrays to determine the effects of the forced expression of SREBP1c on the gene expression profile of rat islets. (
  • Then, we tested the significant changes in single genes by different methods like t test, Significance Analysis of Microarrays, and Bayesian ANOVA analysis. (
  • In the field of molecular biology , gene expression profiling is the measurement of the activity (the expression ) of thousands of genes at once, to create a global picture of cellular function. (
  • The tool is at the heart of a new study that divides similar-looking kidney tumors into subtypes depending on which of thousands of genes are turned on or off. (
  • Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. (
  • Transcriptome analysis experiments can characterize transcriptional activity (coding and non-coding), focus on a subset of relevant target genes and transcripts, or profile thousands of genes at once to create a global picture of cell function. (
  • Researchers analyzed thousands of genes in lymphoma biopsy samples from patients with DLBCL and determined that the activity of as few as 17 genes could be used to predict patients' response to treatment. (
  • Scientists use the pattern and intensity of light emitted to determine the activity of each of the chip's thousands of genes. (
  • This technology allows us to determine the expression level of tens of thousands of genes at once," Perou said. (
  • By using an array containing many DNA samples, scientists can determine, in a single experiment, the expression levels of hundreds or thousands of genes within a cell by measuring the amount of mRNA bound to each site on the array. (
  • Heat maps of gene expression values show how experimental conditions influenced production (expression) of mRNA for a set of genes. (
  • Genes contain the instructions for making messenger RNA ( mRNA ), but at any moment each cell makes mRNA from only a fraction of the genes it carries. (
  • Expression profiling experiments often involve measuring the relative amount of mRNA expressed in two or more experimental conditions. (
  • This topic will focus on the role of mRNA in the cell, platforms for profiling mRNA expression, the challenges in interpreting the data from these analyses, and the emerging clinical applications of gene expression measurements. (
  • While almost all cells in an organism contain the entire genome of the organism, only a small subset of those genes is expressed as messenger RNA (mRNA) at any given time, and their relative expression can be evaluated. (
  • Analysis revealed activation of several key pathways including genes involved in glucose metabolism, mRNA translation, and cytoskeletal remodeling. (
  • Gene expression refers to the transcription of the information contained within DNA, the repository of genetic information, into messenger RNA (mRNA) molecules that are then translated into the proteins that perform most of the cells' critical functions. (
  • Scientists then study the kinds and amounts of mRNA produced by a cell to learn which genes are expressed, which in turn provides insights into how the cell responds to its changing needs. (
  • With the aid of a computer, and the use of fluorescent "tags," the amount of mRNA bound to the spots on the microarray can be visualized and precisely measured, generating a profile of gene expression in the cell. (
  • The Mouse RiboPure™-Blood RNA isolation Kit and GLOBINclear™ Mouse/Rat Globin mRNA depletion technology were used to determine their potential benefits for gene expression profiling. (
  • Traces from 1:20 dilution of one representative whole blood aRNA sample and duplicate non-diluted GLOBINclear Kit samples were overlaid to observe the effects of globin mRNA depletion on aRNA profile. (
  • A multiplex quantitative mRNA gene expression assay in the transfected primary duodenal cells via the transfection reagent and AgNPs with pIREGFP-H5 revealed expression of interleukin (IL)-18, IL-15, and IL-12β. (
  • fined a ranked list of HIF-target genes and experimentally validated ANKRD37 as a novel HIF-1 target. (
  • We describe a method to sort single mammalian cells and to quantify the expression of up to 96 target genes of interest in each cell. (
  • While many SREBP target genes have recently been defined in a combinatorial analysis of gene profiles of livers from SREBP2 and SREBP1a-expressing mice ( 10 ), no information on the targets for SREBP1c in the islet or β-cell are presently available at the transcriptome level. (
  • These patterns will identify critical target genes, discern possible mechanisms involved in ER-mediated modulation of sperm parameters and discover roles for genes with unknown function. (
  • A transcriptomic profiling of these phenotypes will elucidate the affected signaling pathways, reveal their similarities and differences, and clarify whether AMD's phenotypes represent a single disease or entities of an assemblage of diseases. (
  • The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously promises a significant advance in understanding toxic mechanisms to ultimately aid in protection of public health. (
  • Genes comprising 71 metabolic pathways were assessed in each pair, and only five pathways showed consistent changes (decreases) in subjects with schizophrenia. (
  • The present report demonstrates that only five of the metabolic pathways examined showed consistent changes (decreases) in subjects with schizophrenia and that four of these groups are linked together by the presence of overlapping gene members. (
  • Expression profiling revealed marked up-regulation of energy, protein translation, and cytoskeletal remodeling pathways in mesothelioma. (
  • Within H-MM, four independently validated patient clusters overexpressing nonoverlapping sets of genes that form cognate pathways/networks that have potential biological importance in multiple myeloma were identified. (
  • The biological pathways with altered gene expression after UV-light exposure were distinct for each subtype and contained oncogenic related functions such as perturbation of cell cycle, apoptosis, proliferation and differentiation. (
  • Genes that were differentially expressed between BCP ALL subtypes were enriched to distinct signaling pathways with dic(9;20) enriched to TP53 signaling, t(9;22) to interferon signaling, as well as high hyperdiploidy and t(12;21) to apoptosis signaling. (
  • We generated expression profiles of 93 genes in 363 specific cells from L1 stage larvae and found that cells with identical fates can be formed by different gene regulatory pathways. (
  • Multiple genes in diverse pathways have been differentially expressed in the rabbit aneurysm model. (
  • 14 We believe that global analysis of multiple genes will provide information useful in identifying important functional pathways involved in the pathobiology of aneurysms. (
  • In the present study, we extended our previous work and applied the microarray technology to study the global expression of genes at 2 time points following experimental aneurysm creation, to study temporal changes in multiple pathways potentially important in aneurysm pathology. (
  • Our findings lay the groundwork for establishing gene expression profiles that may aid in the diagnosis and prognosis of pediatric ACT, and in the identification of signaling pathways that contribute to this disease. (
  • Among the genes identified by sequence similarity were several involved in photosynthetic pathways, including fucoxanthin-chlorophyll a/c light harvesting protein and a C4-specific pyruvate, orthophosphate dikinase. (
  • The observed differences in gene expression have to be further analyzed in order to gain insight into the molecular pathways leading to sporadic early-onset CRC. (
  • Microarray analysis of these cells also revealed a unique gene fingerprint with key signaling pathways involved in autoimmunity being modulated. (
  • Gene expression profiling technologies like RNA sequencing (RNA-seq) enable a more comprehensive characterization of compounds by measuring the activity of molecular pathways. (
  • Consequently, reliable pathway insights can be obtained at high throughput and relatively low cost while not being limited to a predefined set of genes or pathways. (
  • Because the list of gamma-secretase substrates is growing quickly and this enzyme is a cancer and Alzheimer's disease therapeutic target, the mapping of gamma-secretase activity susceptible gene transcription is important for sharpening our view of specific affected genes, molecular functions and biological pathways. (
  • DE genes were functioning in fatty acid oxidation, signaling pathways and immune-related pathways. (
  • We believe that large-scale gene expression study may present promising new insights on hormone effects through still unclear multiple pathways. (
  • The aim of this study was to identify the genes showing an altered expression in LGMD2A patients and the possible pathways they are implicated in. (
  • Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. (
  • At the facility, researchers will use image analysis technology and molecular biology processes to generate gene expression data for drug and drug target discovery, the company said. (
  • Evaluation of assembly and disassembly expression profiles provides a necessary step for defining the complex cellular and molecular networks involved in regulating flagellar length change. (
  • Gerami and colleagues (2015a) assessed the prognostic accuracy of gene expression profiling for molecular staging of cutaneous melanoma in a multicenter cohort study of 217 individuals undergoing sentinel lymph node biopsy (SLNB). (
  • The unique pattern of gene expression for a given cell or tissue is referred to as its molecular signature. (
  • To better understand the molecular mechanisms underlying this resistance in B. tabaci , gene profiles between the thiamethoxam-resistant and thiamethoxam-susceptible strains were investigated using the suppression subtractive hybridization (SSH) library approach. (
  • To better understand the molecular mechanisms underlying this transformation, we performed a comparative analysis using gene expression profiling of A2B5 + oligodendrocyte progenitors and O4 + oligodendrocytes. (
  • This initiative, which provides a natural complement to Foundation Medicine's comprehensive genomic profiling (CGP) suite of molecular information tests, further enhances support for the Company's biopharma partners in the efficient identification of known and novel genomic and expression-based biomarkers of response for investigational and approved personalized cancer therapies, including new and existing cancer immunotherapies. (
  • The company offers a full suite of comprehensive genomic profiling assays to identify the molecular alterations in a patient's cancer and match them with relevant targeted therapies, immunotherapies and clinical trials. (
  • Different molecular subgroups within PTCL unspecified have been identified associated to different expression profiles. (
  • Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. (
  • In this study, we use gene expression profiling (GEP) to characterize the molecular profile of H-MM, with a view of gaining some insights about its biology, and to study the heterogeneity within H-MM. (
  • Molecular classification of human carcinomas by use of gene expression signatures. (
  • This three-day meeting will address key issues concerning genetics, genotype profiling and gene expressions in the broader context of molecular biology, evolutionary biology, bioinformatics, Genomics and Case studies. (
  • This will undoubtedly lead to the development of focused cancer therapy protocols that are specific to the multigene expression signature and molecular markers of particular tumor types. (
  • The aim of this study was to compare early-onset CRC tumor RNAseq gene expression profiles to late-onset CRC profiles available through The Cancer Genome Atlas (TCGA) in order to gain insight into the molecular changes leading to early-onset CRC. (
  • METHODOLOGY/PRINCIPAL FINDINGS: To identify genes and molecular functions transcriptionally affected by gamma-secretase activity, the cellular transcriptomes of Chinese hamster ovary (CHO) cells with enhanced and inhibited gamma-secretase activity were analyzed and compared by cDNA microarray. (
  • CONCLUSIONS/SIGNIFICANCE: Investigating the effects of gamma-secretase activity on gene transcription has revealed several affected clusters of molecular functions and, more specifically, 21 genes that hold significant potential for a better understanding of the biology of gamma-secretase and its roles in cancer and Alzheimer's disease pathology. (
  • FRIENDSWOOD, Texas--( BUSINESS WIRE )--Castle Biosciences, Inc., a provider of molecular diagnostics to improve cancer treatment, today announced results of an independent study with its noninvasive gene expression profile test, verifying the accuracy and utility of the assay to identify risk of metastasis in patients diagnosed with Stage I or II cutaneous melanoma. (
  • As only some smokers develop COPD with emphysema, we explored the molecular pathogenesis of early-stage COPD with emphysema using gene expression profiling of human lung tissues. (
  • Ten muscle samples from LGMD2A patients with in which molecular diagnosis was ascertained were investigated using array technology to analyze gene expression profiling as compared to ten normal muscle samples. (
  • CONCLUSIONS: This study identifies deep , phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals. (
  • This project will further examine the physiological (i.e. sperm counts and quality) and molecular (i.e. testicular and epididymal gene expression profiles) effects of developmental exposure to DES and investigate the effects of genistein (GEN) and o,p'-dichlorodiphenyltrichlorothane (o,p'-DDT), two environmentally relevant, albeit weak estrogenic endocrine disruptors. (
  • For the purposes of risk assessment, elucidating correlations between physiological effects and changes at the molecular level (i.e. modulation of gene expression profiles) is critically important in order to establish potential mechanisms of action and to confirm that changes in the expression of gene networks translate into the manifestation of a toxic response. (
  • Unsupervised hierarchical clustering readily distinguished tumors from normal samples, and further identified three subclasses of prostate tumors based on distinct patterns of gene expression. (
  • Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification. (
  • We analyzed expression profiles of 12,625 transcripts in prostate tumors from patients with distinct clinical outcomes after therapy as well as metastatic human prostate cancer xenografts in nude mice. (
  • We examined one group of samples (21 tumors) to discover the recurrence predictor genes and then validated the predictive power of these genes in a different set (79 tumors). (
  • Brooks and Zhao analyzed the genes that were turned on or off in kidney tumors removed by their collaborators at Umea University in Sweden. (
  • The laboratory test is a signature of 31 genes, 28 discriminating genes and 3 control genes, that classifies tumors as class 1 (low risk of metastasis) or class 2 (high risk of metastasis), using reverse transcription polymerase chain reaction (RT-PCR) on formalin-fixed paraffin-embedded (FFPE) primary tumor tissue specimens obtained from either biopsy or excision of a cutaneous melanoma. (
  • The clinical validity of the DecisionDx-Melanoma test was evaluated in a prospective, multicenter study of class 1 cutaneous melanoma tumors which analyzed microarray expression data to identify a prognostic 28-gene signature to predict risk of metastasis (Gerami, 2015b). (
  • The investigators suggested their preliminary analysis indicates the 28-gene signature is an independent predictor of metastasis risk in the studied cohort of cutaneous melanoma tumors. (
  • In the context of cancer, gene expression profiling has been used to more accurately classify tumors. (
  • Presented below are ways that gene expression profiling has been used to more precisely classify tumors into subgroups, often with clinical effect. (
  • We found that gene expression-based grouping of tumors is a more powerful survival predictor than histologic grade or age. (
  • The ability of the large scale and 44 gene set expression signatures to group tumors into strong survival groups was validated with an additional external and independent data set from another institution composed of 50 additional gliomas. (
  • This demonstrates that large-scale gene expression analysis and subset analysis of gliomas reveals unrecognized heterogeneity of tumors and is efficient at selecting prognosis-related gene expression differences which are able to be applied across institutions. (
  • Profiling gene expression in patients' tumors may help clinicians decide which patients are suitable candidates for standard therapy and which should consider other options for treatment. (
  • These genes highlight aspects of the tumors that affected response to therapy, including how fast tumor cells were dividing and from what type of normal lymphocyte (a type of white blood cell) the tumor originated. (
  • To provide additional insight into the nature of ACT, we determined the gene expression profiles of 24 pediatric tumors (five adenomas, 18 carcinomas, and one undetermined) and seven normal adrenal glands. (
  • To do this, they used a self-organizing map (SOM) methodology to define clusters of tumors on the basis of gene expression profiles. (
  • Gene expression profiles or signatures are groups of genes that are differentially expressed among tumors or diseased lesions, reflecting differences in biological features of the tissues. (
  • The scientists predict that with the continuously increasing number of reads at reduced costs, RNASeq, a.k.a. whole transcriptome shotgun sequencing, will become affordable for standard differential gene-expression analysis. (
  • Perform transcriptome profiling for hundreds to tens of thousands of single cells in one experiment. (
  • Illumina offers comprehensive next-generation sequencing (NGS) solutions that provide high-quality gene expression and transcriptome analysis data for a broad range of sample types. (
  • RNA-Seq provides a unique combination of transcriptome-wide coverage, sensitivity, and accuracy for a comprehensive view of gene expression changes. (
  • Discover novel gene isoforms, profile gene expression for select targets of interest, analyze the whole coding transcriptome, and accurately perform transcript abundance and fold-change measurement. (
  • Discover alternative transcripts, gene fusions, and allele-specific expression patterns with a clear, complete view of the coding transcriptome. (
  • The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3′-tag digital gene-expression protocol. (
  • Whole transcriptome expression profiling is historically performed using hybridization-based microarray methods. (
  • In this study, we sequenced the antennal transcriptome of H. illucens adults to identify chemosensory genes. (
  • Transcriptome analysis comparing healthy trees to HLB-affected citrus both before and after heat treatment demonstrated that post-treatment transcriptional expression patterns more closely resembled the expression patterns of healthy controls for most differentially expressed genes and that genes involved with plant-bacterium interactions are upregulated after heat treatment. (
  • Genes with extensive sequence similarity may comprise a significant portion of a given transcriptome. (
  • Our study identified differences in gene expression in subjects with COPD according to emphysema status using RNA-Seq transcriptome analysis. (
  • A group of Dutch researchers compared deep sequencing-based gene-expression analysis using the Illumina whole genome sequencer to five microarray-based platforms. (
  • Escherichia coli MG1655 acid-inducible genes were identified by whole-genome expression profiling. (
  • Whole genome expression profiling of E. coli cells growing on minimal glucose medium revealed that gadA , gadB , hdeA , and hdeB were induced relative to growth on rich medium ( 25 ). (
  • Whole genome gene expression profiling of fibroblasts from each XP complementation group was assessed before and after UV-light exposure. (
  • Prohealth Profiling of temperature-induced changes in Borrelia burgdorferi gene expression by using whole genome arrays. (
  • Identification of differentially expressed genes in human bladder cancer through genome-wide gene expression profiling. (
  • This study illustrates the powerful potential of the analysis of genome-wide gene expression to define distinct pathologies and identify classes of cancer. (
  • Building on Foundation Medicine's existing DNA and RNA sequencing platforms, GEP has the potential to provide insights into gene expression signatures that may serve as predictive biomarkers of immunotherapy response. (
  • The study identified four tumor gene expression patterns that may serve as biomarkers of prognosis, including tumor recurrence or metastasis, for patients with head and neck squamous cell cancer and for whom aggressive therapy might be best. (
  • To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of incident primary OSCC, oral dysplasia, and clinically normal oral tissue from surgical patients without head and neck cancer or preneoplastic oral lesions (controls), using Affymetrix U133 2.0 Plus arrays. (
  • This study involves a comprehensive, multi-modal, and integrative assessment of biomarkers implicated in the pathophysiology of PTSD, including measuring differences in whole-blood gene expression and other blood biomarkers of key neurobiological systems, an approach critical to informing risk and resilience prediction algorithms for PTSD, and to develop novel psychopharmacologic approaches for the treatment of this disabling condition in disaster responders and other trauma survivors. (
  • The aim of this study was to identify genes that are expressed differently in the course of BC progression and to establish new biomarkers for BC. (
  • We identified several genes as promising candidates for diagnostic biomarkers of human BC and the CKS2 gene not only as a potential biomarker for diagnosing, but also for staging human BC. (
  • Quantitative data on global gene expression offer the opportunity not only to indicate or confirm exposure to specific chemical classes but also to identify biomarkers (single genes or patterns of gene expression) that are indicative of the initiation/presence of toxicant mechanisms or that can be linked to specific pathology ( 2 , 3 ). (
  • Moreover, results from these studies may identify novel gene targets that are involved in the toxicity of endocrine disruptors that could lead to the development of biomarkers for reproductive toxicants. (
  • The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. (
  • DNAStar recently introduced QSeq, the first product to use the company's disk sort alignment algorithm for quantitative RNASeq applications and digital gene-expression experiments. (
  • Expression of specific genes from each category was further characterized at higher resolution by using quantitative real-time PCR (qRT-PCR). (
  • The level of fluorescence at a particular spot provides quantitative information about the expression of the particular gene corresponding to the spotted cDNA sequence. (
  • Microarray analysis offers the option of unbiased, quantitative, and reproducible tumor evaluation by simultaneously evaluating thousands of individual gene expression measurements. (
  • Differential expression of these four genes was confirmed by quantitative reverse transcription-PCR. (
  • These results demonstrate insights that become possible using computational approaches to analyze quantitative expression from many genes in parallel using a digital gene expression atlas. (
  • Further real-time quantitative PCR analyses revealed that the antennae-enriched unigenes also exhibited significant differences in expression between males and females. (
  • Distinct patterns of gene expression, validated by quantitative real-time PCR and Western blot analysis, were identified that distinguish normal adrenal cortex from tumor. (
  • Comparative expression of genes involved in osmoregulation, detoxification, signal transduction, metabolism, and transcription factor was analyzed through quantitative RT-PCR. (
  • Differences in gene expression underlie central questions in plant biology extending from gene function to evolutionary mechanisms and quantitative traits. (
  • The ability to distinguish between paralogs (e.g. gene family members) and alleles on a genome-wide scale is key to understanding the genetic basis of quantitative traits in diverse plant populations. (
  • According to the small amplitude of expression alterations observed in whole blood, more quantitative technique and larger sample sizes will be needed to be able to investigate whether significant single genes are differentially expressed in HRT versus non-HRT users. (
  • Liver disease-specific and shared gene lists were created and genes identified as highly expressed in hereditary haemochromatosis HCC (HH-HCC) were validated using quantitative RT-PCR. (
  • Most of the genome is selectively repressed, a property that is governed by the regulation of gene expression, mostly at the level of transcription (ie, the production of messenger RNA from the DNA). (
  • Expression profiling reveals off-target gene regulation by RNAi. (
  • Functional enrichment analysis indicated that differentially expressed genes were associated with the regulation of actin cytoskeleton, focal adhesion, tight junction, adherens junction as well as antigen processing and presentation. (
  • We used microarray profiling to examine gene regulation associated with flagellar length change in the green alga Chlamydomonas reinhardtii . (
  • Reductions in expression were identified for genes involved in the regulation of ornithine and polyamine metabolism, the mitochondrial malate shuttle system, the transcarboxylic acid cycle, aspartate and alanine metabolism, and ubiquitin metabolism. (
  • Transcriptional changes included genes required for cell adhesion, actin cytoskeleton regulation, and fatty acid and cholesterol biosynthesis. (
  • Reverter A, Hudson N, Nagaraj S, Perez Enciso M, Dalrymple B. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. (
  • Among the 6 most highly up-regulated genes, CKS2 was the only gene with a significantly greater level of up-regulation in invasive than in superficial BC (p = 0.04). (
  • The set includes genes involved in cell-cycle regulation, chromatin remodeling and cell adhesion. (
  • Sterol regulatory element binding proteins (SREBPs) including the splice variants SREBP1a and SREBP1c, as well as SREBP2 (encoded by a distinct gene), are involved in the regulation of fatty acid and cholesterol synthesis in a variety of mammalian tissues ( 1 ). (
  • it was recently reported that natural antisense transcripts are involved in the regulation of gene expression. (
  • Tsix , the antisense transcript of X-inactive specific transcript ( Xist ) gene, was demonstrated to be involved in the regulation of the Xist gene which mediates X chromosome inactivation ( 15 ). (
  • Genes participating in the ubiquitin proteasome degradation pathway were found to be deregulated in LGMD2A patients, suggesting that regulation of this pathway may be under the control of calpain 3 activity. (
  • Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). (
  • We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. (
  • In general, individual gene/protein assays alone or in combination with histologic features are neither predictive of survival of glioma patients nor able to guide therapeutic decisions. (
  • The discovery of the predictive genes relied on DNA microarray technology, which allows researchers to determine which genes are active within cells. (
  • Many of the predictive genes suggest that a patient's immune response to the tumor is important for achieving a cure with chemotherapy. (
  • Genes differentially expressed in ischemic stroke were identified and analyzed for predictive ability to discriminate stroke from control subjects. (
  • 6-8 We previously reported a 29-probe set expression profile predictive of IS. (
  • Gene expression profiles were associated with oral cancer-free survival and used to develop multivariate predictive models for oral cancer prediction. (
  • Gene lists from cladograms' nodes were processed in Genomatix GePS to reveal the affected signaling pathway networks. (
  • Taken cautiously, significant enrichments in biological process of genes with small changes after HRT use were observed (e.g., receptor and transporter activities, immune response, frizzled signaling pathway, actin filament organization, and glycogen metabolism). (
  • These findings show that profiling gene expression changes in specific cell-types harboring memory traces provides a powerful entry point to identify new genes involved in learning and memory. (
  • Gene chip findings healing versus non healing wounds. (
  • Our findings suggest novel functions for 3'UTRs, as well as caution in the use of 3'UTR sequence probes to analyze gene expression. (
  • These findings underscore the important role plasmid-encoded genes may play in adjustment of B. burgdorferi to growth under diverse environmental conditions. (
  • Finally, the upregulation of IL-32 and immunoglobulin genes may induce the eosinophil chemoattraction explaining the inflammatory findings observed in presymptomatic stages. (
  • Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. (
  • Multivariate analysis of prognostic factors in CLL: clinical stage, IGVH gene mutational status, and loss or mutation of the p53 gene are independent prognostic factors. (
  • We further describe a list of 44 genes whose expression patterns reliably classify gliomas into previously unrecognized biological and prognostic groups: these genes are outstanding candidates for use in histology-independent classification of high-grade gliomas. (
  • Three gene expression-based prognostic breast cancer tests have been licensed for use. (
  • To summarize evidence on the validity and utility of 3 gene expression-based prognostic breast cancer tests: Oncotype DX (Genomic Health, Redwood City, California), MammaPrint (Agendia BV, Amsterdam, the Netherlands), and H/I (AvariaDX, Carlsbad, California). (
  • In gene expression test systems for breast cancer prognosis, an algorithm is applied to such measurements to yield a result that can be used by physicians as a prognostic marker, in combination with clinicopathological factors, to assess the risk of cancer recurrence (e.g., distant metastasis). (
  • Gene expression profiles have been used to develop prognostic models of cancer outcome and to identify markers for diagnosis and classification of cancers ( 9-11 ). (
  • Eventually the group wants to narrow those 259 genes to a smaller subset that can accurately distinguish between cancers. (
  • Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. (
  • We measured the gene expression profiles of a subset of the patient samples and searched for their association with oral cancer-free survival (OCFS) time. (
  • ZAP-70 expression identifies a chronic lymphocytic leukemia subtype with unmutated immunoglobulin genes, inferior clinical outcome, and distinct gene expression profiles. (
  • A laboratory method that identifies all of the genes in a cell or tissue that are making messenger RNA. (
  • Expression profiling identifies genes involved in neoplastic transformation of serous ovarian cancer. (
  • Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. (
  • To better characterize C. glabrata , JCVI performed RNA sequencing (RNAseq) analysis from mouse peritoneal fluid and abscesses from a time course experiment to assess gene expression changes over time. (
  • Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. (
  • There are some specific marker genes identified whose expression patterns can be used to characterize different cell types. (
  • Characterize the function of the differentially upregulated and downregulated genes identified by comparing the gene expression profiles of primary and metastatic cells in these patients. (
  • have profiled similar expression patterns for large numbers of additional genes during flagellar assembly. (
  • For this reason alone, it is clear that additional genes must participate in the glutamate-dependent AR, but these genes remain to be identified ( 9 ). (
  • Functional genomics provides a comprehensive approach for identification of additional genes involved in AR. (
  • Additional genes that could be important in our understanding of the pathogenesis of mesothelioma, aiding in diagnosis, or improving targets for therapy were also identified. (
  • An average of 4753 and 5965 additional genes was called Present after globin depletion for Donor 37 and Donor 45, respectively. (
  • Conclusions- This study replicated our previously reported gene expression profile in a larger cohort and identified additional genes that discriminate ischemic stroke from relevant control groups. (
  • and (2) to identify additional genes that discriminate IS from vascular risk factor ( S ex, A ge and V ariation in V ascular functionalit Y [SAVVY]) control subjects and myocardial infarction (MI) control subjects. (
  • The activity (expression) of specific genes within breast tumor cells has been found to be associated with the chance of disease recurrence. (
  • Several forms of animal behavior are known to be influenced by the activity of specific genes ( 1 , 2 ). (
  • Results We found 29 differentially expressed (DE) genes between 'attack' and 'after treatment', after subtracting non-migraine specific genes, i.e. genes related to a general pain/stress response. (
  • This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function. (
  • We describe the gene expression profiles during these phases and tested 33 selected candidate genes for deficits in LTM formation using RNAi knockdown. (
  • Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. (
  • On the other hand, no changes in the expression of the key β-cell transcription factor pancreatic duodenum homeobox-1 (PDX-1) or in the glucose transporter, Glut2 or glucokinase, were apparent after overexpression of SREBP1c in islets ( 6 ), although these genes were reported to be downregulated by SREBP1c in a study of candidate genes in the INS-1 cell line ( 4 ). (
  • For instance, skin cells, liver cells and nerve cells turn on (express) somewhat different genes and that is in large part what makes them different. (
  • Gene expression profiling tests (Oncotype DX, MammaPrint, others) analyze a number of different genes within your cancer cells to predict your risk of cancer recurrence. (
  • A total of 6878 cDNAs were analyzed in this study, estimated to represent ∼5500 different genes (perhaps ∼40% of genes in the honey bee genome) ( 17 , 18 ). (
  • BACKGROUND: Processing by gamma-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a diverse array of cellular and biological processes. (
  • We investigated global gene expression profiles from HCC arising in different liver diseases to test whether HCC development is driven by expression of common or different genes, which could provide new diagnostic markers or therapeutic targets. (
  • Sequence based techniques, like RNA-Seq , provide information on the sequences of genes in addition to their expression level. (
  • the sequence tells us what the cell could possibly do, while the expression profile tells us what it is actually doing at a point in time. (
  • d) for each distinctly sized amplification product detected in step (c), calculating a cycle number, C t , where the amount of that amplification product crosses a predefined threshold, and correlating the threshold cycle with the amount of a nucleic acid having a sequence of interest in said sample, wherein said method provides an amplification profile and a relative abundance for members of said set of nucleic acid sequences of interest. (
  • Supplementary Table 1-Primer sequence of selected genes designed for qRT-PCR. (
  • To date, however, microarray analyses have been applied almost exclusively to model species for which gene sequence data are abundant. (
  • We show the utility of microarray approaches for the study of gene expression in a species for which, at the onset of our investigation, sequence data were unavailable. (
  • Sequence based techniques, like serial analysis of gene expression (SAGE, SuperSAGE) are also used for gene expression profiling . (
  • More than 90 million clean sequence tags were generated and compared with the P. sojae genome and its 19,027 predicted genes. (
  • These expressed sequence tags (ESTs) belong to several functional categories based on their gene ontology annotation. (
  • The HiCEP method is an amplified fragment length polymorphism (AFLP)-based gene expression profiling method that requires no prior sequence information and has a reduced rate of false positives and a high degree of detection of both coding and non-coding transcripts. (
  • a growing number of chemosensory genes have also been identified from many other Dipteran species based on sequence similarity. (
  • First Monoploid Reference Sequence of Sugarcane For the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species - sorghum. (
  • The first step in gene discovery was to establish a complementary DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. (
  • Several genes that may be involved in domoic acid synthesis were also revealed through sequence similarity, for example, glutamate dehydrogenase and 5-oxo-L-prolinase. (
  • 0.1 with respect to null adenovirus) changes in the expression of 1,238 genes or expressed sequence tags, of which 1,180 (95.3%) were upregulated. (
  • However, resolving expression of closely related genes (e.g. alleles and gene family members) is challenging on a genome-wide scale due to extensive sequence similarity and frequently incomplete genome sequence data. (
  • The extent of these sequence similarities in maize and other complex genomes poses a clear challenge to delineation of gene-specific function. (
  • Using cDNA sequence database, Kiyosawa et al predicted that sense and antisense transcripts were produced from 15% of mouse gene loci ( 13 ) and demonstrated via microarray analysis that 1,947 sense and antisense transcripts were expressed in mice ( 14 ). (
  • Thus, although these genes may indeed play a role in the biology of gliomas, their utility as diagnostic markers is not yet clear, perhaps due to heterogeneity within the tumor groupings. (
  • The first studies on expression profiling of PTCL have also revealed heterogeneity at this level, mainly regarding the PTCL NOS subgroup. (
  • The C. elegans cell lineage provides a unique opportunity to look at how cell lineage affects patterns of gene expression. (
  • Patterns of gene expression in brains of single nursing bees differ predictably from those of foraging bees. (
  • In addition, pediatric adrenocortical carcinomas were found to share similar patterns of gene expression when compared with those published for adult ACT. (
  • These included similar temporal patterns of gene expression and over 300 injury-responsive genes. (
  • In response to a cellular perturbation, changes in gene expression take place that result in the expression of hundreds of gene products and the suppression of others. (
  • Understanding the changes in gene expression in fishes exposed to hypoxic stress could reveal novel mechanisms of tolerance that may shed new light on hypoxia and ischemia in higher vertebrates. (
  • Understanding the tissue-specific and temporal changes in gene expression in fishes exposed to hypoxia could reveal new mechanisms of hypoxia tolerance and shed light on the evolution of this adaptive response in vertebrates. (
  • Microarray studies have been used to relate changes in behavior with changes in gene expression in the brain ( 3 - 7 ). (
  • Together, our results provide first evidence for a specific effect of EE on T cell differentiation and its associated changes in gene expression profile. (
  • RESULTS: Despite tissue -specific changes in expression dominating the injury responses of each tissue , injury-induced changes in gene expression were nonetheless shared between the two axon -regenerative CNS regions that were not shared with the non-regenerative region. (
  • The General Linear Model (GLM) will be used as a novel statistical approach to discern dose-dependent and temporal associations between effects on sperm quality and changes in gene expression profiles. (
  • and ( ii ) tissue-specific patterns of expression reflect the different metabolic roles of tissues during hypoxia. (
  • The principal hypothesis underlying a toxicogenomic or pharmacogenomic strategy is that chemical-specific patterns of altered gene expression will be revealed using high-density microarray analysis of tissues from exposed organisms. (
  • This invention provides information on differentially expressed genes in malignant tissue of gastric, colon and pancreatic adenocarcinomas as compared to their corresponding adjacent non-malignant tissues. (
  • The genes encoding 1-pyrroline-5-carboxylate synthetase (P5CS), glutathione S-transferase (GST), superoxide dismutase (SOD), serine threonine-protein kinase (STK), serine threonine protein phosphatase (PSP), aldehyde dehydrogenase (AD), leucoanthocyanidin dioxygenase/anthocyanin synthase (LD/AS), HSP, MYB, and WRKY have shown upregulation in response to drought stress condition in leaf tissues. (
  • Using RNA-Seq, we evaluated 16,676 genes expressed in lung tissues. (
  • Tissues from these CNS regions (frog ONC eye , tadpole SCI hindbrain , frog SCI hindbrain ) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. (
  • Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. (
  • Expression profiling offers the opportunity to analyze gene expression changes in mesothelioma in an unbiased manner. (
  • The human genome contains on the order of 25,000 genes which work in concert to produce on the order of 1,000,000 distinct proteins. (
  • This is due to alternative splicing , and also because cells make important changes to proteins through posttranslational modification after they first construct them, so a given gene serves as the basis for many possible versions of a particular protein. (
  • While knowledge of the precise proteins a cell makes ( proteomics ) is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global picture possible in a single experiment. (
  • The phenotypic expression of these genes, through the synthesis of specific proteins, involves interaction with environmental signals that trigger activation of particular genes. (
  • Many genes required for oligodendrocyte differentiation were upregulated in O4 + oligodendrocytes, including numerous genes encoding myelin proteins. (
  • Chemosensory genes encode proteins involved directly in the detection of odorants. (
  • Differential expression of many genes and proteins, including matrix metalloproteinases and their inhibitors, cathepsins, caspases, and proinflammatory molecules, have been implicated in the pathobiology of human intracranial aneurysms. (
  • 2 - 5 Small previous studies have focused on involvement of individual genes or proteins in the progression and rupture of aneurysms. (
  • MammaPrint, Oncotype DX, IHC4 and Mammostrat are tests for certain genes or proteins found in breast cancer tumours. (
  • The mapping of interactions of proteins encoded by the validated genes exclusively relied on evidence-based data and revealed broad effects on Wnt pathway members, including WNT3A and DVL3. (
  • Transcription and translation underlie gene expression. (
  • Most transcription factors, inflammatory genes, and structural genes showed underexpression at both time points. (
  • Among the 21 validated genes, the strikingly decreased transcription of PTPRG and AMN1 and increased transcription of UPP1 potentially support data on cell cycle disturbances relevant to cancer, stem cell and neurodegenerative diseases' research. (
  • Intriguingly, the transcription of TERA, a gene of unknown function, is affected by gamma-secretase activity and was significantly altered in the analyzed human Alzheimer's disease brain cortices. (
  • Conversely, expression of most transcription factor genes was downregulated (MYC, FOS and EGR1). (
  • 1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes. (
  • Gene expression analysis studies can provide a snapshot of actively expressed genes and transcripts under various conditions. (
  • NGS-based RNA sequencing (RNA-Seq) methods can quantify and profile any active gene or transcript, including novel transcripts. (
  • Illumina RNA-Seq solutions provide precise measurement of strand orientation, uniform coverage, and high confidence mapping of alternate transcripts and gene fusions. (
  • When a gene is active in a cell, it produces RNA copies known as transcripts. (
  • To measure the activity of genes, researchers use the RNA transcripts to make a fluorescent gene probe. (
  • The HiCEP method was developed to address the shortcomings in gene expression profiling and provide a sensitive method for detecting a large proportion of transcripts in both known and unknown genes, with a low false positive rate. (
  • 1. A method to identify targets for cancer treatment, said method comprising identifying differently expressing genes in tumor tissue and adjacent healthy tissue by comparing expression of transcripts in SHH-analysis and cDNA micorarray analysis. (
  • Resulting sequences resolve gene-specific transcripts independent of a sequenced genome. (
  • The 3′-UTR profile resolved 12 unique cellulose synthase ( CesA ) transcripts in maize ovaries and identified previously uncharacterized members of a histone H1 gene family. (
  • Our results demonstrate the potential of 3′-UTR profiling for resolving gene- and allele-specific transcripts. (
  • Despite rapid advances in expression profiling techniques, the capacity to distinguish among closely related transcripts on a genome-wide scale remains a challenge. (
  • In microarray analyses, cross hybridization of similar transcripts to a given oligonucleotide probe may confound expression of individual genes. (
  • Sense and antisense transcripts of the genes, Apoa4, Hp, Fgb and Fgg, exhibited concordant upregulation during the course of liver regeneration. (
  • Our data provide useful information for comparative studies on the differentiation and evolution of Dipteran chemosensory gene families. (
  • 2020), Comparative gene expression profiling between o. (
  • Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. (
  • Our analysis suggests a more complex transcriptional profile of the phenotypes than expected. (
  • Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage. (
  • Although many genes involved in learning and memory formation have been identified, little is known about the genetic mechanisms required for changing the transcriptional program during different phases of long-term memory (LTM) formation. (
  • I: Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. (
  • Single genes with the most pronounced transcriptional susceptibility to gamma-secretase activity were evaluated by real-time PCR. (
  • hTERT expression and prognosis in B-chronic lymphocytic leukemia. (
  • Orchard JA, Ibbotson RE, Davis Z. ZAP-70 expression and prognosis in chronic lymphocytic leukaemia. (
  • Analyses of gene expression can be clinically useful for disease classification, diagnosis, prognosis, and tailoring treatment to underlying genetic determinants of pharmacologic response. (
  • The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. (
  • Gene expression technologies show great promise to improve predictions of prognosis and treatment benefit for women with early-stage breast cancer. (
  • This guidance document was developed as a special controls guidance to support the classification of gene expression profiling test systems for breast cancer prognosis into class II (special controls). (
  • A gene expression profiling test system for breast cancer prognosis is a device that measures the RNA expression level of multiple genes and combines this information to yield a signature (pattern or classifier or index) to aid in prognosis of previously diagnosed breast cancer. (
  • This guidance provides recommendations to manufacturers regarding preparation of premarket notifications and labeling for a gene expression profiling test system for breast cancer prognosis. (
  • A gene expression profiling test system for breast cancer prognosis is not intended for diagnosis, or to predict or detect response to therapy, or to select the optimal therapy for patients. (
  • This guidance is issued in conjunction with a Federal Register notice announcing the classification of gene expression profiling test systems for breast cancer prognosis. (
  • Any firm submitting a 510(k) premarket notification for a gene expression profiling test system for breast cancer prognosis will need to address the issues covered in this special controls guidance. (
  • The study, titled "Estimation of Prognosis in Invasive Melanoma Using a Gene Expression Profile Test" is an independent, single-center performance study of 257 successfully tested, consecutively consented patients, some of whom were previously diagnosed. (
  • Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. (
  • A new study says the technology can be modified to profile more tissue samples simultaneously and with greater efficiency. (
  • He said the new tool he and his colleagues developed looks for larger groups of genes - equivalent to searching for pitchforks rather than needles - and therefore are more likely to turn up again in future studies. (
  • Our study provides a comprehensive picture of the gene expression landscape in hepatocytes grown on different substrate stiffness, offering insights into the role of substrate stiffness in hepatic pathology. (
  • The patterns of differential gene expression associated with hypoxic stress in aquatic animals, for instance fishes, remain largely unknown. (
  • Differential gene expression analysis showed 1,574 differentially upregulated and 1,200 downregulated gene expression profiles when comparing early-onset versus late-onset tumor profiles. (
  • Principal component analysis and differential gene expression analysis were carried out using R Bioconductor. (
  • 05). Multiple genes implicated in vessel wall remodeling were found to be elevated at 2 weeks and at 12 weeks. (
  • Gene lists defined by cladogram nodes showed that the AMD-related deregulations occurring in the neural retina were different from those in RPE-choroidal tissue. (
  • We performed gene expression analysis on mesothelioma tissue specimens from 16 patients and compared these to 4 control pleural tissue samples using cDNA microarray filters with 4132 clones. (
  • Gene expression profiles are typically obtained one at a time by hybridizing a single tissue sample to a single array on an individual glass slide. (
  • Microarray studies were filtered to identify those that profiled the same tissue in normoxia and hypoxia on Affymetrix platform and used at least two replicates and provided raw data. (
  • Tissue-specific expression profiles of the identified OBPs, CSPs and SNMPs were investigated using RT-PCR. (
  • b A three- tissue comparison was designed to parse out core sets of genes most closely associated with successful CNS axon regeneration. (
  • A popular approach to class discovery involves grouping similar genes or samples together using one of the many existing clustering methods such the traditional k-means or hierarchical clustering , or the more recent MCL [8] and clust [9] methods. (
  • With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. (
  • We used a genomics approach to identify C. reinhardtii genes showing changes in expression during flagellar disassembly. (
  • Together, our results highlight the usefulness of this discovery-driven experimental strategy to identify genes relevant to oligodendrocyte differentiation and myelination. (
  • The purpose of this study was to use microarray analysis to identify specific gene expression changes in mesothelioma compared with normal mesothelium. (
  • One potentially useful approach to solve these issues would be to identify specific gene expression changes in cancerous mesothelial cells. (
  • Our second goal was to identify genes that could be involved in the pathophysiology of mesothelioma or that might serve as diagnostic markers to improve the accuracy of tumor classification. (
  • The results implicate GPC6 as a novel determinant of BMD, and also identify abnormal skeletal phenotypes in knockout mice associated with a further 100 prioritized genes. (
  • 9 - 13 Our group previously reported the use of a rabbit-specific gene chip to identify the differential expression of genes in the experimental aneurysms at a single time point. (
  • Mapping Heat Resistance in Yeasts In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures. (
  • They used the commercially available Affymetrix microarray DNA chips and screened 6,817 genes to identify 1,100 genes expressed differently in the AML and ALL classes. (
  • Therefore, the focus of this thesis was to identify and initiate characterization of actively expressed genes that control cell growth and physiology in P. multiseries, with the specific goal of identifying genes that may play a significant role in toxin production. (
  • Recently, microarray analyses were performed to identify novel genes involved in liver regeneration. (
  • To identify temperature-responsive genes, genome arrays containing 1,662 putative B. burgdorferi open reading frames (ORFs) were prepared on nylon membranes and employed to assess gene expression in B. burgdorferi B31 grown at 23 and 35 degrees C. Differences in expression of more than 3.5 orders of magnitude could be readily discerned and quantitated. (
  • With Drosophila melanogaster as a model system, we profiled transcriptomic changes in the mushroom body-a memory center in the fly brain-at distinct time intervals during appetitive olfactory LTM formation using the targeted DamID technique. (
  • The tests are based on distinct gene lists, using 2 different technologies. (
  • Expression of distinct RNAs from 3' untranslated regions. (
  • Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate, 0.40). (
  • In developing a drug, one may perform gene expression profiling experiments to help assess the drug's toxicity, perhaps by looking for changing levels in the expression of cytochrome P450 genes, which may be a biomarker of drug metabolism. (
  • HIF-1α mediates the expression of a series of genes involved in both cellular and systemic responses to hypoxia, leading to enhanced anaerobic metabolism and induced erythropoiesis and angiogenesis ( 2 ). (
  • Products of these genes are associated not only with flagellar structure and motility but also with other cellular responses, including signal transduction and metabolism. (
  • From the ten libraries, 722 gene expression-pattern clusters were obtained and the top 16 clusters, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and noncoding RNA metabolism. (
  • In the present study, we wished to determine whether transcript levels in more than 70 different gene groups involved in cellular metabolism, which could impact the quality of neuronal communication, were altered in a larger sample of subjects with schizophrenia and whether the effects on these gene groups were interrelated. (
  • The acid-induced genes represented only five functional grouping categories, including eight genes involved in metabolism, nine associated with cell envelope structures or modifications, two encoding chaperones, six regulatory genes, and six unknown genes. (
  • As noted in the article genomic profiles aren't necessarily cheap, and they aren't necessarily value added in some cases when cost is taken into account. (
  • Bringing together Foundation Medicine's unique combination of comprehensive genomic sequencing and gene expression could help determine which therapeutic approach is right for each patient and each tumor type as we develop new classes of personalized cancer treatments with our biopharma partners. (
  • RNA-Sequences were analyzed at gene level (differential expression analysis) and at network level, and we integrated transcriptomic and genomic data. (
  • Several gene expression profiling tests exist, and many are being studied in clinical trials. (
  • This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. (
  • This document addresses gene expression profiling to assist in the risk stratification and clinical management of cutaneous and uveal (ocular) melanoma. (
  • The information derived from gene expression profiling often helps in predicting the patient's clinical outcome. (
  • CAMBRIDGE, Mass.--( BUSINESS WIRE )-- Foundation Medicine, Inc. (NASDAQ:FMI) today announced a comprehensive gene expression profiling (GEP) program to support precision oncology clinical research and development. (
  • and the benefits of Foundation Medicine's gene expression profiling program to biopharma partners, including optimizing clinical research development programs and drug development. (
  • In addition, the expression level of NF-kB pathway genes allowed to differentiate two PTCL subgroups, and this difference could have clinical interest. (
  • Gene arrays are already providing valuable and useful biological and clinical information and in a handful of years will probably become diagnostic tools in addition to the spectacular biology tools they already are. (
  • These profiles represent further refinement of gene expression as a diagnostic tool in patients with acute IS, which could be used to aid in the diagnosis of stroke in the context of clinical information and evaluation. (
  • Careful analysis and record keeping will allow doctors to correlate expression profiles with patients' responses to treatment and clinical outcomes. (
  • Gene expression profile was measured in 86 of 162 OPL patients who were enrolled in a clinical chemoprevention trial that used the incidence of oral cancer development as a prespecified endpoint. (
  • In this report, we demonstrate that gene expression profile can significantly improve the prediction of OSCC development over clinical and histologic variables in OPL patients and the significant genes may be promising targets for cancer prevention. (
  • OUTLINE: Fresh biopsy samples are collected for gene expression profiling and other biomarker/laboratory analyses. (
  • Forward and stepwise logistic regression analyses identified 10 successive combinations of genes which expression differentiated OSCC from controls. (
  • One of the challenges is to preserve valid gene expression profiles from sample collection to isolation and how to maximize RNA yields and purity for sensitive downstream analyses. (
  • Results from these statistical analyses will be compared in order to reveal common gene expression patterns. (
  • Developed as part of the NCI's Cancer Genome Anatomy Project, the Lymphochip is particularly useful for finding differences in gene expression among lymphoid cancers. (
  • Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin. (
  • Differences in gene expression were also identified between adrenocortical adenomas and carcinomas. (
  • Transcript profiles revealed siRNA-specific rather than target-specific signatures, including direct silencing of nontargeted genes containing as few as eleven contiguous nucleotides of identity to the siRNA. (
  • None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. (
  • Four gene signatures whose expression changed relative to baseline (before wound induction by the pre-treatment biopsy) were identified. (
  • Two additional signatures were observed which included preferentially pro-inflammatory genes in the early post-treatment biopsies (2 days after pre-treatment biopsies) and repair and angiogenesis genes in the later (4 to 8 days) biopsies. (
  • In order to maximize the potential of personalized cancer therapy, we need a comprehensive biomarker strategy that includes not only tumor mutational changes and signatures but robust readouts of gene expression, requiring deep expertise in next generation DNA and RNA sequencing," said Vincent Miller, M.D., chief medical officer at Foundation Medicine. (
  • 25% of the down-regulated genes were linked to cell adhesion/surface and 21% to cytoskeleton/cell membrane. (
  • A microarray consisting of genes related to cell adhesion, apoptosis, cell signaling, growth, inflammation, vascular remodeling, and oxidative stress was constructed by using rabbit nucleotide sequences. (
  • Expression of cell adhesion molecules and antioxidant enzymes was down-regulated at 2 weeks but was not significantly different from that of controls at 12 weeks. (
  • Upregulated genes were mostly those related to extracellular matrix (different collagens), cell adhesion (fibronectin), muscle development (myosins and melusin) and signal transduction. (
  • Togo et al reported 23 genes, including Karyopherin α1 and interleukin-1 receptor associated kinase-1 ( IRAK-1 ), as novel genes involved in the early phase of liver regeneration by microarray analysis ( 9 ). (
  • Data Mining Tool software (Affymetrix) was used to separate genes in clusters based on their expression patterns over time. (
  • We identified small clusters of genes discriminating recurrent versus nonrecurrent disease with 90% and 75% accuracy in two independent cohorts of patients. (
  • Single-cell global gene expression profiling showed that undifferentiated cells fell into two clusters delineated by expression of DLL1 and its binding partner syntenin. (
  • Adjuvant chemotherapy guided by a 21-gene expression assay in breast cancer. (
  • The DecisionDx-Melanoma test (Castle Bioscience, Inc., Friendswood, TX) is a multigene expression assay designed to predict metastasis in individuals with stage I or stage II cutaneous melanoma who have no sign of disease beyond the original tumor. (
  • Berger and colleagues (2016) performed a retrospective chart review of 156 individuals with cutaneous melanoma who were consecutively tested with the DecisionDx-Melanoma gene expression profile assay at three dermatology and three surgical oncology practices between May 2013 and December 2015. (
  • This unit describes methods that allow these clones to be used as hybridization detectors in a highly parallel assay of gene expression. (
  • Changes in testicular and epididymal gene expression levels will be examined at 15 and 45 weeks of age using a customized genome-scale expression array assay. (
  • The EGAPP™ Working Group (EWG) found no direct or indirect evidence linking tumor gene expression profiling of women with breast cancer to improved health outcomes. (
  • Can Tumor Gene Expression Improve Outcomes in Patients with Breast Cancer? (
  • Selected genes were investigated further using immunohistochemistry in 86 HCC arising in liver disorders with varied aetiology. (
  • This is the first study to define Candida global gene expression during deep-seated human infection. (
  • Recently, microarray analysis studying global gene expression of a human intracranial aneurysm was reported. (
  • Global gene expression profiling was performed for 4 normal (control) livers as well as 8 background liver and 7 HCC from 3 patients with hereditary haemochromatosis (HH) undergoing surgery. (
  • Using the latest microarray technology, researchers are creating gene expression profiles of people who have suffered strokes and other cerebrovascular disorders and comparing those to the gene expression profiles of healthy subjects and those who have suffered other cardiovascular events. (
  • Techniques include DNA microarray technology or sequenced-based techniques such as serial analysis of gene expression (SAGE). (
  • Furthermore, we demonstrate that the protein expression levels for two genes, serving as surrogate markers for tumor subtypes, are strong predictors of tumor recurrence, independent of known risk factors. (
  • Giorgi C, Yeo GW, Stone ME, Katz DB, Burge C, Turrigiano G, Moore MJ (2007) The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. (
  • We showed that genes related to presynaptic secretory function, and the gene encoding the regulator of G-protein signaling 4 (RGS4), were consistently decreased in subjects with schizophrenia. (
  • At the O4 + stage, there was an increase in expression of a novel proline-rich transmembrane protein (Prmp). (
  • Potentially important up-regulated genes included gp96 , lung resistance-related protein, galectin-3 binding protein, the M r 67,000 laminin receptor (on tumor vessels), and voltage-dependent anion channels. (
  • In this gene expression profiling study, we show that H-MM is defined by a protein biosynthesis signature that is primarily driven by a gene dosage mechanism as a result of trisomic chromosomes. (
  • However, more detailed protein expression experiments should be carried out. (
  • Ewen K, Baker M, Wilhelm D, Aitken R, Koopman P. Global survey of protein expression during gonadal sex determination in mice. (
  • and c) modulating under-expression by increasing bioavailability of under-expressed protein. (
  • By contrast, overexpression of constitutively active AMP-activated protein kinase (AMPK), expected to promote lipolysis, altered the expression of 752 genes, of which 702 (93%) were upregulated. (
  • Green fluorescent protein expression was observed after 36 hours, peaked at 48 hours, and remained stable for up to 60 hours. (
  • In addition, green fluorescent protein expression generally increased with increasing DNA concentration and time. (
  • Through gene expression profiling, researchers are working to find ways to monitor brain health and predict future strokes, aneurysms, and hemorrhages. (
  • If all of the standard factors that doctors use to predict the chance of your cancer returning show that your risk is very small, then gene expression profiling tests probably aren't necessary. (
  • Patterns of genes that are active in tumor cells can predict whether patients with diffuse large B-cell lymphoma (DLBCL) are likely to be cured by chemotherapy, scientists reported today in the New England Journal of Medicine. (
  • We're able to reliably predict the survival of these patients using data from a small number of genes, indicating that this technique should be entirely manageable for routine use," said National Cancer Institute (NCI) investigator Louis M. Staudt, M.D, Ph.D., the senior author on the study. (
  • From these genes, the investigators created a formula that could be used to predict survival following chemotherapy. (
  • To predict behavior from gene expression profiles in a natural context would demonstrate a more robust relation between genes and behavior than is commonly thought to exist ( 9 ). (
  • The robustness of DGE combined with supervised classification by nearest shrunken centroids (NSC) was validated experimentally and by comparison with published expression data for large sets of ALL samples. (
  • Microarray DNA chip technology has been used for the first time to demonstrate the feasibility of cancer classification on the basis of gene-expression profile analysis. (
  • This study clearly shows that future cancer classification could be based on gene-expression profiles. (
  • Here we report a cDNA microarray-based study in prostate cancer leading to the identification of biologically and clinically relevant gene-expression tumor subtypes. (
  • but all you need to do is increase the number of genes to increase your confidence that you've made a positive identification. (
  • Identification of the components and mechanisms involved in flagellar structure and function has begun to elucidate the signal transduction networks, but the genes involved remain incompletely understood ( D avenport and Y oder 2005 ). (
  • An important aspect of understanding coordination of flagellar structure and function is identification of genes whose expression is regulated during flagellar assembly and disassembly. (
  • DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR genotyping. (
  • We reasoned that comparing A2B5 + oligodendrocyte progenitors to O4 + oligodendrocytes would be a productive screening method for identification of genes important for myelination and the establishment of axon-glia interactions. (
  • DNA labeled with fluorophores (target) is prepared from a sample such as a tumor biopsy and is hybridized to the complementary DNA (cDNA) sequences on the gene chip. (
  • The purpose of the biopsy arm is to determine whether there are similar patterns of genes being turned on and/or turned off among people with healing and non-healing wounds. (
  • These differences between macro and microvascular ECs were reflected in differences in expression of genes involved in a range of biological processes. (
  • Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. (
  • Two newly characterized germinal center B-cell-associated genes, GCET1 and GCET2, have differential expression in normal and neoplastic B cells. (
  • Sometimes, a scientist already has an idea of what is going on, a hypothesis , and he or she performs an expression profiling experiment with the idea of potentially disproving this hypothesis. (
  • Using this and other modifications, they completed a study of gene expression in ovarian cancer in a single experiment. (
  • As each microarray experiment often generates large amounts of expression data, it is often difficult for researchers without background in bioinformatics to extrac. (
  • However, nine acid-inducible genes are clustered in the gadA region, including hdeA , which encodes a putative periplasmic chaperone, and four putative regulatory genes. (
  • Indeed, microarray profiling studies have identified clinically relevant gene-expression subtypes in leukemia ( 6 , 7 ), lymphoma ( 8 ), breast cancer ( 9 , 10 ), and lung cancer ( 11 - 13 ). (
  • Although DNA microarray studies of prostate cancer have identified genes differentially expressed in tumor compared to nontumor samples ( 14 - 18 ) and genes whose expression correlates with tumor grade, metastasis, and disease recurrence ( 14 , 17 , 19 , 20 ), to date, tumor subtypes based on gene expression have not been appreciated. (
  • PAIs defined by the expression profile of the prostate cancer recurrence predictor signature 1 for 21 prostate carcinoma samples constituting a signature discovery (training) data set. (
  • Gene expression profiling for breast cancer: What is it? (
  • For women with early-stage breast cancer that is sensitive to hormones, gene expression profiling tests are used to determine whether they are likely to benefit from adjuvant chemotherapy. (
  • Whether these genes were being actively used by a particular cancer could reveal whether that cancer was likely to spread aggressively and need more vigorous treatment. (
  • Due to lowering costs, RNA-Sequencing is becoming more common as a method for cancer gene expression profiling. (
  • Of note, similar gene expression patterns associated with metastatic behaviour of breast cancer tumor cells have also been found in breast cancer of dog, the most common tumor of the female dog. (
  • This review highlights the gene expression profile of androgen independent prostate cancer and the possible mechanisms that results in transformation to such treatment resistant state. (
  • Compare the gene expression profiles of pancreatic cancer cells from the primary and metastatic sites in patients with metastatic pancreatic cancer. (
  • One prominent cluster, cluster 1, is characterized by high expression of cancer testis antigen and proliferation-associated genes. (
  • Expression analysis of delta-catenin and prostate-specific membrane antigen: their potential as diagnostic markers for prostate cancer. (
  • Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. (
  • Large-scale gene expression profiling is an effective strategy for understanding the progression of bladder cancer (BC). (
  • Furthermore, an examination of the class predictor genes provides useful insights into cancer pathogenesis. (
  • The authors then tested whether the gene expression data could be used in 'class discovery', the automatic discovery of new classes of cancer. (
  • 3. The method of claim 2, wherein the cancer is gastric cancer, and the upregulated genes are selected from the group consisting of RCC2, DUSP14, and NEK2. (
  • 4. The method of claim 2, wherein the cancer is colon cancer, and the upregulated genes are selected from the group consisting of JPH1, RPAT and GTPBP4. (
  • 5. The method of claim 2, wherein the cancer is pancreatic adenocarcinoma, and the upregulated genes are selected from the group consisting of CALU, PMEPA1 and BHLHE40. (
  • All patients underwent the DecisionDx ® -Melanoma gene expression profile test, measuring the activity of 31 genes known to be associated with progression in this cancer. (
  • This study is then an exploratory research comparing the genome-wide expression profile of ∼20,000 genes in whole-blood samples according to the use of HRT in a cross-sectional analysis within the prospective follow-up study "Norwegian Women and Cancer study (NOWAC). (
  • The study objective was to determine the value of gene expression profiling in predicting oral cancer development. (
  • Functional pathway analysis revealed proteasome machinery, MYC , and ribosomal components as the top gene sets associated with oral cancer risk. (
  • In multiple independent data sets, the expression profiles of the genes can differentiate head and neck cancer from normal mucosa. (
  • Our results show that gene expression profiles may improve the prediction of oral cancer risk in OPL patients and the significant genes identified may serve as potential targets for oral cancer chemoprevention. (
  • However, to assess the value of expression profiles in predicting cancer risk, samples must be collected before cancer diagnosis in a prospective setting, which takes years with high cost and is therefore difficult to do in practice. (
  • Cluster analysis has placed a group of down regulated genes in the upper left corner. (
  • The Polymerase Chain Reaction (PCR), with its sensitive and selective amplification of specific nucleic acid sequences has become a research tool of almost unparalleled importance, with applications in, for example, cloning, gene expression analysis, DNA sequencing, genetic mapping and diagnostics. (
  • Prostate tumor samples were taken from the patients at the time of surgery and subjected to a microarray gene expression analysis as described in Methods. (
  • Analysis and comparison of the gene expression profiles coupled to flagellar assembly and disassembly revealed that each process involves a new and uncharacterized whole-cell response to flagellar length changes. (
  • Our tools provide efficient mechanical disruption of difficult-to-lyse microbes, optimized chemistry for high yields of nucleic acids, and accurate qPCR-based gene expression analysis to facilitate and advance your research. (
  • The Nierman team was also involved in RNAseq analysis with C. albicans mutants in the absence and presence of Caspofungin to determine time course expression in response to Caspofungin with the aim of producing a drug exposure profile. (
  • Classical differential expression analysis and clustering methods are used to discriminate a limited number of cells. (
  • In an attempt to understand the mechanisms of resistance in the Japanese black pine, we created four LongSAGE (serial analysis of gene expression) libraries. (
  • Using SAM analysis, 1804 genes were differentially expressed between proliferating human retinal and choroidal endothelial cells while 76 genes were differentially expressed between unpassaged proliferating human iris and choroidal endothelial cells. (
  • Analysis of differential transcript expression in chickpea during compatible and incompatible interactions with Fusarium oxysporum f. sp. (
  • Subsampling of deep sequencing datasets demonstrated that differential pathway analysis is largely unaffected when reducing the number of genes to this level. (
  • Functional analysis of plant genomes requires methods for resolving differential expression of closely related genes. (
  • Cluster analysis for each chemical will then be performed to sort genes into groups that have responded in a similar fashion. (
  • Genes whose expression patterns were correlated with toxin production were identified by hybridization to a microarray manufactured from 5376 cDNAs. (