Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Oligonucleotide Array Sequence Analysis: 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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Gene Expression Regulation: 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.Reverse Transcriptase Polymerase Chain Reaction: 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.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Cluster Analysis: 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.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.RNA, Messenger: 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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression Regulation, Developmental: 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.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Microdissection: The performance of dissections with the aid of a microscope.Up-Regulation: 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.Cell Line, Tumor: A cell line derived from cultured tumor cells.Reproducibility of Results: 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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.RNA: 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)Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Regulatory Networks: 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.Tumor Markers, Biological: 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.Promoter Regions, Genetic: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Down-Regulation: 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.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.MicroRNAs: 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.DNA, Complementary: 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.Molecular Sequence Data: 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, Cultured: 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.Computational Biology: 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.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Polymerase Chain Reaction: 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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Mice, Inbred C57BLCell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Validation Studies as Topic: Research using processes by which the reliability and relevance of a procedure for a specific purpose are established.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.RNA, Neoplasm: RNA present in neoplastic tissue.Tissue Fixation: 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.Breast Neoplasms: Tumors or cancer of the human BREAST.Mutation: 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.Prognosis: 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.In Situ Hybridization: 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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.DNA Primers: 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.DNA-Binding Proteins: 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.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Multigene Family: 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)Toxicogenetics: 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.Protein Array Analysis: 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.Gene Library: 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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.Neoplasm Proteins: 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.Models, Biological: 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.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Apoptosis: 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.Genome, Human: 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.Disease Models, Animal: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Blotting, Western: 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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Gene Ontology: 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.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Lasers: 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.Tumor Cells, Cultured: 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.Models, Genetic: 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.Mice, Knockout: 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.Chromatin Immunoprecipitation: 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.Blotting, Northern: 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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Repressor Proteins: 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.Nucleic Acid Hybridization: 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)Cell Cycle: 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.Nuclear Proteins: 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.Genes, Plant: The functional hereditary units of PLANTS.RNA, Small Interfering: 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.Laser Capture Microdissection: 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, Reporter: 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.Homeodomain Proteins: 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 Transformation, Neoplastic: 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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Tissue Array Analysis: 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.Lymphoma, Large B-Cell, Diffuse: 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.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.RNA Interference: 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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Biological Markers: 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.Formaldehyde: 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)Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Epithelial Cells: 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.Transfection: 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.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Multiple Myeloma: 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.Stress, Physiological: 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.Flow Cytometry: 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.Arabidopsis: 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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Epigenesis, Genetic: 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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Proteome: The protein complement of an organism coded for by its genome.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Gene Dosage: 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.Predictive Value of Tests: 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.Embryo, Mammalian: 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.Proteins: 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.Sensitivity and Specificity: 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)Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Membrane Proteins: 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.Amino Acid Sequence: 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.Neoplasms: 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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Inflammation: 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.Gene Knockdown Techniques: 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.Biopsy: Removal and pathologic examination of specimens in the form of small pieces of tissue from the living body.Disease Progression: 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.RNA, Complementary: 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)Rats, Sprague-Dawley: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Protein Binding: 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.Prostatic Neoplasms: Tumors or cancer of the PROSTATE.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Reference Standards: 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, Plasma Cell: Neoplasms associated with a proliferation of a single clone of PLASMA CELLS and characterized by the secretion of PARAPROTEINS.Gene Deletion: 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.Embryonic Stem Cells: 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.DNA: 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, Developmental: Genes that determine the fate of a cell or CELLS in a region of the embryo during EMBRYONIC DEVELOPMENT.Biomarkers, Pharmacological: Measurable biological parameters that serve for drug development, safety and dosing (DRUG MONITORING).Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Antineoplastic Agents: Substances that inhibit or prevent the proliferation of NEOPLASMS.Wnt Proteins: 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.Muscle, Skeletal: 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.Luciferases: 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.Leukocytes, Mononuclear: 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.Histones: 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.NF-kappa B: 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.Stem Cells: Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.Brain: 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.Neoplasm Invasiveness: Ability of neoplasms to infiltrate and actively destroy surrounding tissue.Cell Survival: 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.Lung Neoplasms: Tumors or cancer of the LUNG.Comparative Genomic Hybridization: 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.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Lung: Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.Cytokines: 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.DNA Probes: 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.RNA Stability: 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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Arabidopsis Proteins: 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.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Postmortem Changes: Physiological changes that occur in bodies after death.Bacterial Proteins: Proteins found in any species of bacterium.Drug Resistance, Neoplasm: Resistance or diminished response of a neoplasm to an antineoplastic agent in humans, animals, or cell or tissue cultures.Cloning, Molecular: 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.Oxidative Stress: 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).Zebrafish: 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.Lymphoma, B-Cell: A group of heterogeneous lymphoid tumors generally expressing one or more B-cell antigens or representing malignant transformations of B-lymphocytes.Paraffin: 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.Oncogenes: Genes whose gain-of-function alterations lead to NEOPLASTIC CELL TRANSFORMATION. They include, for example, genes for activators or stimulators of CELL PROLIFERATION such as growth factors, growth factor receptors, protein kinases, signal transducers, nuclear phosphoproteins, and transcription factors. A prefix of "v-" before oncogene symbols indicates oncogenes captured and transmitted by RETROVIRUSES; the prefix "c-" before the gene symbol of an oncogene indicates it is the cellular homolog (PROTO-ONCOGENES) of a v-oncogene.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Mice, Inbred BALB CMetabolome: The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Oryza sativa: 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.Response Elements: 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.Case-Control Studies: 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.Single-Cell Analysis: Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.Liver Neoplasms: Tumors or cancer of the LIVER.Embryonic Development: Morphological and physiological development of EMBRYOS.Proto-Oncogene Proteins: 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.Genome-Wide Association Study: 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.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Nerve Tissue ProteinsFrozen Sections: Thinly cut sections of frozen tissue specimens prepared with a cryostat or freezing microtome.Neoplasms, Basal Cell: Neoplasms composed of cells from the deepest layer of the epidermis. The concept does not refer to neoplasms located in the stratum basale.Cell Culture Techniques: Methods for maintaining or growing CELLS in vitro.In Situ Hybridization, Fluorescence: 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.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.Hepatocytes: The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.Carcinoma, Hepatocellular: 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.Plasma Cells: 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)Transforming Growth Factor beta: 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.Cell Movement: The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM 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
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 ...
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 ...
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 ...
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 ...
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
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 http://www.cbs.dtu.dk/services/faro ...
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 ...
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.
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.. 2.4.2.1 Gene Expression Omnibus (GEO).. 2.4.2.2 ...
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.
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.
A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20-200 micro-grams total RNA or 0.5-2 micro-grams poly (A) RNA is typically required for monitoring gene expression. In addition, gene expression profiles from large, heterogeneous cell populations provide complex patterns from which biological data for the target cells may be difficult to extract. In this study, we chose to investigate a widely used mRNA amplification protocol that allows gene expression studies to be performed on samples with limited starting material. We present a quantitative study of the variation and noise present in our data set obtained from experiments with either amplified or non-amplified material. Using analysis of variance (ANOVA) and multiple hypothesis testing, we estimated the impact of amplification on the preservation of gene expression ratios. Both methods showed that the gene expression ratios were not completely preserved between amplified and non
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 ...
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 ...
Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count
Cancer is a disease characterized by uncontrolled cell growth and proliferation. For cancer to develop, genes regulating cell growth and differentiation must be altered; these mutations are then maintained through subsequent cell divisions and are thus present in all cancerous cells. Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. In the context of cancer, gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression profiling often helps in predicting the patients clinical outcome. Oncogenesis is the process by which normal cells acquire the properties of cancer cells leading to the formation of a cancer or tumor (see: tumorigenesis). It is characterized by a molecular reprogramming of a cell to undergo uninhibited cell division, allowing the formation of a malignant mass. The cells forming this mass undergo natural selection: as cells acquire mutations ...
Large amounts of information generated by gene expression profiling will increase implementation of data management tools Gene expression profiling can...
Welcome to the homepage of the GenT er mining tool! GenT er is an application tool for alignment, analysis and mining of gene expression time series. The core algorithm is based on dynamic time warping techniques used in the speech recognition field(1). These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases, as demonstrated on the figure below.. ...
DI-fusion, le Dépôt institutionnel numérique de lULB, est loutil de référencementde la production scientifique de lULB.Linterface de recherche DI-fusion permet de consulter les publications des chercheurs de lULB et les thèses qui y ont été défendues.
In the present study, we established a novel TNBC classification system, the FUSCC classification, by integrating the expression profiles of both mRNAs and lncRNAs. TNBC samples can be clearly classified into four subtypes according to our system: IM, LAR, MES, and BLIS. Each subtype has its own unique transcriptome profile. Furthermore, we filtrated out several subtype-specific lncRNAs and predicted possible functions of these lncRNAs in TNBC biological processes by analyzing the co-expression network between lncRNAs and mRNAs. To the best of our knowledge, the present study is the first to develop a novel TNBC classification system based on the transcriptome profiles of both mRNAs and lncRNAs in a large TNBC cohort.. Several novel findings were revealed in our in-depth transcriptome analysis. First, considering the expanding roles of lncRNAs in tumorigenesis and disease development, we integrated the expression profiles of both mRNAs and lncRNAs in an attempt to comprehensively understand the ...
OBJECTIVES: An inflammatory process following stroke in human brains and systemic inflammatory responses after stroke in humans have been reported by numerous investigators. The aim of the study was to investigate if genes involved in the cyclooxygenase 2 (COX-2) pathway are upregulated at peripheral level in patients after transient ischaemic attack (TIA) and stroke. DESIGN OF STUDY: Blood samples were obtained from two groups of patients undergoing carotid endarterectomy ...
TY - JOUR. T1 - Transcription network construction for large-scale microarray datasets using a high-performance computing approach. AU - Zhu, Mengxia Michelle. AU - Wu, Qishi. PY - 2008/3/4. Y1 - 2008/3/4. N2 - Background: The advance in high-throughput genomic technologies including microarrays has demonstrated the potential of generating a tremendous amount of gene expression data for the entire genome. Deciphering transcriptional networks that convey information on intracluster correlations and intercluster connections of genes is a crucial analysis task in the post-sequence era. Most of the existing analysis methods for genome-wide gene expression profiles consist of several steps that often require human involvement based on experiential knowledge that is generally difficult to acquire and formalize. Moreover, large-scale datasets typically incur prohibitively expensive computation overhead and thus result in a long experiment-analysis research cycle. Results: We propose a parallel ...
The HLX gene encoding a diverged homeobox transcription factor has been found to be up-regulated by vascular endothelial growth factor-A (VEGF-A) in endothelial cells. endothelial growth factor-A (VEGF-A) is the major trigger of vasculogenesis and angiogenesis during embryogenesis and blood-vessel formation in the adult.1,2 It has also been implicated in pathologic angiogenesis in diseases such as cancer, chronic inflammatory disorders, and retinopathy.3 Whereas several peptide products are generated from the VEGF-A gene by differential splicing, the available data suggest that isoform VEGF-A165 is the RAB11FIP4 predominant form responsible for the major angiogenic effects.4 The gene repertoire induced by VEGF-A mainly via VEGF receptor 2 has been investigated by several groups5-7; however, the transcription factors up-regulated by VEGF-A and how they mediate its specific and unique biologic functions remain largely uncharacterized. We have recently identified a group of genes or at least ...
A distinct feature of human being prostate tumor (PCa) is the advancement of osteoblastic (bone-forming) bone fragments metastases. on growth cells and stromal cells, that is certainly, endothelial osteoblasts and cells. In comparison, CXCL1 features as a paracrine aspect through the CXCR2 receptor portrayed in endothelial osteoblasts and cells. Hence, our research reveals a complicated PCa bone fragments metastasis secretome with paracrine and autocrine signaling features that mediate cross-talk among multiple cell types within the growth microenvironment. A specific feature of individual prostate tumor (PCa)1 with fatal potential is certainly the buy 77-95-2 advancement of metastases in bone fragments with a bone-forming phenotype (1). This home of PCa bone fragments metastasis suggests that PCa cells possess exclusive connections with cells in the bone fragments microenvironment. Cells that are known to become present in the bone tissue microenvironment consist of osteoblasts, osteoclasts, ...
We did a genome-wide transcription profiling study of 60 children, with first relapse of ALL enrolled in the relapse trial ALL-REZ BFM 2002 of the BFM study group. Genetic and immunologic subclasses described by gene expression profiling studies of initial ALL (10, 12) were correctly predicted from microarray data in relapse patients, thus proving consistency of microarray-based leukemia subtype classification across different stages of disease. To identify molecular determinants of the major prognostic factors at ALL relapse, we compared prognostic groups of B-cell precursor ALL relapse classified according to each of these factors. No significant gene expression patterns were found to correlate with the prognostic factors site of relapse and MRD. About the most evident prognostic factor time of relapse, we identified significant differences in gene expression between patients with very early and late relapse. We obtained a list of 83 differentially expressed genes mostly up-regulated in very ...
Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total
Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the ...
The developmental transition to motherhood requires gene expression changes that alter the brain to prepare and drive the female to perform maternal behaviors. Furthermore, it is expected that the many physiological changes accompanying pregnancy and postpartum stages will impact brain gene expression patterns. To understand how extensive these gene expression changes are, we examined the global transcriptional response broadly, by examining four different brain regions: hypothalamus, hippocampus, neocortex, and cerebellum. Further, to understand the time course of these changes we performed RNA-sequencing analyses on mRNA derived from virgin females, two pregnancy time points and three postpartum time points. We find that each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions, across the time points. Additionally, several genes previously implicated in underlying postpartum depression change expression. This study serves as a
As shown in Figure 2A and Table 1, GO enriched functions for the 74 overlapped up-regulated genes and 79 overlapped down-regulated genes were involved in a number of biological processes (BP), including cell cycle phase, M phase, mitotic cell cycle, cell cycle process, and cell division for the up-regulated genes, and muscle system process, purine nucleotide metabolic process, negative regulation of cell proliferation, regulation of RNA metabolic process, and transcription for the down-regulated genes. With regard to molecular function (MF), the top six MFs of the up-regulated DEGs were microtubule motor activity, ATP binding, adenyl ribonucleotide binding, purine nucleoside binding, nucleoside binding, and ribonucleotide binding, and the top four MFs of the down-regulated DEGs were transcription factor activity, DNA binding, transcription regulator activity, and cAMP binding (Figure 2B and Table 1). For the cellular component (CC) terms, majority of the up-regulated DEGs were enriched for ...
Release Date: 06/05/2019 Boston University (BU) researchers, in collaboration with researchers at the National Toxicology Program (NTP) and the Broad Institute, have developed and evaluated a new approach to assess whether exposure to a chemical increases a persons long-term cancer risk. The fast, cost-effective method uses gene expression profiling, which measures the activity of a thousand or more genes to capture what is happening in a cell. Based on gene expression profiling data, the researchers were able to infer specific biological changes at the cellular level and predict potential carcinogenicity of chemicals, or the ability of chemicals to cause cancer.. ...
Differential gene expression patterns in developing sexually dimorphic rat brain regions exposed to antiandrogenic, estrogenic, or complex endocrine disruptor mixtures: Glutamatergic synapses as ...
Background: Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian 6 Landrace backcross with extreme phenotypes according to FA profile. Results: We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with
Gene-expression profiling is the most popular method since it provides a total overview of the expression levels in your sample. All protein-coding (poly-A containing) transcripts are consistently and accurately represented. It provides an affordable approach to examine differential gene-expression analysis between groups of samples, such as various treatments, time-points, or disease versus control samples.. Our ISO-accredited service includes all novel features: Unique Molecular Identifiers (UMIs), identification of antisense transcripts, and can handle a broad range of input RNA, starting from 5 ng. It is applicable for FFPE-material or other (partly) degraded and challenging samples (see below).. For whole blood analysis, we offer globin reduction that removes the globin transcripts originating from erythrocytes, so you reduce the sequencing capacity that is required per sample with 30 to 40%. The removal of ribosomal RNA is not necessary, since these transcripts do not contain a poly-A ...
Detailed analysis of the immunological pathways leading to robust vaccine responses has become possible with the application of systems biology, including transcriptomic analysis. Venous blood is usually obtained for such studies but others have obtained capillary blood (e.g. finger-prick). Capillary samples are practically advantageous, especially in children.The aim of this study was to compare gene expression profiles in venous and capillary blood before, 12h and 24h after vaccination with 23-valent pneumococcal polysaccharide or trivalent inactivated seasonal influenza vaccines.Gene expression at baseline was markedly different between venous and capillary samples, with 4940 genes differentially expressed, and followed a different pattern of changes after vaccination. At baseline, multiple pathways were upregulated in venous compared to capillary blood, including transforming growth factor-beta receptor signalling and toll-like receptor cascades. After vaccination with the influenza vaccine, there
h1,D-NetWeaver Overview,/h1, ,p,D-NetWeaver is an application to enable the manipulation and analysis of time course data matrices, such as gene expression data as generated by microarray or RNA-seq experiments. It is specifically geared toward reconstructing gene regulatory networks from time course gene expression data using differential equation network models. ,/p, ,p,It provides the ability to apply six primary steps to gene expression data: ,/p, ,ol, ,li,Significant gene detection,/li, ,li,Clustering,/li, ,li,Smoothing,/li, ,li,Functional enrichment analysis,/li, ,li,Regulation identification (otherwise known as variable selection of differential equation network models) ,/li, ,li,Parameter estimation refinement,/li, ,/ol, ,p,The software provides many data manipulation and data visualization features to assist users in exploring their data and interpreting the results of these six primary steps.,/p, ,p,The end goal is the creation of a dynamic network model. Currently, the only supported ...
Technologies used for high-throughput gene expression analysis.. A. Breast cancer tumors are sampled at the treatment location and shipped to the central laboratory doing the assay, where pathologic review is done to assess cancer cell contents, followed by RNA preparation and integrity evaluation. Suitable samples are used to quantify RNA levels, thus assessing gene expression. When a gene is expressed, the transcription complex copies its DNA sequence into complementary RNA transcripts that are translated into proteins. High-throughput gene expression analysis aims to quantify messenger RNA (mRNA) populations in a given tissue. B. DNA microarray is the molecular biology technique enabling gene expression analysis in MammaPrint. RNA is labeled with fluorescent dye and hybridized against thousands of different nucleotide sequences corresponding to different genes and arrayed on a solid surface (that is, a modified microscope glass slide). On hybridization, fluorescence emitted by single ...
In the present study, we examined the gene expression profile of 25 IGHV4-34 patients including subset #4, #16 and non-subset 4/16 cases. Initially, we compared the gene expression profiles between subset #4 and non-subset 4/16 patients and between subset #16 patients and non-subset 4/16 patients, and detected only few significant differences. This is probably because, overall, non-subset 4/16 IGHV4-34 cases exhibited a more heterogeneous gene expression profile, likely reflecting the structural heterogeneity of their BCR, which would be expected to be responsive to a far wider range of antigens than that recognized by stereotyped subsets. Interestingly, however, we detected distinct differences in gene expression patterns when comparing subset #4 and #16 cases, both of which can be reliably defined at the molecular level based on subset-specific VH CDR3 and subset-biased features of somatic hypermutation.8 This finding is supported by the recent observation that stereotyped subset cases have ...
Neurohormonal activation in heart failure is well established and involves activation of the renin-angiotensin-aldosterone network and the sympathetic nervous system. Associated with this process is the enhanced production of cytokines and other inflammatory factors that have been directly implicated in the pathophysiological progression of heart failure (2, 6, 11, 15). These factors have both direct and indirect effects on cardiac remodeling and can also affect gene expression in other tissues (19). Due to the systemic nature of the disease, we tested the hypothesis that noncardiac tissue can exhibit specific gene expression signatures that associate with cardiovascular events.. By performing blood gene expression profiling analysis, we analyzed ,27,000 transcripts in blood and demonstrated for the first time that blood gene expression varies as a function of patient outcomes (see online data supplement).1 A total of 197 mortality genes were discovered. Intriguingly, a large number ...
Purpose: ATG41 is involved both in autophagy and zinc-deficient growth. The goal of this study is to compare transcriptomic profiles of wild-type and atg41Δ strains to discover autophagy-independent molecular phenotypes for the mutant. The atg1Δ mutant is a control for autophagy activity. Methods: Wild-type and mutant yeast were grown to mid-log phase in replete medium and shifted to zinc-deficient medium for 8 hours, after which, cells were harvested for RNA sequencing to detect differential gene expression. Results: Gene expression data for virtually every gene (~6,000) was obtained with ~12,000,000 reads per sample. Differential gene expression analysis showed that several hundred genes were differentially experessed in the atg41Δ mutant (greater than 2-fold) at an FDR of 0.5. Conclusions: Most strikingly, we found that the atg41Δ mutant transcriptome shows signs that sulfur metabolism is distrupted during zinc-deficinet growth. Expression of Met4 gene targets is increased.
Sigma-Aldrich offers abstracts and full-text articles by [Youichi Higuchi, Motohiro Kojima, Genichiro Ishii, Kazuhiko Aoyagi, Hiroki Sasaki, Atsushi Ochiai].
... Future Conference: GENE EXPRESSION 2018; GENE EXPRESSION 2019; GENE EXPRESSION 2020;
BACKGROUND: Tumorigenesis is characterised by changes in transcriptional control. Extensive transcript expression data have been acquired over the last decade and used to classify prostate cancers. Prostate cancer is, however, a heterogeneous multifocal cancer and this poses challenges in identifying robust transcript biomarkers. METHODS: In this study, we have undertaken a meta-analysis of publicly available transcriptomic data spanning datasets and technologies from the last decade and encompassing laser capture microdissected and macrodissected sample sets. RESULTS: We identified a 33 gene signature that can discriminate between benign tissue controls and localised prostate cancers irrespective of detection platform or dissection status. These genes were significantly overexpressed in localised prostate cancer versus benign tissue in at least three datasets within the Oncomine Compendium of Expression Array Data. In addition, they were also overexpressed in a recent exon-array dataset as well a
The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving Functional Association(s) by Response Overlap (FARO) between microarray gene expression
With advent of high throughput transcriptomic profiling, biomarker identification has been taken to the genomic level. Several studies have been published so far where transcriptomic profiling and consequently biomarker identification in form of single genes, or a signature composed of several genes, has been done on cancer samples, and such data are available in public domain. Gene signatures prognostic for overall, metastasis free or recurrence free survival have been developed using transcriptomic profiling. In several such studies gene signatures have been developed specific for prognostication in particular subtype of a cancer, for instance, a subgroup of population treated with a specific drug. 70 Gene signature Mammaprint® [1], PAM50 [2], OncotypeDx® [3] are some examples of gene signatures of prognostic importance in breast cancer. Similar signatures have also been developed in other cancers such as Colon cancer [4, 5], Liver cancer [6], Lung cancer [7, 8] and Pancreatic Cancer [9] ...
BioMed Research International is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies covering a wide range of subjects in life sciences and medicine. The journal is divided into 55 subject areas.
The diagnosis and treatment of prostate cancer are fields with long histories. Various efforts have led to the progressive understanding of the disease. However, the present criteria of diagnosis and prognosis, as well as the approaches of treatment and surgery, are not sufficiently reliable. Previous gene expression profiling studies on prostate tumors and normal tissues demonstrated the feasibility in characterizing the molecular alterations at the overall mRNA transcript level. However, these transcriptome analyses were based on the old central dogma of "one gene, one mRNA", which may underestimate the complexity of tumorigenesis [23].. Previously, we carried out a study of prostate cancer by exon-junction microarray-based assay and demonstrated the power of this integrated technology in detecting both transcriptional and splicing regulation [25, 29]. In this paper, we present systematic analyses with the focus on using splice isoform profiling for prostate cancer classification. ...
The constant maintenance of both DC and Mϕ cell pools in the lung is essential for effective immune surveillance in pulmonary tissue. Recent reports highlight the role of PBMo that emigrate into the lung and differentiate into both lung DC and Mϕ, thereby serving as a constant supply for the renewal of the lung DC and Mϕ pool [6]. While many studies have investigated monocyte recruitment under inflammatory conditions, little is known about the pathways mediating monocyte trafficking and differentiation in lung tissue under non-inflammatory conditions [27, 31, 32]. Since PBMo are believed to be precursors for lung Mϕ and DC, a global gene expression profiling approach was chosen to reveal crucial differences between these cell types, to better understand their relation to one another, and to identify gene clusters relevant for the migration and differentiation process that takes place under steady-state conditions. Previous microarray studies investigating the relation, differentiation and/or ...
Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal), proximal-distal, and dermal versus nondermal. A set of 337 genes that varied according to these positional divisions was able to group all 47 samples by their anatomic sites of origin. Genes
Behaviourally driven gene expression reveals song nuclei in hummingbird brain.s profile, publications, research topics, and co-authors
Unraveling the relationship between molecular signatures in the brain and their functional, architectonic, and anatomic correlates is an important neuroscientific goal. It is still not well understood whether the diversity demonstrated by histological studies in the human brain is reflected in the spatial patterning of whole brain transcriptional profiles. Using genome-wide maps of transcriptional distribution of the human brain by the Allen Brain Institute, we test the hypothesis that gene expression profiles are specific to anatomically described brain regions. In this work, we demonstrate that this is indeed the case by showing that gene similarity clusters appear to respect conventional basal-cortical and caudal-rostral gradients. To fully investigate the causes of this observed spatial clustering, we test a connectionist hypothesis that states that the spatial patterning of gene expression in the brain is simply reflective of the fiber tract connectivity between brain regions. We find that ...
Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ ...
Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using ...
5-Fluorouracil (5-FU) is the most common chemotherapeutic agent used in the treatment of colorectal cancer, yet objective response rates are low. Recently, camptothecin (CPT) has emerged as an effective alternative therapy. Decisive means to determine treatment, based on the likelihood of response to each of these agents, could greatly enhance the management of this disease. Here, the ability of cDNA microarray-generated basal gene expression profiles to predict apoptotic response to 5-FU and CPT was determined in a panel of 30 colon carcinoma cell lines. Genes whose basal level of expression correlated significantly with 5-FU- and CPT-induced apoptosis were selected, and their predictive power was assessed using a "leave one out" jackknife cross-validation strategy. Selection of the 50 genes best correlated with 5-FU-induced apoptosis, but not 50 randomly selected genes, significantly predicted response to this agent. Importantly, this gene expression profiling approach predicted response more ...
Previous studies indicate that autism spectrum disorders (ASDs) can be conceptualized as the result of multiple rare and common variants that act in combination to shape different aspects of cognition and behavior.
Currently one of the largest online repositories for human and mouse stem cell gene expression data, StemBase was first designed as a simple web-interface to DNA microarray data generated by the Canadian Stem Cell Network to facilitate the discovery of gene functions relevant to stem cell control and differentiation. Since its creation, StemBase has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. As of September 1, 2008, StemBase contains gene expression data (microarray and Serial Analysis of Gene Expression) from 210 stem cell samples in 60 different experiments. StemBase can be used to study gene expression in human and murine stem cells and is available at http://www.stembase.ca .
Data analysis of microarrays has become an area of intense research.[11] Simply stating that a group of genes were regulated by at least twofold, once a common practice, lacks a solid statistical footing. With five or fewer replicates in each group, typical for microarrays, a single outlier observation can create an apparent difference greater than two-fold. In addition, arbitrarily setting the bar at two-fold is not biologically sound, as it eliminates from consideration many genes with obvious biological significance. Rather than identify differentially expressed genes using a fold change cutoff, one can use a variety of statistical tests or omnibus tests such as ANOVA, all of which consider both fold change and variability to create a p-value, an estimate of how often we would observe the data by chance alone. Applying p-values to microarrays is complicated by the large number of multiple comparisons (genes) involved. For example, a p-value of 0.05 is typically thought to indicate ...
The identification of early and stage-specific biomarkers for Alzheimers disease (AD) is critical, as the development of disease-modification therapies may depend on the discovery and validation of such markers. The identification of early reliable biomarkers depends on the development of new diagnostic algorithms to computationally exploit the information in large biological datasets. To identify potential biomarkers from mRNA expression profile data, we used the Logic Mining method for the unbiased analysis of a large microarray expression dataset from the anti-NGF AD11 transgenic mouse model. The gene expression profile of AD11 brain regions was investigated at different neurodegeneration stages by whole genome microarrays. A new implementation of the Logic Mining method was applied both to early (1-3 months) and late stage (6-15 months) expression data, coupled to standard statistical methods. A small number of fingerprinting formulas was isolated, encompassing mRNAs whose expression ...
Transcriptional programs that regulate development are exquisitely controlled in space and time. Elucidating these programs that underlie development is essential to understanding the acquisition of cell and tissue identity. We present microarray expression profiles of a high resolution set of developmental time points within a single Arabidopsis root, and a comprehensive map of nearly all root cell-types. These cell-type specific transcriptional signatures often predict novel cellular functions. A computational pipeline identified dominant expression patterns that demonstrate transcriptional connections between disparate cell types. Dominant expression patterns along the roots longitudinal axis do not strictly correlate with previously defined developmental zones, and in many cases, expression fluctuation along this axis was observed. Both robust co-regulation of gene expression and potential phasing of gene expression were identified between individual roots. Methods that combine these two sets of
Transcriptome analysis of RNAs extracted from livers of wild type or Smurf1 knock out (KO) or Smurf2 KO mice at age of 11 month old. We prepared RNA from the following groups: livers of Wild type (WT) or Smurf1 KO or Smurf2 KO mouse from mixed Black Swiss/129SvEv background at age of 11 month old. The gene expression profiles were compared, and selected genes that showed either increased or decreased expression by a cut-off of 1.5 folds, p| 0.05. The results showed that 1211 genes in the Smurf1-/- livers were differentially expressed over their WT controls, whereas only 302 genes were differentially expressed in the Smurf2-/- livers, and 114 genes were commonly differentially expressed. Many genes that are involved in lipid metabolism were upregulated in Smurf1-/- livers. These results also indicate that Smurf1 plays a more prominent role in the liver than Smurf2.
It is well know that in contrast to moderate physical activity, an acute bout of prolonged, exhaustive exercise such as marathon or half-marathon running can cause adverse effects on immunity as reflected by transient immunosuppression following the event. We used microarray technology as well as other approaches to study the response of selected and non-selected immune-related genes and proteins following an exercise program. The capacity of whole blood cultures to produce cytokines in response to endotoxin (LPS) was studied (Paper I). Further, the early steps of the immune reaction to pathogen contact were evaluated in details using whole blood culture and gene expression profiling approach in athletes before, 30 min after, 3 h after and 24 h after a half-marathon run (Paper II). Gender and menstrual phase dependent differences in cytokine and gene expression profiles of 12 male subjects (M) and 9 women with regular menstrual cycles was also studied in response to an aerobic exercise at 93% of ...
Tumour hypoxia is a driver of breast cancer progression associated with worse prognosis and more aggressive disease. The cellular response to hypoxia is mediated by the hypoxia-inducible transcription factors HIF-1 and HIF-2, whose transcriptional activity is canonically regulated through their oxygen-labile HIF-α subunits. These are constitutively degraded in the presence of oxygen; however, HIF-1α can be stabilised, even at high oxygen concentrations, through the activation of HER receptor signalling. Despite this, there is still limited understanding on how HER receptor signalling interacts with HIF activity to contribute to breast cancer progression in the context of tumour hypoxia. 2D and 3D cell line models were used alongside microarray gene expression analysis and meta-analysis of publicly available gene expression datasets to assess the impact of HER2 overexpression on HIF-1α/HIF-2α regulation and to compare the global transcriptomic response to acute and chronic hypoxia in an isogenic cell
MAPPFinder calculates the percentage of genes measured within each GO term that meet a user-defined criterion, and this measurement is known as the percent changed. MAPPFinder also calculates the percentage of the genes associated with a GO term that are measured in the experiment, and this measurement is known as the percent present. Calculating the percent present is necessary to determine how well represented a GO term is in the dataset.. The GO gene-association files [17] are potentially problematic, because they treat each GO term independently, removing the implicit parent-child relationship. As a result, looking at the GO terms individually is often uninformative because the number of genes associated with any one term is smaller than the actual number of genes involved in that process, component, or function. To address this issue, we calculate the nested percentage for a parent term with all its children below it in the hierarchy. By combining the child terms with their parent, the ...
Prostate cancer (PCa) is a malignancy cause of cancer deaths and frequently diagnosed in male. This study aimed to identify tumor suppressor genes, hub genes and their pathways by combined bioinformatics analysis. A combined analysis method was used for two types of microarray datasets (DNA methylation and gene expression profiles) from the Gene Expression Omnibus (GEO). Differentially methylated genes (DMGs) were identified by the R package minfi and differentially expressed genes (DEGs) were screened out via the R package limma. A total of 4451 DMGs and 1509 DEGs, identified with nine overlaps between DMGs, DEGs and tumor suppressor genes, were screened for candidate tumor suppressor genes. All these nine candidate tumor suppressor genes were validated by TCGA (The Cancer Genome Atlas) database and Oncomine database. And then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed by DAVID (Database for Annotation, Visualization and
International Journal of Plant Genomics is an international, peer-reviewed Open Access journal that publishes novel and advanced original research results of wide interest in all fields of plant genomics, genome technologies and applications of genomic tools in plant breeding. In addition, the journal welcomes field review articles of general interest to plant scientists in plant genomics. Although the journal is dedicated to publish the research results in plant genomics, research articles in genomics of animals or other organisms that are of significance in advancing or potentially applicable to plant genomics are considered for publication in the journal.
Because microarray experiments literally involve the comparison of thousands of data points, the scientific community has grappled with identifying specific guidelines for the conductance, statistical analysis, and interpretation of microarray experiments due to the significant potential for false positives (i.e. , type I error). To this end, the Microarray Gene Expression Data Society, an international organization of molecular biologists, computer scientists, and data analysts, developed standards known as the Minimum Information About a Microarray Experiment (MIAME), which outlines the minimum information that should be reported about a microarray experiment to enable its unambiguous interpretation and reproduction.5 1In addition adhering to the MIAME guidelines, Lucchinetti et al. analyzed their microarray data using a highly sophisticated technique known as gene set enrichment analysis. Gene set enrichment analysis is a computational method that determines whether an a priori defined set of ...
Overall gene expression levels and dynamics related to microbial metabolisms for each Bin-genome.Gene expression levels and changes were calculated (see Supplem
We report here that our initially identified set of predictive genes for detection of lymph node metastasis in patients with head and neck cancer ( 13) is a subset of a larger group of predictive genes. Using a resampling approach, we have identified a large set of 825 genes that can be used for prediction of metastasis. Based on this group of genes, multiple predictive signatures can be made with high predictive accuracy. The phenomenon that different sets of genes can be used for accurate prediction is not exclusive for this study but is becoming apparent in other cancer profiling studies ( 7, 17). Due to minor differences in gene expression, different genes are selected for optimal prediction when the signature is built using different samples, especially when comparing studies that have been done in different institutes ( 3, 12). This instability in gene composition of different predictive signatures is not detrimental as long as the predictive outcome and accuracy remain similar. Different ...
Free Online Library: Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep.(Research Article, Report) by BioMed Research International; Biotechnology industry High technology industry Adipose tissue Analysis Genetic aspects Adipose tissues Genes Messenger RNA Physiological aspects MicroRNA
Tubular carcinoma (TC) is an uncommon special type of breast cancer characterized by an indolent clinical course. Although described as part of a spectrum of related lesions named low-grade breast neoplasia family due to immunophenotypical and genetic similarities, TCs, low-grade invasive ductal carcinomas of no special type (IDC-NSTs), and classic invasive lobular carcinomas (ILCs) significantly differ in terms of histological features and clinical outcome. The aim of this study was to investigate whether pure TCs constitute an entity distinct from low-grade IDC-NSTs and from classic ILCs. To define the transcriptomic differences between TCs and IDC-NSTs and ILCs whilst minimizing the impact of histological grade and molecular subtype on their profiles, we subjected a series of grade- and molecular subtype-matched TCs and IDC-NSTs and molecular subtype-matched TCs and classic ILCs to genome-wide gene expression profiling using oligonucleotide microarrays. Unsupervised and supervised analysis ...
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. Multiple prediction models were developed and compared using CoxBoost algorithm. We observed a marked improvement in prediction accuracy when a gene expression profile was used. With the gene expression profile only, we developed a 29-trancript prediction model that had prediction error rate around 8%. Using the profile in combination with the previously known risk factors, the model showed a similar prediction error rate as the expression profile alone. Because using the previously known risk factors alone had a clear inferior performance (Fig. 1) compared with models 1 and 2, it is clear that the expression profiles have a predictive value beyond the known risk factors. As an alternative way to assess the misclassification rate of genomic predictors in general, we employed a simpler approach, which used DLDA algorithm ...
Purpose: The role and clinical implication of the transmembrane protein with EGF and two follistatin motifs 2 (TMEFF2) in gastric cancer is poorly understood.. Experimental Design: Gene expression profile analyses were performed and Gene Set Enrichment Analysis (GSEA) was used to explore its gene signatures. AGS and MKN45 cells were transfected with TMEFF2 or control plasmids and analyzed for gene expression patterns, proliferation, and apoptosis. TMEFF2 expression was knocked down with shRNAs, and the effects on genome stability were assessed. Interactions between TMEFF2 and SHP-1 were determined by mass spectrometry and immunoprecipitation assays.. Results: Integrated analysis revealed that TMEFF2 expression was significantly decreased in gastric cancer cases and its expression was negatively correlated with the poor pathologic stage, large tumor size, and poor prognosis. GSEA in The Cancer Genome Atlas (TCGA) and Jilin datasets revealed that cell proliferation, apoptosis, and DNA ...
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High-throughput gene expression profiling can identify sets of genes that are differentially expressed between different phenotypes. Discovering marker genes is particularly important in diagnosis of a cancer phenotype. However, gene sets produced to date are too large to be economically viable diagnostics. We use a hybrid decision tree-discriminant analysis to identify small sets of genes, i.e. single genes and gene pairs, which separate normal samples from different stages of tumor samples. Half the samples are selected for training to form the probability distribution of expression values of each gene. The distributions for the tumor and normal phenotypes are then used to classify the test samples. The algorithm also identifies gene pairs by combining the probability distributions to construct a decision tree which is used to determine the class of test samples. After a series of training and testing sessions, genes and gene pairs that classify all samples correctly are recorded. The method ...
Discussion. sAML develops in approximately 40% of patients with MDS and the clinical discrimination between AML and MDS is based on cytomorphological analysis, since patients with MDS have dysplastic hematopoiesis and a myeloblast count of less than 20%, whereas those with a myeloblast count of 20% or more have AML.6 sAML has clinical and biological heterogeneity linked to chromosome aberrations or molecular changes with the association between them suggesting that those mechanisms are significantly involved in leukemogenesis.1 This case report shows evidence that t(8;13)(q22;q11) could be involved in the pathogenesis and severity of AML. The translocation t(8;13) with breakpoints at (8q22) and (13q11) has neither been reported nor described for possible altered genes. The gene expression profile was performed to determine the specific signature in cells from this patient and to try to clarify a new possible molecular pathway involved in disease evolution. Of the 874 genes differentially ...
Abstract Background MI-319 is a synthetic small molecule designed to target the MDM2-P53 interaction. It is closely related to MDM2 antagonists MI-219 and Nutlin-3 in terms of the expected working mechanisms. The purpose of this study was to evaluate anti-lymphoma activity of MI-319 in WSU-FSCCL, a B-cell follicular lymphoma line. For comparison purpose, MI-319, MI-219 and Nutlin-3 were assessed side by side against FSCCL and three other B-cell hematological tumor cell lines in growth inhibition and gene expression profiling experiments. Results MI-319 was shown to bind to MDM2 protein with an affinity slightly higher than that of MI-219 and Nutlin-3. Nevertheless, cell growth inhibition and gene expression profiling experiments revealed that the three compounds have quite similar potency against the tumor cell lines tested in this study. In vitro, MI-319 exhibited the strongest anti-proliferation activity against FSCCL and four patient cells, which all have wild-type p53. Data obtained from Western
Cancer clinical outcome prediction using gene expression profiles has been proposed by the field of translational bioinformatics for better diagnostics, prognostics, and further therapeutics [1]. Somatic mutations and regulation abnormalities in a tumor cell cause substantial gene expression changes [2]. Expression of oncogenes or tumor suppressor genes promotes the malignant phenotype of cancer cells or inhibits cell division, development, or survival of cancer cell [2]. Thus, DNA microarray technologies have been widely used to predict clinical phenotypes such as stage, grade, metastatic status, recurrence, and patient survival in several cancers [3-5]. In terms of translational bioinformatics, accurate phenotype prediction based on the molecular signature can be used clinically to choose the best of several available therapies for a cancer patient.. However, clinical phenotype prediction based on gene expression profiles can vary between independent data sets [6, 7]. One possible explanation ...
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions - Background: The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. Additionally, it is possible to use the distribution of GO terms inherent to each EP to relate that EP as a whole to other EPs. Because GO term annotation is organized in a tree-like cascade of variable granularity, this approach allows the user to relate (e.g., by hierarchical clustering) EPs of varying length and from different platforms (e.g., GeneChip, SAGE, EST library). Results: Here
presents a world view of the new advances within the organic sciences and the adaption of the pathogen to the host vegetation published utilizing NGS. Molecular Omics is now an incredible motive force to benefit the adaption genetics and an excellent problem to the clinical neighborhood, that are resolved throughout the program of the NGS applied sciences. the supply of entire genome sequences, the respective version species for dicot and monocot plant teams, provides a world chance to delineate the identity, functionality and the expression of the genes, to boost new instruments for the identity of the recent genes and pathway id. Genome-wide study instruments, assets and techniques equivalent to facts mining for structural similarities, gene expression profiling on the DNA and RNA point with quick elevate in to be had genome sequencing efforts, expressed series tags (ESTs), RNA-seq, gene expression profiling, triggered deletion mutants and insertional mutants, and gene expression knock-down ...
TY - JOUR. T1 - Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. AU - Jonker, Martijs J.. AU - Melis, Joost P.M.. AU - Kuiper, Raoul V.. AU - van der Hoeven, Tessa V.. AU - Wackers, Paul F.K.. AU - Robinson, Joke. AU - van der Horst, Gijsbertus T.J.. AU - Dollé, Martijn E.T.. AU - Vijg, Jan. AU - Breit, Timo M.. AU - Hoeijmakers, Jan H.J.. AU - Van Steeg, Harry. PY - 2013/10/1. Y1 - 2013/10/1. N2 - Aging and age-related pathology is a result of a still incompletely understood intricate web of molecular and cellular processes. We present a C57BL/6J female mice in vivo aging study of five organs (liver, kidney, spleen, lung, and brain), in which we compare genome-wide gene expression profiles during chronological aging with pathological changes throughout the entire murine life span (13, 26, 52, 78, 104, and 130 weeks). Relating gene expression changes to chronological aging revealed many differentially expressed genes (DEGs), ...
Intellectual disability (ID) is a common developmental disability observed in 1 to 3% of the human population. A possible role for the Angiotensin II type 2 receptor (AGTR2) in brain function, affecting learning, memory, and behavior, has been suggested in humans and rodents. Mice lacking the Agtr2 gene (Agtr2(-/y)) showed significant impairment in their spatial memory and exhibited abnormal dendritic spine morphology. To identify Agtr2 influenced genes and pathways, we performed whole genome microarray analysis on RNA isolated from brains of Agtr2(-/y) and control male mice at embryonic day 15 (E15) and postnatal day one (P1). The gene expression profiles of the Agtr2(-/y) brain samples were significantly different when compared to profiles of the age-matched control brains. We identified 62 differently expressed genes (p, or =0.005) at E15 and in P1 brains of the Agtr2(-/y) mice. We verified the differential expression of several of these genes in brain samples using quantitative RT-PCR. ...
The effective detection and management of muscle-invasive bladder Transition Cell Carcinoma (TCC) continues to be an urgent clinical challenge. While some differences of gene expression and function in papillary (Ta), superficial (T1) and muscle-invasive (≥T2) bladder cancers have been investigated, the understanding of mechanisms involved in the progression of bladder tumors remains incomplete. Statistical methods of pathway-enrichment, cluster analysis and text-mining can extract and help interpret functional information about gene expression patterns in large sets of genomic data. The public availability of patient-derived expression microarray data allows open access and analysis of large amounts of clinical data. Using these resources, we investigated gene expression differences associated with tumor progression and muscle-invasive TCC. Gene expression was calculated relative to Ta tumors to assess progression-associated differences, revealing a network of genes related to Ras/MAPK ...
To extract functional information on genes and processes from large expression datasets, analysis methods are required that can computationally deal with these amounts of data, are tunable to specific research questions, and construct classifiers that are not overspecific to the dataset at hand. To satisfy these requirements, a stepwise procedure that combines elements from principal component analysis and discriminant analysis, was developed to specifically retrieve genes involved in processes of interest and classify samples based upon those genes. In a global expression dataset of 300 gene knock-outs in Saccharomyces cerevisiae, the procedure successfully classified samples with similar cellular component Gene Ontology annotations of the knock-out gene by expression signatures of limited numbers of genes. The genes discriminating mitochondrion from the other subgroups were evaluated in more detail. The thiamine pathway turned out to be one of the processes involved and was successfully ...
By Gaurav Sablok, Sunil Kumar, Saneyoshi Ueno, Jimmy Kuo, Claudio Varotto. Provides a world view of the new advances within the organic sciences and the adaption of the pathogen to the host crops printed utilizing NGS. Molecular Omics is now a massive motive force to benefit the adaption genetics and an exceptional problem to the medical group, that are resolved during the software of the NGS applied sciences. the supply of whole genome sequences, the respective version species for dicot and monocot plant teams, offers an international chance to delineate the id, functionality and the expression of the genes, to increase new instruments for the identity of the recent genes and pathway identity. Genome-wide study instruments, assets and ways reminiscent of info mining for structural similarities, gene expression profiling on the DNA and RNA point with quick raise in on hand genome sequencing efforts, expressed series tags (ESTs), RNA-seq, gene expression profiling, prompted deletion mutants and ...
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 ...
Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed
TY - JOUR. T1 - In vitro global gene expression analyses support the ethnopharmacological use of Achyranthes aspera. AU - Pochi, Subbayan. AU - Sarkar, Malancha. AU - Nathanson, Lubov. AU - Doshi, Nikesh. AU - Lokeshwar, Balakrishna L.. AU - Ardalan, Bach. PY - 2013/12/1. Y1 - 2013/12/1. N2 - Achyranthes aspera (family Amaranthaceae) is known for its anticancer properties. We have systematically validated the in vitro and in vivo anticancer properties of this plant. However, we do not know its mode of action. Global gene expression analyses may help decipher its mode of action. In the absence of identified active molecules, we believe this is the best approach to discover the mode of action of natural products with known medicinal properties. We exposed human pancreatic cancer cell line MiaPaCa-2 (CRL-1420) to 34 g/mL of LE for 24, 48, and 72 hours. Gene expression analyses were performed using whole human genome microarrays (Agilent Technologies, USA). In our analyses, 82 (54/28) genes passed ...
Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Due to the rapid increase in throughputs and decrease in costs of next generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Here, researchers from BGI Shenzhen, present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. They evaluated its performance on transcriptome datasets from rice and mouse. Using as their benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), they assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. AVAILABILITY
TY - JOUR. T1 - Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). AU - Cushman, John C.. AU - Tillett, Richard L.. AU - Wood, Joshua. AU - Branco, Joshua M.. AU - Schlauch, Karen A.. PY - 2008/5/1. Y1 - 2008/5/1. N2 - The common ice plant (Mesembryanthemum crystallinum L.) has emerged as a useful model for molecular genetic studies of Crassulacean acid metabolism (CAM) because CAM can be induced in this species by water deficit or salinity stress. Non-redundant sequence information from expressed sequence tag data was used to fabricate a custom oligonucleotide microarray to compare large-scale mRNA expression patterns in M. crystallinum plants conducting C3 photosynthesis versus CAM. Samples were collected every 4 h over a 24 h time period at the start of the subjective second day from plants grown under constant light and temperature conditions in order to capture variation in mRNA ...
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published
Objective: Complementary and alternative medicine, such as Traditional Chinese Medicine, represents an efficient therapeutic option for obesity control. It was previously reported that acupuncture catgut embedding therapy (ACET) with moxibustion reduces body weight and reverts insulin resistance in obese women. This study aimed to evidence changes in adipokines and gene expression in adipose tissue that could explain the effects of ACET with moxibustion. Design: Overweight/obese women were treated with ACET with moxibustion or sham acupuncture as control. Peripheral blood samples and fat biopsies were taken before and after intervention. Circulating adipokines (leptin, adiponectin, tumor necrosis factor alpha, and resistin) were quantified by enzyme-linked immunosorbent assay. Gene expression in adipose tissue was determined by cDNA microarray assays and assessed by quantitative reverse transcription real-time polymerase chain reaction. Results: ACET with moxibustion did not modify circulating ...
Plukenetia volubilis is a promising oilseed crop due to its seeds being rich in unsaturated fatty acids, especially alpha-linolenic acid. P. volubilis is monoecious, with separate male and female flowers on the same inflorescence. We previously reported that male flowers were converted to female flowers by exogenous cytokinin (6-benzyladenine, 6-BA) treatment in P. volubilis. To identify candidate genes associated with floral sex differentiation of P. volubilis, we performed de novo transcriptome assembly and comparative analysis on control male inflorescence buds (MIB) and female inflorescence buds (FIB) induced by 6-BA using Illumina sequencing technology. A total of 57,664 unigenes with an average length of 979 bp were assembled from 104.1 million clean reads, and 45,235 (78.45%) unigenes were successfully annotated in the public databases. Notably, Gene Ontology analyses revealed that 4193 and 3880 unigenes were enriched in the categories of reproduction and reproductive processes, ...
Recent genome-wide microarray-based research investigations have revealed a high frequency of submicroscopic copy number alterations (CNAs) in the myelodysplastic syndromes (MDS), suggesting microarray-based comparative genomic hybridization (aCGH) has the potential to detect new clinically relevant genomic markers in a diagnostic laboratory. We performed an exploratory study on 30 cases of MDS, myeloproliferative neoplasia (MPN) or evolving acute myeloid leukemia (AML) (% bone marrow blasts ≤ 30%, range 0-30%, median, 8%) by aCGH, using a genome-wide bacterial artificial chromosome (BAC) microarray. The sample data were compared to corresponding cytogenetics, fluorescence in situ hybridization (FISH), and clinical-pathological findings. Previously unidentified imbalances, in particular those considered submicroscopic aberrations (| 10 Mb), were confirmed by FISH analysis. CNAs identified by aCGH were concordant with the cytogenetic/FISH results in 25/30 (83%) of the samples tested. aCGH revealed new
"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 ...
"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, ...
"Unigene EST profile". Unigene. Retrieved 8 May 2012. "Geo Profiles". NCBI. Retrieved 28 April 2012. "Gene Expression Profiles ... Data from NCBI GEO Profile shows that KIAA1958 expression includes many of the tissue types in the human body. Using EMBL-EBI, ... The highest expression in developmental stage is the blastocyst and for health state, it is most found in uterine tumors. ... The gene has these neighbors on chromosome 9: HSDL2: Hydroxysteroid dehydrogenase-like protein 2 plays a role in nucleotide ...
Raspe, Eric; Decraene, Charles; Berx, Geert (2012). "Gene expression profiling to dissect the complexity of cancer biology: ... "Gene Ontology Consortium". Retrieved 1 July 2018.. *^ Smith, Barry (2005). "Relations in biomedical ontologies". Genome Biology ... Ontologies such as the Gene Ontology[3] are being used to annotate the results of biological experiments in a variety of model ... The Gene Ontology itself is a species-neutral graph-theoretical representation of biological types joined together by formally ...
Carrel L, Willard HF (March 2005). "X-inactivation profile reveals extensive variability in X-linked gene expression in females ... in females that are heterozygous at the involved gene or genes than in females that are homozygous at that gene or those genes. ... meaning that the Tsix gene overlaps the Xist gene and is transcribed on the opposite strand of DNA from the Xist gene.[31] Tsix ... Expressed genes on the inactive X chromosome[edit]. A fraction of the genes along the X chromosome escape inactivation on the ...
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 ...
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 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 ...
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. There is a second, less ...
Dominance and overdominance have different consequences for the gene expression profile of the individuals. If overdominance is ... Over-expression of certain genes in the heterozygous offspring. (The size of the circle depicts the expression level of gene A) ... Fewer genes are under-expressed in the homozygous individual. Gene expression in the offspring is equal to the expression of ... Furthermore, for any given gene, the expression should be comparable to the one observed in the fitter of the two parents. ...
"Gene expression profiling in the human pathogenic dermatophyte Trichophyton rubrum during growth on proteins". Eukaryotic cell ...
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 ...
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 ... 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 ... Multiple transcript variants encoding different isoforms have been found for this gene. GRCh38: Ensembl release 89: ...
"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 ...
2005). "Gene expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer". The Lancet. 365 ( ...
"Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proceedings of the ... Gene[edit]. The NDUFB7 gene is located on the p arm of chromosome 19 in position 13.12 and is 6,000 base pairs long.[9][10] ... "Entrez Gene: NDUFB7 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa".. *^ a b c Voet D, Voet JG, Pratt CW (2013). " ... The protein encoded by this gene is an accessory subunit of the multisubunit NADH:ubiquinone oxidoreductase (complex I) that is ...
"Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma". International Journal of Cancer. 118 (5): 1165-72 ... Possible regulatory role of the fusion gene product in wild type SYT expression". Gene. 268 (1-2): 173-82. doi:10.1016/S0378- ... Protein SSXT is a protein that in humans is encoded by the SS18 gene.[5][6][7] ... Gene ontology. Molecular function. • protein binding. • ligand-dependent nuclear receptor transcription coactivator activity. • ...
biography) 2015, "HHMI". 10 questions from Gene Expression Alumni page at the Howard Hughes Medical Institute. Brain Man Makes ... biography) 2009, "Searle Scholars." UChicago News Profile. (biography) 2015, "UChicago News". HHMI Investigator Alumni Bio. ( ... 2006 Lahn's analysis of genes indicates human brain continues to evolve Scientist's Study Of Brain Genes Sparks a Backlash. ... His research also suggested that newly arisen variants of two brain size genes, ASPM and MCPH1, might have been favored by ...
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 ... A reverse northern blot can be used to profile expression levels of particular sets of RNA sequences in a tissue or to ...
"Analysis of microarray experiments of gene expression profiling". American Journal of Obstetrics and Gynecology. 195 (2): 373- ... The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is ... Also, one can measure what genes are expressed and how that expression changes with time or with other factors. There are many ... A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified ( ...
Gene Expression Omnibus (GEO) Profiles. "Large-scale analysis of the human transcriptome (HG-U133A)". https://www.ncbi.nlm.nih. ... Only one other gene in the study had the same trend of increased expression in lower protein diets in both groups: THOC4. THOC4 ... In a study that looked at differences in expression levels of certain genes (including FAM98A) in both young and old men with ... According to Aceview, FAM98A is expressed at 3.9 times the expression of the average gene. Eleven transcripts have been ...
"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. ...
Gene expression Hsromega India portal Biology portal "Faculty of Science". Banaras Hindu University. 2016. Retrieved 4 October ... "Brief Profile of the Awardee". Shanti Swarup Bhatnagar Prize. 2016. Retrieved 28 September 2016. "Indian Fellow - Lakhotia". ... "Fellow profile - Indian Academy of Sciences". Indian Academy of Sciences. 2016. Retrieved 30 September 2016. "NASI fellows". ... His studies also attempted to identify how these genes impact the modulation of apoptosis and neurodegeneration in Drosophila ...
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. ...
2005). "A novel function of differentiation revealed by cDNA microarray profiling of p75NTR-regulated gene expression". ... This article on a gene on human chromosome 19 is a stub. You can help Wikipedia by expanding it. *v ... Neurotrophin-4 (NT-4), also known as neurotrophin-5 (NT-5), is a protein that in humans is encoded by the NTF4 gene.[5] It is a ... Gene ontology. Molecular function. • neurotrophin p75 receptor binding. • receptor binding. • protein binding. • growth factor ...
... 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 ...
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 ...
... Lars Seemann,1 Jason Shulman,2 and Gemunu H. Gunaratne1 ...
... 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. ...
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 ... You dont need that many genes to fix in on someones likely racial identity. Take two genes, SLC24A5 and DARC. There are ... Racial DNA Profiling? posted by Razib @ 10/05/2007 01:13:00 PM Racial DNA Profiling? ...
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, ...
... Wan-dong Liang,1 Yun-tian Bi,2 Hao-yan Wang,3 Sheng ... Genes induced two folds or more different in response to heat shock stress in Clostridium botulinum ATCC 3502 ...
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 ...
Successful Gene Expression Profiling Performed on Embryos. May 14th, 2008 Editors News ... Article abstract in Human Reproduction: Gene expression profiling of human oocytes following in vivo or in vitro maturation. ... Through this, the abstracts and research profiles of our speakers and organizing committee members are getting global ...
... 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 ...
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 ...
For a detailed description of these genes and ESTs, we have created the gene expression profile database that can be accessed ... This cluster analysis allows us to identify genes according to similar expression dynamics. The coordinated expression of genes ... Genome-wide gene expression profiles of the developing mouse hippocampus. Monica Mody, Yanxiang Cao, Zhenzhong Cui, Khoon-Yen ... Genome-wide gene expression profiles of the developing mouse hippocampus. Monica Mody, Yanxiang Cao, Zhenzhong Cui, Khoon-Yen ...
Total RNA was isolated from DCs and gene expression profiling was performed with oligonucleotide microarrays. Using a ... We studied the gene expression patterns of DCs incubated with reagents inducing their activation or inhibition. ... Our findings suggest that the gene expression signature of DCs can provide a molecular classification for use in the selection ... The diagnostic performance of the signature genes was assessed against an independent set of samples, by qRT-PCR. ...
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 ...
MN cells from five healthy donors were pulsed with SC and gene expression profiles of 18,861 genes were assessed in a micro- ... Gene expression profiling of suppressor mechanisms in tuberculosis. Journal. Molecular Immunology. Volume , Issue number. 45 , ... Twenty-eight genes were found to be increased and 60 genes were decreased (FDR = 1%, fold change , 1.4) in response to SC. ... This study (1) identifies the genes that modulate the T helper response, (2) describes their function, and (3) postulates a ...
Home -, Genomics -, Gene Expression Profiling Gene Expression Profiling. * Human Genome-wide Expression Profiling by Multiplex- ... Mouse Targeted Expression Profiling by Multiplex-RT PCR and subsequent NGS * Plate Based Gene Expression Profiling ( ... Human Targeted Expression Profiling by Multiplex-RT PCR and subsequent NGS * ... Next Generation Sequencing Protein Expression Transcription Factors Cell Signaling & Tracking Multiplex Cytokine Assays Gene ...
  • In one FY 2015 study, NTP initiated microRNA profiling of lung tissue after chemical inhalation to understand the mechanisms of pulmonary fibrosis that may lead to better biomarkers in lung tissue or blood. (nih.gov)
  • NTP is evaluating study conditions that may contribute to differential gene expression, such as animal and tissue variability, methods for tissue sampling, and standards for conducting toxicogenomic studies under laboratory conditions. (nih.gov)
  • While micorarrays are a stable and well understood technology for assaying gene expression, NextGen sequencing methods like RNA-Seq should become more common as sequencing costs drop, and bioinformatic pipelines become standardized and integrated with genomic sequencing. (nih.gov)
  • NTP is researching if gene expression pattern analysis can provide indicators of toxicity (1) at earlier time points and (2) at lower doses than is possible for traditional toxicology parameters. (nih.gov)
  • Several FY 2015 toxicogenomic studies used NextGen sequencing technologies, which provided improvements to gene expression analysis, including base-pair level resolution of accuracy and increased sensitivity compared to microarray platforms. (nih.gov)
  • In addition, metabolomics represents a promising area of study, as it can elucidate how chemicals affect metabolism within cells, relative to changes in gene expression. (nih.gov)
  • 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. (wikipedia.org)
  • 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. (genomeweb.com)
  • 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). (unicare.com)
  • A complete list of the transcriptional changes has been compiled into a comprehensive gene profile database ( http://BrainGenomics.Princeton.edu ), which should prove valuable in advancing our understanding of the molecular and genetic programs underlying both the development and the functions of the mammalian brain. (pnas.org)
  • 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. (jneurosci.org)
  • 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. (businesswire.com)
  • 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. (businesswire.com)
  • Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. (wikipedia.org)
  • The unique pattern of gene expression for a given cell or tissue is referred to as its molecular signature. (wikipedia.org)
  • Different molecular subgroups within PTCL unspecified have been identified associated to different expression profiles. (wiley.com)
  • 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. (nih.gov)
  • Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. (diva-portal.org)
  • 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. (aacrjournals.org)
  • Molecular classification of human carcinomas by use of gene expression signatures. (springer.com)
  • 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. (ourglocal.com)
  • 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. (epfl.ch)
  • 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. (epfl.ch)
  • 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. (businesswire.com)
  • 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. (dovepress.com)
  • 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. (epa.gov)
  • 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. (epa.gov)
  • To examine molecular network changes in skeletal muscle after MOV, we conducted a comparative gene expression analysis in wild-type and Vgll2 KO mice under both sedentary and MOV conditions. (frontiersin.org)
  • In this study, we report for the first time a whole genome transcriptional profile analysis of the human monocyte-to-macrophage differentiation and polarized activation processes, describing distinct molecular signatures which shed new light on these processes and reveal new candidate markers. (jimmunol.org)
  • 1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes. (nih.gov)
  • Gene expression analysis studies can provide a snapshot of actively expressed genes and transcripts under various conditions. (illumina.com)
  • NGS-based RNA sequencing (RNA-Seq) methods can quantify and profile any active gene or transcript, including novel transcripts. (illumina.com)
  • Illumina RNA-Seq solutions provide precise measurement of strand orientation, uniform coverage, and high confidence mapping of alternate transcripts and gene fusions. (illumina.com)
  • However, the GLOBINclear process was able to rescue the decreased gene detection observed with RNA samples containing high levels of exogenous globin transcripts. (bio-medicine.org)
  • In contrast, the GLOBINclear Kit rescued the decreased gene detection observed when exogenous globin transcripts were spiked into the HeLa RNA samples. (bio-medicine.org)
  • When a gene is active in a cell, it produces RNA copies known as transcripts. (innovations-report.com)
  • To measure the activity of genes, researchers use the RNA transcripts to make a fluorescent gene probe. (innovations-report.com)
  • 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. (thermofisher.com)
  • 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. (thermofisher.com)
  • Resulting sequences resolve gene-specific transcripts independent of a sequenced genome. (plantphysiol.org)
  • 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. (plantphysiol.org)
  • Our results demonstrate the potential of 3′-UTR profiling for resolving gene- and allele-specific transcripts. (plantphysiol.org)
  • Despite rapid advances in expression profiling techniques, the capacity to distinguish among closely related transcripts on a genome-wide scale remains a challenge. (plantphysiol.org)
  • In microarray analyses, cross hybridization of similar transcripts to a given oligonucleotide probe may confound expression of individual genes. (plantphysiol.org)
  • Sense and antisense transcripts of the genes, Apoa4, Hp, Fgb and Fgg, exhibited concordant upregulation during the course of liver regeneration. (spandidos-publications.com)
  • 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 ). (spandidos-publications.com)
  • By using the Affymetrix GeneChipxa0Rice Genome Arrayxa0to assessxa051xa0279 transcripts, we established a dynamic gene expression profile (GEP) of the early developmental process of rice (Oryza sativa) stamen. (sigmaaldrich.com)
  • Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. (wikipedia.org)
  • Microarray analysis is a highly efficient tool for assessing the expression of a large number of genes simultaneously, and offers a new means to classify cancer and other diseases. (boomerangbooks.com.au)
  • This technology promises to allow investigation of the entire genome on a single chip so that researchers can obtain a global picture of the interactions among thousands of genes simultaneously. (omicsonline.org)
  • Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. (nih.gov)
  • 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. (jcvi.org)
  • 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. (clinicaltrials.gov)
  • Adjuvant chemotherapy guided by a 21-gene expression assay in breast cancer. (mayoclinic.org)
  • 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. (unicare.com)
  • This unit describes methods that allow these clones to be used as hybridization detectors in a highly parallel assay of gene expression. (currentprotocols.com)
  • 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. (epa.gov)
  • This kit was developed to reduce or eliminate the negative effects of globin mRNA on high density oligonucleotide expression profiling, and the resulting enriched RNA is compatible with the RiboPure-Blood Kit and the MessageAmp II aRNA Amplification System . (bio-medicine.org)
  • In this study, the effect of Codonopsis lanceolata fermented by lactic acid on controlling gene expression levels related to obesity was observed in an oligonucleotide chip microarray. (mdpi.com)
  • The first studies on expression profiling of PTCL have also revealed heterogeneity at this level, mainly regarding the PTCL NOS subgroup. (wiley.com)
  • Gene expression profiling revealed that in DLBCL patients who do not respond well to standard chemotherapy, lymphoma cells have activated this pathway, known as NF-kB. (innovations-report.com)
  • In addition, the expression level of NF-kB pathway genes allowed to differentiate two PTCL subgroups, and this difference could have clinical interest. (wiley.com)
  • There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. (mdpi.com)
  • This study profiled the gene expression for the entire irinotecan pathway to provide insights into individualized cancer therapy. (aacrjournals.org)
  • The four colors of the pathway genes are matched to each quartile. (aacrjournals.org)
  • We revealed both genes and pathway potentially involved in the pathophysiology of migraine. (biorxiv.org)
  • Functional pathway analysis revealed proteasome machinery, MYC , and ribosomal components as the top gene sets associated with oral cancer risk. (aacrjournals.org)
  • 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 and clust methods. (wikipedia.org)
  • The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. (springer.com)
  • The level of fluorescence at a particular spot provides quantitative information about the expression of the particular gene corresponding to the spotted cDNA sequence. (wikipedia.org)
  • Differences in gene expression underlie central questions in plant biology extending from gene function to evolutionary mechanisms and quantitative traits. (plantphysiol.org)
  • 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. (plantphysiol.org)
  • 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. (pubmedcentralcanada.ca)
  • Sequence based techniques, like RNA-Seq , provide information on the sequences of genes in addition to their expression level. (wikipedia.org)
  • 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. (wikipedia.org)
  • 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. (google.ca)
  • Supplementary Table 1-Primer sequence of selected genes designed for qRT-PCR. (springer.com)
  • Of 11,000 genes and expressed sequence tags examined, 1,926 showed dynamic changes during hippocampal development from embryonic day 16 to postnatal day 30. (pnas.org)
  • Sequence based techniques, like serial analysis of gene expression (SAGE, SuperSAGE) are also used for gene expression profiling . (primidi.com)
  • 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. (doe.gov)
  • 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. (mit.edu)
  • 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. (mit.edu)
  • 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. (diabetesjournals.org)
  • 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. (plantphysiol.org)
  • Genes with extensive sequence similarity may comprise a significant portion of a given transcriptome. (plantphysiol.org)
  • The extent of these sequence similarities in maize and other complex genomes poses a clear challenge to delineation of gene-specific function. (plantphysiol.org)
  • However, our ability to predict gene function from DNA sequence is poor. (biologists.org)
  • 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. (google.ca)
  • The genetic basis for disease is determined by the inheritance of genes containing specific sequences of deoxyribonucleic acid (DNA). (uptodate.com)
  • The information derived from gene expression profiling often helps in predicting the patient's clinical outcome. (wikipedia.org)
  • 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. (springer.com)
  • One recent study found that chemotherapy might not be helpful for women with gene expression profiling test results that indicate an intermediate risk of recurrence. (mayoclinic.org)
  • Additional study is need in a randomized sample of individuals to determine how gene expression profiling combined with SLNB would contribute to the accurate staging and treatment planning of individuals with cutaneous melanoma. (unicare.com)
  • This is the first study to define Candida global gene expression during deep-seated human infection. (jcvi.org)
  • 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. (innovations-report.com)
  • For this study, researchers used the Lymphochip, a specialized microarray containing 12,000 DNA spots representing genes expressed in normal and malignant lymphoid cells. (innovations-report.com)
  • The purpose of this study was to use microarray analysis to identify specific gene expression changes in mesothelioma compared with normal mesothelium. (aacrjournals.org)
  • In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. (diva-portal.org)
  • Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. (diva-portal.org)
  • 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. (aacrjournals.org)
  • Fifty-three H-MM and 37 NH-MM with adequately good quality RNA for gene expression study were included. (aacrjournals.org)
  • Using this and other modifications, they completed a study of gene expression in ovarian cancer in a single experiment. (genomenewsnetwork.org)
  • The presented transcriptomic data may further be used as resource to study genes acting at different memory phases. (genetics.org)
  • The objectives of this study are to compare the gene expression profiles of retinoblastoma, retinocytoma, and normal retina using microarray data and to determine the expression profiles that correlate with clinical and histologic features. (arvojournals.org)
  • The present study also outlines the high instability of informative gene selection and suggests the usefulness of resampling techniques to obtain an honest assessment of prognosis prediction accuracy. (aacrjournals.org)
  • 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. (cdc.gov)
  • 6 This profile required validation in a second cohort, which has been done in the current study. (ahajournals.org)
  • 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. (doe.gov)
  • Nevertheless, some of the genes identified as SREBP targets in the liver study, including fatty acid synthase and acetyl-CoA carboxylase, were also upregulated by SREBP1c in β-cells ( 3 , 4 ) and in islets ( 6 ), suggesting that this may represent a useful approach to understanding the mechanisms by which SREBP1c overexpression inhibits insulin secretion from islets. (diabetesjournals.org)
  • 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. (businesswire.com)
  • Our study identified differences in gene expression in subjects with COPD according to emphysema status using RNA-Seq transcriptome analysis. (dovepress.com)
  • The study objective was to determine the value of gene expression profiling in predicting oral cancer development. (aacrjournals.org)
  • To systematically study the genes associated with risk of OSCC, we used gene expression profiling on a large cohort of samples of OPL patients. (aacrjournals.org)
  • The long-term objective of this study is to elucidate how developmental exposure to estrogenic substances modulate gene expression profiles, leading to compromised male reproductive fitness at later stages of life. (epa.gov)
  • In this study, it was investigated that the time course of changes in the gene expression of cerebral artery using rabbit SAH model and performed bioinformatic analysis of differentially expressed genes. (omicsonline.org)
  • Results: In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. (sciweavers.org)
  • This study aimed to validate by qPCR the expression of 26 genes, revealed as differentially expressed by other studies, using peripheral blood cells (PBC) of 11 FRDA patients compared to 11 healthy controls. (curefa.org)
  • With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. (wikipedia.org)
  • Together, our results highlight the usefulness of this discovery-driven experimental strategy to identify genes relevant to oligodendrocyte differentiation and myelination. (jneurosci.org)
  • One potentially useful approach to solve these issues would be to identify specific gene expression changes in cancerous mesothelial cells. (aacrjournals.org)
  • 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. (ahajournals.org)
  • 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. (mit.edu)
  • 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. (epa.gov)
  • Here, we analyzed genes differentially expressed in each of the three LMS subtypes as compared to benign leiomyomas and then used the Connectivity Map (cmap) to calculate enrichment scores for the 1309 cmap drugs in order to identify candidate molecules with the potential to induce a benign, leiomyoma-like phenotype in LMS cells. (harvard.edu)
  • Through gene expression profiling, researchers are working to find ways to monitor brain health and predict future strokes, aneurysms, and hemorrhages. (ucdavis.edu)
  • 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. (mayoclinic.org)
  • 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. (innovations-report.com)
  • From these genes, the investigators created a formula that could be used to predict survival following chemotherapy. (innovations-report.com)
  • Microarray gene expression profiling represents a promising technique to predict the prognosis of stage II colon cancer patients. (aacrjournals.org)
  • 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 ). (sciencemag.org)
  • Gene expression profiling can also be used to predict clinical outcome and response to specific therapeutic agents. (boomerangbooks.com.au)
  • Several forms of animal behavior are known to be influenced by the activity of specific genes ( 1 , 2 ). (sciencemag.org)
  • However, some metabolic products may serve as a signaling molecule, which can be perceived by the cells to control the expression of specific genes as the population increases. (asm.org)
  • 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. (biorxiv.org)
  • Two novel genes have also been mapped onto our target chromosome 2 within the congenic interval by radiation hybrid (RH) mapping. (bl.uk)
  • 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 ). (asm.org)
  • 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. (aacrjournals.org)
  • An average of 4753 and 5965 additional genes was called Present after globin depletion for Donor 37 and Donor 45, respectively. (thermofisher.com)
  • Single-cell global gene expression profiling showed that undifferentiated cells fell into two clusters delineated by expression of DLL1 and its binding partner syntenin. (biologists.org)
  • 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. (genetics.org)
  • The tests are based on distinct gene lists, using 2 different technologies. (annals.org)
  • These include genes involved in neuronal proliferation, differentiation, and synapse formation. (pnas.org)
  • 3) Modulation of genes involved in metabolic activities is a prominent feature of macrophage differentiation and polarization. (jimmunol.org)
  • Thus, transcriptome profiling reveals novel molecules and signatures associated with human monocyte-to-macrophage differentiation and polarized activation which may represent candidate targets in pathophysiology. (jimmunol.org)
  • 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. (nih.gov)
  • with LS of size 40, 7 genes were part of all the 100 signatures. (aacrjournals.org)
  • Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. (springer.com)
  • A Gene Expression Profiling of Early Rice Stamen Development that Reveals Inhibition of Photosynthetic Genes by OsMADS58. (sigmaaldrich.com)
  • Several gene expression profiles (GEPs) are clinically available that provide variations on "recurrence risk scores" intended to help doctors and their patients in treatment decision making. (cdc.gov)
  • Focusing on genes where the difference in expression was most dramatic between the two groups of patients, researchers narrowed the key genes down to 17. (innovations-report.com)
  • Compare the gene expression profiles of pancreatic cancer cells from the primary and metastatic sites in patients with metastatic pancreatic cancer. (clinicaltrials.gov)
  • We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 21 patients taking advantage of `second-generation sequencing technology. (diva-portal.org)
  • Using the same random splits, the accuracy of the 23-gene PS was assessed with a DLDA that used learning set patients as reference samples. (aacrjournals.org)
  • Conclusion: This is the first characterization of gene expression profiles in early-onset CRC patients included in the TCGA database. (aacrjournals.org)
  • 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. (businesswire.com)
  • 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. (aacrjournals.org)
  • 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. (pubmedcentralcanada.ca)
  • Our results indicate that surviving 3-day ADX granule cells display lower membrane capacitance, lower relative N-methyl-d-aspartate (NMDA) R1 mRNA expression and higher relative mineralocorticoid receptor (MR), alpha1A voltage-gated Ca-channel, Bcl-2 and NMDA R2C mRNA expression. (uva.nl)
  • These include the cytochrome P450 4A3 gene, which has been well documented as differentially expressed between SHR and WKY kidneys, and the low affinity Na-dependent glucose transporter (SGLT2). (bl.uk)
  • 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. (thermofisher.com)