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.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.Microdissection: The performance of dissections with the aid of a microscope.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.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)Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.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.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.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.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.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.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Mice, Inbred C57BLMutation: 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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.RNA, Neoplasm: RNA present in neoplastic tissue.Validation Studies as Topic: Research using processes by which the reliability and relevance of a procedure for a specific purpose are established.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.Breast Neoplasms: Tumors or cancer of the human BREAST.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.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.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.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.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.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.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.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.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.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.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.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.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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.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.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.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.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.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.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.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)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.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.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, 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.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.Genes, Plant: The functional hereditary units of PLANTS.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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.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.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).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.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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.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.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.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.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.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.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.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.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.Proteome: The protein complement of an organism coded for by its genome.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.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.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.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.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)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.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.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).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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.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.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.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.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.Biopsy: Removal and pathologic examination of specimens in the form of small pieces of tissue from the living body.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)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.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.Antineoplastic Agents: Substances that inhibit or prevent the proliferation of NEOPLASMS.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.Bacterial Proteins: Proteins found in any species of bacterium.Prostatic Neoplasms: Tumors or cancer of the PROSTATE.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Neoplasms, Plasma Cell: Neoplasms associated with a proliferation of a single clone of PLASMA CELLS and characterized by the secretion of PARAPROTEINS.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.Adenocarcinoma: A malignant epithelial tumor with a glandular organization.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.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.Genes, Developmental: Genes that determine the fate of a cell or CELLS in a region of the embryo during EMBRYONIC DEVELOPMENT.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.Biomarkers, Pharmacological: Measurable biological parameters that serve for drug development, safety and dosing (DRUG MONITORING).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.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.Lung: Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.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.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.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.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.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.Neoplasm Invasiveness: Ability of neoplasms to infiltrate and actively destroy surrounding tissue.Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.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.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.Lung Neoplasms: Tumors or cancer of the LUNG.Mice, Inbred BALB CArabidopsis 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.Drug Resistance, Neoplasm: Resistance or diminished response of a neoplasm to an antineoplastic agent in humans, animals, or cell or tissue cultures.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.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).
... for Flammer syndrome have shown a unique gene expression when their lymphozytes underwent gene expression profiling. To have ... Flammer's syndrome is primarily based on the patient's history with its typical features as well as the findings of nail fold ... Vasospastic individuals demonstrate significant similarity to glaucoma patients as revealed by gene expression profiling in ...
It is a simple non-parametric statistical method based on ranks of fold changes. In addition to its use in expression profiling ... Given n genes and k replicates, let e g , i {\displaystyle e_{g,i}} be the fold change and r g , i {\displaystyle r_{g,i}} the ... is the rank of gene g in a list of all n genes sorted by increasing R P {\displaystyle \mathrm {RP} } . Permutation re-sampling ... generate p permutations of k rank lists of length n. calculate the rank products of the n genes in the p permutations. count ...
Rather than identify differentially expressed genes using a fold change cutoff, one can use a variety of statistical tests or ... 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 ...
CCDS34974.1 This gene is a member of the Human CCDS set: CCDS34974. C8orf33 expression profile revealed that this gene was over ... The mRNA secondary structure of 3' and 5' UTR's indicate different fold energies. The 5' UTR region contains a fold energy of - ... According to microarray-assessed tissue expression analysis by NCBI GEO, the gene C8orf33 has average expression levels in most ... The expression of this gene is up-regulated after lithium exposure. C8orf33 is significantly up regulated in breast cancer drug ...
Alekseev OM, Richardson RT, Alekseev O, O'Rand MG (2009). "Analysis of gene expression profiles in HeLa cells in response to ... The crowded environment of the cytosol can accelerate the folding process, since a compact folded protein will occupy less ... which cannot be folded spontaneously. Such proteins violate Anfinsen's dogma, requiring protein dynamics to fold correctly. ... GroEL is a double-ring 14mer with a hydrophobic patch at its opening; it is so large it can accommodate native folding of 54- ...
... is a highly ubiquitously expressed gene that has shown expression in many tissues. "BLAT". UCSC Genome Bioinformatics. " ... "ARMCX5". Gene cards. "NCBI- nucleotide". "NCBI BLAST". "NCBI-protein". "NCBI-EST profiles". ... ARMCX5 contains 3 ARM-like repeats, DUF364, and ARM-type fold. ARMCX5 has 6 splice variants. ARMCX5 has ten orthologs. ARMCX5 ... ARMCX5 is an armadillo repeat-containing protein that is encoded by the X-linked ARMCX5 gene. It is conserved only in Eutheria ...
The expressed sequence tag (or EST) abundance profile also shows ubiquitous/near ubiquitous, expression throughout human ... ACOT9 gene is known primarily for encoding the Acyl-CoA thioesterase 9 protein. Other, less commonly used names for the gene ... These regions are part of a hotdog fold superfamily, which has been found to be used in a variety of cell roles. Predictions ... "ACOT9 gene detail". Mouse Genome Database. Retrieved 2014-06-19. "Gene: Acot9". Ensembl release 75. "Large-scale analysis of ...
They can be used for detection of mutations and expression monitoring, and gene discovery and mapping. The main methods for ... Analytical or capture protein arrays display antigens and antibodies to profile protein or antibody expression in serum. These ... Functional protein arrays display folded and active proteins and are used for screening molecular interactions, studying ... "Multichannel Reverse Transcription-Polymerase Chain Reaction Microdevice for Rapid Gene Expression and Biomarker Analysis". ...
All the major regulatory elements are located within 100 bp upstream of the gene. The profile of EPX expression has been ... The fold of the enzyme is known as the heme peroxidase fold, conserved among all members of this gene family. However, not all ... The fold is highly conserved and seems to be optimized for catalytic function. However, differences exist which unsurprisingly ... At this level, it is more than 30 times the average level of expression over all tissues in the body. Molecular weight: 57 kDa ...
Miao, Y.; Cui, L.; Chen, Z.; Zhang, L (2016). "Gene expression profiling of DMU-212-induced apoptosis and anti-angiogenesis in ... The 5' un-translated region of isoform 1 is relatively short and is predicted to fold into several stem loop domains within ... Expression profiles have also linked elevated TMEM217 expression to bladder cancer and lymphoma. TMEM217 was found to have ... The gene tends to have expression correlated to lymphatic system, vascular/arterial endothelial tissue, and notable expression ...
MicroRNAs function to regulate the expression levels of other genes by several mechanisms. Significantly altered expression of ... Expression levels are lower in the proficient form compared to the deficient, with a more than two-fold change. This altered ... 2009). "Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are ... miR-592 expression is also altered in hepatocellular carcinoma; it has been shown to be downregulated along with nine other ...
"Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer". ... Obiero J, Walker JR, Dhe-Paganon S (2012). "Fold of the conserved DTC domain in Deltex proteins". Proteins. 80 (5): 1495-9. doi ... Deltex E3 ubiquitin ligase 3L is a protein that in humans is encoded by the DTX3L gene. DTX3L functions as an E3 ubiquitin ... "Entrez Gene: Deltex E3 ubiquitin ligase 3L". Retrieved 2017-03-26. Takeyama K, Aguiar RC, Gu L, He C, Freeman GJ, Kutok JL, ...
... as well as the levels of translation of each region to provide insight into global gene expression. Prior to its development, ... Coupling ribosome profiling with ChIP can elucidate how and when newly synthesized proteins are folded. Using the footprints ... There are three main uses of ribosome profiling: identifying translated mRNA regions, observing how nascent peptides are folded ... This technique is different from Polysome Profiling. Ribosome profiling is based on the discovery that the mRNA within a ...
2000). "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proc. Natl. ... Hansen WJ, Cowan NJ, Welch WJ (1999). "Prefoldin-Nascent Chain Complexes in the Folding of Cytoskeletal Proteins". J. Cell Biol ... Prefoldin subunit 2 is a protein that in humans is encoded by the PFDN2 gene. This gene encodes a member of the prefoldin beta ... "Entrez Gene: PFDN2 prefoldin subunit 2". Vainberg IE, Lewis SA, Rommelaere H, et al. (1998). "Prefoldin, a chaperone that ...
"PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2017-05-07. Database, GeneCards Human Gene. "C12orf66 ... In this study, the amount of C12orf66 down-regulation along with the expression of a number of other genes were used as an ... "EST Profile - Hs.505871". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07. Abdul Aziz, Nurul Ainin; Mokhtar, Norfilza M.; Harun, ... Thus, the level of C12orf66 gene expression reflected the survivability of these patients. C12orf66 interacts with the three ...
A 2007 gene expression study found c10orf76 expression to vary inversely with the expression of several other genes, including ... The NCBI (GenBank) gene profile for c10orf76 labels the start of the first transcribed exon as the beginning of the gene. The ... "PHYRE2 Protein Fold Recognition Server". Retrieved 18 April 2013. "IntAct Interaction Database". Retrieved 3 May 2013. Chatr- ... "Geo Profile: Differential Expression of c10orf76 in B-cell leukemia". Retrieved 13 May 2013. "Geo Profile: Differential ...
"Home - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07. Database, GeneCards Human Gene. "C21orf62 Gene - ... "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2017-05-07. "Home - Gene - NCBI". www.ncbi.nlm.nih.gov ... C21orf62 over or under expression is linked to some types of cancerous cells and tumors. There are no known paralogs of ... The C21orf62 gene is 4132 base pairs in length and contains five exons. The mRNA sequence of C21orf62 in humans has one known ...
A more recent profile of the Ly6/uPAR gene family identified 35 human and at least 61 mouse family members in the organisms' ... "Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom". Molecular ... "Three-finger toxin fold for the extracellular ligand-binding domain of the type II activin receptor serine kinase". Nature ... Traditionally, 3FTx genes have been thought to have evolved by repeated events of duplication followed by neofunctionalization ...
... gene expression profiling, epigenetic modifications, CO2 retaining variants, single nucleotide polymorphisms and copy number ... 0.50 diopter cycloplegic refractive change No evidence of optic-disc edema, nerve sheath distention, choroidal folds, globe ... October 2011). "Optic disc edema, globe flattening, choroidal folds, and hyperopic shifts observed in astronauts after long- ... Optic disc edema, globe flattening, choroidal folds, hyperopic shifts and an increased intracranial pressure have been ...
... is correlated with the expression of genes such that the genetic information being utilized in a cell is ... "replication timing profile". Figure 4 shows an example of such a profile across 70,000,000 base pairs of human Chromosome 2. At ... However, it is an intriguing cellular mechanism with links to many poorly understood features of the folding of chromosomes ... We also know that the replication-timing program changes during development, along with changes in the expression of genes. For ...
Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila. Proceeding of ... Enhancing HMM-Based Protein Profile-Profile Alignment with Structural Features and Evolutionary Coupling Information. BMC ... Improving Protein Fold Recognition by Random Forest. BMC Bioinformatics. 15(S11):S14, 2014. paper 3. R. Cao, Z. Wang, Y. Wang, ... Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. BMC Bioinformatics. 14:278, 2013. ...
pH riboregulators regulate gene expression in response to pH changes. The only known pH riboregulator upregulates the alx gene ... RNA polymerase controls the folding of this ncRNA to its 'H' active form. The ribosome binding site of the alx gene is now ... Using Gene Profiles to Design Drugs". Pharmagenomics (2): 48-53 2003. http://pharmtech.findpharma.com/pharmtech/data/ ... The presence or absence of a target molecule determines whether the siRNA downregulates gene expression. In 2007, Rinaudo et al ...
"GDS424 / 59465_r_at / NBPF1, Normal human tissue expression profiling". NCBI Geo Profiles. Retrieved 4 May 2015. "Allen Brain ... In non-primate mammals, the gene sequences of NBPF-like genes have little similarity to the primate NBPF genes. These genes ... Burkhard P, Stetefeld J, Strelkov SV (February 2001). "Coiled coils: a highly versatile protein folding motif". Trends in Cell ... The large amount of NBPF genes in the human genome is most likely due to recent duplications because all of the NBPF genes are ...
Gene expression profiling in ethnic Malays with type 2 diabetes mellitus, with and without diabetic nephropathy. Journal of ... Also, TEX36 has shown to have a two-fold increase in expression levels after exercise, compared to before in endothelial ... GeneCards, Human Gene Database, entry on TEX36, [http://www.genecards.org/cgi-bin/carddisp.pl?gene=TEX36] Ensembl entry on Gene ... The verified gene sequence was confirmed in NCBI on November 26, 2016. The coding region spans 106,622 bases, and within that ...
As expression of immediate-early gene (IEG) in certain brain regions may represent markers of anti-psychotic activity, ... Plasma levels of F-15,063 decreased seven-fold 4 hours after oral administration, and 25-fold after 8 hours. Despite this, ... F-15,063 was tested in several animal models that predict antipsychotic activity to help determine the behavioral profile. ... expression of immediate-early gene mRNA in the prefrontal cortex and striatum was measured. Treatment with F-15,063 resulted in ...
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 patient's clinical outcome. Oncogenesis is the process by which normal cells acquire the properties of cancer cells leading to the ...
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 ...
... , Inc. (NASDAQ: NSTG) is a publicly held biotech company that specializes in development of cancer diagnostics tools. The company's technology enables a wide variety of basic research, translational medicine and in vitro diagnostics applications. The company was founded by Krassen Dimitrov, Amber Ratcliffe, and Dwayne Dunaway in 2003, and is based in Seattle, Washington. NanoString's "nCounter Analysis System" is based on a digital molecular barcoding technology invented by Dimitrov and Dunaway in Leroy Hood's lab at the Institute for Systems Biology (ISB), and became commercially available in 2008. NanoString received a CE-mark designation for selling the Prosigna™ Breast Cancer Prognostic Gene Signature Assay (PAM50-based breast cancer test) in Israel and EU in September 2012, and in September 2013, NanoString received FDA 510(k) clearance for Prosigna. NanoString's nCounter technology is a variation on the DNA microarray and was invented and patented by Krassen ...
... es are the processes vital for a living organism to live, and that shape its capacities for interacting with its environment. Biological processes are made up of many chemical reactions or other events that are involved in the persistence and transformation of life forms.[1] Metabolism and homeostasis are examples. Regulation of biological processes occurs when any process is modulated in its frequency, rate or extent. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. ...
Microarray technology is a powerful tool for genomic analysis. It gives a global view of the genome in a single experiment. Data analysis of the microarray is a vital part of the experiment. Each microarray study comprises multiple microarrays, each giving tens of thousands of data points. Since the volume of data is growing exponentially as microarrays grow larger, the analysis becomes more challenging. In general the greater the volume of data, the more chances arise for erroneous results. Handling such large volumes of data requires high-end computational infrastructures and programs that can handle multiple data formats. There are already programs available for microarray data analysis on various platforms. However, due to rapid development, diversity in microarray technology, and different data formats, there is always the need for more comprehensive and complete microarray data analysis. Proper data processing and quality control are critical to the validity and interpretability of ...
An MA plot is an application of a Bland-Altman plot for visual representation of genomic data. The plot visualises the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values. Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis. Microarray data is often normalized within arrays to control for systematic biases in dye coupling and hybridization efficiencies, as well as other technical biases in the DNA probes and the print tip used to spot the array. By minimizing these systematic variations, true biological differences can be found. To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree ...
In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same mRNA. This phenomenon is then called alternative splicing. Alternative splicing can occur in many ways. Exons can be extended or skipped, or introns can be retained. It is estimated that 95% of transcripts from multiexon genes undergo alternative splicing, some instances of which occur in a tissue-specific manner and/or under specific cellular conditions.[26] Development of high throughput mRNA sequencing technology can help quantify the expression levels of alternatively spliced isoforms. Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the functions of these isoforms.[27][28] Given this complexity, alternative splicing of pre-mRNA transcripts is regulated by a system of trans-acting proteins (activators and repressors) that bind to ...
In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same mRNA. This phenomenon is then called alternative splicing. Alternative splicing can occur in many ways. Exons can be extended or skipped, or introns can be retained. It is estimated that 95% of transcripts from multiexon genes undergo alternative splicing, some instances of which occur in a tissue-specific manner and/or under specific cellular conditions.[26] Development of high throughput mRNA sequencing technology can help quantify the expression levels of alternatively spliced isoforms. Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the functions of these isoforms.[27][28] Given this complexity, alternative splicing of pre-mRNA transcripts is regulated by a system of trans-acting proteins (activators and repressors) that bind to ...
Calcineurin subunit B type 2 is a protein that in humans is encoded by the PPP3R2 gene. Among its related pathways are MAPK signaling pathway and GPCR pathway. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is CHP1. GRCh38: Ensembl release 89: ENSG00000188386 - Ensembl, May 2017 GRCm38: Ensembl release 89: ENSMUSG00000028310 - Ensembl, May 2017 "Human PubMed Reference:". "Mouse PubMed Reference:". Liu L, Zhang J, Yuan J, Dang Y, Yang C, Chen X, Xu J, Yu L (May 2005). "Characterization of a human regulatory subunit of protein phosphatase 3 gene (PPP3RL) expressed specifically in testis". Mol Biol Rep. 32 (1): 41-5. doi:10.1007/s11033-004-4250-4. PMID 15865209. "Entrez Gene: PPP3R2 protein phosphatase 3 (formerly 2B), regulatory subunit B, beta isoform". "PathCards :: MAPK signaling pathway Pathway and related pathways". pathcards.genecards.org. Retrieved ...
... is the activation of genes within specific tissues of an organism at specific times during development. Gene activation patterns vary widely in complexity. Some are straightforward and static, such as the pattern of tubulin, which is expressed in all cells at all times in life. Some, on the other hand, are extraordinarily intricate and difficult to predict and model, with expression fluctuating wildly from minute to minute or from cell to cell. Spatiotemporal variation plays a key role in generating the diversity of cell types found in developed organisms; since the identity of a cell is specified by the collection of genes actively expressed within that cell, if gene expression was uniform spatially and temporally, there could be at most one kind of cell. Consider the gene wingless, a member of the wnt family of genes. ...
... is a subunit of the interleukin 15 receptor that in humans is encoded by the IL15RA gene. The IL-15 receptor is composed of three subunits: IL-15R alpha, CD122, and CD132. Two of these subunits, CD122 and CD132, are shared with the receptor for IL-2, but IL-2 receptor has an additional subunit (CD25). The shared subunits contain the cytoplasmic motifs required for signal transduction, and this forms the basis of many overlapping biological activities of IL15 and IL2, although in vivo the two cytokines have separate biological effects. This may be due to effects of the respective alpha chains, which are unique to each receptor, the kinetics and affinity of cytokine-cytokine receptor binding, or due to the availability and concentration of each cytokine. IL-15Ralpha specifically binds IL15 with very high affinity, and is capable of binding IL-15 independently of other subunits. It is suggested that this property allows IL-15 to be produced by one cell, ...
... " is a common expression, a proverbial phrase, generally used rhetorically to indicate that a particular situation could be a cause for optimism (half full) or pessimism (half empty), or as a general litmus test to simply determine an individual's worldview. The purpose of the question is to demonstrate that the situation may be seen in different ways depending on one's point of view and that there may be opportunity in the situation as well as trouble. This idiom is used to explain how people perceive events and objects. Perception is unique to every individual and is simply one's interpretation of reality. The phrase "Is the glass half empty or half full" can be understood also as a philosophical question. Another perspective comes from psychology, where research has shown that a speaker's choice of frame can reflect their knowledge of the environment, and that listeners can be sensitive to this information. Cooperative principle ...
மரபணு வெளிப்பாடு (Gene expression) என்பது மரபணுவில் இருக்கும் தகவல்கள், தொழிற்படக்கூடிய மரபணு உற்பத்திப்பொருளாக (gene product) மாற்றப்படும் செயல்முறையாகும். மரபணுவிலிருக்கும் மரபணுக் குறியீட்டுப்பகுதியில் (coding region) இருந்து இவ்வகையான மரபணு உற்பத்திப்பொருட்கள் உருவாகின்றன. மரபணு உற்பத்திப்பொருட்கள் உயிர்வேதியியல் பொருட்களாகும். பொதுவாக இந்த மரபணு உற்பத்திப் பொருட்கள் தொழிற்படும் ...
Spatial Gene Expression Profiling of Neurological Disorders. Cedric Uytingco, PhD. In this interview, Cedric Uytingco discusses ... Since all of these involve protein folding into a certain shape, then what wed like to do is to track the changes in shape of ... Novel motion capture-like technology for tracking how proteins fold into certain shape. *Download PDF Copy ... The information in all of the interactions of the amino acid side chains somehow leads to it folding into a proper shape. ...
... and gene expression profiles in liver were evaluated using Affymetrix Mouse GeneChip 1.0 ST array. We identified 42 genes ... mice on hepatic gene expression profile. Wild type, ,i,Wfs1,/i, heterozygous, and homozygous mice were treated with VPA for ... and 9 genes whose regulation by VPA was dependent on genotype. Among the genes that were regulated differentially by VPA ... Treatment with VPA has been shown to upregulate ,i,Wfs1,/i, expression ,i,in vitro,/i,. Aim of the present study was to compare ...
We attempted to analyze the gene expression profile in PTC primary tumors to seek the genes associated with M1 status and ... The differences in gene expression profile between metastatic and non-metastatic PTC, if they exist, are subtle and potentially ... These genes were validated on microarray dataset B. The differential expression was positively confirmed for only two genes: ... However, when analyzed on an independent dataset by qPCR, the IGFBP3 gene showed no differences in expression. Gene group ...
A second approach is to use machine learning to discriminate cell types based on the whole gene expression profiles (GEPs). The ... Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are ... We selected the genes that were significantly enriched (log2 fold-change ,1 and Benjamini-Hochberg adjusted p-value ≤ 0.05) in ... In all 65 samples, the reproduced gene expression profiles were closer to the original gene expression profiles of each B-cell ...
In conclusion, we show that global preamplification simplifies targeted gene expression profiling of small sample sizes by a ... Global preamplification generated 9.3-fold lower yield and 1.6-fold lower reproducibility than target-specific preamplification ... To demonstrate the potential of global preamplification we analysed the expression of 15 genes in 60 single cells. ... The need to perform gene expression profiling using next generation sequencing and quantitative real-time PCR (qPCR) on small ...
Genes up-regulated by 2-fold or greater after radiation exposure in vitro in the MCF7, SF539, and DU145 cells ... Gene Expression Profiling of Breast, Prostate, and Glioma Cells following Single versus Fractionated Doses of Radiation. Mong- ... Gene Expression Profiling of Breast, Prostate, and Glioma Cells following Single versus Fractionated Doses of Radiation ... Gene Expression Profiling of Breast, Prostate, and Glioma Cells following Single versus Fractionated Doses of Radiation ...
This investigation provides the first systematic determination of the cellular and molecular progression of vocal fold (VF) ... Gene Expression Profiling * Gene Expression Regulation, Developmental / genetics * Gene Expression Regulation, Developmental / ... we characterized the expression pattern of SHH pathway genes, and how loss of Shh affects vocal fold development in the mutant ... the stratification of the vocal folds (E13.5-18.5); and (5) the maturation of vocal fold epithelium (postnatal stages). The ...
Gene expression profile datasets and DEGs identification. The DLBCL and noncancerous tissues gene expression profile datasets ... We integrated three gene expression profiles, and then combined the results of MCODE and PPI to identify hub genes. Furthermore ... Gene expression profiles analysis identifies a novel two-gene signature to predict overall survival in diffuse large B-cell ... Differentially expressed genes (DEGs) were computed based on gene expression profiles from GSE32018, GSE56315, and The Cancer ...
Each point represents a gene. Only genes that passed quality controls were plotted. Vertical dashed lines at −log2 fold changes ... The expression profiles of BAVc and TAVc were highly similar. Additional unique genes were identified in BAVc vs. TAVn compared ... Two genes were upregulated, and none were downregulated in BAVc compared with TAVc, suggesting a similar gene expression ... Heat maps presenting the gene expression of the top 10 annotated up- and downregulated genes for each pairwise comparison. ...
The highest intensity indicates a ≥2-fold difference in gene expression. A bar graph below the cluster diagram depicts the ... and infiltrating immune cells to obtain a gene-expression "profile" from each primary tumor. Two patterns of gene expression ... Evaluating our gene set against gene expression found in other types of late-stage cancer would also be useful. Genes ... Total Gene-Expression Patterns. We initially set out to determine whether global gene-expression patterns in the primary tumors ...
For this, we used microarrays to compare the gene expression profiles of sexually mature to immature males. Using a false ... The set of up-regulated genes includes genes involved in neuroendocrine processes, cell-cell signaling, neurogenesis and ... Some of these genes have previously described functions while many others have roles that have yet to be characterized in a ... Interestingly, while genes involved in immune system function were down-regulated in the brains of mature males, changes in the ...
Decreased genes. No.. Gene symbol. Fold change. No.. Gene symbol. Fold change. No.. Gene symbol. Fold change. No.. Gene symbol ... we analyzed the gene and protein expression profiles of RA using the CIA model. A previous gene expression profiling study ... Gene expression profiling. Gene expression analysis was performed using RNA from blood samples from control and CIA mice. In ... 3-fold higher in CIA than in control mice, with the level of Irf7 showing a , 24-fold difference. The expression of five genes ...
Genes with a significant fold change between paired and unpaired are colored. Red indicates significantly higher expression in ... Assessing gene expression profiles during LTM formation. To study temporal gene expression changes in the mushroom body during ... We describe the gene expression profiles during these phases and tested 33 selected candidate genes for deficits in LTM ... Transcriptomics characterization of gene expression profiles during LTM in the MB. Genetic tools available in Drosophila ...
C) Volcano scatter plot of log10(p-value) vs log2(fold change) of transcript expression in NSM neurons relative to the ... 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 ...
Only 57 genes showed a ≥2-fold change in gene expression; 31 genes were downregulated (Table 2) and an additional 26 genes ... we presumed that this was due to altered gene expression affecting the response to Chk1. Global expression profiles were ... Gene expression profiles controlled by Tra1:. As the resistance to chk1+ overexpression appeared to be dependent on HAT ... Analysis of gene expression profiles:. cDNA was prepared from RNA acid extracted from exponentially growing wild-type and tra1- ...
Differentially expressed genes with at least a 2.0-fold difference in expression that was statistically significant (. ) ... d) Gene profile of human neutrophils as assessed by microarray analysis. Clusters of downregulated genes and upregulated genes ... the gene profile of PMNs phagocytizing iRBCs indicated that the RIT2 gene was the top-regulated gene. RIT2, a member of the Ras ... The fold changes in gene expression determined by these two assays were somehow comparable with some differences in magnitude ( ...
Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential ... The mat− sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 ... and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. Methodology/ ... Principal Findings The transcriptomic profiles of the mat+ and mat− strains revealed 157 differentially transcribed genes, and ...
Our RNA expression profiling data suggest that bone marrow cDCs have a distinct pattern of gene expression. For instance, while ... A total of 635 differentially expressed genes (, 5-fold difference and FDR , 0.02) were identified (Supplemental Table 2). Gene ... Surprisingly, the patterns of gene expression for chemokines, chemokine receptors, and certain DC marker genes were strikingly ... RNA expression of both ligands was induced 3- to 4-fold in the bone marrow following cDC ablation (Figure 5, E and F). To ...
A comprehensive microarray analysis was performed in order to compare gene-expression profiles in juvenile and mature cuttings ... However, clustering the expression profiles revealed that the time after induction contributed more significantly to the ... The expression of 42 transcripts annotated as coding for tubulin, MT-associated proteins and kinesin motor proteins was ... differences in expression than the developmental phase of the cuttings or auxin treatment. Most detected differences which were ...
From the analysis, 2416 differentially expressed genes (DEGs) were identified (p , 0.05 and fold change ≥ 1.5). Gene ontology ( ... Gene Expression Profiling in Ischemic Postconditioning to Alleviate Mouse Liver Ischemia/Reperfusion Injury Pengpeng Zhang1, ... In summary, by exploring gene expression profiling in regard to hepatic I/R and IPO using next-generation RNA-Seq, we suggested ... Zhang P, Ming Y, Cheng K, Niu Y, Ye Q. Gene Expression Profiling in Ischemic Postconditioning to Alleviate Mouse Liver Ischemia ...
... fold change , 2 and q-value , 0.05. The DEGs in the fourth column are those genes which have a higher expression amount than ... Gene expression profiles in fathead minnow exposed to 2,4-DNT: correlation with toxicity in mammals. Toxicol Sci. 2006;94:71-82 ... A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat ... We mapped significantly-changed expression patterns of rat genes to human genes, and used HPD pathways to help us interpret ...
The second cluster was enriched in genes associated with muscle contraction (10 genes, fold enrichment 23.48, p-value 4.16E-09 ... Gene expression clustering. Gene expression clustering of differentially expressed genes produced 4 major temporal expression ... Comparison of gene expression profiles obtained by q-PCR (line) and RNA-seq quantification (bar). For this validation, 10 genes ... Clustering of correlated gene expression profiles during lung development in monodelphis and mice. Heatmap of 207 genes with ...
We next performed nonbiased Affymetrix analyses of global gene expression in WAT. Out of ,21,000 genes, ∼125 genes were ... 6A). Several genes involved in the ER folding process were modestly but significantly increased, including well-known ER ... Obesity-associated improvements in metabolic profile through expansion of adipose tissue. J Clin Invest 2007;117:2621-2637pmid: ... Gene expression levels in qPCR analysis were normalized to ribosomal gene L32, which is also used as a loading control in the ...
... first evidence for a specific effect of EE on T cell differentiation and its associated changes in gene expression profile. In ... for a specific effect of enriched environment on T cell differentiation and its associated changes in gene expression profile. ... Microarray analysis of these cells also revealed a unique gene fingerprint with key signaling pathways involved in autoimmunity ... Microarray analysis of these cells also revealed a unique gene fingerprint with key signaling pathways involved in autoimmunity ...
The microarray gene-expression profiling revealed that 1283 genes were enriched (p value , 0.005; fold , 1.5) in the labial CL ... In this study, we characterized the gene-expression profile of the labial CL of the mouse incisor and assessed the expression ... To find markers for epithelial SCs in the mouse incisor, we compared the gene-expression profiles and gene ontology processes ( ... Gene-Expression Profile of the Labial Cervical Loop of the Incisor. ...
  • We describe the gene expression profiles during these phases and tested 33 selected candidate genes for deficits in LTM formation using RNAi knockdown. (genetics.org)
  • This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function. (nih.gov)
  • Here we used high-throughput RNA sequencing to identify candidate genes and processes linked to summer diapause (SD) induction by comparing the transcriptome differences between the most sensitive larval developmental stage of SD and nondiapause (ND). (g3journal.org)
  • A correspondingly precise gene expression map of C. elegans neurons would facilitate the application of genetic methods toward this goal. (nih.gov)
  • Both methods reported Tfrc and B2m the most stably expressed genes and Gapdh the least stable one. (frontiersin.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)
  • Both methods resulted in gene clusters enriched in meiosis-specific genes (from 14- to 55-fold). (labome.org)
  • Sometimes, a scientist already has an idea of what is going on, a hypothesis , and he or she performs an expression profiling experiment with the idea of potentially disproving this hypothesis. (wikipedia.org)
  • More commonly, expression profiling takes place before enough is known about how genes interact with experimental conditions for a testable hypothesis to exist. (wikipedia.org)
  • With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. (wikipedia.org)
  • Our hypothesis is that gene arrays performed on operative specimens from uniformly treated mesothelioma patients could predict survival and time to progression, and could cluster groups of patients as good or poor risk. (aacrjournals.org)
  • The hypothesis is that understanding how these early genes are regulated during the initial multilayering and growth phase of osteoblasts will lead to models of how BMP activity stimulates cell growth, cell migration, multilayering, matrix deposition and remodeling phase that allows subsequent mineralization. (bioscience.org)
  • We tested the hypothesis that global ECT gene expression patterns can be reproducibly quantified and are altered by mechanical load and by tyrosine kinase inhibition, similar to in vivo myocardium. (ahajournals.org)
  • The influence of bevacizumab and ranibizumab on genes involved in signal transduction and cell signaling downstream of VEGF were compared in order to detect possible differences in their mode of action, which are not related to their Fab-antibody fragments. (biomedcentral.com)
  • The comparison also revealed changes in the mammalian gene expression program associated with the initiation of alveologenesis and birth, pointing to subtle differences between the non-functional embryonic lung of the eutherian mouse and the partially functional developing lung of the marsupial Monodelphis neonates. (springer.com)
  • To determine functional differences between the corpus luteum (CL) of the estrous cycle and pregnancy in cows, gene expression profiles were compared using a 15 K bovine oligo DNA microarray. (go.jp)
  • Collectively, the different gene expression profiles may contribute to functional differences between the cyclic and pregnant CL, and chemokines including eotaxin and lymphotactin may regulate CL function during pregnancy in cows. (go.jp)
  • The Brn1 gene was further identified as a direct target of Pax2, as two functional Pax2-binding sites in the promoter and in an upstream regulatory element of Brn1 were essential for lacZ transgene expression at the mid-hindbrain boundary. (biologists.org)
  • Table S3 Number of genes involved in different functional groups up-regulated by TCE treatment. (springer.com)
  • The increasing collection of microarray data represents a valuable source for generating functional hypotheses of uncharacterized genes. (biomedcentral.com)
  • While the major part of DNA microarray datasets were not purposely generated for this objective, they can be useful in generating hypotheses about the functional involvement of genes, especially for those with significant expression patterns across the experimental conditions or over a time span. (biomedcentral.com)
  • It provides a valuable resource of knowledge for model training and validation in generating the hypotheses about the functional involvement of unknown genes. (biomedcentral.com)
  • For example, only two functional categories of genes previously associated with aging in muscle, kidney, and brain were confirmed in ovary: genes associated with complement activation were upregulated, and genes associated with mitochondrial electron transport were downregulated. (biomedcentral.com)
  • Interestingly, while genes involved in immune system function were down-regulated in the brains of mature males, changes in the expression levels of several receptors and channels were observed suggesting that some rewiring is occurring in the brain at sexual maturity. (biomedcentral.com)
  • Messenger RNA expressions of chemokines ( eotaxin , lymphotactin and ENA-78 ) and their receptors ( CCR3 , XCR1 and CXCR2 ) were validated by quantitative real-time PCR. (go.jp)
  • In this study, we identified by gene expression profiling a significant cluster of genes coding for immune-related cell surface receptors strongly up-regulated by hypoxia in monocyte-derived mDCs and characterized one of such receptors, TREM-1, as a new hypoxia-inducible gene in mDCs. (bloodjournal.org)
  • The available data on the expression of Toll-like receptors in chronic lymphocytic leukemia are limited and derive from small series of patients. (haematologica.org)
  • Results Chronic lymphocytic leukemia cells express all Toll-like receptors expressed by normal activated B cells, with high expression of TLR7 and CD180, intermediate expression of TLR1, TLR6, TLR10 and low expression of TLR2 and TLR9. (haematologica.org)
  • Significant differences were identified for selected genes between cases carrying mutated or unmutated IGHV genes or assigned to different subsets with stereotyped B-cell receptors. (haematologica.org)
  • A role for antigen in the development of chronic lymphocytic leukemia (CLL) is strongly suggested by the biased immunoglobulin heavy variable ( IGHV ) gene repertoire of the malignant clones, the prognostic implications of IGHV gene mutational status and the identification of subsets of patients with almost identical, stereotyped B-cell receptors (BcR), who can also exhibit restricted demographic, biological and clinical features. (haematologica.org)
  • The differences in gene expression profile between metastatic and non-metastatic PTC, if they exist, are subtle and potentially detectable only in large datasets. (mdpi.com)
  • Conclusion: However, our results reveal no differences in gene expression between the obese and non-obese, more studies are necessary to precisely delineate the associated mechanisms, particularly those that include groups with different degrees of obesity and patients with diabetes mellitus type 2 because the expression of the main genes that are involved in β-oxidation and glucose level maintenance are affected by these factors. (wur.nl)
  • Differences in gene expression underlie central questions in plant biology extending from gene function to evolutionary mechanisms and quantitative traits. (plantphysiol.org)
  • In RPE cells, NOS3 and PGF were up-regulated and Pla2g12b was down-regulated after exposure to ranibizumab, while PIK3CG was up-regulated and FIGF was down-regulated after exposure to bevacizumab, but the differences in gene expression were minor between drugs (PIK3CGand PGF were down-regulated more by ranibizumab than by bevacizumab). (biomedcentral.com)
  • Microarrays used in combination with fluorescence-activated cell sorting (FACS), is a particularly powerful strategy, because a large number of known and novel genes can be simultaneously assayed in purified populations of cells prospectively isolated from their native microenvironment within the developing brain. (jneurosci.org)
  • Several forms of animal behavior are known to be influenced by the activity of specific genes ( 1 , 2 ). (sciencemag.org)
  • Instead, in both ovary and testis, CR caused small and mostly gonad-specific effects: suppression of ovulation in ovary and activation of testis-specific genes in testis. (biomedcentral.com)
  • Considering the utmost sensitivity and reliability of qRT-PCR, a careful selection of a constitutively expressed gene is required to account for variation in the amount and quality of starting RNA and cDNA synthesis efficiency. (frontiersin.org)
  • We also identified genes that can transmit the known biologic functions initiated by CTGF such as proliferation and extracellular matrix remodelling. (molvis.org)
  • Distances on the plot represent coefficient of variation in mRNA expression levels between samples for the top 500 genes that best distinguish the samples. (nih.gov)
  • The extent of these sequence similarities in maize and other complex genomes poses a clear challenge to delineation of gene-specific function. (plantphysiol.org)
  • This response included a number of genes which are known to be involved in the pathogenesis of malaria and other inflammatory diseases. (hindawi.com)
  • hCTGF induces various groups of genes responsible for a wound healing and inflammatory response in HTFs. (molvis.org)
  • Inflammatory gene polymorphisms may be associated with glioma risk. (cancerindex.org)
  • The purpose of this study was to analyze effects of certain inflammatory gene and some clinical factors on patient survival.The clinical information of 269 glioma patients conceived operation from September 2010 to May 2014 to decide the 1-, 3-year survival rates according to follow-up results and analyze age, gender, the WHO classification, extent of surgical resection, radiotherapy and chemotherapy factors effects on prognosis. (cancerindex.org)
  • 0.005), which represented decreased expression of inflammatory genes (PGE 2 , IL-6) and catabolic genes (MMP3) and represented increased expression of anti-inflammatory and anabolic genes. (biomedcentral.com)
  • Homozygous mutations in the WFS1 gene result in a rare disease-Wolfram syndrome that is characterized by early-onset diabetes mellitus , progressive optic atrophy, diabetes insipidus , and deafness [ 18 , 19 ]. (hindawi.com)
  • Mutations in the WFS1 gene have been reported in patients with bipolar disorder, major depression, schizophrenia, and suicide victims without Wolfram syndrome [ 18 , 19 , 22 - 31 ]. (hindawi.com)
  • Deregulation of Cyclin G highlights an organ intrinsic control of developmental noise, linked to the ETP-interacting domain, and enhanced by mutations in genes encoding members of the Polycomb Repressive complexes PRC1 and PR-DUB. (plos.org)
  • For example, in yeast, the entire coding genome can be placed on one array and now monitor over 300 diverse mutations and chemical treatments compared with wild-type expression patterns of all the yeast genes. (bioscience.org)
  • To demonstrate the potential of global preamplification we analysed the expression of 15 genes in 60 single cells. (nature.com)
  • To demonstrate the applicability of this strategy to rare neuron types, we generated RNA-Seq profiles of the NSM serotonergic neurons that occur as a single bilateral pair of cells in the C. elegans pharynx. (nih.gov)
  • Altogether our data demonstrate the significance of pre-validation of housekeeping genes for accurate normalization and indicates Tfrc and B2m as best endogenous controls in MS. ActB and Gapdh are not recommended in gene expression studies related to current one. (frontiersin.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)
  • Among them were genes important for assimilation of inorganic carbon, suggesting a link between the carbon and iron regulatory networks. (g3journal.org)
  • Hence, our genome-wide expression profiling indicates an unprecedented complexity in the iron regulatory network of cyanobacteria. (g3journal.org)
  • Reversible lysine acetylation has emerged as a central regulatory mechanism for chromosome remodeling, gene transcription, and other biological processes ( 1, 2 ). (aacrjournals.org)
  • Consequently, the IsO is lost upon individual mutation of these regulators, whereas ectopic expression of a single factor activates most other components of the regulatory cascade ( Nakamura, 2001 ). (biologists.org)
  • Headspace exposure of Arabidopsis thaliana to a mixture of the bicyclic monoterpenes α-pinene and β-pinene induced defense, accumulation of reactive oxygen species, and expression of SA - and SAR-related genes, including the SAR regulatory AZELAIC ACID INDUCED1 ( AZI1 ) gene and three of its paralogs. (plantcell.org)
  • Microarray transcript expression data were validated by QPCR for selected regulatory molecules. (ahajournals.org)
  • In both 3T3-L1 adipocytes and adipose tissue from db / db mice, the SPPARγMs generated attenuated and selective gene-regulatory responses, in comparison with full agonists. (aspetjournals.org)
  • These studies provide new insights into the gene-regulatory activity of SPPARγMs as well as novel quantitative indices to facilitate the identification of PPARγ ligands with robust insulin-sensitizing activity and improved tolerance among patients with type 2 diabetes, compared with presently available PPARγ agonist drugs. (aspetjournals.org)
  • This presentation will focus on using microarray data on a clonal osteoblast cell model to analyze the early BMP-2 responsive genes, as well as some of the later genes regulated by BMP2 during different phases of mineralization. (bioscience.org)
  • Beneath each cluster map is the MDS plot of the 70 genes comparing the SD and MF postradiation exposure response. (aacrjournals.org)
  • The figure above represents the output of a two dimensional cluster, in which similar samples (rows, above) and similar gene probes (columns) were organized so that they would lie close together. (wikipedia.org)