Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Microdissection: The performance of dissections with the aid of a microscope.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Cell Line, Tumor: A cell line derived from cultured tumor cells.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Mice, Inbred C57BLCell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Validation Studies as Topic: Research using processes by which the reliability and relevance of a procedure for a specific purpose are established.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.RNA, Neoplasm: RNA present in neoplastic tissue.Tissue Fixation: The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements.Breast Neoplasms: Tumors or cancer of the human BREAST.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Prognosis: A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Toxicogenetics: The study of existing genetic knowledge, and the generation of new genetic data, to understand and thus avoid DRUG TOXICITY and adverse effects from toxic substances from the environment.Protein Array Analysis: Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Disease Models, Animal: Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Gene Ontology: Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Lasers: An optical source that emits photons in a coherent beam. Light Amplification by Stimulated Emission of Radiation (LASER) is brought about using devices that transform light of varying frequencies into a single intense, nearly nondivergent beam of monochromatic radiation. Lasers operate in the infrared, visible, ultraviolet, or X-ray regions of the spectrum.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Genes, Plant: The functional hereditary units of PLANTS.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Laser Capture Microdissection: Techniques using a laser to cut away and harvest a specific cell or cluster of cells from a tissue section while viewing it under the microscope.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Cell Transformation, Neoplastic: Cell changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm, and other attributes conferring the ability to invade, metastasize, and kill.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Tissue Array Analysis: The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips.Lymphoma, Large B-Cell, Diffuse: Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Biological Markers: Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc.Formaldehyde: A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Epithelial Cells: Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Multiple Myeloma: A malignancy of mature PLASMA CELLS engaging in monoclonal immunoglobulin production. It is characterized by hyperglobulinemia, excess Bence-Jones proteins (free monoclonal IMMUNOGLOBULIN LIGHT CHAINS) in the urine, skeletal destruction, bone pain, and fractures. Other features include ANEMIA; HYPERCALCEMIA; and RENAL INSUFFICIENCY.Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.Flow Cytometry: Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Proteome: The protein complement of an organism coded for by its genome.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Predictive Value of Tests: In screening and diagnostic tests, the probability that a person with a positive test is a true positive (i.e., has the disease), is referred to as the predictive value of a positive test; whereas, the predictive value of a negative test is the probability that the person with a negative test does not have the disease. Predictive value is related to the sensitivity and specificity of the test.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Inflammation: A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.Biopsy: Removal and pathologic examination of specimens in the form of small pieces of tissue from the living body.Disease Progression: The worsening of a disease over time. This concept is most often used for chronic and incurable diseases where the stage of the disease is an important determinant of therapy and prognosis.RNA, Complementary: Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Prostatic Neoplasms: Tumors or cancer of the PROSTATE.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Reference Standards: A basis of value established for the measure of quantity, weight, extent or quality, e.g. weight standards, standard solutions, methods, techniques, and procedures used in diagnosis and therapy.Neoplasms, Plasma Cell: Neoplasms associated with a proliferation of a single clone of PLASMA CELLS and characterized by the secretion of PARAPROTEINS.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Genes, Developmental: Genes that determine the fate of a cell or CELLS in a region of the embryo during EMBRYONIC DEVELOPMENT.Biomarkers, Pharmacological: Measurable biological parameters that serve for drug development, safety and dosing (DRUG MONITORING).Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Antineoplastic Agents: Substances that inhibit or prevent the proliferation of NEOPLASMS.Wnt Proteins: Wnt proteins are a large family of secreted glycoproteins that play essential roles in EMBRYONIC AND FETAL DEVELOPMENT, and tissue maintenance. They bind to FRIZZLED RECEPTORS and act as PARACRINE PROTEIN FACTORS to initiate a variety of SIGNAL TRANSDUCTION PATHWAYS. The canonical Wnt signaling pathway stabilizes the transcriptional coactivator BETA CATENIN.Muscle, Skeletal: A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Leukocytes, Mononuclear: Mature LYMPHOCYTES and MONOCYTES transported by the blood to the body's extravascular space. They are morphologically distinguishable from mature granulocytic leukocytes by their large, non-lobed nuclei and lack of coarse, heavily stained cytoplasmic granules.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Stem Cells: Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Neoplasm Invasiveness: Ability of neoplasms to infiltrate and actively destroy surrounding tissue.Cell Survival: The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.Lung Neoplasms: Tumors or cancer of the LUNG.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Lung: Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Postmortem Changes: Physiological changes that occur in bodies after death.Bacterial Proteins: Proteins found in any species of bacterium.Drug Resistance, Neoplasm: Resistance or diminished response of a neoplasm to an antineoplastic agent in humans, animals, or cell or tissue cultures.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Oxidative Stress: A disturbance in the prooxidant-antioxidant balance in favor of the former, leading to potential damage. Indicators of oxidative stress include damaged DNA bases, protein oxidation products, and lipid peroxidation products (Sies, Oxidative Stress, 1991, pxv-xvi).Zebrafish: An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.Lymphoma, B-Cell: A group of heterogeneous lymphoid tumors generally expressing one or more B-cell antigens or representing malignant transformations of B-lymphocytes.Paraffin: A mixture of solid hydrocarbons obtained from petroleum. It has a wide range of uses including as a stiffening agent in ointments, as a lubricant, and as a topical anti-inflammatory. It is also commonly used as an embedding material in histology.Oncogenes: Genes whose gain-of-function alterations lead to NEOPLASTIC CELL TRANSFORMATION. They include, for example, genes for activators or stimulators of CELL PROLIFERATION such as growth factors, growth factor receptors, protein kinases, signal transducers, nuclear phosphoproteins, and transcription factors. A prefix of "v-" before oncogene symbols indicates oncogenes captured and transmitted by RETROVIRUSES; the prefix "c-" before the gene symbol of an oncogene indicates it is the cellular homolog (PROTO-ONCOGENES) of a v-oncogene.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Mice, Inbred BALB CMetabolome: The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Single-Cell Analysis: Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.Liver Neoplasms: Tumors or cancer of the LIVER.Embryonic Development: Morphological and physiological development of EMBRYOS.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Nerve Tissue ProteinsFrozen Sections: Thinly cut sections of frozen tissue specimens prepared with a cryostat or freezing microtome.Neoplasms, Basal Cell: Neoplasms composed of cells from the deepest layer of the epidermis. The concept does not refer to neoplasms located in the stratum basale.Cell Culture Techniques: Methods for maintaining or growing CELLS in vitro.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.Hepatocytes: The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.Carcinoma, Hepatocellular: A primary malignant neoplasm of epithelial liver cells. It ranges from a well-differentiated tumor with EPITHELIAL CELLS indistinguishable from normal HEPATOCYTES to a poorly differentiated neoplasm. The cells may be uniform or markedly pleomorphic, or form GIANT CELLS. Several classification schemes have been suggested.Plasma Cells: Specialized forms of antibody-producing B-LYMPHOCYTES. They synthesize and secrete immunoglobulin. They are found only in lymphoid organs and at sites of immune responses and normally do not circulate in the blood or lymph. (Rosen et al., Dictionary of Immunology, 1989, p169 & Abbas et al., Cellular and Molecular Immunology, 2d ed, p20)Transforming Growth Factor beta: A factor synthesized in a wide variety of tissues. It acts synergistically with TGF-alpha in inducing phenotypic transformation and can also act as a negative autocrine growth factor. TGF-beta has a potential role in embryonal development, cellular differentiation, hormone secretion, and immune function. TGF-beta is found mostly as homodimer forms of separate gene products TGF-beta1, TGF-beta2 or TGF-beta3. Heterodimers composed of TGF-beta1 and 2 (TGF-beta1.2) or of TGF-beta2 and 3 (TGF-beta2.3) have been isolated. The TGF-beta proteins are synthesized as precursor proteins.Cell Movement: The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM of a cell.
"Gene expression profiling in organ transplantation". Int J Nephrol. 2011: 180201. doi:10.4061/2011/180201. PMC 3154482. PMID ... Gene therapy[edit]. Gene therapy is another method that can be used. In this method, the genes that cause the body to reject ... of immune cells radiolabeled in vivo might-similarly to Gene Expression Profiling (GEP)-offer noninvasive testing.[24][25] ... Research is still being conducted, and no gene therapies are being used to date to treat patients.[27][28][29][30] Current ...
"Analysis of microarray experiments of gene expression profiling". American Journal of Obstetrics and Gynecology. 195 (2): 373- ... Genetics attempts to predict how mutations, individual genes and genetic interactions can affect the expression of a phenotype ... The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is ... A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified ( ...
"Expression profiling reveals off-target gene regulation by RNAi". Nature Biotechnology. 21 (6): 635-637. doi:10.1038/nbt831. ... that once processed bring about silencing of a target gene or genes. Any RNA, including endogenous mRNAs or viral RNAs, can be ... Toxic effects due to over-expression of shRNAs: High level expression of shRNAs has been shown to be toxic. Strategies to ... Woods, N. B.; Bottero, V.; Schmidt, M.; Von Kalle, C.; Verma, I. M. (2006). "Gene therapy: Therapeutic gene causing lymphoma". ...
Although these gene-expression profiles look at different individual genes, they seem to classify a given tumor into similar ... October 2005). "Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with ... When specific DNA mutations or gene expression profiles are identified in the cancer cells this may guide the selection of ... This remains the most common method of testing for receptor status, but DNA multi-gene expression profiles can categorize ...
Gene expression profiling of Arabidopsis meiocytes. Plant Biology 13, 784-793. Roig, I., Brieno-Enriquez, M. A., Caldes, M. G ... Genes 2, 152-168. Yang, X., Makaroff, C. A., and Ma, H. (2003). The Arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-finger ...
Cheang MC, van de Rijn M, Nielsen TO (2008). "Gene expression profiling of breast cancer". Annual Review of Pathology. 3: 67-97 ... Rosenberg M, Fuchs E, Le Beau MM, Eddy RL, Shows TB (1991). "Three epidermal and one simple epithelial type II keratin genes ... Lersch R, Stellmach V, Stocks C, Giudice G, Fuchs E (Sep 1989). "Isolation, sequence, and expression of a human keratin K5 gene ... and cell-type-specific expression of a lacZ gene in the adult and during development". Differentiation; Research in Biological ...
"High glucose-altered gene expression in mesangial cells. Actin-regulatory protein gene expression is triggered by oxidative ... It is located between the genes DEPDC7 and PRRG4 and is 500,000 bp downstream from the Wilms Tumor 1 gene (WT1), which is ... ". "NCBI PRR12 Gene". "Genomatix Tools: El Dorado". "NCBI GeoProfiles db; QSER1 GDS596". "NCBI EST Profile db; QSER1". Clarkson ... This condition was studied as differential expression of genes involved in cell cycle regulation had been noted in these cells ...
"Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma". International Journal of Cancer. 118 (5): 1165-72 ... Clark J, Rocques PJ, Crew AJ, Gill S, Shipley J, Chan AM, Gusterson BA, Cooper CS (Aug 1994). "Identification of novel genes, ... Possible regulatory role of the fusion gene product in wild type SYT expression". Gene. 268 (1-2): 173-82. doi:10.1016/S0378- ... Protein SSXT is a protein that in humans is encoded by the SS18 gene.[5][6][7] ...
Forward and reverse suppression subtractive hybridization were used to generate profiles of gene over and under expression, and ... Reverse northern blotting was used in a 2013 study in Gene in which the author identified a number of genes responsible for ... This allows for significantly expanded gene expression profiling. Arrays may be purchased from commercial suppliers tailored to ... Protocol for differential display, reverse northern and qPCR analysis of expression screening of gene expression difference ...
Gene Expression Omnibus (GEO) Profiles. "Large-scale analysis of the human transcriptome (HG-U133A)". https://www.ncbi.nlm.nih. ... Because there are three paralogs of FAM98 in humans, there is a common ancestor of these genes. A strict ortholog, a gene that ... Only one other gene in the study had the same trend of increased expression in lower protein diets in both groups: THOC4. THOC4 ... One of these four genes was FAM98A, though more research must be done to verify that it was FAM98A that was the gene ...
Gene expression Hsromega India portal Biology portal "Faculty of Science". Banaras Hindu University. 2016. Retrieved 4 October ... "Brief Profile of the Awardee". Shanti Swarup Bhatnagar Prize. 2016. Retrieved 28 September 2016. "Indian Fellow - Lakhotia". ... His studies also attempted to identify how these genes impact the modulation of apoptosis and neurodegeneration in Drosophila ... "Fellow profile - Indian Academy of Sciences". Indian Academy of Sciences. 2016. Retrieved 30 September 2016. "NASI fellows". ...
2006). "Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma". Int. J. Cancer. 118 (5): 1165-72. doi: ... Güre AO, Wei IJ, Old LJ, Chen YT (2002). "The SSX gene family: characterization of 9 complete genes". Int. J. Cancer. 101 (5): ... 2003). "A novel fusion gene, SS18L1/SSX1, in synovial sarcoma". Genes Chromosomes Cancer. 37 (2): 195-200. doi:10.1002/gcc. ... This translocation results in the fusion of the synovial sarcoma translocation gene on chromosome 18 to one of the SSX genes on ...
Raspe, Eric; Decraene, Charles; Berx, Geert (2012). "Gene expression profiling to dissect the complexity of cancer biology: ... the characterization of cellular signaling processes has largely focused on identifying the function of individual genes and ... "Gene Ontology Consortium". Retrieved 1 July 2018.. *^ Smith, Barry (2005). "Relations in biomedical ontologies". Genome Biology ... Ontologies such as the Gene Ontology[3] are being used to annotate the results of biological experiments in a variety of model ...
Gene and protein expression[edit]. About 20,000 protein-coding genes are expressed in human cells and nearly 70% of these genes ... "Expression of Human Skin-Specific Genes Defined by Transcriptomics and Antibody-Based Profiling". Journal of Histochemistry & ... Many genes with elevated expression are also shared with skin and other organs that are composed of squamous epithelia.[25] ... Some 250 of these genes are more specifically expressed in the esophagus with less than 50 genes being highly specific. The ...
Carrel L, Willard HF (March 2005). "X-inactivation profile reveals extensive variability in X-linked gene expression in females ... in females that are heterozygous at the involved gene or genes than in females that are homozygous at that gene or those genes. ... meaning that the Tsix gene overlaps the Xist gene and is transcribed on the opposite strand of DNA from the Xist gene.[31] Tsix ... The Xist gene is expressed at high levels on the Xi and is not expressed on the Xa.[41] Many other genes escape inactivation; ...
Reghunathan R, Jayapal M, Hsu LY, Chng HH, Tai D, Leung BP, Melendez AJ (2005). "Expression profile of immune response genes in ... Exons of the lactoferrin gene in oxen have a similar size to the exons of other genes of the transferrin family, whereas the ... It was shown that gene expression increases with age in the duodenum and decreases in the jejunum. The moonlighting glycolytic ... In humans, lactoferrin gene LTF is located on the third chromosome in the locus 3q21-q23. In oxen, the coding sequence consists ...
Carrel L, Willard H (2005). "X-inactivation profile reveals extensive variability in X-linked gene expression in females". ... in females that are heterozygous at the involved gene or genes than in females that are homozygous at that gene or those genes ... The silencing of genes along the Xi occurs soon after coating by Xist RNA. Like Xist, the Tsix gene encodes a large RNA which ... The Xist gene is expressed at high levels on the Xi and is not expressed on the Xa. Many other genes escape inactivation; some ...
Clerk A, Kemp TJ, Zoumpoulidou G, Sugden PH (April 2007). "Cardiac myocyte gene expression profiling during H2O2-induced ... A few of the known genes near C20orf111 are given in the box below with their known function. Genomic DNA Length:14,968 base ... characterization and expression of a gene with a remarkable promoter". EMBO J. 4 (2): 437-43. PMC 554205 . PMID 3839456. NCBI ( ... C20orf111 gene has no clear paralogs in the human genome. However, it has many orthologs in other organisms, and is conserved ...
Research comparing gene expression between primary and metastatic adenocarcinomas identified a subset of genes whose expression ... January 2002). "Gene expression profiling predicts clinical outcome of breast cancer". Nature. 415 (6871): 530-6. doi:10.1038/ ... Additionally, the expression of these metastatic-associated genes was shown to apply to other cancer types in addition to ... Additionally, identifying the genes whose expression is changed in metastasis offers potential targets to inhibit metastasis. ...
Glinsky GV, Glinskii AB, Stephenson AJ, Hoffman RM, Gerald WL (Mar 2004). "Gene expression profiling predicts clinical outcome ... and/or maintenance of the basal expression of pregnancy-specific glycoprotein genes and possibly other TATA box-less genes. Two ... Krueppel-like factor 6 is a protein that in humans is encoded by the KLF6 gene. It is a tumor suppressor gene. This gene ... "Entrez Gene: KLF6 Kruppel-like factor 6". Botella LM, Sánchez-Elsner T, Sanz-Rodriguez F, Kojima S, Shimada J, Guerrero-Esteo M ...
Gene Expression Profiling in Organ Transplantation Naesens, M (2014). "The Histology of Kidney Transplant Failure: A Long-Term ... Gene therapy is another method that can be used. In this method, the genes that cause the body to reject transplants would be ... Cellular magnetic resonance imaging (MRI) of immune cells radiolabeled in vivo might -similarly to Gene Expression Profiling ( ... complex Transplant rejection and genomics Gene Therapy Progress and Prospects: Gene therapy in organ transplantation Gene ...
Over-expression of certain genes in the heterozygous offspring. (The size of the circle depicts the expression level of gene A) ... Dominance and overdominance have different consequences for the gene expression profile of the individuals. If overdominance is ... Fewer genes are under-expressed in the homozygous individual. Gene expression in the offspring is equal to the expression of ... Furthermore, for any given gene, the expression should be comparable to the one observed in the fitter of the two parents. ...
"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the ... Expression data[edit]. Studies for differential expression of genes from RNA-Seq data, as for RT-qPCR and microarrays, demands ... gene sets rather than of single genes.[20] These gene sets might be known biochemical pathways or otherwise functionally ... Include tools for gene expression and genomics.[21]. *R: An open source environment and programming language dedicated to ...
"Identification of a novel oligodendrocyte cell adhesion protein using gene expression profiling". Journal of Neuroscience. 26 ( ... Human CARKD gene has 10 exons and resides on Chromosome 13 at q34. The following genes are near CARKD on the chromosome: COL4A2 ... "Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation ... indicate its expression in almost all tissues. One peculiar expression pattern of CARKD is its differential expression through ...
Fan, Jinhong; Ngai, John (2001). "Onset of Odorant Receptor Gene Expression during Olfactory Sensory Neuron Regeneration". ... There are approximately 1000 different genes that code for the ORs, making them the largest gene family. An odorant will ... The difference in affinities causes differences in activation patterns resulting in unique odorant profiles.[7][8] The ... Bieri, S.; Monastyrskaia, K; Schilling, B (2004). "Olfactory Receptor Neuron Profiling using Sandalwood Odorants". Chemical ...
... classical QTL analyses were combined with gene expression profiling i.e. by DNA microarrays. Such expression QTLs (eQTLs) ... Several genes factor into determining a person's natural skin color, so modifying only one of those genes can change skin color ... The DNA sequence of any genes in this region can then be compared to a database of DNA for genes whose function is already ... It may indicate that plant height is controlled by many genes of small effect, or by a few genes of large effect. ...
... gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global ... Categorizing regulated genes[edit]. Having identified some set of regulated genes, the next step in expression profiling ... is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global ... Gene set analysis demonstrated several major advantages over individual gene differential expression analysis.[17][18] Gene ...
Gene expression (GE) analyses by use of microarrays (MAs) have become an important part of biomedical and clinical research and ... ZAP-70 expression identifies a chronic lymphocytic leukemia subtype with unmutated immunoglobulin genes, inferior clinical ... Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of ... Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med. 2004;350:1617-1628.CrossRefPubMedGoogle ...
Several constitutively expressed genes have been considered as control candidates, because the expression of these genes is ... Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Gene expression browser for web-based search and visualization of characteristics of gene expression. ... Measurement of gene expression profiles in toxicity determination. US6479235. 25 Nov 1998. 12 Nov 2002. Promega Corporation. ...
... of phthalate toxicity in normal human cells and to provide information concerning inter-individual variation and gene- ... Data Mining Tool software (Affymetrix) was used to separate genes in clusters based on their expression patterns over time. ... Gwinn MR, Whipkey DL, Tennant LB, Weston A [2007]. Gene expression profiling of di-n-butyl phthalate in normal human mammary ... Gene Expression Profiles of Di-n-butyl Phthalate in Normal Human Mammary Epithelial Cells. ...
The phenotypic expression of these genes, through the synthesis of specific proteins, involves interaction with envi ... The genetic basis for disease is determined by the inheritance of genes containing specific sequences of deoxyribonucleic acid ... changes in gene expression take place that result in the expression of hundreds of gene products and the suppression of others ... Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U ...
Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity Melanie J. ... Elucidation of β-Oxidation Pathways in Ralstonia eutropha H16 by Examination of Global Gene Expression Christopher J. Brigham, ... A Systems Biology Approach To Modeling Vibrio cholerae Gene Expression under Virulence-Inducing Conditions Sanjat Kanjilal, ... GENE REGULATION. Transcriptomic and Phenotypic Characterization of a Bacillus subtilis Strain without Extracytoplasmic Function ...
Gene expression profiling using micro-arrays is a modern approach for molecular diagnostics. In clinical micro-array studies, ... 2005) Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 21, 171-178.CrossRefGoogle Scholar ... Micro-arrays gene expression profiles statistical classification supervised machine learning gene selection model assessment ... 2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536.CrossRefGoogle Scholar ...
... including direct silencing of nontargeted genes containing as few as eleven contiguous nucleotides of identity to the siRNA. ... Here, we used gene expression profiling to characterize the specificity of gene silencing by siRNAs in cultured human cells. ... Expression profiling reveals off-target gene regulation by RNAi.. Jackson AL1, Bartz SR, Schelter J, Kobayashi SV, Burchard J, ... Transcript profiles revealed siRNA-specific rather than target-specific signatures, ...
Gene expression ratios are depicted by a log2 pseudocolor scale (ratio fold-change is indicated). (a) Forty-one genes ( ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Jacques Lapointe, Chunde Li, John P. ... might be captured by profiling gene expression using DNA microarrays. Indeed, microarray profiling studies have identified ...
Narrow Roads of Gene Land 3. Statistical Methods in Molecular Evolution. The History and Geography of Human Genes. Population ... Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... You dont need that many genes to fix in on someones likely racial identity. Take two genes, SLC24A5 and DARC. There are ... Racial DNA Profiling? posted by Razib @ 10/05/2007 01:13:00 PM Racial DNA Profiling? ...
The expression profile in muscle tissues was dominated by a strong coordinated down-regulation of genes that encode elements of ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, George ... Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Andrew Y. Gracey, Joshua V. Troll, and ...
... to discover the recurrence predictor genes and then validated the predictive power of these genes in a different set (79 tumors ... A gene expression-based recurrence predictor algorithm was informative in predicting the outcome in patients with early-stage ... We analyzed expression profiles of 12,625 transcripts in prostate tumors from patients with distinct clinical outcomes after ... Prostate tumor samples were taken from the patients at the time of surgery and subjected to a microarray gene expression ...
Genes induced two folds or more different in response to heat shock stress in Clostridium botulinum ATCC 3502 ... Gene Expression Profiling of Clostridium botulinum under Heat Shock Stress. Wan-dong Liang,1 Yun-tian Bi,2 Hao-yan Wang,3 Sheng ...
The activity (expression) of specific genes within breast tumor cells has been found to be associated with the chance of ... Tumor Gene Expression Profiling To Predict Risk of Breast Cancer Recurrence: EGAPP™ Recommendation.  alert icon ... Several gene expression profiles (GEPs) are clinically available that provide variations on "recurrence risk scores" intended ... The EGAPP™ Working Group examined the scientific evidence to see whether gene expression profiling is valid and useful for this ...
The diagnostic performance of the signature genes was assessed against an independent set of samples, by qRT-PCR. Our findings ... Total RNA was isolated from DCs and gene expression profiling was performed with oligonucleotide microarrays. Using a ... We studied the gene expression patterns of DCs incubated with reagents inducing their activation or inhibition. ... suggest that the gene expression signature of DCs can provide a molecular classification for use in the selection of anti- ...
Gene expression profiling tests (Oncotype DX, MammaPrint, others) analyze a number of different genes within your cancer cells ... and gene expression profiling can be particularly helpful.. Several gene expression profiling tests exist, and many are being ... Ive heard that a gene expression profiling test might help in planning my treatment. What is it?. Answer From Sandhya Pruthi, ... The results of gene expression profiling tests help doctors determine who may benefit from additional (adjuvant) treatment ...
Gene expression profile/profiling (GEP): The individual pattern of expression of a panel of genes that is regarded as a " ... Gene expression was examined using high-density oligonucleotide arrays. An analysis showed that gene expression profiling of ... class 2 gene expression profile signature and a negative SLNB result and individuals with a class 2 gene expression profile ... "gene expression profile class assignment of different sign for the tumor cells obtained from the two sites or a failed gene ...
Narrow Roads of Gene Land 3. Statistical Methods in Molecular Evolution. The History and Geography of Human Genes. Population ... Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... DNA profiling - The most common form of DNA profiling used for DNA databases (and other DNA-identification applications) is STR ... DNA databases and DNA profiling posted by the @ 3/12/2007 07:25:00 PM DNA databases and DNA profiling ...
Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ... QIAGEN offers a range of solutions for profiling pathogen gene expression. Our tools provide efficient mechanical disruption of ... For fast, one-step qRT-PCR using sequence-specific probes for gene expression analysis Show details ... Which pathogen genes are expressed upon host invasion; which genes are required for virulence; and how does a pathogen evade ...
The fourth and smallest set of genes was down-regulated throughout the study. Early in wound healing the expression of markers ... Gene expression profiling of cutaneous wound healing J Transl Med. 2007 Feb 21;5:11. doi: 10.1186/1479-5876-5-11. ... Results: Four gene signatures whose expression changed relative to baseline (before wound induction by the pre-treatment biopsy ... The largest group was comprised predominantly of inflammatory genes whose expression was increased throughout the study. Two ...
Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles ... The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously ... The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously ... Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles ...
Coverage for coding sequence genes (B) tph-1 and (C) bas-1 and for (D) a small nuclear RNA (snoRNA) gene, ZK643.9. Lighter vs ... 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 ...
Other articles related to gene, gene expression, expression, expression profiling, gene expression profiling, genes:. ... Gene expression profiling In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are ... Gene Expression Profiling - Conclusions. ... Expression profiling provides new information about what genes do under various ... Gene Expression Profiling. In the field of molecular biology, gene expression profiling is the measurement of the activity (the ...
Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously ... the majority of cells within a tumor will share a common profile of gene expression. Gene expression profiling is a technique ... gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression ... This allows for reliable identification of tumor type based on gene expression. A more powerful result of gene expression ...
... solutions for high-quality gene expression and transcriptome analysis and profiling studies. ... While gene expression microarrays are effective for identifying the expression of known genes and transcripts, they cannot ... and high confidence mapping of alternate transcripts and gene fusions. Discover novel gene isoforms, profile gene expression ... Analyze Gene Expression in Single Cells. Highly sensitive RNA-Seq methods enable gene expression analysis of very low-input ...
  • Candida albicans Transcriptional Profiling Within Biliary Fluid From a Patient With Cholangitis, Before and After Antifungal Treatment and Surgical Drainage. (jcvi.org)
  • Although many genes involved in learning and memory formation have been identified, little is known about the genetic mechanisms required for changing the transcriptional program during different phases of long-term memory (LTM) formation. (genetics.org)
  • I: Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. (psu.edu)
  • Because Drosophila Ci and the Gli3, and possibly Gli2, proteins of vertebrates undergo phosphorylation and proteolytic processing in the absence of Hh to yield truncated transcriptional repressor forms, optimal induction of target gene expression is critically determined by the ratio of the activator (Gli act ) vs. the repressor variants (Gli rep ) of these proteins within the nucleus. (genetics.org)
  • Single genes with the most pronounced transcriptional susceptibility to gamma-secretase activity were evaluated by real-time PCR. (epfl.ch)
  • 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)
  • Sequence based techniques, like RNA-Seq , provide information on the sequences of genes in addition to their expression level. (wikipedia.org)
  • the sequence tells us what the cell could possibly do, while the expression profile tells us what it is actually doing at a point in time. (wikipedia.org)
  • d) for each distinctly sized amplification product detected in step (c), calculating a cycle number, C t , where the amount of that amplification product crosses a predefined threshold, and correlating the threshold cycle with the amount of a nucleic acid having a sequence of interest in said sample, wherein said method provides an amplification profile and a relative abundance for members of said set of nucleic acid sequences of interest. (google.ca)
  • Supplementary Table 1-Primer sequence of selected genes designed for qRT-PCR. (springer.com)
  • To date, however, microarray analyses have been applied almost exclusively to model species for which gene sequence data are abundant. (pnas.org)
  • We show the utility of microarray approaches for the study of gene expression in a species for which, at the onset of our investigation, sequence data were unavailable. (pnas.org)
  • The level of fluorescence at a particular spot provides quantitative information about the expression of the particular gene corresponding to the spotted cDNA sequence. (wikipedia.org)
  • Sequence based techniques, like serial analysis of gene expression (SAGE, SuperSAGE) are also used for gene expression profiling . (primidi.com)
  • The HiCEP method is an amplified fragment length polymorphism (AFLP)-based gene expression profiling method that requires no prior sequence information and has a reduced rate of false positives and a high degree of detection of both coding and non-coding transcripts. (thermofisher.com)
  • a growing number of chemosensory genes have also been identified from many other Dipteran species based on sequence similarity. (frontiersin.org)
  • First Monoploid Reference Sequence of Sugarcane For the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species - sorghum. (doe.gov)
  • The first step in gene discovery was to establish a complementary DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. (mit.edu)
  • Several genes that may be involved in domoic acid synthesis were also revealed through sequence similarity, for example, glutamate dehydrogenase and 5-oxo-L-prolinase. (mit.edu)
  • 0.1 with respect to null adenovirus) changes in the expression of 1,238 genes or expressed sequence tags, of which 1,180 (95.3%) were upregulated. (diabetesjournals.org)
  • However, resolving expression of closely related genes (e.g. alleles and gene family members) is challenging on a genome-wide scale due to extensive sequence similarity and frequently incomplete genome sequence data. (plantphysiol.org)
  • Genes with extensive sequence similarity may comprise a significant portion of a given transcriptome. (plantphysiol.org)
  • The extent of these sequence similarities in maize and other complex genomes poses a clear challenge to delineation of gene-specific function. (plantphysiol.org)
  • Using cDNA sequence database, Kiyosawa et al predicted that sense and antisense transcripts were produced from 15% of mouse gene loci ( 13 ) and demonstrated via microarray analysis that 1,947 sense and antisense transcripts were expressed in mice ( 14 ). (spandidos-publications.com)
  • In developing a drug, one may perform gene expression profiling experiments to help assess the drug's toxicity, perhaps by looking for changing levels in the expression of cytochrome P450 genes, which may be a biomarker of drug metabolism. (wikipedia.org)
  • HIF-1α mediates the expression of a series of genes involved in both cellular and systemic responses to hypoxia, leading to enhanced anaerobic metabolism and induced erythropoiesis and angiogenesis ( 2 ). (pnas.org)
  • The acid-induced genes represented only five functional grouping categories, including eight genes involved in metabolism, nine associated with cell envelope structures or modifications, two encoding chaperones, six regulatory genes, and six unknown genes. (asm.org)
  • However, nine acid-inducible genes are clustered in the gadA region, including hdeA , which encodes a putative periplasmic chaperone, and four putative regulatory genes. (asm.org)
  • To identify temperature-responsive genes, genome arrays containing 1,662 putative B. burgdorferi open reading frames (ORFs) were prepared on nylon membranes and employed to assess gene expression in B. burgdorferi B31 grown at 23 and 35 degrees C. Differences in expression of more than 3.5 orders of magnitude could be readily discerned and quantitated. (prohealth.com)
  • Transcript profiles revealed siRNA-specific rather than target-specific signatures, including direct silencing of nontargeted genes containing as few as eleven contiguous nucleotides of identity to the siRNA. (nih.gov)
  • Four gene signatures whose expression changed relative to baseline (before wound induction by the pre-treatment biopsy) were identified. (nih.gov)
  • Two additional signatures were observed which included preferentially pro-inflammatory genes in the early post-treatment biopsies (2 days after pre-treatment biopsies) and repair and angiogenesis genes in the later (4 to 8 days) biopsies. (nih.gov)
  • Thus, transcriptome profiling reveals novel molecules and signatures associated with human monocyte-to-macrophage differentiation and polarized activation which may represent candidate targets in pathophysiology. (jimmunol.org)
  • Gene expression profiling revealed that in DLBCL patients who do not respond well to standard chemotherapy, lymphoma cells have activated this pathway, known as NF-kB. (innovations-report.com)
  • In addition, the expression level of NF-kB pathway genes allowed to differentiate two PTCL subgroups, and this difference could have clinical interest. (wiley.com)
  • There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. (mdpi.com)
  • In this webinar, a workflow will be presented for the processing of 384 cell lysates with RNA-seq to generate expression data analyzed at the pathway level. (xtalks.com)
  • Subsampling of deep sequencing datasets demonstrated that differential pathway analysis is largely unaffected when reducing the number of genes to this level. (xtalks.com)
  • We revealed both genes and pathway potentially involved in the pathophysiology of migraine. (biorxiv.org)
  • For this reason alone, it is clear that additional genes must participate in the glutamate-dependent AR, but these genes remain to be identified ( 9 ). (asm.org)
  • Additional genes that could be important in our understanding of the pathogenesis of mesothelioma, aiding in diagnosis, or improving targets for therapy were also identified. (aacrjournals.org)
  • An average of 4753 and 5965 additional genes was called Present after globin depletion for Donor 37 and Donor 45, respectively. (thermofisher.com)
  • and (2) to identify additional genes that discriminate IS from vascular risk factor ( S ex, A ge and V ariation in V ascular functionalit Y [SAVVY]) control subjects and myocardial infarction (MI) control subjects. (ahajournals.org)
  • The aim of this study was to identify genes that are expressed differently in the course of BC progression and to establish new biomarkers for BC. (sigmaaldrich.com)
  • We identified several genes as promising candidates for diagnostic biomarkers of human BC and the CKS2 gene not only as a potential biomarker for diagnosing, but also for staging human BC. (sigmaaldrich.com)
  • Moreover, results from these studies may identify novel gene targets that are involved in the toxicity of endocrine disruptors that could lead to the development of biomarkers for reproductive toxicants. (epa.gov)
  • With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. (wikipedia.org)
  • One potentially useful approach to solve these issues would be to identify specific gene expression changes in cancerous mesothelial cells. (aacrjournals.org)
  • The results implicate GPC6 as a novel determinant of BMD, and also identify abnormal skeletal phenotypes in knockout mice associated with a further 100 prioritized genes. (labome.org)
  • In this study, we sequenced the antennal transcriptome of H. illucens adults to identify chemosensory genes. (frontiersin.org)
  • Mapping Heat Resistance in Yeasts In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures. (doe.gov)
  • They used the commercially available Affymetrix microarray DNA chips and screened 6,817 genes to identify 1,100 genes expressed differently in the AML and ALL classes. (biomedcentral.com)
  • Therefore, the focus of this thesis was to identify and initiate characterization of actively expressed genes that control cell growth and physiology in P. multiseries, with the specific goal of identifying genes that may play a significant role in toxin production. (mit.edu)
  • Here, we analyzed genes differentially expressed in each of the three LMS subtypes as compared to benign leiomyomas and then used the Connectivity Map (cmap) to calculate enrichment scores for the 1309 cmap drugs in order to identify candidate molecules with the potential to induce a benign, leiomyoma-like phenotype in LMS cells. (harvard.edu)