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.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.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, 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.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.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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.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.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.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.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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)Cell Line, Tumor: A cell line derived from cultured tumor cells.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.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.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.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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)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.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.Microdissection: The performance of dissections with the aid of a microscope.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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 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.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.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.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).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.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.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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Genes, Plant: The functional hereditary units of PLANTS.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.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.RNA, Neoplasm: RNA present in neoplastic tissue.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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.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.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Breast Neoplasms: Tumors or cancer of the human BREAST.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.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.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.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.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.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.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.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.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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.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.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.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Embryonic Development: Morphological and physiological development of EMBRYOS.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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.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.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.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)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.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Validation Studies as Topic: Research using processes by which the reliability and relevance of a procedure for a specific purpose are established.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.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.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.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.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.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.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.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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.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.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.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.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.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.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.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.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).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.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.Genes, Homeobox: Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS.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.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.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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.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.Genes, Insect: The functional hereditary units of INSECTS.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.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.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Nerve Tissue ProteinsGenetic 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.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.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.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.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.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.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Zebrafish Proteins: Proteins obtained from the ZEBRAFISH. Many of the proteins in this species have been the subject of studies involving basic embryological development (EMBRYOLOGY).Body Patterning: The processes occurring in early development that direct morphogenesis. They specify the body plan ensuring that cells will proceed to differentiate, grow, and diversify in size and shape at the correct relative positions. Included are axial patterning, segmentation, compartment specification, limb position, organ boundary patterning, blood vessel patterning, etc.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.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.Bacterial Proteins: Proteins found in any species of bacterium.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.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.Plant Roots: The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.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.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 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.Seeds: The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.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.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)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.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.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.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression 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.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.Plant Leaves: Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)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.Mesoderm: The middle germ layer of an embryo derived from three paired mesenchymal aggregates along the neural tube.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.Lung: Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.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.Neurons: The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.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.Morphogenesis: The development of anatomical structures to create the form of a single- or multi-cell organism. Morphogenesis provides form changes of a part, parts, or the whole organism.Testis: The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.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.Eye ProteinsPlants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Animals, Genetically Modified: ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.Mice, Inbred BALB CSensitivity 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)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Biopsy: Removal and pathologic examination of specimens in the form of small pieces of tissue from the living body.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Intercellular Signaling Peptides and Proteins: Regulatory proteins and peptides that are signaling molecules involved in the process of PARACRINE COMMUNICATION. They are generally considered factors that are expressed by one cell and are responded to by receptors on another nearby cell. They are distinguished from HORMONES in that their actions are local rather than distal.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).Prostatic Neoplasms: Tumors or cancer of the PROSTATE.
"Transcriptional profiling of the heart reveals chamber-specific gene expression patterns". Circulation Research. 93 (12): 1193- ... Its expression is associated with cancer, but the nature of its role is unclear. Most recent data indicate that loss of StarD10 ... "Entrez Gene: STARD10 START domain containing 10". Olayioye MA, Vehring S, Müller P, Herrmann A, Schiller J, Thiele C, Lindeman ... Lai CH, Chou CY, Ch'ang LY, Liu CS, Lin W (May 2000). "Identification of novel human genes evolutionarily conserved in ...
Gene Expression Patterns. 3 (6): 719-26. doi:10.1016/s1567-133x(03)00140-6. PMID 14643679. Richards M, Tan SP, Tan JH, Chan WK ... Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V (2004). "Expression profiling of mammalian microRNAs ... "Vascular gene expression and phenotypic correlation during differentiation of human embryonic stem cells". Developmental ... Lin-28 homolog A is a protein that in humans is encoded by the LIN28 gene. LIN28 encodes an RNA-binding protein that binds to ...
digital atlas of gene expression patterns in the mouse Brito-Babapulle V, Catovsky D (August 1991). "Inversions and tandem ... "EST Profile - Hs.271614". EST Profile Viewer. National Center for Biotechnology Information (NCBI). "GENEPAINT Set ID: EH1992 ... None of this information gives any indication of a specific function but the wide expression of the gene and its high ... The homolog in mice also shows expression throughout the entire body. Several micro-arrays demonstrate the variable expression ...
Chaib H, Cockrell EK, Rubin MA, Macoska JA (2001). "Profiling and verification of gene expression patterns in normal and ... "Profiling of genes differentially expressed between fetal liver and postnatal liver using high-density oligonucleotide DNA ... This gene encodes the 37 kD subunit. This subunit forms a core complex with the 36 and 40 kDa subunits. The core complex ... "Entrez Gene: RFC4 replication factor C (activator 1) 4, 37kDa". Maruyama T, Farina A, Dey A, Cheong J, Bermudez VP, Tamura T, ...
... clustering of gene expression profiles, feature/gene selection, and multi-class, multi-objective feature selection. IEEE ... Zexuan Zhu, Y. S. Ong and M. Dash (2007). "Markov Blanket-Embedded Genetic Algorithm for Gene Selection". Pattern Recognition. ... CS1 maint: Multiple names: authors list (link) Merz, P.; Zell, A. (2002). "Clustering Gene Expression Profiles with Memetic ... Typical heuristic procedures and schemes include the k-gene exchange, edge exchange, first-improvement, and many others. ...
Specifically mRNA transcripts can be used to investigate differences in gene expression patterns. Transcriptome profiling is ... therefore with traditional RNA capture methods one must be cautious in the interpretation of gene expression patterns, as they ... Wolf, Jochen B. W. (March 2013). "Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial ... mask both low-level mRNA expression in single cells and variation in expression between cells. The photoactivatable TIVA tag is ...
Analysis of DNA microarray expression profiles has led to the discovery of a number of genes that are tightly co-regulated. The ... The use of this technology helps researchers monitor changes in expression patterns for large numbers of genes in a given ... Thus, changes in the regulatory patterns of these genes would affect the development of both the fore- and hind-limbs, ... It is likely that these gene groups share common cis- and trans-acting control elements to achieve coordinate expression. ...
Gene expression profiling studies have also attempted to distinguish heterogeneous groups of DLBCL from each other. These ... studies examine thousands of genes simultaneously using a DNA microarray, looking for patterns which may help in grouping cases ... Methods like gene expression profiling and next-generation sequencing may result in more effective and more personalized ... With the apparent success of gene expression profiling in separating biologically distinct cases of DLBCL, NOS, some ...
... receptors RARgamma and TRbeta provide unique time-dependent gene expression profiles for light-activated gene patterning". ... Caged derivates of estradiol were shown to induce gene expression upon uncaging other caged hormones were used to study ... It is now possible to very precisely turn on genes of interest during the development of whole organisms. Small molecules are ... Ando, H.; Futura, T.; Okamoto, H. (2004). "Photo-mediated gene activation by using caged mRNA in zebrafish embryos". Methods ...
Observed gene expression patterns may be functionally linked to a phenotype by an independent knock-down/rescue study in the ... Audic S, Claverie JM (October 1997). "The significance of digital gene expression profiles". Genome Research. 7 (10): 986-95. ... Gene expression is measured against defined standards both for the gene of interest and control genes. The measurement by qPCR ... "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository". Nucleic Acids Research. 30 (1): 207-10 ...
Coexpression: Predicted association between genes based on observed patterns of simultaneous expression of genes. Szklarczyk D ... must be expressed together and have similar phylogenetic profile. ... In molecular biology, STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database and web ... as in other genomes where the genes are not fused). Occurrence: Proteins that have a similar function or an occurrence in the ...
"Cellular pattern of photosynthetic gene expression in developing maize leaves". Genes & Development. 2: 106-115. doi:10.1101/ ... subscription required) "Jane Langdale EMBO profile". people.embo.org. European Molecular Biology Organization. "Professor Jane ... "Cellular pattern of photosynthetic gene expression in developing maize leaves". Genes & Development. 2 (1): 106-115. doi: ... "Cell position and light influence C4 versus C3 patterns of photosynthetic gene expression in maize". The EMBO Journal. 7 (12): ...
"Gene expression profiling of B lymphocytes and plasma cells from Waldenström's macroglobulinemia: comparison with expression ... "Differential characteristics of Waldenström macroglobulinemia according to patterns of familial aggregation". Blood. 115 (22): ... "Gene-expression profiling of Waldenstrom macroglobulinemia reveals a phenotype more similar to chronic lymphocytic leukemia ... WM cells show only minimal changes in cytogenetic and gene expression studies. Their miRNA signature however differs from their ...
... per gene, relatively to an expression profile representing the expression pattern in the bicluster. The e-CCC-Biclustering ... "A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series". ... 4 (8). Aguilar-Ruiz JS (2005). "Shifting and scaling patterns from gene expression data". Bioinformatics. 21 (10): 3840-3845. ... Their paper is still the most important literature in the gene expression biclustering field. In 2001 and 2003, I.S. Dhillon ...
... including personal profiling, document classification, personalized content management, and DNA gene expression analysis. In ... Given a set of multimodal patterns, each presented at a pattern channel, the fusion ART pattern encoding cycle comprises five ... doi:10.1007/s10115-003-0130-9. Tan, A.-H.; Pan (2005). "Predictive Neural Networks for Gene Expression Data Analysis" (PDF). ... By synchronizing pattern coding across multiple pattern channels, fusion ART learns to encode associative mappings across ...
... gene expression profiling studies of human embryos are limited due to legal and ethical issues. Gene expression profiling of ... from which genetic profiling can score the DNA patterns by comparing with ones that have previously been found among embryos in ... In general, embryo profiling for prediction of pregnancy rates focuses mainly on visual profiles and short-term biomarkers ... thereby providing a non-invasive method of embryo profiling. Examples of protein markers evaluated in such profiling include ...
Allows integration of data between other platforms such as gene expression and microRNA profiling. The method looks at ~2 CpG ... These genes include RefSeq genes from the NCBI CCDS Database, cancer genes that show differential methylation patterns during ... A large scale measurement of DNA methylation patterns from a wide selection of genes may enable us to understand better the ... which in the last decade has been recognized to be important in the regulation of gene expression, development and genetic ...
A recent study observed an inverse expression profile of the p15 gene and an antisense ncRNA in leukaemia. A detailed analysis ... with protein coding genes may contribute to localised patterns of chromatin modifications that regulate gene expression during ... where strong epigenetic mechanisms are thought to underlie the embryonic expression profiles of the Hox genes that persist ... "Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells". Cell Stem Cell. 18 (5): 637-652. ...
discuss the gene expression profiles of previously mentioned CREB and ΔFosB as they are involved in cocaine use. These ... Modifications to histones such as methylations and acetylations can change gene expression patterns by activating or ... Addictive behavior observed from long-term cocaine users can be due to changes of the gene expression profiles in the brain's ... Short-term cocaine exposure lead to the same expression profiles of upregulated genes as CREB did creating the reduced ...
Expression of the panda gene is exhibited openly on any coat that is not already white. Markings can show up anywhere on the ... "Franka's OFA Profile". Orthopedic Foundation For Animals. Retrieved 18 November 2016. "Franka's OFA Profile". Orthopedic ... It cannot be "carried" or be passed on without being visible on a dog's pattern/body. "Cynthia Madchen Alspach". Orthopedic ... Panda is a dominant gene. Therefore, the gene must be expressed if a dog has it. ...
Gene expression profiling of acute myeloid leukemia with translocation t(8;16)(p11;p13) and MYST3-CREBBP rearrangement reveals ... a distinctive signature with a specific pattern of HOX gene expression. „Cancer Res". 66 (14), s. 6947-54, Jul 2006. DOI: ... Homeobox gene expression in the intestinal epithelium of adult mice. „J Biol Chem". 266 (5), s. 3246-51, Feb 1991. PMID: ... The MLL fusion gene, MLL-AF4, regulates cyclin-dependent kinase inhibitor CDKN1B (p27kip1) expression. „Proc Natl Acad Sci U S ...
Gene expression patterns shift closer towards specialized functional functional profiles during embryonic development, however ... gene expression profiles of the two brain hemispheres appear asymmetrical at birth. At birth, gene expression profiles appear ... the gene expression profiles become similar between the hemispheres. Given a healthy adult, expression profiles stay relatively ... The gene expression profile of the central nervous system (CNS) is unique. Eighty percent of all human genes are expressed in ...
All expression patterns reflect the wild-type allele for the gene. Categorizing genes as images does not only allow for ... FlyExpress has a primary function of searching between images for similar expression patterns using a specified spatial profile ... The primary images available in FlyExpress are GEMs, or Genome-wide Expression Maps, that display the spatial patterns of genes ... Kumar, S.; Boccia, K.; McCutchan, M.; Ye, J. (2012). "Exploring spatial patterns of gene expression from Fruit Fly ...
... obtained from RNA-seq experiments revealed a complex expression pattern with a group of 22 genes having expression profiles ... Bartlett, D.H. and T.J. Welch, ompH gene expression is regulated by multiple environmental cues in addition to high pressure in ... Welch, TJ, Bartlett, DH, Identification of a regulatory protein required for pressure-responsive gene expression in the deep- ... which detailed microarray work comparing gene expression at sub-optimal, optimal and supra-optimal temperatures and pressure ...
Genomic signature Gene expression profiling Gene expression profiling in cancer Itadani H, Mizuarai S, Kotani H. Can systems ... or gene expression signature is a single or combined group of genes in a cell with a uniquely characteristic pattern of gene ... mRNA samples which acquired levels of gene expression that eventually revealed characteristic gene expression patterns. The ... "Identification of a gene signature in cell cycle pathway for breast cancer prognosis using gene expression profiling data". BMC ...
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. ...
Data analysis of microarrays has become an area of intense research.[11] Simply stating that a group of genes were regulated by at least twofold, once a common practice, lacks a solid statistical footing. With five or fewer replicates in each group, typical for microarrays, a single outlier observation can create an apparent difference greater than two-fold. In addition, arbitrarily setting the bar at two-fold is not biologically sound, as it eliminates from consideration many genes with obvious biological significance. Rather than identify differentially expressed genes using a fold change cutoff, one can use a variety of statistical tests or omnibus tests such as ANOVA, all of which consider both fold change and variability to create a p-value, an estimate of how often we would observe the data by chance alone. Applying p-values to microarrays is complicated by the large number of multiple comparisons ...
... , 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 ...
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 ...
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 ...
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 ...
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 ...
... 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 ...
... 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 ...
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 ...
Evaluating patterns of gene expression may provide more than just a link between genetics and morphology. It is also expected ... Three NTP studies are using Exome-Seq as a means for mutation profiling at a genome-wide scale to understand differences ... NTP is researching if gene expression pattern analysis can provide indicators of toxicity (1) at earlier time points and (2) at ... Gene expression by quantitative polymerase chain reaction (qPCR). Rider/ Tokar. BDE Toxicogenomics Studies:. *2,2,4,4,5- ...
A Functional Approach to Transcriptome Profiling: Linking Gene Expression Patterns to Metabolites that Matter. ... gene expression genomics secondary metabolite transcriptome This is a preview of subscription content, log in to check access. ... Brady SF, Chao CJ, Handelsman J, Clardy J (2001) Cloning and heterologous expression of a natural product biosynthetic gene ... Zangerl AR, Rutledge CE (1996) The probability of attack and patterns of constitutive and induced defense: a test of optimal ...
... Dev Dyn. 2007 Apr ... we show that these genes show a coordinated spatio-temporal expression pattern during epidermal morphogenesis. The expression ... Our observations reveal a coordinated mode of expression of the SSC genes as well as the correlation of their initiation in the ... were among the most highly differentially expressed genes. The three genes encoding the secreted proteins form a cluster in an ...
... Hung-Tsu Cheng,1,2 ... Q. Pan-Hammarström, S. Wen, and L. Hammarström, "Cytokine gene expression profiles in human lymphocytes induced by a formula of ... W.-C. Cheng, W.-Y. Shu, C.-Y. Li et al., "Intra- and inter-individual variance of gene expression in clinical studies," PLoS ... M. K. Kerr and G. A. Churchill, "Experimental design for gene expression microarrays," Biostatistics, vol. 2, no. 2, pp. 183- ...
Previous studies have addressed the issue of profiling gene expression in M1 or M2 macrophage activation in the mouse, leading ... 478 genes) and a cluster of late affected genes (B, 390 genes). Two clusters (D, 1108 genes; E, 945 genes) are associated with ... Apolipoprotein L gene family: tissue-specific expression, splicing, promoter regions; discovery of a new gene. J. Lipid Res. 42 ... The present study was designed to characterize the gene expression profile of human monocytes undergoing differentiation into ...
To obtain a profile of differential gene expression that is associated with the behavioral differences observed between MTLn3- ... genes with different expression patterns and known cellular functions were divided into seven categories of genes predicted ... 7 ⇓ , in general, most genes showed the same pattern of expression with both array and real-time PCR. However, studies have ... We conclude that aligning cell behavior in vivo with patterns of gene expression can lead to new insights into the ...
Mechanisms and Profiling of Gene Expression Patterns in Chemical Mixture Exposure Scenarios. Mortensen, Anne Skjetne ... Targeted Salmon Gene Array (SalArray): A Toxicogenomic Tool for Gene Expression Profiling of Interactions Between Estrogen and ... While a clear pattern of negative effects on ER-mediated gene expression was found in hepatocytes exposed to PCB77, exposure of ... Different gene expression patterns were obtained at similar time-interval with fish from different seasons, demonstrating the ...
Then, normalized gene expression data for the signature genes were extracted from our data set. Gene expression data for ... Gene Expression Profiles Associated with the Presence of a Fibrotic Focus and the Growth Pattern in Lymph Node-Negative Breast ... Gene Expression Profiles Associated with the Presence of a Fibrotic Focus and the Growth Pattern in Lymph Node-Negative Breast ... Gene Expression Profiles Associated with the Presence of a Fibrotic Focus and the Growth Pattern in Lymph Node-Negative Breast ...
... is a transcriptome-profiling technique that allows accurate gene expression profiles to be generated without any need for prior ... Cluster analyses of the altered tags showed that fipronil and endosulfan elicit transcriptome profiles that are more similar to ... Serial analysis of gene expression (SAGE) is a transcriptome-profiling technique that allows accurate gene expression profiles ... Serial analysis of gene expression reveals identifiable patterns in transcriptome profiles of Palaemonetes pugio exposed to ...
Systematic expression profiling of innate immune genes defines a complex pattern of immunosenescence in peripheral and ... Systematic expression profiling of innate immune genes defines a complex pattern of immunosenescence in peripheral and ... The aim of the present study was to systematically examine mRNA expression levels of innate immune genes and proinflammatory ... exhibited an increased expression and/or secretion of proinflammatory cytokines by peripheral and intestinal leukocytes as well ...
Gene expression profiles were different according to dietary patterns, which probably modulate the risk of chronic diseases. ... The objective of this study was to examine gene expression in relation with dietary patterns. Two hundred and fifty four ... IPA reveals that genes differentially expressed for both patterns were present in networks related to the immune and/or ... Two dietary patterns were identified. The Prudent dietary pattern was characterised by high intakes of vegetables, fruits, ...
Having identified some set of regulated genes, the next step in expression profiling involves looking for patterns within the ... gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global ... Finding patterns among regulated genes[edit]. Ingenuity Gene Network Diagram[23] which dynamically assembles genes with known ... is more relevant than knowing how much messenger RNA is made from each gene, gene expression profiling provides the most global ...
... combined deep learning approach that uses data from multiple sources to teach algorithms how to find patterns between genes and ... Artificial intelligence is being harnessed by researchers to track down genes that cause disease. A KAUST team is taking a ... Spatial Gene Expression Profiling of Neurological Disorders. Cedric Uytingco, PhD. In this interview, Cedric Uytingco discusses ... Sticky gene may boost the nerve calming effects of Valium. *New solution can limit spread of wild-released gene drives to ...
... a public database of microarray experiments and gene expression profiles. ... al.: 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res by Yannick Haudry, Hugo Berube, ... as exemplified by archives of gene expression data such as the Gene Expression Omnibus (GEO) [Edgar, 2002] and ArrayExpress ... ArrayExpress - a public database of microarray experiments and gene expression profiles. (2007) by Parkinson ...
We investigate gene expression in CCAM, and hypothesize that CCAM results from an aberration in the signaling pathway during ... Decreased expression of FABP-7 in fetal CCAM compared with normal fetal lung at both the RNA and protein levels suggests FABP-7 ... Validation of differential expression was achieved at the RNA and protein levels. FABP-7 was underexpressed in fetal CCAM ... Candidate differentially expressed genes were selected with log-odds ratio (B) ,0 and false discovery rate ,0.05. ...
The patterns of gene expression found in vitro were compared with in vivo gene expression profiles previously identified in ... The Gene Expression Response of Breast Cancer to Growth Regulators. Patterns and Correlation with Tumor Expression Profiles. ... and compared the patterns of gene regulation to published tumor expression profiles. The complex pattern of response to these ... The power of gene clustering to define both distinct and overlapping patterns of gene expression associated with each drug is ...
Total Gene-Expression Patterns. We initially set out to determine whether global gene-expression patterns in the primary tumors ... 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 ... Gene Expression Associated with Survival. Because we were seeing a survival difference based on unsupervised gene-expression ...
Some TCS genes exhibited diverse patterns of gene expression in response to abiotic stresses as well as exogenous trans-zeatin ... Some TCS genes exhibited diverse patterns of gene expression in response to abi... ... Gene duplication events occurred rarely, which might have resulted from the absence of recent whole-genome duplication event in ... Gene duplication events occurred rarely, which might have resulted from the absence of recent whole-genome duplication event in ...
... the gene expression patterns varied. This study provides the global transcriptome profiles of overwintering buds at different ... To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene expression profiles of ... Based on sequence homology analysis, we summarized the key genes with significant expression differences in poplar and tea ... Based on sequence homology analysis, we summarized the key genes with significant expression differences in poplar and tea ...
Here we identified 9 children with intellectual disability and obesity who have mutations in a gene called MYT1L. This gene is ... and changes to the lettering of genes (which stop the gene from working, mutations) can cause intellectual disability or ... We have identified a new genetic condition caused by MYT1L mutations, further study of this gene will help us understand, and ... Genetic studies have shown that small missing pieces of chromosome (deletions, which remove many genes) ...
Biplot. We used principal component biplots to display the expression profiles of the genes (rows of the data matrix) and the ... To investigate the specificity and stability of lineage-specific gene expression, we included expression patterns of several ... For other gene sets, such as transcription factors or proteolytic genes, the number of genes whose expression was detected in ... Lineage specificity of gene expression patterns. Yuval Kluger, David P. Tuck, Joseph T. Chang, Yasuhiro Nakayama, Ranjana ...
Specific Tandem 3UTR Patterns and Gene Expression Profiles in Mouse Thy1 Germline Stem Cells. . Biblioteca virtual para leer y ... Specific Tandem 3UTR Patterns and Gene Expression Profiles in Mouse Thy1 Germline Stem Cells - Descarga este documento en PDF. ... Specific Tandem 3UTR Patterns and Gene Expression Profiles in Mouse Thy1 Germline Stem Cells. ... To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells ...
"Using mutual information to discover temporal patterns in gene expression data",. abstract = "Finding relations among gene ... Using mutual information to discover temporal patterns in gene expression data. AIP Conference Proceedings. 2006 Dec 1;854:25- ... Using mutual information to discover temporal patterns in gene expression data. In: AIP Conference Proceedings. 2006 ; Vol. 854 ... Fingerprint Dive into the research topics of Using mutual information to discover temporal patterns in gene expression data. ...
Microarray-based RNA profiling of Synechocystis gene expression. Gene expression was measured at different time points over a ... Main temporal patterns of expression response to iron limitation. Expression profiles of four detected clusters with 688, 664, ... and sRNAs were hierarchically clustered based on their expression changes. The expression profiles of protein-coding genes can ... gene expression at time point 0 hr was taken. To exclude genes that did not show expression changes, a minimum standard ...
Here, the accumulation of carotenoids and the expression of genes from carotenoid metabolic and catabolic pathways were ... PSY1 (phythoene synthase) expression showed a positive correlation with the total carotenoid content. Additionally, the PSY1 ... and its expression was inversely correlated with the accumulation of several carotenoids, suggesting that CCD1 is also an ... expression did not correlate with any of the carotenoids. In contrast, ZmCCD1 (carotenoid dioxygenase) was more highly ...
  • While micorarrays are a stable and well understood technology for assaying gene expression, NextGen sequencing methods like RNA-Seq should become more common as sequencing costs drop, and bioinformatic pipelines become standardized and integrated with genomic sequencing. (nih.gov)
  • In one FY 2015 study, NTP initiated microRNA profiling of lung tissue after chemical inhalation to understand the mechanisms of pulmonary fibrosis that may lead to better biomarkers in lung tissue or blood. (nih.gov)
  • NTP is evaluating study conditions that may contribute to differential gene expression, such as animal and tissue variability, methods for tissue sampling, and standards for conducting toxicogenomic studies under laboratory conditions. (nih.gov)
  • Such approaches are crucial in the analysis of cancer as a genetic disease and in the identification of patterns of gene expression that might be used in diagnosis and therapy. (aacrjournals.org)
  • The KAUST model extracts the patterns learned from how genes network and about the similarities among genetic diseases and transfers them to a deep learning model called a graph convolutional network. (news-medical.net)
  • Genetic studies have shown that small missing pieces of chromosome (deletions, which remove many genes) and changes to the lettering of genes (which stop the gene from working, mutations) can cause intellectual disability or obesity. (plos.org)
  • We have identified a new genetic condition caused by MYT1L mutations, further study of this gene will help us understand, and treat, intellectual disability and obesity. (plos.org)
  • These extensive differences in gene expression stand in stark contrast to the much smaller numbers found in previous studies on genetic wing pattern variation, and suggest that environmentally induced phenotypic shifts may arise from very broad systemic processes. (omicsdi.org)
  • To identify additional players involved in regulating MAL gene expression, we carried out a genetic selection for MAL constitutive mutants. (genetics.org)
  • Further genetic analysis demonstrates that RGR1 and SIN4 work in a common pathway and each component of the Mediator Sin4 module plays a distinct role in regulating MAL gene expression. (genetics.org)
  • To identify possible additional players involved in regulating MAL gene expression, we designed a sensitive genetic selection for MAL constitutive (Mal c ) mutants using a MAL61promoter-HIS3 reporter. (genetics.org)
  • Every tumor can have a distinct genetic profile. (stanford.edu)
  • To understand how these orchestrated events collectively produce a functioning nervous system it is necessary to characterize the genetic circuitry underlying the patterning of cell-fate determining events. (nih.gov)
  • Furthermore, there is the thorny issue of genetic redundancy, i.e. another gene-family member can compensate for the lack of a functional gene. (biologists.org)
  • To understand how a detailed knowledge of gene expression will help researchers elucidate genotype-phenotype relationships, one has to understand that the risk factors associated with many human disease conditions are complex and include lifestyle choices, environment and multiple genetic loci. (biologists.org)
  • The Polymerase Chain Reaction (PCR), with its sensitive and selective amplification of specific nucleic acid sequences has become a research tool of almost unparalleled importance, with applications in, for example, cloning, gene expression analysis, DNA sequencing, genetic mapping and diagnostics. (google.ca)
  • Such genetic patterns could be used to predict the aggressiveness of a patient's cancer and ultimately, guide a doctor's choice of therapy based on a patient's expected outcome. (fredhutch.org)
  • We'd like to look at progression of the disease and to examine genetic expression patterns to see if those patterns can predict clinical outcome. (fredhutch.org)
  • Some labs can test a biopsy for genetic changes or patterns linked to specific types of cancer. (cancervic.org.au)
  • Nir HacohenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhile genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternativ. (medworm.com)
  • Subsets of genes most significantly associated with survival were defined, and vascular cell adhesion molecule-1 (VCAM-1) was the gene most predictive for survival. (pnas.org)
  • Principal component analysis revealed strikingly pervasive differences in relative levels of gene expression among cell lineages that involve most of the subsets examined. (pnas.org)
  • Principal components biplots were found to provide a convenient visual display of the contributions of the various genes within the subsets in lineage discrimination. (pnas.org)
  • Netherlands, 2007 PMID 17200149 -- "Gene-expression and immunohistochemical study of specific T-cell subsets and accessory cell types in the transformation and prognosis of follicular lymphoma. (wikibooks.org)
  • To better characterize these cells, we used global gene analysis to determine gene expression patterns among murine CD11c high DC subsets. (jimmunol.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)
  • In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. (nih.gov)
  • During the transition from its innocuous E. coli ancestor, Shigella , the aetiological agent of bacillary dysentery, has undergone drastic genomic rearrangements affecting the polyamine profile. (plos.org)
  • The prospect of pharmacologically modulating the oncogene-tumor suppressor gene balance in DLBCL, including critical targets such as BCL-6, p53, HSP, and nuclear factor-κB, using epigenetic strategies offers the possibility of targeting these diseases at their genomic roots. (bloodjournal.org)
  • To summarize evidence on the validity and utility of 3 gene expression-based prognostic breast cancer tests: Oncotype DX (Genomic Health, Redwood City, California), MammaPrint (Agendia BV, Amsterdam, the Netherlands), and H/I (AvariaDX, Carlsbad, California). (annals.org)
  • The independent Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) Working Group reviewed the scientific evidence to see whether gene expression profiling is valid and useful for determining the risk of breast cancer recurrence that could be prevented by chemotherapy, and developed a recommendation about the appropriate use of this testing in 2009. (cdc.gov)
  • In PLOS this week: intra-tumor heterogeneity patterns, genomic analysis of Thoroughbred horse origins, and more. (genomeweb.com)
  • fined a ranked list of HIF-target genes and experimentally validated ANKRD37 as a novel HIF-1 target. (psu.edu)
  • Taken together, this study represents the first comprehensive survey of target genes regulated by the Hedgehog pathway during vertebrate development. (genetics.org)
  • These patterns will identify critical target genes, discern possible mechanisms involved in ER-mediated modulation of sperm parameters and discover roles for genes with unknown function. (epa.gov)
  • Functional genomics approach using Dynabeads® to find target genes in testicular cancer. (thermofisher.com)
  • General Public: Can Tumor Gene Expression Profiling (GEP) Improve Outcomes in Patients With Breast Cancer? (cdc.gov)
  • More broadly, we demonstrate how the intrinsic heterogeneity of individual cell behaviors can be exploited to discover features of viral and host gene expression that correlate with single-cell outcomes, which will ultimately impact whether or not infections spread. (rsc.org)
  • Most recent data indicate that loss of StarD10 expression in breast cancer is associated with poor outcomes in patients. (wikipedia.org)
  • The estrogenic and xenobiotic biotransformation gene expressions are receptor-mediated processes that are ligand structure-dependent interactions with estrogen-receptor (ER) and aryl hydrocarbon receptor (AhR). (bibsys.no)
  • Different gene expression patterns were obtained at similar time-interval with fish from different seasons, demonstrating the complexity of AhR-ER interactions. (bibsys.no)
  • Affymetrix Santa Clara, CA) to systematically analyze the gene expression changes induced by tumor-stromal interactions. (aacrjournals.org)
  • We also characterized the role of the cyclooxygenase-2 ( COX-2 ) /PTGS2 , a gene identified as markedly induced in both cancer cells and fibroblasts in our coculture system, in the pancreatic tumor-stromal interactions. (aacrjournals.org)
  • To investigate mechanisms of phthalate toxicity in normal human cells and to provide information concerning inter-individual variation and gene-environment interactions. (cdc.gov)
  • We reasoned that comparing A2B5 + oligodendrocyte progenitors to O4 + oligodendrocytes would be a productive screening method for identification of genes important for myelination and the establishment of axon-glia interactions. (jneurosci.org)
  • Eric J BrownSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTransient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which suppresses fork breakage, strand resection, and RPA accumulation. (medworm.com)
  • Brady SF, Chao CJ, Handelsman J, Clardy J (2001) Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. (springer.com)
  • The three genes encoding the secreted proteins form a cluster in an approximately 40-Kb locus on human chromosome 19 and the syntenic region on mouse chromosome 7 known as the stratified epithelium secreted peptides complex (SSC). (nih.gov)
  • Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development. (nih.gov)
  • The DLL1 + cluster had elevated expression of genes associated with endocytosis, integrin-mediated adhesion and receptor tyrosine kinase signalling. (biologists.org)
  • An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis. (nih.gov)
  • We identified 55 bZIP transcription factor-encoding genes in the grapevine ( Vitis vinifera ) genome, and divided them into 10 groups according to the phylogenetic relationship with those in Arabidopsis. (biomedcentral.com)
  • Reinhard KunzeSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaPlants can prepare their defense of impending herbivory, when they previously perceived eggs deposited by herbivores insect which reliably indicates that larvae will soon hatch and feed on the plants. (medworm.com)
  • While a clear pattern of negative effects on ER-mediated gene expression was found in hepatocytes exposed to PCB77, exposure of cells to the more potent AhR-agonist and dioxinlike PCB126 induced transcriptional activation of ER signalling demonstrated by increased Vtg and ERα mRNA and ERα protein levels. (bibsys.no)
  • This is due to alternative splicing , and also because cells make important changes to proteins through posttranslational modification after they first construct them, so a given gene serves as the basis for many possible versions of a particular protein. (wikipedia.org)
  • Decreased expression of FABP-7 in fetal CCAM compared with normal fetal lung at both the RNA and protein levels suggests FABP-7 may have a role in pulmonary development and in the pathogenesis of CCAM. (nature.com)
  • In total, less than a fifth of all protein-coding genes were differentially expressed during the first 72 hr. (g3journal.org)
  • The levels of C - reactive protein were higher in hypertensive patients than normotensives and inflammation-related genes were increased as well. (medsci.org)
  • Human protein-coding gene CCL13. (nih.gov)
  • B. burgdorferi alters gene expression and protein synthesis in response to temperature, pH, and other uncharacterized environmental factors. (asm.org)
  • The hypothesis tested in this study is that dissolved gases, including CO 2 , serve as a signal for B. burgdorferi to alter protein production and gene expression. (asm.org)
  • Second, we apply MOGSA to discover similarities and differences in mRNA, protein and phosphorylation profiles of a small study of stem cell lines and assess the influence of each data type or feature on the total gene-set score. (mcponline.org)
  • Expression of the smooth-muscle proteins alpha-smooth-muscle actin and calponin, and of the intermediate filament protein desmin are parameters of cardiomyocyte maturation in the prenatal rat heart. (springer.com)
  • Right: Two of the genes were also validated as upregulated at their protein level. (thermofisher.com)
  • StAR-related lipid transfer protein 10 (STARD10) or PCTP-like protein is a lipid transfer protein that in humans is encoded by the STARD10 gene. (wikipedia.org)
  • 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)
  • One of the best model systems for understanding pattern formation is segmentation in the fruit fly Drosophila melanogaster . (otago.ac.nz)
  • Twenty years of study of this system has lead to an almost complete understanding of how genes and their product produce the segments of Drosophila. (otago.ac.nz)
  • In conclusion, genes enriched for "immune/inflammatory responses" may be associated with essential hypertension. (medsci.org)
  • Specifically, the relative timing rather than the magnitude of the viral gene expression and innate immune activation correlated with the infection outcome. (rsc.org)
  • Other studies showed that the presence of a fibrotic focus was correlated with the increased expression of hypoxia-inducible factor-1α (Hif-1α) and carbonic anhydrase 9 (CA9), two endogenous hypoxia markers, both in carcinoma cells and intratumoral fibroblasts ( 12 , 13 ). (aacrjournals.org)
  • These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment. (wikipedia.org)
  • Many factors determine whether a gene is on or off, such as the time of day, whether or not the cell is actively dividing, its local environment, and chemical signals from other cells. (wikipedia.org)
  • For instance, skin cells, liver cells and nerve cells turn on (express) somewhat different genes and that is in large part what makes them different. (wikipedia.org)
  • Among the genes identified, the cyclooxygenase-2 ( COX-2 ) /PTGS2 gene was of particular interest because COX-2 expression was markedly augmented in both cell types (cancer cells and fibroblasts) in response to coculture. (aacrjournals.org)
  • Coculture with fibroblasts also induced COX-2 expression in additional pancreatic cancer cells with an unmethylated COX-2 promoter, but not in those with a methylated COX-2 promoter. (aacrjournals.org)
  • Therefore, despite the complex biological nature of metastatic cancer, basic clinical behavior as defined by survival may be determined by the gene-expression patterns expressed within the compilation of primary gross tumor cells. (pnas.org)
  • Moreover, by applying tree-constructing methodologies borrowed from phylogenetics to the expression data from differentiated cells and stem cells, we reconstructed a tree of relationships that resembled the established hematopoietic program of lineage development. (pnas.org)
  • In our case, we have thousands of variables (genes) to use in discriminating among the types of cells, but for each type, we have only a very small number of examples of that type. (pnas.org)
  • In XY individuals, expression of Sry in supporting cell progenitors triggers commitment to a testicular ("male") fate, whereas the absence of Sry expression in XX supporting cells results in ovarian ("female") development , . (prolekare.cz)
  • Heterogeneity among spleen DC became apparent as early as 1989 ( 9 ), and on the basis of CD8α and CD11b expression, these cells were later subdivided into CD11b low CD8α + and CD11b high CD8α − DC ( 10 ). (jimmunol.org)
  • Comparison with the gene expression profiles of purified normal B cell subpopulations, including germinal center (GC), pre-GC (naive), and post-GC (memory) B cells, shows that HCL cells are more related to memory cells, suggesting a derivation from this B cell population. (rupress.org)
  • In the majority of the cases, leukemic hairy cells bear somatic point mutations in their Ig variable genes ( 6 , 7 ), indicating that the cell giving rise to HCL has transited through the germinal center (GC) of peripheral lymphoid organs, where it has been exposed to the hypermutation mechanism ( 8 ). (rupress.org)
  • Nonspecific filtering criteria identified 313 genes differentially expressed in the leukemic cells. (bloodjournal.org)
  • We next identified 19 genes that were differentially expressed in T-ALL cells from patients who either had a relapse or remained in continuous complete remission. (bloodjournal.org)
  • 1 - 3 Based on the expression of lineage-specific antigens and the presence of lineage-specific gene rearrangements, ALL cells are known to be derived from either B- or T-cell precursors. (bloodjournal.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)
  • Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. (rsc.org)
  • Genes to Cells, 14 (2), 243-260. (springer.com)
  • Genes to Cells, 15 (3), 209-228. (springer.com)
  • In in vitro experiments, β-estradiol induced ECM3 gene production in ER-positive breast carcinoma cell lines, whereas TGFβ induced upregulation of the genes leading to ECM3 gene classification, especially in ER-negative breast carcinoma cells and in fibroblasts. (ebscohost.com)
  • In rapidly dividing Escherichia coli cells grown in rich media, most RNA polymerase (RNAP) molecules are engaged in transcribing a small set of genes whose products are primarily involved in translation, most notably rRNAs and tRNAs (stable RNAs) ( 9 , 27 , 69 ). (asm.org)
  • Because of these selective properties, the majority of cells within a tumor will share a common profile of gene expression. (wikipedia.org)
  • Of note, similar gene expression patterns associated with metastatic behaviour of breast cancer tumor cells have also been found in breast cancer of dog, the most common tumor of the female dog. (wikipedia.org)
  • The bZIP gene family has been comprehensively identified or predicted in several plant genomes. (biomedcentral.com)
  • In example 2, the targeted region of a gene has two or more methylated CpG sites in two out of five genomes. (qiagen.com)
  • The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. (rsc.org)