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.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, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.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.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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.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.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.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.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.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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)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.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.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.Genes, Plant: The functional hereditary units of PLANTS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.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.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.Mice, Inbred C57BLDNA 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.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.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)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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.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.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Microdissection: The performance of dissections with the aid of a microscope.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.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.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.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.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.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.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).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.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.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.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.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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.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.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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 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.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)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.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.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.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.Flowers: The reproductive organs of plants.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Reference Standards: A basis of value established for the measure of quantity, weight, extent or quality, e.g. weight standards, standard solutions, methods, techniques, and procedures used in diagnosis and therapy.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.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.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of 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)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)Droughts: Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.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.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.Breast Neoplasms: Tumors or cancer of the human BREAST.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.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.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.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.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.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.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.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.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.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).Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.RNA, Neoplasm: RNA present in neoplastic tissue.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.Bacterial Proteins: Proteins found in any species of bacterium.Formaldehyde: A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)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.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Methapyrilene: Histamine H1 antagonist with sedative action used as a hypnotic and in allergies.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.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.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.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.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.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.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Plant Diseases: Diseases of plants.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.Fixatives: Agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue.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).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.Cell Culture Techniques: Methods for maintaining or growing CELLS in vitro.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.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.Single-Cell Analysis: Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.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.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.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.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.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.Plant Growth Regulators: Any of the hormones produced naturally in plants and active in controlling growth and other functions. There are three primary classes: auxins, cytokinins, and gibberellins.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.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.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.Embryonic Development: Morphological and physiological development of EMBRYOS.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Hepatocytes: The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.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.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.Abscisic Acid: Abscission-accelerating plant growth substance isolated from young cotton fruit, leaves of sycamore, birch, and other plants, and from potatoes, lemons, avocados, and other fruits.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.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).Nerve Tissue ProteinsFish Proteins: Proteins obtained from species of fish (FISHES).Kashin-Beck Disease: Disabling osteochondrodysplasia with OSTEOSCLEROSIS, cone-shaped METAPHYSIS, and shortening of the DIAPHYSIS. It is endemic in parts of Siberia and northern China. Mineral deficiencies (e.g., selenium, iodine), fungal cereal contamination, and water contamination may be contributing factors in its etiology.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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.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.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.Dissection: The separation and isolation of tissues for surgical purposes, or for the analysis or study of their structures.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Lipid Metabolism: Physiological processes in biosynthesis (anabolism) and degradation (catabolism) of LIPIDS.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.Genes, Bacterial: The functional hereditary units of BACTERIA.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.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.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.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.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.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Extracellular Matrix Proteins: Macromolecular organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and usually, sulfur. These macromolecules (proteins) form an intricate meshwork in which cells are embedded to construct tissues. Variations in the relative types of macromolecules and their organization determine the type of extracellular matrix, each adapted to the functional requirements of the tissue. The two main classes of macromolecules that form the extracellular matrix are: glycosaminoglycans, usually linked to proteins (proteoglycans), and fibrous proteins (e.g., COLLAGEN; ELASTIN; FIBRONECTINS; and LAMININ).Mice, Inbred BALB CHost-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Cell SeparationOligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Cold Temperature: An absence of warmth or heat or a temperature notably below an accustomed norm.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Tissue Embedding: The technique of placing cells or tissue in a supporting medium so that thin sections can be cut using a microtome. The medium can be paraffin wax (PARAFFIN EMBEDDING) or plastics (PLASTIC EMBEDDING) such as epoxy resins.Proteome: The protein complement of an organism coded for by its genome.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)Regeneration: The physiological renewal, repair, or replacement of tissue.Mice, SCID: Mice homozygous for the mutant autosomal recessive gene "scid" which is located on the centromeric end of chromosome 16. These mice lack mature, functional lymphocytes and are thus highly susceptible to lethal opportunistic infections if not chronically treated with antibiotics. The lack of B- and T-cell immunity resembles severe combined immunodeficiency (SCID) syndrome in human infants. SCID mice are useful as animal models since they are receptive to implantation of a human immune system producing SCID-human (SCID-hu) hematochimeric mice.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Chiara Boschetti; Adrian Carr; Alastair Cris (November 15, 2012). "Biochemical Diversification through Foreign Gene Expression ... Freeman, Scott; Herron, Jon C (2007). Evolutionary Analysis, 4th edition. San Francisco: Benjamin Cummings. pp. 308-309. ISBN 0 ... However, rotifers were found to possess a substantial amount of foreign genes from possible horizontal gene transfer events. ... can also be caused by direct selection to get rid of genes that have become unnecessary. Therefore, a smaller genome is not a ...
Statistical Analysis of Gene Expression Microarray Data. Wiley-Blackwell.. *^ Terry Speed (2003). Microarray Gene Expression ... Expression data[edit]. Studies for differential expression of genes from RNA-Seq data, as for RT-qPCR and microarrays, demands ... For example, Gene Set Enrichment Analysis (GSEA) considers the perturbation of whole (functionally related) gene sets rather ... "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles". Proceedings of the ...
"Analysis of microarray experiments of gene expression profiling". American Journal of Obstetrics and Gynecology. 195 (2): 373- ... Genetics attempts to predict how mutations, individual genes and genetic interactions can affect the expression of a phenotype ... The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is ... A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified ( ...
... by mutations in the MECP2 gene despite no large-scale changes in expression of MeCP2 being found in microarray analyses. BDNF ... Morris KL (2008). "Epigenetic Regulation of Gene Expression". RNA and the Regulation of Gene Expression: A Hidden Layer of ... They control gene expression including virulence genes in pathogens and are viewed as new targets in the fight against drug- ... There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of ...
"Ingenuity IPA Software - Pathway Analysis, miRNA, NGS, RNA-Seq, Microarrays, Gene Expression, Biomarkers". Ingenuity Systems. ... "Sigma-Aldrich Launches Your Favorite Gene Powered by Ingenuity, Sigma-Aldrich Co" (Press release). Sigma-Aldrich Co., Inc. ... IPA also lets researchers search for information on genes, proteins, chemicals, drugs, and reagents. Resulting information can ... "The Return on Investment for Ingenuity Pathways Analysis within the Pharmaceutical Value Chain", Zimmerman, Reeve, and Golden, ...
"Chromosomal mapping to 15q14 and expression analysis of the human MEIS2 homeobox gene". Mamm Genome. 8 (12): 951-2. doi:10.1007 ... This article on a gene on human chromosome 15 is a stub. You can help Wikipedia by expanding it.. *v ... Gene ontology. Molecular function. • sequence-specific DNA binding. • transcription corepressor activity. • transcription ... Homeobox protein Meis2 is a protein that in humans is encoded by the MEIS2 gene.[5][6] ...
"Repeatability of published microarray gene expression analyses". Nature Genetics. 41 (2): 149-155. doi:10.1038/ng.295. PMID ... The set of available tools has been greatly expanded over the years and Galaxy is now also used for gene expression, genome ... Workflows Workflows are computational analyses that specify all the steps (and parameters) in the analysis, but none of the ... "A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly". Genome Research. 17 (6 ...
According to Scopus the most cited ones are: Ramoni M.F.; Sebastiani P.; Kohane I.S. "Cluster analysis of gene expression ... "Human longevity and common variations in the LMNA gene: a meta-analysis". Aging Cell. 11: 475-481. doi:10.1111/j.1474-9726.2012 ... The corrected version was published in PLOS ONE, and several of the genes found associated with exceptional human longevity ... how an accurate risk prediction model of a complex genetic trait that is modulated by several interacting genes can be built ...
Knowledge-based analysis of microarray gene expression data by using support vector machinesEdit. *MP Brown ... Description: The first application of supervised learning to gene expression data, in particular Support Vector Machines. The ... IEEE Transactions on Pattern Analysis and Machine Intelligence, 1984. Description: introduced 1) MRFs for image analysis 2) the ... Recursive functions of symbolic expressions and their computation by machine, part I[7]Edit. *John McCarthy. ...
Quantitative trait locus which relates gene expression to genotypes. Genetic analysis of gene expression. Characterization of ... Nolan, Rebecca (April 15, 2002). "Liquor Remains Scarce on Sundays in Eugene, Ore., Area". The Register-Guard. Retrieved 2008- ... Massive search strategy for ethanol-related genes. Genetic models of variation in impulsivity and alcoholism. Genetics of ...
Gene Ontology analysis and annotation; Normal tissue expression of interferon regulated genes; Regulatory analysis of ... Interferome comprises the following data sets: Gene expression data of interferon regulated genes from Homo sapiens, Mus ... Interferome is an online bioinformatics database of interferon-regulated genes (IRGs). These Interferon Regulated Genes are ... regulated genes and is regularly updated. It is used by the interferon and cytokine research community both as an analysis tool ...
"Revisiting global gene expression analysis". Cell. 151 (3): 476-82. PMID 23101621. Lin, CY; Lovén, J; Rahl, PB; Paranal, RM; ... Commonly used gene expression experiments interrogate the expression of one (qPCR) or many (microarray, RNA-Seq) genes. These ... Gene expression is regulated by numerous types of proteins that directly or indirectly influence transcription by RNA ... molecules from expressed genes are increased during disease, development, or in response to stimuli. At the subset of genes ...
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995). "Serial analysis of gene expression". Science. 270 (5235): 484-7. doi: ... 2002). "Mutation screening and imprinting analysis of four candidate genes for autism in the 7q32 region". Mol. Psychiatry. 7 ( ... Carboxypeptidase A1 is an enzyme that in humans is encoded by the CPA1 gene. Three different forms of human pancreatic ... 1986). "Assignment of the gene for carboxypeptidase A to human chromosome 7q22----qter and to mouse chromosome 6". Hum. Genet. ...
"Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter ... Gene expression is measured against defined standards both for the gene of interest and control genes. The measurement by qPCR ... a Bioconductor package for differential expression analysis of digital gene expression data". Bioinformatics. 26 (1): 139-40. ... The Cap Analysis of Gene Expression (CAGE) method is a variant of SAGE that sequences tags from the 5' end of an mRNA ...
Dansen TB, Kops GJ, Denis S, et al., Regulation of sterol carrier protein gene expression by the forkhead transcription factor ... Mungall AJ, Palmer SA, Sims SK, et al., The DNA sequence and analysis of human chromosome 6., in Nature, vol. 425, nº 6960, ... Entrez Gene: FOXO3A forkhead box O3A, su ncbi.nlm.nih.gov.. *^ Brunet A, Bonni A, Zigmond MJ, Lin MZ, Juo P, Hu LS, Anderson MJ ... Gene · Codice genetico · Allele · Locus · Ereditarietà · Diversità genetica · Mutazione. Campi della genetica. Genetica formale ...
Brain Gene Expression Analyses in Social Insects". Cold Spring Harbor Symposia on Quantitative Biology. 74: 419-426. doi: ... "Differential gene expression and protein abundance evince ontogenetic bias toward castes in a primitively eusocial wasp". PLOS ... the differential expression in Polistes of larval genes and proteins (also differentially expressed during queen versus caste ... After the gene-centered view of evolution was developed in the mid 1970s, non-reproductive individuals were seen as an extended ...
"Analysis of CD97 expression and manipulation: antibody treatment but not gene targeting curtails granulocyte migration". ... In pre-active lesion, increased expression of CD55 in endothelial cells and robust CD97 expression on infiltrating leukocytes ... Cluster of differentiation 97 is a protein also known as BL-Ac[F2] encoded by the ADGRE5 gene.[5][6][7][8] CD97 is a member of ... cytosolic β-catenin moves into the nucleus to facilitate expression of pro-oncogenic genes.[53][54] Because of its role in ...
Using the entire read may introduce artifacts in the downstream analyses like genome assembly, snp calling, or gene expression ... "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays". Nature Biotechnology. Nature ... In the case of MPSS, these were typically used for sequencing cDNA for measurements of gene expression levels.[39] ... The chemical synthesis and sequence analysis of a dodecadeoxynucleotide which binds to the endolysin gene of bacteriophage ...
"Genome-wide analysis of gene expression in neuroblastomas detected by mass screening". Cancer Lett. 225 (1): 111-20. doi: ... Using gene set enrichment analysis, 569 out of 938 gene sets were hypermethylated and 369 were hypomethylated in cancers.[22] ... This observation led to the speculation that methylation of CpG sites in the promoter of a gene may inhibit gene expression. ... of far more genes than does mutation.. DNA repair genes with hyper/hypo-methylated promoters in cancers[edit]. DNA repair genes ...
Thisse high-throughput gene expression analysis). Information in ZFIN is tightly linked to the web resources of the Zebrafish ... Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the ... The Zebrafish Database Project B. Thisse and C. Thisse (2004). "Fast release clones: a high throughput expression analysis". ... and clones Gene expression Antibodies Sequence alignments (BLAST) Mutants and transgenic lines Anatomy Genetic maps ZFIN also ...
Facilitating web-based gene-expression analysis. Plant Physiology 141(4):1164-6 Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W ... BMC Bioinformatics 7:311 Zimmermann P, Hennig L and W Gruissem (2005) Gene expression analysis and network discovery using ... Spatiotemporal gene expression Prasad A, Suresh Kumar S, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, and P Zimmermann ( ... find conditions that are relevant for your genes of interest GENE SEARCH tools: find genes that are specifically expressed in ...
... serial analysis of gene expression), a gene expression technology for the global and quantitative measurement of gene activity ... Serial analysis of gene expression [2]. Science. 1995 Oct 20;270(5235):484-7. PMID 7570003 Velculescu VE, Zhang L, Zhou W, ... provided some of the first insights into gene expression patterns in eukaryotic cells and the identification of gene expression ... These studies led Velculescu to coin the term transcriptome in a 1997 paper to describe the comprehensive gene expression ...
2006). "Expression, crystallization and preliminary X-ray crystallographic analysis of human agmatinase". Acta Crystallogr. ... Chen FW, Davies JP, Ioannou YA (1998). "Differential gene expression in apoptosis: identification of ribosomal protein 23K, a ... In humans, the enzyme is encoded by the AGMAT gene. As of late 2007, 5 structures have been solved for this class of enzymes, ... "Entrez Gene: AGMAT agmatine ureohydrolase (agmatinase)". Morris SM (2004). "Vertebrate agmatinases: what role do they play in ...
"Comparative sequence and expression analyses of four mammalian VPS4 genes". Gene. 305 (1): 47-59. doi:10.1016/S0378-1119(02) ... and functional expression of the Mus musculus SKD1 gene in yeast demonstrates that the mouse SKD1 and the yeast VPS4 genes are ... The gene encoding this paralog has been mapped to chromosome 16; the gene for the other resides on chromosome 18. VPS4A has ... "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning". Proc. Natl. Acad. Sci ...
1 May 1996). "Analysis of Hox gene expression in the chick limb bud". Development. 122 (5): 1449-66. ISSN 0950-1991. PMID ... This leads to activation of other genes such as Hox genes, FGF genes and BMP genes in the posterior region, setting up digit ... Three phases of activation of the Hox genes results in patterning of the limb parallel to the expression of the Hox genes in a ... Activation of these genes results in a new limb axis that ultimately results in digit development, possibly interpreting gene ...
基因劑量(Gene dosage)會對人類的表現型產生龐大的影響,對於染色體中造成疾病的複寫、省略與分裂等現象的形成擁有一定的角色。例如唐氏症患者(21號染色體為三體)有較高的比率得到阿茲海默症,可能是因為與阿茲海默症有關的類澱粉前趨蛋白基因(位在21號 ... 人類基因組含有許多不同的調控序列,
Weighted gene co-expression network analysis reveal gene clusters and pathways related to rumen development in calves. Do D.N ... Gene co-expression network analysis of transcriptome data has enabled the identification of key genes and important networks ... Weighted gene co-expression network analysis reveal gene clusters and pathways related to rumen development in calves. ... This study used weighted gene co-expression network analysis (WGCNA) approach to (1) detect modules or clusters of ...
Real time PCR analysis showed different expression pattern for catalase and metallothionein encoded genes. Catalase gene ... Metallothionein gene expression was linearly reduced during different levels of drought treatments especially in Zagros and ... In this research the gene expression pattern of Catalase and Metallothionein was studied in response to drought stress ... Whereas, Moghan cultivar showed most transcription for both genes at -8 bar treatment. Overall gene activities, content of ...
Therefore, tag-based gene expression profiling also called "digital gene expression profiling" (DGE) can today provide most ... Serial Analysis of Gene Expression (SAGE) is a transcriptomic technique used by molecular biologists to produce a snapshot of ... 1995). "Serial analysis of gene expression". Science. 270 (5235): 484-7. Bibcode:1995Sci...270..484V. doi:10.1126/science. ... "Gene expression analysis of plant host-pathogen interactions by SuperSAGE". Proceedings of the National Academy of Sciences. ...
Revisiting global gene expression analysis.. Lovén J1, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, ... Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological ... A) Schematic representation of pattern of change in gene expression when levels of total RNA in the two cells is similar. The ... The data represent fold-change of expression in high-Myc vs. low-Myc cells. Each line represents data for an individual gene. ...
... * Biostatistics & Computational Biology * Phase-shifted Analysis of Gene ... Phase-shifted Analysis of Gene Expression (PAGE). Overview. PAGE is a Java-based software for phase-shifted analysis of gene ... Phase 1: Gene expression pattern matrix transformation into -1,0,1 to indicate the direction of expression change from each ... to analyze gene expression from multiple biological conditions across dose and time series experiments. Grouping of gene ...
Dongen S.., Enright A.J. (2014) Detecting MicroRNA Signatures Using Gene Expression Analysis. In: Kasabov N. (eds) Springer ... Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. ... In cases where gene or protein expression data are available, it is possible to detect the signature of miRNA binding events by ... Gene Ontology Gene List miRNA Target Seed Region Hypergeometric Distribution These keywords were added by machine and not by ...
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... the technology and discuss how ddPCR assays can complement existing techniques in gene expression studies and microRNA analysis ... Droplet Digital™ PCR for Gene Copy Number Variation - Duration: 50:53. Bio-Rad Laboratories 5,642 views ...
Genome-wide analysis of gene expression. Definition. Genome-wide analysis of gene expression is the study of transcription at a ... Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture *Yan ... Comparative clinical and genomic analysis of neurofibromatosis type 2-associated cranial and spinal meningiomas *Alexander ... Typically relying on data from microarrays or high throughput sequencing, it can determine what genes or transcript isoforms ...
Gene Expression. This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are ... It gave me ather different results from what I got from Zacks analysis. For example, on HAP South Asian + Onge was 42%, while ... Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs ... DIY admixture analysis. By Razib Khan , July 27, 2011 11:24 am ... Narrow Roads of Gene Land 3. *Natural Selection and Social ...
An analysis of post-mortem brain transcripts led to Alzheimers-related alternative gene splicing and expression events, ... Science Finds Sex-Biased Gene Expression in Mammals, More. In Science this week: comparative analysis of sex differences in ... Transcriptome Analyses Link Alzheimers Disease With Brain Gene Splicing, Expression. Oct 08, 2018 ... Gene Variants Possible Role. An Australian mothers conviction in the deaths of her children may be re-examined after finding ...
Analysis of meniscal degeneration and meniscal gene expression.. Sun Y1, Mauerhan DR, Honeycutt PR, Kneisl JS, Norton JH, ... Investigation of the gene expression profiles of OA meniscal cells may reveal new therapeutic targets for OA therapy and also ... Differential gene expression in OA meniscal cells and normal meniscal cells was examined using Affymetrix microarray and real ... This study sought: 1) to determine the prevalence of meniscal degeneration in OA patients, and 2) to examine gene expression in ...
Open Access journal that publishes research articles as well as review articles in all areas of genome-scale analysis. Topics ... Global Analysis of Cell Type-Specific Gene Expression. David W. Galbraith University of Arizona, Department of Plant Sciences, ... David W. Galbraith, "Global Analysis of Cell Type-Specific Gene Expression," Comparative and Functional Genomics, vol. 4, no. 2 ...
When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or ... Gene Expression Analysis I. When and where genes are expressed (active) in tissues or cells is one of the main determinants of ... Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction ... Several different methods exist for generating gene expression levels for all of the genes in the genome in tissues or even at ...
When and where genes are expressed (active) in tissues or cells is one of the main determinants of what makes that tissue or ... Gene Expression Analysis II. When and where genes are expressed (active) in tissues or cells is one of the main determinants of ... Now, in todays lab were exploring gene expression data in a manner where we can leverage large data sets of gene expression ... is we can do a co-expression analysis and ask what are the genes that show similar patterns of expression in these large data ...
... Mones Abu-Asab,1 Ming Zhang,2 Dennis ... "Endometriosis Gene Expression Heterogeneity and Biosignature: A Phylogenetic Analysis," Obstetrics and Gynecology International ...
New developments in the high-throughput methods for gene expression analysis bring new challenges in data analysis and ... Computational-biology] Bioinformatics for gene expression analysis. Heather Vincent via comp-bio%40net.bio.net (by Heather. ... Moving beyond the pre-processing steps, biological understanding requires the integration of expression data with other types ... and will also be introduced to the most recent methods for transcriptome analysis. For those interested in learning about data ...
... such that the bottleneck in research is shifting from data generation to data analysis. Hierarchical clustering, divisive ... Analysis of large-scale gene expression data Curr Opin Immunol. 2000 Apr;12(2):201-5. doi: 10.1016/s0952-7915(99)00074-6. ... such that the bottleneck in research is shifting from data generation to data analysis. Hierarchical clustering, divisive ...
... howard judelson judelson at ucrac1.ucr.edu Sat Aug 8 17:07:31 ... expression analysis, and gene characterization; experience in such areas would be a plus but is not required. Riverside is ... These include the positional cloning of fungicide resistance genes, the characterization of genes involved in sexual ... development and sporulation, and comparative studies of the structure and expression of mating type loci throughout the genus. ...
... coupled with data analysis using sophisticated statistical algorithms, have provided new insights into pathogenic mechanisms of ... Recent advances in the study of global patterns of gene expression with the use of microarray technology, ... Microarray analysis of gene expression in lupus Arthritis Res Ther. 2003;5(6):279-87. doi: 10.1186/ar1015. Epub 2003 Oct 13. ... Although some patterns of gene expression, including increased expression of immune system cell surface activation molecules, ...
Microarray gene expression analysis is high-throughput method in which many different sized DNA molecules are attached to solid ... Oligonucleotide array sequence analysis - methods, instrumentation; Gene expression profiling; Genome; Gene expression ... annotation analysis as well as network and pathway analysis. Expression comparison of all genes in different cells of the same ... Microarray gene expression analysis is high-throughput method in which many different sized DNA molecules are attached to solid ...
A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Steven Vandenabeele, Katrien Van Der Kelen, ... A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Steven Vandenabeele, Katrien Van Der Kelen, ... A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco Message Subject (Your Name) has sent you a ... A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Steven Vandenabeele, Katrien Van Der Kelen, ...
Scientists have rendered the first gene and protein networks of human aging, an important step in understanding the genetic ... In the first comprehensive survey of gene activity in each cell type composing normal and malignant breast tissue, scientists ... at Dana-Farber Cancer Institute have identified genes in non-cancerous supporting cells that can spur the growth of breast ...
Education: Bioinformatics for gene expression analysis. Submitted by Heather Vincent; posted on Tuesday, February 22, 2011 ... The University of Manchesters distance course in microarray data analysis (octette.cs.man.ac.uk/bioi[...].html), which runs ... New developments in the high-throughput methods bring new challenges in data analysis and management. Error models for ... Moving beyond the pre-processing steps, biological understanding requires the integration of expression data with other types ...
Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles ... The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously ... 2002). Gene expression analysis reveals chemical-specific profiles. Toxicological Sciences, 67(2), 219-231. ... Patterns of gene expression corresponding to liver tissue derived from chemically exposed rats revealed similarity in gene ...
  • A new study discovered thousands of expression quantitative trait loci (eQTLs) in the renal glomerular and tubulointerstitial compartments and integrated these data with other omics data sets to identify genes with roles in the pathogenesis of chronic kidney disease. (nature.com)
  • INPROCEEDINGS{Livak01analysisof, author = {Kenneth J. Livak and Thomas D. Schmittgen}, title = {Analysis of relative gene expression data using real-time quantitative}, booktitle = {PCR and 2 ���CT method. (psu.edu)
  • In addition, we present the derivation and applications of two variations of the 2 ���CT method that may be script copy number and reporting the relative change useful in the analysis of real-time, quantitative PCR data. (psu.edu)
  • Quantitative analysis identified a multitude of regulated gene messages, including several genes involved in extracellular matrix degradation and lipid/steroid metabolism previously reported to be induced by hCG. (bioone.org)
  • Furthermore, a quantitative analysis showed that the inhibitory profiles of both U0126 and wortmannin are constitutive components of the transcriptome profile obtained by inhibition of the EGFR kinase. (riken.jp)
  • Quantitative transcriptome analysis is potentially widely applicable to determine the target proteins and action mechanisms of uncharacterized compounds," concludes Dr Suzuki. (riken.jp)
  • Our study paves the way for quantitative analysis of drug responses at the promoter level, and moreover, is potentially applicable for the evaluation of combinatorial or serial drug treatment in a clinical setting," he adds. (riken.jp)
  • The method of choice for verifying differential RNA expression is real-time PCR (i.e. quantitative reverse transcriptase PCR) via Taqman method or SyberGreen method. (studentdoctor.net)
  • Bao L, Sun Z (2002) Identifying genes related to drug anticancer mechanisms using support vector machine. (springer.com)
  • 2002), we construct a gene interaction network and search for high-scoring subnetworks. (sciweavers.org)
  • This model can be used to study the relationship between the time to event and a set of covariates (gene expressions) in the presence of censoring (Park and Kohane 2002). (oreilly.com)
  • Two novel genes have also been mapped onto our target chromosome 2 within the congenic interval by radiation hybrid (RH) mapping. (bl.uk)
  • To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites, and a genome-wide analysis of transcription. (asm.org)
  • As Wright several times emphasised, it does not provide a method of discovering or proving causal relationships, but if these are known or hypothesised to exist on other grounds, Path Analysis can (in principle) help quantify their relative importance. (gnxp.com)
  • Researchers from the RIKEN Center for Life Science Technologies report a new method to monitor and quantify the activity of gene promoters during the response to a drug, using the advanced gene expression analysis method CAGE followed by single-molecule sequencing. (riken.jp)
  • We present a few example applications of the technology and discuss how ddPCR assays can complement existing techniques in gene expression studies and microRNA analysis. (youtube.com)
  • QuantiGene™ RNA assays are 96- and 384- well, hybridization-based assays that utilize a branched DNA technology for signal amplification for the direct quantitation of gene expression. (thermofisher.com)
  • Applied Biosystems TaqMan Gene Expression Assays consist of a pair of unlabeled PCR primers and a TaqMan probe with an Applied Biosystems FAM or VIC dye label on the 5' end and minor groove binder (MGB) and nonfluorescent quencher (NFQ) on the 3' end. (thermofisher.com)
  • Over 1.8 million predesigned TaqMan Gene Expression Assays covering more than 30 species are available in a single-tube, 96-well plate, 384-well microfluidic card, and Applied Biosystems OpenArray formats. (thermofisher.com)
  • TaqMan Gene Expression Assays are available in easy-to-use 96-well plates and higher-throughput 384-well microfluidic cards. (thermofisher.com)
  • These results were confirmed by (i) phenotypic analyses, (ii) real-time PCR studies, (iii) reporter gene fusion assays, and (iv) previously published reports about representative genes. (asm.org)
  • While few differences were observed in the expression profiles of genes in the 1-carbon cycle, genes previously considered to be overexpressed in EOC (e.g. (mdpi.com)
  • These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. (arxiv.org)
  • The quality control stage ( QC stage ) allows to correct the complicated artificial influence on the experiment result and to determine clusters of genes that should be excluded from the biological analysis due to the artificial nature of these clusters. (msu.su)