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.Oligonucleotide 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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.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)DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.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.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.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.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).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.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.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.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)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.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).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.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.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.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)Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression Regulation: 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.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.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)RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Glass: Hard, amorphous, brittle, inorganic, usually transparent, polymerous silicate of basic oxides, usually potassium or sodium. It is used in the form of hard sheets, vessels, tubing, fibers, ceramics, beads, etc.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.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.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.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.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.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.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.Genetic Variation: Genotypic differences observed among individuals in a population.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.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Software: Sequential operating programs and data which instruct the functioning of a digital computer.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.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.RNA, Neoplasm: RNA present in neoplastic tissue.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.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.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.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Cell Line: Established cell cultures that have the potential to propagate indefinitely.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Quality Control: A system for verifying and maintaining a desired level of quality in a product or process by careful planning, use of proper equipment, continued inspection, and corrective action as required. (Random House Unabridged Dictionary, 2d ed)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.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Cell Line, Tumor: A cell line derived from cultured tumor cells.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.Bacterial Proteins: Proteins found in any species of bacterium.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.DNA, Neoplasm: DNA present in neoplastic tissue.Phosphorothioate Oligonucleotides: Modified oligonucleotides in which one of the oxygens of the phosphate group is replaced with a sulfur atom.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Oligodeoxyribonucleotides, Antisense: Short fragments of DNA that are used to alter the function of target RNAs or DNAs to which they hybridize.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.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.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.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.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.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.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA 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.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Thionucleotides: Nucleotides in which the base moiety is substituted with one or more sulfur atoms.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.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.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Oligoribonucleotides, Antisense: Short fragments of RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Mice, Inbred C57BLMolecular Weight: The sum of the weight of all the atoms in a molecule.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.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Genes, Viral: The functional hereditary units of VIRUSES.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Kinetics: The rate dynamics in chemical or physical systems.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Molecular Probe Techniques: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.

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... to Arrays of Oligonucleotides: Evaluation of Sequence Analysis, In Genome Mapping and Sequencing (Abstracts of papers presented ... Oligonucleotide Arrays [0045]As used herein an "oligonucleotide array" is an array of regularly situated areas on a solid ... binary array, as is described below. V. Use of the Oligonucleotide Arrays for the Sequencing of Nucleic Acids [0128]The arrays ... within the array. As with sorting arrays, an "address" in a partialing array is the oligonucleotide sequence that is present at ...

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... nucleic acid sequences shown in Tables 34, 36, or 38, and wherein the array comprises 10 or more of said oligonucleotides; or b ... Results of analyses to identify equine 3' sequences for use in a gene expression microarray Sequence Number Equine sequences ... equine coding sequences Sequence Number Equine sequences 18,924 Equine coding sequences 981 Equine coding sequences, mRNA 436 ... Longer sequences can be obtained by sequence assembly. For long sequences, the whole sequence is fragmented and each fragment ...

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Geriatric Assessment; Gene Expression; Aging; Lung; Oligonucleotide Array Sequence Analysis Academic: 336-716-4564. Department: ...

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Oligonucleotide Array Sequence Analysis; Proto-Oncogene Protein c-fli-1/genetics; Proto-Oncogene Protein c-fli-1/metabolism; ...

*  Books - Medicine - Terkko Navigator

Cancer cells, DNA microarrays, Data Interpretation, Statistical, Neoplasms, Oligonucleotide Array Sequence Analysis, Research, ... DNA microarray technology and data analysis in cancer research. ...

*  Microarray analysis reveals a mechanism of phenolic polybrominated diphenylether toxicity in zebrafish.

Animals, Ethers, Oligonucleotide Array Sequence Analysis, Polybrominated Biphenyls/*toxicity, Zebrafish Identifiers. URN: urn: ... Microarray analysis reveals a mechanism of phenolic polybrominated diphenylether toxicity in zebrafish.. van Boxtel, Antonius L ... To identify possible mechanisms of toxicity, we used microarray analysis as a diagnostic tool. Zebrafish embryonic fibroblast ( ...

*  Schematic of the DEMON's algorithm work flow.a. Retriev | Open-i

Oligonucleotide Array Sequence Analysis. *Protein Binding. *RNA, Messenger/metabolism. *Reverse Transcriptase Polymerase Chain ... b. For each HMM-promoter pair a score is computed as the ratio between the probability to emit the promoter sequence using the ... b. For each HMM-promoter pair a score is computed as the ratio between the probability to emit the promoter sequence using the ... Methodology: DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all ...

*  TRIM22 interacts with Gag.HOS-CD4/CXCR4 cells were co-t | Open-i

Oligonucleotide Array Sequence Analysis. *RNA, Small Interfering/genetics. *Transfection. *Up-Regulation. *Virus Replication/ ... Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 ... Mutational analyses of TRIM22 showed that the catalytic amino acids Cys15 and Cys18 of the RING domain are required for TRIM22 ...

*  Perp-deficiency promotes tumorigenesis.A) Perp immunofl | Open-i

Oligonucleotide Array Sequence Analysis. *Phosphoproteins/genetics. *Skin/immunology/pathology/radiation effects. *Tissue Array ... Analysis of Perp-deficient mice in a UVB-induced squamous cell skin carcinoma model reveals that Perp ablation promotes both ... C) Kaplan-Meier analysis showing tumor latency in UVB-treated control (Perpfl/fl and Perpfl/+) and K14CreER;Perpfl/fl mice. ... C) Kaplan-Meier analysis showing tumor latency in UVB-treated control (Perpfl/fl and Perpfl/+) and K14CreER;Perpfl/fl mice. ...

*  Synthetic data: evaluation of the size and ratio of con | Open-i

Oligonucleotide Array Sequence Analysis. *RNA/analysis. *RNA, Neoplasm. Related in: MedlinePlus. © Copyright Policy - open- ... Bottom Line: Cross-patient N-of-1-pathways obtains comparable results with conventional genesets enrichment analysis (GSEA) and ... Bottom Line: Cross-patient N-of-1-pathways obtains comparable results with conventional genesets enrichment analysis (GSEA) and ... we applied the N-of-1-pathways statistical analysis component 1000 times in order to estimate the false negative rate (type II ...

*  Families of PhoP BSs submotifs in E. coli K-12 and S. t | Open-i

Molecular Sequence Data. *Nucleic Acid Conformation. *Oligonucleotide Array Sequence Analysis. *Pattern Recognition, Automated ... Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic ... Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic ... and both sequences belong to the same submotif (Figure 3). In contrast, the PhoP BS sequences in the promoters of the E. coli ...

*  Alzheimer's disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signalling

Oligonucleotide Array Sequence Analysis, RNA; Messenger/analysis, Reverse Transcriptase Polymerase Chain Reaction National ... This high-resolution analysis accounted for systematic differences in age, postmortem interval, brain pH, and reference gene ... Our global analysis involved microarray hybridizations of large pools of samples obtained from 114 individuals, using two ... and later employed to verify gene expression differences detected by cDNA microarray analysis. Of several genes verified as ...

*  Patent US6315958 - Flow cell for synthesis of arrays of DNA probes and the like - Google Patents

"Light-Generated Oligonucleotide Arrays for Rapid DNA Sequence Analysis," Proc. Natl. Acad. Sci. USA, Vol. 91, pp. 5022-5026, ... arrays of oligonucleotide probes using such photolithographic techniques wherein the sequence of the oligonucleotide probe at ... This invention pertains generally to the field of biology and particularly to apparatus for use in the analysis and sequencing ... An improved process for synthesizing arrays of DNA probe sequences, polypeptides, and the like, rapidly and efficiently by a ...

*  Patent US6207960 - System and methods for detection of labeled materials - Google Patents

Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. ... Pease et al., "Light-generated oligonucleotide arrays for rapid DNA sequence analysis," Proc. Natl. Acad. Sci, USA, vol. 91, pp ... the arrays for use with the present invention are described in terms of arrays of different oligonucleotide sequences. However ... For example, an array of oligonucleotides containing all possible sequences of length n which is made up of the basis set of ...

*  Patente US6428752 - Cleaning deposit devices that form microarrays and the like - Google Patentes

A mobile-fluid storage device resupplies the deposit device along the array, e.g. in the immediate vicinity of the deposit ... for microscopic analysis, a deposit device, e.g. a pin, cooperating with a fluid source defines a precisely sized drop of fluid ... By repeated action, minute drops of fluid can be deposited precisely in a dense array, preferably under computer control. ... For depositing fluid dots in an array, e.g., ... oligonucleotide arrays for rapid DNA sequence analysis"; Proc. ...

*  Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. - PubMed -...

Oligonucleotide Array Sequence Analysis. *RNA Polymerase II/metabolism. Substances. *Abd-B proteins, Drosophila ... The vertical lines underneath the Sg4 Nipped-B, SA, and Smc1 tracks indicate microarray features predicted by TiMAT analysis to ... and promoter-targeting sequences (PTS, cyan vertical bars) with Nipped-B and PolII binding overlaid on each other illustrates ... The plots show that many sequences are enriched by both Nipped-B and PolII immunoprecipitation, but there is less direct ...

*  GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis. -...

Our analysis revealed that GLI3 directly restricts the expression of regulators of the G(1)-S cell-cycle transition such as ... The analysis of mouse embryos constitutively lacking Gli3 has revealed the essential GLI3 functions in specifying the ... Oligonucleotide Array Sequence Analysis, Polydactyly, RNA, Messenger, Real-Time Polymerase Chain Reaction, S Phase, Stem Cells ... Our analysis revealed that GLI3 directly restricts the expression of regulators of the G(1)-S cell-cycle transition such as ...

*  Flux of transcript patterns during soybean seed development. - PubMed - NCBI

Oligonucleotide Array Sequence Analysis. *Seed Storage Proteins/genetics. *Seeds/genetics. *Seeds/growth & development* ... Diamonds (connected by lines) indicate the ratio according to Array Format 1. Squares indicate the ratio according to Array ... Diamonds (connected by lines) indicate the ratio according to Array Format 1. Squares indicate the ratio according to Array ... Yellow bars represent fold change in Array Format 1; blue bars represent fold change in Array Format 2. Fold changes are based ...

*  Links tagged with <em>'drosophila</em>' | Links tagged with 'drosophila' | Bioinformatics.ca...

oligonucleotide array sequence analysis physical chromosome mapping protein databases research design software design software ... conserved sequence database management systems dna sequence analysis drosophila drosophila proteins expressed sequence tags ... amino acid sequence animals base composition base sequence cluster analysis complementary dna computational biology computer- ... conserved sequence contig mapping database management systems developmental gene expression regulation dna sequence analysis ...

*  Patent US5856174 - Integrated nucleic acid diagnostic device - Google Patents

... sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and ... most notably, nucleic acid based diagnostic applications and de novo sequencing applications. ... in combination with one or more sample analysis operations. For example, the device can integrate several or all of the ... sequence based analyses using an oligonucleotide array and/or size based analyses using, e.g., microcapillary array ...

*  Head and neck tumor sites differ in prevalence and spectrum of p53 alterations but these have limited prognostic value - Bosch ...

Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array. Proc Natl Acad Sci USA 1999; 96: 7382- ... Comparison of TP53 mutations identified by oligonucleotide microarray and conventional DNA sequence analysis. Cancer Res 2000; ... Sequencing analysis of RNA and DNA of exons 1 through 11 shows p53 gene alterations to be present in almost 100% of head and ... Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples. Clin ...

*  Estimating genomic coexpression networks using first-order conditional independence. | Scholars@Duke

Oligonucleotide Array Sequence Analysis * Saccharomyces cerevisiae *About. *Support. *Index. *Manage Scholars Data ...

*  Differential cardiac gene expression during cardiopulmonary bypass: ischemia-independent upregulation of proinflammatory genes....

Oligonucleotide Array Sequence Analysis * Rats * Up-Regulation *About. *Support. *Index. *Manage Scholars Data ... Distinct proinflammatory gene cascades were confirmed by means of category overrepresentation analysis. CONCLUSIONS: This study ... randomized to either 90 minutes of cardiopulmonary bypass or sham control animals were used to perform cDNA microarray analyses ...

Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.Allele-specific oligonucleotide: An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Abscription: During normal transcription, RNA polymerase transcribes a number of short nonproductive oligonucleotides, and this process is called abortive transcription. The trapped RNAPs have been named abscriptases and the synthesis of specific length oligonucleotides called abscription.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Coles PhillipsThermal cyclerProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.Community Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.Copy number analysis: Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patient's sample. Such analysis helps detect chromosomal copy number variation that may cause or may increase risks of various critical disorders.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Assay sensitivity: Assay sensitivity is a property of a clinical trial defined as the ability of a trial to distinguish an effective treatment from a less effective or ineffective intervention. Without assay sensitivity, a trial is not internally valid and is not capable of comparing the efficacy of two interventions.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Antisense therapy: Antisense therapy is a form of treatment for genetic disorders or infections. When the genetic sequence of a particular gene is known to be causative of a particular disease, it is possible to synthesize a strand of nucleic acid (DNA, RNA or a chemical analogue) that will bind to the messenger RNA (mRNA) produced by that gene and inactivate it, effectively turning that gene "off".YjdF RNA motifEukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Chromosome regionsBorosilicate glass: Borosilicate glass is a type of glass with silica and boron trioxide as the main glass-forming constituents. Borosilicate glasses are known for having very low coefficients of thermal expansion (~3 × 10−6 /°C at 20 °C), making them resistant to thermal shock, more so than any other common glass.Fixative (drawing): In drawing, a fixative is a liquid, similar to varnish, which is usually sprayed over a finished piece of artwork, usually a dry media artwork, to better preserve it and prevent smudging.CpG OligodeoxynucleotideAlternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Genetic variation: right|thumbWGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Mac OS X Server 1.0Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Polymerase-endonuclease amplification reaction: Polymerase-endonuclease amplification reaction (PEAR) is a DNA amplification technology for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides.Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Pituitary-specific positive transcription factor 1: POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1), also known as POU1F1, is a transcription factor for growth hormone.Inverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.Genetic imbalance: Genetic imbalance is to describe situation when the genome of a cell or organism has more copies of some genes than other genes due to chromosomal rearrangements or aneuploidy.CS-BLASTInfinite alleles model: The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and American geneticist James F.DNA-binding proteinCertified reference materials: Certified Reference Materials (CRMs) are ‘controls’ or standards used to check the quality and metrological traceability of products, to validate analytical measurement methods, or for the calibration of instruments.Deletion (genetics)Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.GC box: In molecular biology, a GC box is a distinct pattern of nucleotides found in the promoter region of some eukaryotic genes upstream of the TATA box and approximately 110 bases upstream from the transcription initiation site. It has a consensus sequence GGGCGG which is position dependent and orientation independent.List of sequenced eukaryotic genomesExtracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Analytical quality control: Analytical quality control, commonly shortened to AQC refers to all those processes and procedures designed to ensure that the results of laboratory analysis are consistent, comparable, accurate and within specified limits of precision.analytical quality control (AQC) program to ensure the highest level of confidence in reported data Constituents submitted to the analytical laboratory must be accurately described to avoid faulty interpretations, approximations, or incorrect results.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Gene duplication: Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Gene polymorphismTriparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Open reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).

(1/28523) A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays.

Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization.  (+info)

(2/28523) Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents.

The effect of alkyltrimethylammonium ions on the thermostability of natural and modified DNA duplexes has been investigated. We have shown that the use of tetramethylammonium ions TMA+along with the chemical modification of duplexes allow the fine adjustment of T m and the possibility of obtaining several duplex systems with varied isostabilizedtemperatures, some of which show greater stability than those of natural DNA. This approach could be very useful for DNA sequencing by hybridization.  (+info)

(3/28523) Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.  (+info)

(4/28523) Identification of the genes responsive to etoposide-induced apoptosis: application of DNA chip technology.

DNA chip technology was used in an attempt to identify target genes responsible for apoptosis induced by etoposide, a p53 activating topoisomerase II inhibitor used clinically as an antitumor agent. 62 Individual mRNAs whose mass changed significantly were identified after screening oligonucleotide arrays capable of detecting 6591 unique human mRNA species. 12 (Nine induced and three repressed) of the etoposide-responsive genes were further studied by Northern analysis and an agreement rate of 92%, was reached. Among the 12 genes studied, two (WAF1/p21 and PCNA) are known p53 regulatory genes, two (glutathione peroxidase and S100A2 calcium-binding protein) appear to be the novel p53 target genes and the others appear to be p53-independent. Based upon these findings, the signalling pathways that possibly mediate etoposide-induced apoptosis are proposed.  (+info)

(5/28523) Development of an oligonucleotide-specific capture plate hybridization assay for detection of Haemophilus parasuis.

An oligonucleotide-specific capture plate hybridization assay has been developed to rapidly, specifically, and sensitively detect Haemophilus parasuis from nasal swabs. Several in vitro studies have been performed to determine the sensitivity and specificity of the test, and in vivo studies have validated this technique in pigs. Results suggest that the assay detects <100 colony-forming units/ml in a pure culture and gives a positive result when H. parasuis is present in a ratio of 1:10(3)-10(4) in a mixed culture, and the probe does not hybridize with other related species found in the upper respiratory tract. This assay is more sensitive than culture for detection of the microorganism from nasal swabs and lesions.  (+info)

(6/28523) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips.

A chemistry was developed that permits on DNA-arrays both the covalent immobilisation of pre-fabricated nucleic acids-such as oligonucleotides, PCR-products or peptide nucleic acid oligomers-and the in situ synthesis of such compounds on either glass or polypropylene surfaces. Bonding was found to be stable even after some 30 cycles of stripping. Due to a dendrimeric structure of the linker molecule, the loading can be modified in a controlled manner and increased beyond the capacity of glass without negative effects on hybridisation efficiency. Also, the chemistry warrants the modulation of other surface properties such as charge or hydrophobicity. Preferentially, attachment of nucleic acids takes place only via the terminal amino-group of amino-modified oligonucleotides or the terminal hydroxyl-group of unmodified molecules so that the entire molecule is accessible to probe hybridisation. This derivatisation represents a support chemistry versatile enough to serve nearly all current forms of DNA-arrays or microchips.  (+info)

(7/28523) Timely toxicology.

The ToxChip, a DNA microarray chip, allows the monitoring of the expression levels of thousands of different genes at a time, thereby condensing months of painstaking laboratory tasks into a day's work. For toxicology researchers in particular, this tool is important because it promises a more effective way to identify environmental hazards and their effects on DNA. The ToxChip, developed by NIEHS scientists J. Carl Barrett, Cynthia Afshari, and Emile F. Nuwaysir, could transform the way toxicologists approach environmental problems.  (+info)

(8/28523) DNA microarray technology: the anticipated impact on the study of human disease.

One can imagine that, one day, there will be a general requirement that relevant array data be deposited, at the time of publication of manuscripts in which they are described, into a single site made available for the storage and analysis of array data (modeled after the GenBank submission requirements for DNA sequence information). With this system in place, one can anticipate a time when data from thousands of gene expression experiments will be available for meta-analysis, which has the potential to balance out artifacts from many individual studies, thus leading to more robust results and subtle conclusions. This will require that data adhere to some type of uniform structure and format that would ideally be independent of the particular expression technology used to generate it. The pros and cons of various publication modalities for these large electronic data sets have been discussed elsewhere [12], but, practical difficulties aside, general depositing must occur for this technology to reach the broadest range of investigators. Finally, as mentioned at the beginning of this review, it is unfortunate that this important research tool remains largely restricted to a few laboratories that have developed expertise in this area and to a growing number of commercial interests. Ultimately the real value of microarray technology will only be realized when this approach is generally available. It is hoped that issues including platforms, instrumentation, clone availability, and patents [20] will be resolved shortly, making this technology accessible to the broadest range of scientists at the earliest possible moment.  (+info)



microarray

  • Microarray analysis reveals a mechanism of phenolic polybrominated diphenylether toxicity in zebrafish. (diva-portal.org)
  • To identify possible mechanisms of toxicity, we used microarray analysis as a diagnostic tool. (diva-portal.org)
  • By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. (nih.gov)
  • Our global analysis involved microarray hybridizations of large pools of samples obtained from 114 individuals, using two independent sets of microarrays. (diva-portal.org)
  • This approach was first used to investigate levels of expression of a candidate gene (MAO), and later employed to verify gene expression differences detected by cDNA microarray analysis. (diva-portal.org)
  • A subset of these genes on a highly-repetitive 70-mer oligonucleotide microarray was also used to support the results. (nih.gov)

Mice

  • Analysis of Perp-deficient mice in a UVB-induced squamous cell skin carcinoma model reveals that Perp ablation promotes both tumor initiation and progression. (nih.gov)
  • C) Kaplan-Meier analysis showing tumor latency in UVB-treated control (Perpfl/fl and Perpfl/+) and K14CreER;Perpfl/fl mice. (nih.gov)

genomic

  • Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. (nih.gov)
  • Sequences conforming to each specific submotifs (gray boxes) and their genomic source are listed on the right panel. (nih.gov)
  • Search query "genomic sequences" dna will search for links containing the phrase " genomic sequences " and dna . (bioinformatics.ca)

motifs

  • DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. (nih.gov)
  • Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs) using a machine learning method inspired by the "Divide & Conquer" strategy. (nih.gov)
  • Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. (bioinformatics.ca)

Genome

  • The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies. (bioinformatics.ca)

genes

  • Synthetic data: evaluation of the size and ratio of concordant deregulated genes within a pathway required to be found deregulated in the N-of-1-pathways statistical analysis component. (nih.gov)
  • As a result, we collected 69 DNA sequences corresponding to PhoP BSs, where 31 are BSs from 25 E. coli genes and 38 are BSs from 28 Salmonella genes. (nih.gov)

differences

  • The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. (nih.gov)
  • This high-resolution analysis accounted for systematic differences in age, postmortem interval, brain pH, and reference gene expression, and it estimated the effect of disease on mRNA levels, on top of the effect of all other variables. (diva-portal.org)

diagnostic

  • The device is useful in a variety of applications, and most notably, nucleic acid based diagnostic applications and de novo sequencing applications. (google.com.au)

Transcription Factors

  • Y-axis shows fold change, X-axis shows nineteen transcription factors found to increase in expression at the dry seed stage using Array Format 1. (nih.gov)

binding site

  • Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. (nih.gov)
  • Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. (bioinformatics.ca)

support

  • Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. Pat. (google.com)

component

  • We then applied the N-of-1-pathways statistical analysis component to verify if the simulated pathway was found deregulated with a significance threshold (type I error) chosen as an unadjusted p value of ≤0.05. (nih.gov)
  • For each pair (n, r), we applied the N-of-1-pathways statistical analysis component 1000 times in order to estimate the false negative rate (type II error β). (nih.gov)

sites

  • Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria. (nih.gov)

storage

  • A mobile-fluid storage device resupplies the deposit device along the array, e.g. in the immediate vicinity of the deposit locations. (google.es)
  • For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. (google.com.au)

device

  • For depositing fluid dots in an array, e.g., for microscopic analysis, a deposit device, e.g. a pin, cooperating with a fluid source defines a precisely sized drop of fluid of small diameter on a drop carrying surface. (google.es)
  • The device of the invention is generally capable of performing one or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. (google.com.au)