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.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.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.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Systems Biology: Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.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.Sea Urchins: Somewhat flattened, globular echinoderms, having thin, brittle shells of calcareous plates. They are useful models for studying FERTILIZATION and EMBRYO DEVELOPMENT.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.Strongylocentrotus purpuratus: A species of SEA URCHINS in the family Strongylocentrotidae found on the Pacific coastline from Alaska to Mexico. This species serves as a major research model for molecular developmental biology and other fields.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.Neural Networks (Computer): A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Echinodermata: A phylum of the most familiar marine invertebrates. Its class Stelleroidea contains two subclasses, the Asteroidea (the STARFISH or sea stars) and the Ophiuroidea (the brittle stars, also called basket stars and serpent stars). There are 1500 described species of STARFISH found throughout the world. The second class, Echinoidea, contains about 950 species of SEA URCHINS, heart urchins, and sand dollars. A third class, Holothuroidea, comprises about 900 echinoderms known as SEA CUCUMBERS. Echinoderms are used extensively in biological research. (From Barnes, Invertebrate Zoology, 5th ed, pp773-826)Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Stochastic Processes: Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Cell Physiological Phenomena: Cellular processes, properties, and characteristics.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Endoderm: The inner of the three germ layers of an embryo.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.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.Feedback, Physiological: A mechanism of communication with a physiological system for homeostasis, adaptation, etc. Physiological feedback is mediated through extensive feedback mechanisms that use physiological cues as feedback loop signals to control other systems.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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).Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.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.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Proteome: The protein complement of an organism coded for by its genome.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.Body Patterning: The processes occurring in early development that direct morphogenesis. They specify the body plan ensuring that cells will proceed to differentiate, grow, and diversify in size and shape at the correct relative positions. Included are axial patterning, segmentation, compartment specification, limb position, organ boundary patterning, blood vessel patterning, etc.Mesoderm: The middle germ layer of an embryo derived from three paired mesenchymal aggregates along the neural tube.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Immune System Phenomena: The characteristic properties and processes involved in IMMUNITY and an organism's immune response.Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Ectoderm: The outer of the three germ layers of an embryo.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Gastrulation: A process of complicated morphogenetic cell movements that reorganizes a bilayer embryo into one with three GERM LAYERS and specific orientation (dorsal/ventral; anterior/posterior). Gastrulation describes the germ layer development of a non-mammalian BLASTULA or that of a mammalian BLASTOCYST.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Nonlinear Dynamics: The study of systems which respond disproportionately (nonlinearly) to initial conditions or perturbing stimuli. Nonlinear systems may exhibit "chaos" which is classically characterized as sensitive dependence on initial conditions. Chaotic systems, while distinguished from more ordered periodic systems, are not random. When their behavior over time is appropriately displayed (in "phase space"), constraints are evident which are described by "strange attractors". Phase space representations of chaotic systems, or strange attractors, usually reveal fractal (FRACTALS) self-similarity across time scales. Natural, including biological, systems often display nonlinear dynamics and chaos.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.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.Ciona intestinalis: The only species of a cosmopolitan ascidian.Position-Specific Scoring Matrices: Tabular numerical representations of sequence motifs displaying their variability as likelihood values for each possible residue at each position in a sequence. Position-specific scoring matrices (PSSMs) are calculated from position frequency matrices.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Skeleton: The rigid framework of connected bones that gives form to the body, protects and supports its soft organs and tissues, and provides attachments for MUSCLES.Blastula: An early non-mammalian embryo that follows the MORULA stage. A blastula resembles a hollow ball with the layer of cells surrounding a fluid-filled cavity (blastocele). The layer of cells is called BLASTODERM.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Starfish: Echinoderms having bodies of usually five radially disposed arms coalescing at the center.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.Regulon: In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Models, Theoretical: Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Work Simplification: The construction or arrangement of a task so that it may be done with the greatest possible efficiency.Lytechinus: A genus of SEA URCHINS in the family Toxopneustidae possessing trigeminate ambulacral plating.Genes, Plant: The functional hereditary units of PLANTS.Epistasis, Genetic: A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.Protein Interaction Maps: Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.Caenorhabditis elegans: A species of nematode that is widely used in biological, biochemical, and genetic studies.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Neural Crest: The two longitudinal ridges along the PRIMITIVE STREAK appearing near the end of GASTRULATION during development of nervous system (NEURULATION). The ridges are formed by folding of NEURAL PLATE. Between the ridges is a neural groove which deepens as the fold become elevated. When the folds meet at midline, the groove becomes a closed tube, the NEURAL TUBE.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Embryonic Development: Morphological and physiological development of EMBRYOS.Artificial Intelligence: Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.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.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.Data Mining: Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.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.SOXB1 Transcription Factors: A subclass of SOX transcription factors that are expressed in neuronal tissue where they may play a role in the regulation of CELL DIFFERENTIATION. Members of this subclass are generally considered to be transcriptional activators.Uncertainty: The condition in which reasonable knowledge regarding risks, benefits, or the future is not available.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Bacterial Proteins: Proteins found in any species of bacterium.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Corynebacterium glutamicum: A species of gram-positive, asporogenous, non-pathogenic, soil bacteria that produces GLUTAMIC ACID.Wnt Signaling Pathway: A complex signaling pathway whose name is derived from the DROSOPHILA Wg gene, which when mutated results in the wingless phenotype, and the vertebrate INT gene, which is located near integration sites of MOUSE MAMMARY TUMOR VIRUS. The signaling pathway is initiated by the binding of WNT PROTEINS to cells surface WNT RECEPTORS which interact with the AXIN SIGNALING COMPLEX and an array of second messengers that influence the actions of BETA CATENIN.Flowers: The reproductive organs of plants.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.Nerve Net: A meshlike structure composed of interconnecting nerve cells that are separated at the synaptic junction or joined to one another by cytoplasmic processes. In invertebrates, for example, the nerve net allows nerve impulses to spread over a wide area of the net because synapses can pass information in any direction.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.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.Organogenesis: Formation of differentiated cells and complicated tissue organization to provide specialized functions.Genetic Engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.Morphogenesis: The development of anatomical structures to create the form of a single- or multi-cell organism. Morphogenesis provides form changes of a part, parts, or the whole organism.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.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Feedback: A mechanism of communication within a system in that the input signal generates an output response which returns to influence the continued activity or productivity of that system.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)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.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.Nodal Protein: The founding member of the nodal signaling ligand family of proteins. Nodal protein was originally discovered in the region of the mouse embryo primitive streak referred to as HENSEN'S NODE. It is expressed asymmetrically on the left side in chordates and plays a critical role in the genesis of left-right asymmetry during vertebrate development.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Genes, Insect: The functional hereditary units of INSECTS.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Octamer Transcription Factor-3: An octamer transcription factor that is expressed primarily in totipotent embryonic STEM CELLS and GERM CELLS and is down-regulated during CELL DIFFERENTIATION.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Biological Clocks: The physiological mechanisms that govern the rhythmic occurrence of certain biochemical, physiological, and behavioral phenomena.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.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)T-Box Domain Proteins: Proteins containing a region of conserved sequence, about 200 amino acids long, which encodes a particular sequence specific DNA binding domain (the T-box domain). These proteins are transcription factors that control developmental pathways. The prototype of this family is the mouse Brachyury (or T) gene product.Probability: The study of chance processes or the relative frequency characterizing a chance process.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.Pluripotent Stem Cells: Cells that can give rise to cells of the three different GERM LAYERS.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Caenorhabditis elegans Proteins: Proteins from the nematode species CAENORHABDITIS ELEGANS. The proteins from this species are the subject of scientific interest in the area of multicellular organism MORPHOGENESIS.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.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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Paired Box Transcription Factors: A family of transcription factors that control EMBRYONIC DEVELOPMENT within a variety of cell lineages. They are characterized by a highly conserved paired DNA-binding domain that was first identified in DROSOPHILA segmentation genes.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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.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.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.Adaptation, Biological: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Computer Communication Networks: A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)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).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.Animals, Genetically Modified: ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.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.Monte Carlo Method: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.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.Embryonic Induction: The complex processes of initiating CELL DIFFERENTIATION in the embryo. The precise regulation by cell interactions leads to diversity of cell types and specific pattern of organization (EMBRYOGENESIS).Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.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.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).Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Community Networks: Organizations and individuals cooperating together toward a common goal at the local or grassroots level.Escherichia coli K12: A species of gram-negative, rod-shaped bacteria belonging to the K serogroup of ESCHERICHIA COLI. It lives as a harmless inhabitant of the human LARGE INTESTINE and is widely used in medical and GENETIC RESEARCH.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.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 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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Yeasts: A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.Synthetic Biology: A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems.

*  Gene Regulatory Networks - Page 2 - Walhout Lab

Posted in Review , Tagged Caenorhabditis elegans, Gene Regulatory Networks, Metabolic Networks, Metabolism, microRNA, NHR, ... Posted in Publication , Tagged Caenorhabditis elegans, Diet, Gene Regulatory Networks, Metabolic Networks, Metabolism, ... Review: C. elegans metabolic gene regulatory networks govern the cellular economy Posted on May 1, 2014. by adminNovember 2, ... Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response Posted on April 22, 2014. by ...
walhoutlab.umassmed.edu/?tag=gene-regulatory-networks&paged=2

*  From Saccharomyces cerevisiae to human: The important gene co‑expression modules

Guelzim N, Bottani S, Bourgine P and Képès F: Topological and causal structure of the yeast transcriptional regulatory network ... Network‑based systems biology has become an important method for analyzing high‑throughput gene expression data and gene ... Weighted gene co-expression network construction and module detection. Signed network was constructed according to WGCNA ... In the current study, a weighted gene co‑expression network analysis algorithm was applied to construct a gene co‑expression ...
https://spandidos-publications.com/br/7/2/153

*  Evolution of a conserved gene regulatory network among echinoderms

Lastly, this investigation supports the idea of gene regulatory ne twork kernel is a class of gene regulatory network, which ... 2006) The regulatory ge nome. Gene regulatory networks in development and evolution. San Diego, CA: Academic. DAVIDSON, E.H. et ... This suggests that the gene responsible for the initial activation of the skeletogenic gene regulat ory network in sea urchins ... 2003). Spdeadringe r, a sea urchin embryo gene required separately in skeletogenic and oral ectode rm gene regulatory networks ...
digital.lib.usf.edu/SFS0027497/00001

*  Inferring Drosophila gap gene regulatory network: A parameter sensitivity and perturbation analysis

... Journal. BMC Systems ... Background: Inverse modelling of gene regulatory networks (GRNs) capable of simulating continuous spatio-temporal biological ... of a regulatory network in space. The model parameters are estimated by means of model-fitting algorithms. The gene ... As a case study we use the early gap gene segmentation mechanism in Drosophila melanogaster. We consider the limitations of the ...
dare.uva.nl/search?metis.record.id=312422

*  Reconstructing Gene Regulatory Networks through Integration of Pertubation Screen - George Michailidis

... transcriptional regulatory networks by integrating data from perturbation screens and steady state and time course gene ex... ... Reconstructing Gene Regulatory Networks through Integration of Pertubation Screen Michailidis, George University of Michigan ... 2014) Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles. PLoS One 9: ... Reconstructing Gene Regulatory Networks through Integration of Pertubation Screen. Michailidis, George / University of Michigan ...
grantome.com/grant/NIH/R21-GM101719-02

*  Genetic Regulatory Network Analysis for Rpe65 in the Eye of BXD Mice

Genetic Regulatory Network Analysis for ,i,Rpe65,/i, in the Eye of BXD Mice ... Then the gene co-regulatory network analysis was constructed. The genetic genomics approach demonstrates the importance and the ... However, little is known about the genetic regulatory network for Rpe65 and inherited retinal dystrophies. We combined gene ... Genetic Regulatory Network Analysis for Rpe65 in the Eye of BXD Mice p.248 ...
https://scientific.net/AMR.282-283.248

*  Frontiers | On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior |...

Additionally, extending these models to incorporate variable gene decay rates, asynchronous gene response, and synergistic ... Applying our methods to the budding yeast cell-cycle network revealed that although the network is complex, its steady state is ... Additionally, extending these models to incorporate variable gene decay rates, asynchronous gene response, and synergistic ... are relatively simple and interpretable models of gene regulatorynetworks. Specifying these models with fewer parameters while ...
journal.frontiersin.org/article/10.3389/fgene.2013.00263/full

*  1606.03235] Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks

Abstract: Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such ... Quantitative Biology > Molecular Networks. Title: Intrinsic noise and deviations from criticality in Boolean gene-regulatory ... These results suggest that in order to compensate for inherent stochasticity, regulatory and other type of biological networks ... Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Adaptation and Self-Organizing Systems ...
https://arxiv.org/abs/1606.03235

*  Supervised Inference of Gene Regulatory Networks from Positive and Unlabeled Examples | SpringerLink

Gene regulatory network Reverse engineering Inference Machine learning Gene expression Springer Nature is developing a new tool ... Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22( ... Elucidating the structure of gene regulatory networks (GRN), i.e., identifying which genes are under control of which ... 2013) Supervised Inference of Gene Regulatory Networks from Positive and Unlabeled Examples. In: Mamitsuka H., DeLisi C., ...
https://link.springer.com/protocol/10.1007/978-1-62703-107-3_5

*  Research proposal: Evolution of the Dorsal-Ventral gene regulatory network in Drosophila species

Evolution of the Dorsal-Ventral gene regulatory network in Drosophila species ... we will analyze the gene regulatory network or "cis-regulatory module" (CRM) that regulates the patterning of a fly embryo in ... Research proposal: Evolution of the Dorsal-Ventral gene regulatory network in Drosophila species. 2013-02-19T23:25:29Z (GMT) by ... Gene regulation in animals is a highly complex process, and can be likened to a computation that the regulatory machinery ...
https://figshare.com/articles/Research_proposal_Evolution_of_the_Dorsal_Ventral_gene_regulatory_network_in_Drosophila_species/247214

*  Lirias: REVERSE ENGINEERING THE EYE DEVELOPMENTAL GENE REGULATORY NETWORK BY LARGE-SCALE TRANSCRIPTOME PERTURBATIONS

In conclusion, we were able to reverse engineer a gene regulatory network by combining gene expression data and motif discovery ... REVERSE ENGINEERING THE EYE DEVELOPMENTAL GENE REGULATORY NETWORK BY LARGE-SCALE TRANSCRIPTOME PERTURBATIONS. ... Here we aim to unravel transcriptional networks and to elucidate novel aspects of the syntax and semantics of cis-regulatory ... but the overall knowledge of the genomic cis-regulatory code and the emerging transcriptional networks, remains sparse. ...
https://lirias.kuleuven.be/handle/123456789/424929

*  PTO8: Modeling Stochasticity and Robustness in Gene Regulatory Networks (ISMB 2009) - the mind wobbles

For T-helper differentiation, the GR network is reasonably complex (he's using this as the example for the talk). How does the ... Abhishek Garg Looking at stochasticity in nodes and in functions within GR networks. ... Categories Meetings & ConferencesTags abhishek garg, gene regulatory networks, ismb 2009, robustness, stochasticity Leave a ... PTO8: Modeling Stochasticity and Robustness in Gene Regulatory Networks (ISMB 2009). Abhishek Garg ...
https://themindwobbles.wordpress.com/2009/06/29/pto8-modeling-stochasticity-and-robustness-in-gene-regulatory-networks/

*  Affecting the macrophage response to infection by integrating signaling and gene-regulatory networks - pdf download

Affecting the macrophage response to infection by integrating signaling and gene-regulatory networks. . Download books free in ... These genes provided the basis for reconstructing a gene regulatory network that not only accounts for information coming from ... The TLR signaling and gene-regulatory networks were then integrated to develop a modeling framework for macrophage that ... Affecting the macrophage response to infection by integrating signaling and gene-regulatory networks - Download this document ...
books.duhnnae.com/2017/jun8/149821738950-Affecting-the-macrophage-response-to-infection-by-integrating-signaling-and-gene-regulatory-networks.php

*  Real-time in silico experiments on gene regulatory networks and surgery simulation on handheld devices

... Dépôt DSpace/Manakin. ... Real-time in silico experiments on gene regulatory networks and surgery simulation on handheld devices. ... Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions ... form gene regulatory networks to macroscopic soft tissue deformation and cutting. ...
sam.ensam.eu/handle/10985/10254

*  A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis (2014) | BioPreDyn

Finally, a preliminary gene regulatory network is derived from the optimized model parameters.. Outlook: While the focus of ... A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis (2014). ... the approach outlined here is suitable for inferring gene regulatory networks in the embryonic development of any animal, thus ... Methods/Result: In this work, first standardized gene expression profiles are generated from publicly available N. vectensis ...
biopredyn.eu/article/computational-approach-towards-gene-regulatory-network-developing-nematostella-vectensis

*  Federal Register :: Office of Science Financial Assistance Program Notice 02-13; Genomes to Life

Goal 2-Characterize Gene Regulatory Networks Understanding the structure and function of an organism's molecular machines is a ... Goal 2-Characterize Gene Regulatory Networks *Goal 3-Characterize the Functional Repertoire of Complex Microbial Communities in ... This will only come by understanding the complex gene regulatory networks that govern the coordinated formation and behavior of ... tools needed to identify all the components of gene regulatory networks with an initial focus on cis-acting regulatory ...
https://federalregister.gov/documents/2002/02/04/02-2597/office-of-science-financial-assistance-program-notice-02-13-genomes-to-life

*  Search research programmes - Study - Cardiff University

Transcriptional landscaping in plant stem cells: from chromatin to gene regulatory networks. Agriculture depends on the ... Gene expression regulation by RNA-binding proteins during fly development. This project will employ complementary in vivo and ... The complexity of adult brain function is largely met by the networking of a multitude of neurons, but there is also a ... Firing dynamics of thalamic and cortical neural networks during absence epilepsy. Epilepsy is one of the most serious and ...
cardiff.ac.uk/study/postgraduate/research/programmes/search?collection=pgr-courses&f.subjects|s=biology

*  IJMS | Free Full-Text | RUNX1: A MicroRNA Hub in Normal and Malignant Hematopoiesis | HTML

To guarantee the appropriate level of complexity, flexibility, and robustness, these networks rely on transcriptional and post- ... Hematopoietic development is orchestrated by gene regulatory networks that progressively induce lineage-specific ... Gene regulatory networks (GRNs) have evolved in different organisms to guarantee the appropriate level of complexity, ... Pimanda, J.E.; Gottgens, B. Gene regulatory networks governing haematopoietic stem cell development and identity. Int. J. Dev. ...
mdpi.com/1422-0067/14/1/1566/htm

*  Frank Wellmer : Profiles - Trinity Research : Trinity College DublinFrank Wellmer

Gene regulatory networks; Genetics; Genomes, Genomics; Molecular Genetics; Plant Biochemistry; Plant Development; Plant ... Gene network analysis in Arabidopsis thaliana flower development through dynamic gene perturbations, The Plant Journal, 83, ... Wellmer, F. and Riechmann, J.L, Gene networks controlling the initiation of flower development, Trends in Genetics, 26, (12), ... Wellmer, F. and Riechmann, J.L. , Gene network analysis in plant development by genomic technologies., International Journal of ...
tcd.ie/research/profiles/?profile=wellmerf

*  ESMO 2014 Press Release: RAS Testing Only the First Step for Choosing Treatment for Metastatic Colorectal Cancer, Important New...

Our network of National Representatives act as ambassadors of ESMO's mission in their respective country ... Regulatory Information. Clear, relevant information on EU clinical trials and data protection legislation ... versions of the RAS gene. ...
esmo.org/Press-Office/Press-Releases/RAS-Testing-Only-the-First-Step-for-Choosing-Treatment-for-Metastatic-Colorectal-Cancer-Important-New-Data-Show

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Neural immune gene expression variables are measured with qPCR screening, qPCR arrays, and, importantly, use of cDNA ... Here, we present a strategic combination of protocols for direct quantitative analysis of TATS membrane networks in living VMs ... exert remarkable tissue trophic and immune regulatory effects onto different host target cells in vivo. Here we describe the ... The 4T1 cell line has been engineered to constitutively express the firefly luciferase gene (luc2). When mice carrying 4T1-luc2 ...
https://jove.com/visualize/abstract/23300962/long-term-in-vivo-imaging-of-multiple-organs-at-the-single-cell-level

*  Plus it

Accordingly, mice with heterozygous invalidation of the glucokinase gene also increased NPY and reduced POMC gene expression ( ... integration in neuropeptide Y and pro-opio melanocortin networks? Diabetes 56: 1219-1227, 2007. ... Karyopherin alpha2: a control step of glucose-sensitive gene expression in hepatic cells. Biochem J 364: 201-209, 2002. ... Glucokinase regulates reproductive function, glucocorticoid secretion, food intake, and hypothalamic gene expression. ...
ajpendo.physiology.org/content/298/5/E1078

*  Ofd1, a human disease gene, regulates the length and distal structure of centrioles

Inserting an Ofd1-Myc gene into the native genomic context and under control of endogenous regulatory elements restored Ofd1 ... network of e-repositories. ... OFD1, the gene mutated in oral-facial-digital syndrome type 1, ... Identification of the gene for oral-facial-digital type I syndrome. Am J Hum Genet. 2001;68:569-576. [PubMed] ... Ofd1, a human disease gene, regulates the length and distal structure of centrioles. Veena Singla,1 Miriam Romaguera-Ros,2 Jose ...
pubmedcentralcanada.ca/pmcc/articles/PMC2841064/?lang=en-ca

*  NR4A1 Proteins

Study found a marked down-regulated gene expression of the NR4A subfamily (NR4A1, NR4A2 (show NR4A2 Proteins), and NR4A3 (show ... Nuclear Speckle Splicing Regulatory Protein 1 Proteins * Nuclear Transcription Factor Y, alpha Proteins ... antibodies-online network *antibodies-online. * antikoerper-online.de (deutsch) * antibodies-online.com (english) ... Identify the orphan nuclear receptor NR4A1 as a potential early response gene in FGF2 signaling and regulation of sprouty in ...
antibodies-online.com/fc-epsilon-receptor-signaling-pathway-pathway-22/nr4a1-protein-40093/

*  Plus it

Since the effects of miRNAs on gene expression can be complex as discussed earlier, miRNA-based therapy might affect gene ... This is in part indirectly caused by the downregulation of miR-18b in melanoma (17). With regard to cell cycle regulatory genes ... Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions. Oncogene 32: 1959- ... MicroRNAs are small, noncoding RNAs that regulate gene expression of targeted gene(s). The hallmark of cancer model outlined by ...
physiolgenomics.physiology.org/content/45/22/1049

Biological network: A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web.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?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.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.List of systems biology conferences: Systems biology is a biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences.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.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Matrix model: == Mathematics and physics ==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.Sea urchin injury: Sea urchin injuries are caused by contact with sea urchins, and are characterized by puncture wounds inflicted by the animal's brittle, fragile spines.Physical neural network: A physical neural network is a type of artificial neural network in which an electrically adjustable resistance material is used to emulate the function of a neural synapse. "Physical" neural network is used to emphasize the reliance on physical hardware used to emulate neurons as opposed to software-based approaches which simulate neural networks.Hyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.Extracellular: 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.Aaglacrinus: Carboniferoushttp://strata.geology.Flux (metabolism): Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway.Doob decomposition theorem: In the theory of stochastic processes in discrete time, a part of the mathematical theory of probability, the Doob decomposition theorem gives a unique decomposition of every adapted and integrable stochastic process as the sum of a martingale and a predictable process (or "drift") starting at zero. The theorem was proved by and is named for Joseph L.Mac OS X Server 1.0Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.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.MicroRNA and microRNA target database: This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.De novo transcriptome assembly: De novo transcriptome assembly is the method of creating a transcriptome without the aid of a reference genome.Eukaryotic 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.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.Iroquois homeobox factor: Iroquois homeobox factors are a family of homeodomain transcription factors that play a role in many developmental processes.Squamosa promoter binding protein: The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.Zuotin: Z-DNA binding protein 1, also known as Zuotin, is a Saccharomyces cerevisiae yeast gene.Protein–protein interactionPlant Proteome Database: The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.GAI (Arabidopsis thaliana gene)Multiple patterning: Multiple patterning (or multi-patterning) is a class of technologies for manufacturing integrated circuits (ICs), developed for photolithography to enhance the feature density. The simplest case of multiple patterning is double patterning, where a conventional lithography process is enhanced to produce double the expected number of features.Mesenchyme: Mesenchyme is a type of tissue characterized by loosely associated cells that lack polarity and are surrounded by a large extracellular matrix. Mesenchymal cells are able to develop into the tissues of the lymphatic and circulatory systems, as well as connective tissues throughout the body, such as bone and cartilage.List of sequenced eukaryotic genomesVladimir Andreevich Markov: Vladimir Andreevich Markov (; May 8, 1871 – January 18, 1897) was a Russian mathematician, known for proving the Markov brothers' inequality with his older brother Andrey Markov. He died of tuberculosis at the age of 25.DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.ChIP-exo: ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest (transcription factor) binds to the genome. It is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to almost one base pair.Lineage markers: The lineage markers are characteristic molecules for cell lineages, e.g.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.Nonlinear system: In physics and other sciences, a nonlinear system, in contrast to a linear system, is a system which does not satisfy the superposition principle – meaning that the output of a nonlinear system is not directly proportional to the input.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.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.Retortamonas intestinalis: Retortamonas intestinalis is a species of retortamonad which is found in the gastrointestinal tract.Type XXVII collagen: Type XXVII collagen is the protein predicted to be encoded by COL27A1. It was first described by Dr.Midblastula: In developmental biology, midblastula or midblastula transition (MBT) is a stage during the blastula stage of embryonic development in which zygotic gene transcription is activated. There are three major characteristics of pre-MBT embryos.Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Coles PhillipsPisaster ochraceusHuman embryonic stem cells clinical trials: ==Human Embryonic Stem Cell Clinical Trials==Nif regulonSymmetry 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.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.Von Neumann regular ring: In mathematics, a von Neumann regular ring is a ring R such that for every a in R there exists an x in R such that . To avoid the possible confusion with the regular rings and regular local rings of commutative algebra (which are unrelated notions), von Neumann regular rings are also called absolutely flat rings, because these rings are characterized by the fact that every left module is flat.History of research on Caenorhabditis elegans: The nematode worm Caenorhabditis elegans was first studied in the laboratory by Victor Nigon and Ellsworth Dougherty in the 1940s, but came to prominence after being adopted by Sydney Brenner in 1963 as a model organism for the study of developmental biology using genetics. In 1974, Brenner published the results of his first genetic screen, which isolated hundreds of mutants with morphological phenotypes.Drosophila embryogenesis: Drosophila embryogenesis, the process by which Drosophila (fruit fly) embryos form, is a favorite model system for geneticists and developmental biologists studying embryogenesis. The small size, short generation time, and large brood size make it ideal for genetic studies.Truncal neural crest: The truncal neural crest or trunk neural crest is a form of neural crest.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.Immersive technologyMexican International Conference on Artificial Intelligence: MICAI (short for Mexican International Conference on Artificial Intelligence) is the name of an annual conference covering all areas of Artificial Intelligence (AI), held in Mexico. The first MICAI conference was held in 2000.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.Process mining: Process mining is a process management technique that allows for the analysis of business processes based on event logs. The basic idea is to extract knowledge from event logs recorded by an information system.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Indy (gene): Indy, short for I'm not dead yet, is a gene of the model organism, the fruit fly Drosophila melanogaster. Mutant versions of this gene have doubled the average life span of fruit flies in at least one set of experiments, but this result has been subject to controversy.BESS domain: In molecular biology, the BESS domain is a protein domain which has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32), Suvar(3)7 and Stonewall ). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain.Model risk: In finance, model risk is the risk of loss resulting from using models to make decisions, initially and frequently referring to valuing financial securities. However model risk is more and more prevalent in industries other than financial securities valuation, such as consumer credit score, real-time probability prediction of a fraudulent credit card transaction to the probability of air flight passenger being a terrorist.Temporal analysis of products: Temporal Analysis of Products (TAP), (TAP-2), (TAP-3) is an experimental technique for studyingFerric 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.

(1/4873) Where are we in genomics?

Genomic studies provide scientists with methods to quickly analyse genes and their products en masse. The first high-throughput techniques to be developed were sequencing methods. A great number of genomes from different organisms have thus been sequenced. Genomics is now shifting to the study of gene expression and function. In the past 5-10 years genomics, proteomics and high-throughput microarray technologies have fundamentally changed our ability to study the molecular basis of cells and tissues in health and diseases, giving a new comprehensive view. For example, in cancer research we have seen new diagnostic opportunities for tumour classification, and prognostication. A new exciting development is metabolomics and lab-on-a-chip techniques (which combine miniaturization and automation) for metabolic studies. However, to interpret the large amount of data, extensive computational development is required. In the coming years, we will see the study of biological networks dominating the scene in Physiology. The great accumulation of genomics information will be used in computer programs to simulate biologic processes. Originally developed for genome analysis, bioinformatics now encompasses a wide range of fields in biology from gene studies to integrated biology (i.e. combination of different data sets from genes to metabolites). This is systems biology which aims to study biological organisms as a whole. In medicine, scientific results and applied biotechnologies arising from genomics will be used for effective prediction of diseases and risk associated with drugs. Preventive medicine and medical therapy will be personalized. Widespread applications of genomics for personalized medicine will require associations of gene expression pattern with diagnoses, treatment and clinical data. This will help in the discovery and development of drugs. In agriculture and animal science, the outcomes of genomics will include improvement in food safety, in crop yield, in traceability and in quality of animal products (dairy products and meat) through increased efficiency in breeding and better knowledge of animal physiology. Genomics and integrated biology are huge tasks and no single lab can pursue this alone. We are probably at the end of the beginning rather than at the beginning of the end because Genomics will probably change Biology to a greater extent than previously forecasted. In addition, there is a great need for more information and better understanding of genomics before complete public acceptance.  (+info)

(2/4873) A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA.

The two Caenorhabditis elegans gustatory neurons, ASE left (ASEL) and ASE right (ASER) are morphologically bilaterally symmetric, yet left/right asymmetric in function and in the expression of specific chemosensory signaling molecules. The ASEL versus ASER cell-fate decision is controlled by a complex gene regulatory network composed of microRNAs (miRNAs) and transcription factors. Alterations in the activities of each of these regulatory factors cause a complete lateral cell-fate switch. Here, we describe lsy-2, a novel C2H2 zinc finger transcription factor that is required for the execution of the ASEL stable state. In lsy-2 null mutants, the ASEL neuron adopts the complete ASER gene expression profile, including both upstream regulatory and terminal effector genes. The normally left/right asymmetric ASE neurons are therefore ;symmetrized' in lsy-2 mutants. Cell-specific rescue experiments indicate that lsy-2 is required autonomously in ASEL for the activation of ASEL-specifying factors and the repression of ASER-specifying factors. Genetic epistasis experiments demonstrate that lsy-2 exerts its activity by regulating the transcription of the lsy-6 miRNA in the ASEL neuron, thereby making lsy-2 one of the few factors known to control the cell-type specificity of miRNA gene expression.  (+info)

(3/4873) Identification of novel transcriptional networks in response to treatment with the anticarcinogen 3H-1,2-dithiole-3-thione.

3H-1,2-dithiole-3-thione (D3T), an inducer of antioxidant and phase 2 genes, is known to enhance the detoxification of environmental carcinogens, prevent neoplasia, and elicit other protective effects. However, a comprehensive view of the regulatory pathways induced by this compound has not yet been elaborated. Fischer F344 rats were gavaged daily for 5 days with vehicle or D3T (0.3 mmol/kg). The global changes of gene expression in liver were measured with Affymetrix RG-U34A chips. With the use of functional class scoring, a semi-supervised method exploring both the expression pattern and the functional annotation of the genes, the Gene Ontology classes were ranked according to the significance of the impact of D3T treatment. Two unexpected functional classes were identified for the D3T treatment, cytosolic ribosome constituents with 90% of those genes increased, and cholesterol biosynthesis with 91% of the genes repressed. In another novel approach, the differentially expressed genes were evaluated by the Ingenuity computational pathway analysis tool to identify specific regulatory networks and canonical pathways responsive to D3T treatment. In addition to the known glutathione metabolism pathway (P = 0.0011), several other significant pathways were also revealed, including antigen presentation (P = 0.000476), androgen/estrogen biosynthesis (P = 0.000551), fatty acid (P = 0.000216), and tryptophan metabolism (P = 0.000331) pathways. These findings showed a profound impact of D3T on lipid metabolism and anti-inflammatory/immune-suppressive response, indicating a broader cytoprotective effect of this compound than previously expected.  (+info)

(4/4873) A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis.

OBJECTIVE: While rheumatoid arthritis (RA) is considered a prototypical autoimmune disease, the specific roles of B-cells in RA pathogenesis is not fully delineated. METHODS: We performed microarray expression profiling of peripheral blood B-cells from RA patients and controls. Data were analysed using differential gene expression analysis and 'gene networking' analysis (characterizing clusters of functionally inter-relelated genes) to identify both regulatory genes and the pathways in which they participate. Results were confirmed by quantitative real-time polymerase chain reaction and by measuring the levels of 10 serum cytokines involved in the pathways identified. RESULTS: Genes regulating and effecting the cell-cycle, proliferation, apoptosis, autoimmunity, cytokine networks, angiogenesis and neuro-immune regulation were differentially expressed in RA B-cells. Moreover, the serum levels of several soluble factors that modulate these pathways, including IL-1beta, IL-5, IL-6, IL-10, IL-12p40, IL-17 and VEGF were significantly increased in this cohort of RA patients. CONCLUSIONS: These results outline aspects of the multifaceted role B-cells play in RA pathogenesis in which immune dysregulation in RA modulates B-cell biology and thereby contributes to the induction and perpetuation of a pathogenic humoral immune response.  (+info)

(5/4873) Network regulation of calcium signal in stomatal development.

AIM: Each cell is the production of multiple signal transduction programs involving the expression of thousands of genes. This study aims to gain insights into the gene regulation mechanisms of stomatal development and will investigate the relationships among some signaling transduction pathways. METHODS: Nail enamel printing was conducted to observe the stomatal indices of wild type and 10 mutants (plant hormone mutants, Pi-starvation induced CaM mutants and Pi-starvation-response mutant) in Arabidopsis, and their stomatal indices were analyzed by ANOVA. We analyzed the stomatal indices of 10 Arabidopsis mutants were analyzed by a model PRGE (potential relative effect of genes) to research relations among these genes. RESULTS: In wild type and 10 mutants, the stomatal index did not differ with respect to location on the lower epidermis. Compared with wild type, the stomatal indices of 10 mutants all decreased significantly. Moreover, significant changes and interactions might exist between some mutant genes. CONCLUSION: It was the stomatal intensity in Arabidopsis might be highly sensitive to most mutations in genome. While the effect of many gene mutations on the stomatal index might be negative, we also could assume the stomatal development was regulated by a signal network in which one signal transduction change might influence the stomatal development more or less, and the architecture might be reticulate. Furthermore, we could speculate that calcium was a hub in stomatal development signal regulation network, and other signal transduction pathways regulated stomatal development by influencing or being influenced by calcium signal transduction pathways.  (+info)

(6/4873) Versatility and connectivity efficiency of bipartite transcription networks.

The modulation of promoter activity by DNA-binding transcription regulators forms a bipartite network between the regulators and genes, in which a smaller number of regulators control a much lager number of genes. To facilitate representation of gene expression data with the simplest possible network structure, we have characterized the ability of bipartite networks to describe data. This has led to the classification of two types of bipartite networks, versatile and nonversatile. Versatile networks can describe any data of the same rank, and are indistinguishable from one another. Nonversatile networks require constraints to be present in data they describe, which may be used to distinguish between different network topologies. By quantifying the ability of bipartite networks to represent data we were able to define connectivity efficiency, which is a measure of how economic the use of connections is within a network with respect to data representation and generation. We postulated that it may be desirable for an organism to maximize its gene expression range per network edge, since development of a regulatory connection may have some evolutionary cost. We found that the transcriptional regulatory networks of both Saccharomyces cerevisiae and Escherichia coli lie close to their respective connectivity efficiency maxima, suggesting that connectivity efficiency may have some evolutionary influence.  (+info)

(7/4873) Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators.

Deciphering the molecular basis for human erythropoiesis should yield information benefiting studies of the hemoglobinopathies and other erythroid disorders. We used an in vitro erythroid differentiation system to study the developing red blood cell transcriptome derived from adult CD34+ hematopoietic progenitor cells. mRNA expression profiling was used to characterize developing erythroid cells at six time points during differentiation (days 1, 3, 5, 7, 9, and 11). Eleven thousand seven hundred sixty-three genes (20,963 Affymetrix probe sets) were expressed on day 1, and 1,504 genes, represented by 1,953 probe sets, were differentially expressed (DE) with 537 upregulated and 969 downregulated. A subset of the DE genes was validated using real-time RT-PCR. The DE probe sets were subjected to a cluster metric and could be divided into two, three, four, five, or six clusters of genes with different expression patterns in each cluster. Genes in these clusters were examined for shared transcription factor binding sites (TFBS) in their promoters by comparing enrichment of each TFBS relative to a reference set using transcriptional regulatory network analysis. The sets of TFBS enriched in genes up- and downregulated during erythropoiesis were distinct. This analysis identified transcriptional regulators critical to erythroid development, factors recently found to play a role, as well as a new list of potential candidates, including Evi-1, a potential silencer of genes upregulated during erythropoiesis. Thus this transcriptional regulatory network analysis has yielded a focused set of factors and their target genes whose role in differentiation of the hematopoietic stem cell into distinct blood cell lineages can be elucidated.  (+info)

(8/4873) Discovering antibiotic efficacy biomarkers: toward mechanism-specific high content compound screening.

As current antibiotic therapy is increasingly challenged by emerging drug-resistant bacteria, new technologies are required to identify and develop novel classes of antibiotics. A major bottleneck in today's discovery efforts, however, is a lack of an efficient and standardized method for assaying the efficacy of a drug candidate. We propose a new high content screening approach for identifying efficacious molecules suitable for development of antibiotics. Key to our approach is a new microarray-based efficacy biomarker discovery strategy. We first produced a large dataset of transcriptional responses of Bacillus subtilis to numerous structurally diverse antibacterial drugs. Second we evaluated different protocols to optimize drug concentration and exposure time selection for profiling compounds of unknown mechanism. Finally we identified a surprisingly low number of gene transcripts (approximately 130) that were sufficient for identifying the mechanism of novel substances with reasonable accuracy (approximately 90%). We show that the statistics-based approach reveals a physiologically meaningful set of biomarkers that can be related to major bacterial defense mechanisms against antibiotics. We provide statistical evidence that a parallel measurement of the expression of the biomarkers guarantees optimal performance when using expression systems for screening libraries of novel substances. The general approach is also applicable to drug discovery for medical indications other than infectious diseases.  (+info)



expression


  • The HI set was found to be enriched for genes involved in the processes of gene expression, while the HP set was enriched for genes concerned with the cell cycle and genome integrity. (biomedcentral.com)
  • This subset is enriched for genes that participate in the processes of gene expression, itself ( i.e. transcription and translation). (biomedcentral.com)
  • We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Rpe65 expression in the eye of BXD recombinant inbred (RI) mice. (scientific.net)

itself


  • Moreover, the QTL was mapped to within 3 Mb of the location of the gene itself (Rpe65) as a cis-acting QTL. (scientific.net)