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.

Where are we in genomics? (1/4873)

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

  • Elucidation of cellular and gene regulatory networks (GRNs) governing organ development will accelerate progress toward tissue replacement. (nih.gov)
  • Here, we have compiled reference GRNs underlying pancreas development from data mining that integrates multiple approaches, including mutant analysis, lineage tracing, cell purification, gene expression and enhancer analysis, and biochemical studies of gene regulation. (nih.gov)
  • This work reviews some of the most important statistical methods used for modeling of gene regulatory networks (GRNs) and protein-protein interaction (PPI) networks. (hindawi.com)
  • It appears that the problem of inferring the structure of PPI networks is quite different from that of GRNs. (hindawi.com)
  • Performance evaluation criteria for the approaches used for modeling GRNs and PPI networks are also discussed. (hindawi.com)
  • Gene regulatory networks (GRNs) consist of thousands of genes and proteins which are dynamically interacting with each other. (bl.uk)
  • Therefore, both the regulatory structure estimation and dynamics modeling of GRNs are essential for biological research. (bl.uk)
  • However, this stochastic nature requires heavy simulation time to find the steady-state solution of the GRNs where thousands of genes are involved. (bl.uk)
  • It includes applications of a stochastic process theory called G-networks and a reverse engineering technique for large-scale GRNs. (bl.uk)
  • Additionally a series of bioinformatics techniques was applied in brain tumor data to detect disease candidate genes along with their large-scale GRNs. (bl.uk)
  • Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. (uni.lu)
  • In a previous comparative study of the gene regulatory networks (GRNs) that embody the genomic program for embryogenesis in these animals, we discovered an almost perfectly conserved five-gene network subcircuit required for endoderm specification. (caltech.edu)
  • The variation in structure and function of gene regulatory networks (GRNs) participating in organisms development is a key for understanding species-specific evolutionary strategies. (springer.com)
  • To understand the processes of development and evolution of living organisms, the "gene regulatory networks", or GRNs have to be taken into account. (springer.com)
  • In genetic regulatory networks (GRNs), the diffusion rate of mRNA and protein play a key role in regulatory mechanisms of gene expression, especially in translation and transcription. (embs.org)
  • Our approach is to delineate the gene regulatory networks (GRNs) that specify these cells during their development in the embryo , and we use the amphibian experimental model because a wealth of evidence shows that the mechanisms used are conserved in mammals including humans. (xenbase.org)
  • Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. (harvard.edu)
  • It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). (harvard.edu)
  • These highly conserved gene-expression patterns point to widespread conservation of GRNs across the animal kingdom. (biomedcentral.com)
  • Conventional methods to construct synthetic gene regulatory networks (GRNs) need time-consuming trial and error steps, preventing their use in synthetic biology. (nii.ac.jp)
  • I've inferred 6 GRNs (Gene Regulatory Networks) using CLR (Context Likelihood Relat. (biostars.org)
  • Gene Regulatory Networks (GRNs) are reconstructed from the microarray gene expression data through diversified computational approaches. (theiet.org)
  • The generated GRNs hold the potential in determining the real nature of gene pair regulatory interactions. (theiet.org)
  • GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). (peerj.com)
  • In this paper, we study a more sophisticated score function for DBN first proposed by Nir Friedman for stationary DBNs structure learning of both initial and transition networks but has not yet been used for reconstruction of GRNs. (biomedcentral.com)
  • In the previous work, we compared two important computational approaches, Dynamic Bayesian networks (DBNs) and Probabilistic Boolean networks for reconstructing GRNs using a time-series dataset from the Drosophila Interaction Database, and found that DBN outperforms PBN [ 9 ]. (biomedcentral.com)
  • Reconstruction of g e n e r e g u l a t or y n etwor ks (GRNs) explicitly represents the causality of developmental or regulatory process. (rroij.com)
  • An important problem in molecular biology is to identify and understand the gene regulatory networks (GRNs). (rroij.com)
  • This relies on the incorporation of multiple topological characteristics of GRNs like sparsity and hub gene structures into the model formulation. (omictools.com)
  • The proposed techniques such as stochastic modeling (bottom-up) and reverse engineering (top-down) could provide a systematic view of a complex system and an efficient guideline to identify candidate genes or pathways triggering a specific phenotype of a cell. (bl.uk)
  • In Chapter 3 and 4, I describe the development of a novel approach named DINA (Differential Network Analysis) for the identification of differentially co-regulated pathways. (unina.it)
  • I then applied DINA to these networks in order to identify tissue-specific pathways starting from a list of 110 KEGG-annotated pathways. (unina.it)
  • Using these three cell-type specific networks, I demonstrated that DINA can be used to make hypotheses on dysregulated pathways during disease progression. (unina.it)
  • We then reduce this initial network by removing simple mediators (i.e., linear pathways), and formalize the resulting regulatory core into logical rules that govern the dynamics of each of the network components as a function of the states of its regulators. (biomedcentral.com)
  • Genes essential to the transmission of the infection signal were first identified using a model of the TLR signaling pathways. (bu.edu)
  • These genes provided the basis for reconstructing a gene regulatory network that not only accounts for information coming from the TLRs, but also regulates key reactions within the pathways. (bu.edu)
  • Given its relevance to aging, diabetes, obesity and cancer, interest in L1 arrest is increasing, and signaling pathways and gene regulatory mechanisms controlling arrest and recovery have been characterized. (genetics.org)
  • Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. (springer.com)
  • These authors observed that the performance of the evaluated methods depends on many factors such as features of the data, network size and topology, as well as parameter settings. (omicsonline.org)
  • The predicted network topology links the very early-activated genes involved in LR initiation to later expressed cell identity markers through a multistep genetic cascade exhibiting both positive and negative feedback loops. (plantcell.org)
  • It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. (warwick.ac.uk)
  • The network shown was generated from microarray data without the use of any prior information, and yet the method managed to identify the strong causal relationships between clock components (TOC1, LHY, ELF3, ELF4, CCA1) and to link these to further key regulators of important processes (e.g. (videolectures.net)
  • The existence of each tier in the regulatory hierarchy is justified by the assignment of a unique task and each invariably performs at least two functions: to activate the regulators in the next tier and to perform one other activity distinct from that of the next tier. (nih.gov)
  • Genes responsive to SMV infection are identified as are their potential miRNA regulators. (gc.ca)
  • A robust IGVH expression signature was obtained, and various TFs emerged as regulators of the signature in most of the reconstructed networks. (biomedcentral.com)
  • Divided into five convenient sections, Gene Regulatory Networks: Methods and Protocols details how each of these approaches contributes to a more thorough understanding of the composition and function of gene regulatory networks, while providing a comprehensive protocol on how to implement them in the laboratory. (springer.com)
  • These approaches have been implemented in-vivo for the investigation of the role of defined gene products within specific neuronal types in regions of the reward circuitry in supporting the development of addiction correlates in mice. (europa.eu)
  • Here, we review primarily bioinformatic approaches to capture this regulatory complexity and look at different algorithmic strategies and associated available software solutions to identify composite cis-elements. (eurekaselect.com)
  • Thus, information-theoretic approaches can deal with steady-state gene expression data or with time-series data given that the sampling interval is long enough to assume that each point is independent of the previous points. (biomedcentral.com)
  • Chapter 2 illustrates a comparative study of the different approaches to reverse-engineering gene networks from gene expression profiles (GEPs) and their limitations. (unina.it)
  • Current state-of-the-art reverse-engineering approaches model gene networks as static processes, i.e. regulatory interactions among genes in the network (such as direct physical interactions or indirect functional interactions) do not change across different conditions or tissue types. (unina.it)
  • In this article, we have shown that by combining advanced network biology approaches with the right experimental models, we are able to reveal novel regulatory circuits controlling multiple hallmarks of glioma. (prolekare.cz)
  • In general, these approaches start by computing the pair-wise MIs between all possible pairs of genes, resulting in an MI matrix. (rroij.com)
  • Understanding how they work together to form a cellular network in a living organism is extremely important in the field of molecular biology. (hindawi.com)
  • Importantly, changes in cellular levels of NAD, a close relative of NADP, had previously been linked to a gene circuit that controls aging and longevity in a large number of different organisms, including yeast but also including animals," said Professor Rolf Sternglanz of Stony Brook University in New York, a co-author of the study. (innovations-report.com)
  • Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. (semanticscholar.org)
  • Gene duplication events during evolutionary history have provided large numbers of new genes that can diverge in function and gain new functions, resulting in new morphological, physiological, and biochemical characteristics of organisms and cellular systems. (plantphysiol.org)
  • Analysis of data produced by such experiments offers potential insight into gene function and regulatory mechanisms. (psu.edu)
  • Specifically, we aimed to understand how these gene expression networks are reorganized following chronic drug exposure, assuming that this knowledge will provide insight into mechanisms underlying the development of addiction. (europa.eu)
  • Biofilm formation and the presence of intrinsic resistance-associated genes are examples of the mechanisms that P. aeruginosa employs to resist chemotherapy. (scielo.br)
  • In addition, this bacterium can become resistant to a broad range of antibiotics through the acquisition of new resistance mechanisms via horizontal gene transfer. (scielo.br)
  • Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and complexity of these models mean that their behaviour is not always intuitive and the underlying mechanisms can be difficult to decipher. (uni.lu)
  • We use this method to predict the regulatory mechanisms that underlie proximodistal (PD) patterning of the developing limb bud. (embopress.org)
  • The second part of my thesis is about the development of GNRevealer, a method for reverse engineering of gene regulatory networks from temporal data. (hu-berlin.de)
  • We showed that it is effective on in silico data sets with a reasonable level of informativeness and demonstrated that accurate prediction of network sparsity is key to elucidate the correct network parameters. (diva-portal.org)
  • Authoritative and accessible, Gene Regulatory Networks: Methods and Protocols aims to provide novices and experienced researchers alike with a comprehensive and timely toolkit to study gene regulatory networks from the point of data generation to processing, visualization, and modeling. (indigo.ca)
  • Then the gene regulatory networks constructed based on complete and incomplete data series are compared in terms of statistics at different levels. (mdpi.com)
  • Using existing data from two separate panels of inbred mice, we will perform quantitative trait locus (QTL) mapping on the gene expression measurements. (epa.gov)
  • By extracting the reproducible QTLs across the two data sets, we will find networks of correlated genes which are likely to share common regulatory control. (epa.gov)
  • Depletion of TRIM28 in human or mouse ES cells triggers the upregulation of a broad range of transposable elements(4,10,11), and recent data based on a few specific examples have pointed to an arms race between hosts and transposable elements as an important driver of KZFP gene selection(5). (epfl.ch)
  • It also considers approximate validation methods based on data for which the generating network is not known, the kind of situation one faces when using real data. (eurekaselect.com)
  • On the basis of gene expression and single nucleotide polymorphism data in the yeast, Saccharomyces cerevisiae , we constructed gene regulatory networks using a two-stage penalized least squares method. (purdue.edu)
  • Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. (gc.ca)
  • how to get genes and their interactions from RNA-Seq data? (biostars.org)
  • I am trying to construct a Gene Regulatory Network from RNA-sequencing data. (biostars.org)
  • To this end, we first integrate published functional and well-curated molecular data of the components and interactions that have been found to be involved in such cell states and transitions into a network of 41 molecular components. (biomedcentral.com)
  • We use both laboratory data from cytometry experiments as well as data simulated from the gold-standard network. (gla.ac.uk)
  • We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. (uminho.pt)
  • Finally, we reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. (uminho.pt)
  • For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same ON and OFF gene expression profiles across multiple samples of experimental data. (uminho.pt)
  • In this work, researchers from the Shanghai Jiao Tong University , China compiled putative TF-gene, miRNA-gene and TF-miRNA regulatory relationships from forward-engineering pipelines and curated them as built-in data libraries. (rna-seqblog.com)
  • Structure Expectation-Maximization (SEM) has been developed for learning Probabilistic network structure from data with hidden variables and missing values [ 13 ]. (biomedcentral.com)
  • In this study, we construct a gene regulatory network of inflammation using data extracted from the Ensembl and JASPAR databases. (biomedcentral.com)
  • In this study, Data mining and dynamic network analyses were integrated to examine the gene regulatory network in the inflammatory response system. (biomedcentral.com)
  • These fluctuations are intrinsic: they are determined by the structure, reaction rates, and species concentrations of the underlying biochemical networks. (pnas.org)
  • The structure of these networks underlies their capacity to buffer intrinsic and extrinsic noise and maintain embryonic morphology. (frontiersin.org)
  • The endoderm arises from a single progenitor, the E cell, and is selected from among three possible fates by a three-state combinatorial regulatory system involving intersecting cell-intrinsic and intercellular signals. (nih.gov)
  • Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. (uminho.pt)
  • Gene Regulatory Networks for Development is an advanced short course that conveys the central conceptual focus of this field, which lies at the conceptual nexus of development, evolution and functional regulatory genomics, to be given at MBL, October 12-24, 2014. (xenbase.org)
  • We are looking for a postdoctoral scientist with expertise in genomics, epigenetics and next-gene. (biostars.org)
  • Regulatory neofunctionalization and subfunctionalization are likely caused by mutational changes within the cis-regulatory region of the duplicated genes, which alter the temporal/spatial expression profile as well as responses to various biotic and abiotic stimuli. (plantphysiol.org)
  • We also found that the regulatory core yields an epigenetic landscape that restricts temporal patterns of progression between the steady states, such that recovered patterns resemble the time-ordered transitions observed during the spontaneous immortalization of epithelial cells, both in vivo and in vitro. (biomedcentral.com)
  • Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (cmu.edu)
  • However, the two-stage temporal Bayes network (2TBN) structure of DBN that specifies correlation between time slices cannot be obtained by score metrics used in REVEAL. (biomedcentral.com)
  • However, the two-stage temporal Bayes network (2TBN) cannot be well recovered by application of REVEAL. (biomedcentral.com)
  • Up mutations in the ompR gene, such as the ompR234 mutation, stimulate laboratory strains of E. coli to grow as a biofilm community rather than in a planktonic state. (asm.org)
  • Mutations in the LRRK2 gene are a risk-factor for developing Parkinson's disease. (meta.org)
  • Importantly, the yeast cell can rapidly respond to changes in its nutritional environment by altering the expression of specific genes that allow it to make use of those different energy sources. (innovations-report.com)
  • We further developed the tools to investigate the function of specific genes in supporting the development of behavioral correlates of drug addiction in mice. (europa.eu)
  • Each PD skeletal element expresses specific genes. (embopress.org)
  • Even though these datasets are still far from comprehensive, and the approach faces many important and difficult challenges, some strategies have begun to make connections between disparate regulatory events and to foster new hypotheses. (biochemj.org)
  • As a result, they have released the cGRNB (combinatorial Gene Regulatory Networks Builder): a web server for constructing combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. (rna-seqblog.com)
  • Once these regulatory structures are revealed, it is necessary to understand their dynamical behaviors since pathway activities could be changed by their given conditions. (bl.uk)
  • DINA is based on the hypothesis that genes belonging to a condition-specific pathway are actively co-regulated only when the pathway is active, independently of their absolute level of expression. (unina.it)
  • He and Levine also coauthored a perspective in the same issue of the journal on the properties of gene regulatory networks. (innovations-report.com)