Gene regulatory networks. Medical search

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.

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.

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

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.

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

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.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

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-based representation of physical systems and phenomena such as chemical processes.

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.

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.

Somewhat flattened, globular echinoderms, having thin, brittle shells of calcareous plates. They are useful models for studying FERTILIZATION and EMBRYO DEVELOPMENT.

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.

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.

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.

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.

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 devoted to knowledge about specific genes and gene products.

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)

The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.

Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.

Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.

Sequential operating programs and data which instruct the functioning of a digital computer.

The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.

The systematic study of the complete DNA sequences (GENOME) of organisms.

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.

The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.

Cellular processes, properties, and characteristics.

Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.

The inner of the three germ layers of an embryo.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

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.

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.

Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.

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.

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).

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.

Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.

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.

Methods for determining interaction between PROTEINS.

The protein complement of an organism coded for by its genome.

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.

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.

The middle germ layer of an embryo derived from three paired mesenchymal aggregates along the neural tube.

Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.

Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.

The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

The characteristic properties and processes involved in IMMUNITY and an organism's immune response.

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.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

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.

The outer of the three germ layers of an embryo.

The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.

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.

The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.

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.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.

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.

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.

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.

The only species of a cosmopolitan ascidian.

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.

Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.

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.

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.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

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.

Echinoderms having bodies of usually five radially disposed arms coalescing at the center.

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.

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.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

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.

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.

The construction or arrangement of a task so that it may be done with the greatest possible efficiency.

A genus of SEA URCHINS in the family Toxopneustidae possessing trigeminate ambulacral plating.

The functional hereditary units of PLANTS.

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.

Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.

A species of nematode that is widely used in biological, biochemical, and genetic studies.

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.

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.

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.

The relationships of groups of organisms as reflected by their genetic makeup.

The portion of an interactive computer program that issues messages to and receives commands from a user.

Morphological and physiological development of EMBRYOS.

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.

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 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.

Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.

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.

A species of fruit fly much used in genetics because of the large size of its chromosomes.

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.

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.

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.

The condition in which reasonable knowledge regarding risks, benefits, or the future is not available.

Elements of limited time intervals, contributing to particular results or situations.

Proteins found in any species of bacterium.

A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.

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.

A species of gram-positive, asporogenous, non-pathogenic, soil bacteria that produces GLUTAMIC ACID.

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.

The reproductive organs of plants.

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.

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.

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.

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.

Formation of differentiated cells and complicated tissue organization to provide specialized functions.

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.

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.

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.

The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.

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.

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)

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.

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.

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.

A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.

The functional hereditary units of INSECTS.

Nucleic acid sequences involved in regulating the expression of genes.

An octamer transcription factor that is expressed primarily in totipotent embryonic STEM CELLS and GERM CELLS and is down-regulated during CELL DIFFERENTIATION.

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

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.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

Application of statistical procedures to analyze specific observed or assumed facts from a particular study.

The physiological mechanisms that govern the rhythmic occurrence of certain biochemical, physiological, and behavioral phenomena.

Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.

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)

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.

The study of chance processes or the relative frequency characterizing a chance process.

Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.

Cells that can give rise to cells of the three different GERM LAYERS.

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.

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.

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.

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.

The genetic complement of a BACTERIA as represented in its DNA.

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.

Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.

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 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.

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.

Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.

In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)

Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.

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)

Proteins obtained from the ZEBRAFISH. Many of the proteins in this species have been the subject of studies involving basic embryological development (EMBRYOLOGY).

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 whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.

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.

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)

Genetic loci associated with a QUANTITATIVE TRAIT.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.

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).

The complete gene complement contained in a set of chromosomes in a fungus.

Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.

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).

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.

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.

Organizations and individuals cooperating together toward a common goal at the local or grassroots level.

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.

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.

Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.

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.

Any method used for determining the location of and relative distances between genes on a chromosome.

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.

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)

These molecules and their interactions comprise a gene regulatory network. A typical gene regulatory network looks something ... Other work has focused on predicting the gene expression levels in a gene regulatory network. The approaches used to model gene ... Thus gene regulatory networks approximate a hierarchical scale free network topology. This is consistent with the view that ... Another widely cited characteristic of gene regulatory network is their abundance of certain repetitive sub-networks known as ...

https://en.wikipedia.org/wiki/Gene_regulatory_network

Plant Gene Regulatory Networks. Methods in Molecular Biology. Vol. 1629. pp. 167-184. doi:10.1007/978-1-4939-7125-1_12. ISBN ... This happens when dCAS9 binds to repressor domains, and in the case of the plants, deactivation of a regulatory gene such as ... In contrast to silencing genes, dCas9 can also be used to activate genes when fused to transcription activating factors. These ... These breaks can lead to gene inactivation or the introduction of heterologous genes through non-homologous end joining and ...

https://en.wikipedia.org/wiki/Cas9

"Identifying gene regulatory networks in schizophrenia". NeuroImage. 53 (3): 839-47. doi:10.1016/j.neuroimage.2010.06.036. PMC ...

https://en.wikipedia.org/wiki/Pritzker_Neuropsychiatric_Disorders_Research_Consortium

The Regulatory Genome: Gene Regulatory Networks In Development And Evolution (2006) ISBN 0-12-088563-8 Hinman, Veronica (2016 ... Hood, L. (2008). "Gene regulatory networks and embryonic specification". Proc. Natl. Acad. Sci. U.S.A. 105 (16): 5955-62. doi: ... Research web page Patent: Gene regulatory networks and methods of interdiction for controlling the differentiation state of a ... which would lead to a long line of investigation that eventually led to his contemporary interest in gene regulatory networks. ...

https://en.wikipedia.org/wiki/Eric_H._Davidson

Thattai, M; A. van Oudenaarden (2001). "Intrinsic noise in gene regulatory networks". PNAS USA. 98 (15): 8614-9. Bibcode: ... and then focused on stochasticity in gene networks biological networks as control systems, and the evolution of small networks ... During his time at MIT his lab started with parallel lines of research in actin dynamics and noise in gene networks, ... Pedraza, J M; A. van Oudenaarden (2005). "Noise propagation in gene networks". Science. 307 (5717): 1965-9. Bibcode:2005Sci... ...

https://en.wikipedia.org/wiki/Alexander_van_Oudenaarden

2007). "Innovation and robustness in complex regulatory gene networks". Proceedings of the National Academy of Sciences, USA. ... 2012). "Mutational Robustness of Gene Regulatory Networks". PLOS ONE. 7 (1): e30591. Bibcode:2012PLoSO...730591V. doi:10.1371/ ... or gene networks. Experimental systems for individual genes include enzyme activity of cytochrome P450, B-lactamase, RNA ... For instance, gene expression is intrinsically noisy. This means that two cells in exactly identical regulatory states will ...

https://en.wikipedia.org/wiki/Robustness_(evolution)

... gene regulatory networks (e.g. Guo et al., 2009), degeneracy (Whitacre et al., 2010), grammatical evolution (de Salabert et al ... "A cellular mechanism for multi-robot construction via evolutionary multi-objective optimization of a gene regulatory network." ... Tim Taylor (2004): "A Genetic Regulatory Network-Inspired Real-Time Controller for a Group of Underwater Robots", Intelligent ...

https://en.wikipedia.org/wiki/Artificial_development

Crombach, Anton; Hogeweg, Paulien (11 July 2008). "Evolution of Evolvability in Gene Regulatory Networks". PLOS Computational ... Draghi, J.; Wagner, G. P. (March 2009). "The evolutionary dynamics of evolvability in a gene network model". Journal of ... These regulatory linkages can be made and changed easily, a phenomenon that Kirschner and Gerhart call "weak regulatory linkage ... expressing different Hox genes). Other forms of regulatory compartmentation include different cell types, developmental stages ...

https://en.wikipedia.org/wiki/Facilitated_variation

Special Section: Gene Regulatory Networks for Development. 340 (2): 438-49. doi:10.1016/j.ydbio.2010.01.031. PMID 20123092. ... In studies of homozygous mice, it has been found that deletion of the MSX1 gene has resulted in a double cleft palate, ... In addition, encoded proteins by PAX9 genes have a 128 amino acid long DNA binding paired domain. Studies suggest that all ... Furthermore, mutations of other genes have been identified in syndromes and congenital abnormalities in which tooth agenesis is ...

https://en.wikipedia.org/wiki/Maxillary_lateral_incisor_agenesis

Erwin, Douglas H.; Davidson, Eric H. (2009). "The evolution of hierarchical gene regulatory networks" (PDF). Nature Reviews ... of gene expression generally flows from few high-level control genes through multiple intermediate genes to peripheral gene ... For instance, genes within GRNs with "optimally pleiotropic" effects, that is, genes that have the most widespread effect on ... This type of architecture implies that high-level control genes tend to be more pleiotropic affecting multiple downstream genes ...

https://en.wikipedia.org/wiki/Developmental_bias

Weighted correlation network analysis Gene regulatory networks Biological network inference Biological network Stuart, Joshua M ... "Gene regulatory network inference resources: A practical overview". Biochimica et Biophysica Acta (BBA) - Gene Regulatory ... whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a ... using gene expression profiles as independent variables Gene Network Reverse Engineering - Hundreds of methods to infer gene ...

https://en.wikipedia.org/wiki/Gene_co-expression_network

The organisms are modeled as gene regulatory networks. The models assume that gene expression is regulated exclusively at the ... Wagner's gene network model is a computational model of artificial gene networks, which explicitly modeled the developmental ... The interactions among genes constitute a gene network that is represented by a N {\displaystyle N} × N {\displaystyle N} ... The product of each gene can regulate the expression level of itself and/or the other genes through cis-regulatory elements. ...

https://en.wikipedia.org/wiki/Wagner's_gene_network_model

At MIT, Bar-Joseph's group developed a novel algorithm to discover regulatory networks of gene modules in yeast. These modules ... "Computational discovery of gene modules and regulatory networks". Nature Biotechnology. 21 (11): 1337-42. doi:10.1038/nbt890. ... Michal Linial Bar-Joseph, Ziv (2003). Inferring interactions, expression programs and regulatory networks from high throughput ... Lee, T. I. (2002). "Transcriptional Regulatory Networks in Saccharomyces cerevisiae". Science. 298 (5594): 799-804. Bibcode: ...

https://en.wikipedia.org/wiki/Ziv_Bar-Joseph

Interested in gene regulatory networks and developmental biology, Arda joined the laboratory of Seung K. Kim [Wikidata] at ... Arda's laboratory aims to delineate the gene regulatory networks that control the development, expansion and function of human ... During her doctorate training in the laboratory of Marian Walhout [Wikidata], she studied gene regulatory networks that pertain ... Arda, H. (2010-07-30). C. Elegans Metabolic Gene Regulatory Networks: A Dissertation. GSBS Dissertations and Theses (Thesis). ...

https://en.wikipedia.org/wiki/H._Efsun_Arda

"Appendages and gene regulatory networks: Lessons from the limbless". Genesis. 56 (1): e23078. doi:10.1002/dvg.23078. PMC ... targeting and observing the presence and activity of these genes and their regulatory enhancers. Many of the genes necessary ... The Shh gene, and genes belonging to the BMP, Hox, T-box, FGF, and Wnt families, all play a pivotal role in cell signaling and ... The Turing system has enabled a number of possible outcomes in the evolutionary steps of patterning networks. Many of the genes ...

https://en.wikipedia.org/wiki/Limb_development

Buckingham, M; Rigby, P (February 2014). "Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis". ... "Entrez Gene: MYOD1 myogenic differentiation 1". Rudnicki MA, Schnegelsberg PN, Stead RH, Braun T, Arnold HH, Jaenisch R (Dec ... Wnt4, Wnt5, and Wnt6 function to increase the expression of both of the regulatory factors but at a more subtle level. ... Setdb1 appears to be necessary to maintain both MyoD expression and also genes that are specific to muscle tissues because ...

https://en.wikipedia.org/wiki/MyoD

Signaling networks typically integrate protein-protein interaction networks, gene regulatory networks, and metabolic networks. ... The complete set of gene products and the interactions among them constitutes gene regulatory networks (GRN). GRNs regulate the ... Jia, Bochao; Xu, Suwa; Xiao, Guanghua; Lamba, Vishal; Liang, Faming (2017). "Learning gene regulatory networks from next ... weighted gene co-expression network analysis is extensively used to identify co-expression modules and intramodular hub genes. ...

https://en.wikipedia.org/wiki/Biological_network

"Gene regulatory networks and epigenetic modifications in cell differentiation". IUBMB Life. 66 (2): 100-109. doi:10.1002/iub. ... Later focusing his attention on bacteriophage lambda, he studied the gene expression of the bacterial virus using its operator- ... role of differential contact in the transcription regulation mechanism and demonstrated the theory in many genetic regulatory ...

https://en.wikipedia.org/wiki/Siddhartha_Roy

T-cell gene regulatory network from the Rothenberg Lab. Zebrafish developmental gene regulatory network from the Yuh Lab. Limb ... Input Gene Regulatory Networks can be drawn by hand. Networks can be built using lists of interactions entered via dialog boxes ... BioTapestry is an interactive tool for modeling and visualizing gene regulatory networks. Sea urchin endomesoderm network from ... Environment And Gene Regulatory Influence Network (EGRIN) for Halobacterium salinarum NRC-1 from the Baliga Lab. ...

https://en.wikipedia.org/wiki/BioTapestry

Interpreting the expression-gene and micro-array data. Identifying the network (regulatory) of genes. Learning evolutionary ... Neural networks, such as recurrent neural networks (RNN), convolutional neural networks (CNN), and Hopfield neural networks ... April 2015). "Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their ... Convolutional neural networks (CNN) are a class of deep neural network whose architecture is based on shared weights of ...

https://en.wikipedia.org/wiki/Machine_learning_in_bioinformatics

The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, 2006. M Ptashne and A Gann. Genes ... The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, 2006. S Barolo and JW Posakony. ... "Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification". Cell. ... Thus, common evolutionary rates could be forcing the genes for certain proteins to evolve together while preventing other genes ...

https://en.wikipedia.org/wiki/Modularity_(biology)

During his doctoral training, his research interests focused on modelling the evolution of gene regulatory networks-he ... Evolutionary modelling of feed forward loops in gene regulatory networks. Biosystems 2008; 91: 231-244. Cooper MB, Loose M, ... The evolutionary influence of binding site organisation on gene regulatory networks. Biosystems 2009; 96: 185-193. "Interview: ...

https://en.wikipedia.org/wiki/Max_Cooper_(music_producer)

"Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks". Hybrid Systems Biology. Lecture Notes in ... In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to a regulatory sequence of ... To introduce a reporter gene into an organism, scientists place the reporter gene and the gene of interest in the same DNA ... the reporter gene's expression is independent of the gene of interest's expression, which is an advantage when the gene of ...

https://en.wikipedia.org/wiki/Reporter_gene

Davidson, Eric H. (2006). The regulatory genome : gene regulatory networks in development and evolution. Amsterdam [Netherlands ... Laubichler, Manfred D.; Renn, Jürgen (2015). "Extended evolution: A Conceptual Framework for Integrating Regulatory Networks ... Newman, Stuart A.; Müller, Gerd B. (2006-01-06), "Genes and Form", Genes in Development, Duke University Press, pp. 38-73, doi: ... "Past climate change on Sky Islands drives novelty in a core developmental gene network and its phenotype". BMC Evolutionary ...

https://en.wikipedia.org/wiki/Extended_evolutionary_synthesis

Yan, Jun; Haifang Wang; Yuting Liu; Chunxuan Shao (October 2008). "Analysis of Gene Regulatory Networks in the Mammalian ... As the E-box is connected to several circadian genes, it is possible that the genes and proteins associated with it are " ... The E-box plays an important role in circadian genes; so far, nine E/E'BOX controlled circadian genes have been identified: ... Gene. 510 (2): 118-125. doi:10.1016/j.gene.2012.08.022. PMID 22960268. Nakahata, Y; Yoshida M; Takano A; Soma H; Yamamoto T; ...

https://en.wikipedia.org/wiki/E-box

Banf M, Rhee SY (January 2017). "Computational inference of gene regulatory networks: Approaches, limitations and opportunities ... A facultative gene is a gene only transcribed when needed as opposed to a constitutive gene. An inducible gene is a gene whose ... Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that ... A constitutive gene is a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when ...

https://en.wikipedia.org/wiki/Gene_expression

... gene regulatory networks, multicellular patterning, chemotaxis, systems neuroscience, the evolution of networks, and the effect ... Systems Biology research includes dynamic gene regulatory networks and systems neuroscience. Some models used are prokaryotes, ... Gene regulation studies include the organization and evolution of the regulatory genome, chromatin composition and ... The Gene Regulation, Stem Cells, and Cancer program focus on mechanisms of gene expression, mechanisms of epigenetic regulation ...

https://en.wikipedia.org/wiki/Centre_for_Genomic_Regulation

He proposed the Probabilistic Boolean Network (PBN) model for gene regulatory networks. PBNs have been extensively used for ... Shmulevich, Ilya; Dougherty, Edward (2002). "Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory ... Shmulevich, Ilya; Dougherty, Edward (2010). Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory ... and modeling gene regulatory networks. He is the Fellow of IEEE and SPIE. Dougherty is the author of 16 books, whose topics ...

https://en.wikipedia.org/wiki/Edward_R._Dougherty

... and control of gene regulatory networks underlying circadian rhythms; and computational analysis for developing diagnostics for ... As a scholar, Doyle applies systems engineering principles to the analysis of regulatory mechanisms in biological systems. His ...

https://en.wikipedia.org/wiki/Francis_J._Doyle_III

Multiscale models of gene regulatory networks focus on synthetic biology applications. Simulations can model all biomolecular ... regulation and induction of gene regulatory networks. Microfluidics, in particular droplet microfluidics, is an emerging tool ... Cells use interacting genes and proteins, which are called gene circuits, to implement diverse function, such as responding to ... Three key components are involved: DNA, RNA and Synthetic biologist designed gene circuits that can control gene expression ...

https://en.wikipedia.org/wiki/Synthetic_biology

Gene. 394 (1-2): 78-86. doi:10.1016/j.gene.2007.02.009. PMID 17383832. Lin T, Suttle DP (May 1995). "UMP synthase activity ... Evidence for a regulatory site". Biochemistry. 19 (26): 6062-8. doi:10.1021/bi00567a018. PMID 6894093. Traut TW, Payne RC (Dec ... "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ... In humans, the gene that codes for this enzyme is located on the long arm of chromosome 3 (3q13). This bifunctional enzyme has ...

https://en.wikipedia.org/wiki/Uridine_monophosphate_synthase

A&E Television Networks. November 16, 2009. Retrieved March 17, 2021. Updated December 9, 2020.{{cite web}}: CS1 maint: ... The fourth candidate was Eugene V. Debs of the Socialist Party. Roosevelt had broken with his former party at the 1912 ... When the war ended the Wilson Administration dismantled the wartime boards and regulatory agencies. Demobilization was chaotic ... History News Network. Columbia College of Arts and Sciences at the George Washington University. Retrieved December 7, 2020. ...

https://en.wikipedia.org/wiki/Woodrow_Wilson

The grouping of imprinted genes within clusters allows them to share common regulatory elements, such as non-coding RNAs and ... Winstead ER (2001-05-07). "The Legacy of Solid Gold". Genome News Network. Lazaraviciute G, Kauser M, Bhattacharya S, Haggarty ... among imprinted genes. It has also been postulated that if the retrotransposed gene is inserted close to another imprinted gene ... geneimprint.com Imprinted Gene and Parent-of-origin Effect Database J. Kimball's Imprinted Genes Site Genomic+imprinting at the ...

https://en.wikipedia.org/wiki/Genomic_imprinting

Human gene HSPA1B is an intron-less gene which encodes for the heat shock protein HSP70-2, a member of the Hsp70 family of ... Rosenzweig R, Nillegoda NB, Mayer MP, Bukau B (November 2019). "The Hsp70 chaperone network". Nature Reviews. Molecular Cell ... August 2013). "The ubiquitin ligase Stub1 negatively modulates regulatory T cell suppressive activity by promoting degradation ... "Entrez Gene: HSPA1A heat shock 70kDa protein 1B". Ito Y, Ando A, Ando H, Ando J, Saijoh Y, Inoko H, Fujimoto H (August 1998). " ...

https://en.wikipedia.org/wiki/HSPA1B

... transcriptional complexes activated by IFN signaling to these specific regulatory elements induces transcription of those genes ... "System-level comparison of protein-protein interactions between viruses and the human type I interferon system network". ... Gene cloning also confirmed that IFN-α was encoded by a family of many related genes. The type II IFN (IFN-γ) gene was also ... elements in gene promoters. Type I IFNs can induce expression of genes with either ISRE or GAS elements, but gene induction by ...

https://en.wikipedia.org/wiki/Interferon

The global network does not accept funding from governments, corporations, or political parties, relying on three million ... Scientific and regulatory agencies around the world have repeatedly and consistently found crops and foods improved through ... "Conservation of a sex-determining gene". Nature. 402 (6762): 601-602. Bibcode:1999Natur.402..601B. doi:10.1038/45130. PMID ... The network comprises 26 independent national/regional organisations in over 55 countries across Europe, the Americas, Africa, ...

https://en.wikipedia.org/wiki/Greenpeace

Promoters are important gene regulatory elements used in tuning synthetically designed genetic circuits and metabolic networks ... Gene promoters are typically located upstream of the gene and can have regulatory elements several kilobases away from the ... Enhancers are regions of the genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene ... There are also studies that measured gene expression in synthetic genes or from one to a few genes controlled by bidirectional ...

https://en.wikipedia.org/wiki/Promoter_(genetics)

United States regulatory policy is governed by the Coordinated Framework for Regulation of Biotechnology This regulatory policy ... refers to foods that have been produced using recent advances in gene technology, such as gene cloning, genesplicing and plant ... Global Agricultural Information Network) report CA12029, United States Department of Agriculture, Foreifn Agricultural Service ... Regulatory and Policy Trends). Business and the Environment 13.11 (Nov 2002): p14(1). GMO Compass Rapeseed Archived 2017-03-29 ...

https://en.wikipedia.org/wiki/Genetically_modified_food_in_North_America

Eugene O. Sykes (Mississippi) served the entire time the FRC existed and was appointed to the FCC in 1934. Henry Adams Bellows ... In that case there is not a denial of the freedom of speech but merely the application of the regulatory power of Congress in a ... There was almost no mention of the radio networks - notably the National Broadcasting Company (NBC) and, a bit later the ... The FRC's regulatory activities, and the public's knowledge of its work, primarily focused on broadcasting stations. However, ...

https://en.wikipedia.org/wiki/Federal_Radio_Commission

... the depletion of SON leads to increased intron retention and exon skipping in hESCs in regulatory genes of the cell cycle and ... "SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells". Nature Cell Biology. 15 (10): ... The SON gene is required for RNA splicing of transcripts encoding the cell-cycle protein TUBG1 and genes maintaining hESC ... Aberrant splicing and de novo heterozygous LoF mutations in SON gene disrupts the process of gene expression and can result in ...

https://en.wikipedia.org/wiki/ZTTK_syndrome

It is unknown whether different persons use similar antibody genes in response to COVID‑19. The severity of the inflammation ... The first COVID‑19 vaccine was granted regulatory approval on 2 December 2020 by the UK medicines regulator MHRA. It was ... The WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers, have established ...

https://en.wikipedia.org/wiki/COVID-19

Checkpoints typically consist of a network of regulatory proteins that monitor and dictate the progression of the cell through ... In general, the binding of pRb to E2F inhibits the E2F target gene expression of certain G1/S and S transition genes including ... October 2002). "Transcriptional regulatory networks in Saccharomyces cerevisiae". Science. 298 (5594): 799-804. Bibcode:2002Sci ... Several gene expression studies in Saccharomyces cerevisiae have identified 800-1200 genes that change expression over the ...

https://en.wikipedia.org/wiki/Cell_cycle

Bacterial small RNAs have been identified as components of many regulatory networks. Twenty sRNAs were experimentally ... When genes of unknown function on CII are disrupted, many types of auxotrophy result, emphasizing that the CII is not merely a ... Many genes are duplicated between the two chromosomes but appear to be differentially regulated. Moreover, many of the open ... Tao Y, Liu D, Yan X, Zhou Z, Lee JK, Yang C (2012). "Network Identification and Flux Quantification of Glucose Metabolism in ...

https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides

Regulatory provisions in the US, EU and elsewhere is in a state of flux, continuously being challenged by developments in ... television networks and other "music users", each of whom receives the right to perform any of the music in the repertoire of ... including genes, proteins and peptide fragments, expression systems, cells, and antibodies, for the field of plant disease The ... When a government owns the resource, the transaction often has to follow legal and regulatory requirements.[citation needed] In ...

https://en.wikipedia.org/wiki/Royalty_payment

... role in regulatory gene-expression networks. In conclusion, though not much is known about the role and mechanism by which ... which have evolved to play a role in complex gene-regulatory networks. The microRNAs are transcribed as part of longer RNA ... Insertion of a SINE upstream of a coding region may result in exon shuffling or changes to the regulatory region of the gene. ... This, in addition to SINEs' direct role in regulatory networks (as discussed in SINEs as long non-coding RNAs) is crucial to ...

https://en.wikipedia.org/wiki/Short_interspersed_nuclear_element

Eugene Thuraisingam - Human rights lawyer Davinder Singh - Continued practising law after retiring from politics in 2006. Ravi ... Accounting and Corporate Regulatory Authority Major General Ravinder Singh, Chief of Army, Singapore Armed Forces Vijakumar ... started the movie magazine on 15 August 1952 to publicise their imported movies before screening at their vast theatre network ...

https://en.wikipedia.org/wiki/List_of_Indians_in_Singapore

The subunit encoded by this gene is a component of the V(0) domain. Mutations in this gene are a cause of both cutis laxa type ... Lee C, Ghoshal K, Beaman KD (Jan 1991). "Cloning of a cDNA for a T cell produced molecule with a putative immune regulatory ... 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635-648. doi:10.1016 ... "Entrez Gene: ATP6V0A2 ATPase, H+ transporting, lysosomal V0 subunit a2". Nishi T, Forgac M (2002). "The vacuolar (H+)-ATPases-- ...

https://en.wikipedia.org/wiki/ATP6V0A2

The gene sequence of the target protein can also be compared to a known sequence and structural information can then be ... iron-regulatory proteins, current drug targets, and proteins predicted to have novel folds. So far, structures have been ... has recently developed a wiki-based approach namely Open protein structure annotation network (TOPSAN) for annotating protein ... Completed genome sequences allow every open reading frame (ORF), the part of a gene that is likely to contain the sequence for ...

https://en.wikipedia.org/wiki/Structural_genomics

Imports of natural gas started in the late 1980s and by the end of the 2010s the pipeline distribution network had been ... In Elbistan district, PM10 averages are over three times the regulatory limit, and in Soma SO2 averages are over four times the ... Efimova, Tatiana; Mazur, Eugene; Migotto, Mauro; Rambali, Mikaela; Samson, Rachel (February 2019). OECD Environmental ... "The Real Costs of Coal: Muğla". Climate Action Network Europe. Archived from the original on 26 January 2019. Retrieved 25 ...

https://en.wikipedia.org/wiki/Coal_in_Turkey

"Entrez Gene: Synemin, intermediate filament protein". Garcia-Pelagio KP, Muriel J, O'Neill A, Desmond P, Lovering R, Lund L, ... This protein has been found to form a linkage between desmin, which is a subunit of the IF network, and the extracellular ... Synemin plays an important regulatory role in the heart and the consequences of its absence are profound. Synemin has ... Genes on human chromosome 15, Wikipedia articles incorporating text from the United States National Library of Medicine). ...

https://en.wikipedia.org/wiki/Synemin

... however no data transmission is available on this network. An 8-tower 4G/LTE 1800 MHz network was installed in November 2018, ... although the latter's genes persist in a hybrid population descended from the last female. Other endemic birds are the white- ... civil or regulatory matters. The Chief Magistrate of Norfolk Island is usually the current Chief Magistrate of the Australian ... A small GSM (2G) mobile network operates on the island across 3 towers, ...

https://en.wikipedia.org/wiki/Norfolk_Island

"Entrez Gene: NFIA nuclear factor I/A". Leahy P, Crawford DR, Grossman G, Gronostajski RM, Hanson RW (March 1999). "CREB binding ... Berry FB, O'Neill MA, Coca-Prados M, Walter MA (February 2005). "FOXC1 transcriptional regulatory activity is impaired by PBX1 ... and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635-48. doi:10.1016/j.cell.2006.09.026. PMID ... Nuclear factor 1 A-type is a protein that in humans is encoded by the NFIA gene. Nuclear factor I (NFI) proteins constitute a ...

https://en.wikipedia.org/wiki/NFIA

He graduated from South Eugene High School. He later attended the University of Oregon, also in Eugene. He served as student ... "Neil's network". Portland Tribune. May 21, 2004. (Webarchive template wayback links, Articles with short description, Short ... through regulatory reform and repair of the state's infrastructure. Goldschmidt oversaw a major expansion of the state's prison ... Politicians from Eugene, Oregon, Portland City Council members (Oregon), South Eugene High School alumni, United States ...

https://en.wikipedia.org/wiki/Neil_Goldschmidt

Like NODs, NLRPs contain C-terminal LRRs, which appear to act as a regulatory domain and may be involved in the recognition of ... NODs signal via N-terminal CARD domains to activate downstream gene induction events, and interact with microbial molecules by ... The PRRs are also tightly connected to the proper function of neuronal networks and tissues, especially because of their ... December 1995). "A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21". Science. 270 (5243): 1804- ...

https://en.wikipedia.org/wiki/Pattern_recognition_receptor

The capture of a large number of RNA molecules enables elucidation of gene regulatory networks, prediction of function of ... RNA probes can be designed for any gene or any sequence within a gene for visualization of mRNA, lncRNA and miRNA in tissues ... In this context, it can help define the spatial-temporal patterns of gene expression within cells and tissues. In biology, a ... This homology can be detected by gene or genome sequencing but also by FISH. For instance, human and chimpanzee chromosomes are ...

https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization

Fox Networks Group Latin America - became Disney Networks Group Latin America in 2021. Fox Networks Group Europe - merging with ... It meets the regulatory requirements of the acquisition process in Mexico. On August 31, 2021, Disney announced that Hotstar in ... Maddaus, Gene (November 22, 2019). "Justice Department Goes to Court to Lift Paramount Consent Decrees". Variety. Archived from ... Fox Networks Group - U.S. division merged with Disney-ABC Television Group to form Walt Disney Television FX Networks FX ...

https://en.wikipedia.org/wiki/Acquisition_of_21st_Century_Fox_by_Disney

This region encompasses regulatory elements, non-coding genes, and the stem cell related POU5F1B gene. Roughly 4% of families ... National Comprehensive Cancer Network - Prostate (2012). "NCCN Clinical Practice Guidelines in Oncology". nccn.org. Archived ... Many genes are involved in inherited risk for prostate cancer. The first gene linked to inherited prostate cancer in families ... The absence of zinc is thought to occur via silencing the gene that produces ZIP1. It is called a tumor suppressor gene product ...

https://en.wikipedia.org/wiki/Prostate_cancer

He also inherited his father's network of political and business allies, in particular Charles Haughey and John Byrne, who both ... Moloney, Eugene (16 March 2006). "Disgraced property tycoon Gallagher dies". Irish Independent. Retrieved 23 September 2021. ... removing it from the regulatory oversight of the Central Bank. This allowed it to lend freely to the Gallagher Group. ...

https://en.wikipedia.org/wiki/Patrick_Gallagher_(businessman)

AP-1 transcription is deeply involved in the modulation of gene expression. Changes in cellular gene expression in the ... Due to the AP-1 regulatory functions in cancer cells, AP-1 modulation is studied as a potential strategy for cancer prevention ... "defines the organizational principles of the transcription factor network that drives the transcriptional programme of ... Wai PY, Mi Z, Gao C, Guo H, Marroquin C, Kuo PC (July 2006). "Ets-1 and runx2 regulate transcription of a metastatic gene, ...

https://en.wikipedia.org/wiki/AP-1_transcription_factor

... the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address this question, we performed an ... Glucocorticoid receptor-dependent gene regulatory networks Phillip Phuc Le 1 , Joshua R Friedman, Jonathan Schug, John E ... Glucocorticoid receptor-dependent gene regulatory networks Phillip Phuc Le et al. PLoS Genet. 2005 Aug. ... Figure 6. A Regulatory Network for the GR Pathway analysis was seeded with the 53 differentially expressed and GR-bound genes, ...

https://pubmed.ncbi.nlm.nih.gov/16110340/

Elucidation of cellular and gene regulatory networks (GRNs) governing organ development will accelerate progress toward tissue ... Figure 3. Endocrine progenitor gene regulatory network See text for details.. Figure 4. Immature β-cell gene regulatory network ... B) Sub-circuits of pancreas gene regulatory network representing canonical network motifs. (C) Pancreatic progenitor gene ... Gene regulatory network of differentiating acinar cells See text for details.. Figure 3. Endocrine progenitor gene regulatory ...

https://www.ncbi.nlm.nih.gov/pubmed/23597482

Using Knowledge Driven Matrix Factorization to Reconstruct Modular Gene Regulatory Network. February 1, 2023. ... Using Knowledge Driven Matrix Factorization to Reconstruct Modular Gene Regulatory Network. Proceedings of the AAAI Conference ... Using Knowledge Driven Matrix Factorization to Reconstruct Modular Gene Regulatory Network. Proceedings of the AAAI Conference ... 2008) Using Knowledge Driven Matrix Factorization to Reconstruct Modular Gene Regulatory Network, Proceedings of the AAAI ...

https://aaai.org/papers/00811-using-knowledge-driven-matrix-factorization-to-reconstruct-modular-gene-regulatory-network/

... This video was recorded at Workshop on ... Gene Regulatory Network Inference: In Silico Hypotheses and Experimental Validation is categorized in the following disciplines ... Gene regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditions ... You just viewed Gene Regulatory Network Inference: In.... Please take a moment to rate this material. ...

https://www.merlot.org/merlot/viewMaterial.htm?id=977410

NIEHS intramural scientists have defined descriptive terms of particular relevance to their own research, and have ranked those terms accordingly. This search feature obtains best-matches with the terms you choose, and shows an overall score based on the scientific rankings.. View our page to search various areas of interest and methodology.. ...

https://tools.niehs.nih.gov/portfolio/index.cfm?do=portfolio.grantDetail&grant_number=R01ES031937

... gene regulatory networks (GRNs) inferred from gene expression data, contain a wealth of information but are defying simple, ... For a concerted approach to a problem of this size, we suggest the establishment of the HUMAN GENE REGULATORY NETWORK PROJECT ... Overview of gene regulatory networks (GRN), transcriptional regulatory networks (TRN), and protein interaction networks (PIN) ... Overview of gene regulatory networks (GRN), transcriptional regulatory networks (TRN), and protein interaction networks (PIN) ...

https://www.mdpi.com/2504-4990/1/1/8

Novel cancer subtyping method based on patient-specific gene regulatory network. Mai Adachi Nakazawa, View ORCID Profile ... Novel cancer subtyping method based on patient-specific gene regulatory network Message Subject (Your Name) has forwarded a ... It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. However, only a ... Our method quantifies patient-specific gene networks, which are estimated from their transcriptome data. By clustering their ...

https://www.biorxiv.org/content/10.1101/2021.03.24.436731v2

... novel time lag based information theoretic approaches to infer gene regulatory networks have been proposed. The results show ... The proposed algorithms were compared to existing approaches on four different biological networks. The resulting networks were ... To circumvent the limitations of the MI metric, we introduce a new method of computing time lags between any pair of genes and ... that the time lags of regulatory effects between any pair of genes play an important role in GRN inference schemes. ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-S6-S19/tables/2

Microarray-based gene expression profiling demonstrated that CBD exerts its immunoregulatory effects in activated memory TMOG ... weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) elucidation of gene interactions. Results were ... Pathways and gene networks mediating the regulatory effects of cannabidiol, a nonpsychoactive cannabinoid, in autoimmune T ... Methods: Herein, using microarray-based gene expression profiling, we describe gene networks and intracellular pathways ...

https://pubmed.ncbi.nlm.nih.gov/27256343/

... we described functions of HB40 in modulating growth and development via the regulation of JUB1 and GA inactivation genes GA2OXs ... Functional characterization and unraveling the Gene Regulatory Networks (GRNs) of HD-Zip transcription factor HB40 (and HB22) ... Functional characterization and unraveling the Gene Regulatory Networks (GRNs) of HD-Zip transcription factor HB40 (and HB22) ... In Chapter 5, we investigated the potential gene regulatory network (GRN) controlled by HB22. ...

https://www.universiteitleiden.nl/onderzoek/onderzoeksoutput/wiskunde-en-natuurwetenschappen/functional-characterization-and-unraveling-the-gene-regulatory-networks-grns-of-hd-zip-transcription-factor-hb40-and-hb22-in-arabidopsis-thaliana

Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. Subtilis. In: Physica A: Statistical ... We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the ... N2 - We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of ... AB - We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of ...

https://pennstate.pure.elsevier.com/en/publications/large-scale-inference-and-graph-theoretical-analysis-of-gene-regu

... the MBL in Woods Hole will host the 5th high level short course on developmental gene regulatory networks. Course directors are ... MBL course: Gene regulatory networks for .... MBL course: Gene regulatory networks for Development. Posted by the Node, on 28 ... In October, the MBL in Woods Hole will host the 5th high level short course on developmental gene regulatory networks. Course ... "This high level short course on developmental gene regulatory networks will be offered to graduate students, postdocs, and PIs ...

https://thenode.biologists.com/mbl-course-gene-regulatory-networks-for-development/news/

IRBMED # 2001-0155 is a Single protocol of the Early Detection Research Network. ... Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. ... Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. IRBMED # 2001- ... Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. IRBMED # 2001- ...

https://edrn.nci.nih.gov/data-and-resources/protocols/443-molecular-profiling-of-cancer-identification-and-characterization-of-candidate-biomarkers-and-regulatory-genes-irbmed-2001-0155/

As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two ... and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. We conclude by ... the joint control of gene expression by global physiological effects and specific regulatory interactions, ... Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities ...

https://inria.hal.science/hal-01247997

... ...

http://papers.gersteinlab.org/papers/svm-echipchip/index-all.html

The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast ... 2015) Inferring orthologous gene regulatory networks using interspecies data fusion. Bioinformatics, 31 (12). i97-i105. doi: ... Gene regulatory networks -- Mathematical models, Species, Bayesian statistical decision theory, Gaussian processes ... Finally, the use of Saccharomyces cerevisiae data and networks to inform inference of networks in the budding yeast ...

http://wrap.warwick.ac.uk/85102/

Gene Regulatory Networks for Development. https://www.mbl.edu/education/courses/gene-regulatory-networks-for-development/ ... Gene Regulatory Networks. Strategic Plan Theme 1: Understanding the Molecular, Cellular, and Structural Basis of Development ... Gap: Our understanding of developmental gene regulatory networks is incomplete. A comprehensive picture is necessary to fully ... Priority: Research aimed at providing comprehensive analyses of gene regulatory networks at the single- and multi-cellular ...

https://www.nichd.nih.gov/about/org/der/branches/dbsvb/Pages/overview.aspx

Inference of Gene Regulatory Network Based on Local Bayesian Networks. Inference of Gene Regulatory Network Based on Local ... The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep ... The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative ... employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes ...

https://pesquisa.bvsalud.org/portal/resource/pt/mdl-27479082

5 Gene regulatory network analysis. After inferring the GRN, BioNERO. allows users to perform some common downstream analyses. ... for a given link between gene A and gene B, we can only say that these genes are coexpressed, but we cannot know whether gene A ... 4 Gene regulatory network inference. BioNERO. requires only 2 objects for GRN inference: the expression data ( ... In this vignette, we will demonstrate how to infer gene regulatory networks (GRNs) from expression data with BioNERO. GRNs ...

http://bioconductor.riken.jp/packages/3.17/bioc/vignettes/BioNERO/inst/doc/vignette_02_GRN_inference.html

We use these data to identify gene regulatory networks unique to cisplatin treated SV, as well as the differentially expressed ... Keywords: cisplatin; differential expression; endocochlear potential; gene regulatory networks; inner ear; scRNA-Seq; stria ... Genes are represented by circles, with genes enriched in cisplatin-treated SV cells to the right and genes enriched in control ... Blue circles are genes that exceed the p-value threshold but not the fold change threshold. Gray circles are genes that do not ...

https://www.pubmed.ncbi.nlm.nih.gov/34566577/

Bioinformatics , Computational biology , Gene expression , Gene regulatory networks , Prostate cancer [Full Text- HTML] [Full ... Comparative Analysis of Prostate Cancer Gene Regulatory Networks via Hub Type Variation ... Gene regulatory networks , Prostate cancer , Transcription factors [Full Text- HTML] [Full Text - PDF] [EndNote] [PMC XML] ...

https://www.ajmb.org/KeywordDetails?id=660

Analysis of gene regulatory networks of maize in response to nitrogen. Genes, 9 (3), p. 151. ISSN 2073-4425 ... In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two ... An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both ... Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and ...

https://irep.ntu.ac.uk/id/eprint/32914/

Intercellular delay regulates the collective period of repressively coupled gene regulatory oscillator networks」の研究トピックを掘り下げます。 ... Intercellular delay regulates the collective period of repressively coupled gene regulatory oscillator networks. In: IEEE ... Intercellular delay regulates the collective period of repressively coupled gene regulatory oscillator networks. IEEE ... Intercellular delay regulates the collective period of repressively coupled gene regulatory oscillator networks. / Wang, ...

https://keio.pure.elsevier.com/ja/publications/intercellular-delay-regulates-the-collective-period-of-repressive

Gene Regulatory Networks. Herbicide Resistance. Microsatellite Instability. Wetlands. Category J. Metal Nanoparticles. ... Genes, MDR. In 2006 this term was restricted to mammalian cells (eukaryotes).. In 2007 the terms definition expanded to ...

https://www.nlm.nih.gov/pubs/techbull/nd06/nd06_medline_data_changes2007.html

Students will spend the first few days learning to program in R and will be introduced to gene regulatory networks and the ... But gene expression in a cell is controlled through complex regulatory processes that involve regulatory genes (transcription ... They will then be given the opportunity to model regulatory networks in a disease model and explore their properties. ... By estimating networks separately for healthy and disease populations and comparing those networks, we can gain insight into ...

https://www.hsph.harvard.edu/biostatistics/diversity/summer-program/research-projects/

We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post- ... transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. ... We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks ( ... also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene ...

https://hal.inrae.fr/view/index/identifiant/hal-02049894

... transcription and gene regulatory networks; coding and noncoding RNA mechanisms of action and function; protein synthesis; the ... A leader in RNA biology, Lorsch studies the initiation of translation, a major step in controlling how genes are expressed. ... gene expression, and development. The results of this research form the foundation for advances in diagnosing, preventing, ... including the development of models and algorithms related to biological networks organization and dynamic processes. The ...

https://www.nih.gov/about-nih/what-we-do/nih-almanac/national-institute-general-medical-sciences-nigms

Chromatin, epigenetics and gene regulatory networks. *Cell fate decisions during development and tumorigenesis ... Elucidation of gene networks (Figure 1) associated with specific biological phenotypes thus becomes key to understanding the ... ESCs, derived from the inner cell mass of the blastocyst, are an ideal model system for understanding gene networks controlling ... Reconstruction and characterization of gene networks regulating stem cell identity. *Investigation into how signaling cascades ...

https://www.niehs.nih.gov/research/atniehs/labs/escbl/pi/systemsbiology/index.cfm

This process is tightly orchestrated by a cardiac gene regulatory network (GRN), which ensures the precise spatio-temporal ... Alterations of the timing or spatial localisation of gene expression can have a significant impact in cardiac ontogeny and may ... In particular, we focus on studies utilising high-throughput technologies to systematically dissect gene expression patterns, ... This process is tightly orchestrated by a cardiac gene regulatory network (GRN), which ensures the precise spatio-temporal ...

https://db.cngb.org/stomics/publications/34170300

... identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene ... Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo , has broad implications for GRN ... we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans ... Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient ...

https://www.cardioscience.ox.ac.uk/publications/1088424

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)
Causal networks, e.g., gene regulatory networks (GRNs) inferred from gene expression data, contain a wealth of information but are defying simple, straightforward and low-budget experimental validations. (mdpi.com)
The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. (warwick.ac.uk)
The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. (bvsalud.org)
To overcome the limitations, in this work we present a novel algorithm , namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. (bvsalud.org)
Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. (bvsalud.org)
In particular, the decomposition strategy with local Bayesian networks not only effectively reduce the computational cost of BN due to much smaller sizes of local GRNs, but also identify the directions of the regulations . (bvsalud.org)
In this vignette, we will demonstrate how to infer gene regulatory networks (GRNs) from expression data with BioNERO. (riken.jp)
GRNs display interactions between regulators (e.g., transcription factors or miRNAs) and their targets (e.g., genes). (riken.jp)
This function will infer GRNs with GENIE3, ARACNE and CLR, calculate average ranks for each interaction and filter the resulting network based on the optimal scale-free topology (SFT) fit. (riken.jp)
a regression-tree based algorithm that decomposes the prediction of GRNs for n genes into n regression problems. (riken.jp)
We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. (inrae.fr)
We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. (inrae.fr)
Abstract Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). (ox.ac.uk)
Gene regulatory networks (GRNs) represent how interactions between ligands, receptors, and other regulatory factors are integrated to drive gene expression and establish cell state and ultimately function. (biologists.com)

To address this question, we performed an orthogonal analysis to identify direct targets of the GR. First, we analyzed the expression profile of mouse livers in the presence or absence of exogenous glucocorticoid, resulting in over 1,300 differentially expressed genes. (nih.gov)
Different physical states, or phenotypes, are often characterized based on differentially expressed genes. (harvard.edu)

Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. (medlineplus.gov)

In October, the MBL in Woods Hole will host the 5th high level short course on developmental gene regulatory networks. (biologists.com)
This high level short course on developmental gene regulatory networks will be offered to graduate students, postdocs, and PI's who wish to adapt or advance network approaches to their own research. (biologists.com)
Our understanding of developmental gene regulatory networks is incomplete. (nih.gov)
Research aimed at providing comprehensive analyses of gene regulatory networks at the single- and multi-cellular level for all developmental stages using model organisms and human cell-based models. (nih.gov)
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish. (cngb.org)
2. Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era. (cngb.org)
5. Assessing regulatory information in developmental gene regulatory networks. (nih.gov)
6. The function of architecture and logic in developmental gene regulatory networks. (nih.gov)
7. Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids. (nih.gov)
8. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. (nih.gov)
9. Building developmental gene regulatory networks. (nih.gov)
14. Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. (nih.gov)
19. Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development. (nih.gov)

This video was recorded at Workshop on Probabilistic Modelling of Networks and Pathways, Sheffield 2007. (merlot.org)
Herein, using microarray-based gene expression profiling, we describe gene networks and intracellular pathways involved in CBD-induced suppression of these activated memory TMOG cells. (nih.gov)
Cells that were more CSF-like had increased expression of genes linked to T cell exhaustion and TH1 function pathways and decreased expression of TH cell differentiation and interleukin-7 signaling pathways. (genomeweb.com)
Existing genetic regulatory pathways analysis tools allow researchers to map their experimental data onto gene networks, but do not allow researchers to actively simulate dynamic perturbations to specific nodes. (nih.gov)

In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two microarray studies have been used to infer components of the nitrogen-response network. (ntu.ac.uk)
This package can be used to infer gene regulatory networks from high-throughput gene expression data using different algorithms within the same framework. (archives-ouvertes.fr)

The literature is replete with various approaches to extracting gene regulatory networks from microarray profiling data. (merlot.org)

Context: Inferring gene regulatory networks (GRN) from high-throughput gene expression data is a challenging task for which different strategies have been developed. (archives-ouvertes.fr)
3. Low-order conditional independence graphs for inferring genetic networks. (nih.gov)
4. Inferring gene regulatory networks from multiple microarray datasets. (nih.gov)
9. Inferring gene regulatory networks from time series data using the minimum description length principle. (nih.gov)
14. Inferring Boolean networks with perturbation from sparse gene expression data: a general model applied to the interferon regulatory network. (nih.gov)
20. Inferring cellular networks using probabilistic graphical models. (nih.gov)

Using established computational tools, we integrated and represented these networks in frameworks that should enhance understanding of the surging output of genomic-scale genetic and epigenetic studies of pancreas development and diseases such as diabetes and pancreatic cancer. (nih.gov)
By employing a computational, linear correlative procedure to generate these networks, and by analyzing the networks from a graph theoretical perspective, we are able to verify the biological viability of our inferred networks, and we demonstrate that our networks' graph-theoretical properties are remarkably similar to those of other biological systems. (elsevier.com)
Further research that uses this information to create predictive computational models of the complex gene regulatory networks that coordinate vertebrate embryogenesis. (nih.gov)
Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory -based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. (bvsalud.org)
1. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. (nih.gov)
6. EXAMINE: a computational approach to reconstructing gene regulatory networks. (nih.gov)
This initiative encourages research to develop new, or adapt existing, computational and statistical approaches to aggregate, mine, and conduct integrative analyses of single-cell and bulk tissue multi-omic datasets from brain samples (e.g., gene expression, chromatin state, histone modifications, DNA methylation, etc.) to achieve new insights into the biology of psychiatric disorders. (nih.gov)

We then executed genome-wide location analysis on chromatin from the same livers, identifying more than 300 promoters that are bound by the GR. Intersecting the two lists yielded 53 genes whose expression is functionally dependent upon the ligand-bound GR. Further network and sequence analysis of the functional targets enabled us to suggest interactions between the GR and other transcription factors at specific target genes. (nih.gov)
In this study, the researchers model lateral inhibition, with a GRN model that has both Notch ligand, and Notch ligand repressor as the target genes of the receiver cells. (biologists.com)
Knowing involvement of jag1a ligand in the GRN, the researchers set out to identify 'ligand repressor' genes, which are Notch target genes that repress jag1a . (biologists.com)

Encouragingly, the model network reveal some of the known regulatory interactions in the literature. (merlot.org)
Regulatory interactions which are either confirmed or not confirmed by this experiment will be used to define Bayesian priors for iterative retraining of the state space model by including the time series data collected from the perturbed system. (merlot.org)
mRNA of purified TMOG was then subjected to Illumina microarray analysis followed by ingenuity pathway analysis (IPA), weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) elucidation of gene interactions. (nih.gov)
As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two applications in the model bacterium Escherichia coli in some detail: the joint control of gene expression by global physiological effects and specific regulatory interactions, and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. (hal.science)
Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. (ox.ac.uk)
Subtle perturbations in gene networks are likely to cause much of inherited disease susceptibility, but understanding how complex genotypes and environmental interactions result in disease will require experimental systems biology using model organisms. (nih.gov)

Elucidation of gene networks (Figure 1) associated with specific biological phenotypes thus becomes key to understanding the molecular basis of development and pathogenesis. (nih.gov)

2005). Analysis of the biological implications of these network models is still on-going, but preliminary analysis has already revealed some promising novel biological hypotheses relating to the transcriptional response of bacterial cells adapting to the temperature shift. (merlot.org)
We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. (inrae.fr)
13. A graph-based approach to systematically reconstruct human transcriptional regulatory modules. (nih.gov)
18. Gene networks as a tool to understand transcriptional regulation. (nih.gov)
19. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. (nih.gov)

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. (gersteinlab.org)
18. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. (nih.gov)

Moreover, we review measurement models that have been proposed to interpret primary fluorescence data and inference methods for estimating gene expression profiles from these data. (hal.science)
Results: In this work, we introduce GReNaDIne (Gene Regulatory Network Data-driven Inference), a Python package that implements 18 machine learning data-driven gene regulatory network inference methods. (archives-ouvertes.fr)

We developed an algorithm, PANDA, that models gene regulation as a communication process between TFs and their targets. (harvard.edu)
Similar to eukaryotic miRNAs, many of these bacterial RNAs act by base pairing with mRNA targets to modulate mRNA stability and translation and are integral to most regulatory networks. (nih.gov)

Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and NLP15 as candidate regulators of genes repressed under low Nitrogen conditions, while bZIP108 might play a role in gene activation. (ntu.ac.uk)
The Jothi group is interested in understanding how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation, and apply this knowledge to aid in the development of diagnostic and therapeutic strategies for cancer and other diseases. (nih.gov)
5. Gene transcription in the zebrafish embryo: regulators and networks. (cngb.org)

Inference of Gene Regulatory Network Based on Local Bayesian Networks. (bvsalud.org)
2. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. (nih.gov)

Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. (nih.gov)
One major focus of our research has been the identification and characterization of small, regulatory RNAs in E. coli. (nih.gov)
CIT): Women Scientists Advisory WSA Anita Roberts Lecture The hidden secrets of small genes One major focus of our research has been the identification and characterization of small, regulatory RNAs in E. coli. (nih.gov)

In particular, we focus on studies utilising high-throughput technologies to systematically dissect gene expression patterns, both temporally and spatially during heart development. (cngb.org)

In 2012, two studies (Garnett et al and Barretina et al) attempted to correlate large numbers of gene expression, mutation, and copy number measurements in hundreds of cancer cell lines with sensitivities to hundreds of different drugs, with the goal of finding genes or mutations that might indicate certain kinds of cancers with vulnerabilities to specific drugs. (harvard.edu)
Mutations in the TFAP2A gene cause a condition called branchio-oculo-facial syndrome, which is characterized by skin anomalies on the neck, malformations of the eyes and ears, and distinctive facial features. (medlineplus.gov)
Most TFAP2A gene mutations involved in this condition change single protein building blocks (amino acids) in the transcription factor AP-2α protein. (medlineplus.gov)
TFAP2A gene mutations disrupt the development of structures derived from the branchial arches, which results in the characteristic features of branchio-oculo-facial syndrome. (medlineplus.gov)

These proteins regulate genes that help control cell division and the self-destruction (apoptosis) of cells that are no longer needed. (medlineplus.gov)

Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. (nih.gov)

Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities characterizing gene expression. (hal.science)
In order to assess whether her6 or her9 are directly responsible for repressing jag1a, they over-expressed these genes with a notochord-specific promoter. (biologists.com)
Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. (nih.gov)

During development and in response to environmental insults, various signaling cascades culminate in the activation of appropriate master transcription factors (TFs) and chromatin remodeling enzymes to establish gene expression programs controlling cell fate decisions. (nih.gov)

Reconstruction of gene networks controlling cellular response or fate. (nih.gov)
16. Fast calculation of pairwise mutual information for gene regulatory network reconstruction. (nih.gov)

The understanding of the regulatory networks controlling the adaptation of bacteria to changes in their environment is critically dependent on the ability to monitor the dynamics of gene expression. (hal.science)
In both frameworks, information about network similarity is captured via graph kernels, with the networks additionally informed by species-specific time series gene expression data, when available, using Gaussian processes to model the dynamics of gene expression. (warwick.ac.uk)

B) Sub-circuits of pancreas gene regulatory network representing canonical network motifs. (nih.gov)
Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates. (ox.ac.uk)

While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. (nih.gov)
In Chapter 2, we described functions of HB40 in modulating growth and development via the regulation of JUB1 and GA inactivation genes GA2OXs. (universiteitleiden.nl)
The goal of this initiative is to encourage research that will advance our understanding of brain cell type-specific gene regulation to elucidate the pathogenesis of mental disorders. (nih.gov)

In addition to studies aimed at identifying and understanding the roles of gene variants, environmental perturbations, and other factors causing structural birth defects, DBCAB supports studies intended to advance our understanding of the fundamental processes underlying the formation and differentiation of the embryo. (nih.gov)

Model networks were inferred from the data using the variational Bayesian state space modelling approach of Beal et al. (merlot.org)

We conclude by discussing some current trends in the use of fluorescent reporter genes. (hal.science)
Their single cell RNA-seq analysis revealed her6 and her9 as highly co-expressed genes with jag1a , and fluorescent in situ hybridization of her6 and her9 mRNA showed out-of-phase pattern with jag1a . (biologists.com)

Hilger-Eversheim K, Moser M, Schorle H, Buettner R. Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. (medlineplus.gov)

Putative Arabidopsis homologues of maize genes were used to query the Biological General Repository for Interaction Datasets (BioGRID) network, which yielded the potential involvement of three transcription factors (TFs) (GLK5, MADS64 and bZIP108) and a Calcium-dependent protein kinase. (ntu.ac.uk)
An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both microarray studies, along with genes for Asparagine Synthetase, a dual-specific protein kinase and a protein phosphatase. (ntu.ac.uk)
Interestingly, while it was initially assumed these small RNAs are encoded as independent genes, recent studies have shown that many small RNAs are derived from the 3' end of protein coding genes and the distinction between coding and noncoding is becoming increasingly blurred. (nih.gov)
12. Fitting a geometric graph to a protein-protein interaction network. (nih.gov)
The TFAP2A gene provides instructions for making a protein called transcription factor AP-2 alpha (AP-2α). (medlineplus.gov)
As its name suggests, this protein is a transcription factor, which means it attaches (binds) to specific regions of DNA and helps control the activity of particular genes. (medlineplus.gov)
Without this function, the protein cannot control the activity of genes during development. (medlineplus.gov)

We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. (elsevier.com)

He is now developing new functional bionanomaterials for drug and gene delivery for cancer therapy and for cancer targeting. (nih.gov)
Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology-derived functional networks to discover clusters of genes that share both similar expression patterns and functions. (nih.gov)

Inference of Genome-Scale Gene Regulatory Networks: Are There Differences in Biological and Clinical Validations? (mdpi.com)
By clustering their quantified networks, our method allows for cancer subtyping, taking into consideration the differences in the molecular systems of patients. (biorxiv.org)
At the gene expression level, however, they noted a number of differences. (genomeweb.com)
These differences in gene expression were particularly noticeable in clonally expanded T cells among MS patients. (genomeweb.com)
Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role. (genomeweb.com)

We present a modeling and simulation suite, GRANITE, (Genetic Regulatory Analysis of Networks Investigational Tools Environment), an agent-based approach to modeling large, complex, and dynamic systems. (nih.gov)

Our long-term goal is to develop predictive models of gene function with a specific focus on sex differentiation in the germline. (nih.gov)
Predictive models for gene and pathway function will be important for diagnosis and ultimately intervention, fulfilling the promise of the human genome project. (nih.gov)

When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state -of-the- art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. (bvsalud.org)

Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes. (nih.gov)

Although many of these methods have produced networks which appear biologically plausible, based on circumstantial evidence from the literature, very little work has been done on validating the model networks experimentally. (merlot.org)
Such information can provide empirical support to regulatory decision making that has historically relied on non-statistical and non-data- based methods. (harvard.edu)

Time series microarray data collected from this mutant strain should directly address the question of whether the expression of genes involved in aerobic/anaerobic metabolism during re-adaptation to 37oC is dependent on the expression of hns. (merlot.org)
Our method quantifies patient-specific gene networks, which are estimated from their transcriptome data. (biorxiv.org)
This project will combine time-varying data on emissions from over 1000 power plants in the US and measures of air pollution (and population health) at 10s of thousands of US zip codes to learn about the network defining how regulatory interventions at specific power plants spill across the country to impact the air people breathe. (harvard.edu)
5. Stochastic dynamic modeling of short gene expression time-series data. (nih.gov)
10. Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. (nih.gov)
17. Ensemble learning of genetic networks from time-series expression data. (nih.gov)

This process is tightly orchestrated by a cardiac gene regulatory network (GRN), which ensures the precise spatio-temporal deployment of genes critical for heart formation. (cngb.org)
20. Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo. (nih.gov)

It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. (biorxiv.org)

Results on in silico benchmarks demonstrate that joint inference, and leveraging of known networks between species, offers better accuracy than standalone inference. (warwick.ac.uk)
Our ultimate goal is to determine how the collective action of genes results in an individual with specific characteristics, development, and disease susceptibilities. (nih.gov)

Microarray-based gene expression profiling demonstrated that CBD exerts its immunoregulatory effects in activated memory TMOG cells via (a) suppressing proinflammatory Th17-related transcription, (b) by promoting T cell exhaustion/tolerance, (c) enhancing IFN-dependent anti-proliferative program, (d) hampering antigen presentation, and (d) inducing antioxidant milieu resolving inflammation. (nih.gov)
But gene expression in a cell is controlled through complex regulatory processes that involve regulatory genes (transcription factors, or TFs) activating or deactivating the expression of other genes. (harvard.edu)
Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo , has broad implications for GRN discovery and investigation. (ox.ac.uk)
GRN components are usually identified by perturbation experiments, which reveal the critical genes for the action of interest, such as cell fate decision or pattern formation. (biologists.com)
In this network, the sender cell presents Notch ligand, which induces Notch intracellular domain (NICD) cleavage in the receiver cells, activating transcription of both ligand and ligand repressors. (biologists.com)
NEW YORK - T cells isolated from the cerebrospinal fluid of people with multiple sclerosis express higher levels of genes linked to T cell activation and cytotoxicity than those from the CSF of healthy people, according to a new single-cell RNA sequencing study. (genomeweb.com)
For instance, genes involved in TCR engagement and T cell activation were more highly expressed among MS patients compared to controls. (genomeweb.com)
Many of these genes were linked to T cell activation, cytotoxicity, and an effector phenotype. (genomeweb.com)

Our model places a number of genes at the higher level of the hierarchy ("hubs") in the temperature shifted network, including hns and hybC. (merlot.org)
The model also indicates that hns downregulates genes involved in aerobic metabolism and upregulates genes involved in anaerobic metabolism. (merlot.org)
Based on a published gene regulatory oscillator model, we analyze the collective period of delay-coupled biological oscillators using the multivariable harmonic balance technique. (elsevier.com)
They will then be given the opportunity to model regulatory networks in a disease model and explore their properties. (harvard.edu)
We show that GRANITE is expressive enough to capture any kind of interaction network, can modularly use any kinetic model, is computationally tractable and scalable, and allows researchers to interact and dynamically perturb the system at different hierarchical levels to learn its rules for emergent behavior. (nih.gov)

Y. Tamada and Y. Okuno have a patent application on the method for identification of patient-specific network used in this study through the technology licensing organization in Kyoto University. (biorxiv.org)
Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. (nih.gov)
Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D. Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. (nih.gov)

Understanding the relationships between genes is crucial to identify the genetic program of organisms. (mdpi.com)
This study aims to build a genetic network for the yeast genome by recognizing interacting genes. (mdpi.com)
Cells follow a genetic blueprint composed of complex webs of interacting genes. (nih.gov)
1. New probabilistic graphical models for genetic regulatory networks studies. (nih.gov)
7. A Markovian approach to the control of genetic regulatory networks. (nih.gov)
8. External control in Markovian genetic regulatory networks: the imperfect information case. (nih.gov)
15. Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks. (nih.gov)

Anatomy14

Organisms20

Chemicals and Drugs24

Analytical, Diagnostic and Therapeutic Techniques and Equipment29

Psychiatry and Psychology2

Phenomena and Processes65

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science22

Health Care11

Where are we in genomics? (1/4873)

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

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

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

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

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

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

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

No images available that match "gene regulatory networks"

Gene Regulatory Networks

Models, Genetic

Gene Expression Profiling

Computational Biology

Algorithms

Systems Biology

Transcription Factors

Gene Expression Regulation, Developmental

Computer Simulation

Models, Biological

Oligonucleotide Array Sequence Analysis

Sea Urchins

Gene Expression Regulation

Strongylocentrotus purpuratus

Signal Transduction

Neural Networks (Computer)

Bayes Theorem

Databases, Genetic

Echinodermata

Embryo, Nonmammalian

Metabolic Networks and Pathways

Stochastic Processes

Software

Evolution, Molecular

Genomics

MicroRNAs

Transcriptome

Cell Physiological Phenomena

Nucleotide Motifs

Endoderm

Transcription, Genetic

Cluster Analysis

Feedback, Physiological

Gene Expression Regulation, Bacterial

Models, Statistical

Homeodomain Proteins

Gene Expression Regulation, Plant

Regulatory Elements, Transcriptional

Saccharomyces cerevisiae

Protein Interaction Mapping

Proteome

Arabidopsis

Body Patterning

Mesoderm

Cell Differentiation

Genes, Regulator

Genome

Immune System Phenomena

Markov Chains

Binding Sites

Chromatin Immunoprecipitation

Ectoderm

Biological Evolution

Gastrulation

Cell Lineage

Promoter Regions, Genetic

Gene Expression Regulation, Fungal

Nonlinear Dynamics

Escherichia coli

Reproducibility of Results

Ciona intestinalis

Position-Specific Scoring Matrices

Vertebrates

Skeleton

Blastula

Phenotype

Molecular Sequence Data

Starfish

Embryonic Stem Cells

Regulon

Base Sequence

Mutation

Models, Theoretical

Work Simplification

Lytechinus

Genes, Plant

Epistasis, Genetic

Protein Interaction Maps

Caenorhabditis elegans

Drosophila