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  • expression
  • The stringent response, σ H -dependent gene expression and sporulation in Bacillus subtilis . (springer.com)
  • This data typically include gene expression measurements of wild type and mutant cells in response to a given stimulus. (paperity.org)
  • Independent regulation of gene expression level and noise by histone modifications. (amedeo.com)
  • Expression profiles reflect gene expression levels for different replicates or strains studied in different physico-chemical, temporal or culture medium conditions. (biomedcentral.com)
  • Although the cost of biological experiments diminishes, gene expression data is often acquired under a limited number of replicates and conditions compared to the number of genes. (biomedcentral.com)
  • In this scenario, advanced statistical methods and algorithms are becoming fundamental to decipher the dynamics of biochemical mechanisms such those involved in the regulation of gene expression. (ed.ac.uk)
  • Here, we present a computational study in which we determine an optimal gene regulatory network from the spatiotemporal dynamics of gene expression patterns in a complex 2D growing tissue (non‐isotropic and heterogeneous growth rates). (embopress.org)
  • The process of mapping experimental gene expression data of Meis, Hoxa11 and Hoxa13 to the 2D limb bud model. (embopress.org)
  • The general regulatory model uses the RA and FGF morphogen gradients as inputs and should explain the expression patterns of the PD markers as outputs: Meis, Hoxa11 and Hoxa13 over time and space. (embopress.org)
  • A gene co-expression network (GCN) is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. (wikipedia.org)
  • Having gene expression profiles of a number of genes for several samples or experimental conditions, a gene co-expression network can be constructed by looking for pairs of genes which show a similar expression pattern across samples, since the transcript levels of two co-expressed genes rise and fall together across samples. (wikipedia.org)
  • The concept of gene co-expression networks was first introduced by Butte and Kohane in 1999 as relevance networks. (wikipedia.org)
  • Bute and Kohane used this approach later with mutual information as the co-expression measure and using gene expression data for constructing the first gene co-expression network. (wikipedia.org)
  • A good number of methods have been developed for constructing gene co-expression networks. (wikipedia.org)
  • In first step, a co-expression measure is selected and a similarity score is calculated for each pair of genes using this measure. (wikipedia.org)
  • Then, a threshold is determined and gene pairs which have a similarity score higher than the selected threshold are considered to have significant co-expression relationship and are connected by an edge in the network. (wikipedia.org)
  • The input data for constructing a gene co-expression network is often represented as a matrix. (wikipedia.org)
  • If we have the gene expression values of m genes for n samples (conditions), the input data would be an m×n matrix, called expression matrix. (wikipedia.org)
  • Each element in this matrix shows how similar the expression level of two genes change together. (wikipedia.org)
  • The expression values of a gene for different samples can be represented as a vector, thus calculating the co-expression measure between a pair of genes is the same as calculating the selected measure for two vectors of numbers. (wikipedia.org)
  • Pearson's correlation coefficient, Mutual Information, Spearman's rank correlation coefficient and Euclidean distance are the four mostly used co-expression measures for constructing gene co-expression networks. (wikipedia.org)
  • Euclidean distance measures the geometric distance between two vectors, and so considers both the direction and the magnitude of the vectors of gene expression values. (wikipedia.org)
  • Mutual information measures how much knowing the expression levels of one gene reduces the uncertainty about the expression levels of another. (wikipedia.org)
  • Spearman's rank correlation is the Pearson's correlation calculated for the ranks of gene expression values in a gene expression vector. (wikipedia.org)
  • Gene co-expression networks can be interpreted as association networks between variables that measure transcript abundances. (wikipedia.org)
  • These networks have been used to provide a systems biologic analysis of DNA microarray data, RNA-seq data, miRNA data etc. weighted gene co-expression network analysis is widely used to identify co-expression modules and intramodular hub genes. (wikipedia.org)
  • Teichmann's research investigates gene expression and protein complex assembly using both wet laboratory and computational biology techniques. (wikipedia.org)
  • The RegCreative jamboree was stimulated by a community initiative to curate in perpetuity the genomic sequences which have been experimentally determined to control gene expression. (wikipedia.org)
  • Bayesian
  • Dondelinger, F., Lébre, S., Husmeier, D.: Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure. (springer.com)
  • Two branches of graphical representations of distributions are commonly used, namely, Bayesian networks and Markov random fields. (wikipedia.org)
  • Local independences and global independences are equivalent in Bayesian networks. (wikipedia.org)
  • This type of graphical model is known as a directed graphical model, Bayesian network, or belief network. (wikipedia.org)
  • Classic machine learning models like hidden Markov models, neural networks and newer models such as variable-order Markov models can be considered special cases of Bayesian networks. (wikipedia.org)
  • Both directed acyclic graphs and undirected graphs are special cases of chain graphs, which can therefore provide a way of unifying and generalizing Bayesian and Markov networks. (wikipedia.org)
  • neural network
  • For example, they suggest that a learning system can be seen as being subject to architectural constraints during development, an idea that gave birth to the neural network field of constructivist modelling. (wikipedia.org)
  • Volume 2 contains a variety of neural network models that investigate how these representations change during learning (including models from Randy O'Reilly, Matthew Schlesinger and Yuko Munakata). (wikipedia.org)
  • Known for pioneering the field of modelling and performance evaluation of computer systems and networks throughout Europe, he invented the random neural network and the eponymous G-networks. (wikipedia.org)
  • His inventions include the design of the first random access fibre-optics local area network, a patented admission control technique for ATM networks, a neural network based anomaly detector for brain magnetic resonance scans, and the cognitive packet network routing protocol to offer quality of service to users. (wikipedia.org)
  • microarray
  • Many genome-scale data are available in soybean including genomic sequence, transcriptomics (microarray, RNA-seq), proteomics and metabolomics datasets, together with growing knowledge of soybean in gene, microRNAs, pathways, and phenotypes. (missouri.edu)
  • dynamical
  • Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. (royalsocietypublishing.org)
  • Ruet, P., Thieffry, D.: Graphic requirements for multistability and attractive cycles in a boolean dynamical framework. (springer.com)
  • A Boolean network is a particular kind of sequential dynamical system, where time and states are discrete, i.e. both the set of variables and the set of states in the time series each have a bijection onto an integer series. (wikipedia.org)
  • Since a Boolean network has only 2N possible states, a trajectory will sooner or later reach a previously visited state, and thus, since the dynamics are deterministic, the trajectory will fall into a steady state or cycle called an attractor (though in the broader field of dynamical systems a cycle is only an attractor if perturbations from it lead back to it). (wikipedia.org)
  • In dynamical systems theory, the structure and length of the attractors of a network corresponds to the dynamic phase of the network. (wikipedia.org)
  • experimental
  • It has many useful tools including Affymetrix probeID search, gene family search, multiple gene/metabolite analysis, motif prediction tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. (missouri.edu)
  • Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. (springer.com)
  • Graph
  • If the network structure of the model is a directed acyclic graph, the model represents a factorization of the joint probability of all random variables. (wikipedia.org)
  • A Markov random field, also known as a Markov network, is a model over an undirected graph. (wikipedia.org)
  • Degree (or connectivity, a distinct usage from that used in graph theory) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network. (wikipedia.org)
  • discrete
  • Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. (springer.com)
  • Modularity refers to the ability of a system to organize discrete, individual units that can overall increase the efficiency of network activity and, in a biological sense, facilitates selective forces upon the network. (wikipedia.org)
  • A Boolean network consists of a discrete set of Boolean variables each of which has a Boolean function (possibly different for each variable) assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. (wikipedia.org)
  • Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. (wikipedia.org)
  • model
  • A qualitative simulation method is used to model the sporulation network and simulate the response of the cell to nutrient deprivation. (springer.com)
  • Streck A, Siebert H: Extensions for LTL model checking of Thomas networks. (fu-berlin.de)
  • The Process Hitting (PH) is a recently introduced framework to model concurrent processes. (springer.com)
  • PH is suitable to model Biological Regulatory Networks (BRNs) with complete or partial knowledge of cooperations between regulators by defining the most permissive dynamics with respect to these constraints. (springer.com)
  • The simulation based on this model, though currently limited in scope in terms of the biology it represents, supports the utility of the Halley and Winkler branching process model in describing the behaviour of stem cell gene regulatory networks. (york.ac.uk)
  • This work is important since it provides a general statistical framework to model complex dynamics in gene regulatory networks. (ed.ac.uk)
  • This network reveals a new model of PD regulation which we call the "crossover model", because the proximal morphogen (RA) controls the distal boundary of Hoxa11, while conversely the distal morphogens (FGFs) control the proximal boundary. (embopress.org)
  • This suggests a potential model for module evolution whereby modules form from a system's tendency to resist maximizing connections to create more efficient and compartmentalized network topologies. (wikipedia.org)
  • EVE is a simulation framework that is able to model predictive internal models around of complex environments. (wikipedia.org)
  • Boolean networks have been used in biology to model regulatory networks. (wikipedia.org)
  • pathways
  • With the rapid expansion of human understanding of cell, molecular, and chemical biology, a vast set of data has been generated on the metabolic pathways, signal-transductional pathways, and gene regulatory networks. (wikipedia.org)
  • sequences
  • The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new TFBS recognition algorithms. (wikipedia.org)
  • topology
  • Such theoretical studies have revealed that biological networks share many features with other networks such as the Internet or social networks, e.g. their network topology. (wikipedia.org)
  • This set of functions in effect determines a topology (connectivity) on the set of variables, which then become nodes in a network. (wikipedia.org)
  • The conditions of stability are the same in the case of networks with scale-free topology where the in-and out-degree distribution is a power-law distribution: P ( K ) ∝ K − γ {\displaystyle P(K)\propto K^{-\gamma }} , and ⟨ K i n ⟩ = ⟨ K o u t ⟩ {\displaystyle \langle K^{in}\rangle =\langle K^{out}\rangle } , since every out-link from a node is an in-link to another. (wikipedia.org)
  • promoters
  • They are major regulatory units and around 50% of CpG islands are located in gene promoter regions, while another 25% lie in gene bodies, often serving as alternative promoters. (wikipedia.org)
  • genomic sequences
  • It provides the genomic sequences and gene annotation of 8 different HLA-homozygous typing haplotypes (listed below), their resulting variations (see Data below) and ancestral relationships. (ucl.ac.uk)
  • The RegCreative jamboree was stimulated by a community initiative to curate in perpetuity the genomic sequences which have been experimentally determined to control gene expression. (wikipedia.org)
  • sequence
  • Key steps include the analysis of these factors: The range of variation of traits Covariation among traits (scatterplots and correlations, principal component analysis) Architecture of larger networks of traits Quantitative trait locus mapping and causal models of the linkage between sequence differences and phenotype differences Traits and molecular expression data sets are submitted by researchers directly or are extracted from repositories such as National Center for Biotechnology Information Gene Expression Omnibus. (wikipedia.org)
  • Another example of structural variability is seen in vertebrates, in which 3 paralogues of subunits of the cyclin-dependent kinase module have evolved by 3 independent gene duplication events followed by sequence divergence. (wikipedia.org)
  • These progressed from Sanger sequencing of Expressed Sequence Tag libraries, to chemical tag-based methods (e.g., serial analysis of gene expression), and finally to the current technology, next-gen sequencing of cDNA (notably RNA-Seq). (wikipedia.org)
  • phenotypes
  • Researchers and students typically retrieve sets of genotypes and phenotypes from one or more families and use built-in statistical and mapping functions to explore relations among variables and to assemble networks of associations. (wikipedia.org)
  • There are tools on the site for a wide range of functions that range from simple graphical displays of variation in gene expression or other phenotypes, scatter plots of pairs of traits (Pearson or rank order), construction of both simple and complex network graphs, analysis of principal components and synthetic traits, QTL mapping using marker regression, interval mapping, and pair scans for epistatic interactions. (wikipedia.org)
  • varies
  • E-Infrastructure serves to the download probabilistic models for nonlinear partial differential equations and construct processed for important performance recovered by the FoodStress, most commonly fear that varies to find widely essential genes of guidelines. (pd19.org)
  • A variety of parameters are considered when designing and conducting RNA-Seq experiments: Tissue specificity: Gene expression varies within and between tissues, and RNA-Seq measures this mix of cell types. (wikipedia.org)
  • The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation. (wikipedia.org)
  • Thus
  • For example, learning when nutrients are going to be present in the environment allows the organism to selectively express genes that will take up the food source, thus allowing the organism to harvest energy. (wikipedia.org)
  • biological
  • Modularity refers to the ability of a system to organize discrete, individual units that can overall increase the efficiency of network activity and, in a biological sense, facilitates selective forces upon the network. (wikipedia.org)
  • regulation
  • These records were obtained by manual curation of 828 publications by 45 ORegAnno users from the gene regulation community. (wikipedia.org)
  • The RegCreative jamboree was the first opportunity for these groups to meet to be able to accurately assess the current state of knowledge in gene regulation and to begin to develop standards by which to curate regulatory information. (wikipedia.org)
  • regions
  • Links are given to the Sanger Institute Vega database from which sequences and gene annotation can be downloaded, and to the same regions in the UCSC browser for those who prefer that approach. (ucl.ac.uk)
  • In total, 39 researchers contributed 184 TFBS and 317 Regulatory Regions from 96 papers. (wikipedia.org)
  • neural
  • This hypothesis originated from neurological studies that found that there is an inverse relationship between the number of neural connections and the overall efficiency (more connections seemed to limit the overall performance speed/precision of the network). (wikipedia.org)
  • Complex
  • The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. (lmu.de)
  • Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. (lmu.de)
  • EVE is a simulation framework that is able to model predictive internal models around of complex environments. (wikipedia.org)
  • copies
  • Constructional selection: When a gene exists in many duplicated copies, it may be maintained because of the many connections it has (also termed pleiotropy). (wikipedia.org)
  • current
  • There, you can save your current network in a variety of formats. (string-db.org)
  • from there you can proceed to evidence views that each summarize evidence of a single type, for your current network. (string-db.org)
  • An existing model of cancer chemotherapy is reintroduced and placed within current investigative frameworks regarding approaches to treatment optimization. (aimsciences.org)
  • allows
  • Once logged in, the server will store the pages you visited, and also allows you to upload gene sets and other data. (string-db.org)
  • None of these frameworks allows, by itself, a convenient and complete categorization of the great variety of issues in marketing ethics Contrary to popular impressions, not all marketing is adversarial, and not all marketing is stacked in favour of the marketer. (wikipedia.org)
  • data
  • Gene mapping data sets were incorporated for several mouse recombinant inbred strains. (wikipedia.org)
  • Users can also download the primary data sets as text files, Excel, or in the case of network graphs, as SBML. (wikipedia.org)
  • Control
  • Contemporary cybernetics began as an interdisciplinary study connecting the fields of control systems, electrical network theory, mechanical engineering, logic modeling, evolutionary biology, neuroscience, anthropology, and psychology in the 1940s, often attributed to the Macy Conferences. (wikipedia.org)
  • Individuals
  • Individuals who ensure regulatory compliance and prepare submissions, as well as those whose main job function is clinical affairs or quality assurance are all considered regulatory professionals. (raps.org)
  • different
  • These mRNAs are different from those produced by conventional splicing as they are produced by two or more gene loci. (wikipedia.org)
  • single
  • Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. (biomedcentral.com)
  • Approved Bt genes include single and stacked (event names bracketed) configurations of: Cry1A.105 (MON89034), CryIAb (MON810), CryIF (1507), Cry2Ab (MON89034), Cry3Bb1 (MON863 and MON88017), Cry34Ab1 (59122), Cry35Ab1 (59122), mCry3A (MIR604), and Vip3A (MIR162), in both corn and cotton. (wikipedia.org)
  • found
  • The scientists recognized some of these genes as similar to those found in other venom-producing insects, but about half of the 79 candidate venom genes seemed unique to the wasps. (technologynetworks.com)
  • together
  • Join other regulatory professionals as you navigate the gray together. (raps.org)
  • created a series of models that compared the efficiency of various evolved network topologies in an environment where performance, their only metric for selection, was taken into account, and another treatment where performance as well as the connectivity cost were factored together. (wikipedia.org)
  • whole
  • Stakeholder-oriented framework, analyzing ethical problems on the basis of whom they affect (e.g. consumers, competitors, society as a whole). (wikipedia.org)
  • professionals
  • The Code of Ethics provides regulatory professionals with core values that hold them to the highest standards of professional conduct. (raps.org)
  • For 20 years, our flagship publication, Fundamentals of US Regulatory Affairs, has been giving regulatory professionals the insights and answers they need, right at their fingertips. (raps.org)