• Many of these models contain transcriptional interactions for which the regulatory effects (inducer versus repressor) are ambiguous and cannot be determined from publicly available expression profiles. (biomedcentral.com)
  • The new data support two out of three novel regulatory pathways predicted to mediate expression changes downstream of the yeast transcriptional regulator SWI4 . (biomedcentral.com)
  • Finally, a practical method to measure the immunocompetence status is established, using elements of the theory of small random graphs and taking into account the characteristics of the immune networks, established through transcriptional studies, of patients with severe COVID-19 and healthy patients, assuming that both types of patients were vaccinated with an effective biological against SARS-CoV-2. (biorxiv.org)
  • However, the inherent complexity of transcriptional signatures, with thousands of differentially expressed genes, makes them hard to interpret, thus giving poor mechanistic insights and hampering translation to clinics. (biomedcentral.com)
  • Whenever you are signaling training typically do not work with TFs, chromatin-centered inference out-of TF craft only methods the result off TF binding into the chromatin, which may or may not end up in transcriptional changes of their address genes, while TF hobby inferred away from target gene term can be confounded by indirect outcomes. (micsem.org)
  • Through the analysis of large populations of posterior distributions we are able to quantify the relationships between single-cell transcriptional states and dynamic cellular responses, paving the way for more detailed mappings between gene expression states and dynamic cell fates. (biorxiv.org)
  • A major goal of our research program is the identification of the direct transcriptional targets of these factors to unravel the regulatory networks controlling limb development. (nih.gov)
  • A transcriptional and metabolic framework for secondary wall formation in arabidopsis. (mpg.de)
  • transcription factors differentially activated (brown), and pathway activities as determined by their footprints on gene expression (pink). (saezlab.org)
  • Multiple miRNA-mRNA prediction databases were searched by differentially expressed genes (DEGs) to obtain pairs of a miRNA-DEG regulatory network. (frontiersin.org)
  • Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. (frontiersin.org)
  • describe a novel method to identify potential transcription factors from a list of differentially expressed genes using textual similarity between the genes and transcription factors reported in the literature [ 30 ]. (biomedcentral.com)
  • These data have spawned a variety of methods to infer the structure of gene-regulatory networks or to study their high-level properties, as recently reviewed [ 5 ]. (biomedcentral.com)
  • We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells. (nature.com)
  • Here, we use the signed, directed interactions in Omnipath as a prior knowledge network and we make use of an integer linear programming (ILP) mathematical formulation to infer regulatory signalling network topology from gene expression data. (saezlab.org)
  • Under the framework of Bayesian parameter inference and model selection, the available data is used along with prior knowledge to infer a posterior parameter distribution for the model [ 5 ]. (biorxiv.org)
  • Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. (biomedcentral.com)
  • The increasingly growing fraction of cancer driver mutations emerging from sequencing studies of protein kinase genes appeared to be inactivating or kinase-dead leading to the loss of function. (utoronto.ca)
  • Genomic data such as somatic mutations in cancer can be condensed into information about which pathways are mutated in a statistically significant way. (saezlab.org)
  • Once their activities have been estimated, transcription factors and signaling pathways signatures can be linked to upstream perturbations (drugs, ligands, mutations, etc.) using network-based approaches such as so-called causal reasoning methods. (saezlab.org)
  • Along with strong driver mutations and passenger mutations predicted to have neutral effects, the team's analysis pointed to a set of passenger mutations suspected of having intermediate effects on genes from immune, metabolic, and other pathways. (genomeweb.com)
  • They also explored potential passenger mutation interactions with transcription factor binding sites and other regulatory features in the genome and looked at the relationship between proposed passenger mutations and tumor features overall - from the apparent mutational processes at play to the mutation patterns in tumor sub-clones. (genomeweb.com)
  • Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
  • We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
  • In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
  • There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
  • However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. (researchgate.net)
  • To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. (researchgate.net)
  • In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. (researchgate.net)
  • Her lab focuses on mutations that cause changes in gene expression by affecting a process called alternative splicing of RNA. (ucsc.edu)
  • One in eight women in the United States will develop breast cancer in her lifetime, yet only about 15 percent of these cancers have been linked to inherited gene mutations. (ucsc.edu)
  • Mouse genetics have spotlighted many mutations affecting this process, and a wealth of embryologic information from experimental manipulations in chick has uncovered a network of inductive tissue interactions, providing a rich conceptual framework for molecular analysis. (nih.gov)
  • Recent genome sequencing studies have shown that the somatic mutations that drive cancer development are distributed across a large number of genes. (princeton.edu)
  • Since cancer mutations are hypothesized to target a relatively small number of cellular signaling and regulatory pathways, a common practice is to assess whether known pathways are enriched for mutated genes. (princeton.edu)
  • We recently reported a procedure for inferring gene-regulatory network models by integrating gene-expression profiles with high-throughput measurements of protein interactions [ 18 ]. (biomedcentral.com)
  • Databases used to create the NicheNet model are mentioned and referred to in the Methods section Collection of ligand-receptor, intracellular signaling and gene regulatory interactions , in Supplementary Table 1 and in the Supplementary Notes . (nature.com)
  • We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. (hindawi.com)
  • a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
  • The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
  • These networks range from those involving gene regulatory and protein-protein interactions underlying intracellular signalling pathways, and single-cell responses, to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism ( Subramanian 2015 ). (biorxiv.org)
  • The allosteric interactions and regulation of molecular chaperones and protein kinases allow for molecular communication and event coupling in signal transduction networks. (utoronto.ca)
  • The synergistic roles of the Hsp90-Cdc37 chaperone machinery and protein kinases in biology and disease have stimulated extensive structural and functional studies of regulatory mechanisms underlying the Hsp90-kinase interactions. (utoronto.ca)
  • Allosteric interactions of the Hsp90 with cochaperones and protein kinase clients can determine regulatory mechanisms and cellular functions of many signaling proteins and cascades. (utoronto.ca)
  • They cautioned that the additive effects model used in the current study "did not incorporate the effects of epistatic interactions," but noted that "our current framework can be extended by using more complex models that capture both additive and epistatic variance. (genomeweb.com)
  • T]he FunSeq tool assigns a molecular functional impact score to a mutation based on various features," the authors explained, such as "inter-species conservation, gain or break of transcription factor motifs, disruption of known enhancer-gene interactions, and centrality in the gene regulatory or protein-interaction network. (genomeweb.com)
  • The miRNA-mRNA interactions were verified by dual-luciferase reporter gene assays and experiments using mimics miRNA or their inhibitors. (frontiersin.org)
  • We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes. (nature.com)
  • It works out a great ligand-target gene interaction rating, and you may predicated on this, predicts phone-mobile interactions. (micsem.org)
  • Developmental processes such as axis formation and organogenesis employ regulatory components and interactions that are often also used in normal tissue renewal/homeostasis in the adult organism, as well as contributing to the pathogenesis of disease when aberrantly reactivated. (nih.gov)
  • coarse-grained and fine-grained models, where the former contain less detail on interactions between genes. (biomedcentral.com)
  • However, building dynamic models with high predictive power requires an amount of reliable quantitative data which is often not available in large-scale networks with hundreds of players and interactions. (biomedcentral.com)
  • Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). (rna-seqblog.com)
  • In addition, we will have regular interactions with the permanent staff at Physical Chemistry and will get to meet students in their fi nal studies thereby enlarging our network and creating possibilities for future recruitment. (lu.se)
  • Here, making use of coupled data: single-cell gene expression and dynamic molecular measurements, we develop new methods for parameter inference. (biorxiv.org)
  • In application to the Ca 2+ signaling pathway, we show that cell predecessor-informed priors accelerate inference of the Ca 2+ model parameters in single cells. (biorxiv.org)
  • This leads us to the central question underlying this work: can the integration of singlecell gene expression data into a framework for dynamic modeling and inference improve our understanding of the cellular phenotypes of interest? (biorxiv.org)
  • We address this question below using novel computational methods for single-cell data-informed parameter inference of Ca 2+ dynamics coupled with an innovative dataset jointly measuring dynamics and gene expression in the same single cells [ 7 ]. (biorxiv.org)
  • Both inference and analysis of this kind of model are difficult tasks, thus global, (high-level), analysis of the network, has its attractions. (biomedcentral.com)
  • To develop text mining and data mining techniques to support automated extraction and inference of regulatory pathways from biomedical literature and experimental data. (arizona.edu)
  • Current focuses of the Arizona BioPathway research include automatic extraction of regulatory pathway relations from biomedical literature using NLP techniques, inference of genetic networks from genomic data using data mining approaches, and the integration of existing knowledge and text/data mining results of regulatory pathways using a variety of biomedical ontologies. (arizona.edu)
  • Gene regulatory network inference using fused LASSO on multiple data sets. (mpg.de)
  • Recent advances in genomics and computational biology are enabling construction of large-scale models of gene-regulatory networks. (biomedcentral.com)
  • Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. (nature.com)
  • Computational models of regulatory networks can be used in "forward" simulations to generate synthetic gene expression profiles. (uea.ac.uk)
  • Comparing these synthetic profiles to empirically measured gene expression data gives some indication how well a computational RGN model corresponds to the real RGN. (uea.ac.uk)
  • The MDP will use transsys, a computational framework for RGN modelling. (uea.ac.uk)
  • The results of biophysical and computational systems biology analyses combined with proteomics experiments have been integrated into a graph-based network model of allosteric regulation. (utoronto.ca)
  • Based on these findings, we developed a computational synthetic biology framework for design and re-engineering signal transduction networks and pathways that involve cross-talk between molecular chaperones and protein kinase clients. (utoronto.ca)
  • We have developed a powerful computational framework for revealing the genetic basis of bacterial traits by correlating the inheritance patterns of genes and phenotypes across all the sequenced bacterial genomes (Jim et al. (columbia.edu)
  • The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host protection against pathogens. (biorxiv.org)
  • This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. (cancerindex.org)
  • Ca 2+ signaling is a highly conserved pathway that regulates a host of cellular responses in epithelial cells: from death and division to migration and molecule secretion, as well as collective behaviors from organogenesis to wound healing [ 8 ]. (biorxiv.org)
  • Identifying the direct target promoters of developmental gene-regulators will be critical to understand how these regulators function and to link regulatory cascades in developmental genetic programs to the basic cellular processes that drive morphogenesis of anatomic structures. (nih.gov)
  • Thus, understanding how normal transcription programs are regulated during development may also help to decipher abnormal gene expression patterns in tumors and devise new strategies to intercept cellular targets driving tumor cell behavior. (nih.gov)
  • The term "oncotarget" encompasses all molecules, pathways, cellular functions, cell types, and even tissues that can be viewed as targets relevant to cancer as well as other diseases. (oncotarget.com)
  • Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. (biomedcentral.com)
  • An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. (biomedcentral.com)
  • CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. (biomedcentral.com)
  • CellNetAnalyzer (CNA) is a graphical user interface for MATLAB providing a comprehensive toolbox for structural and functional analysis of different types of cellular networks. (biomedcentral.com)
  • The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. (oregonstate.edu)
  • I thus uncover these circuits of connected drivers which cause tumorigenesis through the perturbation of overlapping cellular pathways in a pan-cancer manner across 15 malignancies. (biomedcentral.com)
  • One step in this direction is thus to understand exactly which downstream genes and cellular processes become affected in the outcome of driver alterations. (biomedcentral.com)
  • Understand and simulate the development of complex traits such as biological pathways (Senescence and Jasmonate) and plant morphology. (niab.com)
  • Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. (biomedcentral.com)
  • Regulatory gene networks are generally a central biological mechanism of decoding genetic information that confers adaptive capabilities into phenotypic responses and other traits. (uea.ac.uk)
  • The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)
  • This provides a knowledge scaffold for identifying central pathways whose genetic or chemical targeting may potentiate drug sensitivity. (columbia.edu)
  • By applying this framework to mild resistance, we have identified a large number of loci whose genetic perturbations significantly affect antibiotic sensitivity. (columbia.edu)
  • Olariu V, Manesso E, commitment and Peterson C. 2017 A deterministic method for estimating free energy genetic network reprogramming paths landscapes with applications to cell commitment and reprogramming paths. (lu.se)
  • DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. (nature.com)
  • Yeast microarrays for genome wide parallel genetic and gene expression analysis. (nature.com)
  • Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
  • We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
  • Limb development is a particularly attractive model for unraveling the function and interaction of such regulatory components, because it is very accessible to study and is extremely well conserved between genetic (mouse) and embryologic (chick) model organisms and humans. (nih.gov)
  • The research goal of Arizona BioPathway is to develop novel machine learning and Natural Language Processing (NLP) techniques to support efficient and effective data and text analysis in biomedical fields, particularly, the analysis of genetic regulatory pathways which are crucial for biological processes such as gene regulation and cancer development. (arizona.edu)
  • The text mining component of Arizona BioPathway is designed to extract genetic regulatory pathway relations from biomedical literature. (arizona.edu)
  • Visualisation is an effective analysis tool for complex networks. (cmcrc.com)
  • Our framework is based on the tight integration of analysis, visualisation and interaction methods. (cmcrc.com)
  • The application of the systems biology approach to the analysis of a gene regulatory network is demonstrated with a case study of the regulation of p21 by multiple miRNAs [ 4 ]. (hindawi.com)
  • In particular, the long-term steady-state analysis of such an integrated network provides insight into the system and its properties. (sdsu.edu)
  • This thesis presents an extension to the pseudo-stoichiometric matrix framework for the steady-state analysis of gene regulatory networks. (sdsu.edu)
  • A modified pathway analysis algorithm determines steady states for the given Boolean network. (sdsu.edu)
  • Steady states for the pseudo-stoichiometric matrix can be calculated by Extreme Pathway Analysis (EPA). (sdsu.edu)
  • We report the results of integrative systems biology studies of the Hsp90 chaperone and protein kinases with an atomic level analysis of the communication pathways regulating conformational equilibrium of theses protein systems in signaling networks. (utoronto.ca)
  • Network modelling and percolation analysis approaches were used to emulate thermal unfolding and characterize conformational landscapes of a wide range of protein kinases, revealing that chaperone dependency of protein kinase clients may be linked with the elevated conformational mobility of their inactive states induced by dynamic and energetic polarization of kinase lobes. (utoronto.ca)
  • 100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)
  • The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. (nih.gov)
  • Furthermore, we have developed a genome-wide epistasis analysis framework that efficiently reveals the organization of these genes within signaling and regulatory networks such as the Rcs phosphorelay pathway and the cyclic-di-GMP second-messenger system. (columbia.edu)
  • Our strategy starts with the calculation of drug-gene correlations and is followed by a pathway-oriented filtering and a network-diffusion analysis across the interactome. (biomedcentral.com)
  • Although providing a rich account of disease biology, these studies have failed to yield better drug therapies, as causality and response to drug perturbations cannot be inferred directly from two-state (diseased vs. healthy) differential gene expression analysis [ 2 , 3 ]. (biomedcentral.com)
  • Provided that the panel of cell lines is large enough, this approach allows for a new type of gene expression analysis where basal expression levels are correlated to drug response phenotypes. (biomedcentral.com)
  • METHODS: We evaluated the relationship between clinical features and OTX2-AS1 expression, prognostic factors, and the significant involvement of OTX2-AS1 in function using various statistical methods, such as Kaplan-Meier method, Cox regression analysis, Gene Set Enrichment Analysis (GSEA), and immune infiltration analysis. (bvsalud.org)
  • PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). (frontiersin.org)
  • Further weighted gene co-expression network analysis (WGCNA) uncovered that turquoise and yellow gene modules were tightly linked to antioxidant enzymes activity and ion content, respectively. (frontiersin.org)
  • For this purpose multi-dimensional data from different levels were KU-60019 needed for the integrative and system-level analysis including gene expression data regulatory data epigenetic data and pathway/network data. (biobender.com)
  • At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. (biomedcentral.com)
  • This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. (biomedcentral.com)
  • This paper concentrates on quantitative modelling of gene regulatory networks (GRNs) using DNA microarray data, as this is more informative than qualitative analysis of biological data. (biomedcentral.com)
  • Herein we introduce CellNetAnalyzer , a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. (biomedcentral.com)
  • The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. (biomedcentral.com)
  • CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. (biomedcentral.com)
  • Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks. (biomedcentral.com)
  • It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. (biomedcentral.com)
  • Systems biology aims at a holistic analysis of biological networks. (biomedcentral.com)
  • CNA extends its predecessor FluxAnalyzer , originally developed for metabolic network analysis [ 7 ], by new methods for signalling and regulatory networks, i.e. for networks where signal flows are dominating (in contrast to mass flows in metabolic networks). (biomedcentral.com)
  • Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. (oregonstate.edu)
  • Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. (oregonstate.edu)
  • There are two main reasons why the catalogs of cancer drivers produced by the aforementioned projects and others need to be broken down into related sets of genes for deeper analysis. (biomedcentral.com)
  • The ultimate goal of Arizona BioPathway is to provide biomedical researchers with a platform of pathway-related literature abstraction, data analysis and knowledge integration, thus to support the development of scientific hypotheses and discovery of new knowledge. (arizona.edu)
  • Importantly, their approach has the potential to identify transcription factors that might be indirectly regulating the genes and, thus, would not be recognized by sequence-based analysis of the expressed gene promoters. (biomedcentral.com)
  • Including 4 multidrug-resistant tuberculosis isolates from Australia citizens epidemiologically linked to the TSPZ into the transmission network analysis revealed 2 probable cross-border transmission events. (cdc.gov)
  • As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.com)
  • Although microRNAs (miRNAs) are physically small, they have been shown to play an important role in gene regulation [ 1 ]. (hindawi.com)
  • Biophysical modeling of allosteric regulation in the protein kinases has offered additional insights into organizing principles of kinase activation by molecular chaperones that may be orchestrated by a cross-talk between key regulatory regions. (utoronto.ca)
  • Network-defined modularity of interacting components and cross-talk in signal transduction networks are quantified through molecular mechanism of allosteric regulation. (utoronto.ca)
  • A rapid overview of this morphologic scheme provides the framework for further studying the processes and regulation involved in development. (medscape.com)
  • We present a computationally efficient strategy for de novo identification of subnetworks in an interaction network that are mutated in a statistically significant number of patients. (princeton.edu)
  • The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. (nih.gov)
  • My lab previously identified several transcription factors (homeobox genes and T-box genes) involved in formation and patterning of both the primary embryonic axis and the limb axis in vertebrates. (nih.gov)
  • We are analyzing the normal developmental function of early transcription factors that regulate digit patterning (Gli3, 5'Hoxd), with the long-term aim of linking regulatory cascades and patterned gene expression to the morphogenesis of specific structures. (nih.gov)
  • DNA Microarray technology enables us to measure mRNA concentrations in a cell for a large number of genes at the same time. (biomedcentral.com)
  • This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (cancerindex.org)
  • These methods are available to the wider scientific community through the Immcantation framework , which provides a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets, with a focus on B cell receptor (BCR) repertoire profiling. (yale.edu)
  • The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). (biomedcentral.com)
  • MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)
  • Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich. (saezlab.org)
  • Perturbation-response genes reveal signaling footprints in cancer gene expression. (saezlab.org)
  • We apply our approach to 189 drugs tested in 671 cancer cell lines and observe a connection between gene expression levels of the modules and mechanisms of action of the drugs. (biomedcentral.com)
  • Daniel Kim's lab studies the role of long noncoding RNA molecules (lncRNAs) in gene expression and cancer. (ucsc.edu)
  • The application of systems biology principles to developmental biology promises to reveal the quantitative interrelationships between signaling and regulatory systems necessary to support robust physiological processes, and thereby provide a framework for the interpretation of the pathology (especially cancer) resulting from gross or subtle disturbances in these interrelationships. (nih.gov)
  • To demonstrate the power of this technology, we will generate a molecular disease fingerprint allowing differentiation between three clinically indistinguishable yet biochemically distinct disease pathways underlying the deadly brain cancer glioblastoma multiforme. (nih.gov)
  • Exploiting the aforementioned catalogs of driver genes, for example, we recently revealed the mutational landscape of chromatin regulatory factors (CRFs) in cancer [ 5 ]. (biomedcentral.com)
  • For both types of networks, the abstract network model can be set-up and edited via a Network Composer and input masks (see Figure 2 ) or, alternatively, via ASCII (text) files. (biomedcentral.com)
  • The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism. (nih.gov)
  • We introduce an alternative approach that examines mutated genes in the context of a genome-scale gene interaction network. (princeton.edu)
  • Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)
  • The catalog of driver genes involved in the development of several malignancies has grown in recent years, as a result of whole-exome and whole-genome analyses of cohorts of tumors, mainly within the framework of large international consortia [ 3 , 4 ]. (biomedcentral.com)
  • The data mining component is designed to extract gene regulatory relations from genomic and proteomic data including DNA microarray by machine learning techniques such as Bayesian networks. (arizona.edu)
  • Linkages extracted from heterogeneous genomic data sources provide different evidence about gene functional relations. (arizona.edu)
  • The data source networks, NicheNet's ligand-target matrix and the processed ligand treatment and case study expression datasets are available on Zenodo ( https://doi.org/10.5281/zenodo.3260758 ) 59 . (nature.com)
  • DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. (nih.gov)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • In this study, we used 7 publicly available microarray datasets to identify gene signatures related to recurrence in optimally debulked SOC patients, and validated their expressions in an independent clinic cohort of 127 patients using immunohistochemistry (IHC). (oncotarget.com)
  • We test these algorithms on a large human protein-protein interaction network using somatic mutation data from glioblastoma and lung adenocarcinoma samples. (princeton.edu)
  • Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. (biomedcentral.com)
  • A qualitative mathematical model of the notion of immunocompetence is developed, based on the formalism of Memory Evolutive Systems (MES), from which, immunocompetence is defined as an emergent structure of a higher order arising from the signal networks that are established between effector cells and molecules of the immune response in the presence of a given antigen. (biorxiv.org)
  • The molecular mechanisms underlying the response to wounding, which is spatially structred into a local and a systemic response, and to other challenges have extensively been studied, and key pathways, mediated by signalling molecules including jasmonic acid, salicylic acid and ethylene, have been identified. (uea.ac.uk)
  • Our study offers a systems-based perspective on drug design and re-engineering of signaling networks by unravelling relationships between protein kinase networks with molecular chaperones and binding specificity of targeted kinase drugs. (utoronto.ca)
  • Such as [ 131 ], modified this new TieDIE signaling network diffusion algorithm [ 132 ] so you're able to phosphoproteomics and transcriptomics data discover druggable kinase pathways. (micsem.org)
  • In this paper, we present a new dynamic Bayesian network (DBN) framework embedded with structural expectation maximization (SEM) to model gene relationship. (sciweavers.org)
  • It is well-suited for analyzing the time-series data and can deal with cyclical structures that can not be tackled by static Bayesian network. (sciweavers.org)
  • We trained a Bayesian machine learning neural network model to generate a neuroimaging phenotype and AD score representing the probability of AD using structural MRI data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Cohort (cut-off 0.5, AUC 0.92, PPV 0.90, NPV 0.93). (cdc.gov)
  • Examples include biological networks such as phylogenetic network, gene regulatory network, metabolic pathways and protein‐protein interaction networks. (cmcrc.com)
  • Gene regulatory networks capture interaction patterns and mechanics of how gene expression is regulated based on signals and components that are internal or external to the organism. (sdsu.edu)
  • Toward a proteome-scale map of the human protein-protein interaction network. (nature.com)
  • First, we use a diffusion process on the interaction network to define a local neighborhood of "influence" for each mutated gene in the network. (princeton.edu)
  • Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. (rna-seqblog.com)
  • Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. (mpg.de)
  • In addition we will address important areas of modern epidemiology such as the influence of early life factors on adult health and disease, but also the importance of the gene-diet-microbiota interaction for body function and health. (lu.se)
  • The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. (cancerindex.org)
  • In this work, we describe expression patterns and proliferation/apoptosis assays to uncover homologous regulatory pathways in the catshark Scyliorhinus canicula. (sharkyear.com)
  • Dual-luciferase reporter gene assays demonstrated Arhgap11a as the target of miR-211-5p. (frontiersin.org)
  • Together with metabolic networks and signal networks, they provide a functional description of cell processes. (sdsu.edu)
  • Among our primary findings is the emerging evidence that a small number of functional motifs may be utilized by the chaperone and protein kinases to act collectively as central regulators of the intermolecular communications, ATP hydrolysis, and protein client binding in signaling networks. (utoronto.ca)
  • By showcasing a family of cyclin-dependent (CDK) kinases that display a broad repertoire of chaperone dependencies, we discovered that unique functional dynamics signatures and chaperone addiction of CDK4 and CDK7 client proteins can explain divergences in their regulatory mechanisms that require a confluence of events, including formation of the inhibitory ternary complex, substrate recruitment and activation loop phosphorylation. (utoronto.ca)
  • In the case of gene expression, a number of functional features can be extracted. (saezlab.org)
  • Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
  • Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
  • The experimental part of the project will produce a data set of gene expression measurements from various Arabidopsis mutants with altered wounding responses. (uea.ac.uk)
  • The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. (nature.com)
  • We are experimenting various techniques to learn regulatory networks from microarray data, either with existing prior knowledge or in combination with other types of biological experimental data, e.g. (arizona.edu)
  • In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms. (genomeweb.com)
  • We hypothesized that a high fat diet in non-human primates would induce changes in hepatic chromatin structure resulting in altered expression of fetal genes critical to the development of childhood and adult obesity. (nih.gov)
  • In the case of network construction in Saccharomyces cerevisiae , there has been a lack of both suitable, well-characterized parts (promoters and regulators) as well as a standardized platform for DNA assembly and delivery of gene circuits. (atcc.org)
  • This study demonstrates the feasibility for the quick and easy construction of gene circuits for delivery into S. cerevisiae and the utility of a fully characterized set of diverse promoters, activators, and repressors. (atcc.org)
  • To systematically study these pathways by modulating individual components-or in the case of synthetic biology, building new network architectures by creating DNA circuit-it is critical to control multiple genes simultaneously under tightly regulated or inducible expression. (atcc.org)
  • Nevertheless, to date, the actual misregulation of genes or processes downstream these cliques has not been systematically proven or exploited with the purpose of identifying them. (biomedcentral.com)
  • However, if we are to accurately model large gene networks in complex organisms, including fly, worm, mouse, and human, automated procedures will be essential for analyzing the network, choosing the best new experiments to test the model, conducting the experiments, and integrating the resulting data. (biomedcentral.com)
  • We applied the new method to learning the regulatory network and the metabolic pathway from Saccharomyces Cerevisiae cell cycle gene expression data. (sciweavers.org)
  • We present NicheNet ( https://github.com/saeyslab/nichenetr ), a method that predicts ligand-target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. (nature.com)
  • In addition, we provide tutorials on model validation (evaluation of target gene and ligand activity), model construction and parameter optimization such that users can benchmark their methods against NicheNet and construct their own models (for example, with their own data sources to include more cell type specificity). (nature.com)
  • Recent technological advances have led to the production of a big data and complex networks in many domains. (cmcrc.com)
  • This talk will present a framework for visual analytics of big data. (cmcrc.com)
  • I will present a number of case studies using various networks derived from big data, in particular biological networks and social networks. (cmcrc.com)
  • For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. (hindawi.com)
  • Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
  • The systems biology approach, combining data-driven modeling and model-driven experiments, provides a systematic and comprehensive perspective on the regulatory roles of miRNAs in gene regulatory networks [ 3 - 5 ]. (hindawi.com)
  • In this project we will develop and use a statistsical approach to discriminate alternative RGN models based on the consistence of their synthetic profiles with a data set of empirical gene expression measurements. (uea.ac.uk)
  • I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
  • Additionally, it is possible to use gene expression data to estimate the activity status of transcription factor (TF) proteins by looking at the mRNA levels of its direct targets (TF footprint). (saezlab.org)
  • Here, we can combine phosphoproteomic, transcriptomic and metabolomics data to find causal paths linking signaling, gene-regulatory, and metabolic processes. (saezlab.org)
  • Network biology offers means to integrate a large amount of omics data [ 18 ]. (biomedcentral.com)
  • A variety of one another causal need and you can head usage of entry to info is found in strategies like CellOracle [ 129 ] and you can Inferelator3.0 [ 130 ] that use chromatin accessibility data so you can describe the fresh new cellphone-type certain earlier in the day regulating circle that is following simple by knowledge an excellent regularized linear regression model towards the gene phrase data. (micsem.org)
  • Unified KU-60019 framework for data integration PM needs thorough investigation of every individual's medical and hereditary details for the delivery of individualized health care. (biobender.com)
  • a unified construction to assist in integration of heterogeneous data including ontology-based frameworks for digital health information. (biobender.com)
  • The so-called joint learning approach is promising to learn the network more accurately, avoiding bias and incompleteness inherited by a particular type of data. (arizona.edu)
  • The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. (biomedcentral.com)
  • Arizona BioPathway is also aimed at the creation of a framework for pathway-related knowledge integration and visualization using a combination of various approaches. (arizona.edu)
  • We have experimented with two different approaches of natural language processing (NLP) to extract the pathway relations, shallow parsing and full parsing. (arizona.edu)
  • To increase the precision, both approaches use relevant biomedical lexicons such as Gene Ontology (GO), HUGO Gene Nomenclature, and the Specialist Lexicon of UMLS to filter the extracted relations. (arizona.edu)
  • Gene expression profiling has become a mainstay approach to characterize cell properties and status, unveiling links between gene activities and disease phenotypes. (biomedcentral.com)
  • Take single-cell gene expression as an example: even if the overwhelming majority of the genes measured in a given experiment contain very little information about the phenotypes under investigation (say 90-95%, for sake of argument) that still leaves hundreds or thousands of genes that do contain relevant information. (biorxiv.org)
  • With a large enough set of snapshots, it should be theoretically possible to uncover the underlying gene regulatory network (GRN) [ 6 ]. (biomedcentral.com)
  • This has opened up the possibility to carry out systematic studies to uncover the repertoire of functionally related groups of driver genes. (biomedcentral.com)
  • The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)
  • IRE1α-XBP1 were essential for expansion of activated mouse and human NK cells and are situated downstream of the mammalian target of rapamycin signaling pathway. (cancerindex.org)
  • Network biology strategies like module detection are able to digest the outcome of large-scale pharmacogenomic initiatives, thereby contributing to their interpretability and improving the characterization of the drugs screened. (biomedcentral.com)
  • Hazard characterization the best features of existing guidance, frameworks, and models using a weight-of-evidence (WoE) approach. (cdc.gov)
  • As a fundamental step, CNA facilitates the construction of network projects which can represent either a mass-flow (stoichiometric, metabolic) or a signal-flow (signal transduction/regulatory) network. (biomedcentral.com)
  • Journal Article Genes (Basel) · December 16, 2021 Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. (duke.edu)
  • Exploring gene regulatory network is a key topic in molecular biology. (sciweavers.org)
  • Complex behavior within eukaryotic cells manifest from layered regulatory networks changing the transcription of many genes. (atcc.org)
  • Figure 7: Illustration of steps to determine a network in Homo sapiens using the metagraph concept, where each metanode represents a set of orthologous eukaryotic genes from the COG database 53 . (nature.com)
  • To simplify drug signatures, we have developed a network-based methodology to identify functionally coherent gene modules. (biomedcentral.com)
  • High density arrays of extraordinarily sensitive integrated microring resonators will allow many gene and protein signatures to be simultaneously quantitated from a single patient sample. (nih.gov)
  • It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). (cancerindex.org)
  • Recently, miRNA-messenger RNA (mRNA) regulatory relationships have been confirmed during biological processes, including osteogenic differentiation. (frontiersin.org)
  • Even with only a few hundred genes retained, this is more than enough in theory to characterize any possible number of cell states or arbitrarily complex dynamical processes. (biorxiv.org)
  • These factors operate in signaling pathways that are used extensively in a number of processes in both the embryo and adult. (nih.gov)
  • Imposed upon this gross morphological description is the modern understanding of gene expression and protein elucidation, which bring about these developmental processes. (medscape.com)
  • It regulates Sp7 protein expression and induces expression of major bone matrix protein genes, such as Col1a1, Spp1, Ibsp, Bglap2, and Fn1 ( 7 , 8 ). (frontiersin.org)
  • Finally, we prove the predictive capability of the modules and demonstrate how they can be used as gene sets in conventional enrichment analyses. (biomedcentral.com)
  • Doug Kellogg's lab is working to elucidate these mechanisms, using biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. (ucsc.edu)
  • Finally, and as a result of defining the underlying immune pattern as a small random graph, it is possible to estimate the probability that an individual is immunocompetent to a given antigen, using information from the immune cell networks involved in the response to SARS-CoV-2 in patients with severe COVID-19 and healthy patients. (biorxiv.org)
  • Because of their similar structural and developmental features, gene expression patterns were described over the four developmental stages of both tooth and scale buds in the catshark. (sharkyear.com)
  • These gene expression patterns differ from mouse tooth development, and discrepancies are also observed between tooth and scale development within the catshark. (sharkyear.com)
  • However, homologous signaling pathways are involved in growth and morphogenesis with variations in their respective expression patterns. (sharkyear.com)
  • Surprisingly, we discover using ODeGP that increasing cell density results in rapid generation of oscillations in the Bmal1 gene, thus highlighting our method's ability to discover unexpected and new patterns. (edu.in)
  • Similarities in the topology of gene expression pattern, including Bmp signaling pathway, suggest that mouse molar development is more similar to scale bud development in the catshark. (sharkyear.com)