A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

scientific article

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/jcb/ThijsMLRMRM02
P356DOI10.1089/10665270252935566
P698PubMed publication ID12015892
P5875ResearchGate publication ID11355588

P50authorStephane RombautsQ30347488
Kathleen MarchalQ38318457
Gert ThijsQ51878942
Yves MoreauQ55638172
Bart De MoorQ61089673
P2093author name stringPierre Rouzé
Magali Lescot
P433issue2
P304page(s)447-464
P577publication date2002-01-01
P1433published inJournal of Computational BiologyQ6295003
P1476titleA Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
P478volume9

Reverse relations

cites work (P2860)
Q390482889p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response
Q34488540A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
Q33285303A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.
Q33332464A novel Bayesian DNA motif comparison method for clustering and retrieval
Q42059367A novel approach to identifying regulatory motifs in distantly related genomes
Q21284367A reexamination of information theory-based methods for DNA-binding site identification
Q34681576A survey of motif discovery methods in an integrated framework
Q34483140A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.
Q80357997ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis
Q45241844AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach.
Q24801141Ab initio identification of putative human transcription factor binding sites by comparative genomics
Q30492890Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes
Q46671627An ER-directed transcriptional response to unfolded protein stress in the absence of conserved sensor-transducer proteins in Giardia lamblia
Q37368357An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters
Q58911794An Improved Scoring Matrix for Multiple Sequence Alignment
Q38336920An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro
Q35568934An integrated approach to reconstructing genome-scale transcriptional regulatory networks
Q42552788Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis
Q38358691Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
Q38387841BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements
Q35063740Bayesian centroid estimation for motif discovery
Q33284530Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites
Q33243426Bounded search for de novo identification of degenerate cis-regulatory elements
Q41807993Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements
Q45173306Characterization of Citrus sinensis type 1 mitochondrial alternative oxidase and expression analysis in biotic stress
Q28508122Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor
Q88089952Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato
Q50091022Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium
Q34499593Comprehensive human transcription factor binding site map for combinatory binding motifs discovery
Q24803783Computational analysis of core promoters in the Drosophila genome
Q35176291Computational approaches to identify promoters and cis-regulatory elements in plant genomes
Q47595367Computational discovery of soybean promoter cis-regulatory elements for the construction of soybean cyst nematode-inducible synthetic promoters.
Q28768266Conservation of Toll-Like Receptor Signaling Pathways in Teleost Fish
Q38507571Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans
Q47943164DLocalMotif: a discriminative approach for discovering local motifs in protein sequences
Q38832361DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Q24805271Detecting DNA regulatory motifs by incorporating positional trends in information content
Q46432897Detoxification and transcriptome response in Arabidopsis seedlings exposed to the allelochemical benzoxazolin-2(3H)-one.
Q55339904DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data.
Q34601566Direct targets of the transcription factors ABA-Insensitive(ABI)4 and ABI5 reveal synergistic action by ABI4 and several bZIP ABA response factors
Q33509178Discovering multiple realistic TFBS motifs based on a generalized model
Q52676244Diversity and motif conservation in protein 3D structural landscape: exploration by a new multivariate simulation method.
Q46819599Dynamic histone acetylation of late embryonic genes during seed germination
Q33250099EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
Q46130685Early genomic responses to salicylic acid in Arabidopsis.
Q35175504Encoded expansion: an efficient algorithm to discover identical string motifs.
Q42788843Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels.
Q33898983Escherichia coli genome-wide promoter analysis: identification of additional AtoC binding target elements
Q33281058Evolutionary hierarchies of conserved blocks in 5'-noncoding sequences of dicot rbcS genes
Q36851106ExactSearch: a web-based plant motif search tool
Q39389402FabR regulates Salmonella biofilm formation via its direct target FabB.
Q58910993Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation
Q33304533Fine-tuning enhancer models to predict transcriptional targets across multiple genomes
Q42620155G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis
Q34480404Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis
Q34372952Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis
Q52022081Genome-specific higher-order background models to improve motif detection.
Q50469313Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance.
Q44302198Genomic analysis of the unfolded protein response in Arabidopsis shows its connection to important cellular processes
Q39804560Gibbs Recursive Sampler: finding transcription factor binding sites
Q41668767GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis
Q35217899Global analysis of gene expression using GeneChip microarrays.
Q30440986Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
Q35959527Hexanucleotide motifs mediate recruitment of the RNA elimination machinery to silent meiotic genes.
Q34569841How does DNA sequence motif discovery work?
Q24337202IFNβ-dependent increases in STAT1, STAT2, and IRF9 mediate resistance to viruses and DNA damage
Q35208563INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis
Q42623225Identification and expression analyses of MYB and WRKY transcription factor genes in Papaver somniferum L.
Q33300586Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes
Q46819603Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis.
Q30000999Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
Q30886390Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data
Q34118625Identification of putative cancer genes through data integration and comparative genomics between plants and humans.
Q46528847Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis
Q40900566Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
Q33543169Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.
Q24807196In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
Q59102293In silico identification of metazoan transcriptional regulatory regions
Q33373950In silico identification of short nucleotide sequences associated with gene expression of pollen development in rice
Q80676035In vivo characterization of plant promoter element interaction using synthetic promoters
Q47388358Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes
Q21146414Interdependency of brassinosteroid and auxin signaling in Arabidopsis
Q92127777Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries
Q38308772Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea
Q24811129Limitations and potentials of current motif discovery algorithms
Q30950386MINER: exploratory analysis of gene interaction networks by machine learning from expression data.
Q28710347MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences
Q24607812MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
Q33855706Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself.
Q33750923Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster
Q33407820ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
Q35795230Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila
Q33237075More robust detection of motifs in coexpressed genes by using phylogenetic information.
Q41904319Motif Discovery in Physiological Datasets: A Methodology for Inferring Predictive Elements
Q36701644Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.
Q38290437Opposite effects of Mn2+ and Zn2+ on PsaR-mediated expression of the virulence genes pcpA, prtA, and psaBCA of Streptococcus pneumoniae
Q35914205PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis
Q45144291Patterns of coordinate down-regulation of ARE-containing transcripts following immune cell activation.
Q43176979Performance evaluation of DNA motif discovery programs.
Q33274647Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria
Q24801249Plant viral intergenic DNA sequence repeats with transcription enhancing activity
Q37288720Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction
Q35658253Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes
Q31115343Post-transcriptional regulation of the trypanosome heat shock response by a zinc finger protein
Q33306761Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms
Q33829278Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
Q31150555Probabilistic inference of transcription factor binding from multiple data sources
Q38300604Production and secretion stress caused by overexpression of heterologous alpha-amylase leads to inhibition of sporulation and a prolonged motile phase in Bacillus subtilis
Q83115961Promoter motifs of olfactory receptor genes expressed in distinct topographic patterns
Q30648026PromoterCAD: Data-driven design of plant regulatory DNA.
Q27499384Quantifying similarity between motifs
Q46661343Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis
Q36018331Regulation of ykrL (htpX) by Rok and YkrK, a novel type of regulator in Bacillus subtilis
Q64088804Review of Different Sequence Motif Finding Algorithms
Q64109188Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
Q38337501Rice MADS3 regulates ROS homeostasis during late anther development
Q41786650SBP-domain transcription factors as possible effectors of cryptochrome-mediated blue light signalling in the moss Physcomitrella patens
Q29346663SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1.
Q36692787Searching the Human Genome for Snail and Slug With DNA@Home
Q31081595SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
Q34017089Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.
Q30000845Systematic identification of functional plant modules through the integration of complementary data sources
Q24813630T-Reg Comparator: an analysis tool for the comparison of position weight matrices
Q24812021TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.
Q41998237The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis
Q33264001The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine
Q38347503The auxin-induced transcriptome for etiolated Arabidopsis seedlings using a structure/function approach
Q28536112The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option
Q44860608The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root apex
Q29346567The novel transcriptional regulator SczA mediates protection against Zn2+ stress by activation of the Zn2+-resistance gene czcD in Streptococcus pneumoniae
Q45202915The pea SAD short-chain dehydrogenase/reductase: quinone reduction, tissue distribution, and heterologous expression.
Q30893938Toucan: deciphering the cis-regulatory logic of coregulated genes.
Q34318696Towards a theoretical understanding of false positives in DNA motif finding
Q99571943Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes
Q34510476Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores
Q40475119Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis.
Q42062317Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons
Q38322422Transcriptome-based identification of the Sinorhizobium meliloti NodD1 regulon.
Q33369976Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse
Q30383377Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins.
Q33523886Variable structure motifs for transcription factor binding sites
Q40151559Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation.
Q25254981cisRED: a database system for genome-scale computational discovery of regulatory elements
Q42676785iTriplet, a rule-based nucleic acid sequence motif finder
Q38351315info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.
Q51912727p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm.
Q42696449ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

Search more.