ArticleGenome research2008
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
- Perspectives of CRISPR/Cas-mediatedHorticulture research · 2020Review
- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model.BioMed research international · 2017Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.Bioinformatics (Oxford, England) · 2015Article
- Article
- Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.Nucleic acids research · 2012Article
- Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.BMC bioinformatics · 2012Article
- Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.Genome biology · 2011Article
- Visualization and exploration of conserved regulatory modules using ReXSpecies 2.BMC evolutionary biology · 2011Article
- Towards an evolutionary model of transcription networks.PLoS computational biology · 2011Article
- Article
- Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.PLoS computational biology · 2010Article
- Genome-wide prediction of transcription factor binding sites using an integrated model.Genome biology · 2010Article
- Genomic analyses reveal a conserved glutathione homeostasis pathway in the invertebrate chordate Ciona intestinalis.Physiological genomics · 2009Article
- Exhaustive search for over-represented DNA sequence motifs with CisFinder.DNA research : an international journal for rapid publication of reports on genes and genomes · 2009Article
- Cellular targeting for cochlear gene therapy.Advances in oto-rhino-laryngology · 2009Review
- Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a predetermined alignment result, GibbsModule iteratively updates the core motif shared by coexpressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared with peer algorithms on a number of synthetic and real data sets. Applying GibbsModule to analyze the binding regions of the Krüppel-like factor (KLF) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published KLF motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. The SOX2 motif was found to be a collaborating motif to the KLF motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and nonfunctional binding sites. All seven tested binding sites in GibbsModule-predicted CRMs had higher ChIP signals as compared with the other seven tested binding sites located outside of predicted CRMs. GibbsModule is available at (http://biocomp.bioen.uiuc.edu/GibbsModule).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.