ArticleNucleic acids research2003
Toucan: deciphering the cis-regulatory logic of coregulated genes.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 3 of them syntheses that pooled it.
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Who cites it
98 citing papers in PubMed, 3 syntheses or guidelines pooled it, 196 citations in OpenAlex.
- Pooled it
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- Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.BMC bioinformatics · 2006Pooled it
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- cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.Nature methods · 2019Article
- Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression.Scientific reports · 2016Article
- NF-κB and IRF pathways: cross-regulation on target genes promoter level.BMC genomics · 2015Article
- An integrated functional genomic analysis identifies the antitumorigenic mechanism of action for PPARγ in lung cancer cells.Genomics data · 2015Article
- An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.Bioinformatics and biology insights · 2015Article
- Summarizing and exploring data of a decade of cytokinin-related transcriptomics.Frontiers in plant science · 2015Article
- Inhibition of cancer cell proliferation by PPARγ is mediated by a metabolic switch that increases reactive oxygen species levels.Cell metabolism · 2014Article
- Evolutionary tinkering of the expression of PDF1s suggests their joint effect on zinc tolerance and the response to pathogen attack.Frontiers in plant science · 2014Article
- Large-scale investigation of human TF-miRNA relations based on coexpression profiles.BioMed research international · 2014Article
- Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.Briefings in bioinformatics · 2013Article
- Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm.Algorithms for molecular biology : AMB · 2013Article
- Genetic architecture of gene expression in the chicken.BMC genomics · 2013Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
TOUCAN is a Java application for the rapid discovery of significant cis-regulatory elements from sets of coexpressed or coregulated genes. Biologists can automatically (i) retrieve genes and intergenic regions, (ii) identify putative regulatory regions, (iii) score sequences for known transcription factor binding sites, (iv) identify candidate motifs for unknown binding sites, and (v) detect those statistically over-represented sites that are characteristic for a gene set. Genes or intergenic regions are retrieved from Ensembl or EMBL, together with orthologs and supporting information. Orthologs are aligned and syntenic regions are selected as candidate regulatory regions. Putative sites for known transcription factors are detected using our MotifScanner, which scores position weight matrices using a probabilistic model. New motifs are detected using our MotifSampler based on Gibbs sampling. Binding sites characteristic for a gene set--and thus statistically over-represented with respect to a reference sequence set--are found using a binomial test. We have validated Toucan by analyzing muscle-specific genes, liver-specific genes and E2F target genes; we have easily detected many known binding sites within intergenic DNA and identified new biologically plausible sites for known and unknown transcription factors. Software available at http://www.esat.kuleuven.ac. be/ approximately dna/BioI/Software.html.
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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 OpenQuestion graph.