ArticleNucleic acids research2008
Positional distribution of human transcription factor binding sites.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes.BMC genomics · 2019Article
- Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study.Human molecular genetics · 2019Article
- Weighting sequence variants based on their annotation increases the power of genome-wide association studies in dairy cattle.Genetics, selection, evolution : GSE · 2019Article
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- Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.Cell reports · 2018Article
- MicroRNA-transcription factor interactions and their combined effect on target gene expression in colon cancer cases.Genes, chromosomes & cancer · 2018Article
- Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.Scientific reports · 2018Article
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- A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.PLoS computational biology · 2017Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a method for estimating the positional distribution of transcription factor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs: OCT4, SOX2, NANOG, HNF1A, HNF4A, HNF6, FOXA2, USF1 and CREB1. The data were obtained from a genome-wide coverage of promoter regions from 8-kb upstream of the transcription start site (TSS) to 2-kb downstream. The number of target genes of each TF ranges from few hundred to several thousand. We found that for each of the nine TFs the estimated binding site distribution is closely approximated by a mixture of two components: a narrow peak, localized within 300-bp upstream of the TSS, and a distribution of almost uniform density within the tested region. Using Gene Ontology (GO) and Enrichment analysis, we were able to associate (for each of the TFs studied) the target genes of both types of binding with known biological processes. Most GO terms were enriched either among the proximal targets or among those with a uniform distribution of binding sites. For example, the three stemness-related TFs have several hundred target genes that belong to 'development' and 'morphogenesis' whose binding sites belong to the uniform distribution.
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