ArticleBMC genomics2013
Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
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- Single-Cell Transcriptome Analysis Reveals Development-Specific Networks at Distinct Synchronized Antral Follicle Sizes in Sheep Oocytes.International journal of molecular sciences · 2024Article
- Cellular specificity of androgen receptor, coregulators, and pioneer factors in prostate cancer.Endocrine oncology (Bristol, England) · 2022Review
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Pioneer factors and their in vitro identification methods.Molecular genetics and genomics : MGG · 2020Review
- GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy.Nature communications · 2017Article
- Glucocorticoids and Reproduction: Traffic Control on the Road to Reproduction.Trends in endocrinology and metabolism: TEM · 2017Review
- Differential effects of HTLV-1 Tax oncoprotein on the different estrogen-induced-ER α-mediated transcriptional activities.Cell cycle (Georgetown, Tex.) · 2016Article
- Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets.Bioinformatics (Oxford, England) · 2015Article
- Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs.Nucleic acids research · 2015Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCell type and TF specific interactions between Transcription Factors (TFs) and cofactors are essential for transcriptional regulation through recruitment of general transcription machinery to gene promoter regions and their identification heavily reliant on protein interaction assays.
resultsUsing TF targeted chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) data from Encyclopedia of DNA Elements (ENCODE), we report cell type and TF specific TF-cofactor interactions captured in vivo through enrichments of non target cofactor binding site motifs within ChIP-seq peaks. We observe enrichments in both known and novel cofactor motifs.
conclusionsGiven the regulatory implications which TF and cofactor interactions have on a cell's phenotype, their identification is necessary but challenging. Here we present the findings to our analyses surrounding the investigation of TF-cofactor interactions encoded within TF ChIP-seq peaks. Novel cofactor binding site enrichments observed provides valuable insight into TF and cell type specific interactions driving TF interactions.
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