ArticleNucleic acids research2011
CENTDIST: discovery of co-associated factors by motif distribution.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- TF-COMB - Discovering grammar of transcription factor binding sites.Computational and structural biotechnology journal · 2022Article
- NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information.Biology direct · 2020Article
- The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation.Haematologica · 2020Article
- Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules.Frontiers in genetics · 2020Article
- An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.Genome research · 2019Article
- TICA: Transcriptional Interaction and Coregulation Analyzer.Genomics, proteomics & bioinformatics · 2018Article
- Molecular and cellular mechanisms of castration resistant prostate cancer.Oncology letters · 2018Review
- Che-1 is targeted by c-Myc to sustain proliferation in pre-B-cell acute lymphoblastic leukemia.EMBO reports · 2018Article
- Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs.Frontiers in genetics · 2018Article
- Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo.Nature communications · 2017Article
- The logic of transcriptional regulator recruitment architecture atGenome research · 2017Article
- LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes.Scientific reports · 2017Article
- Analysis of Co-Associated Transcription Factors via Ordered Adjacency Differences on Motif Distribution.Scientific reports · 2017Article
- Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data.BMC genomics · 2017Article
- Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein.Molecular oncology · 2016Article
- MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis.Nature communications · 2016Article
- Citrullination-acetylation interplay guides E2F-1 activity during the inflammatory response.Science advances · 2016Article
- Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver.Molecular endocrinology (Baltimore, Md.) · 2015Article
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Authors and funding
5 authors.
Funding
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Abstract
Transcription factors (TFs) do not function alone but work together with other TFs (called co-TFs) in a combinatorial fashion to precisely control the transcription of target genes. Mining co-TFs is thus important to understand the mechanism of transcriptional regulation. Although existing methods can identify co-TFs, their accuracy depends heavily on the chosen background model and other parameters such as the enrichment window size and the PWM score cut-off. In this study, we have developed a novel web-based co-motif scanning program called CENTDIST (http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/). In comparison to current co-motif scanning programs, CENTDIST does not require the input of any user-specific parameters and background information. Instead, CENTDIST automatically determines the best set of parameters and ranks co-TF motifs based on their distribution around ChIP-seq peaks. We tested CENTDIST on 14 ChIP-seq data sets and found CENTDIST is more accurate than existing methods. In particular, we applied CENTDIST on an Androgen Receptor (AR) ChIP-seq data set from a prostate cancer cell line and correctly predicted all known co-TFs (eight TFs) of AR in the top 20 hits as well as discovering AP4 as a novel co-TF of AR (which was missed by existing methods). Taken together, CENTDIST, which exploits the imbalanced nature of co-TF binding, is a user-friendly, parameter-less and powerful predictive web-based program for understanding the mechanism of transcriptional co-regulation.
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