ArticleNucleic acids research2002
Predicting transcription factor synergism.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 93 citations in OpenAlex.
- Genome-Wide Characterization and Expression Analysis of Heat Shock Transcription Factors in Two Cultivars of Rice (International journal of molecular sciences · 2026Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- A self-attention model for inferring cooperativity between regulatory features.Nucleic acids research · 2021Article
- A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.Nucleic acids research · 2019Article
- Investigating transcription factor synergism in humans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Heterogeneity of transcription factor binding specificity models within and across cell lines.Genome research · 2016Article
- Modeling co-occupancy of transcription factors using chromatin features.Nucleic acids research · 2016Article
- PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.BMC bioinformatics · 2015Article
- Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.PloS one · 2015Article
- The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.Briefings in bioinformatics · 2014Article
- CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.Nucleic acids research · 2014Article
- Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes.Bioinformatics and biology insights · 2014Article
- Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.Nucleic acids research · 2013Article
- Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.Genome research · 2013Article
- A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.BMC genomics · 2012Article
- Inferring transcription factor complexes from ChIP-seq data.Nucleic acids research · 2011Article
- Simplified method to predict mutual interactions of human transcription factors based on their primary structure.PloS one · 2011Article
- On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence.BMC bioinformatics · 2010Article
- Functional annotation of novel lineage-specific genes using co-expression and promoter analysis.BMC genomics · 2010Article
- Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays.Molecular bioSystems · 2009Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional regulation is mediated by a battery of transcription factor (TF) proteins, that form complexes involving protein-protein and protein-DNA interactions. Individual TFs bind to their cognate cis-elements or transcription factor-binding sites (TFBS). TFBS are organized on the DNA proximal to the gene in groups confined to a few hundred base pair regions. These groups are referred to as modules. Various modules work together to provide the combinatorial regulation of gene transcription in response to various developmental and environmental conditions. The sets of modules constitute a promoter model. Determining the TFs that preferentially work in concert as part of a module is an essential component of understanding transcriptional regulation. The TFs that act synergistically in such a fashion are likely to have their cis-elements co-localized on the genome at specific distances apart. We exploit this notion to predict TF pairs that are likely to be part of a transcriptional module on the human genome sequence. The computational method is validated statistically, using known interacting pairs extracted from the literature. There are 251 TFBS pairs up to 50 bp apart and 70 TFBS pairs up to 200 bp apart that score higher than any of the known synergistic pairs. Further investigation of 50 pairs randomly selected from each of these two sets using PubMed queries provided additional supporting evidence from the existing biological literature suggesting TF synergism for these novel pairs.
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Registered trials
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.