ArticleGenome biology2004
Identifying combinatorial regulation of transcription factors and binding motifs.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 174 citations in OpenAlex.
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- Causal Discovery in High-dimensional, Multicollinear Datasets.Frontiers in epidemiology · 2022Article
- Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast.NPJ systems biology and applications · 2021Review
- Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.Nucleic acids research · 2021Article
- Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades.PloS one · 2021Article
- An osmolality/salinity-responsive enhancer 1 (OSRE1) in intron 1 promotes salinity induction of tilapia glutamine synthetase.Scientific reports · 2020Article
- FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo.Developmental cell · 2018Article
- DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.Bioinformatics (Oxford, England) · 2017Article
- Modeling co-occupancy of transcription factors using chromatin features.Nucleic acids research · 2016Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling.Frontiers in plant science · 2016Article
- Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data.Current genomics · 2015Article
- Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome.Molecular bioSystems · 2015Article
- Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.PloS one · 2015Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundCombinatorial interaction of transcription factors (TFs) is important for gene regulation. Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important.
resultsHere we use a novel method that integrates chromatin immunoprecipitation (ChIP) data with microarray expression data and with combinatorial TF-motif analysis. We systematically identify combinations of transcription factors and of motifs. The various combinations of TFs involved multiple binding mechanisms. We reconstruct a new combinatorial regulatory map of the yeast cell cycle in which cell-cycle regulation can be drawn as a chain of extended TF modules. We find that the pairwise combination of a TF for an early cell-cycle phase and a TF for a later phase is often used to control gene expression at intermediate times. Thus the number of distinct times of gene expression is greater than the number of transcription factors. We also see that some TF modules control branch points (cell-cycle entry and exit), and in the presence of appropriate signals they can allow progress along alternative pathways.
conclusionsCombining different data sources can increase statistical power as demonstrated by detecting TF interactions and composite TF-binding motifs. The original picture of a chain of simple cell-cycle regulators can be extended to a chain of composite regulatory modules: different modules may share a common TF component in the same pathway or a TF component cross-talking to other pathways.
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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.