ArticleNucleic acids research2005
Identifying cooperative transcriptional regulations using protein-protein interactions.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 46 citations in OpenAlex.
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.Plant physiology · 2017Article
- CoopTFD: a repository for predicted yeast cooperative transcription factor pairs.Database : the journal of biological databases and curation · 2016Article
- Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets.PloS one · 2016Article
- YCRD: Yeast Combinatorial Regulation Database.PloS one · 2016Article
- cDREM: inferring dynamic combinatorial gene regulation.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast.BMC genomics · 2015Article
- PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.BMC bioinformatics · 2015Article
- Identifying cooperative transcription factors in yeast using multiple data sources.BMC systems biology · 2014Article
- A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms.BMC systems biology · 2014Article
- Functional and topological characterization of transcriptional cooperativity in yeast.BMC research notes · 2012Article
- Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance.Physiological genomics · 2011Article
- Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk.Journal of the Royal Society, Interface · 2011Article
- A knowledge-based method to predict the cooperative relationship between transcription factors.Molecular diversity · 2010Article
- Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.BMC bioinformatics · 2010Article
- Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.Nucleic acids research · 2009Article
- Peroxisome proliferator-activated receptor-gamma regulates the expression of alveolar macrophage macrophage colony-stimulating factor.Journal of immunology (Baltimore, Md. : 1950) · 2008Article
- Topological comparison of methods for predicting transcriptional cooperativity in yeast.BMC genomics · 2008Article
- High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae.Genome biology · 2008Article
- Prediction of synergistic transcription factors by function conservation.Genome biology · 2007Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cooperative transcriptional activations among multiple transcription factors (TFs) are important to understand the mechanisms of complex transcriptional regulations in eukaryotes. Previous studies have attempted to find cooperative TFs based on gene expression data with gene expression profiles as a measure of similarity of gene regulations. In this paper, we use protein-protein interaction data to infer synergistic binding of cooperative TFs. Our fundamental idea is based on the assumption that genes contributing to a similar biological process are regulated under the same control mechanism. First, the protein-protein interaction networks are used to calculate the similarity of biological processes among genes. Second, we integrate this similarity and the chromatin immuno-precipitation data to identify cooperative TFs. Our computational experiments in yeast show that predictions made by our method have successfully identified eight pairs of cooperative TFs that have literature evidences but could not be identified by the previous method. Further, 12 new possible pairs have been inferred and we have examined the biological relevances for them. However, since a typical problem using protein-protein interaction data is that many false-positive data are contained, we propose a method combining various biological data to increase the prediction accuracy.
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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.