ArticleProceedings of the National Academy of Sciences of the United States of America2004
Interacting models of cooperative gene regulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed, 121 citations in OpenAlex.
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- Emergence of co-expression in gene regulatory networks.PloS one · 2021Article
- Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.PloS one · 2018Article
- Predicting gene expression in massively parallel reporter assays: A comparative study.Human mutation · 2017Article
- Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma.Scientific reports · 2017Article
- A novel statistical approach for identification of the master regulator transcription factor.BMC bioinformatics · 2017Article
- Systematic identification of protein combinations mediating chromatin looping.Nature communications · 2016Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- Prediction of fine-tuned promoter activity from DNA sequence.F1000Research · 2016Article
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- Genome-wide in silico prediction of gene expression.Bioinformatics (Oxford, England) · 2012Article
- One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.Nucleic acids research · 2012Article
- Comparison of targeted maximum likelihood and shrinkage estimators of parameters in gene networks.Statistical applications in genetics and molecular biology · 2012Article
- A self-organized model for cell-differentiation based on variations of molecular decay rates.PloS one · 2012Article
- Specific silencing of the REST target genes in insulin-secreting cells uncovers their participation in beta cell survival.PloS one · 2012Article
- Structural constraints in collaborative competition of transcription factors against the nucleosome.Journal of molecular biology · 2011Article
- Predicting promoter activities of primary human DNA sequences.Nucleic acids research · 2011Article
- ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Uncovering transcriptional interactions via an adaptive fuzzy logic approach.BMC bioinformatics · 2009Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Cooperativity between transcription factors is critical to gene regulation. Current computational methods do not take adequate account of this salient aspect. To address this issue, we present a computational method based on multivariate adaptive regression splines to correlate the occurrences of transcription factor binding motifs in the promoter DNA and their interactions to the logarithm of the ratio of gene expression levels. This allows us to discover both the individual motifs and synergistic pairs of motifs that are most likely to be functional, and enumerate their relative contributions at any arbitrary time point for which mRNA expression data are available. We present results of simulations and focus specifically on the yeast cell-cycle data. Inclusion of synergistic interactions can increase the prediction accuracy over linear regression to as much as 1.5- to 3.5-fold. Significant motifs and combinations of motifs are appropriately predicted at each stage of the cell cycle. We believe our multivariate adaptive regression splines-based approach will become more significant when applied to higher eukaryotes, especially mammals, where cooperative control of gene regulation is absolutely essential.
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