ArticleGenome research2005
Discovering regulatory binding-site modules using rule-based learning.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 51 citations in OpenAlex.
- R.ROSETTA: an interpretable machine learning framework.BMC bioinformatics · 2021Article
- Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers.BMC bioinformatics · 2014Article
- A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.BMC plant biology · 2011Article
- Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis.BMC genomics · 2009Article
- Genetic evidence for a role of adiponutrin in the metabolism of apolipoprotein B-containing lipoproteins.Human molecular genetics · 2009Article
- A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana.BMC systems biology · 2009Article
- Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3.BMC genomics · 2008Article
- Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.BMC bioinformatics · 2008Article
- The C1C2: a framework for simultaneous model selection and assessment.BMC bioinformatics · 2008Article
- Associating transcription factor-binding site motifs with target GO terms and target genes.Nucleic acids research · 2008Article
- High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae.Genome biology · 2008Article
- Predicting gene expression from sequence: a reexamination.PLoS computational biology · 2007Article
- Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors.BMC systems biology · 2007Article
- Enhancer responses to similarly distributed antagonistic gradients in development.PLoS computational biology · 2007Article
- Global gene expression analysis and regulation of the principal genes expressed in bovine placenta in relation to the transcription factor AP-2 family.Reproductive biology and endocrinology : RB&E · 2007Article
- Data mining for gene networks relevant to poor prognosis in lung cancer via backward-chaining rule induction.Cancer informatics · 2007Article
- Using local gene expression similarities to discover regulatory binding site modules.BMC bioinformatics · 2006Article
- Modelling gene regulation networks via multivariate adaptive splines.Cancer genomics & proteomicsArticle
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors regulate expression by binding selectively to sequence sites in cis-regulatory regions of genes. It is therefore reasonable to assume that genes regulated by the same transcription factors should all contain the corresponding binding sites in their regulatory regions and exhibit similar expression profiles as measured by, for example, microarray technology. We have used this assumption to analyze genome-wide yeast binding-site and microarray expression data to reveal the combinatorial nature of gene regulation. We obtained IF-THEN rules linking binding-site combinations (binding-site modules) to genes with particular expression profiles, and thereby provided testable hypotheses on the combinatorial coregulation of gene expression. We showed that genes associated with such rules have a significantly higher probability of being bound by the same transcription factors, as indicated by a genome-wide location analysis, than genes associated with only common binding sites or similar expression. Furthermore, we also found that such genes were significantly more often biologically related in terms of Gene Ontology annotations than genes only associated with common binding sites or similar expression. We analyzed expression data collected under different sets of stress conditions and found many binding-site modules that are conserved over several of these condition sets, as well as modules that are specific to particular biological responses. Our results on the reoccurrence of binding sites in different modules provide specific data on how binding sites may be combined to allow a large number of expression outcomes using relatively few transcription factors.
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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.