ArticleBMC bioinformatics2005
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 33 citations in OpenAlex.
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- A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining.BMC medical genomics · 2008Article
- Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets.BMC systems biology · 2008Article
- High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae.Genome biology · 2008Article
- A systematic approach to detecting transcription factors in response to environmental stresses.BMC bioinformatics · 2007Article
- Underlying principles of natural selection in network evolution: systems biology approach.Evolutionary bioinformatics online · 2007Article
- Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.BMC bioinformatics · 2007Article
- Reconstructing dynamic regulatory maps.Molecular systems biology · 2007Article
- Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.BMC bioinformatics · 2006Article
- iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.Nucleic acids research · 2006Article
- Ranked prediction of p53 targets using hidden variable dynamic modeling.Genome biology · 2006Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene expression programs depend on recognition of cis elements in promoter region of target genes by transcription factors (TFs), but how TFs regulate gene expression via recognition of cis elements is still not clear. To study this issue, we define the cis-regulatory circuit of a gene as a system that consists of its cis elements and the interactions among their recognizing TFs and develop a dynamic model to study the functional architecture and dynamics of the circuit. This is in contrast to traditional approaches where a cis-regulatory circuit is constructed by a mutagenesis or motif-deletion scheme. We estimate the regulatory functions of cis-regulatory circuits using microarray data.
resultsA novel cross-gene identification scheme is proposed to infer how multiple TFs coordinate to regulate gene transcription in the yeast cell cycle and to uncover hidden regulatory functions of a cis-regulatory circuit. Some advantages of this approach over most current methods are that it is based on data obtained from intact cis-regulatory circuits and that a dynamic model can quantitatively characterize the regulatory function of each TF and the interactions among the TFs. Our method may also be applicable to other genes if their expression profiles have been examined for a sufficiently long time.
conclusionIn this study, we have developed a dynamic model to reconstruct cis-regulatory circuits and a cross-gene identification scheme to estimate the regulatory functions of the TFs that control the regulation of the genes under study. We have applied this method to cell cycle genes because the available expression profiles for these genes are long enough. Our method not only can quantify the regulatory strengths and synergy of the TFs but also can predict the expression profile of any gene having a subset of the cis elements studied.
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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.