| Inference of transcriptional regulatory network by two-stage constrained space factor analysis. | |
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MedLine Citation:
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PMID: 16144806 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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MOTIVATION: Microarray gene expression and cross-linking chromatin immunoprecipitation data contain voluminous information that can help the identification of transcriptional regulatory networks at the full genome scale. Such high-throughput data are noisy however. In contrast, from the biomedical literature, we can find many evidenced transcription factor (TF)-target gene binding relationships that have been elucidated at the molecular level. But such sporadically generated knowledge only offers glimpses on limited patches of the network. How to incorporate this valuable knowledge resource to build more reliable network models remains a question. RESULTS: We present a modified factor analysis approach. Our algorithm starts with the evidenced TF-gene linkages. It iterates between the network configuration estimation step and the connection strength estimation step, using the high-throughput data, till convergence. We report two comprehensive regulatory networks obtained for Saccharomyces cerevisiae, one under the normal growth condition and the other under the environmental stress condition. SUPPLEMENTARY INFORMATION: http://kiefer.stat.ucla.edu/lap2/download/bti656_supplement.pdf. |
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Authors:
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Tianwei Yu; Ker-Chau Li |
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Publication Detail:
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Type: Journal Article; Research Support, U.S. Gov't, Non-P.H.S. Date: 2005-09-06 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 21 ISSN: 1367-4803 ISO Abbreviation: Bioinformatics Publication Date: 2005 Nov |
Date Detail:
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Created Date: 2005-10-24 Completed Date: 2006-01-05 Revised Date: 2008-11-21 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 4033-8 Citation Subset: IM |
Affiliation:
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Department of Statistics, University of California-Los Angeles, Los Angeles, CA 90095-1554, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms* Computer Simulation Factor Analysis, Statistical Gene Expression Profiling / methods* Gene Expression Regulation / physiology* Models, Genetic* Pattern Recognition, Automated / methods Proteome / metabolism* Signal Transduction / physiology* Transcription Factors / metabolism* Transcriptional Activation / physiology |
| Chemical | |
Reg. No./Substance:
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0/Proteome; 0/Transcription Factors |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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