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Yu T and Li KC  (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8

Abstract: 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.

Status: Published Type: Journal Article | Research Support, U.S. Gov't, Non-P.H.S. PubMed ID: 16144806

Topics addressed in this paper

Number of different genes curated to this paper: 57

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
ABF1 ACE2 ADR1 BAS1 CBF1 CUP9 DAL82 FKH1 FKH2 GAT1
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Computational analysis yg ball
Omics yg ball
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Topics Genes linked to topics (#11 - 20 )
GCN4 GCR1 GCR2 GLN3 GZF3 HAP1 HAP2 HAP3 HAP4 HAP5
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Topics Genes linked to topics (#21 - 30 )
HIR3 HSF1 INO2 INO4 LEU3 MAC1 MET31 MET4 MIG1 MSN2
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Topics Genes linked to topics (#31 - 40 )
MSN4 OAF1 PDR1 PHO2 PPR1 RAP1 REB1 RIM101 RLM1 ROX1
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RPN4 RTG1 RTG3 SFL1 SKN7 STE12 STP1 STP2 SUM1 SWI4
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Topics Genes linked to topics (#51 - 57 )
SWI5 SWI6 TEC1 THI2 UME6 XBP1 YAP1
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Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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