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Wu WS, et al.  (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421

Abstract: ABSTRACT: BACKGROUND: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation. RESULTS: Integrating gene expression and ChIP-chip data, we develop a method, called MOdule Finding Algorithm (MOFA), for reconstructing TRMs of the yeast cell cycle. MOFA identified 87 TRMs, which together contain 336 distinct genes regulated by 40 TFs. Using various kinds of data, we validated the biological relevance of the identified TRMs. Our analysis shows that different combinations of a fairly small number of TFs are responsible for regulating a large number of genes involved in different cell cycle phases and that there may exist crosstalk between the cell cycle and other cellular processes. MOFA is capable of finding many novel TF-target gene relationships and can determine whether a TF is an activator or/and a repressor. Finally, MOFA refines some clusters proposed by previous studies and provides a better understanding of how the complex expression program of the cell cycle is regulated. CONCLUSIONS: MOFA was developed to reconstruct TRMs of the yeast cell cycle. Many of these TRMs are in agreement with previous studies. Further, MOFA inferred many interesting modules and novel TF combinations. We believe that computational analysis of multiple types of data will be a powerful approach to studying complex biological systems when more and more genomic resources such as genome-wide protein activity data and protein-protein interaction data become available.

Status: Published Type: Journal Article PubMed ID: 17010188

Topics addressed in this paper

Number of different genes curated to this paper: 99

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
ABF1 ACE2 AGA2 ARP7 BUD9 CDC20 CIN5 CLB2 CLB4 CLB6
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Omics yg ball
Primary Literature blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball

Topics Genes linked to topics (#11 - 20 )
CLN1 CST6 DAT1 DIG1 DUN1 EXG1 FKH1 FKH2 GAL4 GAS1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#21 - 30 )
GAT3 GIN4 HAP1 HAP4 HHF1 HHF2 HHT1 HHT2 HIR1 HIR2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#31 - 40 )
HIR3 HSP150 HST4 HTA1 HTB1 IRC8 IRR1 IXR1 KIN3 MBP1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#41 - 50 )
MCM1 MCM3 MMR1 MNN1 MSA1 MSN4 MTC6 NDD1 NRG1 OCH1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#51 - 60 )
PCL1 PCL2 PDR1 PDS5 PHD1 PHO4 PIG1 PSA1 RAD27 RAD51
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball
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Topics Genes linked to topics (#61 - 70 )
RAP1 RAX2 REB1 RIM1 RLM1 RNR1 SIM1 SKN7 SMP1 SPO12
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#71 - 80 )
STB1 STE12 SUR7 SUT1 SWE1 SWI4 SWI5 SWI6 TEC1 TEL2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#81 - 90 )
UME6 UTR2 YAP5 YAP6 YBL111C YBL112C YBL113C YEL075C YEL076C YEL076C-A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball
Substrates/Ligands/Cofactors blue ball blue ball blue ball
Jump to Summary Chart for:
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Topics Genes linked to topics (#91 - 99 )
YER189W YLR464W YOX1 YPR202W YPR203W YRF1-2 YRF1-3 YRF1-5 YRF1-6
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cell Cycle Phase Involved blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Computational analysis blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball
Substrates/Ligands/Cofactors blue ball

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