Method
High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae
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* Corresponding author: Won-Ki Huh wkh@snu.ac.kr
- † Equal contributors
1 Department of Bioinformatics, Dong-a Seetech Research Institute, Seoul 135-010, Republic of Korea
2 School of Biological Sciences and Research Center for Functional Cellulomics, Institute of Microbiology, Seoul National University, Seoul 151-747, Republic of Korea
3 Computational Biology Division, TGEN, N 5th St, Phoenix, Arizona 85004, USA
Genome Biology 2008, 9:R2 doi:10.1186/gb-2008-9-1-r2
Published: 3 January 2008Additional files
Additional data file 1:
Filtering steps for obtaining reliable candidate regulators.
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Additional data file 2:
Matrices representing overall information about EPMs of the nitrogen depletion and the cell cycle conditions.
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Additional data file 3:
Detailed descriptions of condition-specific features of EPMs with their average gene expression profiles
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Additional data file 4:
Case studies that describe the RMs and their regulators in several cell cycle EPMs, heat shock EPM 0 and nitrogen depletion EPM 2.
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Additional data file 5:
Matrices describing nitrogen depletion EPM 0, which includes various functional gene groups that formed several EPMs in other conditions.
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Additional data file 6:
Numbers of overlapped regulators among three conditions.
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Additional data file 7:
Enriched functional categories for the target genes of all confirmed transcription factors.
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Additional data file 8:
Relative nucleosome occupancy levels on the promoters of condition-specific target genes of Uga3 and Yap1
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Additional data file 9:
Regulatory networks among transcription factors under the heat shock and the nitrogen depletion conditions.
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Additional data file 10:
Enriched functional categories for the targets of FFL groups.
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Additional data file 11:
Matrices describing all EPMs and RMs, including lists of synergistic pairs of regulators.
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Additional data file 12:
Possible regulatory relationships among transcription factors in the same EPM.
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Additional data file 13:
Detailed descriptions of RMs in nitrogen depletion EPM 12 and a comparison with the modules determined using other algorithms.
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Additional data file 14:
Criteria for choosing appropriate cut-off values.
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