Genome Biology
Volume 9
Issue 1

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High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

Hun-Goo Lee^*¹^,2 , Hyo-Soo Lee^*¹ , Sang-Hoon Jeon¹ , Tae-Hoon Chung³ , Young-Sung Lim¹ and Won-Ki Huh²

¹Department of Bioinformatics, Dong-a Seetech Research Institute, Seoul 135-010, Republic of Korea

²School of Biological Sciences and Research Center for Functional Cellulomics, Institute of Microbiology, Seoul National University, Seoul 151-747, Republic of Korea

³Computational Biology Division, TGEN, N 5th St, Phoenix, Arizona 85004, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R2doi:10.1186/gb-2008-9-1-r2


Published:	3 January 2008

Subject areas: Genome studies, Methods, Model organisms

Additional 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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