Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states
- Equal contributors
1 Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
2 Current address: Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-751, Republic of Korea
3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
BMC Biology 2014, 12:4 doi:10.1186/1741-7007-12-4Published: 24 January 2014
Additional file 1: Figure S1:
Strand specificity of RNA polymerase (RNAP) binding. Figure S2. Sequence motifs of σ-factors. Figure S3. The majority of σ38-specific promoters were bound by σ70 when rpoS is missing. Figure S4. Examples of up-regulated and down-regulated genes when rpoS was knocked out. Figure S5. Comparison of transcriptional regulation by two major σ-factors, σ70 and σ38, in two closely related bacteria. Figure S6. Comparison of transcriptional level of σ-factors and their anti-σ-factors. Figure S7. Purine and pyrimidine preferences at transcription start site (TSS) and −1 site. Figure S8. Number of TSSs found in one or multiple conditions. Figure S9. Clusters of Orthologous Groups (COG) clustering analysis of σ-factor regulons.
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Additional file 2: Table S1:
Escherichia coli strains and culture conditions for chromatin immunoprecipitation and microarray (ChIP-chip) experiments.
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Additional file 3: Table S2:
RRNA polymerase (RNAP) and σ-factor binding regions in Escherichia coli.
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Additional file 4: Table S3:
Binding intensities of RNA polymerase (RNAP) and σ-factor binding regions.
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Additional file 5: Table S5:
Comparison of σ-factor binding regions with known binding regions.
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Additional file 6: Table S4:
Identified TSSs of Escherichia coli under four different conditions.
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Additional file 7: Table S6:
Reconstructed σ-factor-transcription unit gene (σ-TUG) network in Escherichia coli.
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Additional file 8: Table S7:
Transcription levels of Escherichia coli genes in the wild type and the ΔrpoS strain.
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