Auxotrophic and Prototrophic Conditional Genetic Networks Reveal the Functional Rewiring of Transcription Factors in Escherichia coli
Gagarinova et al. (2021)
Supporting Materials
Tables
- Supplementary Tables 1-12: Table S1-12
- Supplementary Table 1. TF genes targeted for genetic screening.
- Supplementary Table 2. TF gene pairs with significant GI scores in static networks.
- Supplementary Table 3. Functional crosstalk between enriched bioprocesses in RM network.
- Supplementary Table 4. Correlation score of GI gene pairs in static (RM, MM) and differential (DF) networks.
- Supplementary Table 5. Bioprocesses enriched with GIs involving global or local TF regulators.
- Supplementary Table 6. Number of GIs identified per orphan TF.
- Supplementary Table 7. Inter-connectivity of orphan TFs with annotated genes in enriched bioprocesses.
- Supplementary Table 8. YneJ binding sites under carbon-limiting conditions by ChIP-seq.
- Supplementary Table 9. Gene pairs with differential (DF) GI scores.
- Supplementary Table 10. Autocorrelated TF genes and their corresponding single gene deletion mutant strain fitness from phenotypic genetic screen (Tong et al., 2020).
- Supplementary Table 11. TF gene pairs connecting distinct modules in differential network.
- Supplementary Table 12. YdiP binding sites under carbon-limiting conditions by ChIP-seq.
- Supplementary Tables 13-17: Table S13-17
- Supplementary Table 13. Phylogenetic profiles of each TF target across 4,409 species in 17 bacterial phyla.
- Supplementary Table 14. Conserved TFs with epistatic connections from static and differential (DF) networks in each of the assigned bioprocesses.
- Supplementary Table 15. Co-conserved interprocess gene pairs connected by GIs in static and differential (DF) networks.
- Supplementary Table 16. Protein-BLAST searches to determine putative TF paralogs.
- Supplementary Table 17. Bacterial strains and oligonucleotides used in this study.
ChIP-seq
- ChIP raw bed files ChIP raw bed files
- Ynej_ChIP_Tryptone_peaks.bed
- Ynej_ChIP_Putrescine_peaks.bed
- Ydip_ChIP_RM15_Ydip.bed
- Ydip_ChIP_MM15_Ydip.bed
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E-mail questions or comments to: sadhna.phanse@utoronto.ca