Figure 1

Comparing manually curated, and predicted transcription factors (TFs). Manually-curated TFs were obtained from RegulonDB [6] for E. coli K12, and from DBTBS [16] for B. subtilis 168. Predictions were based on matches to Pfam and Superfamily DNA-binding domains reported at the DBD [17]. (A, D) Venn diagrams comparing curated and predicted TFs. (B, E) P-cubic of curated TFs. (C, F) P-cubic of predicted TF-coding genes. The p-cubic of any set of TF-coding genes is below the p-cubic of the corresponding set of other genes, showing that TF-coding genes have lower co-occurrences than other genes. Since predicted TF-coding genes behave similarly to curated TF-coding genes, predicted TF-coding genes might be enough to test if TF-coding genes in other prokaryotes have lower co-occurrences than genes coding for proteins other than TFs.