PMC:2726282 / 2926-4393 JSONTXT

{"project":"2_test","denotations":[{"id":"18599074-16381895-62517914","span":{"begin":215,"end":216},"obj":"16381895"},{"id":"18599074-11967538-62517915","span":{"begin":377,"end":379},"obj":"11967538"},{"id":"18599074-15604458-62517915","span":{"begin":377,"end":379},"obj":"15604458"},{"id":"18599074-10734204-62517916","span":{"begin":709,"end":711},"obj":"10734204"},{"id":"18599074-12582243-62517916","span":{"begin":709,"end":711},"obj":"12582243"},{"id":"18599074-14572541-62517917","span":{"begin":981,"end":983},"obj":"14572541"},{"id":"18599074-14572541-62517918","span":{"begin":1066,"end":1068},"obj":"14572541"}],"text":"Available experimental data point to more than 3000 regulatory interactions between TFs and their regulated genes in E. coli. This information is integrated and documented in a specialised database called RegulonDB.8 Global analyses of this huge network have already been published, emphasising a hierarchical organisation and statistically overrepresented regulatory motifs.9–11 Here, our aim is to analyse the flow of regulatory information within the network of transcriptional interactions among TFs and sigmas (E. coli transcriptional cross-regulatory network). This network encompasses 115 TFs and 7 sigma factors, i.e., around one-third of the total predicted TF proteins in this bacterium (Fig. 1).12,13 On average, every TF is connected to two other TFs (i.e., more technically, the mean degree of the regulatory graph is 2.74). However, the connectivity distribution of TFs is not uniform, with a small fraction of global TFs with high out-degrees dominating the network.15 Seven global regulators were defined previously based on a collection of criteria:15 (i) number of regulated genes; (ii) number of regulated genes encoding for TFs; (iii) propensity of cooperative regulation of targets with the aid of other TFs; (iv) ability to directly affect the expression of a variety of promoters that use different sigma factors; (v) belonging to evolutionary families with few paralogs; and (vi) heterogeneity of the functional classes of the regulated genes."}