PMC:1852316 / 43837-44653 JSONTXT

{"project":"2_test","denotations":[{"id":"17397539-14681419-1689501","span":{"begin":432,"end":434},"obj":"14681419"}],"text":"Our methodology requires a preliminary TRN which is used as the training set in all three methodologies presented below. We gathered this training set from EcoCyc [14]. EcoCyc describes E. coli operons, promoters, TFs, and TF binding sites. The database describes the mechanisms of transcriptional regulation of E. coli genes, and contains the most complete description of the genetic network of any organism. EcoCyc and RegulonDB [36] are curated to ensure that their data content is the same. The preliminary TRN used in this study included 984 genes, 144 TFs, and 2007 gene/TF interactions. Out of 2007 gene/TF interactions, 1124 were up regulation, 766 were down regulation, 5 were uncertain, and 112 were dual regulation (both up/down). Basic properties of the preliminary E. coli TRN are illustrated in Fig. 5."}