Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types.

ABSTRACT: Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of Escherichia coli K-12. An RI groups the transcription factor, its effect (positive or negative) and the regulated target, a promoter, a gene or transcription unit. We improved the evidence codes so that specific methods are incorporated and classified into independent groups. On this basis we updated the computation of confidence levels, weak, strong, or confirmed, for the collection of RIs. These updates enabled us to map the RI set to the current collection of HT TF-binding da

SUBMITTER: Lara P 

PROVIDER: S-EPMC10949920 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature