Database files for RegulonDB 10.6. Both the regulatory network and genomic features are extracted by the regulondb_parser.py script.
Relevant DB tables are interactions, genomic_features, and genomic_feature_association under each strain specific schema.
As of December 2020, these files are:
- attenuator_terminator.txt: Anti-terminators
- conformation.txt: regulator active conformations (need to go from active regulator => protein)
- gene.txt: gene information
- gene_product_link.txt: gene to protein (protein/RNA)
- genetic_network.txt: regulatory relationships
- object_external_db_link.txt: cross-references to other DBs
- object_synonym.txt: synonyms for ECK accession
- object_properties.txt: a catch-all file for a lot of object properties, used to generate display pages; includes genes, sRNAs, operons, promoters, binding sites, etc
- product.txt: product (protein/RNA) information
- product_tf_link.txt: product => transcription factor relationships
- promoter.txt: promoter details
- promoter_feature.txt: promoter properties, included TATA box locations
- regulatory_interaction.txt: interactions between regulators and associated genetic elements
- rfam.txt: riboswitches
- shine_dalgarno.txt: SD boxes
- sigma_tmp.txt: Sigma factor details
- srna_interaction: short RNA => gene regulatory interactions
- site.txt: DNA binding site details
- terminators.txt: terminator properties, including rho (in)dependent
- tf_gene_interaction: transcription factor => gene interactions
- tu_gene_link.txt: transcription unit memberships
These relationships don't appear to be documented anywhere, so these files may change or disappear as RegulonDB is updated.