RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Gama-Castro,S., Jiménez-Jacinto,V., Peralta-Gil,M., Santos-Zavaleta,A., Peñaloza-Spinola,M.I., Contreras-Moreira,B. [..] & Collado-Vides,J.. RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research, 36: D120-D124.. 2008, Vol. , p. -2008.
RegulonDB (http://regulondb.ccg.unam.mx/) is the
primary reference database offering curated knowl-
edge of the transcriptional regulatory network
of Escherichia coli K12, currently the best-known
electronically encoded database of the genetic
regulatory network of any free-living organism.
This paper summarizes the improvements, new
biology and new features available in version 6.0.
Curation of original literature is, from now on, up to
date for every new release. All the objects are
supported by their corresponding evidences, now
classified as strong or weak. Transcription factors
are classified by origin of their effectors and by
gene ontology class. We have now computational
predictions for p54 and five different promoter types
of the p70 family, as well as their corresponding 210
and À35 boxes. In addition to those curated from
the literature, we added about 300 experimentally
mapped promoters coming from our own high-
throughput mapping efforts. RegulonDB v.6.0 now
expands beyond transcription initiation, including
RNA regulatory elements, specifically riboswitches,
attenuators and small RNAs, with their known asso-
ciated targets. The data can be accessed through
overviews of correlations about gene regulation.
RegulonDB associated original literature, together
with more than 4000 curation notes, can now be
searched with the Textpresso text mining engine.
RegulonDB (http://regulondb.ccg.unam.mx/) is the
primary reference database offering curated knowl-
edge of the transcriptional regulatory network
of Escherichia coli K12, currently the best-known
electronically encoded database of the genetic
regulatory network of any free-living organism.
This paper summarizes the improvements, new
biology and new features available in version 6.0.
Curation of original literature is, from now on, up to
date for every new release. All the objects are
supported by their corresponding evidences, now
classified as strong or weak. Transcription factors
are classified by origin of their effectors and by
gene ontology class. We have now computational
predictions for p54 and five different promoter types
of the p70 family, as well as their corresponding 210
and À35 boxes. In addition to those curated from
the literature, we added about 300 experimentally
mapped promoters coming from our own high-
throughput mapping efforts. RegulonDB v.6.0 now
expands beyond transcription initiation, including
RNA regulatory elements, specifically riboswitches,
attenuators and small RNAs, with their known asso-
ciated targets. The data can be accessed through
overviews of correlations about gene regulation.
RegulonDB associated original literature, together
with more than 4000 curation notes, can now be
searched with the Textpresso text mining engine.