%0 Journal Article %1 SantosZavaleta2019RegulonDB %A Santos-Zavaleta, A %A Salgado, H %A Gama-Castro, S %A Sánchez-Pérez, M %A Gómez-Romero, L %A Ledezma-Tejeida, D %A García-Sotelo, J S %A Alquicira-Hernández, K %A Muñiz-Rascado, L J %A Peña-Loredo, P %A Ishida-Gutiérrez, C %A Velázquez-Ramírez, D A %A Del Moral-Chávez, V %A Bonavides-Martínez, C %A Méndez-Cruz, C F %A Galagan, J %A Collado-Vides, J %D 2019 %J Nucleic Acids Res %K database transcriptional-regulatory-network %N D1 %P 212-212 %R 10.1093/nar/gky1077 %T RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 %U https://www.ncbi.nlm.nih.gov/pubmed/30395280 %V 47 %X RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.

@article{SantosZavaleta2019RegulonDB, abstract = {RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.}, added-at = {2019-05-04T14:00:59.000+0200}, author = {Santos-Zavaleta, A and Salgado, H and Gama-Castro, S and S{\'a}nchez-P{\'e}rez, M and G{\'o}mez-Romero, L and Ledezma-Tejeida, D and Garc{\'i}a-Sotelo, J S and Alquicira-Hern{\'a}ndez, K and Mu{\~n}iz-Rascado, L J and Pe{\~n}a-Loredo, P and Ishida-Guti{\'e}rrez, C and Vel{\'a}zquez-Ram{\'i}rez, D A and Del Moral-Ch{\'a}vez, V and Bonavides-Mart{\'i}nez, C and M{\'e}ndez-Cruz, C F and Galagan, J and Collado-Vides, J}, biburl = {https://www.bibsonomy.org/bibtex/2813d0dda216727d250f2c76ceb92d78c/karthikraman}, description = {RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. - PubMed - NCBI}, doi = {10.1093/nar/gky1077}, interhash = {31a885f8d731357c7cb2e16f6ff67f47}, intrahash = {813d0dda216727d250f2c76ceb92d78c}, journal = {Nucleic Acids Res}, keywords = {database transcriptional-regulatory-network}, month = jan, number = {D1}, pages = {212-212}, pmid = {30395280}, timestamp = {2019-05-04T14:00:59.000+0200}, title = {RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30395280}, volume = 47, year = 2019 }