The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Open accessAbstract
RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge 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 sigma(54) and five different promoter types of the sigma(70) family, as well as their corresponding -10 and -35 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 associated 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.
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Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Salgado, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj156 · Cited by 368
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Research works printed but not linked: 16
- Keseler, 2005, Nucleic Acids Research, 33, D334, 10.1093/nar/gki108 · DOI · Paper page
- Gutierrez-Rios, 2003, Genome Research, 13, 2435, 10.1101/gr.1387003 · DOI
- Schaefer, 1995, Analytical biochemistry, 227, 255, 10.1006/abio.1995.1279 · DOI · Paper page
- Huerta, 2003, Journal of molecular biology, 333, 261, 10.1016/j.jmb.2003.07.017 · DOI · Paper page
- Martinez-Antonio, 2006, Trends in microbiology, 14, 22, 10.1016/j.tim.2005.11.002 · DOI
- Nudler, 2004, Trends in biochemical sciences, 29, 11, 10.1016/j.tibs.2003.11.004 · DOI · Paper page
- Griffiths-Jones, 2005, Nucleic Acids Research, 33, D121, 10.1093/nar/gki081 · DOI · Paper page
- Yanofsky, 1981, Nature; Physical Science (London), 289, 751, 10.1038/289751a0 · DOI · Paper page
- Dubnau, 1984, CRC critical reviews in biochemistry, 16, 103, 10.3109/10409238409102300 · DOI
- Lovett, 1990, Journal of Bacteriology, 172, 1, 10.1128/jb.172.1.1-6.1990 · DOI
- Merino, 2005, Trends in genetics : TIG, 21, 260, 10.1016/j.tig.2005.03.002 · DOI
- 2007, Current opinion in microbiology, 10, 93, 10.1016/j.mib.2007.03.017 · DOI
- M ller, 2004, PLoS biology, 2, e309, 10.1371/journal.pbio.0020309 · DOI · Paper page
- Rodriguez-Penagos, 2007, BMC bioinformatics [electronic resource], 8, 293, 10.1186/1471-2105-8-293 · DOI
- Kersey, 2005, Nucleic Acids Research, 33, D297, 10.1093/nar/gki039 · DOI
- 2004, Bioinformatics, 20, 2307, 10.1093/bioinformatics/bth216 · doi:10.1093/bioinformatics/bth216
Cited by
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012776 · Cited by 2,131
“To validate the network predictions we used 3433 experimentally confirmed regulatory interactions among 1471 genes that have been curated in RegulonDB version 6.4 [40].”
MethodInfluentialCOBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745
“• Gene regulatory networks involve transcription and translation events and their control 12,14 .”
Self-citationPathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Karp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
Metadata
- Authors
- Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martinez-Flores, I., Salgado, H., Bonavides-Martinez, C., Abreu-Goodger, C., Rodriguez-Penagos, C., Miranda-Rios, J., Morett, E., Merino, E., Huerta, A. M., Trevino-Quintanilla, L., & Collado-Vides, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-12-23
- Volume
- 36
- Issue
- Database
- Pages
- D120-D124
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2127057035
- Cited by
- 491
- References
- 2
- FWCI
- 32.82
- Type
- journal article
- Language
- en
- Open access
- gold
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- Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martinez-Flores, I., Salgado, H., Bonavides-Martinez, C., Abreu-Goodger, C., Rodriguez-Penagos, C., Miranda-Rios, J., Morett, E., Merino, E., Huerta, A. M., Trevino-Quintanilla, L., & Collado-Vides, J. (2007). RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research. https://doi.org/10.1093/nar/gkm994
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
