RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

被引：274

作者：

Gama-Castro, Socorro ^{[1
]}

Salgado, Heladia ^{[1
]}

Peralta-Gil, Martin ^{[1
]}

Santos-Zavaleta, Alberto ^{[1
]}

Muniz-Rascado, Luis ^{[1
]}

Solano-Lira, Hilda ^{[1
]}

Jimenez-Jacinto, Veronica ^{[2
]}

Weiss, Verena ^{[1
]}

Garcia-Sotelo, Jair S. ^{[1
]}

Lopez-Fuentes, Alejandra ^{[1
]}

Porron-Sotelo, Liliana ^{[1
]}

Alquicira-Hernandez, Shirley ^{[1
]}

Medina-Rivera, Alejandra ^{[1
]}

Martinez-Flores, Irma ^{[1
]}

Alquicira-Hernandez, Kevin ^{[1
]}

Martinez-Adame, Ruth ^{[1
]}

Bonavides-Martinez, Cesar ^{[1
]}

Miranda-Rios, Juan ^{[3
]}

Huerta, Araceli M. ^{[1
]}

Mendoza-Vargas, Alfredo ^{[4
]}

Collado-Torres, Leonardo ^{[5
]}

Taboada, Blanca ^{[6
]}

Vega-Alvarado, Leticia ^{[6
]}

Olvera, Maricela ^{[4
]}

Olvera, Leticia ^{[4
]}

Grande, Ricardo ^{[2
]}

Morett, Enrique ^{[4
]}

Collado-Vides, Julio ^{[1
]}

机构：

[1] Univ Nacl Autonoma Mexico, Programa Genom Computac, Ctr Ciencias Genom, Cuernavaca 62100, Morelos, Mexico

[2] Univ Nacl Autonoma Mexico, Unidad Univ Secuenciac Masiva ADN, Inst Biotecnol, Cuernavaca 62100, Morelos, Mexico

[3] Univ Nacl Autonoma Mexico, Inst Invest Biomed, Mexico City 04510, DF, Mexico

[4] Univ Nacl Autonoma Mexico, Dept Ingn Celular & Biocatalisis, Inst Biotecnol, Cuernavaca 62100, Morelos, Mexico

[5] Winter Genom, Mexico City 07300, DF, Mexico

[6] Univ Nacl Autonoma Mexico, Ctr Ciencias Aplicadas & Desarrollo Tecnol, Mexico City 04510, DF, Mexico

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkq1110

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. The major conceptual change since 3 years ago is an expanded biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. We call these genetic sensory response units, or Gensor Units. We have initiated their high-level curation, with graphic maps and superreactions with links to other databases. Additional connectivity uses expandable submaps. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

引用

页码：D98 / D105

页数：8

共 20 条

[1] Bioinformatics Resources for the Study of Gene Regulation in Bacteria [J].

Collado-Vides, Julio ;

Salgado, Heladia ;

Morett, Enrique ;

Gama-Castro, Socorro ;

Jimenez-Jacinto, Veronica ;

Martinez-Flores, Irma ;

Medina-Rivera, Alejandra ;

Muniz-Rascado, Luis ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto .

JOURNAL OF BACTERIOLOGY, 2009, 191 (01) :23-31

[2] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[3] Many Microbe Microarrays Database: Uniformly normalized affymetrix compendia with structured experimental metadata [J].

Faith, Jeremiah J. ;

Driscoll, Michael E. ;

Fusaro, Vincent A. ;

Cosgrove, Elissa J. ;

Hayete, Boris ;

Juhn, Frank S. ;

Schneider, Stephen J. ;

Gardner, Timothy S. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D866-D870

[4] CellDesigner 3.5: A versatile modeling tool for biochemical networks [J].

Funahashi, Akira ;

Matsuoka, Yukiko ;

Jouraku, Akiya ;

Morohashi, Mineo ;

Kikuchi, Norihiro ;

Kitano, Hiroaki .

PROCEEDINGS OF THE IEEE, 2008, 96 (08) :1254-1265

[5]

Funahashi Akira, 2003, Biosilico, V1, P159, DOI 10.1016/S1478-5382(03)02370-9

[6] RegulonDB (version 6.0):: gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation [J].

Gama-Castro, Socorro ;

Jimenez-Jacinto, Veronica ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto ;

Penaloza-Spinola, Monica I. ;

Contreras-Moreira, Bruno ;

Segura-Salazar, Juan ;

Muniz-Rascado, Luis ;

Martinez-Flores, Irma ;

Salgado, Heladia ;

Bonavides-Martinez, Cesar ;

Abreu-Goodger, Cei ;

Rodriguez-Penagos, Carlos ;

Miranda-Rios, Juan ;

Morett, Enrique ;

Merino, Enrique ;

Huerta, Araceli M. ;

Trevino-Quintanilla, Luis ;

Collado-Vides, Julio .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D120-D124

[7] DNA-binding characteristics of the Escherichia coli CytR regulator:: a relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker [J].

Jorgensen, CI ;

Kallipolitis, BH ;

Valentin-Hansen, P .

MOLECULAR MICROBIOLOGY, 1998, 27 (01) :41-50

[8]

Kanehisa M, 2002, NOVART FDN SYMP, V247, P91

[9] EcoCyc: A comprehensive view of Escherichia coli biology [J].

Keseler, Ingrid M. ;

Bonavides-Martinez, Cesar ;

Collado-Vides, Julio ;

Gama-Castro, Socorro ;

Gunsalus, Robert P. ;

Johnson, D. Aaron ;

Krummenacker, Markus ;

Nolan, Laura M. ;

Paley, Suzanne ;

Paulsen, Ian T. ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto ;

Glennon Shearer, Alexander ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D464-D470

[10]

Langmead B., GENOME BIOL, V10, pR2

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