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

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Gama Castro, Socorro ^a   Salgado, Heladia ^a   Peralta Gil, Martin ^a   Santos Zavaleta, Alberto ^a   Muniz Rascado, Luis ^a   Solano Lira, Hilda ^a   Jimenez Jacinto, Verónica ^b   Weiss, Verena ^a   García Sotelo, Jair S ^a   López Fuentes, Alejandra ^a   Porrón Sotelo, Liliana ^a   Alquicira Hernández, Shirley ^a   Medina Rivera, Alejandra ^a   Martínez Flores, Irma ^a   Alquicira Hernández, Kevin ^a   Martínez Adame, Ruth ^a   Bonavides Martínez, César ^a   Miranda Ríos, Juan ^c   Huerta, Araceli M ^a   Mendoza Vargas, Alfredo ^b   Collado Torres, Leonardo ^d   Taboada, Blanca ^c   Vega Alvarado, Leticia ^c   Olvera, Maricela ^b   Olvera, Leticia ^b   Grande, Ricardo ^b   Morett, Enrique ^b   Collado Vides, Julio ^a   more..

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^d NONE   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIOSENSOR; COMPUTER GRAPHICS; DNA BINDING MOTIF; ESCHERICHIA COLI K 12; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC SENSORY RESPONSE UNIT; INFORMATION SYSTEM; PRIORITY JOURNAL; REGULONDB VERSION 7.0; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

BINDING SITES; DATABASES, GENETIC; ESCHERICHIA COLI K12; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; SIGNAL TRANSDUCTION; SYSTEMS INTEGRATION; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI K12;

EID: 78651299341     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1110     Document Type: Article

References (20)

1. Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juarez, K., Contreras-Moreira, B. et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One, 4, e7526.
2. Funahashi, A., Tanimura, N., Morohashi, M. and Kitano, H. (2003) CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. BIOSILICO, 1, 159-162.
3. Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N. and Kitano, H. (2008) CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proc. IEEE, 96, 1254-1265.
4. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R2.
5. Medina-Rivera, A., Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H., Collado-Vides, J. and van Helden, J. (2010) Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res., doi:1093/nar/GKQ710.
6. Novichkov, P.S., Laikova, O.N., Novichkova, E.S., Gelfand, M.S., Arkin, A.P., Dubchak, I. and Rodionov, D.A. (2010) RegPrecise: A database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res., 38, D111-118.
7. Thomas-Chollier, M., Sand, O., Turatsinze, J.V., Janky, R., Defrance, M., Vervisch, E., Brohee, S. and van Helden, J. (2008) RSAT: Regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-127.
8. Smith, M.W. and Neidhardt, F.C. (1983) Proteins induced by aerobiosis in Escherichia coli. J. Bacteriol., 154, 344-350.
9. Neidhardt, F.C. and Savageau, M.A. (1996) Regulation beyond the operon. In Neidhardt, F.C., Curtiss, R. III, Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B. et al. (eds), Escherichia coli and Salmonella: Cellular and Molecular Biology, Vol. 2. ASM Press, Washington, D.C., pp. 1310-1324.
10. Pedersen, H. and Valentin-Hansen, P. (1997) Protein-induced fit: The CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member. EMBO J., 16, 2108-2118.
11. Jorgensen, C.I., Kallipolitis, B.H. and Valentin-Hansen, P. (1998) 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. Mol. Microbiol., 27, 41-50.
12. Toledano, M.B., Kullik, I., Trinh, F., Baird, P.T., Schneider, T.D. and Storz, G. (1994) Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: A mechanism for differential promoter selection. Cell, 78, 897-909.
13. 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) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
14. Faith, J.J., Driscoll, M.E., Fusaro, V.A., Cosgrove, E.J., Hayete, B., Juhn, F.S., Schneider, S.J. and Gardner, T.S. (2008) Many Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res., 36, D866-D870.
15. Collado-Vides, J., Salgado, H., Morett, E., Gama-Castro, S., Jimenez-Jacinto, V., Martinez-Flores, I., Medina-Rivera, A., Muniz-Rascado, L., Peralta-Gil, M. and Santos-Zavaleta, A. (2009) Bioinformatics resources for the study of gene regulation in bacteria. J. Bacteriol., 191, 23-31.
16. Gama-Castro, S., Jiménez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martínez-Flores, I., Salgado, H. et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12, beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res., 36(Database issue), D120-D124.
17. Ulrich, L.E. and Zhulin, I.B. (2007) MiST: A microbial signal transduction database. Nucleic Acids Res., 35, D386-D390.
18. Kanehisa, M. (2002) The KEGG database. Novartis Found. Symp., 247, 91-101, discussion 101-3, 119-28, 244-252.
19. Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T. et al. (2009) EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res., 37, D464-D470.
20. Karp, P.D., Paley, S. and Romero, P. (2002) The Pathway Tools software. Bioinformatics, 18(Suppl. 1), S225-S232.