EcoCyc: Fusing model organism databases with systems biology

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Keseler, Ingrid M ^a   Mackie, Amanda ^b   Peralta Gil, Martin ^c   Santos Zavaleta, Alberto ^c   Gama Castro, Socorro ^c   Bonavides Martínez, César ^c   Fulcher, Carol ^a   Huerta, Araceli M ^c   Kothari, Anamika ^a   Krummenacker, Markus ^a   Latendresse, Mario ^a   Muñiz Rascado, Luis ^c   Ong, Quang ^a   Paley, Suzanne ^a   Schröder, Imke ^d   Shearer, Alexander G ^a   Subhraveti, Pallavi ^a   Travers, Mike ^a   Weerasinghe, Deepika ^a   Weiss, Verena ^c   Collado Vides, Julio ^c   Gunsalus, Robert P ^d   Paulsen, Ian ^b   Karp, Peter D ^a   more..

^a SRI INTERNATIONAL   (United States)

^b MACQUARIE UNIVERSITY   (Australia)

^c INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DKSA PROTEIN; GUANOSINE 3' DIPHOSPHATE 5' DIPHOSPHATE; RNA POLYMERASE; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BINDING AFFINITY; BINDING SITE; COMPUTER INTERFACE; DATA ANALYSIS; ESCHERICHIA COLI; GENE IDENTIFICATION; GENETIC DATABASE; GENOME ANALYSIS; INFORMATION STORAGE; NOMENCLATURE; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; SEQUENCE ANALYSIS; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION; WEB BROWSER;

BINDING SITES; DATABASES, GENETIC; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; INTERNET; MEMBRANE TRANSPORT PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; POSITION-SPECIFIC SCORING MATRICES; PROMOTER REGIONS, GENETIC; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI K12;

EID: 84876556918     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1027     Document Type: Article

References (29)

1. Latendresse, M., Krummenacker, M., Trupp, M. and Karp, P.D. (2012) Construction and completion of flux balance models from pathway databases. Bioinformatics, 28, 388-396.
2. Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases. Nucleic Acids Res., 40, D742-D753.
3. Paul, B.J., Barker, M.M., Ross, W., Schneider, D.A., Webb, C., Foster, J.W. and Gourse, R.L. (2004) DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 118, 311-322.
4. Lemke, J.J., Sanchez-Vazquez, P., Burgos, H.L., Hedberg, G., Ross, W. and Gourse, R.L. (2011) Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA. Proc. Natl Acad. Sci. USA, 108, 5712-5717.
5. Barker, M.M., Gaal, T., Josaitis, C.A. and Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol., 305, 673-688.
6. Srivatsan, A. and Wang, J.D. (2008) Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol., 11, 100-105.
7. Paul, B.J., Berkmen, M.B. and Gourse, R.L. (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc. Natl Acad. Sci. USA, 102, 7823-7828.
8. Costanzo, A., Nicoloff, H., Barchinger, S.E., Banta, A.B., Gourse, R.L. and Ades, S.E. (2008) ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms. Mol. Microbiol., 67, 619-632.
9. Grote, A., Klein, J., Retter, I., Haddad, I., Behling, S., Bunk, B., Biegler, I., Yarmolinetz, S., Jahn, D. and Munch, R. (2009) PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res., 37, D61-D65.
10. Novichkov, P.S., Brettin, T.S., Novichkova, E.S., Dehal, P.S., Arkin, A.P., Dubchak, I. and Rodionov, D.A. (2012) RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res., 40, W604-W608.
11. Perez, A.G., Angarica, V.E., Vasconcelos, A.T. and Collado-Vides, J. (2007) Tractor-DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. Nucleic Acids Res., 35, D132-D136.
12. Oberto, J. (2010) FITBAR: a web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics, 11, 554.
13. Medina-Rivera, A., Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H., Collado-Vides, J. and van Helden, J. (2011) Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res., 39, 808-824.
14. Huerta, A.M. and Collado-Vides, J. (2003) Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol., 333, 261-278.
15. Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M. et al. (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res., 35, 7577-7590.
16. Bochner, B.R., Gadzinski, P. and Panomitros, E. (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res., 11, 1246-1255.
17. Lang, V.J., Leystra-Lantz, C. and Cook, R.A. (1987) Characterization of the specific pyruvate transport system in Escherichia coli K-12. J. Bacteriol., 169, 380-385.
18. Saier, M.H. Jr, Tran, C.V. and Barabote, R.D. (2006) TCDB: the transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res., 34, D181-D186.
19. AbuOun, M., Suthers, P.F., Jones, G.I., Carter, B.R., Saunders, M.P., Maranas, C.D., Woodward, M.J. and Anjum, M.F. (2009) Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J. Biol. Chem., 284, 29480-29488.
20. Baumler, D.J., Peplinski, R.G., Reed, J.L., Glasner, J.D. and Perna, N.T. (2011) The evolution of metabolic networks of E. coli. BMC Syst. Biol., 5, 182.
21. Yoon, S.H., Han, M.J., Jeong, H., Lee, C.H., Xia, X.X., Lee, D.H., Shim, J.H., Lee, S.Y., Oh, T.K. and Kim, J.F. (2012) Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol, 13, R37.
22. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L. and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol., 2, 2006.0008.
23. Joyce, A.R., Reed, J.L., White, A., Edwards, R., Osterman, A., Baba, T., Mori, H., Lesely, S.A., Palsson, B.O. and Agarwalla, S. (2006) Experimental and computational assessment of conditionally essential genes in Escherichia coli. J. Bacteriol., 188, 8259-8271.
24. Patrick, W.M., Quandt, E.M., Swartzlander, D.B. and Matsumura, I. (2007) Multicopy suppression underpins metabolic evolvability. Mol. Biol. Evol., 24, 2716-2722.
25. Gerdes, S.Y., Scholle, M.D., Campbell, J.W., Balazsi, G., Ravasz, E., Daugherty, M.D., Somera, A.L., Kyrpides, N.C., Anderson, I., Gelfand, M.S. et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol., 185, 5673-5684.
26. Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V. and Palsson, B.O. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, 121.
27. Blattner, F.R., Plunkett, G. 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1462.
28. Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B.L., Mori, H. et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol., 2, 2006.0007.
29. Riley, M., Abe, T., Arnaud, M.B., Berlyn, M.K., Blattner, F.R., Chaudhuri, R.R., Glasner, J.D., Horiuchi, T., Keseler, I.M., Kosuge, T. et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res., 34, 1-9.