ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D495-D501

  Sajed, Tanvir ^a   Marcu, Ana ^a   Ramirez, Miguel ^a   Pon, Allison ^a   Guo, An Chi ^a   Knox, Craig ^a   Wilson, Michael ^a   Grant, Jason R ^a   Djoumbou, Yannick ^a   Wishart, David S ^a,b  

^a UNIVERSITY OF ALBERTA   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BIOCHEMISTRY; COMPUTER INTERFACE; DATA BASE; ESCHERICHIA COLI; ESCHERICHIA COLI METABOLOME DATABASE; INFORMATION RETRIEVAL; MASS SPECTROMETRY; METABOLOME; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; OPERON; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; CHEMICAL DATABASE; CHEMISTRY; ESCHERICHIA COLI K 12; GENETICS; METABOLISM;

ESCHERICHIA COLI PROTEIN;

DATABASES, CHEMICAL; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; METABOLOME;

EID: 84976870059     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1060     Document Type: Article

References (29)

1. Sawitzke, J.A., Thomason, L.C., Costantino, N., Bubunenko, M., Datta, S. and Court, D.L. (2007) Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond. Methods in Enzymology, 421, 171-199.
2. Blattner, F.R., Plunkett, G. III, 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, 777, 1452-1462.
3. Salgado, H., Moreno-Hagelsieb, G., Smith, T. and Collado-Vides, J. (2000) Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci., 97, 6652-6657.
4. Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., Fulcher, C., Huerta, A.M., Kothari, A., Karp, P.D. et al. (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res., 41, D605-D612.
5. Misra, R.V., Horler, R.S., Reindl, W., Goryanin, I.I. and Thomas, G.H. (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res., 33, D329-D333.
6. Sundararaj, S., Guo, A.C., Habibi-Nazhad, B., Rouani, M., Stothard, P., Ellison, M. and Wishart, D.S. (2004) The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res., 32, D293-D295.
7. Zhou, J. and Rudd, K.E. (2013) EcoGene 3.0. Nucleic Acids Res., 41, D613-D624.
8. Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J.S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A. et al. (2013) RegulonDB (version 8.0): omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
9. Croft, D., Mundo, A.F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M.R. et al. (2014). The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
10. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., Holland, T.A., Keseler, I.M., Kothari, A., Karp, P.D. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 42, D459-D471.
11. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
12. Werf, M., Overkamp, K., Muilwijk, B., Coulier, L. and Hankemeier, T. (2007) Microbial metabolomics: Toward a platform with full metabolome coverage. Anal. Biochem., 370, 17-25.
13. Winder, C., Dunn, W., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. and Goodacre, R. (2008) Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites. Anal. Chem., 80, 2939-2948.
14. Bennett, B., Kimball, E., Gao, M., Osterhout, R., Van Dien, S. and Rabinowitz, J. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol., 5, 593-599.
15. Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A. et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 316, 593-597.
16. Guo, A.C., Jewison, T., Wilson, M., Liu, Y., Knox, C., Djoumbou, Y., Lo, P., Mandal, R., Krishnamurthy, R. and Wishart, D.S. (2012) ECMDB: The E. coli Metabolome Database. Nucleic Acids Res., 41, D625-D630.
17. Jewison, T., Su, Y., Disfany, F.M., Liang, Y., Knox, C., Maciejewski, A., Poelzer, J., Huynh, J., Zhou, Y., Wishart, D.S. et al. (2014) SMPDB 2.0: Big improvements to the Small Molecule Pathway Database. Nucleic Acids Res., 42, D478-D484.
18. Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M. and Wishart, D.S. (2015) Pathways with PathWhiz. Nucleic Acids Res., 43, W552-W559.
19. Allen, F., Pon, A., Wilson, M., Greiner, R. and Wishart, D.S. (2014) CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res., 42, W94-W99.
20. Allen, F., Greiner, R. and Wishart, D.S. (2014) Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics, 11, 98-110.
21. Wolf, S., Schmidt, S., Müller-Hannemann, M. and Neumann, S. (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC bioinformatics., 11, 148-159.
22. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K. et al. (2010) MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass Spectrom., 45, 703-714.
23. Ulrich, E., Akutsu, H., Doreleijers, J., Harano, Y., Ioannidis, Y., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z. et al. (2007) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
24. Wishart, D.S., Arndt, D., Pon, A., Sajed, T., Guo, A.C., Djoumbou, Y., Knox, C., Wilson, M., Liang, Y., Grant, J. et al. (2015) T3DB: the toxic exposome database. Nucleic Acids Res., 43, D928-D934.
25. UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
26. Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E. et al. (2013) HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res., 41, D801-D807.
27. Smith, C.A., I'Maille, G., Want, E.J., Qin, C., Trauger, S.A., Brandon, T.R., Custodio, D.E., Abagyan, R. and Siuzdak, G. (2005) METLIN: A metabolite mass spectral database. Ther. Drug Monit., 27, 747-751.
28. De Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S. and Steinbeck, C. (2009). Chemical entities of biological interest: An update. Nucleic Acids Res., 38, D249-D254.
29. Fahy, E., Subramaniam, S., Murphy, R., Nishijima, M., Raetz, C., Shimizu, T., Spener, F., van Meer, G., Wakelam, M. and Dennis, E. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res., 50, S9-S14.