YMDB 2.0: A significantly expanded version of the yeast metabolome database

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D440-D445

  Ramirez Gaona, Miguel ^a   Marcu, Ana ^a   Pon, Allison ^a   Guo, An Chi ^a   Sajed, Tanvir ^a   Wishart, Noah A ^a   Karu, Naama ^a   Feunang, Yannick Djoumbou ^a   Arndt, David ^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; BIOCHEMISTRY; CONTROLLED STUDY; DATA BASE; FUNGAL GENOME; FUNGAL METABOLISM; METABOLOME; NONHUMAN; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; YEAST METABOLOME DATABASE 2.0; BIOLOGY; FACTUAL DATABASE; METABOLISM; METABOLOMICS; PROCEDURES; SOFTWARE; WEB BROWSER; YEAST;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; METABOLIC NETWORKS AND PATHWAYS; METABOLOME; METABOLOMICS; SOFTWARE; WEB BROWSER; YEASTS;

EID: 85016134736     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1058     Document Type: Article

References (26)

1. Song, G., Balakrishnan, R., Binkley, G., Costanzo, M.C., Dalusag, K., Demeter, J., Engel, S., Hellerstedt, S.T., Karra, K., Hitz, B.C. et al. (2016) Integration of new alternative reference strain genome sequences into the saccharomyces genome database. Database (Oxford), 2016, baw074.
2. Mortimer, R.K. and Johnston, J.R. (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics, 113, 35-43.
3. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M. et al. (1996) Life with 6000 genes. Science, 274, 563-567.
4. Sheppard, T.K., Hitz, B.C., Engel, S.R., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M.C., Dalusag, K.S., Demeter, J., Hellerstedt, S.T. et al. (2016) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res., 44, D698-D702.
5. Güldener, U., Münsterkötter, M., Kastenmüller, G., Strack, N., van Helden, J., Lemer, C., Richelles, J., Wodak, S.J., García-Martínez, J., Pérez-Ortín, J.E. et al. (2005) CYGD: the comprehensive yeast genome database. Nucleic Acids Res., 33, D364-D368.
6. Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C.A., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A. et al. (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 44, D471-D480.
7. Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S. et al. (2005) The reactome pathway knowledgebase. Nucleic Acids Res., 44, D481-D487.
8. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res., 44, D457-D462.
9. Heavner, B.D., Smallbone, K., Price, N.D. and Walker, L.P. (2013) Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford), 2013, bat059.
10. Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A.C., Knox, C., Wilson, M., Grant, J.R., Djoumbou, Y. and Wishart, D.S. (2016) ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res., 44, D495-D501.
11. Jewison, T., Knox, C., Neveu, V., Djoumbou, Y., Guo, A.C., Lee, J., Liu, P., Mandal, R., Krishnamurthy, R., Sinelnikov, I. et al. (2012) YMDB: the yeast metabolome database. Nucleic Acids Res., 40, D815-D820.
12. Han, X. (2016) Lipidomics for studying metabolism. Nat. Rev. Endocrinol., 12, 668-679.
13. Sitepu, I.R., Ignatia, L., Franz, A.K., Wong, D.M., Faulina, S.A., Tsui, M., Kanti, A. and Boundy-Mills, K. (2012) An improved high-throughput Nile red fluorescence assay for estimating intracellular lipids in a variety of yeast species. J. Microbiol. Methods, 91, 321-328.
14. Rattray, J.B, Schibeci, A. and Kidby, D.K. (1975) Lipids of yeasts. Bacteriol. Rev., 39, 197-231.
15. Baile, M.G., Lu, Y.W. and Claypool, S.M. (2014) The topology and regulation of cardiolipin biosynthesis and remodeling in yeast. Chem. Phys. Lipids, 179, 25-31.
16. 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.
17. Pon, A., Jewison, T., Liang, Y., Knox, C., Maciejewski, A., Wilson, M. and Wishart, D.S. (2015) Pathways with Path Whiz. Nucleic Acids Res., 43, W552-W559.
18. UniProt Consortium (2007) The universal protein resource (UniProt). Nucleic Acids Res., 35, D193-D197.
19. Smith, C.A., O'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.
20. Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
21. 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.
22. Allen, F., Pon, A., Wilson, M., Greiner, R. and Wishart, D. (2014) CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res., 42, W94-W99.
23. Allen, F., Pon, A., Greiner, R. and Wishart, D. (2016) Computational prediction of electron ionization mass spectra to assist in GC/MS compound Identification. Anal. Chem., 88, 7689-7697.
24. Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res., 36, D344-D350.
25. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
26. Fahy, E., Subramaniam, S., Murphy, R.C., Nishijima, M., Raetz, C.R.H., Shimizu, T., Spener, F., van Meer, G., Wakelam, M.J.O. and Dennis, E.A. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res., 50(Suppl), S9-S14.