Using the reactome database

Current Protocols in Bioinformatics

Volumn , Issue SUPPL.38, 2012, Pages

  Haw, Robin ^a   Stein, Lincoln ^a  

^a ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

Author keywords

Biological pathway; Database; Interaction network; Pathway; Pathway analysis; Pathway visualization; Reaction; Reactome

Indexed keywords

ARTICLE; BIOINFORMATICS; DNA REPAIR; DNA SEQUENCE; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PEER REVIEW; PRIORITY JOURNAL; PROTEIN DATABASE; RNA SEQUENCE; ZEBRA FISH; CLASSIFICATION; COMPUTER INTERFACE; GENE EXPRESSION PROFILING; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION; ANIMAL; FACTUAL DATABASE; INTERNET; PROTEOMICS; SPECIES DIFFERENCE;

DANIO RERIO; RATTUS;

PROTEOME;

DATABASES, PROTEIN; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION; USER-COMPUTER INTERFACE; ANIMALS; DATABASES, FACTUAL; HUMANS; INTERNET; METABOLIC NETWORKS AND PATHWAYS; PROTEOMICS; SPECIES SPECIFICITY;

EID: 84866781251     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0807s38     Document Type: Article

References (9)

1. Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kalatskaya, I., Mahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., and Stein, L. 2011. Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Res. 39:D691-D697.
2. Joshi-Tope, G., Vastrik, I., Gopinath, G.R., Matthews, L., Schmidt, E., Gillespie, M., D'Eustachio, P., Jassal, B., Lewis, S., Wu, G., Birney, E., and Stein, L. 2003. The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists. Cold Spring Harbor Symposia on Quantitative Biology LXVIII:237-244.
3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
4. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277-D280.
5. Krieger, C.J., Zhang, P., Mueller, L.A., Wang, A., Paley, S., Arnaud, M., Pick, J., Rhee, S.Y., and Karp, P.D. 2004. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32:D438-D442.
6. Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S., and Thomas, P.D. 2009. PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 38:D204-D210.
7. Peri, S., Navarro, J.D., Amanchy, R., Kristiansen, T.Z., Jonnalagadda, C.K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T.K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H.N., Rashmi, B.P., Ramya, M.A., Zhao, Z., Chandrika, K.N., Padma, N., Harsha, H.C., Yatish, A.J., Kavitha, M.P., Menezes, M., Choudhury, D.R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S.K., Madavan, V., Joseph, A., Wong, G.W., Schiemann, W.P., Constantinescu, S.N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G.C., Dang, C.V., Garcia, J.G., Pevsner, J., Jensen, O.N., Roepstorff, P., Deshpande, K.S., Chinnaiyan, A.M., Hamosh, A., Chakravarti, A., and Pandey, A. 2003. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 10:2363-2371.
8. Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., and Evelo, C. 2008. WikiPathways: Pathway editing for the people. PLoS Biol. 22:e184.
9. Schaefer, C.F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T., and Buetow, K.H. 2008. PID: The Pathway Interaction Database. Nucleic Acids Res. 37:D674-D679.