NeXO Web: The NeXO ontology database and visualization platform

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Dutkowski, Janusz ^a   Ono, Keiichiro ^a   Kramer, Michael ^a   Yu, Michael ^a   Pratt, Dexter ^a   Demchak, Barry ^a   Ideker, Trey ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION ALGORITHM; COMPUTER INTERFACE; CONCEPTUAL FRAMEWORK; GENE INTERACTION; GENE ONTOLOGY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NETWORK EXTRACTED ONTOLOGY; PRIORITY JOURNAL; PROBABILITY; PROCESS DESIGN; PROCESS DEVELOPMENT; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES; WEB BROWSER; COMPUTER GRAPHICS; EPISTASIS; GENE REGULATORY NETWORK; GENETIC DATABASE; INTERNET; PROTEIN ANALYSIS; CELL COMPARTMENTALIZATION; CYTOSOL; DATA ANALYSIS SOFTWARE; NEXO WEB; ONLINE SYSTEM; PROTEIN INTERACTION; RIBOSOME; VALIDATION PROCESS;

COMPUTER GRAPHICS; DATABASES, GENETIC; EPISTASIS, GENETIC; GENE ONTOLOGY; GENE REGULATORY NETWORKS; INTERNET; PROTEIN INTERACTION MAPPING;

EID: 84891817932     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1192     Document Type: Article

References (11)

1. Musen, M.A., Noy, N.F., Shah, N.H., Whetzel, P.L., Chute, C.G., Story, M.A., Smith, B. and NCBO team (2012) The National Center for Biomedical Ontology. J. Am. Med. Inform. Assoc., 19, 190-195.
2. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255.
3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
4. Dutkowski, J., Kramer, M., Surma, M.A., Balakrishnan, R., Cherry, J.M., Krogan, N.J. and Ideker, T. (2013) A gene ontology inferred from molecular networks. Nat. Biotechnol., 31, 38-45.
5. Huntley, R.P., Binns, D., Dimmer, E., Barrell, D., O'Donovan, C. and Apweiler, R. (2009) QuickGO: a user tutorial for the web-based Gene Ontology browser. Database, 2009, bap010.
6. Carbon, S., Ireland, A., Mungall, C.J., Shu, S., Marshall, B., Lewis, S., AmiGO Hub and Web Presence Working Group. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics, 25, 288-289.
7. Gene Ontology Consortium. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res., 40, D559-D564.
8. Lee, I., Li, Z. and Marcotte, E.M. (2007) An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One, 2, e988.
9. Park, Y. and Bader, J.S. (2011) Resolving the structure of interactomes with hierarchical agglomerative clustering. BMC Bioinformatics, 12(Suppl. 1), S44.
10. Hillenmeyer, M.E., Fung, E., Wildenhain, J., Pierce, S.E., Hoon, S., Lee, W., Proctor, M., St Onge, R.P., Tyers, M., Koller, D. et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science, 320, 362-365.
11. Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.