NDEx, the Network Data Exchange

Cell Systems

Volumn 1, Issue 4, 2015, Pages 302-305

  Pratt, Dexter ^a   Chen, Jing ^a   Welker, David ^a   Rivas, Ricardo ^a   Pillich, Rudolf ^a   Rynkov, Vladimir ^a   Ono, Keiichiro ^a   Miello, Carol ^b   Hicks, Lyndon ^b   Szalma, Sandor ^c   Stojmirovic, Aleksandar ^c   Dobrin, Radu ^c   Braxenthaler, Michael ^d   Kuentzer, Jan ^e   Demchak, Barry ^a   Ideker, Trey ^a,f  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b PFIZER INC   (United States)

^c JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

^d Roche Pharmaceuticals   (United States)

^e ROCHE DIAGNOSTICS GMBH   (Germany)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER NETWORK; COMPUTER PROGRAM; DATA PROCESSING; INFORMATION SYSTEM; PRIORITY JOURNAL; PUBLICATION; RESEARCH;

EID: 84951102783     PISSN: None     EISSN: 24054712     Source Type: Journal    
DOI: 10.1016/j.cels.2015.10.001     Document Type: Article

References (27)

1. Bandyopadhyay, S., Kelley, R., and Ideker, T. (2006). Discovering regulated networks during HIV-1 latency and reactivation. Proceedings of the 2006 Pacific Symposium on Biocomputing, pp. 354-366.
2. A. Califano, A.J. Butte, S. Friend, T. Ideker, and E. Schadt Leveraging models of cell regulation and GWAS data in integrative network-based association studies Nat. Genet. 44 2012 841 847
3. E.G. Cerami, B.E. Gross, E. Demir, I. Rodchenkov, O. Babur, N. Anwar, N. Schultz, G.D. Bader, and C. Sander Pathway Commons, a web resource for biological pathway data Nucleic Acids Res. 39 2011 D685 D690
4. H.-Y. Chuang, E. Lee, Y.-T. Liu, D. Lee, and T. Ideker Network-based classification of breast cancer metastasis Mol. Syst. Biol. 3 2007 140
5. P. Ciccarese, S. Soiland-Reyes, K. Belhajjame, A.J.G. Gray, C. Goble, and T. Clark PAV ontology: provenance, authoring and versioning J. Biomed. Semantics 4 2013 37
6. D. Croft, A.F. Mundo, R. Haw, M. Milacic, J. Weiser, G. Wu, M. Caudy, P. Garapati, M. Gillespie, M.R. Kamdar, and et al. The Reactome pathway knowledgebase Nucleic Acids Res. 42 2014 D472 D477
7. CyNetShare (2014). http://cynetshare.ucsd.edu.
8. E. Demir, M.P. Cary, S. Paley, K. Fukuda, C. Lemer, I. Vastrik, G. Wu, P. D'Eustachio, C. Schaefer, J. Luciano, and et al. The BioPAX community standard for pathway data sharing Nat. Biotechnol. 28 2010 935 942
9. DublinCore (2012). Dublin Core Metadata Element Set, Version 1.1 http://www.dublincore.org/documents/dces/.
10. R.T. Fielding, and R.N. Taylor Principled design of the modern Web architecture ACM Trans. Internet Technol. 2 2002 115 150
11. A. Franceschini, D. Szklarczyk, S. Frankild, M. Kuhn, M. Simonovic, A. Roth, J. Lin, P. Minguez, P. Bork, C. von Mering, and L.J. Jensen STRING v9.1: protein-protein interaction networks, with increased coverage and integration Nucleic Acids Res. 41 2013 D808 D815
12. M. Hofree, J.P. Shen, H. Carter, A. Gross, and T. Ideker Network-based stratification of tumor mutations Nat. Methods 10 2013 1108 1115
13. M. Kanehisa, and S. Goto KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 28 2000 27 30
14. N. Le Novère, B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, and et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Res. 34 2006 D689 D691
15. H. Mi, Q. Dong, A. Muruganujan, P. Gaudet, S. Lewis, and P.D. Thomas PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Res. 38 2010 D204 D210
16. H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 27 1999 29 34
17. OpenBEL (2011). OpenBEL http://www.openbel.org.
18. S. Orchard, M. Ammari, B. Aranda, L. Breuza, L. Briganti, F. Broackes-Carter, N.H. Campbell, G. Chavali, C. Chen, N. del-Toro, and et al. The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases Nucleic Acids Res. 42 2014 D358 D363
19. A.R. Pico, T. Kelder, M.P. van Iersel, K. Hanspers, B.R. Conklin, and C. Evelo WikiPathways: pathway editing for the people PLoS Biol. 6 2008 e184
20. PROV-O (2013). PROV-O: The PROV Ontology http://www.w3.org/TR/prov-o/.
21. QIAGEN (2015). Ingenuity Pathway Analysis (IPA, QIAGEN Redwood City, www.qiagen.com/ingenuity).
22. C.F. Schaefer, K. Anthony, S. Krupa, J. Buchoff, M. Day, T. Hannay, and K.H. Buetow PID: the Pathway Interaction Database Nucleic Acids Res. 37 2009 D674 D679
23. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
24. C. Stark, B.J. Breitkreutz, A. Chatr-Aryamontri, L. Boucher, R. Oughtred, M.S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, and et al. The BioGRID Interaction Database: 2011 update Nucleic Acids Res. 39 2011 D698 D704
25. M.P. van Iersel, T. Kelder, A.R. Pico, K. Hanspers, S. Coort, B.R. Conklin, and C. Evelo Presenting and exploring biological pathways with PathVisio BMC Bioinformatics 9 2008 399
26. Vandin, F., Clay, P., Upfal, E., and Raphael, B.J. (2012). Discovery of mutated subnetworks associated with clinical data in cancer. Proceedings of the 2012 Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, pp. 55-66.
27. D. Warde-Farley, S.L. Donaldson, O. Comes, K. Zuberi, R. Badrawi, P. Chao, M. Franz, C. Grouios, F. Kazi, C.T. Lopes, and et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function Nucleic Acids Res. 38 2010 W214 W220