PathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D419-D426

  Rahmati, Sara ^a   Abovsky, Mark ^b   Pastrello, Chiara ^b   Jurisica, Igor ^a,b,c,d  

^a UNIVERSITY OF TORONTO   (Canada)

^b PRINCESS MARGARET HOSPITAL   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d INSTITUTE OF NEUROIMMUNOLOGY   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; MITOGEN ACTIVATED PROTEIN KINASE; NOTCH1 RECEPTOR; SHC TRANSFORMING PROTEIN 1; UVOMORULIN;

ALGORITHM; ARTICLE; DATA ANALYSIS SOFTWARE; DATA BASE; GENE; GENE ONTOLOGY; HUMAN; MOLECULAR GENETICS; MUTATION RATE; PREDICTION; PROTEIN PROTEIN INTERACTION; PTPRD GENE; RANDOMIZATION; SIGNAL TRANSDUCTION; TUMOR GENE; BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC DATABASE; PROCEDURES; PROTEIN ANALYSIS; SOFTWARE; SYSTEMS BIOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

EID: 85016149337     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1082     Document Type: Article

References (33)

1. Chuang, H.-Y., Lee, E., Liu, Y.-T., Lee, D. and Ideker, T. (2007) Network-based classifcation of breast cancer metastasis. Mol. Syst. Biol., 3, 140.
2. Przulj, N., Wigle, D. and Jurisica, I. (2004) Functional topology in a network of protein interactions. Bioinformatics, 20, 340-348.
3. Bild, A.H., Yao, G., Chang, J.T., Wang, Q., Potti, A., Chasse, D., Joshi, M.B., Harpole, D., Lancaster, J.M., Berchuck, A. et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439, 353-357.
4. Kotlyar, M., Pastrello, C., Sheahan, N. and Jurisica, I. (2016) Integrated interactions database: tissue-specifc view of the human and model organism interactomes. Nucleic Acids Res., 44, D536-D541.
5. Yang, X., Coulombe-Huntington, J., Kang, S., Sheynkman, G.M., Hao, T., Richardson, A., Sun, S., Yang, F., Shen, Y.A., Murray, R.R. et al. (2016) Widespread expansion of protein interaction capabilities by alternative splicing. Cell, 164, 805-817.
6. Snider, J., Kotlyar, M., Saraon, P., Yao, Z., Jurisica, I. and Stagljar, I. (2015) Fundamentals of protein interaction network mapping. Mol. Syst. Biol., 11, 848-848.
7. Khatri, P., Sirota, M. and Butte, A.J. (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol., 8, e1002375.
8. Kandasamy, K., Mohan, S., Raju, R., Keerthikumar, S., Kumar, G.S.S., Venugopal, A.K., Telikicherla, D., Navarro, D.J., Mathivanan, S., Pecquet, C. et al. (2010) NetPath: a public resource of curated signal transduction pathways. Genome Biol., 11, R3.
9. Jewison, T., Su, Y., Disfany, F.M., Liang, Y., Knox, C., MacIejewski, A., Poelzer, J., Huynh, J., Zhou, Y., Arndt, D. et al. (2014) SMPDB 2.0: Big improvements to the small molecule pathway database. Nucleic Acids Res., 42, D478-D484.
10. 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.
11. Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F. and McKay, S. (2016) The Reactome pathway Knowledgebase. Nucleic Acids Res., 44, D481-D487.
12. Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C.-Y. and Wei, L. (2011) KOBAS 2.0: a web server for annotation and identifcation of enriched pathways and diseases. Nucleic Acids Res., 39, W316-W322.
13. Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc., 4, 44-57.
14. Sreenivasaiah, P.K., Rani, S., Cayetano, J., Arul, N. and Kim, D.H. (2012) IPAVS: Integrated pathway resources, analysis and visualization system. Nucleic Acids Res., 40, D803-D808.
15. Mi, H., Poudel, S., Muruganujan, A., Casagrande, J.T. and Thomas, P.D. (2016) PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res., 44, D336-D342.
16. Belinky, F., Nativ, N., Stelzer, G., Zimmerman, S., Iny Stein, T., Safran, M. and Lancet, D. (2015) PathCards: Multi-source consolidation of human biological pathways. Database: The Journal of Biological Databases and Curation, 2015, bav006.
17. Cerami, E.G., Gross, B.E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G.D. and Sander, C. (2011) Pathway commons, a web resource for biological pathway data. Nucleic Acids Res., 39, D685-D690.
18. Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E.L., Bohler, A., Mélius, J., Waagmeester, A., Sinha, S.R., Miller, R. et al. (2015) WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res., doi:10.1093/nar/gkv1024.
19. Herwig, R., Hardt, C., Lienhard, M. and Kamburov, A. (2016) Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat Protoc., 11, 1889-1907.
20. Glaab, E., Baudot, A., Krasnogor, N., Schneider, R. and Valencia, A. (2012) EnrichNet: Network-based gene set enrichment analysis. Bioinformatics, 28, i451-i457.
21. Huang, Y.J., Hang, D., Lu, L.J., Tong, L., Gerstein, M.B. and Montelione, G.T. (2008) Targeting the human cancer pathway protein interaction network by structural genomics. Mol. Cell Proteomics, 7, 2048-2060.
22. Kotlyar, M., Pastrello, C., Pivetta, F., Lo Sardo, A., Cumbaa, C., Li, H., Naranian, T., Niu, Y., Ding, Z., Vafaee, F. et al. (2014) In silico prediction of physical protein interactions and characterization of interactome orphans. Nat. Methods, 12, 79-84.
23. Becker, K.G., Barnes, K.C., Bright, T.J. and Wang, S.A. (2004) The genetic association database. Nat. Genet., 36, 431-432.
24. Forbes, S.A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
25. Culhane, A.C., Schröder, M.S., Sultana, R., Picard, S.C., Martinelli, E.N., Kelly, C., Haibe-Kains, B., Kapushesky, M., St Pierre, A.A., Flahive, W. et al. (2012) GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res., 40, D1060-D1066.
26. Wagner, A.H., Coffman, A.C., Ainscough, B.J., Spies, N.C., Skidmore, Z.L., Campbell, K.M., Krysiak, K., Pan, D., McMichael, J.F., Eldred, J.M. et al. (2016) DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res., 44, D1036-D1044.
27. Rask-Andersen, M., Masuram, S. and Schiöth, H.B. (2014) The druggable genome: evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annu. Rev. Pharmacol. Toxicol., 54, 9-26.
28. Zhao, S., Sedwick, D. and Wang, Z. (2015) Genetic alterations of protein tyrosine phosphatases in human cancers. Oncogene, 34, 3885-3894.
29. Hanahan, D. and Weinberg, R.A. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674.
30. Leiserson, M.D.M., Vandin, F., Wu, H.-T., Dobson, J.R., Eldridge, J. V, Thomas, J.L., Papoutsaki, A., Kim, Y., Niu, B., McLellan, M. et al. (2014) Pan-cancer network analysis identifes combinations of rare somatic mutations across pathways and protein complexes. Nat. Genet., 47, 106-114.
31. Boroughs, L.K. and DeBerardinis, R.J. (2015) Metabolic pathways promoting cancer cell survival and growth. Nat. Cell Biol., 17, 351-359.
32. Li, Y.H., Tavallaee, G., Tokar, T., Nakamura, A., Sundararajan, K., Weston, A., Sharma, A., Mahomed, N.N., Gandhi, R., Jurisica, I. and Kapoor, M. (2016) Identifcation of synovial fuid microRNA signature in knee osteoarthritis: differentiating early-and late-stage knee osteoarthritis. Osteoarthr. Cartil., 24, 1577-1586.
33. Nakamura, A., Rampersaud, Y.R., Sharma, A., Lewis, S.J., Wu, B., Datta, P., Sundararajan, K., Endisha, H., Rossomacha, E., Rockel, J.S. 2016 et al. (2016) Identifcation of microRNA-181a-5p and microRNA-4454 as mediators of facet cartilage degeneration. JCI Insight, 1, e86820.