ComPPI: A cellular compartment-specific database for protein-protein interaction network analysis

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D485-D493

  Veres, Daniel V ^a   Gyurkó, Dávid M ^a   Thaler, Benedek ^a,b   Szalay, Kristóf Z ^a   Fazekas, Dávid ^c   Korcsmáros, Tamás ^c,d,e   Csermely, Peter ^a  

^a SEMMELWEIS UNIVERSITY   (Hungary)

^b BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^c EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^d EARLHAM INSTITUTE   (United Kingdom)

^e INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ANIMAL; CELL COMPARTMENTALIZATION; HUMAN; INTERNET; METABOLISM; PROTEIN ANALYSIS; PROTEIN DATABASE;

ANIMALS; CELL COMPARTMENTATION; DATABASES, PROTEIN; HUMANS; INTERNET; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 84941083034     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1007     Document Type: Article

References (50)

1. Hao, N. and O'Shea, E. K. (2012) Signal-dependent dynamics of transcription factor translocation controls gene expression. Nat. Struct. Mol. Biol., 19, 31-39.
2. Firth, S. M. and Baxter, R. C. (2002) Cellular actions of the insulin-like growth factor binding proteins. Endocr. Rev., 23, 824-854.
3. Azar, W. J., Zivkovic, S., Werther, G. A. and Russo, V. C. (2014) IGFBP-2 nuclear translocation is mediated by a functional NLS sequence and is essential for its pro-tumorigenic actions in cancer cells. Oncogene, 33, 578-588.
4. Semenza, G. L. (2009) Regulation of oxygen homeostasis by hypoxia-inducible factor 1. Physiology (Bethesda), 24, 97-106.
5. Koh, G. C. K. W., Porras, P., Aranda, B., Hermjakob, H. and Orchard, S. E. (2012) Analyzing protein-protein interaction networks. J. Proteome Res., 11, 2014-2031.
6. Vidal, M., Cusick, M. E. and Barabási, A.-L. (2011) Interactome networks and human disease. Cell, 144, 986-998.
7. Bulusu, K. C., Tym, J. E., Coker, E. A., Schierz, A. C. and Al-Lazikani, B. (2014) canSAR: updated cancer research and drug discovery knowledgebase. Nucleic Acids Res., 42, D1040-D1047.
8. De Las Rivas, J. and Fontanillo, C. (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput. Biol., 6, e1000807.
9. Von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
10. Kamburov, A., Stelzl, U., Lehrach, H. and Herwig, R. (2013) The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res., 41, D793-D800.
11. UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
12. Wiwatwattana, N. and Kumar, A. (2005) Organelle DB: a cross-species database of protein localization and function. Nucleic Acids Res., 33, D598-D604.
13. Levy, E. D., Landry, C. R. and Michnick, S. W. (2009) How perfect can protein interactomes be? Sci. Signal., 2, pe11.
14. Sprinzak, E., Sattath, S. and Margalit, H. (2003) How reliable are experimental protein-protein interaction data? J. Mol. Biol., 327, 919-923.
15. Lee, K., Sung, M.-K., Kim, J., Kim, K., Byun, J., Paik, H., Kim, B., Huh, W.-K. and Ideker, T. (2014) Proteome-wide remodeling of protein location and function by stress. Proc. Natl. Acad. Sci. U. S. A., 111, E3157-E3166.
16. Nastou, K. C., Tsaousis, G. N., Kremizas, K. E., Litou, Z. I. and Hamodrakas, S. J. (2014) The human plasma membrane peripherome: visualization and analysis of interactions. Biomed. Res. Int., 2014, 397145.
17. Sprenger, J., Fink, J. L. and Teasdale, R. D. (2006) Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformat., 7, Suppl. 5:S3.
18. Chautard, E., Ballut, L., Thierry-Mieg, N. and Ricard-Blum, S. (2009) MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics, 25, 690-691.
19. 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. Nat. Genet., 25, 25-29.
20. Patil, A., Nakai, K. and Nakamura, H. (2011) HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res., 39, D744-D749.
21. Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
22. Faria, D., Schlicker, A., Pesquita, C., Bastos, H., Ferreira, A. E. N., Albrecht, M. and Falcão, A. O. (2012) Mining GO annotations for improving annotation consistency. PLoS ONE, 7, e40519.
23. Barsky, A., Gardy, J. L., Hancock, R. E. W. and Munzner, T. (2007) Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 23, 1040-1042.
24. Huang, H., McGarvey, P. B., Suzek, B. E., Mazumder, R., Zhang, J., Chen, Y. and Wu, C. H. (2011) A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics, 27, 1190-1191.
25. Wein, S. P., Côté, R. G., Dumousseau, M., Reisinger, F., Hermjakob, H. and Vizcaíno, J. A. (2012) Improvements in the Protein Identifier Cross-Reference service. Nucleic Acids Res., 40, W276-W280.
26. Murali, T., Pacifico, S., Yu, J., Guest, S., Roberts, G. G. and Finley, R. L. (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res., 39, D736-D743.
27. Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al., (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Res., 37, D767-D772.
28. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stümpflen, V., Mewes, H.-W. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
29. Chatr-Aryamontri, A., Breitkreutz, B.-J., Heinicke, S., Boucher, L., Winter, A., Stark, C., Nixon, J., Ramage, L., Kolas, N., O'Donnell, L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
30. Yu, H., Tardivo, L., Tam, S., Weiner, E., Gebreab, F., Fan, C., Svrzikapa, N., Hirozane-Kishikawa, T., Rietman, E., Yang, X. et al. (2011) Next-generation sequencing to generate interactome datasets. Nat. Methods, 8, 478-480.
31. Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U. and Eisenberg, D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
32. Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., Campbell, N. H., Chavali, G., Chen, C., Del-Toro, N. et al. (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.
33. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A. P., Santonico, E. et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res., 40, D857-D861.
34. Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K. et al. (2009) Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res., 37, D773-D781.
35. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol., 28, 1248-1250.
36. Lu, P., Szafron, D., Greiner, R., Wishart, D. S., Fyshe, A., Pearcy, B., Poulin, B., Eisner, R., Ngo, D. and Lamb, N. (2005) PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res., 33, D147-D153.
37. Pierleoni, A., Martelli, P. L., Fariselli, P. and Casadio, R. (2007) eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res., 35, D208-D212.
38. Sprenger, J., Lynn Fink, J., Karunaratne, S., Hanson, K., Hamilton, N. A. and Teasdale, R. D. (2008) LOCATE: a mammalian protein subcellular localization database. Nucleic Acids Res., 36, D230-D233.
39. Wiwatwattana, N., Landau, C. M., Cope, G. J., Harp, G. A. and Kumar, A. (2007) Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Res., 35, D810-D814.
40. Hoelz, A., Debler, E. W. and Blobel, G. (2011) The structure of the nuclear pore complex. Annu. Rev. Biochem., 80, 613-643.
41. Brameier, M., Krings, A. and MacCallum, R. M. (2007) NucPred-predicting nuclear localization of proteins. Bioinformatics, 23, 1159-1160.
42. Waterson, R. M. and Hill, R. L. (1972) Enoyl Coenzyme A Hydratase (Crotonase): catalytic properties of Crotonase and its possible regulatory role in fatty acid oxidation. J. Biol. Chem., 247, 5258-5265.
43. Hamed, R. B., Batchelar, E. T., Clifton, I. J. and Schofield, C. J. (2008) Mechanisms and structures of crotonase superfamily enzymes-how nature controls enolate and oxyanion reactivity. Cell. Mol. Life Sci., 65, 2507-2527.
44. Turteltaub, W. and Murphy, A. (1987) Subcellular localization and capacity of ß-oxidation and aldehyde dehydrogenase in porcine liver. Arch. Biochem. Biophys., 255, 120-126.
45. Bhattacharyya, T., Karnezis, A. N., Murphy, S. P., Hoang, T., Freeman, B. C., Phillips, B. and Morimoto, R. I. (1995) Cloning and subcellular localization of human mitochondrial hsp70. J. Biol. Chem., 270, 1705-1710.
46. Zhang, J., Sun, M., Li, R., Liu, S., Mao, J., Huang, Y., Wang, B., Hou, L., Ibrahim, M. M. and Tang, J. (2013) Ech1 is a potent suppressor of lymphatic metastasis in hepatocarcinoma. Biomed. Pharmacother., 67, 557-560.
47. Yeh, C.-S., Wang, J.-Y., Cheng, T.-L., Juan, C.-H., Wu, C.-H. and Lin, S.-R. (2006) Fatty acid metabolism pathway play an important role in carcinogenesis of human colorectal cancers by microarray-bioinformatics analysis. Cancer Lett., 233, 297-308.
48. Chen, Z., Dai, Y.-C., Chen, Z.-X., Xie, J.-P., Zeng, W., Lin, Y.-Y. and Tan, Q.-H. (2013) Knockdown of ECHS1 protein expression inhibits hepatocellular carcinoma cell proliferation via suppression of Akt activity. Crit. Rev. Eukaryot. Gene Exp., 23, 275-282.
49. Liu, X., Feng, R. and Du, L. (2010) The role of enoyl-CoA hydratase short chain 1 and peroxiredoxin 3 in PP2-induced apoptosis in human breast cancer MCF-7 cells. FEBS Lett., 584, 3185-3192.
50. Fisk, H. A., Mattison, C. P. and Winey, M. (2003) Human Mps1 protein kinase is required for centrosome duplication and normal mitotic progression. Proc. Natl. Acad. Sci. U. S. A., 100, 14875-14880.