STRING v10: Protein-protein interaction networks, integrated over the tree of life

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D447-D452

  Szklarczyk, Damian ^a   Franceschini, Andrea ^a   Wyder, Stefan ^a   Forslund, Kristoffer ^b   Heller, Davide ^a   Huerta Cepas, Jaime ^b   Simonovic, Milan ^a   Roth, Alexander ^a   Santos, Alberto ^c   Tsafou, Kalliopi P ^c   Kuhn, Michael ^d,e   Bork, Peer ^b   Jensen, Lars J ^c   Von Mering, Christian ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^e MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; DATA ANALYSIS SOFTWARE; GENETIC ALGORITHM; NONHUMAN; ORTHOLOGY; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; STRING DATABASE; CLASSIFICATION; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETICS; INTERNET; METABOLISM;

PROTEIN;

DATABASES, PROTEIN; GENE EXPRESSION PROFILING; INTERNET; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 84941051170     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1003     Document Type: Article

References (40)

1. 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.
2. Lee, D., Redfern, O. and Orengo, C. (2007) Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol., 8, 995-1005.
3. Ouzounis, C. A., Coulson, R. M., Enright, A. J., Kunin, V. and Pereira-Leal, J. B. (2003) Classification schemes for protein structure and function. Nat. Rev. Genet., 4, 508-519.
4. Bairoch, A. and Boeckmann, B. (1994) The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res., 22, 3578-3580.
5. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
6. Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R. et al. (2014) The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
7. Sherman, B. T., Huang Da, W., Tan, Q., Guo, Y., Bour, S., Liu, D., Stephens, R., Baseler, M. W., Lane, H. C. and Lempicki, R. A. (2007) DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics, 8, 426-437.
8. Gibson, T. J. (2009) Cell regulation: determined to signal discrete cooperation. Trends Biochem. Sci., 34, 471-482.
9. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res., 40, D841-D846.
10. 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.
11. 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.
12. 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.
13. Schaefer, M. H., Fontaine, J. F., Vinayagam, A., Porras, P., Wanker, E. E. and Andrade-Navarro, M. A. (2012) HIPPIE: Integrating protein interaction networks with experiment based quality scores. PloS One, 7, e31826.
14. Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkman, F. S., Cesareni, G. et al. (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods, 9, 345-350.
15. 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.
16. Luo, Q., Pagel, P., Vilne, B. and Frishman, D. (2011) DIMA 3.0: Domain Interaction Map. Nucleic Acids Res., 39, D724-D729.
17. McDowall, M. D., Scott, M. S. and Barton, G. J. (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res., 37, D651-D656.
18. Schmitt, T., Ogris, C. and Sonnhammer, E. L. (2014) FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res., 42, D380-D388.
19. Zhang, Q. C., Petrey, D., Garzon, J. I., Deng, L. and Honig, B. (2013) PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res., 41, D828-D833.
20. Baspinar, A., Cukuroglu, E., Nussinov, R., Keskin, O. and Gursoy, A. (2014) PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Res., 42, W285-W289.
21. Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D. and Morris, Q. (2013) GeneMANIA prediction server 2013 update. Nucleic Acids Res., 41, W115-W122.
22. Niu, Y., Otasek, D. and Jurisica, I. (2010) Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics, 26, 111-119.
23. Valencia, A. and Pazos, F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol., 12, 368-373.
24. Huynen, M. A., Snel, B., Von Mering, C. and Bork, P. (2003) Function prediction and protein networks. Curr. Opin. Struct. Biol., 15, 191-198.
25. Lewis, A. C., Saeed, R. and Deane, C. M. (2010) Predicting protein-protein interactions in the context of protein evolution. Mol. Biosyst., 6, 55-64.
26. Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., Von Mering, C. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.
27. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P. et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
28. Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
29. Letunic, I., Doerks, T. and Bork, P. (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res., 40, D302-D305.
30. Gaudet, P., Argoud-Puy, G., Cusin, I., Duek, P., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Zahn-Zabal, M., Zwahlen, C. et al. (2013) neXtProt: organizing protein knowledge in the context of human proteome projects. J. Proteome Res., 12, 293-298.
31. Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H. et al. (2010) GeneCards Version 3: the human gene integrator. Database, 2010, 1-16.
32. UniProt Consortium, X (2014) Activities at the Universal Protein Resource (UniProt). Nucleic acids research, 42, D191-D198.
33. Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T. H., Von Mering, C., Jensen, L. J. and Bork, P. (2014) STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res., 42, D401-D407.
34. Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M. et al. (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res., 42, D231-D239.
35. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. and Eisenberg, D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
36. Eisen, M. B., Spellman, P. T., Brown, P. O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A., 95, 14863-14868.
37. Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
38. Hobohm, U., Scharf, M., Schneider, R. and Sander, C. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
39. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
40. Csárdi, G. and Nepusz, T. (2006) The igraph software package for complex network research. Inter. J. Comp. Syst., 1695, 1-9.