The Negatome database: A reference set of non-interacting protein pairs

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Smialowski, Pawel ^a,b   Pagel, Philipp ^a,b   Wong, Philip ^a   Brauner, Barbara ^a   Dunger, Irmtraud ^a   Fobo, Gisela ^a   Frishman, Goar ^a   Montrone, Corinna ^a   Rattei, Thomas ^b   Frishman, Dmitrij ^a,b   Ruepp, Andreas ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC ALGORITHM; HIGH THROUGHPUT SCREENING; NEGATOME DATABASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; FUNGAL GENOME; GENETIC DATABASE; HUMAN; INFORMATION RETRIEVAL; INTERNET; METABOLISM; METHODOLOGY; NUCLEIC ACID DATABASE; PROTEIN TERTIARY STRUCTURE; SACCHAROMYCES CEREVISIAE;

PROTEIN;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; GENOME, FUNGAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SACCHAROMYCES CEREVISIAE; SOFTWARE;

EID: 75549083088     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1026     Document Type: Article

References (40)

1. Shoemaker, B.A. and Panchenko, A.R. (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol., 3, e42.
2. Huang, H. and Bader, J.S. (2009) Precision and recall estimates for two-hybrid screens. Bioinformatics, 25, 372-378.
3. Ben-Hur, A. and Noble, W.S. (2005) Kernel methods for predicting protein-protein interactions. Bioinformatics, 21(Suppl. 1), i38-i46.
4. Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F. and Gerstein, M. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449-453.
5. Guldener, U., Munsterkotter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.W. and Stumpflen, V. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res., 34, D436-D441.
6. 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.
7. Li, X.L., Tan, S.H. and Ng, S.K. (2006) Improving domain-based protein interaction prediction using biologically significant negative datasets. Int. J. Data Min. Bioinform., 1, 138-149.
8. Browne, F., Wang, H., Zheng, H. and Azuaje, F. (2009) GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction. Source Code Biol. Med., 4, 2.
9. Sanchez-Graillet, O. and Poesio, M. (2007) Negation of proteinprotein interactions: analysis and extraction. Bioinformatics, 23, i424-i432.
10. Jansen, R. and Gerstein, M. (2004) Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr. Opin. Microbiol., 7, 535-545.
11. Chen, X.W. and Liu, M. (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21, 4394-4400.
12. Shen, J., Zhang, J., Luo, X., Zhu, W., Yu, K., Chen, K., Li, Y. and Jiang, H. (2007) Predicting protein-protein interactions based only on sequences information. Proc. Natl Acad. Sci. USA, 104, 4337-4341.
13. Guo, Y., Yu, L., Wen, Z. and Li, M. (2008) Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res., 36, 3025-3030.
14. Ben-Hur, A. and Noble, W.S. (2006) Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics, 7(Suppl. 1), S2.
15. Grigoriev, A. (2003) On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res., 31, 4157-4161.
16. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale datasets of protein-protein interactions. Nature, 417, 399-403.
17. Kouranov, A., Xie, L., de la Cruz, J., Chen, L., Westbrook, J., Bourne, P.E. and Berman, H.M. (2006) The RCSB PDB information portal for structural genomics. Nucleic Acids Res., 34, D302-D305.
18. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C. et al. (2004) The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat. Biotechnol., 22, 177-183.
19. Collaborative_Computational_Project. (1994) The CCP4 suite: programs for protein crystallography. Acta. Crystallogr. D Biol. Crystallogr., 50, 760-763.
20. Winn, M.D. (2003) An overview of the CCP4 project in protein crystallography: an example of a collaborative project. J. Synchrotron. Radiat., 10, 23-25.
21. UniProt-Consortium. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
22. Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M. and Bairoch, A. (2007) UniProtKB/Swiss-Prot: the manually annotated section of the UniProt knowledgebase. Methods Mol. Biol., 406, 89-112.
23. Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R. et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res., 35, D561-D565.
24. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stumpflen, V., Mewes, H.W. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
25. Ruepp, A., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Stransky, M., Waegele, B., Schmidt, T., Doudieu, O.N., Stumpflen, V. et al. (2008) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 36, D646-D650.
26. Snyder, H., Mensah, K., Hsu, C., Hashimoto, M., Surgucheva, I.G., Festoff, B., Surguchov, A., Masliah, E., Matouschek, A. and Wolozin, B. (2005) beta-Synuclein reduces proteasomal inhibition by alpha-synuclein but not gamma-synuclein. J. Biol. Chem., 280, 7562-7569.
27. Busino, L., Bassermann, F., Maiolica, A., Lee, C., Nolan, P.M., Godinho, S.I., Draetta, G.F. and Pagano, M. (2007) SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins. Science, 316, 900-904.
28. Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R. et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
29. Stein, A., Russell, R.B. and Aloy, P. (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res., 33, D413-D417.
30. Finn, R.D., Marshall, M. and Bateman, A. (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
31. von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. and Bork, P. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res., 35, D358-D362.
32. Liu, C.T., Yuan, S. and Li, K.C. (2009) Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae. Nucleic Acids Res., 37, 526-532.
33. Guo, T., Hua, S., Ji, X. and Sun, Z. (2004) DBSubLoc: database of protein subcellular localization. Nucleic Acids Res., 32, D122-D124.
34. Resnik, P. (1995) Using information content to evaluate semantic similarity in a taxonomy. In 14th International Conference Research on Computational Linguistics. IJCAI-95, Montreal, Canada, Vol. 1, pp. 448-453.
35. Couto, F.M., Silva, M.J. and Coutinho, P.M. (2005) Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. In 14th ACM International Conference on Information and Knowledge Management. ACM, Bremen, Germany, pp. 343-344.
36. Jiang, J. and Conrath, D. (1998) International Conference Research on Computational Linguistics. ROCLING X, Taiwan, Vol. 1.
37. Froehlich, H. (2008) GOSim package (version 1.1.5.4). 1.1.5.4 ed.
38. R_Development_Core_Team. (2009) R language (version 2.9.1). Vienna, Austria.
39. 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.
40. Pagel, P., Wong, P. and Frishman, D. (2004) A domain interaction map based on phylogenetic profiling. J. Mol. Biol., 344, 1331-1346.