An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Jain, Shobhit ^a,b   Bader, Gary D ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR COMPONENTS; CONFIDENCE ASSESSMENT; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; SEMANTIC SIMILARITY; SEMANTIC SIMILARITY MEASUREMENT; SEMANTIC SIMILARITY MEASURES; TOPOLOGICAL CLUSTERING;

CLUSTERING ALGORITHMS; GENE EXPRESSION; KNOWLEDGE REPRESENTATION; PHYSIOLOGY; YEAST;

PROTEINS;

HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN DATABASE; SEMANTICS;

ALGORITHMS; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPPING; PROTEINS; SEMANTICS;

EID: 78149449890     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-562     Document Type: Article

References (53)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
2. Li D, Liu W, Liu Z, Wang J, Liu Q, Zhu Y, He F. PRINCESS, a protein interaction confidence evaluation system with multiple data sources. Mol Cell Proteomics 2008, 7(6):1043-1052.
3. Patil A, Nakamura H. Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 2005, 6:100.
4. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 2005, 23(8):951-959.
5. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957-968.
6. Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics 2003, 19(5):635-642.
7. Chen Y, Xu D. Genome-scale protein function prediction in yeast Saccharomyces cerevisiae through integrating multiple sources of high-throughput data. Pac Symp Biocomput 2005, 10:471-482.
8. Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS One 2007, 2(3):e337.
9. Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Med Genomics 2008, 1:28.
10. Resnik P. Using information content to evaluate semantic similarity in a taxonomy. IJCAI'95: Proceedings of the 14th international joint conference on Artificial intelligence 1995, San Francisco, CA, USA: Morgan Kaufmann Publishers Inc..
11. Lin D. An Information-Theoretic Definition of Similarity. Proceedings of the 15th International Conference on Machine Learning 1998, 296-304. Morgan Kaufmann.
12. Jiang JJ, Conrath DW. Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy. International Conference Research on Computational Linguistics (ROCLING X) 1997, 9008.
13. Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302.
14. Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23(10):1274-1281.
15. Tao Y, Sam L, Li J, Friedman C, Lussier YA. Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 2007, 23(13):i529-i538.
16. Pesquita C, Faria D, Bastos H, Falcao AO, Couto FM. Evaluating GO-based Semantic Similarity Measures. ISMB/ECCB 2007 SIG Meeting Program Materials, International Society for Computational Biology 2007,
17. Pesquita C, Faria D, Falcao AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol 2009, 5(7):e1000443.
18. Xia K, Dong D, Han JDJ. IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics 2006, 7:508.
19. Yu H, Gao L, Tu K, Guo Z. Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene 2005, 352:75-81.
20. Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, Siani-Rose MA. A knowledge-based clustering algorithm driven by Gene Ontology. J Biopharm Stat 2004, 14(3):687-700.
21. Wu H, Su Z, Mao F, Olman V, Xu Y. Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res 2005, 33(9):2822-2837.
22. del Pozo A, Pazos F, Valencia A. Defining functional distances over gene ontology. BMC Bioinformatics 2008, 9:50.
23. Lei Z, Dai Y. Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics 2006, 7:491.
24. Guo X, Liu R, Shriver CD, Hu H, Liebman MN. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22(8):967-973.
25. Pesquita C, Faria D, Bastos H, Ferreira AEN, Falcao AO, Couto FM. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 2008, 9(Suppl 5):S4.
26. Xu T, Du L, Zhou Y. Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics 2008, 9:472.
27. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health). 2005, Secaucus, NJ, USA: Springer-Verlag New York, Inc..
28. Schlicker A, Albrecht M. FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 2008, (36 Database):D434-D439.
29. Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Rubio A. Correlation between Gene Expression and GO Semantic Similarity. IEEE/ACM Trans Comput Biol Bioinformatics 2005, 2(4):330-338.
30. Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. Ontology engineering. Nature Biotechnology 2010, 28:128-130.
31. Zhang P, Zhang J, Sheng H, Russo JJ, Osborne B, Bue-tow K. Gene functional similarity search tool (GF-SST). BMC Bioinformatics 2006, 7:135.
32. Couto FM, Silva MJ, Coutinho PM. Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. CIKM 05:Proceedings of the 14th ACM international conference on Information and knowledge management 2005, 343-344. New York, NY, USA: ACM.
33. Pesquita C, Pessoa D, Faria D, Couto F. CESSM: Collaborative Evaluation of Semantic Similarity Measures. JB2009: Challenges in Bioinformatics 2009,
34. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, (34 Database):D535-D539.
35. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, Onge PS, Ghanny S, Lam MHY, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440(7084):637-643.
36. Hofer A, Bussiere C, Johnson AW. Mutational analysis of the ribosomal protein Rpl10 from yeast. J Biol Chem 2007, 282(45):32630-32639.
37. West M, Hedges JB, Chen A, Johnson AW. Defining the order in which Nmd3p and Rpl10p load onto nascent 60 S ribosomal subunits. Mol Cell Biol 2005, 25(9):3802-3813.
38. Eisinger DP, Dick FA, Denke E, Trumpower BL. SQT1, which encodes an essential WD domain protein of Saccharomyces cerevisiae, suppresses dominant-negative mutations of the ribosomal protein gene QSR1. Mol Cell Biol 1997, 17(9):5146-5155.
39. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi AL, Tavernier J, Hill DE, Vidal M. High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322(5898):104-110.
40. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
41. Strasser K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondon AG, Aguilera A, Struhl K, Reed R, Hurt E. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 2002, 417(6886):304-308.
42. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440(7084):631-636.
43. Chavez S, Beilharz T, Rondon AG, Erdjument-Bromage H, Tempst P, Svejstrup JQ, Lithgow T, Aguilera A. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J 2000, 19(21):5824-5834.
44. Saccharomyces Genome Database. 2010, , http://downloads.yeastgenome.org/
45. Consortium U The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, (38 Database):D142-D148. Consortium U.
46. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res 2000, 28:289-291.
47. Deane CM, Salwinski L, Xenarios I, Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349-356.
48. Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9:405.
49. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 2010, 38(Suppl):W214-W220.
50. van Rossum G. Python Reference Manual. Tech. rep., Centrum Wiskunde & Informatica 1995, , http://www.python.org/
51. Azuaje F, Al-Shahrour F, Dopazo J. Ontology-driven approaches to analyzing data in functional genomics. Methods Mol Biol 2006, 316:67-86.
52. Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26(7):976-978.
53. Faller AJ. An Average Correlation Coefficient. Journal of Applied Metereology 1981, 20:203-205.