IRefR: An R package to manipulate the iRefIndex consolidated protein interaction database

BMC Bioinformatics

Volumn 12, Issue 1, 2011, Pages

  Mora, Antonio ^a   Donaldson, Ian M ^a  

^a UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY INTERACTIONS; COMPARISON OF METHODS; DATA REPRESENTATIONS; EXPERIMENTAL METHODS; PROTEIN COMPLEXES; PROTEIN INTERACTION; REDUNDANCY RESOLUTION; REPRODUCIBILITIES;

COMPLEX NETWORKS; REDUNDANCY;

PROTEINS;

PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; HUMAN; METABOLISM; MOUSE; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; RAT; REPRODUCIBILITY;

ANIMALS; DATABASES, PROTEIN; HUMANS; MICE; PROTEIN INTERACTION MAPS; PROTEINS; RATS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 82055171942     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-455     Document Type: Article

References (31)

1. Razick S, Magklaras G, Donaldson IM. iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9(1):405. 10.1186/1471-2105-9-405, 2573892, 18823568.
2. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, (33 Database):D418-424.
3. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res 2001, 29(1):242-245. 10.1093/nar/29.1.242, 29820, 11125103.
4. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic acids research 2011, (39 Database):D698-704.
5. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic acids research 2010, (38 Database):D497-501.
6. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic acids research 2002, 30(1):303-305. 10.1093/nar/30.1.303, 99070, 11752321.
7. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic acids research 2009, (37 Database):D767-772.
8. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H. The IntAct molecular interaction database in 2010. Nucleic acids research 2010, (38 Database):D525-531.
9. Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G. MINT, the molecular interaction database: 2009 update. Nucleic acids research 2010, (38 Database):D532-539.
10. Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic acids research 2006, (34 Database):D436-441.
11. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Ruepp A, Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834. 10.1093/bioinformatics/bti115, 15531608.
12. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082. 10.1093/bioinformatics/bti273, 15657099.
13. The R project for statistical computing. , http://www.r-project.org
14. Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) 2010, baq023.
15. Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Literature curation of protein interactions: measuring agreement across major public databases. Database (Oxford) 2010, baq026.
16. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC biology 2007, 5:44. 10.1186/1741-7007-5-44, 2189715, 17925023.
17. MITAB2.6 format for iRefIndex. , http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex_8.0
18. The igraph library. , http://igraph.sourceforge.net
19. Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal 2006, Complex Systems.
20. graph: A package to handle graph data structures. , http://www.bioconductor.org/packages/release/bioc/html/graph.html
21. RBGL: R BOOST Graphical library. , http://cran.r-project.org/web/packages/RBGL/index.html
22. Stojmirovic A, Yu YK. ppiTrim: constructing non-redundant and up-to-date interactomes. Database: the journal of biological databases and curation 2011, 2011:bar036.
23. Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Interaction databases on the same page. Nat Biotechnol 29(5):391-393.
24. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular systems biology 2007, 3:89. 1847948, 17353931.
25. Yu J, Finley RL. Combining multiple positive training sets to generate confidence scores for protein-protein interactions. Bioinformatics 2009, 25(1):105-111. 10.1093/bioinformatics/btn597, 2638943, 19010802.
26. Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M. An experimentally derived confidence score for binary protein-protein interactions. Nat Methods 2009, 6(1):91-97. 10.1038/nmeth.1281, 2976677, 19060903.
27. Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 8(7):528-529.
28. Clauset A, Shalizi CR, Newman MEJ. Power-law distributions in empirical data. SIAM Review 2009, 51(4):661-703.
29. The PSIMex Consortium. , http://www.psimex.org
30. PSICQUIC Web Services. , http://code.google.com/p/psicquic
31. PSI-MI TAB format. , http://code.google.com/p/psicquic/wiki/MITAB25Format