IRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Razick, Sabry ^a   Mora, Antonio ^a   Michalickova, Katerina ^a   Boddie, Paul ^a   Donaldson, Ian M ^a  

^a UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CURATION; DATA FILTERING; DATA SET; EDGE FEATURES; MULTIPLE NODES; PLUG-IN DEVELOPERS; PROTEIN INTERACTION; SOURCE DATA;

DATA MINING; PROTEINS; VISUALIZATION;

DATA VISUALIZATION;

PROTEIN;

ARTICLE; COMPUTER PROGRAM; DATA BASE; DATA MINING; GENETIC DATABASE; METABOLISM; PROTEIN ANALYSIS; PROTEIN DATABASE;

DATA MINING; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DATABASES, PROTEIN; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 80053539569     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-388     Document Type: Article

References (27)

1. 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.
2. 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):D535-539.
3. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res 2008, (36 Database):D646-650.
4. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, (32 Database):D449-451.
5. 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 Res 2010, (38 Database):D525-531.
6. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13(10):2363-2371. 10.1101/gr.1680803, 403728, 14525934.
7. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. MINT: the Molecular INTeraction database. Nucleic Acids Res 2007, (35 Database):D572-574.
8. Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 2006, (34 Database):D436-441.
9. 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.
10. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082. 10.1093/bioinformatics/bti273, 15657099.
11. Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9:405. 10.1186/1471-2105-9-405, 2573892, 18823568.
12. 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, 2010. baq023.
13. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
14. iRefScape wiki page. , http://irefindex.uio.no/wiki/README_Cytoscape_plugin
15. Babnigg G, Giometti CS. A database of unique protein sequence identifiers for proteome studies. Proteomics 2006, 6(16):4514-4522. 10.1002/pmic.200600032, 16858731.
16. Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Literature curation of protein interactions: measuring agreement across major public databases. Database (Oxford) 2010, 2010:baq026.
17. Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Interaction databases on the same page. Nat Biotechnol 29(5):391-393.
18. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 2007, 25(3):309-316. 10.1038/nbt1295, 17344885.
19. McKusick VA. Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 2007, 80(4):588-604. 10.1086/514346, 1852721, 17357067.
20. Disease Groups. , http://donaldson.uio.no/wiki/DiG:_Disease_groups
21. Nguyen TP, Jordan F. A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. BMC Syst Biol 2010, 4:103. 10.1186/1752-0509-4-103, 2924296, 20670417.
22. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284.
23. iRefIndex. , http://irefindex.uio.no
24. UniProt Canonical Sequences. , http://www.uniprot.org/faq/30
25. Razick S, Donaldson IM. Design and prototype of a system to integrate and visualize biological interaction data. 2010, 399. Oslo: Universitetet i Oslo, Institutt for informatikk.
26. Java JTable Java JTable., http://download.oracle.com/javase/6/docs/api/javax/swing/JTable.html
27. 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, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 2007, 3:89. 1847948, 17353931.