Protein Interaction Resources

A collection of resources related to retrieving and working with protein interaction data.

This table accompanies a talk on Protein Interaction Resources given for Metoder i biomedisinsk laboratoriemedisin.

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Name	Location	Notes and references
ID Mapping Service
UniProt	http://www.uniprot.org/	See the ID Mapping Tab
DAVID	http://david.abcc.ncifcrf.gov/	DAVID
Ensemble BioMart	http://www.ensembl.org/index.html	See the BioMart Link
CyThesaurus	http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/ID_Mapping_Examples http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/	A Cytoscape Plugin. Uses BridgeDb
Advanced Network Merge	http://www.cytoscape.org/cgi-bin/moin.cgi/Advanced_Network_Merge_and_ID_Mapping#API_Design	Cytoscape plugin. Uses BridgeDb
The Synergizer	http://llama.med.harvard.edu/synergizer/translate/	Synergizer
BridgeDB	http://www.bridgedb.org./	For programmatic access. http://www.biomedcentral.com/1471-2105/11/5/abstract
PICR	http://www.ebi.ac.uk/Tools/webservices/clients/picr	For programmatic access.
Primary Interaction Databases
IMEx	http://imex.sourceforge.net	International Molecular Exchange Consortium
IMEx	http://imex.sourceforge.net/doc/imex-CurationManual.pdf	IMEx curation manual
BIND	http://bond.unleashedinformatics.com	Biomolecular Interaction Network Database (Inactive)4
DIP	http://dip.doe-mbi.ucla.edu	Database of Interacting Proteins1 [1]
IntAct	http://www.ebi.ac.uk/intact	Interaction database at EBI1 [2, 3]
MINT	http://mint.bio.uniroma2.it/mint	Molecular Interaction Database2 [4]
MPACT	http://mips.gsf.de/genre/proj/mpact	Representation of Interaction Data at MIPS2 [5]
MatrixDB	http://matrixdb.ibcp.fr	Extracellular Matrix interactions Database2
BioGRID	http://www.thebiogrid.org	General Repository for Interaction Datasets3 [6]
MPIDB	http://www.jcvi.org/mpidb	The Microbial Protein Interaction Database3 [7]
HPRD	http://www.hprd.org	Human Protein Reference Database [8, 9]
MPPI	http://mips.gsf.de/proj/ppi	The MIPS Mammalian Protein-Protein Interaction Database [10]
Pathguide	http://www.pathguide.org	A listing of multiple interaction and pathway databases [11]
B. Text-mining resources
BioNLP	http://zope.bioinfo.cnio.es/bionlp_tools	A recent compilation of text-mining tools. [12]
iHOP	http://www.ihop-net.org/UniPub/iHOP	Information Hyperlinked Over Proteins [13]
EBIMed	http://www.ebi.ac.uk/Rebholz-srv/ebimed	PubMed abstract markup of for biological concepts. [14]
FACTA	http://text0.mib.man.ac.uk/software/facta	Finding Associated Concepts with Text Analysis [15]
PubGene	http://www.pubgene.org	Gene-centric retrieval of literature networks. [16]
InfoPubMed	https://www-tsujii.is.s.u-tokyo.ac.jp/info-pubmed	Interactions between genes in PubMed abstracts
Chillibot	http://www.chilibot.net	Relationships between genes, proteins or keywords in PubMed [17]
MedEvi	http://www.ebi.ac.uk/tc-test/textmining/medevi	Context-specific searches of PubMed abstracts. [18]
FABLE	http://fable.chop.edu	Fast Automated Biomedical Literature Extraction
PLN2L	http://zope.bioinfo.cnio.es/plan2l/plan2l.html	Text mining resource specific to Arabidopsis Thaliana PMID 19520768
BioText	http://biosearch.berkeley.edu	Full-text search engine for open source articles. [19]
Reflect	http://reflect.ws	Web-browser plugin for markup of gene, protein and small-molecule names PMID 19513049
C. Predicted Protein Interactions
OPHID/I2D	http://ophid.utoronto.ca	Predicted Protein Interaction Database [20, 21]
InteroPorc	http://biodev.extra.cea.fr/interoporc	Predicted interactions based on orthologous protein clusters. [22]
FunCoup	http://funcoup.sbc.su.se	Networks of Functional Coupling
STRING	http://string.embl.de	Search Tool for Retrieval of Interacting Genes/Proteins [23]
Predictome	http://visant.bu.edu	Predicted interactions using a number of methods. [24, 25]
PRISM	http://prism.ccbb.ku.edu.tr/prism	Predicted protein interactions by structural mapping. [26]
InterPreTS	http://www.russell.embl.de/cgi-bin/interprets2	Interaction Prediction through Tertiary Structure [27, 28]
3did	http://gatealoy.pcb.ub.es/3did	3D interacting domains [29]
DIMA	http://mips.gsf.de/genre/proj/dima	Domain Interaction Map [30]
D. Interaction Confidence Scores and Consolidation
DASMI	http://dasmi.bioinf.mpi-inf.mpg.de	Distributed Annotation Server for Molecular Interactions
PRINCESS	http://61.50.138.118/PICASSO/index.html	Protein Interaction Confidence Evaluation System with Multiple Sources [31]
iRefIndex	http://irefindex.uio.no	Interaction reference index. [32]
E. Integrated tools for visualization and analysis
STRING	http://string.embl.de	Search Tool for Retrieval of Interacting Genes/Proteins [23]
STITCH	http://stitch.embl.de	Search Tool for Interactions of Chemicals with proteins [33]
DILIMOT	http://dilimot.embl.de	Discovery of Linear Motifs [34]
VisAnt	http://visant.bu.edu	Integrative Visual Analysis Tool for Biological Networks and Pathways [35]
Cytoscape	http://www.cytoscape.org	Application for visualizing and analyzing biological networks. [36]
PC	http://www.pathwaycommons.org/pc/	Pathway Commons. Interaction and pathway database integration.5
MiMI	http://mimi.ncibi.org	Michigan Molecular Interaction Database5 [37]
BioNetBuilder	http://err.bio.nyu.edu/cytoscape/bionetbuilder	Interaction data retrieval from multiple databases5. [38]
R	http://www.r-project.org	Free software environment for statistical computing and graphics.
Bioconductor	http://bioconductor.org	Open software for analysis of genomic data. [39]
FunCoup	http://funcoup.sbc.su.se	Networks of Functional Coupling
PPISpider	http://mips.gsf.de/proj/ppispider	Induction of protein interaction subgraphs from lists of proteins.
Torque	http://www.cs.tau.ac.il/~bnet/torque.html	Topology-Free Querying of Protein Interaction Networks PMID 19491310.
CPDB	http://cpdb.molgen.mpg.de	Consensus Path Database with overrepresentation analysis. [40]
SPIKE	http://www.cs.tau.ac.il/~spike	Signaling Pathway Integrated Knowledge Engine [41]
Complex Detection
CME	http://www.kyb.tuebingen.mpg.de/~georgii/dme.htm	Dense module enumeration on a weighted graph PMID 19213739
Commercial Resources
GeneGo	http://www.genego.com
Ingenuity	http://www.ingenuity.com
Ariadne	http://www.ariadnegenomics.com
Other related resources
COSMIC	http://www.sanger.ac.uk/perl/genetics/CGP/cosmic	Catalogue of somatic mutations in cancer.

1. 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 issue):D449-451.

2. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A et al: IntAct: an open source molecular interaction database. Nucleic Acids Res 2004, 32(Database issue):D452-455.

3. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R et al: IntAct--open source resource for molecular interaction data. Nucleic Acids Res 2007, 35(Database issue):D561-565.

4. 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 issue):D572-574.

5. 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 issue):D436-441.

6. 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 issue):D535-539.

7. Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, Uetz P: MPIDB: the microbial protein interaction database. Bioinformatics 2008, 24(15):1743-1744.

8. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM et al: Human protein reference database--2006 update. Nucleic Acids Res 2006, 34(Database issue):D411-414.

9. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg 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. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW et al: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21(6):832-834.

11. Bader GD, Cary MP, Sander C: Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34(Database issue):D504-506.

12. Krallinger M, Valencia A, Hirschman L: Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biology 2008, 9(Suppl 2).

13. Hoffmann R: Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds. Current protocols in bioinformatics / editoral board, Andreas D Baxevanis [et al 2007, Chapter 1:Unit1 16.

14. Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P: EBIMed--text crunching to gather facts for proteins from Medline. Bioinformatics 2007, 23(2):e237-244.

15. Tsuruoka Y, Tsujii J, Ananiadou S: FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 2008.

16. Jenssen TK, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28(1):21-28.

17. Chen H, Sharp BM: Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 2004, 5:147.

18. Kim JJ, Pezik P, Rebholz-Schuhmann D: MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline. Bioinformatics 2008, 24(11):1410-1412.

19. Hearst MA, Divoli A, Guturu H, Ksikes A, Nakov P, Wooldridge MA, Ye J: BioText Search Engine: beyond abstract search. Bioinformatics 2007, 23(16):2196-2197.

20. Brown KR, Jurisica I: Online predicted human interaction database. Bioinformatics 2005, 21(9):2076-2082.

21. Brown KR, Jurisica I: Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 2007, 8(5):R95.

22. Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H: InteroPORC: automated inference of highly conserved protein interaction networks. Bioinformatics 2008, 24(14):1625-1631.

23. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P: STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 2007, 35(Database issue):D358-362.

24. Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C: Predictome: a database of putative functional links between proteins. Nucleic Acids Res 2002, 30(1):306-309.

25. Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C: VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res 2007, 35(Web Server issue):W625-632.

26. Keskin O, Nussinov R, Gursoy A: Prism: protein-protein interaction prediction by structural matching. Methods in molecular biology (Clifton, NJ 2008, 484:505-521.

27. Aloy P, Russell RB: InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 2003, 19(1):161-162.

28. Aloy P, Russell RB: Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A 2002, 99(9):5896-5901.

29. Stein A, Panjkovich A, Aloy P: 3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic acids research 2008.

30. Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stumpflen V, Frishman D: DIMA 2.0--predicted and known domain interactions. Nucleic Acids Res 2008, 36(Database issue):D651-655.

31. 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.

32. Razick S, Magklaras G, Donaldson IM: iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9(1):405.

33. Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P: STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 2008, 36(Database issue):D684-688.

34. Neduva V, Russell RB: DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res 2006, 34(Web Server issue):W350-355.

35. Hu Z, Snitkin ES, DeLisi C: VisANT: an integrative framework for networks in systems biology. Briefings in bioinformatics 2008, 9(4):317-325.

36. 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.

37. Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P et al: Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res 2007, 35(Database issue):D566-571.

38. Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R: BioNetBuilder: automatic integration of biological networks. Bioinformatics 2007, 23(3):392-393.

39. Huber W, Carey VJ, Long L, Falcon S, Gentleman R: Graphs in molecular biology. BMC Bioinformatics 2007, 8 Suppl 6:S8.

40. Kamburov A, Wierling C, Lehrach H, Herwig R: ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res 2008.

41. Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R et al: SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 2008, 9:110.

Footnotes

1. Archival member of IMEx

2. Topical member of IMEx

3. Observing member of IMEx

4. Inactive member of IMEx

5. Available via a Cytoscape plugin

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