| 1 |
AraNet - Probabilistic Functional Gene Network of Arabidopsis thalianahttp://www.functionalnet.org/aranet |
| A resource of interactions in plant proteins (Arabidopsis thaliana). Provides both experimental & predicted interactions. Provides interactions based on the proteins' sequence conservation/similarity. Provides functional associations for the interactions. Provides the pathway and other proteins involved, along with the interactions, for a given set of proteins. Predicted interaction based on gene expression. Provides interactions along with their functional associations. Interactions can be restricted to a given experimental evidence. |
| | Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol. 2010 Feb;28(2):149-56. Epub 2010 Jan 31. PubMed PMID: 20118918; PubMed Central PMCID: PMC2857375. |
| 2010 | 100 |
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| 2 |
AtPID - Arabidopsis thaliana Protein Interactome Databasehttp://www.megabionet.org/atpid |
| A database of interactions in plant proteins (Arabidopsis thaliana). Provides predicted interactions based on gene expression, genomic data, Gene Ontology terms, orthology. Provides domain interactions. Provides functional associations for the interactions. |
| | Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008. Epub 2007 Oct 25. PubMed PMID: 17962307; PubMed Central PMCID: PMC2238993. |
| 2007 | 100 |
URL could not be retrieved (20/12/2011). |
| 3 |
MiMI - Michigan Molecular Interactionhttp://mimi.ncibi.org |
| Collects protein interaction data from multiple PPI databases. Provides interactions along with their functional associations. |
| | Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720. |
| 2006 | 100 |
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| 4 |
MINT - Molecular INTeractionhttp://mint.bio.uniroma2.it |
| A database that provides PPIs of experimental importance. It also identifies interactions among the given list of proteins. Provides options to curate data for the database. |
| | Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett. 2002 Feb 20;513(1):135-40. Review. PubMed PMID: 11911893. |
| 2002 | 100 |
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| 5 |
MitoInteractome - Mitochondrial Protein Interactome Databasehttp://mitointeractome.kobic.kr |
| A resource specific to mitochondrial PPIs. Predicts interactions based on the domain/interfaces/sites. Provides inferred interactions (e.g., human interactions inferred from mouse & rat). |
| | Reja R, Venkatakrishnan AJ, Lee J, Kim BC, Ryu JW, Gong S, Bhak J, Park D. MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. BMC Genomics. 2009 Dec 3;10 Suppl 3:S20. PubMed PMID: 19958484; PubMed Central PMCID: PMC2788373. |
| 2009 | 100 |
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| 6 |
PINT - Protein-protein Interactions Thermodynamichttp://www.bioinfodatabase.com/pint |
| A resource that provides the kinetics/thermodynamics of the interactions. Considers only PubMed for retrieving PPIs. Provides options for uploading or submitting the interaction data. |
| | Kumar MD, Gromiha MM. PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D195-8. PubMed PMID: 16381844 |
| 2006 | 100 |
URL could not be retrieved (20/12/2011). License is required for commercial use |
| 7 |
STRING - Search Tool for the Retrieval of Interacting Genes/Proteinshttp://string.embl.de |
| A database that predicts protein-interactions based on co-expression, genomic data, gene fusion. Also collects PPIs from multiple databases. Provides information on the function of interactions. Can also query with multiple genes/proteins. |
| | Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000 Sep 15;28(18):3442-4. PubMed PMID: 10982861; PubMed Central PMCID: PMC110752. |
| 2000 | 100 |
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