Molecular interactions external databases
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Protein-proteinProtein-DNAProtein-RNADNA-DNAmiRNA-mRNAGenetic
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Database NameURLExp.Pred.Exp.Pred.Exp.Pred.Exp.Pred.Exp.Pred.Exp.Pred.Molecular interaction typesAggregate or Source
Pulled into Alliance?
Data sharing agreement?
AssigneeSpeciesdownload formatLicenseNotesDownload notes
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IMExhttp://www.imexconsortium.org/XXXXprotein-protein, protein-DNA, protein-RNA, DNA-DNAAggregateYesYes
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DIPhttps://dip.mbi.ucla.edu/dip/index.jspXXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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IntActhttps://www.ebi.ac.uk/intact/XXXXprotein-protein, protein-DNA, protein-RNA, DNA-DNASourceYes, via IMExYes, via IMEx
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MINThttps://mint.bio.uniroma2.it/XXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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UniProthttps://www.uniprot.orgXXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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mpidbhttps://www.ebi.ac.uk/intact/ Xprotein-proteinSourceYes, via IMExYes, via IMEx
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matrixdbhttp://matrixdb.univ-lyon1.fr/ Xprotein-proteinSourceYes, via IMExYes, via IMEx
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InnateDBhttp://www.innatedb.com/ Xprotein-proteinSourceYes, via IMExYes, via IMEx
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mbinfohttp://www.mechanobio.info/ Xprotein-proteinSourceYes, via IMExYes, via IMEx
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I2Dhttp://iid.ophid.utoronto.ca/iid/ XXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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Molecular Connectionshttp://www.molecularconnections.com/XXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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NTNUwww.ntnu.no/home XXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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bhf-uclhttp://www.ucl.ac.uk/functional-gene-annotation/psicquic/Tabs/bhf-ucl-datasetXXprotein-protein, protein-DNASourceYes, via IMExYes, via IMEx
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HPIDbhttp://hpidb.igbb.msstate.edu/index.html Xprotein-proteinSourceYes, via IMExYes, via IMEx
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BioGRIDhttps://thebiogrid.org/XXprotein-proteinSourceYesYes
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miRDBhttp://www.mirdb.org/Xpredicted miRNA targetsPrediction sourceNoNo
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TargetScanhttp://www.targetscan.org/vert_72/Xpredicted miRNA targetsPrediction sourceNoNo
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DIANA tools (set)http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=site%2FtoolsXXmany sub-DBsAggregateNoNo
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TarBasehttp://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2FindexXexperimentally confirmed miRNA targetsSourceNoNo
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mircroCLIPhttp://carolina.imis.athena-innovation.gr/diana_team/microCLIP/index.htmlXCLIP identified miRNA targetsSource?NoNo
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miRGen v.3http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=mirgenv3%2FindexXTF regulators of miRNA expression (TFs that bind miRNA promoters)SourceNoNo
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LncBase v.2http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2FindexXXpredicted and experimentally confirmed miRNA targetsSourceNoNo
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mirExTra v2.0http://carolina.imis.athena-innovation.gr/mirextra/Xpredicted miRNA targetsPrediction sourceNoNo
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microT-CDShttp://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/indexXXpredicted and experimentally confirmed miRNA targetsSourceNoNo
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MR-microtThttp://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mrmicrot/indexXpredicted miRNA targetsPrediction sourceNoNo
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miRWalk 2.0http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/XXpredicted and experimentally confirmed miRNA targetsSourceNoNo
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Cupidhttp://cupidtool.sourceforge.net/Xpredicted miRNA targetsPrediction sourceNoNo
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miRecordshttp://c1.accurascience.com/miRecords/Xexperimentally confirmed miRNA targetsSourceNoNo
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starBasehttps://web.archive.org/web/20110222111721/http://starbase.sysu.edu.cn/XXpredicted miRNA targets and CLIP identified miRNA targetsSourceNoNo
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CLIPdb/POSTAR2http://lulab.life.tsinghua.edu.cn/postar2/rbp2.phpXXprotein-RNA, miRNA targets (predicted and experimental)SourceNoNo
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PicTarhttps://web.archive.org/web/20080724163022/http://pictar.bio.nyu.edu/Xpredicted miRNA targetsPrediction sourceNoNo
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RepTarhttp://reptar.ekmd.huji.ac.il/ (dead link)Xpredicted miRNA targetsPrediction sourceNoNo
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RNA22https://cm.jefferson.edu/rna22/Xpredicted miRNA targetsPrediction sourceNoNo
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MBStarhttps://www.isical.ac.in/~bioinfo_miu/MBStar30.htmXpredicted miRNA targetsPrediction sourceNoNo
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PITAhttps://genie.weizmann.ac.il/pubs/mir07/mir07_data.htmlXpredicted miRNA targetsPrediction sourceNoNo
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miRGator v3.0http://mirgator.kobic.re.kr/XXpredicted and experimentally confirmed miRNA targetsAggregateNoNo
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mirTarbasehttp://mirtarbase.mbc.nctu.edu.tw/php/index.phpXexperimentally confirmed miRNA targetsSourceNoNo
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miRTarhttp://mirtar.mbc.nctu.edu.tw/human/Xpredicted miRNA targetsPrediction sourceNoNo
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miRTarCLIPhttp://mirtarclip.mbc.nctu.edu.tw/XCLIP identified miRNA targetsSourceNoNo
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miRSelhttps://services.bio.ifi.lmu.de:1047/mirsel/Xtext-mining identified miRNA targets(Prediction?) SourceNoNo
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comiRNethttp://comirnet.di.uniba.it:8080/Xpredicted miRNA targetsPrediction sourceNoNo
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miRNAMaphttp://mirnamap.mbc.nctu.edu.tw/html/about.htmlXexperimentally confirmed miRNA targetsSourceNoNo
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miRGatehttp://mirgate.bioinfo.cnio.es/miRGate/Xexperimentally confirmed miRNA targetsSourceNoNo
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PDIdbhttp://melolab.org/pdidb/web/content/linksXprotein-DNAAggregateNoNo
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hPDIhttp://bioinfo.wilmer.jhu.edu/PDI/Xprotein-DNA?NoNo
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MISThttp://fgrtools.hms.harvard.edu/MIST/XXXXprotein-protein (and genetic) interactions both experimental and predicted/inferredAggregate of BioGRID, IntAct, mentha, DIP, DroID, HPRD, FlyBase, PomBase
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Reactomehttps://reactome.org/XXXXmRNA-miRNA, protein-DNA, protein-RNA, protein-protein, protein-small_molecule, DNA-small_molecule, RNA-small_moleculeSourceNoNoChris49, including all Alliance speciesPSI-MI TAB (all species file 1,016,953 lines)Creative Commons Public Domain (CC0) Licenseinteractions inferred from complexes generated in Reactome pathway curationhttps://reactome.org/download/current/interactors/reactome.all_species.interactions.psi-mitab.txt
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Stringhttps://string-db.org/XXprotein-proteinImporting data from DBs (MINT, HPRD, BIND, DIP, BioGRID, KEGG, Reactome, IntAct, EcoCyc, NCI-Nature Pathway Interaction Database, GO) curating experimentally derived protein–protein interactions from literatures. Also store computationally predicted interactions from text mining, interactions computed from genomic features, and interactions transferred from model organisms based on orthology.NoNoJae2,031 organismstxt, PSI-MI MITAB2.5 All data and download files in STRING are freely available under a 'Creative Commons BY 4.0' license.
When using the data, please provide appropriate credit — and inform users of any changes or additions that you might have made to the data.
STRING has been developed by a consortium of academic institutions including CPR, EMBL, KU, SIB, TUD and UZH.https://string-db.org/cgi/download.pl?sessionId=uzNlRMbPgyqf
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The MIPS Mammalian Protein-Protein Database (MPPI)
http://mips.helmholtz-muenchen.de/proj/ppi/Xprotein-proteinSourceNoNoEdith11 organisms - mouse, rat, humans, dog, hamster, pig, cattle, sheep, rabbit and "mammal"PSI-MI XMLFree to use; just cite papersmost annotations to human (1812), mouse (1177) and rat (468). Not sure when last updatedhttp://mips.gsf.de/proj/ppi/data/mppi.gz
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Human Protein Reference Database
http://www.hprd.org/Xprotein-proteinSourceNoNoChrishumantab-delimited or PSI-MI XMLGNU Lesser General Public License?Have to fill out form and declare will not share with third party (http://hprd.org/download); 39,240 human protein-protein interactions manually curated in-house
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APIDhttp://cicblade.dep.usal.es:8080/APID/init.actionXonly protein-protein, only experiemental as far as I can tellAggregate of BioGRID, DIP, HPRD, IntAct and MINT (poss. Also BioPlex, plus PDB and PDBsum for 3D structure interactions)nono?Jennifer>400, including all Alliance speciesData provided in MITAB formatLicense: CC by-NC 4.0
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CCSB interactome databasehttp://interactome.dfci.harvard.edu/Xworm onlyprotein-protein for worm and yeast; genetic for worm only; proteinFragment-proteinFragment for worm onlysource? They list papers for each data set but don't make it clear whether they got the data straight from the papers or from another source like WB or SGDnono?Jennifer"human", C. elegans, S. cerevisiaeNo actual data or downloads for human, the overview page sends the user to HuRI (http://interactome.baderlab.org/); other downloads tab delimited text, except fragmentome which is an Excel fileno license info"C. elegans Fragmentome": display a list of interactions using one or more of your favorite proteins as search terms. From this list, you can view exactly which fragments of the prey protein were found to interact."interactions" are almost all listed in the download files as just two protein IDs. There are "microarray" and "phenotype" files for worm that have two protein IDs with a number in column 3. For microarray, this is presumably the same number as shown in "vertex-pairs with PCC ≥ 0.874249" and for phenotype this appears to be the same number as shown in "vertex pairs with s > 4.301"
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HuRI (Human Interactome Mapping Project)
http://interactome.baderlab.org/Xprotein-protein interactions
Source -- multiple pulished studies (Vidal lab and Rolland paper: http://www.cell.com/abstract/S0092-8674(14)01422-6); some unpublished studies
nonoEdithhumanPSI-MI TABhttp://interactome.baderlab.org/downloadhttp://interactome.baderlab.org/faq/Multiple files to download - one from each publication; need to register for unpublished data;
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HitPredicthttp://hintdb.hgc.jp/htp/Xonly protein-protein experimentally supportedProtein-protein interactions from IntAct, BioGRID, HPRD, MINT and DIP are combined, annotated and scored. Jae115, including all Alliance speciestext format and PSI-MITAP2.5 formatno license infoThe reliability score is calculated based on the experimental details of each interaction and the sequence, structure and functional annotations of the interacting proteins.http://hintdb.hgc.jp/htp/download.html
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menthahttps://mentha.uniroma2.it/Xprotein-protein
Aggregate from MINT, IntAct, DIP, MatrixDB, BioGRID
nonoJulieAlliance species plus A. thaliana, E.coliMITAB2.5, textno license infofocus on experimentally determined PPIhttps://mentha.uniroma2.it/download.php
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DroIDhttp://www.droidb.org/Index.jspXXXXonly from FBonly from FBXonly from FBprotein-protein, TF-gene, miRNA-gene, geneticSource for some high-throughput PPI. Aggregate for PPI from FlyBase, BioGRID, IntAct, MINT, BIND, TF-gene from REDFly, modENCODE, miRNA-gene from TargetScanFly, MinoTar, modENCODE.nonoJulieD. meltab-delimited text"All data housed at DroID are freely available"http://www.droidb.org/Downloads.jsp
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