max planck institut
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informatik
Database Information
Based on Ensembl 52, UniProt version 15.0, and Pfam version 23.
Affymetrix probeset data were taken from the NetAffx release of 03/09.
Reactome data were downloaded 04/09/09.
WikiPathway data were downloaded 06/17/09.
Omim data were downloaded 04/03/09.
Mappings between Ensembl, Entrez, and UniProt were downloaded via BioMart (using Ensembl 52).
DDI dataset version 1.
Structural domain-domain interaction datasets:iPfam version 21; 3did version of November 2007
Predicted domain-domain interaction datasets: InterDom version 2.0; LLZ; DPEA; DIMA version 2.0, consisting of 3 subsets (domain profiling, DPEA, and string); LDSC consisting of 2 sets: all interactions and a core subset; RDFF; RCDP50; APMM consisting of 2 sets: APMM1 and APMM2; LP; PINS; IPPRI
Based on Ensembl 54, UniProt version 15.10, and Pfam version 24.
Affymetrix probeset data were taken from the NetAffx release of 07/09.
Reactome data were downloaded 11/13/09.
WikiPathway data were downloaded 11/13/09.
Omim data were downloaded 11/12/09.
Mappings between Ensembl, Entrez, and UniProt were downloaded via BioMart (using Ensembl 54).
DDI dataset version 2 (same as 1, but includes UniDomInt).
Structural domain-domain interaction datasets:iPfam version 21; 3did version of November 2007
Predicted domain-domain interaction datasets: InterDom version 2.0; LLZ; DPEA; DIMA version 2.0, consisting of 3 subsets (domain profiling, DPEA, and string); LDSC consisting of 2 sets: all interactions and a core subset; RDFF; RCDP50; APMM consisting of 2 sets: APMM1 and APMM2; LP; PINS; IPPRI; UniDomInt
Based on Ensembl 55, UniProt version 15.6, and Pfam version 24.
Affymetrix probeset data were taken from the NetAffx release of 11/09.
Reactome data were downloaded 08/09/10.
WikiPathway data were downloaded 08/09/10.
Omim data were downloaded 08/09/10.
Mappings between Ensembl, Entrez, and UniProt were downloaded via BioMart (using Ensembl 55).
DDI dataset version 2 (same as 1, but includes UniDomInt).
Structural domain-domain interaction datasets:iPfam version 21; 3did version of November 2007
Predicted domain-domain interaction datasets: InterDom version 2.0; LLZ; DPEA; DIMA version 2.0, consisting of 3 subsets (domain profiling, DPEA, and string); LDSC consisting of 2 sets: all interactions and a core subset; RDFF; RCDP50; APMM consisting of 2 sets: APMM1 and APMM2; LP; PINS; IPPRI; UniDomInt
Please note: the Affymetrix probesets are mapped to Ensembl transcripts according to their genomic coordinates as given by the respective NetAffx release.
The DomainGraph plugin uses an embedded database by Apache Derby.
The database will be installed locally in the user's Cytoscape directory upon first usage. Exon Array data will also be stored in this local database to remain confidential data locally.