List of data sources in TargetMine

At the moment, the biological data in TargetMine for most part is limited to human, rat and mouse, the most studied model organisms in biomedical field. The data sources compiled in TargetMine are summarized in the following table.

Data Organism [1] Source
Genome annotation H, R, M Entrez Gene
Protein annotation H, R, M UniProt (including Swiss-Prot and TrEMBL)
Protein domain H, R, M InterPro
Pathways H, R, M KEGG Pathway, Reactome [2]
H NCI Pathway interaction database
Gene-gene interactions H, R, M BioGRID, iRefIndex [3]
Gene Ontology and GO annotation H, R, M Gene Ontology,
UniProt-GOA [4]
Protein 3D structure Entire dataset wwPDB, SIFTS
Structural classification - SCOP, CATH
CATH protein domain assignments H, R, M Gene3D
Orthologues / Paralogues H, R, M KEGG Orthology,
TargetMine’s mapping
Transcription factor H ORegAnno, Amadeus, HTRI Database
Enzyme H, R, M ENZYME
Chemical compounds Entire dataset DrugBank [5], ChEMBL [6],
PubChem BioAssay [7],
Ligand Expo, DrugEBIlity, ChEBI
Disease Ontology and
DO annotation
H Disease Ontology,
Disease Ontology Annotatioin [8]
miRNA Entire dataset miRBase
miRNA target H, R, M miRTarBase [9]
Genome-Wide Association Studies H NHGRI GWAS Catalog
Microarray probe annotation H, R, M NetAffx Annotation Files [10]

Notes:

  1. H: human, R: rat, M: mouse.
  2. KEGG Pathway, Reactome, are integrated using the species specific files.
  3. BIOGRID, iRefIndex data are integrated from species specific files but may still contain a few cross-species interactions.
  4. UniProtKB GOA are integrated using the species specific files including those tagged with IEA evidence. However, IEA annotations are excluded when doing the enrichment analysis on the list analysis pages.
  5. DrugBank drug-target associations include all the target types including “off-target”.
  6. See the ChEMBL data set page for more details.
  7. Pubchem BioAssay data here only incorporate “bioactive” compounds.
  8. From BMC Genomics 10 Suppl 1:S6
  9. miRTarBase data are integrated using the species specific files and contain all support types including that labeled “weak”.
  10. The whole transcript (WT) probe sets are not included so far.

For the version information, please check TargetMine data sources page .