OverView
The User Interface Portal to access all the integrated data from the Knowledge Management Center is PHAROS. This portal allows for browsing, free text searches, filters on the 4 different protein classes that IDG is focused on (Kinase, GPCR, Ion Channel, Nuclear Receptor)
Explore: PHAROS Here
Datasources
A wide range of biomedical datasets have been integrated by IDG-KMC with integration activities led by the Icahn School of Medicine at Mt. Sinai via the Harmonizome, and by UNM via the Target Central Research Database (TCRD), which integrates Harmonizome datasets, CPR (Jensen Lab) datasets, EMBL-EBI datasets, and the Drug Target Ontology (DTO) from U. Miami. TCRD integration methodology involves importation by value or by reference to external sources, as informed by performance, provenance, and other design criteria. The User Interface Portal (UIP) Pharos relies on TCRD for data. The following table summarizes the datasets integrated by IDG-KMC at the time of this writing.
Datasource |
Content |
ISMMS: Ma'ayan Lab |
Harmonizome datasets: 114 diverse datasets normalized to attribute tables and weighted bi-partite graphs |
U. Copenhagen: Jensen Lab |
DISEASES, TISSUES, COMPARTMENT, and PubMed text-mining scores |
U. Miami: Schurer Lab |
Drug Target Ontology |
EMBL-EBI |
ChEMBL bioactivities, SureChEMBL patent associations |
Antibodypedia.com |
antibody interactions |
BioPlex |
protein-protein Interactions |
Drugable |
epigenomic associations |
DrugCentral (UNM) |
approved drugs [chemical structures, indications, contraindications, etc.] |
Ensembl Cross |
Protein, transcript and gene identifiers |
Gene Ontology |
Gene annotations |
GTEx |
RNA expression data and derived tissue specificity scores |
GWAS Catalog |
genome wide association |
HGNC |
Hugo gene nomenclature |
HPA |
Human Protein Atlas Protein and RNA expression data and derived tissue specificity scores |
HPM |
Human Proteome Map mass spec expression data and derived tissue specificity scores |
IMPC |
mouse phenotype associations |
AnimalTFDB |
Known transcription factors |
JAX/MGI |
Mouse/Human Orthology Phenotypes |
Panther |
protein class hierarchy |
PubChem |
MLP Assay Info |
PubMed |
gene-associated PubMed identifiers |
NCBI Gene |
gene RIFs |
NIH RePORTER |
NIH funding data associated to targets via Jensen Lab tagging (currently only 2010-2014) |
OMIM |
confirmed phenotype associations |
TIN-X (UNM) |
importance / novelty scores based on Jensen Lab tagging |
TMHMM Predictions |
Results of TMHMM predictions on target protein sequences |
Is House |
HK Gene List from RNASeq (Erez & LevanonFollow Link) |
UniProt |
protein annotations |
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