This page provides a variety of information on concepts and methods used in the Pharos inerface as well as a description of terms used to describe the data from the Target Central Resource Database.

Definitions

Target Development Level

Tclin These targets have activities in DrugDB (i.e., approved drugs) with known mechanism of action that satisfy the activity thresholds detailed below
Tchem These targets have activities in ChEMBL that satisfy the activity thresholds detailed below. In some cases, targets have been manually migrated to Tchem by human curation based on small molecule activities from other sources.
Tbio These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria:
  • target is above the cutoff criteria for Tdark
  • target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code
  • target has confirmed OMIM phenotype(s)
Tdark These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria:
  • A PubMed text-mining score from Jensen Lab < 5
  • ≤ 3 Gene RIFs
  • ≤ 50 Antibodies available according to http://antibodypedia.com

Data Sources

The goal of the IDG KMC is to integrate a variety of data sources to shed light on unstudied and understudied targets. To achieve this we have pulled together data on protein targets, small molecule activity, genomic behavior and disease links. For a list of datasources, and their associated entity counts, see the About Pharos page. A visual representation of all targets and their representation in all IDG datasources can be viewed here. Over time we anticipate incorporating other relevant data sources.

Harmonogram

The Harmonogram visualizes gene appearance in the Harmonizome resources using interactive clustergrams. Genes are shown as rows and resources are shown as columns. The gene occurrence value is normalized relative to the occurrence of other genes in the resource - the darker the tile the more the gene occurs in the resource. The NIH Reporter Grants Linked to NCBI Genes column shows the number of grants linked to each gene and this column is highlighted in blue. The resources are classified into Resource Groups, e.g., Disease or Phenotype Associations, and they are color coded using the column triangles.

You can view clustergrams for different gene classes, e.g., kinases, using the buttons on the sidebar. The ordering of the clustergram can be changed by clicking the reordering buttons or by double-clicking the row or column labels. For instance, double-clicking the NIH Reporter Grants column in Kinases view and zooming into the top of the clustergram reveals that EGFR is the kinase associated with the most grants.

If you have more questions take a look at the Frequently Asked Questions or contact us at pharos@mail.nih.gov