dcGO - A comprehensive domain-centric ontology resource for post-genomic research on functions, phenotypes, diseases and more   

Phenotype similarity network (PSnet): Cross-linking phenotypes and other ontolgoies based on shared domains

  • For a given phenotype, the search for similar phenotypes examines:

    • The extent of shared domain annotations (both at the superfamily and family levels) against the overlaps that would be expected by chance. The search reports Z-score to indicate the strength of the overlap, P-value for the significance and FDR (accounting for multiple hypothesis testing) as well;
    • The information content (IC) of annotated domains using an IC-based similarity metric, that is, the sum of the IC among overlapping domains divided by the sum of the IC among domains in union.

  • Ways to access PSnet:

    • Via BO Hierarchy, where the logoprovides a direct link to the results page;
    • Via Faceted Search, where ontology terms returned by the search will be presented with the logoproviding a direct link to the results page.

Quick start to mining the dcGO resource

  • SCOP domains (LINKTO SCOP Hierarchy and sTOL)
    • SCOP unique identifier (sunid) of a SCOP, e.g. 46458
    • SCOP name or part thereof, e.g. hemoglobin
    • Enrichment analysis for a list of input protein domains via dcGO Enrichment.
  • Genomes (LINKTO SUPERFAMILY database and sTOL)
    • A common organism name, e.g. human
    • A genome name or part thereof, e.g. Homo sapiens

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