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.
Common words (e.g., "and" and "the"), and commonly occurring but specialized words (e.g., "domain", "function") will be removed from the search.
For multi-word searches, an entire phrase (AND) search is run first. If not found, any word (OR) is used instead.
Faceted research results will be organized and linked to the relevant pages, including one or more (if found) of:
- SCOP Hierarchy for SCOP domains and their annotations;
- GO Hierarchy for GO terms and their annotated domains/supra-domains;
- BO Hierarchy for terms from Biomedical Ontologies that are not GO, and domains/supra-domains being annotated;
- PSnet for cross-linking similar phenotypes based on domain annotations shared;
- sTOL for the distribution of individual domain and GO/BO-annotated domains over the tree, and enriched GO/BO terms for extant and ancestral genomes;
- dcGO Predictor for function, phenotype and disease predictions of >80 million sequences in >2,000 genomes, UniProt and hundreds of meta-genomes.
- dcGO Enrichment for the identification of the GO/BO terms enriched within a list of input domains.
- dcGO Pevo for exploring architecture plasticity potentials of dcGO terms during eukaryotic evolution.