Functions, Disease Phenotypes, Their Enrichment Scoring and Networks

Gene functions are sourced from Gene Ontology (GO), while phenotype terms are from Human Phenotype Ontology (HPO).

Function and phenotype scores in Q-omics, are calculated based on the GSEA (Gene Set Enrichment Analysis) score using Fisher's exact test.

Gene network in NetCrafter, are calculated based on weighted Tanimoto scores of contributing functions or phenotypes to gene pairs.

* GO terms used in Q-omics functions

GO functions in Q-omics, consists of ~7,000 "biological process" terms, each of which contain genes with ≥ 3 and ≤300.

* HPO terms used in Q-omics phenotypes

HPO phenotypes in Q-omics, consists of ~8,000 terms, each of which contain genes with ≥ 3 and ≤300.

* GSEA scores used in Q-omics function/phenotype scores

Geneset enrichment analysis (GSEA) score quantifies the over-representation of genes associated with a specific GO biological process or HPO disease phenotype within a ranked list of genes, indicating the functional/phenotypic enrichment of the gene set.

For RNA expression, protein abundance, or CRISPR/shRNA efficacy data, GSEA scores are calculated within the given functional or phenotypic categories. These scores are embedded as function or phenotype scores for selected lists of genes, proteins, or CRISPR/shRNA data.

Functional & Disease phenotype term search