Table 1 Comparison of features used in the three gene prioritization applications
From: Improved human disease candidate gene prioritization using mouse phenotype
Feature type | SUSPECTS | ENDEAVOUR | ToppGene |
|---|---|---|---|
Sequence Features & Annotations | Gene length Homology Base composition | Blast cis-element Transcriptional motifs | Not used |
Gene Annotations | Gene Ontology | Gene Ontology | Gene Ontology Mouse Phenotype |
Transcript Features | Gene expression | Gene expression EST expression | Gene expression |
Protein Features | Protein domains | Protein domains Protein interactions Pathways | Protein domains Protein interactions Pathways |
Literature | Not used | Keywords in abstracts | Co-citation (PMIDs) |