Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

Table 1 The statistics for the reconciliation of gene names between the anatomical profiles from the Monarch, and the PPI networks from STRING for zebrafish and mouse

	Zebrafish	Mouse
Number of genes in the original anatomical profiles	5405	14,652
Number of anatomical entities in the original anatomical profiles	960	1537
Number of genes directly matched to the PPI network using the gene name (round 1)	2527	8166
Number of genes matched using the Ensembl IDs (round 2)	402	378
Number of genes matched using synonyms in the STRING database (round 3)	119	63
Number of final gene matches to the PPI network (in all 3 rounds)/Number of genes in the reconciled anatomical profiles	3048	8607
Number of anatomical entities in the reconciled anatomical profiles	943	1524
Number of final gene mismatches	2357	6045
Number of genes kept in the anatomical profiles after filtering out the entities with fewer than 10 gene annotations	3037	8606
Number of anatomical entities kept in the anatomical profiles after filtering out the entities with fewer than 10 gene annotations	294	850

ISSN: 1471-2105