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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

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

  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