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Table 8 Comparison of homology inference between FIGENIX's pipeline and Homologene

From: FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

Gene Family Query Gene* Paralogy relationship missed Co-orthology relationship missed Orthologs not detected in Taxa Different orthology assignment
Notch Human Notch1 Notch2, Notch3, and Notch4 are not detected as paralogs of Notch1. Notch2, Notch3, and Notch4 are not detected as co-orthologous to Drosophila N. Amphibian Ray-finned fish Cephalochordata Arachnida 3 different C.elegans genes are detected for Hs Notch1, Notch2, and Notch3, suggesting that duplications giving rise to this family took place before the divergence between protostomes and deuterostomes, and that Notch2, and Notch3 were lost in Drosophila.
Calnexin/Calreticulin Human Calnexin Calmegin and Calreticulin are not detected as paralogs of Calnexin. Calmegin is not detected as a Human co-ortholog to Drosophila CG9906 gene. Amphibian Ray-finned fish Calmegin is detected to be orthologous to another Drosophila gene than CG9906, suggesting Calmegin and Calnexin already existed as two duplicates before the divergence between protostomes and deuterostomes and Calmegin was secondary lost in C. elegans
ENPEP/TRHDE/LNPEP/ERAP/LRAP/ANPEP Human TRHDE ENPEP, LNPEP, ERAP, LRAP, and ANPEP are not detected as paralogous to TRHDE. None None Each human gene of this family has been assigned a distinct ortholog in protostomes (e.g. Drosophila) suggesting this multigenic family emerged before the separation of Protostomes and Deuterostomes.
PSMB5/PSMB8 Human PSMB5 PSMB8 is not detected as paralogous to PSMB5 PSMB8 is not detected as co-orthologous to the same Drosophila gene than PSMB5. Ray-finned fish Avian Cephalochordata. Amphibian PSMB5 and PSMB8 are each assigned a distinct Drosophila ortholog suggesting they already existed as two copies in the last common ancestor of human and Drosophila.
PSMB7/PSMB10 Human PSMB7 PSMB10 is not detected as paralogous to PSMB7. PSMB10 is not detected as co-orthologous to the same Drosophila gene than PSMB7. Ray-finned fish Avian Cephalochordata. Amphibian PSMB7 and PSMB10 are each assigned a distinct Drosophila ortholog suggesting they already existed as two copies in the last common ancestor of human and Drosophila.
Cathepsins L, M, P, R Human Cathepsin R Cathepsins L, M and P are not detected as paralogous to Cathepsin R. None Amphibian Avian Ray-finned fish Each cathepsin gene is assigned a distinct drosophila ortholog suggesting the cathepsin family emerged before the separation between human and Drosophila.
Tpp2 Human Tpp2 None (not a multigenic family) None Drosophila None
ERP57 (GPR58) Human GRP58 None (not a multigenic family) None Fungi Bovine Schistosoma Avian None
HSPA5 (GRP78) Human HSPA5 None (not a multigenic family) None Amphibian Aplysia Lepidopteran Avian Schistosoma None
TAP1, TAP2, ABCB9, MDR1 Human TAP1 TAP2, ABCB9, and MDR1 are not detected as paralogous to TAP1. None Drosophila Avian Amphibian Ray-finned fish TAP1, and TAP2 are each assigned a distinct C.elegans ortholog and none in Drosophila, suggesting there was already two copies of these genes in the last common ancestor of these two species, and that the two copies were secondary lost in the Drosophila lineage.
PSME1, PSME2, PSME3 Human PSME1 PSME2, and PSME3 are not detected as paralogous to PSME1. None Protostomes Ray-finned fish None
THOP1, NLN Human THOP1 NLN is not detected as paralogous to THOP1 NLN is not detected as co-orthologous to the same N.crassa gene than THOP1. Amphibian Bacteria None
  1. *Query gene is identical to the Query gene we used for phylogenetic reconstruction with FIGENIX's phylogenomic inference pipeline.