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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.