PantherDB Orthologs

PantherDB (Protein Analysis Through Evolutionary Relationships) provides gene orthology data derived from phylogenetic trees. The AllOrthologs file contains pairwise ortholog relationships between genes across multiple species.

Data is downloaded from: http://data.pantherdb.org/ftp/ortholog/current_release/AllOrthologs.tar.gz

Additionally, NCBI gene_info is used for identifier mapping when direct database mappings are not available.

Species Included

• Human (NCBITaxon:9606)
• Mouse (NCBITaxon:10090)
• Rat (NCBITaxon:10116)
• Dog (NCBITaxon:9615)
• Cow (NCBITaxon:9913)
• Pig (NCBITaxon:9823)
• Chicken (NCBITaxon:9031)
• Frog (NCBITaxon:8364)
• Zebrafish (NCBITaxon:7955)
• Fruit fly (NCBITaxon:7227)
• C. elegans (NCBITaxon:6239)
• Dictyostelium (NCBITaxon:44689)
• Aspergillus nidulans (NCBITaxon:227321)
• Fission yeast (NCBITaxon:4896)
• Baker's yeast (NCBITaxon:4932)

Ortholog Associations

Gene identifiers from the PantherDB file are mapped to standard CURIE namespaces (HGNC, MGI, RGD, SGD, ZFIN, FB, WB, PomBase, dictyBase, Xenbase, ENSEMBL). When a direct mapping is not available, NCBI gene IDs are used as a fallback via a lookup table, with UniProtKB as a last resort. ENSEMBL version numbers are stripped (e.g. ENSG00000123456.1 becomes ENSG00000123456).

Rows where either species is not in the supported taxon set are skipped.

Biolink Captured:

• biolink:GeneToGeneHomologyAssociation
  • id (UUID)
  • subject (gene CURIE)
  • predicate (biolink:orthologous_to)
  • object (gene CURIE)
  • has_evidence (PANTHER.FAMILY ID)
  • aggregator_knowledge_source (["infores:monarchinitiative"])
  • primary_knowledge_source (infores:panther)
  • knowledge_level (knowledge_assertion)
  • agent_type (not_provided)

Citation

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science. 2022;31(1):8-22. doi: 10.1002/pro.4218. PMID: 34717010

License

MIT