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The overall workflow is shown below. The details can be found in Mi2013, Mi2016, Mi2017 .
How is a PANTHER gene tree constructed?
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Biologically meaningful family names are assigned by biologist curators (Thomas2003). The curator either assigns a family a more general functional name that applies to all genes in the family (e.g., NUCLEAR HORMONE RECEPTOR) or finds the largest subfamily name (Y) and names the family Y-RELATED. If in the latter case the largest subfamily is “unnamed” then the family is not named.
How are subfamilies named
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? Why are some subfamilies not named?
The name of a subfamily is transferred from the representative member of the subfamily (Mi2016). If a subfamily contains an annotated SwissProt entry from any of the 12 model organisms (human, mouse, rat, chicken, zebrafish, fruit fly, C. elegans, budding yeast, fission yeast, D. discoideum, Arabidopsis, and E. coli.), then the curated ‘protein name’ is used to name the subfamily. If a subfamily does not contain any SwissProt entries from the model organisms, but contains SwissProt entries from other organisms, the most common SwissProt protein name is used as the subfamily name. If a subfamily does not contain any members from the SwissProt database, a protein name from the TrEMBL entry is automatically selected as the subfamily name. If no name can be found, the subfamily is labeled with ‘unnamed’.
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