6120d02a6aa7faf052299967d8bace2d2d706ad3 hiram Mon Dec 15 13:06:28 2025 -0800 one additional color code definition for paralogous annotations refs #35776 diff --git src/hg/makeDb/trackDb/TOGAv2.html src/hg/makeDb/trackDb/TOGAv2.html index 995cce59d39..40a83b03d08 100644 --- src/hg/makeDb/trackDb/TOGAv2.html +++ src/hg/makeDb/trackDb/TOGAv2.html @@ -78,30 +78,35 @@
  •   "missing": <50% of the CDS is present in the query and the middle 80% of the CDS exhibits no inactivating mutation. There is currently no evidence for transcript loss; however, the uncertainty is higher as more than half of the CDS is missing. Note that Missing transcripts can also arise if no genome alignment chain spans the transcript.
  •   "uncertain loss": there is at least one inactivating mutation in the middle 80% of the CDS, but evidence is not strong enough to classify the transcript as lost. These transcripts may or may not encode a functional protein.
  •   "lost": typically several inactivating mutations are present, thus there is strong evidence that the transcript is unlikely to encode a functional protein.
    • +
  •   + "paralogous": Special category. Transcript is classified as paralogous +by TOGA2’s machine learning classifier and these are only retained if the respective query locus does not have +an orthologous projection. Transcripts in this color have enough inactivating mutations or missing sequence + such that there loss status is "missing" or "deleted".

    • Clicking on a transcript provides additional information about the orthology classification, inactivating mutations, the query's nucleotide/protein sequence, and protein/exon alignments.

    Credits

    This data was prepared by the Michael Hiller's Lab

    References