Going deeper in the tracktability pipe and output file I was surprised by the numbers of hit in the “Antibody pipeline buckets” (seems a bit large, not what have been reported).
Unfortunately, a quick look at the list turned on red alert light in my mind, let me explain:
One example (among many others) is PDE9A, a classic cytoplasmic phosphodiesterase.
There’s actually three “hits” reported in all the Antibodies tracktability buckets: Bucket #4, #5 and #9.
If I’m not mistaken, #4 is “Uniprot Loc”: looking at it, it described it cytoplasmic, and membrane ruffles associated (i.e. intracellular fully – uniport is ok on this one). That should not give a one point to bucket #4.
Next point is for bucket #9 i.e. HPA:
clear enough, HPA report “Located in Nucleoplasm, Plasma membrane, Cytosol (Single cell variability)” hurm hurm…everywhere. Ok, on this one HPA is just wrong, plasma membrane yes indeed but not extracellular. (That the downside of HPA, I don’t think in fact considering the considerable bias it should even be consider having it’s own bucket in the Abs target assessment, but that is another matter of debate )
I could not check the Bucket #5, as it is “(GO CC) Targets with GO CC terms indicative for plasma membrane, extracellular region/matrix, or secretion - high confidence “ however I don’t know own to access such data directly, so could not argument.
Another example if you would like, PRKCA: same bucket highlighted (4-5-9), same problem with bucket 9, but bucket 4 is ‘worse’: uniport announce plasma membrane associated but against there is no distinguo between extra and intracellular (and the answer is: intra…). In term of Abs drug development/trackability that’s a huge difference.
Last example is HDAC8 (Histone deacetylase 8): this one take one point only, in bucket #5. I would love to understand why (as it’s obviously wrong) if you may pinpoint me to the right direction to understand the bucket 5 please
Thanks a lot for the discussion!