Hello OpenTargets team again!
Just wanted to get an idea of what baseline expression (-1) on the human protein atlas for tissues means - does it mean that either the protein wasn’t detected or that it was not measured?
Also, please can we have a bit more info on the unit of expression used?
Many thanks
Hi!
We ingest our data directly from the Human Protein Atlas (Downloadable data - The Human Protein Atlas) and you can see a description of how they record expression in their FAQs under “How is the protein expression scored?” (Help - The Human Protein Atlas) .
When we ingest the data we take their values (not detected, low, medium, high) and map them to a numeric representation (0, 1, 2, 3) in order to display them in the platform widgets. Because of the way we store the data internally (protein baseline data is paired with RNA baseline data from the same gene and tissue/cell type) there are instances where one gene-tissue/cell type combination has RNA but no protein or vice versa. When you see -1 it is an Open Targets placeholder which means that data was not available in the HPA for that particular gene-tissue/cel type combination.
Hope that’s helpful,
Tobi
Indeed very useful,
Many thanks again team OT!