N=3610, annotation:(type:signal) AND reviewed:yes AND organism:"Homo sapiens (Human) [9606]"
I'm looking for an up-to-date resource on human cell-surface proteins - such as a database of all known human cell-surface markers, or a program that predicts trans-membrane domains based on protein name or AA sequence.
Ideally this resource would also be cross-linked to mass-spec or expression data by cell type.
The application is oncology cell therapy target identification.
Thanks
-Ben
2 answers
An old problem with no "clean" solutions but some approximations you might find useful. I am also intepreting some of your "or"s as "and"s
- Selecting "(annotation:(type:signal) AND organism:"Homo sapiens [9606]") AND reviewed:yes" in UniProt gives 3,467, substituting keyword:"Cell membrane" gives 2871. The latter may be cleaner in Swiss-Prot than TrEMBL
- You can explore intersects with the four mass-spec cross references (but PRIDE seems over-occupied) or the transcript expression sources but I dont know how to link these with cell types, and its likely to be noisy if you do (try BIOMART just for the intersects)
- For oncology targets in general you should look at https://cansar.icr.ac.uk/
- This is the type of data you realy want http://www.ncbi.nlm.nih.gov/pubmed/24555563 but I'm not sure how far off a selectable UniProt x-ref might be
hmmer and blast will give you protein domains: http://hmmer.janelia.org
You could also check out http://www.immgen.org/, this would only work if you're interested in immune system cells however. This would be a potential source of cell-specific expression.
Several groups are working towards this, e.g. Cell ontology is trying to integrate GO and protein ontology, but like cdsouthan said, there's not a good solution just yet.
You could also use either a list of targets (gene/protein expression) or use GEO to pull gene expression data for relevant cell or tissue types and then filter the lists using gene ontology.
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