Hi! I got a list of proteins found in human sample (urine).
It looks like a list of IPI identifiers (can be converted to gene symbols or ensemble IDs)
Example:
IPI Accession Number
IPI00745872
IPI00022426
IPI00513767
IPI00022420 (+2)
IPI00022429 (+1)
IPI00024284 (+1)
Do you know any web services that can predict origin tissue from list of detected proteins? Something like GO enrichment, but tissue/cell line oriented?
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Vova Naumov
2 answers
Although not best practice, try DAVID (http://david.abcc.ncifcrf.gov/), it provides some info on tissue source to have a glance.
In your case (using IPI_ID) and selecting UP_TISSUE annotation one can get:
Liver (5/5)
Plasma (3/5)
Urine (2/5)
Fetal liver(2/5)
The recently published portal Human Proteome Map (HPM) has protein expression data from "multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues." Similar work has been made available in the ProteomicsDB resource.
Hope this helps.
Laurent
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