Predict tissue origin by protein expression

Question

[Vova Naumov]

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?

Answer 1

[mikhail.shugay]

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)

Answer 2

[Laurent]

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