Question: Predict tissue origin by protein expression
1
gravatar for Vova Naumov
4.9 years ago by
Vova Naumov220
Russia, Moscow
Vova Naumov220 wrote:

Hi! I got a list of proteins found in human sample (urine).

It looks like a list of ipi identifers (can be converted to gene symbols or ensemble id's)

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?

mass-spectrometry protein • 1.2k views
ADD COMMENTlink modified 4.9 years ago by Laurent1.6k • written 4.9 years ago by Vova Naumov220
1
gravatar for mikhail.shugay
4.9 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

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)

ADD COMMENTlink written 4.9 years ago by mikhail.shugay3.3k
1
gravatar for Laurent
4.9 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

The recently published Human Proteome Map (HPM) portal 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

ADD COMMENTlink written 4.9 years ago by Laurent1.6k
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