Proteome profiling?

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Kambiz
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Proteome profiling?

Postby Kambiz » Sun Apr 15, 2012 8:52 pm

Dear All

I have a first generation proteomics question. I have collected 2000 proteins from human seminal plasma for a paper. The information you will get out: Molecular function, cellular localization, biological function using DAVID or Panther software; KEGG pathway, Chromosome distribution, pI distribution, MW distribution. Are there other information which can be extracted from a list of proteins? Can we make a theoretical protein-protein interaction map using STRING software? I will be very happy if you can suggest other information which can be extracted out of protein list I have.

Thank you all,
Kambiz
Kambiz Gilany, Ph.D.
Assistant Professor
Avicenna Research Institute (ARI)

Evin, Tehran, Iran
P.O. Box: 19615-1177

Tel: +98-21-22432020 Ext. 427
Fax: +98 21 22432021

Website: http://www.avicenna.ac.ir/index.php/en

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Doug
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Postby Doug » Sun Apr 15, 2012 11:19 pm

You could use STRING but I would recommend Cytoscape. It is a little confusing at first but well worth the effort. It doesn't take too long to figure it out. You can view only the proteins you identified and all of their protein interactions. You can modify the plots a lot. For example you can change node sizes to reflect number of identified peptides or change the color of the nodes to reflect protein quantitation.

You might want to look at what kinases or transcription factors are present. That can give you an idea of what is going on with your sample.

Also, check out www.hprd.org/ and uniprot. They each have a lot of protein info. You can look for enrichment of proteins with certain domains (e.g. zinc finger) or proteins with certain modifiable residues. For example, maybe your list of proteins is enriched or depleted for proteins with known glycosylation sites.

Kambiz
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Postby Kambiz » Mon Apr 16, 2012 12:41 am

Thanks.

I have collected the uniprot accession numbers. However, where can I find the software for enrichment of certain domains, at the expasy site?
Kambiz Gilany, Ph.D.
Assistant Professor
Avicenna Research Institute (ARI)

Evin, Tehran, Iran
P.O. Box: 19615-1177

Tel: +98-21-22432020 Ext. 427
Fax: +98 21 22432021

Website: http://www.avicenna.ac.ir/index.php/en

aky
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Postby aky » Mon Apr 16, 2012 2:52 am

For Cytoscape, you can try APID2NET plugin in cytoscape to pull out known interactions for the proteins you enter(uniprot accessions will do). Then you can color the proteins found in your study. There are other plugins in Cytoscape like PiNGO for GO enrichment.

I found the tool STRAP(http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/) very easier to use with just a list of uniprot accessions and it does the rest pretty hassle-free. here is the link to the paper

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Doug
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Postby Doug » Mon Apr 16, 2012 7:43 am

Kambiz,

Unfortunately, I don't know of a tool to do these enrichments. You would just need to do a fisher's exact test for each attribute. This can be done in R.


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