motif finding

[Hosup Lee]

Hi,

Thanks for your help for previous questions.

I am now wondering if EGAN can search and find proteins containing a
specific domain (like PDZ domain) from a set of protein list.

There is programs like motifscan that is for finding motif in one
protein.

What I want is to list all proteins containing specific domain from a
set of proteins (or genes) of proteomics.

Thanks again.

[ucsf egan]

Yes, you can do exactly that.  Just make sure that the Conserved Domain (CDD) Association Node data set is being loaded into EGAN - check the Association Data section of the Launch EGAN Wizard.

Then all you need to do in EGAN is to show the Conserved Domain Node Table, search it for your domain of interest (e.g. PDZ), and then hit the green sun button in the row for the Conserved Domain you are interested in.  That button will show that domain as an association node and all genes that are annotated with that domain.

It's a great way to characterize and perform a functional analysis of a domain, since you can then compare that gene set against experiments and also use that gene set to perform enrichment analyses.

Please post if you have any more questions!

Best,

Jesse

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