Import file to EGAN

[Hosup Lee]

Hi,

I am a beginner to use EGAN.

I have questions about a file for importing to EGAN.

My file is excel file from proteomics containing protein list and
uniprot ID only.

I am wondering how I should modify it to import to EGAN.

Any helps will be highly appreciated.

[ucsf egan]

Hello!

Thanks for writing.  I'm happy to help you use EGAN for proteomics (and other) data.  For starters, I suggest that you read some of the documentation files available from the Docs page on the EGAN website (http://akt.ucsf.edu/EGAN/documentation.php)

If you have a file that just contains UniProt IDs, you can simply launch EGAN and click the gray G button in the bottom of the Network View and choose to specify your own gene set.  Paste your gene list into the dialog and choose the UniProt/SwissProt mapping file from the pulldown menu.

There is one thing you will probably want to do beforehand, however - in the Launch EGAN Wizard, go to section 5) Gene Nodes and for the "Background" option, choose the UniProt/SwissProt file from the pulldown menu.  This will ensure that the only genes loaded into EGAN are genes that have UniProt/SwissProt IDs and will therefore provide the most accurate enrichment statistics.

If you have statistics/confidence/p-values for your protein IDs, let me know.  In that case you will want to define an experiment file and specify that file in the Launch EGAN Wizard (you will still want to specify the "Background" option as described above).

Good luck and please let me know if I can clarify any of those explanations or answer any more questions.

Regards,

Jesse 

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