Protein IDs Imported to EGAN

[燕 张]

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
completed IPI (International Protein Index) IDs .I'm wondering which
mapping file and "background" I should choose.

Any helps will be highly appreciated.

[ucsf egan]

Greetings!

Thanks for posting this question.

Unfortunately IPI to Entrez mapping files are not part of the pre-
collated set available in EGAN. But do not despair, there are some
good solutions available.

1) Use the ID converter at BioMart (http://central.biomart.org/
converter/#!/ID_converter/gene_ensembl_config_2) to convert your IPI
IDs into something else (UniProt might be the most lossless - but
there are a wide array of options including Entrez Gene itself). A
disclosure - I haven't actually used that tool yet, but it seems
awesome.

2) You could create your own IPI to Entrez Gene mapping file. The
mapping file format is tab-delimited text with 3+ columns:

IPI ID
blank column
Entrez Gene ID

You can include additional Entrez Gene ID columns if there exist more
genes for a given IPI ID.

Please post again should you have any more comments/questions.

Good luck!

Jesse