Help using BiNGO with Escherichia Coli

[Sammy Pontrelli]

I did an online tutorial for BiNGO and it worked fine (for yeast), but I can't get E.coli to work. 

I have a list of genes that I want to put into BiNGO and have them grouped by gene type/association. 

I downloaded the file gene_association.ecocyc and set that to be the annotation file in BiNGO. 

When I put my gene list in, it says "Some category labels in the annotation file are not defined in the ontology.... For now they will be ignored" . So I press OK.

There are around 400 genes that I am imputing, but only around 30 of them show up in the list that's generated in BiNGO.

What am I doing wrong? Am I misunderstanding something?

Thanks! 

[piet molenaar]

Hi Sammy,

Mostly this is due to different ids in the shared name column.

Can you send me your network?

Cheers,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626