How to run BiNGO with non-model species

[Manoj Kumar]

Hi,

I am trying to run BiNGO for GO enrichment. I have prepared a list of input data. Since I am working on non-model species, I could not find the list of "select of organism/annotation" at BiNGO. Therefore, I tried to download a gaf file of Arabidopsis from http://current.geneontology.org/products/pages/downloads.html. However, Cytoscape do not support the file. Please let me know how to prepare annotation file for the non-model species for GO enrichment.

Input file format:

SE_09258   =0008152
SE_09257   =0003824
SE_29668   =0050896
SE_13599   =0008152
SE_13596   =0009987

[Scooter Morris]

You can check out the BiNGO manual here.  Note that the first line of the file should contain something like:

(species=Saccharomyces cerevisiae)(type=Biological Process)(curator=GO)

so BiNGO can figure out the species and the GO branch this annotation file applies to.

-- scooter

[Manoj Kumar]

Hi,

Thank you for your reply. I am working on non-model species. I prepared a following custom annotation file and downloaded an ontology (.obo) as reference file from GO database. As I noticed that the ontology file for BiNGO should be in specific categories format (e.g. isa:, partof: parts). Please let me know how to update the .obo file, which downloaded from GO database. Does, BiNGO work for non-model species.

(species=Sequoiadendron giganteum)(type=Biological Process)(curator=GO)
SE_1200 = 0003673
SE_0215 = 0046087
SE_0321 = 0046088
SE_7892 = 0046089

[Scooter Morris]

That should work fine.  According to the manual, you should be able to download the entire .obo file and then select just the BIological Process branch from the "Select namespace" menu.

-- scooter