GOstats for non model organism

Question

[najibveto]

Hello everyone

I have a set of genes and I blast them using Blast2GO, now I want to use GOstats to do GO enrichment analysis. Which format should I export the file from blast2GO?

Because I export them as GAF v.2 but didn't show evidence or gene_id.

[najibveto]

HELLO

IT GAVE A TABLE LIKE THIS ONE:

!Generated by Blast2GO
!Note: This is a beta function of Blast2GO
!Date: 20151119
!gaf-version: 2.0
B2G    gi|345500363|dbj|AB618555.1|    gi|345500363|dbj|AB618555.1|    GO:0016021    GO_REF:nd    ND         C    AB618555.1    NA    NA    taxon:0    20151119    B2G
B2G    gi|345500363|dbj|AB618555.1|    gi|345500363|dbj|AB618555.1|    GO:0015377    GO_REF:nd    ND         F    AB618555.1    NA    NA    taxon:0    20151119    B2G
B2G    gi|345500363|dbj|AB618555.1|    gi|345500363|dbj|AB618555.1|    GO:0006811    GO_REF:nd    ND         P    AB618555.1    NA    NA    taxon:0    20151119    B2G
B2G    gi|345500363|dbj|AB618555.1|    gi|345500363|dbj|AB618555.1|    GO:0055085    GO_REF:nd    ND         P    AB618555.1    NA    NA    taxon:0    20151119    B2G

[seta]

It sounds that GO enrichment analysis can be done using blast2go, did you try it?

Answer 1

[Michael]

There should be a gene or transcript id in the GAF file, possibly show an example. Evidence code is IEA for all automatic annotations.

Answer 2

[sgoetz123]

If you want to perform Enrichment Analysis with GOstat, rather than Blast2GO, you can export the functional annotation (GO terms) you generated with Blast2GO in GOstat format and upload them with "Upload Custom GO Annotations" at http://gostat.wehi.edu.au/cgi-bin/customGOindexes.pl.

You can export the GOstat format from Blast2GO directly from the menu File -> Export -> Export Annotations -> Export Annotations (.annot). You can simply choose GOstat format or define your own format with the "custom format" option.

You might also want to try the Fisher's Exact Test in Blast2GO. Just like in GOstat you have to define your test set and have your datasets annotations loaded. Blast2GO offers FDR multiple testing correction, one- or two-sided tests, enriched GO graphs visualization, reduce enricht terms to most specifics, bar-charts, text export, etc.