Genes Under Go Category

Question

[upendrakumar.devisetty]

I have done GO enrichment analysis using GOSeq and got the lits of GO terms associated with my DE genes. Then i used REVIGO to visualize the list of GO terms and found some interesting clustering. Now my question is how do i know how many genes are there in that particular cluster and also whether those genes are up or down regulated?

Thanks Upendra

Answer 1

[Sukhi Singh]

Each gene must display multiple GO id's. So, you have to make a table, where column1 is GO id's , column 2 is p-val, column 3 you have to generate, which will say Gene Name (so this repeat for the gene name which has multiple GO id's) and column 4 with the FPKM/RPKM value. So, you Revigo control(input) file will look like this

% GOterm        enrichment_P-value    Gene    FPKM
GO:0022402      1.74E-15    Elf1    2.3
GO:0007049      5.43E-1    Elf1    3.5
GO:0010447      2.74E-8    Nanog    -1.3
GO:0000027      2.43E-3    Nanog    -3.5

Now, in the scatter plot, just sort the axis by userValue_3 and you should see clusters which are based on your expression value.

Cheers