Question: Genes Under Go Category
gravatar for upendrakumar.devisetty
6.5 years ago by
United States
upendrakumar.devisetty350 wrote:

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

go clustering • 2.4k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 6.5 years ago by upendrakumar.devisetty350
gravatar for Sukhdeep Singh
6.5 years ago by
Sukhdeep Singh9.7k
Sukhdeep Singh9.7k wrote:

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.


ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Sukhdeep Singh9.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 655 users visited in the last hour