Question: GO term analysis
0
gravatar for manasa22.reddy
2.3 years ago by
United States
manasa22.reddy40 wrote:

enter image description herewe have done micro array analysis for 3 conditions,we have separated all the deg for all three conditions and we have performed gene set enrichment analysis for deg genes for all three conditions.Now i have 3 files related to 3 conditions with following columns(gene set enrichment analysis)

GO Term Universe set
No. of genes
No. of input genes
No. of overlapping genes
p-value Gene IDs
now I have to make some analysis,like what are the GO process that are represented or affected commonly at all 3 conditions.I need some pictorial representation as below,enter image description here

ADD COMMENTlink modified 2.3 years ago by Benn6.6k • written 2.3 years ago by manasa22.reddy40
0
gravatar for Benn
2.3 years ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

Why not use a venn diagram, like suggested in your previous post? finding overlapping go terms

Or use Cytoscape enrichment map. However, with enrichment map you can only compare two conditions in one graph. Comparing 3 conditions in one enrichment map would be too much to understand for the human brain I guess?

ADD COMMENTlink written 2.3 years ago by Benn6.6k

yeah iam working on venn diagrams ,but i also need to plot a graph which is somewhat like the image i have linked in post.

ADD REPLYlink written 2.3 years ago by manasa22.reddy40

I don't see an image...

ADD REPLYlink written 2.3 years ago by Benn6.6k

figure no 6 in follwing article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148957/

ADD REPLYlink written 2.3 years ago by manasa22.reddy40

That looks like a bar plot/chart to me. You can make bar plots in R or even in excel/graphpad, if you don't know how to code.

ADD REPLYlink written 2.3 years ago by Benn6.6k
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