How to perform gene ontology analysis with list of upregulated and down regulated genes?

Question

[John]

Hi,

I have found ~3000 upregulated genes and ~3000 downregulated genes using RSEM & EBSeq.

Using this gene list, how can I perform a Gene ontology analysis in a best way. I would like to produce good diagrams. Please advise best data bases for GO and softwares for diagrams. My data has neural cell types.

I am a beginner, please help

[cpad0112]

6000 affected genes (up/down) may not be good number for GO analysis and DAGs from GO analysis will be huge. Did you use any cut off (FC, p, q values etc) in your analysis?

[John]

Hi, Thanks for your reply, yeah.. I fixed FDR= 0.05, then I had 6000 genes totally I segregated them by taking Fold change <1 and Fold change >1 to get up& down regulated genes. Is this okay?

p.s. providing FDR is to subset the data which has PPDE greater than or equal to 0.95.

Answer 1

[arta]

You can use topGo or GOstats. Once you get results, you can plot results using ggplot2. Or if you would like to do pathway enrichments, you can use Pathview.

There are online tools as well such as Gorilla which outputs as diagrams as well as raw output.

[John]

thank you, I will check them!

Answer 2

[taoi2]

I recommend you to visit //toppgene.cchmc.org .

[John]

Sure, Thanks ............!