Question: How to perform gene ontology analysis with list of upregulated and down regulated genes?
0
gravatar for John
2.3 years ago by
John210
United States
John210 wrote:

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

rna-seq R • 1.6k views
ADD COMMENTlink modified 2.3 years ago by taoi210 • written 2.3 years ago by John210
1

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?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by cpad011213k

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by John210
2
gravatar for arta
2.3 years ago by
arta580
Sweden
arta580 wrote:

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.

ADD COMMENTlink written 2.3 years ago by arta580

thank you, I will check them!

ADD REPLYlink written 2.3 years ago by John210
1
gravatar for taoi2
2.3 years ago by
taoi210
taoi210 wrote:

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

ADD COMMENTlink written 2.3 years ago by taoi210

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

ADD REPLYlink written 2.3 years ago by John210
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