Question: Deferentially expressed genes
gravatar for mahfuz.290066
15 months ago by
kagoshima University Japan
mahfuz.29006610 wrote:

Hello, I am a new guy in the RNA seq study. I found 989 up regulated and 1009 down regulated genes from the NGS data after sorting out on the basis of FDR, FC and P value. But I don't know how can I do further downstream analysis like GO or pathway or any other (maybe I don't know). And also how can I represent my data in my article. I will be very happy if anybody gives me a full guideline. thank you.

next-gen • 534 views
ADD COMMENTlink modified 15 months ago by EagleEye5.3k • written 15 months ago by mahfuz.29006610

Did you read any other articles with RNAseq data already? They can give you an idea of how to present your data.

You don't tell very much about your own study (such as which organism, which tool you've used for differential analysis), so it's hard to suggest how to do downstream analysis.

I usually go for GO analysis with goseq and use gogadget if I have a lot of enriched GO terms. But there are 100s of other GO or pathway tools available.

ADD REPLYlink written 15 months ago by b.nota3.9k

Very very thanks for your reply. i worked with melanoma in human. I got my differentially expressed genes by analyzing through CLC workbench Actually, i read some of the papers. But i did not get a clear idea what should i do with the GO terms or how can i find a melanoma triggering pathways. I got my GO terms by using panther. is there any reference recommended paper???

ADD REPLYlink written 15 months ago by mahfuz.29006610

CLC bio has a Blast2GO plug-in available, but you may need to purchase it. This plug-in should come with KO Pathway Analysis too. In the output for the GO and KO analyses each term has a P-value associated with it based on the gene enrichment. I have used/published the negative log of the p-value of the enrichment and displayed it using a heatmap, as my study was a timecourse experiment. If you have groups you can perhaps use a similar set-up.

ADD REPLYlink written 15 months ago by theobroma221.1k
gravatar for EagleEye
15 months ago by
EagleEye5.3k wrote:

Hi, try GeneSCF.

Also check these posts,

C: Gene ontology comparsion between up- and down-regulated genes

A: gene ontology visualisation

ADD COMMENTlink modified 15 months ago • written 15 months ago by EagleEye5.3k
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