Gene Ontology Analysis

Question

[arpa530]

Hello,

I am doing RNA-Seq analysis and found more than 500 significantly differentially expressed genes. Next, I have finished the gene ontology analysis by using the GOStats package in R. But in the output file, I couldn't see whether any "GO-terms" enriched or depleted. I have tried to find in the "GOstats" package but failed to do so.

I need your help regarding this issue.

Thanks,

[Ben]

Did not you obtain any GO terms? if so, you cany try other tools, such DAVID, goprofile.

Answer 1

[EagleEye]

Gene ontology comparsion between up- and down-regulated genes

Answer 2

[arpa530]

Hi, Thanks for your response. Unfortunately, it didn't say clearly about the GOstats package. I only need to know which "GO-terms" are enriched or depleted. But I couldn't find no such thing in the "GOstats" vignette.

[EagleEye]

If you have information from GOstats, such as P-value, number of genes from your list involved in each term. You can rank the terms with p-values and number of genes. The terms which comes in top rank are the enriched terms for your set of genes. The link I provided in earlier post is the way of presenting your enriched terms.

If GOstats does not have more information, you can try other tools. But you should be careful in choosing your tools since many of the tools are having oudated resource/database. I can recommend you to use GeneSCF.