some questions to do GO enrichment analysis

Question

[lkianmehr]

Hello,

I have a list of MOUSE genes (from RNA-seq analysis) include 800 up and 7150 down regulated from DESeq2 . I did GO enrichment analysis for up-regulated genes by DAVID, and got 3 list of functional groups (84 GO term for Molecular function, 57 GO term for cellular component and 163 Go term for biological process). now I have number of questions that would appreciate if help me to get answer

1- most of these GO term in each group are subset of each other. how can I put them in one group and how they should be seleced based on each functional groups ?

2- can I trust to DAVID results for GO enrichment analysis to put them in the article or is better to try with the other one like GOseq which is specificlly for RNA-seq (cause I am new in R, it's a bit difficult)?

3- because of limited option of DAVID to accept up to 3000 genes, can I do GO analysis just for Up-regulated genes, if not what is your suggestion?

thanks in advane for any help

Answer 1

[EagleEye]

Hello,

1) Use REVIGO (input the results from your analysis, GOID and P-values/FDR) to visualize your GO results in broad categories.

2) Since DAVID is recently updated after a long wait. I am sure that the information is now updated. If you have doubts, you can also verify the results with GeneSCF (it access realtime data from Gene Ontology repository).

3) If you have more than 3000 genes try GeneSCF, it will be slow but more reliable.