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