We de novo assembly our transcriptome using Trinity, then aligned and quantified using RSEM's Perl script
run_RSEM_align_n_estimate.pl supplied with Trinity. This resulted two results, say
RSEM.genes.results. We performed differential gene expression analysis using edgeR supplied with Trinity, using the gene-based
RSEM.genes.results rather than isoforms. Then a lot of DE genes were generated according to the instructions of Trinity here.
So, the gene-based DE genes contained a lot of isoforms. (such as tables in this page of Trinity)
MY QUESTION is: When we got these DE genes and want to find which GO categories or KEGG pathways were involved in these DE genes. Should we extract all isoforms of the DE genes then feed them to Blast2GO? Or any other approaches?
Any suggestions and criticism will be appreciated. Thanks!