I am a beginner of RNAseq study. I am working on the transcriptome of non model species, mussel and snail. Now I have done exposure experiments and RNAseq to determine the toxicity mechanism.
Now I have performed DESeq2 and EBSeq, I have a list of DEGs. As the molecular information of my target species is limited, most of the assembled unigene/transcript don't have any functional annotation, and BLAST hit to NCBI nr. Say only 20% DEGs have their BLAST hit to public databases.
I would like to ask how can I fully use the DGE data to reveal the toxic effect and mechanism? How can I deal with the 80% DEGs without annotation?
I also performed GAGE using the whole transcriptome at background. again the unannotated may cause the few or no enriched pathway/GO returned from GAGE ><"".
Please kindly give me some suggestions of data analysis and how to utilize the result data.