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Old 07-08-2015, 06:20 AM   #1
jack Ip
Junior Member
Location: HK

Join Date: Jul 2015
Posts: 2
Default How to fully use the list of DEGs in non model species?


I am a beginner of RNAseq study. I am working on the transcriptome of non model species, mussel and snail. In my first part of study, I have investigated the transcriptome of my target species. And then, 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.

Many thanks,
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