Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
1
0
Entering edit mode
leo_CD • 0
@leo_cd-17901
Last seen 5.1 years ago

Dear all,

I've a dataset of around 150 RNAseq from different patients and after performing quantification of transcript with Salmon. I'm interested in founding immunologic signature correlate with the expression of a specific gene isoform.

So I've retrieve the abundance (TPM) of that isoform among my 150 RNAseq and I'm using this as a continuous phenotype into GSEA.

Then I've performed gene summarization of my Salmon output using tximport and I'm using this as my expression table (TPM) for GSEA.

Since I've only one replicate for each phenotype I'm trying to found the best method to rank my genes. I've tried to performed a DESeq2 analysis of my dataset using again the abundance of that isoform as my condition and taking the wald score to rank my genes.

Overall I'm not confident I'm taking the best approach to found those signature correlate to the expression of that specific isoform and seeking for your help.

Best Regards,

Leo

deseq2 gsea tpm rnaseq salmon rna seq • 1.2k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 24 minutes ago
United States

My approach would probably be to compute the vst() of the dataset and then rank transcripts/genes by correlation to the transcript of interests.

ADD COMMENT

Login before adding your answer.

Traffic: 648 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6