Diffrential expression analysis of human vs. mouse
0
0
Entering edit mode
Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 17 days ago
Germany

Hi,

I was wondering if it is possible to run DESeq ( or for that reason any other tool for differential expression analysis) to identify  significant differences between two organisms (for our research human and mouse).

I know that we have two different sets of genes, but what if we can overcome this problem by giving the genes a neutral ID based on a common variable and take only the genes which are present in both data sets.

We have several RNA-Seq data sets with multiple samples (=replica) from different brain layers  in mouse and human.  We are doing a DE analysis (DESeq2) to find out which genes are significantly changing between the different brain layers. But we are also interested in changes in the same layer but between the two organisms.

How does it looks like from the statistical point of view?

any ideas?

thanks,

Assa

deseq2 cuffdiff differential gene expression • 1.5k views
ADD COMMENT
0
Entering edit mode

You'll need to tell us your experimental design.  In general, what you are describing is not usually possible to do directly.

ADD REPLY
0
Entering edit mode

I have edited the question and hope it is a bit clearer now.

I was thinking that since DESeq2 needs "only" a count table, why not just take the human samples from layer A and compare them with the samples of layer A from the mouse.

For common probe names I was thinking about taking the gene symbol as a unified ID and than only take the genes which are in both data sets (not in the RNA-Seq results, but from the complete data set, e.g. gtf file).

ADD REPLY

Login before adding your answer.

Traffic: 866 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