RNA-seq gene expression between 2 cells types

Question

[ilyco]

Hi,

This is probably a silly question. I have RNA-seq data which corresponds to two cell types (2 replicates each).

Is there any consecrated way of finding which genes are expressed in both cell types as opposed to just the ones which are differentially expressed between the two cell types? (I have used the R Bioconductor DESeq2 pipeline for differential expression).

Thank you in advance!

[Phil S.]

I guess you can just use the genenames of the expressed ones in the first cell line to filter for the the second and report if they also have expression....

[rinaladist]

Hi, do you have a best way out yet for your problem? because I have the same silly question. I hope you can share with me the experience you had.

Thank you

Answer 1

[Luyi Tian]

I think there is no universal solution for this question. If you define the genes which have zero expression value as non-expressive, this question can be solved by just filter out the zero expressed genes. But in most cases the genes with small expression value could be noise. It depend on your sequencing tech and read depth.

you could read this article for more information:

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.