Co-Expression of All Genes with a Single Gene (Spatial Transcriptomics)
Entering edit mode
12 days ago
ivingan • 0

Hi all,

I am struggle to figure out a solution to a (seemingly) simple. Using Seurat, I would like to find which genes are most highly expressed with individual marker genes spatial transcriptomic dataset.

I have an integrated dataset from mouse brains with the samples coming from 2 separate conditions (stim and ctrl). I also have a list neuronal activity marker genes (e.g., X, Y, Z). I would like to find which genes are correlated in their expression with each of these marker genes between the two conditions. In other words, which genes are co-expressed with X in the stim and in the ctrl condition, with Y in the stim and ctrl condition, and so on.

I don't have any sample code at this moment, I am quite a novice at coding and bioinformatic data analysis.

Closest I've gotten to finding a similar user issue is this [inconclusive and closed thread1 from 5 years ago.

Any help would be useful. Thank you!

Transcriptomics Correlation Seurat scRNA-seq Spatial-Transcriptomics • 180 views
Entering edit mode

If you are truly interested in examining co-expression then perhaps trying WGCNA on pseudobulk counts data generated from each cluster and sample may be the route to go


Login before adding your answer.

Traffic: 1016 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6