co-expression analysis from a scRNA-seq data

Question

[BenHu]

I have downloaded a public expression matrix for a scRNA-seq. Does anyone know how to perform Gene-Gene Co-expression, like this paper Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain. Best,

Answer 1

[Kevin Blighe]

Hey,

You can read the methods of the work that you cite, and, in that way, follow what the authors did. Go here and then go to STAR Methods.

The 2 sections within those methods that you will want to review are

• ICA based analysis and clustering
• Correlation analysis across cell populations

Kevin

[BenHu]

if I know how to do that, I wouldn't ask this question.

[Kevin Blighe]

Hello, which part, specifically, are you finding it difficult to follow? I took a closer look myself and can deduce the following rough steps to help you get started:

Step 1 - filtering

• Filter out cells with fewer than 400 expressed genes
• Filter include highly variable genes across all tissues (you can use your own metrics, if you wish)

Step 2 - ICA (independent component analysis)

• Convert highly variable gene matrices to Z-scores ("[The] selected genes were then centered and scaled across all cells")
• Perform ICA using fastICA package in R, configured to output the first 60 components, and performed separately on each tissue.

Step 3 - KNN clustering

Perform clustering on the 60 ICA components using the cluster implementation in Seurat. Basically, re-use Seurat's functions FindNeighbors() and FindClusters(). I use these in a function in a package that I'm currently developing, to give you an idea: https://github.com/kevinblighe/scToolkit/blob/master/R/clusKNN.R

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That should bring you up to the line "To identify finer substructure among these classes, classes with more than 200 cells were selected for subclustering", whereby they then commence a second round of ICA on a finer subset of genes, it seems.

Unfortunately, following bioinformatics methods can be a nightmare, because it is impossible to accurately write in English language the minute details that are required to comprise a comprehensive methodology.

[Kristoffer Vitting-Seerup]

You might also want to take a look at this article to get ideas for alternatives to pearson correlation.