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Can you extract genes for cluster signatures in CIBERSORTx

Hi all, just have a question about running CIBERSORTx.

So let's say that we used LM22 as the signature matrix, is it possible to extract the genes which define a particular cell type's signature in CIBERSORTx?

From another post: "CIBERSORTx performs a feature selection and therefore typically does not use all genes in the signature matrix."

So I understand that some genes may not be used in the signature matrix, but is there a way to determine which genes were used to define a cell type, and extract these named genes as a list?

I want to see the expression of genes defining a particular cell type, and so I need to know what the signature genes are in this cluster. (I'm aware that this isn't strictly necessary, but I've been asked if this is possible).

Thanks for any assistance offered.

cibersortx deconvolution spatial-deconvolution single-cell rna-seq
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written by smac97 • smac97

1 answer

Okay I think by doing the "Impute cell expression" step I've managed to achieve what I was trying to do.

Basically, if you do the "Impute cell expression" step and use the same data as in the "Impute cell fractions" step, then you get an expression matrix with the genes for the transcriptome for each cell type.

If you extract the names of these genes after ordering in decreasing order, for the cell type you're interested in, then you can get the original expression values of each of these genes in your sample groups and use them to make plots.

Hope that makes sense, I'll leave this up as a possible solution in case anyone else comes across this.

If anyone has a direct method to my original question, I'd still love to hear it.

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written by smac97 • smac97

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