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I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of a cluster is the genes which are highly expressed (high counts) in the cells of that cluster. Let's say cluster A has 200 genes. My questions are:

Can I say that those 200 genes are marker genes for cluster A? How to determine which marker genes are positive marker genes and which are negative marker genes?

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In scRNA-seq clusters are groups of cells with similar transcriptomes typically defined by graph based methods (e.g. leiden, louvain) or more rarely k-means.

Marker genes could be genes that are known to be highly expressed (or better specifically expressed) in a particular cell type (e.g. CD3E is a T cell marker). You can visualize the expression of such marker genes on a UMAP/t-SNE without doing any clustering.

When talking about positive and negative markers, I assume the reference is too differentially expressed genes between different clusters. Typically simple differential expression tests are conducted (e.g. Wilcoxon rank sum) between each individual cluster and the other collective clusters. The upregulated differentially expressed genes could be considered positive markers and downregulated genes negative markers.

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  • $\begingroup$ What do you mean upregulated and and downregulated? I do not understand about them? Also, the 200 genes I mentioned, basically we cannot say those genes are marker genes for cluster A? $\endgroup$
    – MK Huda
    Jun 9, 2021 at 19:37
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A positive marker is a gene that is overexpressed in a cell population compared to other populations.

A negative marker is a gene that is underexpressed in a cell population compared to other populations.

I think the Seurat FindMarkers function has an option to output Log2FoldChange as well as the marker names. In this case the positive markers will have a positive Log2FoldChange, and the negative markers will have a negative Log2FoldChange.

Both positive and negative markers can be used to describe a cell population. In the research that I've done in the past, there's a particular type of dendritic cell that is only distinguished from another dendritic cell type based on cell surface markers that it doesn't have; our own name for these DCs was "Triple negative".

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