Marker genes of Transcriptomic explorer

Technical
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1

Hi,

I’m trying to identify marker genes for each cell cluster in “multiple cortical areas” snRNA data sets,

It would be great if you could help me with the following questions:

  1. What was the algorithm for selecting this list of “marker genes” in Transcriptomics Explorer :: Allen Brain Atlas: Cell Types?

  2. Does the “marker genes” provided on the y-axis include all markers of the cell-specific clusters?

2.1. If yes, then are the marker genes for each cell-specific cluster those genes with non-zero expression values in the heat-map?

2.2. And if the y-axis does not include all the cell-specific marker genes, then is there a way you could suggest for extracting a complete set of marker genes? such as thresholding or filtering the trimmed means of gene expression in each cell-specific cluster?

  1. Why are the cell-specific marker genes in multiple cortical areas dataset -provided by Cytosplore- different from those provided by the transcriptomic explorer?

  2. How can I extract the cell-specific gene sets (rather than marker genes) for each cluster?

I appreciate your help,
Bests,

2

Hi @nmeo,

The genes presented by default in the Transcriptomics explorer manually curated based on the intersection of computational marker gene selection (using various methods) and literature search for biologically meaningful genes. These are by no means a complete set of marker genes, and there are many different ways to define them and it is hard to say which method is best. Here is an example review article. We often use scrattch.hicat or Seurat for our analysis pipelines, including marker gene definition, while Cytosplore uses a method that is less computationally intensive. I don’t understand what you mean by “cell-specific gene sets (rather than marker genes)”, but feel free to clarify if I didn’t already address it.

Best,
Jeremy