Ranking genes by a conservation score which includes enhancers
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9 weeks ago

Hi all,

Is there a method or package (R or python) which can compute a conservation score which includes enhancers (proximal and or distal) between mouse and human genes? I am training a model on single cell rnaseq data using mouse gene expression data to run it on human gene expression to detect a rare cell type. I am considering filtering genes out by their conservations score. What would be a good exclusion criteria using conservation?

scrna-seq enhancers conservation • 213 views
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Rather than doing this why not deriving a gene signature from these rare cells and scoring your human samples with it, for example using UCell. Then see whether it credibly exists, and validate using FACS.

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Our lab only uses publicly available data we don't do experiments ourselves so FACS is out of the question. Also the training data was collected with FACS. Calling it a cell type is not entirely accurate its a transient cell state that we know is in human cells as well, but its a question of if the genes involved are the same.

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Thanks for the suggestion about UCell I will try this out.

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