Gene expression analysis between three different tissues
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Margot • 0
Last seen 8 months ago
United States


I have the transcriptome of three different cell types (e.g. macrophages, neurons and T cells) and I am looking to evaluate tissue specific gene expression across these three cell types. For example, mpeg1 is a macrophage specific gene and therefore I see its expression enriched in macrophages and not in the other cells when I compare the normalized reads expression. Is this comparison of normalized reads count enough to compare/claim tissue specific gene expression? I have more than 3 biological replicates per condition and sequencing depth of more than 50 M reads per sample. I have been just plotting normalized reads from DESeq2 and just doing a 2-way anova with multiple comparison test (tukey) to do statistics.

I understand that since DE analysis is a pair-wise comparison only, is there a better way to go about this analysis? I am looking to plot the results and get an statistical test without having to do DGE for all the comparisons possible (3 cell types against each other).

Thanks in advance, Margot

DESeq2 RNAseq • 318 views
Entering edit mode
Last seen 1 day ago
United States

There is a comprehensive vignette for DESeq2 that explains how to analyze your data. It should answer all your questions.

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