cell annotation question - rnaseq
Suppose I had results from an RNA-seq differential expression analysis on two populations: diseased and non diseased tissue. I IDed X genes for which there was an increase in expression within the diseased tissue group. How would I go about determining which specific cell type it would be based on the expression profile of these X genes?
1 answer
Obvious approach - check if genes with differential expression are markers (example - CD4 == T-lymphocyte). another approach is search for cell expression profile database (for example http://www.ebi.ac.uk/gxa/baseline/experiments) and compare profiles of your experiment with database, look for tools that compare expression profiles.
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