Hi,

I've been reproducing steps in the manual here - https://bioconductor.org/packages/release/bioc/vignettes/TissueEnrich/inst/doc/TissueEnrich.html.

I supplied 147 differentially expressed genes to the GeneSet function. Out of 147 - 82 genes are unmapped, and the number of unique genes across all the tissues is 29, which means that 36 genes are not present in the output object. Does it mean they are not specific (enriched/enhanced) and are expressed in all the tissues or how exactly should I interpret this?

Thanks in advance.

Hi,

In TissueEnrich, we are dividing the genes into six different groups which are specified in our paper (http://doi.org/10.1093/bioinformatics/bty890). The 36 genes could be in the other three non-tissue specific gene groups (Not Expressed, Expressed In all, or Mixed). You can also confirm that by checking the tissue-specificity of a particular gene by using "Tissue-Specific Genes" tab in our web tool (http://tissueenrich.gdcb.iastate.edu/).

Regards, Ashish Jain