TissueEnrich - Tissue-specific gene enrichment analysis
The TissueEnrich package is used to calculate enrichment
of tissue-specific genes in a set of input genes. For example,
the user can input the most highly expressed genes from RNA-Seq
data, or gene co-expression modules to determine which
tissue-specific genes are enriched in those datasets.
Tissue-specific genes were defined by processing RNA-Seq data
from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx
(Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using
the algorithm from the HPA (Uhlén et al. 2015).The
hypergeometric test is being used to determine if the
tissue-specific genes are enriched among the input genes. Along
with tissue-specific gene enrichment, the TissueEnrich package
can also be used to define tissue-specific genes from
expression datasets provided by the user, which can then be
used to calculate tissue-specific gene enrichments.