A benchmark of gene expression tissue-specificity metrics

Abstract

One of the major properties of genes is their expression pattern. Notably, genes are often classified as tissue specific or housekeeping. This property is of interest to molecular evolution as an explanatory factor of, e.g. evolutionary rate, as well as a functional feature which may in itself evolve. While many different methods of measuring tissue specificity have been proposed and used for such studies, there has been no comparison or benchmarking of these methods to our knowledge, and little justification of their use. In this study, we compare nine measures of tissue specificity. Most methods were established for ESTs and microarrays, and several were later adapted to RNA-seq. We analyse their capacity to distinguish gene categories, their robustness to the choice and number of tissues used and their capture of evolutionary conservation signal.

Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study

“…The resulting BAM files were then processed using StringTie for estimation of expression levels (Pertea et al, 2015), in which the transcripts per kilo base million (TPM) normalized method was employed. The TAU method proposed by Yanai et al (2005) was applied on the expression matrix to detect genes that were constitutively expressed or expressed in specific tissues (Kryuchkova & Robinson-Rechavi, 2015). Genes with TAU scores lower than 0.2 were defined as constitutively expressed genes while those with TAU scores higher than 0.99 were defined as tissue-specific genes.…”

Epigenomic profiling of primate LCLs reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

“…This value ranges from 0, for housekeeping genes, to 1, for tissue-specific genes (values above 0.8 are used to identify tissue-specific genes) 68 . Tissue-specificity indices were calculated for all genes included in the latest GTEx release 65 .…”