Comprehensive Comparison of Large-Scale Tissue Expression Datasets

PeerJ. 2015 Jun 30;3:e1054. doi: 10.7717/peerj.1054. eCollection 2015.

Abstract

For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface.

Keywords: Databases; Immunohistochemistry; Mass spectrometry; Microarrays; RNA sequencing; Tissue expression; Tissue-specificity.

Grant support

This work was in part supported by the Novo Nordisk Foundation [NNF14CC0001], by the National Institutes of Health [U54 CA189205-01], and by CSIRO’s OCE Science Leader program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.