TISSUES 2.0: an integrative web resource on mammalian tissue expression

TLDR

Physiological and molecular similarities between model organisms and humans enable translation of findings, aiding the understanding of biological processes in normal and disease states. Researchers need resources that compile multi‑organism tissue expression data to identify similarities and differences at the molecular level. The database assigns comparable confidence scores to gene–tissue associations across multiple evidence sources using a scoring scheme, and is available through a web interface and the STRING Cytoscape app. Analysis of dataset agreement revealed that the quality of datasets, rather than technology or organism, primarily determines concordance across and within species. Database URL: http://tissues.jensenlab.org/.

Abstract

Physiological and molecular similarities between organisms make it possible to translate findings from simpler experimental systems—model organisms—into more complex ones, such as human. This translation facilitates the understanding of biological processes under normal or disease conditions. Researchers aiming to identify the similarities and differences between organisms at the molecular level need resources collecting multi-organism tissue expression data. We have developed a database of gene–tissue associations in human, mouse, rat and pig by integrating multiple sources of evidence: transcriptomics covering all four species and proteomics (human only), manually curated and mined from the scientific literature. Through a scoring scheme, these associations are made comparable across all sources of evidence and across organisms. Furthermore, the scoring produces a confidence score assigned to each of the associations. The TISSUES database (version 2.0) is publicly accessible through a user-friendly web interface and as part of the STRING app for Cytoscape. In addition, we analyzed the agreement between datasets, across and within organisms, and identified that the agreement is mainly affected by the quality of the datasets rather than by the technologies used or organisms compared. Database URL: http://tissues.jensenlab.org/