Human pathways in animal models: possibilities and limitations. Issue 4 (1st February 2021)

• Record Type: Journal Article
• Authors: Doncheva, Nadezhda T; Palasca, Oana; Yarani, Reza; Litman, Thomas; Anthon, Christian; Groenen, Martien A M; Stadler, Peter F; Pociot, Flemming; Jensen, Lars J; Gorodkin, Jan
• Is Part Of: Nucleic acids research. Volume 49:Issue 4(2021)
• Page Start: 1859
• Page End: 1871
• Publication Date: 2021-02-01
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab012
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Animal models are crucial for advancing our knowledge about the molecular pathways involved in human diseases. However, it remains unclear to what extent tissue expression of pathways in healthy individuals is conserved between species. In addition, organism-specific information on pathways in animal models is often lacking. Within these limitations, we explore the possibilities that arise from publicly available data for the animal models mouse, rat, and pig. We approximate the animal pathways activity by integrating the human counterparts of curated pathways with tissue expression data from the models. Specifically, we compare whether the animal orthologs of the human genes are expressed in the same tissue. This is complicated by the lower coverage and worse quality of data in rat and pig as compared to mouse. Despite that, from 203 human KEGG pathways and the seven tissues with best experimental coverage, we identify 95 distinct pathways, for which the tissue expression in one animal model agrees better with human than the others. Our systematic pathway-tissue comparison between human and three animal modes points to specific similarities with human and to distinct differences among the animal models, thereby suggesting the most suitable organism for modeling a human pathway or tissue. Graphical Abstract: