Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science, [2005]-

Proteins*/metabolism ; Proteomics*; Animals ; Brain/metabolism ; Mice ; Rats

The increasingly large amount of proteomics data in the public domain enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.
Competing Interests: The authors have declared that no competing interests exist.

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United Kingdom WT_ Wellcome Trust; 208391/Z/17/Z United Kingdom WT_ Wellcome Trust; BB/T019670/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/T019557/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council

0 (Proteins)

Date Created: 20220617 Date Completed: 20220704 Latest Revision: 20240831

20240831

PMC9246241

10.1371/journal.pcbi.1010174

35714157