ArticlePLoS computational biology2022
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 18 citations in OpenAlex.
- Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.PLoS computational biology · 2024Pooled it
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- AI/ML-Assisted Detection ofInternational journal of molecular sciences · 2025Article
- An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.Proteomics · 2025Article
- Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.Journal of proteome research · 2025Article
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.Journal of proteome research · 2024Article
- EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.Nucleic acids research · 2024Review
- Expression Atlas update: insights from sequencing data at both bulk and single cell level.Nucleic acids research · 2024Article
- A systems approach reveals species differences in hepatic stress response capacity.Toxicological sciences : an official journal of the Society of Toxicology · 2023Article
- Integrated View of Baseline Protein Expression in Human Tissues.Journal of proteome research · 2023Article
- The ProteomeXchange consortium at 10 years: 2023 update.Nucleic acids research · 2023Article
- Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.Scientific data · 2022Article
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Authors and funding
11 authors at 2 institutions in 1 country.
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Abstract
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.
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