ArticleJournal of proteome research2023
Integrated View of Baseline Protein Expression in Human Tissues.
Article in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.PLoS computational biology · 2024Pooled it
- Thermoreversible cell-derived extracellular matrix only hydrogel (CEOgel): Development, characterization, and applications.Materials today. Bio · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease.Integrative and comparative biology · 2025Review
- Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.Journal of proteome research · 2025Article
- Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging.eLife · 2025Article
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study.Scientific reports · 2024Article
- 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
- Toward an Integrated Machine Learning Model of a Proteomics Experiment.Journal of proteome research · 2023Review
- The ProteomeXchange consortium at 10 years: 2023 update.Nucleic acids research · 2023Article
- Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.PLoS computational biology · 2022Article
- Expression Atlas update: gene and protein expression in multiple species.Nucleic acids research · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.