ArticleMolecular & cellular proteomics : MCP2017
Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.
Article in Molecular & cellular proteomics : MCP, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 2 syntheses or guidelines pooled it, 176 citations in OpenAlex.
- Preclinical Analysis of Bone Marrow-Derived Stem Cell Therapy Response and Transcriptomic Overlap Analysis in a Severe Alcoholic Hepatitis Mouse Model.Gut and liver · 2026Pooled it
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers.Cell reports. Medicine · 2025Trial
- Scalable clinical proteomics from DNA/RNA extraction flowthroughs enables integrated proteogenomic profiling from a single cancer biopsy.Clinical proteomics · 2026Article
- Multi-omic analyses of the same sample using metabolomics, lipidomics, proteomics, phosphoproteomics, and glycoproteomics.Chemical communications (Cambridge, England) · 2026Article
- How physiology solves the gene-centric impasse.Experimental physiology · 2026Review
- Early innate immune signatures correlate with Ad26.COV2.S vaccine durability and protective efficacy.bioRxiv : the preprint server for biology · 2026Article
- The proteomic landscape and temporal dynamics of human and mouse gastruloid development.Nature cell biology · 2026Article
- A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.Nature biotechnology · 2026Article
- SR2P: an efficient stacking method to predict protein abundance from gene expression in spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- Article
- Integrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity.Nature communications · 2025Article
- Cholesterol Regulates Airway Epithelial Cell Differentiation by Inhibiting p53 Nuclear Translocation.International journal of molecular sciences · 2025Article
- Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome.NPJ biofilms and microbiomes · 2025Article
- From morphology to single-cell molecules: high-resolution 3D histology in biomedicine.Molecular cancer · 2025Review
- Multiomics Identifies Potential Molecular Profiles Associated With Outcomes After BRAF-Targeted Therapy in Patients With BRAF V600E-Mutated Advanced Solid Tumors.JCO precision oncology · 2025Article
- Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics.Nature cancer · 2025Article
- A novel method for endometrial cancer patient stratification considering ARID1A protein expression and activity with effective use of multi-omics data.Computational and structural biotechnology journal · 2025Article
- Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics.International journal of molecular sciences · 2024Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 11 institutions in 1 country.
Funding
Abstract
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies.
Indexed as
Identifiers
What OpenQuestion holds
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.