ArticleMolecular & cellular proteomics : MCP2018
Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction.
Article in Molecular & cellular proteomics : MCP, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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Who cites it
7 citing papers in PubMed, 11 citations in OpenAlex.
- Comparison of the stage-dependent mitochondrial changes in response to pressure overload between the diseased right and left ventricle in the rat.Basic research in cardiology · 2024Article
- Higher-order modular regulation of the human proteome.Molecular systems biology · 2023Article
- Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (Non-coding RNA · 2022Article
- Review
- Understanding genomics and the immune environment of penile cancer to improve therapy.Nature reviews. Urology · 2020Review
- Article
- Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition.Molecular & cellular proteomics : MCP · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Genes are often coexpressed with their genomic neighbors, even if these are functionally unrelated. For small expression changes driven by genetic variation within the same cell type, non-functional mRNA coexpression is not propagated to the protein level. However, it is unclear if protein levels are also buffered against any non-functional mRNA coexpression accompanying large, regulated changes in the gene expression program, such as those occurring during cell differentiation. Here, we address this question by analyzing mRNA and protein expression changes for housekeeping genes across 20 mouse tissues. We find that a large proportion of mRNA coexpression is indeed non-functional and does not lead to coexpressed proteins. Chromosomal proximity of genes explains a proportion of this nonfunctional mRNA coexpression. However, the main driver of non-functional mRNA coexpression across mouse tissues is epigenetic similarity. Both factors together provide an explanation for why monitoring protein coexpression outperforms mRNA coexpression data in gene function prediction. Furthermore, this suggests that housekeeping genes translocating during evolution within genomic subcompartments might maintain their broad expression pattern.
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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.