Cited by 1,248RNA Research and SplicingRNA and protein synthesis mechanismsGene Regulatory Network Analysis

Global signatures of protein and mRNA expression levels

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de Sousa Abreu, Raquel, Penalva, Luiz O, Marcotte, Edward M, Vogel, Christine·2009·Molecular BioSystems

Abstract

Cellular states are determined by differential expression of the cell’s proteins. The relationship between protein and mRNA expression levels informs about the combined outcomes of translation and protein degradation which are, in addition to transcription and mRNA stability, essential contributors to gene expression regulation. This review summarizes the state of knowledge about large-scale measurements of absolute protein and mRNA expression levels, and the degree of correlation between the two parameters. We summarize the information that can be derived from comparison of protein and mRNA expression levels and discuss how corresponding sequence characteristics suggest modes of regulation.

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Crossref · 10.1039/b908315d

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  • The correlation between proteomes and corresponding transcriptomes was only 0.4 to 0.45, capturing important differences between transcriptome and proteome.

    “As the correlation between the proteomes and the corresponding transcriptomes was only 0.4 to 0.45,our analysis captured important differences between transcriptome and proteome30,31 (Fig. 2c).”

    From Cell type- and brain region-resolved mouse brain proteome (2015) · cites this paper as [30]

    The section ‘Steady-state concentrations of protein molecules per mRNA and their correlates’ (page not provided) reports that several measurements have R² around 0.4 and that much of the variation in protein levels is not explained by mRNA levels. It does not give 0.4–0.45 as a general correlation coefficient: that figure is approximately a squared Pearson correlation, and the reported values vary across organisms. The citing authors’ statement about what their own analysis captured is their inference, not a finding attributed to this source. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • The use of high-resolution MS and RNA-Seq may account for the higher correlations between transcriptomes and proteomes observed here than in previous studies.

    “The use of high-resolution MS and RNA-Seq may account for the fact that higher correlations between transcriptomes and proteomes are observed here than in previous studies”

    From Deep proteome and transcriptome mapping of a human cancer cell line (2011) · cites this paper as de Sousa Abreu et al, 2009

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Research works printed but not linked: 4

  1. [24]Ralston A Nat. Educ 2008 1 1 http://www.nature.com/scitable/topicpage/Simultaneous-Gene-Transcription-and-Translation-in-Bacteria-1025.
  2. [40]Vijay-Kumar S Bugg CE Wilkinson KD Vierstra RD Hatfield PM Cook WJ J. Biol. Chem 1987 262 13 6396 6399 3032965
  3. [157]Seigel GM Hackam AS Ganguly A Mandell LM Gonzalez-Fernandez F Mol. Vision 2007 13 823 832 PMC2768758 17615543
  4. [163]Kondoh N Shuda M Tanaka K Wakatsuki T Hada A Yamamoto M Anticancer Res 2001 21 4A 2429 2433 11724303

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Authors
de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M., & Vogel, C.
Affiliations
  • Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio a , TX, USA
  • The University of Texas at San Antonio Health Science Center (US)
  • The University of Texas at Austin (US)
Corresponding author
Vogel, Christine
Venue
Molecular BioSystems
Published
2009-10-01
Volume
5
Issue
12
Pages
1512-1526
ISSN
  • 1742-2051 (ISSN-L)
  • 1742-206X
OpenAlex
W2056710301
Cited by
1,248
References
187
Citations by year
2026: 32 · 2025: 58 · 2024: 76 · 2023: 99 · 2022: 108 · 2021: 91 · 2020: 99 · 2019: 104 · 2018: 93 · 2017: 85 · 2016: 78 · 2015: 85 · 2014: 85 · 2013: 60 · 2012: 43
FWCI
2.42
Type
journal article
Language
en
Open access
Locations
  • Molecular BioSystems (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Cancer Research Institute
  • National Institute of General Medical Sciences (R01GM076536)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
protein abundance, mRNA levels, mRNA-protein correlation, gene expression regulation, translation (biology), protein degradation, mRNA stability, large-scale proteomics
MeSH terms
Escherichia coli, Humans, Proteins, RNA, Messenger, Protein Biosynthesis, Yeasts, Computational Biology, Ubiquitination

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