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Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
Published on: July 29, 2022
Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation
Gabriel Ostlund1, Erik L L Sonnhammer
1Stockholm Bioinformatics Centre, Science for Life Laboratory, Solna, Sweden. Gabriel.Ostlund@sbc.su.se
Gene
|February 14, 2012
Summary
Messenger RNA (mRNA) and protein levels often differ. This study identifies subsets where mRNA expression strongly correlates with protein abundance, improving biological predictions.
Area of Science:
- Molecular Biology
- Genomics
- Proteomics
Background:
- Messenger RNA (mRNA) expression is frequently used as a surrogate for protein expression.
- The direct correlation between mRNA and protein levels is not fully understood.
- Investigating gene pair coexpression at mRNA and protein levels is crucial.
Purpose of the Study:
- To examine the correlation between mRNA and protein expression and coexpression.
- To identify subsets with high mRNA-protein coherence.
- To understand the relationship between mRNA and protein abundance.
Main Methods:
- Analysis of mRNA and protein expression data.
- Calculation of Spearman correlation for expression and coexpression.
- Application of a quality measure to identify high-coherence subsets.
- Restriction of analysis to functionally coupled genes.
Main Results:
- Initial low correlations were observed between mRNA and protein for both expression (0.12) and coexpression (0.06).
- High-quality subsets achieved higher correlations: 0.31 for expression and 0.34 for coexpression.
- A significant correlation of 0.49 was reached for coexpression in functionally coupled genes.
Conclusions:
- The relationship between mRNA and protein levels is complex and varies significantly.
- A methodology was developed to identify subsets with strong mRNA-protein correlation.
- This approach enhances the reliability of using mRNA levels as a proxy for protein abundance in specific biological contexts.
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