ArticleMolecular systems biology2022
The impact of genomic variation on protein phosphorylation states and regulatory networks.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 32 citations in OpenAlex.
- A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness.Science (New York, N.Y.) · 2025Article
- Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.Nature communications · 2025Article
- Analysis of Limited Proteolysis-Coupled Mass Spectrometry Data.Molecular & cellular proteomics : MCP · 2025Article
- Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents.Nature genetics · 2025Article
- AI-empowered perturbation proteomics for complex biological systems.Cell genomics · 2024Article
- A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects.bioRxiv : the preprint server for biology · 2024Article
- Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast.International journal of molecular sciences · 2024Review
- Article
- The cAMP-PKA signalling crosstalks with CWI and HOG-MAPK pathways in yeast cell response to osmotic and thermal stress.Microbial cell (Graz, Austria) · 2024Review
- Genetic effects on molecular network states explain complex traits.Molecular systems biology · 2023Article
- Multi-Omics Studies in Historically Excluded Populations: The Road to Equity.Clinical pharmacology and therapeutics · 2023Review
- The impact of genomic variation on protein phosphorylation states and regulatory networks.Molecular systems biology · 2022Article
- Arsenic perception and signaling: The yet unexplored world.Frontiers in plant science · 2022Review
Corrections and comments
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Authors and funding
14 authors at 7 institutions in 4 countries.
Funding
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well-defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
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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 Socratic graph.