ArticleMolecular bioSystems2011
Relating protein adduction to gene expression changes: a systems approach.
Article in Molecular bioSystems, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.
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- Histone Adduction and Its Functional Impact on Epigenetics.Chemical research in toxicology · 2017Article
- Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.Molecular & cellular proteomics : MCP · 2017Article
- Covalent Modification of CDK2 by 4-Hydroxynonenal as a Mechanism of Inhibition of Cell Cycle Progression.Chemical research in toxicology · 2016Article
- 4-Hydroxy-nonenal-A Bioactive Lipid Peroxidation Product.Biomolecules · 2015Review
- Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.PLoS computational biology · 2015Article
- Quantitative chemoproteomics for site-specific analysis of protein alkylation by 4-hydroxy-2-nonenal in cells.Analytical chemistry · 2015Article
- Alkylation damage by lipid electrophiles targets functional protein systems.Molecular & cellular proteomics : MCP · 2014Article
- RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal.Molecular bioSystems · 2013Article
- Peptidyl-prolyl cis/trans-isomerase A1 (Pin1) is a target for modification by lipid electrophiles.Chemical research in toxicology · 2013Article
- Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis.PloS one · 2013Article
- SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets.Integrative biology : quantitative biosciences from nano to macro · 2012Article
- Protein modification by oxidized phospholipids and hydrolytically released lipid electrophiles: Investigating cellular responses.Biochimica et biophysica acta · 2012Review
- Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCα invasive signaling axis.Science signaling · 2012Article
- Inflammation and cancer: chemical approaches to mechanisms, imaging, and treatment.The Journal of organic chemistry · 2012Article
- Cell signalling by reactive lipid species: new concepts and molecular mechanisms.The Biochemical journal · 2012Review
- A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Modification of proteins by reactive electrophiles such as the 4-hydroxy-2-nonenal (HNE) plays a critical role in oxidant-associated human diseases. However, little is known about protein adduction and the mechanism by which protein damage elicits adaptive effects and toxicity. We developed a systems approach for relating protein adduction to gene expression changes through the integration of protein adduction, gene expression, protein-DNA interaction, and protein-protein interaction data. Using a random walk strategy, we expanded a list of responsive transcription factors inferred from gene expression studies to upstream signaling networks, which in turn allowed overlaying protein adduction data on the network for the prediction of stress sensors and their associated regulatory mechanisms. We demonstrated the general applicability of transcription factor-based signaling network inference using 103 known pathways. Applying our workflow on gene expression and protein adduction data from HNE-treatment not only rediscovered known mechanisms of electrophile stress but also generated novel hypotheses regarding protein damage sensors. Although developed for analyzing protein adduction data, the framework can be easily adapted for phosphoproteomics and other types of protein modification data.
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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 OpenQuestion graph.