ArticlePLoS genetics2010
Proteomic changes resulting from gene copy number variations in cancer cells.
Article in PLoS genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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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
75 citing papers in PubMed, 143 citations in OpenAlex.
- Peripheral complement C4 protein in schizophrenia: Association with gene copy number and immune cell subtypes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transcriptomic and proteomic ramifications of segmental amplification inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quantitative proteomics analysis of triple-negative breast cancers.NPJ precision oncology · 2025Article
- Understanding the molecular diversity of synapses.Nature reviews. Neuroscience · 2025Review
- Article
- Post-transcriptional regulation of Dufour's gland reproductive signals in bumble bees.BMC genomics · 2024Article
- Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model.Cell genomics · 2024Article
- Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model.bioRxiv : the preprint server for biology · 2024Article
- Article
- Functional Impact of Protein-RNA Variation in Clinical Cancer Analyses.Molecular & cellular proteomics : MCP · 2023Article
- Higher-order modular regulation of the human proteome.Molecular systems biology · 2023Article
- Proteomic Markers for Mechanobiological Properties of Metastatic Cancer Cells.International journal of molecular sciences · 2023Review
- High-Frequency (30 MHz-6 GHz) Breast Tissue Characterization Stabilized by Suction Force for Intraoperative Tumor Margin Assessment.Diagnostics (Basel, Switzerland) · 2023Article
- Recent advances in the field of single-cell proteomics.Translational oncology · 2023Article
- Recent revelations and future directions using single-cell technologies in chronic lymphocytic leukemia.Frontiers in oncology · 2023Review
- High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities.Cancer research · 2022Article
- Extensive protein dosage compensation in aneuploid human cancers.Genome research · 2022Article
- Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics.PLoS biology · 2022Article
- Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures.Molecules (Basel, Switzerland) · 2022Article
- Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease.The FEBS journal · 2022Review
15 more citing papers are in PubMed but not listed here.
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 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Along the transformation process, cells accumulate DNA aberrations, including mutations, translocations, amplifications, and deletions. Despite numerous studies, the overall effects of amplifications and deletions on the end point of gene expression--the level of proteins--is generally unknown. Here we use large-scale and high-resolution proteomics combined with gene copy number analysis to investigate in a global manner to what extent these genomic changes have a proteomic output and therefore the ability to affect cellular transformation. We accurately measure expression levels of 6,735 proteins and directly compare them to the gene copy number. We find that the average effect of these alterations on the protein expression is only a few percent. Nevertheless, by using a novel algorithm, we find the combined impact that many of these regional chromosomal aberrations have at the protein level. We show that proteins encoded by amplified oncogenes are often overexpressed, while adjacent amplified genes, which presumably do not promote growth and survival, are attenuated. Furthermore, regulation of biological processes and molecular complexes is independent of general copy number changes. By connecting the primary genome alteration to their proteomic consequences, this approach helps to interpret the data from large-scale cancer genomics efforts.
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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.