ArticleBMC medical genetics2019
Copy number variation is highly correlated with differential gene expression: a pan-cancer study.
Article in BMC medical genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
180 citing papers in PubMed, 342 citations in OpenAlex.
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Exploring copy number alterations (CNAs) to gain new insight into SCLC heterogeneity.Molecular biology reports · 2026Review
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- Dissecting cancer in a non-mammalian model: genomic insights from lemon frost geckos.BMC biology · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Buffering of gene dosage response curves for human complex traits.Cell genomics · 2026Article
- Integration of GWAS and eQTL analysis reveals regulatory CNVs for fatty acid traits in cattle.iScience · 2026Article
- FGD3 as a prognostic and immunological biomarker: a pan-cancer analysis of its role in tumor progression and the immune landscape.Cancer cell international · 2026Article
- Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda.Molecular biology and evolution · 2026Article
- Phenotypic and genotypic characterization of single circulating tumor cells in the follow-up of high-grade serous ovarian cancer.Molecular oncology · 2026Article
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- Genomic, Clinical, and Spatial Predictors of Durable Response to BRAF/MEK Inhibition inbioRxiv : the preprint server for biology · 2026Article
- GEMap: A comprehensive gene essentiality map for drug discovery.Acta pharmaceutica Sinica. B · 2026Article
- Analysis of CGG repeat numbers in the FMR1 gene among women of childbearing age in Northeast Sichuan.BMC genomic data · 2026Article
- Generation and characterization of a HEK293 cell line optimized for recombinant adeno-associated virus production.Biotechnology reports (Amsterdam, Netherlands) · 2026Article
- Extending differential gene expression testing to handle genome aneuploidy in cancer.PLoS computational biology · 2026Article
- Septins buffer actomyosin forces to protect the nucleus from genotoxic mechanical stress.bioRxiv : the preprint server for biology · 2026Article
- Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models.Nature genetics · 2026Article
- Multi-omics driven computational framework for cancer molecular subtype classification.Scientific reports · 2025Article
120 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
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types.
methodsIn this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship.
resultsOur results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases.
conclusionsThis study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
Indexed as
Identifiers
What OpenQuestion holds
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.