ArticleBMC bioinformatics2009
Integrated analysis of DNA copy number and gene expression microarray data using gene sets.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Multiple Testing of Mix-and-Match Feature Sets in Multi-Omics.Statistics in medicine · 2026Article
- CiberAMP: AnBiology · 2022Article
- Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction.BMC cancer · 2021Article
- High prevalence of APOA1/C3/A4/A5 alterations in luminal breast cancers among young women in East Asia.NPJ breast cancer · 2021Article
- Review
- Imbalance between genomic gain and loss identifies high-risk neuroblastoma patients with worse outcomes.Neoplasia (New York, N.Y.) · 2021Article
- Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways.Entropy (Basel, Switzerland) · 2020Article
- Chemopreventive targeted treatment of head and neck precancer by Wee1 inhibition.Scientific reports · 2020Article
- In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer.International journal of molecular sciences · 2018Article
- Cancer Subtype Discovery Using Prognosis-Enhanced Neural Network Classifier in Multigenomic Data.Technology in cancer research & treatment · 2018Article
- SegCorr a statistical procedure for the detection of genomic regions of correlated expression.BMC bioinformatics · 2017Article
- iGC-an integrated analysis package of gene expression and copy number alteration.BMC bioinformatics · 2017Article
- Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse.Oncotarget · 2016Article
- Exocytosis of polyubiquitinated proteins in bortezomib-resistant leukemia cells: a role for MARCKS in acquired resistance to proteasome inhibitors.Oncotarget · 2016Article
- Nonlinear Joint Latent Variable Models and Integrative Tumor Subtype Discovery.Statistical analysis and data mining · 2016Article
- Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack.BMC bioinformatics · 2016Article
- An Integrated Approach for RNA-seq Data Normalization.Cancer informatics · 2016Article
- Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential.BMC systems biology · 2015Review
- Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA.Briefings in bioinformatics · 2015Article
- Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles.BioMed research international · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes.
resultsWe propose to analyse copy number and expression array data using gene sets, rather than individual genes. The proposed model is robust and sensitive. We re-analysed two publicly available datasets as illustration. These two independent breast cancer datasets yielded similar patterns of association between gene dosage and gene expression levels, in spite of different platforms having been used. Our comparisons show a clear advantage to using sets of genes' expressions to detect associations with long-spanning, low-amplitude copy number aberrations. In addition, our model allows for using additional explanatory variables and does not require mapping between copy number and expression probes.
conclusionWe developed a general and flexible tool for integration of multiple microarray data sets, and showed how the identification of genes whose expression is affected by copy number aberrations provides a powerful approach to prioritize putative targets for functional validation.
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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.