ArticleBriefings in bioinformatics2012
Lessons from a decade of integrating cancer copy number alterations with gene expression profiles.
Article in Briefings in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 2 of them syntheses that pooled it.
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
27 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.PloS one · 2014Pooled it
- Hashimoto's thyroiditis influences tumor cell states and intratumoral microbiota in papillary thyroid carcinoma.iScience · 2026Article
- Multiple Testing of Mix-and-Match Feature Sets in Multi-Omics.Statistics in medicine · 2026Article
- Obscurin: A multitasking giant in the fight against cancer.Biochimica et biophysica acta. Reviews on cancer · 2021Review
- MVisAGe Identifies Concordant and Discordant Genomic Alterations of Driver Genes in Squamous Tumors.Cancer research · 2018Article
- Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes.Oncotarget · 2018Article
- Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data.Scientific reports · 2017Article
- iGC-an integrated analysis package of gene expression and copy number alteration.BMC bioinformatics · 2017Article
- FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change.Nucleic acids research · 2016Article
- Identifying candidate drivers of drug response in heterogeneous cancer by mining high throughput genomics data.BMC genomics · 2016Article
- Article
- Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack.BMC bioinformatics · 2016Article
- Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets.BMC genomics · 2015Article
- Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.Nature communications · 2015Article
- Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential.BMC systems biology · 2015Review
- An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer.Scientific reports · 2015Article
- Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours.Human genomics · 2015Article
- Transcriptome Analysis in Domesticated Species: Challenges and Strategies.Bioinformatics and biology insights · 2015Review
- Article
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.
Funding
Abstract
Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression profiles and somatic copy number alterations (CNA) information on the same patients identified using microarray platforms. In response, many algorithms and software packages are available for integrating these paired data. Surprisingly, there has been no serious attempt to review the currently available methodologies or the novel insights brought using them. In this work, we discuss the quantitative relationships observed between CNA and gene expression in multiple cancer types and biological milestones achieved using the available methodologies. We discuss the conceptual evolution of both, the step-wise and the joint data integration methodologies over the last decade. We conclude by providing suggestions for building efficient data integration methodologies and asking further biological questions.
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.