ArticlePloS one2014
High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 40 citations in OpenAlex.
- Foundation models and deep learning for cancer drug response prediction: a framework for data, metrics, and validation.Briefings in bioinformatics · 2026Review
- Article
- CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations.Cancer research · 2023Article
- Identification of ATP1B1, a key copy number driver gene in diffuse large B-cell lymphoma and potential target for drugs.Annals of translational medicine · 2022Article
- A Validation Framework for Somatic Copy Number Detection in Targeted Sequencing Panels.The Journal of molecular diagnostics : JMD · 2022Article
- Landscape of allele-specific transcription factor binding in the human genome.Nature communications · 2021Article
- Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains.Nature communications · 2021Article
- Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products.Molecular oncology · 2021Article
- CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics.Nucleic acids research · 2021Article
- RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB.Cancer research · 2019Article
- An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines.Cancer research · 2019Review
- A pan-cancer study of the transcriptional regulation of uricogenesis in human tumours: pathological and pharmacological correlates.Bioscience reports · 2018Article
- Overcoming Resistance to DNA-Targeted Agents by Epigenetic Activation of Schlafen 11 (Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
- Synthesis and Biological Evaluation of New Madecassic Acid Derivatives Targeting ERK Cascade Signaling.Frontiers in chemistry · 2018Article
- Targeting DNA repair and replication stress in the treatment of ovarian cancer.International journal of clinical oncology · 2017Review
- The NCI-60 Methylome and Its Integration into CellMiner.Cancer research · 2017Article
- microRNAs and Acute Myeloid Leukemia Chemoresistance: A Mechanistic Overview.Frontiers in oncology · 2017Review
- Phosphorylated fraction of H2AX as a measurement for DNA damage in cancer cells and potential applications of a novel assay.PloS one · 2017Article
- Public data and open source tools for multi-assay genomic investigation of disease.Briefings in bioinformatics · 2016Review
- 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
5 authors at 4 institutions in 1 country.
Funding
Abstract
Array-based comparative genomic hybridization (aCGH) is a powerful technique for detecting gene copy number variation. It is generally considered to be robust and convenient since it measures DNA rather than RNA. In the current study, we combine copy number estimates from four different platforms (Agilent 44 K, NimbleGen 385 K, Affymetrix 500 K and Illumina Human1Mv1_C) to compute a reliable, high-resolution, easy to understand output for the measure of copy number changes in the 60 cancer cells of the NCI-DTP (the NCI-60). We then relate the results to gene expression. We explain how to access that database using our CellMiner web-tool and provide an example of the ease of comparison with transcript expression, whole exome sequencing, microRNA expression and response to 20,000 drugs and other chemical compounds. We then demonstrate how the data can be analyzed integratively with transcript expression data for the whole genome (26,065 genes). Comparison of copy number and expression levels shows an overall medium high correlation (median r = 0.247), with significantly higher correlations (median r = 0.408) for the known tumor suppressor genes. That observation is consistent with the hypothesis that gene loss is an important mechanism for tumor suppressor inactivation. An integrated analysis of concurrent DNA copy number and gene expression change is presented. Limiting attention to focal DNA gains or losses, we identify and reveal novel candidate tumor suppressors with matching alterations in transcript level.
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.