ArticlePloS one2011
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis 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, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- A multigene support vector machine predictor for metastasis of cutaneous melanoma.Molecular medicine reports · 2018Pooled it
- labelSeg: segment annotation for tumor copy number alteration profiles.Briefings in bioinformatics · 2024Article
- EphA3 deficiency in the hypothalamus promotes high-fat diet-induced obesity in mice.Journal of biomedical research · 2022Article
- Potential Biomarker Identification by RNA-Seq Analysis in Antibiotic-Related Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS): A Pilot Study.Toxicological sciences : an official journal of the Society of Toxicology · 2022Article
- Construction and validation of a prognostic risk model of angiogenesis factors in skin cutaneous melanoma.Aging · 2022Article
- Review
- T cell-induced CSF1 promotes melanoma resistance to PD1 blockade.Science translational medicine · 2018Article
- Article
- MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cells.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Melanoma metastasis: new concepts and evolving paradigms.Oncogene · 2014Review
- The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome.Genome research · 2013Article
- Systems biology approaches for discovering biomarkers for traumatic brain injury.Journal of neurotrauma · 2013Review
- RNA-Seq and human complex diseases: recent accomplishments and future perspectives.European journal of human genetics : EJHG · 2013Review
- Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays.Nature nanotechnology · 2013Article
- Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
- WLS inhibits melanoma cell proliferation through the β-catenin signalling pathway and induces spontaneous metastasis.EMBO molecular medicine · 2012Article
- Human mitochondrial DNA: roles of inherited and somatic mutations.Nature reviews. Genetics · 2012Review
- Loss of fragile histidine triad and amplification of 1p36.22 and 11p15.5 in primary gastric adenocarcinomas.World journal of gastroenterology · 2012Article
- SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer.BMC cancer · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 8 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer genomes frequently contain somatic copy number alterations (SCNA) that can significantly perturb the expression level of affected genes and thus disrupt pathways controlling normal growth. In melanoma, many studies have focussed on the copy number and gene expression levels of the BRAF, PTEN and MITF genes, but little has been done to identify new genes using these parameters at the genome-wide scale. Using karyotyping, SNP and CGH arrays, and RNA-seq, we have identified SCNA affecting gene expression ('SCNA-genes') in seven human metastatic melanoma cell lines. We showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. Since few of these alterations were recurrent across our samples, we used a protein network-guided approach to determine whether any pathways were enriched in SCNA-genes in one or more samples. From this unbiased genome-wide analysis, we identified 28 significantly enriched pathway modules. Comparison with two large, independent melanoma SCNA datasets showed less than 10% overlap at the individual gene level, but network-guided analysis revealed 66% shared pathways, including all but three of the pathways identified in our data. Frequently altered pathways included WNT, cadherin signalling, angiogenesis and melanogenesis. Additionally, our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma. Our study demonstrates the utility of network-guided approaches, for both large and small datasets, to identify pathways recurrently perturbed in 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.