ArticleNucleic acids research2017
Cooperative genomic alteration network reveals molecular classification across 12 major cancer types.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers.PLoS computational biology · 2024Article
- Pediatric Pan-Central Nervous System Tumor Methylome Analyses Reveal Immune-Related LncRNAs.Frontiers in immunology · 2022Article
- Transcriptomic heterogeneity of driver gene mutations reveals novel mutual exclusivity and improves exploration of functional associations.Cancer medicine · 2021Article
- Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization.Experimental & molecular medicine · 2021Review
- Identification of novel prognostic biomarkers by integrating multi-omics data in gastric cancer.BMC cancer · 2021Article
- AtMAD: Arabidopsis thaliana multi-omics association database.Nucleic acids research · 2021Article
- Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma.Frontiers in genetics · 2021Article
- Genome-wide methylation patterns predict clinical benefit of immunotherapy in lung cancer.Clinical epigenetics · 2020Article
- DNMIVD: DNA methylation interactive visualization database.Nucleic acids research · 2020Article
- Article
- Co-occurrence and Mutual Exclusivity Analysis of DNA Methylation Reveals Distinct Subtypes in Multiple Cancers.Frontiers in cell and developmental biology · 2020Article
- Identification of a Six-lncRNA Signature With Prognostic Value for Breast Cancer Patients.Frontiers in genetics · 2020Article
- Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data.Journal of translational medicine · 2019Article
- Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis.Epigenetics · 2019Article
- A pan-cancer atlas of cancer hallmark-associated candidate driver lncRNAs.Molecular oncology · 2018Article
- SEECancer: a resource for somatic events in evolution of cancer genome.Nucleic acids research · 2018Article
- Article
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11 authors.
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Abstract
The accumulation of somatic genomic alterations that enables cells to gradually acquire growth advantage contributes to tumor development. This has the important implication of the widespread existence of cooperative genomic alterations in the accumulation process. Here, we proposed a computational method HCOC that simultaneously consider genetic context and downstream functional effects on cancer hallmarks to uncover somatic cooperative events in human cancers. Applying our method to 12 TCGA cancer types, we totally identified 1199 cooperative events with high heterogeneity across human cancers, and then constructed a pan-cancer cooperative alteration network. These cooperative events are associated with genomic alterations of some high-confident cancer drivers, and can trigger the dysfunction of hallmark associated pathways in a co-defect way rather than single alterations. We found that these cooperative events can be used to produce a prognostic classification that can provide complementary information with tissue-of-origin. In a further case study of glioblastoma, using 23 cooperative events identified, we stratified patients into molecularly relevant subtypes with a prognostic significance independent of the Glioma-CpG Island Methylator Phenotype (GCIMP). In summary, our method can be effectively used to discover cancer-driving cooperative events that can be valuable clinical markers for patient stratification.
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