ArticlePloS one2010
A network of cancer genes with co-occurring and anti-co-occurring mutations.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies.Molecular biotechnology · 2025Review
- A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations.Cell reports methods · 2024Article
- Nucleotide-based genetic networks: Methods and applications.Journal of biosciences · 2022Article
- Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma.Cold Spring Harbor molecular case studies · 2020Article
- DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden.PloS one · 2020Article
- Aberrantly high expression of the CUB and zona pellucida-like domain-containing protein 1 (CUZD1) in mammary epithelium leads to breast tumorigenesis.The Journal of biological chemistry · 2018Article
- Percolation transition of cooperative mutational effects in colorectal tumorigenesis.Nature communications · 2017Article
- Genomic analysis reveals frequent TRAF7 mutations in intraneural perineuriomas.Annals of neurology · 2017Article
- Cooperative genomic alteration network reveals molecular classification across 12 major cancer types.Nucleic acids research · 2017Article
- Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis.Oncotarget · 2016Article
- Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas.Nature genetics · 2016Article
- Biological Networks for Cancer Candidate Biomarkers Discovery.Cancer informatics · 2016Review
- Fast randomization of large genomic datasets while preserving alteration counts.Bioinformatics (Oxford, England) · 2014Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO.Science (New York, N.Y.) · 2013Article
- Voting-based cancer module identification by combining topological and data-driven properties.PloS one · 2013Article
- An analysis of substitution, deletion and insertion mutations in cancer genes.Nucleic acids research · 2012Article
- Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling.Frontiers in physiology · 2012Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Certain cancer genes contribute to tumorigenesis in a manner of either co-occurring or mutually exclusive (anti-co-occurring) mutations; however, the global picture of when, where and how these functional interactions occur remains unclear. This study presents a systems biology approach for this purpose. After applying this method to cancer gene mutation data generated from large-scale and whole genome sequencing of cancer samples, a network of cancer genes with co-occurring and anti-co-occurring mutations was constructed. Analysis of this network revealed that genes with co-occurring mutations prefer direct signaling transductions and that the interaction relations among cancer genes in the network are related with their functional similarity. It was also revealed that genes with co-occurring mutations tend to have similar mutation frequencies, whereas genes with anti-co-occurring mutations tend to have different mutation frequencies. Moreover, genes with more exons tend to have more co-occurring mutations with other genes, and genes having lower local coherent network structures tend to have higher mutation frequency. The network showed two complementary modules that have distinct functions and have different roles in tumorigenesis. This study presented a framework for the analysis of cancer genome sequencing outputs. The presented data and uncovered patterns are helpful for understanding the contribution of gene mutations to tumorigenesis and valuable in the identification of key biomarkers and drug targets for cancer.
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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.