ArticlePloS one2013
Pathway-based analysis using genome-wide association data from a Korean non-small cell lung cancer study.
Article in PloS one, 2013. 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.
- Significance ofInternational journal of medical sciences · 2024Article
- Genomic regions associated with pseudorabies virus infection status in naturally infected feral swine (Frontiers in genetics · 2023Article
- Genetic Variants ofFrontiers in oncology · 2021Article
- Observational
- Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP.Mammalian genome : official journal of the International Mammalian Genome Society · 2018Article
- A Decade of GWAS Results in Lung Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2018Review
- Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Identification of Prognostic Genes and Pathways in Lung Adenocarcinoma Using a Bayesian Approach.Cancer informatics · 2017Article
- Genetic variant in DNA repair gene GTF2H4 is associated with lung cancer risk: a large-scale analysis of six published GWAS datasets in the TRICL consortium.Carcinogenesis · 2016Article
- Complex roles of NRAGE on tumor.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2016Review
- NRAGE promotes the malignant phenotype of hepatocellular carcinoma.Oncology letters · 2016Article
- Pathway, in silico and tissue-specific expression quantitative analyses of oesophageal squamous cell carcinoma genome-wide association studies data.International journal of epidemiology · 2016Article
- Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions.Human molecular genetics · 2015Article
- Polycyclic aromatic hydrocarbons: from metabolism to lung cancer.Toxicological sciences : an official journal of the Society of Toxicology · 2015Review
- Genetic variants in the inositol phosphate metabolism pathway and risk of different types of cancer.Scientific reports · 2015Article
- Pathway-Based Genome-Wide Association Studies for Plasma Triglycerides in Obese Females and Normal-Weight Controls.PloS one · 2015Article
- Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Pathway-based analysis, used in conjunction with genome-wide association study (GWAS) techniques, is a powerful tool to detect subtle but systematic patterns in genome that can help elucidate complex diseases, like cancers. Here, we stepped back from genetic polymorphisms at a single locus and examined how multiple association signals can be orchestrated to find pathways related to lung cancer susceptibility. We used single-nucleotide polymorphism (SNP) array data from 869 non-small cell lung cancer (NSCLC) cases from a previous GWAS at the National Cancer Center and 1,533 controls from the Korean Association Resource project for the pathway-based analysis. After mapping single-nucleotide polymorphisms to genes, considering their coding region and regulatory elements (±20 kbp), multivariate logistic regression of additive and dominant genetic models were fitted against disease status, with adjustments for age, gender, and smoking status. Pathway statistics were evaluated using Gene Set Enrichment Analysis (GSEA) and Adaptive Rank Truncated Product (ARTP) methods. Among 880 pathways, 11 showed relatively significant statistics compared to our positive controls (PGSEA≤0.025, false discovery rate≤0.25). Candidate pathways were validated using the ARTP method and similarities between pathways were computed against each other. The top-ranked pathways were ABC Transporters (PGSEA<0.001, PARTP = 0.001), VEGF Signaling Pathway (PGSEA<0.001, PARTP = 0.008), G1/S Check Point (PGSEA = 0.004, PARTP = 0.013), and NRAGE Signals Death through JNK (PGSEA = 0.006, PARTP = 0.001). Our results demonstrate that pathway analysis can shed light on post-GWAS research and help identify potential targets for cancer susceptibility.
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