ArticleHuman heredity2014
Beyond GWAS in COPD: probing the landscape between gene-set associations, genome-wide associations and protein-protein interaction networks.
Article in Human heredity, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Pulmonary comorbidities in psoriasis are associated with a high risk of respiratory failure.The Journal of international medical research · 2023Article
- Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease.Respiratory research · 2022Article
- Genetic variation in genes regulating skeletal muscle regeneration and tissue remodelling associated with weight loss in chronic obstructive pulmonary disease.Journal of cachexia, sarcopenia and muscle · 2021Article
- Functional Gene Variants in Chronic Obstructive Pulmonary Disease: The Search Continues.American journal of respiratory cell and molecular biology · 2021Article
- An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate.BMC medical genomics · 2020Article
- Integrated transcriptomic correlation network analysis identifies COPD molecular determinants.Scientific reports · 2020Article
- Genetics of COPD.Annual review of physiology · 2020Review
- Genetic Advances in Chronic Obstructive Pulmonary Disease. Insights from COPDGene.American journal of respiratory and critical care medicine · 2019Review
- Integrative Genomics Analysis Identifies ACVR1B as a Candidate Causal Gene of Emphysema Distribution.American journal of respiratory cell and molecular biology · 2019Article
- Whole exome sequencing analysis in severe chronic obstructive pulmonary disease.Human molecular genetics · 2018Article
- Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module.Scientific reports · 2018Article
- Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci.American journal of respiratory and critical care medicine · 2018Article
- Prediction of microRNA and gene target from an integrated network in chronic obstructive pulmonary disease based on canonical correlation analysis.Technology and health care : official journal of the European Society for Engineering and Medicine · 2018Article
- Exome Array Analysis Identifies a Common Variant in IL27 Associated with Chronic Obstructive Pulmonary Disease.American journal of respiratory and critical care medicine · 2016Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
Abstract
objectivesTo use a systems biology approach to integrate genotype and protein-protein interaction (PPI) data to identify disease network modules associated with chronic obstructive pulmonary disease (COPD) and to perform traditional pathway analysis.
methodsWe utilized a standard gene-set association approach (FORGE) using gene-based association analysis and gene-set definitions from the molecular signatures database (MSigDB). As a discovery step, we analyzed GWAS results from 2 well-characterized COPD cohorts: COPDGene and GenKOLS. We used a third well-characterized COPD case-control cohort for replication: ECLIPSE. Next, we used dmGWAS, a method that integrates GWAS results with PPI, to identify COPD disease modules.
resultsNo gene-sets reached experiment-wide significance in either discovery population. We identified a consensus network of 10 genes identified in modules by integrating GWAS results with PPI that replicated in COPDGene, GenKOLS, and ECLIPSE. Members of 4 gene-sets were enriched among these 10 genes: (i) lung adenocarcinoma tumor-sequencing genes, (ii) IL-7 pathway genes, (iii) kidney cell response to arsenic, and (iv) CD4 T-cell responses. Further, several genes have also been associated with pathophysiology relevant to COPD including KCNK3, NEDD4L, and RIN3. In particular, KCNK3 has been associated with pulmonary arterial hypertension, a common complication in advanced COPD.
conclusionWe report a set of new genes that may influence the etiology of COPD that would not have been identified using traditional GWAS and pathway analyses alone.
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