ArticlePLoS genetics2011
Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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.
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Who cites it
33 citing papers in PubMed.
- Trial
- A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity.American journal of human genetics · 2021Article
- SNPs in the interleukin-12 signaling pathway are associated with breast cancer risk in Puerto Rican women.Oncotarget · 2020Article
- Pathway-Wide Genetic Risks in Chlamydial Infections Overlap between Tissue Tropisms: A Genome-Wide Association Scan.Mediators of inflammation · 2018Article
- Article
- Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei.Scientific reports · 2017Article
- Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2016Article
- Comparison of significant single nucleotide polymorphisms selections in GWAS for complex traits.Journal of applied genetics · 2016Article
- Sparse regression models for unraveling group and individual associations in eQTL mapping.BMC bioinformatics · 2016Article
- Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy.Human genetics · 2016Article
- Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study.Scientific reports · 2015Article
- Robust Multi-Network Clustering via Joint Cross-Domain Cluster Alignment.Proceedings. IEEE International Conference on Data Mining · 2015Article
- Gene set analysis: A step-by-step guide.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2015Review
- Solving the genetic puzzle of systemic lupus erythematosus.Pediatric nephrology (Berlin, Germany) · 2015Review
- Fast and robust group-wise eQTL mapping using sparse graphical models.BMC bioinformatics · 2015Article
- Trachoma and Ocular Chlamydial Infection in the Era of Genomics.Mediators of inflammation · 2015Review
- Functional and genomic context in pathway analysis of GWAS data.Trends in genetics : TIG · 2014Review
- Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis.BMC genomics · 2014Article
- Genetic susceptibility to nosocomial pneumonia, acute respiratory distress syndrome and poor outcome in patients at risk of critical illness.Inflammation · 2014Article
- Systems analysis of high-throughput data.Advances in experimental medicine and biology · 2014Review
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2 authors.
Funding
Abstract
Genome-wide association studies (GWAS) have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However, while typical GWAS analysis techniques treat markers individually, complex diseases (cancers, diabetes, and Alzheimers, amongst others) are unlikely to have a single causative gene. Thus, there is a pressing need for multi-SNP analysis methods that can reveal system-level differences in cases and controls. Here, we present a novel multi-SNP GWAS analysis method called Pathways of Distinction Analysis (PoDA). The method uses GWAS data and known pathway-gene and gene-SNP associations to identify pathways that permit, ideally, the distinction of cases from controls. The technique is based upon the hypothesis that, if a pathway is related to disease risk, cases will appear more similar to other cases than to controls (or vice versa) for the SNPs associated with that pathway. By systematically applying the method to all pathways of potential interest, we can identify those for which the hypothesis holds true, i.e., pathways containing SNPs for which the samples exhibit greater within-class similarity than across classes. Importantly, PoDA improves on existing single-SNP and SNP-set enrichment analyses, in that it does not require the SNPs in a pathway to exhibit independent main effects. This permits PoDA to reveal pathways in which epistatic interactions drive risk. In this paper, we detail the PoDA method and apply it to two GWAS: one of breast cancer and the other of liver cancer. The results obtained strongly suggest that there exist pathway-wide genomic differences that contribute to disease susceptibility. PoDA thus provides an analytical tool that is complementary to existing techniques and has the power to enrich our understanding of disease genomics at the systems-level.
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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.