Trial reportGenetic epidemiology2012
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.
Trial report in Genetic epidemiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A method for gene-based pathway analysis using genomewide association study summary statistics reveals nine new type 1 diabetes associations.Genetic epidemiology · 2014Pooled it
- Springer: An R package for bi-level variable selection of high-dimensional longitudinal data.Frontiers in genetics · 2023Article
- Interep: An R Package for High-Dimensional Interaction Analysis of the Repeated Measurement Data.Genes · 2022Article
- Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.Scientific reports · 2020Article
- Semiparametric Bayesian variable selection for gene-environment interactions.Statistics in medicine · 2020Article
- Penalized Variable Selection for Lipid-Environment Interactions in a Longitudinal Lipidomics Study.Genes · 2019Article
- A Selective Review of Multi-Level Omics Data Integration Using Variable Selection.High-throughput · 2019Review
- Integration of Enhancer-Promoter Interactions with GWAS Summary Results Identifies Novel Schizophrenia-Associated Genes and Pathways.Genetics · 2018Article
- Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia.Genetic epidemiology · 2018Article
- Airway Mucosal Host Defense Is Key to Genomic Regulation of Cystic Fibrosis Lung Disease Severity.American journal of respiratory and critical care medicine · 2018Article
- A NOVEL AND EFFICIENT ALGORITHM FOR DE NOVO DISCOVERY OF MUTATED DRIVER PATHWAYS IN CANCER.The annals of applied statistics · 2017Article
- Adaptive gene- and pathway-trait association testing with GWAS summary statistics.Bioinformatics (Oxford, England) · 2016Article
- Article
- A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants.American journal of human genetics · 2015Article
- Testing for polygenic effects in genome-wide association studies.Genetic epidemiology · 2015Article
- Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study.Environmental health perspectives · 2015Article
- Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes.American journal of human genetics · 2015Article
- Prioritization of candidate genes in QTL regions based on associations between traits and biological processes.BMC plant biology · 2014Article
- Multiple comparisons in genetic association studies: a hierarchical modeling approach.Statistical applications in genetics and molecular biology · 2014Article
- A set-based association test identifies sex-specific gene sets associated with type 2 diabetes.Frontiers in genetics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Gene-set analyses have been widely used in gene expression studies, and some of the developed methods have been extended to genome wide association studies (GWAS). Yet, complications due to linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs), and variable numbers of SNPs per gene and genes per gene-set, have plagued current approaches, often leading to ad hoc "fixes." To overcome some of the current limitations, we developed a general approach to scan GWAS SNP data for both gene-level and gene-set analyses, building on score statistics for generalized linear models, and taking advantage of the directed acyclic graph structure of the gene ontology when creating gene-sets. However, other types of gene-set structures can be used, such as the popular Kyoto Encyclopedia of Genes and Genomes (KEGG). Our approach combines SNPs into genes, and genes into gene-sets, but assures that positive and negative effects of genes on a trait do not cancel. To control for multiple testing of many gene-sets, we use an efficient computational strategy that accounts for LD and provides accurate step-down adjusted P-values for each gene-set. Application of our methods to two different GWAS provide guidance on the potential strengths and weaknesses of our proposed gene-set analyses.
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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.