ArticleBMC medical genomics2010
Pathway analysis comparison using Crohn's disease genome wide association studies.
Article in BMC medical genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
21 citing papers in PubMed.
- Genomics of posttraumatic stress disorder in veterans: Methods and rationale for Veterans Affairs Cooperative Study #575B.International journal of methods in psychiatric research · 2019Article
- Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs inFrontiers in pharmacology · 2018Article
- Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies.PLoS genetics · 2018Article
- The statistical properties of gene-set analysis.Nature reviews. Genetics · 2016Review
- Very early-onset inflammatory bowel disease: gaining insight through focused discovery.Inflammatory bowel diseases · 2015Review
- Gene-based and pathway-based genome-wide association study of alcohol dependence.Shanghai archives of psychiatry · 2015Article
- Towards the identification of the loci of adaptive evolution.Methods in ecology and evolution · 2015Review
- Pathway-based analysis tools for complex diseases: a review.Genomics, proteomics & bioinformatics · 2014Review
- MultiBLUP: improved SNP-based prediction for complex traits.Genome research · 2014Article
- Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies.Human molecular genetics · 2014Article
- Supervised categorical principal component analysis for genome-wide association analyses.BMC genomics · 2014Article
- Article
- Pathway analysis using genome-wide association study data for coronary restenosis--a potential role for the PARVB gene.PloS one · 2013Article
- Uncovering networks from genome-wide association studies via circular genomic permutation.G3 (Bethesda, Md.) · 2012Article
- Pathway analysis of genomic data: concepts, methods, and prospects for future development.Trends in genetics : TIG · 2012Review
- Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem.BMC proceedings · 2011Article
- Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease dataset.BMC research notes · 2011Article
- Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana.PLoS biology · 2011Article
- Gene set analysis of genome-wide association studies: methodological issues and perspectives.Genomics · 2011Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe use of biological annotation such as genes and pathways in the analysis of gene expression data has aided the identification of genes for follow-up studies and suggested functional information to uncharacterized genes. Several studies have applied similar methods to genome wide association studies and identified a number of disease related pathways. However, many questions remain on how to best approach this problem, such as whether there is a need to obtain a score to summarize association evidence at the gene level, and whether a pathway, dominated by just a few highly significant genes, is of interest.
methodsWe evaluated the performance of two pathway-based methods (Random Set, and Binomial approximation to the hypergeometric test) based on their applications to three data sets of Crohn's disease. We consider both the disease status as a phenotype as well as the residuals after conditioning on IL23R, a known Crohn's related gene, as a phenotype.
resultsOur results show that Random Set method has the most power to identify disease related pathways. We confirm previously reported disease related pathways and provide evidence for IL-2 Receptor Beta Chain in T cell Activation and IL-9 signaling as Crohn's disease associated pathways.
conclusionsOur results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight.
Indexed as
Identifiers
What OpenQuestion holds
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.