ArticleBiostatistics (Oxford, England)2013
Empirical pathway analysis, without permutation.
Article in Biostatistics (Oxford, England), 2013. 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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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
14 citing papers in PubMed.
- TransCONFIRM: Identification of a Genetic Signature of Response to Fulvestrant in Advanced Hormone Receptor-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Trial
- A Comparison of Testing Procedures for Detecting Short- and Long-Term Effects of Biomarkers for Cancer Screening.Statistics in medicine · 2026Article
- Gene set selection via LASSO penalized regression (SLPR).Nucleic acids research · 2017Article
- A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.PLoS computational biology · 2017Article
- Unsupervised gene set testing based on random matrix theory.BMC bioinformatics · 2016Article
- Pathway analysis for RNA-Seq data using a score-based approach.Biometrics · 2016Article
- Monte Carlo simulation of OLS and linear mixed model inference of phenotypic effects on gene expression.PeerJ · 2016Article
- Article
- Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci.Human molecular genetics · 2015Article
- A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants.American journal of human genetics · 2015Article
- Spectral gene set enrichment (SGSE).BMC bioinformatics · 2015Article
- Principal component gene set enrichment (PCGSE).BioData mining · 2015Article
- Genome scale modeling in systems biology: algorithms and resources.Current genomics · 2014Article
- 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
3 authors.
Funding
Abstract
Resampling-based expression pathway analysis techniques have been shown to preserve type I error rates, in contrast to simple gene-list approaches that implicitly assume the independence of genes in ranked lists. However, resampling is intensive in computation time and memory requirements. We describe accurate analytic approximations to permutations of score statistics, including novel approaches for Pearson's correlation, and summed score statistics, that have good performance for even relatively small sample sizes. Our approach preserves the essence of permutation pathway analysis, but with greatly reduced computation. Extensions for inclusion of covariates and censored data are described, and we test the performance of our procedures using simulations based on real datasets. These approaches have been implemented in the new R package safeExpress.
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.