ArticleBioinformatics (Oxford, England)2014
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC).
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Optimizing gene set annotations combining GO structure and gene expression data.BMC systems biology · 2018Article
- Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.BioData mining · 2017Article
- Spectral gene set enrichment (SGSE).BMC bioinformatics · 2015Article
- An Independent Filter for Gene Set Testing Based on Spectral Enrichment.IEEE/ACM transactions on computational biology and bioinformaticsArticle
- Combining rules, background knowledge and change patterns to maintain semantic annotations.AMIA ... Annual Symposium proceedings. AMIA SymposiumArticle
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Abstract
motivationGene set enrichment has become a critical tool for interpreting the results of high-throughput genomic experiments. Inconsistent annotation quality and lack of annotation specificity, however, limit the statistical power of enrichment methods and make it difficult to replicate enrichment results across biologically similar datasets.
resultsWe propose a novel algorithm for optimizing gene set annotations to best match the structure of specific empirical data sources. Our proposed method, entropy minimization over variable clusters (EMVC), filters the annotations for each gene set to minimize a measure of entropy across disjoint gene clusters computed for a range of cluster sizes over multiple bootstrap resampled datasets. As shown using simulated gene sets with simulated data and Molecular Signatures Database collections with microarray gene expression data, the EMVC algorithm accurately filters annotations unrelated to the experimental outcome resulting in increased gene set enrichment power and better replication of enrichment results. AVAILABILITY AND IMPLEMENTATION: http://cran.r-project.org/web/packages/EMVC/index.html.
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