ArticleBioinformatics (Oxford, England)2008
Gene set enrichment analysis using linear models and diagnostics.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
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- Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data.NAR genomics and bioinformatics · 2023Article
- Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture.Genome biology · 2022Article
- TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation.Briefings in bioinformatics · 2022Article
- Analysis of transcriptomic data sets supports the role of IL-6 in NETosis and immunothrombosis in severe COVID-19.BMC genomic data · 2021Article
- Potential Genes and Pathways of Neonatal Sepsis Based on Functional Gene Set Enrichment Analyses.Computational and mathematical methods in medicine · 2018Article
- FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.Bioinformatics (Oxford, England) · 2017Article
- Article
- Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data.PloS one · 2017Article
- Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification.Briefings in bioinformatics · 2016Article
- Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.Nature medicine · 2016Article
- Overlapping Group Logistic Regression with Applications to Genetic Pathway Selection.Cancer informatics · 2016Article
- A network model for angiogenesis in ovarian cancer.BMC bioinformatics · 2015Article
- BicOverlapper 2.0: visual analysis for gene expression.Bioinformatics (Oxford, England) · 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
3 authors at 2 institutions in 1 country.
Funding
Abstract
motivationGene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and also to evaluate model fit and explore model expansion.
resultsWe demonstrate this methodology on an adult acute lymphoblastic leukemia (ALL) dataset, using GSEA based on chromosome-band mapping of genes. Individual residuals, grouped or aggregated by chromosomal loci, indicate problematic samples and potential data-entry errors, and help identify hyperdiploidy as a factor playing a key role in expression for this dataset. Subsequent analysis pinpoints suspected DNA copy number abnormalities of specific samples and chromosomes (most prevalent are chromosomes X, 21 and 14), and also reveals significant expression differences between the hyperdiploid and diploid groups on other chromosomes (most prominently 19, 22, 3 and 13)--differences which are apparently not associated with copy number. AVAILABILITY: Software for the statistical tools demonstrated in this article is available as Bioconductor package GSEAlm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.