Research graph
References from Assessment of Gene Set Enrichment Analysis using curated RNA-seq-based benchmarks. Local targets link to admitted publications; unresolved targets remain external evidence.
Identifying significantly impacted pathways: a comprehensive review and assessment
2019 · External reference
Gene set analysis: challenges, opportunities, and future research
10.3389/fgene.2020.00654 · 2020 · External reference
Popularity and performance of bioinformatics software: the case of gene set analysis
2021 · External reference
On the influence of several factors on pathway enrichment analysis
10.1093/bib/bbac143 · 2022 · External reference
Molecular signatures database (MSigDB) 3.0
10.1093/bioinformatics/btr260 · 2011 · External reference
Ten years of pathway analysis: current approaches and outstanding challenges
10.1371/journal.pcbi.1002375 · 2012 · External reference
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity
10.1371/journal.pone.0079217 · 2013 · External reference
Comparative study on gene set and pathway topology-based enrichment methods
10.1186/s12859-015-0751-5 · 2015 · External reference
Empirical comparison of structure-based pathway methods
10.1093/bib/bbv049 · 2016 · External reference
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
10.1093/bib/bbv069 · 2016 · External reference
Gene set analysis methods: a systematic comparison
10.1186/s13040-018-0166-8 · 2018 · External reference
A critical comparison of topology-based pathway analysis methods
10.1371/journal.pone.0191154 · 2018 · External reference
A comparative study of topology-based pathway enrichment analysis methods
2019 · External reference
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
10.1093/bioinformatics/btz447 · 2019 · External reference
Toward a gold standard for benchmarking gene set enrichment analysis
10.1093/bib/bbz158 · 2020 · External reference
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
10.1038/ng1180 · 2003 · External reference
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
10.1073/pnas.0506580102 · 2005 · External reference
Multiple sources of bias confound functional enrichment analysis of global -omics data
10.1186/s13059-015-0761-7 · 2015 · External reference
Urgent need for consistent standards in functional enrichment analysis
10.1371/journal.pcbi.1009935 · 2022 · External reference
Comprehensive and integrative genomic characterization of hepatocellular carcinoma
10.1016/j.cell.2017.05.046 · 2017 · External reference
KEGG: integrating viruses and cellular organisms
10.1093/nar/gkaa970 · 2021 · External reference
The reactome pathway knowledgebase
2020 · External reference
The Gene Ontology resource: enriching a GOld mine
10.1093/nar/gkaa1113 · 2021 · External reference
Unresolved reference
External reference
The Chernobyl Tissue Bank: integrating research on radiation-induced thyroid cancer
10.1088/0952-4746/32/1/n77 · 2012 · External reference
The genomic landscape of Mongolian hepatocellular carcinoma
10.1038/s41467-020-18186-1 · 2020 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles
10.1038/s41598-019-43282-8 · 2019 · External reference
Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples
10.1038/s41598-020-71521-w · 2020 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
10.2202/1544-6115.1027 · 2004 · External reference
Unresolved reference
External reference
Down-weighting overlapping genes improves gene set analysis
10.1186/1471-2105-13-136 · 2012 · External reference
Avoiding the pitfalls of gene set enrichment analysis with setrank
10.1186/s12859-017-1571-6 · 2017 · External reference
Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap
10.1038/s41596-018-0103-9 · 2019 · External reference
Permutation p-values should never be zero: Calculating exact p-values when permutations are randomly drawn
2010 · External reference
Unresolved reference
2007 · External reference
Systematic determination of genetic network architecture
10.1038/10343 · 1999 · External reference
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
10.1093/nar/gkn923 · 2009 · External reference
Pathway studio—the analysis and navigation of molecular networks
10.1093/bioinformatics/btg290 · 2003 · External reference
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
10.1038/nprot.2008.211 · 2009 · External reference
g:Profiler-a web server for functional interpretation of gene lists (2016 update)
10.1093/nar/gkw199 · 2016 · External reference
Causal analysis approaches in Ingenuity Pathway Analysis
10.1093/bioinformatics/btt703 · 2014 · External reference
Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays
10.1073/pnas.0502674102 · 2005 · External reference
pROC: an open-source package for R and S+ to analyze and compare ROC curves
10.1186/1471-2105-12-77 · 2011 · External reference
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
10.1093/bioinformatics/btp616 · 2010 · External reference
Differential expression analysis for sequence count data
10.1186/gb-2010-11-10-r106 · 2010 · External reference
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
10.1186/gb-2014-15-2-r29 · 2014 · External reference
The limitations of simple gene set enrichment analysis assuming gene independence
10.1177/0962280212460441 · 2016 · External reference
Introducing the FAIR Principles for research software
10.1038/s41597-022-01710-x · 2022 · External reference
