ArticleBMC bioinformatics2017
Avoiding the pitfalls of gene set enrichment analysis with SetRank.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 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
85 citing papers in PubMed.
- Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.Science (New York, N.Y.) · 2019Trial
- Article
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Genetic Determinants of T-Cell Homeostasis in Critical Illness: An Exploratory Analysis of Immune Gene Variants and TREC Dynamics.Journal of personalized medicine · 2026Article
- Blood-Based Epigenetic Signatures in Brazilian Males With Alcohol Use Disorder.Addiction biology · 2026Article
- A Ponatinib-Associated Transcriptomic Signature: Implications for Cardiovascular Toxicity.International journal of molecular sciences · 2026Article
- Ten common mistakes that could ruin your enrichment analysis.PLoS computational biology · 2026Article
- Candidate miRNA Regulators of Blood Transcriptional Signatures for Differential Diagnosis of Chronic Lymphocytic Leukemia and Multiple Myeloma: A Comprehensive In Silico Study.Current issues in molecular biology · 2026Article
- Coral Genetic Structure in the Western Indian Ocean Mirrors Ocean Circulation and Thermal Stress History.Evolutionary applications · 2026Article
- Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB.PLoS genetics · 2026Article
- Global coral genomic vulnerability explains recent reef losses.Nature communications · 2025Article
- Modelling of the Systemic Inflammatory Host Response in Relation to the Microbiome of the Endodontic Infection.International endodontic journal · 2025Article
- InCURA: integrative gene clustering based on transcription factor binding sites.Nucleic acids research · 2025Article
- SomaModules: A Pathway Enrichment Approach Tailored to SomaScan Data.Journal of proteome research · 2025Article
- Comprehensive identification of hub mRNAs and lncRNAs in colorectal cancer using galaxy: an in silico transcriptome analysis.Discover oncology · 2025Article
- Genomic and cellular responses to aspirin in colonic organoids from African- and European-Americans.Physiological genomics · 2025Article
- Beyond hemoglobin: Critical role of 2,3-bisphosphoglycerate mutase in kidney function and injury.Acta physiologica (Oxford, England) · 2025Article
- Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis.RNA (New York, N.Y.) · 2024Article
- Multi-Omics Analysis Identified Drug Repurposing Targets for Chronic Obstructive Pulmonary Disease.International journal of molecular sciences · 2024Article
- The response to single-gene duplication implicates translation as a key vulnerability in aneuploid yeast.PLoS genetics · 2024Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe purpose of gene set enrichment analysis (GSEA) is to find general trends in the huge lists of genes or proteins generated by many functional genomics techniques and bioinformatics analyses.
resultsHere we present SetRank, an advanced GSEA algorithm which is able to eliminate many false positive hits. The key principle of the algorithm is that it discards gene sets that have initially been flagged as significant, if their significance is only due to the overlap with another gene set. The algorithm is explained in detail and its performance is compared to that of other methods using objective benchmarking criteria. Furthermore, we explore how sample source bias can affect the results of a GSEA analysis.
conclusionsThe benchmarking results show that SetRank is a highly specific tool for GSEA. Furthermore, we show that the reliability of results can be improved by taking sample source bias into account. SetRank is available as an R package and through an online web interface.
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.