ArticleScientific reports2014
Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Marked intestinal trans-differentiation by autoimmune gastritis along with ectopic pancreatic and pulmonary trans-differentiation.Journal of gastroenterology · 2024Article
- Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.Briefings in bioinformatics · 2022Article
- On the influence of several factors on pathway enrichment analysis.Briefings in bioinformatics · 2022Review
- Autoimmune gastritis induces aberrant DNA methylation reflecting its carcinogenic potential.Journal of gastroenterology · 2022Article
- DecoPath: a web application for decoding pathway enrichment analysis.NAR genomics and bioinformatics · 2021Article
- Gaussian Embedding for Large-scale Gene Set Analysis.Nature machine intelligence · 2020Article
- Article
- Gene Set Analysis: Challenges, Opportunities, and Future Research.Frontiers in genetics · 2020Review
- Identification of Key circRNAs/lncRNAs/miRNAs/mRNAs and Pathways in Preeclampsia Using Bioinformatics Analysis.Medical science monitor : international medical journal of experimental and clinical research · 2019Article
- Identification of marker genes and pathways specific to precancerous duodenal adenomas and early stage adenocarcinomas.Journal of gastroenterology · 2019Article
- The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling.Frontiers in genetics · 2019Article
- Data-driven human transcriptomic modules determined by independent component analysis.BMC bioinformatics · 2018Article
- Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.Frontiers in plant science · 2016Article
- Regulated genes in mesenchymal stem cells and gastric cancer.World journal of stem cells · 2015Article
- Integrating phenotypic small-molecule profiling and human genetics: the next phase in drug discovery.Trends in genetics : TIG · 2015Review
- Toxicity prediction from toxicogenomic data based on class association rule mining.Toxicology reports · 2014Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet there are no guidelines for the choice of collections and the impact of such choice, if any, is unknown. Here we compare each of the standard gene set collections in the context of a large dataset of drug response in human cancer cell lines. We define and test a new collection based on gene co-expression in cancer cell lines to compare the performance of the standard collections to an externally derived cell line based collection. The results show that GSEA findings vary significantly depending on the collection chosen for analysis. Henceforth, collections should be carefully selected and reported in studies that leverage GSEA.
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