ArticleBioinformatics (Oxford, England)2021
Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer.iScience · 2025Article
- Comparative investigation of immune-related biomarkers related to alopecia areata subtypes.Archives of medical science : AMS · 2025Article
- Identification of Shared Pathways and Molecules Between Type 2 Diabetes and Lung Adenocarcinoma and the Impact of High Glucose Environment on Lung Adenocarcinoma.International journal of endocrinology · 2025Article
- Stress-induced premature senescence in high five cell cultures: a principal factor in cell-density effects.Bioresources and bioprocessing · 2024Article
- RAD51 High-Expressed Hepatocellular Carcinomas Are Associated With High Cell Proliferation.The Journal of surgical research · 2024Article
- Identification and Immune Characteristics Study of Pyroptosis‑Related Genes in Endometriosis.Biochemical genetics · 2024Article
- Identification of novel genes associated with atherosclerosis in Bama miniature pig.Animal models and experimental medicine · 2024Article
- Identification of potential biological processes and key genes in diabetes-related stroke through weighted gene co-expression network analysis.BMC medical genomics · 2024Article
- Transcriptome analysis reveals the impact of NETs activation on airway epithelial cell EMT and inflammation in bronchiolitis obliterans.Scientific reports · 2023Article
- Identification of key biomarkers and associated pathways of pancreatic cancer using integrated transcriptomic and gene network analysis.Saudi journal of biological sciences · 2023Article
- Single-cell transcriptome profiling highlights the role of APP in blood vessels in assessing the risk of patients with proliferative diabetic retinopathy developing Alzheimer's disease.Frontiers in cell and developmental biology · 2023Article
- Prognostic Significance of mRNA Expression RBBP8 or Its Methylation in Gliomas.Cellular and molecular neurobiology · 2023Article
- Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility.Frontiers in molecular biosciences · 2023Article
- Identification of key genes in the pathogenesis of preeclampsia via bioinformatic analysis and experimental verification.Frontiers in endocrinology · 2023Article
- Identification of the effects of COVID-19 on patients with pulmonary fibrosis and lung cancer: a bioinformatics analysis and literature review.Scientific reports · 2022Review
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3 authors.
Funding
Abstract
motivationGene Set Enrichment Analysis (GSEA) is an algorithm widely used to identify statistically enriched gene sets in transcriptomic data. However, GSEA cannot examine the enrichment of two gene sets or pathways relative to one another. Here we present Differential Gene Set Enrichment Analysis (DGSEA), an adaptation of GSEA that quantifies the relative enrichment of two gene sets.
resultsAfter validating the method using synthetic data, we demonstrate that DGSEA accurately captures the hypoxia-induced coordinated upregulation of glycolysis and downregulation of oxidative phosphorylation. We also show that DGSEA is more predictive than GSEA of the metabolic state of cancer cell lines, including lactate secretion and intracellular concentrations of lactate and AMP. Finally, we demonstrate the application of DGSEA to generate hypotheses about differential metabolic pathway activity in cellular senescence. Together, these data demonstrate that DGSEA is a novel tool to examine the relative enrichment of gene sets in transcriptomic data. AVAILABILITY AND IMPLEMENTATION: DGSEA software and tutorials are available at https://jamesjoly.github.io/DGSEA/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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