ArticleBMC bioinformatics2020
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers, 2 of them syntheses that pooled it.
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Who cites it
107 citing papers in PubMed, 2 syntheses or guidelines pooled it, 158 citations in OpenAlex.
- Cross-species systems analysis distinguishes inflammatory remodeling from primary mucus secretory failure in inflammatory bowel disease.Frontiers in immunology · 2026Pooled it
- Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages.International journal of molecular sciences · 2020Pooled it
- Home-based high-intensity exercise training during neoadjuvant chemotherapy is associated with favorable chemotherapy outcomes and tumor microenvironment remodeling in breast cancer.Cell communication and signaling : CCS · 2026Trial
- Perturbation of metabolic pathways associated with exposure of human renal proximal tubular cells to nephrotoxic pollutants and drugs.Toxicology · 2026Article
- Study of blood linear RNA nominates CD55 and DLD as early-stage biomarkers for Parkinson's disease.Brain : a journal of neurology · 2026Article
- Fatty Acid-Binding Protein 5 Potentially Regulates the Proliferation and Metastasis of Uveal Melanoma Cells Through the PI3K/AKT/mTOR Signaling Pathway.CNS neuroscience & therapeutics · 2026Article
- IAN, an intelligent system for omics data analysis and discovery.Cell reports methods · 2026Article
- Circulating multi-omic signature of disease severity and cholangiocarcinoma in primary sclerosing cholangitis.Hepatology communications · 2026Article
- Multi-omics links microbial dysbiosis, systemic inflammation, and metabolomic disruptions to SNAE risk in treated HIV.JCI insight · 2026Article
- SOPA and SIMPA: normalized single-sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers.Briefings in bioinformatics · 2026Article
- A multi-omics study reveals pathway-level insights and predictive biomarkers in pediatric TB.Clinical proteomics · 2026Article
- PINK1‑mediated mitophagy enhances breast cancer proliferation through metabolic reprogramming.Oncology reports · 2026Article
- Gut microbiota remodeling inZoological research · 2026Article
- Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.Briefings in bioinformatics · 2026Article
- Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution.Nature communications · 2026Article
- Article
- Multi-omics links microbial dysbiosis, systemic inflammation and metabolomic disruptions to SNAE risk in treated HIV.bioRxiv : the preprint server for biology · 2026Article
- Oncogenic SOX9-TRAIP signaling drives gastric cancer progression by mediating the degradation of the CPEB3-mTORC1 tumor suppressor axis.World journal of surgical oncology · 2026Article
- Unlocking the power of extracellular vesicles: multi-omics integration for cancer biomarker discovery.Biomarker research · 2026Review
- Early multi-omic signatures and machine learning models predict cardiomyocyte differentiation efficiency and enable robust hPSC differentiation to cardiomyocytes.bioRxiv : the preprint server for biology · 2026Article
47 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundGaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of different tools and algorithms have been developed so far. Among those, the gene set enrichment analysis (GSEA) proved to control both type I and II errors well. In recent years the call for a combined analysis of multiple omics layers became prominent, giving rise to a few multi-omics enrichment tools. Each of these has its own drawbacks and restrictions regarding its universal application.
resultsHere, we present the multiGSEA package aiding to calculate a combined GSEA-based pathway enrichment on multiple omics layers. The package queries 8 different pathway databases and relies on the robust GSEA algorithm for a single-omics enrichment analysis. In a final step, those scores will be combined to create a robust composite multi-omics pathway enrichment measure. multiGSEA supports 11 different organisms and includes a comprehensive mapping of transcripts, proteins, and metabolite IDs.
conclusionsWith multiGSEA we introduce a highly versatile tool for multi-omics pathway integration that minimizes previous restrictions in terms of omics layer selection, pathway database availability, organism selection and the mapping of omics feature identifiers. multiGSEA is publicly available under the GPL-3 license at https://github.com/yigbt/multiGSEA and at bioconductor: https://bioconductor.org/packages/multiGSEA .
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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.