Single-sample gene set enrichment analysis reveals the clinical implications of immune-related genes in ovarian cancerdoi:10.3389/fmolb.2024.1426274Weiwei GongMingqin KuangHongxi ChenYiheng LuoKeli YouBin ZhangYueyang LiuFrontiers in Molecular Biosciences...
Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal ... A Grigoriadis,A Mackay,JS Reis-Filho,... - 《Breast Cancer Research》 被引量: 268发表: 2006年 Physiological parameter system A physiolog...
The preranked based gene set enrichment analysis (GSEA) of the selected pathways that are related COVID-19 disease mechanism28 (as listed in Fig. 4c) is measured using the fgsea function in the R package fgsea v1.22.045. Significant pathways are defined with adjusted p-value <0.05. ...
Secondly, gene set activities can be projected onto individual cells, thus providing a natural approach to perform single-cell gene set enrichment analysis. This flexible framework enables the study of different types of regulatory mechanisms depending on the observations modelled. For example, it can...
Gene Set Enrichment Analysis GO: Gene Ontology MSigDB: Molecular Signatures Database AUC: Area under the curve TPM: Transcripts per million DEMRGs: Differential Expressed Metabolism-Related Genes SVM-RFE: Support vector machine recursive feature elimination IHC: Immunohistochemistry HPA: Human...
Using conventional all-patients analysis, we obtained 2056 up-regulated and 4836 down-regulated genes in the tumour samples compared to the adjacent normal samples (Additional file2). Gene set enrichment analysis (GSEA) of the up- and down-regulated genes showed enrichment of cell cycle-related ...
Heatmap showing the enrichment scores from single sample GSEA analysis using our general gene set categories.Danny, A. Milner JrNathalie, PochetMalkie, KrupkaChris, WilliamsKarl, SeydelTerrie, E. TaylorYves, Van de PeerAviv, RegevDyann, Wirth...
Gene-set enrichment analysis workshop - available through the Orchestra platform (search “WEHI Masterclass Day 4: Functional Analysis, single sample gene set analysis”). Getting Started These instructions will get you to install the package up and running on your local machine. If you experience...
GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7. Article PubMed PubMed Central Google Scholar Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies...
The functional enrichment analysis module and pathway analysis module were used to perform metabolic pathway analysis for the blood metabolites that were identified by the IVW method, as mentioned above. The metabolic pathway analysis tested 183 human metabolic pathways from two metabolite set libraries...