Aspects also include identifying an enriched gene set Gbased at least in part upon the mutation enrichment score and the differentiation enrichment score.Chaya LevovitzLaxmi ParidaKahn Rhrissorrakrai
Gene Set Enrichment Analysis (GSEA) and its variations aim to discover collections of genes that show moderate but coordinated differences in expression. However, such techniques may be ineffective if many individual genes in a phenotype-related gene set have weak discriminative power. A potential ...
GSEA analysis for oncogenic signature gene sets. (a) Enrichment plot of GSEA analysis for HCT-116. (b) Enrichment plot of GSEA analysis for LoVo. Enrichment plot on the whole transcriptome of the CRC cell lines showing the up-regulation of KRAS signaling oncogenic signature in HCT-116 vs SW...
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework...
Summary: GeoDiver is an online web application for performing Differential Gene Expression Analysis (DGEA) and Generally Applicable Gene-set Enrichment Analysis (GAGE) on gene expression datasets from the publicly available Gene Expression Omnibus (GEO). The output produced includes numerous high quality...
and used the DGCA wrapper function to perform gene ontology (GO) enrichment analysis based on the GOstats R package (version 2.34) [42] and org.Hs.eg.db GO annotation R package (version 3.1.2). For the GO enrichment analysis, we used genes identified in gene pairs with q < 0.01,...
Combined with GO annotations and KEGG pathway enrichment analysis, the expression of two early-ripening related genes and six aroma formation related genes was significantly up-regulated in YH-20-1; while, in YH-20-2, only one early-ripening related gene was significantly up-regulated. Moreover...
According to the Gene Ontology annotation, 15 genes are linked to the GO-terms DNA or nucleotide binding, indicating a possible role of these genes in transcription regulation. Furthermore, GO-category enrichment analysis revealed that electron carrier activity is over-represented, involving only ...
Gene Set Enrichment Analysis (GSEA) has been applied widely as a tool for gene-set analyses. We describe here some critical problems with GSEA and propose an alternative method by extending the single-gene analysis method, Significance Analysis of Microarray (SAM), to gene-set analyses (SAM-GS...
The Construction and Validation of a Novel Ferroptosis-Related Gene Signature in Parkinson's Disease The GSE8397 dataset includes GPL96 and GPL97 platforms. The differential genes were analyzed by immune infiltration and Gene Set Enrichment Analysis (GSEA)... T Liu,H Wu,J Wei - 《International ...