Gene set enrichment analysisIngenuity pathway analysisSheng-ji Hua-yu (SJHY) formula is a Chinese herbal prescription for diabetic ulcers (DUs) treatment, which can accelerate wound reconstruction and shorten the healing time. However, its mechanism role maintains unclear. To elucidate the molecular ...
setSize:富集到该pathway的基因数 enrichmentScore:富集分数(ES),即GSEA的核心 NES:归一化后的Enrichment score(ES) pvalue/p.adjust/qvalues:p值/矫正后p值/FDR值 rank:在基因集中对ES分数贡献最大的核心基因在genelist排序中的位置(按照log2fc从大到小的排序) leading_edge:三个指标的含义(如下) tag:核心...
GSEA(Gene Set Enrichment Analysis; 基因集合富集分析) 富集是将一组基因根据一些先验的知识(也就是常见的注释)进行分类的过程。也就是物以类聚。我们一般会想到最常见的是GO/KEGG(pathway)富集,其思路是先筛选差异基因(也就是不同的处理后基因组里发生表达变化的那些基因。如果培养条件没有发生变化,那么细胞在短...
Originally, gene set/pathway enrichment analysis was mainly used to assess whether a specific gene annotation is significantly enriched with extremely deregulated genes. However, this method is very flexible and can be adapted for many different uses. For example, associations between drugs and their ...
lnc和信号通路的调控网络 lncRNA Target Pathway Network 面议 产品介绍 基因富集分析 (Gene Set Enrichment Analysis,GSEA)通过基因在两类样本中的差异表达程度排序,检验预先设定的基因集是否在这个排序表的顶端或者底端富集,检测差异基因的表达在已定义的功能或者通路分组中是否有共同的表达趋势,从另一个角度来解读生物...
Choosing a ranking metric in Gene Set Enrichment Analysis has critical impact on results of pathway enrichment analysis. The absolute value of Moderated Welch Test has the best overall sensitivity and Minimum Significant Difference has the best overall specificity of gene set analysis. When the number...
GAGE is a widely used method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior perf...
DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primar
STAGEs: A web-based tool that integrates data visualization and pathway enrichment analysis for gene expression studies Article Open access 02 May 2023 reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization Article Open...
Stars indicate significant enrichment (FWER-adjusted p < 0.05). A number of metabolic pathway genes are differentially expressed. B: KEGG pathways affected by deletion of GCN5A. Plotted normalized enrichment scores (NES) for bradyzoite gene sets. A positive NES indicates that the gene set ...