2. module member-ship 简称MM, 将该基因的表达量与module的第一主成分,即module eigengene进行相关性分析就可以得到MM值,所以MM值本质上是一个相关系数,如果基因和某个module的MM值为0,说明二者根本不相关,该基因不属于这个module; 如果MM的绝对值接近1,说明基因与该module相关性很高。 在WGCNA中,计算基因与modul...
2,纵坐标:对应模块的eigengene。 官网给出的解释是这个样子的: Eigengene,即每个模块的第一主成分。 这里小编自己的理解就是这个模块有134个样本,n个基因,然后用pca主成分分析对这n个基因进行降维取其第一主成分作为这个模块的特征。 3,图中的小格子中的数值代表什么? 这里我们得到横坐标的表型性状向量和纵坐标的...
+ Differential module eigengene (DME) analysis + + + Module trait correlation + + + Enrichment analysis + + + Exploring modules in external datasets + + Projecting modules to new datasets + + + Module preservation and reproducibility + + + Cross-species and cross-modality an...
To better explain the method of determining clustering center in this paper, the concept of module eigengene (ME) is introduced: In GCNA, a vector ME is often used to represent the expression profiles of all genes in a gene module (cluster). Generally, Principal Component Analysis (PCA) is...
The module eigengene expression, adjacency matrix heatmap, Module-Trait relationships, and co-expression gene modules were calculated based on Pearson correlation. Finally, the module "lightpink1" consisting of RD26 and SRMT was selected and their co-expressed genes corresponding to salt tol- erance...
Chapter 9 - Preservation module prediction by weighted differentially coexpressed gene network analysis (WDCGNA) of HIV-1 disease: a case study for cancerDifferentially coexpressed genes (DCEGs)Differentially expressed genes (DEGs)Eigengene network of differential coexpression modules...
b Module–trait relationships presenting the significance of the module eigengene correlation with traits. The left panel provides a color key to the nine modules. The color scale on right shows the module-trait correlation ranging from − 1 (green) to 1 (red). c The significantly enriched...
Overview of the toxicogenomic module associations with pathogenesis (TXG-MAP) for analysis of liver gene expression changes. (a) Module 69 consists of co-induced genes; genes are ordered clockwise starting at the hub gene (Mbd2), with decreasing correlation against the module eigengene. Nodes are...
High dimensional weighted gene co-expression network analysis - module preservation updates · smorabit/hdWGCNA@3624dd2
Despite investment in toxicogenomics, nonclinical safety studies are still used to predict clinical liabilities for new drug candidates. Network-based approaches for genomic analysis help overcome challenges with whole-genome transcriptional profiling us