官方注释: Figure 1: Visualizing the gene network using a heatmap plot. The heatmap depicts the Topological Overlap Matrix(TOM) among all genes in the analysis. Light color represents low overlap and progressively darker red color represents higher overlap. Blocks of darker colors along the diagona...
GWAS-linked genes (L2G score > 0.5) have borders colored in an orange to red gradient (count of GWAS-linked traits). d, Simplified heatmap of one the clusters in a concerning allergic reactions (node and edge color code are the same as in c). In this case, two modules were ...
(D) regulatory effects of TFs on individual genes with “red” as activation, “blue” as depression, and “white” as no regulatory effects; (E) a heatmap of TF protein activities across biological samples of multiple conditions with “red” as enhanced activity, “green” as reduced ...
Below each local Manhattan plot is displayed the LD heatmap. Color coding within the LD heatmap ranges from white to black and the parameter for estimating pairwise LD was R square. The white color within the LD heatmap corresponds to an R-square value of 0, whereas the black color ...
Heatmap of topological metrics computed for Cancer Genes Network.Vashisht, ShikhaBagler, Ganesh
# First, smooth expression for a cleaner plot ccells <- xdyn$cells expSmoothed <- grnKsmooth(expDat, ccells, BW=0.03) # Plot a heatmap of the dynamic TFs tfstoplot<-intersect(dgenes,mmTFs) dynTFs<-xdyn dynTFs$genes<-dynTFs$genes[names(dynTFs$genes) %in% tfstoplot] hm_dyn(exp...
An alternative is a multi-dimensional scaling plot; an example is presented in Figure 2B. Relationships among modules can be summarized by a hierarchical clustering dendrogram of their eigengenes, or by a heatmap plot of the corresponding eigengene network (function labeledHeatmap), illustrated in ...
The target genes were then all subjected to the Database for Annotation, Visualization, and Integrated Discovery (DAVID, https://david.ncifcrf.gov/) to carry out GO and KEGG enrichment for functional enrichment analysis. P-values were derived from the DAVID database and set to below 0.05 [...
In all panels, the P value was obtained by using a two-sided t test. In the boxplots (B, G), each box shows the interquartile range (IQR between Q1 and Q3) for the corresponding set. The central mark (horizontal line) shows the median and the dots show the rest of the ...
Complex diseases are inherently multifaceted, and the associated data are often heterogeneous, making linking interactions across genes, metabolites, RNA, proteins, cellular functions, and clinically relevant phenotypes a high-priority challenge. Disease