PMC

PPI network and module analysis network. (a) (left) Normal group-common target PPI network between hepatitis B data and predicted targets of YZHG; (right) module analysis of the CytoHubba plug-in identified the top 10 genes to construct key module network 1. (b) (left) The hepatitis B-hepatitis B-related hepatocellular carcinoma data and the PPI network of YZHG; (right) module analysis was performed using the CytoHubba plug-in to obtain the top 10 genes and construct key module network 2. (c) (left) Hepatitis C PPI data and PPI network of YZHG; (right) the top 10 genes were obtained to construct key module network 3 after the CytoHubba plug-in module analysis. (d) (left) PPI network of hepatitis C-related cirrhosis-hepatitis C-related hepatocellular carcinoma; (right) module analysis of the CytoHubba plug-in identified the top 10 genes to construct key module network 4. Left: orange circle represents a common target, and purple means related protein information obtained by PPI. Right: the top five genes with the highest scores are represented by yellow to red, and the redder the color, the higher the MCC score.

A. The heatmap of lncRNAs and mRNAs in the module 1 based on expression. The columns represented 6 samples and the rows represented lncRNAs and their mRNA neighbors. Labels on the right were the names of lncRNAs and mRNAs. B. The heatmap of lncRNAs and mRNAs in the module 2 based on expression data. The columns represented 6 samples and the rows represented lncRNAs and their mRNA neighbors. Labels on the right were the names of lncRNAs and mRNAs. C. The ceRNA module network of module 1 extracted from global triple network. D. The ceRNA module network of module 2 extracted from global triple network. F. The triple network of lncRNA FAM13A-AS1 extracted from global triple network. E. The triple network of lncRNA LINC00648 extracted from global triple network.

(A) Entire PPI network. (B) PPI network of module 1. (C) PPI network of module 2. (D) PPI network of module 3.

Construction of co-expression modules of ovarian cancers based on lncRNA data (left column) and mRNA data (right column). A Analysis of network topology for various soft-threshold powers, including the scale-free fit index (y-axis) and the mean connectivity (degree, y-axis). B Check scale-free topology, and here the adjacency matrix was defined using soft-thresholds with beta = 3 for lncRNA data, and with beta = 4 for mRNA data. C Clustering dendrograms of lncRNAs or mRNAs, with dissimilarity based on topological overlap, together with assigned module colors. As a result, six co-expression modules (co-expression green module, co-expression turquoise module, co-expression yellow module, co-expression blue module, co-expression brown module, co-expression gray module) were constructed from lnRNA data, and 14 co-expression modules from mRNA data (co-expression magenta module, co-expression tan module, co-expression green module, co-expression black module, co-expression yellow module, co-expression green-yellow module, co-expression red module, co-expression turquoise module, co-expression purple module, co-expression blue module, co-expression pink module, co-expression brown module, co-expression salmon module, co-expression gray module). D The heatmap depicts the topological overlap matrix (TOM) among all lncRNAs or all mRNAs. E Visualizing the gene network using a heatmap plot