Figure 4

Cholesterol biosynthesis theme analysis. (A) Cholesterol biosynthesis theme from enrichment map. (B) Cholesterol biosynthesis-associated heatmap. (C) Network of interactions among moxLDL-SMC cholesterol metabolism related genes, as retrieved by the GeneMANIA website, colored by gene expression at 3h (node center) and 21h (node border). Red indicates up-regulation, blue indicates down-regulation and white indicates no differential expression or no expression data available. Circles represent genes and connecting lines represent interactions between genes. The network was generated using a GeneMANIA query of 43 cholesterol synthesis related genes (large circles) differentially expressed at either 3h or 21h. GeneMANIA retrieved known and predicted interactions between these genes and added extra genes (smaller white circles) that are strongly connected to query genes (we used the default setting of 20 additional connecting genes). Light blue lines indicate pathway interactions from the Reactome pathway database, dark blue lines indicate experimentally determine physical interactions, from various protein interaction databases included in GeneMANIA, and brown lines indicate predicted interactions, mostly from the I2D database of protein interactions predicted from experimentally determined physical interactions in other species. GeneMANIA advanced settings were used to search only physical, pathway and the default set of predicted networks. We excluded co-expression, co-localization and genetic interaction networks from the search to focus the analysis on higher confidence physical and pathway interactions.