Fig. 2

Components of gene regulatory networks (GRNs) and a schematic overview for performing perturbation analyses in Multioviz. a Visualization of the components making up a GRN. Here, variables (e.g., SNPs and genes) are represented as nodes. The shape of these nodes are different depending on the molecular level that they represent and the color scheme describes the significance level of each variable according to a statistical model (e.g., p-value or PIP). Insignificant SNPs are more yellow and more statistically important SNPs are depicted in red. Similarly, insignificant genes are light blue, while significant genes are dark blue. b Directed edges are used to map nodes between molecular levels (e.g., SNPs reside in the boundaries of genes) [18]. Since we do not assume to have access to temporal information, interactions between variables on the same molecular level are represented by undirected edges. There are three classes of edges between and within molecular levels: no connectivity, sparse connectivity, and complete connectivity. Here, the first molecular level has no connectivity since there are no direct interactions between SNPs. However, the second molecular level has complete connectivity because there is an interaction between all genes. The nodes and edges together form a visual representation of a GRN. c To emulate perturbation analyses, Multioviz allows users to select molecular variables (i.e., nodes), delete them, and rerun the statistical analysis to generate a new GRN. To perform this type of analysis within in the Multioviz interface, users simply highlight the variable of interest by (1) clicking on the node and selecting “Edit”, (2) clicking on “Delete selected”, and then (3) clicking “Rerun” under the “Perturb” left drop-down menu. An overview of the Multioviz interface can be found in Fig. 3