dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Figure 2
In-depth analysis for network-level understanding.
(A) Heatmap visualisation of the semantic similarity between pairs of domains according to their annotations by Disease Ontology (DO). (B) Network representation of the pairwise domain semantic similarity. It is a weighted and undirected network, with edge thickness indicating semantic similarity between a pair of domains/nodes. Nodes are labeled by both numeric id and textual description. (C) A table listing GOMF terms and their annotated domains (used as domain seeds for random walk with restart, RWR). Notably, terms used here are only those with at least 3 annotatable domains that are also in the domain network (see Figure 2B). (D) Contact (statistical significance) network between GOMF terms in Figure 2C, as estimated by RWR on the domain network in Figure 2B. Only those significant contacts/edges (adjusted p-values<0.1) are shown, with thickness indicating the contact strength (z-score).