Figure 2: How to predict disease-gene or function-gene relationships across species.

(a) The objective is to predict gene-related functions or diseases across species by leveraging known annotations. (b) Network-based methods can annotate diseases or functions for genes across species by aligning networks or by embedding networks into a shared, low-dimensional feature space where a supervised learning model is then trained to propagate annotations. (c) Phylogenetic profile-based methods identify co-presence or co-absence of genes throughout evolutionary history, implying closely related functions among these genes. This relationship is then used to propagate annotations across species. (d) Disease and function annotations can be transferred by combining ontologies across species. Genes with similar functions or disease associations across species can then be identified through the ontology structure.