In addition, these networks can be constructed based on shared pathways [35], shared miRNA [36], shared protein complex [37], shared disease ontology [38] and disease comorbidity [39].
We have taken a computational approach to studying disease relationships through 1) systematic identification of disease associated genes by literature mining, 2) associating diseases to biological pathways where disease genes are enriched, and 3) linking diseases together based on shared pathways.
Here we describe our method to construct a network of human phenotypes (traits and diseases) based on shared biological pathways of the associated genes.
The authors of the Ukrainian study commented that the apparent similarity between birth-month patterns for both types of diabetes has implications for exploring hypotheses based on shared etiological pathways.
We also note that a disease similarity network can be constructed based on shared disease gene [30], shared pathways [35], shared miRNA [36], shared protein complex [37], shared disease ontology [38] and disease comorbidity [39].
Specifically, we were also able to construct a pathway network following the same logic as the HDN (Section "Human disease networks"): connecting pathways based on shared phenotypes, as well as a bipartite graph with links between PTs and pathways.
The concept of this function-based approach (FBA) quite differs from the physical entity-based approach (PEBA) which identifies pathway cross-talks based on shared components and protein-protein interaction.
Pathway databases associate an organism's proteins with molecular functions, represent these as reactions, and group the reactions based on shared components: the output of one reaction might be the input, catalyst or regulator of a second, and so on.
