In both cases, additional annotations can be added to the visualization to improve interpretation of the modules, e.g., to indicate the functional annotation of the genes, and interactivity can be used to accelerate the exploration of the modules.
The approach performs well when evaluated against similar tools and smaller overall module size allows for more specific functional annotation and facilitates the interpretation of these modules.
All this leaves the biological interpretation of these modules murky – surely there must be more than five regulatory systems across the life cycle of these species, and if so then what do these module groupings really reflect?
This remark corroborates that the corner-stone of our method, i.e. the integration of different kinds of data, fulfils more successfully the biological interpretation of the term 'functional module'.
We use biological annotation data from Gene Onotology (GO); (Ashburner, 2000) and Kyoto Encylcopedia of Gene and Genome (KEGG) (Kanehisa et al., 2006) to assist the interpretation of the inferred gene modules.
The interpretation of a module's substructure is further facilitated by the integration of other data types.
A limitation of these methods is that they still are not a gene-gene network, therefore, interpretation of the meaning of each module is difficult, varying with each cluster.
The smaller distribution of module sizes associated with Walktrap-GM highlights a more specific and informative set of biological interactions that facilitates interpretation of modules; where the functional annotation of larger modules that may otherwise be too general to be meaningful.
For easier interpretation of the relationships between expression and methylation modules, we use the same module labels for modules that show significant overlap.
The first interpretation keeps the view that a step of the module coincides with an instant, whereas in the second interpretation new instants are introduced by the refined clocks, but these instants are not visible to the outside.
