Proteomaps based on Gene Ontology

Proteomaps can be created based on any user-defined hierarchy tree. The following images of S. cerevisiae proteome (data from Lu et al., 2007) were created with the widely used and flexible Gene Ontology (GO).

Ontologies such as GO need to be adapted to form a tree graph. In GO ontologies, many non-terminal nodes are under several more general terms simultaneously. In addition, GO - being a directed acyclic graph rather than a tree - contains terms that are located at different distances from the root. Finally, the dynamic nature of GO contains for some genes more than 10 levels and we find that for proteomaps a more compact 3-level hierarchy is easier to visually comprehend.

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