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not relevant. Nevertheless, comparing the relationships between the
modules derived from expression data from these organisms may
give us new insights into the global organization of their transcription
programs.
It is useful to provide graphic visualizations of the higher-order
module organization. To this end, we have proposed two complementary
presentations. A module tree [Fig. 8(a)] summarizes the entire com-
pendium of transcription modules identified by the ISA at different res-
olutions. Similar modules detected for different stringencies on
coexpression are connected by lines and form the branches of the mod-
ule tree. Branches may merge if several modules that emerge at a higher
threshold converge into the same module when iterated at a lower
Fig. 8. Visualization of large-scale expression data. (a) Module trees summarize the
transcription modules identified by the ISA at different resolutions (rectangles).
Similar modules identified for different stringencies on coexpression are connected by
lines and form the branches of the module tree. Branches may merge if several mod-
ules that emerge at a higher threshold converge into the same module when iterated
at a lower threshold (transversal lines). (b) All modules identified at the same resolu-
tion are represented on a plane such that their distances reflect the regulatory
relations. Modules induced under similar conditions are closer to each other, while
large distances indicate inverse activation.
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