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Schema Diagram


Schema for regulatory network graphs

Schema for regulatory network graphs showing the types of nodes (every graph node must be one of these types) and the allowed connections between them. In the schema, there are three Central Dogma nodes for gene, mRNA and protein, along with suitable relationships.  These nodes are augmented with transcriptional regulatory elements at the single-site and module/cassette level.  Both protein:protein complexes and protein:DNA complexes receive their own node types.  There are also three nodes types for reactions involving protein: degradation, assembly, and state modification such as ubiqitination, neddylation, or phosphorylation.  Each of these could have been drawn as a kind of link rather than node, except that we know they often involve three or more protein components and it is hard to draw or compute with three-headed arrows. We therefore transform them to a standard bipartite graph representation as a simple way to handle the problem. This design will enable us to produce large regulatory networks as an “unrolled” version of this schema, in which each schema node has many instances and each schema link (between nodes of type A and B, let us say) corresponds to many actual links between individual nodes of type A and B.  Such a network is consistent with the schema of the Figure above..

Architecture Diagram - Top Level
Architecture Diagram

Designed by Brandon King
kingb at