ugraph {SubpathwayMiner}R Documentation

The undirected graph list based on enzyme commission (EC) numbers constructed from KEGG metabolic pathways

Description

Undirected graph list based on enzyme commission (EC) numbers constructed from KEGG pathways.

Format

A list of graph

Details

Generally, A metabolic pathway can be considered as a graph with chemical compounds as nodes and enzymes as edges.

We simplify metabolic pathways. Each metabolic pathway is converted to an undirected graph with enzymes as nodes. Two enzymes are connected by an edge if their corresponding reactions have a common compound. Chemical compounds are then omitted from graphs. .

If we consider the direction of reaction. The pathway will be a directed graph.

Note that each graph in uGraph or dGraph is constructed from metabolic pathways and one pathway can only build not more than one graph.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

References

Ogata,H., Fujibuchi,W., Goto,S. and Kanehisa,M. (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res., 20, 4021-4028.

See Also

dGraph,KOuGraph


[Package SubpathwayMiner version 2.0 Index]