Direct access to this object is deprecated.
pathways(species, "kegg") instead.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.
Pathway topology conversion
KEGG pathway were retrieved in KGML format from the KEGG ftp site.
KEGG database provides separate xml files, one for each pathway. A pathway is therefore define by all the reactions described within each file.
Pathway nodes often correspond to multiple gene products. These can be divided into protein complexes (proteins linked by protein-protein interactions) and groups made of alternative members (genes with similar biochemical functions). Thus, when considering signal propagation these groups are considered differently. The first kind (hereafter group AND) should be expanded into a clique (all proteins connected to the others), while the second (hereafter group OR) should be expanded without connection among them. In the KGML format there are two ways of defining nodes with multiple elements: protein complexes (group AND defined by entry type=``group'') and groups with alternative members (group OR defined by entry type=``gene'').
Compound mediated interactions are interactions for which a compound acts as a bridge between two elements. Since chemical compounds are not usually measured with high-throughput technology, they should be removed from the network to analyse gene signals. However, the trivial elimination of the compounds, without signal propagation, will strongly bias the topology interrupting the signals that pass through them. If element 'A' is linked to compound 'c' and compound 'c' is linked to element 'B', element 'A' should be linked to element 'B'. Within the KGML format there are two different ways of describing a compound mediated interaction: i) direct interaction type=``PPrel'' ('A' interacts whit 'B' through compound 'c' ) and ii) indirect one type=``PCrel'' ('A' interacts to compound 'c' and 'c' interacts with 'B').
Not all compounds are considered for the propagation because some of them (for example: H2O, ATP, ADP) are highly frequent in map descriptions and the signal propagation through them would lead to chains too long. Compounds not considered for propagation are not characteristic of a specific reaction, but act as secondary substrates/products widely shared among different processes.
graphite allows the user to see the single/multiple relation types that characterized an edge. The type of edges have been kept as much as possible similar to those annotated in the original data format. Some new types have been introduced due to topological conversion needs.