This set of Python scripts works to merge pathway related table metadata (omics profiles, non-KEGG pathway metadata) from external platforms like R and Cytoscape to automate common tasks in the visualization process.
A mechanism to handle both of these issues is to merge all pathways from detailed metabolism categories that are categorized under the same more general metabolism categories provided in KEGG.
From PathwayAPI, 87 PDSs are derived from the non-merged pathways (derived from 75 different pathways; Additional file 2: Table S1), of which, 23 belong to pathways merge-able in PathwayAPI via LCS.
For the highest completeness, we employed a network of functional coupling that was drawn up using the methodology of the data integration tool FunCoup [ 13], and then merged with curated pathways from Kyoto Encyclopedia of Genes and Genomes (KEGG), protein complex data from CORUM, and a special network from glioblastoma data.
The small drop of 5 PDSs (from 87) suggests that merging the pathways (based on the LCS approach) did not make any major change to the overall results.
Beyond facilitating the interpretation of pathways in a gene-oriented manner, the approach also assigns unique identifiers to nodes, enabling merging graphs from different pathways.
This strategy has the additional advantage of providing enough sites in each individual gene set to be used as neutral reference, without the need of merging sites from different pathways.
We recently developed an integrated pathway database, PathwayAPI [ 3], which utilises a novel pathway merging approach based on pathway name matches (Longest Common Substring matching; LCS) [ 3].
Another variant of the TGF-β pathway was also among the top 30 pathways (26th place), as was the 'joint pathway' (TGF_joint, 8th place), which was created by merging the genes from the two pathways (see Materials and methods).
As a result, many published pathway-based application (Jimeno et al., 2008; Pangas et al., 2008; Setlur et al., 2007; Xu et al., 2007) or evaluation (Liu et al., 2007; Song and Black, 2008) in microarray data analysis used a couple of hundred well-curated non-redundant pathways merged from KEGG and other public annotation systems like Biocarta and/or Gene Ontology (GO).
