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The results are summarised in the pathway map shown in Fig. 3.
The pathway map was constructed from Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) (Kanehisa and Goto 2000), and identified proteins were adapted to this map.
For the pathway map, Student's t-test analysis coupled with Bonferroni correction was performed between treatment and control values to highlight individual metabolite trends and metabolite networks were constructed using KEGG pathway maps web tool (http://www.genome.jp/kegg/).jp/kegg/
The results are listed in a search result panel and are also visually highlighted by red markers placed onto the respective components on the pathway map.
Search results are directly shown within the pathway map, marked with red pins on the nodes as well as gray lines highlighting the corresponding edges for reactions.
Therefore, the pathway map should be able to be freely edited and annotated by adding nodes, edges or data, as in WikiPathways [46].
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Finally, the pathway maps that provide the necessary compounds for the conserved pathway maps are connected to the pathway-map network, until there are no more suitable pathway maps to be added.
When a pathway map includes several products that can be the initial substrates of the pathway-map network, this pathway map will be frequently accepted at the "extension of the pathway-map network" process.
A pathway map that can provide the initial substrates of the pathway-map network was chosen randomly from those other than the components of the pathway-map network, and was connected into the pathway-map network to create a new one.
Starting from the conserved pathway mapsγ, 10,000 sets of organism-specific pathway mapsγ were determined by expanding the pathway-map networks described in the Methods.
Further, a description, various synonyms, the CAS number, chemical formula, a reference picture (structural formula for compounds, image of the pathway-map for pathways), molecular weight, and mass are added as human-readable annotation, if available.
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CEO of Professional Science Editing for Scientists @ prosciediting.com