In this representation, chemical compounds, reactions and pathways may be represented in the same vectorial space.
With this description, chemical compounds, reactions and pathways can be concomitantly represented in the same vectorial space.
Nevertheless, TLR seems to be the main pathway triggered by these compounds, and similar pathways may be triggered by actual microbes in infected tissues.
RiceCyc is a new compound and pathway database obtained from known literature pathways and by computational approaches obtained from the fully sequenced rice genomes.
We developed perl scripts using the pathway tools software [ 42- 44] to obtain information on the reactions, compounds and metabolic pathways involved in the metabolism of the K12 strain of Escherichia coli.
PathRanker's functions are completely flexible allowing for either an analysis of the complete KEGG network or more tailored analysis of pathways between specific compounds and KEGG pathway groups.
"Our ultimate goal is to identify compounds and aging pathways that are relevant to humans in the hope that we contribute to making humans live longer, healthier lives," said lead author Ethan Sarnoski, graduate student in the Department of Molecular, Cellular & Developmental Biology.
ePlatton considerably reduced the redundancy of the ligand set of targets and made it easy to deduce the possible relationship between compounds and targets, pathways and side effects.
Depending on the species there may be specificity for particular sulfur compounds and metabolic pathways are not necessarily restricted to sulfur (Kirkwood et al. 2005, 2007a, b).
When all pathway mappings were converged, we were able to ascertain the presence of 398 enzymes, 584 reactions, 598 compounds and 152 pathways (Table 3).
