During stationary phase, energy metabolism is limited and primarily consists of pathways that scavenge potential nutrients from the medium and from within the cell [56].
The IPA library consists of pathways from the mouse, human and rat genomes; therefore, identified pathways were based on homologous genes from the bovine genome.
MetaCyc consists of pathways, reactions, enzymes and metabolites together with literature information from more than 600 species, ranging from microbes to plants and human [ 17].
*Number of reactions categorized in a subsystem or found to be neighboring each metabolite Perturbations under aerobic conditions largely consisted of pathways involved in mediating the NADH and NADPH balance.
As in previous treatments, [ 22, 25], we consider a network consisting of two pathways, the X pathway and the Y pathway (Fig. 1A).
The total number of proteins/genes consisting of those pathways is 8614.
The ranked list of 2-fold differentially expressed genes was compared with a curated database consisting of molecular pathways and publicly available microarray experiments (Additional file 6).
We showed a visualization of a sub-graph consisting of 7 pathways and 34 GOBP terms that intersected with the MI response.
The complement is a complex system consisting of 3 pathways (classical, alternative and lectin), which helps to kill and clear pathogens.
The non-canonical Wnt signalling pathway consists of Wnt/Ca2+ pathway and Wnt/c-Jun N-terminal kinase (JNK) (planar cell polarity) pathway (Cohen et al, 2008).
Count matrices generated for pathway-level comparisons consisted of 353 pathways and a matrix of KO terms comprised of 4,399 KO terms generated for gene-level comparisons.
