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With pathway enrichment analysis, we got the main biochemical pathways and signal transduction pathways in which DEGs involved.
The KEGG pathway enrichment analysis of DEGs was also performed with the whole genome background as a reference to find the main biochemical pathways and signal transduction pathways in which DEGs involved.
We included in the model the main biochemical pathways, carbon, nitrogen, sulphur and phosphate metabolism, taking into account the cellular distribution of the components and the reactions (see Methods and Figure 1).
With a totally different approach, in another study, the main biochemical pathways in the different metabolisms were integrated in a generic stoichiometric model called the metabolic spreadsheet[ 15, 23].
To further identify the biological pathways that are active in bermudagrass, the 8067 unigenes annotated by blast analysis against KAAS (KEGG Automatic Annotation Server) were classified into five main biochemical pathways: 'cellular processes', 'environmental information processing'genetictinformationion processing'metabolismism' and 'organismal systems'.
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The main biochemical pathway of caspase-independent cell apoptosis was elucidated as the results of release of mitochondrial intermembrane space (IMS) proteins and inhibition of respiratory chain.
The reasons for the difference can be attributed mainly to the different approaches taken to reconstruct the CIN, and the filtering mechanisms applied to remove compounds that are not directly relevant for main biochemical pathway routes such as co-factors.
KEGG is a major public database of biological pathways, and significant enrichment in KEGG categories can identify differentially expressed genes involved in the main biochemical metabolic pathways and signal transduction pathways.
The five main KEGG biochemical pathways were represented: metabolism (2349 contigs), genetic information processing (2082), organism system (851), cellular processes (764) and environmental information processing (783).
Evidences reveal that many biochemical pathways associated with hyperglycaemia can increase the production of ROS (Huang et al. 2011).
With significant enrichment pathways, we could discern the main biochemical and signal transduction pathways.
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basic biochemical pathways
core biochemical pathways
main biochemical parameters
main biochemical targets
main biochemical components
main biochemical compounds
main biochemical characteristics
main biochemical determinants
main biochemical reactions
main biochemical processes
main biochemical means
main biochemical properties
main biochemical groups
main biochemical effects
main metabolic pathways
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