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To test how gene duplication and associated gene expression variation may shape Arabidopsis metabolism, I focused on transcripts associated with specific metabolic pathways using the AraCyc databases predictions [20], [21].
Out of these, 197 genes could be associated with different metabolic pathways using the RiceCYC 1.2.
MapMan software (Thimm et al. 2004) was used to visualize the distribution of DEGs into different bins and their appearance in different metabolic pathways using Oryza - specific mapping file.
MapMan analysis of the secondary metabolic pathways using the differentially expressed genes derived from (a) comparison C + F vs C, and (b) comparison W + F vs W. Red arrows indicate the pathways enriched in up-regulated genes.
In this study, we demonstrate production of C-4 carboxylic acids non-native to the host, specifically crotonic and butyric acids, from methane in an engineered M. buryatense 5GB1C by diversion of carbon flux through the acetyl-CoA node of central 'sugar' linked metabolic pathways using reverse β-oxidation pathway genes.
It also implies that there is potential for discovery of new genes in this organism and possibly of new gene networks and metabolic pathways using the assembled data.
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Knowledge of the metabolic pathways used by anaerobic bacteria to break down hydrocarbons has allowed us to identify unique intermediate compounds that can be used as biomarkers for in situ activity.
Analysis of the Sulfobacillus genomes illuminates metabolic pathways used in various transformations of carbon, nitrogen, and sulfur metabolism (summarized Figure 5 and Additional file 5: Table S2).
Shown in Table 2. is the distribution of the unigenes into general metabolic pathways used by KEGG.
The metabolic pathways used are those of the Kyoto Encyclopedia of Genes and Genomes (KEGG) [ 46].
The metabolic pathways used by tsetse combine standard pathways used by most organisms with pathways specific to tsetse.
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