As can be seen in Additional file 3: Table S2 and Figure 4, most affected pathways contained differentially expressed genes from several different treatments.
Interestingly, metabolic pathways contain the most abundant DEGs whereby most of the genes were down-regulated after the four challenges.
Tumor suppressive autophagic pathways contain some key regulators, most notably Beclin-1, UVRAG, Bif-1, ATG5, p53 and FoxO1.
The three most significantly overrepresented pathways containing these TWIST1 co-expressed genes were: Focal adhesion pathway (Fisher's exact P = 1.0 × 10-8), ECM-receptor interaction pathway (Fisher's exact P = 9.9 × 10-7), and TGF-beta signaling pathway (Fisher's exact P = 2.6 × 10-4) (Additional file 3: Table S10).
The most highly induced pathways contained components of jasmonic acid biosynthesis, flavonoid biosynthesis, 13-lipoxygenase pathway, and phenylpropanoid biosynthesis, which demonstrated that the jasmonic acid defense pathway was involved in the localized resistant reaction of G. max [PI 88788] to H. glycines [ 14].
The KEGG pathways contain the genes assigned to these pathways.
Genes involved in sensory perception pathways contained most of the genetic variation, primarily SNPs (27%) and CNVs (60%).
Metabolic pathways (735 unigenes), pathways in cancer (186 unigenes) and biosynthesis of secondary metabolites (155 unigenes) were the three pathways containing most unigenes.
While most gene-families and pathways contained almost no differentially expressed genes in the tolerant genotype (Table 2), two gene-families, that is, trypsins and neurexins, did have a number of differentially expressed genes in the tolerant genotype.
The categories of plant hormone signal transduction and metabolic pathways contained the most targets, at 14.93%.
