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In the study of positive selection, concentration of genes in particular, apparently selected pathways is commonly tested.
These groups were then assessed for enrichment in genes belonging to the selected pathways using Ingenuity Pathways Analysis (IPA) (http://www.ingenuity.com, release March 2014).
Techniques initiating signals at defined starting points and cellular locations are attractive to elucidate the output of selected pathways.
The plots of gene abundance at the wood surface against abundance in the wood centre show first that the selected pathways are always present at the surface when they are detected in the wood centre (Figure 6).
Genes assigned to the selected pathways in the enriched modules (FDR < 0.05) were further included in the seed gene list (DNAJB1 and ENC1 for Nrf2 pathway and ARNT and PRKCA for AhR pathway).
The PAS of the two selected pathways had a significant positive correlation to the TGI of the tumorgrafts (R 2=0.8754, P value=0.0061 and R 2=0.7166, P value=0.0335, respectively).
Further, we selected pathways that were unique to the two patients in this study.
Subsequently, selected pathways were drawn manually for biological phenomenon highlighted by the correlations of molecular abundance.
The MetaCore software (GeneGo Inc, St Joseph, MI) was used to identify common molecular pathways at both doses and to create regulatory networks for selected pathways.
A full list of these pathways is found in Tables S2, S3 and S4, while selected pathways are presented in Figure 5B.
Datasets containing both up-regulated and down-regulated genes were also analyzed in selected pathways pertaining to cell cycle progression at G1/S and G2/M.
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