Online resource 1Validation of gene expression of the microarray with PTGS2 real-time qPCR. Correlation of microarray and qPCR-data from 0% PDX (a); 1% PDX (b); and 2% PDX (c).
Online resource 2 (a)Multivariate analysis of variance (50-50 MANOVA) for two first principal components of the PCA. The effect of polydextrose, PDX is statistically significant with p<0.001. (b) Analysis of variance for linear model calculated using values projected on vector separating the medium-only and butyrate. Effect of PDX is statistically significant with p<0.001.
Online resource 3The density estimates for distribution of the sample projections onto the vector separating the medium (black vertical line) and butyrate (turquoise blue vertical line). The green color column indicates the 0% PDX, red color column 1% PDX, and blue color column 2% PDX.
Online resource 4Differentially up-regulated (a) and down-regulated (b) genes disclosed by 1% PDX. In the genes marked with asterisk (*) the regulative effect brought out by PDX was beyond the effect of butyrate.
Online resource 5 Differentially up-regulated (a) and down-regulated (b) genes disclosed by 2% PDX. In the genes marked with (*) the regulative effect brought out by PDX was beyond the effect of butyrate.
Online resource 6 Cell cycle pathway as illustrated byGenMAPP. Genes regulated by 1% PDX (a) or by 2% PDX (b). The rectangles representing the genes are divided into four subsections for V1-V4 as indicated in the bottom part of figure (b). The red color indicates up-regulation and green color down-regulation, while a rectangle without color indicates a gene non-regulated by PDX.
Online resource 7 Apoptosis pathway as illustrated by GenMAPP. Genes regulated by 1% PDX (a) or by 2% PDX (b). The rectangles representing the genes are divided into four subsections for V1-V4 as indicated in the bottom part of figure (b). The red color indicates up-regulation and green color down-regulation, while a rectangle without color indicates a gene non-regulated by PDX.
Online resource 8 PPAR responsive gene regulation. (a) Schematic illustration of PPAR binding to peroxisome proliferator response element (PPRE) together with a nuclear coreceptor and coactivators. In the unliganded state, PPAR interacts with anti-repressor complex; the deacetylated state activity of corepressor inhibits gene transcription. Upon binding of ligands, PPAR heterodimerises with RXR and recruits the coactivator containing histone acetylase activity and facilitates transcription of various genes (adapted from [44]); (b) Expression pattern of genes involved in PPAR-mediated gene regulation or PPARtarget genes. The genes written in bold-case are found in (a) and are part of the activation complex, whereas the rest are PPAR target genes. The genes marked with asterisk (*) were regulated by PDX beyond the effect of butyrate.