DOI: 10.5281/zenodo.10676552
title: Supplementary Tables Chapter 6 - Coco Duizer

description: Supplementary Tables Chapter 6 - Coco Duizer

Table 1. DEG HT29 ADP-heptose Flagellin.Differentially expressed genes in HT-29 cells after stimulation with ADP-heptose or flagellin as calculated using DESeq2. Genes with a minimum fold-increase of 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table 2. VENN HT-29 ADP-heptose Flagellin.Differentially expressed genes, as calculated in Table 1, that are uniquely upregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-up), uniquely upregulated in flagellin-stimulated HT-29 cells (HT-29 Flagellin-up), or upregulated in both ADP-heptose-, and flagellin-stimulated HT-29 cells (HT-29 ADP-heptose-up:HT-29 Flagellin-up).

Table 3. Table 3 - KEGG Enrichment HT-29 ADP-heptose Flagellin.Upregulated pathways and genesets as calculated by KEGG over-representation analysis and KEGG gene set enrichtment analysis (GSEA) in HT-29 cells following stimulation with ADP-heptose or flagellin. Pathways and geneset with an adjusted p value of <0.05 are shown.

Table 4. DEG Organoids Flagellin.Differentially expressed genes in rectal organoids after stimulation with flagellin as calculated using DESeq2. Genes with a minimum fold-increase of 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table 5. DEG PBMC ADP-heptose LPS.Differentially expressed genes in PBMCs after stimulation with ADP-heptose or LPS as calculated using DESeq2. Genes with a minimum fold-increase of 1 and 2 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction are shown. Upregulated genes are shown in green, downregulated genes are shown in red.

Table 6. VENN PBMC ADP-heptose LPS.Differentially expressed genes, as calculated in Table 5, that are uniquely upregulated in ADP-heptose-stimulated PBMCs (PBMC ADP-heptose-up), uniquely upregulated in LPS-stimulated PBMC (PBMC LPS-up), or upregulated in both ADP-heptose-, and LPS-stimulated PBMC (PBMC ADP-heptose-up:PBMC LPS-up), or that are uniquely downregulated in ADP-heptose-stimulated PBMCs (PBMC ADP-heptose-down), uniquely downregulated in LPS-stimulated PBMC (PBMC LPS-down), or downregulated in both ADP-heptose-, and LPS-stimulated PBMC (PBMC ADP-heptose-down:PBMC LPS-down). Genes in the VENN diagram and this table had a minimum fold-increase of 1 with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction.

Table 7. KEGG Enrichment PBMC ADP-heptose LPS.Differentially regulated pathways and genesets as calculated by KEGG over-representation analysis and KEGG gene set enrichtment analysis (GSEA) in PBMCs following stimulation with ADP-heptose or LPS. Pathways and geneset with an adjusted p value of <0.05 are shown.

Table 8. VENN HT-29 PBMC ADP-heptose.Differentially expressed genes, as calculated in Tables 1 and 5, that are uniquely upregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-up), uniquely upregulated in ADP-heptose-stimulated PBMC (PBMC ADP-heptose-up), or upregulated in both ADP-heptose-stimulated HT-29 cells and PBMCs (HT-29 ADP-heptose-up:PBMC ADP-heptose-up), or are uniquely downregulated in ADP-heptose-stimulated HT-29 cells (HT-29 ADP-heptose-down), uniquely downregulated in ADP-heptose-stimulated PBMC (PBMC ADP-heptose-down), or downregulated in both ADP-heptose-stimulated HT-29 cells and PBMCs (HT-29 ADP-heptose-down:PBMC ADP-heptose-down). Genes in the VENN diagram and this table had a minimum fold-increase of 2 (HT-29 cells) or 1 (PBMCs) with a false discovery rate of 0.05 as calculated by Benjamini-Hochberg correction.

Table 9. KEGG Enrichment HT-29 PBMC ADP-heptose.Differentially regulated pathways as calculated by KEGG over-representation analysis in HT-29 and PBMCs following stimulation with ADP-heptose. Pathways with an adjusted p value of <0.05 are shown.