Table 4.
SAM-GS results (only top 10 rows are shown)
| Gene Set Name/Pathway | GS Size | GS P Value (0 ↔ <1/nb Permutations) | GS q Value | oGS Size | Genes Evaluated in Our Study Belonging to the Stated Pathway |
|---|---|---|---|---|---|
| SIG_CD40 PATHWAY MAP | 1 | 0.02 | 0.386 | 34 | MAPKAPK5 |
| ST_p38_MAPK_Pathway | 1 | 0.02 | 0.386 | 34 | MAPKAPK5 |
| FRASOR_ER_ DOWN | 1 | 0.045 | 0.386 | 68 | KYNU |
| HTERT_DOWN | 1 | 0.045 | 0.386 | 64 | KYNU |
| NFKB_ INDUCED | 7 | 0.08 | 0.386 | 106 | CCL20/FN1/IL15/IL1B/IL6/IL8/TNF |
| X41bbPathway | 2 | 0.08 | 0.386 | 18 | IFNG/IL4 |
| MAP00380_ Tryptophan_ metabolism | 3 | 0.085 | 0.386 | 42 | HAAO/KYNU/TDO2 |
| StemPathway | 3 | 0.09 | 0.386 | 15 | IL4/IL6/IL8 |
| CR_IMMUNE_ FUNCTION | 6 | 0.105 | 0.386 | 50 | IFNG/IL10/IL13/IL15/IL1B/IL4 |
| MAP00340_ Histidine_ metabolism | 1 | 0.12 | 0.386 | 20 | HNMT |
| 89 genes in current study | 89 | 0.185 | 0.386 | 89 | AADAT/AHR/C4BPA/CALR/CCBL2/CCL20/ CD3E/CD74/CLDN1/CLDN12/CLDN15/ CLDN16/CLDN2/CLDN3/CLDN4/CLDN7/ CPSF1/CTNNA1/CTNNB1/DLG1/FGFR4/ FN1/FOXP3/GOT2/GPBAR1/GUCA2B/ HAAO/HNMT/HRH1/HRH2/IDO1/IDO2/ IFIT3/IFNG/IL10/IL13/IL15/IL17A/IL1B/ IL2RA/IL4/IL6/IL8/INADL/KITLG/KMO/ KYNU/MAGI1/MAPKAPK5/MKNK2/MPP5/ MPP7/MYLK/NR1H4/OCLN/P2RY4/ PDZD3/PPP1CB/PPP2R5C/PRG2/PVRL3/ QPRT/RBP2/SLC10A2/SLC6A4/SLC9A1/ SOS1/TDO2/TFF1/TGFB1/TJP1/TJP2/TJP3/ TLR1/TLR2/TLR3/TLR4/TLR5/TLR6/TLR7/ TLR8/TLR9/TNF/TNFSF14/TNFSF15/ TPH1/TPSAB1/TPSB2/VIP |
SAM-GS, Significance Analysis of Microarray to Gene-Set Analyses; GS size, number of genes in the gene set/pathway; GS P value, permutation test for no association between the gene expression of the gene set and the binary phenotype (IBS-D compared with controls); GS q value, to account for multiple comparisons when multiple gene sets are tested, one might consider FDR instead of type I error probability; oGS, original number of genes in the pathway/gene set (for example, there were 106 genes in the NFKB_INDUCED pathway, where 7 genes from our study were found); Genes in Pathway, the genes in our study found in the pathway/gene set (for example, there are 7 genes from our study overlapping with NFKB_INDUCED pathway; the genes are CCL20, FN1, IL15, IL1B, IL6, IL8, and TNF).