Table 4.
Summary of GSEA Analysis
| Gene Set(Pathway) | Genes within Gene Set (Top 20 only) | NES | FDR | |
|---|---|---|---|---|
| 1 | DAC_BLADDER_UP(IFN signaling) | OAS2, MX1, IF144L, OAS1, CXCL2, TNFSF10, STC1, IFIT3, STAT1, ICAM1, MMP1, IRF7, CIS, MX2, C3, IL13RA2, TNFAIP3, HBEGF, NT5E, SLP1 | 2.38 | 0.000 |
| 2 | IFNA_UV-CMV_COMMON_HCMV_6HRS_UP (IFN and inflammatory signaling pathways) | OAS2, RSAD2, MX1, IFI44L, OAS1, IF127, OASL, TNFSF10, IFIT3, INDO, ISG20, CIORF38, TDRD7, STXI1, BAZIA, SAMHD1, TLR3, IRF7, GCH1, MX2 | 2.37 | 0.000 |
| 3 | DAC_IFN_BLADDER_UP (IFN signaling) | OAS2, MX1, OAS1, CXCL2, TNFSF10, IFIT3, STAT1, ICAM1, IRF7, CIS, MX2, C3, ILI3RA2, TNFAIP3, SLP1, CCL5, CCL20 | 2.36 | 0.000 |
| 4 | TAKEDA_NUP8_HOXA9_3D_UP (IFN signaling) | OAS2, RSAD2, MX1, IFI44L, OAS3, OAS1, CTSG, HERC5, IF127, OASL, IFIT3, IFIT1, IFIT2, IFIH1, CCL18, INDO, PLSCR1, DDX58, EPSTI1, DST | 2.35 | 0.000 |
| 5 | IFNA_HCMV_6HRS_UP (IFN and inflammatory signaling pathways) | OAS2, RSAD2, MX1, 1F144L, OAS1, IF127, OASL, TNFSF10, IFIT3, INDO, PLSCR1, ISG20, STAT1, TRIM22, IFIT5, CIORF38, TDRD7, STXI1, ZBTB20, BAZIA | 2.32 | 0.000 |
| 6 | CMV_HCMV_TIMECOURSE_12HRS_UP (IFN and inflammatory signaling_pathways) | OAS2, RSAD2, MX1, OAS1, OASL, TNFSF10, IFIT3, ISG20, CH25H, B4GALT5, IRF7, SOD2, PRPF19, MX2, GBP2, TNFAIP6, RARRES3, RHOB, CCL5, NR4A3 | 2.28 | 0.000 |
| 7 | TAKEDA_NUP8_HOXA9_8D_UP (IFN signaling) | OAS2, RSAD2, MX1, IFI44L, OAS3, OAS1, CTSG, HERC5, IFI27, LXN, NR4A2, IFIT3, IFIT1, IFIT2, DHRS3, C20ORF103, IFIH1, MTSS1, INDO, DDX58 | 2.18 | 0.001 |
| 8 | BENNETT_SLE_UP (IFN signaling) | OAS2, MX1, IFI44L, OAS1, OASL, TNFSF10, IFIT3, PLSCR1, CAMP, STAT1, C2, TAP1, IFI35, TDRD7, IFITM3, IRF7, APOBEC3C, MX2, SERPING1, LY6E | 2.14 | 0.002 |
| 9 | TAKEDA_NUP8_HOXA9_10D_UP (IFN signaling) | OAS2, RSAD2, MX1, IFI44L, OAS3, OAS1, HERC5, DCAL1, IFI27, OASL, NR4A2, IFIT3, IFIT1, IFIT2, DHRS3, CD38, C20ORF103, IFIH1, INDO, DDX58 | 2.12 | 0.003 |
| 10 | IFNALPHA_NL_UP (IFN signaling) | RSAD2, MX1, IFI44L, IF127, TNFSF10, PLSCR1, VCAM1, STAT1, IFITM1, UBE2D3, BST2, IRF7, CALR, MX2, HLA-E, PIAS4, KIAA0409, UBE2L6, AKR7A2, PSME1 | 2.10 | 0.004 |
| 11 | SANA_TNFA_ENDOTHELIAL_UP (IFN, inflammatory, and immune signaling pathways) | IL8, OAS2, MX1, IFI44L, OAS3, OAS1, CXCL2, CX3CL1, IFIT1, CXCL3, IFIH1, FIJ20035, PARP14, VCAM1, BIRC3, UBD, CCL2, GBP1, OXR1, NFKBIA | 2.07 | 0.006 |
| 12 | SANA_IFNG_ENDOTHELIAL_UP (IFN, inflammatory, and immune signaling pathways) | OAS2, MX1, IFI44L, QAS1, TNFSF10, CX3CL1, NOD27, IFIH1, INDO, ILI8BP, FLJ20035, PARP14, TNCRNA, STAT1, UBD, DTX3L, GBP1, LAP3, C17ORF27, CXCL9 | 2.04 | 0.008 |
| 13 | NTHIPATHWAY (NF-κB signaling-related to inflammation) | ILIB, IL8, DUSP1, NFKBIA, NR3C1, EP300, CREBBP, TGFBR1, IKBKB, MAP2K6, TLR2, RELA, MAPK14, MAPK11, TGFBR2, CHUK, MAP3K7, NFKB1, MYD88, MAP2K3 | 2.04 | 0.008 |
| 14 | GALINDO_ACT_UP (Inflammatory and apoptosis signaling) | IL1B, CXCL2, ILI8RAP, ILIRN, PTGS2, PDGFB, LILRB4, DUSP1, NFKB1A, IER3, FOSL1, CSF3, ICAM1, CCL3, RREB1, TNFSF9, BCL3, UBC, TNFAIP2, CCL4 | 2.04 | 0.008 |
| 15 | CMV_UV-CMV_COMMON_HCMV_6HRS_UP (IFN and inflammatory signaling) | RSAD2, MX1, OASL, NR4A2, IFIT3, ILI1, ZC3HAV1, RIPK1, PMAIP1, POLG2, ATF3, CREM, GCH1, C12ORF22, PSCD1, NR4A3, BTRC, SLC745, NR4A1 | 2.03 | 0.007 |
GSEA analysis of the microarray results for Aβ treatment versus control helped in identifying gene sets correlated predominately with inflammation. Pathway 13, NTHIPATHWAY is identified as one of the inflammatory gene sets of particular interest, such as IL-β and IL-8, the top-ranked genes in this set. All gene sets can be accessed at the Molecular Signatures Database, http://www.broad.mit.edu/gsea/msigdb/index.jsp (provided in the public domain by the Broad Institute at Massachusetts Institute of Technology, Cambridge, MA).