Skip to main content
. 2018 Mar 2;118(8):1062–1073. doi: 10.1038/s41416-018-0025-x

Table 1.

Pathway enrichment analysis using Reactome of genes significantly overexpressed in decitabine/TSA-treated HMCLs

Gene set name k/K # Genes in Gene Set (K) # Genes in Overlap (k) P-value FDR q-value Genes
Interferon alpha/beta signaling (R) 0.0069 67 18 0.0000 5.98E-13 IFITM1, IFITM2, IFIT1, IFIT3, IFIT2, RSAD2, IFI27, EGR1, STAT1, XAF1, OASL, OAS1, OAS2, IRF7, IRF6, USP18, GBP2, MX1
Interferon gamma signaling (R) 0.0074 72 17 0.0000 1.52E-11 TRIM22, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, CD44, HLA-DQB1, STAT1, HLA-DPB1, HLA-DRA, OASL, OAS1, OAS2, IRF7, IRF6, GBP2, GBP1
Inflammatory bowel disease (IBD) (K) 0.0068 66 13 0.0000 6.70E-08 GATA3, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, STAT4, STAT1, HLA-DPB1, IL4R, HLA-DRA
Allograft rejection (K) 0.0039 38 10 0.0000 2.37E-07 PRF1, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Graft-versus-host disease (K) 0.0043 42 10 0.0000 5.03E-07 PRF1, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Asthma (K) 0.0032 31 9 0.0000 5.03E-07 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Cell adhesion molecules (CAMs) (K) 0.0148 144 16 0.0000 8.00E-07 ALCAM, SDC4, SDC2, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, CDH1, NRCAM, SELL, HLA-DRA, CD6
Antigen processing and presentation (K) 0.0080 78 11 0.0000 1.02E-05 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HSPA1A, HSPA2, HLA-DRA
Intestinal immune network for IgA production (K) 0,0049 48 9 0.0000 1.15E-05 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Systemic lupus erythematosus (K) 0.0138 135 13 0.0000 5.28E-05 C3, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HIST1H2AE, HIST1H2BG, HIST1H2BD, HLA-DRA
TCR signaling (R) 0.0067 65 8 0.0000 8.54E-04 PAG1, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DPB1, HLA-DRA
MHC class II antigen presentation (R) 0.0091 89 9 0.0001 0.001 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Rheumatoid arthritis (K) 0.0092 90 9 0.0001 0.001 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA
Phagosome (K) 0.0158 154 11 0.0002 0.003 C3, HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DMA, HLA-DMB, HLA-DPB1, CLEC7A, HLA-DRA
Costimulation by the CD28 family (R) 0.0064 62 7 0.0002 0.003 HLA-DQA1, HLA-DRB5, HLA-DRB1, HLA-DPA1, HLA-DQB1, HLA-DPB1, HLA-DRA
IL12 signaling mediated by STAT4 (N) 0.0031 30 5 0.0003 0.005 PRF1, HLA-DRB1, STAT4, HLA-DRA, ETV5
Validated transcriptional targets of TAp63 isoforms (N) 0.0050 49 6 0.0003 0.006 EGR2, CDKN1A, MFGE8, NQO1, IGFBP3, PMAIP1
T-cell activation (P) 0.0083 81 7 0.0009 0.01 HLA-DQA1, HLA-DPA1, HLA-DMA, HLA-DMB, ITPR1, HLA-DRA, PIK3CD
Direct p53 effectors (N) 0.0135 132 9 0.0009 0.01 ATF3, TGFA, SFN, CDKN1A, DUSP1, HSPA1A, CD82, IGFBP3, PMAIP1
ECM–receptor interaction (K) 0.0089 87 7 0.0013 0.01 SDC4, FN1, COL1A1, COL1A2, CD44, ITGA7, LAMB3
IL4-mediated signaling events (N) 0.0066 64 6 0.0013 0.02 EGR2, PARP14, COL1A1, COL1A2, IL13RA2, IL4R
Proteoglycans in cancer (K) 0.0209 204 11 0.0016 0.02 CBLB, ANK3, SDC4, SDC2, FN1, CDKN1A, CD44, FLNB, ITPR1, HPSE, PIK3CD
p53 signaling pathway (K) 0.0070 68 6 0.0018 0.02 SFN, CDKN1A, CD82, SESN3, IGFBP3, PMAIP1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes (N) 0.0048 47 5 0.0020 0.02 CBLB, GATA3, EGR1, EGR2, GBP3
Apoptotic execution phase (R) 0.0048 47 5 0.0020 0.02 GSN, TJP2, CDH1, H1F0, DSP
Proteoglycan syndecan-mediated signaling events (N) 0.0004 4 2 0.0026 0.03 SDC4, SDC2
ErbB1 downstream signaling (N) 0.0103 100 7 0.0028 0.03 NCKAP1, EPS8, SFN, EGR1, DUSP1, CHN2, STAT1

Gene annotation and networks were generated with the Reactome Functional Interaction Cytoscape plugin (http://www.cytoscape.org/)