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/)