Table 4.

Biological pathways differentially represented in T12 surveillance biopsy samples from the three groups on the basis of whole-genome microarrays

Parameter	Gene Numbera	Normal (n = 25) versus IF Alone (n = 24)			Normal (n = 25) versus IF+i (n = 16)			IF Alone (n = 24) versus IF+i (n = 16)
		Gene Number P < 0.05b	% Increasedc	Pd	Gene Number P < 0.05	% Increasedc	P	Gene Number P < 0.05	% Increasedc	P
All detectable pathway-assigned genes	13,601	528			5469			5380
Death receptor signaling	51	7	86	0.003	24	83	0.2	24	75	0.2
CCR5 signaling in macrophages	43	6	100	0.005	21	76	0.2	22	64	0.08
Starch and sucrose metabolism	47	6	100	0.009	15	67	0.9	17	41	0.8
α-Adrenergic signaling	65	7	100	0.015	29	59	0.3	32	50	0.1
Macropinocytosis	57	6	100	0.02	30	67	0.04	23	61	0.5
CCR3 signaling in eosinophils	80	7	100	0.04	34	53	0.4	39	38	0.07
Chemokine signaling	53	5	80	0.05	24	67	0.3	28	50	0.03
Antigen presentation pathway	28	2	100	0.3	26	92	0.00001	20	90	0.0006
CTLA4 signaling in cytotoxic T lymphocytes	66	1	100	0.9	41	68	0.0003	38	66	0.002
T helper cell differentiation	22	2	100	0.2	17	100	0.0005	14	100	0.02
IL-4 signaling	56	2	100	0.6	35	77	0.0006	31	74	0.01
CD28 signaling in T helper cells	81	2	100	0.8	47	79	0.0009	44	75	0.004
CTL-mediated apoptosis of target cells	16	1	100	0.5	13	85	0.001	11	82	0.02
Dendritic cell maturation	98	6	100	0.1	55	87	0.001	50	74	0.01
Toll-like receptor signaling	40	2	100	0.5	25	64	0.004	19	58	0.2
Role of PKR in IFN induction and antiviral response	33	0	–	1.0	21	67	0.006	21	57	0.004
NK cell signaling	72	3	100	0.5	40	73	0.006	44	64	0.0002
IFN signaling	24	3	100	0.06	16	94	0.008	12	100	0.2
T cell receptor signaling	72	2	100	0.8	39	74	0.01	38	68	0.01
Calcium-induced T lymphocyte apoptosis	33	2	100	0.3	20	75	0.01	18	72	0.06
Role of pattern recognition receptors in recognition of bacteria and viruses	60	3	100	0.4	33	85	0.01	31	81	0.04
Hepatic fibrosis/hepatic stellate cell activation	99	6	83	0.2	51	78	0.02	40	68	0.5
NF-κB signaling	102	3	100	0.8	52	69	0.02	40	63	0.6
Fcγ receptor–mediated phagocytosis in macrophages and monocytes	78	1	100	1.0	41	71	0.02	42	64	0.007
Glycosphingolipid biosynthesis, neolactoseries	16	1	0	0.5	11	55	0.02	10	60	0.05
Role of NFAT in regulation of the immune response	123	5	100	0.5	61	72	0.02	61	66	0.01
B cell receptor signaling	116	6	83	0.3	57	70	0.03	57	60	0.02
EGF signaling	42	1	100	0.8	23	48	0.04	19	42	0.3
Fc ϵ RI signaling	69	3	100	0.5	34	56	0.08	37	46	0.02
fMLP signaling in neutrophils	82	5	100	0.2	39	64	0.1	41	56	0.03
GM-CSF signaling	56	2	50	0.6	29	62	0.05	29	59	0.04
CXCR4 signaling	114	6	100	0.3	48	54	0.4	54	43	0.05

^aRefers to total number of detectable genes within each biological pathway. Biological pathway nomenclature derived from Ingenuity Pathways Analysis software (Ingenuity Systems).

^bRefers to the number of pathway genes with significantly altered expression (by t test) between groups.

^cRefers to the proportion of the significantly altered genes that demonstrated increased expression in IF alone compared with normal, IF+i compared with normal, or IF+i compared with IF alone, respectively.

^dRefers to the result of Fisher exact test for overrepresentation of pathway-specific genes in one group compared with the other.