Detection of EBV Infection and Gene Expression in Oral Cancer from Patients in Taiwan by Microarray Analysis

Table 3

Arbitrary viral gene expression levels in EBV-negative oral cancer specimens.

Spot on Chip(a)	Case Number(b) and Gene Expression Level(c)										Mean(d)	Mean + 2SD(e)
	6	15	20	27	31	38	40	41	50	54
1	1429	1794	1034	999	4215	1428	7001	1610	1956	2418	2388	6122
2	124	646	835	449	1966	539	3649	235	11	504	896	3116
3	5	660	988	0	701	1	148	0	0	139	264	1008
4	139	204	222	0	392	0	48	0	0	6	101	371
5	25	518	1490	0	1016	0	182	0	17	747	400	1457
6	36	8997	6073	7026	1456	3038	11046	1531	3268	2999	4547	11722
R	3778	1766	2435	3905	3459	6762	11277	2487	3788	4620	4428	9976
27	153	256	1109	1	1503	138	135	0	0	254	355	1392
28	0	6621	1534	1683	6549	2578	10069	84	27	49	2919	10060
29	0	75	42	0	206	0	76	0	0	0	40	173
30	4	3	6	0	64	0	88	0	0	0	17	80
31	439	110	136	0	102	0	113	0	0	0	90	361
32	0	0	55	0	695	0	2	0	0	0	75	512
33	98	4	7	0	502	0	0	0	0	1164	178	938
34	23	390	937	0	4344	0	56	0	0	603	635	3321
35	224	1036	1158	1464	1793	814	2524	342	0	1006	1036	2564
36	525	2286	1127	93	1208	0	1	150	164	23	558	2075
37	0	139	9	2	286	0	0	0	11	0	45	235
38	0	76	27	0	364	0	0	0	4	0	47	275
39	0	147	76	0	2410	45	0	0	42	0	272	1777
40	0	0	61	0	284	0	8	0	0	0	35	214
41	0	0	12	0	684	0	0	4	0	12	71	502
42	0	17	0	0	357	0	4	0	0	0	38	262
43	25	18	0	0	847	0	73	0	0	0	96	626
44	177	1233	566	12	802	0	0	509	421	0	372	1207
45	0	118	322	0	571	43	0	18	74	0	115	492
46	0	221	0	0	181	0	0	4	75	4	49	217
47	0	54	71	0	345	0	0	0	12	0	48	263
48	0	46	0	0	689	0	8	4	18	0	77	508
49	0	6	91	0	923	0	3	0	4	0	103	682
50	2	14	145	8	751	0	1	0	0	10	93	564
51	15	51	60	0	114	0	0	0	2	93	34	120
52	421	5377	1626	3518	3597	643	1388	2389	4402	1548	2491	5812
53	1	1001	119	0	1046	0	0	12	140	0	232	1073
54	0	14	346	0	755	0	0	0	27	0	114	613
55	0	3801	465	49	4006	0	4	0	251	0	858	4084
56	0	60	57	6	654	0	0	0	0	0	78	486
57	0	28	336	0	1213	0	0	0	0	0	158	928
58	0	1	285	0	1593	0	0	0	0	144	202	1198
59	17	0	184	0	2132	87	28	0	0	38	249	1577
60	10	166	0	0	536	0	13	0	121	0	85	423
61	1	1217	152	0	350	0	0	17	200	6	194	951
62	0	501	68	2	784	0	0	0	306	324	199	746
63	0	162	0	0	590	0	0	0	59	0	81	454
64	2	21	152	0	1234	0	0	0	4	21	143	915
65	6	0	74	2	1442	0	12	0	5	0	154	1060
66	2	39	4	0	5235	0	4	0	0	64	535	3838
67	17	9450	8745	2722	18077	7441	11458	5385	241	7549	7109	18009
68	582	209	407	0	488	0	0	0	633	0	232	769
69	116	726	22	82	1261	0	0	0	523	85	282	1132
70	15	177	0	281	85	0	0	0	57	2	62	254
71	1	62	21	0	65	0	0	0	261	0	41	204
72	0	273	0	0	306	0	0	0	42	0	62	304
73	80	23	14	0	1017	75	0	0	0	0	121	754
74	16	0	0	0	85	0	0	0	0	41	14	71
75	1650	6	1059	26	455	1113	1475	69	0	3792	965	3326
76	−186	−178	267	0	1227	0	0	0	47	1	118	936
77	279	294	7	0	26	22	0	0	446	0	107	440
78	14	443	0	0	72	0	38	17	691	0	128	607
79	2	84	3	0	612	0	0	21	457	0	118	566
80	345	1752	904	2625	1894	5532	2065	1122	10422	3957	3062	9067
81	3810	239	153	0	802	0	0	0	118	0	512	2881
82	1423	333	855	0	657	0	0	0	716	0	398	1393
83	1237	324	410	0	400	0	0	0	262	0	263	1035
84	229	67	98	443	584	0	121	236	144	0	192	573
85	38	13	0	1	778	0	3	0	448	0	128	663
86	4422	2490	945	413	931	0	12	734	1141	4	1109	3876
87	1258	246	106	26	798	0	80	7	118	0	264	1111
88	701	99	247	152	122	0	7	0	343	0	167	609
89	1710	108	94	89	1045	0	0	138	341	0	353	1495
90r	1649	1917	1637	25454	5125	12036	16692	16458	31646	7670	12028	33016

(a) The 172-kbp EBV genome was PCR-amplified to produce 71 consecutive DNA fragments that were subsequently fabricated onto EBV-chip. These viral DNA fragments were given Arabic numbers, except for the internal W-repeated region (as R), as indicated at the left and their residing genes were cited in Figure 1.
(b) Ten oral cancer specimens shown here are determined to be EBV-negative by the criteria described in the Materials and Methods Section, and the numbers correspond to the patient number shown in Table 1.
(c) The gene expression levels were represented as the arbitrary numbers of hybridization signals (blue-spots on EBV-chips) digitalized by ScanAlyze program [32]. Owing to the highly sensitive tyramide-biotin signal amplification method, some spots on the EBV-chips hybridized to the cDNA samples from the EBV-negative tissues still revealed viral gene expression signals, which were considered as the background signals.
(d) Mean values with their standard deviations (SDs) of the background gene expression levels for all spots were calculated.
(e) The values of means plus two-time SD were obtained as the threshold expression levels for calculating the viral gene expression levels in EBV-positive tissue samples (Figure 2).