Table 5

Thirty common cancer genes differentially expressed more than threefold accompanied by a p value of <0.05 in at least one of the Dukes’ compared with normal mucosa

Probe set ID	Gene name	UG cluster	Cyto band	Left colon: sigmoid and rectosigmoid							Right colon: caecum
Probe set ID	Gene name	UG cluster	Cyto band	Nsig med*	Bsig med†	Csig med‡	Avg FC NvB§	p Value NvB¶	Avg FC NvC	p Value NvC††	Ncae med**	Bcae med††	Ccae med‡‡	Avg FC NvB§§	p Value NvB	Avg FC NvC	p Value NvC
*Nsig med, median derived from “signal” of 10 normal mucosae of the sigmoid and rectosigmoid.
†Bsig med, median derived from “signal” of eight Dukes’ B adenocarcinomas of the sigmoid and rectosigmoid.
‡Csig med, median derived from “signal” of seven Dukes’ C adenocarcinomas of the sigmoid and rectosigmoid.
§Avg FC NvB, fold change, corresponding to the “signal ratio” of Nsig med/Bsig med or Nsig med/Csig med, was calculated from the “signal log ratio”.
¶p value NvB, probability that a variant would assume a value greater than or equal to the observed value strictly by chance.
**Ncae med, median derived from “signal” of 10 normal mucosae of the caecum.
††Bcae med, median derived from “signal” of five Dukes’ B adenocarcinomas of the caecum.
‡‡Ccae med, median derived from “signal” of five Dukes’ C adenocarcinomas of the caecum.
§§Avg FC NvB, fold change, corresponding to the “signal ratio” of Ncae med/Bcae med or Ncae med/Ccae med, was calculated from the “signal log ratio”.
UG cluster, UniGene cluster (http://www.ncbi.nlm.nih.gov/UniGene).
D87292_at	TST thiosulfate sulfurtransferase (rhodanese)	Hs.248267	22q13.1	2492	1166	489	−2.1	0.002	−4.5	0.001	2649	1089	749	−1.0	0.766	−3.6	0.008
HG2614-HT2710_at	Collagen type viii alpha 1			35	96	244	1.7	0.006	5.6	0.001	19	38	69	1.3	0.766	5.2	0.032
HG2755-HT2862_at	T-Plastin			58	163	321	2.0	0.010	3.8	0.001	47	135	284	1.4	0.365	3.7	0.016
HG2981-HT3125_s_at	Epican alt. splice 1			13	58	75	4.3	0.001	5.6	0.001	16	78	75	1.7	0.484	4.1	0.032
HG4312-HT4582_s_at	Transcription factor Iiia			268	858	462	3.0	0.000	1.8	0.001	245	556	781	1.9	0.075	3.1	0.032
J03910_rna1_at	Metallothionein-IG (MT1G)	Hs.173451	16q13	2252	409	148	−6.9	0.010	−12.3	0.001	1417	219	279	−1.6	0.766	−9.7	0.032
J04970_at	Carboxypeptidase M	Hs.169765	12q15	60	21	21	−3.9	0.000	−2.8	0.001	55	21	19	−1.8	0.266	−3.3	0.032
L12350_at	Thrombospondin 2 (THBS2)	Hs.108623	6q27	22	85	448	2.0	0.004	13.2	0.001	24	53	136	−1.6	0.921	6.1	0.032
L12760_s_at	Phosphoenolpyruvate carboxykinase (PCK1)	Hs.1872	20q13.31	755	106	40	−4.2	0.001	−11.0	0.001	510	35	12	−3.2	0.187	−22.4	0.032
L22524_s_at	Metalloproteinase; MMP-7			5	37	570	6.1	0.001	83.2	0.001	7	62	179	6.0	0.044	23.0	0.032
L76465_at	NAD+ dependent 15 hydroxyprostaglandin dehydrogenase (PGDH)	Hs.77348	4q34–q35	213	61	21	−4.5	0.001	−7.7	0.001	211	41	11	−4.5	0.012	−16.9	0.095
M10942_at	Metallothionein-Ie gene (hMT-Ie)	Hs.74170	16q13	989	134	302	−5.2	0.002	−3.7	0.001	551	228	274	−1.7	0.266	−3.6	0.016
M12759_at	Ig J chain gene			687	117	95	−3.3	0.013	−7.9	0.001	1189	227	60	1.1	0.484	−22.1	0.032
M12963_s_at	Class I alcohol dehydrogenase (ADH1) alpha subunit	Hs.73843	4q21–q23	1724	260	59	−7.1	0.008	−38.8	0.001	1647	282	31	−3.8	0.044	−46.7	0.095
M22324_at	Aminopeptidase N/CD13	Hs.1239	15q25–q26	565	117	198	−3.6	0.002	−2.9	0.001	2169	357	128	−2.8	0.266	−9.0	0.016
M26576_cds2_at	Alpha-1 collagen type IV			105	332	764	2.0	0.010	5.0	0.001	107	233	429	1.4	0.187	−0.3	0.016
M77349_at	Transforming growth factor-beta induced gene product (BIGH3)	Hs.118787	5q31	307	1735	2618	5.3	0.000	8.0	0.001	253	582	1933	2.1	0.187	−0.2	0.008
M87860_at	S-lac lectin L-14-II (LGALS2)			232	40	12	−5.3	0.001	−7.4	0.001	57	35	7	−1.0	0.766	−7.8	0.016
S78187_at	CDC25Hu2 = cdc25+ homologue	Hs.153752	20p13	129	612	304	4.2	0.000	1.6	0.006	218	814	640	3.3	0.024	3.4	0.032
U05861_at	Hepatic dihydrodiol dehydrogenase			173	54	22	−3.8	0.041	−6.8	0.008	99	43	32	−3.4	0.044	−2.4	0.548
U14528_at	Sulfate transporter (DTD)	Hs.29981	5q31–q34	620	137	23	−4.3	0.001	−20.1	0.001	679	85	18	−1.8	0.619	−28.1	0.032
U18018_at	E1A enhancer binding protein (E1A-F)	Hs.77711	17q21	54	350	226	9.4	0.000	3.7	0.025	67	340	261	3.3	0.012	4.4	0.008
U20758_rna1_at	Osteopontin gene	Hs.313	4q21–q25	11	46	463	2.2	0.010	15.1	0.001	15	80	120	4.6	0.004	12.8	0.056
U70663_at	Zinc finger transcription factor hEZF (EZF)	Hs.7934	9q31	605	76	44	−6.2	0.001	−8.8	0.001	587	124	71	−3.0	0.123	−10.3	0.008
U77643_at	K12 protein precursor	Hs.95655	17q25	422	160	148	−3.0	0.000	−3.4	0.001	536	146	165	−1.7	0.187	−3.1	0.016
U78551_at	Gall bladder mucin MUC5B	Hs.102482	11p15	465	75	26	−3.8	0.010	−5.5	0.003	154	421	111	4.7	0.044	−3.4	0.548
X54925_at	MMP1 matrix metalloproteinase 1; type I interstitial collagenase	Hs.83169	11q22.3	12	129	945	7.3	0.001	31.8	0.005	10	248	244	16.9	0.004	36.7	0.056
X59770_at	IL-1R2 type II interleukin-1 receptor	Hs.25333	2q12–q22	427	48	65	−6.4	0.000	−4.5	0.001	160	54	66	−1.7	0.365	−2.9	0.016
X63629_at	p cadherin	Hs.2877	16q22	14	214	134	11.2	0.000	6.6	0.001	15	218	142	5.1	0.123	8.4	0.016
Z80345_rna1_s_at	SCAD	Hs.127610	12q22–qter	285	121	41	−3.0	0.001	−7.5	0.001	399	181	55	−1.3	0.484	−7.0	0.032