Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma

Table 3

Comparison of mean signals and standard deviation (sdv) of genes which were recently described as predictive for lymphatic metastasis in colorectal carcinomas [12], between 31 amplified RNA samples of colon carcinomas and 24 RNA samples of colon carcinomas not amplified prior to microarray hybridization.

Group					Colon carcinoma		Colon carcinoma
Samples; n					31		24
Stage UICC					III		III
Amplified					yes		no
ProbeSet ID	gb	Gene	Bases	fold change log2 mean amplified versus non amplified	log2 mean	log2 sdev	log2 mean	log2 sdev
205433_at	NM_000055	BCHE	64562	1.05	4.36	0.71	4.16	0.21
211044_at	BC006333	TRIM14	49,926	0.8	3.37	0.18	4.22	0.24
37547_at	U85995	PTHB1	476,529	1.32	5.63	0.61	4.25	0.17
215973_at	AF036973	HCG4P6	1060	0.89	4.07	0.36	4.56	0.21
214376_at	AI263044	EST	363	0.99	4.53	0.36	4.55	0.14
216489_at	AB046836	TRPM3	911,872	0.75	3.46	0.16	4.62	0.2
211201_at	M95489	FSHR	192,237	0.76	3.55	0.21	4.65	0.16
214068_at	AF070610	BEAN	56,130	0.74	3.45	0.41	4.66	0.21
216063_at	N55205	HBBP1	1742	0.79	3.75	0.21	4.72	0.24
219791_s_at	NM_024748	FLJ11539	11,373	0.77	3.67	0.43	4.77	0.2
209353_s_at	BC001205	SIN3B	50,947	0.92	4.37	0.23	4.77	0.29
211381_x_at	AF168617	SPAG11	15,917	0.76	3.63	0.22	4.78	0.35
207021_at	NM_007009	ZPBP	155,788	0.74	3.57	0.2	4.85	0.17
220227_at	NM_024883	CDH4	684,743	0.74	3.77	0.19	5.12	0.38
210701_at	D85939	CFDP1	139,780	1	5.12	0.42	5.12	0.22
220156_at	NM_024593	EFCAB1	11,825	0.76	4.04	0.17	5.32	0.28
209883_at	AF288389	GLT25D2	101,898	0.89	4.67	0.77	5.25	0.19
207031_at	NM_001189	BAPX1	3661	1.04	5.54	0.67	5.32	0.29
206885_x_at	NM_022559	GH1	1636	0.76	4.14	0.27	5.47	0.25
212963_at	BF968960	TM2D1	44,379	0.83	4.6	0.41	5.55	0.27
207897_at	NM_001883	CRHR2	46,857	0.81	4.59	0.16	5.67	0.32
222083_at	AW024233	GLYAT	23,218	0.64	3.69	0.21	5.72	0.37
214149_s_at	AI252582	ATP6V0E	51,138	0.86	5.07	0.49	5.87	0.58
220332_at	NM_006580	CLDN16	22,493	0.82	4.71	0.25	5.75	0.21
220944_at	NM_020393	PGLYRP4	18,721	0.78	4.57	0.27	5.84	0.52
219170_at	NM_024333	FSD1	19,171	0.91	5.35	0.24	5.9	0.36
221113_s_at	NM_016087	WNT16	15,738	1.03	6.15	0.17	5.95	0.28
221431_s_at	NM_030959	OR12D3	948	0.68	4.08	0.23	6.03	0.31
207936_x_at	NM_006604	RFPL3	6277	0.64	3.96	0.36	6.16	0.47
204303_s_at	NM_014772	KIAA0427	324,158	0.99	6.01	0.31	6.09	0.17
210272_at	M29873	CYP2B7P1	26,394	0.74	4.69	0.23	6.35	0.38
207984_s_at	NM_005374	MPP2	32,387	0.64	4.07	0.25	6.36	0.26
208227_x_at	NM_021721	ADAM22	262,753	0.69	4.55	0.31	6.56	0.35
213847_at	NM_006262	PRPH	4997	0.84	5.63	0.33	6.71	0.42
215544_s_at	AL121891	UBOX5	14,320	0.85	5.83	0.23	6.85	0.31
336_at	D38081	TBXA2R	12,155	0.74	5.03	0.24	6.84	0.28
209402_s_at	AF047338	SLC12A4	24,296	1	6.97	0.26	7	0.25
221629_x_at	AF151022	LOC51236	2948	0.83	6.04	0.58	7.29	0.5
219071_x_at	NM_016458	C8orf30A	2948	1.03	8.12	0.71	7.92	0.52
56829_at	H61826	NIBP	726,091	0.82	6.83	0.27	8.29	0.3
205835_s_at	AW975818	YTHDC2	81,572	0.9	4.11	0.17	4.59	0.19
213254_at	N64803	TNRC6B	290,992	0.93	6.15	0.23	6.65	0.38
34764_at	D21851	LARS2	160,261	1.01	7.13	0.63	7.04	0.51
209711_at	N80922	SLC35D1	50,402	1.32	10.2	0.52	7.73	0.45
203073_at	NM_007357	COG2	51,491	1	8.11	0.51	8.07	0.3
209174_s_at	BC000978	FLJ20259	64,363	1.07	8.71	0.32	8.17	0.25
221884_at	BE466525	EVI1	64,236	1.25	10.56	0.66	8.46	0.46
218160_at	NM_014222	NDUFA8	15,762	1.22	11.3	0.38	9.24	0.47
201386_s_at	AF279891	DHX15	57,098	1.08	10.44	0.66	9.64	0.52
202753_at	NM_014814	PSMD6	13,281	1.14	11.46	0.44	10.03	0.46