Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses

Table 1 Top 30 probes. Thirty probes of highest value v(s). 1st column: gene name in Hugo Gene nomenclature; 2nd column: reference of the Affymetrix DNA probe; 3rd column, v(s): probe valuation; 4th to 6th columns, p(s), n(s), c(s): numbers of pcr and nopcr correct predictions and total number c(s) = p(s) + n(s) of correct predictions for the 21 PCR and 61 NoPCR cases of the learning set.

Gene	Probe	v(s)	p(s)	n(s)	c(s)	p value (t test)	rank among probe sets according to p value by t test
BTG3	213134_x_at	0.61	12	40	52	2,96E-05	58
BTG3	205548_s_at	0.61	12	40	52	3,31E-05	62
GATA3	209604_s_at	0.59	15	29	44	0,00020015	148
GATA3	209603_at	0.49	12	26	38	0,00029983	186
THRAP2	212207_at	0.46	8	34	42	2,56E-08	3
SCCPDH	201826_s_at	0.46	12	22	34	0,00033299	194
SIL	205339_at	0.45	10	27	37	0,00049604	233
KRT7	209016_s_at	0.45	6	38	44	0,00248585	539
MCM5	201755_at	0.45	7	35	42	0,00281786	567
NME3	204862_s_at	0.44	10	25	35	2,45E-05	52
METRN	219051_x_at	0.44	11	22	33	1,71E-06	19
PDE4B	211302_s_at	0.43	9	27	36	0,00824095	1062
PHF15	212660_at	0.42	7	32	39	2,83E-05	57
SSR1	200891_s_at	0.42	7	32	39	0,00187004	466
PISD	202392_s_at	0.42	11	20	31	6,61E-05	92
MELK	204825_at	0.41	8	28	36	0,00012238	120
CA12	215867_x_at	0.41	10	22	32	4,42E-05	74
CA12	214164_x_at	0.41	10	22	32	4,70E-05	77
MAPK3	212046_x_at	0.41	10	22	32	9,07E-06	31
GATA3	209602_s_at	0.41	13	13	26	0,00068129	269
BBS4	212745_s_at	0.41	3	42	45	1,25E-07	4
DAPK1	203139_at	0.41	9	24	33	0,0006761	266
SAS	203226_s_at	0.40	7	29	36	8,70E-05	106
FLJ10916	219044_at	0.40	8	26	34	1,30E-06	15
E2F3	203693_s_at	0.40	8	26	34	0,00044243	219
AHNAK	220016_at	0.40	9	23	32	0,0001449	129
KLHDC3	214383_x_at	0.40	9	23	32	0,00071442	279
SFRS12	212721_at	0.40	9	23	32	5,34E-05	87
SRPK1	202200_s_at	0.39	6	31	37	0,00067356	265
CXCR4	217028_at	0.39	8	25	33	0,00098699	339

ISSN: 1471-2105