Table 4.

Genes associated with pathologic CR in basal-like breast cancer

	Probe set	Gene symbol	Fold difference of means between residual disease and pathologic CR
1	213060_s_at*	CHI3L2	4.117
2	200052_s_at	ILF2	2.645
3	213338_at	RIS1	3.181
4	214433_s_at*	SELENBP1	2.735
5	204319_s_at	RGS10	2.183
6	213005_s_at	ANKRD15	2.517
7	221561_at	SOAT1	2.156
8	212190_at	SERPINE2	2.448
9	209387_s_at	TM4SF1	3.096
10	221727_at	PC4	1.842
11	213716_s_at	SECTM1	2.183
12	203165_s_at	SLC33A1	1.826
13	207414_s_at	PACE4	1.732
14	201819_at	SCARB1	2.118
15	217983_s_at	RNASET2	1.915
16	214540_at	HIST1H2BO	1.864
17	218538_s_at	MRS2L	1.794
18	202506_at	SSFA2	1.678
19	215071_s_at	HIST1H2AC	2.099
20	202988_s_at	RGS1	2.328
21	220624_s_at	ELF5	2.521
22	221505_at*	ANP32E	2.51
23	208370_s_at	DSCR1	2.332
24	204407_at	TTF2	1.913
25	218398_at	MRPS30	1.595
26	213754_s_at	TRIM26	1.844
27	210147_at	ART3	3.943
28	204809_at	CLPX	1.813
29	202035_s_at	SFRP1	6.461
30	209389_x_at	DBI	1.792
31	201897_s_at	CKS1B	1.937
32	209142_s_at	UBE2G1	1.746
33	209340_at	UAP1	1.724
34	203362_s_at	MAD2L1	1.967
35	217028_at	CXCR4	2.097
36	205044_at*	GABRP	6.224
37	36711_at	MAFF	2.271
38	202023_at	EFNA1	1.721
39	212915_at	PDZRN3	2.539
40	217851_s_at	C20orf45	1.734
41	211762_sat	KPNA2	1.849
42	213134_x_at*	BTG3	2.007
43	204162_at	KNTC2	2.283
44	212276_at	LPIN1	2.219
45	219768_at	B7-H4	1.843
46	209551_at	MGC11061	1.925
47	203744_at	HMGB3	1.457
48	200975_at	PPT1	1.628
49	221931_s_at	SEC13L	1.796
50	209786_at	HMGN4	1.63
51	218963_s_at	KRT23	3.088
52	219209_at	MDA5	2.337
53	214214_s_at	C1QBP	1.799
54	209656_s_at	TM4SF10	2.645
55	203706_s_at*	FZD7	2.603
56	206055_sat	SNRPA1	1.799
57	204825_at	MELK	1.735
58	212762_s_at	TCF7L2	1.928
59	203423_at	RBP1	1.82
60	210605_s_at*	MFGE8	2.085
61	214835_s_at	SUCLG2	1.576

NOTE: There are 72 probes sets significant by SAM, corresponding to 61 genes. The median false discovery rate among the 72 significant genes is 0.04. Genes are ranked by significance.