Table 4.

Genes associated with pathologic CR in basal-like breast cancer

Probe setGene symbolFold difference of means between residual disease and pathologic CR
1213060_s_at*CHI3L24.117
2200052_s_atILF22.645
3213338_atRIS13.181
4214433_s_at*SELENBP12.735
5204319_s_atRGS102.183
6213005_s_atANKRD152.517
7221561_atSOAT12.156
8212190_atSERPINE22.448
9209387_s_atTM4SF13.096
10221727_atPC41.842
11213716_s_atSECTM12.183
12203165_s_atSLC33A11.826
13207414_s_atPACE41.732
14201819_atSCARB12.118
15217983_s_atRNASET21.915
16214540_atHIST1H2BO1.864
17218538_s_atMRS2L1.794
18202506_atSSFA21.678
19215071_s_atHIST1H2AC2.099
20202988_s_atRGS12.328
21220624_s_atELF52.521
22221505_at*ANP32E2.51
23208370_s_atDSCR12.332
24204407_atTTF21.913
25218398_atMRPS301.595
26213754_s_atTRIM261.844
27210147_atART33.943
28204809_atCLPX1.813
29202035_s_atSFRP16.461
30209389_x_atDBI1.792
31201897_s_atCKS1B1.937
32209142_s_atUBE2G11.746
33209340_atUAP11.724
34203362_s_atMAD2L11.967
35217028_atCXCR42.097
36205044_at*GABRP6.224
3736711_atMAFF2.271
38202023_atEFNA11.721
39212915_atPDZRN32.539
40217851_s_atC20orf451.734
41211762_satKPNA21.849
42213134_x_at*BTG32.007
43204162_atKNTC22.283
44212276_atLPIN12.219
45219768_atB7-H41.843
46209551_atMGC110611.925
47203744_atHMGB31.457
48200975_atPPT11.628
49221931_s_atSEC13L1.796
50209786_atHMGN41.63
51218963_s_atKRT233.088
52219209_atMDA52.337
53214214_s_atC1QBP1.799
54209656_s_atTM4SF102.645
55203706_s_at*FZD72.603
56206055_satSNRPA11.799
57204825_atMELK1.735
58212762_s_atTCF7L21.928
59203423_atRBP11.82
60210605_s_at*MFGE82.085
61214835_s_atSUCLG21.576
  • 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.