. Author manuscript; available in PMC: 2014 Jul 24.

Published in final edited form as: Breast Cancer Res Treat. 2010 Dec 9;125(3):785–795. doi: 10.1007/s10549-010-1280-6

Table 2.

Class comparison test between IBC and Non-IBC in tumor subgroups

Significantly differentially expressed probe sets (n=18,940) with t-test
No. of patients (IBC/Non-IBC)	ALL		ER+/HER2−		HER2+		ER−/HER2−
	82 (25/57)		27 (5/22)		29 (12/17)		26 (8/18)
	No. of Genes	Global P value^*	No. of Genes	Global P value^*	No. of Genes	Global P value^*	No. of Genes	Global P value^*
Parametric p value^†
0.05	1214	0.209	927	0.372	2065	0.051	989	0.279
0.01	268	0.167	195	0.318	508	0.043	144	0.462
0.005	130	0.177	90	0.388	265	0.039	68	0.458
0.001	25	0.188	23	0.311	61	0.030	16	0.353

Efron-Tibshirani’s GSA test P-value^* with prior defined gene sets
No. of patients (IBC/Non-IBC) GeneList GeneSets	No. of genes	ALL		ER+/HER2−		HER2+		ER−/HER2−
		82 (25/57)		27 (5/22)		29 (12/17)		26 (8/18)
		P -value^‡	Directions	P -value^‡	Directions	P -value^‡	Directions	P -value^‡	Directions
Wnt gene set¹⁵	17	0.545	Non-IBC	0.375	IBC	0.415	Non-IBC	0.040	IBC
Laere genes¹³	36	0.395	IBC	0.315	Non-IBC	0.330	Non-IBC	0.195	IBC
Bieche genes⁴	54	0.245	IBC	0.015	IBC	0.180	Non-IBC	0.300	IBC
CD44 related signatures¹⁶	55	0.135	Non-IBC	0.140	Non-IBC	0.055	Non-IBC	0.415	Non-IBC
Bertucci genes¹⁴	71	0.230	Non-IBC	0.560	IBC	0.045	IBC	0.010	Non-IBC

IBC: Inflammatory Breast Cancer; ER: Estrogen Receptor.

Global p value shows the probability of getting at least the same number of genes significant on a t-test (at the specified p level) by chance if there are no real differences between IBC and Non-IBC.

^†

The parametric p-value was derived from t-test.

^‡

The Efron and Tibshirani gene set analysis method that employs “maxmean” statistics (under 1000 permutations).