BMC Genomics

Table 1 Top 10 TF binding profiles with significantly different activities between ER+ and ER- breast cancer samples in the Veer and the Wang datasets

From: REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer

The Veer data
Cell line	TF	Condition	Lab	RAS	Location	P-value	FDR
T47d	Eralphaa	Gen1h	Haib	6.424	0.174	0	0.005
T47d	Eralphaa	Estradia1h	Haib	6.424	0.174	0	0.011
T47d	Foxa1	Dmso2	Haib	5.427	0.174	0	0.036
T47d	Gata3	Dmso2	Haib	5.263	0.174	0	0.039
T47d	P300	Dmso2	Haib	4.372	0.180	0.002	0.266
Hepg2	Foxa1		Haib	3.905	0.158	0.001	0.413
T47d	Eralphaa	Dmso2	Haib	3.946	0.247	0.012	0.438
Ecc1	Eralphaa	Estradia1h	Haib	4.006	0.126	0	0.457
Mcf7	Cmyc	Estro	Broad	1.710	0.637	0.206	0.695
H1hesc	Ctcf		Broad	1.710	0.106	0.184	0.701
The Wang data
Cell line	TF	Condition	Lab	RAS	Location	P-value	FDR
T47d	Eralphaa	Gen1h	Haib	6.538	0.135	0	0.003
T47d	Eralphaa	Estradia1h	Haib	6.538	0.135	0	0.007
T47d	Gata3	Dmso2	Haib	4.874	0.189	0.006	0.142
T47d	Foxa1	Dmso2	Haib	5.076	0.189	0.003	0.142
Ecc1	Eralphaa	Estradia1h	Haib	4.953	0.094	0	0.146
Ecc1	Eralphaa	Gen1h	Haib	3.929	0.126	0.005	0.872
Hl60	Ctcf		Uw	-1.042	0.704	0.365	0.901
H1hesc	Sin3ak20		Haib	0.735	0.233	0.454	0.921
Gm19239	Ctcf		Broad	-0.917	0.035	0.417	0.801
A549	Gr	Dexd	Haib	0.725	0.281	0.444	0.924

The “Location” column shows the percentile of genes at which the maximum deviation is observed. TF binding profiles with a FDR<0.25 are highlighted in bold.

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