Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach

Table 1 Summary of the GO functions revealed for each gene set

Gene Group^a		No.	Gene^b	Gene Function^c				Resistance^d	p-value^e
				F _p	F _a	F _m	F _i
4 h	S₁ ∩ S₃	423		no	no	no	yes	n/d	< 0.05
	U₁ ∩ U₃	0		n/a	n/a	n/a	n/a	n/a	n/a
	D₁ ∩ D₃	1	DAPK1	no	yes	no	no	inherent	< 0.05
	U₁ ∩ D₃	0		n/a	n/a	n/a	n/a	n/a	n/a
	D₁ ∩ U₃	0		n/a	n/a	n/a	n/a	n/a	n/a
	U ₁	12	BCL2L2	yes	no	no	no	inherent	< 0.05
	U ₃	11		yes	no	yes	no	inherent	< 0.05
	D ₁	23	DAP	no	yes	yes	no	inherent	< 0.05
			CASP1	no	yes	no	no	inherent	< 0.05
			CDC25	yes	no	no	no	acquired	< 0.05
	^D 3	22	IL24	no	yes	no	no	inherent	< 0.05
72 h	S₄ ∩ S₅	433		no	yes	yes	no	n/d	< 0.05
	U₄ ∩ U₅	0		n/a	n/a	n/a	n/a	n/a	n/a
	D₄ ∩ D₅	0		n/a	n/a	n/a	n/a	n/a	n/a
	U₄ ∩ D₅	1	KIT	yes	no	no	no	acquired	< 0.05
	D₄ ∩ U₅	1	MADD	n/d	n/d	n/d	n/d	n/d	< 0.05
	U ₄	9	BCL2	yes	no	no	no	acquired	< 0.05
	U ₅	12	BIRC5	yes	no	no	no	acquired	< 0.05
	D ₄	19	BCL2L2	yes	no	no	no	acquired	< 0.05
	D ₅	18	IKBKE	no	yes	no	yes	~ inherent	< 0.05
			PPP3CC	no	yes	no	no	~ inherent	< 0.05
clusters	^C 1	4		n/a	n/a	n/a	n/a	n/a	n/a
	^C 2	11		n/d	n/d	n/d	n/d	n/a	n/a
	^C 3	14		no	yes	no	no	inherent	< 0.05
	^C 4	25		n/a	n/a	n/a	n/a	n/a	n/a
	^C 5	17		yes	yes	no	no	n/d	< 0.05
	^C 6	10		no	yes	no	no	inherent	< 0.05
	^C 7	19		yes	no	yes	no	acquired	< 0.05

^a S_i, U_i, and D_i correspond to groups which include genes constantly expressed, up-regulated, and down-regulated in experiment i, respectively, and C_i to a cluster of genes showing similar expression profile. Subscript i is varying from 1 to 5 and refers to each experimental setup, ^b Selected genes from each gene set, ^c F_p = is related to apoptosis evasion and cell cycle progression, F_a = is related to apoptosis induction and cell cycle arrest, F_m = is related to metabolic processes, F_i = is related to the regulation of IκB/NFκB, n/a = not available, and n/d = not defined, ^d ~ inherent = probably inherent, ^e Each p-value corresponds either to the one-sided Fisher exact test of the GO-based analysis of the respective gene set, or, in case of a single gene, to the intensity-dependent Z-score.