Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal

Chechlinska, Magdalena; Siwicki, Jan Konrad; Gos, Monika; Oczko-Wojciechowska, Malgorzata; Jarzab, Michal; Pfeifer, Aleksandra; Jarzab, Barbara; Steffen, Jan

doi:10.1186/1471-2164-10-261

BMC Genomics

Table 2 Gene expression signature of T lymphocyte cell cycle exit.

From: Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal

	Probe set	Gene symbol	Description	Fold-change (after IL-2 withdrawal vs. before)	Paired design		Non-paired design
					Parametric p-value	FDR¹	Parametric p-value	FDR
Up-regulated
1	1555878_at	RPS24	ribosomal protein S24	3.21	0.0003	0.30	<0.0001	0.03
2	201471_s_at	SQSTM1	sequestosome 1	2.48	0.0002	0.30	0.0004	0.09
3	226831_at	NA	NA	2.04	0.0004	0.30	<0.0001	<0.01
4	1555446_s_at	TMEM1	transmembrane protein 1	2.04	<0.0001	0.30	<0.0001	<0.01
5	218684_at	LRRC8D	leucine rich repeat containing 8 family, member D	1.72	0.0007	0.30	0.0003	0.09
6	208091_s_at	ECOP	EGFR-coamplified and overexpressed protein	1.69	0.0006	0.30	<0.0001	0.06
7	244803_at	YY1AP1	YY1 associated protein 1	1.66	0.0002	0.30	0.0004	0.09
8	209006_s_at	C1orf63	chromosome 1 open reading frame 63	1.65	0.0006	0.30	0.0007	0.10
9	213702_x_at	ASAH1	N-acylsphingosine amidohydrolase (acid ceramidase) 1	1.59	<0.0001	0.30	<0.0001	0.02
10	212833_at	SLC25A46	solute carrier family 25, member 46	1.58	0.0006	0.30	0.0005	0.10
11	212310_at	MIA3	melanoma inhibitory activity family, member 3	1.50	0.0007	0.30	<0.0001	0.03
12	1562612_at	ME2	malic enzyme 2, NAD(+)-dependent, mitochondrial	1.47	<0.0001	0.309	<0.0001	<0.01
13	230161_at	CD99	CD99 molecule	1.45	0.0005	0.30	<0.0001	<0.01
Down-regulated
1	1553101_a_at	ALKBH5	alkB, alkylation repair homolog 5 (E. coli)	0.72	0.0003	0.23	0.0009	0.11
2	201968_s_at	PGM1	phosphoglucomutase 1	0.64	0.0006	0.22	0.0006	0.10
3	206055_s_at	SNRPA1	small nuclear ribonucleoprotein polypeptide	0.62	0.0005	0.22	0.0005	0.10
4	228146_at	C17orf51	chromosome 17 open reading frame 51	0.55	0.0007	0.22	0.0007	0.10
5	207339_s_at	LTB	lymphotoxin beta (TNF superfamily, member 3)	0.54	0.0002	0.22	0.0008	0.11
6	201170_s_at	BHLHB2	basic helix-loop-helix domain containing, class B, 2	0.53	<0.0001	0.22	<0.0001	0.04
7	202932_at	YES1	v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1	0.50	0.0008	0.224	0.0009	0.11
8	206999_at	IL12RB2	interleukin 12 receptor, beta 2	0.49	0.0002	0.22	0.0005	0.10
9	201041_s_at	DUSP1	dual specificity phosphatase 1	0.44	0.0005	0.21	<0.0001	0.05
10	202081_at	IER2	immediate early response 2	0.43	0.0005	0.21	0.0009	0.11
11	227262_at	HAPLN3	hyaluronan and proteoglycan link protein 3	0.41	0.0005	0.20	0.0006	0.10
12	218551_at	RP5-1077B9.4	invasion inhibitory protein 45	0.41	0.0004	0.20	0.0006	0.10
13	212590_at	RRAS2	related RAS viral (r-ras) oncogene homolog 2	0.40	0.0002	0.20	0.0002	0.07
14	226283_at	WDR51B	WD repeat domain 51B	0.39	0.0004	0.20	<0.0001	0.01
15	219681_s_at	RAB11FIP1	RAB11 family interacting protein 1 (class I)	0.38	0.0004	0.20	<0.0001	0.03
16	219255_x_at	IL17RB	interleukin 17 receptor B	0.38	0.0004	0.20	0.0005	0.10
17	224156_x_at	IL17RB	interleukin 17 receptor B	0.37	0.0007	0.20	0.0006	0.10
18	210845_s_at	PLAUR	plasminogen activator, urokinase receptor	0.36	0.0004	0.20	0.0003	0.08
19	214508_x_at	CREM	cAMP responsive element modulator	0.30	0.0007	0.20	<0.0001	0.05
20	209488_s_at	RBPMS	RNA binding protein with multiple splicing	0.28	0.0007	0.20	<0.0001	0.05
21	223217_s_at	NFKBIZ	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	0.25	0.0008	0.20	0.0005	0.10
22	209193_at	PIM1	pim-1 oncogene	0.20	<0.0001	0.20	<0.0001	<0.01
23	225262_at	FOSL2	FOS-like antigen 2	0.17	0.0004	0.20	0.0006	0.10
24	227599_at	C3orf59	chromosome 3 open reading frame 59	0.17	<0.0001	0.19	<0.0001	<0.01
25	244035_at	BCL2	B-cell CLL/lymphoma 2	0.16	0.0008	0.19	0.0009	0.11
26	202859_x_at	IL8	interleukin 8	0.15	0.0009	0.19	0.0006	0.10
27	211506_s_at	IL8	interleukin 8	0.10	0.0003	0.19	0.0002	0.07
28	203821_at	HBEGF	heparin-binding EGF-like growth factor	0.06	0.0004	0.19	0.0002	0.07
29	207844_at	IL13	interleukin 13	0.05	<0.0001	0.19	0.0007	0.10
30	214637_at	OSM	oncostatin M	0.05	0.0002	0.18	<0.0001	<0.01
31	203373_at	SOCS2	suppressor of cytokine signaling 2	0.04	0.0001	0.17	<0.0001	0.03
32	205266_at	LIF	leukemia inhibitory factor (cholinergic differentiation factor)	0.04	0.0003	0.17	<0.0001	0.03
33	203372_s_at	SOCS2	suppressor of cytokine signaling 2	0.03	0.0002	0.17	<0.0001	0.03
34	208891_at	DUSP6	dual specificity phosphatase 6	0.03	0.0002	0.17	<0.0001	<0.01
35	223377_x_at	CISH	cytokine inducible SH2-containing protein	0.03	<0.0001	0.16	<0.0001	<0.01
36	223961_s_at	CISH	cytokine inducible SH2-containing protein	0.03	<0.0001	0.14	<0.0001	0.01
37	221223_x_at	CISH	cytokine inducible SH2-containing protein	0.03	<0.0001	0.13	<0.0001	<0.01
38	208893_s_at	DUSP6	dual specificity phosphatase 6	0.02	<0.0001	0.13	<0.0001	<0.01
39	230170_at	OSM	oncostatin M	0.02	0.0002	0.13	<0.0001	<0.01
40	208892_s_at	DUSP6	dual specificity phosphatase 6	0.02	0.0010	0.05	<0.0001	0.03

Common genes identified as significantly changed (p < 0.001) in a paired analysis and in a non-paired block analysis.
¹FDR – False Discovery Rate

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