Table 2.

Selected genes with differential expression in T cells from CVID with impaired T cell proliferation comparing healthy controls and XLA patients

UniGene	Gene name	Fold changea	Absolute differencea	q-valueb (%)	Normal in vitrob responsec
Cell cycle-related
Hs.77311	BTG3	1·69	54	3·02	up
Hs.252587	Securin (PTTG1)	1·55	98	0·39	up
Hs.14125	PA26	0·62	−85	0·39
Hs.79070	v-myc	0·47	−302	0·39	up
Hs.106070	p57Kip2	0·41	−75	3·12
Apoptosis-related
Hs.73172	GFI-1	2·28	88	0·39	up
Hs.211600	TNF-α ip3 (A20)	1·98	352	3·02	nc
Hs.82359	Fas	1·56	89	0·39	nc
Hs.159428	Bax	1·55	28	4·93
Hs.79241	Bcl2	0·67	−149	0·39	up
Hs.83429	TRAIL	0·66	−134	3·96	up
Hs.3280	Caspase 6	0·60	−50	0·70	up
Hs.5353	Caspase 10	0·54	−45	0·39
Hs.79428	BNIP3 (Bcl2-ip)	0·54	−54	0·39	nc
Signal transduction
Hs.301746	RAP2A	2·24	350	0·39
Hs.239527	RAP2B	1·94	51	0·39
Hs.74631	CD147 (Basigin)	1·67	80	1·18
Hs.177534	MKP-5 (DUSP10)	1·51	36	1·37
Hs.239818	PI-3-K	0·64	−33	1·37	down
Hs.83428	p105 (NFɛB1)	0·63	−106	0·39	up
Hs.115907	DAGKD	0·63	−102	3·56	down
Hs.29877	Txk	0·55	−97	1·37	down
Hs.348	CAMK4	0·51	−55	0·95	down
Hs.80395	MAL	0·50	−342	0·39	down
Hs.121128	BRDG1 (STAP1)	0·50	−25	3·02
Hs.44865	LEF-1	0·47	−727	0·39
cAMP-associated
Hs.301946	AKAP13	1·59	141	2·60
Hs.42322	AKAP2	1·52	48	3·02	nc
Hs.433700	PKIA	0·66	−38	0·95
Hs.78746	PDE8A	0·48	−58	0·39
Hs.337616	PDE3B	0·45	−89	0·39
Cell-to-cell communication
Hs.856	IFN-γ	3·11	106	0·39	up
Hs.74011	LAG-3	2·13	77	0·39	up
Hs.342874	TGFβR3	1·67	98	4·46	down
Hs.814	HLA-DP b1	1·66	623	3·02	down
Hs.272409	T-box 21 (T-bet)	1·62	219	3·02	up
Hs.2259	CD3γ	1·54	171	0·39	down
Hs.181097	OX-40 l	0·65	−40	3·56	nc
Hs.75545	IL-4R	0·61	−96	0·39	nc
Hs.64310	IL-11Rα	0·61	−75	0·39	down
Hs.232068	ZEB-1	0·61	−47	0·95	nc
Hs.82065	gp130 (IL-6Rβ)	0·61	−26	3·96	nc
Hs.193400	IL-6Rα (CD126)	0·60	−60	2·10
Hs.428	Flt-3LG	0·59	−55	0·39	down
Hs.890	LTβ	0·58	−857	3·02	nc
Hs.1369	DAF (CD55)	0·53	−122	0·39	nc
Hs.154299	Thrombin-RL	0·50	−32	0·39	down
Hs.289019	LTBP3	0·46	−71	3·02
Adhesion/migration
Hs.75703	MIP-1β (CCL4)	1·96	294	0·70	up
Hs.241392	RANTES (CCL5)	1·70	919	0·39	down
Hs.75626	LFA-3 (CD58)	1·56	58	0·39
Hs.78913	CX3CR1	1·55	928	1·53	down
Hs.137548	CD84	1·52	102	4·93
Hs.433303	ICAM-2	0·58	−388	0·39	down
Hs.1652	CCR7	0·39	−753	0·39	down
Hs.227730	Integrin α6	0·37	−195	0·39	down
TCRγδ-associated
Hs.274509	TCRγ c2	2·81	956	0·39	nc
Hs.382367	Galectin-1	1·93	511	0·39
Hs.112259	TCRγ v9	1·89	995	0·39	nc
Hs.87450	Cathepsin W	1·80	389	3·12	nc
Hs.268531	Granzyme M	1·60	125	3·56
Hs.73895	4–1BB	1·60	21	3·56	up
Hs.54457	CD81	1·57	301	0·39
Hs.74647	TCRα	0·62	−26	2·10	nc
Cytotoxic T cell-associated
Hs.348264	Granzyme H	2·87	1629	0·39
Hs.132906	CRACC	2·01	95	0·39
Hs.10306	NKG7 (GMP-17)	2·00	1638	0·39
Hs.41682	NKG2A (CD159A)	1·95	431	0·39
Hs.85258	CD8α	1·88	664	0·39	nc
Hs.146322	KLRG1	1·81	314	1·53	down
Hs.90708	Granzyme A	1·68	724	0·95	nc
Hs.105806	Granulysin	1·64	922	2·10
Hs.81743	CD160 (BY55)	1·63	123	3·56
Hs.1051	Granzyme B	1·61	547	3·02	up
Hs.157872	2B4 (CD244)	1·57	68	2·60
Hs.411106	Perforin	1·52	1146	0·70

^aFold change and absolute difference (abs. diff.) comparing mean expression in the CVID samples versus mean expression in the control and XLA samples.

^bq-value is a significance estimate for the proportion (%) of false positive genes, corrected for multiple testing by permutation analyses [16,17]. A q-value = 5% corresponds to P = 0·05.

^cIndicates the response to in vitro activation in microarray experiments by Diehn et al. [23].