Section V

Previous

Table of Contents

Next

Table S15. Probe sets most strongly associated with time to progression or relapse in the training set

	U133 probe set	Gene description	Symbol	Location	GenBank reference	UniGene reference	P valuea	cFDRb
1	60471_at§*	Homo sapiens transcribed sequence with strong similarity to protein ref:NP_079108.1 hypothetical protein FLJ22439	---	---	AA625133	Hs.512736	0.0001	0.4864
2	202283_at§	serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	SERPINF1	Chr:17p13.1	NM_002615	Hs.173594	0.0001	0.4872
3	200682_s_at	ubiquitin-conjugating enzyme E2L 3	UBE2L3	Chr:22q11.21	BG531983	Hs.108104	0.0004	0.4885
4	217208_s_at	discs, large homolog 1 (Drosophila)	DLG1	Chr:3q29	AL121981	Hs.389893	0.0004	0.4886
5	203063_at§*	protein phosphatase 1F (PP2C domain containing)	PPM1F	Chr:22q11.22	NM_014634	Hs.278441	0.0004	0.4886
6	40420_at	serine/threonine kinase 10	STK10	Chr:5q35.1	AB015718	Hs.16134	0.0004	0.4888
7	210720_s_at	amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein	APBA2BP	Chr:20q11.22	AB039947	Hs.324104	0.0004	0.4889
8	209011_at	triple functional domain (PTPRF interacting)	TRIO	Chr:5p15.1-p14	BF223718	Hs.367689	0.0005	0.4891
9	218117_at	ring-box 1	RBX1	Chr:22q13.2	NM_014248	Hs.373992	0.0005	0.4891
10	60528_at	phospholipase A2, group IVB (cytosolic)	PLA2G4B	Chr:15q11.2-q21.3	N71116	Hs.198161	0.0005	0.4896
11	38269_at	protein kinase D2	PRKD2	Chr:19q13.2	AL050147	Hs.205431	0.0005	0.4896
12	219457_s_at	Ras and Rab interactor 3	RIN3	Chr:14q32.13	NM_024832	Hs.413374	0.0008	0.4911
13	209707_at	phosphatidylinositol glycan, class K	PIGK	Chr:1p31.1	AF022913	Hs.293653	0.0008	0.4914
14	218184_at	tubby like protein 4	TULP4	Chr:6q25-q26	NM_020245	Hs.102237	0.0009	0.4917
15	214682_at	polycystic kidney disease 1 (autosomal dominant)	PKD1	Chr:16p13.3	AK023376	Hs.75813	0.0009	0.4917
16	212656_at	hepatocellularcarcinoma-associated antigen HCA557a	DKFZP586D0919	Chr:12q13.2	AF110399	Hs.435643	0.0009	0.4919
17	212129_at	non-imprinted in Prader-Willi/Angelman syndrome 2	NIPA2	Chr:15q11.2	AI589507	Hs.512761	0.0010	0.4921
18	202650_s_at	KIAA0195 gene product	KIAA0195	Chr:17q25.3	NM_014738	Hs.301132	0.0010	0.4923
19	209553_at	KIAA0804 protein	KIAA0804	Chr:3q28	BC001001	Hs.361493	0.0010	0.4924
20	203241_at	UV radiation resistance associated gene	UVRAG	Chr:11q13.5	NM_003369	Hs.13137	0.0010	0.4925
21	217329_x_at	---	---	---	AF042164	---	0.0011	0.4927
22	201381_x_at	Siah-interacting protein	SIP	Chr:1q24-q25	AF057356	Hs.27258	0.0012	0.4930
23	209039_x_at	EH-domain containing 1	EHD1	Chr:11q13	AF001434	Hs.155119	0.0012	0.4933
24	37384_at	protein phosphatase 1F (PP2C domain containing)	PPM1F	Chr:22q11.22	D86995	Hs.278441	0.0013	0.4935
25	202308_at	sterol regulatory element binding transcription factor 1	SREBF1	Chr:17p11.2	NM_004176	Hs.426528	0.0013	0.4935
26	212096_s_at	mitochondrial tumor suppressor gene 1	MTSG1	Chr:8p22	AL096842	Hs.7946	0.0013	0.4935
27	221945_at	KIAA1940 protein	KIAA1940	Chr:2p13.2	AA906578	Hs.23158	0.0013	0.4936
28	200773_x_at	prothymosin, alpha (gene sequence 28)	PTMA	Chr:2q35-q36	NM_002823	Hs.459927	0.0013	0.4937
29	219933_at	glutaredoxin 2	GLRX2	Chr:1q31.2-q31.3	NM_016066	Hs.458283	0.0014	0.4940
30	219416_at	scavenger receptor class A, member 3	SCARA3	Chr:8p21	NM_016240	Hs.128856	0.0014	0.4941
31	218336_at	prefoldin 2	PFDN2	Chr:1q23.1	NM_012394	Hs.298229	0.0014	0.4942
32	211113_s_at	ATP-binding cassette, sub-family G (WHITE), member 1	ABCG1	Chr:21q22.3	U34919	Hs.369055	0.0014	0.4943
33	219033_at	hypothetical protein FLJ21308	FLJ21308	Chr:5q11.2	NM_024615	Hs.310185	0.0015	0.4943
34	216033_s_at	FYN oncogene related to SRC, FGR, YES	FYN	Chr:6q21	S74774	Hs.390567	0.0015	0.4944
35	202530_at	mitogen-activated protein kinase 14	MAPK14	Chr:6p21.3-p21.2	NM_001315	Hs.79107	0.0017	0.4954
36	44146_at	glucocorticoid modulatory element binding protein 2	GMEB2	Chr:20q13.33	AA045183	Hs.28906	0.0017	0.4955
37	214061_at	unknown MGC21654 product	MGC21654	Chr:8q24.13	AI017564	Hs.95631	0.0017	0.4955
38	211096_at	---	---	---	BC003111	---	0.0018	0.4959
39	203662_s_at	tropomodulin 1	TMOD1	Chr:9q22.3	NM_003275	Hs.374849	0.0019	0.4960
40	45653_at	polymerase delta-interacting protein 1	PDIP1	Chr:16p11.2	AW026481	Hs.106817	0.0019	0.4961
41	203047_at	serine/threonine kinase 10	STK10	Chr:5q35.1	NM_005990	Hs.16134	0.0019	0.4962
42	217586_x_at	Homo sapiens transcribed sequence with weak  similarity to protein ref:NP_062553.1 (H.sapiens)  hypothetical protein FLJ11267 [Homo sapiens]	---	---	N35922	Hs.269852	0.0019	0.4962
43	218890_x_at	mitochondrial ribosomal protein L35	MRPL35	Chr:2p11.2	NM_016622	Hs.433439	0.0020	0.4963
44	218226_s_at	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa	NDUFB4	Chr:3q13.33	NM_004547	Hs.227750	0.0020	0.4964
45	218896_s_at	ELG protein	HSA277841	Chr:17p13.3	NM_018553	Hs.120963	0.0021	0.4967
46	213880_at	G protein-coupled receptor 49	GPR49	Chr:12q22-q23	AL524520	Hs.166705	0.0022	0.4970
47	219539_at	gem (nuclear organelle) associated protein 6	GEMIN6	Chr:2p22.3	NM_024775	Hs.143818	0.0022	0.4972
48	201840_at	neural precursor cell expressed, developmentally down-regulated 8	NEDD8	Chr:14q11.2	NM_006156	Hs.75512	0.0023	0.4975
49	218461_at	protein x 0004	MGC14560	Chr:12q24.13	NM_016301	Hs.284164	0.0024	0.4976
50	212477_at	centaurin, beta 2	CENTB2	Chr:3q29	D26069	Hs.410715	0.0024	0.4976

^a summary p represents a combined p value for the significance of association of expression with outcome in each treatment protocol as compared with the gamma distribution of three similarly transformed independent variables.
^b conditional false discovery rate (cFDR) estimated using the LOESS histogram.
^§ Probe sets with p-values less than or equal a = 0.001 in all 68 leave-one-out GMS assessments (jack-knife procedure).
* Significant in a multivariable Cox regression analysis including all probes selected by the jackknife procedure.