Table 1. The 45 genes most significantly associated with survival based on Cox proportional-hazards regression analysis.

	Proportion*	P value survival†	clust2/clust1‡	P value clust2/clust1§	Expression for longer survival¶	Gene description
1	0.71	0.0001	1.86	0.0092	Up	VCAM-1
2	0.41	0.0007	1.45	0.0022	Up	CGI-10 protein
3	0.41	0.0002	1.41	0.0061	Up	EST
4	0.35	0.0001	1.46	0.0027	Up	EST
5	0.31	0.0001	1.18	0.1175	Up	EST
6	0.29	0.0007	1.10	0.3698	Up	cDNA DKFZp586l1823
7	0.25	0.0006	1.06	0.5411	Up	EST
8	0.24	0.0007	1.11	0.3292	Up	Guanylate cyclase 1, soluble α2
9	0.23	0.0009	1.17	0.1185	Up	Homo sapiens clone 24987
10	0.23	0.0008	1.12	0.1576	Up	Ring finger protein 15
11	0.22	0.0005	0.94	0.4678	Up	Glutamate receptor, AMPA 1
12	0.19	0.0006	0.99	0.8342	Up	EST
13	0.18	0.0006	1.16	0.1125	Up	TRANCE, TNF-related ligand
14	0.17	0.0004	1.18	0.0190	Up	Thyroid hormone receptor interactor 11
15	0.16	0.0005	1.15	0.0555	Up	EST
16	0.14	0.0002	1.02	0.8083	Up	A kinase (PRKA) anchor protein 7
17	0.13	0.0007	1.02	0.7726	Up	cDNA FLJ13496 fis
18	0.11	0.0000	1.11	0.1456	Up	GTP-binding protein ragB
19	0.16	0.0002	0.70	0.0000	Down	Tubulin-α4
20	0.12	0.0002	0.83	0.0010	Down	fos-related antigen 1
21	0.12	0.0004	1.06	0.3067	Down	EST
22	0.12	0.0003	0.93	0.1250	Down	Multifunctional polypeptide similar to SAICAR synthetase
23	0.12	0.0006	1.00	0.9833	Down	Interferon-induced protein with tetratricopeptide repeats 1
24	0.10	0.0003	1.03	0.5846	Down	Protease, serine, 2 (trypsin 2)
25	0.09	0.0000	0.82	0.0001	Down	Ribosomal protein L27a
26	0.09	0.0005	1.03	0.5952	Down	ADP-ribosylation factor 4-like
27	0.09	0.0001	1.01	0.8006	Down	Solute carrier family 9 (Na+/H+ exchanger) isoform 1
28	0.07	0.0006	0.91	0.0475	Down	GAS2-related on chromosome 22
29	0.07	0.0003	1.06	0.2109	Down	Guanylate cyclase 1, soluble, β3
30	0.07	0.0001	1.01	0.7728	Down	Matrix Gla protein
31	0.07	0.0007	0.98	0.6387	Down	GPR1, G protein-coupled receptor
32	0.07	0.0001	1.02	0.6866	Down	Troponin I, cardiac
33	0.07	0.0002	0.95	0.2839	Down	TNF receptor-associated factor 2
34	0.07	0.0000	0.97	0.4729	Down	Glutathione S-transferase θ2
35	0.07	0.0002	1.05	0.2258	Down	BRCA2
36	0.05	0.0008	0.80	0.0000	Down	Replication factor C (activator 1) 4 (37 kDa)
37	0.05	0.0002	1.01	0.8859	Down	TYRO protein tyrosine kinase-binding protein
38	0.05	0.0001	0.93	0.1051	Down	MafG
39	0.04	0.0006	0.95	0.2372	Down	Collagen XIV, α1; undulin
40	0.04	0.0006	1.01	0.8032	Down	Kinesin heavy chain member 2
41	0.03	0.0002	1.05	0.2256	Down	Macrophage migration inhibitory factor
42	0.03	0.0001	1.02	0.6427	Down	Mitogen-activated protein kinase 1
43	0.02	0.0000	0.91	0.0164	Down	CD 97 antigen
44	0.02	0.0006	1.00	0.9715	Down	Surfactant, pulmonary-associated protein B
45	0.02	0.0005	1.03	0.4154	Down	RIP protein kinase

^*Proportion of patients with a log-ratio value of the gene differing from the median >0.5 for each gene. The median expression of a gene is defined as the median level of expression of that gene across all 58 patients. The higher the proportion means a greater variability in expression of that gene across the patient population.

^†The level of significance of the gene's association with survival.

^‡Average fold difference of the expression of the gene between the two major patient groups identified by unsupervised clustering (Fig. 1a). Cluster 1 patients had the shorter mean survival (351 vs. 611 days). The average fold difference is 2 to the power of the difference in mean log ratios for the two clusters.

^§Level of significance comparing expression of the genes between the two clusters based on the unsupervised analysis.

^¶Relative expression level of each gene related to longer patient survival. Calculations were based on the sign of the regression coefficient associated with each gene in the Cox proportional-hazards model. A negative coefficient yields improved survival with increased (up) expression, and a positive coefficient yields improved survival with decreased (down) expression.