TABLE VI.

The ranks and the p-values of the 24 target pathways for SPIA (all genes) and pDis analysis (all genes). The improvement factor based on Fig. 2 is calculated for each data set considering 5% significance threshold using FDR-corrected p-values. The average improvement factor shows that pDis analysis (all genes) improves the results 43.75% compared to SPIA (all genes). Twelve target pathways were found to be significant in pDis analysis (all genes) while only one target pathways have significant FDR-corrected p-values in SPIA (all genes). As shown, the average p-value and rank for the target pathways are lower (i.e. better) in the pDis analysis (all genes) than in SPIA (all genes).

	GEO ID	Target pathway	SPIA (all genes)			pDis analysis (all genes)			Improvement Compared to SPIA (all genes)
			p-values	FDR	ranks	p-values	FDR	ranks
1	GSE1297	Alzheimer’s Disease	0.095	0.414	22.72	5e-06	5.7e-05	4.74	+1
2	GSE5281	Alzheimer’s Disease	0.661	0.880	73.48	5e-06	3.6e-05	7.29	+1
3	GSE5281	Alzheimer’s Disease	0.060	0.255	23.10	5e-06	2.6e-05	9.85	+1
4	GSE5281	Alzheimer’s Disease	0.332	0.695	47.72	5e-06	2.6e-05	9.85	+1
5	GSE20153	Parkinson’s disease	0.021	0.170	11.36	0.002	0.008	21.53	+1
6	GSE20291	Parkinson’s disease	0.020	0.174	10.98	5e-06	2.2e-05	11.67	+1
7	GSE8762	Huntington’s disease	0.955	0.992	96.21	5e-06	1.6e-05	15.32	+1
8	GSE4107	Colorectal Cancer	0.010	0.101	9.84	0.002	0.009	20.43	+1
9	GSE8671	Colorectal Cancer	0.991	1.00	98.48	0.116	0.248	46.71	+0.5
10	GSE9348	Colorectal Cancer	0.197	0.433	45.45	0.054	0.172	31.02	+0.5
11	GSE14762	Renal Cancer	0.004	0.025	15.90	0.029	0.062	46.71	−1
12	GSE781	Renal Cancer	0.074	0.338	21.21	0.998	0.998	100	−0.5
13	GSE15471	Pancreatic Cancer	0.039	0.125	30.68	0.168	0.247	67.88	−0.5
14	GSE16515	Pancreatic Cancer	0.046	0.144	31.81	0.121	0.242	49.63	−0.5
15	GSE19728	Glioma	0.301	0.502	59.84	5e-06	2.2e-05	11.31	+1
16	GSE21354	Glioma	0.026	0.118	21.96	5e-06	2.1e-05	12.04	+1
17	GSE6956	Prostate Cancer	0.083	0.543	15.15	0.031	0.124	24.45	−0.5
18	GSE6956	Prostate Cancer	0.027	0.294	8.71	0.001	0.013	6.56	+1
19	GSE3467	Thyroid Cancer	0.936	0.990	93.93	0.018	0.061	28.83	+0.5
20	GSE3678	Thyroid Cancer	0.951	0.977	94.69	0.201	0.364	54.38	+0.5
21	GSE9476	Acute myeloid leukemia	0.512	0.793	62.87	5e-06	9.7e-05	2.92	+1
22	GSE18842	Non-Small Cell Lung Cancer	0.294	0.591	49.24	0.496	0.635	78.10	−0.5
23	GSE19188	Non-Small Cell Lung Cancer	0.712	0.824	86.36	0.874	0.925	93.43	−0.5
24	GSE3585	Dilated cardiomyopathy	0.471	0.801	57.95	0.093	0.364	25.54	+0.5
Average			0.325	0.507	45.40	0.133	0.186	32.51	+11/24=43.75%