TABLE V.

The ranks and the p-values of the 24 target pathways for GSEA 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 37.5% compared to GSEA. Twelve target pathways were found to be significant in pDis analysis (all genes) while only 2 target pathways have significant FDR-corrected p-values in GSEA. 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 GSEA.

	GEO ID	Target pathway	GSEA			pDis analysis (all genes)			Improvement Compared to GSEA
			p-values	FDR	ranks	p-values	FDR	ranks
1	GSE1297	Alzheimer’s Disease	5e-06	4e-05	5.75	5e-06	5.7e-05	4.74	+0.5
2	GSE5281	Alzheimer’s Disease	5e-06	4e-05	3.59	5e-06	3.6e-05	7.29	−0.5
3	GSE5281	Alzheimer’s Disease	5e-06	4e-04	5.75	5e-06	2.6e-05	9.85	−0.5
4	GSE5281	Alzheimer’s Disease	5e-06	4e-05	7.19	5e-06	2.6e-05	9.85	−0.5
5	GSE20153	Parkinson’s disease	0.995	1	96.40	0.002	0.008	21.53	+1
6	GSE20291	Parkinson’s disease	5e-06	4e-05	6.83	5e-06	2.2e-05	11.67	−0.5
7	GSE8762	Huntington’s disease	5e-06	0.08	6.83	5e-06	1.6e-05	15.32	+1
8	GSE4107	Colorectal Cancer	0.081	0.171	35.25	0.002	0.009	20.43	+1
9	GSE8671	Colorectal Cancer	0.312	0.625	56.83	0.116	0.248	46.71	−0.5
10	GSE9348	Colorectal Cancer	0.118	0.283	33.81	0.054	0.172	31.02	+0.5
11	GSE14762	Renal Cancer	0.148	0.261	45.32	0.029	0.062	46.71	−0.5
12	GSE781	Renal Cancer	0.356	0.584	58.27	0.998	0.998	100	−0.5
13	GSE15471	Pancreatic Cancer	0.020	0.038	38.84	0.168	0.247	67.88	−1
14	GSE16515	Pancreatic Cancer	0.002	0.019	16.54	0.121	0.242	49.63	−1
15	GSE19728	Glioma	0.069	0.121	50.35	5e-06	2.2e-05	11.31	+1
16	GSE21354	Glioma	0.114	0.248	43.88	5e-06	2.1e-05	12.04	+1
17	GSE6956	Prostate Cancer	0.023	0.170	22.30	0.031	0.124	24.45	−0.5
18	GSE6956	Prostate Cancer	0.016	0.068	17.98	0.001	0.013	6.56	+1
19	GSE3467	Thyroid Cancer	0.463	0.682	71.22	0.018	0.061	28.83	+0.5
20	GSE3678	Thyroid Cancer	0.182	0.353	40.28	0.201	0.364	54.38	−0.5
21	GSE9476	Acute myeloid leukemia	0.4662	0.808	56.83	5e-06	9.7e-05	2.92	+1
22	GSE18842	Non-Small Cell Lung Cancer	0.414	0.727	63.30	0.496	0.635	78.10	−0.5
23	GSE19188	Non-Small Cell Lung Cancer	0.870	0.995	87.76	0.874	0.925	93.43	−0.5
24	GSE3585	Dilated cardiomyopathy	0.874	1	88.48	0.093	0.364	25.54	+0.5
Average			0.23	0.34	39.98	0.133	0.186	32.51	+2.5/24=10%