TABLE IV.

The ranks and the p-values of the 24 target pathways for GSA 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 33.3% compared to GSA. Twelve target pathways were found to be significant in pDis analysis (all genes) while non of the target pathways have significant FDR-corrected p-values in GSA. As shown, the average p-value for the target pathways are lower (i.e. better) in the pDis analysis (all genes) than in GSA.

	GEO ID	Target pathway	GSA			pDis analysis (all genes)			Improvement Compared to GSA
			p-values	FDR	ranks	p-values	FDR	ranks
1	GSE1297	Alzheimer’s Disease	0.100	0.514	19.42	5e-06	5.7e-05	4.74	+1.0
2	GSE5281	Alzheimer’s Disease	0.316	0.872	33.09	5e-06	3.6e-05	7.29	+1.0
3	GSE5281	Alzheimer’s Disease	0.116	0.488	23.74	5e-06	2.6e-05	9.85	+1.0
4	GSE5281	Alzheimer’s Disease	0.164	0.537	27.69	5e-06	2.6e-05	9.85	+1.0
5	GSE20153	Parkinson’s disease	0.542	0.885	54.67	0.002	0.008	21.53	+1.0
6	GSE20291	Parkinson’s disease	0.246	0.629	35.61	5e-06	2.2e-05	11.67	+1.0
7	GSE8762	Huntington’s disease	0.154	0.876	15.10	5e-06	1.6e-05	15.32	+1.0
8	GSE4107	Colorectal Cancer	0.154	0.764	20.14	0.002	0.009	20.43	+1.0
9	GSE8671	Colorectal Cancer	0.002	0.069	2.87	0.116	0.248	46.71	−0.5
10	GSE9348	Colorectal Cancer	0.032	0.342	9.35	0.054	0.172	31.02	−0.5
11	GSE14762	Renal Cancer	0.132	0.600	21.58	0.029	0.062	46.71	−0.5
12	GSE781	Renal Cancer	0.492	0.865	56.47	0.998	0.998	100	−0.5
13	GSE15471	Pancreatic Cancer	0.112	0.622	17.98	0.168	0.247	67.88	−0.5
14	GSE16515	Pancreatic Cancer	0.062	0.625	8.63	0.121	0.242	49.63	−0.5
15	GSE19728	Glioma	0.136	0.548	24.46	5e-06	2.2e-05	11.31	1.0
16	GSE21354	Glioma	0.128	0.547	22.66	5e-06	2.1e-05	12.04	+1.0
17	GSE6956	Prostate Cancer	0.060	0.440	9.35	0.031	0.124	24.45	−0.5
18	GSE6956	Prostate Cancer	0.032	0.451	6.47	0.001	0.013	6.56	+1.0
19	GSE3467	Thyroid Cancer	0.152	0.687	20.14	0.018	0.061	28.83	−0.5
20	GSE3678	Thyroid Cancer	0.464	0.814	56.11	0.201	0.364	54.38	+ 0.5
21	GSE9476	Acute myeloid leukemia	0.128	0.902	10.07	5e-06	9.7e-05	2.92	+1.0
22	GSE18842	Non-Small Cell Lung Cancer	0.156	0.6992	20.86	0.496	0.635	78.10	−0.5
23	GSE19188	Non-Small Cell Lung Cancer	0.446	0.844	48.92	0.874	0.925	93.43	−0.5
24	GSE3585	Dilated cardiomyopathy	0.866	0.919	91.36	0.093	0.364	25.54	+0.5
Average			0.216	0.647	27.368	0.133	0.186	32.51	+8/24=33.3%