TABLE I.

The twenty-four data sets from the GEO database used to evaluate the pathway analysis methods compared in this paper. Each data set corresponds to a disease for which there is a target pathway in KEGG.

	GEO ID	Pubmed	Reference	Disease	Target Pathway
1	GSE1297	14769913	[6]	Alzheimer’s Disease	hsa05010
2	GSE5281	17077275	[27]	Alzheimer’s Disease	hsa05010
3	GSE5281	17077275	[27]	Alzheimer’s Disease	hsa05010
4	GSE5281	17077275	[27]	Alzheimer’s Disease	hsa05010
5	GSE20153	20926834	[61]	Parkinson’s disease	hsa05012
6	GSE20291	15965975	[60]	Parkinson’s disease	hsa05012
7	GSE8762	17724341	[40]	Huntington’s disease	hsa05016
8	GSE4107	17317818	[16]	Colorectal Cancer	hsa05210
9	GSE8671	18171984	[41]	Colorectal Cancer	hsa05210
10	GSE9348	20143136	[15]	Colorectal Cancer	hsa05210
11	GSE14762	19252501	[58]	Renal Cancer	hsa05211
12	GSE781	14641932	[26]	Renal Cancer	hsa05211
13	GSE15471	19260470	[1]	Pancreatic Cancer	hsa05212
14	GSE16515	19732725	[36]	Pancreatic Cancer	hsa05212
15	GSE19728	NA	NA	Glioma	hsa05214
16	GSE21354	NA	NA	Glioma	hsa05214
17	GSE6956	18245496	[56]	Prostate Cancer	hsa05215
18	GSE6956	18245496	[56]	Prostate Cancer	hsa05215
19	GSE3467	16365291	[13]	Thyroid Cancer	hsa05216
20	GSE3678	NA	NA	Thyroid Cancer	hsa05216
21	GSE9476	17910043	[44]	Acute myeloid leukemia	hsa05221
22	GSE18842	20878980	[42]	Non-Small Cell Lung Cancer	hsa05223
23	GSE19188	20421987	[17]	Non-Small Cell Lung Cancer	hsa05223
24	GSE3585	17045896	[3]	Dilated cardiomyopathy	hsa05414