Comparative study on gene set and pathway topology-based enrichment methods

BMC Bioinformatics

Table 2 Summary of 36 datasets used in benchmark analysis

GEO accession	Disease/Target pathway	Samples	Ref.
GSE781	Renal cell carcinoma	17	[36]
GSE1297	Alzheimer’s disease	16	[37]
GSE3467	Thyroid cancer	18	[38]
GSE3585	Dilated cardiomyopathy	12	[39]
GSE3678	Thyroid cancer	14	---
GSE4107	Colorectal cancer	22	[40]
GSE5281_EC	Alzheimer’s disease	21	[41]
GSE5281_HIP	Alzheimer’s disease	23	[41]
GSE5281_VCX	Alzheimer’s disease	31	[41]
GSE6956AA	Prostate cancer	10	[42]
GSE6956C	Prostate cancer	16	[42]
GSE8671	Colorectal cancer	64	[43]
GSE8762	Huntington’s disease	22	[44]
GSE9348	Colorectal cancer	82	[45]
GSE9476	Acute myeloid leukemia	63	[46]
GSE14762	Renal cell carcinoma	21	[47]
GSE15471	Pancreatic cancer	70	[48]
GSE16515	Pancreatic cancer	30	[49]
GSE18842	Non-small cell lung cancer	88	[50]
GSE19188	Non-small cell lung cancer	153	[51]
GSE19728	Glioma	21	[52]
GSE20153	Parkinson’s disease	16	[53]
GSE20291	Parkinson’s disease	33	[54]
GSE21354	Glioma	17	[52]
GSE1145	Dilated cardiomyopathy	26	---
GSE14924_CD4	Acute myeloid leukemia	20	[55]
GSE14924_CD8	Acute myeloid leukemia	21	[55]
GSE16759	Alzheimer’s disease	8	[56]
GSE19420	Type II diabetes mellitus	24	[57]
GSE20164	Parkinson’s disease	11	[53]
GSE23878	Colorectal cancer	38	[58]
GSE24739_G0	Chronic myeloid leukemia	12	[59]
GSE24739_G1	Chronic myeloid leukemia	12	[59]
GSE32676	Pancreatic cancer	32	[60]
GSE4183	Colorectal cancer	23	[61]
GSE7305	Endometrial cancer	20	[62]
Total:		1127

The benchmark datasets were retrieved from KEGGandMetacoreDzPathwaysGEO and KEGGdzPathwaysGEO R-packages. The columns of summary table represent the accession number from GEO database, the name of target pathway, the number of samples for each dataset and the reference of original publication

ISSN: 1471-2105