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Table 2 Summary of 36 datasets used in benchmark analysis

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

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  
  1. 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