Table 1

The 24 data sets used to assess the proposed gene set analysis method
GEOID Pubmed Ref. Disease/Target pathway KEGGID Tissue
1 GSE1297 14769913 [20] Alzheimer’s Disease hsa05010 Hippocampal CA1
2 GSE5281 17077275 [21] Alzheimer’s Disease hsa05010 Brain, Entorhinal Cortex
3 GSE5281 17077275 [21] Alzheimer’s Disease hsa05010 Brain, hippocampus
4 GSE5281 17077275 [21] Alzheimer’s Disease hsa05010 Brain, Primary visual cortex
5 GSE20153 20926834 [22] Parkinson’s disease hsa05012 Lymphoblasts
6 GSE20291 15965975 [23] Parkinson’s disease hsa05012 Postmortem brain putamen
7 GSE8762 17724341 [24] Huntington’s disease hsa05016 Lymphocytes (blood)
8 GSE4107 17317818 [25] Colorectal Cancer hsa05210 Mucosa
9 GSE8671 18171984 [26] Colorectal Cancer hsa05210 Colon
10 GSE9348 20143136 [27] Colorectal Cancer hsa05210 Colon
11 GSE14762 19252501 [28] Renal Cancer hsa05211 Kidney
12 GSE781 14641932 [29] Renal Cancer hsa05211 Kidney
13 GSE15471 19260470 [30] Pancreatic Cancer hsa05212 Pancreas
14 GSE16515 19732725 [31] Pancreatic Cancer hsa05212 Pancreas
15 GSE19728 - Glioma hsa05214 Brain
16 GSE21354 - Glioma hsa05214 Brain, Spine
17 GSE6956 18245496 [32] Prostate Cancer hsa05215 Prostate
18 GSE6956 18245496 [32] Prostate Cancer hsa05215 Prostate
19 GSE3467 16365291 [33] Thyroid Cancer hsa05216 Thyroid
20 GSE3678 - Thyroid Cancer hsa05216 Thyroid
21 GSE9476 17910043 [34] Acute myeloid leukemia hsa05221 Blood, Bone marrow
22 GSE18842 20878980 [35] Non-Small Cell Lung Cancer hsa05223 Lung
23 GSE19188 20421987 [36] Non-Small Cell Lung Cancer hsa05223 Lung
24 GSE3585 17045896 [37] Dilated cardiomyopathy hsa05414 Heart

Each data set comes from tissues affected by a specific disease. The KEGG pathway describing that disease is henceforth considered to be the target pathway. The analysis methods were compared in terms of their ability to rank the target pathway as high as possible in the analysis of each data set.

Tarca et al.

Tarca et al. BMC Bioinformatics 2012 13:136   doi:10.1186/1471-2105-13-136

Open Data