Skip to main content
. 2014 Mar 21;4:4411. doi: 10.1038/srep04411

Table 5. Characteristics of datasets/tasks used in this study. “N” is number of subjects with complete coverage of data from all available modalities in a given dataset. “N(0)” and “N(1)” denote number of subjects for classes “0” and “1”, respectively. The encoding of classes is given in the second column.

Dataset short name Phenotypic response variable definition and encoding N(0) N(1) Gene Expression miRNA Expression Protein expression Clinical Tumor Imaging GWAS DNA Methylation Somatic Mutations Copy Number
Breast cancer patient samples from The Cancer Genome Atlas (TCGA), N = 240
TCGA_BRCA1.R1 Neoplasm disease stages I*, II* (0) vs. III*, IV* (1) 124 111 X   X X     X X  
TCGA_BRCA1.R2 Lymph node stage N0* (0) vs. N1*, N2*, N3* (1) 183 50 X   X X     X X  
TCGA_BRCA1.R3 Tumor stages T1*, T2* (0) vs. T3*, T4* (1) 203 37 X   X X     X X  
TCGA_BRCA1.R4 Estrogen receptor negative (0) vs. positive (1) 57 176 X   X X     X X  
TCGA_BRCA1.R5 Progesterone receptor negative (0) vs. positive (1) 89 144 X   X X     X X  
TCGA_BRCA1.R6 survived 2 years (0) or not (1) 96 7 X   X X     X X  
TCGA_BRCA1.R7 survived 3 years (0) or not (1) 62 13 X   X X     X X  
TCGA_BRCA1.R8 survived 4 years (0) or not (1) 45 13 X   X X     X X  
Breast cancer patient samples from The Cancer Genome Atlas (TCGA), N = 160
TCGA_BRCA2.R1 Neoplasm disease stages I*, II* (0) vs. III*, IV* (1) 57 101 X   X X     X X  
TCGA_BRCA2.R2 Lymph node stage N0* (0) vs. N1*, N2*, N3* (1) 107 52 X   X X     X X  
TCGA_BRCA2.R3 Tumor stages T1*, T2* (0) vs. T3*, T4* (1) 129 30 X   X X     X X  
TCGA_BRCA2.R4 Estrogen receptor negative (0) vs. positive (1) 39 121 X   X X     X X  
TCGA_BRCA2.R5 Progesterone receptor negative (0) vs. positive (1) 60 100 X   X X     X X  
TCGA_BRCA2.R6 survived 2 years (0) or not (1) 94 6 X   X X     X X  
TCGA_BRCA2.R7 survived 3 years (0) or not (1) 71 9 X   X X     X X  
TCGA_BRCA2.R8 survived 4 years (0) or not (1) 38 14 X   X X     X X  
Ovarian cancer patient samples from The Cancer Genome Atlas (TCGA), N = 397
TCGA_OVCA.R1 Lymphatic invasion present (1) vs. absent (0) 47 87 X   X X     X X  
TCGA_OVCA.R2 Neoplasm histologic grade G1,G2 (0) vs. G3,G4 (1) 52 325 X   X X     X X  
TCGA_OVCA.R3 Tumor stages T1*, T2* (0) vs. T3*, T4* (1) 30 350 X   X X     X X  
TCGA_OVCA.R4 Venous invasion present (1) vs. absent (0) 40 53 X   X X     X X  
TCGA_OVCA.R5 survived 1 year (1) or not (0) 271 32 X   X X     X X  
TCGA_OVCA.R6 survived 2 years (1) or not (0) 206 68 X   X X     X X  
TCGA_OVCA.R7 survived 3 years (1) or not (0) 153 98 X   X X     X X  
TCGA_OVCA.R8 survived 4 years (1) or not (0) 85 148 X   X X     X X  
TCGA_OVCA.R9 survived 5 years (1) or not (0) 55 168 X   X X     X X  
TCGA_OVCA.R10 survived 6 years (1) or not (0) 30 182 X   X X     X X  
TCGA_OVCA.R11 survived 7 years (1) or not (0) 19 189 X   X X     X X  
Prostate cancer patient samples from Memorial Sloan-Kettering Cancer Center (MSKCC), N = 92
MSKCC_PRCA.R1 Lymph node stage N0 (0) vs. N1 (1) 62 12 X X   X         X
MSKCC_PRCA.R2 Primary (0) vs. metastatic (1) 79 13 X X   X         X
MSKCC_PRCA.R3 Tumor stages T1 (0) vs. T2, T3, T4 (1) 53 35 X X   X         X
Oral squamous cell carcinoma patient samples from the European project NeoMark, N = 106
NEOMARK.R1 Recurrence (1) vs. no recurrence (0) of oral squam. cell cancer 71 6 X     X X        
Breast cancer patient samples from the UK-Canada project METABRIC, N = 1950
METABRIC.R1 ER_Expr positive (1) vs. negative (0) 463 1487 X     X   X      
METABRIC.R2 HER2_Expr positive (1) vs. negative (0) 1710 240 X     X   X      
METABRIC.R3 PR_Expr positive (1) vs. negative (0) 920 1030 X     X   X      
METABRIC.R4 Grade 1 (0) vs. 2,3 (1) 167 1783 X     X   X      
METABRIC.R5 Grade 1,2 (0) vs. 3 (1) 1018 932 X     X   X      
METABRIC.R6 Stage 0 (0) vs. Stages 1,2,3,4 (1) 509 1441 X     X   X      
METABRIC.R7 Stages 0,1 (0) vs. Stages 2,3,4 (1) 1005 945 X     X   X      
METABRIC.R8 Stages 0,1,2 (0) vs. Stages 3,4 (1) 1825 125 X     X   X      
METABRIC.R9 Stages 0,1,2,3 (0) vs. Stage 4 (1) 1940 10 X     X   X      
METABRIC.R10 survived 1 year (1) or not (0) 27 1878 X     X   X      
METABRIC.R11 survived 2 years (1) or not (0) 102 1767 X     X   X      
METABRIC.R12 survived 3 years (1) or not (0) 184 1634 X     X   X      
METABRIC.R13 survived 4 years (1) or not (0) 279 1482 X     X   X      
METABRIC.R14 survived 5 years (1) or not (0) 340 1328 X     X   X      
METABRIC.R15 survived 6 years (1) or not (0) 387 1138 X     X   X      
METABRIC.R16 survived 7 years (1) or not (0) 424 1013 X     X   X