Skip to main content

Advertisement

Table 2 Fold difference in the expression values of informative probe sets for 6 different prediction problems in different data sets.

From: Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems

Data set IBC versus Non-IBC p53 mutation versus normal PIK3 mutation versus normal
Receptor status ER-negative ER-positive ER-negative ER-positive ER-negative ER-positive
Phenotype IBC Non-IBC IBC Non-IBC mutation normal mutation normal mutation normal mutation normal
Pts # 19 vs 27 6 vs 31 44 vs 11 14 vs 31 8 vs 49 15 vs 57
Feature # 10 100 10 100 10 100 10 100 10 100 10 100
FDR q value 1.000 1.000 0.280 0.500 0.14 0.33 0.49 0.6 0.08 0.09 0.24 0.55
Fold difference *             
< 0.5 0 20 0 2 1 9 2 29 0 0 0 17
≥0.5 - < 1.0 4 55 1 41 1 37 5 47 1 23 6 50
≥1.0 - < 1.2 2 11 1 10 1 11 1 11 3 18 1 17
≥1.2 - < 1.5 3 12 4 18 2 15 1 9 4 21 2 10
≥1.5 - < 2.0 0 0 2 20 2 22 1 4 1 23 0 5
≥2.0 - < 3.0 0 1 2 9 3 6 0 0 1 14 1 1
≥3.0 - < 4.0 1 1 0 0 0 0 0 0 0 1 0 0
≥4.0 0 0 0 0 0 0 0 0 0 0 0 0
Data set WANG TRANSBIG Mainz          
Receptor status ER-negative ER-positive ER-negative ER-positive ER-negative ER-positive       
Recurrence Yes No Yes No Yes No Yes No Yes No Yes No
Pts # 29 vs 50 29 vs 50 18 vs 45 23 vs 112 11 vs 20 30 vs 139       
Feature # 10 100 10 100 10 100 10 100 10 100 10 100
FDR q value 0.2 0.26 0.004 0.02 0.820 0.91 0.010 0.03 0.47 0.58 0.01 0.03
Fold difference *             
< 0.5 2 35 3 68 2 26 1 26 1 13 3 59
≥0.5 - < 1.0 6 51 7 30 4 47 5 52 5 44 5 26
≥1.0 - < 1.2 0 7 0 2 3 21 2 12 0 5 1 3
≥1.2 - < 1.5 0 5 0 0 1 6 1 8 1 16 0 0
≥1.5 - < 2.0 1 1 0 0 0 0 1 2 2 17 1 2
≥2.0 - < 3.0 1 1 0 0 0 0 0 0 0 3 0 0
≥3.0 - < 4.0 0 0 0 0 0 0 0 0 1 2 0 0
≥4.0 0 0 0 0 0 0 0 0 0 0 0 0
  1. * Log2 Difference = abs(mean log2 intensity for group1 - mean log2 intensity for group 2) where "abs" is absolute value.
  2. The numbers of probe sets with a given level of differential expression are shown for the 6 comparisons. Analyses were performed separately for Estrogen Receptor (ER)-positive and ER-negative cancers. IBC = inflammatory breast cancer, PI3K = Phosphatidylinositol-3 kinase, FDR = false discovery rate. The WANG, TRANSBIG, Mainz data sets correspond to references 2, 3 and 28. Probe sets with mean log2 transformed expression difference > 1 between comparisons groups are highlighted in bold.