Estrogen Receptor ER IHC ErbB2
Her2 IHC
(3+ score)
Specificity:
88.1 % (37/42)
Sensitivity:
97.3 % (71/73)
Specificity:
97.7 % (42/43)
Sensitivity:
55.6 % (10/18)
Specificity:
92.2 % (39/42)
Sensitivity:
87.3 % (89/102)
Specificity:
100 % (104/104)
Sensitivity:
35.1 % (13/37)
Specificity:
92.9 % (39/42)
Sensitivity:
94.7 % (54/57)
Specificity:
94.4 % (75/79)
Sensitivity:
77.8 % (7/9)
Supplementary Figure 7: Derivation of cutoff values for ER and ErbB2 Affymetrix expression data.
To derive cutoff values for ER (ProbeSet 205225_at) and ErbB2 (ProbeSet 216836_s_at) Affymetrix expression data two normal distributions were fitted to the observed distributions of expression values (Venables & Ripley, Modern Applied Statistics with S. Springer 2002). Specifity and sensitivity of the derived cutoff values were obtained from datasets with available immunohistochemical or biochemical data on ER and HER2 status. Data are presented here from three exemplary datasets with available immunohistochemical data for both ER and HER2.
dataset Frankfurt
Density
-0.20 -0.15 -0.10 -0.05 0.00 0.05 0
2 4 6 8
-0.2 -0.1 0.0 0.1
0 2 4 6
dataset expO
Density
-0.2 -0.1 0.0 0.1
0 1 2 3 4 5
dataset New York
Density
-0.1 0.0 0.1 0.2
0 2 4 6 8
dataset Frankfurt
Density
-0.1 0.0 0.1 0.2 0.3
0 2 4 6 8 10
dataset expO
Density
-0.2 -0.1 0.0 0.1 0.2
0 1 2 3 4 5 6
dataset New York
Density
Suppl. Figure 8: Quality of Plexin B1 Affymetrix measurements in different datasets.
The correlation of Plexin B1 expression with the ER status of the tumor was used as a criterium for data quality of Plexin B1 expression measurements in different Affymetrix datasets. Dataset F (Rotterdam) was excluded from the study based on the low difference in expression between ER positive and negative tumors.
-0.2000 0.0000 0.2000
norm. PLXNB1 (215807_s_at)
Frankfurt
-0.2000 0.0000 0.2000
negative
-0.2000 0.0000 0.2000
Hamburg
New York
ER status positive
norm. PLXNB1 (215807_s_at)norm. PLXNB1 (215807_s_at)
A
B
C
-0.4000 -0.2000 0.0000 0.2000
-0.4000 -0.2000 0.0000 0.2000
-0.4000 -0.2000 0.0000 0.2000
Oxford
Villejuif
Rotterdam
negative
ER status positive
norm. PLXNB1 (215807_s_at)norm. PLXNB1 (215807_s_at)norm. PLXNB1 (215807_s_at)
D
E
F
Suppl. Figure 9: Annual hazard rates of disease recurrence.
The annual hazard rates of disease recurrence are plotted according to Plexin B1 expression among cases with ER positive tumors (A) and according to ER status among all cases (B).
months
120 100
80 60
40 20
0
Haz a rd
0.007
0.006
0.005
0.004
0.003
0.002
0.001
Plexin B1 among ER positive tumors
low Plexin B1 high Plexin B1
A
0.020
0.015
0.010
0.005
0.000
ER positive ER negative
months
Haz a rd
120 100
80 60
40 20
0
ER status
B
23
Suppl. Table 4: Univariate analysis of standard parameters and PlexinB1 expression in relation to disease free survival.
All samples ER positive tumors only
Parameter: n= Hazard Ratio P-Value n= Hazard Ratio P-Value
ER status positive vs negative 762 0.5 <0.001 - - -
Lymph node status LNN vs. N1 595 0.8 0.3 443 0.9 0.5
Age > 50 years vs < 50 years 603 1.0 0.8 450 1.0 1.0
Pathological grading poor vs. well/intermediate 603 2.0 <0.001 475 1.8 0.002
Tumor size >2cm vs ≤2cm 603 2.2 <0.001 450 2.2 <0.001
ErbB2 status positive vs negative 762 1.6 0.01 580 1.7 0.04
