1. Red: stable co-clustering Blue: no co-clustering
Supplementary Figure 1
Red: stable co-clustering Blue: no co-clustering
2-cluster
3-cluster
Results of NMF in 74 samples from the WG dataset
These plots show how often each pair of samples (74x74 pairings) were in the same cluster during 20 iterations of NMF. Dark red means the samples were always in the same cluster and dark blue means they never were. There is support for 2, 3, and 4 stable cluster assignments by NMF. K5 and K6 are unstable.
4-cluster
5-cluster

2. Supplementary Figure 2

3. Supplementary Figure 3

4. Supplementary Figure 4
P=0.16
EGFR mutation

5. Supplementary Figure 5

6. Supplementary Figure 6
EGFR mutation
KRAS mutation

7. 26 10 16 14 5 7 17 104 n=199 DUSP4 deletion p16 deletion EGFR mutation
Supplementary Figure 7
p=0.0001
DUSP4 deletion
p16 deletion 26 10 16 14 5 7 p=
p=0.007 17
104
EGFR mutation
n=199

8. Wild type EGFR EGFR del19 EGFR L858R
Supplementary Figure 8
6E-16
Wild type
EGFR
EGFR
del19
EGFR
L858R
5E-16
4E-16
DUSP4 mRNA conc (uM)
3E-16
2E-16
1E-16
WT - No EGF
WT - 2 hrs
WT - 4 hrs
WT - 30 min
WT - 1 hr
WT - 6 hrs
del19 - No EGF
del min
del hrs
del hrs
del hrs
L858R - No EGF
del hr
L858R - 30 min
L858R - 2 hrs
L858R - 4 hrs
L858R - 1 hr
L858R - 6 hrs

9. Supplementary Figure 9 A B GFP DUSP4-GFP H358 H1650 H1650 DUSP4 Vector
70KD
DUSP4-GFP
27KD
GFP
ACTIN
H358
H1650
H1650

10. Supplementary Figure 10
H1650 cells
24hrs after
electroporation
H1650 cells
after one week selection
GFP
DUSP4-GFP