Kidney Renal Clear Cell Carcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 43 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXA2 and FOXA3 transcription factor networks 107
Nephrin/Neph1 signaling in the kidney podocyte 77
Syndecan-4-mediated signaling events 77
Ephrin A reverse signaling 72
Glypican 2 network 67
PDGFR-alpha signaling pathway 66
IL4-mediated signaling events 55
Syndecan-1-mediated signaling events 54
Wnt signaling 52
LPA4-mediated signaling events 50
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXA2 and FOXA3 transcription factor networks 107 4965 46 -0.85 0.035 1000 -1000 -0.1 -1000
Nephrin/Neph1 signaling in the kidney podocyte 77 2646 34 -0.13 0.031 1000 -1000 -0.037 -1000
Syndecan-4-mediated signaling events 77 5220 67 -0.34 0.063 1000 -1000 -0.046 -1000
Ephrin A reverse signaling 72 504 7 -0.084 0.01 1000 -1000 -0.007 -1000
Glypican 2 network 67 270 4 -0.034 -0.006 1000 -1000 0.002 -1000
PDGFR-alpha signaling pathway 66 2915 44 -0.14 0.038 1000 -1000 -0.053 -1000
IL4-mediated signaling events 55 5015 91 -0.69 0.54 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 54 1860 34 -0.16 0.031 1000 -1000 -0.049 -1000
Wnt signaling 52 370 7 -0.092 0.028 1000 -1000 -0.02 -1000
LPA4-mediated signaling events 50 606 12 -0.14 0.009 1000 -1000 -0.021 -1000
Signaling events mediated by the Hedgehog family 50 2627 52 -0.26 0.054 1000 -1000 -0.048 -1000
IL23-mediated signaling events 50 3050 60 -0.48 0.031 1000 -1000 -0.13 -1000
EPO signaling pathway 49 2713 55 -0.21 0.031 1000 -1000 -0.051 -1000
Endothelins 47 4561 96 -0.19 0.031 1000 -1000 -0.069 -1000
amb2 Integrin signaling 46 3795 82 -0.23 0.04 1000 -1000 -0.047 -1000
BMP receptor signaling 43 3541 81 -0.2 0.054 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 42 896 21 -0.11 0.045 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 41 3136 76 -0.38 0.044 1000 -1000 -0.13 -1000
Signaling mediated by p38-alpha and p38-beta 40 1803 44 -0.14 0.03 1000 -1000 -0.03 -1000
IL6-mediated signaling events 40 3042 75 -0.51 0.04 1000 -1000 -0.066 -1000
Noncanonical Wnt signaling pathway 39 1030 26 -0.092 0.03 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 36 3436 93 -0.11 0.074 1000 -1000 -0.066 -1000
p75(NTR)-mediated signaling 35 4488 125 -0.27 0.08 1000 -1000 -0.071 -1000
IL12-mediated signaling events 33 2875 87 -0.24 0.053 1000 -1000 -0.092 -1000
Calcium signaling in the CD4+ TCR pathway 33 1031 31 -0.21 0.03 1000 -1000 -0.059 -1000
Angiopoietin receptor Tie2-mediated signaling 33 2959 88 -0.19 0.039 1000 -1000 -0.09 -1000
Fc-epsilon receptor I signaling in mast cells 32 3140 97 -0.23 0.038 1000 -1000 -0.062 -1000
Reelin signaling pathway 31 1739 56 -0.13 0.077 1000 -1000 -0.049 -1000
Effects of Botulinum toxin 31 827 26 -0.11 0.031 1000 -1000 -0.02 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 31 2158 68 -0.29 0.087 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 31 1657 52 -0.09 0.031 1000 -1000 -0.024 -1000
Thromboxane A2 receptor signaling 30 3160 105 -0.11 0.031 1000 -1000 -0.052 -1000
Arf6 signaling events 29 1859 62 -0.11 0.061 1000 -1000 -0.041 -1000
IL27-mediated signaling events 29 1487 51 -0.13 0.072 1000 -1000 -0.054 -1000
LPA receptor mediated events 29 3016 102 -0.11 0.031 1000 -1000 -0.069 -1000
Glucocorticoid receptor regulatory network 28 3257 114 -0.36 0.09 1000 -1000 -0.066 -1000
Glypican 1 network 27 1311 48 -0.089 0.038 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 26 1388 52 -0.076 0.047 1000 -1000 -0.046 -1000
VEGFR1 specific signals 26 1510 56 -0.074 0.031 1000 -1000 -0.053 -1000
Signaling events regulated by Ret tyrosine kinase 25 2097 82 -0.08 0.031 1000 -1000 -0.071 -1000
HIF-2-alpha transcription factor network 25 1095 43 -0.22 0.063 1000 -1000 -0.063 -1000
Signaling events mediated by VEGFR1 and VEGFR2 25 3180 125 -0.05 0.045 1000 -1000 -0.055 -1000
EPHB forward signaling 24 2076 85 -0.093 0.045 1000 -1000 -0.07 -1000
Paxillin-independent events mediated by a4b1 and a4b7 22 822 37 -0.21 0.065 1000 -1000 -0.037 -1000
Neurotrophic factor-mediated Trk receptor signaling 22 2713 120 -0.11 0.084 1000 -1000 -0.057 -1000
Visual signal transduction: Cones 21 816 38 -0.066 0.041 1000 -1000 -0.021 -1000
IFN-gamma pathway 21 1429 68 -0.12 0.043 1000 -1000 -0.061 -1000
Integrins in angiogenesis 21 1811 84 -0.18 0.067 1000 -1000 -0.061 -1000
Signaling events mediated by PTP1B 20 1556 76 -0.11 0.037 1000 -1000 -0.051 -1000
S1P1 pathway 20 731 36 -0.073 0.03 1000 -1000 -0.046 -1000
BCR signaling pathway 20 2041 99 -0.076 0.061 1000 -1000 -0.068 -1000
Plasma membrane estrogen receptor signaling 20 1772 86 -0.14 0.054 1000 -1000 -0.065 -1000
FOXM1 transcription factor network 20 1026 51 -0.015 0.11 1000 -1000 -0.14 -1000
JNK signaling in the CD4+ TCR pathway 19 333 17 -0.013 0.031 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 18 1204 65 -0.16 0.044 1000 -1000 -0.065 -1000
Ephrin B reverse signaling 18 888 48 -0.037 0.031 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 17 945 54 -0.089 0.043 1000 -1000 -0.06 -1000
Canonical Wnt signaling pathway 17 884 51 -0.073 0.042 1000 -1000 -0.062 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1402 78 -0.21 0.037 1000 -1000 -0.057 -1000
Aurora B signaling 17 1174 67 -0.18 0.059 1000 -1000 -0.041 -1000
Ceramide signaling pathway 16 1284 76 -0.11 0.076 1000 -1000 -0.047 -1000
IL1-mediated signaling events 16 1042 62 -0.1 0.055 1000 -1000 -0.059 -1000
Class IB PI3K non-lipid kinase events 16 48 3 -0.015 0.015 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 15 949 61 -0.073 0.08 1000 -1000 -0.056 -1000
PLK1 signaling events 15 1328 85 -0.11 0.044 1000 -1000 -0.038 -1000
FoxO family signaling 15 1001 64 -0.38 0.078 1000 -1000 -0.072 -1000
Stabilization and expansion of the E-cadherin adherens junction 15 1112 74 -0.11 0.073 1000 -1000 -0.07 -1000
Ras signaling in the CD4+ TCR pathway 15 260 17 -0.017 0.052 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 14 1124 76 -0.18 0.056 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 14 565 39 -0.054 0.031 1000 -1000 -0.031 -1000
IL2 signaling events mediated by PI3K 14 820 58 -0.036 0.048 1000 -1000 -0.052 -1000
Caspase cascade in apoptosis 13 1033 74 -0.094 0.062 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 13 646 47 -0.21 0.045 1000 -1000 -0.046 -1000
Syndecan-3-mediated signaling events 13 465 35 -0.057 0.08 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 13 293 22 -0.049 0.031 1000 -1000 -0.049 -1000
E-cadherin signaling events 13 68 5 0.005 0.024 1000 -1000 0.008 -1000
Syndecan-2-mediated signaling events 12 870 69 -0.11 0.052 1000 -1000 -0.044 -1000
ceramide signaling pathway 12 615 49 -0.026 0.043 1000 -1000 -0.05 -1000
Class I PI3K signaling events 12 918 73 -0.056 0.073 1000 -1000 -0.054 -1000
TCGA08_retinoblastoma 12 98 8 -0.004 0.028 1000 -1000 -0.007 -1000
Regulation of Telomerase 12 1268 102 -0.22 0.064 1000 -1000 -0.072 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 12 419 33 -0.1 0.057 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 12 1222 97 -0.055 0.058 1000 -1000 -0.058 -1000
Regulation of Androgen receptor activity 12 842 70 -0.18 0.051 1000 -1000 -0.047 -1000
ErbB4 signaling events 11 765 69 -0.072 0.043 1000 -1000 -0.053 -1000
Signaling mediated by p38-gamma and p38-delta 11 173 15 -0.043 0.028 1000 -1000 -0.035 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 11 495 45 -0.039 0.078 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 11 612 54 -0.077 0.066 1000 -1000 -0.058 -1000
TCGA08_rtk_signaling 11 298 26 -0.11 0.062 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 10 282 28 -0.005 0.048 1000 -1000 -0.025 -1000
Osteopontin-mediated events 10 400 38 -0.032 0.055 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 10 866 85 -0.083 0.051 1000 -1000 -0.057 -1000
Hedgehog signaling events mediated by Gli proteins 10 659 65 -0.21 0.08 1000 -1000 -0.046 -1000
Nectin adhesion pathway 10 666 63 -0.016 0.053 1000 -1000 -0.057 -1000
S1P3 pathway 10 437 42 -0.026 0.041 1000 -1000 -0.049 -1000
E-cadherin signaling in keratinocytes 10 450 43 -0.058 0.033 1000 -1000 -0.045 -1000
Regulation of nuclear SMAD2/3 signaling 9 1323 136 -0.1 0.1 1000 -1000 -0.058 -1000
Insulin-mediated glucose transport 9 314 32 -0.081 0.057 1000 -1000 -0.04 -1000
mTOR signaling pathway 9 529 53 -0.079 0.045 1000 -1000 -0.043 -1000
Insulin Pathway 9 675 74 -0.047 0.067 1000 -1000 -0.048 -1000
S1P4 pathway 9 229 25 -0.002 0.046 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 9 413 44 -0.077 0.05 1000 -1000 -0.039 -1000
PLK2 and PLK4 events 8 25 3 0.008 0.027 1000 -1000 -0.017 -1000
Aurora C signaling 8 61 7 -0.001 0.033 1000 -1000 -0.009 -1000
S1P5 pathway 8 150 17 -0.008 0.031 1000 -1000 -0.016 -1000
RXR and RAR heterodimerization with other nuclear receptor 8 465 52 -0.05 0.058 1000 -1000 -0.075 -1000
IGF1 pathway 8 480 57 -0.08 0.069 1000 -1000 -0.059 -1000
Signaling events mediated by PRL 8 275 34 -0.043 0.045 1000 -1000 -0.049 -1000
a4b1 and a4b7 Integrin signaling 7 37 5 0.019 0.035 1000 -1000 0.003 -1000
TRAIL signaling pathway 7 365 48 0 0.068 1000 -1000 -0.037 -1000
TCGA08_p53 7 49 7 -0.007 0.028 1000 -1000 -0.012 -1000
E-cadherin signaling in the nascent adherens junction 7 603 76 -0.038 0.053 1000 -1000 -0.071 -1000
BARD1 signaling events 6 390 57 -0.057 0.071 1000 -1000 -0.052 -1000
Aurora A signaling 6 395 60 -0.1 0.06 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 6 441 68 -0.081 0.057 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 6 276 40 -0.055 0.056 1000 -1000 -0.022 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 559 83 -0.081 0.057 1000 -1000 -0.043 -1000
Arf6 trafficking events 6 465 71 -0.052 0.054 1000 -1000 -0.036 -1000
Canonical NF-kappaB pathway 5 207 39 -0.027 0.06 1000 -1000 -0.037 -1000
Arf6 downstream pathway 5 226 43 -0.045 0.046 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 5 310 58 -0.03 0.053 1000 -1000 -0.043 -1000
Paxillin-dependent events mediated by a4b1 5 190 36 -0.056 0.058 1000 -1000 -0.043 -1000
Atypical NF-kappaB pathway 5 178 31 0 0.037 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class II 4 318 75 -0.038 0.058 1000 -1000 -0.03 -1000
Arf1 pathway 4 231 54 -0.001 0.051 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 3 359 104 -0.059 0.072 1000 -1000 -0.046 -1000
Rapid glucocorticoid signaling 3 68 20 0 0.036 1000 -1000 -0.004 -1000
Alternative NF-kappaB pathway 3 40 13 0 0.055 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 2 67 23 -0.028 0.057 1000 -1000 -0.036 -1000
Circadian rhythm pathway 2 62 22 -0.01 0.058 1000 -1000 -0.056 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 21 27 0 0.073 1000 -1000 -0.039 -1000
Total 2806 161047 7203 -15 7 131000 -131000 -6.4 -131000
FOXA2 and FOXA3 transcription factor networks

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.56 0.45 -10000 0 -1 166 166
PCK1 -0.62 0.62 -10000 0 -1.4 146 146
HNF4A -0.72 0.55 -10000 0 -1.2 215 215
KCNJ11 -0.56 0.5 -10000 0 -1.1 162 162
AKT1 -0.19 0.21 -10000 0 -0.57 52 52
response to starvation -0.025 0.039 -10000 0 -0.19 1 1
DLK1 -0.56 0.48 -10000 0 -1.1 157 157
NKX2-1 -0.14 0.18 0.36 6 -0.42 55 61
ACADM -0.56 0.45 -10000 0 -1 175 175
TAT -0.32 0.24 -10000 0 -0.74 64 64
CEBPB -0.015 0.07 -10000 0 -0.38 10 10
CEBPA -0.028 0.1 -10000 0 -0.49 18 18
TTR -0.48 0.36 -10000 0 -0.92 140 140
PKLR -0.62 0.52 -10000 0 -1.2 178 178
APOA1 -0.7 0.53 -10000 0 -1.3 164 164
CPT1C -0.58 0.47 -10000 0 -1.1 164 164
ALAS1 -0.28 0.22 -10000 0 -0.77 26 26
TFRC -0.38 0.3 -10000 0 -0.8 103 103
FOXF1 0.007 0.11 -10000 0 -0.51 20 20
NF1 0.035 0.01 -10000 0 -10000 0 0
HNF1A (dimer) -0.06 0.16 -10000 0 -0.55 38 38
CPT1A -0.56 0.45 -10000 0 -1 177 177
HMGCS1 -0.55 0.45 -10000 0 -1 162 162
NR3C1 -0.014 0.067 -10000 0 -0.26 6 6
CPT1B -0.62 0.5 -10000 0 -1.2 167 167
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.005 -10000 0 -10000 0 0
GCK -0.59 0.48 -10000 0 -1.1 179 179
CREB1 -0.042 0.083 -10000 0 -0.24 19 19
IGFBP1 -0.42 0.46 -10000 0 -1.2 84 84
PDX1 -0.27 0.25 -10000 0 -0.61 110 110
UCP2 -0.56 0.45 -10000 0 -1 177 177
ALDOB -0.69 0.58 -10000 0 -1.3 184 184
AFP -0.24 0.28 -10000 0 -0.77 65 65
BDH1 -0.58 0.47 -10000 0 -1.1 180 180
HADH -0.55 0.48 -10000 0 -1.1 152 152
F2 -0.85 0.62 -10000 0 -1.4 219 219
HNF1A -0.06 0.16 -10000 0 -0.55 38 38
G6PC -0.46 0.6 -10000 0 -1.4 125 125
SLC2A2 -0.51 0.62 -10000 0 -1.6 97 97
INS 0.031 0.06 0.21 13 -10000 0 13
FOXA1 -0.19 0.23 -10000 0 -0.44 193 193
FOXA3 -0.18 0.22 -10000 0 -0.48 118 118
FOXA2 -0.63 0.55 -10000 0 -1.2 178 178
ABCC8 -0.57 0.48 -10000 0 -1.1 159 159
ALB -0.28 0.36 -10000 0 -0.85 103 103
Nephrin/Neph1 signaling in the kidney podocyte

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.095 0.19 0.36 147 -10000 0 147
KIRREL -0.022 0.12 -10000 0 -0.57 19 19
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.095 0.19 -10000 0 -0.36 147 147
PLCG1 0.03 0.006 -10000 0 -10000 0 0
ARRB2 0.03 0.018 -10000 0 -0.35 1 1
WASL 0.028 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.074 0.19 -10000 0 -0.34 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.062 0.14 -10000 0 -0.32 80 80
FYN -0.089 0.16 0.29 7 -0.32 124 131
mol:Ca2+ -0.072 0.18 -10000 0 -0.34 122 122
mol:DAG -0.072 0.18 -10000 0 -0.34 122 122
NPHS2 -0.071 0.16 -10000 0 -0.39 86 86
mol:IP3 -0.072 0.18 -10000 0 -0.34 122 122
regulation of endocytosis -0.066 0.16 -10000 0 -0.3 120 120
Nephrin/NEPH1/podocin/Cholesterol -0.084 0.18 -10000 0 -0.34 123 123
establishment of cell polarity -0.095 0.19 -10000 0 -0.36 147 147
Nephrin/NEPH1/podocin/NCK1-2 -0.053 0.18 -10000 0 -0.32 113 113
Nephrin/NEPH1/beta Arrestin2 -0.066 0.16 -10000 0 -0.3 120 120
NPHS1 -0.13 0.23 -10000 0 -0.46 144 144
Nephrin/NEPH1/podocin -0.075 0.17 -10000 0 -0.32 124 124
TJP1 0.031 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.006 -10000 0 -10000 0 0
NCK2 0.031 0.006 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.071 0.18 -10000 0 -0.34 121 121
CD2AP 0.029 0.028 -10000 0 -0.56 1 1
Nephrin/NEPH1/podocin/GRB2 -0.073 0.18 -10000 0 -0.34 123 123
GRB2 0.031 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.1 0.17 0.3 7 -0.33 132 139
cytoskeleton organization -0.087 0.16 -10000 0 -0.39 78 78
Nephrin/NEPH1 -0.062 0.14 -10000 0 -0.27 116 116
Nephrin/NEPH1/ZO-1 -0.055 0.17 -10000 0 -0.35 79 79
Syndecan-4-mediated signaling events

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.11 0.19 -10000 0 -0.53 48 48
Syndecan-4/Syndesmos -0.29 0.27 -10000 0 -0.63 143 143
positive regulation of JNK cascade -0.28 0.25 -10000 0 -0.58 152 152
Syndecan-4/ADAM12 -0.34 0.29 -10000 0 -0.65 171 171
CCL5 -0.014 0.14 -10000 0 -0.41 47 47
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.039 -10000 0 -0.56 2 2
ITGA5 0.023 0.067 -10000 0 -0.56 6 6
SDCBP 0.029 0.019 -10000 0 -0.34 1 1
PLG -0.22 0.24 -10000 0 -0.43 251 251
ADAM12 -0.079 0.2 -10000 0 -0.42 112 112
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.043 -10000 0 -0.49 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.059 0.043 -10000 0 -0.2 1 1
Syndecan-4/Laminin alpha1 -0.32 0.28 -10000 0 -0.63 160 160
Syndecan-4/CXCL12/CXCR4 -0.3 0.27 -10000 0 -0.62 152 152
Syndecan-4/Laminin alpha3 -0.3 0.27 -10000 0 -0.62 152 152
MDK -0.034 0.16 -10000 0 -0.43 65 65
Syndecan-4/FZD7 -0.3 0.27 -10000 0 -0.63 146 146
Syndecan-4/Midkine -0.32 0.28 -10000 0 -0.64 163 163
FZD7 0.025 0.048 -10000 0 -0.38 6 6
Syndecan-4/FGFR1/FGF -0.28 0.25 -10000 0 -0.59 151 151
THBS1 0.018 0.085 -10000 0 -0.52 11 11
integrin-mediated signaling pathway -0.3 0.27 -10000 0 -0.6 163 163
positive regulation of MAPKKK cascade -0.28 0.25 -10000 0 -0.58 152 152
Syndecan-4/TACI -0.32 0.28 -10000 0 -0.65 158 158
CXCR4 0.018 0.086 -10000 0 -0.56 10 10
cell adhesion 0.017 0.071 0.21 3 -0.44 8 11
Syndecan-4/Dynamin -0.3 0.27 -10000 0 -0.63 145 145
Syndecan-4/TSP1 -0.3 0.28 -10000 0 -0.63 153 153
Syndecan-4/GIPC -0.3 0.27 -10000 0 -0.63 146 146
Syndecan-4/RANTES -0.31 0.28 -10000 0 -0.64 155 155
ITGB1 0.031 0.004 -10000 0 -10000 0 0
LAMA1 -0.016 0.16 -10000 0 -0.53 39 39
LAMA3 0.01 0.092 -10000 0 -0.38 23 23
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCA 0.063 0.13 0.96 8 -0.44 1 9
Syndecan-4/alpha-Actinin -0.3 0.27 -10000 0 -0.63 146 146
TFPI -0.025 0.17 -10000 0 -0.53 45 45
F2 -0.2 0.24 -10000 0 -0.44 229 229
alpha5/beta1 Integrin 0.039 0.052 -10000 0 -0.41 6 6
positive regulation of cell adhesion -0.31 0.26 -10000 0 -0.61 164 164
ACTN1 0.027 0.04 -10000 0 -0.56 2 2
TNC -0.02 0.15 -10000 0 -0.46 47 47
Syndecan-4/CXCL12 -0.3 0.28 -10000 0 -0.64 151 151
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0.023 0.014 -10000 0 -10000 0 0
CXCL12 0.011 0.098 -10000 0 -0.46 18 18
TNFRSF13B -0.044 0.17 -10000 0 -0.43 73 73
FGF2 0.013 0.098 -10000 0 -0.52 15 15
FGFR1 0.028 0.02 -10000 0 -0.34 1 1
Syndecan-4/PI-4-5-P2 -0.3 0.27 -10000 0 -0.63 146 146
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.015 0.11 -10000 0 -0.4 27 27
cell migration -0.018 0.02 -10000 0 -10000 0 0
PRKCD 0.021 0.054 -10000 0 -0.33 9 9
vasculogenesis -0.29 0.26 -10000 0 -0.6 153 153
SDC4 -0.31 0.3 -10000 0 -0.67 144 144
Syndecan-4/Tenascin C -0.31 0.28 -10000 0 -0.64 163 163
Syndecan-4/PI-4-5-P2/PKC alpha -0.047 0.034 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.29 0.27 -10000 0 -0.63 146 146
MMP9 -0.079 0.19 -10000 0 -0.41 108 108
Rac1/GTP 0.017 0.073 0.21 3 -0.45 8 11
cytoskeleton organization -0.28 0.26 -10000 0 -0.6 143 143
GIPC1 0.027 0.051 -10000 0 -0.51 4 4
Syndecan-4/TFPI -0.32 0.28 -10000 0 -0.62 162 162
Ephrin A reverse signaling

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.047 0.14 -9999 0 -0.3 107 107
EFNA5 -0.084 0.21 -9999 0 -0.47 101 101
FYN -0.032 0.14 -9999 0 -0.33 65 65
neuron projection morphogenesis -0.047 0.14 -9999 0 -0.3 107 107
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.047 0.14 -9999 0 -0.3 107 107
EPHA5 0.01 0.07 -9999 0 -0.34 17 17
Glypican 2 network

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.034 0.16 -9999 0 -0.43 65 65
GPC2 -0.006 0.13 -9999 0 -0.45 33 33
GPC2/Midkine -0.029 0.15 -9999 0 -0.33 86 86
neuron projection morphogenesis -0.029 0.15 -9999 0 -0.33 86 86
PDGFR-alpha signaling pathway

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.12 0.23 -10000 0 -0.45 135 135
PDGF/PDGFRA/CRKL -0.063 0.17 -10000 0 -0.38 74 74
positive regulation of JUN kinase activity -0.016 0.14 -10000 0 -0.31 59 59
CRKL 0.031 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.08 0.16 -10000 0 -0.32 135 135
AP1 -0.13 0.27 0.45 1 -0.88 40 41
mol:IP3 -0.087 0.16 -10000 0 -0.33 130 130
PLCG1 -0.087 0.16 -10000 0 -0.33 130 130
PDGF/PDGFRA/alphaV Integrin -0.063 0.17 -10000 0 -0.32 129 129
RAPGEF1 0.029 0.028 -10000 0 -0.56 1 1
CRK 0.031 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.086 0.16 -10000 0 -0.33 130 130
CAV3 0 0 -10000 0 -10000 0 0
CAV1 0.02 0.069 -10000 0 -0.53 7 7
SHC/Grb2/SOS1 -0.015 0.14 -10000 0 -0.31 59 59
PDGF/PDGFRA/Shf -0.067 0.17 -10000 0 -0.32 133 133
FOS -0.14 0.26 0.32 1 -0.86 40 41
JUN -0.033 0.045 -10000 0 -0.44 4 4
oligodendrocyte development -0.063 0.17 -10000 0 -0.32 129 129
GRB2 0.031 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:DAG -0.087 0.16 -10000 0 -0.33 130 130
PDGF/PDGFRA -0.12 0.22 -10000 0 -0.45 135 135
actin cytoskeleton reorganization -0.064 0.17 -10000 0 -0.32 132 132
SRF 0.02 0.022 -10000 0 -0.41 1 1
SHC1 0.03 0.007 -10000 0 -10000 0 0
PI3K -0.036 0.15 -10000 0 -0.34 58 58
PDGF/PDGFRA/Crk/C3G -0.038 0.15 -10000 0 -0.34 67 67
JAK1 -0.08 0.16 -10000 0 -0.32 129 129
ELK1/SRF -0.061 0.12 -10000 0 -0.32 66 66
SHB 0.03 0.006 -10000 0 -10000 0 0
SHF 0.026 0.053 -10000 0 -0.47 5 5
CSNK2A1 0.038 0.017 -10000 0 -10000 0 0
GO:0007205 -0.091 0.16 -10000 0 -0.42 73 73
SOS1 0.031 0.006 -10000 0 -10000 0 0
Ras protein signal transduction -0.016 0.14 -10000 0 -0.31 59 59
PDGF/PDGFRA/SHB -0.064 0.17 -10000 0 -0.32 132 132
PDGF/PDGFRA/Caveolin-1 -0.065 0.17 -10000 0 -0.32 124 124
ITGAV 0.029 0.019 -10000 0 -0.34 1 1
ELK1 -0.084 0.14 -10000 0 -0.39 66 66
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.064 0.17 -10000 0 -0.32 132 132
JAK-STAT cascade -0.08 0.16 -10000 0 -0.32 129 129
cell proliferation -0.067 0.17 -10000 0 -0.32 133 133
IL4-mediated signaling events

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.47 0.52 -10000 0 -1.3 98 98
STAT6 (cleaved dimer) -0.49 0.55 -10000 0 -1.3 119 119
IGHG1 -0.15 0.16 -10000 0 -0.45 8 8
IGHG3 -0.45 0.5 -10000 0 -1.2 112 112
AKT1 -0.23 0.32 -10000 0 -0.97 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.36 -10000 0 -1.3 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.25 0.37 -10000 0 -1.1 43 43
THY1 -0.48 0.54 -10000 0 -1.3 99 99
MYB -0.015 0.14 -10000 0 -0.4 47 47
HMGA1 0.017 0.076 -10000 0 -0.39 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.44 -10000 0 -1 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.37 -10000 0 -1.1 41 41
SP1 0.028 0.031 -10000 0 -10000 0 0
INPP5D 0.027 0.039 -10000 0 -0.56 2 2
SOCS5 0.039 0.024 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.56 -10000 0 -1.3 114 114
SOCS1 -0.31 0.34 -10000 0 -0.79 104 104
SOCS3 -0.27 0.35 -10000 0 -1.1 48 48
FCER2 -0.42 0.48 -10000 0 -1.2 92 92
PARP14 0.026 0.031 -10000 0 -0.56 1 1
CCL17 -0.53 0.59 -10000 0 -1.4 124 124
GRB2 0.031 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.32 -10000 0 -0.97 37 37
T cell proliferation -0.48 0.56 -10000 0 -1.3 108 108
IL4R/JAK1 -0.47 0.53 -10000 0 -1.3 99 99
EGR2 -0.51 0.56 -10000 0 -1.4 100 100
JAK2 -0.022 0.044 -10000 0 -10000 0 0
JAK3 0.009 0.11 -10000 0 -0.5 20 20
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
JAK1 0.008 0.025 -10000 0 -10000 0 0
COL1A2 -0.18 0.33 -10000 0 -1.5 19 19
CCL26 -0.53 0.6 -10000 0 -1.5 106 106
IL4R -0.5 0.58 -10000 0 -1.4 99 99
PTPN6 0.04 0.03 -10000 0 -0.54 1 1
IL13RA2 -0.54 0.59 -10000 0 -1.4 115 115
IL13RA1 -0.022 0.045 -10000 0 -10000 0 0
IRF4 -0.19 0.43 -10000 0 -1.4 41 41
ARG1 -0.13 0.18 -10000 0 -0.83 9 9
CBL -0.29 0.38 -10000 0 -0.95 70 70
GTF3A 0.018 0.047 -10000 0 -0.34 1 1
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.025 0.062 -10000 0 -10000 0 0
IRF4/BCL6 -0.16 0.39 -10000 0 -1.3 38 38
CD40LG -0.007 0.14 -10000 0 -0.53 28 28
MAPK14 -0.3 0.4 -10000 0 -1 68 68
mitosis -0.21 0.29 -10000 0 -0.88 42 42
STAT6 -0.57 0.72 -10000 0 -1.6 110 110
SPI1 0.021 0.078 -10000 0 -0.51 9 9
RPS6KB1 -0.2 0.28 -10000 0 -0.86 39 39
STAT6 (dimer) -0.57 0.74 -10000 0 -1.6 110 110
STAT6 (dimer)/PARP14 -0.51 0.6 -10000 0 -1.4 114 114
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.39 -10000 0 -1.1 49 49
FRAP1 -0.23 0.32 -10000 0 -0.97 42 42
LTA -0.5 0.57 -10000 0 -1.4 104 104
FES 0.026 0.055 -10000 0 -0.56 4 4
T-helper 1 cell differentiation 0.54 0.63 1.5 110 -10000 0 110
CCL11 -0.59 0.6 -10000 0 -1.4 144 144
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.38 -10000 0 -1.2 41 41
IL2RG -0.003 0.13 -10000 0 -0.44 35 35
IL10 -0.51 0.57 -10000 0 -1.4 103 103
IRS1 0.009 0.094 -10000 0 -0.39 23 23
IRS2 -0.005 0.11 -10000 0 -0.36 43 43
IL4 -0.11 0.11 -10000 0 -0.25 50 50
IL5 -0.44 0.54 -10000 0 -1.3 88 88
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.4 -10000 0 -0.96 103 103
COL1A1 -0.28 0.49 -10000 0 -1.6 47 47
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.56 -10000 0 -1.4 99 99
IL2R gamma/JAK3 0.002 0.14 -10000 0 -0.4 45 45
TFF3 -0.5 0.57 -10000 0 -1.4 104 104
ALOX15 -0.48 0.52 -10000 0 -1.3 104 104
MYBL1 0.017 0.069 -10000 0 -0.34 16 16
T-helper 2 cell differentiation -0.4 0.47 -10000 0 -1.1 112 112
SHC1 0.03 0.007 -10000 0 -10000 0 0
CEBPB 0.023 0.059 -10000 0 -0.35 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.36 -10000 0 -1.1 43 43
mol:PI-3-4-5-P3 -0.23 0.32 -10000 0 -0.97 42 42
PI3K -0.24 0.36 -10000 0 -1.1 42 42
DOK2 0.015 0.088 -10000 0 -0.54 11 11
ETS1 0.027 0.084 -10000 0 -0.52 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.31 -10000 0 -1 32 32
ITGB3 -0.48 0.54 -10000 0 -1.3 102 102
PIGR -0.69 0.67 -10000 0 -1.5 165 165
IGHE 0.033 0.061 0.25 7 -10000 0 7
MAPKKK cascade -0.18 0.29 -10000 0 -0.93 32 32
BCL6 0.027 0.048 -10000 0 -0.56 3 3
OPRM1 -0.47 0.52 -10000 0 -1.2 112 112
RETNLB -0.47 0.52 -10000 0 -1.2 112 112
SELP -0.5 0.57 -10000 0 -1.4 104 104
AICDA -0.51 0.57 -10000 0 -1.3 117 117
Syndecan-1-mediated signaling events

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.069 -10000 0 -0.53 7 7
CCL5 -0.014 0.14 -10000 0 -0.41 47 47
SDCBP 0.029 0.019 -10000 0 -0.34 1 1
FGFR/FGF2/Syndecan-1 -0.15 0.19 -10000 0 -0.46 80 80
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.14 0.2 -10000 0 -0.46 78 78
Syndecan-1/Syntenin -0.14 0.19 0.29 2 -0.45 76 78
MAPK3 -0.13 0.18 -10000 0 -0.5 52 52
HGF/MET 0.008 0.11 -10000 0 -0.43 21 21
TGFB1/TGF beta receptor Type II 0.023 0.069 -10000 0 -0.53 7 7
BSG 0.026 0.048 -10000 0 -0.38 6 6
keratinocyte migration -0.14 0.19 -10000 0 -0.46 78 78
Syndecan-1/RANTES -0.16 0.2 0.29 1 -0.46 93 94
Syndecan-1/CD147 -0.13 0.2 0.28 1 -0.47 69 70
Syndecan-1/Syntenin/PIP2 -0.13 0.18 0.27 2 -0.44 76 78
LAMA5 0.021 0.074 -10000 0 -0.53 8 8
positive regulation of cell-cell adhesion -0.13 0.18 0.26 2 -0.43 76 78
MMP7 -0.15 0.24 -10000 0 -0.44 175 175
HGF -0.011 0.13 -10000 0 -0.44 38 38
Syndecan-1/CASK -0.14 0.18 -10000 0 -0.44 81 81
Syndecan-1/HGF/MET -0.14 0.21 -10000 0 -0.54 63 63
regulation of cell adhesion -0.12 0.18 0.42 1 -0.49 51 52
HPSE 0.003 0.12 -10000 0 -0.51 24 24
positive regulation of cell migration -0.15 0.19 -10000 0 -0.46 80 80
SDC1 -0.15 0.19 -10000 0 -0.46 84 84
Syndecan-1/Collagen -0.15 0.19 -10000 0 -0.46 80 80
PPIB 0.03 0.018 -10000 0 -0.34 1 1
MET 0.023 0.054 -10000 0 -0.47 5 5
PRKACA 0.031 0.003 -10000 0 -10000 0 0
MMP9 -0.073 0.19 -10000 0 -0.41 108 108
MAPK1 -0.13 0.18 0.27 1 -0.49 53 54
homophilic cell adhesion -0.15 0.19 -10000 0 -0.46 81 81
MMP1 -0.13 0.24 -10000 0 -0.46 151 151
Wnt signaling

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.092 0.17 -9999 0 -0.35 112 112
FZD6 0.028 0.033 -9999 0 -0.45 2 2
WNT6 -0.057 0.19 -9999 0 -0.46 82 82
WNT4 -0.061 0.19 -9999 0 -0.44 90 90
FZD3 0.027 0.02 -9999 0 -0.34 1 1
WNT5A 0.002 0.092 -9999 0 -0.38 24 24
WNT11 -0.027 0.16 -9999 0 -0.42 59 59
LPA4-mediated signaling events

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.006 0.066 -10000 0 -0.36 15 15
ADCY5 -0.033 0.11 -10000 0 -0.36 49 49
ADCY6 0.005 0.017 -10000 0 -0.35 1 1
ADCY7 0.003 0.033 -10000 0 -0.35 4 4
ADCY1 -0.012 0.075 -10000 0 -0.32 23 23
ADCY2 -0.1 0.14 -10000 0 -0.27 177 177
ADCY3 0.004 0.029 -10000 0 -0.35 3 3
ADCY8 -0.14 0.15 -10000 0 -0.28 226 226
PRKCE 0.009 0.02 -10000 0 -0.41 1 1
ADCY9 0.005 0.017 -10000 0 -0.35 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.091 0.14 0.25 20 -0.3 86 106
Signaling events mediated by the Hedgehog family

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.16 0.25 -10000 0 -0.6 84 84
IHH -0.12 0.23 -10000 0 -0.51 111 111
SHH Np/Cholesterol/GAS1 -0.007 0.096 -10000 0 -0.33 27 27
LRPAP1 0.027 0.048 -10000 0 -0.56 3 3
dorsoventral neural tube patterning 0.007 0.096 0.33 27 -10000 0 27
SMO/beta Arrestin2 -0.1 0.2 -10000 0 -0.53 42 42
SMO -0.11 0.2 -10000 0 -0.54 47 47
AKT1 -0.053 0.16 -10000 0 -0.63 23 23
ARRB2 0.03 0.018 -10000 0 -0.35 1 1
BOC 0.02 0.072 -10000 0 -0.56 7 7
ADRBK1 0.027 0.048 -10000 0 -0.56 3 3
heart looping -0.11 0.2 -10000 0 -0.53 47 47
STIL -0.09 0.16 -10000 0 -0.42 46 46
DHH N/PTCH2 -0.018 0.15 -10000 0 -0.35 72 72
DHH N/PTCH1 -0.12 0.19 -10000 0 -0.49 59 59
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
DHH -0.017 0.15 -10000 0 -0.48 43 43
PTHLH -0.26 0.39 -10000 0 -0.96 92 92
determination of left/right symmetry -0.11 0.2 -10000 0 -0.53 47 47
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
skeletal system development -0.26 0.38 -10000 0 -0.94 92 92
IHH N/Hhip -0.15 0.21 -10000 0 -0.39 168 168
DHH N/Hhip -0.074 0.19 -10000 0 -0.33 143 143
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.2 -10000 0 -0.53 47 47
pancreas development -0.084 0.2 -10000 0 -0.42 118 118
HHAT 0.027 0.037 -10000 0 -0.42 3 3
PI3K 0.037 0.042 -10000 0 -0.3 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.085 -10000 0 -0.41 17 17
somite specification -0.11 0.2 -10000 0 -0.53 47 47
SHH Np/Cholesterol/PTCH1 -0.1 0.16 -10000 0 -0.44 51 51
SHH Np/Cholesterol/PTCH2 -0.016 0.11 -10000 0 -0.33 38 38
SHH Np/Cholesterol/Megalin -0.038 0.14 -10000 0 -0.36 65 65
SHH -0.016 0.1 -10000 0 -0.34 41 41
catabolic process -0.12 0.18 -10000 0 -0.42 76 76
SMO/Vitamin D3 -0.11 0.19 -10000 0 -0.49 52 52
SHH Np/Cholesterol/Hhip -0.055 0.14 -10000 0 -0.35 66 66
LRP2 -0.047 0.2 -10000 0 -0.54 62 62
receptor-mediated endocytosis -0.13 0.21 -10000 0 -0.52 67 67
SHH Np/Cholesterol/BOC -0.002 0.091 -10000 0 -0.32 27 27
SHH Np/Cholesterol/CDO -0.007 0.11 -10000 0 -0.36 31 31
mesenchymal cell differentiation 0.054 0.14 0.34 66 -10000 0 66
mol:Vitamin D3 -0.093 0.18 -10000 0 -0.44 50 50
IHH N/PTCH2 -0.087 0.18 -10000 0 -0.38 103 103
CDON 0.012 0.1 -10000 0 -0.55 15 15
IHH N/PTCH1 -0.12 0.19 -10000 0 -0.43 76 76
Megalin/LRPAP1 -0.018 0.15 -10000 0 -0.4 63 63
PTCH2 -0.004 0.13 -10000 0 -0.45 33 33
SHH Np/Cholesterol -0.008 0.082 -10000 0 -0.32 23 23
PTCH1 -0.12 0.18 -10000 0 -0.43 76 76
HHIP -0.085 0.2 -10000 0 -0.42 118 118
IL23-mediated signaling events

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.39 0.52 -10000 0 -1.3 80 80
IL23A -0.37 0.51 -10000 0 -1.3 72 72
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.52 -10000 0 -1.3 79 79
positive regulation of T cell mediated cytotoxicity -0.43 0.6 -10000 0 -1.5 88 88
ITGA3 -0.36 0.49 -10000 0 -1.3 72 72
IL17F -0.24 0.31 0.49 1 -0.76 72 73
IL12B -0.059 0.15 -10000 0 -0.46 55 55
STAT1 (dimer) -0.4 0.56 -10000 0 -1.4 86 86
CD4 -0.36 0.48 -10000 0 -1.2 74 74
IL23 -0.37 0.48 -10000 0 -1.3 68 68
IL23R -0.069 0.22 -10000 0 -1.3 12 12
IL1B -0.39 0.54 -10000 0 -1.4 71 71
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.38 0.5 -10000 0 -1.3 83 83
TYK2 -0.006 0.053 -10000 0 -0.59 2 2
STAT4 0.015 0.092 -10000 0 -0.54 12 12
STAT3 0.031 0.005 -10000 0 -10000 0 0
IL18RAP -0.004 0.12 -10000 0 -0.49 23 23
IL12RB1 -0.025 0.11 -10000 0 -0.52 20 20
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.014 0.1 -10000 0 -0.41 21 21
IL23R/JAK2 -0.075 0.22 -10000 0 -1.2 12 12
positive regulation of chronic inflammatory response -0.43 0.6 -10000 0 -1.5 88 88
natural killer cell activation 0.006 0.009 0.054 3 -10000 0 3
JAK2 -0.007 0.041 -10000 0 -10000 0 0
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.03 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.35 0.45 -10000 0 -1.2 69 69
ALOX12B -0.42 0.55 -10000 0 -1.3 98 98
CXCL1 -0.48 0.59 -10000 0 -1.4 118 118
T cell proliferation -0.43 0.6 -10000 0 -1.5 88 88
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A -0.18 0.25 0.42 1 -0.59 61 62
PI3K -0.37 0.53 -10000 0 -1.3 83 83
IFNG -0.032 0.054 -10000 0 -0.13 69 69
STAT3 (dimer) -0.35 0.5 -10000 0 -1.2 81 81
IL18R1 -0.001 0.12 -10000 0 -0.56 18 18
IL23/IL23R/JAK2/TYK2/SOCS3 -0.22 0.35 -10000 0 -1 39 39
IL18/IL18R -0.007 0.15 -10000 0 -0.48 30 30
macrophage activation -0.018 0.019 -10000 0 -0.05 3 3
TNF -0.4 0.55 -10000 0 -1.4 76 76
STAT3/STAT4 -0.38 0.54 -10000 0 -1.3 83 83
STAT4 (dimer) -0.4 0.56 -10000 0 -1.4 87 87
IL18 0.006 0.086 -10000 0 -0.44 15 15
IL19 -0.36 0.48 -10000 0 -1.2 88 88
STAT5A (dimer) -0.4 0.56 -10000 0 -1.4 85 85
STAT1 0.028 0.031 -10000 0 -0.34 3 3
SOCS3 0.002 0.12 -10000 0 -0.46 27 27
CXCL9 -0.39 0.52 -10000 0 -1.3 82 82
MPO -0.4 0.52 -10000 0 -1.3 93 93
positive regulation of humoral immune response -0.43 0.6 -10000 0 -1.5 88 88
IL23/IL23R/JAK2/TYK2 -0.48 0.74 -10000 0 -1.8 84 84
IL6 -0.44 0.57 -10000 0 -1.4 105 105
STAT5A 0.028 0.039 -10000 0 -0.56 2 2
IL2 -0.001 0.069 -10000 0 -0.35 14 14
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.009 0.054 3 -10000 0 3
CD3E -0.38 0.51 -10000 0 -1.3 76 76
keratinocyte proliferation -0.43 0.6 -10000 0 -1.5 88 88
NOS2 -0.4 0.52 -10000 0 -1.3 93 93
EPO signaling pathway

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.057 0.16 0.47 1 -0.57 2 3
CRKL -0.071 0.14 0.33 9 -0.46 2 11
mol:DAG -0.085 0.15 0.25 2 -0.34 104 106
HRAS -0.049 0.15 0.35 17 -0.44 5 22
MAPK8 -0.094 0.15 0.25 1 -0.31 111 112
RAP1A -0.07 0.15 0.37 11 -0.46 2 13
GAB1 -0.072 0.14 0.34 9 -0.49 3 12
MAPK14 -0.092 0.15 0.25 1 -0.3 108 109
EPO -0.21 0.25 -10000 0 -0.44 229 229
PLCG1 -0.088 0.15 -10000 0 -0.34 104 104
EPOR/TRPC2/IP3 Receptors 0.01 0.059 -10000 0 -0.38 7 7
RAPGEF1 0.029 0.028 -10000 0 -0.56 1 1
EPO/EPOR (dimer)/SOCS3 -0.12 0.18 -10000 0 -0.36 123 123
GAB1/SHC/GRB2/SOS1 -0.048 0.14 0.29 6 -0.44 3 9
EPO/EPOR (dimer) -0.14 0.19 -10000 0 -0.32 231 231
IRS2 -0.083 0.15 0.36 10 -0.44 9 19
STAT1 -0.081 0.16 0.26 2 -0.34 100 102
STAT5B -0.085 0.16 0.25 2 -0.34 101 103
cell proliferation -0.084 0.15 0.34 8 -0.29 104 112
GAB1/SHIP/PIK3R1/SHP2/SHC -0.06 0.13 -10000 0 -0.47 6 6
TEC -0.071 0.14 0.34 9 -0.46 2 11
SOCS3 0.002 0.12 -10000 0 -0.46 27 27
STAT1 (dimer) -0.079 0.16 0.26 2 -0.34 100 102
JAK2 0.015 0.031 -10000 0 -10000 0 0
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
EPO/EPOR (dimer)/JAK2 -0.067 0.15 -10000 0 -0.28 105 105
EPO/EPOR -0.14 0.19 -10000 0 -0.32 231 231
LYN 0.027 0.041 -10000 0 -0.57 2 2
TEC/VAV2 -0.066 0.14 0.29 3 -0.45 2 5
elevation of cytosolic calcium ion concentration 0.01 0.058 -10000 0 -0.38 7 7
SHC1 0.03 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.1 0.17 -10000 0 -0.34 109 109
mol:IP3 -0.085 0.15 0.25 2 -0.34 104 106
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.07 0.15 0.31 4 -0.48 10 14
SH2B3 0.011 0.049 -10000 0 -0.56 2 2
NFKB1 -0.093 0.15 0.25 1 -0.3 108 109
EPO/EPOR (dimer)/JAK2/SOCS3 -0.095 0.14 0.27 1 -0.3 117 118
PTPN6 -0.076 0.14 0.3 2 -0.28 100 102
TEC/VAV2/GRB2 -0.057 0.14 0.29 3 -0.44 2 5
EPOR 0.01 0.059 -10000 0 -0.38 7 7
INPP5D 0.027 0.039 -10000 0 -0.56 2 2
mol:GDP -0.05 0.14 0.29 6 -0.45 3 9
SOS1 0.031 0.006 -10000 0 -10000 0 0
PLCG2 0.015 0.079 -10000 0 -0.38 17 17
CRKL/CBL/C3G -0.058 0.14 0.29 3 -0.46 3 6
VAV2 -0.07 0.14 0.34 9 -0.46 2 11
CBL -0.072 0.14 0.34 8 -0.46 2 10
SHC/Grb2/SOS1 -0.069 0.12 -10000 0 -0.44 2 2
STAT5A -0.086 0.16 0.25 2 -0.34 103 105
GRB2 0.031 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.067 0.15 -10000 0 -0.54 4 4
LYN/PLCgamma2 0.031 0.071 -10000 0 -0.31 14 14
PTPN11 0.031 0.005 -10000 0 -10000 0 0
BTK -0.077 0.15 0.34 9 -0.45 8 17
BCL2 -0.069 0.19 0.42 3 -0.79 11 14
Endothelins

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.04 0.25 0.27 49 -0.55 61 110
PTK2B 0.028 0.02 -10000 0 -0.34 1 1
mol:Ca2+ -0.028 0.29 0.45 1 -1 31 32
EDN1 -0.028 0.22 0.24 47 -0.54 58 105
EDN3 -0.013 0.11 -10000 0 -0.34 48 48
EDN2 -0.099 0.22 -10000 0 -0.47 120 120
HRAS/GDP -0.035 0.26 0.33 5 -0.74 43 48
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.031 0.24 -10000 0 -0.71 40 40
ADCY4 -0.052 0.24 0.33 1 -0.63 47 48
ADCY5 -0.073 0.25 0.33 1 -0.62 58 59
ADCY6 -0.04 0.21 0.33 1 -0.58 42 43
ADCY7 -0.045 0.22 0.33 1 -0.56 48 49
ADCY1 -0.055 0.23 0.33 1 -0.65 43 44
ADCY2 -0.13 0.25 -10000 0 -0.56 76 76
ADCY3 -0.042 0.22 0.33 1 -0.59 44 45
ADCY8 -0.16 0.25 -10000 0 -0.52 97 97
ADCY9 -0.043 0.21 0.33 1 -0.57 43 44
arachidonic acid secretion -0.04 0.25 0.4 4 -0.67 44 48
ETB receptor/Endothelin-1/Gq/GTP -0.028 0.21 -10000 0 -0.6 41 41
GNAO1 0.006 0.1 -10000 0 -0.41 26 26
HRAS 0.027 0.047 -10000 0 -0.56 3 3
ETA receptor/Endothelin-1/G12/GTP 0.015 0.26 0.38 59 -0.52 53 112
ETA receptor/Endothelin-1/Gs/GTP 0.01 0.27 0.36 60 -0.53 58 118
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.055 0.29 -10000 0 -0.64 62 62
EDNRB -0.008 0.14 -10000 0 -0.55 28 28
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.084 0.3 -10000 0 -0.72 55 55
CYSLTR1 -0.046 0.28 -10000 0 -0.7 49 49
SLC9A1 -0.016 0.17 0.2 44 -0.41 45 89
mol:GDP -0.052 0.29 0.33 5 -0.8 45 50
SLC9A3 -0.17 0.44 -10000 0 -0.87 102 102
RAF1 -0.066 0.27 0.4 2 -0.8 40 42
JUN -0.022 0.28 0.45 1 -0.94 30 31
JAK2 -0.037 0.25 0.27 51 -0.56 58 109
mol:IP3 -0.044 0.26 0.24 2 -0.76 42 44
ETA receptor/Endothelin-1 0.003 0.32 0.44 64 -0.64 59 123
PLCB1 0 0.13 -10000 0 -0.55 24 24
PLCB2 0.01 0.11 -10000 0 -0.51 18 18
ETA receptor/Endothelin-3 -0.002 0.15 -10000 0 -0.32 55 55
FOS -0.076 0.3 0.49 2 -0.88 46 48
Gai/GDP -0.14 0.3 -10000 0 -0.63 101 101
CRK 0.031 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.076 0.34 0.32 2 -0.85 57 59
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
PRKCB1 -0.045 0.25 0.22 2 -0.72 43 45
GNAQ 0.03 0.01 -10000 0 -10000 0 0
GNAZ 0.024 0.06 -10000 0 -0.49 6 6
GNAL 0.017 0.08 -10000 0 -0.42 14 14
Gs family/GDP -0.038 0.26 0.36 3 -0.71 44 47
ETA receptor/Endothelin-1/Gq/GTP -0.015 0.22 0.36 1 -0.62 39 40
MAPK14 -0.04 0.22 -10000 0 -0.64 43 43
TRPC6 -0.035 0.32 0.45 1 -1.1 31 32
GNAI2 0.023 0.014 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.029 -10000 0 -0.56 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.23 -10000 0 -0.68 42 42
ETB receptor/Endothelin-2 -0.081 0.21 -10000 0 -0.38 131 131
ETB receptor/Endothelin-3 -0.017 0.13 -10000 0 -0.31 70 70
ETB receptor/Endothelin-1 -0.026 0.23 -10000 0 -0.55 58 58
MAPK3 -0.073 0.3 0.49 2 -0.83 51 53
MAPK1 -0.072 0.3 0.5 2 -0.83 49 51
Rac1/GDP -0.037 0.25 0.33 4 -0.72 42 46
cAMP biosynthetic process -0.12 0.26 0.28 4 -0.62 69 73
MAPK8 -0.045 0.37 0.48 1 -1.2 36 37
SRC 0.028 0.039 -10000 0 -0.56 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.036 0.17 -10000 0 -0.48 45 45
p130Cas/CRK/Src/PYK2 -0.044 0.28 0.5 3 -0.83 42 45
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.036 0.25 0.33 4 -0.72 42 46
COL1A2 -0.069 0.34 0.39 2 -0.87 49 51
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.069 0.22 -10000 0 -0.44 92 92
mol:DAG -0.044 0.26 0.24 2 -0.76 42 44
MAP2K2 -0.065 0.28 0.56 2 -0.71 55 57
MAP2K1 -0.062 0.27 0.43 2 -0.7 53 55
EDNRA 0.012 0.17 0.24 38 -0.51 24 62
positive regulation of muscle contraction -0.018 0.23 0.26 47 -0.5 53 100
Gq family/GDP -0.02 0.26 -10000 0 -0.74 41 41
HRAS/GTP -0.055 0.28 0.41 2 -0.76 45 47
PRKCH -0.048 0.25 -10000 0 -0.77 40 40
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCA -0.044 0.25 -10000 0 -0.72 42 42
PRKCB -0.048 0.27 0.28 9 -0.76 45 54
PRKCE -0.043 0.25 0.24 1 -0.72 42 43
PRKCD -0.056 0.25 -10000 0 -0.76 41 41
PRKCG -0.053 0.26 -10000 0 -0.72 45 45
regulation of vascular smooth muscle contraction -0.094 0.36 0.52 2 -1 47 49
PRKCQ -0.052 0.26 0.26 1 -0.72 46 47
PLA2G4A -0.05 0.28 0.4 4 -0.77 44 48
GNA14 0.01 0.11 -10000 0 -0.55 16 16
GNA15 0.021 0.077 -10000 0 -0.52 9 9
GNA12 0.028 0.01 -10000 0 -10000 0 0
GNA11 0.024 0.064 -10000 0 -0.52 6 6
Rac1/GTP 0.015 0.26 0.38 59 -0.52 53 112
MMP1 -0.19 0.39 0.68 2 -0.97 82 84
amb2 Integrin signaling

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.003 0.13 -10000 0 -0.49 18 18
alphaM/beta2 Integrin/GPIbA 0.004 0.12 -10000 0 -0.41 26 26
alphaM/beta2 Integrin/proMMP-9 -0.051 0.17 -10000 0 -0.34 81 81
PLAUR 0.012 0.091 -10000 0 -0.4 21 21
HMGB1 0.004 0.038 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.014 0.1 -10000 0 -0.47 14 14
AGER -0.039 0.14 -10000 0 -0.45 42 42
RAP1A 0.031 0.006 -10000 0 -10000 0 0
SELPLG 0.019 0.082 -10000 0 -0.56 9 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.052 0.18 -10000 0 -0.43 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.073 0.19 -10000 0 -0.41 108 108
CYR61 0.007 0.11 -10000 0 -0.46 22 22
TLN1 0.029 0.028 -10000 0 -0.56 1 1
Rap1/GTP -0.1 0.18 -10000 0 -0.48 51 51
RHOA 0.023 0.014 -10000 0 -10000 0 0
P-selectin oligomer -0.008 0.14 -10000 0 -0.52 32 32
MYH2 -0.16 0.2 -10000 0 -0.43 114 114
MST1R -0.015 0.13 -10000 0 -0.42 38 38
leukocyte activation during inflammatory response -0.11 0.17 -10000 0 -0.36 94 94
APOB -0.17 0.24 -10000 0 -0.44 192 192
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.01 0.095 -10000 0 -0.4 22 22
JAM3 0.019 0.083 -10000 0 -0.54 10 10
GP1BA 0.012 0.1 -10000 0 -0.53 15 15
alphaM/beta2 Integrin/CTGF 0.003 0.12 -10000 0 -0.47 21 21
alphaM/beta2 Integrin -0.13 0.2 -10000 0 -0.44 87 87
JAM3 homodimer 0.019 0.083 -10000 0 -0.54 10 10
ICAM2 0.025 0.058 -10000 0 -0.52 5 5
ICAM1 0.018 0.088 -10000 0 -0.54 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.13 0.2 -10000 0 -0.45 80 80
cell adhesion 0.004 0.12 -10000 0 -0.41 26 26
NFKB1 -0.11 0.23 0.38 4 -0.47 88 92
THY1 0.012 0.1 -10000 0 -0.52 16 16
RhoA/GDP 0.017 0.011 -10000 0 -10000 0 0
Lipoprotein(a) -0.11 0.16 -10000 0 -0.27 213 213
alphaM/beta2 Integrin/LRP/tPA 0.016 0.13 -10000 0 -0.49 20 20
IL6 -0.18 0.31 0.38 2 -0.74 86 88
ITGB2 -0.005 0.081 -10000 0 -0.58 7 7
elevation of cytosolic calcium ion concentration 0.008 0.14 -10000 0 -0.5 21 21
alphaM/beta2 Integrin/JAM2/JAM3 0.017 0.12 -10000 0 -0.39 28 28
JAM2 0.016 0.089 -10000 0 -0.52 12 12
alphaM/beta2 Integrin/ICAM1 -0.018 0.17 -10000 0 -0.45 40 40
alphaM/beta2 Integrin/uPA/Plg -0.14 0.18 -10000 0 -0.37 117 117
RhoA/GTP -0.16 0.21 -10000 0 -0.46 115 115
positive regulation of phagocytosis -0.091 0.17 -10000 0 -0.6 29 29
Ron/MSP -0.021 0.14 -10000 0 -0.34 66 66
alphaM/beta2 Integrin/uPAR/uPA 0.01 0.14 -10000 0 -0.5 21 21
alphaM/beta2 Integrin/uPAR 0.004 0.13 -10000 0 -0.46 21 21
PLAU 0.012 0.085 -10000 0 -0.36 22 22
PLAT 0.019 0.073 -10000 0 -0.49 9 9
actin filament polymerization -0.15 0.19 -10000 0 -0.41 112 112
MST1 -0.011 0.12 -10000 0 -0.45 33 33
alphaM/beta2 Integrin/lipoprotein(a) -0.1 0.17 -10000 0 -0.36 94 94
TNF -0.14 0.27 0.38 3 -0.75 51 54
RAP1B 0.03 0.018 -10000 0 -0.34 1 1
alphaM/beta2 Integrin/uPA 0.004 0.12 -10000 0 -0.48 16 16
fibrinolysis -0.14 0.18 -10000 0 -0.37 117 117
HCK 0.021 0.074 -10000 0 -0.53 8 8
dendritic cell antigen processing and presentation -0.13 0.2 -10000 0 -0.45 80 80
VTN -0.068 0.18 -10000 0 -0.4 107 107
alphaM/beta2 Integrin/CYR61 0.001 0.13 -10000 0 -0.45 22 22
LPA -0.006 0.098 -10000 0 -0.34 35 35
LRP1 0.019 0.082 -10000 0 -0.56 9 9
cell migration -0.062 0.17 -10000 0 -0.43 51 51
FN1 0.004 0.11 -10000 0 -0.42 27 27
alphaM/beta2 Integrin/Thy1 0.006 0.13 -10000 0 -0.49 21 21
MPO -0.029 0.16 -10000 0 -0.43 60 60
KNG1 -0.11 0.21 -10000 0 -0.41 145 145
RAP1/GDP 0.04 0.015 -10000 0 -0.2 1 1
ROCK1 -0.16 0.2 -10000 0 -0.47 93 93
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.23 0.24 -10000 0 -0.44 251 251
CTGF 0.009 0.1 -10000 0 -0.49 18 18
alphaM/beta2 Integrin/Hck 0.01 0.12 -10000 0 -0.52 17 17
ITGAM -0.008 0.092 -10000 0 -0.54 11 11
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.004 0.16 -10000 0 -0.46 34 34
HP -0.16 0.23 -10000 0 -0.42 189 189
leukocyte adhesion -0.06 0.19 -10000 0 -0.6 28 28
SELP -0.008 0.14 -10000 0 -0.52 32 32
BMP receptor signaling

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.14 0.23 -10000 0 -0.4 166 166
SMAD6-7/SMURF1 0.052 0.04 -10000 0 -0.35 3 3
NOG -0.15 0.25 -10000 0 -0.46 172 172
SMAD9 -0.062 0.23 -10000 0 -0.66 51 51
SMAD4 0.03 0.006 -10000 0 -10000 0 0
SMAD5 -0.063 0.14 -10000 0 -0.48 26 26
BMP7/USAG1 -0.15 0.21 -10000 0 -0.36 207 207
SMAD5/SKI -0.045 0.16 0.27 2 -0.48 25 27
SMAD1 -0.001 0.06 -10000 0 -0.48 2 2
BMP2 0.016 0.092 -10000 0 -0.54 12 12
SMAD1/SMAD1/SMAD4 0.013 0.07 -10000 0 -0.45 2 2
BMPR1A 0.03 0.006 -10000 0 -10000 0 0
BMPR1B -0.14 0.24 -10000 0 -0.45 167 167
BMPR1A-1B/BAMBI -0.079 0.18 -10000 0 -0.36 103 103
AHSG 0 0.091 -10000 0 -0.34 30 30
CER1 0 0 -10000 0 -10000 0 0
BMP2-4/CER1 0.008 0.1 -10000 0 -0.32 37 37
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.048 0.14 -10000 0 -0.45 29 29
BMP2-4 (homodimer) 0.007 0.12 -10000 0 -0.37 38 38
RGMB 0.026 0.027 -10000 0 -0.34 2 2
BMP6/BMPR2/BMPR1A-1B -0.048 0.17 -10000 0 -0.33 84 84
RGMA -0.01 0.14 -10000 0 -0.49 37 37
SMURF1 0.028 0.01 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.063 0.14 -10000 0 -0.41 42 42
BMP2-4/USAG1 -0.079 0.18 -10000 0 -0.39 92 92
SMAD6/SMURF1/SMAD5 -0.043 0.15 -10000 0 -0.49 20 20
SOSTDC1 -0.12 0.23 -10000 0 -0.45 146 146
BMP7/BMPR2/BMPR1A-1B -0.1 0.2 -10000 0 -0.37 128 128
SKI 0.029 0.028 -10000 0 -0.56 1 1
BMP6 (homodimer) 0.014 0.092 -10000 0 -0.5 14 14
HFE2 0.001 0.098 -10000 0 -0.34 34 34
ZFYVE16 0.028 0.01 -10000 0 -10000 0 0
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
BMP2-4/CHRD 0.004 0.15 -10000 0 -0.43 37 37
SMAD5/SMAD5/SMAD4 -0.046 0.16 0.27 2 -0.47 25 27
MAPK1 0.031 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.036 0.13 -10000 0 -0.42 22 22
BMP7 (homodimer) -0.08 0.2 -10000 0 -0.42 112 112
NUP214 0.029 0.028 -10000 0 -0.56 1 1
BMP6/FETUA 0.011 0.092 -10000 0 -0.27 37 37
SMAD1/SKI 0.004 0.076 0.32 1 -0.57 1 2
SMAD6 0.026 0.055 -10000 0 -0.56 4 4
CTDSP2 0.031 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.007 0.12 -10000 0 -0.39 26 26
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.18 0.25 -10000 0 -0.46 203 203
BMPR2 (homodimer) 0.03 0.007 -10000 0 -10000 0 0
GADD34/PP1CA 0.054 0.046 -10000 0 -0.5 2 2
BMPR1A-1B (homodimer) -0.086 0.18 -10000 0 -0.32 160 160
CHRDL1 -0.2 0.25 -10000 0 -0.45 219 219
ENDOFIN/SMAD1 0.003 0.072 0.32 1 -0.58 1 2
SMAD6-7/SMURF1/SMAD1 0.024 0.081 -10000 0 -0.55 1 1
SMAD6/SMURF1 0.028 0.01 -10000 0 -10000 0 0
BAMBI -0.001 0.13 -10000 0 -0.52 27 27
SMURF2 0.03 0.018 -10000 0 -0.34 1 1
BMP2-4/CHRDL1 -0.12 0.2 -10000 0 -0.39 124 124
BMP2-4/GREM1 -0.12 0.2 -10000 0 -0.39 118 118
SMAD7 0.031 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.058 0.23 -10000 0 -0.61 56 56
SMAD1/SMAD6 0.004 0.07 -10000 0 -0.58 1 1
TAK1/SMAD6 0.039 0.017 -10000 0 -10000 0 0
BMP7 -0.08 0.2 -10000 0 -0.42 112 112
BMP6 0.014 0.092 -10000 0 -0.5 14 14
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.041 0.14 -10000 0 -0.42 30 30
PPM1A 0.029 0.009 -10000 0 -10000 0 0
SMAD1/SMURF2 0.004 0.075 0.32 1 -0.58 1 2
SMAD7/SMURF1 0.041 0.016 -10000 0 -10000 0 0
CTDSPL 0.021 0.028 -10000 0 -0.34 2 2
PPP1CA 0.029 0.039 -10000 0 -0.56 2 2
XIAP 0.031 0.003 -10000 0 -10000 0 0
CTDSP1 0.027 0.039 -10000 0 -0.56 2 2
PPP1R15A 0.028 0.037 -10000 0 -0.42 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.2 -10000 0 -0.49 73 73
CHRD -0.007 0.14 -10000 0 -0.49 33 33
BMPR2 0.03 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.07 0.15 -10000 0 -0.41 48 48
BMP4 -0.004 0.13 -10000 0 -0.47 30 30
FST -0.087 0.21 -10000 0 -0.43 115 115
BMP2-4/NOG -0.093 0.2 -10000 0 -0.4 109 109
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.083 0.19 -10000 0 -0.35 112 112
EGFR-dependent Endothelin signaling events

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.027 0.048 -9999 0 -0.56 3 3
EGFR 0.007 0.11 -9999 0 -0.51 18 18
EGF/EGFR -0.071 0.19 -9999 0 -0.36 108 108
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.015 0.15 -9999 0 -0.32 64 64
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.1 -9999 0 -0.55 15 15
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.23 -9999 0 -0.45 135 135
EGF/EGFR dimer/SHC -0.045 0.16 -9999 0 -0.37 68 68
mol:GDP -0.019 0.15 -9999 0 -0.32 64 64
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.024 0.17 -9999 0 -0.56 43 43
GRB2/SOS1 0.045 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.03 0.13 -9999 0 -0.3 67 67
SHC1 0.03 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.019 0.14 -9999 0 -0.3 67 67
FRAP1 -0.067 0.11 -9999 0 -0.3 64 64
EGF/EGFR dimer -0.073 0.18 -9999 0 -0.34 131 131
SOS1 0.031 0.006 -9999 0 -10000 0 0
GRB2 0.031 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.011 0.16 -9999 0 -0.47 49 49
HIF-1-alpha transcription factor network

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.17 0.51 -10000 0 -1.4 50 50
HDAC7 0.028 0.048 -10000 0 -0.56 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.17 0.41 -10000 0 -1.1 53 53
SMAD4 0.03 0.012 -10000 0 -10000 0 0
ID2 -0.17 0.51 -10000 0 -1.4 49 49
AP1 -0.013 0.14 -10000 0 -0.34 61 61
ABCG2 -0.18 0.52 -10000 0 -1.4 54 54
HIF1A -0.008 0.083 -10000 0 -0.39 2 2
TFF3 -0.19 0.53 -10000 0 -1.4 53 53
GATA2 0.004 0.11 -10000 0 -0.5 20 20
AKT1 -0.013 0.1 -10000 0 -0.49 4 4
response to hypoxia -0.036 0.1 -10000 0 -0.35 13 13
MCL1 -0.17 0.5 -10000 0 -1.4 50 50
NDRG1 -0.17 0.52 -10000 0 -1.4 50 50
SERPINE1 -0.19 0.52 -10000 0 -1.4 57 57
FECH -0.17 0.51 -10000 0 -1.4 50 50
FURIN -0.17 0.51 -10000 0 -1.4 50 50
NCOA2 -0.02 0.12 -10000 0 -0.56 19 19
EP300 -0.021 0.14 -10000 0 -0.34 37 37
HMOX1 -0.18 0.52 -10000 0 -1.4 50 50
BHLHE40 -0.2 0.49 -10000 0 -1.4 51 51
BHLHE41 -0.18 0.52 -10000 0 -1.4 51 51
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.034 0.14 -10000 0 -0.43 10 10
ENG 0.002 0.15 0.4 3 -0.62 13 16
JUN 0.022 0.06 -10000 0 -0.53 5 5
RORA -0.17 0.51 -10000 0 -1.4 50 50
ABCB1 -0.16 0.42 -10000 0 -1.2 61 61
TFRC -0.17 0.51 -10000 0 -1.4 51 51
CXCR4 -0.18 0.52 -10000 0 -1.4 49 49
TF -0.24 0.53 -10000 0 -1.4 60 60
CITED2 -0.18 0.51 -10000 0 -1.4 51 51
HIF1A/ARNT -0.27 0.75 -10000 0 -2.1 50 50
LDHA -0.028 0.19 -10000 0 -1.1 12 12
ETS1 -0.17 0.52 -10000 0 -1.4 50 50
PGK1 -0.17 0.51 -10000 0 -1.4 50 50
NOS2 -0.19 0.52 -10000 0 -1.4 55 55
ITGB2 -0.18 0.52 -10000 0 -1.4 50 50
ALDOA -0.17 0.51 -10000 0 -1.4 50 50
Cbp/p300/CITED2 -0.21 0.53 -10000 0 -1.4 56 56
FOS -0.034 0.16 -10000 0 -0.44 59 59
HK2 -0.17 0.52 -10000 0 -1.4 50 50
SP1 0.018 0.051 -10000 0 -10000 0 0
GCK -0.13 0.42 -10000 0 -1.2 50 50
HK1 -0.17 0.51 -10000 0 -1.4 50 50
NPM1 -0.18 0.49 -10000 0 -1.4 50 50
EGLN1 -0.17 0.5 -10000 0 -1.4 50 50
CREB1 0.036 0.01 -10000 0 -10000 0 0
PGM1 -0.17 0.51 -10000 0 -1.4 50 50
SMAD3 0.03 0.012 -10000 0 -10000 0 0
EDN1 -0.17 0.45 -10000 0 -1.2 61 61
IGFBP1 -0.24 0.53 -10000 0 -1.3 62 62
VEGFA -0.13 0.39 0.5 1 -1 48 49
HIF1A/JAB1 -0.003 0.065 -10000 0 -0.34 1 1
CP -0.23 0.55 -10000 0 -1.4 56 56
CXCL12 -0.18 0.52 -10000 0 -1.4 50 50
COPS5 0.007 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4 0.044 0.018 -10000 0 -10000 0 0
BNIP3 -0.18 0.51 -10000 0 -1.4 50 50
EGLN3 -0.18 0.53 -10000 0 -1.5 50 50
CA9 -0.18 0.53 -10000 0 -1.5 50 50
TERT -0.18 0.51 -10000 0 -1.4 54 54
ENO1 -0.17 0.51 -10000 0 -1.4 50 50
PFKL -0.17 0.51 -10000 0 -1.4 50 50
NCOA1 0.022 0.019 -10000 0 -10000 0 0
ADM -0.18 0.52 -10000 0 -1.4 51 51
ARNT 0.001 0.083 -10000 0 -0.38 2 2
HNF4A -0.044 0.19 -10000 0 -0.56 53 53
ADFP -0.2 0.49 -10000 0 -1.4 52 52
SLC2A1 -0.12 0.38 0.5 1 -1 45 46
LEP -0.19 0.51 -10000 0 -1.4 53 53
HIF1A/ARNT/Cbp/p300 -0.16 0.43 -10000 0 -1.1 54 54
EPO -0.38 0.5 -10000 0 -1 139 139
CREBBP -0.021 0.14 -10000 0 -0.33 38 38
HIF1A/ARNT/Cbp/p300/HDAC7 -0.16 0.46 -10000 0 -1.2 51 51
PFKFB3 -0.17 0.52 -10000 0 -1.4 50 50
NT5E -0.18 0.52 -10000 0 -1.4 52 52
Signaling mediated by p38-alpha and p38-beta

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.068 0.27 -10000 0 -0.99 27 27
MKNK1 0.03 0.006 -10000 0 -10000 0 0
MAPK14 -0.011 0.12 -10000 0 -0.33 41 41
ATF2/c-Jun -0.019 0.13 -10000 0 -0.56 15 15
MAPK11 -0.023 0.15 -10000 0 -0.4 49 49
MITF -0.036 0.16 -10000 0 -0.44 49 49
MAPKAPK5 -0.023 0.14 -10000 0 -0.41 46 46
KRT8 -0.026 0.15 -10000 0 -0.41 49 49
MAPKAPK3 0.02 0.039 -10000 0 -0.42 3 3
MAPKAPK2 0.03 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.028 0.19 -10000 0 -0.52 49 49
CEBPB -0.027 0.14 -10000 0 -0.41 47 47
SLC9A1 -0.03 0.17 -10000 0 -0.45 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.022 0.14 -10000 0 -0.4 48 48
p38alpha-beta/MNK1 -0.003 0.17 -10000 0 -0.42 48 48
JUN -0.017 0.13 -10000 0 -0.55 15 15
PPARGC1A -0.063 0.2 -10000 0 -0.44 85 85
USF1 -0.022 0.15 -10000 0 -0.41 47 47
RAB5/GDP/GDI1 -0.017 0.12 -10000 0 -0.35 32 32
NOS2 -0.073 0.3 -10000 0 -1.1 32 32
DDIT3 -0.027 0.16 -10000 0 -0.42 49 49
RAB5A 0.023 0.014 -10000 0 -10000 0 0
HSPB1 -0.005 0.15 0.29 33 -0.37 40 73
p38alpha-beta/HBP1 -0.005 0.16 -10000 0 -0.43 43 43
CREB1 -0.029 0.17 -10000 0 -0.47 50 50
RAB5/GDP 0.017 0.01 -10000 0 -10000 0 0
EIF4E -0.026 0.14 -10000 0 -0.39 43 43
RPS6KA4 -0.027 0.16 -10000 0 -0.44 48 48
PLA2G4A -0.031 0.14 -10000 0 -0.4 45 45
GDI1 -0.026 0.16 -10000 0 -0.42 48 48
TP53 -0.043 0.18 -10000 0 -0.51 47 47
RPS6KA5 -0.031 0.16 -10000 0 -0.44 51 51
ESR1 -0.035 0.16 -10000 0 -0.43 54 54
HBP1 0.028 0.01 -10000 0 -10000 0 0
MEF2C -0.029 0.16 -10000 0 -0.46 45 45
MEF2A -0.023 0.14 -10000 0 -0.41 47 47
EIF4EBP1 -0.037 0.18 -10000 0 -0.5 51 51
KRT19 -0.14 0.23 -10000 0 -0.42 137 137
ELK4 -0.022 0.14 -10000 0 -0.4 48 48
ATF6 -0.021 0.14 -10000 0 -0.4 47 47
ATF1 -0.028 0.16 -10000 0 -0.46 49 49
p38alpha-beta/MAPKAPK2 -0.001 0.16 -10000 0 -0.42 47 47
p38alpha-beta/MAPKAPK3 -0.017 0.16 -10000 0 -0.42 49 49
IL6-mediated signaling events

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.29 0.28 -10000 0 -0.77 63 63
CRP -0.36 0.37 -10000 0 -0.99 82 82
cell cycle arrest -0.34 0.33 -10000 0 -0.86 89 89
TIMP1 -0.24 0.25 -10000 0 -0.74 45 45
IL6ST -0.026 0.14 -10000 0 -0.56 28 28
Rac1/GDP -0.12 0.17 -10000 0 -0.46 57 57
AP1 -0.03 0.14 -10000 0 -0.63 8 8
GAB2 0.03 0.018 -10000 0 -0.34 1 1
TNFSF11 -0.37 0.37 -10000 0 -0.95 98 98
HSP90B1 -0.013 0.061 -10000 0 -0.75 1 1
GAB1 0.03 0.028 -10000 0 -0.56 1 1
MAPK14 -0.08 0.18 -10000 0 -0.59 34 34
AKT1 0.028 0.049 -10000 0 -0.49 2 2
FOXO1 0.034 0.048 -10000 0 -0.48 1 1
MAP2K6 -0.098 0.16 -10000 0 -0.44 60 60
mol:GTP -0.003 0.004 -10000 0 -10000 0 0
MAP2K4 -0.17 0.18 -10000 0 -0.54 49 49
MITF -0.1 0.16 -10000 0 -0.42 64 64
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.039 -10000 0 -0.56 2 2
A2M -0.008 0.24 -10000 0 -1.5 12 12
CEBPB 0.025 0.056 -10000 0 -0.34 10 10
GRB2/SOS1/GAB family/SHP2 -0.016 0.097 -10000 0 -0.6 7 7
STAT3 -0.36 0.37 -10000 0 -0.94 88 88
STAT1 -0.016 0.12 -10000 0 -0.86 8 8
CEBPD -0.3 0.29 -10000 0 -0.78 71 71
PIK3CA 0.031 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.042 -10000 0 -0.3 6 6
JUN 0.024 0.057 -10000 0 -0.52 5 5
PIAS3/MITF -0.1 0.15 -10000 0 -0.42 55 55
MAPK11 -0.085 0.19 -10000 0 -0.58 39 39
STAT3 (dimer)/FOXO1 -0.24 0.25 -10000 0 -0.69 56 56
GRB2/SOS1/GAB family -0.036 0.16 -10000 0 -0.5 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.085 0.16 -10000 0 -0.4 64 64
GRB2 0.031 0.006 -10000 0 -10000 0 0
JAK2 0.03 0.007 -10000 0 -10000 0 0
LBP -0.4 0.37 0.44 1 -0.89 135 136
PIK3R1 0.024 0.052 -10000 0 -0.42 6 6
JAK1 0.021 0.021 -10000 0 -10000 0 0
MYC -0.3 0.29 -10000 0 -0.78 73 73
FGG -0.51 0.46 -10000 0 -1.1 166 166
macrophage differentiation -0.34 0.33 -10000 0 -0.86 89 89
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.18 -10000 0 -0.39 72 72
JUNB -0.29 0.28 -10000 0 -0.81 53 53
FOS -0.032 0.16 -10000 0 -0.44 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.16 -10000 0 -0.42 75 75
STAT1/PIAS1 -0.13 0.16 -10000 0 -0.43 56 56
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.042 -10000 0 -0.54 1 1
STAT3 (dimer) -0.36 0.37 -10000 0 -0.93 89 89
PRKCD -0.21 0.23 0.47 2 -0.61 61 63
IL6R 0.005 0.095 -10000 0 -0.54 13 13
SOCS3 -0.069 0.26 0.43 1 -0.98 24 25
gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.1 -10000 0 -0.36 28 28
Rac1/GTP -0.14 0.18 -10000 0 -0.47 66 66
HCK 0.02 0.074 -10000 0 -0.53 8 8
MAPKKK cascade 0.002 0.1 -10000 0 -0.66 6 6
bone resorption -0.35 0.34 -10000 0 -0.86 101 101
IRF1 -0.27 0.3 -10000 0 -0.8 57 57
mol:GDP -0.13 0.17 -10000 0 -0.44 73 73
SOS1 0.03 0.007 -10000 0 -10000 0 0
VAV1 -0.13 0.17 -10000 0 -0.45 73 73
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.065 0.2 -10000 0 -0.63 37 37
PTPN11 -0.001 0.047 -10000 0 -0.92 1 1
IL6/IL6RA -0.091 0.17 -10000 0 -0.33 140 140
gp130 (dimer)/TYK2/TYK2/LMO4 0.012 0.1 -10000 0 -0.36 29 29
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.099 -10000 0 -0.36 28 28
IL6 -0.12 0.22 -10000 0 -0.45 134 134
PIAS3 0.03 0.006 -10000 0 -10000 0 0
PTPRE 0.04 0.043 -10000 0 -0.56 2 2
PIAS1 0.031 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.084 0.14 -10000 0 -0.36 67 67
LMO4 0.009 0.026 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.33 0.32 -10000 0 -0.84 88 88
MCL1 0.04 0.061 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.014 0.15 -9999 0 -0.54 36 36
GNB1/GNG2 -0.081 0.17 -9999 0 -0.41 56 56
mol:DAG -0.084 0.15 -9999 0 -0.41 44 44
PLCG1 -0.086 0.15 -9999 0 -0.42 44 44
YES1 -0.088 0.16 -9999 0 -0.41 60 60
FZD3 0.027 0.02 -9999 0 -0.34 1 1
FZD6 0.028 0.033 -9999 0 -0.45 2 2
G protein -0.076 0.16 -9999 0 -0.42 44 44
MAP3K7 -0.079 0.13 -9999 0 -0.4 38 38
mol:Ca2+ -0.081 0.14 -9999 0 -0.4 44 44
mol:IP3 -0.084 0.15 -9999 0 -0.41 44 44
NLK 0 0.096 -9999 0 -0.91 5 5
GNB1 0.03 0.007 -9999 0 -10000 0 0
CAMK2A -0.085 0.14 -9999 0 -0.42 45 45
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.092 0.17 -9999 0 -0.35 112 112
CSNK1A1 0.024 0.013 -9999 0 -10000 0 0
GNAS -0.087 0.16 -9999 0 -0.41 61 61
GO:0007205 -0.085 0.14 -9999 0 -0.42 38 38
WNT6 -0.057 0.19 -9999 0 -0.46 82 82
WNT4 -0.061 0.19 -9999 0 -0.44 90 90
NFAT1/CK1 alpha -0.076 0.16 -9999 0 -0.45 42 42
GNG2 0.025 0.048 -9999 0 -0.56 3 3
WNT5A 0.002 0.092 -9999 0 -0.38 24 24
WNT11 -0.027 0.16 -9999 0 -0.42 59 59
CDC42 -0.087 0.15 -9999 0 -0.4 56 56
TCR signaling in naïve CD8+ T cells

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.031 0.22 0.32 11 -0.6 44 55
FYN -0.076 0.3 0.34 8 -0.8 50 58
LAT/GRAP2/SLP76 -0.06 0.22 0.28 2 -0.6 50 52
IKBKB 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.025 0.19 0.35 19 -0.48 45 64
B2M 0.031 0.006 -10000 0 -10000 0 0
IKBKG 0 0.067 0.12 33 -0.18 23 56
MAP3K8 0.027 0.046 -10000 0 -0.45 4 4
mol:Ca2+ -0.017 0.029 0.084 5 -0.091 40 45
integrin-mediated signaling pathway 0.036 0.035 -10000 0 -0.35 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.054 0.27 0.39 10 -0.7 51 61
TRPV6 0.074 0.37 1.1 48 -0.58 9 57
CD28 0.006 0.11 -10000 0 -0.52 20 20
SHC1 -0.072 0.28 0.35 11 -0.77 49 60
receptor internalization -0.084 0.31 0.34 1 -0.8 56 57
PRF1 -0.081 0.35 -10000 0 -1.2 37 37
KRAS 0.031 0.005 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.007 0.16 0.33 17 -0.4 37 54
LAT -0.083 0.29 0.39 4 -0.72 61 65
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.03 0.16 -10000 0 -0.44 60 60
CD3E -0.02 0.16 -10000 0 -0.46 49 49
CD3G -0.031 0.18 -10000 0 -0.5 54 54
RASGRP2 -0.001 0.038 0.086 2 -0.18 15 17
RASGRP1 -0.015 0.2 0.33 25 -0.51 40 65
HLA-A 0.03 0.008 -10000 0 -10000 0 0
RASSF5 0.026 0.048 -10000 0 -0.56 3 3
RAP1A/GTP/RAPL 0.037 0.036 -10000 0 -0.35 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.092 0.2 43 -0.14 22 65
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.041 0.079 -10000 0 -0.25 42 42
PRKCA -0.012 0.12 0.18 8 -0.3 37 45
GRAP2 0.016 0.094 -10000 0 -0.56 12 12
mol:IP3 -0.047 0.16 0.2 21 -0.46 46 67
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.095 0.36 -10000 0 -0.78 65 65
ORAI1 -0.066 0.29 0.64 1 -0.92 44 45
CSK -0.08 0.29 0.39 2 -0.8 49 51
B7 family/CD28 -0.064 0.3 0.34 2 -0.9 41 43
CHUK 0.03 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.096 0.35 0.35 2 -0.88 57 59
PTPN6 -0.081 0.29 0.3 2 -0.79 51 53
VAV1 -0.08 0.29 0.43 2 -0.8 49 51
Monovalent TCR/CD3 -0.061 0.26 -10000 0 -0.64 55 55
CBL 0.031 0.004 -10000 0 -10000 0 0
LCK -0.084 0.32 0.34 6 -0.85 53 59
PAG1 -0.078 0.29 0.34 4 -0.79 50 54
RAP1A 0.031 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.096 0.35 0.34 2 -0.9 55 57
CD80 -0.01 0.14 -10000 0 -0.49 35 35
CD86 0.016 0.091 -10000 0 -0.57 11 11
PDK1/CARD11/BCL10/MALT1 -0.027 0.11 -10000 0 -0.3 44 44
HRAS 0.027 0.048 -10000 0 -0.56 3 3
GO:0035030 -0.07 0.22 0.3 2 -0.67 43 45
CD8A -0.053 0.18 -10000 0 -0.43 85 85
CD8B -0.062 0.19 -10000 0 -0.43 95 95
PTPRC 0.015 0.09 -10000 0 -0.53 12 12
PDK1/PKC theta -0.03 0.24 0.43 22 -0.61 44 66
CSK/PAG1 -0.075 0.28 0.36 4 -0.79 47 51
SOS1 0.031 0.006 -10000 0 -10000 0 0
peptide-MHC class I 0.044 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.063 0.26 -10000 0 -0.75 45 45
STIM1 -0.005 0.11 0.94 2 -0.91 3 5
RAS family/GTP 0.027 0.1 0.22 31 -0.2 28 59
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.098 0.36 0.35 1 -0.91 56 57
mol:DAG -0.062 0.13 -10000 0 -0.39 51 51
RAP1A/GDP 0.017 0.049 0.12 31 -10000 0 31
PLCG1 0.03 0.006 -10000 0 -10000 0 0
CD247 0.015 0.092 -10000 0 -0.52 13 13
cytotoxic T cell degranulation -0.073 0.32 -10000 0 -1 38 38
RAP1A/GTP 0 0.014 -10000 0 -0.07 12 12
mol:PI-3-4-5-P3 -0.036 0.22 0.35 12 -0.57 47 59
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.058 0.22 0.26 6 -0.6 48 54
NRAS 0.031 0.006 -10000 0 -10000 0 0
ZAP70 -0.012 0.14 -10000 0 -0.46 40 40
GRB2/SOS1 0.045 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.065 0.21 0.31 1 -0.6 49 50
MALT1 0.028 0.039 -10000 0 -0.56 2 2
TRAF6 0.03 0.028 -10000 0 -0.56 1 1
CD8 heterodimer -0.075 0.24 -10000 0 -0.49 105 105
CARD11 -0.016 0.14 -10000 0 -0.43 44 44
PRKCB -0.016 0.13 0.16 7 -0.34 37 44
PRKCE -0.011 0.12 0.19 8 -0.3 37 45
PRKCQ -0.047 0.26 0.35 18 -0.67 51 69
LCP2 0.016 0.067 -10000 0 -0.56 6 6
BCL10 0.03 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.016 0.17 0.34 19 -0.41 44 63
IKK complex 0.032 0.1 0.19 83 -0.13 18 101
RAS family/GDP -0.002 0.013 -10000 0 -0.082 3 3
MAP3K14 -0.008 0.13 0.28 15 -0.34 35 50
PDPK1 -0.018 0.19 0.38 21 -0.45 44 65
TCR/CD3/MHC I/CD8/Fyn -0.11 0.38 0.37 1 -0.99 54 55
p75(NTR)-mediated signaling

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.041 0.043 -10000 0 -0.41 4 4
Necdin/E2F1 0.014 0.12 -10000 0 -0.42 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.024 0.17 -10000 0 -0.42 49 49
NGF (dimer)/p75(NTR)/BEX1 -0.13 0.23 -10000 0 -0.45 114 114
NT-4/5 (dimer)/p75(NTR) -0.006 0.14 -10000 0 -0.38 50 50
IKBKB 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.022 0.16 0.46 2 -0.44 42 44
IKBKG 0.027 0.048 -10000 0 -0.56 3 3
BDNF -0.059 0.2 -10000 0 -0.48 81 81
MGDIs/NGR/p75(NTR)/LINGO1 -0.001 0.17 -10000 0 -0.48 45 45
FURIN 0.028 0.043 -10000 0 -0.49 3 3
proBDNF (dimer)/p75(NTR)/Sortilin -0.032 0.19 -10000 0 -0.41 73 73
LINGO1 -0.002 0.13 -10000 0 -0.54 27 27
Sortilin/TRAF6/NRIF 0.036 0.036 -10000 0 -10000 0 0
proBDNF (dimer) -0.059 0.2 -10000 0 -0.48 81 81
NTRK1 -0.014 0.13 -10000 0 -0.41 45 45
RTN4R 0.012 0.092 -10000 0 -0.41 20 20
neuron apoptosis -0.047 0.18 0.45 2 -0.59 32 34
IRAK1 0.03 0.028 -10000 0 -0.56 1 1
SHC1 -0.037 0.16 -10000 0 -0.45 50 50
ARHGDIA 0.028 0.039 -10000 0 -0.56 2 2
RhoA/GTP 0.017 0.011 -10000 0 -10000 0 0
Gamma Secretase 0.08 0.041 -10000 0 -0.3 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.012 0.17 -10000 0 -0.44 49 49
MAGEH1 0.031 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.01 0.2 -10000 0 -0.46 66 66
Mammalian IAPs/DIABLO 0.062 0.077 -10000 0 -0.32 15 15
proNGF (dimer) -0.025 0.16 -10000 0 -0.5 48 48
MAGED1 0.03 0.025 -10000 0 -0.34 2 2
APP 0.03 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.011 0.065 -10000 0 -0.34 15 15
ZNF274 0.031 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.022 0.15 -10000 0 -0.4 51 51
NGF -0.025 0.16 -10000 0 -0.5 48 48
cell cycle arrest -0.017 0.16 0.49 2 -0.39 47 49
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.026 0.15 -10000 0 -0.49 33 33
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.014 0.13 -10000 0 -0.39 35 35
NCSTN 0.03 0.007 -10000 0 -10000 0 0
mol:GTP -0.007 0.17 -10000 0 -0.45 52 52
PSENEN 0.031 0.004 -10000 0 -10000 0 0
mol:ceramide -0.037 0.16 -10000 0 -0.44 51 51
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.015 0.13 -10000 0 -0.45 25 25
p75(NTR)/beta APP 0.007 0.12 -10000 0 -0.38 40 40
BEX1 -0.16 0.23 -10000 0 -0.42 197 197
mol:GDP -0.051 0.16 -10000 0 -0.45 52 52
NGF (dimer) -0.23 0.21 -10000 0 -0.42 207 207
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.018 0.17 -10000 0 -0.46 44 44
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
RAC1/GTP -0.005 0.14 -10000 0 -0.4 45 45
MYD88 0.017 0.056 -10000 0 -0.56 4 4
CHUK 0.03 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.006 0.17 -10000 0 -0.45 52 52
RHOB 0.012 0.1 -10000 0 -0.55 15 15
RHOA 0.023 0.014 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.041 0.036 -10000 0 -0.32 4 4
NT3 (dimer) -0.012 0.15 -10000 0 -0.49 38 38
TP53 -0.046 0.15 0.4 3 -0.55 15 18
PRDM4 -0.035 0.15 -10000 0 -0.43 48 48
BDNF (dimer) -0.27 0.22 -10000 0 -0.44 236 236
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
SORT1 0.027 0.048 -10000 0 -0.56 3 3
activation of caspase activity 0.017 0.17 -10000 0 -0.42 49 49
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.01 0.17 -10000 0 -0.43 51 51
RHOC 0.029 0.028 -10000 0 -0.56 1 1
XIAP 0.031 0.003 -10000 0 -10000 0 0
MAPK10 -0.048 0.18 0.41 4 -0.51 40 44
DIABLO 0.031 0.005 -10000 0 -10000 0 0
SMPD2 -0.038 0.16 -10000 0 -0.44 51 51
APH1B 0.029 0.039 -10000 0 -0.56 2 2
APH1A 0.03 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.008 0.18 -10000 0 -0.47 52 52
PSEN1 0.029 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.043 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.018 0.18 -10000 0 -0.46 56 56
MAPK8 -0.047 0.17 0.37 4 -0.5 41 45
MAPK9 -0.047 0.16 0.39 2 -0.54 30 32
APAF1 0.031 0.005 -10000 0 -10000 0 0
NTF3 -0.012 0.15 -10000 0 -0.49 38 38
NTF4 0.011 0.066 -10000 0 -0.34 15 15
NDN -0.008 0.15 -10000 0 -0.55 31 31
RAC1/GDP 0.021 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.006 0.17 -10000 0 -0.45 43 43
p75 CTF/Sortilin/TRAF6/NRIF 0.073 0.039 -10000 0 -0.32 3 3
RhoA-B-C/GTP -0.007 0.17 -10000 0 -0.45 52 52
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0 0.18 -10000 0 -0.36 72 72
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.013 0.18 -10000 0 -0.38 74 74
PRKACB 0.03 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.023 0.15 -10000 0 -0.35 79 79
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.51 20 20
BIRC2 0.031 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.18 0.73 1 -0.48 39 40
BAD -0.035 0.18 0.51 5 -0.54 31 36
RIPK2 0.028 0.026 -10000 0 -0.34 2 2
NGFR -0.018 0.16 -10000 0 -0.52 41 41
CYCS -0.034 0.15 -10000 0 -0.43 46 46
ADAM17 0.03 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.013 0.16 -10000 0 -0.43 45 45
BCL2L11 -0.034 0.18 0.48 5 -0.53 31 36
BDNF (dimer)/p75(NTR) -0.056 0.2 -10000 0 -0.39 106 106
PI3K 0.006 0.17 -10000 0 -0.44 47 47
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.011 0.17 -10000 0 -0.43 50 50
NDNL2 0.031 0.004 -10000 0 -10000 0 0
YWHAE 0.031 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.019 -10000 0 -0.34 1 1
NGF (dimer)/p75(NTR) -0.03 0.19 -10000 0 -0.46 66 66
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.011 0.17 -10000 0 -0.44 49 49
TRAF6 0.03 0.028 -10000 0 -0.56 1 1
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCZ 0.02 0.074 -10000 0 -0.53 8 8
PLG -0.23 0.24 -10000 0 -0.44 251 251
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.071 0.2 -10000 0 -0.43 89 89
SQSTM1 0.024 0.014 -10000 0 -10000 0 0
NGFRAP1 0.03 0.028 -10000 0 -0.56 1 1
CASP3 -0.028 0.17 0.49 5 -0.48 33 38
E2F1 0.026 0.046 -10000 0 -0.45 4 4
CASP9 0.03 0.007 -10000 0 -10000 0 0
IKK complex 0.001 0.18 -10000 0 -0.54 28 28
NGF (dimer)/TRKA -0.031 0.16 -10000 0 -0.35 86 86
MMP7 -0.15 0.24 -10000 0 -0.44 175 175
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.17 -10000 0 -0.41 50 50
MMP3 -0.018 0.12 -10000 0 -0.34 54 54
APAF-1/Caspase 9 -0.028 0.13 -10000 0 -0.51 23 23
IL12-mediated signaling events

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.053 0.16 -10000 0 -0.47 39 39
TBX21 -0.11 0.43 -10000 0 -1.3 44 44
B2M 0.027 0.017 -10000 0 -10000 0 0
TYK2 0.024 0.052 -10000 0 -0.59 2 2
IL12RB1 0.005 0.12 -10000 0 -0.51 20 20
GADD45B -0.064 0.37 -10000 0 -1.2 32 32
IL12RB2 -0.075 0.18 -10000 0 -0.37 119 119
GADD45G -0.084 0.4 -10000 0 -1.2 38 38
natural killer cell activation 0.004 0.019 -10000 0 -10000 0 0
RELB 0.028 0.039 -10000 0 -0.56 2 2
RELA 0.031 0.003 -10000 0 -10000 0 0
IL18 0.015 0.087 -10000 0 -0.44 15 15
IL2RA -0.029 0.16 -10000 0 -0.43 60 60
IFNG -0.12 0.23 -10000 0 -0.44 150 150
STAT3 (dimer) -0.061 0.33 -10000 0 -0.9 43 43
HLA-DRB5 -0.004 0.12 -10000 0 -0.42 33 33
FASLG -0.12 0.46 -10000 0 -1.3 47 47
NF kappa B2 p52/RelB -0.088 0.41 -10000 0 -1.1 47 47
CD4 0.02 0.068 -10000 0 -0.56 6 6
SOCS1 0.009 0.096 -10000 0 -0.4 23 23
EntrezGene:6955 -0.003 0.01 -10000 0 -10000 0 0
CD3D -0.036 0.16 -10000 0 -0.45 60 60
CD3E -0.026 0.15 -10000 0 -0.46 49 49
CD3G -0.037 0.18 -10000 0 -0.51 54 54
IL12Rbeta2/JAK2 -0.037 0.14 -10000 0 -0.26 105 105
CCL3 -0.12 0.45 -10000 0 -1.3 50 50
CCL4 -0.1 0.42 -10000 0 -1.3 37 37
HLA-A 0.027 0.016 -10000 0 -10000 0 0
IL18/IL18R 0.03 0.16 -10000 0 -0.49 30 30
NOS2 -0.12 0.48 -10000 0 -1.4 52 52
IL12/IL12R/TYK2/JAK2/SPHK2 -0.048 0.16 -10000 0 -0.48 36 36
IL1R1 -0.093 0.4 -10000 0 -1.2 39 39
IL4 -0.004 0.019 -10000 0 -10000 0 0
JAK2 0.025 0.032 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.17 0.52 -10000 0 -1.2 67 67
RAB7A -0.033 0.3 0.59 1 -0.91 31 32
lysosomal transport -0.028 0.29 0.59 1 -0.85 31 32
FOS -0.17 0.47 -10000 0 -1.3 60 60
STAT4 (dimer) -0.076 0.39 0.48 1 -1.1 45 46
STAT5A (dimer) -0.15 0.42 -10000 0 -1.1 55 55
GZMA -0.1 0.44 -10000 0 -1.3 44 44
GZMB -0.11 0.42 -10000 0 -1.3 39 39
HLX 0.01 0.1 -10000 0 -0.52 17 17
LCK -0.12 0.47 -10000 0 -1.3 49 49
TCR/CD3/MHC II/CD4 -0.081 0.31 -10000 0 -0.92 40 40
IL2/IL2R -0.009 0.17 -10000 0 -0.39 60 60
MAPK14 -0.064 0.4 -10000 0 -1.2 36 36
CCR5 -0.16 0.44 -10000 0 -1.2 56 56
IL1B -0.017 0.15 -10000 0 -0.47 42 42
STAT6 0.004 0.1 -10000 0 -0.34 2 2
STAT4 0.015 0.092 -10000 0 -0.54 12 12
STAT3 0.031 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 -10000 0 -0.34 3 3
NFKB1 0.031 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.048 -10000 0 -0.56 3 3
IL12B -0.034 0.15 -10000 0 -0.44 55 55
CD8A -0.056 0.18 -10000 0 -0.43 85 85
CD8B -0.065 0.19 -10000 0 -0.43 95 95
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.053 0.16 0.47 39 -10000 0 39
IL2RB 0.006 0.12 -10000 0 -0.52 21 21
proteasomal ubiquitin-dependent protein catabolic process -0.057 0.34 0.51 2 -0.93 44 46
IL2RG -0.005 0.13 -10000 0 -0.45 35 35
IL12 -0.028 0.15 -10000 0 -0.34 71 71
STAT5A 0.028 0.039 -10000 0 -0.56 2 2
CD247 0.009 0.092 -10000 0 -0.52 13 13
IL2 0.015 0.064 -10000 0 -0.34 14 14
SPHK2 0.027 0.048 -10000 0 -0.56 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.002 0.13 -10000 0 -0.55 23 23
IL12/IL12R/TYK2/JAK2 -0.15 0.59 -10000 0 -1.6 48 48
MAP2K3 -0.071 0.4 -10000 0 -1.2 39 39
RIPK2 0.028 0.026 -10000 0 -0.34 2 2
MAP2K6 -0.069 0.4 -10000 0 -1.2 39 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.016 0.082 -10000 0 -0.56 9 9
IL18RAP 0.004 0.12 -10000 0 -0.49 23 23
IL12Rbeta1/TYK2 0.022 0.11 -10000 0 -0.41 20 20
EOMES -0.24 0.44 -10000 0 -1.2 54 54
STAT1 (dimer) -0.13 0.36 -10000 0 -0.85 65 65
T cell proliferation -0.024 0.28 0.46 6 -0.74 40 46
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.006 0.12 -10000 0 -0.57 18 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.064 0.3 -10000 0 -0.79 46 46
ATF2 -0.047 0.35 0.54 2 -1 35 37
Calcium signaling in the CD4+ TCR pathway

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.008 0.042 -10000 0 -0.34 2 2
NFATC2 -0.034 0.1 -10000 0 -0.35 36 36
NFATC3 -0.007 0.035 -10000 0 -10000 0 0
CD40LG -0.16 0.26 0.37 2 -0.64 70 72
PTGS2 -0.17 0.26 0.36 1 -0.61 84 85
JUNB 0.022 0.071 -10000 0 -0.51 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.028 -10000 0 -10000 0 0
CaM/Ca2+ 0.001 0.028 -10000 0 -10000 0 0
CALM1 0.018 0.023 -10000 0 -10000 0 0
JUN 0.011 0.065 -10000 0 -0.5 6 6
mol:Ca2+ -0.009 0.019 -10000 0 -0.31 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.012 -10000 0 -10000 0 0
FOSL1 -0.025 0.15 -10000 0 -0.41 59 59
CREM 0.03 0.018 -10000 0 -0.34 1 1
Jun/NFAT1-c-4/p21SNFT -0.073 0.18 -10000 0 -0.45 41 41
FOS -0.044 0.16 -10000 0 -0.45 59 59
IFNG -0.21 0.3 0.37 2 -0.6 139 141
AP-1/NFAT1-c-4 -0.16 0.3 -10000 0 -0.67 77 77
FASLG -0.17 0.27 0.36 1 -0.59 96 97
NFAT1-c-4/ICER1 -0.041 0.12 -10000 0 -0.38 19 19
IL2RA -0.18 0.27 0.37 2 -0.6 96 98
FKBP12/FK506 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.15 0.24 0.37 2 -0.58 70 72
JunB/Fra1/NFAT1-c-4 -0.062 0.16 -10000 0 -0.44 36 36
IL4 -0.16 0.23 -10000 0 -0.54 84 84
IL2 0 0.13 -10000 0 -1 6 6
IL3 -0.019 0.14 -10000 0 -0.93 9 9
FKBP1A 0.03 0.006 -10000 0 -10000 0 0
BATF3 0.007 0.11 -10000 0 -0.51 20 20
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.033 -10000 0 -0.45 2 2
Angiopoietin receptor Tie2-mediated signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.015 0.35 -10000 0 -1 45 45
NCK1/PAK1/Dok-R -0.051 0.13 -10000 0 -0.44 46 46
NCK1/Dok-R -0.032 0.4 -10000 0 -1.2 41 41
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.007 0.058 0.25 23 -10000 0 23
RELA 0.031 0.003 -10000 0 -10000 0 0
SHC1 0.03 0.008 -10000 0 -10000 0 0
Rac/GDP 0.021 0.007 -10000 0 -10000 0 0
F2 -0.19 0.25 0.27 10 -0.45 214 224
TNIP2 0.027 0.048 -10000 0 -0.56 3 3
NF kappa B/RelA -0.003 0.37 -10000 0 -1.1 41 41
FN1 0.004 0.11 -10000 0 -0.42 27 27
PLD2 -0.056 0.41 -10000 0 -1.3 41 41
PTPN11 0.031 0.005 -10000 0 -10000 0 0
GRB14 -0.015 0.14 -10000 0 -0.43 45 45
ELK1 -0.035 0.36 -10000 0 -1.1 41 41
GRB7 0.021 0.077 -10000 0 -0.56 8 8
PAK1 0.031 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.02 0.4 -10000 0 -1.2 44 44
CDKN1A 0.013 0.27 -10000 0 -0.7 48 48
ITGA5 0.023 0.067 -10000 0 -0.56 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.038 0.4 -10000 0 -1.2 42 42
CRK 0.031 0.005 -10000 0 -10000 0 0
mol:NO 0.025 0.27 0.46 4 -0.72 47 51
PLG -0.17 0.41 -10000 0 -1.4 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.016 0.32 -10000 0 -0.94 44 44
GRB2 0.031 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.053 -10000 0 -0.42 6 6
ANGPT2 -0.028 0.35 -10000 0 -1.1 36 36
BMX -0.09 0.43 -10000 0 -1.4 42 42
ANGPT1 -0.013 0.35 -10000 0 -1.3 26 26
tube development -0.003 0.3 -10000 0 -0.79 50 50
ANGPT4 -0.032 0.17 -10000 0 -0.46 57 57
response to hypoxia -0.007 0.02 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.061 0.45 -10000 0 -1.4 41 41
alpha5/beta1 Integrin 0.039 0.052 -10000 0 -0.41 6 6
FGF2 0.013 0.098 -10000 0 -0.51 15 15
STAT5A (dimer) 0.002 0.34 -10000 0 -0.92 50 50
mol:L-citrulline 0.025 0.27 0.46 4 -0.72 47 51
AGTR1 -0.08 0.21 -10000 0 -0.46 102 102
MAPK14 -0.055 0.44 -10000 0 -1.4 44 44
Tie2/SHP2 -0.044 0.36 -10000 0 -1.2 37 37
TEK -0.054 0.4 -10000 0 -1.4 37 37
RPS6KB1 -0.005 0.33 -10000 0 -0.95 45 45
Angiotensin II/AT1 -0.056 0.15 -10000 0 -0.33 103 103
Tie2/Ang1/GRB2 -0.043 0.44 -10000 0 -1.4 41 41
MAPK3 -0.043 0.36 -10000 0 -1.1 42 42
MAPK1 -0.046 0.36 -10000 0 -1.2 41 41
Tie2/Ang1/GRB7 -0.047 0.44 -10000 0 -1.4 41 41
NFKB1 0.031 0.004 -10000 0 -10000 0 0
MAPK8 -0.057 0.42 -10000 0 -1.3 41 41
PI3K -0.031 0.41 -10000 0 -1.2 45 45
FES -0.048 0.43 -10000 0 -1.4 42 42
Crk/Dok-R -0.03 0.4 -10000 0 -1.2 42 42
Tie2/Ang1/ABIN2 -0.045 0.44 -10000 0 -1.4 41 41
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.001 0.31 -10000 0 -0.88 46 46
STAT5A 0.029 0.039 -10000 0 -0.56 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.002 0.33 -10000 0 -0.96 43 43
Tie2/Ang2 -0.041 0.42 -10000 0 -1.2 49 49
Tie2/Ang1 -0.064 0.47 -10000 0 -1.5 41 41
FOXO1 -0.007 0.33 -10000 0 -0.9 49 49
ELF1 0.029 0.04 -10000 0 -10000 0 0
ELF2 -0.053 0.42 -10000 0 -1.3 41 41
mol:Choline -0.048 0.38 -10000 0 -1.2 41 41
cell migration -0.027 0.076 -10000 0 -0.24 46 46
FYN -0.019 0.34 -10000 0 -0.93 50 50
DOK2 0.015 0.088 -10000 0 -0.54 11 11
negative regulation of cell cycle 0.02 0.25 -10000 0 -0.63 48 48
ETS1 0.009 0.12 -10000 0 -0.41 28 28
PXN 0.015 0.28 0.5 3 -0.77 43 46
ITGB1 0.031 0.004 -10000 0 -10000 0 0
NOS3 0.013 0.31 0.47 4 -0.84 47 51
RAC1 0.028 0.01 -10000 0 -10000 0 0
TNF -0.035 0.17 -10000 0 -0.42 67 67
MAPKKK cascade -0.048 0.38 -10000 0 -1.2 41 41
RASA1 0.028 0.01 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.045 0.44 -10000 0 -1.4 41 41
NCK1 0.03 0.006 -10000 0 -10000 0 0
vasculogenesis 0.032 0.25 0.42 6 -0.63 47 53
mol:Phosphatidic acid -0.048 0.38 -10000 0 -1.2 41 41
mol:Angiotensin II 0 0.006 -10000 0 -10000 0 0
mol:NADP 0.025 0.27 0.46 4 -0.72 47 51
Rac1/GTP -0.002 0.3 -10000 0 -0.87 44 44
MMP2 -0.062 0.42 -10000 0 -1.3 43 43
Fc-epsilon receptor I signaling in mast cells

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.015 0.09 -10000 0 -0.56 11 11
LAT2 -0.026 0.15 -10000 0 -0.52 24 24
AP1 -0.012 0.2 -10000 0 -0.64 29 29
mol:PIP3 0.016 0.22 0.43 32 -0.6 26 58
IKBKB 0.034 0.16 0.31 57 -0.32 25 82
AKT1 -0.014 0.14 0.38 14 -0.47 13 27
IKBKG 0.032 0.16 0.31 54 -0.32 26 80
MS4A2 -0.02 0.16 -10000 0 -0.53 42 42
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
MAP3K1 0.007 0.16 0.3 32 -0.51 23 55
mol:Ca2+ 0.026 0.18 0.39 35 -0.42 26 61
LYN 0.027 0.041 -10000 0 -0.58 2 2
CBLB -0.026 0.14 -10000 0 -0.48 25 25
SHC1 0.03 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.03 0.074 -10000 0 -0.32 17 17
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.027 0.039 -10000 0 -0.56 2 2
PLD2 -0.028 0.15 0.34 14 -0.39 36 50
PTPN13 -0.011 0.18 0.36 3 -0.66 21 24
PTPN11 0.027 0.017 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.011 0.15 0.46 16 -0.38 15 31
SYK 0.025 0.056 -10000 0 -0.56 4 4
GRB2 0.031 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.041 0.17 -10000 0 -0.59 29 29
LAT -0.042 0.16 -10000 0 -0.5 32 32
PAK2 -0.01 0.17 0.36 8 -0.58 24 32
NFATC2 -0.049 0.17 -10000 0 -0.59 37 37
HRAS -0.018 0.19 0.31 4 -0.63 27 31
GAB2 0.03 0.018 -10000 0 -0.34 1 1
PLA2G1B -0.21 0.38 0.43 1 -0.83 128 129
Fc epsilon R1 -0.016 0.17 -10000 0 -0.41 58 58
Antigen/IgE/Fc epsilon R1 -0.01 0.16 -10000 0 -0.38 57 57
mol:GDP -0.024 0.2 -10000 0 -0.68 27 27
JUN 0.024 0.058 -10000 0 -0.52 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.053 -10000 0 -0.42 6 6
FOS -0.031 0.16 -10000 0 -0.44 59 59
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.023 0.15 -10000 0 -0.42 39 39
CHUK 0.032 0.16 0.31 54 -0.32 25 79
KLRG1 -0.024 0.13 -10000 0 -0.48 22 22
VAV1 -0.034 0.16 -10000 0 -0.57 27 27
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.026 0.14 -10000 0 -0.41 35 35
negative regulation of mast cell degranulation -0.008 0.14 -10000 0 -0.46 21 21
BTK -0.024 0.2 -10000 0 -0.77 22 22
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.031 0.18 -10000 0 -0.59 28 28
GAB2/PI3K/SHP2 -0.034 0.12 -10000 0 -0.49 15 15
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.02 0.14 -10000 0 -0.53 22 22
RAF1 -0.23 0.42 -10000 0 -0.91 128 128
Fc epsilon R1/FcgammaRIIB/SHIP -0.002 0.19 -10000 0 -0.39 64 64
FCER1G 0.023 0.068 -10000 0 -0.51 7 7
FCER1A -0.034 0.17 -10000 0 -0.47 60 60
Antigen/IgE/Fc epsilon R1/Fyn -0.001 0.16 -10000 0 -0.36 57 57
MAPK3 -0.21 0.39 -10000 0 -0.83 128 128
MAPK1 -0.21 0.39 -10000 0 -0.83 128 128
NFKB1 0.031 0.004 -10000 0 -10000 0 0
MAPK8 0.012 0.19 -10000 0 -0.78 20 20
DUSP1 0.005 0.1 -10000 0 -0.56 15 15
NF-kappa-B/RelA 0.018 0.076 0.16 25 -0.22 13 38
actin cytoskeleton reorganization -0.009 0.18 0.37 3 -0.65 21 24
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.17 -10000 0 -0.59 24 24
FER -0.028 0.14 -10000 0 -0.42 34 34
RELA 0.031 0.003 -10000 0 -10000 0 0
ITK -0.018 0.11 -10000 0 -0.52 19 19
SOS1 0.031 0.006 -10000 0 -10000 0 0
PLCG1 -0.009 0.2 0.44 5 -0.67 26 31
cytokine secretion 0.003 0.047 -10000 0 -10000 0 0
SPHK1 -0.037 0.15 -10000 0 -0.49 31 31
PTK2 -0.012 0.19 0.38 3 -0.72 20 23
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.03 0.17 -10000 0 -0.6 27 27
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.027 0.23 0.38 52 -0.59 27 79
MAP2K2 -0.22 0.4 -10000 0 -0.85 128 128
MAP2K1 -0.22 0.39 -10000 0 -0.85 127 127
MAP2K7 0.029 0.039 -10000 0 -0.56 2 2
KLRG1/SHP2 -0.013 0.13 0.25 1 -0.48 18 19
MAP2K4 0.015 0.17 -10000 0 -0.91 15 15
Fc epsilon R1/FcgammaRIIB -0.013 0.19 -10000 0 -0.41 66 66
mol:Choline -0.027 0.14 0.34 14 -0.38 36 50
SHC/Grb2/SOS1 0.02 0.15 -10000 0 -0.51 17 17
FYN 0.025 0.048 -10000 0 -0.56 3 3
DOK1 0.026 0.055 -10000 0 -0.56 4 4
PXN -0.005 0.18 0.46 5 -0.64 20 25
HCLS1 -0.029 0.16 -10000 0 -0.53 25 25
PRKCB 0.029 0.19 0.35 54 -0.46 27 81
FCGR2B 0.004 0.11 -10000 0 -0.46 24 24
IGHE 0 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.009 0.14 -10000 0 -0.48 21 21
LCP2 0.016 0.068 -10000 0 -0.56 6 6
PLA2G4A -0.03 0.15 -10000 0 -0.5 28 28
RASA1 0.028 0.01 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.027 0.14 0.34 14 -0.38 36 50
IKK complex 0.038 0.14 0.29 57 -0.25 17 74
WIPF1 0.029 0.028 -10000 0 -0.56 1 1
Reelin signaling pathway

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.034 -10000 0 -0.41 2 2
VLDLR 0.025 0.049 -10000 0 -0.43 5 5
CRKL 0.031 0.004 -10000 0 -10000 0 0
LRPAP1 0.027 0.048 -10000 0 -0.56 3 3
FYN 0.025 0.048 -10000 0 -0.56 3 3
ITGA3 0.023 0.062 -10000 0 -0.47 7 7
RELN/VLDLR/Fyn -0.031 0.14 -10000 0 -0.36 45 45
MAPK8IP1/MKK7/MAP3K11/JNK1 0.077 0.078 -10000 0 -0.49 6 6
AKT1 -0.038 0.097 -10000 0 -0.34 16 16
MAP2K7 0.029 0.039 -10000 0 -0.56 2 2
RAPGEF1 0.029 0.028 -10000 0 -0.56 1 1
DAB1 -0.013 0.11 -10000 0 -0.34 49 49
RELN/LRP8/DAB1 -0.052 0.15 -10000 0 -0.35 65 65
LRPAP1/LRP8 0.028 0.073 -10000 0 -0.27 24 24
RELN/LRP8/DAB1/Fyn -0.042 0.15 -10000 0 -0.33 67 67
DAB1/alpha3/beta1 Integrin -0.04 0.15 -10000 0 -0.47 12 12
long-term memory -0.13 0.2 -10000 0 -0.38 139 139
DAB1/LIS1 -0.03 0.15 -10000 0 -0.33 61 61
DAB1/CRLK/C3G -0.038 0.15 -10000 0 -0.46 11 11
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
DAB1/NCK2 -0.029 0.16 -10000 0 -0.34 47 47
ARHGEF2 0.03 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.13 0.23 -10000 0 -0.44 154 154
CDK5R1 0.03 0.018 -10000 0 -0.34 1 1
RELN -0.089 0.2 -10000 0 -0.42 119 119
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
RELN/LRP8/Fyn -0.038 0.15 -10000 0 -0.36 48 48
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.2 -10000 0 -0.37 140 140
MAPK8 0.027 0.048 -10000 0 -0.56 3 3
RELN/VLDLR/DAB1 -0.046 0.14 -10000 0 -0.34 61 61
ITGB1 0.031 0.004 -10000 0 -10000 0 0
MAP1B -0.06 0.14 -10000 0 -0.34 66 66
RELN/LRP8 -0.038 0.15 -10000 0 -0.37 49 49
GRIN2B/RELN/LRP8/DAB1/Fyn -0.054 0.17 -10000 0 -0.34 85 85
PI3K 0.037 0.042 -10000 0 -0.3 6 6
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.039 0.05 -10000 0 -0.34 7 7
RAP1A -0.048 0.14 0.46 4 -0.43 11 15
PAFAH1B1 0.031 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.06 -10000 0 -0.49 6 6
CRLK/C3G 0.043 0.024 -10000 0 -0.41 1 1
GRIN2B -0.021 0.13 -10000 0 -0.38 55 55
NCK2 0.031 0.006 -10000 0 -10000 0 0
neuron differentiation -0.022 0.12 -10000 0 -0.41 26 26
neuron adhesion -0.047 0.14 0.35 8 -0.45 12 20
LRP8 0.012 0.085 -10000 0 -0.36 22 22
GSK3B -0.036 0.092 -10000 0 -0.33 13 13
RELN/VLDLR/DAB1/Fyn -0.036 0.14 -10000 0 -0.32 62 62
MAP3K11 0.029 0.039 -10000 0 -0.56 2 2
RELN/VLDLR/DAB1/P13K -0.036 0.1 -10000 0 -0.29 46 46
CDK5 0.026 0.04 -10000 0 -0.56 2 2
MAPT -0.055 0.19 0.67 5 -0.52 58 63
neuron migration -0.039 0.14 0.4 4 -0.41 16 20
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.022 0.12 -10000 0 -0.41 26 26
RELN/VLDLR -0.024 0.15 -10000 0 -0.34 50 50
Effects of Botulinum toxin

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.001 0.048 -10000 0 -0.28 12 12
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.014 0.083 -10000 0 -0.24 45 45
STXBP1 0.024 0.056 -10000 0 -0.45 6 6
ACh/CHRNA1 -0.075 0.15 -10000 0 -0.29 140 140
RAB3GAP2/RIMS1/UNC13B 0.031 0.076 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.01 0.11 -10000 0 -0.35 46 46
mol:ACh -0.003 0.054 0.09 44 -0.13 50 94
RAB3GAP2 0.03 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.002 0.1 -10000 0 -0.33 13 13
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.075 0.15 -10000 0 -0.28 140 140
UNC13B 0.03 0.006 -10000 0 -10000 0 0
CHRNA1 -0.11 0.22 -10000 0 -0.44 140 140
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.016 0.11 -10000 0 -0.28 54 54
SNAP25 -0.029 0.099 -10000 0 -0.29 56 56
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.021 0.15 -10000 0 -0.43 51 51
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.016 0.053 -10000 0 -0.24 17 17
STX1A/SNAP25 fragment 1/VAMP2 0.002 0.1 -10000 0 -0.33 13 13
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.087 0.23 -10000 0 -0.53 89 89
NFATC2 -0.074 0.24 -10000 0 -0.71 33 33
NFATC3 -0.013 0.09 -10000 0 -0.28 11 11
CD40LG -0.23 0.38 -10000 0 -1.1 52 52
ITCH 0.027 0.053 -10000 0 -10000 0 0
CBLB 0.026 0.054 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.45 -10000 0 -1.1 86 86
JUNB 0.022 0.071 -10000 0 -0.51 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.066 -10000 0 -0.29 15 15
T cell anergy 0.003 0.11 -10000 0 -0.49 16 16
TLE4 -0.046 0.17 -10000 0 -0.58 23 23
Jun/NFAT1-c-4/p21SNFT -0.14 0.36 -10000 0 -1.1 34 34
AP-1/NFAT1-c-4 -0.23 0.46 -10000 0 -1.3 48 48
IKZF1 -0.05 0.2 -10000 0 -0.72 25 25
T-helper 2 cell differentiation -0.11 0.26 -10000 0 -0.72 53 53
AP-1/NFAT1 -0.084 0.22 -10000 0 -0.59 38 38
CALM1 0.032 0.042 -10000 0 -10000 0 0
EGR2 -0.14 0.38 -10000 0 -1.5 24 24
EGR3 -0.14 0.36 -10000 0 -1.3 27 27
NFAT1/FOXP3 -0.12 0.28 -10000 0 -0.61 86 86
EGR1 -0.029 0.15 -10000 0 -0.44 51 51
JUN 0.002 0.068 -10000 0 -0.54 5 5
EGR4 -0.002 0.092 -10000 0 -0.35 29 29
mol:Ca2+ 0.002 0.045 -10000 0 -0.34 3 3
GBP3 -0.091 0.27 -10000 0 -0.79 49 49
FOSL1 -0.025 0.15 -10000 0 -0.41 59 59
NFAT1-c-4/MAF/IRF4 -0.13 0.34 -10000 0 -1 35 35
DGKA -0.052 0.19 -10000 0 -0.62 26 26
CREM 0.03 0.018 -10000 0 -0.34 1 1
NFAT1-c-4/PPARG -0.13 0.31 -10000 0 -1 34 34
CTLA4 -0.15 0.3 -10000 0 -0.68 85 85
NFAT1-c-4 (dimer)/EGR1 -0.14 0.34 -10000 0 -1.1 33 33
NFAT1-c-4 (dimer)/EGR4 -0.13 0.33 -10000 0 -1 35 35
FOS -0.052 0.16 -10000 0 -0.45 59 59
IFNG -0.29 0.5 -10000 0 -1.2 87 87
T cell activation -0.089 0.21 -10000 0 -0.86 9 9
MAF 0.022 0.072 -10000 0 -0.56 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.087 0.24 1 13 -10000 0 13
TNF -0.16 0.34 -10000 0 -1 37 37
FASLG -0.21 0.51 -10000 0 -1.6 49 49
TBX21 -0.023 0.12 -10000 0 -0.53 18 18
BATF3 0.007 0.11 -10000 0 -0.51 20 20
PRKCQ 0.009 0.094 -10000 0 -0.47 15 15
PTPN1 -0.046 0.17 -10000 0 -0.63 16 16
NFAT1-c-4/ICER1 -0.12 0.32 -10000 0 -1 34 34
GATA3 -0.006 0.12 -10000 0 -0.41 39 39
T-helper 1 cell differentiation -0.28 0.48 -10000 0 -1.2 87 87
IL2RA -0.25 0.4 -10000 0 -0.99 79 79
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.047 0.17 -10000 0 -0.59 21 21
E2F1 0.031 0.046 -10000 0 -0.45 4 4
PPARG 0.02 0.041 -10000 0 -0.56 2 2
SLC3A2 -0.05 0.18 -10000 0 -0.62 25 25
IRF4 -0.022 0.15 -10000 0 -0.42 54 54
PTGS2 -0.24 0.38 -10000 0 -1 55 55
CSF2 -0.21 0.35 -10000 0 -1 47 47
JunB/Fra1/NFAT1-c-4 -0.13 0.35 -10000 0 -1.1 31 31
IL4 -0.12 0.27 -10000 0 -0.76 53 53
IL5 -0.21 0.35 -10000 0 -1 47 47
IL2 -0.091 0.21 -10000 0 -0.88 9 9
IL3 -0.056 0.15 -10000 0 -1 9 9
RNF128 0.01 0.13 -10000 0 -0.56 22 22
NFATC1 -0.088 0.24 -10000 0 -1 13 13
CDK4 0.074 0.17 0.73 5 -10000 0 5
PTPRK -0.048 0.17 -10000 0 -0.63 18 18
IL8 -0.25 0.39 -10000 0 -1 59 59
POU2F1 0.028 0.033 -10000 0 -0.45 2 2
Visual signal transduction: Rods

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.031 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.009 0.034 -10000 0 -0.24 8 8
Metarhodopsin II/Arrestin 0.01 0.041 -10000 0 -0.2 17 17
PDE6G/GNAT1/GTP 0.011 0.064 -10000 0 -0.22 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.011 0.049 -10000 0 -0.35 8 8
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.034 0.14 -10000 0 -0.38 47 47
mol:Na + -0.044 0.14 -10000 0 -0.32 73 73
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.031 0.17 -10000 0 -0.38 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.039 0.15 -10000 0 -0.32 73 73
CNGB1 -0.001 0.096 -10000 0 -0.34 33 33
RDH5 -0.004 0.14 -10000 0 -0.54 28 28
SAG 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.065 0.13 0.41 2 -0.39 23 25
Na + (4 Units) -0.043 0.13 -10000 0 -0.31 67 67
RGS9 -0.065 0.2 -10000 0 -0.47 89 89
GNB1/GNGT1 -0.05 0.18 -10000 0 -0.39 94 94
GNAT1/GDP -0.031 0.14 -10000 0 -0.33 69 69
GUCY2D -0.026 0.15 -10000 0 -0.41 57 57
GNGT1 -0.09 0.23 -10000 0 -0.54 95 95
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.031 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.097 -10000 0 -0.36 24 24
mol:11-cis-retinal -0.004 0.14 -10000 0 -0.54 28 28
mol:cGMP -0.012 0.11 -10000 0 -0.31 39 39
GNB1 0.03 0.007 -10000 0 -10000 0 0
Rhodopsin 0.004 0.12 -10000 0 -0.35 44 44
SLC24A1 0.031 0.003 -10000 0 -10000 0 0
CNGA1 -0.032 0.17 -10000 0 -0.47 58 58
Metarhodopsin II 0.009 0.037 -10000 0 -0.18 17 17
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family -0.003 0.12 -10000 0 -0.33 39 39
RGS9BP -0.011 0.14 -10000 0 -0.44 41 41
Metarhodopsin II/Transducin -0.057 0.14 -10000 0 -0.33 87 87
GCAP Family/Ca ++ 0.014 0.079 -10000 0 -0.27 32 32
PDE6A/B 0.002 0.11 -10000 0 -0.36 35 35
mol:Pi -0.031 0.17 -10000 0 -0.38 67 67
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.036 0.14 -10000 0 -0.32 84 84
PDE6B -0.002 0.13 -10000 0 -0.55 26 26
PDE6A 0.012 0.064 -10000 0 -0.34 14 14
PDE6G 0.012 0.09 -10000 0 -0.4 20 20
RHO 0.012 0.07 -10000 0 -0.34 17 17
PDE6 -0.031 0.18 -10000 0 -0.46 41 41
GUCA1A 0.015 0.057 -10000 0 -0.34 11 11
GC2/GCAP Family 0.014 0.079 -10000 0 -0.27 32 32
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.004 0.12 -10000 0 -0.5 23 23
Thromboxane A2 receptor signaling

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.01 0.11 -10000 0 -0.52 17 17
GNB1/GNG2 -0.036 0.072 -10000 0 -0.2 63 63
AKT1 -0.008 0.12 0.31 3 -0.3 37 40
EGF -0.11 0.23 -10000 0 -0.45 135 135
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0 0.1 0.39 2 -0.44 16 18
mol:Ca2+ -0.005 0.15 0.34 3 -0.33 65 68
LYN -0.001 0.093 0.39 1 -0.43 13 14
RhoA/GTP -0.005 0.058 -10000 0 -0.16 16 16
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.013 0.16 0.36 3 -0.37 66 69
GNG2 0.025 0.048 -10000 0 -0.56 3 3
ARRB2 0.03 0.018 -10000 0 -0.35 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.005 0.14 -10000 0 -0.64 16 16
G beta5/gamma2 -0.047 0.097 -10000 0 -0.27 63 63
PRKCH -0.016 0.17 0.39 2 -0.39 66 68
DNM1 -0.006 0.13 -10000 0 -0.49 32 32
TXA2/TP beta/beta Arrestin3 -0.013 0.054 -10000 0 -0.21 28 28
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.009 0.1 -10000 0 -0.51 17 17
G12 family/GTP -0.019 0.13 -10000 0 -0.32 57 57
ADRBK1 0.027 0.048 -10000 0 -0.56 3 3
ADRBK2 0.03 0.028 -10000 0 -0.56 1 1
RhoA/GTP/ROCK1 0.029 0.026 -10000 0 -0.35 1 1
mol:GDP 0.001 0.13 0.42 28 -0.37 2 30
mol:NADP 0.011 0.098 -10000 0 -0.56 13 13
RAB11A 0.031 0.003 -10000 0 -10000 0 0
PRKG1 -0.015 0.16 -10000 0 -0.56 36 36
mol:IP3 -0.016 0.18 0.42 2 -0.42 65 67
cell morphogenesis 0.029 0.026 -10000 0 -0.35 1 1
PLCB2 -0.038 0.25 0.45 2 -0.6 65 67
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.035 0.12 0.39 1 -0.45 17 18
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.098 -10000 0 -0.49 13 13
RHOA 0.023 0.014 -10000 0 -10000 0 0
PTGIR 0.007 0.12 -10000 0 -0.53 20 20
PRKCB1 -0.017 0.18 0.39 2 -0.41 68 70
GNAQ 0.03 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.011 0.098 -10000 0 -0.56 13 13
TXA2/TXA2-R family -0.036 0.24 0.46 2 -0.57 68 70
LCK -0.009 0.11 0.39 2 -0.43 21 23
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.005 0.1 -10000 0 -0.37 27 27
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.12 -10000 0 -0.55 17 17
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.11 -10000 0 -0.51 12 12
MAPK14 -0.001 0.11 0.28 5 -0.24 53 58
TGM2/GTP -0.022 0.2 -10000 0 -0.49 61 61
MAPK11 -0.003 0.12 0.27 7 -0.26 59 66
ARHGEF1 -0.004 0.083 -10000 0 -0.21 33 33
GNAI2 0.023 0.014 -10000 0 -10000 0 0
JNK cascade -0.016 0.18 0.43 2 -0.41 68 70
RAB11/GDP 0.031 0.004 -10000 0 -10000 0 0
ICAM1 -0.006 0.14 0.37 2 -0.31 64 66
cAMP biosynthetic process -0.016 0.17 0.42 2 -0.39 64 66
Gq family/GTP/EBP50 0 0.096 0.24 1 -0.31 24 25
actin cytoskeleton reorganization 0.029 0.026 -10000 0 -0.35 1 1
SRC 0 0.092 -10000 0 -0.5 10 10
GNB5 0.031 0.003 -10000 0 -10000 0 0
GNB1 0.03 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.039 0.12 0.33 4 -0.38 28 32
VCAM1 -0.014 0.16 0.32 3 -0.37 64 67
TP beta/Gq family/GDP/G beta5/gamma2 -0.005 0.14 -10000 0 -0.64 16 16
platelet activation -0.002 0.15 0.34 7 -0.32 63 70
PGI2/IP 0.005 0.084 -10000 0 -0.38 20 20
PRKACA 0 0.097 -10000 0 -0.37 23 23
Gq family/GDP/G beta5/gamma2 -0.004 0.13 -10000 0 -0.48 25 25
TXA2/TP beta/beta Arrestin2 -0.023 0.13 -10000 0 -0.54 27 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.12 -10000 0 -0.41 29 29
mol:DAG -0.021 0.2 0.42 2 -0.47 67 69
EGFR 0.007 0.11 -10000 0 -0.51 18 18
TXA2/TP alpha -0.032 0.23 0.48 2 -0.55 64 66
Gq family/GTP 0.001 0.071 -10000 0 -0.27 26 26
YES1 0.002 0.093 0.39 2 -0.42 13 15
GNAI2/GTP -0.002 0.1 -10000 0 -0.43 18 18
PGD2/DP 0.006 0.076 -10000 0 -0.34 20 20
SLC9A3R1 0.017 0.09 -10000 0 -0.56 11 11
FYN 0.001 0.1 0.51 3 -0.43 15 18
mol:NO 0.011 0.098 -10000 0 -0.56 13 13
GNA15 0.021 0.076 -10000 0 -0.51 9 9
PGK/cGMP 0 0.13 -10000 0 -0.39 38 38
RhoA/GDP 0.022 0.014 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.02 0.14 -10000 0 -0.6 15 15
NOS3 0.012 0.098 -10000 0 -0.56 13 13
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCA -0.012 0.17 0.39 2 -0.38 63 65
PRKCB -0.015 0.18 0.33 7 -0.41 68 75
PRKCE -0.011 0.17 0.38 3 -0.38 65 68
PRKCD -0.034 0.17 0.38 2 -0.41 68 70
PRKCG -0.02 0.18 0.43 2 -0.42 67 69
muscle contraction -0.03 0.22 0.46 2 -0.52 68 70
PRKCZ -0.014 0.16 0.41 2 -0.37 65 67
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta 0.015 0.12 -10000 0 -0.42 25 25
PRKCQ -0.018 0.17 0.35 3 -0.39 68 71
MAPKKK cascade -0.03 0.22 0.43 2 -0.51 66 68
SELE -0.016 0.16 0.32 3 -0.37 65 68
TP beta/GNAI2/GDP/G beta/gamma 0.017 0.12 -10000 0 -0.54 12 12
ROCK1 0.03 0.028 -10000 0 -0.56 1 1
GNA14 0.01 0.11 -10000 0 -0.55 16 16
chemotaxis -0.044 0.26 0.47 2 -0.63 66 68
GNA12 0.028 0.01 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.064 -10000 0 -0.52 6 6
Rac1/GTP 0.021 0.007 -10000 0 -10000 0 0
Arf6 signaling events

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.025 0.058 -10000 0 -0.28 13 13
ARNO/beta Arrestin1-2 0.016 0.11 -10000 0 -0.96 4 4
EGFR 0.007 0.11 -10000 0 -0.51 18 18
EPHA2 0.023 0.06 -10000 0 -0.49 6 6
USP6 0.022 0.058 -10000 0 -0.35 11 11
IQSEC1 0.023 0.014 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.073 0.18 -10000 0 -0.34 131 131
ARRB2 0 0.045 -10000 0 -0.3 1 1
mol:GTP 0.014 0.048 0.14 8 -0.28 6 14
ARRB1 0.026 0.055 -10000 0 -0.56 4 4
FBXO8 0.031 0.004 -10000 0 -10000 0 0
TSHR -0.032 0.17 -10000 0 -0.48 55 55
EGF -0.11 0.23 -10000 0 -0.45 135 135
somatostatin receptor activity 0 0 0.001 27 -0.001 42 69
ARAP2 0.028 0.039 -10000 0 -0.56 2 2
mol:GDP -0.042 0.13 0.21 9 -0.33 49 58
mol:PI-3-4-5-P3 0 0 0.001 19 -0.001 26 45
ITGA2B -0.037 0.17 -10000 0 -0.45 65 65
ARF6 0.029 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.075 -10000 0 -0.38 9 9
ADAP1 0.02 0.065 -10000 0 -0.45 8 8
KIF13B 0.021 0.052 -10000 0 -0.34 9 9
HGF/MET 0.008 0.11 -10000 0 -0.43 21 21
PXN 0.03 0.018 -10000 0 -0.34 1 1
ARF6/GTP -0.031 0.13 0.24 26 -0.32 44 70
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.055 0.16 -10000 0 -0.36 70 70
ADRB2 0.015 0.067 -10000 0 -0.44 9 9
receptor agonist activity 0 0 0 26 0 36 62
actin filament binding 0 0 0.001 27 -0.001 43 70
SRC 0.028 0.039 -10000 0 -0.56 2 2
ITGB3 0.016 0.084 -10000 0 -0.43 15 15
GNAQ 0.03 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 35 -0.001 30 65
ARF6/GDP -0.01 0.14 0.3 2 -0.46 25 27
ARF6/GDP/GULP/ACAP1 -0.04 0.17 0.28 3 -0.43 46 49
alphaIIb/beta3 Integrin/paxillin/GIT1 0.02 0.13 -10000 0 -0.34 40 40
ACAP1 0 0.12 -10000 0 -0.46 29 29
ACAP2 0.03 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.002 0.065 -10000 0 -0.2 44 44
EFNA1 0.021 0.069 -10000 0 -0.53 7 7
HGF -0.011 0.13 -10000 0 -0.44 38 38
CYTH3 0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.011 0.11 -10000 0 -1.2 4 4
NCK1 0.03 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 34 0 36 70
endosomal lumen acidification 0 0 0.001 10 -0.001 44 54
microtubule-based process 0 0 -10000 0 0 3 3
GULP1 -0.014 0.15 -10000 0 -0.48 40 40
GNAQ/ARNO 0.028 0.11 -10000 0 -1.1 4 4
mol:Phosphatidic acid 0 0 0 7 -10000 0 7
PIP3-E 0 0 0 13 0 10 23
MET 0.023 0.054 -10000 0 -0.47 5 5
GNA14 0.01 0.11 -10000 0 -0.55 16 16
GNA15 0.021 0.076 -10000 0 -0.51 9 9
GIT1 0.028 0.039 -10000 0 -0.56 2 2
mol:PI-4-5-P2 0 0 0.001 34 -0.001 35 69
GNA11 0.024 0.064 -10000 0 -0.52 6 6
LHCGR -0.012 0.11 -10000 0 -0.34 43 43
AGTR1 -0.079 0.21 -10000 0 -0.46 102 102
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.064 -10000 0 -0.19 44 44
IPCEF1/ARNO -0.036 0.15 -10000 0 -0.81 7 7
alphaIIb/beta3 Integrin -0.018 0.15 -10000 0 -0.34 75 75
IL27-mediated signaling events

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.069 -10000 0 -0.53 7 7
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.072 0.21 0.68 29 -10000 0 29
IL27/IL27R/JAK1 -0.07 0.24 -10000 0 -0.98 19 19
TBX21 -0.093 0.2 0.51 1 -0.61 35 36
IL12B -0.037 0.15 -10000 0 -0.43 55 55
IL12A -0.016 0.087 -10000 0 -0.39 23 23
IL6ST -0.019 0.14 -10000 0 -0.57 28 28
IL27RA/JAK1 -0.028 0.21 -10000 0 -1.3 11 11
IL27 -0.015 0.12 -10000 0 -0.43 31 31
TYK2 0.011 0.048 -10000 0 -0.58 2 2
T-helper cell lineage commitment -0.04 0.13 0.18 33 -0.31 62 95
T-helper 2 cell differentiation 0.072 0.21 0.68 29 -10000 0 29
T cell proliferation during immune response 0.072 0.21 0.68 29 -10000 0 29
MAPKKK cascade -0.072 0.21 -10000 0 -0.68 29 29
STAT3 0.031 0.005 -10000 0 -10000 0 0
STAT2 0.029 0.033 -10000 0 -0.45 2 2
STAT1 0.027 0.031 -10000 0 -0.34 3 3
IL12RB1 0.007 0.11 -10000 0 -0.49 20 20
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.13 0.22 0.51 1 -0.59 46 47
IL27/IL27R/JAK2/TYK2 -0.073 0.22 -10000 0 -0.7 29 29
positive regulation of T cell mediated cytotoxicity -0.072 0.21 -10000 0 -0.68 29 29
STAT1 (dimer) -0.1 0.28 0.54 1 -0.91 28 29
JAK2 0.016 0.025 -10000 0 -10000 0 0
JAK1 0.029 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.057 0.21 -10000 0 -0.67 28 28
T cell proliferation -0.12 0.22 -10000 0 -0.56 59 59
IL12/IL12R/TYK2/JAK2 -0.12 0.28 -10000 0 -0.92 39 39
IL17A -0.041 0.13 0.18 31 -0.31 62 93
mast cell activation 0.072 0.21 0.68 29 -10000 0 29
IFNG -0.027 0.054 -10000 0 -0.12 82 82
T cell differentiation -0.007 0.01 -10000 0 -0.023 86 86
STAT3 (dimer) -0.057 0.2 -10000 0 -0.68 27 27
STAT5A (dimer) -0.058 0.21 -10000 0 -0.68 28 28
STAT4 (dimer) -0.062 0.23 -10000 0 -0.73 31 31
STAT4 0.015 0.092 -10000 0 -0.54 12 12
T cell activation -0.004 0.02 0.12 11 -10000 0 11
IL27R/JAK2/TYK2 -0.042 0.23 -10000 0 -1.2 13 13
GATA3 -0.037 0.24 0.76 2 -1.4 12 14
IL18 -0.002 0.058 -10000 0 -0.31 15 15
positive regulation of mast cell cytokine production -0.055 0.2 -10000 0 -0.65 27 27
IL27/EBI3 -0.01 0.12 -10000 0 -0.37 39 39
IL27RA -0.04 0.22 -10000 0 -1.4 11 11
IL6 -0.11 0.22 -10000 0 -0.44 134 134
STAT5A 0.028 0.039 -10000 0 -0.56 2 2
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.003 0.11 0.57 11 -10000 0 11
IL1B -0.023 0.1 -10000 0 -0.33 42 42
EBI3 0.001 0.098 -10000 0 -0.46 18 18
TNF -0.032 0.11 -10000 0 -0.33 54 54
LPA receptor mediated events

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.13 -10000 0 -0.33 46 46
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.12 0.33 2 -0.51 9 11
AP1 -0.046 0.16 -10000 0 -0.38 46 46
mol:PIP3 -0.034 0.12 -10000 0 -0.53 10 10
AKT1 -0.033 0.14 0.28 7 -0.43 21 28
PTK2B -0.033 0.13 0.3 1 -0.43 25 26
RHOA -0.066 0.15 0.2 2 -0.3 108 110
PIK3CB 0.029 0.028 -10000 0 -0.56 1 1
mol:Ca2+ -0.007 0.11 0.31 2 -0.49 15 17
MAGI3 0.023 0.056 -10000 0 -0.37 9 9
RELA 0.031 0.003 -10000 0 -10000 0 0
apoptosis -0.023 0.11 -10000 0 -0.31 49 49
HRAS/GDP 0.02 0.035 -10000 0 -0.41 3 3
positive regulation of microtubule depolymerization -0.06 0.15 0.3 5 -0.4 42 47
NF kappa B1 p50/RelA -0.023 0.14 -10000 0 -0.54 14 14
endothelial cell migration -0.033 0.14 -10000 0 -0.38 58 58
ADCY4 -0.043 0.15 -10000 0 -0.43 50 50
ADCY5 -0.057 0.16 -10000 0 -0.44 56 56
ADCY6 -0.037 0.14 -10000 0 -0.41 47 47
ADCY7 -0.037 0.14 -10000 0 -0.42 47 47
ADCY1 -0.043 0.14 -10000 0 -0.43 45 45
ADCY2 -0.09 0.18 -10000 0 -0.49 64 64
ADCY3 -0.037 0.14 -10000 0 -0.42 46 46
ADCY8 -0.11 0.18 -10000 0 -0.48 63 63
ADCY9 -0.037 0.14 -10000 0 -0.42 45 45
GSK3B -0.031 0.12 0.26 3 -0.42 24 27
arachidonic acid secretion -0.041 0.14 -10000 0 -0.4 55 55
GNG2 0.025 0.048 -10000 0 -0.56 3 3
TRIP6 0.014 0.081 -10000 0 -0.65 5 5
GNAO1 -0.037 0.13 -10000 0 -0.36 53 53
HRAS 0.027 0.048 -10000 0 -0.56 3 3
NFKBIA -0.02 0.13 0.33 3 -0.5 16 19
GAB1 0.03 0.028 -10000 0 -0.56 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.2 -10000 0 -0.94 18 18
JUN 0.024 0.058 -10000 0 -0.52 5 5
LPA/LPA2/NHERF2 0.021 0.088 -10000 0 -0.39 17 17
TIAM1 -0.007 0.24 -10000 0 -1.2 18 18
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 -0.008 0.12 0.38 1 -0.5 15 16
PLCB3 0.009 0.095 -10000 0 -0.4 17 17
FOS -0.031 0.16 -10000 0 -0.44 59 59
positive regulation of mitosis -0.041 0.14 -10000 0 -0.4 55 55
LPA/LPA1-2-3 -0.005 0.14 -10000 0 -0.36 49 49
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
stress fiber formation -0.022 0.13 0.48 2 -0.41 23 25
GNAZ -0.027 0.12 -10000 0 -0.36 50 50
EGFR/PI3K-beta/Gab1 -0.026 0.12 -10000 0 -0.56 10 10
positive regulation of dendritic cell cytokine production -0.006 0.14 -10000 0 -0.36 49 49
LPA/LPA2/MAGI-3 0.025 0.073 -10000 0 -0.36 12 12
ARHGEF1 -0.001 0.12 0.34 5 -0.32 33 38
GNAI2 -0.026 0.11 -10000 0 -0.34 46 46
GNAI3 -0.023 0.12 -10000 0 -0.35 46 46
GNAI1 -0.018 0.11 -10000 0 -0.34 39 39
LPA/LPA3 0.009 0.048 -10000 0 -0.23 14 14
LPA/LPA2 0.011 0.07 -10000 0 -0.4 11 11
LPA/LPA1 -0.028 0.14 -10000 0 -0.38 56 56
HB-EGF/EGFR -0.043 0.13 -10000 0 -0.38 38 38
HBEGF -0.048 0.13 -10000 0 -0.3 92 92
mol:DAG -0.008 0.12 0.38 1 -0.5 15 16
cAMP biosynthetic process -0.053 0.16 0.38 6 -0.4 56 62
NFKB1 0.031 0.004 -10000 0 -10000 0 0
SRC 0.028 0.039 -10000 0 -0.56 2 2
GNB1 0.03 0.007 -10000 0 -10000 0 0
LYN -0.017 0.14 0.33 4 -0.53 17 21
GNAQ 0.006 0.06 -10000 0 -0.35 9 9
LPAR2 0.018 0.085 -10000 0 -0.52 11 11
LPAR3 0.013 0.062 -10000 0 -0.35 13 13
LPAR1 -0.033 0.18 -10000 0 -0.5 52 52
IL8 -0.087 0.19 0.42 1 -0.46 60 61
PTK2 -0.028 0.12 -10000 0 -0.34 46 46
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
CASP3 -0.023 0.11 -10000 0 -0.31 49 49
EGFR 0.007 0.11 -10000 0 -0.51 18 18
PLCG1 -0.001 0.082 -10000 0 -0.42 11 11
PLD2 -0.029 0.13 0.34 1 -0.34 48 49
G12/G13 0.014 0.11 -10000 0 -0.31 35 35
PI3K-beta -0.055 0.14 -10000 0 -0.47 22 22
cell migration 0.009 0.078 -10000 0 -0.28 19 19
SLC9A3R2 0.017 0.086 -10000 0 -0.56 10 10
PXN -0.024 0.12 0.3 1 -0.42 23 24
HRAS/GTP -0.043 0.15 -10000 0 -0.41 55 55
RAC1 0.028 0.01 -10000 0 -10000 0 0
MMP9 -0.073 0.19 -10000 0 -0.41 108 108
PRKCE 0.029 0.028 -10000 0 -0.56 1 1
PRKCD -0.011 0.12 0.41 3 -0.48 15 18
Gi(beta/gamma) -0.036 0.14 -10000 0 -0.4 52 52
mol:LPA -0.005 0.033 -10000 0 -0.2 7 7
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.14 -10000 0 -0.58 12 12
MAPKKK cascade -0.041 0.14 -10000 0 -0.4 55 55
contractile ring contraction involved in cytokinesis -0.07 0.14 0.19 2 -0.3 110 112
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.005 0.088 -10000 0 -0.35 22 22
GNA15 0 0.082 -10000 0 -0.38 16 16
GNA12 0.028 0.01 -10000 0 -10000 0 0
GNA13 0.03 0.005 -10000 0 -10000 0 0
MAPT -0.063 0.15 0.3 5 -0.42 42 47
GNA11 0.002 0.079 -10000 0 -0.41 12 12
Rac1/GTP 0.01 0.21 -10000 0 -1 18 18
MMP2 -0.033 0.14 -10000 0 -0.38 58 58
Glucocorticoid receptor regulatory network

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.016 0.12 -10000 0 -0.95 4 4
SMARCC2 0.031 0.016 -10000 0 -10000 0 0
SMARCC1 0.022 0.019 -10000 0 -10000 0 0
TBX21 -0.051 0.19 -10000 0 -0.75 25 25
SUMO2 0.027 0.029 0.55 1 -10000 0 1
STAT1 (dimer) 0.029 0.057 -10000 0 -0.36 9 9
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 -0.004 0.12 -10000 0 -0.41 36 36
GR alpha/HSP90/FKBP51/HSP90 0.033 0.12 0.32 7 -0.33 12 19
PRL -0.033 0.12 -10000 0 -0.62 4 4
cortisol/GR alpha (dimer)/TIF2 0.067 0.22 0.51 38 -0.45 4 42
RELA -0.042 0.11 -10000 0 -0.27 37 37
FGG -0.094 0.32 0.46 35 -0.52 118 153
GR beta/TIF2 0.03 0.12 0.32 14 -0.38 11 25
IFNG -0.36 0.46 -10000 0 -1.1 106 106
apoptosis -0.057 0.21 0.75 6 -0.63 27 33
CREB1 0.03 0.007 -10000 0 -10000 0 0
histone acetylation 0.015 0.15 0.38 24 -0.42 14 38
BGLAP -0.015 0.11 -10000 0 -0.57 3 3
GR/PKAc 0.052 0.089 0.3 10 -0.3 1 11
NF kappa B1 p50/RelA -0.073 0.19 -10000 0 -0.48 49 49
SMARCD1 0.031 0.015 -10000 0 -10000 0 0
MDM2 0.038 0.092 0.27 27 -10000 0 27
GATA3 -0.004 0.13 -10000 0 -0.4 39 39
AKT1 0.023 0.03 0.23 1 -0.38 2 3
CSF2 -0.005 0.12 0.47 3 -0.58 4 7
GSK3B 0.025 0.016 -10000 0 -10000 0 0
NR1I3 -0.03 0.22 0.74 6 -0.67 18 24
CSN2 0.057 0.17 0.35 64 -0.31 7 71
BRG1/BAF155/BAF170/BAF60A 0.055 0.061 -10000 0 -0.32 6 6
NFATC1 0.028 0.039 -10000 0 -0.56 2 2
POU2F1 0.028 0.038 -10000 0 -0.45 2 2
CDKN1A 0.02 0.098 -10000 0 -1.9 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.012 0.19 1 -10000 0 1
SFN -0.081 0.2 -10000 0 -0.41 118 118
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.01 0.15 0.34 3 -0.35 26 29
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.035 0.28 0.64 10 -0.77 34 44
JUN -0.17 0.19 -10000 0 -0.5 62 62
IL4 -0.032 0.11 -10000 0 -0.35 26 26
CDK5R1 0.028 0.02 -10000 0 -0.36 1 1
PRKACA 0.031 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.22 0.22 29 -0.46 121 150
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.044 0.12 0.32 7 -0.37 9 16
cortisol/GR alpha (monomer) 0.09 0.26 0.62 46 -0.41 6 52
NCOA2 0.005 0.12 -10000 0 -0.56 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.11 0.17 -10000 0 -0.5 59 59
AP-1/NFAT1-c-4 -0.33 0.3 -10000 0 -0.7 134 134
AFP -0.21 0.34 -10000 0 -1.5 23 23
SUV420H1 0.031 0.003 -10000 0 -10000 0 0
IRF1 0.035 0.16 0.46 6 -0.84 7 13
TP53 0.044 0.052 -10000 0 -0.7 2 2
PPP5C 0.029 0.039 -10000 0 -0.56 2 2
KRT17 -0.31 0.42 -10000 0 -1.1 87 87
KRT14 -0.2 0.41 -10000 0 -1.4 46 46
TBP 0.036 0.011 -10000 0 -10000 0 0
CREBBP 0.066 0.097 0.33 40 -0.29 4 44
HDAC1 0.029 0.009 -10000 0 -10000 0 0
HDAC2 0.029 0.01 -10000 0 -10000 0 0
AP-1 -0.33 0.3 -10000 0 -0.7 135 135
MAPK14 0.026 0.014 -10000 0 -10000 0 0
MAPK10 0.02 0.069 0.23 1 -0.56 6 7
MAPK11 0.015 0.089 0.55 1 -0.56 10 11
KRT5 -0.34 0.43 -10000 0 -1.1 91 91
interleukin-1 receptor activity 0 0.005 -10000 0 -10000 0 0
NCOA1 0.031 0.014 -10000 0 -10000 0 0
STAT1 0.029 0.057 -10000 0 -0.36 9 9
CGA -0.027 0.11 0.24 3 -0.33 24 27
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.049 0.13 0.38 21 -0.41 2 23
MAPK3 0.024 0.042 0.23 1 -0.56 2 3
MAPK1 0.027 0.017 0.25 1 -10000 0 1
ICAM1 -0.12 0.27 -10000 0 -0.73 50 50
NFKB1 -0.042 0.11 -10000 0 -0.27 34 34
MAPK8 -0.1 0.15 -10000 0 -0.46 29 29
MAPK9 0.022 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.061 0.22 0.76 6 -0.67 27 33
BAX 0.02 0.12 -10000 0 -1.3 3 3
POMC -0.1 0.29 -10000 0 -1.4 15 15
EP300 0.07 0.095 0.33 41 -0.27 3 44
cortisol/GR alpha (dimer)/p53 0.089 0.22 0.56 33 -0.75 2 35
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.071 0.22 14 -10000 0 14
SGK1 0.062 0.22 0.73 1 -1.5 6 7
IL13 -0.15 0.22 -10000 0 -0.75 29 29
IL6 -0.24 0.42 -10000 0 -0.98 91 91
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.12 0.18 -10000 0 -0.8 11 11
IL2 -0.2 0.24 -10000 0 -0.75 34 34
CDK5 0.024 0.04 -10000 0 -0.56 2 2
PRKACB 0.03 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
IL8 -0.18 0.35 -10000 0 -0.84 75 75
CDK5R1/CDK5 0.036 0.035 0.23 1 -0.41 2 3
NF kappa B1 p50/RelA/PKAc -0.03 0.16 -10000 0 -0.38 37 37
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.081 0.2 0.49 36 -0.46 1 37
SMARCA4 0.029 0.041 -10000 0 -0.56 2 2
chromatin remodeling 0.042 0.14 0.41 18 -0.43 3 21
NF kappa B1 p50/RelA/Cbp 0.005 0.2 0.41 23 -0.48 25 48
JUN (dimer) -0.17 0.19 -10000 0 -0.5 62 62
YWHAH 0.031 0.005 -10000 0 -10000 0 0
VIPR1 -0.077 0.22 -10000 0 -0.79 31 31
NR3C1 0.051 0.16 0.47 26 -0.54 1 27
NR4A1 -0.046 0.18 -10000 0 -0.43 80 80
TIF2/SUV420H1 0.024 0.092 -10000 0 -0.41 19 19
MAPKKK cascade -0.057 0.21 0.75 6 -0.63 27 33
cortisol/GR alpha (dimer)/Src-1 0.087 0.22 0.56 37 -0.64 1 38
PBX1 0.013 0.1 -10000 0 -0.56 13 13
POU1F1 0.02 0.023 -10000 0 -0.34 1 1
SELE -0.17 0.36 -10000 0 -0.95 64 64
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.042 0.14 0.41 18 -0.43 3 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.081 0.2 0.49 36 -0.46 1 37
mol:cortisol 0.044 0.17 0.35 59 -0.26 18 77
MMP1 -0.32 0.5 -10000 0 -1.3 86 86
Glypican 1 network

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.039 0.084 -10000 0 -0.38 16 16
fibroblast growth factor receptor signaling pathway 0.038 0.084 -10000 0 -0.38 16 16
LAMA1 -0.016 0.16 -10000 0 -0.53 39 39
PRNP 0.028 0.033 -10000 0 -0.45 2 2
GPC1/SLIT2 -0.021 0.15 -10000 0 -0.33 78 78
SMAD2 0.011 0.05 -10000 0 -0.32 8 8
GPC1/PrPc/Cu2+ 0.034 0.044 -10000 0 -0.32 6 6
GPC1/Laminin alpha1 0.003 0.13 -10000 0 -0.39 42 42
TDGF1 -0.046 0.15 -10000 0 -0.37 79 79
CRIPTO/GPC1 -0.025 0.12 -10000 0 -0.26 77 77
APP/GPC1 0.038 0.046 -10000 0 -0.38 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.093 -10000 0 -0.35 12 12
FLT1 -0.008 0.14 -10000 0 -0.56 30 30
GPC1/TGFB/TGFBR1/TGFBR2 0.036 0.061 -10000 0 -0.35 8 8
SERPINC1 -0.025 0.15 -10000 0 -0.41 56 56
FYN -0.029 0.097 -10000 0 -0.37 14 14
FGR -0.032 0.1 -10000 0 -0.37 16 16
positive regulation of MAPKKK cascade -0.085 0.17 0.34 4 -0.51 37 41
SLIT2 -0.048 0.18 -10000 0 -0.46 75 75
GPC1/NRG 0.003 0.12 -10000 0 -0.36 39 39
NRG1 -0.012 0.14 -10000 0 -0.49 36 36
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.014 0.15 -10000 0 -0.48 35 35
LYN -0.029 0.095 -10000 0 -0.36 14 14
mol:Spermine 0.005 0.04 -10000 0 -0.38 5 5
cell growth 0.038 0.084 -10000 0 -0.38 16 16
BMP signaling pathway -0.024 0.058 0.52 5 -10000 0 5
SRC -0.029 0.098 -10000 0 -0.4 11 11
TGFBR1 0.03 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.089 0.2 -10000 0 -0.41 121 121
GPC1 0.024 0.058 -10000 0 -0.52 5 5
TGFBR1 (dimer) 0.03 0.006 -10000 0 -10000 0 0
VEGFA 0.005 0.12 -10000 0 -0.56 20 20
BLK -0.076 0.14 -10000 0 -0.39 54 54
HCK -0.033 0.1 -10000 0 -0.38 17 17
FGF2 0.013 0.098 -10000 0 -0.52 15 15
FGFR1 0.028 0.02 -10000 0 -0.34 1 1
VEGFR1 homodimer -0.008 0.14 -10000 0 -0.56 30 30
TGFBR2 0.018 0.056 -10000 0 -0.56 4 4
cell death 0.038 0.046 -10000 0 -0.38 5 5
ATIII/GPC1 -0.002 0.12 -10000 0 -0.3 59 59
PLA2G2A/GPC1 -0.051 0.16 -10000 0 -0.3 123 123
LCK -0.043 0.12 -10000 0 -0.41 31 31
neuron differentiation 0.003 0.12 -10000 0 -0.36 39 39
PrPc/Cu2+ 0.021 0.024 -10000 0 -0.32 2 2
APP 0.03 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.018 0.056 -10000 0 -0.56 4 4
Nongenotropic Androgen signaling

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.007 0.13 -10000 0 -0.33 56 56
regulation of S phase of mitotic cell cycle -0.006 0.097 -10000 0 -0.27 47 47
GNAO1 0.006 0.1 -10000 0 -0.41 26 26
HRAS 0.027 0.047 -10000 0 -0.56 3 3
SHBG/T-DHT -0.004 0.084 -10000 0 -0.28 38 38
PELP1 0.03 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.028 -10000 0 -0.41 2 2
MAP2K1 -0.027 0.1 0.34 1 -0.4 9 10
T-DHT/AR -0.031 0.14 -10000 0 -0.4 59 59
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.007 50 50
GNAI2 0.022 0.014 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.029 -10000 0 -0.56 1 1
mol:GDP -0.046 0.15 -10000 0 -0.45 53 53
cell proliferation -0.066 0.16 0.31 5 -0.47 37 42
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
FOS -0.076 0.23 -10000 0 -0.8 36 36
mol:Ca2+ -0.005 0.022 -10000 0 -0.071 33 33
MAPK3 -0.052 0.14 0.3 6 -0.48 16 22
MAPK1 -0.024 0.089 -10000 0 -0.55 4 4
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 0 0.002 -10000 0 -0.004 64 64
cAMP biosynthetic process -0.017 0.076 0.29 2 -0.26 34 36
GNG2 0.025 0.048 -10000 0 -0.56 3 3
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 64 64
HRAS/GTP 0.01 0.12 -10000 0 -0.31 49 49
actin cytoskeleton reorganization 0.036 0.033 -10000 0 -0.28 2 2
SRC 0.028 0.039 -10000 0 -0.56 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 64 64
PI3K 0.034 0.036 -10000 0 -0.25 6 6
apoptosis 0.047 0.14 0.43 42 -0.26 2 44
T-DHT/AR/PELP1 -0.007 0.13 -10000 0 -0.35 57 57
HRAS/GDP -0.031 0.15 -10000 0 -0.44 54 54
CREB1 -0.051 0.16 0.28 1 -0.46 42 43
RAC1-CDC42/GTP 0.046 0.037 -10000 0 -0.28 2 2
AR -0.042 0.19 -10000 0 -0.55 58 58
GNB1 0.03 0.007 -10000 0 -10000 0 0
RAF1 -0.023 0.1 0.35 1 -0.3 39 40
RAC1-CDC42/GDP -0.005 0.15 -10000 0 -0.41 50 50
T-DHT/AR/PELP1/Src 0.013 0.12 -10000 0 -0.32 50 50
MAP2K2 -0.03 0.11 0.34 1 -0.48 9 10
T-DHT/AR/PELP1/Src/PI3K -0.006 0.097 -10000 0 -0.28 47 47
GNAZ 0.024 0.06 -10000 0 -0.49 6 6
SHBG -0.009 0.14 -10000 0 -0.46 37 37
Gi family/GNB1/GNG2/GDP -0.042 0.15 -10000 0 -0.52 27 27
mol:T-DHT 0 0.003 -10000 0 -0.006 19 19
RAC1 0.028 0.01 -10000 0 -10000 0 0
GNRH1 -0.019 0.098 -10000 0 -0.35 35 35
Gi family/GTP -0.018 0.083 -10000 0 -0.27 31 31
CDC42 0.03 0.006 -10000 0 -10000 0 0
VEGFR1 specific signals

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.01 0.18 -10000 0 -0.69 30 30
VEGFR1 homodimer/NRP1 -0.032 0.18 -10000 0 -0.66 33 33
mol:DAG -0.066 0.21 -10000 0 -0.62 44 44
VEGFR1 homodimer/NRP1/VEGFR 121 -0.025 0.21 -10000 0 -0.73 35 35
CaM/Ca2+ -0.049 0.2 -10000 0 -0.72 30 30
HIF1A 0.011 0.099 -10000 0 -0.38 27 27
GAB1 0.03 0.028 -10000 0 -0.56 1 1
AKT1 -0.05 0.2 0.31 1 -0.68 32 33
PLCG1 -0.066 0.21 -10000 0 -0.62 44 44
NOS3 -0.055 0.22 -10000 0 -0.78 33 33
CBL 0.031 0.004 -10000 0 -10000 0 0
mol:NO -0.043 0.21 0.59 1 -0.73 33 34
FLT1 -0.028 0.2 -10000 0 -0.78 30 30
PGF -0.062 0.19 -10000 0 -0.42 94 94
VEGFR1 homodimer/NRP2/VEGFR121 -0.012 0.23 -10000 0 -0.75 36 36
CALM1 0.029 0.008 -10000 0 -10000 0 0
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 -0.027 0.21 0.29 1 -0.69 34 35
endothelial cell proliferation -0.069 0.21 -10000 0 -0.74 34 34
mol:Ca2+ -0.065 0.2 -10000 0 -0.61 44 44
MAPK3 -0.069 0.18 -10000 0 -0.67 30 30
MAPK1 -0.068 0.18 -10000 0 -0.69 29 29
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
PLGF homodimer -0.062 0.18 -10000 0 -0.42 94 94
PRKACA 0.031 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.02 0.069 -10000 0 -0.53 7 7
VEGFA homodimer 0.005 0.12 -10000 0 -0.56 20 20
VEGFR1 homodimer/VEGFA homodimer -0.025 0.23 -10000 0 -0.78 35 35
platelet activating factor biosynthetic process -0.069 0.17 -10000 0 -0.65 30 30
PI3K -0.032 0.22 -10000 0 -0.73 31 31
PRKCA -0.067 0.19 -10000 0 -0.71 30 30
PRKCB -0.074 0.2 -10000 0 -0.65 39 39
VEGFR1 homodimer/PLGF homodimer -0.066 0.24 -10000 0 -0.65 49 49
VEGFA 0.005 0.12 -10000 0 -0.56 20 20
VEGFB 0.031 0.003 -10000 0 -10000 0 0
mol:IP3 -0.066 0.21 -10000 0 -0.62 44 44
RASA1 -0.024 0.16 -10000 0 -0.63 30 30
NRP2 0.02 0.074 -10000 0 -0.53 8 8
VEGFR1 homodimer -0.028 0.2 -10000 0 -0.78 30 30
VEGFB homodimer 0.031 0.003 -10000 0 -10000 0 0
NCK1 0.03 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.039 0.21 0.29 1 -0.73 32 33
PTPN11 0.031 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.21 -10000 0 -0.72 31 31
mol:L-citrulline -0.043 0.21 0.59 1 -0.73 33 34
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.011 0.21 -10000 0 -0.73 32 32
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.006 0.21 -10000 0 -0.72 35 35
CD2AP 0.029 0.028 -10000 0 -0.56 1 1
PI3K/GAB1 -0.021 0.22 -10000 0 -0.71 30 30
PDPK1 -0.051 0.19 -10000 0 -0.68 30 30
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.22 -10000 0 -0.72 35 35
mol:NADP -0.043 0.21 0.59 1 -0.73 33 34
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
ubiquitin-dependent protein catabolic process 0.009 0.21 -10000 0 -0.71 32 32
VEGFR1 homodimer/NRP2 -0.017 0.2 -10000 0 -0.71 32 32
Signaling events regulated by Ret tyrosine kinase

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.08 0.17 -10000 0 -0.48 38 38
Crk/p130 Cas/Paxillin -0.054 0.12 -10000 0 -0.39 27 27
JUN -0.033 0.11 -10000 0 -0.39 22 22
HRAS 0.027 0.048 -10000 0 -0.56 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.031 0.16 -10000 0 -0.38 50 50
RAP1A 0.031 0.006 -10000 0 -10000 0 0
FRS2 0.031 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.023 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.033 0.16 -10000 0 -0.39 53 53
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.019 0.12 -10000 0 -0.35 28 28
RHOA 0.023 0.014 -10000 0 -10000 0 0
RAP1A/GTP -0.03 0.15 -10000 0 -0.36 55 55
GRB7 0.021 0.077 -10000 0 -0.56 8 8
RET51/GFRalpha1/GDNF -0.032 0.16 -10000 0 -0.38 54 54
MAPKKK cascade -0.04 0.15 -10000 0 -0.51 21 21
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
RET9/GFRalpha1/GDNF/IRS1 -0.027 0.13 -10000 0 -0.34 37 37
lamellipodium assembly -0.036 0.11 -10000 0 -0.32 37 37
RET51/GFRalpha1/GDNF/SHC -0.03 0.16 -10000 0 -0.37 51 51
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.013 0.12 -10000 0 -0.33 28 28
RET9/GFRalpha1/GDNF/Shank3 -0.023 0.14 -10000 0 -0.38 38 38
MAPK3 -0.05 0.14 -10000 0 -0.43 26 26
DOK1 0.026 0.055 -10000 0 -0.56 4 4
DOK6 0 0.13 -10000 0 -0.53 25 25
PXN 0.03 0.018 -10000 0 -0.34 1 1
neurite development -0.052 0.14 -10000 0 -0.46 25 25
DOK5 -0.009 0.13 -10000 0 -0.43 39 39
GFRA1 -0.071 0.19 -10000 0 -0.42 105 105
MAPK8 -0.032 0.11 -10000 0 -0.42 18 18
HRAS/GTP -0.029 0.16 -10000 0 -0.4 46 46
tube development -0.019 0.13 -10000 0 -0.36 37 37
MAPK1 -0.046 0.14 0.43 4 -0.44 23 27
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.014 0.084 -10000 0 -0.26 33 33
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
SRC 0.028 0.039 -10000 0 -0.56 2 2
PDLIM7 0.017 0.057 -10000 0 -0.45 6 6
RET51/GFRalpha1/GDNF/Dok6 -0.036 0.18 -10000 0 -0.4 67 67
SHC1 0.03 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.036 0.17 -10000 0 -0.4 56 56
RET51/GFRalpha1/GDNF/Dok5 -0.051 0.18 -10000 0 -0.4 64 64
PRKCA 0.026 0.044 -10000 0 -0.39 5 5
HRAS/GDP 0.02 0.035 -10000 0 -0.41 3 3
CREB1 -0.019 0.1 -10000 0 -0.33 32 32
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.017 0.093 -10000 0 -0.29 32 32
RET51/GFRalpha1/GDNF/Grb7 -0.038 0.17 -10000 0 -0.4 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.021 0.15 -10000 0 -0.43 52 52
DOK4 0.021 0.072 -10000 0 -0.56 7 7
JNK cascade -0.032 0.11 -10000 0 -0.39 21 21
RET9/GFRalpha1/GDNF/FRS2 -0.015 0.12 -10000 0 -0.34 30 30
SHANK3 0.017 0.088 -10000 0 -0.54 11 11
RASA1 0.028 0.01 -10000 0 -10000 0 0
NCK1 0.03 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.015 0.089 -10000 0 -0.29 33 33
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.03 0.11 -10000 0 -0.37 19 19
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.033 0.12 -10000 0 -0.4 24 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.029 0.12 -10000 0 -0.34 38 38
PI3K -0.057 0.17 -10000 0 -0.49 39 39
SOS1 0.031 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.011 0.14 -10000 0 -0.36 37 37
GRB10 0.027 0.029 -10000 0 -0.56 1 1
activation of MAPKK activity -0.025 0.097 -10000 0 -0.35 13 13
RET51/GFRalpha1/GDNF/FRS2 -0.031 0.16 -10000 0 -0.38 52 52
GAB1 0.03 0.028 -10000 0 -0.56 1 1
IRS1 0.009 0.094 -10000 0 -0.39 23 23
IRS2 -0.005 0.11 -10000 0 -0.36 43 43
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.034 0.13 -10000 0 -0.44 24 24
RET51/GFRalpha1/GDNF/PKC alpha -0.035 0.16 -10000 0 -0.38 57 57
GRB2 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.031 0.003 -10000 0 -10000 0 0
GDNF 0.013 0.057 -10000 0 -0.34 11 11
RAC1 0.028 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.044 0.17 -10000 0 -0.38 59 59
Rac1/GTP -0.038 0.13 -10000 0 -0.4 32 32
RET9/GFRalpha1/GDNF -0.033 0.13 -10000 0 -0.26 100 100
GFRalpha1/GDNF -0.042 0.15 -10000 0 -0.3 100 100
HIF-2-alpha transcription factor network

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.002 0.21 -10000 0 -0.9 18 18
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.026 0.048 -10000 0 -0.56 3 3
TCEB1 0.03 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.003 0.16 -10000 0 -0.54 27 27
EPO -0.22 0.35 -10000 0 -0.68 131 131
FIH (dimer) 0.023 0.027 -10000 0 -10000 0 0
APEX1 0.022 0.027 -10000 0 -10000 0 0
SERPINE1 -0.082 0.34 -10000 0 -0.86 54 54
FLT1 -0.087 0.44 -10000 0 -1.4 43 43
ADORA2A -0.081 0.31 0.41 1 -0.88 42 43
germ cell development -0.077 0.33 -10000 0 -0.83 53 53
SLC11A2 -0.055 0.31 -10000 0 -0.9 39 39
BHLHE40 -0.077 0.31 -10000 0 -0.9 42 42
HIF1AN 0.023 0.027 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.072 0.23 0.35 1 -0.69 32 33
ETS1 0.019 0.099 -10000 0 -0.57 10 10
CITED2 -0.024 0.2 -10000 0 -0.84 19 19
KDR -0.082 0.43 -10000 0 -1.4 42 42
PGK1 -0.057 0.31 -10000 0 -0.88 42 42
SIRT1 0.026 0.01 -10000 0 -10000 0 0
response to hypoxia -0.005 0.006 -10000 0 -10000 0 0
HIF2A/ARNT -0.076 0.45 -10000 0 -1.2 42 42
EPAS1 -0.024 0.18 -10000 0 -0.57 33 33
SP1 0.036 0.013 -10000 0 -10000 0 0
ABCG2 -0.069 0.34 -10000 0 -0.93 46 46
EFNA1 -0.056 0.32 -10000 0 -0.9 42 42
FXN -0.079 0.3 0.41 1 -0.86 42 43
POU5F1 -0.084 0.35 -10000 0 -0.89 53 53
neuron apoptosis 0.063 0.39 1.1 42 -10000 0 42
EP300 0.031 0.005 -10000 0 -10000 0 0
EGLN3 -0.005 0.13 -10000 0 -0.58 23 23
EGLN2 0.021 0.054 -10000 0 -0.57 3 3
EGLN1 0.023 0.026 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.039 0.048 -10000 0 -0.35 4 4
VHL 0.02 0.041 -10000 0 -0.56 2 2
ARNT 0.021 0.028 -10000 0 -10000 0 0
SLC2A1 -0.084 0.32 0.41 1 -0.91 42 43
TWIST1 -0.096 0.32 -10000 0 -0.88 48 48
ELK1 0.034 0.028 -10000 0 -0.34 2 2
HIF2A/ARNT/Cbp/p300 -0.005 0.22 -10000 0 -0.7 28 28
VEGFA -0.066 0.34 -10000 0 -0.97 42 42
CREBBP 0.03 0.007 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.033 0.063 -10000 0 -0.3 14 14
AKT1 -0.015 0.22 0.31 1 -0.66 43 44
PTK2B -0.033 0.21 0.35 4 -0.7 37 41
VEGFR2 homodimer/Frs2 -0.016 0.21 -10000 0 -0.75 34 34
CAV1 0.02 0.069 -10000 0 -0.53 7 7
CALM1 0.029 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.008 0.23 -10000 0 -0.77 36 36
endothelial cell proliferation 0.003 0.21 0.42 11 -0.61 41 52
mol:Ca2+ -0.029 0.21 -10000 0 -0.69 38 38
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.005 0.22 -10000 0 -0.72 35 35
RP11-342D11.1 -0.042 0.21 -10000 0 -0.72 38 38
CDH5 0.012 0.1 -10000 0 -0.56 14 14
VEGFA homodimer 0.037 0.087 -10000 0 -0.34 17 17
SHC1 0.03 0.007 -10000 0 -10000 0 0
SHC2 0.015 0.092 -10000 0 -0.5 14 14
HRAS/GDP -0.001 0.19 -10000 0 -0.62 37 37
SH2D2A -0.018 0.15 -10000 0 -0.45 46 46
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.016 0.22 -10000 0 -0.68 38 38
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.037 0.26 -10000 0 -0.66 56 56
VEGFR1 homodimer -0.008 0.14 -10000 0 -0.56 30 30
SHC/GRB2/SOS1 0.024 0.22 -10000 0 -0.69 36 36
GRB10 -0.032 0.21 -10000 0 -0.71 36 36
PTPN11 0.031 0.005 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
PAK1 0.031 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.007 0.25 -10000 0 -0.82 35 35
HRAS 0.027 0.048 -10000 0 -0.56 3 3
VEGF/Rho/ROCK1/Integrin Complex -0.02 0.16 -10000 0 -0.47 42 42
HIF1A 0.028 0.019 -10000 0 -0.34 1 1
FRS2 0.031 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.004 0.22 -10000 0 -0.71 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.006 0.1 -10000 0 -0.56 14 14
Nck/Pak 0.045 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.012 0.24 -10000 0 -0.8 36 36
mol:GDP 0.01 0.21 -10000 0 -0.67 36 36
mol:NADP -0.001 0.19 0.36 3 -0.58 39 42
eNOS/Hsp90 0.014 0.18 0.4 2 -0.54 38 40
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 -0.03 0.21 -10000 0 -0.7 38 38
HIF1A/ARNT 0.041 0.02 -10000 0 -0.24 1 1
SHB 0.03 0.006 -10000 0 -10000 0 0
VEGFA 0.006 0.12 -10000 0 -0.56 20 20
VEGFC 0.024 0.064 -10000 0 -0.52 6 6
FAK1/Vinculin -0.036 0.23 0.6 1 -0.73 40 41
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.023 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.23 -10000 0 -0.74 37 37
PTPN6 0.029 0.028 -10000 0 -0.56 1 1
EPAS1 -0.002 0.16 -10000 0 -0.51 35 35
mol:L-citrulline -0.001 0.19 0.36 3 -0.58 39 42
ITGAV 0.029 0.019 -10000 0 -0.34 1 1
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.01 0.22 -10000 0 -0.73 35 35
VEGFR2 homodimer/VEGFA homodimer -0.008 0.24 -10000 0 -0.79 38 38
VEGFR2/3 heterodimer -0.033 0.23 -10000 0 -0.75 39 39
VEGFB 0.031 0.003 -10000 0 -10000 0 0
MAPK11 -0.05 0.23 0.43 1 -0.74 42 43
VEGFR2 homodimer -0.036 0.23 -10000 0 -0.85 34 34
FLT1 -0.008 0.14 -10000 0 -0.56 30 30
NEDD4 0.025 0.067 -10000 0 -0.56 6 6
MAPK3 -0.044 0.19 0.36 2 -0.64 39 41
MAPK1 -0.041 0.19 0.39 1 -0.65 38 39
VEGFA145/NRP2 0.018 0.12 -10000 0 -0.48 21 21
VEGFR1/2 heterodimer -0.035 0.27 -10000 0 -0.89 39 39
KDR -0.036 0.23 -10000 0 -0.86 34 34
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.24 -10000 0 -0.76 37 37
SRC 0.028 0.039 -10000 0 -0.56 2 2
platelet activating factor biosynthetic process -0.036 0.21 0.41 4 -0.66 39 43
PI3K -0.03 0.26 -10000 0 -0.83 40 40
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.23 -10000 0 -0.74 37 37
FES -0.034 0.23 -10000 0 -0.75 38 38
GAB1 -0.034 0.27 -10000 0 -0.9 37 37
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.23 -10000 0 -0.74 37 37
CTNNB1 0.023 0.014 -10000 0 -10000 0 0
SOS1 0.031 0.006 -10000 0 -10000 0 0
ARNT 0.03 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.004 0.18 0.4 2 -0.54 38 40
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.23 -10000 0 -0.77 37 37
PI3K/GAB1 -0.011 0.22 -10000 0 -0.7 37 37
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.023 0.22 -10000 0 -0.7 35 35
PRKACA 0.031 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.021 0.23 -10000 0 -0.73 39 39
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
CDC42 -0.033 0.22 -10000 0 -0.75 37 37
actin cytoskeleton reorganization -0.036 0.25 -10000 0 -0.65 56 56
PTK2 -0.05 0.24 -10000 0 -0.79 40 40
EDG1 -0.042 0.21 -10000 0 -0.72 38 38
mol:DAG -0.03 0.21 -10000 0 -0.7 38 38
CaM/Ca2+ -0.013 0.2 -10000 0 -0.66 36 36
MAP2K3 -0.04 0.21 -10000 0 -0.72 37 37
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.01 0.24 -10000 0 -0.75 36 36
PLCG1 -0.03 0.22 -10000 0 -0.72 38 38
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.007 0.22 -10000 0 -0.71 36 36
IQGAP1 0.031 0.004 -10000 0 -10000 0 0
YES1 0.031 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.009 0.23 -10000 0 -0.72 41 41
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.23 -10000 0 -0.75 37 37
cell migration -0.022 0.21 0.32 1 -0.66 36 37
mol:PI-3-4-5-P3 -0.023 0.23 -10000 0 -0.74 40 40
FYN 0.025 0.048 -10000 0 -0.56 3 3
VEGFB/NRP1 -0.022 0.2 -10000 0 -0.68 38 38
mol:NO -0.001 0.19 0.36 3 -0.58 39 42
PXN 0.03 0.018 -10000 0 -0.34 1 1
HRAS/GTP -0.022 0.18 -10000 0 -0.62 37 37
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.016 0.23 -10000 0 -0.75 36 36
VHL 0.02 0.041 -10000 0 -0.56 2 2
ITGB3 0.016 0.084 -10000 0 -0.43 15 15
NOS3 -0.009 0.22 0.52 1 -0.68 39 40
VEGFR2 homodimer/VEGFA homodimer/Sck -0.017 0.25 -10000 0 -0.82 37 37
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCA -0.035 0.2 -10000 0 -0.67 37 37
PRKCB -0.043 0.21 -10000 0 -0.7 38 38
VCL 0.03 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.024 0.22 -10000 0 -0.73 38 38
VEGFR1/2 heterodimer/VEGFA homodimer -0.028 0.29 -10000 0 -0.85 45 45
VEGFA165/NRP2 0.018 0.12 -10000 0 -0.48 21 21
MAPKKK cascade -0.008 0.19 -10000 0 -0.63 34 34
NRP2 0.02 0.074 -10000 0 -0.53 8 8
VEGFC homodimer 0.024 0.063 -10000 0 -0.52 6 6
NCK1 0.03 0.006 -10000 0 -10000 0 0
ROCK1 0.03 0.028 -10000 0 -0.56 1 1
FAK1/Paxillin -0.036 0.23 0.6 1 -0.73 40 41
MAP3K13 -0.035 0.23 -10000 0 -0.74 39 39
PDPK1 -0.022 0.2 -10000 0 -0.63 39 39
EPHB forward signaling

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.053 0.15 -10000 0 -0.3 116 116
cell-cell adhesion 0.035 0.12 0.45 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.027 0.14 -10000 0 -0.36 38 38
ITSN1 0.03 0.006 -10000 0 -10000 0 0
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
SHC1 0.03 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.015 0.1 -10000 0 -0.37 28 28
Ephrin B1/EPHB1 0.013 0.09 -10000 0 -0.25 43 43
HRAS/GDP -0.006 0.14 -10000 0 -0.47 23 23
Ephrin B/EPHB1/GRB7 0.022 0.16 -10000 0 -0.38 45 45
Endophilin/SYNJ1 -0.02 0.11 -10000 0 -0.33 43 43
KRAS 0.031 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.024 0.15 -10000 0 -0.39 41 41
endothelial cell migration 0.04 0.078 -10000 0 -0.33 15 15
GRB2 0.031 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.077 -10000 0 -0.56 8 8
PAK1 -0.022 0.12 -10000 0 -0.51 11 11
HRAS 0.027 0.048 -10000 0 -0.56 3 3
RRAS -0.024 0.13 -10000 0 -0.37 43 43
DNM1 -0.006 0.13 -10000 0 -0.49 32 32
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.12 -10000 0 -0.36 41 41
lamellipodium assembly -0.035 0.12 -10000 0 -0.45 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.002 0.12 -10000 0 -0.4 24 24
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
EPHB2 0.005 0.11 -10000 0 -0.43 26 26
EPHB3 -0.004 0.14 -10000 0 -0.53 28 28
EPHB1 -0.006 0.12 -10000 0 -0.38 40 40
EPHB4 0.023 0.055 -10000 0 -0.56 4 4
mol:GDP -0.023 0.14 0.35 5 -0.43 31 36
Ephrin B/EPHB2 0.018 0.14 -10000 0 -0.35 43 43
Ephrin B/EPHB3 0.013 0.15 -10000 0 -0.36 51 51
JNK cascade -0.011 0.1 0.36 2 -0.37 19 21
Ephrin B/EPHB1 0.012 0.14 -10000 0 -0.37 42 42
RAP1/GDP 0.018 0.14 0.32 7 -0.44 20 27
EFNB2 0.013 0.1 -10000 0 -0.56 14 14
EFNB3 -0.007 0.14 -10000 0 -0.48 34 34
EFNB1 0.025 0.061 -10000 0 -0.56 5 5
Ephrin B2/EPHB1-2 0.009 0.12 -10000 0 -0.26 66 66
RAP1B 0.03 0.018 -10000 0 -0.34 1 1
RAP1A 0.031 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.003 0.14 -10000 0 -0.53 15 15
Rap1/GTP -0.018 0.12 -10000 0 -0.46 16 16
axon guidance -0.053 0.15 -10000 0 -0.3 116 116
MAPK3 -0.008 0.11 0.2 2 -0.5 14 16
MAPK1 -0.008 0.11 0.2 2 -0.47 14 16
Rac1/GDP -0.011 0.13 0.36 1 -0.44 22 23
actin cytoskeleton reorganization -0.026 0.1 -10000 0 -0.42 15 15
CDC42/GDP 0.007 0.14 0.34 8 -0.44 22 30
PI3K 0.045 0.08 -10000 0 -0.33 15 15
EFNA5 -0.084 0.21 -10000 0 -0.47 101 101
Ephrin B2/EPHB4 0.023 0.075 -10000 0 -0.35 17 17
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.12 -10000 0 -0.32 43 43
CDC42 0.03 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.12 -10000 0 -0.47 17 17
PTK2 0.019 0.092 0.53 14 -10000 0 14
MAP4K4 -0.011 0.1 0.36 2 -0.37 19 21
SRC 0.028 0.039 -10000 0 -0.56 2 2
KALRN 0.024 0.058 -10000 0 -0.52 5 5
Intersectin/N-WASP 0.04 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis 0.016 0.16 0.41 31 -0.42 14 45
MAP2K1 -0.006 0.11 -10000 0 -0.49 14 14
WASL 0.028 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.031 0.12 -10000 0 -0.38 20 20
cell migration 0 0.14 0.42 4 -0.52 15 19
NRAS 0.031 0.006 -10000 0 -10000 0 0
SYNJ1 -0.021 0.12 -10000 0 -0.34 43 43
PXN 0.03 0.018 -10000 0 -0.34 1 1
TF -0.093 0.15 -10000 0 -0.46 35 35
HRAS/GTP -0.003 0.14 -10000 0 -0.47 21 21
Ephrin B1/EPHB1-2 0.015 0.11 -10000 0 -0.38 20 20
cell adhesion mediated by integrin 0.035 0.11 0.37 34 -0.32 4 38
RAC1 0.028 0.01 -10000 0 -10000 0 0
mol:GTP -0.001 0.14 -10000 0 -0.36 45 45
RAC1-CDC42/GTP -0.039 0.13 -10000 0 -0.5 19 19
RASA1 0.028 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.001 0.13 0.35 1 -0.44 20 21
ruffle organization 0.013 0.18 0.4 39 -0.52 14 53
NCK1 0.03 0.006 -10000 0 -10000 0 0
receptor internalization -0.044 0.14 -10000 0 -0.45 27 27
Ephrin B/EPHB2/KALRN 0.027 0.15 -10000 0 -0.36 45 45
ROCK1 0 0.097 -10000 0 -0.38 24 24
RAS family/GDP -0.031 0.099 -10000 0 -0.42 16 16
Rac1/GTP -0.03 0.13 -10000 0 -0.49 18 18
Ephrin B/EPHB1/Src/Paxillin -0.006 0.12 -10000 0 -0.36 36 36
Paxillin-independent events mediated by a4b1 and a4b7

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.018 0.07 -10000 0 -0.4 11 11
CRKL 0.031 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
DOCK1 0.03 0.006 -10000 0 -10000 0 0
ITGA4 0.019 0.079 -10000 0 -0.54 9 9
alpha4/beta7 Integrin/MAdCAM1 0.034 0.089 -10000 0 -0.37 12 12
EPO -0.21 0.24 -10000 0 -0.44 229 229
alpha4/beta7 Integrin 0.028 0.087 -10000 0 -0.45 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.061 -10000 0 -0.39 8 8
EPO/EPOR (dimer) -0.14 0.19 -10000 0 -0.32 231 231
lamellipodium assembly 0.015 0.095 0.28 1 -0.6 5 6
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
PI3K 0.037 0.042 -10000 0 -0.3 6 6
ARF6 0.029 0.008 -10000 0 -10000 0 0
JAK2 -0.083 0.13 -10000 0 -0.29 106 106
PXN 0.03 0.018 -10000 0 -0.34 1 1
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
MADCAM1 0.015 0.071 -10000 0 -0.34 17 17
cell adhesion 0.032 0.088 -10000 0 -0.36 12 12
CRKL/CBL 0.045 0.008 -10000 0 -10000 0 0
ITGB1 0.031 0.004 -10000 0 -10000 0 0
SRC -0.002 0.1 -10000 0 -0.35 29 29
ITGB7 0.022 0.072 -10000 0 -0.56 7 7
RAC1 0.028 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.024 0.12 -10000 0 -0.39 32 32
p130Cas/Crk/Dock1 0.022 0.1 -10000 0 -0.5 6 6
VCAM1 -0.006 0.14 -10000 0 -0.55 29 29
RHOA 0.023 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.064 -10000 0 -0.34 9 9
BCAR1 -0.012 0.1 -10000 0 -0.35 28 28
EPOR 0.025 0.051 -10000 0 -0.38 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.031 0.004 -10000 0 -10000 0 0
GIT1 0.028 0.039 -10000 0 -0.56 2 2
Rac1/GTP 0.014 0.098 0.28 1 -0.63 5 6
Neurotrophic factor-mediated Trk receptor signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.006 0.089 -10000 0 -0.3 21 21
NT3 (dimer)/TRKC -0.043 0.2 -10000 0 -0.42 86 86
NT3 (dimer)/TRKB -0.058 0.22 -10000 0 -0.48 77 77
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.04 -10000 0 -0.5 2 2
RAPGEF1 0.029 0.028 -10000 0 -0.56 1 1
BDNF -0.059 0.2 -10000 0 -0.48 81 81
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
DYNLT1 0.028 0.02 -10000 0 -0.34 1 1
NTRK1 -0.014 0.13 -10000 0 -0.41 45 45
NTRK2 -0.069 0.21 -10000 0 -0.48 91 91
NTRK3 -0.053 0.2 -10000 0 -0.49 75 75
NT-4/5 (dimer)/TRKB -0.048 0.19 -10000 0 -0.44 70 70
neuron apoptosis 0.073 0.21 0.56 54 -10000 0 54
SHC 2-3/Grb2 -0.082 0.24 -10000 0 -0.62 54 54
SHC1 0.03 0.007 -10000 0 -10000 0 0
SHC2 -0.079 0.24 -10000 0 -0.64 55 55
SHC3 -0.09 0.24 -10000 0 -0.62 58 58
STAT3 (dimer) 0.031 0.051 -10000 0 -0.35 8 8
NT3 (dimer)/TRKA -0.025 0.18 -10000 0 -0.44 60 60
RIN/GDP 0.006 0.1 0.3 8 -0.28 26 34
GIPC1 0.027 0.051 -10000 0 -0.51 4 4
KRAS 0.031 0.005 -10000 0 -10000 0 0
DNAJA3 -0.045 0.16 -10000 0 -0.49 39 39
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.009 0.11 -10000 0 -0.74 10 10
MAGED1 0.03 0.025 -10000 0 -0.34 2 2
PTPN11 0.031 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.011 0.065 -10000 0 -0.34 15 15
SHC/GRB2/SOS1 0.059 0.018 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.015 0.16 -10000 0 -0.42 46 46
TRKA/NEDD4-2 0.003 0.11 -10000 0 -0.28 58 58
ELMO1 0.023 0.055 -10000 0 -0.56 4 4
RhoG/GTP/ELMO1/DOCK1 0.034 0.038 -10000 0 -0.34 4 4
NGF -0.025 0.16 -10000 0 -0.5 48 48
HRAS 0.027 0.048 -10000 0 -0.56 3 3
DOCK1 0.03 0.006 -10000 0 -10000 0 0
GAB2 0.03 0.018 -10000 0 -0.34 1 1
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.03 0.007 -10000 0 -10000 0 0
FRS2 0.031 0.005 -10000 0 -10000 0 0
DNM1 -0.006 0.13 -10000 0 -0.49 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.03 0.16 -10000 0 -0.47 40 40
mol:GDP 0.004 0.15 0.4 7 -0.44 26 33
NGF (dimer) -0.025 0.16 -10000 0 -0.5 48 48
RhoG/GDP 0.017 0.041 -10000 0 -0.41 4 4
RIT1/GDP 0.013 0.1 0.3 5 -0.3 19 24
TIAM1 0.028 0.039 -10000 0 -0.56 2 2
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
BDNF (dimer)/TRKB -0.066 0.2 -10000 0 -0.41 95 95
KIDINS220/CRKL/C3G 0.043 0.024 -10000 0 -0.41 1 1
SHC/RasGAP 0.04 0.017 -10000 0 -10000 0 0
FRS2 family/SHP2 0.058 0.032 -10000 0 -0.35 2 2
SHC/GRB2/SOS1/GAB1 0.072 0.031 -10000 0 -0.32 1 1
RIT1/GTP 0.021 0.012 -10000 0 -10000 0 0
NT3 (dimer) -0.012 0.15 -10000 0 -0.49 38 38
RAP1/GDP 0.01 0.083 -10000 0 -0.26 16 16
KIDINS220/CRKL 0.031 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.059 0.2 -10000 0 -0.48 81 81
ubiquitin-dependent protein catabolic process -0.013 0.15 -10000 0 -0.4 47 47
Schwann cell development -0.024 0.034 -10000 0 -10000 0 0
EHD4 0.031 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.072 0.035 -10000 0 -0.32 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.039 -10000 0 -0.46 1 1
RAP1B 0.03 0.018 -10000 0 -0.34 1 1
RAP1A 0.031 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.23 -10000 0 -0.56 66 66
ABL1 0.028 0.039 -10000 0 -0.56 2 2
SH2B family/GRB2/SOS1 0.045 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.009 0.11 -10000 0 -0.5 12 12
STAT3 0.031 0.051 -10000 0 -0.35 8 8
axon guidance -0.11 0.22 -10000 0 -0.53 66 66
MAPK3 -0.037 0.14 -10000 0 -0.41 42 42
MAPK1 -0.035 0.14 -10000 0 -0.4 43 43
CDC42/GDP 0.018 0.11 0.34 7 -0.29 19 26
NTF3 -0.012 0.15 -10000 0 -0.49 38 38
NTF4 0.011 0.066 -10000 0 -0.34 15 15
NGF (dimer)/TRKA/FAIM -0.009 0.15 -10000 0 -0.39 44 44
PI3K 0.037 0.042 -10000 0 -0.3 6 6
FRS3 0.028 0.039 -10000 0 -0.56 2 2
FAIM 0.028 0.033 -10000 0 -0.45 2 2
GAB1 0.03 0.028 -10000 0 -0.56 1 1
RASGRF1 -0.057 0.17 -10000 0 -0.5 46 46
SOS1 0.031 0.006 -10000 0 -10000 0 0
MCF2L -0.056 0.18 -10000 0 -0.44 67 67
RGS19 0.028 0.039 -10000 0 -0.56 2 2
CDC42 0.03 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.028 0.1 0.3 1 -0.51 10 11
Rac1/GDP 0.012 0.095 0.28 2 -0.29 19 21
NGF (dimer)/TRKA/GRIT -0.024 0.14 -10000 0 -0.3 86 86
neuron projection morphogenesis -0.026 0.2 -10000 0 -0.83 13 13
NGF (dimer)/TRKA/NEDD4-2 -0.013 0.16 -10000 0 -0.4 47 47
MAP2K1 0.032 0.053 0.42 3 -0.3 1 4
NGFR -0.018 0.16 -10000 0 -0.52 41 41
NGF (dimer)/TRKA/GIPC/GAIP -0.033 0.16 -10000 0 -0.5 32 32
RAS family/GTP/PI3K 0.025 0.039 -10000 0 -0.31 5 5
FRS2 family/SHP2/GRB2/SOS1 0.083 0.038 -10000 0 -0.3 2 2
NRAS 0.031 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.045 0.01 -10000 0 -10000 0 0
PRKCI 0.029 0.019 -10000 0 -0.34 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.01 -10000 0 -10000 0 0
PRKCZ 0.02 0.074 -10000 0 -0.53 8 8
MAPKKK cascade -0.08 0.26 -10000 0 -0.7 63 63
RASA1 0.028 0.01 -10000 0 -10000 0 0
TRKA/c-Abl 0.006 0.11 -10000 0 -0.3 47 47
SQSTM1 0.024 0.014 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.05 0.19 -10000 0 -0.38 96 96
NGF (dimer)/TRKA/p62/Atypical PKCs 0.007 0.13 -10000 0 -0.36 35 35
MATK 0.017 0.086 -10000 0 -0.48 13 13
NEDD4L 0.02 0.066 -10000 0 -0.36 13 13
RAS family/GDP -0.024 0.057 -10000 0 -0.26 10 10
NGF (dimer)/TRKA -0.049 0.16 -10000 0 -0.43 59 59
Rac1/GTP -0.038 0.11 -10000 0 -0.35 35 35
FRS2 family/SHP2/CRK family 0.084 0.037 -10000 0 -0.3 2 2
Visual signal transduction: Cones

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.01 0.12 -9999 0 -0.31 50 50
RGS9BP -0.011 0.14 -9999 0 -0.44 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.018 0.049 -9999 0 -0.2 21 21
mol:ADP 0.002 0.024 -9999 0 -0.24 4 4
GNAT2 0.028 0.019 -9999 0 -0.34 1 1
RGS9-1/Gbeta5/R9AP -0.031 0.17 -9999 0 -0.38 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.033 0.015 -9999 0 -0.2 1 1
GRK7 0.024 0.035 -9999 0 -0.34 4 4
CNGB3 0.016 0.052 -9999 0 -0.35 9 9
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.036 -9999 0 -0.18 17 17
Cone PDE6 -0.01 0.16 -9999 0 -0.34 66 66
Cone Metarhodopsin II 0.016 0.019 -9999 0 -0.18 4 4
Na + (4 Units) 0.018 0.044 -9999 0 -0.18 18 18
GNAT2/GDP -0.014 0.15 -9999 0 -0.32 67 67
GNB5 0.031 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) 0.001 0.033 -9999 0 -10000 0 0
Cone Transducin -0.01 0.13 -9999 0 -0.33 50 50
SLC24A2 0 0 -9999 0 -10000 0 0
GNB3/GNGT2 -0.035 0.16 -9999 0 -0.33 95 95
GNB3 -0.066 0.2 -9999 0 -0.45 92 92
GNAT2/GTP 0.021 0.013 -9999 0 -0.24 1 1
CNGA3 0.009 0.069 -9999 0 -0.34 17 17
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.019 0.049 -9999 0 -0.2 21 21
mol:Pi -0.031 0.17 -9999 0 -0.38 67 67
Cone CNG Channel 0.041 0.059 -9999 0 -0.3 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0 0 -9999 0 -10000 0 0
RGS9 -0.065 0.2 -9999 0 -0.47 89 89
PDE6C 0.018 0.046 -9999 0 -0.34 7 7
GNGT2 0.024 0.061 -9999 0 -0.56 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.022 0.007 -9999 0 -10000 0 0
IFN-gamma pathway

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.018 0.13 -10000 0 -0.28 63 63
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.031 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.011 0.13 0.31 4 -0.44 7 11
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.057 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.09 -10000 0 -0.35 14 14
CaM/Ca2+ -0.015 0.13 -10000 0 -0.27 56 56
RAP1A 0.031 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.032 0.12 -10000 0 -0.28 54 54
AKT1 -0.024 0.12 0.37 9 -0.35 5 14
MAP2K1 -0.04 0.1 0.29 2 -0.32 3 5
MAP3K11 -0.042 0.12 0.3 5 -0.28 53 58
IFNGR1 0.013 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.07 0.17 -10000 0 -0.47 47 47
Rap1/GTP -0.034 0.092 -10000 0 -0.41 1 1
CRKL/C3G 0.043 0.024 -10000 0 -0.41 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.013 0.14 -10000 0 -0.29 55 55
CEBPB 0.009 0.14 0.45 9 -0.51 8 17
STAT3 0.031 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.022 0.2 -10000 0 -1.2 7 7
STAT1 -0.039 0.12 0.3 5 -0.28 49 54
CALM1 0.029 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.12 0.23 -10000 0 -0.44 150 150
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.023 0.12 0.29 7 -0.36 4 11
CEBPB/PTGES2/Cbp/p300 0.007 0.089 -10000 0 -0.42 6 6
mol:Ca2+ -0.02 0.13 -10000 0 -0.28 63 63
MAPK3 -0.014 0.12 0.42 3 -0.84 3 6
STAT1 (dimer) -0.038 0.13 -10000 0 -0.52 14 14
MAPK1 -0.014 0.12 0.42 3 -0.72 4 7
JAK2 0.013 0.03 -10000 0 -10000 0 0
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
JAK1 0.014 0.03 -10000 0 -10000 0 0
CAMK2D 0.031 0.004 -10000 0 -10000 0 0
DAPK1 0.013 0.12 0.4 11 -0.59 7 18
SMAD7 0 0.071 0.22 19 -0.2 6 25
CBL/CRKL/C3G -0.017 0.12 0.3 4 -0.32 4 8
PI3K -0.017 0.12 -10000 0 -0.31 5 5
IFNG -0.12 0.23 -10000 0 -0.44 150 150
apoptosis 0.009 0.12 0.36 12 -0.47 10 22
CAMK2G 0.03 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.031 0.005 -10000 0 -10000 0 0
CAMK2A -0.029 0.15 -10000 0 -0.44 52 52
CAMK2B -0.077 0.2 -10000 0 -0.42 108 108
FRAP1 -0.029 0.12 0.36 9 -0.33 5 14
PRKCD -0.031 0.12 0.35 7 -0.37 6 13
RAP1B 0.03 0.018 -10000 0 -0.34 1 1
negative regulation of cell growth -0.032 0.09 -10000 0 -0.35 14 14
PTPN2 0.031 0.005 -10000 0 -10000 0 0
EP300 0.031 0.005 -10000 0 -10000 0 0
IRF1 -0.031 0.12 0.36 4 -0.55 10 14
STAT1 (dimer)/PIASy -0.025 0.12 0.29 7 -0.33 8 15
SOCS1 -0.003 0.18 -10000 0 -1.4 7 7
mol:GDP -0.018 0.12 0.28 4 -0.3 4 8
CASP1 -0.003 0.082 0.22 19 -0.33 10 29
PTGES2 0.025 0.049 -10000 0 -0.43 5 5
IRF9 0.022 0.06 0.22 14 -10000 0 14
mol:PI-3-4-5-P3 -0.026 0.11 -10000 0 -0.3 5 5
RAP1/GDP -0.018 0.1 -10000 0 -0.42 1 1
CBL -0.041 0.11 0.3 5 -0.27 49 54
MAP3K1 -0.04 0.11 0.3 2 -0.27 46 48
PIAS1 0.031 0.003 -10000 0 -10000 0 0
PIAS4 0.029 0.039 -10000 0 -0.55 2 2
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.09 -10000 0 -0.35 14 14
PTPN11 -0.045 0.11 -10000 0 -0.28 62 62
CREBBP 0.03 0.007 -10000 0 -10000 0 0
RAPGEF1 0.029 0.028 -10000 0 -0.56 1 1
Integrins in angiogenesis

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.005 0.16 -10000 0 -0.5 41 41
alphaV beta3 Integrin 0.037 0.091 -10000 0 -0.37 18 18
PTK2 -0.057 0.19 0.49 2 -0.58 38 40
IGF1R 0.027 0.048 -10000 0 -0.56 3 3
PI4KB 0.029 0.028 -10000 0 -0.56 1 1
MFGE8 0.018 0.085 -10000 0 -0.52 11 11
SRC 0.028 0.039 -10000 0 -0.56 2 2
CDKN1B -0.032 0.13 -10000 0 -0.46 29 29
VEGFA 0.005 0.12 -10000 0 -0.56 20 20
ILK -0.034 0.13 -10000 0 -0.46 30 30
ROCK1 0.03 0.028 -10000 0 -0.56 1 1
AKT1 -0.036 0.12 -10000 0 -0.44 30 30
PTK2B -0.015 0.13 0.36 1 -0.41 35 36
alphaV/beta3 Integrin/JAM-A -0.013 0.14 -10000 0 -0.34 39 39
CBL 0.031 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.1 0.18 -10000 0 -0.36 109 109
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.041 0.098 -10000 0 -0.32 16 16
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.046 0.15 -10000 0 -0.41 48 48
alphaV/beta3 Integrin/Syndecan-1 0.035 0.088 -10000 0 -0.35 14 14
PI4KA 0.03 0.028 -10000 0 -0.56 1 1
IGF-1R heterotetramer/IGF1/IRS1 0.012 0.13 -10000 0 -0.5 12 12
PI4 Kinase 0.042 0.038 -10000 0 -0.74 1 1
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.038 0.087 -10000 0 -0.37 14 14
RPS6KB1 -0.011 0.14 0.47 10 -0.49 10 20
TLN1 0.029 0.028 -10000 0 -0.56 1 1
MAPK3 -0.026 0.14 -10000 0 -0.6 19 19
GPR124 0.01 0.1 -10000 0 -0.56 15 15
MAPK1 -0.026 0.14 -10000 0 -0.6 19 19
PXN 0.03 0.018 -10000 0 -0.34 1 1
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
alphaV/beta3 Integrin/Tumstatin 0.016 0.12 -10000 0 -0.37 38 38
cell adhesion -0.08 0.16 -10000 0 -0.31 111 111
ANGPTL3 -0.18 0.25 -10000 0 -0.45 206 206
VEGFR2 homodimer/VEGFA homodimer/Src 0.017 0.14 -10000 0 -0.44 36 36
IGF-1R heterotetramer 0.027 0.047 -10000 0 -0.56 3 3
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
TGFBR2 0.018 0.056 -10000 0 -0.56 4 4
ITGB3 0.016 0.084 -10000 0 -0.43 15 15
IGF1 0.004 0.11 -10000 0 -0.41 28 28
RAC1 0.028 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.033 0.089 -10000 0 -0.36 17 17
apoptosis 0.029 0.019 -10000 0 -0.34 1 1
CD47 0.029 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.046 0.059 -10000 0 -0.34 5 5
VCL 0.03 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.01 0.13 -10000 0 -0.4 31 31
CSF1 0.026 0.051 -10000 0 -0.51 4 4
PIK3C2A -0.034 0.13 -10000 0 -0.45 32 32
PI4 Kinase/Pyk2 -0.047 0.16 -10000 0 -0.54 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.027 0.15 -10000 0 -0.42 40 40
FAK1/Vinculin -0.033 0.16 0.46 2 -0.46 34 36
alphaV beta3/Integrin/ppsTEM5 0.033 0.09 -10000 0 -0.36 17 17
RHOA 0.023 0.014 -10000 0 -10000 0 0
VTN -0.068 0.18 -10000 0 -0.4 107 107
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
FGF2 0.013 0.098 -10000 0 -0.52 15 15
F11R 0.005 0.076 -10000 0 -0.44 12 12
alphaV/beta3 Integrin/Lactadherin 0.042 0.08 -10000 0 -0.38 11 11
alphaV/beta3 Integrin/TGFBR2 0.031 0.073 -10000 0 -0.37 9 9
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.067 0.063 -10000 0 -0.5 4 4
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
alphaV/beta3 Integrin/Talin 0.045 0.059 -10000 0 -0.35 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.004 0.11 -10000 0 -0.42 27 27
alphaV/beta3 Integrin/Pyk2 0.009 0.13 -10000 0 -0.4 37 37
SDC1 0.008 0.1 -10000 0 -0.44 22 22
VAV3 0.017 0.089 0.36 6 -0.34 17 23
PTPN11 0.031 0.005 -10000 0 -10000 0 0
IRS1 0.009 0.094 -10000 0 -0.39 23 23
FAK1/Paxillin -0.033 0.16 0.63 1 -0.46 34 35
cell migration -0.032 0.14 0.43 2 -0.43 28 30
ITGAV 0.029 0.019 -10000 0 -0.34 1 1
PI3K -0.005 0.13 -10000 0 -0.44 10 10
SPP1 0.01 0.098 -10000 0 -0.43 21 21
KDR -0.012 0.15 -10000 0 -0.56 34 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.019 -10000 0 -0.34 1 1
COL4A3 -0.02 0.16 -10000 0 -0.5 43 43
angiogenesis -0.028 0.15 0.3 3 -0.62 18 21
Rac1/GTP 0.025 0.073 -10000 0 -0.33 13 13
EDIL3 -0.023 0.16 -10000 0 -0.49 46 46
cell proliferation 0.031 0.073 -10000 0 -0.37 9 9
Signaling events mediated by PTP1B

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.11 -10000 0 -0.56 16 16
Jak2/Leptin Receptor -0.016 0.14 0.32 1 -0.48 23 24
PTP1B/AKT1 -0.009 0.097 0.22 3 -0.32 20 23
FYN 0.025 0.048 -10000 0 -0.56 3 3
p210 bcr-abl/PTP1B -0.021 0.095 0.28 3 -0.31 21 24
EGFR 0 0.11 -10000 0 -0.52 18 18
EGF/EGFR -0.06 0.16 -10000 0 -0.35 73 73
CSF1 0.026 0.051 -10000 0 -0.51 4 4
AKT1 0.027 0.04 -10000 0 -0.57 2 2
INSR 0.021 0.077 -10000 0 -0.56 8 8
PTP1B/N-cadherin -0.023 0.12 0.24 1 -0.34 33 34
Insulin Receptor/Insulin -0.008 0.11 0.25 2 -0.36 19 21
HCK 0.021 0.074 -10000 0 -0.53 8 8
CRK 0.031 0.005 -10000 0 -10000 0 0
TYK2 -0.021 0.098 0.31 5 -0.34 17 22
EGF -0.11 0.23 -10000 0 -0.45 135 135
YES1 0.031 0.005 -10000 0 -10000 0 0
CAV1 -0.024 0.12 0.28 10 -0.36 23 33
TXN 0.029 0.019 -10000 0 -0.35 1 1
PTP1B/IRS1/GRB2 -0.007 0.11 0.29 2 -0.38 12 14
cell migration 0.021 0.095 0.31 21 -0.28 3 24
STAT3 0.031 0.005 -10000 0 -10000 0 0
PRLR -0.033 0.16 -10000 0 -0.42 63 63
ITGA2B -0.037 0.17 -10000 0 -0.45 65 65
CSF1R 0.008 0.092 -10000 0 -0.5 14 14
Prolactin Receptor/Prolactin -0.015 0.12 -10000 0 -0.3 69 69
FGR 0.023 0.062 -10000 0 -0.47 7 7
PTP1B/p130 Cas -0.011 0.1 0.24 1 -0.33 21 22
Crk/p130 Cas 0 0.1 0.24 1 -0.37 11 12
DOK1 -0.008 0.13 0.23 9 -0.43 22 31
JAK2 -0.025 0.14 0.26 2 -0.48 24 26
Jak2/Leptin Receptor/Leptin -0.037 0.14 -10000 0 -0.44 22 22
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
PTPN1 -0.021 0.096 0.28 3 -0.31 21 24
LYN 0.027 0.039 -10000 0 -0.56 2 2
CDH2 0.004 0.12 -10000 0 -0.56 21 21
SRC 0.015 0.096 0.31 1 -0.89 4 5
ITGB3 0.015 0.084 -10000 0 -0.43 15 15
CAT1/PTP1B -0.039 0.17 0.3 7 -0.51 30 37
CAPN1 0.027 0.048 -10000 0 -0.57 3 3
CSK 0.027 0.048 -10000 0 -0.56 3 3
PI3K 0.003 0.11 -10000 0 -0.44 10 10
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.031 0.14 -10000 0 -0.45 21 21
negative regulation of transcription -0.024 0.14 0.26 2 -0.47 24 26
FCGR2A 0.024 0.058 -10000 0 -0.52 5 5
FER 0.023 0.041 -10000 0 -0.57 2 2
alphaIIb/beta3 Integrin -0.018 0.15 -10000 0 -0.34 75 75
BLK -0.056 0.18 -10000 0 -0.43 85 85
Insulin Receptor/Insulin/Shc 0.033 0.05 -10000 0 -0.35 7 7
RHOA 0.022 0.014 -10000 0 -10000 0 0
LEPR 0.022 0.067 -10000 0 -0.47 8 8
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
p210 bcr-abl/Grb2 0.031 0.005 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.043 0.2 0.29 2 -0.59 34 36
PRL 0.007 0.053 -10000 0 -0.35 9 9
SOCS3 -0.032 0.28 -10000 0 -1.4 19 19
SPRY2 0.028 0.04 -10000 0 -0.57 2 2
Insulin Receptor/Insulin/IRS1 0.019 0.082 -10000 0 -0.36 13 13
CSF1/CSF1R -0.014 0.11 0.33 1 -0.4 20 21
Ras protein signal transduction 0.013 0.071 0.47 9 -10000 0 9
IRS1 0.009 0.094 -10000 0 -0.39 23 23
INS -0.001 0.003 -10000 0 -10000 0 0
LEP -0.031 0.14 -10000 0 -0.37 63 63
STAT5B -0.016 0.11 0.24 4 -0.37 21 25
STAT5A -0.016 0.11 0.24 4 -0.36 25 29
GRB2 0.031 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.023 0.11 -10000 0 -0.35 27 27
CSN2 -0.004 0.053 0.13 9 -0.15 29 38
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
LAT -0.013 0.14 -10000 0 -0.59 23 23
YBX1 0.037 0.008 -10000 0 -10000 0 0
LCK 0.004 0.12 -10000 0 -0.48 24 24
SHC1 0.03 0.007 -10000 0 -10000 0 0
NOX4 0.009 0.1 -10000 0 -0.48 19 19
S1P1 pathway

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.005 0.16 -10000 0 -0.49 42 42
PDGFRB 0.003 0.11 -10000 0 -0.56 16 16
SPHK1 -0.02 0.15 -10000 0 -0.84 13 13
mol:S1P -0.019 0.13 -10000 0 -0.73 13 13
S1P1/S1P/Gi -0.051 0.17 0.39 1 -0.51 41 42
GNAO1 0.005 0.1 -10000 0 -0.41 26 26
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.16 -10000 0 -0.52 33 33
PLCG1 -0.046 0.16 0.48 1 -0.49 36 37
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.11 -10000 0 -0.56 16 16
GNAI2 0.022 0.016 -10000 0 -10000 0 0
GNAI3 0.03 0.009 -10000 0 -10000 0 0
GNAI1 0.026 0.03 -10000 0 -0.57 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.032 0.13 -10000 0 -0.43 41 41
S1P1/S1P -0.027 0.16 0.24 2 -0.52 32 34
negative regulation of cAMP metabolic process -0.049 0.17 0.39 1 -0.49 41 42
MAPK3 -0.061 0.19 0.44 2 -0.6 38 40
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.011 -10000 0 -10000 0 0
KDR -0.012 0.15 -10000 0 -0.56 34 34
PLCB2 -0.022 0.16 0.29 8 -0.51 31 39
RAC1 0.028 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.12 -10000 0 -0.43 32 32
receptor internalization -0.027 0.14 -10000 0 -0.48 32 32
PTGS2 -0.073 0.27 0.45 2 -0.96 30 32
Rac1/GTP -0.023 0.12 -10000 0 -0.42 31 31
RHOA 0.023 0.014 -10000 0 -10000 0 0
VEGFA 0.005 0.12 -10000 0 -0.56 20 20
negative regulation of T cell proliferation -0.049 0.17 0.39 1 -0.49 41 42
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.061 -10000 0 -0.49 6 6
MAPK1 -0.061 0.19 0.38 1 -0.63 35 36
S1P1/S1P/PDGFB-D/PDGFRB -0.03 0.17 -10000 0 -0.57 31 31
ABCC1 0.03 0.007 -10000 0 -10000 0 0
BCR signaling pathway

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.011 0.16 0.34 10 -0.54 20 30
IKBKB 0.016 0.11 0.32 15 -0.31 9 24
AKT1 -0.008 0.13 0.37 21 -0.26 13 34
IKBKG 0.029 0.1 0.31 14 -0.33 10 24
CALM1 -0.002 0.12 0.6 1 -0.5 14 15
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
MAP3K1 -0.019 0.19 0.37 13 -0.61 24 37
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.13 0.31 3 -0.5 17 20
DOK1 0.026 0.055 -10000 0 -0.56 4 4
AP-1 0.003 0.11 0.3 19 -0.29 18 37
LYN 0.027 0.039 -10000 0 -0.56 2 2
BLNK 0.022 0.065 -10000 0 -0.45 8 8
SHC1 0.03 0.007 -10000 0 -10000 0 0
BCR complex -0.031 0.16 -10000 0 -0.32 94 94
CD22 -0.045 0.17 -10000 0 -0.57 29 29
CAMK2G 0.002 0.11 0.42 2 -0.46 14 16
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
INPP5D 0.027 0.039 -10000 0 -0.56 2 2
SHC/GRB2/SOS1 -0.019 0.12 -10000 0 -0.53 10 10
GO:0007205 -0.002 0.13 0.35 2 -0.51 17 19
SYK 0.025 0.055 -10000 0 -0.56 4 4
ELK1 0 0.13 0.37 3 -0.53 14 17
NFATC1 -0.04 0.15 0.34 8 -0.5 21 29
B-cell antigen/BCR complex -0.031 0.16 -10000 0 -0.32 94 94
PAG1/CSK 0.037 0.055 -10000 0 -0.38 7 7
NFKBIB 0.026 0.048 0.14 21 -0.13 7 28
HRAS -0.004 0.13 0.4 2 -0.6 12 14
NFKBIA 0.026 0.048 0.14 20 -0.12 6 26
NF-kappa-B/RelA/I kappa B beta 0.031 0.044 0.16 15 -10000 0 15
RasGAP/Csk 0 0.15 -10000 0 -0.37 44 44
mol:GDP -0.001 0.13 0.34 2 -0.5 16 18
PTEN 0.03 0.006 -10000 0 -10000 0 0
CD79B 0.015 0.09 -10000 0 -0.48 14 14
NF-kappa-B/RelA/I kappa B alpha 0.031 0.044 0.16 15 -10000 0 15
GRB2 0.031 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.025 0.19 0.37 11 -0.56 25 36
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 -0.004 0.13 0.24 2 -0.52 17 19
CSK 0.027 0.048 -10000 0 -0.56 3 3
FOS -0.025 0.14 0.44 3 -0.48 19 22
CHUK 0.022 0.11 0.3 15 -0.31 16 31
IBTK 0.03 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.016 0.15 0.34 3 -0.59 13 16
PTPN6 -0.045 0.16 -10000 0 -0.57 25 25
RELA 0.031 0.003 -10000 0 -10000 0 0
BCL2A1 0.019 0.041 0.18 6 -0.12 3 9
VAV2 -0.069 0.18 -10000 0 -0.66 24 24
ubiquitin-dependent protein catabolic process 0.029 0.048 0.14 21 -0.12 7 28
BTK -0.027 0.22 -10000 0 -1 21 21
CD19 -0.076 0.18 -10000 0 -0.6 28 28
MAP4K1 -0.01 0.14 -10000 0 -0.48 38 38
CD72 0 0.12 -10000 0 -0.44 30 30
PAG1 0.025 0.055 -10000 0 -0.56 4 4
MAPK14 -0.012 0.16 0.34 16 -0.5 23 39
SH3BP5 0.013 0.074 -10000 0 -0.53 8 8
PIK3AP1 -0.004 0.15 -10000 0 -0.61 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.044 0.21 -10000 0 -0.59 38 38
RAF1 -0.01 0.12 0.43 2 -0.58 11 13
RasGAP/p62DOK/SHIP -0.001 0.15 -10000 0 -0.38 42 42
CD79A -0.058 0.18 -10000 0 -0.41 93 93
re-entry into mitotic cell cycle 0.003 0.11 0.29 19 -0.3 17 36
RASA1 0.028 0.01 -10000 0 -10000 0 0
MAPK3 0.009 0.12 0.37 11 -0.53 10 21
MAPK1 0.005 0.11 0.4 6 -0.48 10 16
CD72/SHP1 -0.038 0.18 -10000 0 -0.64 25 25
NFKB1 0.031 0.004 -10000 0 -10000 0 0
MAPK8 -0.014 0.17 0.36 14 -0.51 23 37
actin cytoskeleton organization -0.044 0.17 0.36 6 -0.54 24 30
NF-kappa-B/RelA 0.061 0.086 0.26 20 -0.28 3 23
Calcineurin 0.025 0.11 -10000 0 -0.46 11 11
PI3K -0.063 0.15 -10000 0 -0.49 25 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 0.14 0.24 1 -0.59 17 18
SOS1 0.031 0.006 -10000 0 -10000 0 0
Bam32/HPK1 -0.037 0.25 -10000 0 -0.84 32 32
DAPP1 -0.045 0.26 -10000 0 -0.97 28 28
cytokine secretion -0.037 0.14 0.34 8 -0.46 21 29
mol:DAG -0.004 0.13 0.24 2 -0.52 17 19
PLCG2 0.015 0.079 -10000 0 -0.38 17 17
MAP2K1 0.003 0.12 0.41 4 -0.55 10 14
B-cell antigen/BCR complex/FcgammaRIIB -0.025 0.16 -10000 0 -0.4 50 50
mol:PI-3-4-5-P3 -0.051 0.1 0.19 1 -0.34 21 22
ETS1 -0.002 0.12 0.53 2 -0.5 14 16
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.008 0.16 -10000 0 -0.39 37 37
B-cell antigen/BCR complex/LYN -0.031 0.16 -10000 0 -0.59 25 25
MALT1 0.028 0.039 -10000 0 -0.56 2 2
TRAF6 0.03 0.028 -10000 0 -0.56 1 1
RAC1 -0.052 0.18 0.32 2 -0.59 24 26
B-cell antigen/BCR complex/LYN/SYK -0.02 0.17 -10000 0 -0.57 25 25
CARD11 -0.003 0.17 0.29 20 -0.62 17 37
FCGR2B 0.004 0.11 -10000 0 -0.46 24 24
PPP3CA 0.031 0.004 -10000 0 -10000 0 0
BCL10 0.03 0.006 -10000 0 -10000 0 0
IKK complex 0.021 0.068 0.22 22 -0.12 3 25
PTPRC 0.016 0.089 -10000 0 -0.52 12 12
PDPK1 -0.026 0.091 0.24 12 -0.24 14 26
PPP3CB 0.03 0.006 -10000 0 -10000 0 0
PPP3CC 0.028 0.01 -10000 0 -10000 0 0
POU2F2 0.023 0.041 0.2 6 -0.12 5 11
Plasma membrane estrogen receptor signaling

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.098 -10000 0 -0.33 18 18
ER alpha/Gai/GDP/Gbeta gamma -0.059 0.21 -10000 0 -0.56 51 51
AKT1 -0.054 0.26 -10000 0 -0.79 47 47
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.26 -10000 0 -0.81 47 47
mol:Ca2+ -0.027 0.14 -10000 0 -0.5 31 31
IGF1R 0.027 0.048 -10000 0 -0.56 3 3
E2/ER alpha (dimer)/Striatin 0.015 0.09 -10000 0 -0.32 29 29
SHC1 0.03 0.007 -10000 0 -10000 0 0
apoptosis 0.05 0.24 0.74 47 -10000 0 47
RhoA/GTP 0.014 0.045 -10000 0 -0.27 8 8
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.021 0.17 -10000 0 -0.54 30 30
regulation of stress fiber formation -0.012 0.054 -10000 0 -0.26 4 4
E2/ERA-ERB (dimer) 0.007 0.094 -10000 0 -0.27 42 42
KRAS 0.031 0.005 -10000 0 -10000 0 0
G13/GTP 0.029 0.048 -10000 0 -0.26 10 10
pseudopodium formation 0.012 0.054 0.26 4 -10000 0 4
E2/ER alpha (dimer)/PELP1 0.029 0.056 -10000 0 -0.29 12 12
GRB2 0.031 0.005 -10000 0 -10000 0 0
GNG2 0.025 0.048 -10000 0 -0.56 3 3
GNAO1 0.006 0.1 -10000 0 -0.41 26 26
HRAS 0.027 0.048 -10000 0 -0.56 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.046 0.21 0.45 1 -0.6 47 48
E2/ER beta (dimer) -0.001 0.082 -10000 0 -0.28 33 33
mol:GDP -0.006 0.092 -10000 0 -0.39 16 16
mol:NADP -0.046 0.21 0.45 1 -0.6 47 48
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 -0.029 0.15 -10000 0 -0.54 29 29
IGF-1R heterotetramer 0.027 0.047 -10000 0 -0.56 3 3
PLCB1 -0.017 0.14 -10000 0 -0.53 24 24
PLCB2 -0.014 0.13 -10000 0 -0.5 27 27
IGF1 0.004 0.11 -10000 0 -0.41 28 28
mol:L-citrulline -0.046 0.21 0.45 1 -0.6 47 48
RHOA 0.023 0.014 -10000 0 -10000 0 0
Gai/GDP -0.14 0.28 -10000 0 -0.57 131 131
JNK cascade -0.001 0.082 -10000 0 -0.28 33 33
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
ESR2 -0.002 0.11 -10000 0 -0.4 33 33
GNAQ 0.03 0.006 -10000 0 -10000 0 0
ESR1 0.015 0.086 -10000 0 -0.48 13 13
Gq family/GDP/Gbeta gamma 0 0.17 -10000 0 -0.77 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.16 -10000 0 -0.98 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.019 0.17 -10000 0 -0.54 27 27
GNAZ 0.024 0.06 -10000 0 -0.49 6 6
E2/ER alpha (dimer) 0.011 0.063 -10000 0 -0.34 13 13
STRN 0.009 0.11 -10000 0 -0.56 17 17
GNAL 0.017 0.08 -10000 0 -0.42 14 14
PELP1 0.031 0.005 -10000 0 -10000 0 0
MAPK11 -0.009 0.089 -10000 0 -0.28 41 41
GNAI2 0.023 0.014 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.029 -10000 0 -0.56 1 1
HBEGF -0.077 0.19 0.3 4 -0.54 47 51
cAMP biosynthetic process 0.002 0.092 -10000 0 -0.34 21 21
SRC -0.054 0.19 -10000 0 -0.56 43 43
PI3K 0.037 0.042 -10000 0 -0.3 6 6
GNB1 0.03 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.021 0.1 -10000 0 -0.42 10 10
SOS1 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.04 0.14 -10000 0 -0.46 31 31
Gs family/GTP 0.008 0.096 -10000 0 -0.35 21 21
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.034 -10000 0 -0.32 3 3
vasodilation -0.042 0.2 0.44 1 -0.56 47 48
mol:DAG -0.029 0.15 -10000 0 -0.54 29 29
Gs family/GDP/Gbeta gamma -0.003 0.099 -10000 0 -0.43 11 11
MSN 0.012 0.057 0.32 2 -10000 0 2
Gq family/GTP 0.001 0.12 -10000 0 -0.48 22 22
mol:PI-3-4-5-P3 -0.048 0.25 -10000 0 -0.78 47 47
NRAS 0.031 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.042 0.2 0.56 47 -0.44 1 48
GRB2/SOS1 0.045 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.001 0.092 -10000 0 -0.38 14 14
NOS3 -0.051 0.23 0.45 1 -0.64 47 48
GNA11 0.024 0.064 -10000 0 -0.52 6 6
MAPKKK cascade -0.033 0.21 0.39 2 -0.59 48 50
E2/ER alpha (dimer)/PELP1/Src -0.026 0.18 0.27 1 -0.49 41 42
ruffle organization 0.012 0.054 0.26 4 -10000 0 4
ROCK2 0.019 0.063 0.33 3 -10000 0 3
GNA14 0.01 0.11 -10000 0 -0.55 16 16
GNA15 0.021 0.076 -10000 0 -0.51 9 9
GNA13 0.031 0.005 -10000 0 -10000 0 0
MMP9 -0.093 0.2 0.32 2 -0.52 57 59
MMP2 -0.056 0.19 -10000 0 -0.55 45 45
FOXM1 transcription factor network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.099 0.38 1.1 1 -1.1 23 24
PLK1 0.036 0.17 -10000 0 -1.5 4 4
BIRC5 0.003 0.27 -10000 0 -1.4 15 15
HSPA1B 0.091 0.38 0.8 1 -1.1 24 25
MAP2K1 0.05 0.044 -10000 0 -10000 0 0
BRCA2 0.083 0.41 0.76 2 -1.2 30 32
FOXM1 0.072 0.53 0.8 2 -1.7 27 29
XRCC1 0.096 0.38 0.83 2 -1.2 22 24
FOXM1B/p19 0.071 0.4 0.73 1 -1.2 25 26
Cyclin D1/CDK4 0.082 0.38 -10000 0 -1.1 29 29
CDC2 0.096 0.4 0.78 2 -1.2 27 29
TGFA 0.078 0.39 0.71 2 -1.1 31 33
SKP2 0.11 0.4 0.88 3 -1.2 25 28
CCNE1 0.028 0.061 -10000 0 -0.38 10 10
CKS1B 0.1 0.38 0.96 2 -1.1 24 26
RB1 0.091 0.24 -10000 0 -1.1 9 9
FOXM1C/SP1 0.081 0.44 -10000 0 -1.4 26 26
AURKB -0.015 0.32 -10000 0 -1.4 22 22
CENPF 0.096 0.4 0.96 2 -1.2 25 27
CDK4 0.036 0.023 -10000 0 -10000 0 0
MYC 0.089 0.35 -10000 0 -1 25 25
CHEK2 0.048 0.057 -10000 0 -0.5 2 2
ONECUT1 0.082 0.39 0.63 1 -1.2 27 28
CDKN2A 0.003 0.11 -10000 0 -0.47 22 22
LAMA4 0.087 0.4 0.8 1 -1.2 28 29
FOXM1B/HNF6 0.059 0.49 -10000 0 -1.6 27 27
FOS 0.034 0.48 0.83 1 -1.2 49 50
SP1 0.031 0.007 -10000 0 -10000 0 0
CDC25B 0.098 0.38 0.83 2 -1.2 23 25
response to radiation 0.021 0.027 -10000 0 -10000 0 0
CENPB 0.098 0.38 0.83 2 -1.2 22 24
CENPA 0.086 0.41 0.83 2 -1.2 30 32
NEK2 0.089 0.41 0.96 2 -1.2 28 30
HIST1H2BA 0.095 0.38 0.71 2 -1.1 27 29
CCNA2 0.028 0.059 -10000 0 -0.38 9 9
EP300 0.031 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.085 0.44 0.82 2 -1.4 24 26
CCNB2 0.088 0.4 1.1 1 -1.2 25 26
CCNB1 0.099 0.41 0.84 2 -1.2 24 26
ETV5 0.098 0.38 0.8 1 -1.1 24 25
ESR1 0.089 0.4 0.8 1 -1.2 26 27
CCND1 0.082 0.4 0.76 2 -1.1 29 31
GSK3A 0.045 0.056 -10000 0 -0.6 2 2
Cyclin A-E1/CDK1-2 0.07 0.076 -10000 0 -0.4 4 4
CDK2 0.036 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.024 0.033 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.093 0.4 -10000 0 -1.3 25 25
GAS1 0.081 0.4 0.8 1 -1.2 28 29
MMP2 0.085 0.41 1.1 1 -1.2 27 28
RB1/FOXM1C 0.079 0.39 -10000 0 -1.2 27 27
CREBBP 0.03 0.007 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.004 0.17 -10000 0 -0.49 37 37
MAP4K1 -0.01 0.14 -10000 0 -0.48 38 38
MAP3K8 0.027 0.046 -10000 0 -0.45 4 4
PRKCB 0.012 0.098 -10000 0 -0.52 15 15
DBNL 0.024 0.048 -10000 0 -0.56 3 3
CRKL 0.031 0.004 -10000 0 -10000 0 0
MAP3K1 -0.013 0.14 -10000 0 -0.64 19 19
JUN 0.003 0.21 -10000 0 -0.9 19 19
MAP3K7 -0.013 0.14 -10000 0 -0.64 19 19
GRAP2 0.016 0.094 -10000 0 -0.56 12 12
CRK 0.031 0.005 -10000 0 -10000 0 0
MAP2K4 0.018 0.17 0.24 28 -0.67 19 47
LAT -0.006 0.12 -10000 0 -0.41 38 38
LCP2 0.016 0.067 -10000 0 -0.56 6 6
MAPK8 0.003 0.22 -10000 0 -0.92 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.01 0.15 -10000 0 -0.68 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.011 0.16 -10000 0 -0.48 37 37
ErbB2/ErbB3 signaling events

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.001 0.025 -10000 0 -0.36 2 2
RAS family/GTP -0.008 0.14 -10000 0 -0.49 20 20
NFATC4 -0.036 0.099 0.27 4 -0.4 13 17
ERBB2IP 0.03 0.01 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.026 -10000 0 -0.34 2 2
mammary gland morphogenesis -0.019 0.11 -10000 0 -0.34 40 40
JUN -0.008 0.098 0.19 2 -0.45 12 14
HRAS 0.027 0.047 -10000 0 -0.56 3 3
DOCK7 -0.033 0.1 -10000 0 -0.41 14 14
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.001 0.13 -10000 0 -0.36 44 44
AKT1 0.005 0.028 -10000 0 -0.42 2 2
BAD 0 0.047 -10000 0 -0.46 4 4
MAPK10 -0.01 0.071 0.18 4 -0.27 11 15
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.02 0.12 -10000 0 -0.37 39 39
RAF1 -0.033 0.13 0.29 2 -0.48 20 22
ErbB2/ErbB3/neuregulin 2 -0.007 0.12 -10000 0 -0.4 32 32
STAT3 0.023 0.12 -10000 0 -0.98 7 7
cell migration 0.005 0.092 0.34 11 -0.25 9 20
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.16 0.26 -10000 0 -0.62 81 81
FOS -0.11 0.19 -10000 0 -0.47 51 51
NRAS 0.03 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.11 -10000 0 -0.34 40 40
MAPK3 -0.13 0.22 -10000 0 -0.52 74 74
MAPK1 -0.13 0.22 -10000 0 -0.52 74 74
JAK2 -0.033 0.1 -10000 0 -0.43 12 12
NF2 0.013 0.038 -10000 0 -0.77 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.022 0.14 -10000 0 -0.41 41 41
NRG1 -0.013 0.14 -10000 0 -0.5 36 36
GRB2/SOS1 0.044 0.01 -10000 0 -10000 0 0
MAPK8 -0.021 0.11 -10000 0 -0.32 35 35
MAPK9 -0.012 0.057 0.18 2 -0.24 9 11
ERBB2 -0.022 0.034 -10000 0 -0.43 3 3
ERBB3 -0.005 0.14 -10000 0 -0.56 27 27
SHC1 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.028 0.01 -10000 0 -10000 0 0
apoptosis 0.004 0.058 0.63 3 -0.15 2 5
STAT3 (dimer) 0.024 0.12 -10000 0 -0.95 7 7
RNF41 -0.006 0.022 -10000 0 -0.33 2 2
FRAP1 0 0.023 -10000 0 -0.35 2 2
RAC1-CDC42/GTP -0.017 0.075 -10000 0 -0.32 10 10
ErbB2/ErbB2/HSP90 (dimer) 0.011 0.037 -10000 0 -0.3 5 5
CHRNA1 -0.15 0.25 -10000 0 -0.64 79 79
myelination -0.036 0.11 0.37 7 -0.39 13 20
PPP3CB -0.031 0.096 -10000 0 -0.44 9 9
KRAS 0.03 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.009 0.13 -10000 0 -0.53 16 16
NRG2 -0.003 0.11 -10000 0 -0.43 27 27
mol:GDP -0.022 0.14 -10000 0 -0.41 41 41
SOS1 0.03 0.006 -10000 0 -10000 0 0
MAP2K2 -0.044 0.13 0.29 2 -0.47 22 24
SRC 0.028 0.039 -10000 0 -0.56 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.034 0.1 -10000 0 -0.42 13 13
MAP2K1 -0.15 0.22 -10000 0 -0.55 42 42
heart morphogenesis -0.019 0.11 -10000 0 -0.34 40 40
RAS family/GDP 0.009 0.14 -10000 0 -0.51 18 18
GRB2 0.03 0.005 -10000 0 -10000 0 0
PRKACA 0.015 0.04 -10000 0 -0.81 1 1
CHRNE 0.002 0.038 0.12 1 -0.2 13 14
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
activation of caspase activity -0.005 0.028 0.41 2 -10000 0 2
nervous system development -0.019 0.11 -10000 0 -0.34 40 40
CDC42 0.03 0.006 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0.1 -10000 0 -0.56 14 14
EPHB2 0.004 0.11 -10000 0 -0.43 26 26
EFNB1 -0.012 0.12 -10000 0 -0.41 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.14 -10000 0 -0.38 32 32
Ephrin B2/EPHB1-2 0.008 0.12 -10000 0 -0.33 37 37
neuron projection morphogenesis -0.006 0.13 -10000 0 -0.36 33 33
Ephrin B1/EPHB1-2/Tiam1 0.001 0.15 -10000 0 -0.4 36 36
DNM1 -0.006 0.13 -10000 0 -0.49 32 32
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.002 0.078 -10000 0 -0.53 9 9
YES1 0.005 0.12 -10000 0 -0.8 9 9
Ephrin B1/EPHB1-2/NCK2 0.004 0.14 -10000 0 -0.39 34 34
PI3K 0.031 0.085 -10000 0 -0.53 8 8
mol:GDP 0 0.15 -10000 0 -0.39 36 36
ITGA2B -0.037 0.17 -10000 0 -0.45 65 65
endothelial cell proliferation 0.022 0.075 -10000 0 -0.35 17 17
FYN 0 0.12 -10000 0 -0.8 9 9
MAP3K7 -0.005 0.083 -10000 0 -0.58 9 9
FGR 0.002 0.12 -10000 0 -0.79 9 9
TIAM1 0.028 0.039 -10000 0 -0.56 2 2
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
RGS3 0.028 0.039 -10000 0 -0.56 2 2
cell adhesion -0.016 0.12 -10000 0 -0.5 13 13
LYN 0.003 0.12 -10000 0 -0.81 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.002 0.11 -10000 0 -0.75 9 9
Ephrin B1/EPHB1-2 -0.005 0.091 -10000 0 -0.63 9 9
SRC 0.006 0.11 -10000 0 -0.76 9 9
ITGB3 0.016 0.084 -10000 0 -0.43 15 15
EPHB1 -0.006 0.12 -10000 0 -0.38 40 40
EPHB4 0.023 0.055 -10000 0 -0.56 4 4
RAC1 0.028 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.075 -10000 0 -0.35 17 17
alphaIIb/beta3 Integrin -0.018 0.15 -10000 0 -0.34 75 75
BLK -0.016 0.13 -10000 0 -0.82 9 9
HCK 0.004 0.11 -10000 0 -0.78 9 9
regulation of stress fiber formation -0.003 0.14 0.39 34 -10000 0 34
MAPK8 -0.003 0.079 0.35 1 -0.52 8 9
Ephrin B1/EPHB1-2/RGS3 0.002 0.15 -10000 0 -0.41 35 35
endothelial cell migration 0.004 0.11 0.37 4 -0.56 8 12
NCK2 0.031 0.006 -10000 0 -10000 0 0
PTPN13 0.027 0.073 -10000 0 -0.67 5 5
regulation of focal adhesion formation -0.003 0.14 0.39 34 -10000 0 34
chemotaxis -0.001 0.15 0.4 35 -10000 0 35
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.14 -10000 0 -0.38 32 32
angiogenesis -0.004 0.09 -10000 0 -0.63 9 9
LCK -0.002 0.12 -10000 0 -0.81 9 9
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.029 0.008 -10000 0 -10000 0 0
VLDLR 0.025 0.049 -10000 0 -0.43 5 5
LRPAP1 0.027 0.048 -10000 0 -0.56 3 3
NUDC 0.03 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.038 0.15 -10000 0 -0.37 49 49
CaM/Ca2+ 0.022 0.006 -10000 0 -10000 0 0
KATNA1 0.029 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.041 0.14 -10000 0 -0.34 49 49
IQGAP1/CaM 0.043 0.013 -10000 0 -10000 0 0
DAB1 -0.013 0.11 -10000 0 -0.34 49 49
IQGAP1 0.031 0.004 -10000 0 -10000 0 0
PLA2G7 -0.027 0.16 -10000 0 -0.44 56 56
CALM1 0.029 0.008 -10000 0 -10000 0 0
DYNLT1 0.028 0.02 -10000 0 -0.34 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.028 0.073 -10000 0 -0.27 24 24
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.031 0.005 -10000 0 -10000 0 0
CDK5R1 0.03 0.018 -10000 0 -0.34 1 1
LIS1/Poliovirus Protein 3A 0.013 0.003 -10000 0 -10000 0 0
CDK5R2 -0.034 0.15 -10000 0 -0.38 69 69
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.052 0.16 -10000 0 -0.37 61 61
YWHAE 0.031 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.027 0.16 0.32 26 -0.5 9 35
MAP1B 0.005 0.032 0.28 1 -0.3 4 5
RAC1 0.017 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.044 0.12 -10000 0 -0.33 42 42
RELN -0.089 0.2 -10000 0 -0.42 119 119
PAFAH/LIS1 0 0.099 -10000 0 -0.35 23 23
LIS1/CLIP170 0.035 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.036 0.11 -10000 0 -0.45 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.11 -10000 0 -0.4 16 16
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.058 0.13 0.24 1 -0.52 10 11
LIS1/IQGAP1 0.035 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.009 -10000 0 -10000 0 0
PAFAH1B1 0.018 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.059 -10000 0 -0.44 7 7
PAFAH1B2 0.02 0.082 -10000 0 -0.56 9 9
MAP1B/LIS1/Dynein heavy chain 0.035 0.029 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.025 0.15 0.32 19 -0.5 8 27
LRP8 0.012 0.085 -10000 0 -0.36 22 22
NDEL1/Katanin 60 -0.03 0.15 0.32 23 -0.5 9 32
P39/CDK5 -0.068 0.14 -10000 0 -0.33 64 64
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.035 0.01 -10000 0 -10000 0 0
CDK5 -0.058 0.12 -10000 0 -0.34 48 48
PPP2R5D 0.029 0.028 -10000 0 -0.56 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.03 0.008 -10000 0 -10000 0 0
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.034 0.14 -10000 0 -0.32 61 61
RELN/VLDLR -0.024 0.15 -10000 0 -0.34 50 50
CDC42 0.018 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.018 0.25 1 -10000 0 1
AES 0.026 0.045 -10000 0 -0.47 3 3
FBXW11 0.024 0.014 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.074 -10000 0 -0.41 12 12
SMAD4 0.03 0.006 -10000 0 -10000 0 0
DKK2 -0.073 0.21 -10000 0 -0.46 98 98
TLE1 0.028 0.033 0.24 1 -0.56 1 2
MACF1 0.031 0.007 -10000 0 -10000 0 0
CTNNB1 -0.014 0.14 0.38 9 -0.41 10 19
WIF1 -0.003 0.089 -10000 0 -0.35 28 28
beta catenin/RanBP3 -0.027 0.12 0.44 10 -0.49 4 14
KREMEN2 -0.026 0.15 -10000 0 -0.42 56 56
DKK1 -0.034 0.17 -10000 0 -0.44 64 64
beta catenin/beta TrCP1 -0.014 0.11 0.52 1 -0.44 5 6
FZD1 0.012 0.098 -10000 0 -0.56 13 13
AXIN2 0 0.14 0.74 2 -1.3 3 5
AXIN1 0.027 0.048 -10000 0 -0.56 3 3
RAN 0.031 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin -0.006 0.14 -10000 0 -0.6 20 20
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.007 0.15 0.31 2 -0.6 12 14
Axin1/APC/GSK3 0.042 0.097 0.31 12 -0.6 3 15
Axin1/APC/GSK3/beta catenin/Macf1 0.009 0.13 0.35 6 -0.55 6 12
HNF1A -0.011 0.15 0.24 1 -0.55 32 33
CTBP1 0.03 0.019 0.25 1 -10000 0 1
MYC -0.011 0.23 0.62 9 -1.6 8 17
RANBP3 0.029 0.039 -10000 0 -0.56 2 2
DKK2/LRP6/Kremen 2 -0.043 0.17 -10000 0 -0.37 70 70
NKD1 -0.025 0.15 -10000 0 -0.42 56 56
TCF4 0.018 0.078 0.24 1 -0.52 9 10
TCF3 0.03 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.03 0.11 -10000 0 -0.32 33 33
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.014 0.12 0.56 7 -0.63 5 12
LEF1 -0.029 0.16 0.24 1 -0.41 62 63
DVL1 0.014 0.052 -10000 0 -0.38 3 3
CSNK2A1 0.031 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.009 0.18 0.32 2 -0.69 19 21
DKK1/LRP6/Kremen 2 -0.016 0.15 -10000 0 -0.41 44 44
LRP6 0.031 0.006 -10000 0 -10000 0 0
CSNK1A1 0.024 0.023 0.25 1 -10000 0 1
NLK 0.031 0.006 -10000 0 -10000 0 0
CCND1 -0.035 0.26 0.68 2 -1.6 12 14
WNT1 -0.012 0.14 -10000 0 -0.48 38 38
GSK3A 0.029 0.039 -10000 0 -0.56 2 2
GSK3B 0.03 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.025 -10000 0 -0.34 2 2
PPP2R5D 0.041 0.11 0.3 24 -0.41 13 37
APC 0.004 0.11 0.39 6 -0.31 27 33
WNT1/LRP6/FZD1 0.021 0.082 0.26 3 -0.28 3 6
CREBBP 0.029 0.019 0.24 1 -10000 0 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.029 0.13 0.31 1 -0.47 23 24
CRKL -0.013 0.11 0.25 1 -0.45 18 19
HRAS 0.001 0.14 -10000 0 -0.51 21 21
mol:PIP3 -0.002 0.11 -10000 0 -0.44 16 16
SPRED1 0.03 0.028 -10000 0 -0.56 1 1
SPRED2 0.031 0.006 -10000 0 -10000 0 0
GAB1 -0.013 0.11 -10000 0 -0.48 18 18
FOXO3 -0.007 0.14 0.44 1 -0.52 18 19
AKT1 -0.008 0.16 0.29 3 -0.5 27 30
BAD -0.008 0.15 0.33 3 -0.5 24 27
megakaryocyte differentiation -0.019 0.12 -10000 0 -0.47 22 22
GSK3B -0.005 0.14 0.32 4 -0.49 22 26
RAF1 -0.006 0.1 0.28 1 -0.43 18 19
SHC1 0.03 0.007 -10000 0 -10000 0 0
STAT3 -0.012 0.11 -10000 0 -0.48 17 17
STAT1 -0.055 0.25 -10000 0 -1.1 20 20
HRAS/SPRED1 0.02 0.12 0.27 1 -0.44 18 19
cell proliferation -0.012 0.11 -10000 0 -0.46 19 19
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
TEC 0.031 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.004 0.13 -10000 0 -0.51 20 20
HRAS/SPRED2 0.02 0.12 0.27 1 -0.43 18 19
LYN/TEC/p62DOK 0.03 0.12 -10000 0 -0.49 16 16
MAPK3 0.01 0.092 0.26 7 -0.33 17 24
STAP1 -0.045 0.14 -10000 0 -0.45 33 33
GRAP2 0.016 0.094 -10000 0 -0.56 12 12
JAK2 -0.05 0.23 -10000 0 -0.98 19 19
STAT1 (dimer) -0.053 0.24 -10000 0 -1 20 20
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.016 0.15 -10000 0 -0.47 26 26
actin filament polymerization -0.015 0.1 -10000 0 -0.46 17 17
LYN 0.027 0.039 -10000 0 -0.56 2 2
STAP1/STAT5A (dimer) -0.034 0.18 -10000 0 -0.64 26 26
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
CBL/CRKL/GRB2 0.022 0.1 -10000 0 -0.43 13 13
PI3K 0.02 0.13 -10000 0 -0.48 16 16
PTEN 0.03 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.3 -10000 0 -1.5 13 13
MAPK8 -0.013 0.11 -10000 0 -0.48 19 19
STAT3 (dimer) -0.011 0.11 -10000 0 -0.46 17 17
positive regulation of transcription 0.014 0.082 0.28 9 -0.26 16 25
mol:GDP 0.006 0.14 -10000 0 -0.5 22 22
PIK3C2B -0.014 0.12 -10000 0 -0.48 19 19
CBL/CRKL 0.001 0.1 -10000 0 -0.44 15 15
FER -0.015 0.11 -10000 0 -0.48 16 16
SH2B3 -0.011 0.11 -10000 0 -0.48 17 17
PDPK1 0.005 0.11 0.32 6 -0.41 13 19
SNAI2 -0.019 0.13 -10000 0 -0.5 24 24
positive regulation of cell proliferation -0.022 0.19 -10000 0 -0.74 21 21
KITLG 0.006 0.1 -10000 0 -0.48 19 19
cell motility -0.022 0.19 -10000 0 -0.74 21 21
PTPN6 0.029 0.029 -10000 0 -0.55 1 1
EPOR 0.015 0.13 -10000 0 -1.3 3 3
STAT5A (dimer) -0.006 0.17 -10000 0 -0.6 23 23
SOCS1 0.009 0.096 -10000 0 -0.4 23 23
cell migration 0.019 0.12 0.48 22 -10000 0 22
SOS1 0.031 0.006 -10000 0 -10000 0 0
EPO -0.21 0.25 -10000 0 -0.44 229 229
VAV1 0.012 0.1 -10000 0 -0.53 16 16
GRB10 -0.013 0.1 -10000 0 -0.48 15 15
PTPN11 0.031 0.007 -10000 0 -10000 0 0
SCF/KIT -0.011 0.12 -10000 0 -0.48 20 20
GO:0007205 0 0.006 -10000 0 -10000 0 0
MAP2K1 -0.003 0.085 0.26 2 -0.34 16 18
CBL 0.031 0.004 -10000 0 -10000 0 0
KIT -0.016 0.26 -10000 0 -1.6 11 11
MAP2K2 -0.005 0.088 0.26 2 -0.34 18 20
SHC/Grb2/SOS1 0.035 0.11 -10000 0 -0.46 14 14
STAT5A -0.008 0.17 -10000 0 -0.62 23 23
GRB2 0.031 0.005 -10000 0 -10000 0 0
response to radiation -0.018 0.12 -10000 0 -0.49 24 24
SHC/GRAP2 0.033 0.068 -10000 0 -0.4 10 10
PTPRO -0.019 0.12 -10000 0 -0.48 22 22
SH2B2 -0.016 0.11 -10000 0 -0.48 17 17
DOK1 0.026 0.055 -10000 0 -0.56 4 4
MATK -0.02 0.13 -10000 0 -0.49 22 22
CREBBP 0.037 0.038 -10000 0 -10000 0 0
BCL2 -0.013 0.26 -10000 0 -1.5 12 12
Aurora B signaling

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.01 0.079 -10000 0 -0.34 13 13
STMN1 -0.003 0.088 -10000 0 -0.31 32 32
Aurora B/RasGAP/Survivin 0.022 0.13 -10000 0 -0.42 31 31
Chromosomal passenger complex/Cul3 protein complex 0 0.096 -10000 0 -0.38 21 21
BIRC5 0.001 0.12 -10000 0 -0.42 32 32
DES -0.18 0.32 -10000 0 -0.64 134 134
Aurora C/Aurora B/INCENP 0.036 0.1 -10000 0 -0.4 15 15
Aurora B/TACC1 0.02 0.079 -10000 0 -0.26 30 30
Aurora B/PP2A 0.022 0.095 -10000 0 -0.31 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.007 0.03 -10000 0 -0.16 11 11
mitotic metaphase/anaphase transition -0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.008 0.1 -10000 0 -0.35 34 34
Cul3 protein complex 0.051 0.051 -10000 0 -0.35 5 5
KIF2C -0.001 0.11 -10000 0 -0.35 33 33
PEBP1 0.031 0.008 -10000 0 -10000 0 0
KIF20A 0 0.1 -10000 0 -0.41 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.019 0.09 -10000 0 -0.3 31 31
SEPT1 0.015 0.083 -10000 0 -0.41 16 16
SMC2 0.029 0.028 -10000 0 -0.56 1 1
SMC4 0.029 0.028 -10000 0 -0.56 1 1
NSUN2/NPM1/Nucleolin 0.016 0.18 0.28 1 -0.72 21 22
PSMA3 0.029 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -10000 0 -10000 0 0
H3F3B 0.004 0.065 -10000 0 -0.35 12 12
AURKB 0.002 0.12 -10000 0 -0.43 32 32
AURKC 0.021 0.073 -10000 0 -0.49 9 9
CDCA8 0.02 0.065 -10000 0 -0.36 13 13
cytokinesis -0.024 0.15 -10000 0 -0.53 31 31
Aurora B/Septin1 0.009 0.17 0.28 1 -0.53 31 32
AURKA 0.021 0.058 -10000 0 -0.35 11 11
INCENP 0.027 0.05 -10000 0 -0.58 3 3
KLHL13 0.022 0.07 -10000 0 -0.46 9 9
BUB1 -0.001 0.12 -10000 0 -0.42 31 31
hSgo1/Aurora B/Survivin 0 0.14 -10000 0 -0.43 36 36
EVI5 0.031 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.011 0.13 -10000 0 -0.45 28 28
SGOL1 0.006 0.085 -10000 0 -0.39 19 19
CENPA -0.009 0.11 -10000 0 -0.39 33 33
NCAPG 0.019 0.075 -10000 0 -0.41 13 13
Aurora B/HC8 Proteasome 0.021 0.09 -10000 0 -0.3 30 30
NCAPD2 0.029 0.028 -10000 0 -0.56 1 1
Aurora B/PP1-gamma 0.023 0.091 -10000 0 -0.3 31 31
RHOA 0.023 0.014 -10000 0 -10000 0 0
NCAPH 0.017 0.076 -10000 0 -0.39 15 15
NPM1 -0.007 0.11 -10000 0 -0.48 19 19
RASA1 0.028 0.01 -10000 0 -10000 0 0
KLHL9 0.03 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.089 -10000 0 -0.3 30 30
PPP1CC 0.031 0.005 -10000 0 -10000 0 0
Centraspindlin 0.024 0.15 -10000 0 -0.47 30 30
RhoA/GDP 0.017 0.011 -10000 0 -10000 0 0
NSUN2 -0.006 0.11 -10000 0 -0.47 20 20
MYLK -0.004 0.086 -10000 0 -0.37 20 20
KIF23 0.019 0.072 -10000 0 -0.37 15 15
VIM -0.009 0.1 -10000 0 -0.33 39 39
RACGAP1 0.03 0.026 -10000 0 -0.36 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.015 0.15 -10000 0 -0.59 23 23
Chromosomal passenger complex -0.001 0.13 -10000 0 -0.41 34 34
Chromosomal passenger complex/EVI5 0.059 0.15 -10000 0 -0.43 32 32
TACC1 0.027 0.029 -10000 0 -0.56 1 1
PPP2R5D 0.029 0.028 -10000 0 -0.56 1 1
CUL3 0.03 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.045 -10000 0 -0.41 5 5
MAP4K4 -0.002 0.1 -10000 0 -0.48 12 12
BAG4 0.029 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide -0.031 0.098 -10000 0 -0.24 59 59
NFKBIA 0.029 0.008 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.51 20 20
BAX -0.007 0.047 -10000 0 -0.29 7 7
RIPK1 0.03 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.084 0.94 3 -0.49 2 5
BAD -0.042 0.082 -10000 0 -0.23 52 52
SMPD1 0.003 0.068 0.25 6 -0.26 5 11
RB1 -0.04 0.085 0.16 2 -0.24 47 49
FADD/Caspase 8 0.004 0.11 -10000 0 -0.52 11 11
MAP2K4 -0.024 0.083 0.18 2 -0.28 19 21
NSMAF 0.029 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.04 0.093 0.19 1 -0.36 19 20
EGF -0.11 0.23 -10000 0 -0.45 135 135
mol:ceramide -0.043 0.09 0.17 2 -0.24 55 57
MADD 0.03 0.028 -10000 0 -0.56 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.012 0.035 -10000 0 -0.31 5 5
ASAH1 0.026 0.031 -10000 0 -0.34 3 3
negative regulation of cell cycle -0.04 0.084 0.16 2 -0.24 47 49
cell proliferation -0.028 0.1 -10000 0 -0.39 19 19
BID 0.005 0.12 -10000 0 -0.71 7 7
MAP3K1 -0.026 0.087 0.19 20 -0.23 40 60
EIF2A -0.027 0.088 0.33 7 -0.49 4 11
TRADD 0.028 0.039 -10000 0 -0.56 2 2
CRADD 0.029 0.028 -10000 0 -0.56 1 1
MAPK3 -0.034 0.087 -10000 0 -0.42 11 11
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.033 0.085 -10000 0 -0.41 10 10
Cathepsin D/ceramide -0.028 0.091 -10000 0 -0.23 57 57
FADD -0.002 0.1 -10000 0 -0.48 11 11
KSR1 -0.046 0.099 0.18 2 -0.26 51 53
MAPK8 -0.029 0.099 -10000 0 -0.32 27 27
PRKRA -0.034 0.089 0.18 9 -0.24 42 51
PDGFA 0.025 0.04 -10000 0 -0.56 2 2
TRAF2 0.028 0.039 -10000 0 -0.56 2 2
IGF1 0.004 0.11 -10000 0 -0.41 28 28
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.043 0.089 0.17 2 -0.24 55 57
CTSD 0.026 0.052 -10000 0 -0.42 6 6
regulation of nitric oxide biosynthetic process 0.046 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.029 0.11 -10000 0 -0.42 19 19
PRKCD 0.016 0.053 -10000 0 -0.34 9 9
PRKCZ 0.02 0.074 -10000 0 -0.53 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.012 0.035 -10000 0 -0.31 5 5
RelA/NF kappa B1 0.046 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.039 -10000 0 -0.56 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.002 0.11 -10000 0 -0.51 11 11
TNFR1A/BAG4/TNF-alpha 0.018 0.11 -10000 0 -0.35 26 26
mol:Sphingosine-1-phosphate 0.012 0.045 -10000 0 -0.41 5 5
MAP2K1 -0.039 0.087 -10000 0 -0.44 10 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.031 0.003 -10000 0 -10000 0 0
CYCS -0.012 0.048 0.16 3 -0.26 7 10
TNFRSF1A 0.031 0.006 -10000 0 -10000 0 0
NFKB1 0.031 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.042 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.03 0.093 0.33 7 -0.34 14 21
TNF-alpha/TNFR1A/FAN 0.018 0.11 -10000 0 -0.35 27 27
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.088 -10000 0 -0.5 8 8
MAP2K2 -0.041 0.085 -10000 0 -0.39 13 13
SMPD3 -0.002 0.093 0.2 2 -0.42 11 13
TNF -0.027 0.16 -10000 0 -0.46 54 54
PKC zeta/PAR4 0.034 0.068 -10000 0 -0.43 9 9
mol:PHOSPHOCHOLINE 0.033 0.098 0.23 65 -0.26 6 71
NF kappa B1/RelA/I kappa B alpha 0.076 0.062 -10000 0 -0.35 6 6
AIFM1 -0.018 0.056 0.16 2 -0.27 8 10
BCL2 0.018 0.086 -10000 0 -0.56 10 10
IL1-mediated signaling events

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.038 0.025 -10000 0 -0.24 3 3
PRKCZ 0.02 0.074 -10000 0 -0.53 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.048 0.14 -10000 0 -0.46 22 22
IRAK/TOLLIP 0.034 0.026 -10000 0 -0.33 1 1
IKBKB 0.029 0.009 -10000 0 -10000 0 0
IKBKG 0.027 0.048 -10000 0 -0.56 3 3
IL1 alpha/IL1R2 -0.082 0.18 -10000 0 -0.31 165 165
IL1A -0.007 0.12 -10000 0 -0.38 40 40
IL1B -0.02 0.12 -10000 0 -0.36 46 46
IRAK/TRAF6/p62/Atypical PKCs 0.052 0.061 -10000 0 -0.49 2 2
IL1R2 -0.1 0.21 -10000 0 -0.41 139 139
IL1R1 0.029 0.033 -10000 0 -0.45 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.019 0.11 -10000 0 -0.5 11 11
TOLLIP 0.031 0.003 -10000 0 -10000 0 0
TICAM2 0.023 0.04 -10000 0 -0.56 2 2
MAP3K3 0.031 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.02 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.08 0.37 1 -0.65 2 3
JUN -0.002 0.06 0.35 6 -0.35 1 7
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.036 0.12 -10000 0 -0.38 22 22
IL1 alpha/IL1R1/IL1RAP/MYD88 0.024 0.1 -10000 0 -0.36 14 14
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.033 0.098 -10000 0 -0.34 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.013 0.12 -10000 0 -0.39 27 27
NFKB1 0.031 0.004 -10000 0 -10000 0 0
MAPK8 0.007 0.057 0.37 6 -0.32 2 8
IRAK1 0.016 0.025 -10000 0 -0.36 1 1
IL1RN/IL1R1 0.014 0.1 -10000 0 -0.29 44 44
IRAK4 0.031 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.019 -10000 0 -0.34 1 1
TRAF6 0.03 0.028 -10000 0 -0.56 1 1
PI3K 0.037 0.042 -10000 0 -0.3 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.034 0.13 -10000 0 -0.44 23 23
CHUK 0.03 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.013 0.12 -10000 0 -0.39 27 27
IL1 beta/IL1R2 -0.077 0.18 -10000 0 -0.42 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0.04 0.028 -10000 0 -0.29 1 1
NF kappa B1 p50/RelA 0.025 0.11 -10000 0 -0.61 5 5
IRAK3 0.026 0.055 -10000 0 -0.56 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.032 0.11 -10000 0 -0.56 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.083 -10000 0 -0.38 14 14
IL1 alpha/IL1R1/IL1RAP 0.027 0.094 -10000 0 -0.35 12 12
RELA 0.031 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.014 -10000 0 -10000 0 0
MYD88 0.017 0.056 -10000 0 -0.56 4 4
IRAK/TRAF6/MEKK3 0.055 0.038 -10000 0 -0.31 1 1
IL1RAP 0.023 0.059 -10000 0 -0.44 7 7
UBE2N 0.031 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.009 0.089 -10000 0 -0.52 6 6
CASP1 0.02 0.082 -10000 0 -0.56 9 9
IL1RN/IL1R2 -0.084 0.18 -10000 0 -0.31 167 167
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.012 0.13 -10000 0 -0.4 28 28
TMEM189-UBE2V1 0.021 0.031 -10000 0 -0.34 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.033 0.12 -10000 0 -0.48 9 9
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
IL1RN -0.009 0.13 -10000 0 -0.4 43 43
TRAF6/TAK1/TAB1/TAB2 0.051 0.026 -10000 0 -10000 0 0
MAP2K6 0.024 0.056 0.37 7 -0.29 1 8
Class IB PI3K non-lipid kinase events

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.015 0.088 0.44 16 -10000 0 16
PI3K Class IB/PDE3B 0.015 0.088 -10000 0 -0.44 16 16
PDE3B 0.015 0.088 -10000 0 -0.44 16 16
Presenilin action in Notch and Wnt signaling

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.11 -10000 0 -0.6 4 4
HDAC1 0.028 0.008 -10000 0 -10000 0 0
AES 0.026 0.045 -10000 0 -0.44 4 4
FBXW11 0.024 0.014 -10000 0 -10000 0 0
DTX1 0.006 0.11 -10000 0 -0.48 22 22
LRP6/FZD1 0.029 0.074 -10000 0 -0.41 12 12
TLE1 0.028 0.028 -10000 0 -0.56 1 1
AP1 -0.033 0.13 -10000 0 -0.35 46 46
NCSTN 0.03 0.007 -10000 0 -10000 0 0
ADAM10 0.027 0.047 -10000 0 -0.56 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.13 -10000 0 -0.67 10 10
NICD/RBPSUH 0.034 0.1 -10000 0 -0.6 4 4
WIF1 0.003 0.088 -10000 0 -0.34 28 28
NOTCH1 0.013 0.1 -10000 0 -0.62 4 4
PSENEN 0.031 0.004 -10000 0 -10000 0 0
KREMEN2 -0.026 0.15 -10000 0 -0.42 56 56
DKK1 -0.034 0.17 -10000 0 -0.44 64 64
beta catenin/beta TrCP1 0.006 0.092 0.28 3 -0.39 8 11
APH1B 0.029 0.039 -10000 0 -0.56 2 2
APH1A 0.03 0.007 -10000 0 -10000 0 0
AXIN1 0.015 0.073 0.28 5 -0.38 5 10
CtBP/CBP/TCF1/TLE1/AES 0.003 0.087 -10000 0 -0.43 8 8
PSEN1 0.029 0.008 -10000 0 -10000 0 0
FOS -0.031 0.16 -10000 0 -0.44 59 59
JUN 0.024 0.058 -10000 0 -0.52 5 5
MAP3K7 0.029 0.008 -10000 0 -10000 0 0
CTNNB1 -0.006 0.11 0.28 7 -0.36 13 20
MAPK3 0.028 0.039 -10000 0 -0.56 2 2
DKK2/LRP6/Kremen 2 -0.044 0.17 -10000 0 -0.37 70 70
HNF1A -0.011 0.15 -10000 0 -0.56 32 32
CTBP1 0.03 0.006 -10000 0 -10000 0 0
MYC -0.007 0.23 -10000 0 -1.2 15 15
NKD1 -0.025 0.15 -10000 0 -0.42 56 56
FZD1 0.011 0.098 -10000 0 -0.56 13 13
NOTCH1 precursor/Deltex homolog 1 0.021 0.12 -10000 0 -0.56 5 5
apoptosis -0.033 0.12 -10000 0 -0.35 46 46
Delta 1/NOTCHprecursor 0.021 0.11 -10000 0 -0.59 4 4
DLL1 0.009 0.1 -10000 0 -0.5 17 17
PPARD -0.004 0.2 -10000 0 -0.97 18 18
Gamma Secretase 0.08 0.041 -10000 0 -0.31 2 2
APC 0.014 0.07 0.28 4 -0.36 4 8
DVL1 0.008 0.058 -10000 0 -0.35 7 7
CSNK2A1 0.031 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.016 0.15 -10000 0 -0.41 44 44
LRP6 0.031 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.014 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 -0.006 0.25 -10000 0 -1.5 13 13
WNT1 -0.012 0.14 -10000 0 -0.49 38 38
Axin1/APC/beta catenin 0.041 0.11 0.48 7 -0.47 4 11
DKK2 -0.073 0.21 -10000 0 -0.46 98 98
NOTCH1 precursor/DVL1 0.027 0.11 -10000 0 -0.62 5 5
GSK3B 0.029 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.025 -10000 0 -0.34 2 2
NOTCH/Deltex homolog 1 0.02 0.12 -10000 0 -0.57 5 5
PPP2R5D 0.026 0.12 0.31 18 -0.45 14 32
MAPK1 0.031 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.018 0.12 -10000 0 -0.33 33 33
RBPJ 0.031 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.009 -10000 0 -10000 0 0
PLK1 signaling events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.036 0.068 0.14 129 -0.17 1 130
BUB1B 0.012 0.055 0.18 9 -0.23 14 23
PLK1 0.01 0.033 0.13 11 -0.14 6 17
PLK1S1 0.013 0.027 0.15 5 -0.2 2 7
KIF2A 0.02 0.082 0.25 40 -0.24 6 46
regulation of mitotic centrosome separation 0.01 0.033 0.13 11 -0.14 6 17
GOLGA2 0.03 0.007 -10000 0 -10000 0 0
Hec1/SPC24 0.018 0.1 -10000 0 -0.32 34 34
WEE1 0.023 0.047 0.24 1 -0.66 1 2
cytokinesis 0.026 0.1 0.23 12 -0.42 10 22
PP2A-alpha B56 0.023 0.15 -10000 0 -0.64 19 19
AURKA 0.012 0.026 0.13 4 -0.14 3 7
PICH/PLK1 0.01 0.067 -10000 0 -0.38 10 10
CENPE 0 0.057 0.24 3 -0.22 20 23
RhoA/GTP 0.017 0.011 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.02 0.082 0.25 40 -0.24 6 46
PPP2CA 0.024 0.013 -10000 0 -10000 0 0
FZR1 0.027 0.048 -10000 0 -0.56 3 3
TPX2 0.013 0.029 0.15 5 -0.15 1 6
PAK1 0.031 0.004 -10000 0 -10000 0 0
SPC24 -0.005 0.14 -10000 0 -0.48 33 33
FBXW11 0.024 0.014 -10000 0 -10000 0 0
CLSPN -0.002 0.072 0.15 1 -0.27 28 29
GORASP1 0.023 0.014 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.019 20 -0.017 4 24
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.018 0.077 11 -0.071 6 17
G2 phase of mitotic cell cycle 0 0.003 0.019 2 -10000 0 2
STAG2 0.029 0.039 -10000 0 -0.56 2 2
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.47 127 127
spindle elongation 0.01 0.033 0.13 11 -0.14 6 17
ODF2 0.03 0.007 -10000 0 -10000 0 0
BUB1 0.003 0.15 -10000 0 -0.69 19 19
TPT1 0.009 0.036 0.14 3 -0.18 11 14
CDC25C 0 0.079 0.16 1 -0.36 17 18
CDC25B 0.028 0.04 -10000 0 -0.35 5 5
SGOL1 -0.036 0.068 0.17 1 -0.14 129 130
RHOA 0.023 0.014 -10000 0 -10000 0 0
CCNB1/CDK1 0.037 0.05 -10000 0 -0.37 3 3
CDC14B 0.008 0.02 -10000 0 -0.42 1 1
CDC20 0.012 0.084 -10000 0 -0.37 21 21
PLK1/PBIP1 0.009 0.033 0.11 4 -0.18 7 11
mitosis -0.002 0.003 0.022 1 -10000 0 1
FBXO5 0.006 0.041 0.16 8 -0.19 3 11
CDC2 0.001 0.002 -10000 0 -0.014 3 3
NDC80 0.019 0.077 -10000 0 -0.46 11 11
metaphase plate congression 0.006 0.058 0.16 1 -0.25 20 21
ERCC6L 0.016 0.064 -10000 0 -0.36 10 10
NLP/gamma Tubulin 0.007 0.027 0.11 7 -0.13 9 16
microtubule cytoskeleton organization 0.009 0.036 0.14 3 -0.18 11 14
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 2 -10000 0 2
PPP1R12A 0.031 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.018 0.072 -10000 0 -0.29 18 18
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.037 -10000 0 -10000 0 0
RAB1A 0.031 0.006 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.027 0.12 12 -0.1 8 20
mitotic prometaphase 0 0.004 0.018 17 -0.013 2 19
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.057 -10000 0 -0.44 5 5
microtubule-based process 0.005 0.066 0.21 1 -0.24 25 26
Golgi organization 0.01 0.033 0.13 11 -0.14 6 17
Cohesin/SA2 0.024 0.037 0.13 3 -0.26 3 6
PPP1CB/MYPT1 0.044 0.011 -10000 0 -10000 0 0
KIF20A 0 0.1 -10000 0 -0.4 26 26
APC/C/CDC20 0.02 0.06 0.17 3 -0.24 18 21
PPP2R1A 0.029 0.039 -10000 0 -0.56 2 2
chromosome segregation 0.009 0.032 0.11 4 -0.18 7 11
PRC1 0.029 0.03 -10000 0 -0.34 3 3
ECT2 0.011 0.053 0.22 15 -0.24 6 21
C13orf34 0.008 0.027 0.11 11 -0.11 6 17
NUDC 0.006 0.059 0.16 1 -0.25 20 21
regulation of attachment of spindle microtubules to kinetochore 0.012 0.055 0.18 9 -0.23 14 23
spindle assembly 0.009 0.031 0.12 12 -0.16 5 17
spindle stabilization 0.014 0.027 0.15 5 -0.2 2 7
APC/C/HCDH1 0.025 0.036 -10000 0 -0.35 4 4
MKLP2/PLK1 0.005 0.067 0.21 1 -0.25 25 26
CCNB1 0.021 0.058 -10000 0 -0.34 11 11
PPP1CB 0.031 0.006 -10000 0 -10000 0 0
BTRC 0.03 0.006 -10000 0 -10000 0 0
ROCK2 -0.016 0.084 -10000 0 -0.4 11 11
TUBG1 0.01 0.039 0.13 4 -0.27 7 11
G2/M transition of mitotic cell cycle 0.003 0.041 -10000 0 -0.36 3 3
MLF1IP 0.007 0.026 -10000 0 -0.3 3 3
INCENP 0.027 0.048 -10000 0 -0.56 3 3
FoxO family signaling

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.38 0.6 -10000 0 -1.4 114 114
PLK1 -0.034 0.22 -10000 0 -1.1 8 8
CDKN1B -0.001 0.13 0.49 1 -0.37 6 7
FOXO3 0.002 0.18 -10000 0 -0.76 15 15
KAT2B 0.024 0.025 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.095 0.19 0.42 1 -0.4 103 104
CAT -0.034 0.2 -10000 0 -0.95 9 9
CTNNB1 0.023 0.014 -10000 0 -10000 0 0
AKT1 0.006 0.059 -10000 0 -0.5 3 3
FOXO1 -0.12 0.2 0.5 1 -0.43 112 113
MAPK10 0.037 0.07 0.2 37 -0.31 5 42
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.078 0.097 0.35 18 -10000 0 18
response to oxidative stress -0.012 0.034 -10000 0 -0.25 2 2
FOXO3A/SIRT1 -0.006 0.18 -10000 0 -0.67 13 13
XPO1 0.031 0.006 -10000 0 -10000 0 0
EP300 -0.005 0.045 -10000 0 -0.34 1 1
BCL2L11 0.016 0.1 -10000 0 -0.9 5 5
FOXO1/SKP2 -0.094 0.18 0.38 1 -0.41 95 96
mol:GDP -0.012 0.034 -10000 0 -0.25 2 2
RAN 0.032 0.005 -10000 0 -10000 0 0
GADD45A 0.047 0.17 -10000 0 -0.72 14 14
YWHAQ 0.03 0.006 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.019 0.11 -10000 0 -0.62 8 8
MST1 -0.009 0.13 -10000 0 -0.45 33 33
CSNK1D 0.027 0.043 -10000 0 -0.49 3 3
CSNK1E 0.03 0.018 -10000 0 -0.34 1 1
FOXO4/14-3-3 family 0.001 0.12 -10000 0 -0.57 9 9
YWHAB 0.03 0.006 -10000 0 -10000 0 0
MAPK8 0.039 0.063 0.21 24 -0.3 3 27
MAPK9 0.026 0.049 0.22 12 -10000 0 12
YWHAG 0.028 0.01 -10000 0 -10000 0 0
YWHAE 0.031 0.005 -10000 0 -10000 0 0
YWHAZ 0.03 0.007 -10000 0 -10000 0 0
SIRT1 0.034 0.014 -10000 0 -10000 0 0
SOD2 -0.029 0.2 0.39 2 -0.67 20 22
RBL2 0.012 0.17 -10000 0 -0.96 5 5
RAL/GDP 0.031 0.031 -10000 0 -10000 0 0
CHUK 0.034 0.022 -10000 0 -10000 0 0
Ran/GTP 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.027 0.048 -10000 0 -0.56 3 3
RAL/GTP 0.036 0.03 -10000 0 -10000 0 0
CSNK1G1 0.031 0.003 -10000 0 -10000 0 0
FASLG -0.091 0.4 -10000 0 -1.5 30 30
SKP2 0.024 0.047 -10000 0 -0.45 4 4
USP7 0.031 0.007 -10000 0 -10000 0 0
IKBKB 0.033 0.021 -10000 0 -10000 0 0
CCNB1 -0.021 0.19 -10000 0 -0.86 8 8
FOXO1-3a-4/beta catenin 0.002 0.15 0.4 2 -0.42 7 9
proteasomal ubiquitin-dependent protein catabolic process -0.093 0.18 0.38 1 -0.4 95 96
CSNK1A1 0.024 0.013 -10000 0 -10000 0 0
SGK1 0.028 0.06 -10000 0 -0.58 4 4
CSNK1G3 0.025 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.012 -10000 0 -10000 0 0
ZFAND5 0.077 0.095 0.46 6 -10000 0 6
SFN -0.081 0.2 -10000 0 -0.41 118 118
CDK2 -0.013 0.054 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.006 0.13 -10000 0 -0.52 16 16
CREBBP -0.014 0.054 -10000 0 -10000 0 0
FBXO32 -0.025 0.18 -10000 0 -0.8 9 9
BCL6 0.004 0.19 -10000 0 -0.85 12 12
RALB 0.032 0.006 -10000 0 -10000 0 0
RALA 0.029 0.01 -10000 0 -10000 0 0
YWHAH 0.031 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.009 0.056 -10000 0 -0.28 12 12
epithelial cell differentiation 0.028 0.068 -10000 0 -0.3 12 12
CYFIP2 0.016 0.069 -10000 0 -0.53 7 7
ENAH 0.03 0.1 0.36 13 -0.38 5 18
EGFR 0.007 0.11 -10000 0 -0.51 18 18
EPHA2 0.023 0.06 -10000 0 -0.49 6 6
MYO6 0.049 0.1 0.4 9 -0.3 13 22
CTNNB1 0.023 0.014 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.04 0.054 -10000 0 -0.35 6 6
AQP5 0.019 0.097 -10000 0 -0.52 5 5
CTNND1 0.031 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.048 0.11 0.42 8 -0.28 14 22
regulation of calcium-dependent cell-cell adhesion 0.026 0.14 0.38 7 -0.34 33 40
EGF -0.11 0.23 -10000 0 -0.45 135 135
NCKAP1 0.03 0.007 -10000 0 -10000 0 0
AQP3 -0.001 0.16 -10000 0 -0.56 25 25
cortical microtubule organization 0.028 0.068 -10000 0 -0.3 12 12
GO:0000145 0.036 0.1 0.39 9 -0.27 14 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.071 -10000 0 -0.3 12 12
MLLT4 0.029 0.009 -10000 0 -10000 0 0
ARF6/GDP -0.009 0.068 -10000 0 -0.48 6 6
ARF6 0.029 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.075 -10000 0 -0.38 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.028 0.083 0.29 2 -0.3 2 4
PVRL2 0.028 0.039 -10000 0 -0.56 2 2
ZYX 0.037 0.093 0.36 4 -0.29 14 18
ARF6/GTP 0.066 0.072 -10000 0 -0.38 7 7
CDH1 0.005 0.12 -10000 0 -0.5 22 22
EGFR/EGFR/EGF/EGF -0.048 0.14 -10000 0 -0.32 60 60
RhoA/GDP 0.03 0.066 -10000 0 -0.28 12 12
actin cytoskeleton organization 0.038 0.096 0.34 8 -0.3 10 18
IGF-1R heterotetramer 0.027 0.047 -10000 0 -0.56 3 3
GIT1 0.028 0.039 -10000 0 -0.56 2 2
IGF1R 0.027 0.048 -10000 0 -0.56 3 3
IGF1 0.004 0.11 -10000 0 -0.41 28 28
DIAPH1 0.031 0.12 -10000 0 -0.69 8 8
Wnt receptor signaling pathway -0.028 0.068 0.3 12 -10000 0 12
RHOA 0.023 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.009 0.069 -10000 0 -0.51 6 6
CTNNA1 0.024 0.013 -10000 0 -10000 0 0
VCL 0.039 0.097 0.34 8 -0.3 10 18
EFNA1 0.021 0.069 -10000 0 -0.53 7 7
LPP 0.032 0.095 0.37 4 -0.31 11 15
Ephrin A1/EPHA2 0.019 0.084 -10000 0 -0.41 11 11
SEC6/SEC8 -0.001 0.058 -10000 0 -0.52 2 2
MGAT3 0.026 0.14 0.39 7 -0.35 33 40
HGF/MET 0.005 0.099 -10000 0 -0.42 10 10
HGF -0.011 0.13 -10000 0 -0.44 38 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.057 -10000 0 -0.28 12 12
actin cable formation 0.073 0.13 0.28 72 -0.38 4 76
KIAA1543 0.032 0.11 0.33 8 -0.34 15 23
KIFC3 0.038 0.099 -10000 0 -0.32 15 15
NCK1 0.03 0.006 -10000 0 -10000 0 0
EXOC3 0.024 0.047 -10000 0 -0.45 4 4
ACTN1 0.042 0.1 0.47 5 -0.31 11 16
NCK1/GIT1 0.042 0.032 -10000 0 -0.41 2 2
mol:GDP 0.028 0.068 -10000 0 -0.3 12 12
EXOC4 0.028 0.01 -10000 0 -10000 0 0
STX4 0.04 0.092 -10000 0 -0.29 14 14
PIP5K1C 0.048 0.11 0.43 8 -0.28 14 22
LIMA1 0.029 0.025 -10000 0 -0.34 2 2
ABI1 0.031 0.004 -10000 0 -10000 0 0
ROCK1 0.049 0.12 0.39 15 -0.44 6 21
adherens junction assembly 0.042 0.16 0.45 14 -0.63 11 25
IGF-1R heterotetramer/IGF1 0.014 0.083 -10000 0 -0.38 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.033 -10000 0 -0.41 2 2
MET 0.023 0.054 -10000 0 -0.47 5 5
PLEKHA7 0.043 0.11 0.36 7 -0.35 17 24
mol:GTP 0.058 0.074 -10000 0 -0.38 9 9
establishment of epithelial cell apical/basal polarity 0.062 0.14 0.37 43 -0.71 2 45
cortical actin cytoskeleton stabilization 0.009 0.056 -10000 0 -0.28 12 12
regulation of cell-cell adhesion 0.038 0.096 0.34 8 -0.3 10 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.057 -10000 0 -0.28 12 12
Ras signaling in the CD4+ TCR pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.015 0.2 0.36 1 -0.67 26 27
MAP3K8 0.026 0.046 -10000 0 -0.45 4 4
FOS -0.017 0.18 0.3 1 -0.73 21 22
PRKCA 0.023 0.046 -10000 0 -0.39 5 5
PTPN7 -0.005 0.12 -10000 0 -0.44 29 29
HRAS 0.027 0.047 -10000 0 -0.56 3 3
PRKCB 0.01 0.099 -10000 0 -0.52 15 15
NRAS 0.03 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.035 -10000 0 -0.32 3 3
MAPK3 -0.015 0.17 -10000 0 -0.7 23 23
MAP2K1 -0.002 0.11 -10000 0 -0.56 13 13
ELK1 0.026 0.029 -10000 0 -0.34 2 2
BRAF 0.006 0.094 -10000 0 -0.49 14 14
mol:GTP 0 0.002 -10000 0 -0.004 64 64
MAPK1 -0.015 0.17 -10000 0 -0.7 23 23
RAF1 -0.003 0.1 -10000 0 -0.56 13 13
KRAS 0.03 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.028 0.033 -10000 0 -0.45 2 2
SVIL 0.031 0.004 -10000 0 -10000 0 0
ZNF318 0.03 0.006 -10000 0 -10000 0 0
JMJD2C -0.001 0.013 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.038 0.14 -10000 0 -0.37 58 58
CARM1 0.029 0.039 -10000 0 -0.56 2 2
PRDX1 0.03 0.006 -10000 0 -10000 0 0
PELP1 0.031 0.005 -10000 0 -10000 0 0
CTNNB1 0.023 0.014 -10000 0 -10000 0 0
AKT1 0.027 0.039 -10000 0 -0.56 2 2
PTK2B 0.028 0.02 -10000 0 -0.34 1 1
MED1 0.031 0.005 -10000 0 -10000 0 0
MAK 0.015 0.094 -10000 0 -0.56 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.022 0.062 -10000 0 -0.56 5 5
GSN 0.026 0.048 -10000 0 -0.56 3 3
NCOA2 0.005 0.12 -10000 0 -0.56 19 19
NCOA6 0.03 0.006 -10000 0 -10000 0 0
DNA-PK 0.056 0.021 -10000 0 -10000 0 0
NCOA4 0.031 0.005 -10000 0 -10000 0 0
PIAS3 0.03 0.006 -10000 0 -10000 0 0
cell proliferation -0.036 0.17 -10000 0 -0.67 27 27
XRCC5 0.03 0.007 -10000 0 -10000 0 0
UBE3A 0.031 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.059 0.17 -10000 0 -0.41 75 75
FHL2 -0.058 0.24 -10000 0 -0.9 31 31
RANBP9 0.03 0.006 -10000 0 -10000 0 0
JMJD1A -0.022 0.058 -10000 0 -0.15 60 60
CDK6 0.025 0.038 -10000 0 -0.42 3 3
TGFB1I1 0.019 0.079 -10000 0 -0.54 9 9
T-DHT/AR/CyclinD1 -0.047 0.16 -10000 0 -0.39 66 66
XRCC6 0.031 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.055 0.17 -10000 0 -0.37 73 73
CTDSP1 0.027 0.039 -10000 0 -0.56 2 2
CTDSP2 0.031 0.005 -10000 0 -10000 0 0
BRCA1 0.027 0.046 -10000 0 -0.45 4 4
TCF4 0.019 0.082 -10000 0 -0.56 9 9
CDKN2A 0.005 0.11 -10000 0 -0.47 22 22
SRF 0.025 0.048 -10000 0 -0.56 1 1
NKX3-1 -0.082 0.21 -10000 0 -0.7 32 32
KLK3 0.006 0.042 0.19 6 -0.22 2 8
TMF1 0.024 0.03 -10000 0 -0.56 1 1
HNRNPA1 0.031 0.005 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 0.012 0.029 -10000 0 -0.41 2 2
T-DHT/AR/Caspase 8 -0.038 0.14 -10000 0 -0.37 57 57
AR -0.069 0.2 -10000 0 -0.57 58 58
UBA3 0.025 0.013 -10000 0 -10000 0 0
PATZ1 0.031 0.005 -10000 0 -10000 0 0
PAWR 0.028 0.039 -10000 0 -0.56 2 2
PRKDC 0.029 0.008 -10000 0 -10000 0 0
PA2G4 0.031 0.005 -10000 0 -10000 0 0
UBE2I 0.03 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.035 0.13 -10000 0 -0.34 60 60
RPS6KA3 0.029 0.033 -10000 0 -0.45 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.37 58 58
LATS2 0.031 0.005 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.34 59 59
Cyclin D3/CDK11 p58 0.021 0.021 -10000 0 -0.41 1 1
VAV3 0.011 0.1 -10000 0 -0.56 15 15
KLK2 -0.035 0.093 -10000 0 -0.44 11 11
CASP8 0.03 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.037 0.17 -10000 0 -0.4 64 64
TMPRSS2 -0.18 0.36 -10000 0 -0.86 87 87
CCND1 0.017 0.09 -10000 0 -0.56 11 11
PIAS1 0.031 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.032 -10000 0 -0.19 1 1
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.029 0.039 -10000 0 -0.56 2 2
T-DHT/AR/CDK6 -0.036 0.14 -10000 0 -0.38 53 53
CMTM2 0.005 0.11 -10000 0 -0.43 25 25
SNURF -0.004 0.14 -10000 0 -0.56 27 27
ZMIZ1 0.006 0.046 -10000 0 -10000 0 0
CCND3 0.029 0.028 -10000 0 -0.56 1 1
TGIF1 0.03 0.018 -10000 0 -0.34 1 1
FKBP4 0.031 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.023 0.067 -10000 0 -0.56 6 6
ANTXR2 0.024 0.067 -10000 0 -0.56 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.012 -10000 0 -0.076 11 11
monocyte activation -0.054 0.18 -10000 0 -0.45 67 67
MAP2K2 0.008 0.086 -10000 0 -0.68 7 7
MAP2K1 -0.002 0.011 -10000 0 -10000 0 0
MAP2K7 -0.004 0.022 -10000 0 -0.3 2 2
MAP2K6 -0.003 0.021 0.098 1 -0.28 2 3
CYAA -0.01 0.05 -10000 0 -0.33 10 10
MAP2K4 -0.002 0.011 0.12 1 -10000 0 1
IL1B -0.022 0.089 0.24 5 -0.25 45 50
Channel 0.03 0.061 -10000 0 -0.35 10 10
NLRP1 -0.007 0.042 0.12 1 -0.26 11 12
CALM1 0.029 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.013 0.1 -10000 0 -0.4 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.012 0.076 11 -10000 0 11
MAPK3 -0.003 0.023 0.12 2 -0.3 2 4
MAPK1 -0.002 0.011 -10000 0 -10000 0 0
PGR -0.02 0.068 -10000 0 -0.24 35 35
PA/Cellular Receptors 0.031 0.066 -10000 0 -0.38 10 10
apoptosis -0.002 0.012 -10000 0 -0.076 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.057 -10000 0 -0.32 11 11
macrophage activation -0.003 0.022 -10000 0 -0.29 2 2
TNF -0.027 0.16 -10000 0 -0.46 54 54
VCAM1 -0.054 0.18 -10000 0 -0.44 75 75
platelet activation -0.013 0.1 -10000 0 -0.4 30 30
MAPKKK cascade -0.002 0.024 0.16 3 -0.14 3 6
IL18 -0.009 0.065 -10000 0 -0.32 15 15
negative regulation of macrophage activation -0.002 0.012 -10000 0 -0.076 11 11
LEF -0.002 0.012 -10000 0 -0.076 11 11
CASP1 -0.003 0.041 -10000 0 -0.2 13 13
mol:cAMP -0.013 0.1 -10000 0 -0.4 30 30
necrosis -0.002 0.012 -10000 0 -0.076 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.029 0.057 -10000 0 -0.33 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.004 0.17 -10000 0 -0.8 15 15
UGCG -0.003 0.14 -10000 0 -0.61 20 20
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.17 0.3 1 -0.6 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.002 0.14 -10000 0 -0.59 21 21
mol:DAG -0.013 0.15 -10000 0 -0.9 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.18 0.29 1 -0.62 23 24
FRAP1 0.005 0.22 0.31 1 -0.76 25 26
FOXO3 0.008 0.2 0.29 2 -0.79 20 22
AKT1 0.004 0.23 0.3 2 -0.89 21 23
GAB2 0.031 0.018 -10000 0 -0.34 1 1
SMPD1 0.022 0.047 -10000 0 -0.7 1 1
SGMS1 0.003 0.15 -10000 0 -0.84 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.031 -10000 0 -0.35 2 2
CALM1 0.029 0.008 -10000 0 -10000 0 0
cell proliferation 0.004 0.16 0.27 1 -0.73 15 16
EIF3A 0.03 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.043 -10000 0 -0.29 6 6
RPS6KB1 0.007 0.12 -10000 0 -1.1 5 5
mol:sphingomyelin -0.013 0.15 -10000 0 -0.9 12 12
natural killer cell activation 0 0.002 -10000 0 -0.011 1 1
JAK3 0.01 0.11 -10000 0 -0.52 20 20
PIK3R1 0.025 0.053 -10000 0 -0.41 6 6
JAK1 0.033 0.007 -10000 0 -10000 0 0
NFKB1 0.031 0.004 -10000 0 -10000 0 0
MYC 0.014 0.2 0.37 3 -0.88 16 19
MYB -0.036 0.26 -10000 0 -1.3 16 16
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.001 0.22 -10000 0 -0.87 21 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.12 -10000 0 -0.96 5 5
mol:PI-3-4-5-P3 0.002 0.21 -10000 0 -0.82 21 21
Rac1/GDP 0.024 0.031 -10000 0 -0.32 2 2
T cell proliferation 0.004 0.19 0.27 4 -0.73 22 26
SHC1 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.028 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.015 -10000 0 -0.042 50 50
PRKCZ 0 0.2 -10000 0 -0.78 22 22
NF kappa B1 p50/RelA 0.034 0.18 0.3 1 -0.65 21 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.009 0.19 -10000 0 -0.77 22 22
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
RELA 0.031 0.003 -10000 0 -10000 0 0
IL2RA -0.029 0.16 -10000 0 -0.43 60 60
IL2RB 0.008 0.12 -10000 0 -0.52 21 21
TERT -0.016 0.11 -10000 0 -0.34 49 49
E2F1 0.003 0.1 -10000 0 -0.45 18 18
SOS1 0.031 0.006 -10000 0 -10000 0 0
RPS6 0.028 0.031 -10000 0 -0.34 3 3
mol:cAMP 0 0.007 0.02 49 -10000 0 49
PTPN11 0.031 0.005 -10000 0 -10000 0 0
IL2RG -0.003 0.13 -10000 0 -0.45 35 35
actin cytoskeleton organization 0.004 0.19 0.27 4 -0.73 22 26
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.016 0.064 -10000 0 -0.34 14 14
PIK3CA 0.032 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.048 0.04 -10000 0 -0.3 2 2
LCK 0.006 0.12 -10000 0 -0.48 24 24
BCL2 0.006 0.2 -10000 0 -0.79 22 22
Caspase cascade in apoptosis

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.005 0.11 -10000 0 -0.5 17 17
ACTA1 -0.023 0.12 -10000 0 -0.52 20 20
NUMA1 0.003 0.12 -10000 0 -0.58 15 15
SPTAN1 -0.018 0.12 -10000 0 -0.53 19 19
LIMK1 -0.002 0.13 0.29 2 -0.53 16 18
BIRC3 0.008 0.11 -10000 0 -0.51 20 20
BIRC2 0.031 0.004 -10000 0 -10000 0 0
BAX 0.029 0.039 -10000 0 -0.56 2 2
CASP10 -0.012 0.088 -10000 0 -0.45 14 14
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.031 0.003 -10000 0 -10000 0 0
PTK2 0.001 0.12 -10000 0 -0.51 17 17
DIABLO 0.031 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.018 0.12 -10000 0 -0.52 19 19
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.028 -10000 0 -0.56 1 1
GSN -0.019 0.12 -10000 0 -0.52 20 20
MADD 0.03 0.028 -10000 0 -0.56 1 1
TFAP2A -0.094 0.29 -10000 0 -0.7 75 75
BID -0.001 0.058 -10000 0 -0.3 13 13
MAP3K1 0.007 0.045 -10000 0 -0.27 3 3
TRADD 0.028 0.039 -10000 0 -0.56 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.044 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.017 0.12 -10000 0 -0.54 20 20
CASP9 0.03 0.007 -10000 0 -10000 0 0
DNA repair -0.001 0.062 0.28 14 -0.18 6 20
neuron apoptosis 0.013 0.14 -10000 0 -0.74 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.006 0.13 -10000 0 -0.58 17 17
APAF1 0.031 0.005 -10000 0 -10000 0 0
CASP6 0.013 0.15 -10000 0 -0.8 11 11
TRAF2 0.028 0.039 -10000 0 -0.56 2 2
ICAD/CAD -0.018 0.12 0.27 1 -0.5 20 21
CASP7 0 0.074 0.3 10 -0.39 4 14
KRT18 0.022 0.041 -10000 0 -0.54 1 1
apoptosis -0.011 0.12 -10000 0 -0.57 17 17
DFFA -0.018 0.12 -10000 0 -0.52 19 19
DFFB -0.019 0.12 -10000 0 -0.52 20 20
PARP1 0.001 0.063 0.19 5 -0.28 14 19
actin filament polymerization -0.001 0.12 0.51 14 -0.28 2 16
TNF -0.027 0.16 -10000 0 -0.46 54 54
CYCS 0.008 0.058 0.16 5 -0.29 10 15
SATB1 0.009 0.14 -10000 0 -0.75 12 12
SLK -0.019 0.11 -10000 0 -0.51 19 19
p15 BID/BAX 0.015 0.074 -10000 0 -0.36 11 11
CASP2 0.012 0.11 0.22 32 -0.46 8 40
JNK cascade -0.007 0.045 0.27 3 -10000 0 3
CASP3 -0.019 0.12 -10000 0 -0.54 20 20
LMNB2 0.027 0.13 0.31 8 -0.56 13 21
RIPK1 0.03 0.006 -10000 0 -10000 0 0
CASP4 0.031 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.062 0.077 -10000 0 -0.32 15 15
negative regulation of DNA binding -0.092 0.28 -10000 0 -0.68 75 75
stress fiber formation -0.019 0.11 -10000 0 -0.5 19 19
GZMB -0.01 0.11 -10000 0 -0.39 31 31
CASP1 0.012 0.05 -10000 0 -0.35 9 9
LMNB1 0.02 0.12 0.31 4 -0.5 11 15
APP 0.013 0.14 -10000 0 -0.76 13 13
TNFRSF1A 0.031 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM -0.009 0.13 -10000 0 -0.58 17 17
LMNA 0.024 0.14 0.3 9 -0.56 14 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.001 0.099 -10000 0 -0.47 9 9
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.02 0.12 0.3 1 -0.54 18 19
APAF-1/Caspase 9 -0.003 0.14 -10000 0 -0.64 19 19
nuclear fragmentation during apoptosis 0.004 0.12 -10000 0 -0.56 15 15
CFL2 0 0.12 0.28 2 -0.53 14 16
GAS2 -0.038 0.13 0.29 1 -0.52 23 24
positive regulation of apoptosis 0.027 0.13 0.29 8 -0.57 12 20
PRF1 0.015 0.093 -10000 0 -0.53 13 13
FAS signaling pathway (CD95)

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.002 0.054 0.29 11 -0.41 1 12
RFC1 0.003 0.049 0.3 10 -10000 0 10
PRKDC 0.005 0.058 0.31 13 -10000 0 13
RIPK1 0.032 0.007 -10000 0 -10000 0 0
CASP7 -0.007 0.099 -10000 0 -0.62 10 10
FASLG/FAS/FADD/FAF1 -0.016 0.078 0.22 3 -0.31 19 22
MAP2K4 -0.043 0.17 0.26 5 -0.49 32 37
mol:ceramide -0.028 0.12 -10000 0 -0.42 24 24
GSN 0 0.06 0.29 11 -0.41 3 14
FASLG/FAS/FADD/FAF1/Caspase 8 -0.022 0.096 -10000 0 -0.38 19 19
FAS 0.019 0.051 -10000 0 -0.56 3 3
BID -0.014 0.032 0.27 5 -10000 0 5
MAP3K1 -0.012 0.13 0.36 4 -0.52 15 19
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
RB1 0.002 0.055 0.29 11 -10000 0 11
CFLAR 0.029 0.04 -10000 0 -0.56 2 2
HGF/MET 0.024 0.11 -10000 0 -0.38 22 22
ARHGDIB 0.003 0.069 0.33 14 -0.31 2 16
FADD 0.023 0.019 -10000 0 -10000 0 0
actin filament polymerization 0.001 0.062 0.41 3 -0.29 11 14
NFKB1 -0.024 0.11 -10000 0 -0.8 4 4
MAPK8 -0.076 0.21 0.32 3 -0.5 69 72
DFFA 0.001 0.043 0.28 8 -10000 0 8
DNA fragmentation during apoptosis -0.001 0.049 0.28 8 -0.41 1 9
FAS/FADD/MET 0.041 0.057 -10000 0 -0.36 6 6
CFLAR/RIP1 0.045 0.033 -10000 0 -0.41 2 2
FAIM3 0.024 0.063 -10000 0 -0.47 7 7
FAF1 0.021 0.021 -10000 0 -10000 0 0
PARP1 0.001 0.047 0.29 9 -10000 0 9
DFFB 0 0.047 0.28 8 -0.41 1 9
CHUK -0.023 0.1 -10000 0 -0.73 4 4
FASLG -0.031 0.15 -10000 0 -0.44 52 52
FAS/FADD 0.029 0.048 -10000 0 -0.42 3 3
HGF -0.011 0.13 -10000 0 -0.44 38 38
LMNA -0.003 0.054 0.41 3 -0.35 2 5
CASP6 0.003 0.049 0.3 10 -10000 0 10
CASP10 0.022 0.018 -10000 0 -10000 0 0
CASP3 0.006 0.061 0.35 12 -10000 0 12
PTPN13 0.025 0.061 -10000 0 -0.56 5 5
CASP8 -0.015 0.045 0.35 6 -10000 0 6
IL6 -0.21 0.48 -10000 0 -1.3 70 70
MET 0.023 0.054 -10000 0 -0.47 5 5
ICAD/CAD 0 0.045 0.34 4 -0.39 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.028 0.12 -10000 0 -0.42 24 24
activation of caspase activity by cytochrome c -0.013 0.032 0.27 5 -10000 0 5
PAK2 0.005 0.071 0.36 13 -10000 0 13
BCL2 0.018 0.086 -10000 0 -0.56 10 10
Syndecan-3-mediated signaling events

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.031 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.017 0.12 -10000 0 -0.48 7 7
Syndecan-3/Neurocan 0.013 0.09 -10000 0 -0.4 18 18
POMC 0.015 0.09 -10000 0 -0.48 14 14
EGFR 0.007 0.11 -10000 0 -0.51 18 18
Syndecan-3/EGFR 0.008 0.099 -10000 0 -0.42 15 15
AGRP 0.021 0.043 -10000 0 -0.34 6 6
NCSTN 0.03 0.007 -10000 0 -10000 0 0
PSENEN 0.031 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.029 0.039 -10000 0 -0.56 2 2
APH1A 0.03 0.007 -10000 0 -10000 0 0
NCAN 0.017 0.064 -10000 0 -0.34 14 14
long-term memory 0.036 0.089 -10000 0 -0.4 13 13
Syndecan-3/IL8 -0.022 0.13 -10000 0 -0.43 19 19
PSEN1 0.029 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.043 0.031 -10000 0 -0.41 2 2
FYN 0.025 0.048 -10000 0 -0.56 3 3
limb bud formation 0.002 0.081 -10000 0 -0.4 17 17
MC4R 0.012 0.061 -10000 0 -0.34 13 13
SRC 0.028 0.039 -10000 0 -0.56 2 2
PTN -0.031 0.16 -10000 0 -0.47 54 54
FGFR/FGF/Syndecan-3 0.002 0.081 -10000 0 -0.41 17 17
neuron projection morphogenesis -0.003 0.12 0.32 1 -0.56 5 6
Syndecan-3/AgRP 0.014 0.087 -10000 0 -0.4 18 18
Syndecan-3/AgRP/MC4R 0.023 0.094 -10000 0 -0.39 18 18
Fyn/Cortactin 0.041 0.034 -10000 0 -0.41 2 2
SDC3 0.002 0.082 -10000 0 -0.41 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.022 0.12 -10000 0 -0.43 19 19
IL8 -0.057 0.18 -10000 0 -0.41 92 92
Syndecan-3/Fyn/Cortactin 0.037 0.091 -10000 0 -0.41 13 13
Syndecan-3/CASK -0.001 0.08 -10000 0 -0.38 18 18
alpha-MSH/MC4R 0.018 0.083 -10000 0 -0.31 26 26
Gamma Secretase 0.08 0.041 -10000 0 -0.3 2 2
IL2 signaling events mediated by STAT5

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.031 0.018 -10000 0 -0.34 1 1
ELF1 -0.003 0.11 -10000 0 -0.35 29 29
CCNA2 0.023 0.056 -10000 0 -0.37 9 9
PIK3CA 0.031 0.007 -10000 0 -10000 0 0
JAK3 0.008 0.11 -10000 0 -0.52 20 20
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
JAK1 0.031 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.002 0.2 -10000 0 -0.81 21 21
SHC1 0.03 0.007 -10000 0 -10000 0 0
SP1 0.029 0.062 -10000 0 -0.39 9 9
IL2RA -0.049 0.21 -10000 0 -0.52 63 63
IL2RB 0.007 0.12 -10000 0 -0.52 21 21
SOS1 0.031 0.006 -10000 0 -10000 0 0
IL2RG -0.004 0.13 -10000 0 -0.45 35 35
G1/S transition of mitotic cell cycle 0.021 0.16 0.4 4 -0.96 10 14
PTPN11 0.031 0.005 -10000 0 -10000 0 0
CCND2 0.009 0.11 -10000 0 -0.83 8 8
LCK 0.004 0.12 -10000 0 -0.48 24 24
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.016 0.064 -10000 0 -0.34 14 14
CDK6 0.025 0.038 -10000 0 -0.42 3 3
CCND3 0.008 0.16 -10000 0 -0.72 16 16
E-cadherin signaling events

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.024 0.093 -9999 0 -0.38 19 19
E-cadherin/beta catenin 0.014 0.088 -9999 0 -0.36 22 22
CTNNB1 0.023 0.014 -9999 0 -10000 0 0
JUP 0.024 0.061 -9999 0 -0.56 5 5
CDH1 0.005 0.12 -9999 0 -0.5 22 22
Syndecan-2-mediated signaling events

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.016 0.075 -10000 0 -0.4 10 10
EPHB2 0.005 0.11 -10000 0 -0.43 26 26
Syndecan-2/TACI -0.014 0.11 -10000 0 -0.35 29 29
LAMA1 -0.016 0.16 -10000 0 -0.53 39 39
Syndecan-2/alpha2 ITGB1 0.044 0.072 -10000 0 -0.3 10 10
HRAS 0.027 0.048 -10000 0 -0.56 3 3
Syndecan-2/CASK 0.01 0.027 -10000 0 -0.31 3 3
ITGA5 0.023 0.067 -10000 0 -0.56 6 6
BAX 0.006 0.088 -10000 0 -1.3 2 2
EPB41 0.024 0.051 -10000 0 -0.38 7 7
positive regulation of cell-cell adhesion 0.028 0.032 -10000 0 -0.42 2 2
LAMA3 0.01 0.092 -10000 0 -0.38 23 23
EZR 0.028 0.02 -10000 0 -0.34 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.043 -10000 0 -0.49 3 3
Syndecan-2/MMP2 0.02 0.065 -10000 0 -0.37 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.059 -10000 0 -0.41 7 7
dendrite morphogenesis 0.018 0.069 -10000 0 -0.35 12 12
Syndecan-2/GM-CSF 0.013 0.049 -10000 0 -0.38 2 2
determination of left/right symmetry 0.013 0.032 -10000 0 -0.37 3 3
Syndecan-2/PKC delta 0.019 0.043 -10000 0 -0.37 2 2
GNB2L1 0.022 0.041 -10000 0 -0.56 2 2
MAPK3 0.007 0.056 -10000 0 -0.57 2 2
MAPK1 0.009 0.048 -10000 0 -0.34 2 2
Syndecan-2/RACK1 0.033 0.063 -10000 0 -0.64 3 3
NF1 0.031 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.032 -10000 0 -0.37 3 3
ITGA2 0.019 0.074 -10000 0 -0.53 8 8
MAPK8 0.012 0.046 -10000 0 -0.41 5 5
Syndecan-2/alpha2/beta1 Integrin 0.029 0.11 -10000 0 -0.33 32 32
Syndecan-2/Kininogen -0.053 0.13 -10000 0 -0.35 46 46
ITGB1 0.031 0.004 -10000 0 -10000 0 0
SRC 0.051 0.094 0.35 1 -0.62 4 5
Syndecan-2/CASK/Protein 4.1 0.025 0.039 -10000 0 -0.33 3 3
extracellular matrix organization 0.026 0.059 -10000 0 -0.42 7 7
actin cytoskeleton reorganization 0.016 0.075 -10000 0 -0.4 10 10
Syndecan-2/Caveolin-2/Ras 0.041 0.057 -10000 0 -0.48 4 4
Syndecan-2/Laminin alpha3 0.02 0.06 -10000 0 -0.35 5 5
Syndecan-2/RasGAP 0.044 0.064 -10000 0 -0.62 3 3
alpha5/beta1 Integrin 0.039 0.052 -10000 0 -0.41 6 6
PRKCD 0.016 0.053 -10000 0 -0.34 9 9
Syndecan-2 dimer 0.018 0.07 -10000 0 -0.35 12 12
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.052 0.082 -10000 0 -0.68 3 3
RHOA 0.023 0.014 -10000 0 -10000 0 0
SDCBP 0.029 0.019 -10000 0 -0.34 1 1
TNFRSF13B -0.044 0.17 -10000 0 -0.43 73 73
RASA1 0.028 0.01 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.034 0.059 -10000 0 -0.41 7 7
Syndecan-2/Synbindin 0.031 0.03 -10000 0 -0.37 2 2
TGFB1 0.023 0.069 -10000 0 -0.53 7 7
CASP3 0.015 0.05 -10000 0 -0.42 2 2
FN1 0.004 0.11 -10000 0 -0.42 27 27
Syndecan-2/IL8 -0.022 0.12 -10000 0 -0.35 31 31
SDC2 0.013 0.032 -10000 0 -0.37 3 3
KNG1 -0.11 0.21 -10000 0 -0.41 145 145
Syndecan-2/Neurofibromin 0.031 0.026 -10000 0 -0.4 1 1
TRAPPC4 0.031 0.004 -10000 0 -10000 0 0
CSF2 0.006 0.069 -10000 0 -0.34 17 17
Syndecan-2/TGFB1 0.026 0.059 -10000 0 -0.42 7 7
Syndecan-2/Syntenin/PI-4-5-P2 0.028 0.032 -10000 0 -0.42 2 2
Syndecan-2/Ezrin 0.033 0.038 -10000 0 -0.34 2 2
PRKACA 0.024 0.035 -10000 0 -0.37 1 1
angiogenesis -0.022 0.12 -10000 0 -0.34 31 31
MMP2 0.01 0.095 -10000 0 -0.4 22 22
IL8 -0.057 0.18 -10000 0 -0.41 92 92
calcineurin-NFAT signaling pathway -0.014 0.11 -10000 0 -0.35 29 29
ceramide signaling pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0 0.12 -10000 0 -0.53 15 15
BAG4 0.029 0.009 -10000 0 -10000 0 0
BAD 0.007 0.063 0.34 4 -0.31 5 9
NFKBIA 0.029 0.008 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.51 20 20
BAX 0.008 0.061 0.25 9 -0.37 3 12
EnzymeConsortium:3.1.4.12 0.004 0.034 0.11 7 -0.11 16 23
IKBKB 0.005 0.12 0.34 3 -0.49 15 18
MAP2K2 0.006 0.078 0.29 7 -0.42 6 13
MAP2K1 0.007 0.071 0.32 5 -0.37 5 10
SMPD1 0.008 0.037 0.17 5 -0.17 2 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.008 0.13 0.32 1 -0.54 14 15
MAP2K4 0.021 0.073 0.22 33 -0.28 1 34
protein ubiquitination 0.007 0.13 0.35 5 -0.52 15 20
EnzymeConsortium:2.7.1.37 0.01 0.083 0.34 7 -0.4 6 13
response to UV 0 0.001 0.004 10 -0.003 4 14
RAF1 0.003 0.069 0.3 5 -0.35 7 12
CRADD 0.029 0.028 -10000 0 -0.56 1 1
mol:ceramide 0.008 0.05 0.16 10 -0.17 11 21
I-kappa-B-alpha/RELA/p50/ubiquitin 0.039 0.013 -10000 0 -10000 0 0
MADD 0.03 0.028 -10000 0 -0.56 1 1
MAP3K1 0.019 0.071 0.21 33 -0.21 3 36
TRADD 0.028 0.039 -10000 0 -0.56 2 2
RELA/p50 0.031 0.003 -10000 0 -10000 0 0
MAPK3 0.009 0.08 0.29 6 -0.44 6 12
MAPK1 0.009 0.074 0.3 6 -0.37 6 12
p50/RELA/I-kappa-B-alpha 0.043 0.015 -10000 0 -10000 0 0
FADD -0.002 0.12 0.33 1 -0.52 15 16
KSR1 0.004 0.071 0.23 7 -0.3 12 19
MAPK8 0.019 0.075 0.24 19 -0.26 3 22
TRAF2 0.028 0.039 -10000 0 -0.56 2 2
response to radiation 0 0.001 0.004 5 -0.003 1 6
CHUK 0.004 0.12 0.3 2 -0.49 15 17
TNF R/SODD 0.042 0.015 -10000 0 -10000 0 0
TNF -0.026 0.16 -10000 0 -0.46 54 54
CYCS 0.014 0.076 0.26 16 -0.26 10 26
IKBKG 0.003 0.13 0.3 3 -0.52 15 18
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.001 0.13 -10000 0 -0.53 16 16
RELA 0.031 0.003 -10000 0 -10000 0 0
RIPK1 0.03 0.006 -10000 0 -10000 0 0
AIFM1 0.009 0.068 0.24 15 -0.39 3 18
TNF/TNF R/SODD 0.018 0.11 -10000 0 -0.35 26 26
TNFRSF1A 0.031 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 5 -0.003 1 6
CASP8 0.023 0.11 -10000 0 -0.74 8 8
NSMAF 0 0.12 0.29 2 -0.51 15 17
response to hydrogen peroxide 0 0.001 0.004 10 -0.003 4 14
BCL2 0.018 0.086 -10000 0 -0.56 10 10
Class I PI3K signaling events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.014 0.057 0.29 1 -0.65 2 3
DAPP1 -0.033 0.19 0.27 4 -0.63 28 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.028 0.24 0.32 2 -0.78 30 32
mol:DAG 0.025 0.13 0.23 75 -0.3 22 97
HRAS 0.031 0.049 -10000 0 -0.56 3 3
RAP1A 0.033 0.012 -10000 0 -10000 0 0
ARF5/GDP 0.04 0.088 0.24 3 -0.42 11 14
PLCG2 0.015 0.079 -10000 0 -0.38 17 17
PLCG1 0.03 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.04 -10000 0 -0.56 2 2
mol:GTP -0.011 0.05 0.3 2 -0.31 7 9
ARF1/GTP 0.019 0.072 0.27 1 -0.46 3 4
RHOA 0.023 0.014 -10000 0 -10000 0 0
YES1 0.031 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.011 0.05 0.3 1 -0.3 8 9
ADAP1 0.013 0.086 0.29 2 -0.66 2 4
ARAP3 -0.011 0.049 0.3 2 -0.31 7 9
INPPL1 0.029 0.039 -10000 0 -0.56 2 2
PREX1 0.029 0.028 -10000 0 -0.56 1 1
ARHGEF6 0.03 0.028 -10000 0 -0.56 1 1
ARHGEF7 0.031 0.005 -10000 0 -10000 0 0
ARF1 0.03 0.007 -10000 0 -10000 0 0
NRAS 0.033 0.012 -10000 0 -10000 0 0
FYN 0.025 0.048 -10000 0 -0.56 3 3
ARF6 0.029 0.008 -10000 0 -10000 0 0
FGR 0.023 0.062 -10000 0 -0.47 7 7
mol:Ca2+ 0.019 0.07 0.21 10 -10000 0 10
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.039 -10000 0 -0.56 2 2
ZAP70 -0.012 0.14 -10000 0 -0.46 40 40
mol:IP3 0.019 0.089 0.17 75 -0.22 14 89
LYN 0.027 0.039 -10000 0 -0.56 2 2
ARF1/GDP 0.05 0.091 0.25 7 -0.42 10 17
RhoA/GDP 0.023 0.068 0.37 3 -0.42 3 6
PDK1/Src/Hsp90 0.053 0.038 -10000 0 -0.35 2 2
BLNK 0.022 0.065 -10000 0 -0.45 8 8
actin cytoskeleton reorganization 0.037 0.11 0.36 12 -0.46 6 18
SRC 0.028 0.039 -10000 0 -0.56 2 2
PLEKHA2 0.004 0.037 -10000 0 -0.35 5 5
RAC1 0.028 0.01 -10000 0 -10000 0 0
PTEN 0.02 0.021 -10000 0 -10000 0 0
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
ARF6/GTP 0.011 0.061 0.29 1 -0.56 3 4
RhoA/GTP 0.009 0.05 0.3 2 -0.4 2 4
Src family/SYK family/BLNK-LAT -0.049 0.23 -10000 0 -0.79 29 29
BLK -0.056 0.18 -10000 0 -0.43 85 85
PDPK1 0.03 0.007 -10000 0 -10000 0 0
CYTH1 0.025 0.086 0.29 8 -0.4 2 10
HCK 0.021 0.074 -10000 0 -0.53 8 8
CYTH3 0.016 0.077 0.29 2 -0.4 2 4
CYTH2 0.021 0.095 0.29 7 -0.57 3 10
KRAS 0.033 0.012 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.028 0.078 -10000 0 -0.44 6 6
SGK1 0.021 0.1 -10000 0 -0.36 23 23
INPP5D 0.027 0.039 -10000 0 -0.56 2 2
mol:GDP 0.037 0.094 0.24 10 -0.46 10 20
SOS1 0.031 0.006 -10000 0 -10000 0 0
SYK 0.025 0.055 -10000 0 -0.56 4 4
ARF6/GDP 0.016 0.06 0.32 2 -0.41 3 5
mol:PI-3-4-5-P3 0.017 0.081 -10000 0 -0.31 7 7
ARAP3/RAP1A/GTP 0.011 0.05 0.3 1 -0.3 8 9
VAV1 0.012 0.1 -10000 0 -0.53 16 16
mol:PI-3-4-P2 0.014 0.04 -10000 0 -0.41 4 4
RAS family/GTP/PI3K Class I 0.073 0.084 0.34 1 -0.3 8 9
PLEKHA1 0.005 0.033 -10000 0 -0.34 4 4
Rac1/GDP 0.041 0.084 0.22 2 -0.43 9 11
LAT -0.006 0.12 -10000 0 -0.41 38 38
Rac1/GTP 0.032 0.08 -10000 0 -0.48 8 8
ITK -0.021 0.068 0.28 1 -0.34 10 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.018 0.16 0.26 73 -0.44 24 97
LCK 0.004 0.12 -10000 0 -0.48 24 24
BTK 0.019 0.098 0.29 9 -0.38 5 14
TCGA08_retinoblastoma

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.024 0.061 -10000 0 -0.49 6 6
CDKN2C 0.028 0.044 -10000 0 -0.48 3 3
CDKN2A 0.008 0.1 -10000 0 -0.44 22 22
CCND2 -0.001 0.045 0.25 11 -10000 0 11
RB1 -0.004 0.057 -10000 0 -0.27 16 16
CDK4 0.001 0.052 0.27 13 -10000 0 13
CDK6 0.001 0.053 0.3 11 -10000 0 11
G1/S progression 0.004 0.059 0.28 15 -0.27 1 16
Regulation of Telomerase

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.084 0.18 -10000 0 -0.79 12 12
RAD9A 0.027 0.046 -10000 0 -0.45 4 4
AP1 -0.011 0.14 -10000 0 -0.34 61 61
IFNAR2 0.027 0.04 -10000 0 -0.56 2 2
AKT1 0.007 0.059 -10000 0 -0.4 5 5
ER alpha/Oestrogen 0.01 0.063 -10000 0 -0.34 13 13
NFX1/SIN3/HDAC complex 0.023 0.078 -10000 0 -0.44 9 9
EGF -0.11 0.23 -10000 0 -0.45 135 135
SMG5 0.03 0.007 -10000 0 -10000 0 0
SMG6 0.029 0.028 -10000 0 -0.56 1 1
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl -0.073 0.18 -10000 0 -0.74 13 13
SAP18 0.031 0.005 -10000 0 -10000 0 0
MRN complex 0.045 0.036 -10000 0 -0.35 1 1
WT1 -0.22 0.26 -10000 0 -0.46 233 233
WRN 0.028 0.01 -10000 0 -10000 0 0
SP1 0.027 0.017 -10000 0 -10000 0 0
SP3 0.03 0.007 -10000 0 -10000 0 0
TERF2IP 0.03 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.053 0.17 -10000 0 -0.71 10 10
Mad/Max 0.041 0.015 -10000 0 -10000 0 0
TERT -0.086 0.19 -10000 0 -0.84 11 11
CCND1 -0.091 0.24 0.48 1 -1.2 14 15
MAX 0.029 0.009 -10000 0 -10000 0 0
RBBP7 0.031 0.004 -10000 0 -10000 0 0
RBBP4 0.03 0.006 -10000 0 -10000 0 0
TERF2 0.027 0.007 -10000 0 -10000 0 0
PTGES3 0.031 0.005 -10000 0 -10000 0 0
SIN3A 0.031 0.003 -10000 0 -10000 0 0
Telomerase/911 0.034 0.046 -10000 0 -10000 0 0
CDKN1B -0.061 0.14 -10000 0 -0.36 55 55
RAD1 0.029 0.009 -10000 0 -10000 0 0
XRCC5 0.03 0.007 -10000 0 -10000 0 0
XRCC6 0.031 0.005 -10000 0 -10000 0 0
SAP30 0.019 0.082 -10000 0 -0.56 9 9
TRF2/PARP2 0.041 0.013 -10000 0 -10000 0 0
UBE3A 0.031 0.004 -10000 0 -10000 0 0
JUN 0.024 0.058 -10000 0 -0.52 5 5
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.011 -10000 0 -10000 0 0
FOS -0.032 0.16 -10000 0 -0.44 59 59
IFN-gamma/IRF1 -0.065 0.17 -10000 0 -0.42 55 55
PARP2 0.03 0.007 -10000 0 -10000 0 0
BLM 0.023 0.061 -10000 0 -0.42 8 8
Telomerase -0.002 0.11 -10000 0 -0.45 13 13
IRF1 0.017 0.074 -10000 0 -0.53 8 8
ESR1 0.014 0.086 -10000 0 -0.48 13 13
KU/TER 0.043 0.012 -10000 0 -10000 0 0
ATM/TRF2 0.044 0.022 -10000 0 -0.38 1 1
ubiquitin-dependent protein catabolic process 0.032 0.068 -10000 0 -0.43 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.032 0.069 -10000 0 -0.44 6 6
HDAC1 0.03 0.006 -10000 0 -10000 0 0
HDAC2 0.026 0.016 -10000 0 -10000 0 0
ATM 0.011 0.021 -10000 0 -0.43 1 1
SMAD3 0.013 0.05 -10000 0 -0.38 7 7
ABL1 0.028 0.039 -10000 0 -0.56 2 2
MXD1 0.03 0.006 -10000 0 -10000 0 0
MRE11A 0.031 0.004 -10000 0 -10000 0 0
HUS1 0.028 0.01 -10000 0 -10000 0 0
RPS6KB1 0.031 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.05 0.18 -10000 0 -0.77 10 10
NR2F2 0.032 0.006 -10000 0 -10000 0 0
MAPK3 -0.001 0.051 -10000 0 -0.26 15 15
MAPK1 0 0.045 -10000 0 -0.24 7 7
TGFB1/TGF beta receptor Type II 0.023 0.069 -10000 0 -0.53 7 7
NFKB1 0.031 0.004 -10000 0 -10000 0 0
HNRNPC 0.03 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.021 -10000 0 -0.43 1 1
NBN 0.029 0.019 -10000 0 -0.34 1 1
EGFR 0.007 0.11 -10000 0 -0.51 18 18
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.073 0.18 -10000 0 -0.34 131 131
MYC 0.018 0.081 -10000 0 -0.52 10 10
IL2 0.01 0.066 -10000 0 -0.35 14 14
KU 0.043 0.012 -10000 0 -10000 0 0
RAD50 0.023 0.03 -10000 0 -0.56 1 1
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
TGFB1 0.023 0.069 -10000 0 -0.53 7 7
TRF2/BLM 0.038 0.041 -10000 0 -0.27 7 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.063 0.18 -10000 0 -0.78 10 10
SP1/HDAC2 0.037 0.027 -10000 0 -10000 0 0
PINX1 0.027 0.029 -10000 0 -0.56 1 1
Telomerase/EST1A -0.054 0.17 -10000 0 -0.71 10 10
Smad3/Myc 0.023 0.074 -10000 0 -0.4 12 12
911 complex 0.051 0.038 -10000 0 -0.35 2 2
IFNG -0.12 0.23 -10000 0 -0.43 150 150
Telomerase/PinX1 -0.056 0.17 -10000 0 -0.7 11 11
Telomerase/AKT1/mTOR/p70S6K -0.006 0.094 -10000 0 -0.46 5 5
SIN3B 0.029 0.039 -10000 0 -0.56 2 2
YWHAE 0.031 0.005 -10000 0 -10000 0 0
Telomerase/EST1B -0.054 0.17 -10000 0 -0.7 10 10
response to DNA damage stimulus 0.005 0.012 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.064 0.046 -10000 0 -0.3 1 1
TRF2/WRN 0.039 0.018 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.054 0.17 -10000 0 -0.71 10 10
E2F1 0.026 0.046 -10000 0 -0.45 4 4
ZNFX1 0.03 0.006 -10000 0 -10000 0 0
PIF1 -0.002 0.12 -10000 0 -0.39 36 36
NCL 0.03 0.008 -10000 0 -10000 0 0
DKC1 0.031 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.035 0.17 -10000 0 -0.46 62 62
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.048 -10000 0 -0.56 3 3
TCEB1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/p53 0.016 0.075 0.33 1 -0.41 7 8
HIF1A 0.002 0.067 -10000 0 -0.34 14 14
COPS5 0.03 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.057 0.06 -10000 0 -0.34 4 4
FIH (dimer) 0.03 0.006 -10000 0 -10000 0 0
CDKN2A 0.005 0.11 -10000 0 -0.47 22 22
ARNT/IPAS -0.005 0.13 -10000 0 -0.33 60 60
HIF1AN 0.03 0.006 -10000 0 -10000 0 0
GNB2L1 0.022 0.041 -10000 0 -0.56 2 2
HIF1A/ARNT 0.015 0.074 0.33 1 -0.41 7 8
CUL2 0.031 0.004 -10000 0 -10000 0 0
OS9 0.031 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.043 0.051 -10000 0 -0.57 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.017 0.074 -10000 0 -0.42 7 7
PHD1-3/OS9 0.05 0.091 -10000 0 -0.32 24 24
HIF1A/RACK1/Elongin B/Elongin C 0.027 0.084 -10000 0 -0.42 9 9
VHL 0.02 0.041 -10000 0 -0.56 2 2
HSP90AA1 0.028 0.026 -10000 0 -0.34 2 2
HIF1A/JAB1 0.014 0.074 -10000 0 -0.33 14 14
EGLN3 0 0.13 -10000 0 -0.56 23 23
EGLN2 0.027 0.048 -10000 0 -0.56 3 3
EGLN1 0.03 0.007 -10000 0 -10000 0 0
TP53 0.031 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.1 0.24 -10000 0 -0.48 123 123
ARNT 0.03 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.029 0.025 -10000 0 -0.34 2 2
HIF1A/p19ARF 0.005 0.099 -10000 0 -0.35 25 25
PDGFR-beta signaling pathway

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.002 0.12 -10000 0 -0.53 17 17
PDGFB-D/PDGFRB/SLAP 0.008 0.11 -10000 0 -0.42 26 26
PDGFB-D/PDGFRB/APS/CBL 0.03 0.083 -10000 0 -0.37 15 15
AKT1 0.048 0.15 0.38 44 -0.51 6 50
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.016 0.14 0.33 3 -0.56 18 21
PIK3CA 0.03 0.007 -10000 0 -10000 0 0
FGR 0.012 0.18 0.32 3 -0.73 16 19
mol:Ca2+ 0.011 0.14 0.3 4 -0.62 16 20
MYC 0.033 0.16 0.4 12 -0.78 10 22
SHC1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.079 -10000 0 -0.29 15 15
LRP1/PDGFRB/PDGFB 0.027 0.1 -10000 0 -0.43 19 19
GRB10 0.027 0.029 -10000 0 -0.56 1 1
PTPN11 0.031 0.005 -10000 0 -10000 0 0
GO:0007205 0.011 0.14 0.3 4 -0.63 16 20
PTEN 0.03 0.006 -10000 0 -10000 0 0
GRB2 0.031 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.077 -10000 0 -0.56 8 8
PDGFB-D/PDGFRB/SHP2 0.021 0.08 -10000 0 -0.41 14 14
PDGFB-D/PDGFRB/GRB10 0.019 0.081 -10000 0 -0.41 14 14
cell cycle arrest 0.008 0.11 -10000 0 -0.42 26 26
HRAS 0.027 0.048 -10000 0 -0.56 3 3
HIF1A 0.04 0.14 0.36 42 -0.48 5 47
GAB1 0.01 0.14 0.33 4 -0.59 17 21
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.011 0.13 0.38 4 -0.54 17 21
PDGFB-D/PDGFRB 0.035 0.075 -10000 0 -0.36 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.02 0.081 -10000 0 -0.41 15 15
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.002 0.12 -10000 0 -0.51 18 18
positive regulation of MAPKKK cascade 0.021 0.08 -10000 0 -0.41 14 14
PIK3R1 0.023 0.052 -10000 0 -0.42 6 6
mol:IP3 0.011 0.14 0.3 4 -0.64 16 20
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.026 0.047 -10000 0 -0.55 3 3
PDGFB-D/PDGFRB/GRB7 0.015 0.093 -10000 0 -0.38 22 22
SHB 0.03 0.006 -10000 0 -10000 0 0
BLK -0.055 0.22 0.32 2 -0.6 48 50
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.021 0.082 -10000 0 -0.41 15 15
BCAR1 0.027 0.048 -10000 0 -0.56 3 3
VAV2 0.011 0.16 0.36 4 -0.64 18 22
CBL 0.031 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.02 0.083 -10000 0 -0.4 16 16
LCK -0.002 0.2 0.32 3 -0.65 27 30
PDGFRB 0.004 0.11 -10000 0 -0.56 16 16
ACP1 0.031 0.006 -10000 0 -10000 0 0
HCK 0.029 0.13 0.32 2 -0.59 11 13
ABL1 0.013 0.15 0.31 6 -0.57 17 23
PDGFB-D/PDGFRB/CBL 0.002 0.16 0.34 1 -0.69 17 18
PTPN1 0.031 0.007 -10000 0 -10000 0 0
SNX15 0.031 0.003 -10000 0 -10000 0 0
STAT3 0.031 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 -10000 0 -0.34 3 3
cell proliferation 0.034 0.15 0.39 13 -0.68 10 23
SLA 0.013 0.094 -10000 0 -0.49 15 15
actin cytoskeleton reorganization 0.022 0.064 0.34 1 -10000 0 1
SRC 0.033 0.11 0.32 2 -0.49 8 10
PI3K -0.005 0.079 -10000 0 -0.48 6 6
PDGFB-D/PDGFRB/GRB7/SHC 0.029 0.083 -10000 0 -0.34 18 18
SH2B2 0.021 0.06 -10000 0 -0.49 6 6
PLCgamma1/SPHK1 0.016 0.14 0.34 3 -0.58 18 21
LYN 0.022 0.14 0.32 2 -0.51 15 17
LRP1 0.019 0.082 -10000 0 -0.56 9 9
SOS1 0.031 0.006 -10000 0 -10000 0 0
STAT5B 0.031 0.005 -10000 0 -10000 0 0
STAT5A 0.028 0.039 -10000 0 -0.56 2 2
NCK1-2/p130 Cas 0.057 0.077 -10000 0 -0.31 3 3
SPHK1 0 0.12 -10000 0 -0.4 34 34
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.011 0.14 0.3 4 -0.64 16 20
PLCG1 0.01 0.14 0.3 4 -0.66 16 20
NHERF/PDGFRB 0.021 0.11 -10000 0 -0.39 25 25
YES1 0.032 0.12 0.33 1 -0.6 8 9
cell migration 0.02 0.11 -10000 0 -0.39 25 25
SHC/Grb2/SOS1 0.058 0.071 -10000 0 -0.3 5 5
SLC9A3R2 0.017 0.086 -10000 0 -0.56 10 10
SLC9A3R1 0.017 0.09 -10000 0 -0.56 11 11
NHERF1-2/PDGFRB/PTEN 0.033 0.1 -10000 0 -0.36 25 25
FYN 0.005 0.17 0.32 2 -0.62 19 21
DOK1 0.043 0.093 -10000 0 -0.32 15 15
HRAS/GTP 0.02 0.035 -10000 0 -0.41 3 3
PDGFB 0.027 0.048 -10000 0 -0.56 3 3
RAC1 0.029 0.17 0.43 6 -0.63 17 23
PRKCD 0.02 0.086 -10000 0 -0.34 13 13
FER 0.019 0.077 -10000 0 -0.32 15 15
MAPKKK cascade 0.023 0.095 0.37 12 -0.31 1 13
RASA1 0.029 0.082 -10000 0 -0.32 13 13
NCK1 0.03 0.006 -10000 0 -10000 0 0
NCK2 0.031 0.006 -10000 0 -10000 0 0
p62DOK/Csk 0.055 0.097 -10000 0 -0.36 13 13
PDGFB-D/PDGFRB/SHB 0.019 0.081 -10000 0 -0.41 15 15
chemotaxis 0.013 0.14 0.31 6 -0.55 17 23
STAT1-3-5/STAT1-3-5 0.045 0.068 -10000 0 -0.34 1 1
Bovine Papilomavirus E5/PDGFRB 0.002 0.079 -10000 0 -0.41 16 16
PTPRJ 0.03 0.018 -10000 0 -0.34 1 1
Regulation of Androgen receptor activity

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.018 0.005 -10000 0 -10000 0 0
SMARCC1 0.012 0.041 -10000 0 -0.77 1 1
REL 0.015 0.095 -10000 0 -0.54 13 13
HDAC7 -0.018 0.11 -10000 0 -0.46 8 8
JUN 0.024 0.058 -10000 0 -0.52 5 5
EP300 0.031 0.005 -10000 0 -10000 0 0
KAT2B 0.023 0.014 -10000 0 -10000 0 0
KAT5 0.03 0.028 -10000 0 -0.56 1 1
MAPK14 0.009 0.036 -10000 0 -0.43 2 2
FOXO1 0.028 0.031 -10000 0 -0.34 3 3
T-DHT/AR -0.001 0.12 -10000 0 -0.46 7 7
MAP2K6 0.023 0.043 -10000 0 -0.57 2 2
BRM/BAF57 0.044 0.012 -10000 0 -10000 0 0
MAP2K4 0.026 0.018 -10000 0 -10000 0 0
SMARCA2 0.03 0.007 -10000 0 -10000 0 0
PDE9A -0.035 0.21 -10000 0 -0.96 19 19
NCOA2 0.005 0.12 -10000 0 -0.56 19 19
CEBPA 0.012 0.096 -10000 0 -0.45 18 18
EHMT2 0.028 0.039 -10000 0 -0.56 2 2
cell proliferation -0.003 0.16 0.44 10 -0.5 17 27
NR0B1 -0.004 0.095 -10000 0 -0.34 33 33
EGR1 -0.027 0.15 -10000 0 -0.43 51 51
RXRs/9cRA 0.043 0.054 -10000 0 -0.32 4 4
AR/RACK1/Src -0.008 0.084 0.31 2 -0.48 7 9
AR/GR -0.016 0.11 0.24 1 -0.39 21 22
GNB2L1 0.022 0.041 -10000 0 </