Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/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 74 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
FOXM1 transcription factor network 149
HIF-1-alpha transcription factor network 124
LPA receptor mediated events 102
TCGA08_retinoblastoma 98
Endothelins 92
Osteopontin-mediated events 89
Syndecan-1-mediated signaling events 88
PDGFR-alpha signaling pathway 81
Nectin adhesion pathway 80
Ephrin B reverse signaling 75
Results

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
FOXM1 transcription factor network 149 7606 51 -0.66 0.022 1000 -1000 -0.014 -1000
HIF-1-alpha transcription factor network 124 9465 76 -0.15 0.035 1000 -1000 -0.008 -1000
LPA receptor mediated events 102 10468 102 -0.085 0.023 1000 -1000 -0.019 -1000
TCGA08_retinoblastoma 98 786 8 -0.022 0.022 1000 -1000 -0.002 -1000
Endothelins 92 8889 96 -0.2 0.023 1000 -1000 -0.006 -1000
Osteopontin-mediated events 89 3386 38 -0.22 0.023 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 88 2994 34 -0.086 0.023 1000 -1000 -0.002 -1000
PDGFR-alpha signaling pathway 81 3571 44 -0.15 0.031 1000 -1000 0.001 -1000
Nectin adhesion pathway 80 5075 63 -0.083 0.031 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 75 3633 48 -0.2 0.051 1000 -1000 -0.031 -1000
TCGA08_p53 74 522 7 -0.069 0.018 1000 -1000 -0.002 -1000
amb2 Integrin signaling 73 6044 82 -0.13 0.034 1000 -1000 0 -1000
Thromboxane A2 receptor signaling 70 7446 105 -0.21 0.052 1000 -1000 -0.025 -1000
Fc-epsilon receptor I signaling in mast cells 70 6812 97 -0.087 0.027 1000 -1000 -0.018 -1000
PLK2 and PLK4 events 68 206 3 -0.002 0.017 1000 -1000 0.017 -1000
Cellular roles of Anthrax toxin 68 2659 39 -0.099 0.022 1000 -1000 -0.004 -1000
TRAIL signaling pathway 67 3244 48 -0.038 0.023 1000 -1000 -0.005 -1000
Syndecan-4-mediated signaling events 65 4416 67 -0.11 0.027 1000 -1000 -0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 63 5395 85 -0.17 0.023 1000 -1000 -0.012 -1000
IL4-mediated signaling events 62 5721 91 -0.33 0.18 1000 -1000 -0.11 -1000
Nongenotropic Androgen signaling 62 3257 52 -0.13 0.066 1000 -1000 -0.013 -1000
IL6-mediated signaling events 60 4502 75 -0.13 0.025 1000 -1000 -0.007 -1000
IGF1 pathway 59 3417 57 -0.022 0.035 1000 -1000 -0.016 -1000
IL23-mediated signaling events 59 3598 60 -0.26 0.025 1000 -1000 -0.002 -1000
IL1-mediated signaling events 57 3565 62 -0.075 0.046 1000 -1000 0 -1000
BARD1 signaling events 55 3189 57 -0.036 0.027 1000 -1000 -0.032 -1000
Integrins in angiogenesis 55 4664 84 -0.056 0.033 1000 -1000 0 -1000
IFN-gamma pathway 53 3666 68 -0.053 0.034 1000 -1000 -0.014 -1000
EPHB forward signaling 52 4504 85 -0.028 0.036 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 50 254 5 0.005 0.019 1000 -1000 0.019 -1000
PLK1 signaling events 50 4260 85 -0.066 0.025 1000 -1000 -0.008 -1000
Noncanonical Wnt signaling pathway 49 1288 26 -0.032 0.026 1000 -1000 -0.015 -1000
Signaling events mediated by the Hedgehog family 48 2521 52 -0.084 0.034 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 47 3504 74 -0.064 0.044 1000 -1000 -0.015 -1000
Wnt signaling 46 323 7 -0.032 0.023 1000 -1000 0.011 -1000
E-cadherin signaling in keratinocytes 46 2005 43 -0.012 0.027 1000 -1000 -0.012 -1000
Signaling events mediated by PTP1B 45 3456 76 -0.092 0.074 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 45 1669 37 -0.04 0.033 1000 -1000 0 -1000
TCR signaling in naïve CD8+ T cells 45 4263 93 -0.051 0.032 1000 -1000 -0.02 -1000
Stabilization and expansion of the E-cadherin adherens junction 45 3401 74 -0.059 0.034 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 45 770 17 -0.024 0.025 1000 -1000 0 -1000
IL12-mediated signaling events 44 3883 87 -0.26 0.026 1000 -1000 -0.057 -1000
Syndecan-2-mediated signaling events 44 3089 69 -0.018 0.028 1000 -1000 0 -1000
Aurora A signaling 44 2671 60 -0.064 0.037 1000 -1000 0 -1000
Canonical Wnt signaling pathway 44 2290 51 -0.19 0.084 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 43 2515 58 -0.11 0.023 1000 -1000 -0.007 -1000
BCR signaling pathway 43 4265 99 -0.057 0.032 1000 -1000 -0.018 -1000
BMP receptor signaling 42 3417 81 -0.073 0.05 1000 -1000 -0.019 -1000
Circadian rhythm pathway 41 919 22 -0.079 0.024 1000 -1000 -0.007 -1000
FoxO family signaling 41 2628 64 -0.27 0.041 1000 -1000 -0.014 -1000
Retinoic acid receptors-mediated signaling 41 2426 58 -0.092 0.029 1000 -1000 0 -1000
Ephrin A reverse signaling 40 284 7 0 0.023 1000 -1000 0 -1000
Reelin signaling pathway 39 2209 56 -0.018 0.056 1000 -1000 -0.001 -1000
HIF-2-alpha transcription factor network 39 1701 43 -0.098 0.041 1000 -1000 -0.094 -1000
E-cadherin signaling in the nascent adherens junction 38 2923 76 -0.06 0.04 1000 -1000 -0.024 -1000
Arf6 downstream pathway 37 1604 43 -0.029 0.031 1000 -1000 -0.022 -1000
FOXA2 and FOXA3 transcription factor networks 37 1704 46 -0.16 0.042 1000 -1000 -0.006 -1000
ErbB2/ErbB3 signaling events 36 2390 65 -0.071 0.023 1000 -1000 -0.023 -1000
Aurora B signaling 36 2431 67 -0.066 0.033 1000 -1000 -0.005 -1000
Paxillin-dependent events mediated by a4b1 35 1275 36 -0.032 0.034 1000 -1000 -0.029 -1000
Plasma membrane estrogen receptor signaling 35 3045 86 -0.057 0.053 1000 -1000 -0.023 -1000
FAS signaling pathway (CD95) 34 1634 47 -0.053 0.041 1000 -1000 -0.01 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 34 1571 45 -0.06 0.038 1000 -1000 -0.001 -1000
ErbB4 signaling events 33 2291 69 -0.069 0.047 1000 -1000 -0.014 -1000
p75(NTR)-mediated signaling 33 4203 125 -0.039 0.055 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 33 858 26 -0.014 0.029 1000 -1000 -0.018 -1000
IL2 signaling events mediated by STAT5 33 738 22 -0.075 0.032 1000 -1000 0.01 -1000
Signaling events mediated by PRL 33 1127 34 -0.014 0.023 1000 -1000 0 -1000
RXR and RAR heterodimerization with other nuclear receptor 32 1710 52 -0.029 0.059 1000 -1000 -0.011 -1000
EGFR-dependent Endothelin signaling events 31 661 21 0 0.041 1000 -1000 0 -1000
S1P3 pathway 31 1336 42 -0.055 0.03 1000 -1000 0 -1000
ceramide signaling pathway 29 1433 49 -0.014 0.038 1000 -1000 0 -1000
Signaling mediated by p38-gamma and p38-delta 29 445 15 -0.049 0.023 1000 -1000 0 -1000
Class I PI3K signaling events 29 2178 73 -0.008 0.042 1000 -1000 -0.005 -1000
Atypical NF-kappaB pathway 28 869 31 0 0.023 1000 -1000 0 -1000
Regulation of Androgen receptor activity 28 2008 70 -0.092 0.034 1000 -1000 -0.011 -1000
E-cadherin signaling events 27 138 5 0.018 0.025 1000 -1000 0.019 -1000
Regulation of Telomerase 26 2739 102 -0.13 0.045 1000 -1000 -0.001 -1000
S1P4 pathway 25 638 25 -0.003 0.03 1000 -1000 0 -1000
Canonical NF-kappaB pathway 24 957 39 0 0.037 1000 -1000 0 -1000
Nephrin/Neph1 signaling in the kidney podocyte 23 786 34 -0.023 0.049 1000 -1000 -0.02 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 23 1291 54 -0.014 0.029 1000 -1000 -0.001 -1000
Arf6 signaling events 23 1454 62 -0.017 0.036 1000 -1000 0 -1000
Glypican 1 network 23 1113 48 -0.021 0.039 1000 -1000 -0.02 -1000
Glucocorticoid receptor regulatory network 23 2651 114 -0.13 0.046 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 23 2779 120 -0.057 0.055 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 22 1695 76 -0.01 0.033 1000 -1000 -0.009 -1000
Presenilin action in Notch and Wnt signaling 22 1345 61 -0.18 0.042 1000 -1000 -0.018 -1000
EPO signaling pathway 22 1220 55 -0.005 0.059 1000 -1000 0 -1000
Signaling mediated by p38-alpha and p38-beta 22 989 44 -0.007 0.033 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 22 1561 68 -0.081 0.094 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 22 2155 97 -0.06 0.046 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 21 262 12 0 0.014 1000 -1000 0 -1000
Regulation of nuclear SMAD2/3 signaling 20 2834 136 -0.13 0.071 1000 -1000 -0.031 -1000
mTOR signaling pathway 20 1103 53 -0.015 0.032 1000 -1000 -0.017 -1000
S1P5 pathway 19 328 17 -0.006 0.023 1000 -1000 -0.01 -1000
p38 MAPK signaling pathway 19 878 44 -0.013 0.044 1000 -1000 0 -1000
Ceramide signaling pathway 18 1428 76 -0.013 0.043 1000 -1000 -0.005 -1000
Signaling events mediated by HDAC Class III 18 734 40 -0.036 0.042 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class I 18 1892 104 -0.036 0.053 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 18 2351 125 -0.019 0.055 1000 -1000 -0.025 -1000
Class IB PI3K non-lipid kinase events 18 54 3 -0.019 0.019 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 17 1396 82 -0.008 0.057 1000 -1000 -0.021 -1000
Syndecan-3-mediated signaling events 16 582 35 -0.01 0.035 1000 -1000 0 -1000
Regulation of p38-alpha and p38-beta 16 909 54 -0.006 0.057 1000 -1000 0 -1000
Arf6 trafficking events 16 1140 71 -0.025 0.033 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 15 269 17 -0.003 0.044 1000 -1000 0 -1000
Hedgehog signaling events mediated by Gli proteins 15 1004 65 -0.006 0.054 1000 -1000 -0.004 -1000
Class I PI3K signaling events mediated by Akt 15 1050 68 -0.026 0.047 1000 -1000 -0.011 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 15 524 33 -0.003 0.053 1000 -1000 0 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 14 1187 83 -0.006 0.048 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 14 380 27 -0.013 0.047 1000 -1000 -0.013 -1000
Insulin Pathway 14 1056 74 -0.01 0.063 1000 -1000 -0.013 -1000
Insulin-mediated glucose transport 13 435 32 0 0.033 1000 -1000 0 -1000
Calcium signaling in the CD4+ TCR pathway 13 422 31 -0.002 0.09 1000 -1000 -0.024 -1000
VEGFR1 specific signals 13 738 56 0 0.039 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 12 918 75 -0.033 0.058 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 12 342 28 0 0.036 1000 -1000 0 -1000
S1P1 pathway 12 467 36 -0.001 0.028 1000 -1000 -0.014 -1000
Glypican 2 network 12 49 4 0.021 0.029 1000 -1000 0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 11 255 23 -0.012 0.043 1000 -1000 0.001 -1000
Effects of Botulinum toxin 11 308 26 0 0.041 1000 -1000 0 -1000
IL27-mediated signaling events 11 604 51 -0.006 0.033 1000 -1000 -0.027 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1048 88 -0.028 0.058 1000 -1000 -0.042 -1000
Alternative NF-kappaB pathway 11 154 13 0 0.056 1000 -1000 0 -1000
Aurora C signaling 10 71 7 0 0.033 1000 -1000 0 -1000
Arf1 pathway 8 472 54 -0.011 0.032 1000 -1000 -0.001 -1000
Rapid glucocorticoid signaling 7 157 20 0 0.025 1000 -1000 0 -1000
Visual signal transduction: Rods 7 405 52 0 0.066 1000 -1000 0 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 7 558 78 -0.012 0.036 1000 -1000 -0.02 -1000
Visual signal transduction: Cones 1 74 38 0 0.064 1000 -1000 0 -1000
Total 4910 283494 7203 -8 5.2 131000 -131000 -1.5 -131000
FOXM1 transcription factor network

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
NFATC3 -0.43 0.59 -10000 0 -1.2 192 192
PLK1 -0.061 0.29 -10000 0 -1.3 30 30
BIRC5 -0.065 0.3 -10000 0 -1.3 31 31
HSPA1B -0.44 0.59 -10000 0 -1.1 209 209
MAP2K1 0.001 0.044 -10000 0 -0.16 3 3
BRCA2 -0.45 0.6 -10000 0 -1.2 195 195
FOXM1 -0.66 0.96 -10000 0 -1.7 209 209
XRCC1 -0.44 0.59 -10000 0 -1.1 197 197
FOXM1B/p19 -0.54 0.66 -10000 0 -1.3 216 216
Cyclin D1/CDK4 -0.44 0.55 -10000 0 -1 229 229
CDC2 -0.5 0.67 -10000 0 -1.3 206 206
TGFA -0.39 0.52 -10000 0 -0.97 211 211
SKP2 -0.44 0.6 -10000 0 -1.2 198 198
CCNE1 0 0.048 -10000 0 -0.13 70 70
CKS1B -0.44 0.6 -10000 0 -1.1 202 202
RB1 -0.36 0.45 -10000 0 -0.89 201 201
FOXM1C/SP1 -0.54 0.72 -10000 0 -1.3 214 214
AURKB -0.07 0.3 -10000 0 -1.3 33 33
CENPF -0.48 0.62 -10000 0 -1.2 219 219
CDK4 0.008 0.026 -10000 0 -0.13 9 9
MYC -0.4 0.52 -10000 0 -0.98 219 219
CHEK2 -0.003 0.05 -10000 0 -0.14 25 25
ONECUT1 -0.44 0.57 -10000 0 -1.1 214 214
CDKN2A 0.013 0.021 0.084 2 -0.12 10 12
LAMA4 -0.48 0.62 -10000 0 -1.2 214 214
FOXM1B/HNF6 -0.55 0.72 -10000 0 -1.4 215 215
FOS -0.52 0.64 -10000 0 -1.2 236 236
SP1 0.021 0.011 -10000 0 -0.038 11 11
CDC25B -0.44 0.59 -10000 0 -1.1 199 199
response to radiation -0.012 0.032 -10000 0 -10000 0 0
CENPB -0.43 0.59 -10000 0 -1.2 192 192
CENPA -0.44 0.59 -10000 0 -1.2 195 195
NEK2 -0.45 0.61 -10000 0 -1.2 206 206
HIST1H2BA -0.43 0.59 -10000 0 -1.1 196 196
CCNA2 0.01 0.033 -10000 0 -0.12 29 29
EP300 0.022 0.009 -10000 0 -0.12 2 2
CCNB1/CDK1 -0.58 0.79 -10000 0 -1.5 199 199
CCNB2 -0.47 0.62 -10000 0 -1.2 210 210
CCNB1 -0.48 0.65 -10000 0 -1.3 201 201
ETV5 -0.5 0.63 -10000 0 -1.2 225 225
ESR1 -0.47 0.61 -10000 0 -1.2 222 222
CCND1 -0.44 0.56 -10000 0 -1 230 230
GSK3A 0.002 0.042 -10000 0 -0.16 10 10
Cyclin A-E1/CDK1-2 -0.038 0.099 -10000 0 -0.16 170 170
CDK2 0.015 0.024 -10000 0 -0.13 14 14
G2/M transition of mitotic cell cycle -0.015 0.038 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.49 0.66 -10000 0 -1.3 210 210
GAS1 -0.45 0.6 -10000 0 -1.2 197 197
MMP2 -0.53 0.64 -10000 0 -1.2 243 243
RB1/FOXM1C -0.5 0.58 -10000 0 -1.1 230 230
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
HIF-1-alpha transcription factor network

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
PKM2 -0.12 0.34 -9999 0 -0.54 171 171
HDAC7 -0.001 0.006 -9999 0 -0.06 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.062 0.33 -9999 0 -0.57 114 114
SMAD4 0.023 0.007 -9999 0 -0.12 1 1
ID2 -0.12 0.34 -9999 0 -0.54 171 171
AP1 -0.03 0.087 -9999 0 -0.15 162 162
ABCG2 -0.12 0.34 -9999 0 -0.54 171 171
HIF1A -0.016 0.09 -9999 0 -0.12 163 163
TFF3 -0.13 0.34 -9999 0 -0.54 178 178
GATA2 0.02 0.023 -9999 0 -0.097 18 18
AKT1 -0.004 0.072 -9999 0 -0.1 120 120
response to hypoxia -0.02 0.064 -9999 0 -0.1 135 135
MCL1 -0.12 0.34 -9999 0 -0.54 171 171
NDRG1 -0.13 0.35 -9999 0 -0.56 176 176
SERPINE1 -0.13 0.33 -9999 0 -0.53 175 175
FECH -0.12 0.34 -9999 0 -0.54 170 170
FURIN -0.12 0.34 -9999 0 -0.54 171 171
NCOA2 0.023 0.013 -9999 0 -0.1 5 5
EP300 0.001 0.089 -9999 0 -0.22 28 28
HMOX1 -0.13 0.34 -9999 0 -0.55 172 172
BHLHE40 -0.13 0.33 -9999 0 -0.54 170 170
BHLHE41 -0.13 0.33 -9999 0 -0.54 170 170
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.035 0.12 -9999 0 -0.17 65 65
ENG 0.006 0.089 -9999 0 -0.17 54 54
JUN 0.014 0.033 -9999 0 -0.12 31 31
RORA -0.12 0.34 -9999 0 -0.54 170 170
ABCB1 -0.024 0.1 -9999 0 -0.74 4 4
TFRC -0.14 0.35 -9999 0 -0.55 182 182
CXCR4 -0.14 0.35 -9999 0 -0.55 185 185
TF -0.12 0.34 -9999 0 -0.54 173 173
CITED2 -0.12 0.34 -9999 0 -0.54 170 170
HIF1A/ARNT -0.077 0.44 -9999 0 -0.7 125 125
LDHA -0.088 0.3 -9999 0 -0.99 54 54
ETS1 -0.13 0.35 -9999 0 -0.55 173 173
PGK1 -0.13 0.34 -9999 0 -0.54 176 176
NOS2 -0.13 0.33 -9999 0 -0.54 170 170
ITGB2 -0.14 0.35 -9999 0 -0.56 180 180
ALDOA -0.12 0.34 -9999 0 -0.54 171 171
Cbp/p300/CITED2 -0.11 0.36 -9999 0 -0.62 136 136
FOS -0.005 0.053 -9999 0 -0.12 95 95
HK2 -0.12 0.34 -9999 0 -0.54 176 176
SP1 0.031 0.009 -9999 0 -0.11 1 1
GCK 0.003 0.12 -9999 0 -0.41 1 1
HK1 -0.12 0.34 -9999 0 -0.54 169 169
NPM1 -0.12 0.34 -9999 0 -0.54 171 171
EGLN1 -0.12 0.34 -9999 0 -0.54 171 171
CREB1 0.023 0.028 -9999 0 -0.075 42 42
PGM1 -0.13 0.34 -9999 0 -0.55 175 175
SMAD3 0.022 0.016 -9999 0 -0.12 7 7
EDN1 -0.035 0.19 -9999 0 -1 15 15
IGFBP1 -0.12 0.34 -9999 0 -0.54 169 169
VEGFA -0.089 0.29 -9999 0 -0.51 136 136
HIF1A/JAB1 -0.005 0.085 -9999 0 -0.16 93 93
CP -0.14 0.35 -9999 0 -0.57 181 181
CXCL12 -0.14 0.35 -9999 0 -0.55 182 182
COPS5 0.019 0.023 -9999 0 -0.11 15 15
SMAD3/SMAD4 0.029 0.033 -9999 0 -0.13 21 21
BNIP3 -0.13 0.34 -9999 0 -0.54 180 180
EGLN3 -0.15 0.35 -9999 0 -0.55 185 185
CA9 -0.14 0.34 -9999 0 -0.54 187 187
TERT -0.12 0.34 -9999 0 -0.54 170 170
ENO1 -0.12 0.34 -9999 0 -0.54 170 170
PFKL -0.12 0.34 -9999 0 -0.54 170 170
NCOA1 0.023 0.009 -9999 0 -0.12 2 2
ADM -0.13 0.34 -9999 0 -0.54 180 180
ARNT -0.008 0.069 -9999 0 -0.095 163 163
HNF4A 0.027 0.009 -9999 0 -0.12 2 2
ADFP -0.14 0.35 -9999 0 -0.55 184 184
SLC2A1 -0.094 0.29 -9999 0 -0.52 133 133
LEP -0.12 0.34 -9999 0 -0.54 170 170
HIF1A/ARNT/Cbp/p300 -0.072 0.34 -9999 0 -0.58 118 118
EPO -0.073 0.28 -9999 0 -0.57 90 90
CREBBP -0.001 0.09 -9999 0 -0.22 29 29
HIF1A/ARNT/Cbp/p300/HDAC7 -0.075 0.35 -9999 0 -0.6 116 116
PFKFB3 -0.13 0.34 -9999 0 -0.55 171 171
NT5E -0.15 0.35 -9999 0 -0.56 193 193
LPA receptor mediated 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
GNB1/GNG2 -0.021 0.073 -10000 0 -0.13 137 137
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.092 -10000 0 -0.19 91 91
AP1 -0.058 0.073 -10000 0 -0.13 252 252
mol:PIP3 -0.051 0.063 -10000 0 -0.13 166 166
AKT1 -0.014 0.07 0.15 1 -0.16 53 54
PTK2B -0.028 0.066 -10000 0 -0.14 122 122
RHOA -0.008 0.053 -10000 0 -0.35 6 6
PIK3CB 0.015 0.029 -10000 0 -0.12 24 24
mol:Ca2+ -0.004 0.039 -10000 0 -0.11 38 38
MAGI3 0.019 0.025 -10000 0 -0.12 18 18
RELA 0.023 0.009 -10000 0 -0.12 2 2
apoptosis -0.034 0.069 -10000 0 -0.16 120 120
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
positive regulation of microtubule depolymerization -0.018 0.06 -10000 0 -0.12 124 124
NF kappa B1 p50/RelA -0.04 0.062 -10000 0 -0.13 140 140
endothelial cell migration -0.085 0.14 -10000 0 -0.22 249 249
ADCY4 -0.042 0.098 -10000 0 -0.2 134 134
ADCY5 -0.045 0.098 -10000 0 -0.2 141 141
ADCY6 -0.042 0.098 -10000 0 -0.2 133 133
ADCY7 -0.042 0.097 -10000 0 -0.2 133 133
ADCY1 -0.042 0.097 -10000 0 -0.2 133 133
ADCY2 -0.042 0.097 -10000 0 -0.2 134 134
ADCY3 -0.043 0.098 -10000 0 -0.2 134 134
ADCY8 -0.048 0.099 -10000 0 -0.2 137 137
ADCY9 -0.045 0.1 -10000 0 -0.2 140 140
GSK3B -0.024 0.063 -10000 0 -0.13 125 125
arachidonic acid secretion -0.04 0.092 -10000 0 -0.19 128 128
GNG2 0.021 0.018 -10000 0 -0.12 9 9
TRIP6 0.001 0.051 -10000 0 -0.25 20 20
GNAO1 -0.04 0.073 -10000 0 -0.11 250 250
HRAS 0.023 0.006 -10000 0 -0.12 1 1
NFKBIA -0.03 0.084 -10000 0 -0.21 73 73
GAB1 0.02 0.022 -10000 0 -0.12 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.023 0.22 -10000 0 -0.87 37 37
JUN 0.014 0.032 -10000 0 -0.12 30 30
LPA/LPA2/NHERF2 -0.009 0.035 -10000 0 -0.062 140 140
TIAM1 -0.04 0.26 -10000 0 -1 37 37
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:IP3 -0.004 0.039 -10000 0 -0.11 38 38
PLCB3 -0.003 0.032 -10000 0 -0.05 140 140
FOS -0.005 0.052 -10000 0 -0.12 95 95
positive regulation of mitosis -0.04 0.092 -10000 0 -0.19 128 128
LPA/LPA1-2-3 -0.037 0.06 -10000 0 -0.097 249 249
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
stress fiber formation -0.025 0.073 -10000 0 -0.19 42 42
GNAZ -0.034 0.071 -10000 0 -0.11 248 248
EGFR/PI3K-beta/Gab1 -0.053 0.065 -10000 0 -0.14 166 166
positive regulation of dendritic cell cytokine production -0.037 0.06 -10000 0 -0.097 249 249
LPA/LPA2/MAGI-3 -0.008 0.035 -10000 0 -0.061 134 134
ARHGEF1 -0.019 0.062 -10000 0 -0.12 127 127
GNAI2 -0.034 0.07 -10000 0 -0.1 249 249
GNAI3 -0.039 0.077 -10000 0 -0.11 250 250
GNAI1 -0.044 0.081 -10000 0 -0.11 271 271
LPA/LPA3 -0.021 0.031 -10000 0 -0.052 249 249
LPA/LPA2 -0.02 0.031 -10000 0 -0.052 249 249
LPA/LPA1 -0.051 0.082 -10000 0 -0.13 249 249
HB-EGF/EGFR -0.003 0.059 -10000 0 -0.13 77 77
HBEGF 0.004 0.039 -10000 0 -0.077 96 96
mol:DAG -0.004 0.039 -10000 0 -0.11 38 38
cAMP biosynthetic process -0.045 0.096 -10000 0 -0.2 134 134
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
SRC 0.023 0.008 -10000 0 -0.12 2 2
GNB1 0.023 0.006 -10000 0 -0.12 1 1
LYN -0.03 0.089 -10000 0 -0.22 75 75
GNAQ -0.012 0.038 -10000 0 -0.069 124 124
LPAR2 0 0 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.033 0.049 -10000 0 -0.083 249 249
IL8 -0.084 0.15 -10000 0 -0.37 96 96
PTK2 -0.028 0.062 -10000 0 -0.09 247 247
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
CASP3 -0.034 0.07 -10000 0 -0.16 120 120
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PLCG1 -0.007 0.041 -10000 0 -0.067 135 135
PLD2 -0.026 0.059 -10000 0 -0.086 249 249
G12/G13 -0.019 0.072 -10000 0 -0.14 127 127
PI3K-beta -0.039 0.059 -10000 0 -0.19 48 48
cell migration -0.011 0.078 -10000 0 -0.22 49 49
SLC9A3R2 0.017 0.029 -10000 0 -0.12 24 24
PXN -0.026 0.075 -10000 0 -0.19 42 42
HRAS/GTP -0.041 0.093 -10000 0 -0.19 128 128
RAC1 0.023 0.002 -10000 0 -10000 0 0
MMP9 0 0.05 -10000 0 -0.12 81 81
PRKCE 0.021 0.017 -10000 0 -0.12 8 8
PRKCD -0.004 0.044 -10000 0 -0.12 45 45
Gi(beta/gamma) -0.042 0.096 -10000 0 -0.19 139 139
mol:LPA -0.033 0.049 -10000 0 -0.083 249 249
TRIP6/p130 Cas/FAK1/Paxillin -0.021 0.091 -10000 0 -0.16 136 136
MAPKKK cascade -0.04 0.092 -10000 0 -0.19 128 128
contractile ring contraction involved in cytokinesis -0.008 0.053 -10000 0 -0.35 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.009 0.029 -10000 0 -0.056 131 131
GNA15 -0.01 0.034 -10000 0 -0.064 124 124
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MAPT -0.019 0.061 -10000 0 -0.12 124 124
GNA11 -0.009 0.028 -10000 0 -0.056 123 123
Rac1/GTP -0.025 0.24 -10000 0 -0.92 37 37
MMP2 -0.085 0.14 -10000 0 -0.22 249 249
TCGA08_retinoblastoma

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
CDKN2B 0.017 0.017 -10000 0 -0.067 11 11
CDKN2C 0.008 0.044 -10000 0 -0.12 58 58
CDKN2A 0.015 0.021 -10000 0 -0.12 10 10
CCND2 0.015 0.052 0.12 107 -10000 0 107
RB1 -0.022 0.061 0.09 1 -0.12 136 137
CDK4 0.022 0.068 0.13 138 -0.12 17 155
CDK6 0.014 0.073 0.13 131 -0.13 39 170
G1/S progression 0.019 0.065 0.12 138 -10000 0 138
Endothelins

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
AKT1 -0.074 0.13 0.27 6 -0.25 167 173
PTK2B 0.022 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.04 0.16 -10000 0 -0.49 40 40
EDN1 -0.056 0.11 0.2 6 -0.18 204 210
EDN3 0.019 0.024 -10000 0 -0.12 16 16
EDN2 0.018 0.027 -10000 0 -0.12 21 21
HRAS/GDP -0.067 0.14 -10000 0 -0.3 110 110
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.049 0.11 0.2 3 -0.23 110 113
ADCY4 -0.058 0.11 0.2 6 -0.2 162 168
ADCY5 -0.06 0.11 0.2 5 -0.2 166 171
ADCY6 -0.057 0.11 0.2 6 -0.2 159 165
ADCY7 -0.056 0.11 0.2 6 -0.2 159 165
ADCY1 -0.057 0.11 0.2 6 -0.2 158 164
ADCY2 -0.057 0.11 0.2 6 -0.2 160 166
ADCY3 -0.058 0.11 0.2 6 -0.2 161 167
ADCY8 -0.066 0.11 0.2 4 -0.2 173 177
ADCY9 -0.059 0.11 0.2 6 -0.2 160 166
arachidonic acid secretion -0.13 0.23 -10000 0 -0.44 154 154
ETB receptor/Endothelin-1/Gq/GTP -0.021 0.081 -10000 0 -0.18 78 78
GNAO1 0.011 0.041 -10000 0 -0.12 50 50
HRAS 0.022 0.006 -10000 0 -0.12 1 1
ETA receptor/Endothelin-1/G12/GTP -0.052 0.14 0.32 6 -0.23 158 164
ETA receptor/Endothelin-1/Gs/GTP -0.049 0.13 0.3 6 -0.22 150 156
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.13 0.19 0.28 6 -0.35 202 208
EDNRB -0.012 0.053 -10000 0 -0.088 152 152
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.073 0.14 0.28 6 -0.26 150 156
CYSLTR1 -0.082 0.14 0.28 5 -0.28 150 155
SLC9A1 -0.042 0.088 0.19 6 -0.18 123 129
mol:GDP -0.078 0.15 0.21 2 -0.31 116 118
SLC9A3 -0.057 0.16 -10000 0 -0.44 45 45
RAF1 -0.09 0.18 -10000 0 -0.37 127 127
JUN -0.08 0.27 -10000 0 -0.78 62 62
JAK2 -0.08 0.14 0.27 6 -0.25 174 180
mol:IP3 -0.051 0.12 -10000 0 -0.25 97 97
ETA receptor/Endothelin-1 -0.084 0.17 0.36 6 -0.29 172 178
PLCB1 0.011 0.034 -10000 0 -0.12 33 33
PLCB2 0.019 0.019 -10000 0 -0.12 9 9
ETA receptor/Endothelin-3 -0.02 0.077 0.16 5 -0.13 135 140
FOS -0.17 0.34 -10000 0 -0.85 107 107
Gai/GDP 0.012 0.071 -10000 0 -0.56 4 4
CRK 0.021 0.016 -10000 0 -0.12 7 7
mol:Ca ++ -0.098 0.16 0.27 3 -0.32 161 164
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
PRKCB1 -0.051 0.11 -10000 0 -0.25 96 96
GNAQ 0.019 0.017 -10000 0 -0.12 6 6
GNAZ 0.022 0.012 -10000 0 -0.12 4 4
GNAL 0.021 0.019 -10000 0 -0.12 10 10
Gs family/GDP -0.066 0.14 -10000 0 -0.29 110 110
ETA receptor/Endothelin-1/Gq/GTP -0.042 0.12 0.21 4 -0.23 101 105
MAPK14 -0.027 0.086 -10000 0 -0.19 86 86
TRPC6 -0.042 0.17 -10000 0 -0.52 36 36
GNAI2 0.022 0.01 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 36 36
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.031 0.089 -10000 0 -0.2 84 84
ETB receptor/Endothelin-2 0.004 0.048 -10000 0 -0.11 46 46
ETB receptor/Endothelin-3 0.007 0.043 -10000 0 -0.1 38 38
ETB receptor/Endothelin-1 -0.048 0.1 0.17 4 -0.18 165 169
MAPK3 -0.16 0.3 -10000 0 -0.73 113 113
MAPK1 -0.16 0.31 -10000 0 -0.74 112 112
Rac1/GDP -0.067 0.14 -10000 0 -0.3 110 110
cAMP biosynthetic process -0.039 0.1 0.2 6 -0.19 124 130
MAPK8 -0.057 0.19 -10000 0 -0.5 70 70
SRC 0.023 0.009 -10000 0 -0.12 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.034 0.096 -10000 0 -0.24 70 70
p130Cas/CRK/Src/PYK2 -0.053 0.15 -10000 0 -0.37 69 69
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.066 0.14 -10000 0 -0.3 111 111
COL1A2 -0.14 0.23 0.28 5 -0.46 166 171
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.022 0.079 0.16 5 -0.13 139 144
mol:DAG -0.051 0.12 -10000 0 -0.25 97 97
MAP2K2 -0.12 0.23 -10000 0 -0.54 118 118
MAP2K1 -0.12 0.23 -10000 0 -0.53 117 117
EDNRA -0.049 0.1 0.2 6 -0.17 189 195
positive regulation of muscle contraction -0.059 0.12 0.24 6 -0.21 160 166
Gq family/GDP -0.044 0.14 -10000 0 -0.29 98 98
HRAS/GTP -0.068 0.14 -10000 0 -0.29 108 108
PRKCH -0.051 0.12 -10000 0 -0.24 104 104
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.056 0.12 -10000 0 -0.25 104 104
PRKCB -0.053 0.11 -10000 0 -0.24 101 101
PRKCE -0.05 0.11 -10000 0 -0.24 104 104
PRKCD -0.054 0.12 -10000 0 -0.25 103 103
PRKCG -0.049 0.12 -10000 0 -0.25 95 95
regulation of vascular smooth muscle contraction -0.2 0.4 -10000 0 -1 107 107
PRKCQ -0.058 0.12 -10000 0 -0.25 109 109
PLA2G4A -0.14 0.25 -10000 0 -0.48 154 154
GNA14 0.018 0.022 -10000 0 -0.12 11 11
GNA15 0.02 0.018 -10000 0 -0.12 8 8
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA11 0.021 0.015 -10000 0 -0.12 5 5
Rac1/GTP -0.052 0.14 0.32 6 -0.23 159 165
MMP1 0.016 0.14 0.24 2 -0.6 15 17
Osteopontin-mediated events

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
IKK alpha homodimer -0.046 0.11 -9999 0 -0.23 114 114
NF kappa B1 p50/RelA/I kappa B alpha -0.067 0.17 -9999 0 -0.33 132 132
alphaV/beta3 Integrin/Osteopontin/Src -0.038 0.11 -9999 0 -0.19 165 165
AP1 -0.12 0.16 -9999 0 -0.3 185 185
ILK -0.046 0.099 -9999 0 -0.22 105 105
bone resorption -0.041 0.11 -9999 0 -0.19 153 153
PTK2B 0.023 0.009 -9999 0 -0.12 2 2
PYK2/p130Cas -0.022 0.11 -9999 0 -0.2 116 116
ITGAV 0.008 0.036 -9999 0 -0.12 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0 0.069 -9999 0 -0.12 127 127
alphaV/beta3 Integrin/Osteopontin -0.041 0.12 -9999 0 -0.22 131 131
MAP3K1 -0.05 0.1 -9999 0 -0.2 132 132
JUN 0.013 0.032 -9999 0 -0.12 30 30
MAPK3 -0.063 0.12 -9999 0 -0.26 138 138
MAPK1 -0.064 0.13 -9999 0 -0.26 138 138
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.053 0.1 -9999 0 -0.2 144 144
ITGB3 0 0.047 -9999 0 -0.12 70 70
NFKBIA -0.08 0.16 -9999 0 -0.33 139 139
FOS -0.006 0.053 -9999 0 -0.12 95 95
CD44 0.011 0.038 -9999 0 -0.12 42 42
CHUK 0.021 0.013 -9999 0 -0.12 4 4
PLAU -0.22 0.4 -9999 0 -1 107 107
NF kappa B1 p50/RelA -0.067 0.17 -9999 0 -0.37 117 117
BCAR1 0.023 0.01 -9999 0 -0.12 3 3
RELA 0.023 0.009 -9999 0 -0.12 2 2
alphaV beta3 Integrin -0.027 0.087 -9999 0 -0.17 119 119
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.047 0.1 -9999 0 -0.21 127 127
VAV3 -0.054 0.11 -9999 0 -0.22 140 140
MAP3K14 -0.053 0.11 -9999 0 -0.22 135 135
ROCK2 0.019 0.021 -9999 0 -0.12 12 12
SPP1 0.009 0.034 -9999 0 -0.12 31 31
RAC1 0.023 0.002 -9999 0 -10000 0 0
Rac1/GTP -0.05 0.1 -9999 0 -0.2 145 145
MMP2 -0.13 0.16 -9999 0 -0.28 244 244
Syndecan-1-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
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CCL5 0.006 0.042 -9999 0 -0.12 55 55
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
FGFR/FGF2/Syndecan-1 -0.083 0.12 -9999 0 -0.25 135 135
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.072 0.12 -9999 0 -0.24 140 140
Syndecan-1/Syntenin -0.076 0.13 -9999 0 -0.24 153 153
MAPK3 -0.06 0.12 -9999 0 -0.27 84 84
HGF/MET -0.017 0.074 -9999 0 -0.11 198 198
TGFB1/TGF beta receptor Type II 0.019 0.023 -9999 0 -0.12 14 14
BSG 0.022 0.012 -9999 0 -0.12 4 4
keratinocyte migration -0.071 0.12 -9999 0 -0.23 140 140
Syndecan-1/RANTES -0.086 0.14 -9999 0 -0.25 167 167
Syndecan-1/CD147 -0.062 0.12 -9999 0 -0.29 82 82
Syndecan-1/Syntenin/PIP2 -0.074 0.12 -9999 0 -0.23 153 153
LAMA5 0.019 0.025 -9999 0 -0.12 17 17
positive regulation of cell-cell adhesion -0.073 0.12 -9999 0 -0.22 153 153
MMP7 -0.021 0.059 -9999 0 -0.12 144 144
HGF 0.02 0.022 -9999 0 -0.12 14 14
Syndecan-1/CASK -0.079 0.12 -9999 0 -0.24 135 135
Syndecan-1/HGF/MET -0.086 0.13 -9999 0 -0.24 171 171
regulation of cell adhesion -0.058 0.11 -9999 0 -0.26 86 86
HPSE 0.013 0.034 -9999 0 -0.12 34 34
positive regulation of cell migration -0.083 0.12 -9999 0 -0.25 135 135
SDC1 -0.084 0.12 -9999 0 -0.25 135 135
Syndecan-1/Collagen -0.083 0.12 -9999 0 -0.25 135 135
PPIB 0.023 0.003 -9999 0 -10000 0 0
MET 0.001 0.047 -9999 0 -0.12 71 71
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
MMP9 0 0.05 -9999 0 -0.12 81 81
MAPK1 -0.061 0.12 -9999 0 -0.27 83 83
homophilic cell adhesion -0.082 0.12 -9999 0 -0.25 135 135
MMP1 -0.007 0.058 -9999 0 -0.12 116 116
PDGFR-alpha signaling pathway

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
PDGFRA -0.004 0.045 -10000 0 -0.13 59 59
PDGF/PDGFRA/CRKL -0.008 0.067 -10000 0 -0.13 119 119
positive regulation of JUN kinase activity 0.01 0.066 -10000 0 -0.1 119 119
CRKL 0.023 0.009 -10000 0 -0.12 2 2
PDGF/PDGFRA/Caveolin-3 -0.008 0.067 -10000 0 -0.14 101 101
AP1 -0.15 0.26 -10000 0 -0.67 107 107
mol:IP3 -0.007 0.046 -10000 0 -0.071 151 151
PLCG1 -0.007 0.046 -10000 0 -0.071 151 151
PDGF/PDGFRA/alphaV Integrin -0.036 0.092 -10000 0 -0.16 166 166
RAPGEF1 0.023 0 -10000 0 -10000 0 0
CRK 0.022 0.016 -10000 0 -0.12 7 7
mol:Ca2+ -0.007 0.046 -10000 0 -0.071 151 151
CAV3 0.022 0.01 -10000 0 -0.12 3 3
CAV1 0.012 0.038 -10000 0 -0.12 42 42
SHC/Grb2/SOS1 0.011 0.067 -10000 0 -0.1 119 119
PDGF/PDGFRA/Shf -0.008 0.067 -10000 0 -0.13 119 119
FOS -0.14 0.26 -10000 0 -0.66 107 107
JUN -0.019 0.044 0.26 4 -0.13 31 35
oligodendrocyte development -0.036 0.092 -10000 0 -0.16 166 166
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:DAG -0.007 0.046 -10000 0 -0.071 151 151
PDGF/PDGFRA -0.004 0.045 -10000 0 -0.13 59 59
actin cytoskeleton reorganization -0.008 0.067 -10000 0 -0.13 115 115
SRF 0.024 0.022 -10000 0 -0.068 24 24
SHC1 0.023 0.001 -10000 0 -10000 0 0
PI3K -0.013 0.084 -10000 0 -0.13 153 153
PDGF/PDGFRA/Crk/C3G 0.009 0.06 -10000 0 -0.11 91 91
JAK1 0.004 0.031 -10000 0 -0.074 61 61
ELK1/SRF -0.011 0.065 -10000 0 -0.13 107 107
SHB 0.023 0.008 -10000 0 -0.12 2 2
SHF 0.023 0.008 -10000 0 -0.12 2 2
CSNK2A1 0.031 0.021 0.064 22 -0.1 6 28
GO:0007205 -0.022 0.07 -10000 0 -0.14 109 109
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Ras protein signal transduction 0.01 0.066 -10000 0 -0.1 119 119
PDGF/PDGFRA/SHB -0.008 0.067 -10000 0 -0.13 115 115
PDGF/PDGFRA/Caveolin-1 -0.018 0.079 -10000 0 -0.12 178 178
ITGAV 0.012 0.033 -10000 0 -0.12 31 31
ELK1 -0.023 0.068 -10000 0 -0.12 144 144
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PDGF/PDGFRA/Crk -0.009 0.067 -10000 0 -0.13 122 122
JAK-STAT cascade 0.004 0.031 -10000 0 -0.074 61 61
cell proliferation -0.008 0.066 -10000 0 -0.13 119 119
Nectin adhesion pathway

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
PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
alphaV beta3 Integrin -0.018 0.081 -9999 0 -0.16 107 107
PTK2 -0.074 0.15 -9999 0 -0.31 143 143
positive regulation of JNK cascade -0.053 0.11 -9999 0 -0.27 120 120
CDC42/GDP -0.046 0.17 -9999 0 -0.36 120 120
Rac1/GDP -0.045 0.17 -9999 0 -0.35 120 120
RAP1B 0.019 0.019 -9999 0 -0.12 10 10
RAP1A 0.021 0.011 -9999 0 -0.12 3 3
CTNNB1 0.022 0.007 -9999 0 -0.12 1 1
CDC42/GTP -0.046 0.15 -9999 0 -0.32 120 120
nectin-3/I-afadin -0.021 0.08 -9999 0 -0.16 123 123
RAPGEF1 -0.062 0.17 -9999 0 -0.38 119 119
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.075 0.19 -9999 0 -0.43 119 119
PDGFB-D/PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
TLN1 -0.038 0.097 -9999 0 -0.16 160 160
Rap1/GTP -0.064 0.12 -9999 0 -0.28 120 120
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
Rap1/GTP/I-afadin 0.015 0.06 -9999 0 -0.11 88 88
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.021 0.08 -9999 0 -0.16 123 123
PVR 0.022 0.012 -9999 0 -0.12 4 4
Necl-5(dimer) 0.022 0.012 -9999 0 -0.12 4 4
mol:GDP -0.068 0.2 -9999 0 -0.43 120 120
MLLT4 0.014 0.032 -9999 0 -0.12 30 30
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K -0.009 0.085 -9999 0 -0.11 183 183
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.017 0.049 -9999 0 -0.11 71 71
positive regulation of lamellipodium assembly -0.06 0.12 -9999 0 -0.28 130 130
PVRL1 0.023 0.01 -9999 0 -0.12 3 3
PVRL3 0.003 0.046 -9999 0 -0.12 67 67
PVRL2 0.019 0.023 -9999 0 -0.12 15 15
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
CDH1 0.021 0.015 -9999 0 -0.12 6 6
CLDN1 -0.003 0.051 -9999 0 -0.12 88 88
JAM-A/CLDN1 -0.03 0.087 -9999 0 -0.12 221 221
SRC -0.083 0.21 -9999 0 -0.48 119 119
ITGB3 0.005 0.046 -9999 0 -0.12 67 67
nectin-1(dimer)/I-afadin/I-afadin 0.017 0.049 -9999 0 -0.11 71 71
FARP2 -0.065 0.19 -9999 0 -0.42 120 120
RAC1 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.004 0.073 -9999 0 -0.12 124 124
nectin-1/I-afadin 0.017 0.049 -9999 0 -0.11 71 71
nectin-2/I-afadin 0.012 0.054 -9999 0 -0.11 89 89
RAC1/GTP/IQGAP1/filamentous actin 0.017 0.045 -9999 0 -0.11 57 57
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.004 0.072 -9999 0 -0.12 123 123
CDC42/GTP/IQGAP1/filamentous actin 0.017 0.044 -9999 0 -0.12 49 49
F11R 0.023 0.007 -9999 0 -0.12 1 1
positive regulation of filopodium formation -0.053 0.11 -9999 0 -0.27 120 120
alphaV/beta3 Integrin/Talin -0.052 0.11 -9999 0 -0.2 155 155
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.012 0.054 -9999 0 -0.11 89 89
nectin-2(dimer)/I-afadin/I-afadin 0.012 0.054 -9999 0 -0.11 89 89
PIP5K1C -0.046 0.1 -9999 0 -0.17 177 177
VAV2 -0.078 0.21 -9999 0 -0.44 130 130
RAP1/GDP -0.046 0.16 -9999 0 -0.33 120 120
ITGAV 0.012 0.033 -9999 0 -0.12 31 31
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.008 0.074 -9999 0 -0.12 132 132
nectin-3(dimer)/I-afadin/I-afadin -0.021 0.08 -9999 0 -0.16 123 123
Rac1/GTP -0.052 0.16 -9999 0 -0.34 130 130
PTPRM -0.056 0.11 -9999 0 -0.2 177 177
E-cadherin/beta catenin/alpha catenin 0.031 0.071 -9999 0 -0.18 27 27
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.023 0.002 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.007 0.041 -10000 0 -0.12 51 51
EPHB2 0.022 0.021 -10000 0 -0.12 11 11
EFNB1 0.023 0.019 -10000 0 -0.067 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.055 -10000 0 -0.15 11 11
Ephrin B2/EPHB1-2 0.011 0.061 -10000 0 -0.1 102 102
neuron projection morphogenesis 0.029 0.046 -10000 0 -0.15 11 11
Ephrin B1/EPHB1-2/Tiam1 0.04 0.056 -10000 0 -0.1 49 49
DNM1 0.022 0.02 -10000 0 -0.12 11 11
cell-cell signaling 0.002 0.004 -10000 0 -10000 0 0
MAP2K4 -0.12 0.21 -10000 0 -0.47 151 151
YES1 -0.19 0.31 -10000 0 -0.71 151 151
Ephrin B1/EPHB1-2/NCK2 0.051 0.043 -10000 0 -0.093 26 26
PI3K -0.13 0.22 -10000 0 -0.47 156 156
mol:GDP 0.039 0.055 -10000 0 -0.1 49 49
ITGA2B 0.023 0.006 -10000 0 -0.12 1 1
endothelial cell proliferation 0.001 0.057 -10000 0 -0.094 143 143
FYN -0.2 0.31 -10000 0 -0.71 151 151
MAP3K7 -0.13 0.22 -10000 0 -0.5 151 151
FGR -0.18 0.31 -10000 0 -0.69 151 151
TIAM1 0.015 0.032 -10000 0 -0.12 29 29
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
RGS3 0.023 0.006 -10000 0 -0.12 1 1
cell adhesion -0.12 0.2 -10000 0 -0.45 153 153
LYN -0.2 0.31 -10000 0 -0.71 151 151
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.28 -10000 0 -0.64 151 151
Ephrin B1/EPHB1-2 -0.15 0.24 -10000 0 -0.54 151 151
SRC -0.18 0.31 -10000 0 -0.69 151 151
ITGB3 0.005 0.046 -10000 0 -0.12 67 67
EPHB1 0.018 0.032 -10000 0 -0.12 29 29
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.058 -10000 0 -0.094 143 143
alphaIIb/beta3 Integrin 0.011 0.053 -10000 0 -0.14 38 38
BLK -0.18 0.31 -10000 0 -0.69 151 151
HCK -0.19 0.31 -10000 0 -0.7 151 151
regulation of stress fiber formation -0.049 0.043 0.092 26 -10000 0 26
MAPK8 -0.12 0.2 -10000 0 -0.44 151 151
Ephrin B1/EPHB1-2/RGS3 0.051 0.043 -10000 0 -0.095 26 26
endothelial cell migration -0.12 0.18 -10000 0 -0.41 154 154
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTPN13 -0.012 0.057 -10000 0 -0.13 110 110
regulation of focal adhesion formation -0.049 0.043 0.092 26 -10000 0 26
chemotaxis -0.049 0.042 0.094 26 -10000 0 26
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
Rac1/GTP 0.038 0.05 -10000 0 -0.15 11 11
angiogenesis -0.15 0.23 -10000 0 -0.53 151 151
LCK -0.18 0.31 -10000 0 -0.69 151 151
TCGA08_p53

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
CDKN2A 0.007 0.012 -10000 0 -0.076 10 10
TP53 -0.05 0.11 0.18 14 -0.24 126 140
Senescence -0.069 0.13 0.18 14 -0.26 158 172
Apoptosis -0.069 0.13 0.18 14 -0.26 158 172
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.002 0.01 0.056 9 -0.083 4 13
MDM4 0.018 0.023 -10000 0 -0.12 15 15
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.029 0.082 -9999 0 -0.13 181 181
alphaM/beta2 Integrin/GPIbA 0.022 0.058 -9999 0 -0.11 77 77
alphaM/beta2 Integrin/proMMP-9 -0.005 0.08 -9999 0 -0.13 130 130
PLAUR 0.018 0.023 -9999 0 -0.12 14 14
HMGB1 0.023 0.008 -9999 0 -0.041 1 1
alphaM/beta2 Integrin/Talin 0.015 0.069 -9999 0 -0.12 97 97
AGER 0.022 0.017 -9999 0 -0.068 15 15
RAP1A 0.021 0.011 -9999 0 -0.12 3 3
SELPLG 0.02 0.021 -9999 0 -0.12 12 12
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.034 0.069 -9999 0 -0.15 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 0 0.05 -9999 0 -0.12 81 81
CYR61 0.002 0.047 -9999 0 -0.12 70 70
TLN1 0.021 0.013 -9999 0 -0.12 4 4
Rap1/GTP -0.099 0.15 -9999 0 -0.28 175 175
RHOA 0.023 0.006 -9999 0 -0.12 1 1
P-selectin oligomer 0.018 0.026 -9999 0 -0.12 20 20
MYH2 -0.12 0.15 -9999 0 -0.28 219 219
MST1R 0.017 0.028 -9999 0 -0.12 23 23
leukocyte activation during inflammatory response 0.027 0.052 -9999 0 -0.091 77 77
APOB 0.023 0.01 -9999 0 -0.12 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.015 0.059 -9999 0 -0.12 131 131
JAM3 0.02 0.02 -9999 0 -0.12 11 11
GP1BA 0.023 0.009 -9999 0 -0.12 2 2
alphaM/beta2 Integrin/CTGF 0.004 0.073 -9999 0 -0.12 119 119
alphaM/beta2 Integrin -0.12 0.16 -9999 0 -0.33 158 158
JAM3 homodimer 0.02 0.02 -9999 0 -0.12 11 11
ICAM2 0.017 0.028 -9999 0 -0.12 23 23
ICAM1 0 0.048 -9999 0 -0.12 75 75
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.16 -9999 0 -0.33 158 158
cell adhesion 0.022 0.058 -9999 0 -0.11 77 77
NFKB1 0.022 0.07 -9999 0 -0.22 23 23
THY1 -0.002 0.048 -9999 0 -0.12 77 77
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Lipoprotein(a) 0.03 0.013 -9999 0 -0.062 11 11
alphaM/beta2 Integrin/LRP/tPA -0.017 0.087 -9999 0 -0.12 209 209
IL6 0.007 0.094 -9999 0 -0.34 17 17
ITGB2 0.013 0.032 -9999 0 -0.097 37 37
elevation of cytosolic calcium ion concentration -0.015 0.1 -9999 0 -0.15 153 153
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.062 -9999 0 -0.1 84 84
JAM2 0.015 0.034 -9999 0 -0.12 34 34
alphaM/beta2 Integrin/ICAM1 0.005 0.087 -9999 0 -0.12 149 149
alphaM/beta2 Integrin/uPA/Plg -0.005 0.087 -9999 0 -0.13 142 142
RhoA/GTP -0.13 0.16 -9999 0 -0.29 219 219
positive regulation of phagocytosis -0.078 0.14 -9999 0 -0.28 139 139
Ron/MSP 0.027 0.031 -9999 0 -0.087 36 36
alphaM/beta2 Integrin/uPAR/uPA -0.014 0.1 -9999 0 -0.16 153 153
alphaM/beta2 Integrin/uPAR 0.012 0.077 -9999 0 -0.15 89 89
PLAU -0.006 0.054 -9999 0 -0.12 101 101
PLAT -0.002 0.049 -9999 0 -0.12 80 80
actin filament polymerization -0.12 0.14 -9999 0 -0.27 219 219
MST1 0.022 0.012 -9999 0 -0.12 4 4
alphaM/beta2 Integrin/lipoprotein(a) 0.031 0.054 -9999 0 -0.091 77 77
TNF 0.015 0.076 -9999 0 -0.26 16 16
RAP1B 0.019 0.019 -9999 0 -0.12 10 10
alphaM/beta2 Integrin/uPA -0.019 0.091 -9999 0 -0.15 143 143
fibrinolysis -0.006 0.086 -9999 0 -0.13 142 142
HCK 0.019 0.023 -9999 0 -0.12 15 15
dendritic cell antigen processing and presentation -0.12 0.16 -9999 0 -0.33 158 158
VTN 0.023 0.008 -9999 0 -0.12 2 2
alphaM/beta2 Integrin/CYR61 -0.01 0.08 -9999 0 -0.13 146 146
LPA 0.021 0.018 -9999 0 -0.12 9 9
LRP1 0.015 0.032 -9999 0 -0.12 29 29
cell migration -0.043 0.086 -9999 0 -0.13 235 235
FN1 -0.012 0.055 -9999 0 -0.12 115 115
alphaM/beta2 Integrin/Thy1 -0.026 0.085 -9999 0 -0.13 201 201
MPO 0.023 0.006 -9999 0 -0.12 1 1
KNG1 0.023 0.01 -9999 0 -0.12 3 3
RAP1/GDP 0.015 0.05 -9999 0 -0.12 62 62
ROCK1 -0.12 0.15 -9999 0 -0.28 211 211
ELA2 0.022 0.01 -9999 0 -0.12 3 3
PLG 0.023 0.008 -9999 0 -0.12 2 2
CTGF 0.012 0.035 -9999 0 -0.12 37 37
alphaM/beta2 Integrin/Hck 0.018 0.07 -9999 0 -0.14 81 81
ITGAM 0.021 0.019 -9999 0 -0.11 9 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.03 0.066 -9999 0 -0.11 82 82
HP -0.034 0.062 -9999 0 -0.12 194 194
leukocyte adhesion -0.009 0.088 -9999 0 -0.17 69 69
SELP 0.018 0.026 -9999 0 -0.12 20 20
Thromboxane A2 receptor signaling

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
TGM2 0.005 0.046 -10000 0 -0.12 67 67
GNB1/GNG2 -0.069 0.081 -10000 0 -0.18 197 197
AKT1 -0.055 0.11 -10000 0 -0.19 197 197
EGF 0.02 0.021 -10000 0 -0.12 13 13
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.026 0.029 -10000 0 -0.11 7 7
mol:Ca2+ -0.095 0.15 -10000 0 -0.29 200 200
LYN 0.024 0.032 -10000 0 -0.13 9 9
RhoA/GTP -0.036 0.069 -10000 0 -0.12 200 200
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.17 -10000 0 -0.34 198 198
GNG2 0.02 0.018 -10000 0 -0.12 9 9
ARRB2 0.022 0.013 -10000 0 -0.12 5 5
TP alpha/Gq family/GDP/G beta5/gamma2 0.027 0.048 -10000 0 -0.24 13 13
G beta5/gamma2 -0.09 0.11 -10000 0 -0.23 196 196
PRKCH -0.12 0.18 -10000 0 -0.35 198 198
DNM1 0.02 0.02 -10000 0 -0.12 11 11
TXA2/TP beta/beta Arrestin3 0.017 0.014 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.023 0.006 -10000 0 -0.12 1 1
G12 family/GTP -0.12 0.13 -10000 0 -0.29 199 199
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
ADRBK2 0.015 0.031 -10000 0 -0.12 28 28
RhoA/GTP/ROCK1 0.028 0.021 -10000 0 -0.1 14 14
mol:GDP 0.05 0.12 0.23 95 -10000 0 95
mol:NADP 0.023 0 -10000 0 -10000 0 0
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
PRKG1 0.018 0.026 -10000 0 -0.12 19 19
mol:IP3 -0.12 0.19 -10000 0 -0.36 199 199
cell morphogenesis 0.027 0.021 -10000 0 -0.1 14 14
PLCB2 -0.17 0.25 -10000 0 -0.49 198 198
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.026 0.029 -10000 0 -0.12 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.032 -10000 0 -0.14 7 7
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PTGIR 0.023 0.002 -10000 0 -10000 0 0
PRKCB1 -0.12 0.19 -10000 0 -0.37 199 199
GNAQ 0.021 0.015 -10000 0 -0.12 6 6
mol:L-citrulline 0.023 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.18 0.26 -10000 0 -0.51 198 198
LCK 0.026 0.029 -10000 0 -0.11 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.042 0.026 -10000 0 -0.12 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.061 -10000 0 -0.43 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.041 0.028 -10000 0 -0.12 7 7
MAPK14 -0.073 0.12 -10000 0 -0.22 200 200
TGM2/GTP -0.14 0.21 -10000 0 -0.4 205 205
MAPK11 -0.072 0.12 -10000 0 -0.22 199 199
ARHGEF1 -0.053 0.094 -10000 0 -0.17 199 199
GNAI2 0.022 0.01 -10000 0 -0.12 3 3
JNK cascade -0.13 0.19 -10000 0 -0.38 198 198
RAB11/GDP 0.023 0.007 -10000 0 -0.12 1 1
ICAM1 -0.11 0.16 -10000 0 -0.32 198 198
cAMP biosynthetic process -0.11 0.17 -10000 0 -0.33 205 205
Gq family/GTP/EBP50 0.018 0.042 -10000 0 -0.14 28 28
actin cytoskeleton reorganization 0.027 0.021 -10000 0 -0.1 14 14
SRC 0.026 0.029 -10000 0 -0.11 6 6
GNB5 0.022 0.01 -10000 0 -0.12 3 3
GNB1 0.023 0.006 -10000 0 -0.12 1 1
EGF/EGFR 0.018 0.057 -10000 0 -0.13 38 38
VCAM1 -0.12 0.17 -10000 0 -0.34 198 198
TP beta/Gq family/GDP/G beta5/gamma2 0.027 0.048 -10000 0 -0.24 13 13
platelet activation -0.093 0.16 -10000 0 -0.29 198 198
PGI2/IP 0.015 0.017 -10000 0 -0.15 6 6
PRKACA 0.021 0.022 -10000 0 -0.15 8 8
Gq family/GDP/G beta5/gamma2 0.027 0.046 -10000 0 -0.22 13 13
TXA2/TP beta/beta Arrestin2 0.016 0.032 -10000 0 -0.26 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.021 0.021 -10000 0 -0.14 8 8
mol:DAG -0.14 0.21 -10000 0 -0.41 198 198
EGFR 0.015 0.03 -10000 0 -0.12 25 25
TXA2/TP alpha -0.15 0.23 -10000 0 -0.44 205 205
Gq family/GTP 0.014 0.036 -10000 0 -0.14 25 25
YES1 0.024 0.032 -10000 0 -0.14 8 8
GNAI2/GTP 0.02 0.03 -10000 0 -0.12 7 7
PGD2/DP 0.017 0.004 -10000 0 -0.076 1 1
SLC9A3R1 0.016 0.03 -10000 0 -0.12 26 26
FYN 0.02 0.035 -10000 0 -0.13 13 13
mol:NO 0.023 0 -10000 0 -10000 0 0
GNA15 0.021 0.017 -10000 0 -0.12 8 8
PGK/cGMP 0.028 0.016 -10000 0 -0.057 19 19
RhoA/GDP 0.023 0.006 -10000 0 -0.12 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.041 0.045 -10000 0 -0.15 7 7
NOS3 0.023 0 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.35 200 200
PRKCB -0.12 0.18 -10000 0 -0.34 198 198
PRKCE -0.12 0.18 -10000 0 -0.35 198 198
PRKCD -0.12 0.19 -10000 0 -0.37 198 198
PRKCG -0.12 0.19 -10000 0 -0.37 198 198
muscle contraction -0.16 0.24 -10000 0 -0.47 198 198
PRKCZ -0.11 0.17 -10000 0 -0.33 198 198
ARR3 0.023 0.006 -10000 0 -0.12 1 1
TXA2/TP beta 0.033 0.035 -10000 0 -0.12 11 11
PRKCQ -0.12 0.18 -10000 0 -0.35 199 199
MAPKKK cascade -0.15 0.22 -10000 0 -0.43 198 198
SELE -0.094 0.15 -10000 0 -0.28 198 198
TP beta/GNAI2/GDP/G beta/gamma 0.052 0.035 -10000 0 -0.14 5 5
ROCK1 0.023 0.009 -10000 0 -0.12 2 2
GNA14 0.02 0.02 -10000 0 -0.12 11 11
chemotaxis -0.21 0.3 -10000 0 -0.6 196 196
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
GNA11 0.022 0.013 -10000 0 -0.12 5 5
Rac1/GTP 0.015 0.015 -10000 0 -0.15 5 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.019 -9999 0 -0.12 10 10
LAT2 -0.033 0.11 -9999 0 -0.2 138 138
AP1 -0.069 0.18 -9999 0 -0.36 120 120
mol:PIP3 -0.037 0.14 -9999 0 -0.26 128 128
IKBKB -0.014 0.083 -9999 0 -0.15 127 127
AKT1 -0.025 0.07 -9999 0 -0.13 116 116
IKBKG -0.014 0.082 -9999 0 -0.15 125 125
MS4A2 0.027 0.014 -9999 0 -0.13 3 3
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
MAP3K1 -0.038 0.13 -9999 0 -0.28 99 99
mol:Ca2+ -0.027 0.11 -9999 0 -0.2 128 128
LYN 0.02 0.014 -9999 0 -0.12 4 4
CBLB -0.032 0.1 -9999 0 -0.2 131 131
SHC1 0.023 0.001 -9999 0 -10000 0 0
RasGAP/p62DOK -0.005 0.066 -9999 0 -0.11 134 134
positive regulation of cell migration 0.011 0.009 -9999 0 -0.076 6 6
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.008 0.05 -9999 0 -0.1 72 72
PTPN13 -0.087 0.19 -9999 0 -0.44 94 94
PTPN11 0.021 0.013 -9999 0 -0.12 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.034 0.11 -9999 0 -0.24 84 84
SYK 0.016 0.028 -9999 0 -0.12 21 21
GRB2 0.023 0.006 -9999 0 -0.12 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.26 130 130
LAT -0.032 0.1 -9999 0 -0.2 137 137
PAK2 -0.044 0.14 -9999 0 -0.29 108 108
NFATC2 -0.003 0.062 -9999 0 -0.35 14 14
HRAS -0.048 0.15 -9999 0 -0.28 132 132
GAB2 0.007 0.041 -9999 0 -0.12 52 52
PLA2G1B 0.017 0.11 -9999 0 -0.91 8 8
Fc epsilon R1 0.003 0.062 -9999 0 -0.094 129 129
Antigen/IgE/Fc epsilon R1 0.006 0.055 -9999 0 -0.079 130 130
mol:GDP -0.058 0.17 -9999 0 -0.32 132 132
JUN 0.014 0.032 -9999 0 -0.12 30 30
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
FOS -0.005 0.052 -9999 0 -0.12 95 95
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.037 0.11 -9999 0 -0.21 139 139
CHUK -0.017 0.085 -9999 0 -0.17 103 103
KLRG1 -0.015 0.088 -9999 0 -0.18 105 105
VAV1 -0.034 0.11 -9999 0 -0.2 133 133
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.032 0.1 -9999 0 -0.2 137 137
negative regulation of mast cell degranulation -0.027 0.086 -9999 0 -0.2 80 80
BTK -0.065 0.19 -9999 0 -0.42 91 91
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.1 -9999 0 -0.19 154 154
GAB2/PI3K/SHP2 -0.045 0.059 -9999 0 -0.14 117 117
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.003 0.072 -9999 0 -0.23 40 40
RAF1 0.011 0.12 -9999 0 -0.98 8 8
Fc epsilon R1/FcgammaRIIB/SHIP -0.008 0.083 -9999 0 -0.12 184 184
FCER1G 0.002 0.044 -9999 0 -0.12 63 63
FCER1A 0.018 0.027 -9999 0 -0.12 20 20
Antigen/IgE/Fc epsilon R1/Fyn 0.002 0.065 -9999 0 -0.1 95 95
MAPK3 0.015 0.11 -9999 0 -0.92 8 8
MAPK1 0.014 0.11 -9999 0 -0.92 8 8
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.008 0.13 -9999 0 -0.53 27 27
DUSP1 -0.004 0.051 -9999 0 -0.12 90 90
NF-kappa-B/RelA -0.005 0.062 -9999 0 -0.12 100 100
actin cytoskeleton reorganization -0.065 0.19 -9999 0 -0.5 67 67
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.037 0.14 -9999 0 -0.25 138 138
FER -0.032 0.1 -9999 0 -0.2 135 135
RELA 0.023 0.009 -9999 0 -0.12 2 2
ITK -0.004 0.049 -9999 0 -0.26 11 11
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG1 -0.055 0.17 -9999 0 -0.31 133 133
cytokine secretion -0.005 0.044 -9999 0 -0.088 100 100
SPHK1 -0.033 0.1 -9999 0 -0.2 138 138
PTK2 -0.069 0.21 -9999 0 -0.53 66 66
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.27 133 133
EDG1 0.011 0.009 -9999 0 -0.076 6 6
mol:DAG -0.035 0.14 -9999 0 -0.26 126 126
MAP2K2 0.011 0.11 -9999 0 -0.93 8 8
MAP2K1 0.013 0.11 -9999 0 -0.92 8 8
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
KLRG1/SHP2 -0.014 0.084 -9999 0 -0.17 95 95
MAP2K4 0.012 0.12 -9999 0 -0.84 11 11
Fc epsilon R1/FcgammaRIIB -0.009 0.09 -9999 0 -0.13 184 184
mol:Choline -0.008 0.05 -9999 0 -0.1 72 72
SHC/Grb2/SOS1 -0.012 0.12 -9999 0 -0.19 138 138
FYN 0.012 0.037 -9999 0 -0.12 40 40
DOK1 0.022 0.015 -9999 0 -0.12 6 6
PXN -0.059 0.19 -9999 0 -0.48 66 66
HCLS1 -0.035 0.12 -9999 0 -0.23 117 117
PRKCB -0.026 0.11 -9999 0 -0.2 128 128
FCGR2B 0.004 0.044 -9999 0 -0.12 61 61
IGHE -0.001 0.003 -9999 0 -10000 0 0
KLRG1/SHIP -0.027 0.087 -9999 0 -0.2 80 80
LCP2 0.013 0.033 -9999 0 -0.12 31 31
PLA2G4A -0.045 0.11 -9999 0 -0.22 131 131
RASA1 0.021 0.011 -9999 0 -0.12 3 3
mol:Phosphatidic acid -0.008 0.05 -9999 0 -0.1 72 72
IKK complex -0.006 0.068 -9999 0 -0.14 89 89
WIPF1 0.02 0.02 -9999 0 -0.12 11 11
PLK2 and PLK4 events

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
PLK2 -0.002 0.049 -9999 0 -0.12 82 82
PLK4 0.017 0.028 -9999 0 -0.12 22 22
regulation of centriole replication -0.002 0.047 -9999 0 -0.09 102 102
Cellular roles of Anthrax toxin

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
ANTXR1 0.007 0.042 -10000 0 -0.12 55 55
ANTXR2 0.013 0.035 -10000 0 -0.12 36 36
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.013 -10000 0 -0.033 102 102
monocyte activation -0.099 0.16 -10000 0 -0.35 157 157
MAP2K2 0.006 0.052 -10000 0 -0.66 3 3
MAP2K1 0 0.015 -10000 0 -0.028 104 104
MAP2K7 0 0.014 -10000 0 -0.029 81 81
MAP2K6 -0.005 0.024 -10000 0 -0.044 111 111
CYAA -0.015 0.047 -10000 0 -0.11 102 102
MAP2K4 0 0.016 -10000 0 -0.031 81 81
IL1B -0.009 0.036 -10000 0 -0.075 93 93
Channel -0.002 0.058 -10000 0 -0.12 102 102
NLRP1 0 0.015 -10000 0 -0.031 81 81
CALM1 0.022 0.014 -10000 0 -0.12 5 5
negative regulation of phagocytosis 0.001 0.054 -10000 0 -0.46 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.013 0.033 102 -10000 0 102
MAPK3 0 0.015 -10000 0 -0.052 17 17
MAPK1 -0.001 0.018 -10000 0 -0.032 108 108
PGR -0.011 0.026 -10000 0 -0.055 124 124
PA/Cellular Receptors -0.004 0.064 -10000 0 -0.13 102 102
apoptosis -0.007 0.013 -10000 0 -0.033 102 102
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.057 -10000 0 -0.11 102 102
macrophage activation 0.003 0.017 -10000 0 -0.053 27 27
TNF 0.02 0.02 -10000 0 -0.12 11 11
VCAM1 -0.099 0.16 -10000 0 -0.36 157 157
platelet activation 0.001 0.054 -10000 0 -0.46 7 7
MAPKKK cascade 0.003 0.02 0.048 50 -10000 0 50
IL18 -0.011 0.039 -10000 0 -0.077 109 109
negative regulation of macrophage activation -0.007 0.013 -10000 0 -0.033 102 102
LEF -0.007 0.013 -10000 0 -0.033 102 102
CASP1 -0.005 0.024 -10000 0 -0.043 106 106
mol:cAMP 0.001 0.055 -10000 0 -0.46 7 7
necrosis -0.007 0.013 -10000 0 -0.033 102 102
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.001 0.055 -10000 0 -0.11 102 102
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.001 0.046 -9999 0 -0.12 69 69
positive regulation of NF-kappaB transcription factor activity -0.021 0.079 -9999 0 -0.12 206 206
MAP2K4 -0.008 0.086 -9999 0 -0.23 36 36
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
TNFRSF10B 0.022 0.014 -9999 0 -0.12 5 5
TNFRSF10A 0.019 0.021 -9999 0 -0.12 12 12
SMPD1 -0.013 0.053 -9999 0 -0.1 131 131
IKBKG 0.023 0.008 -9999 0 -0.12 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.023 -9999 0 -0.12 15 15
TRAIL/TRAILR2 -0.02 0.078 -9999 0 -0.12 201 201
TRAIL/TRAILR3 -0.02 0.075 -9999 0 -0.12 208 208
TRAIL/TRAILR1 -0.025 0.082 -9999 0 -0.15 138 138
TRAIL/TRAILR4 -0.021 0.079 -9999 0 -0.12 206 206
TRAIL/TRAILR1/DAP3/GTP -0.006 0.069 -9999 0 -0.11 144 144
IKK complex 0.006 0.079 -9999 0 -0.28 33 33
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.015 0.021 -9999 0 -0.14 10 10
MAPK3 0.006 0.032 -9999 0 -0.073 73 73
MAP3K1 -0.008 0.086 -9999 0 -0.25 26 26
TRAILR4 (trimer) 0.019 0.023 -9999 0 -0.12 15 15
TRADD 0.023 0.006 -9999 0 -0.12 1 1
TRAILR1 (trimer) 0.019 0.021 -9999 0 -0.12 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.011 0.082 -9999 0 -0.14 140 140
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 0.005 0.034 -9999 0 -0.074 75 75
TRAIL/TRAILR1/FADD/TRADD/RIP 0.015 0.073 -9999 0 -0.17 20 20
mol:ceramide -0.013 0.053 -9999 0 -0.1 131 131
FADD 0.023 0.009 -9999 0 -0.12 2 2
MAPK8 -0.007 0.085 -9999 0 -0.22 43 43
TRAF2 0.023 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.025 -9999 0 -0.12 18 18
CHUK 0.021 0.013 -9999 0 -0.12 4 4
TRAIL/TRAILR1/FADD -0.007 0.074 -9999 0 -0.12 139 139
DAP3 0.023 0.007 -9999 0 -0.12 1 1
CASP10 -0.038 0.098 -9999 0 -0.2 130 130
JNK cascade -0.021 0.079 -9999 0 -0.12 206 206
TRAIL (trimer) 0.001 0.046 -9999 0 -0.12 69 69
TNFRSF10C 0.019 0.025 -9999 0 -0.12 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD 0.004 0.069 -9999 0 -0.098 144 144
TRAIL/TRAILR2/FADD -0.002 0.071 -9999 0 -0.12 131 131
cell death -0.013 0.052 -9999 0 -0.1 131 131
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.079 -9999 0 -0.14 133 133
TRAILR2 (trimer) 0.022 0.014 -9999 0 -0.12 5 5
CASP8 -0.001 0.11 -9999 0 -0.66 15 15
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.019 0.071 -9999 0 -0.091 134 134
Syndecan-4-mediated signaling events

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
PTK2 -0.11 0.2 -10000 0 -0.37 178 178
Syndecan-4/Syndesmos -0.079 0.18 -10000 0 -0.4 102 102
positive regulation of JNK cascade -0.1 0.18 -10000 0 -0.4 114 114
Syndecan-4/ADAM12 -0.093 0.18 -10000 0 -0.4 105 105
CCL5 0.006 0.042 -10000 0 -0.12 55 55
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
DNM2 0.02 0.022 -10000 0 -0.12 13 13
ITGA5 0.013 0.036 -10000 0 -0.12 38 38
SDCBP 0.021 0.01 -10000 0 -0.12 2 2
PLG 0.027 0.011 0.062 10 -0.1 2 12
ADAM12 -0.01 0.06 -10000 0 -0.12 129 129
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.019 -10000 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.008 0.009 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.087 0.18 -10000 0 -0.41 103 103
Syndecan-4/CXCL12/CXCR4 -0.1 0.19 -10000 0 -0.42 114 114
Syndecan-4/Laminin alpha3 -0.092 0.18 -10000 0 -0.42 106 106
MDK 0.021 0.014 -10000 0 -0.12 5 5
Syndecan-4/FZD7 -0.085 0.18 -10000 0 -0.41 102 102
Syndecan-4/Midkine -0.08 0.18 -10000 0 -0.4 102 102
FZD7 0.015 0.031 -10000 0 -0.12 27 27
Syndecan-4/FGFR1/FGF -0.067 0.17 -10000 0 -0.38 103 103
THBS1 -0.003 0.052 -10000 0 -0.12 91 91
integrin-mediated signaling pathway -0.096 0.18 -10000 0 -0.41 105 105
positive regulation of MAPKKK cascade -0.1 0.18 -10000 0 -0.4 114 114
Syndecan-4/TACI -0.078 0.18 -10000 0 -0.4 102 102
CXCR4 0.012 0.032 -10000 0 -0.12 30 30
cell adhesion -0.053 0.095 -10000 0 -0.19 165 165
Syndecan-4/Dynamin -0.08 0.18 -10000 0 -0.4 102 102
Syndecan-4/TSP1 -0.1 0.18 -10000 0 -0.41 110 110
Syndecan-4/GIPC -0.08 0.18 -10000 0 -0.4 102 102
Syndecan-4/RANTES -0.094 0.19 -10000 0 -0.42 105 105
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
LAMA1 0 0.052 -10000 0 -0.12 90 90
LAMA3 0.006 0.043 -10000 0 -0.12 57 57
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA 0.002 0.051 0.079 4 -0.15 40 44
Syndecan-4/alpha-Actinin -0.081 0.18 -10000 0 -0.41 103 103
TFPI 0.018 0.026 -10000 0 -0.12 19 19
F2 0.02 0.016 -10000 0 -0.12 4 4
alpha5/beta1 Integrin 0.017 0.048 -10000 0 -0.1 75 75
positive regulation of cell adhesion -0.095 0.18 -10000 0 -0.4 111 111
ACTN1 0.022 0.011 -10000 0 -0.12 3 3
TNC -0.004 0.053 -10000 0 -0.12 95 95
Syndecan-4/CXCL12 -0.099 0.18 -10000 0 -0.43 103 103
FGF6 0.022 0.012 -10000 0 -0.12 4 4
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CXCL12 -0.002 0.05 -10000 0 -0.12 85 85
TNFRSF13B 0.023 0 -10000 0 -10000 0 0
FGF2 0.023 0.008 -10000 0 -0.12 2 2
FGFR1 0.008 0.043 -10000 0 -0.12 56 56
Syndecan-4/PI-4-5-P2 -0.088 0.17 -10000 0 -0.4 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.055 -10000 0 -0.12 115 115
cell migration -0.005 0.004 -10000 0 -10000 0 0
PRKCD 0.023 0.019 -10000 0 -0.12 8 8
vasculogenesis -0.097 0.18 -10000 0 -0.4 110 110
SDC4 -0.089 0.18 -10000 0 -0.43 102 102
Syndecan-4/Tenascin C -0.1 0.18 -10000 0 -0.42 105 105
Syndecan-4/PI-4-5-P2/PKC alpha -0.006 0.007 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.084 0.18 -10000 0 -0.41 102 102
MMP9 0.002 0.05 -10000 0 -0.12 81 81
Rac1/GTP -0.053 0.097 -10000 0 -0.19 163 163
cytoskeleton organization -0.076 0.17 -10000 0 -0.39 102 102
GIPC1 0.019 0.023 -10000 0 -0.12 15 15
Syndecan-4/TFPI -0.08 0.18 -10000 0 -0.4 102 102
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.018 0.078 -10000 0 -0.12 194 194
CRKL -0.027 0.11 -10000 0 -0.33 39 39
mol:PIP3 -0.002 0.049 0.22 24 -10000 0 24
AKT1 0.005 0.038 0.17 23 -0.1 7 30
PTK2B 0.023 0.009 -10000 0 -0.12 2 2
RAPGEF1 -0.022 0.11 -10000 0 -0.32 37 37
RANBP10 0.023 0.009 -10000 0 -0.12 2 2
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
HGF/MET/SHIP2 -0.002 0.068 -10000 0 -0.11 123 123
MAP3K5 -0.015 0.11 -10000 0 -0.3 42 42
HGF/MET/CIN85/CBL/ENDOPHILINS 0.011 0.067 -10000 0 -0.096 127 127
AP1 -0.04 0.075 -10000 0 -0.14 168 168
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis -0.17 0.32 -10000 0 -0.76 125 125
STAT3 (dimer) -0.021 0.098 -10000 0 -0.27 38 38
GAB1/CRKL/SHP2/PI3K -0.016 0.13 -10000 0 -0.29 60 60
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.015 0.11 -10000 0 -0.32 37 37
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.018 0.025 -10000 0 -0.12 18 18
PTEN 0.022 0.008 -10000 0 -0.12 1 1
ELK1 -0.021 0.057 0.25 12 -0.12 6 18
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.016 0.08 -10000 0 -0.19 66 66
PAK1 0.003 0.041 0.16 22 -0.1 23 45
HGF/MET/RANBP10 0 0.067 -10000 0 -0.11 119 119
HRAS -0.084 0.21 -10000 0 -0.48 123 123
DOCK1 -0.027 0.11 -10000 0 -0.32 44 44
GAB1 -0.033 0.12 -10000 0 -0.34 39 39
CRK -0.028 0.11 -10000 0 -0.33 39 39
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.073 0.19 -10000 0 -0.42 123 123
JUN 0.014 0.032 -10000 0 -0.12 30 30
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.028 0.077 -10000 0 -0.16 123 123
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
cell morphogenesis -0.029 0.12 -10000 0 -0.21 140 140
GRB2/SHC -0.006 0.078 -10000 0 -0.14 129 129
FOS -0.005 0.052 -10000 0 -0.12 95 95
GLMN 0.004 0.015 0.076 8 -0.055 18 26
cell motility -0.021 0.057 0.25 12 -0.12 6 18
HGF/MET/MUC20 -0.011 0.061 -10000 0 -0.092 198 198
cell migration -0.006 0.077 -10000 0 -0.14 129 129
GRB2 0.023 0.006 -10000 0 -0.12 1 1
CBL 0.023 0.006 -10000 0 -0.12 1 1
MET/RANBP10 -0.015 0.074 -10000 0 -0.12 189 189
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.019 0.092 -10000 0 -0.16 155 155
MET/MUC20 -0.028 0.068 -10000 0 -0.12 188 188
RAP1B -0.021 0.1 -10000 0 -0.3 40 40
RAP1A -0.02 0.1 -10000 0 -0.3 41 41
HGF/MET/RANBP9 -0.002 0.07 -10000 0 -0.12 127 127
RAF1 -0.077 0.2 -10000 0 -0.46 124 124
STAT3 -0.019 0.097 -10000 0 -0.16 148 148
cell proliferation -0.036 0.13 -10000 0 -0.25 127 127
RPS6KB1 -0.018 0.076 -10000 0 -0.26 37 37
MAPK3 -0.025 0.074 0.68 5 -10000 0 5
MAPK1 -0.021 0.091 0.7 8 -10000 0 8
RANBP9 0.022 0.014 -10000 0 -0.12 5 5
MAPK8 -0.017 0.12 -10000 0 -0.33 53 53
SRC -0.016 0.086 -10000 0 -0.14 155 155
PI3K -0.022 0.091 -10000 0 -0.16 133 133
MET/Glomulin -0.003 0.049 -10000 0 -0.096 93 93
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K1 -0.068 0.19 -10000 0 -0.42 124 124
MET 0.001 0.047 -10000 0 -0.12 71 71
MAP4K1 -0.016 0.11 -10000 0 -0.33 34 34
PTK2 0.021 0.015 -10000 0 -0.12 6 6
MAP2K2 -0.07 0.19 -10000 0 -0.43 124 124
BAD 0.008 0.036 0.16 23 -0.091 7 30
MAP2K4 -0.012 0.1 -10000 0 -0.26 46 46
SHP2/GRB2/SOS1/GAB1 -0.03 0.12 -10000 0 -0.23 131 131
INPPL1 0.021 0.018 -10000 0 -0.12 9 9
PXN 0.022 0.013 -10000 0 -0.12 5 5
SH3KBP1 0.021 0.019 -10000 0 -0.12 10 10
HGS -0.022 0.071 -10000 0 -0.15 119 119
PLCgamma1/PKC 0.011 0.028 -10000 0 -0.1 29 29
HGF 0.02 0.022 -10000 0 -0.12 14 14
RASA1 0.021 0.011 -10000 0 -0.12 3 3
NCK1 0.02 0.019 -10000 0 -0.12 9 9
PTPRJ 0.02 0.019 -10000 0 -0.12 10 10
NCK/PLCgamma1 -0.014 0.085 -10000 0 -0.15 134 134
PDPK1 0.002 0.042 0.19 24 -0.11 6 30
HGF/MET/SHIP -0.011 0.061 -10000 0 -0.092 198 198
IL4-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 -0.17 0.46 -10000 0 -1 86 86
STAT6 (cleaved dimer) -0.26 0.38 -10000 0 -0.94 108 108
IGHG1 -0.032 0.2 -10000 0 -0.59 11 11
IGHG3 -0.16 0.42 -10000 0 -0.93 94 94
AKT1 -0.12 0.34 -10000 0 -0.76 86 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.34 -10000 0 -0.83 74 74
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.37 -10000 0 -0.84 85 85
THY1 -0.33 0.62 -10000 0 -1.2 168 168
MYB 0.01 0.04 -10000 0 -0.12 48 48
HMGA1 0.012 0.038 -10000 0 -0.12 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.33 -10000 0 -0.68 94 94
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.13 0.37 -10000 0 -0.82 89 89
SP1 -0.001 0.049 -10000 0 -0.09 109 109
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.017 0.023 -10000 0 -0.086 3 3
STAT6 (dimer)/ETS1 -0.17 0.45 -10000 0 -0.96 100 100
SOCS1 -0.097 0.32 -10000 0 -0.65 95 95
SOCS3 -0.11 0.34 -10000 0 -0.9 51 51
FCER2 -0.099 0.33 -10000 0 -0.76 45 45
PARP14 0.014 0.033 -10000 0 -0.12 30 30
CCL17 -0.15 0.44 -10000 0 -0.99 84 84
GRB2 0.023 0.006 -10000 0 -0.12 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.078 0.27 -10000 0 -0.6 74 74
T cell proliferation -0.18 0.47 -10000 0 -1 102 102
IL4R/JAK1 -0.17 0.46 -10000 0 -1 96 96
EGR2 -0.15 0.45 -10000 0 -1 77 77
JAK2 0.013 0.051 -10000 0 -0.15 16 16
JAK3 0.023 0.016 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
JAK1 0.024 0.021 -10000 0 -0.12 2 2
COL1A2 -0.24 0.54 -10000 0 -1.3 112 112
CCL26 -0.16 0.46 -10000 0 -1 84 84
IL4R -0.17 0.49 -10000 0 -1.1 90 90
PTPN6 0.023 0.018 -10000 0 -0.12 2 2
IL13RA2 -0.16 0.45 -10000 0 -1 81 81
IL13RA1 0.015 0.048 -10000 0 -0.13 13 13
IRF4 0 0.13 -10000 0 -0.85 2 2
ARG1 -0.001 0.16 -10000 0 -0.79 4 4
CBL -0.1 0.31 -10000 0 -0.64 94 94
GTF3A -0.013 0.055 -10000 0 -0.097 148 148
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL13RA1/JAK2 0.004 0.092 -10000 0 -0.17 74 74
IRF4/BCL6 -0.004 0.12 -10000 0 -0.84 2 2
CD40LG 0.031 0.012 -10000 0 -0.12 2 2
MAPK14 -0.11 0.32 -10000 0 -0.67 96 96
mitosis -0.11 0.32 -10000 0 -0.71 86 86
STAT6 -0.18 0.51 -10000 0 -1.1 92 92
SPI1 0.027 0.021 -10000 0 -0.12 12 12
RPS6KB1 -0.1 0.31 -10000 0 -0.68 87 87
STAT6 (dimer) -0.18 0.51 -10000 0 -1.1 91 91
STAT6 (dimer)/PARP14 -0.19 0.47 -10000 0 -1 96 96
mast cell activation 0.001 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.12 0.36 -10000 0 -0.81 82 82
FRAP1 -0.12 0.34 -10000 0 -0.76 87 87
LTA -0.15 0.44 -10000 0 -1 82 82
FES 0.023 0.01 -10000 0 -0.12 3 3
T-helper 1 cell differentiation 0.18 0.5 1.1 91 -10000 0 91
CCL11 -0.19 0.47 -10000 0 -1 96 96
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.12 0.35 -10000 0 -0.8 81 81
IL2RG 0.001 0.05 -10000 0 -0.12 82 82
IL10 -0.15 0.44 -10000 0 -1 81 81
IRS1 0.02 0.022 -10000 0 -0.12 14 14
IRS2 0.022 0.016 -10000 0 -0.12 7 7
IL4 0.002 0.14 -10000 0 -10000 0 0
IL5 -0.15 0.44 -10000 0 -1 69 69
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.14 0.43 -10000 0 -0.88 96 96
COL1A1 -0.31 0.6 -10000 0 -1.3 143 143
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.47 -10000 0 -1 88 88
IL2R gamma/JAK3 -0.007 0.072 -10000 0 -0.13 109 109
TFF3 -0.17 0.47 -10000 0 -1 87 87
ALOX15 -0.15 0.44 -10000 0 -1 82 82
MYBL1 0.017 0.028 -10000 0 -0.12 22 22
T-helper 2 cell differentiation -0.15 0.42 -10000 0 -0.87 102 102
SHC1 0.023 0.001 -10000 0 -10000 0 0
CEBPB 0.023 0.032 -10000 0 -0.12 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.36 -10000 0 -0.8 90 90
mol:PI-3-4-5-P3 -0.12 0.34 -10000 0 -0.76 86 86
PI3K -0.13 0.37 -10000 0 -0.82 87 87
DOK2 0.02 0.021 -10000 0 -0.12 12 12
ETS1 0.013 0.035 -10000 0 -0.12 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.074 0.26 -10000 0 -0.59 75 75
ITGB3 -0.2 0.51 -10000 0 -1.1 99 99
PIGR -0.18 0.46 -10000 0 -1 89 89
IGHE 0.001 0.059 0.16 18 -0.16 9 27
MAPKKK cascade -0.072 0.26 -10000 0 -0.58 75 75
BCL6 0.018 0.02 -10000 0 -0.12 10 10
OPRM1 -0.15 0.44 -10000 0 -0.99 85 85
RETNLB -0.15 0.44 -10000 0 -0.99 84 84
SELP -0.16 0.44 -10000 0 -1 82 82
AICDA -0.15 0.42 -10000 0 -0.97 82 82
Nongenotropic Androgen signaling

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
PTK2 0.01 0.009 -10000 0 -0.077 6 6
GNB1/GNG2 0.011 0.059 -10000 0 -0.1 97 97
regulation of S phase of mitotic cell cycle -0.018 0.085 -10000 0 -0.16 134 134
GNAO1 0.011 0.041 -10000 0 -0.12 50 50
HRAS 0.022 0.006 -10000 0 -0.12 1 1
SHBG/T-DHT 0.015 0.005 -10000 0 -0.061 2 2
PELP1 0.022 0.009 -10000 0 -0.12 2 2
AKT1 0.01 0.012 -10000 0 -0.076 10 10
MAP2K1 -0.013 0.061 -10000 0 -0.11 114 114
T-DHT/AR -0.014 0.06 -10000 0 -0.12 123 123
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 104 104
GNAI2 0.022 0.01 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 36 36
mol:GDP -0.048 0.097 -10000 0 -0.25 95 95
cell proliferation -0.063 0.16 -10000 0 -0.37 108 108
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
FOS -0.13 0.29 -10000 0 -0.7 108 108
mol:Ca2+ -0.008 0.022 -10000 0 -0.044 116 116
MAPK3 -0.042 0.11 -10000 0 -0.25 111 111
MAPK1 -0.032 0.1 -10000 0 -0.21 109 109
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:IP3 -0.001 0.002 -10000 0 -0.004 104 104
cAMP biosynthetic process 0.01 0.016 0.058 18 -10000 0 18
GNG2 0.02 0.018 -10000 0 -0.12 9 9
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 104 104
HRAS/GTP 0.006 0.054 -10000 0 -0.092 89 89
actin cytoskeleton reorganization 0.016 0.048 -10000 0 -0.1 67 67
SRC 0.022 0.009 -10000 0 -0.13 2 2
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 104 104
PI3K 0.008 0.055 -10000 0 -0.1 98 98
apoptosis 0.066 0.17 0.38 114 -10000 0 114
T-DHT/AR/PELP1 0.002 0.054 -10000 0 -0.096 125 125
HRAS/GDP -0.027 0.1 -10000 0 -0.23 97 97
CREB1 -0.071 0.18 -10000 0 -0.41 114 114
RAC1-CDC42/GTP 0.023 0.052 -10000 0 -0.1 67 67
AR 0.008 0.038 -10000 0 -0.12 43 43
GNB1 0.023 0.006 -10000 0 -0.12 1 1
RAF1 -0.008 0.053 -10000 0 -0.096 79 79
RAC1-CDC42/GDP -0.015 0.1 -10000 0 -0.22 98 98
T-DHT/AR/PELP1/Src 0.014 0.053 -10000 0 -0.098 88 88
MAP2K2 -0.015 0.062 -10000 0 -0.12 116 116
T-DHT/AR/PELP1/Src/PI3K -0.018 0.086 -10000 0 -0.16 134 134
GNAZ 0.022 0.012 -10000 0 -0.12 4 4
SHBG 0.023 0.008 -10000 0 -0.12 2 2
Gi family/GNB1/GNG2/GDP 0.001 0.077 -10000 0 -0.24 34 34
mol:T-DHT -0.001 0.001 -10000 0 -0.003 76 76
RAC1 0.023 0.002 -10000 0 -10000 0 0
GNRH1 0.011 0.009 -10000 0 -0.076 6 6
Gi family/GTP -0.018 0.07 -10000 0 -0.15 99 99
CDC42 0.023 0.002 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.074 0.32 -10000 0 -0.76 75 75
CRP -0.064 0.3 -10000 0 -0.72 71 71
cell cycle arrest -0.092 0.36 -10000 0 -0.78 90 90
TIMP1 -0.11 0.35 -10000 0 -0.75 107 107
IL6ST 0.016 0.03 -10000 0 -0.083 34 34
Rac1/GDP -0.019 0.17 -10000 0 -0.35 78 78
AP1 -0.059 0.21 -10000 0 -0.45 99 99
GAB2 0.01 0.042 -10000 0 -0.12 52 52
TNFSF11 -0.064 0.3 -10000 0 -0.74 67 67
HSP90B1 0.005 0.18 -10000 0 -1.2 12 12
GAB1 0.021 0.022 -10000 0 -0.12 13 13
MAPK14 -0.028 0.16 -10000 0 -0.47 50 50
AKT1 -0.017 0.15 -10000 0 -0.36 60 60
FOXO1 -0.015 0.14 -10000 0 -0.35 58 58
MAP2K6 -0.029 0.15 -10000 0 -0.36 73 73
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.027 0.2 -10000 0 -0.39 94 94
MITF -0.02 0.14 -10000 0 -0.33 75 75
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.016 -10000 0 -0.12 7 7
A2M -0.12 0.38 -10000 0 -1.2 62 62
CEBPB 0.023 0.036 -10000 0 -0.11 37 37
GRB2/SOS1/GAB family/SHP2 -0.03 0.17 0.24 5 -0.37 94 99
STAT3 -0.1 0.38 -10000 0 -0.84 91 91
STAT1 -0.087 0.28 -10000 0 -0.84 68 68
CEBPD -0.072 0.32 -10000 0 -0.74 75 75
PIK3CA 0.021 0.017 -10000 0 -0.12 7 7
PI3K 0.009 0.066 -10000 0 -0.13 98 98
JUN 0.014 0.032 -10000 0 -0.12 30 30
PIAS3/MITF -0.013 0.14 -10000 0 -0.31 75 75
MAPK11 -0.028 0.16 -10000 0 -0.46 51 51
STAT3 (dimer)/FOXO1 -0.087 0.34 -10000 0 -0.68 106 106
GRB2/SOS1/GAB family 0.004 0.12 0.22 5 -0.25 66 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.12 -10000 0 -0.27 73 73
GRB2 0.025 0.008 -10000 0 -0.12 1 1
JAK2 0.017 0.025 -10000 0 -0.12 17 17
LBP -0.04 0.25 -10000 0 -0.59 63 63
PIK3R1 0.016 0.031 -10000 0 -0.12 28 28
JAK1 0.022 0.015 -10000 0 -0.043 17 17
MYC -0.13 0.4 -10000 0 -0.88 109 109
FGG -0.064 0.3 -10000 0 -0.72 72 72
macrophage differentiation -0.092 0.36 -10000 0 -0.78 90 90
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.093 -10000 0 -0.15 96 96
JUNB -0.11 0.37 -10000 0 -0.86 89 89
FOS -0.005 0.052 -10000 0 -0.12 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.022 0.15 -10000 0 -0.35 74 74
STAT1/PIAS1 -0.031 0.18 -10000 0 -0.34 96 96
GRB2/SOS1/GAB family/SHP2/PI3K -0.023 0.15 -10000 0 -0.28 116 116
STAT3 (dimer) -0.1 0.38 -10000 0 -0.84 89 89
PRKCD -0.044 0.25 -10000 0 -0.5 97 97
IL6R 0.019 0.024 -10000 0 -0.083 23 23
SOCS3 -0.044 0.21 -10000 0 -0.93 25 25
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.079 -10000 0 -0.15 81 81
Rac1/GTP -0.023 0.18 -10000 0 -0.38 80 80
HCK 0.019 0.023 -10000 0 -0.12 15 15
MAPKKK cascade -0.048 0.22 -10000 0 -0.49 98 98
bone resorption -0.058 0.29 -10000 0 -0.69 67 67
IRF1 -0.13 0.41 -10000 0 -0.94 98 98
mol:GDP -0.024 0.16 -10000 0 -0.35 79 79
SOS1 0.02 0.027 -10000 0 -0.12 20 20
VAV1 -0.025 0.16 -10000 0 -0.35 79 79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.027 0.17 -10000 0 -0.43 68 68
PTPN11 -0.006 0.16 -10000 0 -0.83 19 19
IL6/IL6RA 0.007 0.062 -10000 0 -0.13 67 67
gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.061 -10000 0 -0.12 69 69
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.077 -10000 0 -0.14 94 94
IL6 0.005 0.049 -10000 0 -0.1 85 85
PIAS3 0.02 0.022 -10000 0 -0.12 14 14
PTPRE 0.022 0.018 0.086 10 -10000 0 10
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.003 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.014 0.097 -10000 0 -0.21 77 77
LMO4 0.021 0.023 -10000 0 -0.077 16 16
STAT3 (dimer)/PIAS3 -0.088 0.35 -10000 0 -0.77 89 89
MCL1 -0.014 0.16 -10000 0 -0.61 20 20
IGF1 pathway

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
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTK2 0.021 0.015 -10000 0 -0.12 6 6
CRKL -0.005 0.055 -10000 0 -0.12 96 96
GRB2/SOS1/SHC 0.035 0.042 -10000 0 -0.12 32 32
HRAS 0.023 0.006 -10000 0 -0.12 1 1
IRS1/Crk -0.001 0.057 -10000 0 -0.12 96 96
IGF-1R heterotetramer/IGF1/PTP1B 0.007 0.062 -10000 0 -0.12 94 94
AKT1 -0.01 0.059 -10000 0 -0.099 146 146
BAD -0.008 0.056 -10000 0 -0.1 112 112
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.006 0.055 -10000 0 -0.12 96 96
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.063 -10000 0 -0.12 109 109
RAF1 -0.004 0.09 -10000 0 -0.49 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.009 0.071 -10000 0 -0.11 118 118
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.005 0.063 -10000 0 -0.13 96 96
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
RPS6KB1 -0.012 0.063 -10000 0 -0.11 146 146
GNB2L1 0.023 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.006 0.077 0.2 6 -0.39 11 17
PXN 0.022 0.013 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.021 0.046 -10000 0 -0.12 52 52
HRAS/GTP -0.003 0.053 -10000 0 -0.1 94 94
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.021 0.069 -10000 0 -0.12 48 48
IGF-1R heterotetramer 0.012 0.033 -10000 0 -0.091 42 42
IGF-1R heterotetramer/IGF1/IRS/Nck 0.008 0.063 -10000 0 -0.12 96 96
Crk/p130 Cas/Paxillin 0.02 0.061 -10000 0 -0.099 90 90
IGF1R 0.012 0.033 -10000 0 -0.091 42 42
IGF1 0.001 0.047 -10000 0 -0.074 129 129
IRS2/Crk 0.003 0.055 -10000 0 -0.11 91 91
PI3K -0.001 0.077 -10000 0 -0.11 154 154
apoptosis -0.003 0.056 0.12 59 -10000 0 59
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
PRKCD -0.016 0.095 -10000 0 -0.2 97 97
RAF1/14-3-3 E 0.007 0.082 -10000 0 -0.42 11 11
BAD/14-3-3 0.003 0.059 -10000 0 -0.12 59 59
PRKCZ -0.009 0.059 -10000 0 -0.11 111 111
Crk/p130 Cas/Paxillin/FAK1 0.004 0.068 -10000 0 -0.14 58 58
PTPN1 0.023 0.006 -10000 0 -0.12 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.018 0.097 -10000 0 -0.21 94 94
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.019 0.061 -10000 0 -0.094 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IRS1/NCK2 0.001 0.058 -10000 0 -0.12 96 96
GRB10 0.022 0.014 -10000 0 -0.12 5 5
PTPN11 -0.007 0.058 -10000 0 -0.12 97 97
IRS1 -0.012 0.059 -10000 0 -0.13 96 96
IRS2 -0.006 0.054 -10000 0 -0.12 97 97
IGF-1R heterotetramer/IGF1 -0.013 0.077 -10000 0 -0.16 96 96
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDPK1 -0.012 0.063 -10000 0 -0.1 152 152
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKD1 -0.022 0.099 -10000 0 -0.21 102 102
SHC1 0.023 0.001 -10000 0 -10000 0 0
IL23-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
CCL2 -0.26 0.57 -9999 0 -1.2 127 127
IL23A -0.2 0.5 -9999 0 -1.2 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.5 -9999 0 -1.2 94 94
positive regulation of T cell mediated cytotoxicity -0.22 0.56 -9999 0 -1.3 93 93
ITGA3 -0.24 0.54 -9999 0 -1.2 124 124
IL17F -0.11 0.32 -9999 0 -0.69 98 98
IL12B 0.016 0.04 -9999 0 -10000 0 0
STAT1 (dimer) -0.22 0.54 -9999 0 -1.2 99 99
CD4 -0.21 0.52 -9999 0 -1.2 101 101
IL23 -0.18 0.48 -9999 0 -1.2 86 86
IL23R 0.002 0.089 -9999 0 -10000 0 0
IL1B -0.22 0.54 -9999 0 -1.3 94 94
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.47 -9999 0 -1.1 88 88
TYK2 0.013 0.034 -9999 0 -0.14 7 7
STAT4 0.02 0.02 -9999 0 -0.12 11 11
STAT3 0.022 0.011 -9999 0 -0.12 3 3
IL18RAP 0.022 0.018 -9999 0 -0.12 8 8
IL12RB1 0.015 0.03 -9999 0 -0.15 1 1
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
IL12Rbeta1/TYK2 0.021 0.04 -9999 0 -0.11 8 8
IL23R/JAK2 -0.001 0.12 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.22 0.56 -9999 0 -1.3 93 93
natural killer cell activation 0 0.008 -9999 0 -10000 0 0
JAK2 0.011 0.046 -9999 0 -0.12 17 17
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
RELA 0.022 0.009 -9999 0 -0.12 2 2
positive regulation of dendritic cell antigen processing and presentation -0.17 0.46 -9999 0 -1.1 87 87
ALOX12B -0.18 0.47 -9999 0 -1.1 88 88
CXCL1 -0.23 0.52 -9999 0 -1.1 119 119
T cell proliferation -0.22 0.56 -9999 0 -1.3 93 93
NFKBIA 0.016 0.028 -9999 0 -0.12 21 21
IL17A -0.072 0.26 -9999 0 -0.54 92 92
PI3K -0.2 0.51 -9999 0 -1.2 97 97
IFNG -0.004 0.026 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.48 -9999 0 -1.1 99 99
IL18R1 0.02 0.022 -9999 0 -0.12 14 14
IL23/IL23R/JAK2/TYK2/SOCS3 -0.084 0.28 -9999 0 -0.6 87 87
IL18/IL18R 0.015 0.061 -9999 0 -0.11 78 78
macrophage activation -0.009 0.021 -9999 0 -0.044 83 83
TNF -0.19 0.5 -9999 0 -1.2 88 88
STAT3/STAT4 -0.2 0.51 -9999 0 -1.2 96 96
STAT4 (dimer) -0.21 0.53 -9999 0 -1.2 93 93
IL18 0.004 0.046 -9999 0 -0.12 66 66
IL19 -0.18 0.47 -9999 0 -1.1 89 89
STAT5A (dimer) -0.21 0.53 -9999 0 -1.2 95 95
STAT1 0.014 0.03 -9999 0 -0.12 25 25
SOCS3 0.015 0.031 -9999 0 -0.12 28 28
CXCL9 -0.26 0.56 -9999 0 -1.2 130 130
MPO -0.18 0.47 -9999 0 -1.1 88 88
positive regulation of humoral immune response -0.22 0.56 -9999 0 -1.3 93 93
IL23/IL23R/JAK2/TYK2 -0.24 0.61 -9999 0 -1.4 93 93
IL6 -0.2 0.48 -9999 0 -1.1 92 92
STAT5A 0.022 0.012 -9999 0 -0.12 4 4
IL2 0.025 0.014 -9999 0 -0.13 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.008 -9999 0 -10000 0 0
CD3E -0.2 0.5 -9999 0 -1.2 91 91
keratinocyte proliferation -0.22 0.56 -9999 0 -1.3 93 93
NOS2 -0.18 0.47 -9999 0 -1.1 94 94
IL1-mediated signaling events

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
UBC13/UEV1A 0.014 0.022 -10000 0 -0.14 11 11
PRKCZ 0.023 0 -10000 0 -10000 0 0
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 7 7
ERC1 0.016 0.029 -10000 0 -0.12 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.063 0.15 -10000 0 -0.3 127 127
IRAK/TOLLIP 0.028 0.026 -10000 0 -0.11 16 16
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
IKBKG 0.023 0.008 -10000 0 -0.12 2 2
IL1 alpha/IL1R2 0.014 0.048 -10000 0 -0.15 23 23
IL1A 0.017 0.029 -10000 0 -0.12 24 24
IL1B 0.002 0.039 -10000 0 -0.083 84 84
IRAK/TRAF6/p62/Atypical PKCs 0.037 0.059 -10000 0 -0.16 16 16
IL1R2 0.006 0.045 -10000 0 -0.12 64 64
IL1R1 0.003 0.046 -10000 0 -0.12 68 68
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.065 0.15 0.16 1 -0.29 135 136
TOLLIP 0.023 0.01 -10000 0 -0.12 3 3
TICAM2 0.021 0.014 -10000 0 -0.12 5 5
MAP3K3 0.023 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.034 0.05 -10000 0 -0.15 34 34
IKK complex/ELKS 0.024 0.093 -10000 0 -0.24 52 52
JUN 0.011 0.047 -10000 0 -0.17 26 26
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.052 0.12 -10000 0 -0.21 143 143
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.002 0.077 -10000 0 -0.11 137 137
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.087 -10000 0 -0.17 69 69
IL1 beta fragment/IL1R1/IL1RAP -0.057 0.1 -10000 0 -0.15 246 246
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 0.014 0.049 -10000 0 -0.17 27 27
IRAK1 0.016 0.022 -10000 0 -0.088 22 22
IL1RN/IL1R1 -0.008 0.07 -10000 0 -0.11 167 167
IRAK4 0.019 0.02 -10000 0 -0.12 10 10
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
PI3K 0.007 0.065 -10000 0 -0.13 98 98
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.075 0.15 -10000 0 -0.3 139 139
CHUK 0.021 0.013 -10000 0 -0.12 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.057 0.1 -10000 0 -0.15 246 246
IL1 beta/IL1R2 -0.036 0.089 -10000 0 -0.15 182 182
IRAK/TRAF6/TAK1/TAB1/TAB2 0.046 0.055 -10000 0 -0.19 18 18
NF kappa B1 p50/RelA -0.051 0.12 -10000 0 -0.21 150 150
IRAK3 0.009 0.041 -10000 0 -0.12 52 52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.05 0.12 -10000 0 -0.22 132 132
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.031 0.11 -10000 0 -0.27 63 63
IL1 alpha/IL1R1/IL1RAP -0.014 0.078 -10000 0 -0.13 134 134
RELA 0.023 0.009 -10000 0 -0.12 2 2
MAP3K7IP1 0.023 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.015 -10000 0 -0.12 6 6
MYD88 0.023 0.006 -10000 0 -0.12 1 1
IRAK/TRAF6/MEKK3 0.04 0.031 -10000 0 -0.097 23 23
IL1RAP 0.009 0.038 -10000 0 -0.12 44 44
UBE2N 0.023 0.007 -10000 0 -0.12 1 1
IRAK/TRAF6 -0.047 0.099 -10000 0 -0.19 141 141
CASP1 0.006 0.04 -10000 0 -0.12 50 50
IL1RN/IL1R2 0.01 0.053 -10000 0 -0.14 34 34
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.045 0.1 -10000 0 -0.14 246 246
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.038 0.13 -10000 0 -0.29 97 97
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL1RN 0.018 0.025 -10000 0 -0.12 17 17
TRAF6/TAK1/TAB1/TAB2 0.042 0.052 -10000 0 -0.12 43 43
MAP2K6 0.015 0.05 -10000 0 -0.18 25 25
BARD1 signaling events

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
BARD1/CSTF1 0.016 0.052 -10000 0 -0.12 70 70
ATM 0.018 0.022 -10000 0 -0.12 13 13
UBE2D3 0.023 0.001 -10000 0 -10000 0 0
PRKDC 0.021 0.016 -10000 0 -0.12 7 7
ATR 0.02 0.014 -10000 0 -0.12 5 5
UBE2L3 0.022 0.011 -10000 0 -0.12 3 3
FANCD2 -0.009 0.096 -10000 0 -0.24 72 72
protein ubiquitination -0.016 0.087 -10000 0 -0.16 78 78
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.022 0.066 -10000 0 -0.14 67 67
MRE11A 0.02 0.017 -10000 0 -0.12 8 8
DNA-PK 0.026 0.06 -10000 0 -0.14 61 61
FA complex/FANCD2/Ubiquitin 0.01 0.093 -10000 0 -0.33 26 26
FANCF 0.022 0.011 -10000 0 -0.12 3 3
BRCA1 0.015 0.029 -10000 0 -0.12 24 24
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
CDK2/Cyclin E1 -0.016 0.076 -10000 0 -0.12 192 192
FANCG 0.021 0.016 -10000 0 -0.12 7 7
BRCA1/BACH1/BARD1 -0.001 0.07 -10000 0 -0.13 126 126
FANCE 0.023 0 -10000 0 -10000 0 0
FANCC 0.022 0.013 -10000 0 -0.12 5 5
NBN 0.021 0.013 -10000 0 -0.12 4 4
FANCA 0.021 0.019 -10000 0 -0.12 10 10
DNA repair -0.015 0.11 -10000 0 -0.31 44 44
BRCA1/BARD1/ubiquitin -0.001 0.07 -10000 0 -0.13 126 126
BARD1/DNA-PK 0.027 0.076 -10000 0 -0.14 81 81
FANCL 0.019 0.023 -10000 0 -0.12 14 14
mRNA polyadenylation -0.016 0.052 0.12 70 -10000 0 70
BRCA1/BARD1/CTIP/M/R/N Complex -0.036 0.14 -10000 0 -0.33 74 74
BRCA1/BACH1/BARD1/TopBP1 0.009 0.072 -10000 0 -0.13 105 105
BRCA1/BARD1/P53 -0.027 0.092 -10000 0 -0.12 257 257
BARD1/CSTF1/BRCA1 0.013 0.065 -10000 0 -0.12 95 95
BRCA1/BACH1 0.015 0.029 -10000 0 -0.12 24 24
BARD1 0.016 0.029 -10000 0 -0.12 23 23
PCNA 0.019 0.017 -10000 0 -0.12 7 7
BRCA1/BARD1/UbcH5C 0.015 0.063 -10000 0 -0.12 89 89
BRCA1/BARD1/UbcH7 0.013 0.064 -10000 0 -0.12 94 94
BRCA1/BARD1/RAD51/PCNA 0 0.085 -10000 0 -0.12 157 157
BARD1/DNA-PK/P53 -0.009 0.096 -10000 0 -0.19 62 62
BRCA1/BARD1/Ubiquitin -0.001 0.07 -10000 0 -0.13 126 126
BRCA1/BARD1/CTIP -0.011 0.083 -10000 0 -0.13 160 160
FA complex 0.018 0.074 -10000 0 -0.31 17 17
BARD1/EWS 0.018 0.049 -10000 0 -0.12 63 63
RBBP8 0.011 0.029 -10000 0 -0.076 48 48
TP53 0.01 0.029 -10000 0 -0.12 24 24
TOPBP1 0.021 0.015 -10000 0 -0.12 6 6
G1/S transition of mitotic cell cycle 0.027 0.091 0.12 257 -10000 0 257
BRCA1/BARD1 -0.013 0.09 -10000 0 -0.16 78 78
CSTF1 0.023 0.007 -10000 0 -0.12 1 1
BARD1/EWS-Fli1 0.002 0.044 -10000 0 -0.12 62 62
CDK2 0.018 0.023 -10000 0 -0.12 14 14
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.015 0.03 -10000 0 -0.12 26 26
RAD50 0.021 0.015 -10000 0 -0.12 6 6
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.07 -10000 0 -0.13 126 126
EWSR1 0.023 0.001 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.049 -9999 0 -0.12 59 59
alphaV beta3 Integrin 0 0.073 -9999 0 -0.13 107 107
PTK2 -0.029 0.13 -9999 0 -0.28 88 88
IGF1R 0.013 0.031 -9999 0 -0.12 28 28
PI4KB 0.022 0.014 -9999 0 -0.12 5 5
MFGE8 0.006 0.043 -9999 0 -0.12 57 57
SRC 0.023 0.008 -9999 0 -0.12 2 2
CDKN1B -0.006 0.087 -9999 0 -0.34 30 30
VEGFA 0.019 0.02 -9999 0 -0.12 11 11
ILK 0.013 0.04 -9999 0 -0.31 3 3
ROCK1 0.023 0.009 -9999 0 -0.12 2 2
AKT1 0.014 0.037 -9999 0 -0.28 3 3
PTK2B -0.011 0.063 -9999 0 -0.11 140 140
alphaV/beta3 Integrin/JAM-A 0.014 0.068 -9999 0 -0.1 114 114
CBL 0.023 0.006 -9999 0 -0.12 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0 0.073 -9999 0 -0.13 107 107
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.071 -9999 0 -0.11 111 111
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.095 -9999 0 -0.25 51 51
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.074 -9999 0 -0.13 113 113
PI4KA 0.021 0.016 -9999 0 -0.12 7 7
IGF-1R heterotetramer/IGF1/IRS1 -0.055 0.086 -9999 0 -0.16 153 153
PI4 Kinase 0.028 0.032 -9999 0 -0.12 24 24
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
alphaV/beta3 Integrin/Osteopontin -0.029 0.098 -9999 0 -0.16 166 166
RPS6KB1 -0.056 0.081 -9999 0 -0.16 164 164
TLN1 0.021 0.013 -9999 0 -0.12 4 4
MAPK3 -0.054 0.14 -9999 0 -0.34 102 102
GPR124 0.023 0.01 -9999 0 -0.12 3 3
MAPK1 -0.055 0.14 -9999 0 -0.34 102 102
PXN 0.022 0.013 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
alphaV/beta3 Integrin/Tumstatin 0 0.073 -9999 0 -0.13 107 107
cell adhesion -0.03 0.097 -9999 0 -0.18 118 118
ANGPTL3 0.023 0.01 -9999 0 -0.12 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.044 -9999 0 -0.11 39 39
IGF-1R heterotetramer 0.013 0.031 -9999 0 -0.12 28 28
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
TGFBR2 0.02 0.02 -9999 0 -0.12 11 11
ITGB3 0.005 0.046 -9999 0 -0.12 67 67
IGF1 0.007 0.045 -9999 0 -0.12 62 62
RAC1 0.023 0.002 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.001 0.072 -9999 0 -0.13 107 107
apoptosis 0.012 0.033 -9999 0 -0.12 31 31
CD47 0.021 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/CD47 -0.01 0.083 -9999 0 -0.14 126 126
VCL 0.021 0.014 -9999 0 -0.12 5 5
alphaV/beta3 Integrin/Del1 -0.029 0.083 -9999 0 -0.14 161 161
CSF1 0.013 0.033 -9999 0 -0.12 31 31
PIK3C2A -0.013 0.1 -9999 0 -0.35 44 44
PI4 Kinase/Pyk2 0.001 0.059 -9999 0 -0.14 49 49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.001 0.079 -9999 0 -0.12 140 140
FAK1/Vinculin -0.016 0.11 -9999 0 -0.23 93 93
alphaV beta3/Integrin/ppsTEM5 0 0.073 -9999 0 -0.13 107 107
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VTN 0.023 0.008 -9999 0 -0.12 2 2
BCAR1 0.023 0.01 -9999 0 -0.12 3 3
FGF2 0.023 0.008 -9999 0 -0.12 2 2
F11R 0.022 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/Lactadherin -0.028 0.088 -9999 0 -0.14 173 173
alphaV/beta3 Integrin/TGFBR2 -0.005 0.079 -9999 0 -0.14 113 113
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.015 0.075 -9999 0 -0.12 112 112
HSP90AA1 0.023 0.004 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.004 0.074 -9999 0 -0.12 123 123
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.012 0.055 -9999 0 -0.12 115 115
alphaV/beta3 Integrin/Pyk2 0 0.072 -9999 0 -0.16 49 49
SDC1 0.021 0.019 -9999 0 -0.12 10 10
VAV3 -0.012 0.074 -9999 0 -0.14 118 118
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
IRS1 0.02 0.022 -9999 0 -0.12 14 14
FAK1/Paxillin -0.013 0.11 -9999 0 -0.24 73 73
cell migration -0.011 0.11 -9999 0 -0.23 74 74
ITGAV 0.012 0.033 -9999 0 -0.12 31 31
PI3K 0.006 0.083 -9999 0 -0.17 61 61
SPP1 0.012 0.031 -9999 0 -0.12 28 28
KDR 0.021 0.019 -9999 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0.033 -9999 0 -0.12 31 31
COL4A3 0.023 0.008 -9999 0 -0.12 2 2
angiogenesis -0.055 0.16 -9999 0 -0.37 102 102
Rac1/GTP -0.007 0.074 -9999 0 -0.18 54 54
EDIL3 -0.006 0.056 -9999 0 -0.12 110 110
cell proliferation -0.005 0.078 -9999 0 -0.14 113 113
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.08 -10000 0 -0.13 111 111
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.023 0.009 -10000 0 -0.12 2 2
STAT1 (dimer)/Cbp/p300 -0.019 0.13 -10000 0 -0.22 127 127
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.08 -10000 0 -0.15 101 101
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.093 -10000 0 -0.2 135 135
CaM/Ca2+ 0.01 0.077 -10000 0 -0.14 75 75
RAP1A 0.021 0.011 -10000 0 -0.12 3 3
STAT1 (dimer)/SHP2 -0.017 0.092 -10000 0 -0.18 97 97
AKT1 -0.014 0.081 -10000 0 -0.17 90 90
MAP2K1 -0.007 0.068 -10000 0 -0.15 77 77
MAP3K11 -0.006 0.066 -10000 0 -0.12 104 104
IFNGR1 0.016 0.026 -10000 0 -0.12 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.015 0.082 -10000 0 -0.27 30 30
Rap1/GTP -0.023 0.056 -10000 0 -0.16 59 59
CRKL/C3G 0.034 0.01 -10000 0 -0.093 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.024 0.079 -10000 0 -0.12 106 106
CEBPB -0.014 0.15 -10000 0 -0.38 62 62
STAT3 0.022 0.011 -10000 0 -0.12 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.11 -10000 0 -0.71 5 5
STAT1 -0.018 0.086 0.11 2 -0.19 81 83
CALM1 0.022 0.014 -10000 0 -0.12 5 5
IFN-gamma (dimer) 0.01 0.038 -10000 0 -0.12 43 43
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
STAT1 (dimer)/PIAS1 -0.015 0.091 -10000 0 -0.18 93 93
CEBPB/PTGES2/Cbp/p300 -0.036 0.11 -10000 0 -0.29 70 70
mol:Ca2+ 0.005 0.078 -10000 0 -0.13 111 111
MAPK3 -0.009 0.12 -10000 0 -0.44 19 19
STAT1 (dimer) -0.041 0.15 -10000 0 -0.27 133 133
MAPK1 -0.013 0.13 -10000 0 -0.47 24 24
JAK2 0.016 0.026 -10000 0 -0.12 17 17
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
JAK1 0.02 0.012 -10000 0 -0.059 5 5
CAMK2D 0.018 0.024 -10000 0 -0.12 16 16
DAPK1 -0.014 0.16 -10000 0 -0.48 48 48
SMAD7 -0.009 0.064 -10000 0 -0.12 100 100
CBL/CRKL/C3G 0.018 0.068 -10000 0 -0.14 55 55
PI3K -0.004 0.092 -10000 0 -0.17 99 99
IFNG 0.01 0.038 -10000 0 -0.12 43 43
apoptosis -0.017 0.13 0.22 1 -0.39 48 49
CAMK2G 0.023 0.006 -10000 0 -0.12 1 1
STAT3 (dimer) 0.022 0.011 -10000 0 -0.12 3 3
CAMK2A 0.023 0.006 -10000 0 -0.12 1 1
CAMK2B 0.023 0.008 -10000 0 -0.12 2 2
FRAP1 -0.012 0.077 -10000 0 -0.16 87 87
PRKCD -0.016 0.086 -10000 0 -0.18 94 94
RAP1B 0.019 0.019 -10000 0 -0.12 10 10
negative regulation of cell growth -0.053 0.093 -10000 0 -0.2 135 135
PTPN2 0.023 0.006 -10000 0 -0.12 1 1
EP300 0.022 0.01 -10000 0 -0.12 2 2
IRF1 -0.038 0.13 -10000 0 -0.27 111 111
STAT1 (dimer)/PIASy -0.015 0.089 0.19 3 -0.18 84 87
SOCS1 0.008 0.095 -10000 0 -1.2 3 3
mol:GDP 0.015 0.065 -10000 0 -0.14 55 55
CASP1 -0.031 0.095 -10000 0 -0.17 153 153
PTGES2 0.022 0.01 -10000 0 -0.12 3 3
IRF9 0.004 0.071 -10000 0 -0.15 74 74
mol:PI-3-4-5-P3 -0.013 0.084 -10000 0 -0.17 95 95
RAP1/GDP 0.006 0.073 -10000 0 -0.17 56 56
CBL -0.005 0.066 -10000 0 -0.14 84 84
MAP3K1 -0.008 0.071 -10000 0 -0.13 105 105
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
PIAS4 0.023 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.093 -10000 0 -0.2 135 135
PTPN11 -0.009 0.067 -10000 0 -0.13 105 105
CREBBP 0.02 0.016 -10000 0 -0.12 6 6
RAPGEF1 0.023 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.011 0.049 -10000 0 -0.097 90 90
cell-cell adhesion 0.023 0.04 0.14 40 -10000 0 40
Ephrin B/EPHB2/RasGAP 0.016 0.076 -10000 0 -0.099 144 144
ITSN1 0.022 0.011 -10000 0 -0.12 3 3
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SHC1 0.023 0.001 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.022 0.033 -10000 0 -0.12 24 24
Ephrin B1/EPHB1 0.024 0.028 -10000 0 -0.12 8 8
HRAS/GDP -0.002 0.07 -10000 0 -0.14 89 89
Ephrin B/EPHB1/GRB7 0.018 0.071 -10000 0 -0.096 120 120
Endophilin/SYNJ1 -0.001 0.052 -10000 0 -0.087 125 125
KRAS 0.014 0.034 -10000 0 -0.12 33 33
Ephrin B/EPHB1/Src 0.023 0.067 -10000 0 -0.092 110 110
endothelial cell migration 0.001 0.071 -10000 0 -0.11 146 146
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GRB7 0.018 0.025 -10000 0 -0.12 18 18
PAK1 -0.003 0.057 -10000 0 -0.16 29 29
HRAS 0.023 0.006 -10000 0 -0.12 1 1
RRAS -0.006 0.056 -10000 0 -0.096 128 128
DNM1 0.02 0.02 -10000 0 -0.12 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0 0.049 -10000 0 -0.087 111 111
lamellipodium assembly -0.023 0.04 -10000 0 -0.14 40 40
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.051 -10000 0 -0.16 31 31
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
EPHB2 0.02 0.02 -10000 0 -0.12 11 11
EPHB3 0.019 0.023 -10000 0 -0.12 15 15
EPHB1 0.016 0.032 -10000 0 -0.12 29 29
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
mol:GDP -0.01 0.079 -10000 0 -0.17 100 100
Ephrin B/EPHB2 0.012 0.066 -10000 0 -0.097 124 124
Ephrin B/EPHB3 0.011 0.065 -10000 0 -0.095 124 124
JNK cascade 0.014 0.045 -10000 0 -0.1 57 57
Ephrin B/EPHB1 0.013 0.063 -10000 0 -0.095 110 110
RAP1/GDP 0 0.084 -10000 0 -0.15 101 101
EFNB2 0.007 0.041 -10000 0 -0.12 51 51
EFNB3 0.018 0.027 -10000 0 -0.12 20 20
EFNB1 0.021 0.019 -10000 0 -0.12 10 10
Ephrin B2/EPHB1-2 0.006 0.061 -10000 0 -0.1 102 102
RAP1B 0.019 0.019 -10000 0 -0.12 10 10
RAP1A 0.021 0.011 -10000 0 -0.12 3 3
CDC42/GTP 0.008 0.078 -10000 0 -0.18 32 32
Rap1/GTP -0.028 0.045 -10000 0 -0.14 60 60
axon guidance 0.011 0.049 -10000 0 -0.096 90 90
MAPK3 0.008 0.063 -10000 0 -0.19 18 18
MAPK1 0.008 0.063 -10000 0 -0.18 19 19
Rac1/GDP 0.001 0.079 -10000 0 -0.16 99 99
actin cytoskeleton reorganization -0.025 0.045 -10000 0 -0.14 46 46
CDC42/GDP 0.001 0.079 -10000 0 -0.16 88 88
PI3K 0.004 0.074 -10000 0 -0.11 146 146
EFNA5 0.014 0.033 -10000 0 -0.12 31 31
Ephrin B2/EPHB4 0 0.058 -10000 0 -0.095 143 143
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.08 -10000 0 -0.26 18 18
CDC42 0.023 0.002 -10000 0 -10000 0 0
RAS family/GTP -0.025 0.042 -10000 0 -0.13 55 55
PTK2 -0.001 0.05 -10000 0 -0.2 32 32
MAP4K4 0.015 0.045 -10000 0 -0.1 57 57
SRC 0.023 0.008 -10000 0 -0.12 2 2
KALRN 0.015 0.033 -10000 0 -0.12 31 31
Intersectin/N-WASP 0.031 0.023 -10000 0 -0.14 8 8
neuron projection morphogenesis 0.005 0.07 -10000 0 -0.16 45 45
MAP2K1 0.005 0.066 -10000 0 -0.2 16 16
WASL 0.023 0.008 -10000 0 -0.12 2 2
Ephrin B1/EPHB1-2/NCK1 0.036 0.055 -10000 0 -0.11 56 56
cell migration 0.002 0.077 -10000 0 -0.15 98 98
NRAS 0.022 0.011 -10000 0 -0.12 3 3
SYNJ1 -0.001 0.052 -10000 0 -0.088 125 125
PXN 0.022 0.013 -10000 0 -0.12 5 5
TF -0.001 0.049 -10000 0 -0.081 128 128
HRAS/GTP 0.01 0.063 -10000 0 -0.15 31 31
Ephrin B1/EPHB1-2 0.032 0.039 -10000 0 -0.11 27 27
cell adhesion mediated by integrin 0.014 0.047 0.1 103 -10000 0 103
RAC1 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0.011 0.069 -10000 0 -0.16 31 31
RAC1-CDC42/GTP -0.024 0.039 -10000 0 -0.13 41 41
RASA1 0.021 0.011 -10000 0 -0.12 3 3
RAC1-CDC42/GDP 0.009 0.081 -10000 0 -0.15 88 88
ruffle organization 0.004 0.057 -10000 0 -0.13 42 42
NCK1 0.02 0.019 -10000 0 -0.12 9 9
receptor internalization 0 0.049 -10000 0 -0.082 126 126
Ephrin B/EPHB2/KALRN 0.019 0.073 -10000 0 -0.097 132 132
ROCK1 0.017 0.028 -10000 0 -0.097 24 24
RAS family/GDP -0.028 0.049 -10000 0 -0.15 47 47
Rac1/GTP -0.024 0.041 -10000 0 -0.14 40 40
Ephrin B/EPHB1/Src/Paxillin 0 0.071 -10000 0 -0.14 101 101
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
ITGB7 0.019 0.023 -9999 0 -0.12 15 15
ITGA4 0.015 0.029 -9999 0 -0.12 24 24
alpha4/beta7 Integrin 0.005 0.065 -9999 0 -0.13 107 107
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 102 102
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.011 0.057 0.19 48 -10000 0 48
BUB1B -0.029 0.1 -10000 0 -0.22 93 93
PLK1 -0.01 0.049 -10000 0 -0.1 95 95
PLK1S1 -0.003 0.022 -10000 0 -0.049 81 81
KIF2A -0.007 0.047 -10000 0 -0.11 79 79
regulation of mitotic centrosome separation -0.01 0.049 -10000 0 -0.1 95 95
GOLGA2 0.023 0.006 -10000 0 -0.12 1 1
Hec1/SPC24 -0.015 0.088 -10000 0 -0.15 139 139
WEE1 -0.015 0.077 -10000 0 -0.24 37 37
cytokinesis -0.052 0.14 -10000 0 -0.29 125 125
PP2A-alpha B56 -0.039 0.24 -10000 0 -0.7 64 64
AURKA -0.026 0.092 -10000 0 -0.25 76 76
PICH/PLK1 -0.025 0.1 -10000 0 -0.18 143 143
CENPE -0.005 0.046 -10000 0 -0.11 74 74
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
positive regulation of microtubule depolymerization -0.007 0.047 -10000 0 -0.11 79 79
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.023 0 -10000 0 -10000 0 0
TPX2 -0.034 0.1 -10000 0 -0.26 92 92
PAK1 0.016 0.029 -10000 0 -0.12 24 24
SPC24 0.016 0.03 -10000 0 -0.12 25 25
FBXW11 0.023 0.003 -10000 0 -10000 0 0
CLSPN 0 0.035 -10000 0 -0.12 17 17
GORASP1 0.023 0.006 -10000 0 -0.12 1 1
metaphase -0.001 0.004 -10000 0 -0.014 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.022 -10000 0 -0.049 81 81
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.009 49 49
STAG2 0.02 0.02 -10000 0 -0.12 11 11
GRASP65/GM130/RAB1/GTP 0.017 0.031 -10000 0 -10000 0 0
spindle elongation -0.01 0.049 -10000 0 -0.1 95 95
ODF2 0.021 0.014 -10000 0 -0.12 5 5
BUB1 -0.066 0.25 -10000 0 -0.76 64 64
TPT1 0.001 0.035 -10000 0 -0.16 17 17
CDC25C -0.016 0.095 -10000 0 -0.38 33 33
CDC25B 0.015 0.024 -10000 0 -0.13 14 14
SGOL1 -0.011 0.057 -10000 0 -0.19 48 48
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CCNB1/CDK1 -0.029 0.13 -10000 0 -0.24 138 138
CDC14B 0.011 0.004 -10000 0 -0.084 1 1
CDC20 0.016 0.026 -10000 0 -0.12 19 19
PLK1/PBIP1 -0.004 0.042 -10000 0 -0.097 73 73
mitosis 0.003 0.009 0.025 71 -0.011 1 72
FBXO5 -0.02 0.07 -10000 0 -0.16 87 87
CDC2 0.007 0.04 -10000 0 -0.12 48 48
NDC80 0.008 0.038 -10000 0 -0.12 43 43
metaphase plate congression 0 0.042 -10000 0 -0.21 12 12
ERCC6L -0.034 0.12 -10000 0 -0.23 136 136
NLP/gamma Tubulin -0.002 0.029 -10000 0 -0.08 49 49
microtubule cytoskeleton organization 0.001 0.035 -10000 0 -0.16 17 17
G2/M transition DNA damage checkpoint 0 0.002 0.01 16 -10000 0 16
PPP1R12A 0.022 0.008 -10000 0 -0.12 1 1
interphase 0 0.002 0.01 16 -10000 0 16
PLK1/PRC1-2 -0.015 0.095 -10000 0 -0.16 133 133
GRASP65/GM130/RAB1/GTP/PLK1 0.023 0.053 -10000 0 -0.12 45 45
RAB1A 0.023 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.011 0.051 -10000 0 -0.11 94 94
mitotic prometaphase -0.001 0.003 0.02 6 -0.01 23 29
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.057 -10000 0 -0.25 14 14
microtubule-based process -0.01 0.072 -10000 0 -0.13 112 112
Golgi organization -0.01 0.049 -10000 0 -0.1 95 95
Cohesin/SA2 -0.003 0.054 -10000 0 -0.12 85 85
PPP1CB/MYPT1 0.024 0.039 -10000 0 -0.14 29 29
KIF20A 0.009 0.037 -10000 0 -0.12 42 42
APC/C/CDC20 -0.005 0.069 -10000 0 -0.13 102 102
PPP2R1A 0.022 0.009 -10000 0 -0.12 2 2
chromosome segregation -0.004 0.042 -10000 0 -0.096 73 73
PRC1 0.015 0.03 -10000 0 -0.12 25 25
ECT2 -0.021 0.072 -10000 0 -0.15 105 105
C13orf34 -0.01 0.05 -10000 0 -0.11 87 87
NUDC 0 0.042 -10000 0 -0.21 12 12
regulation of attachment of spindle microtubules to kinetochore -0.028 0.099 -10000 0 -0.22 93 93
spindle assembly -0.005 0.037 -10000 0 -0.082 83 83
spindle stabilization -0.003 0.022 -10000 0 -0.049 81 81
APC/C/HCDH1 0.025 0.007 -10000 0 -0.089 2 2
MKLP2/PLK1 -0.01 0.073 -10000 0 -0.13 112 112
CCNB1 0.014 0.027 -10000 0 -0.12 20 20
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.023 0.002 -10000 0 -10000 0 0
ROCK2 -0.015 0.094 -10000 0 -0.29 49 49
TUBG1 0 0.039 -10000 0 -0.17 19 19
G2/M transition of mitotic cell cycle -0.044 0.12 -10000 0 -0.24 136 136
MLF1IP 0.01 0.011 -10000 0 -0.078 8 8
INCENP 0.022 0.009 -10000 0 -0.12 2 2
Noncanonical Wnt signaling pathway

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
NFATC2 0.02 0.019 -9999 0 -0.12 10 10
GNB1/GNG2 -0.011 0.1 -9999 0 -0.23 68 68
mol:DAG -0.018 0.095 -9999 0 -0.21 76 76
PLCG1 -0.018 0.097 -9999 0 -0.21 76 76
YES1 -0.029 0.1 -9999 0 -0.26 63 63
FZD3 0.013 0.032 -9999 0 -0.12 30 30
FZD6 0.017 0.024 -9999 0 -0.12 15 15
G protein -0.008 0.1 -9999 0 -0.22 68 68
MAP3K7 -0.014 0.084 -9999 0 -0.18 82 82
mol:Ca2+ -0.017 0.093 -9999 0 -0.2 76 76
mol:IP3 -0.018 0.095 -9999 0 -0.21 76 76
NLK 0.026 0.045 -9999 0 -0.98 1 1
GNB1 0.023 0.006 -9999 0 -0.12 1 1
CAMK2A -0.015 0.087 -9999 0 -0.19 76 76
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.032 0.1 -9999 0 -0.18 162 162
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
GNAS -0.028 0.097 -9999 0 -0.25 61 61
GO:0007205 -0.021 0.092 -9999 0 -0.21 76 76
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.023 0.01 -9999 0 -0.12 3 3
NFAT1/CK1 alpha -0.01 0.11 -9999 0 -0.22 82 82
GNG2 0.02 0.018 -9999 0 -0.12 9 9
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 83 83
CDC42 -0.024 0.095 -9999 0 -0.24 63 63
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.084 0.19 -10000 0 -0.4 137 137
IHH -0.001 0.048 -10000 0 -0.075 143 143
SHH Np/Cholesterol/GAS1 0.022 0.029 -10000 0 -0.098 19 19
LRPAP1 0.018 0.023 -10000 0 -0.12 15 15
dorsoventral neural tube patterning -0.022 0.029 0.097 19 -10000 0 19
SMO/beta Arrestin2 -0.01 0.11 -10000 0 -0.28 10 10
SMO -0.019 0.11 -10000 0 -0.31 8 8
AKT1 -0.018 0.11 -10000 0 -0.33 40 40
ARRB2 0.022 0.013 -10000 0 -0.12 5 5
BOC 0.011 0.038 -10000 0 -0.12 44 44
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
heart looping -0.018 0.1 -10000 0 -0.3 8 8
STIL -0.017 0.082 -10000 0 -0.15 137 137
DHH N/PTCH2 0.034 0.011 -10000 0 -0.15 1 1
DHH N/PTCH1 -0.019 0.099 -10000 0 -0.18 137 137
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
DHH 0.023 0.01 -10000 0 -0.12 3 3
PTHLH -0.072 0.18 -10000 0 -0.38 137 137
determination of left/right symmetry -0.018 0.1 -10000 0 -0.3 8 8
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
skeletal system development -0.072 0.18 -10000 0 -0.37 137 137
IHH N/Hhip 0.016 0.039 -10000 0 -0.097 27 27
DHH N/Hhip 0.029 0.024 -10000 0 -0.14 1 1
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.018 0.1 -10000 0 -0.3 8 8
pancreas development 0.017 0.029 -10000 0 -0.12 25 25
HHAT 0.022 0.011 -10000 0 -0.12 3 3
PI3K 0.007 0.065 -10000 0 -0.13 98 98
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.035 -10000 0 -0.12 35 35
somite specification -0.018 0.1 -10000 0 -0.3 8 8
SHH Np/Cholesterol/PTCH1 -0.013 0.086 -10000 0 -0.15 137 137
SHH Np/Cholesterol/PTCH2 0.03 0.014 -10000 0 -0.099 5 5
SHH Np/Cholesterol/Megalin 0.007 0.039 -10000 0 -0.1 20 20
SHH 0.022 0.011 -10000 0 -0.085 5 5
catabolic process -0.033 0.11 -10000 0 -0.21 137 137
SMO/Vitamin D3 -0.01 0.097 -10000 0 -0.24 8 8
SHH Np/Cholesterol/Hhip 0.027 0.02 -10000 0 -0.098 5 5
LRP2 -0.015 0.063 -10000 0 -0.12 150 150
receptor-mediated endocytosis -0.02 0.098 -10000 0 -0.21 58 58
SHH Np/Cholesterol/BOC 0.02 0.034 -10000 0 -0.11 23 23
SHH Np/Cholesterol/CDO 0.018 0.037 -10000 0 -0.098 40 40
mesenchymal cell differentiation -0.026 0.02 0.098 5 -10000 0 5
mol:Vitamin D3 -0.012 0.088 -10000 0 -0.15 137 137
IHH N/PTCH2 0.021 0.031 -10000 0 -0.14 3 3
CDON 0.013 0.035 -10000 0 -0.12 35 35
IHH N/PTCH1 -0.028 0.11 -10000 0 -0.21 137 137
Megalin/LRPAP1 -0.01 0.065 -10000 0 -0.092 200 200
PTCH2 0.023 0.008 -10000 0 -0.12 2 2
SHH Np/Cholesterol 0.018 0.012 -10000 0 -0.1 4 4
PTCH1 -0.033 0.11 -10000 0 -0.21 137 137
HHIP 0.017 0.029 -10000 0 -0.12 25 25
Caspase cascade in apoptosis

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
TOP1 0.005 0.11 0.16 16 -0.24 60 76
ACTA1 0.023 0.073 0.15 60 -0.21 16 76
NUMA1 0.001 0.11 0.16 16 -0.25 67 83
SPTAN1 0.019 0.077 0.15 61 -0.2 20 81
LIMK1 0.025 0.072 0.15 62 -0.22 14 76
BIRC3 -0.005 0.052 -10000 0 -0.12 93 93
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
BAX 0.023 0 -10000 0 -10000 0 0
CASP10 0.005 0.036 -10000 0 -0.072 88 88
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.008 0.14 0.17 7 -0.32 64 71
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
apoptotic nuclear changes 0.019 0.076 0.15 61 -0.2 20 81
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.009 -10000 0 -0.12 2 2
GSN 0.021 0.074 0.15 58 -0.22 17 75
MADD 0.023 0.006 -10000 0 -0.12 1 1
TFAP2A -0.031 0.15 -10000 0 -0.47 50 50
BID 0.01 0.037 -10000 0 -0.22 5 5
MAP3K1 0.008 0.082 -10000 0 -0.36 22 22
TRADD 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.025 0.04 -10000 0 -0.16 22 22
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.006 0.076 0.14 37 -0.22 23 60
CASP9 0.022 0.014 -10000 0 -0.12 5 5
DNA repair -0.024 0.074 0.26 22 -0.14 61 83
neuron apoptosis -0.026 0.16 -10000 0 -0.57 41 41
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.009 0.1 0.17 34 -0.26 31 65
APAF1 0.021 0.014 -10000 0 -0.12 5 5
CASP6 -0.055 0.25 -10000 0 -0.78 59 59
TRAF2 0.023 0 -10000 0 -10000 0 0
ICAD/CAD 0.028 0.069 0.15 59 -0.2 14 73
CASP7 0.044 0.077 0.19 106 -0.19 6 112
KRT18 -0.014 0.12 -10000 0 -0.56 22 22
apoptosis -0.006 0.13 0.18 29 -0.31 61 90
DFFA 0.025 0.072 0.15 61 -0.22 14 75
DFFB 0.025 0.072 0.15 63 -0.22 14 77
PARP1 0.024 0.074 0.14 61 -0.26 22 83
actin filament polymerization -0.025 0.069 0.2 15 -0.15 58 73
TNF 0.02 0.02 -10000 0 -0.12 11 11
CYCS -0.005 0.05 -10000 0 -0.21 22 22
SATB1 -0.063 0.24 -10000 0 -0.75 60 60
SLK 0.018 0.077 0.15 61 -0.21 18 79
p15 BID/BAX 0.016 0.044 -10000 0 -0.25 5 5
CASP2 0.008 0.066 -10000 0 -0.24 17 17
JNK cascade -0.008 0.082 0.36 22 -10000 0 22
CASP3 0.023 0.077 0.16 63 -0.23 14 77
LMNB2 -0.002 0.099 -10000 0 -0.26 63 63
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP4 0.015 0.029 -10000 0 -0.12 23 23
Mammalian IAPs/DIABLO -0.019 0.083 -10000 0 -0.13 159 159
negative regulation of DNA binding -0.03 0.15 -10000 0 -0.47 50 50
stress fiber formation 0.018 0.076 0.15 61 -0.21 18 79
GZMB 0.006 0.044 -10000 0 -0.098 78 78
CASP1 -0.064 0.14 -10000 0 -0.28 149 149
LMNB1 -0.028 0.14 -10000 0 -0.28 103 103
APP -0.027 0.17 -10000 0 -0.58 41 41
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.002 -10000 0 -10000 0 0
VIM -0.003 0.13 0.18 30 -0.32 58 88
LMNA -0.008 0.11 -10000 0 -0.27 73 73
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.07 -10000 0 -0.23 21 21
LRDD 0.022 0.015 -10000 0 -0.12 6 6
SREBF1 0.024 0.074 0.15 63 -0.22 14 77
APAF-1/Caspase 9 0.028 0.11 0.26 15 -0.75 8 23
nuclear fragmentation during apoptosis 0.001 0.11 0.16 16 -0.24 67 83
CFL2 0.025 0.07 0.15 57 -0.2 15 72
GAS2 0.023 0.072 0.15 58 -0.21 15 73
positive regulation of apoptosis -0.014 0.12 -10000 0 -0.3 67 67
PRF1 0.014 0.035 -10000 0 -0.12 37 37
Wnt signaling

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
Noncanonical Wnts/FZD -0.032 0.1 -9999 0 -0.18 162 162
FZD6 0.017 0.024 -9999 0 -0.12 15 15
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.023 0.01 -9999 0 -0.12 3 3
FZD3 0.013 0.032 -9999 0 -0.12 30 30
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 83 83
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.006 0.11 -10000 0 -0.22 82 82
adherens junction organization -0.008 0.12 -10000 0 -0.26 70 70
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.098 -10000 0 -0.24 53 53
FMN1 -0.003 0.11 -10000 0 -0.25 69 69
mol:IP3 -0.003 0.093 -10000 0 -0.21 67 67
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.11 -10000 0 -0.27 67 67
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
AKT1 0 0.098 -10000 0 -0.25 50 50
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.006 0.13 -10000 0 -0.36 49 49
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.1 -10000 0 -0.24 68 68
VASP -0.002 0.11 -10000 0 -0.25 68 68
ZYX -0.004 0.11 -10000 0 -0.26 67 67
JUB -0.006 0.11 -10000 0 -0.25 70 70
EGFR(dimer) -0.001 0.11 -10000 0 -0.26 70 70
E-cadherin/beta catenin-gamma catenin 0.027 0.052 -10000 0 -0.11 63 63
mol:PI-3-4-5-P3 0.003 0.1 -10000 0 -0.25 54 54
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.003 0.11 -10000 0 -0.26 54 54
FYN -0.012 0.11 -10000 0 -0.27 68 68
mol:Ca2+ -0.003 0.091 -10000 0 -0.2 67 67
JUP 0.019 0.021 -10000 0 -0.12 12 12
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:DAG -0.003 0.093 -10000 0 -0.21 67 67
CDH1 0.02 0.015 -10000 0 -0.12 6 6
RhoA/GDP 0.002 0.098 -10000 0 -0.24 53 53
establishment of polarity of embryonic epithelium -0.001 0.1 -10000 0 -0.25 68 68
SRC 0.023 0.008 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
RHOA 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
CASR 0 0.087 -10000 0 -0.2 66 66
RhoA/GTP 0.005 0.089 -10000 0 -0.23 48 48
AKT2 -0.001 0.098 -10000 0 -0.24 54 54
actin cable formation 0 0.1 -10000 0 -0.24 69 69
apoptosis 0.005 0.099 0.24 59 -10000 0 59
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
mol:GDP -0.006 0.098 -10000 0 -0.21 75 75
PIP5K1A -0.002 0.11 -10000 0 -0.25 68 68
PLCG1 -0.004 0.095 -10000 0 -0.21 67 67
Rac1/GTP 0.004 0.11 -10000 0 -0.24 71 71
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.01 0.041 -10000 0 -0.12 51 51
Jak2/Leptin Receptor -0.042 0.13 -10000 0 -0.37 56 56
PTP1B/AKT1 -0.059 0.1 -10000 0 -0.24 96 96
FYN 0.012 0.037 -10000 0 -0.12 40 40
p210 bcr-abl/PTP1B -0.074 0.1 -10000 0 -0.26 94 94
EGFR 0.015 0.03 -10000 0 -0.12 25 25
EGF/EGFR -0.057 0.1 -10000 0 -0.23 103 103
CSF1 0.013 0.033 -10000 0 -0.12 31 31
AKT1 0.021 0.019 -10000 0 -0.12 10 10
INSR 0.021 0.017 -10000 0 -0.12 8 8
PTP1B/N-cadherin -0.092 0.12 -10000 0 -0.24 186 186
Insulin Receptor/Insulin -0.03 0.091 -10000 0 -0.21 75 75
HCK 0.019 0.023 -10000 0 -0.12 15 15
CRK 0.022 0.016 -10000 0 -0.12 7 7
TYK2 -0.067 0.1 -10000 0 -0.25 95 95
EGF 0.018 0.022 -10000 0 -0.12 13 13
YES1 0.02 0.018 -10000 0 -0.12 8 8
CAV1 -0.055 0.096 -10000 0 -0.23 93 93
TXN 0.019 0.014 -10000 0 -0.12 5 5
PTP1B/IRS1/GRB2 -0.053 0.11 -10000 0 -0.24 101 101
cell migration 0.074 0.1 0.26 94 -10000 0 94
STAT3 0.021 0.011 -10000 0 -0.12 3 3
PRLR 0.014 0.042 -10000 0 -0.12 55 55
ITGA2B 0.022 0.006 -10000 0 -0.12 1 1
CSF1R 0.014 0.031 -10000 0 -0.12 28 28
Prolactin Receptor/Prolactin 0.035 0.035 -10000 0 -0.17 2 2
FGR 0.023 0.006 -10000 0 -0.12 1 1
PTP1B/p130 Cas -0.062 0.1 -10000 0 -0.25 94 94
Crk/p130 Cas -0.051 0.1 -10000 0 -0.24 92 92
DOK1 -0.055 0.094 -10000 0 -0.24 79 79
JAK2 -0.05 0.13 -10000 0 -0.4 54 54
Jak2/Leptin Receptor/Leptin -0.054 0.12 -10000 0 -0.25 120 120
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
PTPN1 -0.074 0.1 -10000 0 -0.26 94 94
LYN 0.021 0.013 -10000 0 -0.12 4 4
CDH2 -0.014 0.056 -10000 0 -0.12 121 121
SRC -0.007 0.053 -10000 0 -0.61 2 2
ITGB3 0.004 0.046 -10000 0 -0.12 67 67
CAT1/PTP1B -0.056 0.12 -10000 0 -0.26 99 99
CAPN1 0.02 0.013 -10000 0 -0.12 4 4
CSK 0.023 0.009 -10000 0 -0.12 2 2
PI3K -0.032 0.1 -10000 0 -0.2 101 101
mol:H2O2 0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.048 0.12 -10000 0 -0.24 114 114
negative regulation of transcription -0.049 0.13 -10000 0 -0.39 54 54
FCGR2A 0.013 0.03 -10000 0 -0.12 26 26
FER 0.019 0.017 -10000 0 -0.12 8 8
alphaIIb/beta3 Integrin 0.008 0.053 -10000 0 -0.14 38 38
BLK 0.022 0.013 -10000 0 -0.12 5 5
Insulin Receptor/Insulin/Shc 0.043 0.022 -10000 0 -0.11 7 7
RHOA 0.021 0.007 -10000 0 -0.12 1 1
LEPR 0.018 0.028 -10000 0 -0.12 22 22
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
p210 bcr-abl/Grb2 0.023 0.006 -10000 0 -0.12 1 1
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.001 0.085 -10000 0 -0.23 36 36
PRL 0.027 0.012 -10000 0 -0.13 3 3
SOCS3 -0.027 0.22 -10000 0 -1.2 20 20
SPRY2 -0.008 0.054 -10000 0 -0.12 103 103
Insulin Receptor/Insulin/IRS1 0.039 0.03 -10000 0 -0.11 13 13
CSF1/CSF1R -0.076 0.13 -10000 0 -0.26 138 138
Ras protein signal transduction 0.028 0.034 0.098 29 -0.14 6 35
IRS1 0.02 0.022 -10000 0 -0.12 14 14
INS 0.022 0.011 -10000 0 -0.12 3 3
LEP 0.023 0.006 -10000 0 -0.12 1 1
STAT5B -0.059 0.1 -10000 0 -0.24 96 96
STAT5A -0.061 0.1 -10000 0 -0.25 93 93
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDGFB-D/PDGFRB -0.067 0.1 -10000 0 -0.24 104 104
CSN2 0.04 0.027 -10000 0 -10000 0 0
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
LAT -0.082 0.19 -10000 0 -0.5 88 88
YBX1 0.033 0.015 -10000 0 -0.15 3 3
LCK 0.022 0.015 -10000 0 -0.12 6 6
SHC1 0.023 0.001 -10000 0 -10000 0 0
NOX4 -0.021 0.062 -10000 0 -0.12 156 156
Paxillin-independent events mediated by a4b1 and a4b7

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 -0.003 0.075 -9999 0 -0.16 90 90
CRKL 0.023 0.009 -9999 0 -0.12 2 2
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
DOCK1 0.019 0.02 -9999 0 -0.12 11 11
ITGA4 0.015 0.029 -9999 0 -0.12 24 24
alpha4/beta7 Integrin/MAdCAM1 0.032 0.059 -9999 0 -0.1 79 79
EPO 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta7 Integrin 0.005 0.065 -9999 0 -0.13 107 107
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.022 0.016 -9999 0 -0.12 7 7
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 102 102
EPO/EPOR (dimer) 0.032 0.019 -9999 0 -0.079 15 15
lamellipodium assembly 0.004 0.086 -9999 0 -0.35 18 18
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K 0.007 0.065 -9999 0 -0.13 98 98
ARF6 0.023 0.003 -9999 0 -10000 0 0
JAK2 0.003 0.081 -9999 0 -0.18 74 74
PXN 0.022 0.013 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
MADCAM1 0.023 0.006 -9999 0 -0.12 1 1
cell adhesion 0.03 0.058 -9999 0 -0.1 79 79
CRKL/CBL 0.033 0.013 -9999 0 -0.14 2 2
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC -0.037 0.074 -9999 0 -0.13 188 188
ITGB7 0.019 0.023 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.04 0.09 -9999 0 -0.15 188 188
p130Cas/Crk/Dock1 -0.021 0.075 -9999 0 -0.16 78 78
VCAM1 -0.018 0.059 -9999 0 -0.12 139 139
RHOA 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.033 0.057 -9999 0 -0.099 75 75
BCAR1 -0.032 0.067 -9999 0 -0.11 188 188
EPOR 0.02 0.021 -9999 0 -0.12 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.023 0.006 -9999 0 -0.12 1 1
GIT1 0.022 0.013 -9999 0 -0.12 5 5
Rac1/GTP 0.004 0.089 -9999 0 -0.36 18 18
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.004 0.14 -10000 0 -0.32 67 67
FYN -0.047 0.18 -10000 0 -0.4 89 89
LAT/GRAP2/SLP76 -0.01 0.15 -10000 0 -0.32 81 81
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 -0.009 0.13 -10000 0 -0.3 78 78
B2M 0.022 0.007 -10000 0 -10000 0 0
IKBKG 0.008 0.044 -10000 0 -0.091 67 67
MAP3K8 0.023 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.004 0.011 -10000 0 -0.034 48 48
integrin-mediated signaling pathway 0.021 0.035 -10000 0 -0.096 44 44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.024 0.18 -10000 0 -0.42 78 78
TRPV6 0.003 0.017 -10000 0 -0.13 7 7
CD28 0.022 0.01 -10000 0 -0.12 3 3
SHC1 -0.019 0.16 -10000 0 -0.4 65 65
receptor internalization -0.015 0.14 -10000 0 -0.35 65 65
PRF1 -0.019 0.18 -10000 0 -0.79 20 20
KRAS 0.014 0.034 -10000 0 -0.12 33 33
GRB2 0.023 0.006 -10000 0 -0.12 1 1
COT/AKT1 0.004 0.11 -10000 0 -0.24 77 77
LAT -0.019 0.16 -10000 0 -0.4 65 65
EntrezGene:6955 0 0.003 -10000 0 -0.022 3 3
CD3D 0.008 0.044 -10000 0 -0.12 58 58
CD3E 0.015 0.033 -10000 0 -0.12 29 29
CD3G 0.002 0.05 -10000 0 -0.12 78 78
RASGRP2 0.007 0.015 -10000 0 -0.049 1 1
RASGRP1 -0.017 0.14 -10000 0 -0.29 89 89
HLA-A 0.02 0.019 -10000 0 -0.12 8 8
RASSF5 0.02 0.022 -10000 0 -0.12 13 13
RAP1A/GTP/RAPL 0.022 0.035 -10000 0 -0.096 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.05 -10000 0 -0.089 82 82
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.054 -10000 0 -0.14 83 83
PRKCA -0.005 0.08 -10000 0 -0.18 76 76
GRAP2 0.022 0.012 -10000 0 -0.12 4 4
mol:IP3 -0.045 0.099 0.096 4 -0.27 77 81
EntrezGene:6957 0 0.004 -10000 0 -0.022 3 3
TCR/CD3/MHC I/CD8 -0.015 0.13 -10000 0 -0.36 52 52
ORAI1 0 0.023 -10000 0 -0.15 7 7
CSK -0.019 0.16 -10000 0 -0.4 65 65
B7 family/CD28 -0.008 0.16 -10000 0 -0.35 75 75
CHUK 0.021 0.013 -10000 0 -0.12 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.027 0.18 -10000 0 -0.44 67 67
PTPN6 -0.024 0.16 -10000 0 -0.4 66 66
VAV1 -0.023 0.16 -10000 0 -0.4 70 70
Monovalent TCR/CD3 -0.016 0.096 -10000 0 -0.2 98 98
CBL 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.037 0.18 -10000 0 -0.39 84 84
PAG1 -0.02 0.16 -10000 0 -0.4 64 64
RAP1A 0.021 0.011 -10000 0 -0.12 3 3
TCR/CD3/MHC I/CD8/LCK -0.029 0.17 -10000 0 -0.42 70 70
CD80 0.019 0.024 -10000 0 -0.12 16 16
CD86 0.013 0.033 -10000 0 -0.12 32 32
PDK1/CARD11/BCL10/MALT1 -0.027 0.066 -10000 0 -0.18 78 78
HRAS 0.023 0.006 -10000 0 -0.12 1 1
GO:0035030 -0.017 0.13 -10000 0 -0.31 75 75
CD8A 0.023 0.012 -10000 0 -0.13 3 3
CD8B 0.021 0.017 -10000 0 -0.13 7 7
PTPRC -0.004 0.05 -10000 0 -0.12 86 86
PDK1/PKC theta -0.016 0.15 -10000 0 -0.35 78 78
CSK/PAG1 -0.015 0.16 -10000 0 -0.39 64 64
SOS1 0.017 0.027 -10000 0 -0.12 20 20
peptide-MHC class I 0.012 0.073 -10000 0 -0.19 58 58
GRAP2/SLP76 -0.015 0.17 -10000 0 -0.37 81 81
STIM1 -0.002 0.032 -10000 0 -0.17 18 18
RAS family/GTP 0.007 0.07 -10000 0 -0.14 73 73
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.15 -10000 0 -0.37 65 65
mol:DAG -0.042 0.089 -10000 0 -0.23 82 82
RAP1A/GDP 0.005 0.026 -10000 0 -0.045 82 82
PLCG1 0.018 0.025 -10000 0 -0.12 18 18
CD247 0.024 0.004 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.017 0.18 -10000 0 -0.7 23 23
RAP1A/GTP -0.002 0.009 -10000 0 -0.037 25 25
mol:PI-3-4-5-P3 -0.016 0.15 -10000 0 -0.35 78 78
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.051 0.13 0.12 3 -0.33 76 79
NRAS 0.022 0.011 -10000 0 -0.12 3 3
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
GRB2/SOS1 0.021 0.046 -10000 0 -0.12 52 52
LAT/GRAP2/SLP76/VAV1 -0.013 0.15 -10000 0 -0.33 79 79
MALT1 0.018 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
CD8 heterodimer 0.032 0.017 -10000 0 -0.081 7 7
CARD11 0.018 0.028 -10000 0 -0.12 22 22
PRKCB -0.03 0.064 -10000 0 -0.17 82 82
PRKCE 0 0.08 -10000 0 -0.18 76 76
PRKCQ -0.024 0.17 -10000 0 -0.39 79 79
LCP2 0.013 0.033 -10000 0 -0.12 31 31
BCL10 0.023 0.001 -10000 0 -10000 0 0
regulation of survival gene product expression -0.005 0.12 -10000 0 -0.26 78 78
IKK complex 0.007 0.044 -10000 0 -0.084 53 53
RAS family/GDP -0.006 0.01 -10000 0 -0.034 41 41
MAP3K14 0.008 0.088 -10000 0 -0.18 77 77
PDPK1 -0.007 0.13 -10000 0 -0.28 78 78
TCR/CD3/MHC I/CD8/Fyn -0.031 0.19 -10000 0 -0.49 67 67
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.001 0.089 -10000 0 -0.18 90 90
epithelial cell differentiation 0.028 0.06 -10000 0 -0.12 71 71
CYFIP2 0.02 0.017 -10000 0 -0.12 8 8
ENAH 0.008 0.057 -10000 0 -0.13 54 54
EGFR 0.015 0.03 -10000 0 -0.12 25 25
EPHA2 0.02 0.021 -10000 0 -0.12 13 13
MYO6 0.009 0.058 -10000 0 -0.12 71 71
CTNNB1 0.022 0.007 -10000 0 -0.12 1 1
ABI1/Sra1/Nap1 0.03 0.05 -10000 0 -0.12 54 54
AQP5 -0.059 0.15 -10000 0 -0.32 123 123
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.05 -10000 0 -0.11 71 71
regulation of calcium-dependent cell-cell adhesion 0.013 0.051 -10000 0 -0.11 71 71
EGF 0.02 0.021 -10000 0 -0.12 13 13
NCKAP1 0.023 0.004 -10000 0 -10000 0 0
AQP3 0.011 0.077 -10000 0 -0.27 27 27
cortical microtubule organization 0.028 0.06 -10000 0 -0.12 71 71
GO:0000145 0.007 0.046 -10000 0 -0.1 71 71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.062 -10000 0 -0.12 71 71
MLLT4 0.014 0.032 -10000 0 -0.12 30 30
ARF6/GDP -0.023 0.051 -10000 0 -0.17 46 46
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.063 -10000 0 -0.11 77 77
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.014 0.06 -10000 0 -0.19 32 32
PVRL2 0.019 0.023 -10000 0 -0.12 15 15
ZYX 0.01 0.055 -10000 0 -0.12 71 71
ARF6/GTP 0.034 0.064 -10000 0 -0.17 19 19
CDH1 0.021 0.015 -10000 0 -0.12 6 6
EGFR/EGFR/EGF/EGF 0.015 0.063 -10000 0 -0.18 28 28
RhoA/GDP 0.03 0.059 -10000 0 -0.11 75 75
actin cytoskeleton organization 0.007 0.06 -10000 0 -0.13 71 71
IGF-1R heterotetramer 0.013 0.031 -10000 0 -0.12 28 28
GIT1 0.022 0.013 -10000 0 -0.12 5 5
IGF1R 0.013 0.031 -10000 0 -0.12 28 28
IGF1 0.007 0.045 -10000 0 -0.12 62 62
DIAPH1 -0.022 0.2 -10000 0 -0.56 71 71
Wnt receptor signaling pathway -0.028 0.06 0.12 71 -10000 0 71
RHOA 0.023 0.006 -10000 0 -0.12 1 1
RhoA/GTP -0.022 0.05 -10000 0 -0.17 45 45
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
VCL 0.007 0.062 -10000 0 -0.13 71 71
EFNA1 0.014 0.031 -10000 0 -0.12 28 28
LPP 0.011 0.055 -10000 0 -0.11 73 73
Ephrin A1/EPHA2 0.011 0.064 -10000 0 -0.18 32 32
SEC6/SEC8 -0.021 0.05 -10000 0 -0.19 35 35
MGAT3 0.013 0.052 -10000 0 -0.11 71 71
HGF/MET -0.006 0.072 -10000 0 -0.18 48 48
HGF 0.02 0.022 -10000 0 -0.12 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.089 -10000 0 -0.18 90 90
actin cable formation 0.011 0.08 -10000 0 -0.19 52 52
KIAA1543 0.012 0.05 -10000 0 -0.1 71 71
KIFC3 0.014 0.051 -10000 0 -0.11 71 71
NCK1 0.02 0.019 -10000 0 -0.12 9 9
EXOC3 0.023 0.009 -10000 0 -0.12 2 2
ACTN1 0.012 0.058 -10000 0 -0.12 71 71
NCK1/GIT1 0.022 0.043 -10000 0 -0.14 32 32
mol:GDP 0.028 0.06 -10000 0 -0.12 71 71
EXOC4 0.023 0.007 -10000 0 -0.12 1 1
STX4 0.013 0.052 -10000 0 -0.11 71 71
PIP5K1C 0.014 0.051 -10000 0 -0.11 71 71
LIMA1 0.019 0.023 -10000 0 -0.12 14 14
ABI1 0.022 0.009 -10000 0 -0.12 2 2
ROCK1 0.01 0.061 -10000 0 -0.15 46 46
adherens junction assembly 0.021 0.059 -10000 0 -0.21 18 18
IGF-1R heterotetramer/IGF1 -0.002 0.071 -10000 0 -0.16 53 53
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.012 0.054 -10000 0 -0.11 89 89
MET 0.001 0.047 -10000 0 -0.12 71 71
PLEKHA7 0.013 0.053 -10000 0 -0.11 71 71
mol:GTP 0.027 0.062 -10000 0 -0.11 77 77
establishment of epithelial cell apical/basal polarity 0.012 0.063 -10000 0 -0.18 37 37
cortical actin cytoskeleton stabilization -0.001 0.089 -10000 0 -0.18 90 90
regulation of cell-cell adhesion 0.007 0.06 -10000 0 -0.13 71 71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.089 -10000 0 -0.18 90 90
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.024 0.13 -9999 0 -0.26 111 111
MAP3K8 0.021 0.009 -9999 0 -0.12 2 2
FOS -0.013 0.092 -9999 0 -0.28 27 27
PRKCA 0.008 0.038 -9999 0 -0.12 42 42
PTPN7 0.017 0.013 -9999 0 -10000 0 0
HRAS 0.022 0.006 -9999 0 -0.12 1 1
PRKCB -0.003 0.006 -9999 0 -0.01 187 187
NRAS 0.021 0.011 -9999 0 -0.12 3 3
RAS family/GTP 0.025 0.043 -9999 0 -0.11 38 38
MAPK3 0.003 0.067 -9999 0 -0.44 6 6
MAP2K1 -0.015 0.09 -9999 0 -0.29 45 45
ELK1 0.016 0.02 -9999 0 -0.13 6 6
BRAF -0.015 0.084 -9999 0 -0.3 40 40
mol:GTP -0.001 0.002 -9999 0 -0.003 175 175
MAPK1 0 0.075 -9999 0 -0.44 9 9
RAF1 -0.016 0.083 -9999 0 -0.29 45 45
KRAS 0.014 0.034 -9999 0 -0.12 33 33
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.002 0.095 -10000 0 -0.22 50 50
TBX21 -0.085 0.28 -10000 0 -0.71 63 63
B2M 0.024 0.006 -10000 0 -10000 0 0
TYK2 0.015 0.029 -10000 0 -0.13 7 7
IL12RB1 0.016 0.025 -10000 0 -0.066 3 3
GADD45B -0.096 0.33 -10000 0 -0.91 59 59
IL12RB2 0.014 0.033 -10000 0 -0.12 17 17
GADD45G -0.083 0.28 -10000 0 -0.78 54 54
natural killer cell activation -0.003 0.019 -10000 0 -0.039 51 51
RELB 0.022 0.011 -10000 0 -0.12 3 3
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL18 0.005 0.046 -10000 0 -0.12 66 66
IL2RA 0.021 0.018 -10000 0 -0.12 9 9
IFNG 0.013 0.037 -10000 0 -0.12 41 41
STAT3 (dimer) -0.077 0.27 -10000 0 -0.6 90 90
HLA-DRB5 -0.014 0.057 -10000 0 -0.12 119 119
FASLG -0.087 0.28 -10000 0 -0.76 53 53
NF kappa B2 p52/RelB -0.081 0.28 -10000 0 -0.63 86 86
CD4 0.012 0.029 -10000 0 -0.12 21 21
SOCS1 0.017 0.03 -10000 0 -0.12 26 26
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.004 0.045 -10000 0 -0.12 58 58
CD3E 0.012 0.033 -10000 0 -0.12 29 29
CD3G -0.001 0.051 -10000 0 -0.12 78 78
IL12Rbeta2/JAK2 0.009 0.063 -10000 0 -0.14 52 52
CCL3 -0.11 0.33 -10000 0 -0.85 65 65
CCL4 -0.094 0.28 -10000 0 -0.63 87 87
HLA-A 0.021 0.018 -10000 0 -0.12 8 8
IL18/IL18R 0.025 0.076 -10000 0 -0.12 82 82
NOS2 -0.086 0.26 -10000 0 -0.57 96 96
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.092 -10000 0 -0.23 43 43
IL1R1 -0.18 0.43 -10000 0 -1 103 103
IL4 0.026 0.021 -10000 0 -0.11 3 3
JAK2 0.012 0.034 -10000 0 -0.12 18 18
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.42 30 30
RAB7A -0.067 0.27 -10000 0 -0.7 60 60
lysosomal transport -0.062 0.26 -10000 0 -0.65 62 62
FOS -0.26 0.49 -10000 0 -1.1 126 126
STAT4 (dimer) -0.077 0.28 -10000 0 -0.63 87 87
STAT5A (dimer) -0.086 0.28 -10000 0 -0.62 88 88
GZMA -0.12 0.35 -10000 0 -0.88 72 72
GZMB -0.11 0.32 -10000 0 -0.84 60 60
HLX 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.096 0.29 -10000 0 -0.67 85 85
TCR/CD3/MHC II/CD4 -0.11 0.21 -10000 0 -0.36 182 182
IL2/IL2R 0.013 0.068 -10000 0 -0.1 116 116
MAPK14 -0.089 0.31 -10000 0 -0.71 82 82
CCR5 -0.067 0.25 -10000 0 -0.63 60 60
IL1B 0.005 0.044 -10000 0 -0.12 47 47
STAT6 -0.024 0.13 -10000 0 -0.32 48 48
STAT4 0.02 0.02 -10000 0 -0.12 11 11
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT1 0.014 0.03 -10000 0 -0.12 25 25
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
NFKB2 0.023 0.009 -10000 0 -0.12 2 2
IL12B 0.017 0.023 -10000 0 -0.038 2 2
CD8A 0.024 0.01 -10000 0 -0.12 3 3
CD8B 0.023 0.016 -10000 0 -0.12 7 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.001 0.094 0.22 50 -10000 0 50
IL2RB 0.019 0.023 -10000 0 -0.12 15 15
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.26 -10000 0 -0.58 87 87
IL2RG -0.002 0.049 -10000 0 -0.12 82 82
IL12 0.004 0.063 -10000 0 -0.13 58 58
STAT5A 0.022 0.012 -10000 0 -0.12 4 4
CD247 0.021 0.01 -10000 0 -10000 0 0
IL2 0.023 0.01 -10000 0 -0.12 3 3
SPHK2 0.023 0.01 -10000 0 -0.12 3 3
FRAP1 0.022 0.012 -10000 0 -0.12 4 4
IL12A -0.001 0.05 -10000 0 -0.12 70 70
IL12/IL12R/TYK2/JAK2 -0.1 0.31 -10000 0 -0.7 87 87
MAP2K3 -0.083 0.3 -10000 0 -0.68 84 84
RIPK2 0.013 0.034 -10000 0 -0.12 34 34
MAP2K6 -0.1 0.31 -10000 0 -0.7 86 86
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.009 0.031 -10000 0 -0.13 23 23
IL18RAP 0.022 0.02 -10000 0 -0.12 8 8
IL12Rbeta1/TYK2 0.024 0.037 -10000 0 -0.12 5 5
EOMES 0.018 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.1 0.28 -10000 0 -0.6 100 100
T cell proliferation -0.064 0.22 -10000 0 -0.5 86 86
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.025 -10000 0 -0.12 14 14
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.21 -10000 0 -0.53 90 90
ATF2 -0.081 0.29 -10000 0 -0.65 85 85
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.018 0.069 -9999 0 -0.16 81 81
EPHB2 0.02 0.02 -9999 0 -0.12 11 11
Syndecan-2/TACI 0.014 0.042 -9999 0 -0.11 46 46
LAMA1 0 0.052 -9999 0 -0.12 90 90
Syndecan-2/alpha2 ITGB1 -0.005 0.079 -9999 0 -0.11 167 167
HRAS 0.023 0.006 -9999 0 -0.12 1 1
Syndecan-2/CASK -0.001 0.038 -9999 0 -0.11 46 46
ITGA5 0.013 0.036 -9999 0 -0.12 38 38
BAX 0.025 0.02 -9999 0 -10000 0 0
EPB41 0.02 0.018 -9999 0 -0.12 9 9
positive regulation of cell-cell adhesion 0.004 0.049 -9999 0 -0.1 83 83
LAMA3 0.006 0.043 -9999 0 -0.12 57 57
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.038 -9999 0 -0.12 44 44
Syndecan-2/MMP2 -0.015 0.066 -9999 0 -0.16 69 69
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.008 0.06 -9999 0 -0.11 104 104
dendrite morphogenesis 0.011 0.048 -9999 0 -0.12 48 48
Syndecan-2/GM-CSF 0.014 0.043 -9999 0 -0.11 47 47
determination of left/right symmetry 0.012 0.025 -9999 0 -0.066 50 50
Syndecan-2/PKC delta 0.01 0.048 -9999 0 -0.12 53 53
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
MAPK3 0.014 0.038 -9999 0 -0.094 47 47
MAPK1 0.013 0.039 -9999 0 -0.096 47 47
Syndecan-2/RACK1 0.025 0.042 -9999 0 -0.087 53 53
NF1 0.018 0.02 -9999 0 -0.12 10 10
FGFR/FGF/Syndecan-2 0.012 0.025 -9999 0 -0.066 50 50
ITGA2 0.011 0.037 -9999 0 -0.12 41 41
MAPK8 0.02 0.023 -9999 0 -0.1 1 1
Syndecan-2/alpha2/beta1 Integrin 0.006 0.07 -9999 0 -0.11 119 119
Syndecan-2/Kininogen 0.014 0.043 -9999 0 -0.11 46 46
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC 0.018 0.036 -9999 0 -0.078 53 53
Syndecan-2/CASK/Protein 4.1 0.009 0.045 -9999 0 -0.1 61 61
extracellular matrix organization 0.01 0.048 -9999 0 -0.12 52 52
actin cytoskeleton reorganization -0.018 0.068 -9999 0 -0.16 81 81
Syndecan-2/Caveolin-2/Ras 0.01 0.061 -9999 0 -0.11 97 97
Syndecan-2/Laminin alpha3 0 0.058 -9999 0 -0.14 60 60
Syndecan-2/RasGAP 0.028 0.05 -9999 0 -0.15 7 7
alpha5/beta1 Integrin 0.017 0.048 -9999 0 -0.1 75 75
PRKCD 0.02 0.018 -9999 0 -0.12 8 8
Syndecan-2 dimer 0.011 0.048 -9999 0 -0.12 48 48
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.047 -9999 0 -0.14 7 7
RHOA 0.023 0.006 -9999 0 -0.12 1 1
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
TNFRSF13B 0.023 0 -9999 0 -10000 0 0
RASA1 0.021 0.011 -9999 0 -0.12 3 3
alpha2/beta1 Integrin 0.008 0.06 -9999 0 -0.11 104 104
Syndecan-2/Synbindin 0.007 0.051 -9999 0 -0.12 55 55
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CASP3 0.01 0.043 -9999 0 -0.1 53 53
FN1 -0.012 0.055 -9999 0 -0.12 115 115
Syndecan-2/IL8 0.001 0.055 -9999 0 -0.13 61 61
SDC2 0.012 0.025 -9999 0 -0.066 50 50
KNG1 0.023 0.01 -9999 0 -0.12 3 3
Syndecan-2/Neurofibromin 0.008 0.05 -9999 0 -0.13 51 51
TRAPPC4 0.016 0.025 -9999 0 -0.12 17 17
CSF2 0.023 0.008 -9999 0 -0.12 2 2
Syndecan-2/TGFB1 0.01 0.048 -9999 0 -0.12 52 52
Syndecan-2/Syntenin/PI-4-5-P2 0.005 0.05 -9999 0 -0.1 83 83
Syndecan-2/Ezrin 0.012 0.04 -9999 0 -0.097 50 50
PRKACA 0.008 0.045 -9999 0 -0.11 52 52
angiogenesis 0.001 0.055 -9999 0 -0.13 61 61
MMP2 -0.015 0.059 -9999 0 -0.12 131 131
IL8 0.004 0.047 -9999 0 -0.12 70 70
calcineurin-NFAT signaling pathway 0.014 0.042 -9999 0 -0.11 46 46
Aurora A signaling

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
Aurora A/GADD45A 0 0.075 -10000 0 -0.18 72 72
BIRC5 0.018 0.023 -10000 0 -0.12 15 15
NFKBIA 0.013 0.038 0.11 7 -0.13 24 31
CPEB1 0.02 0.022 -10000 0 -0.12 14 14
AKT1 0.017 0.026 0.11 7 -0.095 13 20
NDEL1 0.023 0.006 -10000 0 -0.12 1 1
Aurora A/BRCA1 -0.007 0.069 -10000 0 -0.13 113 113
NDEL1/TACC3 0.005 0.075 -10000 0 -0.16 77 77
GADD45A 0.014 0.032 -10000 0 -0.12 30 30
GSK3B 0.022 0.013 0.069 15 -0.12 3 18
PAK1/Aurora A 0.003 0.071 -10000 0 -0.17 71 71
MDM2 0.02 0.02 -10000 0 -0.12 11 11
JUB 0.018 0.024 -10000 0 -0.12 16 16
TPX2 0.017 0.017 -10000 0 -0.07 15 15
TP53 -0.064 0.13 -10000 0 -0.25 182 182
DLG7 0.012 0.025 0.11 2 -0.057 41 43
AURKAIP1 0.02 0.021 -10000 0 -0.12 12 12
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.005 0.08 -10000 0 -0.17 77 77
G2/M transition of mitotic cell cycle -0.007 0.069 -10000 0 -0.13 113 113
AURKA -0.005 0.078 0.14 3 -0.2 69 72
AURKB 0.008 0.044 -10000 0 -0.2 19 19
CDC25B 0.006 0.066 -10000 0 -0.25 29 29
G2/M transition checkpoint -0.002 0.067 -10000 0 -0.14 95 95
mRNA polyadenylation 0.005 0.061 -10000 0 -0.15 69 69
Aurora A/CPEB 0.005 0.061 -10000 0 -0.15 69 69
Aurora A/TACC1/TRAP/chTOG 0.005 0.09 -10000 0 -0.18 79 79
BRCA1 0.015 0.029 -10000 0 -0.12 24 24
centrosome duplication 0.002 0.071 -10000 0 -0.17 71 71
regulation of centrosome cycle 0.005 0.074 -10000 0 -0.16 77 77
spindle assembly 0.004 0.089 -10000 0 -0.18 79 79
TDRD7 0.014 0.031 -10000 0 -0.12 28 28
Aurora A/RasGAP/Survivin 0.003 0.082 -10000 0 -0.16 84 84
CENPA 0.012 0.046 -10000 0 -0.25 13 13
Aurora A/PP2A 0.007 0.068 -10000 0 -0.16 69 69
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.026 0.095 -10000 0 -0.23 80 80
negative regulation of DNA binding -0.064 0.13 -10000 0 -0.25 182 182
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.034 0.011 -10000 0 -10000 0 0
RASA1 0.021 0.011 -10000 0 -0.12 3 3
Ajuba/Aurora A -0.002 0.068 -10000 0 -0.14 95 95
mitotic prometaphase 0.002 0.018 0.072 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.077 0.14 3 -0.2 69 72
TACC1 0.014 0.035 -10000 0 -0.12 35 35
TACC3 0.014 0.032 -10000 0 -0.12 29 29
Aurora A/Antizyme1 0.004 0.076 -10000 0 -0.16 77 77
Aurora A/RasGAP 0.004 0.073 -10000 0 -0.18 70 70
OAZ1 0.017 0.025 -10000 0 -0.12 17 17
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.02 0.019 0.071 9 -0.12 8 17
GIT1 0.022 0.013 -10000 0 -0.12 5 5
GIT1/beta-PIX/PAK1 0.037 0.036 -10000 0 -0.11 21 21
Importin alpha/Importin beta/TPX2 0.017 0.017 -10000 0 -0.07 15 15
PPP2R5D 0.022 0.013 -10000 0 -0.12 5 5
Aurora A/TPX2 -0.004 0.083 -10000 0 -0.2 78 78
PAK1 0.016 0.029 -10000 0 -0.12 24 24
CKAP5 0.021 0.013 -10000 0 -0.12 4 4
Canonical Wnt signaling pathway

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
HDAC1 0.037 0.047 0.11 118 -0.087 10 128
AES 0.036 0.043 0.099 125 -0.11 10 135
FBXW11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 67 67
SMAD4 0.022 0.007 -10000 0 -0.12 1 1
DKK2 0.023 0.01 -10000 0 -0.12 3 3
TLE1 0.033 0.038 0.1 86 -0.11 8 94
MACF1 0.016 0.026 -10000 0 -0.12 18 18
CTNNB1 0.021 0.097 0.18 8 -0.34 23 31
WIF1 0.02 0.021 -10000 0 -0.12 13 13
beta catenin/RanBP3 0.084 0.19 0.38 135 -0.35 13 148
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 34 34
beta catenin/beta TrCP1 0.034 0.095 0.19 8 -0.35 20 28
FZD1 0.023 0.006 -10000 0 -0.12 1 1
AXIN2 -0.037 0.16 -10000 0 -0.82 11 11
AXIN1 0.023 0.011 -10000 0 -0.12 3 3
RAN 0.024 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.036 0.083 -10000 0 -0.5 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.023 0.11 0.24 8 -0.28 40 48
Axin1/APC/GSK3 0.027 0.06 -10000 0 -0.25 16 16
Axin1/APC/GSK3/beta catenin/Macf1 0.03 0.068 -10000 0 -0.26 16 16
HNF1A 0.037 0.038 0.1 113 -0.12 3 116
CTBP1 0.037 0.04 0.1 113 -0.11 7 120
MYC -0.17 0.44 -10000 0 -1.3 75 75
RANBP3 0.023 0.009 -10000 0 -0.12 2 2
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 33 33
NKD1 0.022 0.012 -10000 0 -0.12 4 4
TCF4 0.036 0.042 0.1 121 -0.091 8 129
TCF3 0.037 0.039 0.1 110 -0.12 5 115
WNT1/LRP6/FZD1/Axin1 0.044 0.044 -10000 0 -0.097 37 37
Ran/GTP 0.018 0.012 -10000 0 -0.14 3 3
CtBP/CBP/TCF/TLE1/AES 0.08 0.23 0.45 130 -0.34 12 142
LEF1 0.012 0.056 0.097 78 -0.11 73 151
DVL1 0.027 0.076 -10000 0 -0.33 18 18
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.025 0.14 -10000 0 -0.32 56 56
DKK1/LRP6/Kremen 2 0.027 0.047 -10000 0 -0.11 35 35
LRP6 0.014 0.033 -10000 0 -0.12 32 32
CSNK1A1 0.04 0.044 0.11 124 -0.13 1 125
NLK 0.017 0.021 -10000 0 -0.13 11 11
CCND1 -0.19 0.45 -10000 0 -1.3 84 84
WNT1 0.023 0.009 -10000 0 -0.12 2 2
GSK3A 0.021 0.019 -10000 0 -0.12 10 10
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
FRAT1 0.023 0.006 -10000 0 -0.12 1 1
PPP2R5D 0.018 0.044 -10000 0 -0.2 16 16
APC 0.022 0.033 -10000 0 -0.085 37 37
WNT1/LRP6/FZD1 0.018 0.056 -10000 0 -0.25 9 9
CREBBP 0.035 0.038 0.1 105 -0.1 5 110
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.019 0.16 -10000 0 -0.69 21 21
UGCG -0.001 0.079 -10000 0 -0.73 5 5
AKT1/mTOR/p70S6K/Hsp90/TERT -0.031 0.16 -10000 0 -0.31 103 103
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0 0.078 -10000 0 -0.71 5 5
mol:DAG -0.042 0.2 -10000 0 -0.9 29 29
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.04 0.18 -10000 0 -0.38 99 99
FRAP1 -0.053 0.2 -10000 0 -0.43 100 100
FOXO3 -0.053 0.2 -10000 0 -0.41 107 107
AKT1 -0.059 0.21 -10000 0 -0.45 105 105
GAB2 0.007 0.041 -10000 0 -0.12 52 52
SMPD1 0.006 0.042 -10000 0 -0.52 1 1
SGMS1 -0.029 0.16 -10000 0 -0.68 29 29
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 -0.005 0.05 -10000 0 -0.11 85 85
CALM1 0.022 0.014 -10000 0 -0.12 5 5
cell proliferation -0.039 0.16 -10000 0 -0.31 98 98
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.008 0.067 -10000 0 -0.13 98 98
RPS6KB1 -0.03 0.18 -10000 0 -0.82 23 23
mol:sphingomyelin -0.042 0.2 -10000 0 -0.9 29 29
natural killer cell activation -0.001 0.003 -10000 0 -0.011 29 29
JAK3 0.022 0.016 -10000 0 -0.065 13 13
PIK3R1 0.015 0.033 -10000 0 -0.1 36 36
JAK1 0.022 0.013 -10000 0 -0.048 11 11
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MYC -0.11 0.32 -10000 0 -0.86 81 81
MYB -0.061 0.28 -10000 0 -1.1 40 40
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.039 0.16 -10000 0 -0.32 107 107
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.17 -10000 0 -0.76 23 23
mol:PI-3-4-5-P3 -0.037 0.16 -10000 0 -0.31 107 107
Rac1/GDP 0.007 0.051 -10000 0 -0.11 70 70
T cell proliferation -0.032 0.14 -10000 0 -0.29 107 107
SHC1 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.018 -10000 0 -0.04 83 83
PRKCZ -0.033 0.15 -10000 0 -0.3 107 107
NF kappa B1 p50/RelA -0.035 0.19 -10000 0 -0.38 107 107
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.12 -10000 0 -0.32 51 51
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL2RA 0.02 0.018 -10000 0 -0.12 9 9
IL2RB 0.019 0.024 -10000 0 -0.086 24 24
TERT 0.023 0 -10000 0 -10000 0 0
E2F1 -0.016 0.12 -10000 0 -0.42 42 42
SOS1 0.017 0.027 -10000 0 -0.12 20 20
RPS6 0.023 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0.009 0.019 80 -10000 0 80
PTPN11 0.021 0.012 -10000 0 -0.12 3 3
IL2RG -0.001 0.05 -10000 0 -0.11 90 90
actin cytoskeleton organization -0.032 0.14 -10000 0 -0.29 107 107
GRB2 0.022 0.007 -10000 0 -0.12 1 1
IL2 0.023 0.014 -10000 0 -0.058 11 11
PIK3CA 0.02 0.019 -10000 0 -0.067 17 17
Rac1/GTP 0.02 0.056 -10000 0 -0.11 70 70
LCK 0.022 0.017 -10000 0 -0.09 9 9
BCL2 -0.034 0.17 -10000 0 -0.41 60 60
BCR signaling 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
JUN -0.025 0.11 -10000 0 -0.25 78 78
IKBKB 0.013 0.078 0.19 15 -0.22 30 45
AKT1 -0.008 0.06 0.14 12 -0.15 50 62
IKBKG 0.012 0.067 0.16 1 -0.2 29 30
CALM1 -0.009 0.11 0.16 4 -0.28 53 57
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
MAP3K1 -0.029 0.13 -10000 0 -0.33 64 64
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
mol:Ca2+ -0.013 0.11 0.16 4 -0.3 53 57
DOK1 0.022 0.015 -10000 0 -0.12 6 6
AP-1 -0.015 0.077 0.14 1 -0.18 79 80
LYN 0.02 0.013 -10000 0 -0.12 4 4
BLNK 0.014 0.033 -10000 0 -0.12 32 32
SHC1 0.023 0.001 -10000 0 -10000 0 0
BCR complex 0.028 0.026 -10000 0 -0.076 33 33
CD22 -0.04 0.1 -10000 0 -0.22 107 107
CAMK2G -0.004 0.1 0.15 4 -0.28 46 50
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0.052 -10000 0 -0.14 38 38
GO:0007205 -0.013 0.11 0.16 4 -0.3 53 57
SYK 0.016 0.027 -10000 0 -0.12 21 21
ELK1 -0.009 0.11 0.16 4 -0.29 52 56
NFATC1 -0.014 0.084 0.15 4 -0.23 56 60
B-cell antigen/BCR complex 0.028 0.026 -10000 0 -0.076 33 33
PAG1/CSK 0.032 0.02 -10000 0 -0.097 13 13
NFKBIB 0.008 0.045 -10000 0 -0.13 46 46
HRAS -0.002 0.088 0.14 1 -0.25 46 47
NFKBIA 0.011 0.041 -10000 0 -0.12 36 36
NF-kappa-B/RelA/I kappa B beta 0.014 0.043 -10000 0 -0.12 43 43
RasGAP/Csk 0.023 0.068 -10000 0 -0.088 128 128
mol:GDP -0.012 0.11 0.15 4 -0.29 54 58
PTEN 0.022 0.008 -10000 0 -0.12 1 1
CD79B 0.023 0.006 -10000 0 -0.12 1 1
NF-kappa-B/RelA/I kappa B alpha 0.014 0.04 -10000 0 -0.11 43 43
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PI3K/BCAP/CD19 -0.029 0.13 -10000 0 -0.37 59 59
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:IP3 -0.013 0.11 0.16 4 -0.3 53 57
CSK 0.023 0.009 -10000 0 -0.12 2 2
FOS -0.023 0.11 0.15 2 -0.29 58 60
CHUK -0.003 0.095 0.16 1 -0.25 55 56
IBTK 0.019 0.017 -10000 0 -0.12 7 7
CARD11/BCL10/MALT1/TAK1 0.006 0.1 0.19 1 -0.25 54 55
PTPN6 -0.036 0.095 -10000 0 -0.24 72 72
RELA 0.023 0.009 -10000 0 -0.12 2 2
BCL2A1 0.009 0.034 -10000 0 -0.081 51 51
VAV2 -0.031 0.11 -10000 0 -0.31 56 56
ubiquitin-dependent protein catabolic process 0.012 0.045 -10000 0 -0.12 46 46
BTK -0.051 0.25 -10000 0 -1.1 33 33
CD19 -0.032 0.096 -10000 0 -0.21 88 88
MAP4K1 0.019 0.023 -10000 0 -0.12 15 15
CD72 0.023 0.006 -10000 0 -0.12 1 1
PAG1 0.022 0.015 -10000 0 -0.12 6 6
MAPK14 -0.022 0.11 -10000 0 -0.28 65 65
SH3BP5 0.021 0.015 -10000 0 -0.12 6 6
PIK3AP1 -0.01 0.11 0.17 4 -0.33 47 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.013 0.14 -10000 0 -0.29 86 86
RAF1 0.001 0.084 0.13 1 -0.24 43 44
RasGAP/p62DOK/SHIP 0.015 0.062 -10000 0 -0.084 132 132
CD79A 0.016 0.032 -10000 0 -0.12 29 29
re-entry into mitotic cell cycle -0.014 0.077 0.14 1 -0.18 78 79
RASA1 0.021 0.011 -10000 0 -0.12 3 3
MAPK3 0.008 0.074 0.13 3 -0.22 37 40
MAPK1 0.008 0.074 0.13 3 -0.22 37 40
CD72/SHP1 -0.026 0.095 -10000 0 -0.22 72 72
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 -0.023 0.11 -10000 0 -0.29 64 64
actin cytoskeleton organization -0.024 0.098 -10000 0 -0.28 56 56
NF-kappa-B/RelA 0.022 0.096 -10000 0 -0.23 51 51
Calcineurin 0.013 0.1 -10000 0 -0.25 49 49
PI3K -0.038 0.075 -10000 0 -0.23 55 55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.013 0.11 0.17 4 -0.34 44 48
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Bam32/HPK1 -0.042 0.18 -10000 0 -0.54 47 47
DAPP1 -0.057 0.19 -10000 0 -0.6 47 47
cytokine secretion -0.013 0.08 0.15 4 -0.21 56 60
mol:DAG -0.013 0.11 0.16 4 -0.3 53 57
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
MAP2K1 0.005 0.079 0.13 1 -0.22 41 42
B-cell antigen/BCR complex/FcgammaRIIB 0.009 0.063 -10000 0 -0.11 101 101
mol:PI-3-4-5-P3 -0.034 0.057 0.094 1 -0.18 54 55
ETS1 -0.007 0.098 0.15 2 -0.27 51 53
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.029 0.069 -10000 0 -0.1 98 98
B-cell antigen/BCR complex/LYN -0.037 0.1 -10000 0 -0.22 95 95
MALT1 0.018 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 -0.026 0.1 -10000 0 -0.29 56 56
B-cell antigen/BCR complex/LYN/SYK -0.004 0.091 -10000 0 -0.22 53 53
CARD11 -0.01 0.11 0.16 4 -0.29 53 57
FCGR2B 0.004 0.044 -10000 0 -0.12 61 61
PPP3CA 0.021 0.014 -10000 0 -0.12 5 5
BCL10 0.023 0.001 -10000 0 -10000 0 0
IKK complex 0.012 0.038 0.1 17 -0.091 29 46
PTPRC -0.004 0.05 -10000 0 -0.12 86 86
PDPK1 -0.01 0.054 0.13 13 -0.13 52 65
PPP3CB 0.023 0.007 -10000 0 -0.12 1 1
PPP3CC 0.023 0.01 -10000 0 -0.12 3 3
POU2F2 0.011 0.033 -10000 0 -0.076 52 52
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.035 0.09 -9999 0 -0.12 247 247
SMAD6-7/SMURF1 0.042 0.03 -9999 0 -0.14 11 11
NOG 0.017 0.028 -9999 0 -0.12 23 23
SMAD9 0.02 0.049 -9999 0 -0.54 2 2
SMAD4 0.022 0.007 -9999 0 -0.12 1 1
SMAD5 0 0.092 -9999 0 -0.29 31 31
BMP7/USAG1 -0.073 0.092 -9999 0 -0.17 226 226
SMAD5/SKI 0.012 0.091 -9999 0 -0.27 31 31
SMAD1 0.021 0.073 -9999 0 -0.28 26 26
BMP2 0.022 0.013 -9999 0 -0.12 5 5
SMAD1/SMAD1/SMAD4 -0.003 0.065 -9999 0 -0.25 26 26
BMPR1A 0.02 0.014 -9999 0 -0.12 4 4
BMPR1B 0.008 0.041 -9999 0 -0.12 52 52
BMPR1A-1B/BAMBI -0.025 0.086 -9999 0 -0.14 159 159
AHSG 0.023 0.008 -9999 0 -0.12 2 2
CER1 0.022 0.012 -9999 0 -0.12 4 4
BMP2-4/CER1 0.033 0.039 -9999 0 -0.12 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.004 0.098 -9999 0 -0.27 43 43
BMP2-4 (homodimer) 0.02 0.041 -9999 0 -0.086 71 71
RGMB 0.023 0.008 -9999 0 -0.12 2 2
BMP6/BMPR2/BMPR1A-1B 0.013 0.076 -9999 0 -0.12 114 114
RGMA 0.021 0.017 -9999 0 -0.12 8 8
SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.005 0.076 -9999 0 -0.22 42 42
BMP2-4/USAG1 -0.012 0.069 -9999 0 -0.12 116 116
SMAD6/SMURF1/SMAD5 0.012 0.092 -9999 0 -0.27 32 32
SOSTDC1 -0.017 0.062 -9999 0 -0.12 148 148
BMP7/BMPR2/BMPR1A-1B -0.033 0.092 -9999 0 -0.13 221 221
SKI 0.023 0.01 -9999 0 -0.12 3 3
BMP6 (homodimer) 0.02 0.022 -9999 0 -0.12 14 14
HFE2 0.023 0.008 -9999 0 -0.12 2 2
ZFYVE16 0.02 0.018 -9999 0 -0.12 8 8
MAP3K7 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/CHRD 0.033 0.038 -9999 0 -0.11 16 16
SMAD5/SMAD5/SMAD4 0.01 0.094 -9999 0 -0.27 36 36
MAPK1 0.021 0.016 -9999 0 -0.12 7 7
TAK1/TAB family 0.023 0.095 -9999 0 -0.22 48 48
BMP7 (homodimer) -0.01 0.055 -9999 0 -0.12 109 109
NUP214 0.023 0.007 -9999 0 -0.12 1 1
BMP6/FETUA 0.032 0.017 -9999 0 -10000 0 0
SMAD1/SKI 0.033 0.072 -9999 0 -0.26 26 26
SMAD6 0.02 0.02 -9999 0 -0.12 11 11
CTDSP2 0.022 0.009 -9999 0 -0.12 2 2
BMP2-4/FETUA 0.033 0.039 -9999 0 -0.12 15 15
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
GREM1 0.008 0.044 -9999 0 -0.12 59 59
BMPR2 (homodimer) 0.021 0.014 -9999 0 -0.12 5 5
GADD34/PP1CA 0.031 0.047 -9999 0 -0.12 45 45
BMPR1A-1B (homodimer) -0.011 0.08 -9999 0 -0.13 157 157
CHRDL1 -0.008 0.054 -9999 0 -0.12 104 104
ENDOFIN/SMAD1 0.03 0.075 -9999 0 -0.27 27 27
SMAD6-7/SMURF1/SMAD1 0.05 0.075 -9999 0 -0.25 27 27
SMAD6/SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BAMBI -0.004 0.054 -9999 0 -0.12 98 98
SMURF2 0.022 0.013 -9999 0 -0.12 4 4
BMP2-4/CHRDL1 -0.014 0.072 -9999 0 -0.12 138 138
BMP2-4/GREM1 0.023 0.049 -9999 0 -0.12 31 31
SMAD7 0.023 0.003 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.028 0.052 -9999 0 -0.36 4 4
SMAD1/SMAD6 0.033 0.072 -9999 0 -0.26 26 26
TAK1/SMAD6 0.027 0.035 -9999 0 -0.14 21 21
BMP7 -0.01 0.055 -9999 0 -0.12 109 109
BMP6 0.02 0.022 -9999 0 -0.12 14 14
MAP3K7IP2 0.02 0.016 -9999 0 -0.12 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.003 0.082 -9999 0 -0.25 32 32
PPM1A 0.023 0.001 -9999 0 -10000 0 0
SMAD1/SMURF2 0.031 0.074 -9999 0 -0.27 26 26
SMAD7/SMURF1 0.031 0.024 -9999 0 -0.14 10 10
CTDSPL 0.023 0.006 -9999 0 -0.12 1 1
PPP1CA 0.023 0.002 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.022 0.011 -9999 0 -0.12 3 3
PPP1R15A 0.019 0.025 -9999 0 -0.12 18 18
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.002 0.079 -9999 0 -0.21 50 50
CHRD 0.023 0.006 -9999 0 -0.12 1 1
BMPR2 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.004 0.086 -9999 0 -0.24 42 42
BMP4 0.009 0.042 -9999 0 -0.12 54 54
FST 0.004 0.048 -9999 0 -0.12 74 74
BMP2-4/NOG 0.027 0.047 -9999 0 -0.12 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.023 0.09 -9999 0 -0.12 222 222
Circadian rhythm pathway

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
chromatin modification -0.067 0.31 -10000 0 -1 52 52
CLOCK 0.017 0.024 -10000 0 -0.056 40 40
TIMELESS/CRY2 -0.063 0.31 -10000 0 -1 50 50
DEC1/BMAL1 0.024 0.038 -10000 0 -0.13 25 25
ATR 0.02 0.014 -10000 0 -0.12 5 5
NR1D1 -0.01 0.11 -10000 0 -0.52 2 2
ARNTL 0.018 0.023 -10000 0 -0.05 47 47
TIMELESS -0.079 0.32 -10000 0 -1.1 50 50
NPAS2 0.003 0.048 -10000 0 -0.096 93 93
CRY2 0.023 0 -10000 0 -10000 0 0
mol:CO 0.001 0.042 0.13 50 -10000 0 50
CHEK1 0.012 0.034 -10000 0 -0.12 34 34
mol:HEME -0.001 0.042 -10000 0 -0.13 50 50
PER1 0.022 0.013 -10000 0 -0.12 5 5
BMAL/CLOCK/NPAS2 0.001 0.086 -10000 0 -0.12 154 154
BMAL1/CLOCK -0.033 0.19 -10000 0 -0.56 55 55
S phase of mitotic cell cycle -0.067 0.31 -10000 0 -1 52 52
TIMELESS/CHEK1/ATR -0.07 0.32 -10000 0 -1 52 52
mol:NADPH -0.001 0.042 -10000 0 -0.13 50 50
PER1/TIMELESS -0.063 0.31 -10000 0 -1.1 50 50
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.023 0.01 -10000 0 -0.12 3 3
FoxO family signaling

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
G6PC 0.022 0.061 -9999 0 -0.41 1 1
PLK1 -0.15 0.36 -9999 0 -0.84 86 86
CDKN1B -0.052 0.19 -9999 0 -0.35 120 120
FOXO3 -0.13 0.32 -9999 0 -0.6 135 135
KAT2B -0.011 0.027 -9999 0 -0.045 197 197
FOXO1/SIRT1 0.024 0.066 -9999 0 -0.24 15 15
CAT -0.16 0.38 -9999 0 -0.86 94 94
CTNNB1 0.022 0.007 -9999 0 -0.12 1 1
AKT1 0.009 0.038 -9999 0 -0.063 56 56
FOXO1 0.015 0.066 -9999 0 -0.27 11 11
MAPK10 0.013 0.042 -9999 0 -0.1 39 39
mol:GTP 0 0.003 -9999 0 -10000 0 0
FOXO4 0.011 0.13 -9999 0 -0.34 42 42
response to oxidative stress -0.008 0.029 -9999 0 -0.052 107 107
FOXO3A/SIRT1 -0.14 0.3 -9999 0 -0.48 208 208
XPO1 0.022 0.01 -9999 0 -0.12 2 2
EP300 0.024 0.01 -9999 0 -0.12 2 2
BCL2L11 0.005 0.086 -9999 0 -1.3 2 2
FOXO1/SKP2 0.021 0.07 -9999 0 -0.25 18 18
mol:GDP -0.008 0.029 -9999 0 -0.052 107 107
RAN 0.024 0.003 -9999 0 -10000 0 0
GADD45A -0.083 0.27 -9999 0 -0.71 66 66
YWHAQ 0.023 0.003 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.085 -9999 0 -0.27 20 20
MST1 0.007 0.034 -9999 0 -0.056 46 46
CSNK1D 0.023 0.001 -9999 0 -10000 0 0
CSNK1E 0.022 0.015 -9999 0 -0.12 6 6
FOXO4/14-3-3 family 0.013 0.12 -9999 0 -0.26 59 59
YWHAB 0.023 0.007 -9999 0 -0.12 1 1
MAPK8 0.016 0.041 -9999 0 -0.12 30 30
MAPK9 0.016 0.041 -9999 0 -0.12 27 27
YWHAG 0.02 0.021 -9999 0 -0.12 13 13
YWHAE 0.022 0.014 -9999 0 -0.12 5 5
YWHAZ 0.023 0.003 -9999 0 -10000 0 0
SIRT1 0.02 0.008 -9999 0 -10000 0 0
SOD2 -0.092 0.3 -9999 0 -0.69 85 85
RBL2 -0.079 0.26 -9999 0 -0.67 50 50
RAL/GDP 0.019 0.043 -9999 0 -0.13 26 26
CHUK 0.007 0.034 -9999 0 -0.058 45 45
Ran/GTP 0.017 0.014 -9999 0 -0.14 3 3
CSNK1G2 0.023 0.01 -9999 0 -0.12 3 3
RAL/GTP 0.022 0.044 -9999 0 -0.12 26 26
CSNK1G1 0.023 0.008 -9999 0 -0.12 2 2
FASLG 0.007 0.067 -9999 0 -1.2 1 1
SKP2 0.018 0.024 -9999 0 -0.12 16 16
USP7 0.02 0.02 -9999 0 -0.12 10 10
IKBKB 0.007 0.036 -9999 0 -0.057 57 57
CCNB1 -0.18 0.42 -9999 0 -0.99 97 97
FOXO1-3a-4/beta catenin -0.037 0.21 -9999 0 -0.38 100 100
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.069 -9999 0 -0.25 18 18
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
SGK1 -0.011 0.027 -9999 0 -0.045 197 197
CSNK1G3 0.022 0.007 -9999 0 -0.12 1 1
Ran/GTP/Exportin 1 0.027 0.032 -9999 0 -0.12 24 24
ZFAND5 0.019 0.12 -9999 0 -0.49 11 11
SFN 0.014 0.031 -9999 0 -0.12 28 28
CDK2 0.022 0.023 -9999 0 -0.12 14 14
FOXO3A/14-3-3 -0.006 0.13 -9999 0 -0.31 54 54
CREBBP 0.025 0.016 -9999 0 -0.12 6 6
FBXO32 -0.27 0.51 -9999 0 -1.1 149 149
BCL6 -0.12 0.34 -9999 0 -0.82 79 79
RALB 0.023 0.008 -9999 0 -0.12 1 1
RALA 0.023 0.009 -9999 0 -0.12 2 2
YWHAH 0.021 0.015 -9999 0 -0.12 6 6
Retinoic acid receptors-mediated signaling

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
HDAC1 0.019 0.019 -10000 0 -0.12 10 10
HDAC3 0.023 0.002 -10000 0 -10000 0 0
VDR 0.019 0.022 -10000 0 -0.12 13 13
Cbp/p300/PCAF 0.02 0.044 -10000 0 -0.13 43 43
EP300 0.022 0.009 -10000 0 -0.12 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.093 -10000 0 -0.21 65 65
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -0.12 1 1
AKT1 0.019 0.089 0.17 80 -0.18 46 126
RAR alpha/9cRA/Cyclin H -0.015 0.12 -10000 0 -0.21 112 112
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.081 -10000 0 -0.2 59 59
CDC2 0.006 0.04 -10000 0 -0.12 48 48
response to UV -0.001 0.007 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.007 0.061 -10000 0 -0.15 51 51
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.009 0.035 -10000 0 -0.12 36 36
RXRs/RARs/NRIP1/9cRA -0.041 0.19 -10000 0 -0.45 81 81
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
NCOA3 0.021 0.011 -10000 0 -0.12 3 3
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARG 0.02 0.016 -10000 0 -0.12 6 6
RAR gamma1/9cRA 0.024 0.028 -10000 0 -0.088 31 31
MAPK3 0.021 0.015 -10000 0 -0.12 5 5
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
MAPK8 0.019 0.018 -10000 0 -0.12 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.034 0.14 -10000 0 -0.32 92 92
RARA 0.01 0.055 -10000 0 -0.14 45 45
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.086 -10000 0 -0.21 60 60
PRKCA 0.008 0.043 -10000 0 -0.09 77 77
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.06 0.2 -10000 0 -0.5 84 84
RXRG -0.005 0.069 -10000 0 -0.18 55 55
RXRA -0.034 0.11 -10000 0 -0.21 96 96
RXRB 0.005 0.062 -10000 0 -0.18 45 45
VDR/Vit D3/DNA 0.009 0.035 -10000 0 -0.12 36 36
RBP1 0.01 0.035 -10000 0 -0.12 36 36
CRBP1/9-cic-RA -0.018 0.064 -10000 0 -0.13 138 138
RARB 0.012 0.036 -10000 0 -0.12 33 33
PRKCG 0.018 0.024 -10000 0 -0.052 50 50
MNAT1 0.023 0.007 -10000 0 -0.12 1 1
RAR alpha/RXRs -0.019 0.16 -10000 0 -0.36 80 80
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.014 0.13 -10000 0 -0.28 82 82
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.098 -10000 0 -0.23 60 60
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.057 0.2 -10000 0 -0.5 84 84
positive regulation of DNA binding -0.019 0.11 -10000 0 -0.2 112 112
NRIP1 -0.092 0.31 -10000 0 -0.96 58 58
RXRs/RARs -0.046 0.17 -10000 0 -0.4 90 90
RXRs/RXRs/DNA/9cRA -0.04 0.14 -10000 0 -0.32 91 91
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
CDK7 0.018 0.023 -10000 0 -0.12 15 15
TFIIH 0.029 0.053 -10000 0 -0.13 46 46
RAR alpha/9cRA 0.024 0.07 -10000 0 -0.19 28 28
CCNH 0.02 0.022 -10000 0 -0.12 13 13
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
RAR gamma2/9cRA 0.025 0.05 -10000 0 -0.096 66 66
Ephrin A reverse 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
MAPKKK cascade 0.017 0.041 -9999 0 -0.088 70 70
EFNA5 0.014 0.033 -9999 0 -0.12 31 31
FYN 0.007 0.042 -9999 0 -0.12 41 41
neuron projection morphogenesis 0.017 0.041 -9999 0 -0.088 70 70
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.017 0.041 -9999 0 -0.089 70 70
EPHA5 0.023 0.008 -9999 0 -0.12 2 2
Reelin signaling pathway

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
CDK5R1/CDK5 0.021 0.042 -9999 0 -0.14 25 25
VLDLR 0.01 0.038 -9999 0 -0.12 42 42
CRKL 0.023 0.009 -9999 0 -0.12 2 2
LRPAP1 0.018 0.023 -9999 0 -0.12 15 15
FYN 0.012 0.037 -9999 0 -0.12 40 40
ITGA3 0.013 0.034 -9999 0 -0.12 33 33
RELN/VLDLR/Fyn -0.005 0.073 -9999 0 -0.13 102 102
MAPK8IP1/MKK7/MAP3K11/JNK1 0.056 0.042 -9999 0 -0.093 30 30
AKT1 -0.015 0.078 -9999 0 -0.15 114 114
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
RAPGEF1 0.023 0 -9999 0 -10000 0 0
DAB1 0.023 0.01 -9999 0 -0.12 3 3
RELN/LRP8/DAB1 0.025 0.042 -9999 0 -0.11 21 21
LRPAP1/LRP8 0.015 0.054 -9999 0 -0.12 72 72
RELN/LRP8/DAB1/Fyn 0.02 0.055 -9999 0 -0.097 62 62
DAB1/alpha3/beta1 Integrin -0.006 0.069 -9999 0 -0.14 61 61
long-term memory 0.016 0.062 -9999 0 -0.13 21 21
DAB1/LIS1 0.016 0.067 -9999 0 -0.14 25 25
DAB1/CRLK/C3G 0.012 0.057 -9999 0 -0.13 21 21
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
DAB1/NCK2 0.019 0.067 -9999 0 -0.14 22 22
ARHGEF2 0.023 0.009 -9999 0 -0.12 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.001 0.051 -9999 0 -0.12 86 86
CDK5R1 0.023 0.006 -9999 0 -0.12 1 1
RELN 0 0.053 -9999 0 -0.12 91 91
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
RELN/LRP8/Fyn 0.01 0.06 -9999 0 -0.12 61 61
GRIN2A/RELN/LRP8/DAB1/Fyn 0.015 0.066 -9999 0 -0.14 20 20
MAPK8 0.021 0.015 -9999 0 -0.12 6 6
RELN/VLDLR/DAB1 0.011 0.055 -9999 0 -0.1 71 71
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
MAP1B -0.006 0.056 -9999 0 -0.11 95 95
RELN/LRP8 0.015 0.058 -9999 0 -0.12 53 53
GRIN2B/RELN/LRP8/DAB1/Fyn 0.029 0.06 -9999 0 -0.14 12 12
PI3K 0.007 0.065 -9999 0 -0.13 98 98
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.004 0.064 -9999 0 -0.12 113 113
RAP1A 0.005 0.05 -9999 0 -0.13 26 26
PAFAH1B1 0.021 0.018 -9999 0 -0.12 9 9
MAPK8IP1 0.017 0.029 -9999 0 -0.12 24 24
CRLK/C3G 0.034 0.01 -9999 0 -0.093 3 3
GRIN2B 0.02 0.02 -9999 0 -0.12 11 11
NCK2 0.023 0.006 -9999 0 -0.12 1 1
neuron differentiation 0.018 0.056 -9999 0 -0.18 23 23
neuron adhesion -0.004 0.061 -9999 0 -0.13 68 68
LRP8 0.02 0.021 -9999 0 -0.12 12 12
GSK3B -0.011 0.074 -9999 0 -0.14 115 115
RELN/VLDLR/DAB1/Fyn 0.007 0.066 -9999 0 -0.11 103 103
MAP3K11 0.022 0.013 -9999 0 -0.12 5 5
RELN/VLDLR/DAB1/P13K -0.018 0.083 -9999 0 -0.16 113 113
CDK5 0.015 0.032 -9999 0 -0.12 30 30
MAPT 0.01 0.016 -9999 0 -0.093 5 5
neuron migration -0.013 0.079 -9999 0 -0.19 52 52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.018 0.056 -9999 0 -0.18 23 23
RELN/VLDLR 0.008 0.07 -9999 0 -0.11 121 121
HIF-2-alpha transcription factor network

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
MMP14 -0.098 0.3 -10000 0 -0.93 63 63
oxygen homeostasis 0.001 0.01 -10000 0 -10000 0 0
TCEB2 0.023 0.006 -10000 0 -0.12 1 1
TCEB1 0.022 0.011 -10000 0 -0.12 3 3
VHL/Elongin B/Elongin C/HIF2A 0.008 0.11 -10000 0 -0.21 63 63
EPO 0.004 0.18 -10000 0 -0.38 46 46
FIH (dimer) 0.023 0.013 -10000 0 -0.12 1 1
APEX1 0.02 0.026 -10000 0 -0.1 13 13
SERPINE1 -0.014 0.19 -10000 0 -0.37 66 66
FLT1 -0.022 0.22 -10000 0 -0.75 43 43
ADORA2A -0.01 0.17 -10000 0 -0.36 57 57
germ cell development -0.018 0.19 -10000 0 -0.37 78 78
SLC11A2 -0.011 0.19 -10000 0 -0.38 67 67
BHLHE40 -0.013 0.18 -10000 0 -0.36 68 68
HIF1AN 0.023 0.013 -10000 0 -0.12 1 1
HIF2A/ARNT/SIRT1 0.012 0.14 -10000 0 -0.27 55 55
ETS1 0.027 0.036 -10000 0 -0.11 33 33
CITED2 0.025 0.079 -10000 0 -0.86 3 3
KDR -0.022 0.22 -10000 0 -0.74 43 43
PGK1 -0.014 0.2 -10000 0 -0.4 71 71
SIRT1 0.023 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.022 0.23 -10000 0 -0.42 58 58
EPAS1 -0.009 0.11 -10000 0 -0.21 90 90
SP1 0.016 0.035 -10000 0 -0.077 60 60
ABCG2 -0.007 0.19 -10000 0 -0.38 60 60
EFNA1 -0.02 0.2 -10000 0 -0.39 84 84
FXN -0.011 0.17 -10000 0 -0.37 55 55
POU5F1 -0.02 0.2 -10000 0 -0.38 78 78
neuron apoptosis -0.021 0.23 0.41 58 -10000 0 58
EP300 0.022 0.009 -10000 0 -0.12 2 2
EGLN3 -0.001 0.051 -10000 0 -0.12 87 87
EGLN2 0.023 0.014 -10000 0 -0.12 2 2
EGLN1 0.023 0.014 -10000 0 -0.12 2 2
VHL/Elongin B/Elongin C 0.041 0.031 -10000 0 -0.12 17 17
VHL 0.021 0.016 -10000 0 -0.12 7 7
ARNT 0.023 0.021 -10000 0 -0.12 4 4
SLC2A1 -0.024 0.19 -10000 0 -0.4 70 70
TWIST1 -0.01 0.17 -10000 0 -0.37 56 56
ELK1 0.028 0.018 -10000 0 -0.1 9 9
HIF2A/ARNT/Cbp/p300 0.008 0.15 -10000 0 -0.28 58 58
VEGFA -0.013 0.2 -10000 0 -0.41 63 63
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.011 0.14 -9999 0 -0.41 51 51
KLHL20 -0.013 0.085 -9999 0 -0.19 70 70
CYFIP2 0.02 0.017 -9999 0 -0.12 8 8
Rac1/GDP 0.011 0.093 -9999 0 -0.23 57 57
ENAH -0.012 0.13 -9999 0 -0.4 52 52
AP1M1 0.021 0.017 -9999 0 -0.12 8 8
RAP1B 0.019 0.019 -9999 0 -0.12 10 10
RAP1A 0.021 0.011 -9999 0 -0.12 3 3
CTNNB1 0.022 0.007 -9999 0 -0.12 1 1
CDC42/GTP 0.009 0.071 -9999 0 -0.2 37 37
ABI1/Sra1/Nap1 -0.028 0.049 -9999 0 -0.14 74 74
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.055 -9999 0 -0.1 65 65
RAPGEF1 -0.002 0.12 -9999 0 -0.34 51 51
CTNND1 0.023 0.004 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.012 0.14 -9999 0 -0.42 51 51
CRK -0.007 0.12 -9999 0 -0.37 51 51
E-cadherin/gamma catenin/alpha catenin 0.024 0.061 -9999 0 -0.13 63 63
alphaE/beta7 Integrin 0.026 0.034 -9999 0 -0.11 33 33
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
NCKAP1 0.023 0.004 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.015 0.06 -9999 0 -0.11 88 88
DLG1 -0.012 0.14 -9999 0 -0.42 51 51
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.05 -9999 0 -0.15 56 56
MLLT4 0.014 0.032 -9999 0 -0.12 30 30
ARF6/GTP/NME1/Tiam1 0.018 0.057 -9999 0 -0.11 74 74
PI3K -0.029 0.065 -9999 0 -0.2 56 56
ARF6 0.023 0.003 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.017 0.054 -9999 0 -0.16 44 44
TIAM1 0.015 0.032 -9999 0 -0.12 29 29
E-cadherin(dimer)/Ca2+ 0.032 0.061 -9999 0 -0.12 71 71
AKT1 0.004 0.049 -9999 0 -0.12 55 55
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
CDH1 0.02 0.015 -9999 0 -0.12 6 6
RhoA/GDP 0.012 0.092 -9999 0 -0.22 57 57
actin cytoskeleton organization -0.008 0.064 -9999 0 -0.14 71 71
CDC42/GDP 0.012 0.092 -9999 0 -0.22 57 57
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.08 -9999 0 -0.19 68 68
ITGB7 0.019 0.023 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.035 0.066 -9999 0 -0.13 71 71
E-cadherin/Ca2+/beta catenin/alpha catenin 0.022 0.051 -9999 0 -0.11 68 68
mol:GDP 0 0.1 -9999 0 -0.26 56 56
CDC42/GTP/IQGAP1 0.017 0.044 -9999 0 -0.12 49 49
JUP 0.02 0.021 -9999 0 -0.12 12 12
p120 catenin/RhoA/GDP 0.016 0.095 -9999 0 -0.23 55 55
RAC1/GTP/IQGAP1 0.017 0.045 -9999 0 -0.11 57 57
PIP5K1C/AP1M1 0.033 0.014 -9999 0 -0.14 1 1
RHOA 0.023 0.006 -9999 0 -0.12 1 1
CDC42 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
positive regulation of S phase of mitotic cell cycle -0.014 0.063 -9999 0 -0.12 121 121
NME1 0.016 0.029 -9999 0 -0.12 23 23
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.013 0.14 -9999 0 -0.42 53 53
regulation of cell-cell adhesion -0.019 0.051 -9999 0 -0.18 37 37
WASF2 -0.002 0.036 -9999 0 -0.078 70 70
Rap1/GTP 0.012 0.081 -9999 0 -0.22 38 38
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.04 0.064 -9999 0 -0.1 79 79
CCND1 -0.018 0.076 -9999 0 -0.14 121 121
VAV2 -0.021 0.18 -9999 0 -0.46 67 67
RAP1/GDP 0.015 0.088 -9999 0 -0.23 41 41
adherens junction assembly -0.012 0.14 -9999 0 -0.4 53 53
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.022 0.009 -9999 0 -0.12 2 2
PIP5K1C 0.023 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.033 0.065 -9999 0 -0.17 24 24
E-cadherin/beta catenin 0.007 0.057 -9999 0 -0.23 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.01 0.13 -9999 0 -0.4 51 51
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
Rac1/GTP -0.06 0.11 -9999 0 -0.32 67 67
E-cadherin/beta catenin/alpha catenin 0.025 0.06 -9999 0 -0.13 68 68
ITGAE 0.023 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.14 -9999 0 -0.43 51 51
Arf6 downstream pathway

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
PLAUR -0.029 0.22 -10000 0 -0.83 39 39
regulation of axonogenesis -0.005 0.06 0.19 38 -10000 0 38
myoblast fusion 0.001 0.1 0.38 39 -10000 0 39
mol:GTP -0.001 0.066 -10000 0 -0.22 45 45
regulation of calcium-dependent cell-cell adhesion -0.006 0.088 0.21 55 -10000 0 55
ARF1/GTP 0.013 0.055 -10000 0 -0.16 47 47
mol:GM1 -0.002 0.049 -10000 0 -0.16 45 45
mol:Choline 0.004 0.052 -10000 0 -0.15 46 46
lamellipodium assembly -0.007 0.12 -10000 0 -0.41 46 46
MAPK3 0.005 0.087 -10000 0 -0.28 46 46
ARF6/GTP/NME1/Tiam1 0.007 0.089 -10000 0 -0.22 55 55
ARF1 0.018 0.027 -10000 0 -0.12 21 21
ARF6/GDP -0.001 0.11 -10000 0 -0.38 39 39
ARF1/GDP 0.004 0.1 -10000 0 -0.33 46 46
ARF6 0.016 0.035 -10000 0 -0.12 37 37
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
TIAM1 0.014 0.034 -10000 0 -0.12 29 29
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.004 0.088 -10000 0 -0.28 46 46
actin filament bundle formation -0.006 0.1 0.34 46 -10000 0 46
KALRN 0.002 0.082 -10000 0 -0.29 39 39
RAB11FIP3/RAB11A 0.031 0.023 -10000 0 -0.13 11 11
RhoA/GDP 0.007 0.11 -10000 0 -0.34 46 46
NME1 0.014 0.03 -10000 0 -0.12 23 23
Rac1/GDP 0.007 0.1 -10000 0 -0.34 46 46
substrate adhesion-dependent cell spreading -0.001 0.065 -10000 0 -0.22 45 45
cortical actin cytoskeleton organization -0.007 0.12 -10000 0 -0.41 46 46
RAC1 0.023 0.002 -10000 0 -10000 0 0
liver development -0.001 0.065 -10000 0 -0.22 45 45
ARF6/GTP -0.001 0.066 -10000 0 -0.22 45 45
RhoA/GTP 0.015 0.057 -10000 0 -0.17 46 46
mol:GDP -0.005 0.11 -10000 0 -0.36 46 46
ARF6/GTP/RAB11FIP3/RAB11A 0.028 0.052 -10000 0 -0.13 46 46
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PLD1 0 0.06 -10000 0 -0.18 45 45
RAB11FIP3 0.023 0.01 -10000 0 -0.12 3 3
tube morphogenesis -0.007 0.12 -10000 0 -0.41 46 46
ruffle organization 0.005 0.06 -10000 0 -0.19 38 38
regulation of epithelial cell migration -0.001 0.065 -10000 0 -0.22 45 45
PLD2 0.01 0.051 -10000 0 -0.16 46 46
PIP5K1A 0.005 0.06 -10000 0 -0.19 38 38
mol:Phosphatidic acid 0.004 0.052 -10000 0 -0.15 46 46
Rac1/GTP -0.008 0.12 -10000 0 -0.41 46 46
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.052 0.28 -10000 0 -0.62 61 61
PCK1 -0.15 0.4 -10000 0 -1.1 81 81
HNF4A -0.1 0.36 -10000 0 -0.74 108 108
KCNJ11 -0.008 0.27 -10000 0 -0.64 38 38
AKT1 -0.002 0.16 -10000 0 -0.32 42 42
response to starvation -0.018 0.045 -10000 0 -0.12 77 77
DLK1 -0.023 0.28 -10000 0 -0.64 48 48
NKX2-1 -0.007 0.15 -10000 0 -0.53 1 1
ACADM -0.064 0.3 -10000 0 -0.64 77 77
TAT -0.022 0.2 -10000 0 -0.56 18 18
CEBPB 0.021 0.032 -10000 0 -0.11 30 30
CEBPA 0.029 0.015 -10000 0 -0.12 5 5
TTR 0.013 0.16 -10000 0 -0.83 4 4
PKLR -0.041 0.26 -10000 0 -0.6 51 51
APOA1 -0.16 0.48 -10000 0 -1 112 112
CPT1C -0.048 0.27 -10000 0 -0.61 54 54
ALAS1 -0.01 0.19 -10000 0 -1 4 4
TFRC -0.099 0.4 -10000 0 -0.96 82 82
FOXF1 0.015 0.012 -10000 0 -0.11 5 5
NF1 0.024 0.026 -10000 0 -0.13 12 12
HNF1A (dimer) 0.042 0.018 -10000 0 -0.13 5 5
CPT1A -0.058 0.29 -10000 0 -0.65 63 63
HMGCS1 -0.055 0.28 -10000 0 -0.64 61 61
NR3C1 0.035 0.017 -10000 0 -0.11 5 5
CPT1B -0.042 0.26 -10000 0 -0.61 51 51
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.013 -10000 0 -0.14 2 2
GCK -0.041 0.26 -10000 0 -0.61 49 49
CREB1 -0.008 0.069 -10000 0 -0.17 74 74
IGFBP1 -0.012 0.16 -10000 0 -0.52 8 8
PDX1 0.03 0.17 -10000 0 -0.77 4 4
UCP2 -0.089 0.33 -10000 0 -0.69 91 91
ALDOB -0.008 0.26 -10000 0 -0.62 40 40
AFP 0.018 0.05 -10000 0 -0.3 3 3
BDH1 -0.066 0.3 -10000 0 -0.64 73 73
HADH -0.017 0.28 -10000 0 -0.65 45 45
F2 -0.06 0.33 -10000 0 -0.82 41 41
HNF1A 0.042 0.018 -10000 0 -0.13 5 5
G6PC 0.026 0.075 -10000 0 -0.42 1 1
SLC2A2 0.024 0.18 -10000 0 -0.66 2 2
INS 0.009 0.012 0.16 1 -0.13 2 3
FOXA1 0.035 0.03 -10000 0 -0.21 2 2
FOXA3 0.004 0.096 -10000 0 -0.19 79 79
FOXA2 -0.003 0.32 -10000 0 -0.69 47 47
ABCC8 -0.007 0.26 -10000 0 -0.64 37 37
ALB 0.018 0.051 -10000 0 -0.3 3 3
ErbB2/ErbB3 signaling events

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
USP8 0.012 0.012 -10000 0 -0.057 15 15
RAS family/GTP 0.005 0.084 -10000 0 -0.17 55 55
NFATC4 0.001 0.053 0.18 6 -0.12 39 45
ERBB2IP 0.02 0.019 -10000 0 -0.12 10 10
HSP90 (dimer) 0.023 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0 0.066 0.19 7 -0.12 83 90
JUN 0.004 0.071 0.18 1 -10000 0 1
HRAS 0.023 0.006 -10000 0 -0.12 1 1
DOCK7 -0.005 0.066 0.19 6 -0.15 53 59
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.018 0.06 0.21 7 -0.1 87 94
AKT1 0.01 0.012 -10000 0 -0.077 10 10
BAD 0.013 0.011 -10000 0 -0.056 13 13
MAPK10 0.002 0.045 0.14 6 -0.1 41 47
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.07 0.2 7 -0.13 83 90
RAF1 -0.004 0.084 -10000 0 -0.18 60 60
ErbB2/ErbB3/neuregulin 2 0.005 0.054 -10000 0 -0.11 87 87
STAT3 -0.005 0.18 -10000 0 -0.93 21 21
cell migration 0.001 0.052 0.16 5 -0.12 40 45
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.062 0.21 -10000 0 -0.52 68 68
FOS -0.071 0.2 -10000 0 -0.41 128 128
NRAS 0.021 0.011 -10000 0 -0.12 3 3
mol:Ca2+ 0 0.066 0.19 7 -0.12 83 90
MAPK3 -0.039 0.17 -10000 0 -0.46 49 49
MAPK1 -0.041 0.17 -10000 0 -0.42 64 64
JAK2 -0.005 0.065 0.19 6 -0.15 51 57
NF2 0.013 0.046 -10000 0 -0.73 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.012 0.053 0.13 8 -0.17 30 38
NRG1 0.021 0.017 -10000 0 -0.12 8 8
GRB2/SOS1 0.02 0.046 -10000 0 -0.12 52 52
MAPK8 -0.011 0.092 0.18 6 -0.19 97 103
MAPK9 0.003 0.044 0.14 5 -0.11 35 40
ERBB2 0 0.048 0.27 15 -0.093 4 19
ERBB3 0.013 0.031 -10000 0 -0.12 27 27
SHC1 0.023 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
apoptosis -0.009 0.017 0.13 4 -10000 0 4
STAT3 (dimer) -0.005 0.18 -10000 0 -0.9 21 21
RNF41 0.013 0.012 -10000 0 -0.046 17 17
FRAP1 0.013 0.011 -10000 0 -0.056 14 14
RAC1-CDC42/GTP -0.005 0.05 -10000 0 -0.12 44 44
ErbB2/ErbB2/HSP90 (dimer) 0.012 0.028 -10000 0 -0.11 22 22
CHRNA1 -0.025 0.14 -10000 0 -0.35 47 47
myelination 0 0.053 0.18 6 -0.15 20 26
PPP3CB -0.001 0.058 0.18 6 -0.13 43 49
KRAS 0.014 0.034 -10000 0 -0.12 33 33
RAC1-CDC42/GDP 0.017 0.074 -10000 0 -0.14 83 83
NRG2 0.023 0.006 -10000 0 -0.12 1 1
mol:GDP 0.012 0.052 0.13 8 -0.17 30 38
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K2 -0.01 0.09 -10000 0 -0.18 77 77
SRC 0.023 0.008 -10000 0 -0.12 2 2
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.001 0.062 0.19 5 -0.12 84 89
MAP2K1 -0.041 0.16 -10000 0 -0.39 61 61
heart morphogenesis 0 0.066 0.19 7 -0.12 83 90
RAS family/GDP 0.012 0.084 -10000 0 -0.17 58 58
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.01 0.048 -10000 0 -0.77 2 2
CHRNE 0.01 0.019 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.012 0.077 10 -10000 0 10
nervous system development 0 0.066 0.19 7 -0.12 83 90
CDC42 0.023 0.002 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex -0.049 0.17 -9999 0 -0.36 97 97
STMN1 0.019 0.019 -9999 0 -0.068 23 23
Aurora B/RasGAP/Survivin 0.017 0.073 -9999 0 -0.16 72 72
Chromosomal passenger complex/Cul3 protein complex -0.002 0.089 -9999 0 -0.25 47 47
BIRC5 0.018 0.024 -9999 0 -0.12 15 15
DES -0.03 0.23 -9999 0 -0.94 33 33
Aurora C/Aurora B/INCENP 0.033 0.039 -9999 0 -0.11 33 33
Aurora B/TACC1 0.014 0.048 -9999 0 -0.095 82 82
Aurora B/PP2A 0.02 0.048 -9999 0 -0.12 59 59
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.006 0.062 -9999 0 -0.19 53 53
mitotic metaphase/anaphase transition 0.002 0.005 -9999 0 -10000 0 0
NDC80 0.009 0.032 -9999 0 -0.08 55 55
Cul3 protein complex 0.016 0.056 -9999 0 -0.11 57 57
KIF2C -0.066 0.21 -9999 0 -0.51 88 88
PEBP1 0.022 0.008 -9999 0 -0.12 1 1
KIF20A 0.009 0.038 -9999 0 -0.12 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.012 0.058 -9999 0 -0.13 80 80
SEPT1 0.022 0.013 -9999 0 -0.12 5 5
SMC2 0.015 0.03 -9999 0 -0.12 25 25
SMC4 0.018 0.025 -9999 0 -0.12 17 17
NSUN2/NPM1/Nucleolin -0.025 0.17 -9999 0 -0.64 36 36
PSMA3 0.019 0.02 -9999 0 -0.12 11 11
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B -0.002 0.065 -9999 0 -0.21 48 48
AURKB 0.019 0.027 -9999 0 -0.12 19 19
AURKC 0.023 0.006 -9999 0 -0.12 1 1
CDCA8 0.019 0.021 -9999 0 -0.12 11 11
cytokinesis -0.04 0.2 -9999 0 -0.46 76 76
Aurora B/Septin1 -0.022 0.19 -9999 0 -0.43 74 74
AURKA 0.015 0.027 -9999 0 -0.12 20 20
INCENP 0.021 0.011 -9999 0 -0.12 2 2
KLHL13 -0.001 0.052 -9999 0 -0.12 91 91
BUB1 0.017 0.025 -9999 0 -0.12 17 17
hSgo1/Aurora B/Survivin 0.011 0.078 -9999 0 -0.16 78 78
EVI5 0.021 0.015 -9999 0 -0.12 6 6
RhoA/GTP -0.023 0.18 -9999 0 -0.37 87 87
SGOL1 0.016 0.028 -9999 0 -0.12 22 22
CENPA -0.037 0.18 -9999 0 -0.36 91 91
NCAPG 0.01 0.036 -9999 0 -0.12 39 39
Aurora B/HC8 Proteasome 0.007 0.064 -9999 0 -0.15 72 72
NCAPD2 0.015 0.029 -9999 0 -0.12 24 24
Aurora B/PP1-gamma 0.012 0.059 -9999 0 -0.13 81 81
RHOA 0.023 0.006 -9999 0 -0.12 1 1
NCAPH 0.019 0.02 -9999 0 -0.12 10 10
NPM1 -0.011 0.12 -9999 0 -0.41 40 40
RASA1 0.021 0.011 -9999 0 -0.12 3 3
KLHL9 0.023 0.007 -9999 0 -0.12 1 1
mitotic prometaphase -0.001 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.064 -9999 0 -0.15 72 72
PPP1CC 0.022 0.005 -9999 0 -10000 0 0
Centraspindlin -0.032 0.19 -9999 0 -0.39 91 91
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
NSUN2 -0.01 0.11 -9999 0 -0.39 41 41
MYLK -0.005 0.067 -9999 0 -0.21 52 52
KIF23 0.013 0.033 -9999 0 -0.12 31 31
VIM 0.016 0.026 -9999 0 -0.084 28 28
RACGAP1 0.018 0.024 -9999 0 -0.12 16 16
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.02 0.12 -9999 0 -0.37 58 58
Chromosomal passenger complex -0.037 0.17 -9999 0 -0.34 94 94
Chromosomal passenger complex/EVI5 0.032 0.085 -9999 0 -0.18 57 57
TACC1 0.014 0.035 -9999 0 -0.12 35 35
PPP2R5D 0.022 0.013 -9999 0 -0.12 5 5
CUL3 0.023 0.004 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.023 0.009 -10000 0 -0.12 2 2
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
DOCK1 0.019 0.02 -10000 0 -0.12 11 11
ITGA4 0.015 0.029 -10000 0 -0.12 24 24
RAC1 0.023 0.002 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.005 0.065 -10000 0 -0.13 107 107
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.016 -10000 0 -0.12 7 7
alpha4/beta1 Integrin 0.02 0.059 -10000 0 -0.12 76 76
alpha4/beta7 Integrin/Paxillin 0.021 0.055 -10000 0 -0.1 80 80
lamellipodium assembly 0 0.12 -10000 0 -0.3 64 64
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.007 0.065 -10000 0 -0.13 98 98
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.021 0.013 -10000 0 -0.12 4 4
PXN 0.021 0.014 -10000 0 -0.07 13 13
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
ARF6/GTP 0.031 0.051 -10000 0 -0.14 11 11
cell adhesion 0.026 0.061 -10000 0 -0.098 96 96
CRKL/CBL 0.033 0.013 -10000 0 -0.14 2 2
alpha4/beta1 Integrin/Paxillin 0.022 0.053 -10000 0 -0.1 77 77
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
ITGB7 0.019 0.023 -10000 0 -0.12 15 15
ARF6/GDP 0.02 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.021 0.082 -10000 0 -0.17 77 77
p130Cas/Crk/Dock1 0.034 0.041 -10000 0 -0.11 36 36
VCAM1 -0.018 0.059 -10000 0 -0.12 139 139
alpha4/beta1 Integrin/Paxillin/Talin 0.028 0.062 -10000 0 -0.098 96 96
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.055 -10000 0 -0.14 11 11
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
mol:GDP -0.032 0.054 0.14 11 -10000 0 11
CBL 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GIT1 0.022 0.013 -10000 0 -0.12 5 5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.028 0.062 -10000 0 -0.098 96 96
Rac1/GTP -0.002 0.13 -10000 0 -0.32 64 64
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.036 0.049 -10000 0 -0.093 64 64
ER alpha/Gai/GDP/Gbeta gamma 0.005 0.095 -10000 0 -0.26 56 56
AKT1 -0.056 0.23 -10000 0 -0.6 80 80
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.057 0.23 -10000 0 -0.61 80 80
mol:Ca2+ 0.011 0.068 -10000 0 -0.24 30 30
IGF1R 0.013 0.031 -10000 0 -0.12 28 28
E2/ER alpha (dimer)/Striatin 0.014 0.047 -10000 0 -0.1 74 74
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis 0.053 0.22 0.58 80 -10000 0 80
RhoA/GTP -0.016 0.034 -10000 0 -0.14 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.1 -10000 0 -0.25 61 61
regulation of stress fiber formation -0.007 0.049 0.14 39 -10000 0 39
E2/ERA-ERB (dimer) 0.018 0.041 -10000 0 -0.099 61 61
KRAS 0.014 0.034 -10000 0 -0.12 33 33
G13/GTP 0.014 0.042 -10000 0 -0.091 74 74
pseudopodium formation 0.007 0.049 -10000 0 -0.14 39 39
E2/ER alpha (dimer)/PELP1 0.017 0.041 -10000 0 -0.099 62 62
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GNG2 0.02 0.018 -10000 0 -0.12 9 9
GNAO1 0.011 0.041 -10000 0 -0.12 50 50
HRAS 0.023 0.006 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.013 0.13 -10000 0 -0.32 72 72
E2/ER beta (dimer) 0.017 0.004 -10000 0 -0.076 1 1
mol:GDP 0.002 0.076 -10000 0 -0.24 46 46
mol:NADP -0.013 0.13 -10000 0 -0.32 72 72
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:IP3 0.011 0.07 -10000 0 -0.25 30 30
IGF-1R heterotetramer 0.013 0.031 -10000 0 -0.12 28 28
PLCB1 0.01 0.072 -10000 0 -0.26 30 30
PLCB2 0.016 0.068 -10000 0 -0.26 27 27
IGF1 0.007 0.045 -10000 0 -0.12 62 62
mol:L-citrulline -0.013 0.13 -10000 0 -0.32 72 72
RHOA 0.023 0.006 -10000 0 -0.12 1 1
Gai/GDP 0.022 0.062 -10000 0 -0.54 3 3
JNK cascade 0.017 0.004 -10000 0 -0.076 1 1
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
ESR2 0.023 0.006 -10000 0 -0.12 1 1
GNAQ 0.021 0.015 -10000 0 -0.12 6 6
ESR1 0.018 0.024 -10000 0 -0.12 15 15
Gq family/GDP/Gbeta gamma 0.03 0.063 -10000 0 -0.3 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.092 -10000 0 -0.49 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.006 0.1 -10000 0 -0.25 61 61
GNAZ 0.022 0.012 -10000 0 -0.12 4 4
E2/ER alpha (dimer) 0.002 0.046 -10000 0 -0.13 60 60
STRN 0.022 0.012 -10000 0 -0.12 4 4
GNAL 0.021 0.019 -10000 0 -0.12 10 10
PELP1 0.023 0.008 -10000 0 -0.12 2 2
MAPK11 0.021 0.003 -10000 0 -0.056 1 1
GNAI2 0.022 0.01 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 36 36
HBEGF -0.025 0.1 -10000 0 -0.25 70 70
cAMP biosynthetic process 0.015 0.033 -10000 0 -0.086 46 46
SRC 0.004 0.097 -10000 0 -0.24 65 65
PI3K 0.007 0.065 -10000 0 -0.13 98 98
GNB1 0.023 0.006 -10000 0 -0.12 1 1
G13/GDP/Gbeta gamma 0.022 0.076 -10000 0 -0.2 48 48
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IGF-1R heterotetramer/IGF1 -0.039 0.073 -10000 0 -0.21 75 75
Gs family/GTP 0.021 0.035 -10000 0 -0.087 46 46
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.043 -10000 0 -0.11 38 38
vasodilation -0.012 0.12 -10000 0 -0.31 72 72
mol:DAG 0.011 0.07 -10000 0 -0.25 30 30
Gs family/GDP/Gbeta gamma 0.005 0.068 -10000 0 -0.2 48 48
MSN 0.007 0.051 -10000 0 -0.14 39 39
Gq family/GTP 0.015 0.072 -10000 0 -0.27 28 28
mol:PI-3-4-5-P3 -0.054 0.22 -10000 0 -0.59 80 80
NRAS 0.022 0.011 -10000 0 -0.12 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.012 0.12 0.31 72 -10000 0 72
GRB2/SOS1 0.021 0.046 -10000 0 -0.12 52 52
RhoA/GDP 0.013 0.077 -10000 0 -0.22 48 48
NOS3 -0.015 0.13 -10000 0 -0.34 72 72
GNA11 0.022 0.013 -10000 0 -0.12 5 5
MAPKKK cascade -0.006 0.15 -10000 0 -0.43 57 57
E2/ER alpha (dimer)/PELP1/Src 0.002 0.11 -10000 0 -0.26 61 61
ruffle organization 0.007 0.049 -10000 0 -0.14 39 39
ROCK2 0.01 0.049 -10000 0 -0.15 24 24
GNA14 0.02 0.02 -10000 0 -0.12 11 11
GNA15 0.021 0.017 -10000 0 -0.12 8 8
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MMP9 -0.012 0.1 -10000 0 -0.25 64 64
MMP2 -0.019 0.1 -10000 0 -0.26 69 69
FAS signaling pathway (CD95)

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
SPTAN1 0.003 0.039 0.15 3 -0.26 10 13
RFC1 0.003 0.04 0.16 4 -0.26 10 14
PRKDC 0.003 0.039 0.16 4 -0.25 10 14
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP7 0.002 0.091 -10000 0 -0.45 16 16
FASLG/FAS/FADD/FAF1 0.036 0.085 0.16 118 -0.17 43 161
MAP2K4 -0.001 0.11 -10000 0 -0.3 41 41
mol:ceramide 0.004 0.096 -10000 0 -0.26 38 38
GSN 0.002 0.038 0.16 1 -0.26 10 11
FASLG/FAS/FADD/FAF1/Caspase 8 0.041 0.09 0.16 111 -0.25 19 130
FAS 0.016 0.026 -10000 0 -0.12 17 17
BID 0.005 0.017 0.25 2 -0.067 4 6
MAP3K1 0 0.093 -10000 0 -0.32 28 28
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
RB1 0.001 0.041 0.16 4 -0.25 11 15
CFLAR 0.022 0.011 -10000 0 -0.12 3 3
HGF/MET -0.053 0.089 -10000 0 -0.14 248 248
ARHGDIB -0.002 0.043 0.16 3 -0.28 10 13
FADD 0.022 0.01 -10000 0 -0.12 2 2
actin filament polymerization -0.002 0.038 0.25 10 -0.16 1 11
NFKB1 -0.039 0.2 -10000 0 -0.73 40 40
MAPK8 -0.002 0.12 -10000 0 -0.36 36 36
DFFA 0.003 0.04 0.16 4 -0.25 11 15
DNA fragmentation during apoptosis 0.004 0.04 0.16 4 -0.25 11 15
FAS/FADD/MET -0.015 0.082 -10000 0 -0.13 168 168
CFLAR/RIP1 0.03 0.027 -10000 0 -0.15 10 10
FAIM3 0.022 0.013 -10000 0 -0.12 5 5
FAF1 0.021 0.015 -10000 0 -0.12 5 5
PARP1 0.004 0.037 0.16 4 -0.24 10 14
DFFB 0.004 0.04 0.16 4 -0.25 11 15
CHUK -0.035 0.19 -10000 0 -0.7 40 40
FASLG 0.022 0.013 -10000 0 -0.12 4 4
FAS/FADD 0.012 0.058 -10000 0 -0.13 81 81
HGF 0.02 0.022 -10000 0 -0.12 14 14
LMNA 0 0.046 0.14 4 -0.26 13 17
CASP6 -0.002 0.05 0.16 4 -0.29 12 16
CASP10 0.019 0.02 -10000 0 -0.12 10 10
CASP3 -0.002 0.045 0.18 4 -0.28 11 15
PTPN13 -0.011 0.055 -10000 0 -0.12 110 110
CASP8 -0.005 0.019 0.14 7 -10000 0 7
IL6 -0.039 0.21 -10000 0 -0.75 36 36
MET 0.001 0.047 -10000 0 -0.12 71 71
ICAD/CAD 0.007 0.038 0.15 2 -0.22 12 14
FASLG/FAS/FADD/FAF1/Caspase 10 0.004 0.097 -10000 0 -0.27 38 38
activation of caspase activity by cytochrome c 0.005 0.017 0.25 2 -0.067 4 6
PAK2 0.003 0.04 0.16 4 -0.25 11 15
BCL2 0.016 0.031 -10000 0 -0.12 28 28
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.012 -9999 0 -0.12 4 4
Caspase 8 (4 units) 0.023 0.085 -9999 0 -0.25 34 34
NEF 0.005 0.007 -9999 0 -0.066 5 5
NFKBIA -0.001 0.039 -9999 0 -0.073 88 88
BIRC3 -0.058 0.13 -9999 0 -0.28 123 123
CYCS 0.013 0.071 -9999 0 -0.22 31 31
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
CD247 0.028 0.008 -9999 0 -0.11 1 1
MAP2K7 0.018 0.092 -9999 0 -0.38 17 17
protein ubiquitination 0.021 0.067 -9999 0 -0.22 17 17
CRADD 0.023 0.009 -9999 0 -0.12 2 2
DAXX 0.022 0.012 -9999 0 -0.12 4 4
FAS 0.016 0.025 -9999 0 -0.12 17 17
BID 0.02 0.065 -9999 0 -0.24 30 30
NF-kappa-B/RelA/I kappa B alpha -0.021 0.11 -9999 0 -0.18 148 148
TRADD 0.023 0.006 -9999 0 -0.12 1 1
MAP3K5 0.018 0.025 -9999 0 -0.12 17 17
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
FADD 0.023 0.009 -9999 0 -0.12 2 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.11 -9999 0 -0.18 148 148
MAPK8 0.019 0.09 -9999 0 -0.36 18 18
APAF1 0.021 0.014 -9999 0 -0.12 5 5
TRAF1 0.023 0.001 -9999 0 -10000 0 0
TRAF2 0.023 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.068 -9999 0 -0.26 28 28
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.02 0.075 -9999 0 -0.22 27 27
CHUK 0.021 0.07 -9999 0 -0.24 17 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.069 -9999 0 -0.11 85 85
TCRz/NEF 0.029 0.014 -9999 0 -0.16 2 2
TNF 0.02 0.02 -9999 0 -0.12 11 11
FASLG 0.029 0.02 -9999 0 -0.33 1 1
NFKB1 0.004 0.031 -9999 0 -0.059 71 71
TNFR1A/BAG4/TNF-alpha 0.038 0.034 -9999 0 -0.11 20 20
CASP6 -0.041 0.21 -9999 0 -0.53 80 80
CASP7 -0.059 0.19 -9999 0 -0.41 119 119
RELA 0.004 0.032 -9999 0 -0.058 68 68
CASP2 0.023 0.009 -9999 0 -0.12 2 2
CASP3 -0.06 0.2 -9999 0 -0.41 119 119
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
TNFR1A/BAG4 0.027 0.034 -9999 0 -0.14 18 18
CASP8 0.023 0.004 -9999 0 -10000 0 0
CASP9 0.022 0.014 -9999 0 -0.12 5 5
MAP3K14 0.022 0.071 -9999 0 -0.2 28 28
APAF-1/Caspase 9 -0.028 0.12 -9999 0 -0.22 125 125
BCL2 0.019 0.087 -9999 0 -0.32 20 20
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.048 0.2 -10000 0 -0.69 41 41
epithelial cell differentiation -0.039 0.19 -10000 0 -0.65 41 41
ITCH 0.027 0.027 0.085 4 -0.072 29 33
WWP1 -0.053 0.29 -10000 0 -1.2 34 34
FYN 0.012 0.037 -10000 0 -0.12 40 40
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PRL 0.023 0.01 -10000 0 -0.12 3 3
neuron projection morphogenesis -0.016 0.16 -10000 0 -0.53 40 40
PTPRZ1 0.021 0.017 -10000 0 -0.12 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.18 -10000 0 -0.59 40 40
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.19 -10000 0 -0.66 40 40
ADAM17 0.023 0.031 0.085 2 -0.085 34 36
ErbB4/ErbB4 -0.036 0.22 -10000 0 -0.8 38 38
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.054 0.2 -10000 0 -0.7 41 41
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.038 0.18 -10000 0 -0.61 44 44
GRIN2B -0.036 0.18 -10000 0 -0.58 44 44
ErbB4/ErbB2/betacellulin -0.041 0.18 -10000 0 -0.64 41 41
STAT1 0.014 0.03 -10000 0 -0.12 25 25
HBEGF 0.018 0.026 -10000 0 -0.12 20 20
PRLR 0.009 0.042 -10000 0 -0.12 55 55
E4ICDs/ETO2 -0.046 0.2 -10000 0 -0.79 34 34
axon guidance -0.062 0.23 -10000 0 -0.8 42 42
NEDD4 0.024 0.034 0.085 7 -0.081 42 49
Prolactin receptor/Prolactin receptor/Prolactin 0.024 0.032 -10000 0 -0.072 56 56
CBFA2T3 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/HBEGF -0.033 0.18 -10000 0 -0.65 39 39
MAPK3 -0.017 0.16 -10000 0 -0.55 40 40
STAT1 (dimer) -0.058 0.21 -10000 0 -0.75 39 39
MAPK1 -0.018 0.16 -10000 0 -0.55 40 40
JAK2 0.017 0.025 -10000 0 -0.12 17 17
ErbB4/ErbB2/neuregulin 1 beta -0.031 0.18 -10000 0 -0.64 40 40
NRG1 0.021 0.027 -10000 0 -0.07 30 30
NRG3 0.005 0.048 -10000 0 -0.12 73 73
NRG2 0.023 0.006 -10000 0 -0.12 1 1
NRG4 0.002 0.047 -10000 0 -0.12 70 70
heart development -0.062 0.23 -10000 0 -0.8 42 42
neural crest cell migration -0.031 0.18 -10000 0 -0.63 40 40
ERBB2 0.021 0.027 -10000 0 -0.067 32 32
WWOX/E4ICDs -0.046 0.2 -10000 0 -0.79 34 34
SHC1 0.023 0.001 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.069 0.2 -10000 0 -0.6 50 50
apoptosis 0.047 0.2 0.66 43 -10000 0 43
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.046 0.2 -10000 0 -0.79 34 34
ErbB4/ErbB2/epiregulin -0.031 0.18 -10000 0 -0.64 40 40
ErbB4/ErbB4/betacellulin/betacellulin -0.056 0.2 -10000 0 -0.78 36 36
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.029 0.19 -10000 0 -0.64 41 41
MDM2 -0.033 0.2 -10000 0 -0.74 38 38
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.025 0.17 -10000 0 -0.57 42 42
STAT5A -0.057 0.22 -10000 0 -0.77 42 42
ErbB4/EGFR/neuregulin 1 beta -0.036 0.18 -10000 0 -0.63 41 41
DLG4 0.023 0.008 -10000 0 -0.12 2 2
GRB2/SHC 0.032 0.02 -10000 0 -0.13 8 8
E4ICDs/TAB2/NCoR1 -0.041 0.2 -10000 0 -0.74 37 37
STAT5A (dimer) -0.039 0.21 -10000 0 -0.73 41 41
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 7 7
STAT5B (dimer) -0.052 0.22 -10000 0 -0.77 42 42
LRIG1 0.01 0.036 -10000 0 -0.12 39 39
EREG 0.021 0.017 -10000 0 -0.12 8 8
BTC 0.011 0.038 -10000 0 -0.12 43 43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.062 0.23 -10000 0 -0.81 42 42
ERBB4 -0.034 0.22 -10000 0 -0.8 38 38
STAT5B 0.023 0.006 -10000 0 -0.12 1 1
YAP1 0.002 0.076 -10000 0 -0.5 11 11
GRB2 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/neuregulin 4 -0.05 0.18 -10000 0 -0.55 52 52
glial cell differentiation 0.04 0.2 0.73 37 -10000 0 37
WWOX 0.023 0.006 -10000 0 -0.12 1 1
cell proliferation -0.069 0.21 -10000 0 -0.57 64 64
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.02 0.048 -10000 0 -0.13 49 49
Necdin/E2F1 0.017 0.046 -10000 0 -0.088 84 84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.038 0.049 -10000 0 -0.1 53 53
NGF (dimer)/p75(NTR)/BEX1 -0.008 0.054 -10000 0 -0.075 214 214
NT-4/5 (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.083 10 10
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 0.009 0.045 -10000 0 -0.1 64 64
IKBKG 0.023 0.008 -10000 0 -0.12 2 2
BDNF 0.023 0.01 -10000 0 -0.12 3 3
MGDIs/NGR/p75(NTR)/LINGO1 0.04 0.031 -10000 0 -0.12 13 13
FURIN 0.02 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75(NTR)/Sortilin 0.035 0.042 -10000 0 -0.12 34 34
LINGO1 0.018 0.026 -10000 0 -0.12 19 19
Sortilin/TRAF6/NRIF 0.004 0.054 -10000 0 -0.17 23 23
proBDNF (dimer) 0.022 0.01 -10000 0 -0.12 3 3
NTRK1 0.023 0.006 -10000 0 -0.12 1 1
RTN4R 0.021 0.018 -10000 0 -0.12 9 9
neuron apoptosis -0.039 0.12 -10000 0 -0.35 36 36
IRAK1 0.02 0.022 -10000 0 -0.12 13 13
SHC1 0.019 0.011 -10000 0 -0.062 10 10
ARHGDIA 0.016 0.032 -10000 0 -0.12 29 29
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
Gamma Secretase 0.035 0.067 -10000 0 -0.097 88 88
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.025 0.051 -10000 0 -0.11 62 62
MAGEH1 0.018 0.023 -10000 0 -0.12 15 15
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.021 0.051 -10000 0 -0.11 54 54
Mammalian IAPs/DIABLO -0.018 0.083 -10000 0 -0.13 159 159
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.02 0.019 -10000 0 -0.12 10 10
APP 0.022 0.008 -10000 0 -0.12 1 1
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.023 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.029 0.027 -10000 0 -0.1 12 12
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.042 0.098 62 -0.1 33 95
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.062 -10000 0 -0.15 62 62
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.028 0.022 -10000 0 -0.087 19 19
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
mol:GTP 0.022 0.034 -10000 0 -0.093 43 43
PSENEN 0.016 0.03 -10000 0 -0.12 25 25
mol:ceramide 0.016 0.034 -10000 0 -0.11 34 34
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.004 0.09 -10000 0 -0.3 30 30
p75(NTR)/beta APP 0.022 0.044 -10000 0 -0.13 43 43
BEX1 -0.016 0.062 -10000 0 -0.12 146 146
mol:GDP 0.006 0.01 -10000 0 -0.067 10 10
NGF (dimer) -0.028 0.064 -10000 0 -0.1 198 198
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.041 -10000 0 -0.11 21 21
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
RAC1/GTP 0.025 0.016 -10000 0 -0.07 14 14
MYD88 0.023 0.006 -10000 0 -0.12 1 1
CHUK 0.021 0.013 -10000 0 -0.12 4 4
NGF (dimer)/p75(NTR)/PKA 0.022 0.034 -10000 0 -0.093 43 43
RHOB 0.022 0.013 -10000 0 -0.12 5 5
RHOA 0.023 0.006 -10000 0 -0.12 1 1
MAGE-G1/E2F1 0.032 0.018 -10000 0 -0.087 12 12
NT3 (dimer) -0.003 0.055 -10000 0 -0.12 101 101
TP53 0.011 0.047 -10000 0 -0.13 40 40
PRDM4 0.017 0.032 -10000 0 -0.1 34 34
BDNF (dimer) -0.02 0.069 -10000 0 -0.096 204 204
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SORT1 0.02 0.018 -10000 0 -0.12 8 8
activation of caspase activity 0.034 0.047 -10000 0 -0.1 53 53
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.032 0.042 -10000 0 -0.11 40 40
RHOC 0.023 0.002 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.022 0.055 -10000 0 -0.17 24 24
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
SMPD2 0.016 0.034 -10000 0 -0.11 34 34
APH1B 0.014 0.031 -10000 0 -0.12 28 28
APH1A 0.023 0.009 -10000 0 -0.12 2 2
proNGF (dimer)/p75(NTR)/Sortilin 0.02 0.038 -10000 0 -0.1 47 47
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
APAF-1/Pro-Caspase 9 0.025 0.04 -10000 0 -0.16 22 22
NT3 (dimer)/p75(NTR) 0.012 0.046 -10000 0 -0.076 119 119
MAPK8 0.022 0.058 -10000 0 -0.19 24 24
MAPK9 0.022 0.054 -10000 0 -0.18 21 21
APAF1 0.021 0.014 -10000 0 -0.12 5 5
NTF3 -0.003 0.055 -10000 0 -0.12 101 101
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.008 0.044 -10000 0 -0.12 59 59
RAC1/GDP 0.016 0.015 -10000 0 -0.15 5 5
RhoA-B-C/GDP 0.04 0.035 -10000 0 -0.084 34 34
p75 CTF/Sortilin/TRAF6/NRIF 0.038 0.058 -10000 0 -0.12 62 62
RhoA-B-C/GTP 0.022 0.034 -10000 0 -0.092 43 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.045 -10000 0 -0.093 40 40
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.046 0.046 -10000 0 -0.1 40 40
PRKACB 0.02 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75 ECD 0.022 0.044 -10000 0 -0.12 45 45
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.005 0.052 -10000 0 -0.12 93 93
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
neuron projection morphogenesis 0.003 0.056 0.099 49 -0.13 47 96
BAD 0.02 0.06 -10000 0 -0.18 24 24
RIPK2 0.013 0.034 -10000 0 -0.12 34 34
NGFR 0.021 0.018 -10000 0 -0.12 9 9
CYCS 0.014 0.042 -10000 0 -0.11 49 49
ADAM17 0.019 0.02 -10000 0 -0.12 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.049 -10000 0 -0.11 55 55
BCL2L11 0.02 0.06 -10000 0 -0.18 27 27
BDNF (dimer)/p75(NTR) 0.032 0.017 -10000 0 -0.082 12 12
PI3K 0.021 0.054 -10000 0 -0.11 64 64
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.033 0.039 -10000 0 -0.1 36 36
NDNL2 0.023 0.009 -10000 0 -0.12 2 2
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
NGF (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.083 10 10
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.029 0.046 -10000 0 -0.11 49 49
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0 -10000 0 -10000 0 0
PLG 0.023 0.008 -10000 0 -0.12 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.05 -10000 0 -0.16 34 34
SQSTM1 0.021 0.015 -10000 0 -0.12 6 6
NGFRAP1 0.022 0.009 -10000 0 -0.12 2 2
CASP3 0.021 0.058 -10000 0 -0.18 23 23
E2F1 0.021 0.016 -10000 0 -0.12 7 7
CASP9 0.022 0.014 -10000 0 -0.12 5 5
IKK complex 0.021 0.08 -10000 0 -0.22 33 33
NGF (dimer)/TRKA 0.017 0.004 -10000 0 -0.076 1 1
MMP7 -0.021 0.059 -10000 0 -0.12 144 144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.042 0.042 -10000 0 -0.096 40 40
MMP3 0.017 0.029 -10000 0 -0.12 24 24
APAF-1/Caspase 9 -0.037 0.06 -10000 0 -0.16 87 87
TCGA08_rtk_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
PDGFRA 0.005 0.043 -10000 0 -0.12 59 59
HRAS 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
AKT 0.001 0.064 0.13 8 -0.12 81 89
FOXO3 0.021 0.017 -10000 0 -0.12 8 8
AKT1 0.021 0.019 -10000 0 -0.12 10 10
FOXO1 0.023 0.008 -10000 0 -0.12 2 2
AKT3 -0.003 0.055 -10000 0 -0.12 101 101
FOXO4 0.023 0 -10000 0 -10000 0 0
MET 0.001 0.047 -10000 0 -0.12 71 71
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PIK3CB 0.015 0.029 -10000 0 -0.12 24 24
NRAS 0.022 0.011 -10000 0 -0.12 3 3
PIK3CG 0.011 0.036 -10000 0 -0.12 39 39
PIK3R3 0.012 0.035 -10000 0 -0.12 36 36
PIK3R2 0.017 0.029 -10000 0 -0.12 25 25
NF1 0.018 0.02 -10000 0 -0.12 10 10
RAS 0.006 0.06 0.15 34 -0.15 43 77
ERBB2 0.02 0.021 -10000 0 -0.12 12 12
proliferation/survival/translation 0.002 0.074 0.22 37 -10000 0 37
PI3K -0.014 0.077 0.13 9 -0.14 112 121
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
KRAS 0.014 0.034 -10000 0 -0.12 33 33
FOXO 0.029 0.037 0.14 9 -0.033 12 21
AKT2 0.019 0.025 -10000 0 -0.12 18 18
PTEN 0.022 0.008 -10000 0 -0.12 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.041 -9999 0 -0.12 52 52
ELF1 0.032 0.023 -9999 0 -0.2 3 3
CCNA2 0.013 0.032 -9999 0 -0.12 29 29
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
JAK3 0.023 0.013 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
JAK1 0.022 0.01 -9999 0 -0.12 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.005 0.13 -9999 0 -0.3 57 57
SHC1 0.024 0.002 -9999 0 -10000 0 0
SP1 0.012 0.054 -9999 0 -0.091 103 103
IL2RA 0.03 0.037 -9999 0 -0.49 2 2
IL2RB 0.02 0.023 -9999 0 -0.12 15 15
SOS1 0.018 0.027 -9999 0 -0.12 20 20
IL2RG -0.001 0.049 -9999 0 -0.12 82 82
G1/S transition of mitotic cell cycle -0.075 0.17 -9999 0 -0.31 157 157
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
CCND2 0 0.087 -9999 0 -0.16 102 102
LCK 0.022 0.015 -9999 0 -0.12 6 6
GRB2 0.023 0.007 -9999 0 -0.12 1 1
IL2 0.023 0.011 -9999 0 -0.12 3 3
CDK6 0.008 0.039 -9999 0 -0.12 47 47
CCND3 -0.003 0.14 -9999 0 -0.56 14 14
Signaling events mediated by PRL

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
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
mol:Halofuginone 0.003 0.025 -10000 0 -0.18 10 10
ITGA1 0.014 0.029 -10000 0 -0.12 24 24
CDKN1A 0.014 0.061 -10000 0 -0.29 19 19
PRL-3/alpha Tubulin 0.014 0.051 -10000 0 -0.14 42 42
mol:Ca2+ 0.018 0.077 0.28 42 -10000 0 42
AGT 0.02 0.02 -10000 0 -0.12 11 11
CCNA2 0 0.093 -10000 0 -0.59 12 12
TUBA1B 0.023 0 -10000 0 -10000 0 0
EGR1 -0.001 0.06 -10000 0 -0.34 12 12
CDK2/Cyclin E1 0.005 0.075 -10000 0 -0.26 24 24
MAPK3 0.014 0.026 -10000 0 -0.071 44 44
PRL-2 /Rab GGTase beta 0.008 0.063 -10000 0 -0.13 89 89
MAPK1 0.013 0.031 -10000 0 -0.083 45 45
PTP4A1 0.002 0.091 -10000 0 -0.57 12 12
PTP4A3 0.011 0.037 -10000 0 -0.12 40 40
PTP4A2 0.022 0.009 -10000 0 -0.12 2 2
ITGB1 0.013 0.027 -10000 0 -0.073 46 46
SRC 0.023 0.008 -10000 0 -0.12 2 2
RAC1 -0.014 0.11 -10000 0 -0.34 55 55
Rab GGTase beta/Rab GGTase alpha 0.012 0.058 -10000 0 -0.13 80 80
PRL-1/ATF-5 -0.003 0.095 -10000 0 -0.54 12 12
RABGGTA 0.023 0.006 -10000 0 -0.12 1 1
BCAR1 0.019 0.076 0.28 42 -10000 0 42
RHOC -0.013 0.11 -10000 0 -0.35 52 52
RHOA -0.014 0.11 -10000 0 -0.34 55 55
cell motility -0.011 0.11 -10000 0 -0.32 58 58
PRL-1/alpha Tubulin 0 0.094 -10000 0 -0.54 12 12
PRL-3/alpha1 Integrin -0.01 0.079 -10000 0 -0.16 99 99
ROCK1 -0.012 0.11 -10000 0 -0.32 58 58
RABGGTB 0.018 0.022 -10000 0 -0.12 12 12
CDK2 0.018 0.023 -10000 0 -0.12 14 14
mitosis 0.002 0.09 -10000 0 -0.57 12 12
ATF5 0.018 0.026 -10000 0 -0.12 19 19
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.021 0.2 -10000 0 -0.97 24 24
VDR 0.019 0.022 -10000 0 -0.12 13 13
FAM120B 0.022 0.011 -10000 0 -0.12 3 3
RXRs/LXRs/DNA/9cRA 0.025 0.095 -10000 0 -0.24 55 55
RXRs/LXRs/DNA/Oxysterols 0.019 0.13 -10000 0 -0.35 60 60
MED1 0.022 0.014 -10000 0 -0.12 5 5
mol:9cRA 0.002 0.017 -10000 0 -0.047 51 51
RARs/THRs/DNA/Src-1 -0.003 0.087 -10000 0 -0.16 107 107
RXRs/NUR77 0.033 0.067 -10000 0 -0.12 27 27
RXRs/PPAR 0.032 0.039 -10000 0 -0.16 5 5
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.009 0.035 -10000 0 -0.12 36 36
RARs/VDR/DNA/Vit D3 0.03 0.056 -10000 0 -0.1 67 67
RARA 0.023 0 -10000 0 -10000 0 0
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARs/RARs/DNA/9cRA 0.025 0.045 -10000 0 -0.094 58 58
RARG 0.021 0.015 -10000 0 -0.12 6 6
RPS6KB1 -0.004 0.09 -10000 0 -0.32 39 39
RARs/THRs/DNA/SMRT -0.002 0.083 -10000 0 -0.16 103 103
THRA 0.022 0.015 -10000 0 -0.12 6 6
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0.035 -10000 0 -0.12 36 36
RXRs/PPAR/9cRA/PGJ2/DNA 0.041 0.073 0.27 14 -0.16 16 30
NR1H4 0.022 0.016 -10000 0 -0.12 7 7
RXRs/LXRs/DNA 0.059 0.086 -10000 0 -0.16 57 57
NR1H2 0.021 0.027 -10000 0 -0.049 52 52
NR1H3 0.02 0.029 -10000 0 -0.095 18 18
RXRs/VDR/DNA/Vit D3 0.039 0.059 -10000 0 -0.12 23 23
NR4A1 0.003 0.049 -10000 0 -0.12 76 76
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.023 0.048 -10000 0 -0.2 10 10
RXRG 0.007 0.05 -10000 0 -0.09 102 102
RXR alpha/CCPG 0.031 0.026 -10000 0 -0.13 7 7
RXRA 0.021 0.025 -10000 0 -0.049 42 42
RXRB 0.024 0.02 -10000 0 -0.037 34 34
THRB 0.012 0.035 -10000 0 -0.12 36 36
PPARG 0.017 0.029 -10000 0 -0.12 24 24
PPARD 0.023 0.008 -10000 0 -0.12 2 2
TNF 0.021 0.13 -10000 0 -0.4 22 22
mol:Oxysterols 0.001 0.015 -10000 0 -0.041 59 59
cholesterol transport 0.019 0.13 -10000 0 -0.34 60 60
PPARA 0.022 0.012 -10000 0 -0.12 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.034 -10000 0 -0.12 33 33
RXRs/NUR77/BCL2 0.013 0.046 -10000 0 -0.15 23 23
SREBF1 0.022 0.13 -10000 0 -0.41 20 20
RXRs/RXRs/DNA/9cRA 0.041 0.073 0.26 14 -0.16 16 30
ABCA1 -0.029 0.27 -10000 0 -0.8 60 60
RARs/THRs 0.027 0.072 -10000 0 -0.1 105 105
RXRs/FXR 0.049 0.056 -10000 0 -0.12 15 15
BCL2 0.016 0.031 -10000 0 -0.12 28 28
EGFR-dependent Endothelin signaling events

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
HRAS 0.023 0.006 -9999 0 -0.12 1 1
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EGF/EGFR 0.013 0.053 -9999 0 -0.092 80 80
EGF/EGFR dimer/SHC/GRB2/SOS1 0.041 0.059 -9999 0 -0.095 69 69
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.014 0.034 -9999 0 -0.12 34 34
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.02 0.021 -9999 0 -0.12 13 13
EGF/EGFR dimer/SHC 0.03 0.046 -9999 0 -0.11 40 40
mol:GDP 0.036 0.056 -9999 0 -0.094 69 69
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.009 0.042 -9999 0 -0.12 54 54
GRB2/SOS1 0.021 0.046 -9999 0 -0.12 52 52
HRAS/GTP 0.023 0.045 -9999 0 -0.13 13 13
SHC1 0.023 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.036 0.052 -9999 0 -0.14 13 13
FRAP1 0.016 0.044 -9999 0 -0.087 69 69
EGF/EGFR dimer 0.016 0.05 -9999 0 -0.11 74 74
SOS1 0.017 0.027 -9999 0 -0.12 20 20
GRB2 0.023 0.006 -9999 0 -0.12 1 1
ETA receptor/Endothelin-1 0.008 0.056 -9999 0 -0.16 34 34
S1P3 pathway

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
PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
mol:S1P -0.002 0.007 -9999 0 -0.029 25 25
S1P1/S1P/Gi 0.008 0.066 -9999 0 -0.22 33 33
GNAO1 0.008 0.042 -9999 0 -0.12 50 50
S1P/S1P3/G12/G13 0.024 0.024 -9999 0 -0.097 16 16
AKT1 0.006 0.059 -9999 0 -0.42 5 5
AKT3 -0.055 0.23 -9999 0 -0.87 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
GNAI2 0.02 0.014 -9999 0 -0.044 15 15
GNAI3 0.02 0.012 -9999 0 -0.12 1 1
GNAI1 0.01 0.036 -9999 0 -0.12 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.002 0.008 -9999 0 -0.015 105 105
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.022 0.015 -9999 0 -0.12 6 6
mol:Ca2+ -0.016 0.089 -9999 0 -0.17 109 109
MAPK3 -0.013 0.085 -9999 0 -0.22 53 53
MAPK1 -0.013 0.085 -9999 0 -0.22 52 52
JAK2 -0.023 0.1 -9999 0 -0.24 74 74
CXCR4 -0.021 0.093 -9999 0 -0.24 63 63
FLT1 0.019 0.019 -9999 0 -0.052 23 23
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
SRC -0.012 0.084 -9999 0 -0.22 50 50
S1P/S1P3/Gi -0.016 0.089 -9999 0 -0.17 109 109
RAC1 0.023 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.085 -9999 0 -0.22 47 47
VEGFA 0.017 0.023 -9999 0 -0.062 31 31
S1P/S1P2/Gi -0.011 0.077 -9999 0 -0.15 108 108
VEGFR1 homodimer/VEGFA homodimer 0.016 0.056 -9999 0 -0.15 45 45
RHOA 0.023 0.006 -9999 0 -0.12 1 1
S1P/S1P3/Gq 0.014 0.044 -9999 0 -0.15 34 34
GNAQ 0.021 0.015 -9999 0 -0.12 6 6
GNAZ 0.02 0.015 -9999 0 -0.12 4 4
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
GNA11 0.022 0.013 -9999 0 -0.12 5 5
Rac1/GTP -0.006 0.086 -9999 0 -0.23 47 47
ceramide signaling pathway

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
MAP4K4 -0.012 0.11 -10000 0 -0.21 120 120
BAG4 0.022 0.012 -10000 0 -0.12 4 4
BAD 0.007 0.036 -10000 0 -0.12 19 19
NFKBIA 0.016 0.027 -10000 0 -0.12 21 21
BIRC3 -0.005 0.052 -10000 0 -0.12 93 93
BAX 0.007 0.036 -10000 0 -0.11 19 19
EnzymeConsortium:3.1.4.12 0 0.027 -10000 0 -0.081 22 22
IKBKB -0.009 0.11 -10000 0 -0.28 40 40
MAP2K2 0.013 0.036 -10000 0 -0.1 23 23
MAP2K1 0.015 0.033 -10000 0 -0.099 20 20
SMPD1 0.005 0.028 -10000 0 -0.094 16 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.32 35 35
MAP2K4 0.007 0.039 -10000 0 -0.11 30 30
protein ubiquitination -0.012 0.11 -10000 0 -0.28 42 42
EnzymeConsortium:2.7.1.37 0.016 0.034 -10000 0 -0.11 12 12
response to UV 0 0 -10000 0 -0.001 8 8
RAF1 0.011 0.034 -10000 0 -0.1 22 22
CRADD 0.023 0.009 -10000 0 -0.12 2 2
mol:ceramide 0.003 0.038 -10000 0 -0.12 20 20
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0.041 -10000 0 -0.097 62 62
MADD 0.023 0.006 -10000 0 -0.12 1 1
MAP3K1 0.004 0.041 -10000 0 -0.12 31 31
TRADD 0.023 0.006 -10000 0 -0.12 1 1
RELA/p50 0.023 0.009 -10000 0 -0.12 2 2
MAPK3 0.017 0.035 -10000 0 -0.1 21 21
MAPK1 0.016 0.037 -10000 0 -0.11 18 18
p50/RELA/I-kappa-B-alpha 0.018 0.05 -10000 0 -0.12 62 62
FADD -0.01 0.11 -10000 0 -0.2 120 120
KSR1 0.008 0.035 -10000 0 -0.11 20 20
MAPK8 0.008 0.042 -10000 0 -0.11 36 36
TRAF2 0.024 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.012 0.11 -10000 0 -0.3 41 41
TNF R/SODD 0.027 0.033 -10000 0 -0.14 18 18
TNF 0.021 0.02 -10000 0 -0.12 11 11
CYCS 0.006 0.038 0.097 1 -0.12 21 22
IKBKG -0.009 0.11 -10000 0 -0.28 37 37
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.22 120 120
RELA 0.023 0.009 -10000 0 -0.12 2 2
RIPK1 0.023 0.011 -10000 0 -0.12 3 3
AIFM1 0.001 0.044 0.097 1 -0.12 36 37
TNF/TNF R/SODD 0.038 0.034 -10000 0 -0.11 20 20
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.12 -10000 0 -0.67 17 17
NSMAF -0.011 0.11 -10000 0 -0.2 120 120
response to hydrogen peroxide 0 0 -10000 0 -0.001 8 8
BCL2 0.016 0.031 -10000 0 -0.12 28 28
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.019 0.015 -9999 0 -0.057 18 18
SNTA1 0.023 0.009 -9999 0 -0.12 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.021 -9999 0 -0.074 21 21
MAPK12 0.01 0.028 -9999 0 -0.062 39 39
CCND1 -0.049 0.14 -9999 0 -0.36 90 90
p38 gamma/SNTA1 0.005 0.058 -9999 0 -0.16 42 42
MAP2K3 0.023 0.006 -9999 0 -0.12 1 1
PKN1 0.016 0.031 -9999 0 -0.12 27 27
G2/M transition checkpoint 0.002 0.045 -9999 0 -0.15 39 39
MAP2K6 0.007 0.03 -9999 0 -0.052 82 82
MAPT 0.007 0.04 -9999 0 -0.13 28 28
MAPK13 0.019 0.019 -9999 0 -0.078 17 17
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.002 0.059 -9999 0 -0.21 39 39
Class I PI3K 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
ARF5/GTP 0.005 0.042 -10000 0 -0.11 49 49
DAPP1 0.006 0.078 -10000 0 -0.25 25 25
Src family/SYK family/BLNK-LAT/BTK-ITK 0.001 0.12 -10000 0 -0.33 40 40
mol:DAG 0.015 0.065 0.16 14 -0.15 37 51
HRAS 0.023 0.007 -10000 0 -0.13 1 1
RAP1A 0.022 0.012 -10000 0 -0.12 3 3
ARF5/GDP 0.003 0.086 -10000 0 -0.2 63 63
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
PLCG1 0.018 0.025 -10000 0 -0.12 18 18
ARF5 0.02 0.019 -10000 0 -0.12 10 10
mol:GTP -0.006 0.038 -10000 0 -0.11 54 54
ARF1/GTP 0.003 0.05 0.16 21 -0.12 41 62
RHOA 0.023 0.006 -10000 0 -0.12 1 1
YES1 0.02 0.018 -10000 0 -0.12 8 8
RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
ADAP1 -0.005 0.036 -10000 0 -0.1 54 54
ARAP3 -0.006 0.037 -10000 0 -0.11 54 54
INPPL1 0.021 0.018 -10000 0 -0.12 9 9
PREX1 0.021 0.017 -10000 0 -0.12 8 8
ARHGEF6 0.014 0.032 -10000 0 -0.12 29 29
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
ARF1 0.018 0.027 -10000 0 -0.12 21 21
NRAS 0.022 0.012 -10000 0 -0.12 3 3
FYN 0.012 0.037 -10000 0 -0.12 40 40
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0.012 0.037 0.092 14 -0.077 37 51
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.032 -10000 0 -0.12 29 29
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
mol:IP3 0.013 0.049 0.11 14 -0.11 37 51
LYN 0.021 0.013 -10000 0 -0.12 4 4
ARF1/GDP 0.003 0.087 -10000 0 -0.2 61 61
RhoA/GDP 0.015 0.066 0.17 19 -0.15 45 64
PDK1/Src/Hsp90 0.042 0.03 -10000 0 -0.12 18 18
BLNK 0.014 0.033 -10000 0 -0.12 32 32
actin cytoskeleton reorganization 0.006 0.086 0.19 17 -0.22 42 59
SRC 0.023 0.008 -10000 0 -0.12 2 2
PLEKHA2 0.013 0.011 -10000 0 -0.056 13 13
RAC1 0.023 0.002 -10000 0 -10000 0 0
PTEN 0.022 0.008 -10000 0 -0.12 1 1
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.006 0.042 -10000 0 -0.11 46 46
RhoA/GTP 0.013 0.051 0.17 22 -0.11 41 63
Src family/SYK family/BLNK-LAT 0.007 0.096 -10000 0 -0.29 31 31
BLK 0.022 0.013 -10000 0 -0.12 5 5
PDPK1 0.023 0.006 -10000 0 -0.12 1 1
CYTH1 -0.005 0.036 -10000 0 -0.1 54 54
HCK 0.019 0.023 -10000 0 -0.12 15 15
CYTH3 -0.005 0.036 -10000 0 -0.1 54 54
CYTH2 -0.005 0.036 -10000 0 -0.1 54 54
KRAS 0.015 0.034 -10000 0 -0.12 33 33
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.053 0.13 22 -0.21 19 41
SGK1 0.009 0.049 -10000 0 -0.21 19 19
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.085 -10000 0 -0.21 60 60
SOS1 0.017 0.027 -10000 0 -0.12 20 20
SYK 0.016 0.027 -10000 0 -0.12 21 21
ARF6/GDP 0.008 0.063 0.17 19 -0.14 47 66
mol:PI-3-4-5-P3 -0.004 0.038 0.084 1 -0.11 54 55
ARAP3/RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
VAV1 0.02 0.019 -10000 0 -0.12 10 10
mol:PI-3-4-P2 0.01 0.011 -10000 0 -0.076 9 9
RAS family/GTP/PI3K Class I 0.026 0.058 0.19 22 -0.11 54 76
PLEKHA1 0.013 0.012 -10000 0 -0.056 17 17
Rac1/GDP 0.004 0.087 -10000 0 -0.2 62 62
LAT 0.022 0.01 -10000 0 -0.12 3 3
Rac1/GTP -0.001 0.1 -10000 0 -0.24 69 69
ITK -0.001 0.039 -10000 0 -0.1 58 58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.083 0.19 14 -0.2 38 52
LCK 0.022 0.015 -10000 0 -0.12 6 6
BTK -0.003 0.043 -10000 0 -0.11 56 56
Atypical NF-kappaB pathway

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
BCL3/RelA 0.03 0.026 -9999 0 -0.093 21 21
FBXW11 0.023 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.041 -9999 0 -0.11 43 43
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.073 -9999 0 -0.19 37 37
NFKBIA 0 0.066 -9999 0 -0.15 79 79
MAPK14 0.023 0.007 -9999 0 -0.12 1 1
NF kappa B1 p105/p50 0.021 0.043 -9999 0 -0.12 42 42
ARRB2 0.014 0.035 -9999 0 -0.2 14 14
REL 0.021 0.016 -9999 0 -0.12 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.042 -9999 0 -0.12 42 42
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.04 -9999 0 -0.11 42 42
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
NF kappa B1 p50 dimer 0.012 0.044 -9999 0 -0.13 49 49
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
NFKB1 0.02 0.013 -9999 0 -0.07 10 10
RELA 0.023 0.009 -9999 0 -0.12 2 2
positive regulation of anti-apoptosis 0.013 0.051 -9999 0 -0.13 53 53
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.02 0.075 -9999 0 -0.2 35 35
SRC 0.023 0.008 -9999 0 -0.12 2 2
PI3K 0.007 0.065 -9999 0 -0.13 98 98
NF kappa B1 p50/RelA 0.013 0.052 -9999 0 -0.13 53 53
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -9999 0 -10000 0 0
SYK 0.016 0.027 -9999 0 -0.12 21 21
I kappa B alpha/PIK3R1 0.008 0.069 -9999 0 -0.14 79 79
cell death 0.019 0.072 -9999 0 -0.19 35 35
NF kappa B1 p105/c-Rel 0.021 0.041 -9999 0 -0.11 43 43
LCK 0.022 0.015 -9999 0 -0.12 6 6
BCL3 0.02 0.022 -9999 0 -0.12 14 14
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.015 -9999 0 -0.069 13 13
SMARCC1 -0.002 0.18 -9999 0 -1.1 14 14
REL 0.02 0.016 -9999 0 -0.12 7 7
HDAC7 -0.018 0.096 -9999 0 -0.17 122 122
JUN 0.015 0.032 -9999 0 -0.12 30 30
EP300 0.022 0.009 -9999 0 -0.12 2 2
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.026 -9999 0 -0.071 36 36
FOXO1 0.023 0.008 -9999 0 -0.12 2 2
T-DHT/AR -0.001 0.11 -9999 0 -0.18 119 119
MAP2K6 0.012 0.035 -9999 0 -0.12 35 35
BRM/BAF57 0.007 0.061 -9999 0 -0.14 71 71
MAP2K4 0.022 0.011 -9999 0 -0.12 3 3
SMARCA2 0.012 0.035 -9999 0 -0.12 36 36
PDE9A -0.092 0.31 -9999 0 -0.86 78 78
NCOA2 0.022 0.013 -9999 0 -0.12 4 4
CEBPA 0.022 0.013 -9999 0 -0.12 5 5
EHMT2 0.023 0.009 -9999 0 -0.12 2 2
cell proliferation -0.011 0.11 -9999 0 -0.25 59 59
NR0B1 0.013 0.037 -9999 0 -0.12 41 41
EGR1 -0.005 0.053 -9999 0 -0.12 98 98
RXRs/9cRA 0.034 0.032 -9999 0 -0.096 4 4
AR/RACK1/Src 0.01 0.073 -9999 0 -0.17 47 47
AR/GR -0.013 0.085 -9999 0 -0.17 104 104
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
PKN1 0.016 0.031 -9999 0 -0.12 27 27
RCHY1 0.018 0.022 -9999 0 -0.12 13 13
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
MAPK8 0.019 0.017 -9999 0 -0.073 9 9
T-DHT/AR/TIF2/CARM1 0.01 0.084 -9999 0 -0.16 71 71
SRC 0.015 0.027 -9999 0 -0.065 18 18
NR3C1 0.021 0.014 -9999 0 -0.12 5 5
KLK3 0.004 0.047 -9999 0 -10000 0 0
APPBP2 0.019 0.016 -9999 0 -0.12 6 6
TRIM24 0.023 0.014 -9999 0 -0.12 5 5
T-DHT/AR/TIP60 -0.014 0.071 -9999 0 -0.15 89 89
TMPRSS2 0.002 0.091 -9999 0 -0.68 4 4
RXRG 0.006 0.047 -9999 0 -0.12 68 68
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.021 0.017 -9999 0 -0.12 8 8
RXRB 0.023 0 -9999 0 -10000 0 0
CARM1 0.019 0.026 -9999 0 -0.12 19 19
NR2C2 0.023 0.006 -9999 0 -0.12 1 1
KLK2 0.019 0.073 -9999 0 -0.25 14 14
AR -0.01 0.075 -9999 0 -0.16 97 97
SENP1 0.022 0.011 -9999 0 -0.12 3 3
HSP90AA1 0.023 0.004 -9999 0 -10000 0 0
MDM2 0.018 0.02 -9999 0 -0.12 11 11
SRY 0.021 0.008 -9999 0 -0.11 2 2
GATA2 0.02 0.021 -9999 0 -0.12 13 13
MYST2 0.022 0.011 -9999 0 -0.12 3 3
HOXB13 0.02 0.027 -9999 0 -0.12 20 20
T-DHT/AR/RACK1/Src 0.006 0.074 -9999 0 -0.17 52 52
positive regulation of transcription 0.02 0.021 -9999 0 -0.12 13 13
DNAJA1 0.02 0.012 -9999 0 -0.13 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.09 -9999 0 -0.28 48 48
NCOA1 0.025 0.033 -9999 0 -0.16 16 16
SPDEF 0.012 0.041 -9999 0 -0.12 49 49
T-DHT/AR/TIF2 -0.007 0.088 -9999 0 -0.21 65 65
T-DHT/AR/Hsp90 -0.004 0.078 -9999 0 -0.15 82 82
GSK3B 0.022 0.011 -9999 0 -0.12 3 3
NR2C1 0.021 0.01 -9999 0 -0.12 2 2
mol:T-DHT 0.013 0.028 -9999 0 -0.044 60 60
SIRT1 0.023 0.003 -9999 0 -10000 0 0
ZMIZ2 0.02 0.013 -9999 0 -0.12 5 5
POU2F1 0.018 0.041 -9999 0 -0.077 77 77
T-DHT/AR/DAX-1 -0.007 0.077 -9999 0 -0.15 87 87
CREBBP 0.021 0.015 -9999 0 -0.12 6 6
SMARCE1 0.023 0.011 -9999 0 -0.12 3 3
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.025 0.057 -9999 0 -0.12 63 63
E-cadherin/beta catenin 0.018 0.053 -9999 0 -0.14 56 56
CTNNB1 0.022 0.007 -9999 0 -0.12 1 1
JUP 0.02 0.021 -9999 0 -0.12 12 12
CDH1 0.021 0.015 -9999 0 -0.12 6 6
Regulation of Telomerase

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
Telomerase catalytic core complex -0.045 0.18 -10000 0 -0.44 63 63
RAD9A 0.023 0 -10000 0 -10000 0 0
AP1 -0.03 0.086 -10000 0 -0.15 161 161
IFNAR2 0.018 0.02 -10000 0 -0.12 8 8
AKT1 0.012 0.041 -10000 0 -0.23 3 3
ER alpha/Oestrogen 0.001 0.046 -10000 0 -0.13 60 60
NFX1/SIN3/HDAC complex 0.01 0.089 -10000 0 -0.24 42 42
EGF 0.02 0.022 -10000 0 -0.12 13 13
SMG5 0.022 0.011 -10000 0 -0.12 3 3
SMG6 0.023 0.01 -10000 0 -0.12 3 3
SP3/HDAC2 0.027 0.031 -10000 0 -0.13 13 13
TERT/c-Abl -0.041 0.17 -10000 0 -0.42 63 63
SAP18 0.023 0.003 -10000 0 -10000 0 0
MRN complex 0.022 0.066 -10000 0 -0.14 67 67
WT1 0.019 0.016 -10000 0 -0.12 5 5
WRN 0.019 0.02 -10000 0 -0.12 10 10
SP1 0.02 0.015 -10000 0 -0.14 1 1
SP3 0.023 0.003 -10000 0 -10000 0 0
TERF2IP 0.023 0.009 -10000 0 -0.12 2 2
Telomerase/Nucleolin -0.032 0.17 -10000 0 -0.38 70 70
Mad/Max 0.032 0.015 -10000 0 -0.078 4 4
TERT -0.047 0.18 -10000 0 -0.45 63 63
CCND1 -0.13 0.36 -10000 0 -0.98 83 83
MAX 0.023 0.004 -10000 0 -10000 0 0
RBBP7 0.021 0.011 -10000 0 -0.12 3 3
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
TERF2 0.025 0.017 0.082 40 -0.11 1 41
PTGES3 0.014 0.035 -10000 0 -0.12 36 36
SIN3A 0.021 0.014 -10000 0 -0.12 5 5
Telomerase/911 0.017 0.095 -10000 0 -0.34 27 27
CDKN1B -0.015 0.096 -10000 0 -0.23 63 63
RAD1 0.02 0.021 -10000 0 -0.12 12 12
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.023 0.001 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.032 -10000 0 -0.09 30 30
UBE3A 0.023 0.004 -10000 0 -10000 0 0
JUN 0.014 0.032 -10000 0 -0.12 30 30
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.014 0.02 -10000 0 -0.15 7 7
FOS -0.005 0.052 -10000 0 -0.12 95 95
IFN-gamma/IRF1 -0.007 0.086 -10000 0 -0.16 114 114
PARP2 0.018 0.025 -10000 0 -0.12 18 18
BLM 0.015 0.031 -10000 0 -0.12 28 28
Telomerase 0.013 0.1 -10000 0 -0.39 24 24
IRF1 0.003 0.059 -10000 0 -0.12 80 80
ESR1 0.017 0.024 -10000 0 -0.12 15 15
KU/TER 0.018 0.058 -10000 0 -0.17 44 44
ATM/TRF2 0.02 0.05 -10000 0 -0.13 53 53
ubiquitin-dependent protein catabolic process 0.014 0.086 -10000 0 -0.25 34 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.014 0.088 -10000 0 -0.25 36 36
HDAC1 0.019 0.019 -10000 0 -0.12 10 10
HDAC2 0.017 0.024 -10000 0 -0.12 12 12
ATM -0.012 0.068 0.14 1 -0.26 40 41
SMAD3 0.019 0.019 -10000 0 -0.07 21 21
ABL1 0.022 0.007 -10000 0 -0.12 1 1
MXD1 0.021 0.017 -10000 0 -0.12 8 8
MRE11A 0.02 0.017 -10000 0 -0.12 8 8
HUS1 0.023 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.014 -10000 0 -0.12 5 5
TERT/NF kappa B1/14-3-3 -0.023 0.17 -10000 0 -0.4 53 53
NR2F2 0.022 0.015 -10000 0 -0.12 5 5
MAPK3 0.021 0.016 -10000 0 -0.09 8 8
MAPK1 0.02 0.017 -10000 0 -0.086 10 10
TGFB1/TGF beta receptor Type II 0.019 0.023 -10000 0 -0.12 14 14
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
HNRNPC 0.022 0.012 -10000 0 -0.12 4 4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.012 0.068 0.14 1 -0.26 40 41
NBN 0.021 0.013 -10000 0 -0.12 4 4
EGFR 0.015 0.03 -10000 0 -0.12 25 25
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.015 0.051 -10000 0 -0.11 74 74
MYC 0.015 0.027 -10000 0 -0.12 20 20
IL2 0.02 0.016 -10000 0 -0.12 3 3
KU 0.018 0.058 -10000 0 -0.17 44 44
RAD50 0.021 0.015 -10000 0 -0.12 6 6
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
TGFB1 0.019 0.023 -10000 0 -0.12 14 14
TRF2/BLM 0.024 0.043 -10000 0 -0.095 57 57
FRAP1 0.022 0.012 -10000 0 -0.12 4 4
KU/TERT -0.033 0.18 -10000 0 -0.41 67 67
SP1/HDAC2 0.025 0.037 -10000 0 -0.11 27 27
PINX1 0.021 0.017 -10000 0 -0.12 8 8
Telomerase/EST1A -0.028 0.16 -10000 0 -0.38 68 68
Smad3/Myc 0.016 0.046 -10000 0 -0.15 29 29
911 complex 0.043 0.024 -10000 0 -0.11 9 9
IFNG 0.009 0.047 -10000 0 -0.096 87 87
Telomerase/PinX1 -0.031 0.17 -10000 0 -0.38 69 69
Telomerase/AKT1/mTOR/p70S6K 0.004 0.11 -10000 0 -0.4 21 21
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Telomerase/EST1B -0.029 0.16 -10000 0 -0.38 69 69
response to DNA damage stimulus -0.004 0.031 0.052 1 -0.12 40 41
MRN complex/TRF2/Rap1 0.045 0.061 -10000 0 -0.11 57 57
TRF2/WRN 0.024 0.041 -10000 0 -0.1 49 49
Telomerase/hnRNP C1/C2 -0.028 0.16 -10000 0 -0.38 68 68
E2F1 0.02 0.018 -10000 0 -0.12 7 7
ZNFX1 0.019 0.021 -10000 0 -0.12 12 12
PIF1 0.023 0.006 -10000 0 -0.12 1 1
NCL 0.022 0.008 -10000 0 -0.12 1 1
DKC1 0.022 0.011 -10000 0 -0.12 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.011 0.041 -9999 0 -0.12 50 50
CDC42/GTP 0.007 0.067 -9999 0 -0.21 23 23
PLCG1 -0.002 0.066 -9999 0 -0.14 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.022 0.01 -9999 0 -0.12 3 3
GNAI3 0.021 0.008 -9999 0 -0.12 1 1
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
cell migration 0.007 0.066 -9999 0 -0.21 23 23
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.001 0.066 -9999 0 -0.14 89 89
MAPK1 -0.001 0.066 -9999 0 -0.14 89 89
S1P/S1P5/Gi -0.003 0.069 -9999 0 -0.15 89 89
GNAI1 0.012 0.035 -9999 0 -0.12 36 36
CDC42/GDP 0.016 0.014 -9999 0 -0.15 4 4
S1P/S1P5/G12 0.016 0.006 -9999 0 -0.12 1 1
RHOA 0.021 0.02 -9999 0 -0.1 14 14
S1P/S1P4/Gi -0.003 0.069 -9999 0 -0.15 89 89
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.012 -9999 0 -0.12 4 4
S1P/S1P4/G12/G13 0.026 0.021 -9999 0 -0.095 16 16
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
CDC42 0.023 0.002 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.019 0.02 -9999 0 -0.055 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.11 -9999 0 -0.26 55 55
ERC1 0.016 0.029 -9999 0 -0.12 24 24
RIP2/NOD2 0.013 0.053 -9999 0 -0.11 84 84
NFKBIA 0.001 0.087 -9999 0 -0.27 43 43
BIRC2 0.021 0.013 -9999 0 -0.12 4 4
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
RIPK2 0.013 0.034 -9999 0 -0.12 34 34
IKBKG 0.012 0.09 -9999 0 -0.32 29 29
IKK complex/A20 0.037 0.095 -9999 0 -0.29 30 30
NEMO/A20/RIP2 0.013 0.034 -9999 0 -0.12 34 34
XPO1 0.022 0.01 -9999 0 -0.12 2 2
NEMO/ATM 0.017 0.099 -9999 0 -0.3 39 39
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.023 0.002 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.025 0.03 -9999 0 -0.12 24 24
IKK complex/ELKS 0.02 0.093 -9999 0 -0.3 30 30
BCL10/MALT1/TRAF6 0.035 0.041 -9999 0 -0.12 31 31
NOD2 0.023 0.006 -9999 0 -0.12 1 1
NFKB1 0.017 0.023 -9999 0 -0.063 32 32
RELA 0.019 0.022 -9999 0 -0.061 30 30
MALT1 0.018 0.026 -9999 0 -0.12 19 19
cIAP1/UbcH5C 0.021 0.047 -9999 0 -0.14 45 45
ATM 0.018 0.022 -9999 0 -0.12 13 13
TNF/TNFR1A 0.025 0.036 -9999 0 -0.11 37 37
TRAF6 0.022 0.009 -9999 0 -0.12 2 2
PRKCA 0.011 0.038 -9999 0 -0.12 42 42
CHUK 0.021 0.013 -9999 0 -0.12 4 4
UBE2D3 0.023 0.001 -9999 0 -10000 0 0
TNF 0.02 0.02 -9999 0 -0.12 11 11
NF kappa B1 p50/RelA 0.029 0.075 -9999 0 -0.15 76 76
BCL10 0.023 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.086 -9999 0 -0.27 43 43
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.02 -9999 0 -0.056 28 28
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
IKK complex 0.029 0.097 -9999 0 -0.29 35 35
CYLD 0.023 0.007 -9999 0 -0.12 1 1
IKK complex/PKC alpha 0.024 0.1 -9999 0 -0.29 34 34
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.023 0.043 0.14 29 -10000 0 29
KIRREL 0.018 0.027 -10000 0 -0.12 20 20
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.023 0.043 -10000 0 -0.14 29 29
PLCG1 0.018 0.025 -10000 0 -0.12 18 18
ARRB2 0.022 0.013 -10000 0 -0.12 5 5
WASL 0.023 0.008 -10000 0 -0.12 2 2
Nephrin/NEPH1/podocin/CD2AP 0.036 0.056 -10000 0 -0.11 66 66
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.053 -10000 0 -0.14 35 35
FYN 0.014 0.034 -10000 0 -0.11 27 27
mol:Ca2+ 0.04 0.048 -10000 0 -0.11 40 40
mol:DAG 0.041 0.048 -10000 0 -0.11 40 40
NPHS2 0.022 0.014 -10000 0 -0.081 7 7
mol:IP3 0.041 0.048 -10000 0 -0.11 40 40
regulation of endocytosis 0.032 0.045 -10000 0 -0.1 29 29
Nephrin/NEPH1/podocin/Cholesterol 0.034 0.035 -10000 0 -0.099 28 28
establishment of cell polarity 0.023 0.043 -10000 0 -0.14 29 29
Nephrin/NEPH1/podocin/NCK1-2 0.049 0.054 -10000 0 -0.1 39 39
Nephrin/NEPH1/beta Arrestin2 0.033 0.046 -10000 0 -0.1 29 29
NPHS1 0.021 0.02 -10000 0 -0.1 12 12
Nephrin/NEPH1/podocin 0.026 0.045 -10000 0 -0.11 29 29
TJP1 0.021 0.01 -10000 0 -0.12 2 2
NCK1 0.02 0.019 -10000 0 -0.12 9 9
NCK2 0.023 0.006 -10000 0 -0.12 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.042 0.049 -10000 0 -0.11 40 40
CD2AP 0.02 0.017 -10000 0 -0.12 7 7
Nephrin/NEPH1/podocin/GRB2 0.046 0.042 -10000 0 -0.11 30 30
GRB2 0.023 0.006 -10000 0 -0.12 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.019 0.029 -10000 0 -0.089 26 26
cytoskeleton organization 0.022 0.047 -10000 0 -0.13 31 31
Nephrin/NEPH1 0.021 0.029 -10000 0 -0.091 29 29
Nephrin/NEPH1/ZO-1 0.027 0.055 -10000 0 -0.13 57 57
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.021 0.014 -10000 0 -0.12 5 5
VLDLR 0.01 0.038 -10000 0 -0.12 42 42
LRPAP1 0.018 0.023 -10000 0 -0.12 15 15
NUDC 0.022 0.011 -10000 0 -0.12 3 3
RELN/LRP8 0.015 0.058 -10000 0 -0.12 53 53
CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
KATNA1 0.02 0.019 -10000 0 -0.12 10 10
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.006 0.047 -10000 0 -0.11 53 53
IQGAP1/CaM 0.016 0.054 -10000 0 -0.15 53 53
DAB1 0.023 0.01 -10000 0 -0.12 3 3
IQGAP1 0.02 0.017 -10000 0 -0.12 7 7
PLA2G7 0.005 0.044 -10000 0 -0.12 62 62
CALM1 0.022 0.014 -10000 0 -0.12 5 5
DYNLT1 0.019 0.022 -10000 0 -0.12 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.015 0.054 -10000 0 -0.12 72 72
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.009 -10000 0 -0.12 2 2
CDK5R1 0.023 0.006 -10000 0 -0.12 1 1
LIS1/Poliovirus Protein 3A 0.013 0.023 -10000 0 -0.12 11 11
CDK5R2 0.023 0.01 -10000 0 -0.12 3 3
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.06 -10000 0 -0.12 71 71
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
NDEL1/14-3-3 E 0.022 0.055 -10000 0 -0.16 19 19
MAP1B -0.014 0.059 0.2 3 -0.2 46 49
RAC1 0.014 0.048 -10000 0 -0.36 7 7
p35/CDK5 0.008 0.053 -10000 0 -0.15 21 21
RELN 0 0.053 -10000 0 -0.12 91 91
PAFAH/LIS1 0.015 0.038 -10000 0 -0.13 14 14
LIS1/CLIP170 0.029 0.027 -10000 0 -0.13 11 11
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.016 0.063 -10000 0 -0.19 20 20
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.014 0.098 -10000 0 -0.21 94 94
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.011 0.052 -10000 0 -0.15 21 21
LIS1/IQGAP1 0.025 0.034 -10000 0 -0.16 13 13
RHOA 0.014 0.047 -10000 0 -0.3 9 9
PAFAH1B1 0.02 0.015 -10000 0 -0.07 15 15
PAFAH1B3 0.014 0.033 -10000 0 -0.12 31 31
PAFAH1B2 0.022 0.012 -10000 0 -0.12 4 4
MAP1B/LIS1/Dynein heavy chain 0.009 0.053 0.13 3 -0.13 50 53
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.064 -10000 0 -0.18 18 18
LRP8 0.02 0.021 -10000 0 -0.12 12 12
NDEL1/Katanin 60 0.02 0.056 -10000 0 -0.16 22 22
P39/CDK5 0.008 0.053 -10000 0 -0.14 21 21
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.028 -10000 0 -0.13 11 11
CDK5 0.004 0.043 -10000 0 -0.098 58 58
PPP2R5D 0.022 0.013 -10000 0 -0.12 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.023 -10000 0 -0.11 11 11
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
RELN/VLDLR/DAB1/LIS1 0.021 0.059 -10000 0 -0.11 27 27
RELN/VLDLR 0.008 0.07 -10000 0 -0.11 121 121
CDC42 0.015 0.044 -10000 0 -0.35 6 6
Arf6 signaling events

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
CENTA1/KIF3B 0.013 0.017 -9999 0 -0.077 18 18
ARNO/beta Arrestin1-2 0.029 0.019 -9999 0 -0.076 11 11
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EPHA2 0.02 0.021 -9999 0 -0.12 13 13
USP6 0.023 0.006 -9999 0 -0.12 1 1
IQSEC1 0.023 0.006 -9999 0 -0.12 1 1
EGFR/EGFR/EGF/EGF 0.016 0.05 -9999 0 -0.11 74 74
ARRB2 0.017 0.018 -9999 0 -0.2 3 3
mol:GTP 0.003 0.006 -9999 0 -10000 0 0
ARRB1 0.02 0.022 -9999 0 -0.12 13 13
FBXO8 0.022 0.011 -9999 0 -0.12 3 3
TSHR 0.013 0.037 -9999 0 -0.12 41 41
EGF 0.02 0.021 -9999 0 -0.12 13 13
somatostatin receptor activity 0 0 -9999 0 0 26 26
ARAP2 0 0 -9999 0 0 25 25
mol:GDP 0.015 0.045 -9999 0 -0.16 25 25
mol:PI-3-4-5-P3 0 0 -9999 0 0 26 26
ITGA2B 0.023 0.006 -9999 0 -0.12 1 1
ARF6 0.023 0.003 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.063 -9999 0 -0.11 77 77
ADAP1 0 0 -9999 0 0 25 25
KIF13B 0.02 0.022 -9999 0 -0.12 13 13
HGF/MET -0.017 0.074 -9999 0 -0.11 198 198
PXN 0.022 0.013 -9999 0 -0.12 5 5
ARF6/GTP 0.023 0.057 -9999 0 -0.2 26 26
EGFR/EGFR/EGF/EGF/ARFGEP100 0.031 0.045 -9999 0 -0.11 40 40
ADRB2 0.023 0.006 -9999 0 -0.12 1 1
receptor agonist activity 0 0 -9999 0 0 26 26
actin filament binding 0 0 -9999 0 0 26 26
SRC 0.023 0.008 -9999 0 -0.12 2 2
ITGB3 0.005 0.046 -9999 0 -0.12 67 67
GNAQ 0.021 0.015 -9999 0 -0.12 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 26 26
ARF6/GDP 0.021 0.05 -9999 0 -0.26 10 10
ARF6/GDP/GULP/ACAP1 0.018 0.06 -9999 0 -0.16 28 28
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.049 -9999 0 -0.096 39 39
ACAP1 0 0 -9999 0 0 12 12
ACAP2 0 0 -9999 0 0 25 25
LHCGR/beta Arrestin2 0.023 0.016 -9999 0 -0.14 3 3
EFNA1 0.014 0.031 -9999 0 -0.12 28 28
HGF 0.02 0.022 -9999 0 -0.12 14 14
CYTH3 0 0 -9999 0 -0.001 26 26
CYTH2 0 0.001 -9999 0 -0.004 26 26
NCK1 0.02 0.019 -9999 0 -0.12 9 9
fibronectin binding 0 0 -9999 0 0 27 27
endosomal lumen acidification 0 0 -9999 0 0 16 16
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.005 0.045 -9999 0 -0.12 63 63
GNAQ/ARNO 0.015 0.007 -9999 0 -0.046 6 6
mol:Phosphatidic acid 0 0 -9999 0 0 25 25
PIP3-E 0.018 0.028 -9999 0 -0.12 22 22
MET 0.001 0.047 -9999 0 -0.12 71 71
GNA14 0.021 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GIT1 0.022 0.013 -9999 0 -0.12 5 5
mol:PI-4-5-P2 0 0 -9999 0 -0.001 26 26
GNA11 0.022 0.013 -9999 0 -0.12 5 5
LHCGR 0.022 0.013 -9999 0 -0.12 5 5
AGTR1 0.022 0.012 -9999 0 -0.12 4 4
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.016 -9999 0 -0.14 3 3
IPCEF1/ARNO 0.026 0.038 -9999 0 -0.082 42 42
alphaIIb/beta3 Integrin 0.011 0.053 -9999 0 -0.14 38 38
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.044 -10000 0 -0.11 29 29
fibroblast growth factor receptor signaling pathway 0.029 0.044 -10000 0 -0.11 29 29
LAMA1 0 0.052 -10000 0 -0.12 90 90
PRNP 0.021 0.014 -10000 0 -0.12 5 5
GPC1/SLIT2 -0.01 0.07 -10000 0 -0.11 177 177
SMAD2 0.024 0.028 -10000 0 -0.1 18 18
GPC1/PrPc/Cu2+ 0.021 0.037 -10000 0 -0.1 48 48
GPC1/Laminin alpha1 0.015 0.043 -10000 0 -0.075 102 102
TDGF1 0.022 0.015 -10000 0 -0.12 6 6
CRIPTO/GPC1 0.032 0.017 -10000 0 -0.075 14 14
APP/GPC1 0.023 0.043 -10000 0 -0.13 42 42
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.024 0.016 -10000 0 -0.11 1 1
FLT1 0.022 0.014 -10000 0 -0.12 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.032 -10000 0 -0.11 18 18
SERPINC1 0.023 0.008 -10000 0 -0.12 2 2
FYN 0.019 0.024 -10000 0 -0.11 1 1
FGR 0.026 0.013 -10000 0 -0.11 1 1
positive regulation of MAPKKK cascade 0.017 0.051 -10000 0 -0.18 16 16
SLIT2 0.001 0.047 -10000 0 -0.12 72 72
GPC1/NRG 0.032 0.019 -10000 0 -0.08 15 15
NRG1 0.021 0.017 -10000 0 -0.12 8 8
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.046 -10000 0 -0.12 42 42
LYN 0.024 0.015 -10000 0 -0.11 1 1
mol:Spermine 0.011 0.01 -10000 0 -0.076 7 7
cell growth 0.029 0.044 -10000 0 -0.11 29 29
BMP signaling pathway -0.021 0.016 0.12 7 -10000 0 7
SRC 0.026 0.014 -10000 0 -0.11 2 2
TGFBR1 0.022 0.01 -10000 0 -0.12 3 3
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.011 0.04 -10000 0 -0.12 48 48
GPC1 0.021 0.016 -10000 0 -0.12 7 7
TGFBR1 (dimer) 0.022 0.01 -10000 0 -0.12 3 3
VEGFA 0.019 0.02 -10000 0 -0.12 11 11
BLK 0.026 0.015 -10000 0 -0.11 2 2
HCK 0.024 0.019 -10000 0 -0.17 1 1
FGF2 0.023 0.008 -10000 0 -0.12 2 2
FGFR1 0.008 0.043 -10000 0 -0.12 56 56
VEGFR1 homodimer 0.022 0.014 -10000 0 -0.12 5 5
TGFBR2 0.02 0.02 -10000 0 -0.12 11 11
cell death 0.023 0.043 -10000 0 -0.13 42 42
ATIII/GPC1 0.033 0.015 -10000 0 -0.077 10 10
PLA2G2A/GPC1 0.024 0.033 -10000 0 -0.075 57 57
LCK 0.026 0.016 -10000 0 -0.17 1 1
neuron differentiation 0.031 0.019 -10000 0 -0.079 15 15
PrPc/Cu2+ 0.006 0.04 -10000 0 -0.14 40 40
APP 0.022 0.008 -10000 0 -0.12 1 1
TGFBR2 (dimer) 0.02 0.02 -10000 0 -0.12 11 11
Glucocorticoid receptor regulatory network

Figure S85.  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 S85.  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 -0.011 0.059 -10000 0 -0.7 2 2
SMARCC2 0.022 0.012 -10000 0 -0.12 4 4
SMARCC1 0.023 0.004 -10000 0 -10000 0 0
TBX21 0.043 0.046 -10000 0 -0.31 1 1
SUMO2 0.021 0.005 -10000 0 -10000 0 0
STAT1 (dimer) -0.007 0.079 -10000 0 -0.17 92 92
FKBP4 0.02 0.019 -10000 0 -0.12 10 10
FKBP5 0.006 0.042 -10000 0 -0.12 55 55
GR alpha/HSP90/FKBP51/HSP90 -0.013 0.081 0.18 1 -0.2 47 48
PRL 0.045 0.057 -10000 0 -0.5 1 1
cortisol/GR alpha (dimer)/TIF2 -0.021 0.11 0.38 3 -0.33 4 7
RELA -0.021 0.076 -10000 0 -0.15 120 120
FGG -0.016 0.1 0.31 2 -0.32 3 5
GR beta/TIF2 -0.006 0.07 0.2 2 -0.2 25 27
IFNG -0.003 0.11 -10000 0 -0.45 2 2
apoptosis -0.053 0.17 -10000 0 -0.4 78 78
CREB1 0.033 0.008 -10000 0 -10000 0 0
histone acetylation 0.025 0.083 0.27 8 -0.26 25 33
BGLAP 0.04 0.083 -10000 0 -0.87 3 3
GR/PKAc 0.028 0.062 0.2 2 -0.14 24 26
NF kappa B1 p50/RelA -0.045 0.15 -10000 0 -0.27 142 142
SMARCD1 0.021 0.018 -10000 0 -0.12 9 9
MDM2 -0.003 0.045 -10000 0 -0.22 8 8
GATA3 0.037 0.022 -10000 0 -0.11 11 11
AKT1 0.015 0.021 0.15 2 -0.13 10 12
CSF2 0.029 0.057 -10000 0 -10000 0 0
GSK3B 0.02 0.012 -10000 0 -0.13 3 3
NR1I3 -0.039 0.15 -10000 0 -0.43 18 18
CSN2 -0.015 0.092 0.26 4 -0.29 3 7
BRG1/BAF155/BAF170/BAF60A 0.042 0.051 -10000 0 -0.11 45 45
NFATC1 0.033 0.012 -10000 0 -0.11 3 3
POU2F1 0.031 0.008 -10000 0 -0.11 1 1
CDKN1A -0.042 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.004 -10000 0 -10000 0 0
SFN 0.014 0.031 -10000 0 -0.12 28 28
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.007 0.086 0.18 1 -0.18 62 63
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.28 -10000 0 -0.72 95 95
JUN 0.021 0.088 -10000 0 -0.28 7 7
IL4 0.046 0.046 -10000 0 -0.3 1 1
CDK5R1 0.022 0.006 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
cortisol/GR alpha (monomer)/AP-1 -0.041 0.08 0.19 15 -0.2 56 71
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.006 0.079 0.18 1 -0.17 44 45
cortisol/GR alpha (monomer) -0.04 0.12 0.42 3 -0.38 3 6
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.014 0.079 -10000 0 -0.18 69 69
AP-1/NFAT1-c-4 -0.011 0.15 -10000 0 -0.39 25 25
AFP 0.016 0.083 -10000 0 -0.56 1 1
SUV420H1 0.021 0.015 -10000 0 -0.12 6 6
IRF1 -0.094 0.23 -10000 0 -0.6 87 87
TP53 0.026 0.034 -10000 0 -10000 0 0
PPP5C 0.022 0.015 -10000 0 -0.12 6 6
KRT17 -0.011 0.15 -10000 0 -0.82 9 9
KRT14 0 0.18 0.48 8 -1.1 12 20
TBP 0.03 0.03 -10000 0 -0.22 6 6
CREBBP 0.022 0.047 0.29 12 -0.13 5 17
HDAC1 0.013 0.019 -10000 0 -0.13 10 10
HDAC2 0.018 0.021 -10000 0 -0.12 12 12
AP-1 -0.012 0.15 -10000 0 -0.4 25 25
MAPK14 0.02 0.008 -10000 0 -0.12 1 1
MAPK10 0.011 0.036 -10000 0 -0.12 38 38
MAPK11 0.021 0.004 -10000 0 -10000 0 0
KRT5 -0.069 0.26 -10000 0 -0.88 46 46
interleukin-1 receptor activity -0.002 0.001 -10000 0 -10000 0 0
NCOA1 0.024 0.01 -10000 0 -0.079 4 4
STAT1 -0.007 0.079 -10000 0 -0.17 92 92
CGA 0.043 0.057 -10000 0 -0.4 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.048 0.11 0.28 5 -0.34 36 41
MAPK3 0.019 0.015 -10000 0 -0.12 5 5
MAPK1 0.019 0.017 -10000 0 -0.12 7 7
ICAM1 -0.13 0.32 -10000 0 -0.79 103 103
NFKB1 -0.032 0.099 -10000 0 -0.18 136 136
MAPK8 0.033 0.074 -10000 0 -0.24 7 7
MAPK9 0.019 0.012 -10000 0 -0.12 3 3
cortisol/GR alpha (dimer) -0.056 0.17 -10000 0 -0.41 79 79
BAX -0.04 0.12 -10000 0 -10000 0 0
POMC 0.03 0.081 -10000 0 -10000 0 0
EP300 0.022 0.045 0.29 12 -0.13 1 13
cortisol/GR alpha (dimer)/p53 -0.046 0.12 0.36 1 -0.36 5 6
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.057 0.26 15 -0.2 7 22
SGK1 -0.001 0.1 0.33 12 -0.31 34 46
IL13 0.022 0.088 -10000 0 -0.52 1 1
IL6 -0.028 0.15 -10000 0 -0.65 14 14
PRKACG 0.023 0.008 -10000 0 -0.12 2 2
IL5 0.025 0.088 -10000 0 -10000 0 0
IL2 0.005 0.11 -10000 0 -0.46 1 1
CDK5 0.013 0.032 -10000 0 -0.12 30 30
PRKACB 0.02 0.02 -10000 0 -0.12 11 11
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
IL8 -0.06 0.23 -10000 0 -0.79 42 42
CDK5R1/CDK5 0.018 0.043 -10000 0 -0.13 32 32
NF kappa B1 p50/RelA/PKAc -0.003 0.12 -10000 0 -0.19 117 117
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.33 2 -0.31 4 6
SMARCA4 0.016 0.031 -10000 0 -0.12 27 27
chromatin remodeling -0.009 0.091 0.26 1 -0.32 13 14
NF kappa B1 p50/RelA/Cbp -0.022 0.14 0.34 7 -0.25 85 92
JUN (dimer) 0.021 0.088 -10000 0 -0.28 7 7
YWHAH 0.021 0.015 -10000 0 -0.12 6 6
VIPR1 0.043 0.044 -10000 0 -10000 0 0
NR3C1 -0.015 0.08 0.26 2 -0.33 10 12
NR4A1 0.01 0.048 -10000 0 -10000 0 0
TIF2/SUV420H1 0.02 0.048 -10000 0 -0.13 50 50
MAPKKK cascade -0.053 0.17 -10000 0 -0.4 78 78
cortisol/GR alpha (dimer)/Src-1 -0.014 0.11 0.39 3 -0.32 3 6
PBX1 0.029 0.014 -10000 0 -0.11 4 4
POU1F1 0.03 0.014 -10000 0 -0.12 4 4
SELE -0.007 0.11 -10000 0 -0.32 11 11
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.009 0.091 0.27 1 -0.32 13 14
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.33 2 -0.31 4 6
mol:cortisol -0.028 0.064 0.22 3 -10000 0 3
MMP1 -0.042 0.17 -10000 0 -0.96 15 15
Neurotrophic factor-mediated Trk receptor signaling

Figure S86.  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 S86.  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 0.023 0.009 -10000 0 -0.12 2 2
RAS family/GTP/Tiam1 0.002 0.065 -10000 0 -0.16 63 63
NT3 (dimer)/TRKC 0.008 0.05 -10000 0 -0.15 18 18
NT3 (dimer)/TRKB 0.023 0.046 -10000 0 -0.12 19 19
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.087 -10000 0 -0.17 94 94
RAPGEF1 0.023 0 -10000 0 -10000 0 0
BDNF 0.023 0.01 -10000 0 -0.12 3 3
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
DYNLT1 0.019 0.022 -10000 0 -0.12 13 13
NTRK1 0.023 0.006 -10000 0 -0.12 1 1
NTRK2 0.019 0.025 -10000 0 -0.12 18 18
NTRK3 0.015 0.033 -10000 0 -0.12 31 31
NT-4/5 (dimer)/TRKB 0.027 0.02 -10000 0 -0.063 26 26
neuron apoptosis -0.043 0.037 -10000 0 -10000 0 0
SHC 2-3/Grb2 0.045 0.039 -10000 0 -10000 0 0
SHC1 0.023 0.001 -10000 0 -10000 0 0
SHC2 0.027 0.034 -10000 0 -10000 0 0
SHC3 0.027 0.034 -10000 0 -10000 0 0
STAT3 (dimer) -0.019 0.1 -10000 0 -0.25 86 86
NT3 (dimer)/TRKA 0.026 0.043 -10000 0 -0.12 11 11
RIN/GDP 0.03 0.062 -10000 0 -0.18 32 32
GIPC1 0.019 0.023 -10000 0 -0.12 15 15
KRAS 0.014 0.034 -10000 0 -0.12 33 33
DNAJA3 0.009 0.042 0.16 14 -0.14 8 22
RIN/GTP 0.017 0.007 -10000 0 -0.076 3 3
CCND1 -0.057 0.18 -10000 0 -0.48 85 85
MAGED1 0.02 0.019 -10000 0 -0.12 10 10
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
RICS 0.017 0.027 -10000 0 -0.12 20 20
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.035 0.042 -10000 0 -0.12 32 32
GRB2 0.023 0.006 -10000 0 -0.12 1 1
NGF (dimer)/TRKA/MATK 0.031 0.01 -10000 0 -0.069 5 5
TRKA/NEDD4-2 0.022 0.042 -10000 0 -0.14 28 28
ELMO1 0.01 0.04 -10000 0 -0.12 48 48
RhoG/GTP/ELMO1/DOCK1 0.009 0.049 -10000 0 -0.12 56 56
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.023 0.006 -10000 0 -0.12 1 1
DOCK1 0.019 0.02 -10000 0 -0.12 11 11
GAB2 0.007 0.041 -10000 0 -0.12 52 52
RIT2 0.023 0.01 -10000 0 -0.12 3 3
RIT1 0.021 0.014 -10000 0 -0.12 5 5
FRS2 0.019 0.023 -10000 0 -0.12 15 15
DNM1 0.02 0.02 -10000 0 -0.12 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.016 -10000 0 -0.12 7 7
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.006 0.044 0.13 3 -0.14 12 15
mol:GDP 0.026 0.083 -10000 0 -0.26 32 32
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.004 0.039 -10000 0 -0.097 68 68
RIT1/GDP 0.029 0.064 -10000 0 -0.19 29 29
TIAM1 0.015 0.032 -10000 0 -0.12 29 29
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
BDNF (dimer)/TRKB 0.043 0.021 -10000 0 -0.11 3 3
KIDINS220/CRKL/C3G 0.034 0.01 -10000 0 -0.093 3 3
SHC/RasGAP 0.025 0.039 -10000 0 -0.14 29 29
FRS2 family/SHP2 0.035 0.041 -10000 0 -0.12 33 33
SHC/GRB2/SOS1/GAB1 0.042 0.048 -10000 0 -0.1 44 44
RIT1/GTP 0.012 0.028 -10000 0 -0.13 20 20
NT3 (dimer) -0.003 0.055 -10000 0 -0.12 101 101
RAP1/GDP 0.017 0.056 -10000 0 -0.17 31 31
KIDINS220/CRKL 0.023 0.009 -10000 0 -0.12 2 2
BDNF (dimer) 0.022 0.01 -10000 0 -0.12 3 3
ubiquitin-dependent protein catabolic process 0.021 0.035 -10000 0 -0.11 28 28
Schwann cell development -0.004 0.009 -10000 0 -0.049 3 3
EHD4 0.023 0.001 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.041 0.051 -10000 0 -0.11 41 41
FRS2 family/SHP2/CRK family/C3G/GAB2 0.013 0.064 -10000 0 -0.13 83 83
RAP1B 0.019 0.019 -10000 0 -0.12 10 10
RAP1A 0.021 0.011 -10000 0 -0.12 3 3
CDC42/GTP 0.031 0.04 -10000 0 -0.15 4 4
ABL1 0.022 0.007 -10000 0 -0.12 1 1
SH2B family/GRB2/SOS1 0.021 0.046 -10000 0 -0.12 52 52
Rap1/GTP 0.023 0.081 -10000 0 -0.25 35 35
STAT3 -0.019 0.1 -10000 0 -0.25 86 86
axon guidance 0.021 0.034 -10000 0 -0.14 4 4
MAPK3 0.024 0.013 -10000 0 -0.21 1 1
MAPK1 0.024 0.014 -10000 0 -0.21 1 1
CDC42/GDP 0.03 0.062 -10000 0 -0.18 29 29
NTF3 -0.003 0.055 -10000 0 -0.12 101 101
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.03 0.012 -10000 0 -0.073 7 7
PI3K 0.007 0.065 -10000 0 -0.13 98 98
FRS3 0.023 0.008 -10000 0 -0.12 2 2
FAIM 0.022 0.012 -10000 0 -0.12 4 4
GAB1 0.02 0.022 -10000 0 -0.12 13 13
RASGRF1 0.01 0.042 0.16 14 -0.14 8 22
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MCF2L 0.008 0.038 -10000 0 -0.12 18 18
RGS19 0.023 0 -10000 0 -10000 0 0
CDC42 0.023 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.11 -10000 0 -0.31 49 49
Rac1/GDP 0.03 0.062 -10000 0 -0.18 29 29
NGF (dimer)/TRKA/GRIT 0.021 0.035 -10000 0 -0.12 28 28
neuron projection morphogenesis -0.042 0.18 -10000 0 -0.82 22 22
NGF (dimer)/TRKA/NEDD4-2 0.021 0.035 -10000 0 -0.12 28 28
MAP2K1 0.021 0.037 -10000 0 -0.091 44 44
NGFR 0.021 0.018 -10000 0 -0.12 9 9
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.047 -10000 0 -0.14 42 42
RAS family/GTP/PI3K -0.003 0.084 -10000 0 -0.18 88 88
FRS2 family/SHP2/GRB2/SOS1 0.046 0.059 -10000 0 -0.11 54 54
NRAS 0.022 0.011 -10000 0 -0.12 3 3
GRB2/SOS1 0.021 0.046 -10000 0 -0.12 52 52
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0 -10000 0 -10000 0 0
MAPKKK cascade 0.027 0.033 -10000 0 -0.4 2 2
RASA1 0.021 0.011 -10000 0 -0.12 3 3
TRKA/c-Abl 0.029 0.031 -10000 0 -0.14 18 18
SQSTM1 0.021 0.015 -10000 0 -0.12 6 6
BDNF (dimer)/TRKB/GIPC 0.041 0.048 -10000 0 -0.1 42 42
NGF (dimer)/TRKA/p62/Atypical PKCs 0.033 0.052 -10000 0 -0.097 66 66
MATK 0.022 0.013 -10000 0 -0.12 5 5
NEDD4L 0.017 0.027 -10000 0 -0.12 21 21
RAS family/GDP -0.013 0.034 -10000 0 -0.13 34 34
NGF (dimer)/TRKA 0.003 0.036 -10000 0 -0.15 8 8
Rac1/GTP -0.016 0.041 -10000 0 -0.13 41 41
FRS2 family/SHP2/CRK family 0.055 0.042 -10000 0 -0.086 37 37
Coregulation of Androgen receptor activity

Figure S87.  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 S87.  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 0.014 0.035 -9999 0 -0.12 35 35
SVIL 0.016 0.031 -9999 0 -0.12 27 27
ZNF318 0.019 0.013 -9999 0 -0.12 5 5
JMJD2C 0.029 0.016 -9999 0 -0.12 6 6
T-DHT/AR/Ubc9 0.017 0.058 -9999 0 -0.11 87 87
CARM1 0.019 0.026 -9999 0 -0.12 19 19
PRDX1 0.022 0.004 -9999 0 -10000 0 0
PELP1 0.022 0.008 -9999 0 -0.12 2 2
CTNNB1 0.023 0.008 -9999 0 -0.12 1 1
AKT1 0.02 0.019 -9999 0 -0.12 10 10
PTK2B 0.024 0.009 -9999 0 -0.12 2 2
MED1 0.02 0.014 -9999 0 -0.12 5 5
MAK 0.008 0.04 -9999 0 -0.12 48 48
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.022 0.018 -9999 0 -0.12 9 9
GSN 0.023 0.011 -9999 0 -0.12 3 3
NCOA2 0.022 0.013 -9999 0 -0.12 4 4
NCOA6 0.024 0.014 -9999 0 -0.12 5 5
DNA-PK 0.023 0.06 -9999 0 -0.14 61 61
NCOA4 0.023 0.004 -9999 0 -10000 0 0
PIAS3 0.021 0.022 -9999 0 -0.12 14 14
cell proliferation 0.004 0.045 -9999 0 -0.49 2 2
XRCC5 0.021 0.01 -9999 0 -0.12 2 2
UBE3A 0.025 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.015 0.059 -9999 0 -0.11 83 83
FHL2 0.017 0.078 -9999 0 -0.67 5 5
RANBP9 0.023 0.014 -9999 0 -0.12 5 5
JMJD1A 0.033 0.024 -9999 0 -0.11 6 6
CDK6 0.008 0.039 -9999 0 -0.12 47 47
TGFB1I1 0.024 0.012 -9999 0 -0.12 4 4
T-DHT/AR/CyclinD1 -0.01 0.078 -9999 0 -0.13 143 143
XRCC6 0.022 0.004 -9999 0 -10000 0 0
T-DHT/AR 0.026 0.077 -9999 0 -0.18 21 21
CTDSP1 0.023 0.011 -9999 0 -0.12 3 3
CTDSP2 0.02 0.009 -9999 0 -0.12 2 2
BRCA1 0.017 0.029 -9999 0 -0.12 24 24
TCF4 0.019 0.017 -9999 0 -0.12 8 8
CDKN2A 0.014 0.021 -9999 0 -0.12 10 10
SRF 0.024 0.03 -9999 0 -0.12 24 24
NKX3-1 0.013 0.086 -9999 0 -0.29 34 34
KLK3 0.014 0.038 -9999 0 -10000 0 0
TMF1 0.022 0.012 -9999 0 -0.12 3 3
HNRNPA1 0.022 0.002 -9999 0 -10000 0 0
AOF2 0.024 0.009 -9999 0 -0.12 2 2
APPL1 0.019 0.014 -9999 0 -0.072 12 12
T-DHT/AR/Caspase 8 0.012 0.061 -9999 0 -0.11 93 93
AR 0.015 0.038 -9999 0 -0.11 44 44
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.021 0.012 -9999 0 -0.12 4 4
PAWR 0.023 0.009 -9999 0 -0.12 2 2
PRKDC 0.02 0.016 -9999 0 -0.12 7 7
PA2G4 0.021 0.009 -9999 0 -0.12 2 2
UBE2I 0.023 0.001 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.014 0.055 -9999 0 -0.1 84 84
RPS6KA3 0.019 0.024 -9999 0 -0.12 15 15
T-DHT/AR/ARA70 0.014 0.062 -9999 0 -0.11 95 95
LATS2 0.022 0.006 -9999 0 -0.12 1 1
T-DHT/AR/PRX1 0.011 0.056 -9999 0 -0.099 97 97
Cyclin D3/CDK11 p58 0.014 0.019 -9999 0 -0.1 14 14
VAV3 0.011 0.037 -9999 0 -0.12 41 41
KLK2 0.016 0.072 -9999 0 -0.29 23 23
CASP8 0.022 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.022 0.065 -9999 0 -0.099 105 105
TMPRSS2 0.005 0.098 -9999 0 -0.3 35 35
CCND1 0.007 0.042 -9999 0 -0.12 54 54
PIAS1 0.025 0.009 -9999 0 -0.12 2 2
mol:T-DHT 0.005 0.007 -9999 0 -0.055 2 2
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.027 0.002 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.008 0.078 -9999 0 -0.13 137 137
CMTM2 0.023 0.006 -9999 0 -0.12 1 1
SNURF 0.021 0.017 -9999 0 -0.12 8 8
ZMIZ1 0.022 0.031 -9999 0 -0.11 27 27
CCND3 0.021 0.018 -9999 0 -0.12 9 9
TGIF1 0.022 0.001 -9999 0 -10000 0 0
FKBP4 0.022 0.019 -9999 0 -0.12 10 10
Presenilin action in Notch and Wnt signaling

Figure S88.  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 S88.  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) 0.016 0.12 -10000 0 -0.48 29 29
HDAC1 0.027 0.027 0.092 19 -0.1 10 29
AES 0.023 0.02 0.063 2 -0.12 10 12
FBXW11 0.023 0.003 -10000 0 -10000 0 0
DTX1 0.023 0.008 -10000 0 -0.12 2 2
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 67 67
TLE1 0.022 0.02 0.075 1 -0.11 10 11
AP1 -0.003 0.071 -10000 0 -0.2 46 46
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
ADAM10 0.021 0.014 -10000 0 -0.12 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.059 0.19 -10000 0 -0.49 55 55
NICD/RBPSUH 0.014 0.12 -10000 0 -0.48 29 29
WIF1 0.02 0.021 -10000 0 -0.12 13 13
NOTCH1 0.001 0.12 -10000 0 -0.51 29 29
PSENEN 0.016 0.03 -10000 0 -0.12 25 25
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 34 34
beta catenin/beta TrCP1 -0.005 0.081 -10000 0 -0.27 30 30
APH1B 0.014 0.031 -10000 0 -0.12 28 28
APH1A 0.023 0.009 -10000 0 -0.12 2 2
AXIN1 -0.001 0.046 0.19 4 -0.2 10 14
CtBP/CBP/TCF1/TLE1/AES 0.037 0.096 0.26 22 -0.26 11 33
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
FOS -0.005 0.052 -10000 0 -0.12 95 95
JUN 0.014 0.032 -10000 0 -0.12 30 30
MAP3K7 0.024 0.017 -10000 0 -0.12 5 5
CTNNB1 -0.016 0.078 -10000 0 -0.28 29 29
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 33 33
HNF1A 0.024 0.014 0.063 2 -0.12 4 6
CTBP1 0.024 0.017 0.065 1 -0.12 7 8
MYC -0.16 0.42 -10000 0 -1.2 75 75
NKD1 0.023 0.012 -10000 0 -0.12 4 4
FZD1 0.023 0.006 -10000 0 -0.12 1 1
NOTCH1 precursor/Deltex homolog 1 0.014 0.12 -10000 0 -0.48 29 29
apoptosis -0.003 0.07 -10000 0 -0.2 46 46
Delta 1/NOTCHprecursor 0.014 0.12 -10000 0 -0.48 29 29
DLL1 0.022 0.012 -10000 0 -0.12 4 4
PPARD 0.001 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.033 0.067 -10000 0 -0.098 88 88
APC -0.004 0.057 0.19 4 -0.37 6 10
DVL1 0.017 0.066 -10000 0 -0.3 20 20
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
MAP3K7IP1 0.026 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.026 0.047 -10000 0 -0.11 35 35
LRP6 0.014 0.033 -10000 0 -0.12 32 32
CSNK1A1 0.022 0.007 -10000 0 -0.12 1 1
NLK 0.029 0.042 -10000 0 -0.22 11 11
CCND1 -0.18 0.43 -10000 0 -1.2 82 82
WNT1 0.023 0.008 -10000 0 -0.12 2 2
Axin1/APC/beta catenin -0.001 0.085 0.2 3 -0.31 21 24
DKK2 0.023 0.01 -10000 0 -0.12 3 3
NOTCH1 precursor/DVL1 0.015 0.13 -10000 0 -0.44 34 34
GSK3B 0.023 0.011 -10000 0 -0.12 3 3
FRAT1 0.024 0.007 -10000 0 -0.12 1 1
NOTCH/Deltex homolog 1 0.016 0.12 -10000 0 -0.48 29 29
PPP2R5D 0.009 0.04 -10000 0 -0.22 10 10
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
WNT1/LRP6/FZD1 0.042 0.045 -10000 0 -0.096 38 38
RBPJ 0.023 0.009 -10000 0 -0.12 2 2
CREBBP 0.017 0.018 -10000 0 -0.11 6 6
EPO signaling pathway

Figure S89.  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 S89.  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 0.015 0.15 -9999 0 -0.45 36 36
CRKL 0.029 0.037 -9999 0 -0.11 9 9
mol:DAG 0.025 0.075 -9999 0 -0.2 47 47
HRAS 0.031 0.045 -9999 0 -0.12 16 16
MAPK8 0.021 0.042 -9999 0 -0.11 45 45
RAP1A 0.026 0.044 -9999 0 -0.16 15 15
GAB1 0.027 0.038 -9999 0 -0.11 11 11
MAPK14 0.021 0.041 -9999 0 -0.11 46 46
EPO 0.025 0.008 -9999 0 -0.12 1 1
PLCG1 0.026 0.077 -9999 0 -0.2 47 47
EPOR/TRPC2/IP3 Receptors 0.022 0.021 -9999 0 -0.12 12 12
RAPGEF1 0.023 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.036 0.042 -9999 0 -0.12 21 21
GAB1/SHC/GRB2/SOS1 0.041 0.053 -9999 0 -0.13 16 16
EPO/EPOR (dimer) 0.034 0.022 -9999 0 -0.11 5 5
IRS2 0.029 0.038 -9999 0 -0.11 10 10
STAT1 0.021 0.099 -9999 0 -0.26 52 52
STAT5B 0.031 0.076 -9999 0 -0.22 30 30
cell proliferation 0.019 0.039 -9999 0 -0.1 46 46
GAB1/SHIP/PIK3R1/SHP2/SHC 0.022 0.046 -9999 0 -0.11 27 27
TEC 0.02 0.044 -9999 0 -0.13 22 22
SOCS3 0.015 0.031 -9999 0 -0.12 28 28
STAT1 (dimer) 0.021 0.098 -9999 0 -0.26 52 52
JAK2 0.019 0.025 -9999 0 -0.12 17 17
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
EPO/EPOR (dimer)/JAK2 0.059 0.054 -9999 0 -0.12 9 9
EPO/EPOR 0.034 0.022 -9999 0 -0.11 5 5
LYN 0.022 0.014 -9999 0 -0.12 4 4
TEC/VAV2 0.021 0.059 -9999 0 -0.13 29 29
elevation of cytosolic calcium ion concentration 0.022 0.021 -9999 0 -0.12 12 12
SHC1 0.023 0.001 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.039 0.053 -9999 0 -0.13 45 45
mol:IP3 0.025 0.075 -9999 0 -0.2 47 47
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.029 0.047 -9999 0 -0.13 17 17
SH2B3 0.024 0.004 -9999 0 -10000 0 0
NFKB1 0.017 0.054 -9999 0 -0.15 45 45
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.059 -9999 0 -0.17 61 61
PTPN6 0.025 0.038 -9999 0 -0.11 10 10
TEC/VAV2/GRB2 0.029 0.062 -9999 0 -0.12 32 32
EPOR 0.022 0.021 -9999 0 -0.12 12 12
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP 0.041 0.053 -9999 0 -0.13 16 16
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG2 0.02 0.02 -9999 0 -0.12 11 11
CRKL/CBL/C3G 0.053 0.041 -9999 0 -0.12 5 5
VAV2 0.028 0.037 -9999 0 -0.11 9 9
CBL 0.029 0.038 -9999 0 -0.12 9 9
SHC/Grb2/SOS1 0.03 0.044 -9999 0 -0.14 15 15
STAT5A 0.029 0.08 -9999 0 -0.23 33 33
GRB2 0.023 0.006 -9999 0 -0.12 1 1
STAT5 (dimer) 0.049 0.089 -9999 0 -0.24 30 30
LYN/PLCgamma2 0.019 0.05 -9999 0 -0.13 56 56
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
BTK 0.022 0.046 -9999 0 -0.15 20 20
BCL2 0.019 0.12 -9999 0 -0.4 25 25
Signaling mediated by p38-alpha and p38-beta

Figure S90.  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 S90.  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 0.006 0.12 -9999 0 -0.76 10 10
MKNK1 0.023 0.006 -9999 0 -0.12 1 1
MAPK14 0.015 0.049 -9999 0 -0.15 25 25
ATF2/c-Jun -0.006 0.11 -9999 0 -0.3 61 61
MAPK11 0.016 0.049 -9999 0 -0.15 24 24
MITF 0.019 0.061 -9999 0 -0.23 21 21
MAPKAPK5 0.02 0.057 -9999 0 -0.23 19 19
KRT8 0.016 0.065 -9999 0 -0.24 25 25
MAPKAPK3 0.022 0.012 -9999 0 -0.12 4 4
MAPKAPK2 0.023 0.009 -9999 0 -0.12 2 2
p38alpha-beta/CK2 0.02 0.072 -9999 0 -0.22 25 25
CEBPB 0.016 0.063 -9999 0 -0.24 21 21
SLC9A1 0.02 0.059 -9999 0 -0.23 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.017 0.069 -9999 0 -0.16 58 58
p38alpha-beta/MNK1 0.033 0.063 -9999 0 -0.2 21 21
JUN -0.007 0.11 -9999 0 -0.3 61 61
PPARGC1A 0.016 0.06 -9999 0 -0.21 23 23
USF1 0.019 0.059 -9999 0 -0.23 21 21
RAB5/GDP/GDI1 0.018 0.051 -9999 0 -0.16 33 33
NOS2 0.011 0.056 -9999 0 -0.24 18 18
DDIT3 0.015 0.06 -9999 0 -0.22 24 24
RAB5A 0.023 0.006 -9999 0 -0.12 1 1
HSPB1 0.019 0.045 -9999 0 -0.19 16 16
p38alpha-beta/HBP1 0.025 0.069 -9999 0 -0.15 47 47
CREB1 0.019 0.071 -9999 0 -0.29 22 22
RAB5/GDP 0.016 0.014 -9999 0 -0.13 5 5
EIF4E 0.02 0.049 -9999 0 -0.18 18 18
RPS6KA4 0.021 0.057 -9999 0 -0.23 19 19
PLA2G4A 0 0.06 -9999 0 -0.15 45 45
GDI1 0.018 0.061 -9999 0 -0.23 24 24
TP53 0.005 0.065 -9999 0 -0.26 22 22
RPS6KA5 0.018 0.059 -9999 0 -0.22 23 23
ESR1 0.01 0.076 -9999 0 -0.25 33 33
HBP1 0.022 0.005 -9999 0 -10000 0 0
MEF2C 0.016 0.067 -9999 0 -0.24 24 24
MEF2A 0.019 0.061 -9999 0 -0.24 20 20
EIF4EBP1 0.02 0.067 -9999 0 -0.26 23 23
KRT19 0.009 0.075 -9999 0 -0.23 36 36
ELK4 0.021 0.056 -9999 0 -0.23 18 18
ATF6 0.019 0.063 -9999 0 -0.26 19 19
ATF1 0.019 0.07 -9999 0 -0.29 21 21
p38alpha-beta/MAPKAPK2 0.033 0.061 -9999 0 -0.2 17 17
p38alpha-beta/MAPKAPK3 0.033 0.061 -9999 0 -0.19 19 19
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S91.  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 S91.  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 0.028 0.018 -10000 0 -0.097 7 7
NFATC2 0.019 0.19 0.35 11 -0.4 53 64
NFATC3 0.059 0.058 0.26 28 -0.24 2 30
CD40LG 0.043 0.14 -10000 0 -0.56 4 4
ITCH 0.025 0.067 -10000 0 -0.28 19 19
CBLB 0.023 0.073 -10000 0 -0.31 19 19
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.039 0.15 -10000 0 -0.49 13 13
JUNB 0.008 0.042 -10000 0 -0.12 53 53
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.06 -10000 0 -0.18 35 35
T cell anergy 0.012 0.088 -10000 0 -0.3 31 31
TLE4 -0.013 0.18 -10000 0 -0.41 72 72
Jun/NFAT1-c-4/p21SNFT 0.081 0.15 -10000 0 -0.56 4 4
AP-1/NFAT1-c-4 0.081 0.19 -10000 0 -0.62 4 4
IKZF1 0.021 0.12 -10000 0 -0.3 28 28
T-helper 2 cell differentiation 0.024 0.14 -10000 0 -0.46 8 8
AP-1/NFAT1 0.008 0.15 0.29 8 -0.26 74 82
CALM1 0.026 0.038 -10000 0 -0.11 34 34
EGR2 0.068 0.15 0.51 9 -0.86 3 12
EGR3 0.07 0.14 0.51 5 -0.52 1 6
NFAT1/FOXP3 0.039 0.14 -10000 0 -0.27 48 48
EGR1 -0.004 0.053 -10000 0 -0.12 98 98
JUN 0.02 0.034 -10000 0 -0.12 31 31
EGR4 0.023 0.014 -10000 0 -0.12 5 5
mol:Ca2+ 0.006 0.031 -10000 0 -0.12 28 28
GBP3 -0.058 0.23 -10000 0 -0.45 128 128
FOSL1 0.021 0.018 -10000 0 -0.12 9 9
NFAT1-c-4/MAF/IRF4 0.094 0.14 -10000 0 -0.57 3 3
DGKA 0.014 0.14 -10000 0 -0.31 53 53
CREM 0.021 0.012 -10000 0 -0.12 4 4
NFAT1-c-4/PPARG 0.082 0.14 -10000 0 -0.62 3 3
CTLA4 0.02 0.1 -10000 0 -0.22 49 49
NFAT1-c-4 (dimer)/EGR1 0.054 0.15 -10000 0 -0.6 4 4
NFAT1-c-4 (dimer)/EGR4 0.09 0.14 -10000 0 -0.61 3 3
FOS 0 0.052 -10000 0 -0.11 96 96
IFNG 0.019 0.14 -10000 0 -0.44 6 6
T cell activation 0.028 0.11 -10000 0 -10000 0 0
MAF 0.023 0.012 -10000 0 -0.12 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.071 0.13 0.61 3 -0.49 26 29
TNF 0.038 0.14 -10000 0 -0.53 5 5
FASLG 0.056 0.15 -10000 0 -0.98 3 3
TBX21 0.026 0.018 -10000 0 -0.13 3 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.019 0.03 -10000 0 -0.12 26 26
PTPN1 0.021 0.13 -10000 0 -0.28 46 46
NFAT1-c-4/ICER1 0.082 0.14 -10000 0 -0.61 3 3
GATA3 0.024 0.02 -10000 0 -0.12 11 11
T-helper 1 cell differentiation 0.018 0.13 -10000 0 -0.43 8 8
IL2RA 0.041 0.15 -10000 0 -0.44 16 16
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.017 0.14 -10000 0 -0.4 24 24
E2F1 0.017 0.044 -10000 0 -0.15 36 36
PPARG 0.017 0.029 -10000 0 -0.12 24 24
SLC3A2 0.015 0.14 -10000 0 -0.31 53 53
IRF4 0.019 0.025 -10000 0 -0.12 18 18
PTGS2 0.035 0.15 -10000 0 -0.57 5 5
CSF2 0.043 0.14 -10000 0 -0.56 4 4
JunB/Fra1/NFAT1-c-4 0.072 0.15 -10000 0 -0.54 4 4
IL4 0.023 0.14 -10000 0 -0.47 8 8
IL5 0.043 0.14 -10000 0 -0.56 4 4
IL2 0.028 0.11 -10000 0 -10000 0 0
IL3 0.012 0.041 -10000 0 -0.38 3 3
RNF128 0.025 0.052 -10000 0 -0.25 7 7
NFATC1 0.071 0.13 0.49 26 -0.62 3 29
CDK4 -0.081 0.28 0.46 1 -1.2 29 30
PTPRK -0.005 0.17 -10000 0 -0.43 58 58
IL8 0.029 0.15 -10000 0 -0.55 6 6
POU2F1 0.031 0.007 -10000 0 -0.12 1 1
PDGFR-beta signaling pathway

Figure S92.  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 S92.  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 0.025 0.071 -10000 0 -0.25 13 13
PDGFB-D/PDGFRB/SLAP 0.02 0.039 -10000 0 -0.08 72 72
PDGFB-D/PDGFRB/APS/CBL 0.022 0.028 -10000 0 -0.073 16 16
AKT1 0.009 0.053 -10000 0 -0.12 44 44
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.069 -10000 0 -0.23 18 18
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
FGR 0.014 0.04 -10000 0 -0.19 5 5
mol:Ca2+ 0.011 0.066 -10000 0 -0.28 14 14
MYC -0.06 0.26 -10000 0 -0.71 76 76
SHC1 0.023 0.001 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.038 -10000 0 -0.087 38 38
LRP1/PDGFRB/PDGFB 0.024 0.052 -10000 0 -0.11 58 58
GRB10 0.022 0.014 -10000 0 -0.12 5 5
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
GO:0007205 0.011 0.067 -10000 0 -0.28 14 14
PTEN 0.022 0.008 -10000 0 -0.12 1 1
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GRB7 0.018 0.025 -10000 0 -0.12 18 18
PDGFB-D/PDGFRB/SHP2 0.018 0.044 -10000 0 -0.091 76 76
PDGFB-D/PDGFRB/GRB10 0.021 0.039 -10000 0 -0.16 9 9
cell cycle arrest 0.02 0.039 -10000 0 -0.079 72 72
HRAS 0.023 0.006 -10000 0 -0.12 1 1
HIF1A 0.007 0.054 -10000 0 -0.13 51 51
GAB1 0.005 0.08 -10000 0 -0.25 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.078 -10000 0 -0.22 32 32
PDGFB-D/PDGFRB 0.032 0.039 -10000 0 -0.095 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.046 -10000 0 -0.12 39 39
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.018 0.086 -10000 0 -0.21 35 35
positive regulation of MAPKKK cascade 0.018 0.044 -10000 0 -0.09 76 76
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
mol:IP3 0.011 0.067 -10000 0 -0.28 14 14
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.009 -10000 0 -0.12 2 2
PDGFB-D/PDGFRB/GRB7 0.017 0.045 -10000 0 -0.087 80 80
SHB 0.023 0.008 -10000 0 -0.12 2 2
BLK 0.014 0.038 -10000 0 -0.2 3 3
PTPN2 0.022 0.008 -10000 0 -0.13 1 1
PDGFB-D/PDGFRB/SNX15 0.024 0.032 -10000 0 -0.081 23 23
BCAR1 0.023 0.01 -10000 0 -0.12 3 3
VAV2 -0.005 0.11 -10000 0 -0.24 82 82
CBL 0.023 0.006 -10000 0 -0.12 1 1
PDGFB-D/PDGFRB/DEP1 0.017 0.045 -10000 0 -0.12 37 37
LCK 0.014 0.039 -10000 0 -0.19 5 5
PDGFRB 0.01 0.042 -10000 0 -0.12 51 51
ACP1 0.021 0.014 -10000 0 -0.12 5 5
HCK -0.001 0.089 -10000 0 -0.45 16 16
ABL1 0.007 0.068 -10000 0 -0.22 20 20
PDGFB-D/PDGFRB/CBL 0.007 0.082 -10000 0 -0.3 14 14
PTPN1 0.022 0.007 -10000 0 -0.13 1 1
SNX15 0.023 0 -10000 0 -10000 0 0
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT1 0.014 0.03 -10000 0 -0.12 25 25
cell proliferation -0.05 0.23 -10000 0 -0.63 76 76
SLA 0.02 0.02 -10000 0 -0.12 11 11
actin cytoskeleton reorganization 0.032 0.041 -10000 0 -0.15 7 7
SRC 0.015 0.038 -10000 0 -0.19 4 4
PI3K -0.021 0.04 -10000 0 -0.12 59 59
PDGFB-D/PDGFRB/GRB7/SHC 0.031 0.041 -10000 0 -0.13 16 16
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.019 0.07 -10000 0 -0.24 18 18
LYN -0.022 0.13 -10000 0 -0.43 48 48
LRP1 0.015 0.032 -10000 0 -0.12 29 29
SOS1 0.017 0.027 -10000 0 -0.12 20 20
STAT5B 0.023 0.006 -10000 0 -0.12 1 1
STAT5A 0.022 0.012 -10000 0 -0.12 4 4
NCK1-2/p130 Cas 0.046 0.051 -10000 0 -0.12 15 15
SPHK1 0.021 0.017 -10000 0 -0.12 8 8
EDG1 0.022 0.015 -10000 0 -0.12 6 6
mol:DAG 0.011 0.067 -10000 0 -0.28 14 14
PLCG1 0.011 0.068 -10000 0 -0.29 14 14
NHERF/PDGFRB 0.025 0.049 -10000 0 -0.12 30 30
YES1 -0.01 0.12 -10000 0 -0.44 32 32
cell migration 0.024 0.048 -10000 0 -0.12 30 30
SHC/Grb2/SOS1 0.044 0.051 -10000 0 -0.12 14 14
SLC9A3R2 0.017 0.029 -10000 0 -0.12 24 24
SLC9A3R1 0.016 0.03 -10000 0 -0.12 26 26
NHERF1-2/PDGFRB/PTEN 0.031 0.056 -10000 0 -0.11 51 51
FYN -0.02 0.12 -10000 0 -0.4 41 41
DOK1 0.021 0.028 -10000 0 -0.11 10 10
HRAS/GTP 0.017 0.008 -10000 0 -0.11 2 2
PDGFB 0.023 0.01 -10000 0 -0.12 3 3
RAC1 -0.023 0.16 -10000 0 -0.4 83 83
PRKCD 0.02 0.03 -10000 0 -0.12 10 10
FER 0.02 0.029 -10000 0 -0.11 11 11
MAPKKK cascade -0.008 0.027 0.059 12 -0.12 14 26
RASA1 0.02 0.03 -10000 0 -0.12 10 10
NCK1 0.02 0.019 -10000 0 -0.12 9 9
NCK2 0.023 0.006 -10000 0 -0.12 1 1
p62DOK/Csk 0.033 0.032 -10000 0 -0.091 18 18
PDGFB-D/PDGFRB/SHB 0.024 0.033 -10000 0 -0.09 13 13
chemotaxis 0.007 0.067 -10000 0 -0.21 20 20
STAT1-3-5/STAT1-3-5 0.021 0.058 -10000 0 -0.14 22 22
Bovine Papilomavirus E5/PDGFRB 0.008 0.029 -10000 0 -0.08 54 54
PTPRJ 0.02 0.019 -10000 0 -0.12 10 10
LPA4-mediated signaling events

Figure S93.  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 S93.  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 0.012 0.014 -9999 0 -0.056 22 22
ADCY5 0.009 0.019 -9999 0 -0.059 41 41
ADCY6 0.013 0.01 -9999 0 -0.056 11 11
ADCY7 0.014 0.009 -9999 0 -0.056 8 8
ADCY1 0.013 0.01 -9999 0 -0.056 11 11
ADCY2 0.013 0.012 -9999 0 -0.056 17 17
ADCY3 0.012 0.013 -9999 0 -0.056 18 18
ADCY8 0.002 0.027 -9999 0 -0.057 98 98
PRKCE 0.01 0.01 -9999 0 -0.076 8 8
ADCY9 0.012 0.012 -9999 0 -0.056 16 16
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.012 0.033 -9999 0 -0.18 12 12
Regulation of nuclear SMAD2/3 signaling

Figure S94.  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 S94.  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
EP300 0.02 0.011 -10000 0 -0.12 2 2
HSPA8 0.023 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.06 0.084 0.2 43 -0.14 28 71
AKT1 0.023 0.021 -10000 0 -0.1 15 15
GSC 0.022 0.094 -10000 0 -1.2 3 3
NKX2-5 0.022 0.015 -10000 0 -0.047 19 19
muscle cell differentiation -0.039 0.081 0.28 20 -10000 0 20
SMAD2-3/SMAD4/SP1 0.049 0.094 -10000 0 -0.2 29 29
SMAD4 0.024 0.039 -10000 0 -0.14 13 13
CBFB 0.023 0.007 -10000 0 -0.12 1 1
SAP18 0.023 0.003 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.052 -10000 0 -0.14 39 39
SMAD3/SMAD4/VDR 0.046 0.073 -10000 0 -0.17 31 31
MYC 0.013 0.028 0.098 5 -0.12 20 25
CDKN2B 0.031 0.12 -10000 0 -1.2 5 5
AP1 0.005 0.1 -10000 0 -0.21 75 75
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.12 -10000 0 -0.32 48 48
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.039 0.055 -10000 0 -0.28 10 10
SP3 0.02 0.015 -10000 0 -0.037 24 24
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.024 0.018 -10000 0 -0.11 7 7
SMAD3/SMAD4/GR 0.035 0.07 0.18 1 -0.15 37 38
GATA3 0.027 0.021 -10000 0 -0.11 11 11
SKI/SIN3/HDAC complex/NCoR1 0.02 0.079 -10000 0 -0.26 26 26
MEF2C/TIF2 0.042 0.064 -10000 0 -0.2 25 25
endothelial cell migration 0.013 0.11 1.2 3 -10000 0 3
MAX 0.023 0.006 0.074 3 -10000 0 3
RBBP7 0.022 0.011 -10000 0 -0.12 3 3
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
RUNX2 0.019 0.023 -10000 0 -0.12 15 15
RUNX3 0.018 0.028 -10000 0 -0.12 22 22
RUNX1 0.019 0.022 -10000 0 -0.12 13 13
CTBP1 0.021 0.016 -10000 0 -0.12 7 7
NR3C1 0.021 0.016 0.074 3 -0.12 5 8
VDR 0.019 0.022 -10000 0 -0.12 13 13
CDKN1A 0.017 0.065 -10000 0 -0.52 1 1
KAT2B -0.001 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.055 0.055 -10000 0 -0.2 11 11
DCP1A 0.023 0.001 -10000 0 -10000 0 0
SKI 0.023 0.01 -10000 0 -0.12 3 3
SERPINE1 -0.013 0.11 -10000 0 -1.2 3 3
SMAD3/SMAD4/ATF2 0.041 0.064 -10000 0 -0.18 19 19
SMAD3/SMAD4/ATF3 0.035 0.062 -10000 0 -0.14 20 20
SAP30 0.023 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.027 0.051 0.14 3 -0.14 40 43
JUN -0.008 0.098 -10000 0 -0.21 73 73
SMAD3/SMAD4/IRF7 0.051 0.059 -10000 0 -0.18 11 11
TFE3 0.018 0.031 -10000 0 -0.084 41 41
COL1A2 -0.13 0.26 -10000 0 -0.64 112 112
mesenchymal cell differentiation -0.041 0.057 0.15 14 -10000 0 14
DLX1 0.021 0.017 -10000 0 -0.12 8 8
TCF3 0.022 0.013 -10000 0 -0.12 5 5
FOS -0.004 0.054 -10000 0 -0.11 102 102
SMAD3/SMAD4/Max 0.046 0.056 0.18 1 -0.16 10 11
Cbp/p300/SNIP1 0.033 0.047 -10000 0 -0.13 38 38
ZBTB17 0.022 0.006 0.081 5 -10000 0 5
LAMC1 0.021 0.083 -10000 0 -0.27 34 34
TGIF2/HDAC complex/SMAD3/SMAD4 0.04 0.061 -10000 0 -0.16 21 21
IRF7 0.024 0.017 -10000 0 -0.12 7 7
ESR1 0.032 0.038 0.098 99 -0.12 11 110
HNF4A 0.023 0.008 -10000 0 -0.12 2 2
MEF2C 0.034 0.061 -10000 0 -0.21 24 24
SMAD2-3/SMAD4 0.049 0.063 -10000 0 -0.17 15 15
Cbp/p300/Src-1 0.029 0.053 -10000 0 -0.13 48 48
IGHV3OR16-13 0.005 0.074 -10000 0 -0.49 12 12
TGIF2/HDAC complex 0.022 0.013 -10000 0 -0.12 4 4
CREBBP 0.02 0.016 -10000 0 -0.12 6 6
SKIL 0.011 0.035 -10000 0 -0.12 35 35
HDAC1 0.02 0.019 -10000 0 -0.12 10 10
HDAC2 0.02 0.021 -10000 0 -0.12 12 12
SNIP1 0.023 0.01 -10000 0 -0.12 3 3
GCN5L2 0.021 0.013 -10000 0 -0.12 4 4
SMAD3/SMAD4/TFE3 0.048 0.072 -10000 0 -0.16 37 37
MSG1/HSC70 0.027 0.031 -10000 0 -0.081 42 42
SMAD2 0.027 0.016 -10000 0 -0.071 8 8
SMAD3 0.022 0.036 -10000 0 -0.1 22 22
SMAD3/E2F4-5/DP1/p107/SMAD4 0.024 0.067 -10000 0 -0.21 22 22
SMAD2/SMAD2/SMAD4 -0.002 0.044 0.12 2 -0.21 17 19
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
MYOD/E2A 0.032 0.015 -10000 0 -0.076 11 11
SMAD2-3/SMAD4/SP1/MIZ-1 0.061 0.092 -10000 0 -0.2 21 21
IFNB1 0.035 0.044 -10000 0 -0.17 9 9
SMAD3/SMAD4/MEF2C 0.058 0.076 -10000 0 -0.22 21 21
CITED1 0.015 0.035 -10000 0 -0.12 35 35
SMAD2-3/SMAD4/ARC105 0.061 0.061 -10000 0 -0.17 11 11
RBL1 0.019 0.022 -10000 0 -0.12 13 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.042 0.067 -10000 0 -0.4 8 8
RUNX1-3/PEBPB2 0.036 0.039 -10000 0 -0.12 27 27
SMAD7 -0.004 0.14 -10000 0 -0.38 37 37
MYC/MIZ-1 0.003 0.063 0.17 5 -0.15 75 80
SMAD3/SMAD4 -0.018 0.099 0.28 3 -0.29 42 45
IL10 0.039 0.044 -10000 0 -0.18 7 7
PIASy/HDAC complex 0.024 0.005 -10000 0 -10000 0 0
PIAS3 0.019 0.022 -10000 0 -0.12 14 14
CDK2 0.017 0.023 -10000 0 -0.12 14 14
IL5 0.039 0.044 -10000 0 -0.25 3 3
CDK4 0.019 0.019 -10000 0 -0.12 9 9
PIAS4 0.024 0.005 -10000 0 -10000 0 0
ATF3 0.011 0.04 -10000 0 -0.12 47 47
SMAD3/SMAD4/SP1 0.028 0.09 -10000 0 -0.2 33 33
FOXG1 0.02 0.019 -10000 0 -0.12 10 10
FOXO3 0.024 0.02 -10000 0 -0.069 23 23
FOXO1 0.025 0.017 -10000 0 -0.071 17 17
FOXO4 0.025 0.016 -10000 0 -0.071 15 15
heart looping 0.034 0.061 -10000 0 -0.21 24 24
CEBPB 0.017 0.032 -10000 0 -0.12 29 29
SMAD3/SMAD4/DLX1 0.044 0.055 -10000 0 -0.15 14 14
MYOD1 0.022 0.013 -10000 0 -0.12 5 5
SMAD3/SMAD4/HNF4 0.045 0.054 -10000 0 -0.16 11 11
SMAD3/SMAD4/GATA3 0.059 0.059 -10000 0 -0.22 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.011 0.035 -10000 0 -0.12 35 35
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.062 -10000 0 -0.14 15 15
SMAD3/SMAD4/SP1-3 0.042 0.097 -10000 0 -0.2 38 38
MED15 0.022 0.012 -10000 0 -0.12 4 4
SP1 -0.004 0.053 -10000 0 -0.093 113 113
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
SIN3A 0.022 0.014 -10000 0 -0.12 5 5
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.071 0.062 -10000 0 -0.16 22 22
ITGB5 0.007 0.094 -10000 0 -0.26 44 44
TGIF/SIN3/HDAC complex/CtBP 0.022 0.078 -10000 0 -0.27 23 23
SMAD3/SMAD4/AR 0.015 0.078 -10000 0 -0.14 54 54
AR 0.009 0.038 -10000 0 -0.12 43 43
negative regulation of cell growth 0.026 0.073 -10000 0 -0.23 29 29
SMAD3/SMAD4/MYOD 0.044 0.055 -10000 0 -0.17 11 11
E2F5 0.02 0.02 -10000 0 -0.12 11 11
E2F4 0.022 0.012 -10000 0 -0.12 4 4
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.068 0.058 -10000 0 -0.16 12 12
SMAD2-3/SMAD4/FOXO1-3a-4 0.041 0.061 -10000 0 -0.31 10 10
TFDP1 0.019 0.022 -10000 0 -0.12 14 14
SMAD3/SMAD4/AP1 0.013 0.11 -10000 0 -0.22 70 70
SMAD3/SMAD4/RUNX2 0.041 0.058 -10000 0 -0.15 14 14
TGIF2 0.022 0.013 -10000 0 -0.12 4 4
TGIF1 0.023 0 -10000 0 -10000 0 0
ATF2 0.022 0.004 -10000 0 -10000 0 0
mTOR signaling pathway

Figure S95.  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 S95.  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
GBL 0.023 0.008 -10000 0 -0.12 2 2
MKNK1 0.023 0.006 -10000 0 -0.12 1 1
mol:PIP3 -0.005 0.043 -10000 0 -0.11 66 66
FRAP1 0.011 0.072 -10000 0 -0.42 13 13
AKT1 0.006 0.057 0.18 19 -0.11 70 89
INSR 0.021 0.017 -10000 0 -0.12 8 8
Insulin Receptor/Insulin 0.028 0.019 -10000 0 -0.077 17 17
mol:GTP 0.023 0.056 0.18 18 -0.13 29 47
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.044 -10000 0 -0.17 32 32
TSC2 0.021 0.017 -10000 0 -0.12 8 8
RHEB/GDP 0.008 0.047 -10000 0 -0.12 34 34
TSC1 0.023 0.006 -10000 0 -0.12 1 1
Insulin Receptor/IRS1 0.02 0.029 -10000 0 -0.22 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.01 0.06 -10000 0 -0.19 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.006 0.084 0.16 14 -0.29 29 43
MAP3K5 -0.004 0.058 -10000 0 -0.27 25 25
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
apoptosis -0.004 0.058 -10000 0 -0.27 25 25
mol:LY294002 0 0 0 16 -0.001 6 22
EIF4B 0.008 0.077 0.16 14 -0.25 31 45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.076 0.17 1 -0.24 30 31
eIF4E/eIF4G1/eIF4A1 -0.007 0.042 -10000 0 -0.26 13 13
KIAA1303 0.023 0.008 -10000 0 -0.12 2 2
PI3K 0.016 0.052 -10000 0 -0.11 69 69
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.053 0.16 16 -0.17 15 31
FKBP1A 0.022 0.012 -10000 0 -0.12 4 4
RHEB/GTP 0.02 0.052 0.14 3 -0.12 34 37
mol:Amino Acids 0 0 0 16 -0.001 6 22
FKBP12/Rapamycin 0.016 0.014 -10000 0 -0.11 7 7
PDPK1 0.005 0.052 0.18 17 -0.1 64 81
EIF4E 0.023 0.001 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.14 -10000 0 -0.49 38 38
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.032 0.061 -10000 0 -10000 0 0
TSC1/TSC2 0.025 0.061 0.19 18 -0.14 29 47
tumor necrosis factor receptor activity 0 0 0.001 6 0 16 22
RPS6 0.023 0.002 -10000 0 -10000 0 0
PPP5C 0.022 0.015 -10000 0 -0.12 6 6
EIF4G1 0.023 0.004 -10000 0 -10000 0 0
IRS1 0.006 0.028 -10000 0 -0.27 5 5
INS 0.023 0.01 -10000 0 -0.12 3 3
PTEN 0.022 0.007 -10000 0 -0.12 1 1
PDK2 0.004 0.054 0.18 17 -0.14 31 48
EIF4EBP1 0.011 0.1 -10000 0 -1.1 5 5
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PPP2R5D 0.014 0.066 -10000 0 -0.37 13 13
peptide biosynthetic process 0.022 0.018 -10000 0 -0.11 6 6
RHEB 0.019 0.022 -10000 0 -0.12 13 13
EIF4A1 0.023 0.007 -10000 0 -0.12 1 1
mol:Rapamycin 0 0.001 0.003 20 -0.002 17 37
EEF2 0.023 0.018 -10000 0 -0.12 6 6
eIF4E/4E-BP1 0.023 0.097 -10000 0 -1 5 5
S1P5 pathway

Figure S96.  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 S96.  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:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.006 0.066 0.2 24 -10000 0 24
GNAI2 0.022 0.01 -10000 0 -0.12 3 3
S1P/S1P5/G12 0.016 0.006 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.041 -10000 0 -0.12 50 50
RhoA/GTP 0.007 0.067 -10000 0 -0.2 24 24
negative regulation of cAMP metabolic process -0.003 0.069 -10000 0 -0.15 89 89
GNAZ 0.022 0.012 -10000 0 -0.12 4 4
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNA12 0.023 0.001 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.003 0.069 -10000 0 -0.15 89 89
RhoA/GDP 0.016 0.016 -10000 0 -0.14 6 6
RHOA 0.023 0.006 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 36 36
p38 MAPK signaling pathway

Figure S97.  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 S97.  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
TRAF6/ASK1 0.01 0.052 -9999 0 -0.14 51 51
TRAF2/ASK1 0.023 0.033 -9999 0 -0.091 42 42
ATM 0.018 0.022 -9999 0 -0.12 13 13
MAP2K3 -0.003 0.12 -9999 0 -0.32 65 65
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.013 0.12 -9999 0 -0.28 63 63
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.015 0.033 -9999 0 -0.12 32 32
TXN -0.003 0.051 -9999 0 -0.21 33 33
CALM1 0.022 0.014 -9999 0 -0.12 5 5
GADD45A 0.014 0.032 -9999 0 -0.12 30 30
GADD45B 0.016 0.029 -9999 0 -0.12 24 24
MAP3K1 0.021 0.015 -9999 0 -0.12 6 6
MAP3K6 0.022 0.012 -9999 0 -0.12 4 4
MAP3K7 0.021 0.014 -9999 0 -0.12 5 5
MAP3K4 0.023 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.023 0.041 -9999 0 -0.11 47 47
TAK1/TAB family 0 0.069 -9999 0 -0.33 22 22
RAC1/OSM/MEKK3 0.044 0.015 -9999 0 -0.097 6 6
TRAF2 0.023 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.1 -9999 0 -0.25 64 64
TRAF6 0.006 0.056 -9999 0 -0.21 32 32
RAC1 0.023 0.002 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.023 0.008 -9999 0 -0.12 2 2
CCM2 0.023 0.001 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.029 0.019 -9999 0 -0.092 13 13
MAPK11 0.023 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.033 0.037 -9999 0 -0.1 32 32
OSM/MEKK3 0.034 0.007 -9999 0 -0.14 1 1
TAOK1 -0.002 0.068 -9999 0 -0.22 46 46
TAOK2 0.003 0.057 -9999 0 -0.2 40 40
TAOK3 -0.004 0.068 -9999 0 -0.21 53 53
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
MAPK14 0.023 0.007 -9999 0 -0.12 1 1
MAP3K7IP2 0.02 0.016 -9999 0 -0.12 7 7
MAP3K5 0.018 0.025 -9999 0 -0.12 17 17
MAP3K10 0.022 0.015 -9999 0 -0.12 6 6
MAP3K3 0.023 0 -9999 0 -10000 0 0
TRX/ASK1 0.009 0.051 -9999 0 -0.18 33 33
GADD45/MTK1/MTK1 0.024 0.058 -9999 0 -0.096 83 83
Ceramide signaling pathway

Figure S98.  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 S98.  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 0.02 0.016 -10000 0 -0.075 15 15
MAP4K4 0.003 0.069 -10000 0 -0.22 22 22
BAG4 0.022 0.012 -10000 0 -0.12 4 4
PKC zeta/ceramide 0.013 0.009 0.071 7 -10000 0 7
NFKBIA 0.016 0.027 -10000 0 -0.12 21 21
BIRC3 -0.005 0.052 -10000 0 -0.12 93 93
BAX 0.01 0.005 -10000 0 -10000 0 0
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
AKT1 0.007 0.02 -10000 0 -0.13 12 12
BAD 0.001 0.01 0.068 5 -10000 0 5
SMPD1 0.009 0.036 -10000 0 -0.14 17 17
RB1 -0.013 0.034 0.063 4 -0.092 80 84
FADD/Caspase 8 0.003 0.095 -10000 0 -0.3 29 29
MAP2K4 -0.001 0.024 0.068 5 -0.093 29 34
NSMAF 0.021 0.014 -10000 0 -0.12 5 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.015 0.068 5 -0.097 7 12
EGF 0.02 0.021 -10000 0 -0.12 13 13
mol:ceramide -0.004 0.01 0.063 7 -10000 0 7
MADD 0.023 0.006 -10000 0 -0.12 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.018 0.022 -10000 0 -0.084 20 20
ASAH1 0.021 0.016 -10000 0 -0.12 7 7
negative regulation of cell cycle -0.013 0.033 0.063 4 -0.091 80 84
cell proliferation 0.017 0.041 -10000 0 -0.11 21 21
BID 0.009 0.079 -10000 0 -0.6 4 4
MAP3K1 -0.003 0.021 0.068 5 -0.1 20 25
EIF2A -0.007 0.043 0.07 4 -0.11 60 64
TRADD 0.023 0.006 -10000 0 -0.12 1 1
CRADD 0.023 0.009 -10000 0 -0.12 2 2
MAPK3 0.009 0.021 0.074 4 -0.1 12 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.023 0.074 4 -0.11 16 20
Cathepsin D/ceramide 0.011 0.012 0.07 6 -0.055 9 15
FADD 0.004 0.068 -10000 0 -0.22 20 20
KSR1 0.001 0.01 0.063 7 -0.054 3 10
MAPK8 0.004 0.039 -10000 0 -0.19 18 18
PRKRA -0.002 0.02 0.063 7 -0.092 20 27
PDGFA 0.02 0.022 -10000 0 -0.12 13 13
TRAF2 0.023 0 -10000 0 -10000 0 0
IGF1 0.007 0.045 -10000 0 -0.12 62 62
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.004 0.01 0.063 7 -10000 0 7
CTSD 0.02 0.02 -10000 0 -0.12 11 11
regulation of nitric oxide biosynthetic process 0.02 0.047 -10000 0 -0.13 48 48
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.019 0.044 -10000 0 -0.12 21 21
PRKCD 0.02 0.018 -10000 0 -0.12 8 8
PRKCZ 0.023 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.018 0.022 -10000 0 -0.084 20 20
RelA/NF kappa B1 0.021 0.047 -10000 0 -0.13 48 48
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.009 -10000 0 -0.12 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.072 -10000 0 -0.24 19 19
TNFR1A/BAG4/TNF-alpha 0.038 0.034 -10000 0 -0.11 20 20
mol:Sphingosine-1-phosphate 0.02 0.016 -10000 0 -0.075 15 15
MAP2K1 0.007 0.016 0.07 5 -0.094 9 14
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.009 -10000 0 -0.12 2 2
CYCS 0.004 0.024 0.13 2 -0.12 15 17
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
TNFR1A/BAG4 0.027 0.034 -10000 0 -0.14 18 18
EIF2AK2 -0.008 0.036 0.068 5 -0.1 54 59
TNF-alpha/TNFR1A/FAN 0.033 0.047 -10000 0 -0.13 35 35
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.12 -10000 0 -0.39 40 40
MAP2K2 0.005 0.019 0.07 4 -0.094 11 15
SMPD3 0.011 0.041 -10000 0 -0.16 15 15
TNF 0.02 0.02 -10000 0 -0.12 11 11
PKC zeta/PAR4 0.033 0.014 -10000 0 -0.11 5 5
mol:PHOSPHOCHOLINE -0.008 0.016 0.092 5 -10000 0 5
NF kappa B1/RelA/I kappa B alpha 0.043 0.059 -10000 0 -0.095 75 75
AIFM1 -0.005 0.036 0.11 2 -0.12 44 46
BCL2 0.016 0.031 -10000 0 -0.12 28 28
Signaling events mediated by HDAC Class III

Figure S99.  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 S99.  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
EP300 0.022 0.009 -10000 0 -0.12 2 2
HDAC4 0.023 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.008 0.002 -10000 0 -10000 0 0
CDKN1A 0.034 0.04 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.023 0 -10000 0 -10000 0 0
FOXO3 0.002 0.049 0.26 18 -10000 0 18
FOXO1 0.023 0.008 -10000 0 -0.12 2 2
FOXO4 0.008 0.064 -10000 0 -0.22 36 36
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
TAT 0.023 0.008 -10000 0 -0.12 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.008 -10000 0 -0.076 5 5
PPARGC1A 0.014 0.034 -10000 0 -0.12 35 35
FHL2 0.02 0.021 -10000 0 -0.12 12 12
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.022 0.044 -10000 0 -0.18 25 25
HIST2H4A 0.008 0.002 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.013 0.036 0.2 18 -0.089 5 23
SIRT1 0.019 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.042 0.021 -10000 0 -0.11 10 10
SIRT1/Histone H1b 0.004 0.073 -10000 0 -0.17 72 72
apoptosis -0.036 0.039 0.14 25 -10000 0 25
SIRT1/PGC1A 0.021 0.028 -10000 0 -0.074 43 43
p53/SIRT1 -0.036 0.081 -10000 0 -0.15 177 177
SIRT1/FOXO4 0.016 0.058 -10000 0 -0.19 36 36
FOXO1/FHL2/SIRT1 0.037 0.026 -10000 0 -0.1 14 14
HIST1H1E -0.006 0.081 -10000 0 -0.2 72 72
SIRT1/p300 0.022 0.039 -10000 0 -0.14 31 31
muscle cell differentiation -0.014 0.02 0.12 11 -10000 0 11
TP53 0.007 0.029 -10000 0 -0.13 24 24
KU70/SIRT1/BAX 0.037 0.039 -10000 0 -0.14 25 25
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
MEF2D 0.023 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.024 -10000 0 -0.14 11 11
ACSS2 0.018 0.01 -10000 0 -0.073 6 6
SIRT1/PCAF/MYOD 0.015 0.02 -10000 0 -0.12 11 11
Signaling events mediated by HDAC Class I

Figure S100.  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 S100.  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
NF kappa B/RelA 0.032 0.075 -10000 0 -0.2 35 35
Ran/GTP/Exportin 1/HDAC1 -0.012 0.04 -10000 0 -0.12 55 55
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.09 -10000 0 -0.26 39 39
SUMO1 0.023 0.009 -10000 0 -0.12 2 2
ZFPM1 0.023 0.01 -10000 0 -0.12 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.036 -10000 0 -0.14 30 30
FKBP3 0.021 0.013 -10000 0 -0.12 4 4
Histones 0.04 0.067 -10000 0 -0.23 18 18
YY1/LSF 0.017 0.063 -10000 0 -0.2 36 36
SMG5 0.022 0.011 -10000 0 -0.12 3 3
RAN 0.023 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.016 0.066 -10000 0 -0.17 51 51
I kappa B alpha/HDAC1 0.012 0.083 -10000 0 -0.24 48 48
SAP18 0.023 0.003 -10000 0 -10000 0 0
RELA 0.017 0.076 -10000 0 -0.22 38 38
HDAC1/Smad7 0.034 0.042 -10000 0 -0.11 41 41
RANGAP1 0.023 0.006 -10000 0 -0.12 1 1
HDAC3/TR2 0.031 0.045 -10000 0 -0.24 11 11
NuRD/MBD3 Complex 0.013 0.098 -10000 0 -0.32 32 32
NF kappa B1 p50/RelA 0.021 0.079 -10000 0 -0.2 46 46
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.02 0.021 -10000 0 -0.12 13 13
GATA1 0.023 0.006 -10000 0 -0.12 1 1
Mad/Max 0.033 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.025 0.094 -10000 0 -0.29 32 32
RBBP7 0.022 0.011 -10000 0 -0.12 3 3
NPC 0.009 0.023 -10000 0 -0.095 27 27
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
MAX 0.023 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.003 -10000 0 -10000 0 0
NFKBIA 0.004 0.082 -10000 0 -0.26 43 43
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.015 0.082 -10000 0 -0.31 22 22
SIN3 complex 0.053 0.032 -10000 0 -0.098 19 19
SMURF1 0.023 0.009 -10000 0 -0.12 2 2
CHD3 0.021 0.016 -10000 0 -0.12 7 7
SAP30 0.023 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
YY1/HDAC3 0.022 0.065 -10000 0 -0.25 19 19
YY1/HDAC2 0.018 0.059 -10000 0 -0.18 37 37
YY1/HDAC1 0.016 0.061 -10000 0 -0.2 36 36
NuRD/MBD2 Complex (MeCP1) 0.013 0.098 -10000 0 -0.31 32 32
PPARG 0.021 0.061 -10000 0 -0.2 35 35
HDAC8/hEST1B 0.037 0.038 -10000 0 -0.12 28 28
UBE2I 0.023 0.001 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
HDAC3/SMRT (N-CoR2) 0.031 0.046 -10000 0 -0.25 10 10
MBD3L2 0.023 0.01 -10000 0 -0.12 3 3
ubiquitin-dependent protein catabolic process 0.034 0.042 -10000 0 -0.11 41 41
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
NuRD/MBD3/MBD3L2 Complex 0.023 0.095 -10000 0 -0.3 32 32
HDAC1 0.019 0.019 -10000 0 -0.12 10 10
HDAC3 0.023 0.044 -10000 0 -0.26 9 9
HDAC2 0.02 0.021 -10000 0 -0.12 12 12
YY1 0.008 0.065 -10000 0 -0.22 36 36
HDAC8 0.021 0.013 -10000 0 -0.12 4 4
SMAD7 0.023 0.003 -10000 0 -10000 0 0
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
MXD1 0.021 0.017 -10000 0 -0.12 8 8
STAT3 0.004 0.079 -10000 0 -0.23 52 52
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.01 -10000 0 -0.12 2 2
YY1/LSF/HDAC1 0.018 0.072 -10000 0 -0.19 43 43
YY1/SAP30/HDAC1 0.025 0.063 -10000 0 -0.17 37 37
EP300 0.022 0.009 -10000 0 -0.12 2 2
STAT3 (dimer non-phopshorylated) 0.004 0.079 -10000 0 -0.23 52 52
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.082 -10000 0 -0.26 43 43
histone deacetylation 0.013 0.097 -10000 0 -0.31 32 32
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.078 -10000 0 -0.26 24 24
nuclear export -0.036 0.038 0.12 28 -10000 0 28
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GATAD2B 0.022 0.009 -10000 0 -0.12 2 2
GATAD2A 0.02 0.021 -10000 0 -0.12 13 13
GATA2/HDAC3 0.032 0.047 -10000 0 -0.25 10 10
GATA1/HDAC1 0.023 0.042 -10000 0 -0.12 41 41
GATA1/HDAC3 0.033 0.044 -10000 0 -0.24 10 10
CHD4 0.022 0.009 -10000 0 -0.12 2 2
TNF-alpha/TNFR1A 0.025 0.036 -10000 0 -0.11 37 37
SIN3/HDAC complex/Mad/Max 0.022 0.078 -10000 0 -0.28 22 22
NuRD Complex 0.023 0.095 -10000 0 -0.3 32 32
positive regulation of chromatin silencing 0.038 0.066 -10000 0 -0.22 18 18
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
MTA2 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.022 0.014 -10000 0 -0.12 5 5
XPO1 0.022 0.01 -10000 0 -0.12 2 2
SUMO1/HDAC1 0.029 0.048 -10000 0 -0.13 30 30
HDAC complex 0.034 0.064 -10000 0 -0.12 67 67
GATA1/Fog1 0.034 0.01 -10000 0 -0.095 3 3
FKBP25/HDAC1/HDAC2 0.027 0.054 -10000 0 -0.12 55 55
TNF 0.02 0.02 -10000 0 -0.12 11 11
negative regulation of cell growth 0.022 0.077 -10000 0 -0.28 22 22
NuRD/MBD2/PRMT5 Complex 0.013 0.098 -10000 0 -0.31 32 32
Ran/GTP/Exportin 1 0.034 0.049 -10000 0 -0.15 30 30
NF kappa B/RelA/I kappa B alpha 0.018 0.079 -10000 0 -0.28 30 30
SIN3/HDAC complex/NCoR1 0.019 0.079 -10000 0 -0.27 27 27
TFCP2 0.021 0.014 -10000 0 -0.12 5 5
NR2C1 0.022 0.01 -10000 0 -0.12 2 2
MBD3 0.023 0.008 -10000 0 -0.12 2 2
MBD2 0.023 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

Figure S101.  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 S101.  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 -0.018 0.081 -9999 0 -0.16 107 107
AKT1 0.019 0.12 -9999 0 -0.32 32 32
PTK2B -0.004 0.08 -9999 0 -0.2 48 48
VEGFR2 homodimer/Frs2 0.025 0.058 -9999 0 -0.27 8 8
CAV1 0.012 0.038 -9999 0 -0.12 42 42
CALM1 0.022 0.014 -9999 0 -0.12 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.03 0.073 -9999 0 -0.24 17 17
endothelial cell proliferation 0.026 0.1 -9999 0 -0.31 21 21
mol:Ca2+ 0.027 0.067 -9999 0 -0.23 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.036 0.083 -9999 0 -0.22 28 28
RP11-342D11.1 0.019 0.062 -9999 0 -0.23 17 17
CDH5 0.022 0.012 -9999 0 -0.12 4 4
VEGFA homodimer 0.038 0.058 -9999 0 -0.1 71 71
SHC1 0.023 0.001 -9999 0 -10000 0 0
SHC2 0.023 0.008 -9999 0 -0.12 2 2
HRAS/GDP 0.03 0.061 -9999 0 -0.24 12 12
SH2D2A 0.023 0.006 -9999 0 -0.12 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.054 0.082 -9999 0 -0.32 9 9
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.036 0.07 -9999 0 -0.23 16 16
VEGFR1 homodimer 0.022 0.014 -9999 0 -0.12 5 5
SHC/GRB2/SOS1 0.055 0.078 -9999 0 -0.26 12 12
GRB10 0.029 0.072 -9999 0 -0.34 11 11
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PAK1 0.016 0.029 -9999 0 -0.12 24 24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.04 0.086 -9999 0 -0.21 31 31
HRAS 0.023 0.006 -9999 0 -0.12 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.019 0.12 -9999 0 -0.3 63 63
HIF1A 0.022 0.01 -9999 0 -0.12 2 2
FRS2 0.019 0.023 -9999 0 -0.12 15 15
oxygen and reactive oxygen species metabolic process 0.034 0.081 -9999 0 -0.22 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.023 0.008 -9999 0 -0.12 2 2
Nck/Pak 0.013 0.056 -9999 0 -0.12 82 82
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.079 -9999 0 -0.22 24 24
mol:GDP 0.041 0.071 -9999 0 -0.25 12 12
mol:NADP 0.037 0.07 -9999 0 -0.29 9 9
eNOS/Hsp90 0.045 0.071 -9999 0 -0.27 9 9
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
mol:IP3 0.027 0.068 -9999 0 -0.24 18 18
HIF1A/ARNT 0.024 0.042 -9999 0 -0.15 28 28
SHB 0.023 0.008 -9999 0 -0.12 2 2
VEGFA 0.022 0.021 -9999 0 -0.085 17 17
VEGFC 0.017 0.029 -9999 0 -0.12 24 24
FAK1/Vinculin -0.007 0.13 -9999 0 -0.38 33 33
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.008 0.094 -9999 0 -0.21 46 46
PTPN6 0.023 0.009 -9999 0 -0.12 2 2
EPAS1 0.025 0.04 -9999 0 -0.13 27 27
mol:L-citrulline 0.037 0.07 -9999 0 -0.29 9 9
ITGAV 0.012 0.033 -9999 0 -0.12 31 31
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.042 0.074 -9999 0 -0.21 21 21
VEGFR2 homodimer/VEGFA homodimer 0.047 0.078 -9999 0 -0.25 17 17
VEGFR2/3 heterodimer 0.028 0.056 -9999 0 -0.28 7 7
VEGFB 0.015 0.032 -9999 0 -0.12 30 30
MAPK11 0.022 0.069 -9999 0 -0.25 17 17
VEGFR2 homodimer 0.028 0.052 -9999 0 -0.34 7 7
FLT1 0.022 0.014 -9999 0 -0.12 5 5
NEDD4 0.023 0.022 -9999 0 -0.1 15 15
MAPK3 0.014 0.064 -9999 0 -0.23 17 17
MAPK1 0.013 0.064 -9999 0 -0.24 17 17
VEGFA145/NRP2 0.002 0.072 -9999 0 -0.15 86 86
VEGFR1/2 heterodimer 0.027 0.058 -9999 0 -0.26 9 9
KDR 0.028 0.052 -9999 0 -0.34 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.033 0.083 -9999 0 -0.28 13 13
SRC 0.023 0.008 -9999 0 -0.12 2 2
platelet activating factor biosynthetic process 0.015 0.066 -9999 0 -0.24 16 16
PI3K 0.034 0.099 -9999 0 -0.3 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.027 0.076 -9999 0 -0.22 21 21
FES 0.03 0.066 -9999 0 -0.23 17 17
GAB1 0.026 0.095 -9999 0 -0.3 26 26
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.07 -9999 0 -0.23 16 16
CTNNB1 0.022 0.007 -9999 0 -0.12 1 1
SOS1 0.017 0.027 -9999 0 -0.12 20 20
ARNT 0.022 0.012 -9999 0 -0.12 4 4
eNOS/Caveolin-1 0.039 0.074 -9999 0 -0.28 10 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.076 -9999 0 -0.22 22 22
PI3K/GAB1 0.027 0.12 -9999 0 -0.34 30 30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.036 0.082 -9999 0 -0.19 29 29
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.06 -9999 0 -0.32 6 6
HSP90AA1 0.023 0.004 -9999 0 -10000 0 0
CDC42 0.03 0.065 -9999 0 -0.29 9 9
actin cytoskeleton reorganization 0.036 0.069 -9999 0 -0.23 16 16
PTK2 -0.015 0.13 -9999 0 -0.4 32 32
EDG1 0.031 0.067 -9999 0 -0.28 11 11
mol:DAG 0.027 0.068 -9999 0 -0.24 18 18
CaM/Ca2+ 0.033 0.068 -9999 0 -0.26 12 12
MAP2K3 0.023 0.064 -9999 0 -0.25 13 13
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.083 -9999 0 -0.35 11 11
PLCG1 0.027 0.068 -9999 0 -0.28 11 11
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.048 0.069 -9999 0 -0.22 16 16
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
YES1 0.02 0.018 -9999 0 -0.12 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.075 -9999 0 -0.24 19 19
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.036 0.07 -9999 0 -0.24 16 16
cell migration -0.002 0.14 -9999 0 -0.38 42 42
mol:PI-3-4-5-P3 0.034 0.094 -9999 0 -0.28 22 22
FYN 0.012 0.037 -9999 0 -0.12 40 40
VEGFB/NRP1 0.027 0.063 -9999 0 -0.21 19 19
mol:NO 0.037 0.07 -9999 0 -0.29 9 9
PXN 0.022 0.013 -9999 0 -0.12 5 5
HRAS/GTP -0.013 0.043 -9999 0 -0.24 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.048 0.077 -9999 0 -0.35 11 11
VHL 0.021 0.016 -9999 0 -0.12 7 7
ITGB3 0.005 0.046 -9999 0 -0.12 67 67
NOS3 0.037 0.076 -9999 0 -0.32 9 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.036 0.07 -9999 0 -0.23 16 16
RAC1 0.023 0.002 -9999 0 -10000 0 0
PRKCA 0.02 0.063 -9999 0 -0.25 13 13
PRKCB 0.02 0.061 -9999 0 -0.27 11 11
VCL 0.021 0.014 -9999 0 -0.12 5 5
VEGFA165/NRP1 0.033 0.064 -9999 0 -0.23 17 17
VEGFR1/2 heterodimer/VEGFA homodimer 0.035 0.072 -9999 0 -0.24 18 18
VEGFA165/NRP2 0.002 0.072 -9999 0 -0.15 86 86
MAPKKK cascade 0.048 0.074 -9999 0 -0.28 13 13
NRP2 0.012 0.036 -9999 0 -0.12 38 38
VEGFC homodimer 0.017 0.029 -9999 0 -0.12 24 24
NCK1 0.02 0.019 -9999 0 -0.12 9 9
ROCK1 0.023 0.009 -9999 0 -0.12 2 2
FAK1/Paxillin -0.004 0.12 -9999 0 -0.37 33 33
MAP3K13 0.024 0.068 -9999 0 -0.23 19 19
PDPK1 0.03 0.085 -9999 0 -0.26 22 22
Class IB PI3K non-lipid kinase events

Figure S102.  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 S102.  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 -0.019 0.025 0.12 18 -10000 0 18
PI3K Class IB/PDE3B 0.019 0.025 -10000 0 -0.12 18 18
PDE3B 0.019 0.025 -10000 0 -0.12 18 18
Signaling events regulated by Ret tyrosine kinase

Figure S103.  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 S103.  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 0.096 -9999 0 -0.39 31 31
Crk/p130 Cas/Paxillin -0.007 0.025 -9999 0 -0.15 7 7
JUN 0.013 0.059 -9999 0 -0.21 22 22
HRAS 0.023 0.006 -9999 0 -0.12 1 1
RET51/GFRalpha1/GDNF/GRB10 0.045 0.038 -9999 0 -0.099 11 11
RAP1A 0.021 0.011 -9999 0 -0.12 3 3
FRS2 0.019 0.023 -9999 0 -0.12 15 15
RAP1A/GDP 0.01 0.034 -9999 0 -0.14 28 28
RET51/GFRalpha1/GDNF/DOK1 0.046 0.038 -9999 0 -0.11 9 9
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.022 0.016 -9999 0 -0.12 7 7
RET9/GFRalpha1/GDNF/Enigma 0.034 0.031 -9999 0 -0.11 7 7
RHOA 0.023 0.006 -9999 0 -0.12 1 1
RAP1A/GTP 0.04 0.041 -9999 0 -0.092 30 30
GRB7 0.018 0.025 -9999 0 -0.12 18 18
RET51/GFRalpha1/GDNF 0.046 0.036 -9999 0 -0.096 8 8
MAPKKK cascade 0.037 0.037 -9999 0 -0.18 5 5
BCAR1 0.023 0.01 -9999 0 -0.12 3 3
RET9/GFRalpha1/GDNF/IRS1 0.034 0.032 -9999 0 -0.099 10 10
lamellipodium assembly 0.025 0.043 -9999 0 -0.17 7 7
RET51/GFRalpha1/GDNF/SHC 0.048 0.034 -9999 0 -0.096 5 5
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
RET9/GFRalpha1/GDNF/SHC 0.037 0.027 -9999 0 -0.099 3 3
RET9/GFRalpha1/GDNF/Shank3 0.037 0.027 -9999 0 -0.1 3 3
MAPK3 0.022 0.033 -9999 0 -0.087 30 30
DOK1 0.022 0.015 -9999 0 -0.12 6 6
DOK6 0.023 0.008 -9999 0 -0.12 2 2
PXN 0.022 0.013 -9999 0 -0.12 5 5
neurite development 0.029 0.039 -9999 0 -0.17 10 10
DOK5 -0.008 0.054 -9999 0 -0.12 103 103
GFRA1 0.011 0.04 -9999 0 -0.12 49 49
MAPK8 0.015 0.061 -9999 0 -0.23 17 17
HRAS/GTP 0.042 0.04 -9999 0 -0.15 9 9
tube development 0.038 0.03 -9999 0 -0.12 7 7
MAPK1 0.022 0.033 -9999 0 -0.087 30 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.017 0.053 -9999 0 -0.16 36 36
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
SRC 0.023 0.008 -9999 0 -0.12 2 2
PDLIM7 0.02 0.021 -9999 0 -0.12 12 12
RET51/GFRalpha1/GDNF/Dok6 0.057 0.035 -9999 0 -0.096 5 5
SHC1 0.023 0.001 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.048 0.035 -9999 0 -0.097 7 7
RET51/GFRalpha1/GDNF/Dok5 -0.003 0.072 -9999 0 -0.1 146 146
PRKCA 0.011 0.038 -9999 0 -0.12 42 42
HRAS/GDP 0.017 0.008 -9999 0 -0.11 2 2
CREB1 0.021 0.072 -9999 0 -0.24 30 30
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.036 -9999 0 -0.14 20 20
RET51/GFRalpha1/GDNF/Grb7 0.042 0.043 -9999 0 -0.11 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.019 0.024 -9999 0 -0.12 17 17
DOK4 0.022 0.012 -9999 0 -0.12 4 4
JNK cascade 0.01 0.063 -9999 0 -0.2 29 29
RET9/GFRalpha1/GDNF/FRS2 0.031 0.037 -9999 0 -0.1 19 19
SHANK3 0.023 0.006 -9999 0 -0.12 1 1
RASA1 0.021 0.011 -9999 0 -0.12 3 3
NCK1 0.02 0.019 -9999 0 -0.12 9 9
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.048 -9999 0 -0.15 33 33
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.022 0.054 -9999 0 -0.16 36 36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.015 0.065 -9999 0 -0.16 60 60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.024 0.049 -9999 0 -0.15 33 33
PI3K 0.034 0.052 -9999 0 -0.19 11 11
SOS1 0.017 0.027 -9999 0 -0.12 20 20
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.046 0.032 -9999 0 -0.12 7 7
GRB10 0.022 0.014 -9999 0 -0.12 5 5
activation of MAPKK activity 0.021 0.054 -9999 0 -0.27 10 10
RET51/GFRalpha1/GDNF/FRS2 0.042 0.043 -9999 0 -0.096 21 21
GAB1 0.02 0.022 -9999 0 -0.12 13 13
IRS1 0.02 0.022 -9999 0 -0.12 14 14
IRS2 0.022 0.016 -9999 0 -0.12 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.029 0.038 -9999 0 -0.2 3 3
RET51/GFRalpha1/GDNF/PKC alpha 0.031 0.052 -9999 0 -0.097 44 44
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
GDNF 0.023 0.008 -9999 0 -0.12 2 2
RAC1 0.023 0.002 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.045 0.039 -9999 0 -0.095 13 13
Rac1/GTP 0.032 0.051 -9999 0 -0.2 7 7
RET9/GFRalpha1/GDNF 0.024 0.026 -9999 0 -0.058 51 51
GFRalpha1/GDNF 0.025 0.031 -9999 0 -0.073 51 51
Syndecan-3-mediated signaling events

Figure S104.  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 S104.  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 0.022 0.011 -9999 0 -0.12 3 3
Syndecan-3/Src/Cortactin -0.001 0.076 -9999 0 -0.26 15 15
Syndecan-3/Neurocan 0.021 0.051 -9999 0 -0.47 5 5
POMC 0.023 0.01 -9999 0 -0.12 3 3
EGFR 0.015 0.03 -9999 0 -0.12 25 25
Syndecan-3/EGFR 0.016 0.053 -9999 0 -0.35 8 8
AGRP 0.023 0.001 -9999 0 -10000 0 0
NCSTN 0.022 0.012 -9999 0 -0.12 4 4
PSENEN 0.016 0.03 -9999 0 -0.12 25 25
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0.031 -9999 0 -0.12 28 28
APH1A 0.023 0.009 -9999 0 -0.12 2 2
NCAN 0.023 0.01 -9999 0 -0.12 3 3
long-term memory 0.018 0.064 -9999 0 -0.32 10 10
Syndecan-3/IL8 0.011 0.056 -9999 0 -0.39 7 7
PSEN1 0.022 0.008 -9999 0 -0.12 1 1
Src/Cortactin 0.03 0.027 -9999 0 -0.12 17 17
FYN 0.012 0.037 -9999 0 -0.12 40 40
limb bud formation 0.006 0.051 -9999 0 -0.43 6 6
MC4R 0 0 -9999 0 -10000 0 0
SRC 0.023 0.008 -9999 0 -0.12 2 2
PTN -0.01 0.055 -9999 0 -0.12 111 111
FGFR/FGF/Syndecan-3 0.006 0.052 -9999 0 -0.43 6 6
neuron projection morphogenesis -0.006 0.068 -9999 0 -0.29 12 12
Syndecan-3/AgRP 0.021 0.051 -9999 0 -0.41 6 6
Syndecan-3/AgRP/MC4R 0.019 0.049 -9999 0 -0.45 5 5
Fyn/Cortactin 0.011 0.055 -9999 0 -0.14 50 50
SDC3 0.006 0.052 -9999 0 -0.5 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.011 0.055 -9999 0 -0.38 7 7
IL8 0.004 0.047 -9999 0 -0.12 70 70
Syndecan-3/Fyn/Cortactin 0.019 0.065 -9999 0 -0.32 10 10
Syndecan-3/CASK 0.005 0.049 -9999 0 -0.47 5 5
alpha-MSH/MC4R 0.017 0.007 -9999 0 -0.076 3 3
Gamma Secretase 0.035 0.067 -9999 0 -0.097 88 88
Regulation of p38-alpha and p38-beta

Figure S105.  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 S105.  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
RIP1/MEKK3 0.03 0.016 -9999 0 -0.12 6 6
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.012 0.035 -9999 0 -0.12 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.011 -9999 0 -0.12 3 3
RAC1-CDC42/GTP/PAK family 0.007 0.055 -9999 0 -0.15 51 51
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.02 0.018 -9999 0 -0.12 8 8
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.023 0 -9999 0 -10000 0 0
FYN 0.012 0.037 -9999 0 -0.12 40 40
MAP3K12 0.022 0.011 -9999 0 -0.12 3 3
FGR 0.023 0.006 -9999 0 -0.12 1 1
p38 alpha/TAB1 0.02 0.083 -9999 0 -0.2 43 43
PRKG1 0.018 0.026 -9999 0 -0.12 19 19
DUSP8 0.023 0.006 -9999 0 -0.12 1 1
PGK/cGMP/p38 alpha 0.014 0.079 -9999 0 -0.2 44 44
apoptosis 0.018 0.079 -9999 0 -0.2 43 43
RAL/GTP 0.024 0.032 -9999 0 -0.12 26 26
LYN 0.021 0.013 -9999 0 -0.12 4 4
DUSP1 -0.004 0.051 -9999 0 -0.12 90 90
PAK1 0.016 0.029 -9999 0 -0.12 24 24
SRC 0.023 0.008 -9999 0 -0.12 2 2
RAC1/OSM/MEKK3/MKK3 0.057 0.021 -9999 0 -0.093 11 11
TRAF6 0.022 0.009 -9999 0 -0.12 2 2
RAC1 0.023 0.002 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.023 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.019 -9999 0 -0.13 8 8
MAPK11 0.005 0.099 -9999 0 -0.28 38 38
BLK 0.022 0.013 -9999 0 -0.12 5 5
HCK 0.019 0.023 -9999 0 -0.12 15 15
MAP2K3 0.023 0.006 -9999 0 -0.12 1 1
DUSP16 0.018 0.025 -9999 0 -0.12 18 18
DUSP10 0.012 0.035 -9999 0 -0.12 36 36
TRAF6/MEKK3 0.028 0.016 -9999 0 -0.091 10 10
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
MAPK14 0.011 0.086 -9999 0 -0.22 44 44
positive regulation of innate immune response 0.008 0.11 -9999 0 -0.3 40 40
LCK 0.022 0.015 -9999 0 -0.12 6 6
p38alpha-beta/MKP7 0.014 0.11 -9999 0 -0.29 41 41
p38alpha-beta/MKP5 0.006 0.12 -9999 0 -0.28 49 49
PGK/cGMP 0.014 0.017 -9999 0 -0.076 19 19
PAK2 0.022 0.011 -9999 0 -0.12 3 3
p38alpha-beta/MKP1 -0.006 0.12 -9999 0 -0.29 55 55
CDC42 0.023 0.002 -9999 0 -10000 0 0
RALB 0.022 0.007 -9999 0 -0.12 1 1
RALA 0.022 0.009 -9999 0 -0.12 2 2
PAK3 0.008 0.044 -9999 0 -0.12 59 59
Arf6 trafficking events

Figure S106.  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 S106.  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
SLC2A4 0.023 0.006 -10000 0 -0.12 1 1
CLTC 0.005 0.082 -10000 0 -0.46 11 11
calcium ion-dependent exocytosis 0.01 0.043 -10000 0 -0.17 16 16
Dynamin 2/GTP 0.013 0.044 -10000 0 -0.1 58 58
EXOC4 0.023 0.007 -10000 0 -0.12 1 1
CD59 0.008 0.061 -10000 0 -0.36 11 11
CPE 0.009 0.027 -10000 0 -0.065 59 59
CTNNB1 0.022 0.007 -10000 0 -0.12 1 1
membrane fusion 0.015 0.036 -10000 0 -0.15 22 22
CTNND1 0.012 0.042 -10000 0 -0.098 57 57
DNM2 0.02 0.022 -10000 0 -0.12 13 13
mol:PI-4-5-P2 0.014 0.048 -10000 0 -0.27 12 12
TSHR 0.013 0.026 -10000 0 -0.068 49 49
INS 0.018 0.017 -10000 0 -10000 0 0
BIN1 0.022 0.013 -10000 0 -0.12 5 5
mol:Choline 0.015 0.036 -10000 0 -0.15 22 22
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.022 -10000 0 -0.072 29 29
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.013 0.044 -10000 0 -0.1 58 58
JUP 0.006 0.065 -10000 0 -0.37 12 12
ASAP2/amphiphysin II 0.026 0.02 -10000 0 -0.1 12 12
ARF6/GTP 0.015 0.02 -10000 0 -0.15 9 9
CDH1 0.004 0.069 -10000 0 -0.4 11 11
clathrin-independent pinocytosis 0.015 0.02 -10000 0 -0.15 9 9
MAPK8IP3 0.023 0.006 -10000 0 -0.12 1 1
positive regulation of endocytosis 0.015 0.02 -10000 0 -0.15 9 9
EXOC2 0.022 0.014 -10000 0 -0.12 5 5
substrate adhesion-dependent cell spreading 0.011 0.1 -10000 0 -0.4 26 26
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.015 -10000 0 -0.12 6 6
regulation of calcium-dependent cell-cell adhesion -0.013 0.08 0.34 15 -10000 0 15
positive regulation of phagocytosis 0.018 0.016 -10000 0 -0.11 8 8
ARF6/GTP/JIP3 0.029 0.019 -10000 0 -0.12 9 9
ACAP1 0.014 0.032 -10000 0 -0.13 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.01 0.06 -10000 0 -0.39 10 10
clathrin heavy chain/ACAP1 0.011 0.066 -10000 0 -0.32 14 14
JIP4/KLC1 0.033 0.04 -10000 0 -0.1 39 39
EXOC1 0.021 0.012 -10000 0 -0.12 3 3
exocyst 0.011 0.11 -10000 0 -0.4 26 26
RALA/GTP 0.014 0.021 -10000 0 -0.13 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.025 0.029 -10000 0 -0.12 21 21
receptor recycling 0.015 0.02 -10000 0 -0.15 9 9
CTNNA1 0.011 0.041 -10000 0 -0.097 56 56
NME1 0.014 0.022 -10000 0 -0.072 29 29
clathrin coat assembly 0.005 0.081 -10000 0 -0.45 11 11
IL2RA 0.009 0.06 -10000 0 -0.38 10 10
VAMP3 0.019 0.016 -10000 0 -0.11 8 8
GLUT4/clathrin heavy chain/ACAP1 0.018 0.065 -10000 0 -0.33 12 12
EXOC6 0.021 0.012 -10000 0 -0.12 3 3
PLD1 0.001 0.057 -10000 0 -0.19 41 41
PLD2 0.018 0.028 -10000 0 -0.19 6 6
EXOC5 0.022 0.011 -10000 0 -0.12 3 3
PIP5K1C 0.014 0.048 -10000 0 -0.27 12 12
SDC1 0.008 0.061 -10000 0 -0.36 11 11
ARF6/GDP 0.011 0.042 -10000 0 -0.099 66 66
EXOC7 0.023 0.001 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.015 0.083 -10000 0 -0.35 15 15
mol:Phosphatidic acid 0.015 0.036 -10000 0 -0.15 22 22
endocytosis -0.025 0.02 0.1 12 -10000 0 12
SCAMP2 0.023 0.009 -10000 0 -0.12 2 2
ADRB2 0.009 0.078 -10000 0 -0.43 11 11
EXOC3 0.023 0.009 -10000 0 -0.12 2 2
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.016 0.045 -10000 0 -0.1 58 58
KLC1 0.021 0.013 -10000 0 -0.12 4 4
AVPR2 0.008 0.079 -10000 0 -0.4 13 13
RALA 0.022 0.009 -10000 0 -0.12 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.013 0.087 -10000 0 -0.32 19 19
JNK signaling in the CD4+ TCR pathway

Figure S107.  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 S107.  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 0.036 0.054 -9999 0 -0.1 61 61
MAP4K1 0.019 0.023 -9999 0 -0.12 15 15
MAP3K8 0.023 0.009 -9999 0 -0.12 2 2
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.023 0.002 -9999 0 -10000 0 0
CRKL 0.023 0.009 -9999 0 -0.12 2 2
MAP3K1 0.021 0.052 -9999 0 -0.19 9 9
JUN -0.003 0.095 -9999 0 -0.49 18 18
MAP3K7 0.021 0.052 -9999 0 -0.18 8 8
GRAP2 0.022 0.012 -9999 0 -0.12 4 4
CRK 0.022 0.016 -9999 0 -0.12 7 7
MAP2K4 0.021 0.058 -9999 0 -0.2 14 14
LAT 0.022 0.01 -9999 0 -0.12 3 3
LCP2 0.013 0.033 -9999 0 -0.12 31 31
MAPK8 0.003 0.096 -9999 0 -0.52 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.031 0.038 -9999 0 -0.17 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.044 0.056 -9999 0 -0.092 64 64
Hedgehog signaling events mediated by Gli proteins

Figure S108.  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 S108.  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 0.019 0.019 -10000 0 -0.12 10 10
HDAC2 0.02 0.021 -10000 0 -0.12 12 12
GNB1/GNG2 0.04 0.034 -10000 0 -0.11 23 23
forebrain development 0.027 0.11 -10000 0 -0.39 25 25
GNAO1 0.011 0.041 -10000 0 -0.12 50 50
SMO/beta Arrestin2 0.035 0.021 -10000 0 -0.14 5 5
SMO 0.024 0.011 -10000 0 -0.12 3 3
ARRB2 0.023 0.014 -10000 0 -0.12 5 5
GLI3/SPOP 0.006 0.11 -10000 0 -0.21 86 86
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
GNAI2 0.023 0.011 -10000 0 -0.12 3 3
SIN3/HDAC complex 0.052 0.031 -10000 0 -0.099 19 19
GNAI1 0.013 0.035 -10000 0 -0.12 36 36
XPO1 0.025 0.01 -10000 0 -0.12 2 2
GLI1/Su(fu) 0.033 0.1 -10000 0 -0.38 26 26
SAP30 0.023 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.011 -10000 0 -0.12 3 3
MIM/GLI2A 0.023 0.034 -10000 0 -0.11 31 31
IFT88 0.016 0.03 -10000 0 -0.12 25 25
GNAI3 0.022 0.009 -10000 0 -0.12 1 1
GLI2 0.036 0.041 -10000 0 -0.22 7 7
GLI3 -0.006 0.11 0.16 2 -0.22 85 87
CSNK1D 0.023 0.001 -10000 0 -10000 0 0
CSNK1E 0.022 0.015 -10000 0 -0.12 6 6
SAP18 0.023 0.003 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.016 0.03 -10000 0 -0.12 25 25
GNG2 0.02 0.018 -10000 0 -0.12 9 9
Gi family/GTP 0.009 0.07 -10000 0 -0.14 88 88
SIN3B 0.021 0.015 -10000 0 -0.12 6 6
SIN3A 0.021 0.014 -10000 0 -0.12 5 5
GLI3/Su(fu) 0.015 0.1 -10000 0 -0.33 27 27
GLI2/Su(fu) 0.054 0.043 -10000 0 -0.21 8 8
FOXA2 0.028 0.084 -10000 0 -0.74 5 5
neural tube patterning 0.027 0.11 -10000 0 -0.39 25 25
SPOP 0.022 0.011 -10000 0 -0.12 3 3
Su(fu)/PIAS1 0.036 0.04 -10000 0 -0.2 13 13
GNB1 0.023 0.006 -10000 0 -0.12 1 1
CSNK1G2 0.023 0.01 -10000 0 -0.12 3 3
CSNK1G3 0.022 0.007 -10000 0 -0.12 1 1
MTSS1 0.023 0.034 -10000 0 -0.11 31 31
embryonic limb morphogenesis 0.027 0.11 -10000 0 -0.39 25 25
SUFU 0.026 0.041 -10000 0 -0.22 12 12
LGALS3 0.018 0.023 -10000 0 -0.12 14 14
catabolic process 0.031 0.1 -10000 0 -0.3 27 27
GLI3A/CBP 0.033 0.022 -10000 0 -0.13 7 7
KIF3A 0.019 0.021 -10000 0 -0.12 12 12
GLI1 0.026 0.11 -10000 0 -0.4 25 25
RAB23 0.023 0.01 -10000 0 -0.12 3 3
CSNK1A1 0.022 0.007 -10000 0 -0.12 1 1
IFT172 0.022 0.014 -10000 0 -0.12 5 5
RBBP7 0.021 0.011 -10000 0 -0.12 3 3
Su(fu)/Galectin3 0.031 0.044 -10000 0 -0.19 16 16
GNAZ 0.023 0.012 -10000 0 -0.12 4 4
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
CSNK1G1 0.023 0.008 -10000 0 -0.12 2 2
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GLI2/SPOP 0.046 0.042 -10000 0 -0.24 6 6
STK36 0.022 0.021 -10000 0 -0.12 12 12
Gi family/GNB1/GNG2/GDP 0.008 0.077 -10000 0 -0.22 31 31
PTCH1 0.033 0.11 -10000 0 -0.53 9 9
MIM/GLI1 0.043 0.11 -10000 0 -0.4 23 23
CREBBP 0.033 0.022 -10000 0 -0.14 7 7
Su(fu)/SIN3/HDAC complex 0.02 0.095 -10000 0 -0.32 27 27
Class I PI3K signaling events mediated by Akt

Figure S109.  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 S109.  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 0.02 0.016 -10000 0 -0.07 16 16
BAD/BCL-XL/YWHAZ 0.039 0.031 -10000 0 -0.095 22 22
CDKN1B 0.013 0.076 -10000 0 -0.33 23 23
CDKN1A 0.017 0.074 -10000 0 -0.33 23 23
FRAP1 0.022 0.012 -10000 0 -0.12 4 4
PRKDC 0.021 0.016 -10000 0 -0.12 7 7
FOXO3 0.016 0.075 -10000 0 -0.32 24 24
AKT1 0.014 0.077 -10000 0 -0.34 23 23
BAD 0.023 0.01 -10000 0 -0.12 3 3
AKT3 -0.004 0.054 -10000 0 -0.2 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.017 0.073 -10000 0 -0.32 23 23
AKT1/ASK1 0.019 0.077 -10000 0 -0.32 23 23
BAD/YWHAZ 0.043 0.025 -10000 0 -0.11 11 11
RICTOR 0.02 0.016 -10000 0 -0.12 7 7
RAF1 0.023 0.003 -10000 0 -10000 0 0
JNK cascade -0.018 0.074 0.31 23 -10000 0 23
TSC1 0.017 0.073 -10000 0 -0.32 23 23
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.078 -10000 0 -0.33 24 24
EP300 0.022 0.009 -10000 0 -0.12 2 2
mol:GDP 0.014 0.076 -10000 0 -0.34 23 23
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.016 0.074 -10000 0 -0.32 23 23
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
TBC1D4 0.018 0.013 -10000 0 -0.04 29 29
MAP3K5 0.018 0.025 -10000 0 -0.12 17 17
MAPKAP1 0.023 0.002 -10000 0 -10000 0 0
negative regulation of cell cycle -0.017 0.072 0.21 29 -10000 0 29
YWHAH 0.021 0.015 -10000 0 -0.12 6 6
AKT1S1 0.017 0.073 -10000 0 -0.32 23 23
CASP9 0.016 0.074 -10000 0 -0.33 23 23
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
p27Kip1/KPNA1 0.021 0.081 -10000 0 -0.31 26 26
GBL 0.023 0.008 -10000 0 -0.12 2 2
PDK1/Src/Hsp90 0.042 0.03 -10000 0 -0.12 18 18
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
SRC 0.023 0.008 -10000 0 -0.12 2 2
AKT2/p21CIP1 0.022 0.067 -10000 0 -0.28 24 24
KIAA1303 0.023 0.008 -10000 0 -0.12 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.071 -10000 0 -0.34 17 17
CHUK 0.014 0.077 -10000 0 -0.33 24 24
BAD/BCL-XL 0.035 0.076 -10000 0 -0.31 23 23
mTORC2 0.047 0.043 -10000 0 -0.1 39 39
AKT2 0.015 0.024 -10000 0 -0.2 5 5
FOXO1-3a-4/14-3-3 family 0.023 0.087 -10000 0 -0.25 33 33
PDPK1 0.023 0.006 -10000 0 -0.12 1 1
MDM2 0.015 0.076 -10000 0 -0.33 23 23
MAPKKK cascade -0.026 0.076 0.32 24 -10000 0 24
MDM2/Cbp/p300 0.032 0.085 -10000 0 -0.33 23 23
TSC1/TSC2 0.018 0.072 -10000 0 -0.31 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.082 -10000 0 -0.32 23 23
glucose import 0.018 0.019 -10000 0 -0.14 5 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0.07 -10000 0 -0.27 15 15
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.02 0.012 -10000 0 -0.031 30 30
GSK3A 0.016 0.075 -10000 0 -0.33 23 23
FOXO1 0.017 0.073 -10000 0 -0.32 23 23
GSK3B 0.016 0.075 -10000 0 -0.33 23 23
SFN 0.014 0.031 -10000 0 -0.12 28 28
G1/S transition of mitotic cell cycle 0.019 0.074 -10000 0 -0.32 23 23
p27Kip1/14-3-3 family 0.028 0.078 -10000 0 -0.32 18 18
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
KPNA1 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.021 -10000 0 -0.12 13 13
RHEB 0.019 0.022 -10000 0 -0.12 13 13
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S110.  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 S110.  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 0.016 0.031 -9999 0 -0.12 28 28
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.023 0.006 -9999 0 -0.12 1 1
TCEB1 0.022 0.011 -9999 0 -0.12 3 3
HIF1A/p53 0.002 0.061 -9999 0 -0.21 32 32
HIF1A 0.007 0.046 -9999 0 -0.19 22 22
COPS5 0.018 0.023 -9999 0 -0.12 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.049 -9999 0 -0.17 9 9
FIH (dimer) 0.023 0.006 -9999 0 -0.12 1 1
CDKN2A 0.015 0.021 -9999 0 -0.12 10 10
ARNT/IPAS 0.028 0.028 -9999 0 -0.14 4 4
HIF1AN 0.023 0.006 -9999 0 -0.12 1 1
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
HIF1A/ARNT 0.014 0.055 -9999 0 -0.19 22 22
CUL2 0.022 0.011 -9999 0 -0.12 3 3
OS9 0.022 0.009 -9999 0 -0.12 2 2
RACK1/Elongin B/Elongin C 0.043 0.025 -9999 0 -0.11 14 14
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.014 0.055 -9999 0 -0.19 23 23
PHD1-3/OS9 0.015 0.065 -9999 0 -0.097 110 110
HIF1A/RACK1/Elongin B/Elongin C 0.035 0.058 -9999 0 -0.25 9 9
VHL 0.021 0.016 -9999 0 -0.12 7 7
HSP90AA1 0.023 0.004 -9999 0 -10000 0 0
HIF1A/JAB1 0.011 0.057 -9999 0 -0.2 25 25
EGLN3 -0.003 0.051 -9999 0 -0.12 87 87
EGLN2 0.023 0.008 -9999 0 -0.12 2 2
EGLN1 0.023 0.009 -9999 0 -0.12 2 2
TP53 0.01 0.029 -9999 0 -0.12 24 24
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.097 -9999 0 -0.53 16 16
ARNT 0.022 0.012 -9999 0 -0.12 4 4
ARD1A 0.018 0.025 -9999 0 -0.12 18 18
RBX1 0.022 0.011 -9999 0 -0.12 3 3
HIF1A/p19ARF 0.004 0.063 -9999 0 -0.22 28 28
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S111.  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 S111.  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 0.021 0.017 -10000 0 -0.12 8 8
NFATC1 0.03 0.064 -10000 0 -0.25 14 14
NFATC2 0.02 0.048 -10000 0 -0.18 16 16
NFATC3 0.024 0.021 -10000 0 -0.24 2 2
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Calcineurin A alpha-beta B1/CABIN1 -0.006 0.081 -10000 0 -0.22 38 38
Exportin 1/Ran/NUP214 0.037 0.039 -10000 0 -0.11 34 34
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.015 0.079 -10000 0 -0.22 28 28
BCL2/BAX 0.029 0.025 -10000 0 -0.074 30 30
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.02 -10000 0 -0.12 12 12
CaM/Ca2+ 0.013 0.02 -10000 0 -0.12 12 12
BAX 0.023 0 -10000 0 -10000 0 0
MAPK14 0.022 0.007 -10000 0 -0.12 1 1
BAD 0.023 0.01 -10000 0 -0.12 3 3
CABIN1/MEF2D 0.006 0.08 -10000 0 -0.21 38 38
Calcineurin A alpha-beta B1/BCL2 0.016 0.031 -10000 0 -0.12 28 28
FKBP8 0.016 0.031 -10000 0 -0.12 27 27
activation-induced cell death of T cells -0.006 0.079 0.2 38 -10000 0 38
KPNB1 0.022 0.009 -10000 0 -0.12 2 2
KPNA2 0.017 0.024 -10000 0 -0.12 15 15
XPO1 0.022 0.01 -10000 0 -0.12 2 2
SFN 0.014 0.031 -10000 0 -0.12 28 28
MAP3K8 0.022 0.009 -10000 0 -0.12 2 2
NFAT4/CK1 alpha 0.029 0.038 -10000 0 -0.15 13 13
MEF2D/NFAT1/Cbp/p300 0.039 0.079 -10000 0 -0.15 46 46
CABIN1 -0.006 0.081 -10000 0 -0.22 38 38
CALM1 0.021 0.014 -10000 0 -0.12 5 5
RAN 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.015 -10000 0 -0.12 6 6
CAMK4 0.016 0.031 -10000 0 -0.12 27 27
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
YWHAH 0.021 0.015 -10000 0 -0.12 6 6
Calcineurin A alpha-beta B1/AKAP79/PKA 0.032 0.017 -10000 0 -0.082 12 12
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
MAPK8 0.021 0.015 -10000 0 -0.12 6 6
MAPK9 0.021 0.011 -10000 0 -0.12 3 3
YWHAG 0.02 0.021 -10000 0 -0.12 13 13
FKBP1A 0.022 0.012 -10000 0 -0.12 4 4
NFAT1-c-4/YWHAQ 0.048 0.071 -10000 0 -0.29 10 10
PRKCH 0.019 0.023 -10000 0 -0.12 15 15
CABIN1/Cbp/p300 0.02 0.052 -10000 0 -0.15 43 43
CASP3 0.022 0.009 -10000 0 -0.12 2 2
PIM1 0.019 0.023 -10000 0 -0.12 15 15
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.012 -10000 0 -0.087 7 7
apoptosis 0.019 0.036 0.14 2 -0.21 11 13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.07 -10000 0 -0.26 16 16
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.021 0.017 -10000 0 -0.12 8 8
JNK2/NFAT4 0.034 0.024 -10000 0 -0.2 3 3
BAD/BCL-XL 0.029 0.028 -10000 0 -0.14 11 11
PRKCD 0.02 0.018 -10000 0 -0.12 8 8
NUP214 0.023 0.007 -10000 0 -0.12 1 1
PRKCZ 0.023 0.001 -10000 0 -10000 0 0
PRKCA 0.011 0.038 -10000 0 -0.12 42 42
PRKCG 0.022 0.016 -10000 0 -0.12 7 7
PRKCQ 0.015 0.03 -10000 0 -0.12 25 25
FKBP38/BCL2 0.023 0.035 -10000 0 -0.14 7 7
EP300 0.022 0.01 -10000 0 -0.12 2 2
PRKCB1 0.015 0.034 -10000 0 -0.12 34 34
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
NFATc/JNK1 0.039 0.068 -10000 0 -0.24 18 18
CaM/Ca2+/FKBP38 0.024 0.028 -10000 0 -0.073 39 39
FKBP12/FK506 0.016 0.014 -10000 0 -0.11 7 7
CSNK1A1 0.017 0.016 -10000 0 -0.085 12 12
CaM/Ca2+/CAMK IV 0.023 0.028 -10000 0 -0.1 14 14
NFATc/ERK1 0.041 0.066 -10000 0 -0.24 14 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.014 0.08 -10000 0 -0.22 29 29
NR4A1 0.017 0.082 -10000 0 -0.19 45 45
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
positive T cell selection 0.024 0.021 -10000 0 -0.24 2 2
NFAT1/CK1 alpha 0.021 0.044 -10000 0 -0.16 18 18
RCH1/ KPNB1 0.011 0.061 -10000 0 -0.13 82 82
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
AKAP5 0.023 0.008 -10000 0 -0.12 2 2
MEF2D 0.023 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.067 -10000 0 -0.24 17 17
CREBBP 0.02 0.016 -10000 0 -0.12 6 6
BCL2 0.016 0.031 -10000 0 -0.12 28 28
Sumoylation by RanBP2 regulates transcriptional repression

Figure S112.  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 S112.  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 0.019 0.019 -9999 0 -0.12 10 10
Ran/GTP/Exportin 1/HDAC4 -0.008 0.033 -9999 0 -0.15 26 26
MDM2/SUMO1 0.033 0.04 -9999 0 -0.11 30 30
HDAC4 0.023 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.043 -9999 0 -0.17 31 31
SUMO1 0.023 0.009 -9999 0 -0.12 2 2
NPC/RanGAP1/SUMO1 0.01 0.036 -9999 0 -0.14 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.02 0.03 -9999 0 -0.13 17 17
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.023 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.022 0.01 -9999 0 -0.12 2 2
SUMO1/HDAC4 0.036 0.035 -9999 0 -0.1 30 30
SUMO1/HDAC1 0.029 0.048 -9999 0 -0.13 30 30
RANGAP1 0.023 0.006 -9999 0 -0.12 1 1
MDM2/SUMO1/SUMO1 0.047 0.043 -9999 0 -0.1 33 33
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.036 -9999 0 -0.14 30 30
Ran/GTP 0.026 0.036 -9999 0 -0.12 30 30
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.02 0.02 -9999 0 -0.12 11 11
UBE2I 0.023 0.001 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.047 -9999 0 -0.15 30 30
NPC 0.009 0.023 -9999 0 -0.095 27 27
PIAS2 0.021 0.018 -9999 0 -0.12 9 9
PIAS1 0.022 0.009 -9999 0 -0.12 2 2
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Insulin Pathway

Figure S113.  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 S113.  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
CBL/APS/CAP 0.034 0.028 -9999 0 -0.089 16 16
TC10/GTP 0.031 0.023 -9999 0 -0.081 15 15
Insulin Receptor/Insulin/IRS1/Shp2 0.05 0.042 -9999 0 -0.1 29 29
HRAS 0.023 0.006 -9999 0 -0.12 1 1
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.013 0.036 -9999 0 -0.12 39 39
FOXO3 0.009 0.065 -9999 0 -0.6 6 6
AKT1 0.016 0.047 -9999 0 -0.12 27 27
INSR 0.023 0.017 -9999 0 -0.12 8 8
Insulin Receptor/Insulin 0.06 0.027 -9999 0 -0.16 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.022 0.014 -9999 0 -0.12 5 5
SORBS1 0.02 0.021 -9999 0 -0.12 12 12
CRK 0.022 0.016 -9999 0 -0.12 7 7
PTPN1 0.025 0.021 -9999 0 -0.16 3 3
CAV1 0.02 0.027 -9999 0 -0.09 13 13
CBL/APS/CAP/Crk-II/C3G 0.051 0.024 -9999 0 -0.1 7 7
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.03 -9999 0 -0.09 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.052 -9999 0 -0.091 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.037 0.054 -9999 0 -0.3 13 13
RPS6KB1 0.014 0.048 -9999 0 -0.13 33 33
PARD6A 0.023 0.009 -9999 0 -0.12 2 2
CBL 0.023 0.006 -9999 0 -0.12 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.009 0.073 -9999 0 -0.68 6 6
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.027 0.055 -9999 0 -0.13 38 38
HRAS/GTP -0.007 0.02 -9999 0 -0.12 6 6
Insulin Receptor 0.023 0.017 -9999 0 -0.12 8 8
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.063 0.034 -9999 0 -0.084 19 19
PRKCI -0.01 0.13 -9999 0 -0.38 62 62
Insulin Receptor/Insulin/GRB14/PDK1 0.008 0.045 -9999 0 -0.13 27 27
SHC1 0.023 0.001 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.021 0.079 -9999 0 -0.47 9 9
PI3K 0.033 0.057 -9999 0 -0.092 76 76
NCK2 0.023 0.006 -9999 0 -0.12 1 1
RHOQ 0.021 0.017 -9999 0 -0.12 8 8
mol:H2O2 0 0.002 -9999 0 -10000 0 0
HRAS/GDP 0.017 0.008 -9999 0 -0.11 2 2
AKT2 0.015 0.048 -9999 0 -0.13 26 26
PRKCZ 0.028 0.063 -9999 0 -0.36 13 13
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0.025 0.02 -9999 0 -0.079 13 13
F2RL2 0.02 0.022 -9999 0 -0.12 14 14
TRIP10 0.021 0.018 -9999 0 -0.12 9 9
Insulin Receptor/Insulin/Shc 0.044 0.02 -9999 0 -0.095 7 7
TC10/GTP/CIP4/Exocyst 0.026 0.026 -9999 0 -0.084 29 29
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.056 0.046 -9999 0 -0.091 38 38
RAPGEF1 0.023 0 -9999 0 -10000 0 0
RASA1 0.021 0.011 -9999 0 -0.12 3 3
NCK1 0.02 0.019 -9999 0 -0.12 9 9
CBL/APS/CAP/Crk-II 0.04 0.024 -9999 0 -0.11 7 7
TC10/GDP 0.014 0.022 -9999 0 -0.11 16 16
Insulin Receptor/Insulin/SHC/GRB10 0.056 0.029 -9999 0 -0.092 15 15
INPP5D 0.012 0.018 -9999 0 -0.086 12 12
SOS1 0.017 0.027 -9999 0 -0.12 20 20
SGK1 -0.002 0.004 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
IRS1 0.02 0.022 -9999 0 -0.12 14 14
p62DOK/RasGAP 0.022 0.08 -9999 0 -0.48 9 9
INS 0.024 0.011 -9999 0 -0.12 3 3
mol:PI-3-4-P2 0.012 0.018 -9999 0 -0.085 12 12
GRB2 0.023 0.006 -9999 0 -0.12 1 1
EIF4EBP1 0.016 0.045 -9999 0 -0.12 31 31
PTPRA 0.024 0.012 -9999 0 -0.098 5 5
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
TC10/GTP/CIP4 0.026 0.026 -9999 0 -0.084 29 29
PDPK1 0.023 0.006 -9999 0 -0.12 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.027 0.049 -9999 0 -0.13 43 43
Insulin Receptor/Insulin/IRS1 0.041 0.027 -9999 0 -0.091 13 13
Insulin Receptor/Insulin/IRS3 0.034 0.023 -9999 0 -0.093 17 17
Par3/Par6 0.046 0.032 -9999 0 -0.089 18 18
Insulin-mediated glucose transport

Figure S114.  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 S114.  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
Insulin responsive Vesicles 0.022 0.073 -10000 0 -0.21 23 23
CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
AKT1 0.021 0.019 -10000 0 -0.12 10 10
AKT2 0.019 0.025 -10000 0 -0.12 18 18
STXBP4 0.018 0.026 -10000 0 -0.12 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.015 0.067 0.18 6 -0.22 15 21
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
CALM1 0.022 0.014 -10000 0 -0.12 5 5
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
TBC1D4 0.02 0.017 -10000 0 -0.07 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.015 -10000 0 -0.12 6 6
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
SNARE/Synip 0.033 0.041 -10000 0 -0.13 19 19
YWHAG 0.02 0.021 -10000 0 -0.12 13 13
ASIP 0.021 0.015 -10000 0 -0.12 6 6
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
AS160/CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
RHOQ 0.021 0.017 -10000 0 -0.12 8 8
GYS1 0.025 0.017 -10000 0 -0.035 31 31
PRKCZ 0.023 0 -10000 0 -10000 0 0
TRIP10 0.021 0.018 -10000 0 -0.12 9 9
TC10/GTP/CIP4/Exocyst 0.026 0.026 -10000 0 -0.084 29 29
AS160/14-3-3 0.024 0.064 -10000 0 -0.19 36 36
VAMP2 0.016 0.032 -10000 0 -0.12 30 30
SLC2A4 0.015 0.071 0.18 6 -0.24 15 21
STX4 0.022 0.012 -10000 0 -0.12 4 4
GSK3B 0.023 0.03 -10000 0 -0.2 7 7
SFN 0.014 0.031 -10000 0 -0.12 28 28
LNPEP 0.017 0.027 -10000 0 -0.12 20 20
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Calcium signaling in the CD4+ TCR pathway

Figure S115.  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 S115.  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 0.025 0.021 -9999 0 -0.11 9 9
NFATC2 0.024 0.022 -9999 0 -0.096 11 11
NFATC3 0.026 0.02 -9999 0 -0.11 8 8
CD40LG 0.045 0.078 -9999 0 -0.22 12 12
PTGS2 0.037 0.089 -9999 0 -0.21 24 24
JUNB 0.007 0.042 -9999 0 -0.12 53 53
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.021 -9999 0 -0.12 12 12
CaM/Ca2+ 0.019 0.021 -9999 0 -0.12 12 12
CALM1 0.024 0.014 -9999 0 -0.12 5 5
JUN 0.017 0.032 -9999 0 -0.12 30 30
mol:Ca2+ 0.002 0.003 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.012 -9999 0 -0.085 7 7
FOSL1 0.021 0.018 -9999 0 -0.12 9 9
CREM 0.021 0.012 -9999 0 -0.12 4 4
Jun/NFAT1-c-4/p21SNFT 0.062 0.06 -9999 0 -0.17 9 9
FOS -0.002 0.052 -9999 0 -0.12 95 95
IFNG 0.041 0.084 -9999 0 -0.23 15 15
AP-1/NFAT1-c-4 0.09 0.11 -9999 0 -0.24 14 14
FASLG 0.044 0.079 -9999 0 -0.22 13 13
NFAT1-c-4/ICER1 0.052 0.038 -9999 0 -0.13 8 8
IL2RA 0.044 0.08 -9999 0 -0.22 15 15
FKBP12/FK506 0.016 0.014 -9999 0 -0.11 7 7
CSF2 0.045 0.079 -9999 0 -0.22 13 13
JunB/Fra1/NFAT1-c-4 0.046 0.06 -9999 0 -0.14 17 17
IL4 0.045 0.079 -9999 0 -0.22 12 12
IL2 0.008 0.015 -9999 0 -10000 0 0
IL3 0.039 0.05 -9999 0 -0.61 3 3
FKBP1A 0.022 0.012 -9999 0 -0.12 4 4
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.031 0.007 -9999 0 -0.12 1 1
VEGFR1 specific signals

Figure S116.  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 S116.  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 0.026 0.056 -9999 0 -0.28 10 10
VEGFR1 homodimer/NRP1 0.014 0.05 -9999 0 -0.4 5 5
mol:DAG 0.022 0.05 -9999 0 -0.26 10 10
VEGFR1 homodimer/NRP1/VEGFR 121 0.019 0.06 -9999 0 -0.29 10 10
CaM/Ca2+ 0.031 0.053 -9999 0 -0.25 10 10
HIF1A 0.029 0.033 -9999 0 -0.23 7 7
GAB1 0.02 0.022 -9999 0 -0.12 13 13
AKT1 0.014 0.071 -9999 0 -0.23 26 26
PLCG1 0.022 0.05 -9999 0 -0.26 10 10
NOS3 0.029 0.059 -9999 0 -0.26 11 11
CBL 0.023 0.006 -9999 0 -0.12 1 1
mol:NO 0.029 0.058 -9999 0 -0.25 11 11
FLT1 0.027 0.05 -9999 0 -0.47 5 5
PGF 0.021 0.018 -9999 0 -0.12 9 9
VEGFR1 homodimer/NRP2/VEGFR121 0.015 0.077 -9999 0 -0.24 22 22
CALM1 0.022 0.014 -9999 0 -0.12 5 5
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
eNOS/Hsp90 0.039 0.062 -9999 0 -0.26 11 11
endothelial cell proliferation 0.006 0.066 -9999 0 -0.3 13 13
mol:Ca2+ 0.022 0.049 -9999 0 -0.26 10 10
MAPK3 0.016 0.045 -9999 0 -0.21 12 12
MAPK1 0.015 0.046 -9999 0 -0.2 14 14
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
PLGF homodimer 0.021 0.018 -9999 0 -0.12 9 9
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.012 0.038 -9999 0 -0.12 42 42
VEGFA homodimer 0.019 0.02 -9999 0 -0.12 11 11
VEGFR1 homodimer/VEGFA homodimer 0.026 0.06 -9999 0 -0.32 10 10
platelet activating factor biosynthetic process 0.017 0.043 -9999 0 -0.22 10 10
PI3K 0.032 0.074 -9999 0 -0.23 22 22
PRKCA 0.016 0.047 -9999 0 -0.23 11 11
PRKCB 0.016 0.044 -9999 0 -0.24 10 10
VEGFR1 homodimer/PLGF homodimer 0.029 0.054 -9999 0 -0.36 6 6
VEGFA 0.019 0.02 -9999 0 -0.12 11 11
VEGFB 0.015 0.032 -9999 0 -0.12 30 30
mol:IP3 0.022 0.05 -9999 0 -0.26 10 10
RASA1 0.02 0.051 -9999 0 -0.24 13 13
NRP2 0.012 0.036 -9999 0 -0.12 38 38
VEGFR1 homodimer 0.027 0.05 -9999 0 -0.47 5 5
VEGFB homodimer 0.015 0.032 -9999 0 -0.12 30 30
NCK1 0.02 0.019 -9999 0 -0.12 9 9
eNOS/Caveolin-1 0.035 0.063 -9999 0 -0.26 10 10
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
mol:PI-3-4-5-P3 0.03 0.073 -9999 0 -0.23 22 22
mol:L-citrulline 0.029 0.058 -9999 0 -0.25 11 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.034 0.072 -9999 0 -0.23 18 18
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.072 -9999 0 -0.26 17 17
CD2AP 0.02 0.017 -9999 0 -0.12 7 7
PI3K/GAB1 0.036 0.077 -9999 0 -0.22 25 25
PDPK1 0.015 0.062 -9999 0 -0.22 22 22
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.07 -9999 0 -0.25 18 18
mol:NADP 0.029 0.058 -9999 0 -0.25 11 11
HSP90AA1 0.023 0.004 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.071 -9999 0 -0.23 18 18
VEGFR1 homodimer/NRP2 0.02 0.06 -9999 0 -0.3 11 11
Signaling events mediated by HDAC Class II

Figure S117.  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 S117.  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
G beta1gamma2/HDAC5 0.053 0.032 -10000 0 -0.098 21 21
HDAC3 0.023 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.007 0.028 -10000 0 -0.11 36 36
GATA1/HDAC4 0.034 0.004 -10000 0 -0.07 1 1
GATA1/HDAC5 0.034 0.004 -10000 0 -0.07 1 1
GATA2/HDAC5 0.032 0.016 -10000 0 -0.07 13 13
HDAC5/BCL6/BCoR 0.033 0.045 -10000 0 -0.12 43 43
HDAC9 0.015 0.031 -10000 0 -0.12 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.031 0.048 -10000 0 -0.12 47 47
HDAC4/ANKRA2 0.028 0.031 -10000 0 -0.14 14 14
HDAC5/YWHAB 0.032 0.02 -10000 0 -0.13 8 8
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.036 -10000 0 -0.14 30 30
GATA2 0.02 0.021 -10000 0 -0.12 13 13
HDAC4/RFXANK 0.025 0.038 -10000 0 -0.11 39 39
BCOR 0.023 0.007 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0 -10000 0 -10000 0 0
HDAC5 0.023 0 -10000 0 -10000 0 0
GNB1/GNG2 0.027 0.035 -10000 0 -0.12 30 30
Histones 0.026 0.035 -10000 0 -0.12 26 26
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
HDAC4 0.023 0 -10000 0 -10000 0 0
XPO1 0.022 0.01 -10000 0 -0.12 2 2
HDAC5/ANKRA2 0.028 0.031 -10000 0 -0.14 14 14
HDAC4/Ubc9 0.034 0.007 -10000 0 -0.14 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.024 -10000 0 -0.12 14 14
TUBA1B 0.023 0 -10000 0 -10000 0 0
HDAC6 0.019 0.023 -10000 0 -0.12 15 15
HDAC5/RFXANK 0.025 0.038 -10000 0 -0.11 39 39
CAMK4 0.016 0.031 -10000 0 -0.12 27 27
Tubulin/HDAC6 0.043 0.019 -10000 0 -10000 0 0
SUMO1 0.023 0.009 -10000 0 -0.12 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
GATA1 0.023 0.006 -10000 0 -0.12 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
NR3C1 0.021 0.014 -10000 0 -0.12 5 5
SUMO1/HDAC4 0.036 0.035 -10000 0 -0.1 30 30
SRF 0.018 0.026 -10000 0 -0.12 20 20
HDAC4/YWHAB 0.032 0.02 -10000 0 -0.13 8 8
Tubulin 0.033 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.031 0.024 -10000 0 -0.12 14 14
GNB1 0.023 0.006 -10000 0 -0.12 1 1
RANGAP1 0.023 0.006 -10000 0 -0.12 1 1
BCL6/BCoR 0.019 0.05 -10000 0 -0.15 43 43
HDAC4/HDAC3/SMRT (N-CoR2) 0.043 0.024 -10000 0 -0.11 8 8
HDAC4/SRF 0.038 0.03 -10000 0 -0.12 5 5
HDAC4/ER alpha 0.018 0.049 -10000 0 -0.12 60 60
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.026 0.035 -10000 0 -0.12 26 26
cell motility 0.043 0.019 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.001 -10000 0 -10000 0 0
HDAC7/HDAC3 0.016 0.014 -10000 0 -0.15 4 4
BCL6 0.019 0.02 -10000 0 -0.12 10 10
HDAC4/CaMK II delta B 0.023 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.028 0.031 -10000 0 -0.14 14 14
ESR1 0.018 0.024 -10000 0 -0.12 15 15
HDAC6/HDAC11 0.029 0.028 -10000 0 -0.15 8 8
Ran/GTP/Exportin 1 0.034 0.049 -10000 0 -0.15 30 30
NPC 0.009 0.023 -10000 0 -0.095 27 27
MEF2C 0.02 0.02 -10000 0 -0.12 11 11
RAN 0.023 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.058 0.038 -10000 0 -0.09 24 24
GNG2 0.02 0.018 -10000 0 -0.12 9 9
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
TUBB2A 0.021 0.017 -10000 0 -0.12 8 8
HDAC11 0.022 0.012 -10000 0 -0.12 4 4
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
RANBP2 0.022 0.01 -10000 0 -0.12 2 2
ANKRA2 0.02 0.021 -10000 0 -0.12 12 12
RFXANK 0.018 0.025 -10000 0 -0.12 17 17
nuclear import -0.033 0.034 0.16 15 -10000 0 15
Sphingosine 1-phosphate (S1P) pathway

Figure S118.  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 S118.  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 0.023 0.01 -9999 0 -0.12 3 3
SPHK1 0.021 0.017 -9999 0 -0.12 8 8
GNAI2 0.022 0.01 -9999 0 -0.12 3 3
mol:S1P 0.018 0.03 -9999 0 -0.18 12 12
GNAO1 0.011 0.041 -9999 0 -0.12 50 50
mol:Sphinganine-1-P 0.021 0.013 -9999 0 -0.07 11 11
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.036 0.034 -9999 0 -0.14 13 13
GNAI3 0.021 0.008 -9999 0 -0.12 1 1
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.022 0.015 -9999 0 -0.12 6 6
S1P1/S1P 0.028 0.029 -9999 0 -0.14 13 13
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.012 0.035 -9999 0 -0.12 36 36
S1P/S1P5/G12 0.026 0.025 -9999 0 -0.13 13 13
S1P/S1P3/Gq 0.022 0.056 -9999 0 -0.22 25 25
S1P/S1P4/Gi 0.002 0.075 -9999 0 -0.16 88 88
GNAQ 0.021 0.015 -9999 0 -0.12 6 6
GNAZ 0.022 0.012 -9999 0 -0.12 4 4
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
GNA11 0.022 0.013 -9999 0 -0.12 5 5
ABCC1 0.021 0.017 -9999 0 -0.12 8 8
S1P1 pathway

Figure S119.  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 S119.  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 0.029 0.053 -9999 0 -0.14 40 40
PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
SPHK1 0.001 0.015 -9999 0 -10000 0 0
mol:S1P 0.015 0.028 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.023 0.072 -9999 0 -0.3 15 15
GNAO1 0.01 0.041 -9999 0 -0.12 50 50
PDGFB-D/PDGFRB/PLCgamma1 0.009 0.087 -9999 0 -0.26 28 28
PLCG1 0.021 0.071 -9999 0 -0.28 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.041 -9999 0 -0.12 51 51
GNAI2 0.022 0.011 -9999 0 -0.12 3 3
GNAI3 0.022 0.009 -9999 0 -0.12 1 1
GNAI1 0.012 0.035 -9999 0 -0.12 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.023 0.046 -9999 0 -0.21 7 7
S1P1/S1P 0.025 0.053 -9999 0 -0.22 8 8
negative regulation of cAMP metabolic process 0.023 0.07 -9999 0 -0.29 15 15
MAPK3 0.022 0.09 -9999 0 -0.44 13 13
calcium-dependent phospholipase C activity -0.001 0.001 -9999 0 -10000 0 0
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
KDR 0.025 0.021 -9999 0 -0.12 11 11
PLCB2 0.025 0.049 -9999 0 -0.2 8 8
RAC1 0.023 0.002 -9999 0 -10000 0 0
RhoA/GTP 0.021 0.046 -9999 0 -0.19 11 11
receptor internalization 0.023 0.05 -9999 0 -0.21 8 8
PTGS2 0.001 0.14 -9999 0 -0.86 10 10
Rac1/GTP 0.021 0.045 -9999 0 -0.19 9 9
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VEGFA 0.023 0.022 -9999 0 -0.11 12 12
negative regulation of T cell proliferation 0.023 0.07 -9999 0 -0.29 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.012 -9999 0 -0.12 4 4
MAPK1 0.021 0.091 -9999 0 -0.44 13 13
S1P1/S1P/PDGFB-D/PDGFRB 0.028 0.065 -9999 0 -0.24 11 11
ABCC1 0.021 0.017 -9999 0 -0.12 8 8
Glypican 2 network

Figure S120.  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 S120.  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 0.021 0.014 -9999 0 -0.12 5 5
GPC2 0.023 0.009 -9999 0 -0.12 2 2
GPC2/Midkine 0.029 0.03 -9999 0 -0.12 21 21
neuron projection morphogenesis 0.029 0.03 -9999 0 -0.12 21 21
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S121.  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 S121.  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
SMAD4 0.022 0.007 -10000 0 -0.12 1 1
SMAD2 0.015 0.036 0.19 2 -0.16 9 11
SMAD3 0.027 0.046 -10000 0 -0.15 27 27
SMAD3/SMAD4 -0.012 0.15 -10000 0 -0.36 81 81
SMAD4/Ubc9/PIASy 0.043 0.028 -10000 0 -0.12 16 16
SMAD2/SMAD2/SMAD4 0.034 0.064 0.17 2 -0.17 18 20
PPM1A 0.023 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.014 -10000 0 -0.12 5 5
SMAD2/SMAD4 0.027 0.033 0.16 2 -0.14 9 11
MAP3K1 0.021 0.015 -10000 0 -0.12 6 6
TRAP-1/SMAD4 0.025 0.042 -10000 0 -0.14 31 31
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
NUP214 0.023 0.007 -10000 0 -0.12 1 1
CTDSP1 0.022 0.011 -10000 0 -0.12 3 3
CTDSP2 0.022 0.009 -10000 0 -0.12 2 2
CTDSPL 0.023 0.006 -10000 0 -0.12 1 1
KPNB1 0.022 0.009 -10000 0 -0.12 2 2
TGFBRAP1 0.022 0.007 -10000 0 -0.12 1 1
UBE2I 0.023 0.001 -10000 0 -10000 0 0
NUP153 0.02 0.018 -10000 0 -0.12 9 9
KPNA2 0.017 0.024 -10000 0 -0.12 15 15
PIAS4 0.023 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

Figure S122.  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 S122.  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 0.011 0.006 -9999 0 -0.076 3 3
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.033 0.016 -9999 0 -0.14 2 2
STXBP1 0.02 0.02 -9999 0 -0.12 11 11
ACh/CHRNA1 0.013 0.025 -9999 0 -0.062 51 51
RAB3GAP2/RIMS1/UNC13B 0.041 0.029 -9999 0 -0.11 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.023 0.006 -9999 0 -0.12 1 1
mol:ACh 0.005 0.011 -9999 0 -0.076 4 4
RAB3GAP2 0.022 0.009 -9999 0 -0.12 2 2
STX1A/SNAP25/VAMP2 0.039 0.031 -9999 0 -0.1 8 8
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.013 0.025 -9999 0 -0.062 51 51
UNC13B 0.021 0.016 -9999 0 -0.12 7 7
CHRNA1 0.011 0.04 -9999 0 -0.12 48 48
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 0.015 0.023 -9999 0 -0.061 41 41
SNAP25 0.004 0.018 -9999 0 -0.19 2 2
VAMP2 0.004 0.016 -9999 0 -0.18 2 2
SYT1 0.014 0.035 -9999 0 -0.12 37 37
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.024 0.013 -9999 0 -0.056 14 14
STX1A/SNAP25 fragment 1/VAMP2 0.039 0.031 -9999 0 -0.1 8 8
IL27-mediated signaling events

Figure S123.  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 S123.  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 0.025 0.034 -10000 0 -0.4 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.001 0.096 0.38 20 -10000 0 20
IL27/IL27R/JAK1 0.027 0.098 -10000 0 -0.95 3 3
TBX21 -0.001 0.081 -10000 0 -0.55 4 4
IL12B 0.024 0.002 -10000 0 -10000 0 0
IL12A 0.001 0.029 -10000 0 -0.076 70 70
IL6ST 0.016 0.027 -10000 0 -0.12 20 20
IL27RA/JAK1 0.01 0.086 -10000 0 -1.1 3 3
IL27 0.023 0.004 -10000 0 -10000 0 0
TYK2 0.021 0.017 -10000 0 -0.12 7 7
T-helper cell lineage commitment 0.014 0.09 -10000 0 -1.2 2 2
T-helper 2 cell differentiation -0.001 0.096 0.38 20 -10000 0 20
T cell proliferation during immune response -0.001 0.096 0.38 20 -10000 0 20
MAPKKK cascade 0.001 0.096 -10000 0 -0.38 20 20
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT2 0.02 0.018 -10000 0 -0.12 9 9
STAT1 0.014 0.03 -10000 0 -0.12 25 25
IL12RB1 0.023 0.006 -10000 0 -0.12 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.001 0.083 -10000 0 -0.5 5 5
IL27/IL27R/JAK2/TYK2 0.001 0.097 -10000 0 -0.39 20 20
positive regulation of T cell mediated cytotoxicity 0.001 0.096 -10000 0 -0.38 20 20
STAT1 (dimer) 0.013 0.11 0.4 1 -0.77 4 5
JAK2 0.016 0.025 -10000 0 -0.12 17 17
JAK1 0.022 0.01 -10000 0 -0.12 2 2
STAT2 (dimer) 0.003 0.1 -10000 0 -0.38 20 20
T cell proliferation -0.001 0.093 -10000 0 -0.37 20 20
IL12/IL12R/TYK2/JAK2 0.026 0.066 -10000 0 -0.72 1 1
IL17A 0.014 0.09 -10000 0 -1.2 2 2
mast cell activation -0.001 0.096 0.38 20 -10000 0 20
IFNG 0.003 0.021 -10000 0 -0.078 4 4
T cell differentiation -0.001 0.004 -10000 0 -0.018 6 6
STAT3 (dimer) 0.003 0.1 -10000 0 -0.38 20 20
STAT5A (dimer) 0.005 0.1 -10000 0 -0.37 20 20
STAT4 (dimer) 0.005 0.1 -10000 0 -0.37 20 20
STAT4 0.02 0.02 -10000 0 -0.12 11 11
T cell activation -0.006 0.011 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 0.008 0.1 -10000 0 -0.84 4 4
GATA3 0.014 0.029 -10000 0 -10000 0 0
IL18 0 0.028 -10000 0 -0.076 66 66
positive regulation of mast cell cytokine production 0.003 0.1 -10000 0 -0.37 20 20
IL27/EBI3 0.033 0.009 -10000 0 -10000 0 0
IL27RA -0.004 0.09 -10000 0 -1.1 3 3
IL6 0.012 0.053 -10000 0 -0.33 3 3
STAT5A 0.022 0.012 -10000 0 -0.12 4 4
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.006 0.046 0.48 3 -10000 0 3
IL1B 0.004 0.024 -10000 0 -0.076 45 45
EBI3 0.023 0.008 -10000 0 -0.12 1 1
TNF 0.01 0.012 -10000 0 -0.076 11 11
Angiopoietin receptor Tie2-mediated signaling

Figure S124.  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 S124.  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 0.023 0.17 -9999 0 -0.68 14 14
NCK1/PAK1/Dok-R -0.028 0.072 -9999 0 -0.32 15 15
NCK1/Dok-R 0.05 0.086 -9999 0 -0.84 2 2
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
mol:beta2-estradiol -0.008 0.012 -9999 0 -10000 0 0
RELA 0.023 0.009 -9999 0 -0.12 2 2
SHC1 0.024 0.002 -9999 0 -10000 0 0
Rac/GDP 0.016 0.015 -9999 0 -0.15 5 5
F2 0.014 0.02 -9999 0 -0.13 4 4
TNIP2 0.021 0.018 -9999 0 -0.12 9 9
NF kappa B/RelA 0.058 0.086 -9999 0 -0.79 2 2
FN1 -0.012 0.055 -9999 0 -0.12 115 115
PLD2 0.042 0.076 -9999 0 -0.87 2 2
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
GRB14 0.013 0.036 -9999 0 -0.12 39 39
ELK1 0.045 0.073 -9999 0 -0.82 2 2
GRB7 0.018 0.025 -9999 0 -0.12 18 18
PAK1 0.016 0.029 -9999 0 -0.12 24 24
Tie2/Ang1/alpha5/beta1 Integrin 0.012 0.1 -9999 0 -0.7 3 3
CDKN1A 0.027 0.18 -9999 0 -0.61 41 41
ITGA5 0.013 0.036 -9999 0 -0.12 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
RasGAP/Dok-R 0.052 0.083 -9999 0 -0.84 2 2
CRK 0.022 0.016 -9999 0 -0.12 7 7
mol:NO 0.03 0.14 -9999 0 -0.5 17 17
PLG 0.042 0.076 -9999 0 -0.87 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
chemokinesis 0.037 0.14 -9999 0 -0.74 6 6
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PIK3R1 0.015 0.031 -9999 0 -0.12 28 28
ANGPT2 -0.028 0.27 -9999 0 -1 39 39
BMX 0.042 0.076 -9999 0 -0.87 2 2
ANGPT1 0.023 0.047 -9999 0 -10000 0 0
tube development 0.01 0.2 -9999 0 -0.69 41 41
ANGPT4 0.023 0.009 -9999 0 -0.12 2 2
response to hypoxia 0.002 0.008 -9999 0 -0.061 2 2
Tie2/Ang1/GRB14 0.044 0.082 -9999 0 -0.88 2 2
alpha5/beta1 Integrin 0.017 0.048 -9999 0 -0.1 75 75
FGF2 0.023 0.01 -9999 0 -0.12 2 2
STAT5A (dimer) 0.025 0.23 -9999 0 -0.78 41 41
mol:L-citrulline 0.03 0.14 -9999 0 -0.5 17 17
AGTR1 0.021 0.016 -9999 0 -0.12 4 4
MAPK14 0.038 0.12 -9999 0 -1 4 4
Tie2/SHP2 0.037 0.081 -9999 0 -0.6 5 5
TEK 0.034 0.087 -9999 0 -0.72 4 4
RPS6KB1 0.026 0.15 -9999 0 -0.71 9 9
Angiotensin II/AT1 0.016 0.018 -9999 0 -0.077 4 4
Tie2/Ang1/GRB2 0.049 0.081 -9999 0 -0.88 2 2
MAPK3 0.042 0.071 -9999 0 -0.81 2 2
MAPK1 0.042 0.073 -9999 0 -0.81 2 2
Tie2/Ang1/GRB7 0.046 0.082 -9999 0 -0.88 2 2
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 0.04 0.076 -9999 0 -0.87 2 2
PI3K 0.025 0.16 -9999 0 -0.92 6 6
FES 0.046 0.097 -9999 0 -1 2 2
Crk/Dok-R 0.056 0.081 -9999 0 -0.84 2 2
Tie2/Ang1/ABIN2 0.048 0.08 -9999 0 -0.88 2 2
blood circulation 0 0 -9999 0 -10000 0 0
negative regulation of caspase activity 0.025 0.16 -9999 0 -0.58 17 17
STAT5A 0.022 0.012 -9999 0 -0.12 4 4
mol:ROS 0 0 -9999 0 -10000 0 0
PTK2 0.025 0.15 -9999 0 -0.74 7 7
Tie2/Ang2 0.003 0.26 -9999 0 -0.93 41 41
Tie2/Ang1 0.041 0.08 -9999 0 -0.92 2 2
FOXO1 0.02 0.18 -9999 0 -0.6 41 41
ELF1 0.03 0.013 -9999 0 -0.097 3 3
ELF2 0.042 0.077 -9999 0 -0.88 2 2
mol:Choline 0.042 0.074 -9999 0 -0.84 2 2
cell migration -0.02 0.045 -9999 0 -0.18 18 18
FYN 0.004 0.23 -9999 0 -0.79 41 41
DOK2 0.02 0.021 -9999 0 -0.12 12 12
negative regulation of cell cycle 0.03 0.17 -9999 0 -0.55 41 41
ETS1 0.022 0.035 -9999 0 -0.12 27 27
PXN 0.028 0.13 -9999 0 -0.57 9 9
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
NOS3 0.028 0.15 -9999 0 -0.56 17 17
RAC1 0.023 0.002 -9999 0 -10000 0 0
TNF 0.029 0.025 -9999 0 -0.12 11 11
MAPKKK cascade 0.042 0.074 -9999 0 -0.84 2 2
RASA1 0.021 0.011 -9999 0 -0.12 3 3
Tie2/Ang1/Shc 0.05 0.081 -9999 0 -0.88 2 2
NCK1 0.02 0.019 -9999 0 -0.12 9 9
vasculogenesis 0.031 0.13 -9999 0 -0.45 17 17
mol:Phosphatidic acid 0.042 0.074 -9999 0 -0.84 2 2
mol:Angiotensin II -0.001 0.009 -9999 0 -10000 0 0
mol:NADP 0.03 0.14 -9999 0 -0.5 17 17
Rac1/GTP 0.03 0.14 -9999 0 -0.73 6 6
MMP2 0.016 0.082 -9999 0 -0.87 2 2
Alternative NF-kappaB pathway

Figure S125.  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 S125.  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
IKK alpha homodimer 0.024 0.04 -9999 0 -0.14 30 30
FBXW11 0.023 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -9999 0 -10000 0 0
CHUK 0.021 0.013 -9999 0 -0.12 4 4
NF kappa B2 p100/RelB 0.056 0.044 -9999 0 -0.091 43 43
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAP3K14 0.023 0.006 -9999 0 -0.12 1 1
NF kappa B1 p50/RelB 0.02 0.048 -9999 0 -0.14 43 43
RELB 0.022 0.011 -9999 0 -0.12 3 3
NFKB2 0.023 0.009 -9999 0 -0.12 2 2
NF kappa B2 p52/RelB 0.029 0.02 -9999 0 -0.1 12 12
regulation of B cell activation 0.028 0.02 -9999 0 -0.1 12 12
Aurora C signaling

Figure S126.  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 S126.  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
INCENP 0.023 0.008 -9999 0 -0.12 2 2
Aurora C/Aurora B/INCENP 0.033 0.037 -9999 0 -0.097 33 33
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.003 0.068 -9999 0 -0.39 16 16
AURKB 0.017 0.026 -9999 0 -0.12 19 19
AURKC 0.023 0.006 -9999 0 -0.12 1 1
Arf1 pathway

Figure S127.  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 S127.  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
coatomer protein complex 0.018 0.009 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.008 0.035 -10000 0 -0.14 14 14
AP2 0.025 0.04 -10000 0 -0.13 33 33
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.016 -10000 0 -0.089 10 10
CLTB 0.022 0.014 -10000 0 -0.12 5 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.034 -10000 0 -0.16 16 16
CD4 0.016 0.027 -10000 0 -0.12 21 21
CLTA 0.023 0.006 -10000 0 -0.12 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
ARFGAP1 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.008 -10000 0 -0.046 5 5
ARF1/GTP 0.011 0.014 -10000 0 -0.12 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.026 -10000 0 -0.15 11 11
mol:Choline 0.009 0.008 -10000 0 -0.045 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.017 0.027 -10000 0 -0.12 21 21
DDEF1 0.008 0.012 -10000 0 -0.2 1 1
ARF1/GDP 0.009 0.004 0.047 1 -0.063 1 2
AP2M1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.018 -10000 0 -0.11 7 7
Rac/GTP 0.016 0.016 -10000 0 -0.15 5 5
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.018 -10000 0 -0.091 3 3
ARFIP2 0.021 0.013 -10000 0 -0.12 5 5
COPA 0.023 0.007 -10000 0 -0.12 1 1
RAC1 0.023 0.002 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.018 0.035 -10000 0 -0.21 11 11
ARF1/GTP/ARHGAP10 0.011 0.016 -10000 0 -0.065 23 23
GGA3 0.022 0.015 -10000 0 -0.12 6 6
ARF1/GTP/Membrin 0.019 0.018 -10000 0 -0.18 2 2
AP2A1 0.021 0.017 -10000 0 -0.12 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0.033 -10000 0 -0.16 16 16
ARF1/GDP/Membrin 0.021 0.019 -10000 0 -0.29 1 1
Arfaptin 2/Rac/GDP 0.029 0.016 -10000 0 -0.086 10 10
CYTH2 0 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.021 -10000 0 -0.08 9 9
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 0.015 -10000 0 -0.15 5 5
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.006 0.077 -10000 0 -0.26 22 22
PLD2 0.009 0.008 -10000 0 -0.046 5 5
ARF-GAP1/v-SNARE 0.012 0 -10000 0 -10000 0 0
PIP5K1A 0.009 0.008 -10000 0 -0.046 5 5
ARF1/GTP/Membrin/GBF1/p115 0.011 0.028 -10000 0 -0.1 14 14
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.008 -10000 0 -0.045 5 5
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -10000 0 -10000 0 0
GOSR2 0.015 0.016 -10000 0 -0.36 1 1
USO1 -0.011 0.094 -10000 0 -0.36 38 38
GBF1 0.001 0.07 -10000 0 -0.36 21 21
ARF1/GTP/Arfaptin 2 0.028 0.021 -10000 0 -0.062 27 27
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.02 0.062 -10000 0 -0.13 75 75
Rapid glucocorticoid signaling

Figure S128.  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 S128.  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
Gs family/GDP/Gbeta gamma 0.034 0.028 -10000 0 -0.093 20 20
MAPK9 0 0.045 -10000 0 -0.21 25 25
adrenocorticotropin secretion 0.011 0.006 -10000 0 -0.076 3 3
GNB1/GNG2 0.025 0.029 -10000 0 -0.095 30 30
GNB1 0.023 0.006 -10000 0 -0.12 1 1
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.03 -10000 0 -0.2 12 12
Gs family/GTP 0.014 0.009 -10000 0 -0.054 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0 0.002 0.017 10 -10000 0 10
GNAL 0.021 0.019 -10000 0 -0.12 10 10
GNG2 0.02 0.018 -10000 0 -0.12 9 9
CRH 0.023 0.01 -10000 0 -0.12 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.039 -10000 0 -0.17 24 24
MAPK11 0.01 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

Figure S129.  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 S129.  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 + 0.023 0.009 -9999 0 -0.12 2 2
GNAT1/GTP 0.017 0.006 -9999 0 -0.076 2 2
Metarhodopsin II/Arrestin 0.031 0.007 -9999 0 -0.056 4 4
PDE6G/GNAT1/GTP 0.025 0.024 -9999 0 -0.06 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.023 0.008 -9999 0 -0.12 2 2
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.039 0.024 -9999 0 -0.12 2 2
mol:Na + 0.053 0.02 -9999 0 -0.3 1 1
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.022 -9999 0 -0.11 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.066 0.021 -9999 0 -0.31 1 1
CNGB1 0.023 0.006 -9999 0 -0.12 1 1
RDH5 0.01 0.041 -9999 0 -0.12 50 50
SAG 0.023 0.01 -9999 0 -0.12 3 3
mol:Ca2+ 0.04 0.018 -9999 0 -0.29 1 1
Na + (4 Units) 0.043 0.018 -9999 0 -0.29 1 1
RGS9 0.018 0.028 -9999 0 -0.12 22 22
GNB1/GNGT1 0.03 0.027 -9999 0 -0.1 21 21
GNAT1/GDP 0.05 0.021 -9999 0 -0.088 2 2
GUCY2D 0.023 0.01 -9999 0 -0.12 3 3
GNGT1 0.019 0.023 -9999 0 -0.12 15 15
GUCY2F 0.023 0.006 -9999 0 -0.12 1 1
GNB5 0.023 0.01 -9999 0 -0.12 3 3
mol:GMP (4 units) 0.031 0.023 -9999 0 -0.1 4 4
mol:11-cis-retinal 0.01 0.041 -9999 0 -0.12 50 50
mol:cGMP 0.057 0.018 -9999 0 -0.12 4 4
GNB1 0.023 0.006 -9999 0 -0.12 1 1
Rhodopsin 0.023 0.035 -9999 0 -0.079 59 59
SLC24A1 0.023 0.009 -9999 0 -0.12 2 2
CNGA1 0.022 0.013 -9999 0 -0.12 5 5
Metarhodopsin II 0.015 0.003 -9999 0 -0.054 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.058 0.018 -9999 0 -0.12 4 4
RGS9BP 0.023 0.01 -9999 0 -0.12 3 3
Metarhodopsin II/Transducin 0.025 0.022 -9999 0 -0.15 7 7
GCAP Family/Ca ++ 0.043 0.015 -9999 0 -0.11 4 4
PDE6A/B 0.033 0.014 -9999 0 -0.07 11 11
mol:Pi 0.042 0.022 -9999 0 -0.11 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.041 0.023 -9999 0 -0.11 8 8
PDE6B 0.022 0.016 -9999 0 -0.12 7 7
PDE6A 0.022 0.012 -9999 0 -0.12 4 4
PDE6G 0.014 0.035 -9999 0 -0.12 36 36
RHO 0.023 0.006 -9999 0 -0.12 1 1
PDE6 0.056 0.035 -9999 0 -0.15 2 2
GUCA1A 0.022 0.01 -9999 0 -0.12 3 3
GC2/GCAP Family 0.058 0.017 -9999 0 -0.12 4 4
GUCA1C 0.022 0.012 -9999 0 -0.12 4 4
GUCA1B 0.023 0.006 -9999 0 -0.12 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S130.  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 S130.  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 0.015 0.058 -10000 0 -0.33 3 3
CRKL 0.013 0.059 -10000 0 -0.31 4 4
HRAS 0.031 0.068 -10000 0 -0.28 6 6
mol:PIP3 0.004 0.068 0.22 4 -0.3 5 9
SPRED1 0.019 0.016 -10000 0 -0.12 6 6
SPRED2 0.022 0.014 -10000 0 -0.12 5 5
GAB1 0.01 0.062 -10000 0 -0.33 4 4
FOXO3 0.019 0.063 -10000 0 -0.31 6 6
AKT1 0.017 0.064 -10000 0 -0.34 5 5
BAD 0.02 0.061 -10000 0 -0.32 5 5
megakaryocyte differentiation 0.012 0.06 -10000 0 -0.32 4 4
GSK3B 0.02 0.062 -10000 0 -0.33 5 5
RAF1 0.03 0.061 -10000 0 -0.26 6 6
SHC1 0.023 0.001 -10000 0 -10000 0 0
STAT3 0.011 0.063 -10000 0 -0.29 7 7
STAT1 0.012 0.12 -10000 0 -0.72 5 5
HRAS/SPRED1 0.031 0.068 -10000 0 -0.25 8 8
cell proliferation 0.011 0.061 -10000 0 -0.3 6 6
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
TEC 0.01 0.038 -10000 0 -0.12 44 44
RPS6KB1 0.01 0.077 -10000 0 -0.31 10 10
HRAS/SPRED2 0.036 0.064 -10000 0 -0.23 8 8
LYN/TEC/p62DOK 0.013 0.086 -10000 0 -0.28 14 14
MAPK3 0.029 0.052 -10000 0 -0.27 4 4
STAP1 0.011 0.061 -10000 0 -0.33 4 4
GRAP2 0.022 0.012 -10000 0 -0.12 4 4
JAK2 0.005 0.12 -10000 0 -0.51 12 12
STAT1 (dimer) 0.008 0.13 -10000 0 -0.7 5 5
mol:Gleevec -0.001 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.03 0.075 -10000 0 -0.29 7 7
actin filament polymerization 0.008 0.059 -10000 0 -0.33 4 4
LYN 0.021 0.013 -10000 0 -0.12 4 4
STAP1/STAT5A (dimer) 0.012 0.09 -10000 0 -0.43 6 6
PIK3R1 0.015 0.031 -10000 0 -0.12 28 28
CBL/CRKL/GRB2 0.033 0.064 -10000 0 -0.31 4 4
PI3K 0.017 0.089 -10000 0 -0.3 15 15
PTEN 0.022 0.008 -10000 0 -0.12 1 1
SCF/KIT/EPO/EPOR 0.03 0.13 -10000 0 -1.3 2 2
MAPK8 0.011 0.062 -10000 0 -0.3 6 6
STAT3 (dimer) 0.011 0.062 -10000 0 -0.28 7 7
positive regulation of transcription 0.028 0.045 -10000 0 -0.22 4 4
mol:GDP 0.03 0.074 -10000 0 -0.3 6 6
PIK3C2B 0.011 0.062 -10000 0 -0.33 4 4
CBL/CRKL 0.024 0.062 -10000 0 -0.36 3 3
FER 0.011 0.061 -10000 0 -0.33 4 4
SH2B3 0.013 0.06 -10000 0 -0.33 4 4
PDPK1 0.007 0.066 0.21 4 -0.26 7 11
SNAI2 0.001 0.065 -10000 0 -0.37 5 5
positive regulation of cell proliferation 0.008 0.1 -10000 0 -0.55 5 5
KITLG 0.02 0.029 -10000 0 -0.12 21 21
cell motility 0.008 0.1 -10000 0 -0.55 5 5
PTPN6 0.022 0.009 -10000 0 -0.12 2 2
EPOR 0.013 0.13 -10000 0 -0.57 18 18
STAT5A (dimer) 0.01 0.094 -10000 0 -0.43 7 7
SOCS1 0.017 0.03 -10000 0 -0.12 26 26
cell migration -0.012 0.06 0.32 4 -10000 0 4
SOS1 0.017 0.027 -10000 0 -0.12 20 20
EPO 0.024 0.008 -10000 0 -0.13 1 1
VAV1 0.02 0.019 -10000 0 -0.12 10 10
GRB10 0.011 0.063 -10000 0 -0.31 6 6
PTPN11 0.021 0.011 -10000 0 -0.12 3 3
SCF/KIT 0.009 0.063 -10000 0 -0.32 5 5
GO:0007205 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 0.029 0.051 -10000 0 -0.2 6 6
CBL 0.023 0.006 -10000 0 -0.12 1 1
KIT 0.005 0.13 -10000 0 -0.73 4 4
MAP2K2 0.028 0.053 -10000 0 -0.19 8 8
SHC/Grb2/SOS1 0.032 0.072 -10000 0 -0.35 4 4
STAT5A 0.01 0.096 -10000 0 -0.44 7 7
GRB2 0.023 0.006 -10000 0 -0.12 1 1
response to radiation 0.001 0.065 -10000 0 -0.36 5 5
SHC/GRAP2 0.034 0.011 -10000 0 -0.084 5 5
PTPRO 0.012 0.061 -10000 0 -0.33 4 4
SH2B2 0.008 0.06 -10000 0 -0.34 4 4
DOK1 0.022 0.015 -10000 0 -0.12 6 6
MATK 0.012 0.061 -10000 0 -0.33 4 4
CREBBP 0.036 0.031 -10000 0 -0.12 9 9
BCL2 0.006 0.15 -10000 0 -0.62 26 26
Visual signal transduction: Cones

Figure S131.  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 S131.  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 0.04 0.012 -9999 0 -0.09 2 2
RGS9BP 0.023 0.01 -9999 0 -0.12 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.031 0.004 -9999 0 -10000 0 0
mol:ADP 0.011 0.004 -9999 0 -0.076 1 1
GNAT2 0.023 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.022 -9999 0 -0.11 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.031 0.004 -9999 0 -0.056 1 1
GRK7 0.023 0.006 -9999 0 -0.12 1 1
CNGB3 0.023 0.006 -9999 0 -0.12 1 1
Cone Metarhodopsin II/X-Arrestin 0.017 0.004 -9999 0 -0.076 1 1
mol:Ca2+ 0.025 0.008 -9999 0 -0.1 1 1
Cone PDE6 0.064 0.024 -9999 0 -0.1 3 3
Cone Metarhodopsin II 0.015 0.003 -9999 0 -0.054 1 1
Na + (4 Units) 0.043 0.01 -9999 0 -0.1 1 1
GNAT2/GDP 0.05 0.021 -9999 0 -0.088 2 2
GNB5 0.023 0.01 -9999 0 -0.12 3 3
mol:GMP (4 units) 0.026 0.005 -9999 0 -0.1 1 1
Cone Transducin 0.043 0.013 -9999 0 -0.097 2 2
SLC24A2 0.022 0.013 -9999 0 -0.12 5 5
GNB3/GNGT2 0.033 0.016 -9999 0 -0.14 2 2
GNB3 0.022 0.01 -9999 0 -0.12 3 3
GNAT2/GTP 0.017 0 -9999 0 -10000 0 0
CNGA3 0.023 0 -9999 0 -10000 0 0
ARR3 0.023 0.006 -9999 0 -0.12 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.031 0.004 -9999 0 -10000 0 0
mol:Pi 0.042 0.022 -9999 0 -0.11 2 2
Cone CNG Channel 0.057 0.008 -9999 0 -0.13 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.022 0.013 -9999 0 -0.12 5 5
RGS9 0.018 0.028 -9999 0 -0.12 22 22
PDE6C 0.023 0.006 -9999 0 -0.12 1 1
GNGT2 0.022 0.013 -9999 0 -0.12 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.023 0.006 -9999 0 -0.12 1 1
Methods & Data
Input

  • Expression Data Normalization = Tumor samples were used to median center the expression data used in this analysis.

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/1971473/2.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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