Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression and copy number 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 107 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
PLK2 and PLK4 events 187
FOXM1 transcription factor network 142
TCGA08_p53 104
HIF-1-alpha transcription factor network 96
Ephrin B reverse signaling 96
Wnt signaling 96
Osteopontin-mediated events 91
LPA receptor mediated events 91
PDGFR-alpha signaling pathway 88
Endothelins 88
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
PLK2 and PLK4 events 187 561 3 -0.011 0.036 1000 -1000 -0.017 -1000
FOXM1 transcription factor network 142 7291 51 -0.52 0.038 1000 -1000 -0.016 -1000
TCGA08_p53 104 730 7 -0.063 0.038 1000 -1000 -0.009 -1000
HIF-1-alpha transcription factor network 96 7370 76 -0.048 0.096 1000 -1000 0 -1000
Ephrin B reverse signaling 96 4651 48 -0.2 0.08 1000 -1000 -0.056 -1000
Wnt signaling 96 678 7 -0.019 0.041 1000 -1000 0.005 -1000
Osteopontin-mediated events 91 3471 38 -0.18 0.041 1000 -1000 -0.015 -1000
LPA receptor mediated events 91 9347 102 -0.047 0.041 1000 -1000 -0.058 -1000
PDGFR-alpha signaling pathway 88 3877 44 -0.12 0.05 1000 -1000 -0.02 -1000
Endothelins 88 8525 96 -0.18 0.044 1000 -1000 -0.02 -1000
Syndecan-1-mediated signaling events 87 2966 34 -0.036 0.04 1000 -1000 -0.005 -1000
Nectin adhesion pathway 84 5306 63 -0.083 0.062 1000 -1000 -0.005 -1000
amb2 Integrin signaling 82 6727 82 -0.083 0.082 1000 -1000 -0.012 -1000
TCGA08_retinoblastoma 82 662 8 -0.012 0.029 1000 -1000 -0.005 -1000
TRAIL signaling pathway 81 3912 48 -0.022 0.042 1000 -1000 -0.017 -1000
Nongenotropic Androgen signaling 78 4060 52 -0.12 0.061 1000 -1000 -0.016 -1000
Thromboxane A2 receptor signaling 76 8061 105 -0.15 0.071 1000 -1000 -0.021 -1000
BARD1 signaling events 75 4322 57 -0.038 0.064 1000 -1000 -0.063 -1000
TCGA08_rtk_signaling 73 1916 26 -0.017 0.04 1000 -1000 -0.019 -1000
Paxillin-dependent events mediated by a4b1 71 2562 36 -0.066 0.069 1000 -1000 -0.054 -1000
Signaling events mediated by the Hedgehog family 69 3620 52 -0.065 0.058 1000 -1000 -0.025 -1000
IL1-mediated signaling events 69 4308 62 -0.045 0.073 1000 -1000 -0.017 -1000
Integrins in angiogenesis 69 5809 84 -0.057 0.056 1000 -1000 -0.017 -1000
Ras signaling in the CD4+ TCR pathway 69 1189 17 -0.002 0.054 1000 -1000 0 -1000
IL6-mediated signaling events 68 5163 75 -0.14 0.05 1000 -1000 -0.029 -1000
Syndecan-4-mediated signaling events 68 4615 67 -0.06 0.046 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 67 6572 97 -0.072 0.046 1000 -1000 -0.043 -1000
IL23-mediated signaling events 67 4069 60 -0.16 0.055 1000 -1000 -0.02 -1000
Signaling events mediated by PRL 66 2250 34 -0.018 0.04 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 65 2544 39 -0.078 0.04 1000 -1000 -0.015 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 65 5550 85 -0.16 0.051 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 65 4990 76 -0.058 0.07 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 64 3310 51 -0.18 0.099 1000 -1000 -0.024 -1000
IGF1 pathway 64 3668 57 -0.022 0.065 1000 -1000 -0.012 -1000
Noncanonical Wnt signaling pathway 63 1644 26 -0.032 0.041 1000 -1000 -0.017 -1000
FoxO family signaling 63 4033 64 -0.2 0.046 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 63 2742 43 -0.026 0.05 1000 -1000 -0.006 -1000
IL2 signaling events mediated by STAT5 61 1359 22 -0.039 0.047 1000 -1000 -0.004 -1000
IL4-mediated signaling events 60 5519 91 -0.23 0.058 1000 -1000 -0.03 -1000
BMP receptor signaling 60 4883 81 -0.02 0.07 1000 -1000 -0.003 -1000
IFN-gamma pathway 60 4124 68 -0.058 0.063 1000 -1000 -0.033 -1000
IL12-mediated signaling events 59 5185 87 -0.19 0.061 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 59 295 5 0.033 0.039 1000 -1000 0.037 -1000
EPHB forward signaling 59 5020 85 -0.055 0.16 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 58 5482 93 -0.082 0.087 1000 -1000 -0.02 -1000
E-cadherin signaling events 56 280 5 0.035 0.049 1000 -1000 0.038 -1000
Paxillin-independent events mediated by a4b1 and a4b7 55 2053 37 -0.02 0.07 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 55 2618 47 -0.058 0.052 1000 -1000 -0.026 -1000
BCR signaling pathway 54 5362 99 -0.075 0.069 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 53 3093 58 -0.079 0.06 1000 -1000 -0.006 -1000
E-cadherin signaling in the nascent adherens junction 53 4070 76 -0.057 0.071 1000 -1000 -0.032 -1000
Syndecan-2-mediated signaling events 52 3641 69 0 0.063 1000 -1000 -0.012 -1000
Plasma membrane estrogen receptor signaling 52 4489 86 -0.09 0.086 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 51 3115 61 -0.16 0.075 1000 -1000 -0.03 -1000
Class I PI3K signaling events 50 3654 73 -0.015 0.05 1000 -1000 -0.017 -1000
ErbB4 signaling events 49 3439 69 -0.07 0.056 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 49 2866 58 -0.064 0.041 1000 -1000 -0.034 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 49 2216 45 -0.058 0.075 1000 -1000 -0.016 -1000
Circadian rhythm pathway 48 1071 22 -0.081 0.044 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 48 2076 43 -0.061 0.069 1000 -1000 -0.077 -1000
Aurora B signaling 48 3257 67 -0.058 0.067 1000 -1000 -0.011 -1000
Caspase cascade in apoptosis 47 3534 74 -0.11 0.051 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 46 552 12 -0.015 0.054 1000 -1000 -0.014 -1000
Reelin signaling pathway 46 2624 56 -0.011 0.095 1000 -1000 -0.008 -1000
Arf6 signaling events 45 2842 62 0 0.082 1000 -1000 0 -1000
EPO signaling pathway 45 2511 55 0 0.072 1000 -1000 -0.012 -1000
PLK1 signaling events 45 3861 85 -0.046 0.051 1000 -1000 -0.012 -1000
Stabilization and expansion of the E-cadherin adherens junction 45 3371 74 -0.076 0.066 1000 -1000 -0.052 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 45 1509 33 -0.005 0.086 1000 -1000 -0.006 -1000
Regulation of Telomerase 44 4540 102 -0.11 0.071 1000 -1000 -0.016 -1000
Regulation of Androgen receptor activity 43 3025 70 -0.081 0.064 1000 -1000 -0.024 -1000
Canonical NF-kappaB pathway 42 1642 39 -0.036 0.065 1000 -1000 -0.017 -1000
p75(NTR)-mediated signaling 42 5318 125 -0.059 0.099 1000 -1000 -0.037 -1000
RXR and RAR heterodimerization with other nuclear receptor 42 2184 52 -0.038 0.095 1000 -1000 -0.017 -1000
Regulation of p38-alpha and p38-beta 41 2258 54 -0.029 0.091 1000 -1000 -0.002 -1000
ErbB2/ErbB3 signaling events 40 2630 65 -0.033 0.047 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 40 858 21 -0.016 0.081 1000 -1000 -0.005 -1000
Neurotrophic factor-mediated Trk receptor signaling 39 4726 120 -0.052 0.09 1000 -1000 -0.022 -1000
Arf6 downstream pathway 38 1651 43 -0.034 0.061 1000 -1000 -0.045 -1000
Insulin-mediated glucose transport 38 1229 32 -0.018 0.047 1000 -1000 -0.017 -1000
mTOR signaling pathway 38 2042 53 -0.053 0.057 1000 -1000 -0.017 -1000
Signaling mediated by p38-gamma and p38-delta 38 572 15 -0.038 0.039 1000 -1000 -0.017 -1000
p38 MAPK signaling pathway 38 1710 44 -0.043 0.072 1000 -1000 0 -1000
Aurora A signaling 37 2234 60 -0.046 0.066 1000 -1000 -0.017 -1000
PDGFR-beta signaling pathway 37 3656 97 -0.036 0.083 1000 -1000 -0.032 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 36 1963 54 -0.017 0.056 1000 -1000 -0.018 -1000
ceramide signaling pathway 36 1806 49 -0.032 0.059 1000 -1000 -0.009 -1000
Syndecan-3-mediated signaling events 36 1276 35 -0.013 0.073 1000 -1000 -0.01 -1000
Regulation of nuclear SMAD2/3 signaling 34 4659 136 -0.091 0.1 1000 -1000 -0.056 -1000
Class I PI3K signaling events mediated by Akt 34 2328 68 -0.034 0.078 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 34 1076 31 -0.016 0.041 1000 -1000 -0.018 -1000
S1P3 pathway 34 1435 42 -0.02 0.054 1000 -1000 -0.009 -1000
Class IB PI3K non-lipid kinase events 34 102 3 -0.039 0.039 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 33 771 23 -0.017 0.066 1000 -1000 -0.006 -1000
JNK signaling in the CD4+ TCR pathway 33 572 17 -0.007 0.079 1000 -1000 -0.007 -1000
Hedgehog signaling events mediated by Gli proteins 33 2199 65 0 0.076 1000 -1000 -0.008 -1000
FOXA2 and FOXA3 transcription factor networks 33 1555 46 -0.12 0.056 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class I 33 3465 104 -0.041 0.076 1000 -1000 -0.041 -1000
S1P4 pathway 33 829 25 -0.013 0.054 1000 -1000 -0.008 -1000
Ephrin A reverse signaling 32 229 7 -0.013 0.04 1000 -1000 -0.008 -1000
S1P5 pathway 32 559 17 -0.007 0.041 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 32 2715 83 -0.013 0.071 1000 -1000 -0.016 -1000
Coregulation of Androgen receptor activity 30 2281 76 -0.011 0.052 1000 -1000 -0.009 -1000
Glypican 1 network 30 1459 48 -0.04 0.069 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 29 820 28 -0.019 0.054 1000 -1000 -0.017 -1000
Signaling events regulated by Ret tyrosine kinase 29 2414 82 -0.009 0.092 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 29 3674 125 -0.023 0.072 1000 -1000 -0.017 -1000
Ceramide signaling pathway 28 2182 76 -0.019 0.081 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 28 366 13 0 0.094 1000 -1000 0 -1000
Nephrin/Neph1 signaling in the kidney podocyte 27 936 34 -0.049 0.086 1000 -1000 -0.046 -1000
Insulin Pathway 27 2002 74 -0.026 0.1 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 26 1957 75 -0.036 0.094 1000 -1000 -0.025 -1000
IL27-mediated signaling events 26 1338 51 -0.008 0.08 1000 -1000 -0.024 -1000
Angiopoietin receptor Tie2-mediated signaling 26 2296 88 -0.045 0.076 1000 -1000 -0.045 -1000
Glucocorticoid receptor regulatory network 25 2927 114 -0.11 0.077 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 25 1023 40 -0.064 0.072 1000 -1000 -0.052 -1000
Calcium signaling in the CD4+ TCR pathway 25 792 31 -0.039 0.084 1000 -1000 -0.014 -1000
Signaling mediated by p38-alpha and p38-beta 24 1073 44 -0.023 0.055 1000 -1000 -0.007 -1000
VEGFR1 specific signals 24 1366 56 -0.027 0.045 1000 -1000 -0.024 -1000
Arf1 pathway 24 1306 54 -0.01 0.052 1000 -1000 -0.009 -1000
Sumoylation by RanBP2 regulates transcriptional repression 23 623 27 -0.031 0.083 1000 -1000 -0.025 -1000
S1P1 pathway 22 812 36 -0.001 0.044 1000 -1000 -0.014 -1000
Effects of Botulinum toxin 21 560 26 -0.01 0.071 1000 -1000 -0.009 -1000
Rapid glucocorticoid signaling 21 430 20 -0.01 0.049 1000 -1000 -0.009 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 19 1319 68 -0.078 0.095 1000 -1000 -0.042 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 19 1489 78 -0.021 0.065 1000 -1000 -0.027 -1000
Aurora C signaling 18 129 7 0 0.063 1000 -1000 -0.001 -1000
Glypican 2 network 18 72 4 0.04 0.055 1000 -1000 0.038 -1000
Arf6 trafficking events 18 1287 71 -0.047 0.05 1000 -1000 -0.038 -1000
Visual signal transduction: Cones 15 605 38 -0.01 0.088 1000 -1000 -0.009 -1000
Visual signal transduction: Rods 14 741 52 -0.018 0.098 1000 -1000 -0.003 -1000
Total 6553 359135 7203 -7.1 8.4 131000 -131000 -2.5 -131000
PLK2 and PLK4 events

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
PLK2 0.026 0.02 -9999 0 0 215 215
PLK4 0.036 0.015 -9999 0 0 83 83
regulation of centriole replication -0.011 0.01 0 263 -9999 0 263
FOXM1 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
NFATC3 -0.35 0.6 -10000 0 -1.2 165 165
PLK1 -0.048 0.31 -10000 0 -1.2 34 34
BIRC5 -0.053 0.32 -10000 0 -1.3 35 35
HSPA1B -0.36 0.6 -10000 0 -1.1 176 176
MAP2K1 0.002 0.07 -10000 0 -10000 0 0
BRCA2 -0.36 0.61 -10000 0 -1.2 167 167
FOXM1 -0.52 0.88 -10000 0 -1.6 174 174
XRCC1 -0.35 0.6 -10000 0 -1.2 166 166
FOXM1B/p19 -0.44 0.66 -10000 0 -1.3 178 178
Cyclin D1/CDK4 -0.36 0.55 -10000 0 -1 180 180
CDC2 -0.42 0.68 -10000 0 -1.3 182 182
TGFA -0.32 0.52 -10000 0 -0.98 175 175
SKP2 -0.35 0.61 -10000 0 -1.2 168 168
CCNE1 0.02 0.029 -10000 0 -0.009 255 255
CKS1B -0.35 0.61 -10000 0 -1.2 168 168
RB1 -0.32 0.48 -10000 0 -0.97 170 170
FOXM1C/SP1 -0.44 0.71 -10000 0 -1.3 179 179
AURKB -0.1 0.4 -10000 0 -1.2 61 61
CENPF -0.39 0.63 -10000 0 -1.2 187 187
CDK4 0.007 0.044 0.11 3 -0.039 166 169
MYC -0.34 0.48 -10000 0 -0.95 183 183
CHEK2 0.005 0.065 -10000 0 -10000 0 0
ONECUT1 -0.36 0.58 -10000 0 -1.1 177 177
CDKN2A 0.026 0.02 0.089 2 -0.034 8 10
LAMA4 -0.39 0.63 -10000 0 -1.2 187 187
FOXM1B/HNF6 -0.46 0.71 -10000 0 -1.4 177 177
FOS -0.43 0.65 -10000 0 -1.2 219 219
SP1 0.036 0.022 -10000 0 -0.033 47 47
CDC25B -0.35 0.61 -10000 0 -1.1 169 169
response to radiation -0.006 0.036 0.088 9 -10000 0 9
CENPB -0.34 0.6 -10000 0 -1.2 162 162
CENPA -0.36 0.6 -10000 0 -1.1 170 170
NEK2 -0.37 0.62 -10000 0 -1.2 173 173
HIST1H2BA -0.35 0.6 -10000 0 -1.1 168 168
CCNA2 0.024 0.029 -10000 0 -0.011 202 202
EP300 0.036 0.014 -10000 0 0 73 73
CCNB1/CDK1 -0.49 0.79 -10000 0 -1.5 175 175
CCNB2 -0.38 0.63 0.8 1 -1.2 181 182
CCNB1 -0.39 0.66 -10000 0 -1.3 173 173
ETV5 -0.37 0.64 -10000 0 -1.2 193 193
ESR1 -0.4 0.62 -10000 0 -1.1 190 190
CCND1 -0.37 0.55 -10000 0 -1 186 186
GSK3A 0.005 0.062 0.15 3 -10000 0 3
Cyclin A-E1/CDK1-2 -0.007 0.11 -10000 0 -0.17 125 125
CDK2 0.029 0.028 -10000 0 -0.018 129 129
G2/M transition of mitotic cell cycle -0.007 0.044 0.095 10 -10000 0 10
FOXM1B/Cbp/p300 -0.41 0.66 -10000 0 -1.3 175 175
GAS1 -0.36 0.6 -10000 0 -1.1 174 174
MMP2 -0.43 0.65 -10000 0 -1.2 219 219
RB1/FOXM1C -0.41 0.59 0.67 1 -1.1 187 188
CREBBP 0.038 0.012 -10000 0 0 54 54
TCGA08_p53

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
CDKN2A -0.007 0.005 0 175 -10000 0 175
TP53 -0.053 0.12 0.18 13 -0.24 149 162
Senescence -0.063 0.12 0.18 13 -0.24 151 164
Apoptosis -0.063 0.12 0.18 13 -0.24 151 164
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.006 0.038 0.3 8 -10000 0 8
MDM4 0.038 0.013 -10000 0 0 57 57
HIF-1-alpha transcription factor network

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
PKM2 0.034 0.34 0.55 49 -0.53 90 139
HDAC7 -0.001 0.004 -10000 0 -0.037 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.03 0.32 0.6 3 -0.59 54 57
SMAD4 0.039 0.012 -10000 0 0 49 49
ID2 0.034 0.33 0.55 50 -0.52 89 139
AP1 0.006 0.085 -10000 0 -0.14 120 120
ABCG2 0.029 0.33 0.56 44 -0.53 89 133
HIF1A 0.031 0.1 0.2 42 -0.13 88 130
TFF3 0.01 0.32 0.55 36 -0.53 87 123
GATA2 0.04 0.019 -10000 0 -0.058 12 12
AKT1 0.042 0.097 0.22 34 -0.11 70 104
response to hypoxia 0.006 0.069 0.15 41 -0.11 47 88
MCL1 0.036 0.34 0.55 47 -0.53 90 137
NDRG1 -0.017 0.29 0.53 27 -0.56 76 103
SERPINE1 -0.01 0.3 0.55 27 -0.53 87 114
FECH 0.031 0.33 0.55 51 -0.53 87 138
FURIN 0.037 0.34 0.55 49 -0.52 90 139
NCOA2 0.038 0.015 -10000 0 -0.001 72 72
EP300 0.045 0.12 0.29 39 -0.24 20 59
HMOX1 0.021 0.33 0.55 43 -0.53 92 135
BHLHE40 -0.024 0.3 0.5 41 -0.52 90 131
BHLHE41 -0.024 0.3 0.5 41 -0.52 90 131
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.096 0.16 0.36 17 -0.19 43 60
ENG 0.02 0.11 0.27 15 -0.2 27 42
JUN 0.036 0.019 -10000 0 -0.005 90 90
RORA 0.034 0.33 0.55 48 -0.52 90 138
ABCB1 0.018 0.097 -10000 0 -0.55 4 4
TFRC -0.007 0.31 0.55 33 -0.54 86 119
CXCR4 0.009 0.33 0.55 40 -0.53 95 135
TF 0.027 0.33 0.55 47 -0.52 88 135
CITED2 0.032 0.33 0.54 49 -0.52 91 140
HIF1A/ARNT 0.018 0.38 -10000 0 -0.65 63 63
LDHA -0.048 0.3 -10000 0 -0.9 55 55
ETS1 0.011 0.33 0.54 35 -0.54 91 126
PGK1 0.032 0.34 0.55 50 -0.54 92 142
NOS2 -0.024 0.3 0.5 41 -0.52 90 131
ITGB2 0.012 0.34 0.55 42 -0.55 93 135
ALDOA 0.041 0.34 0.55 50 -0.53 89 139
Cbp/p300/CITED2 0.014 0.34 0.56 27 -0.59 75 102
FOS 0.027 0.022 -10000 0 -0.049 5 5
HK2 0.035 0.34 0.55 47 -0.53 89 136
SP1 0.048 0.008 -10000 0 -10000 0 0
GCK 0.066 0.15 0.53 5 -10000 0 5
HK1 0.034 0.34 0.54 51 -0.53 90 141
NPM1 0.039 0.34 0.55 50 -0.53 90 140
EGLN1 0.04 0.33 0.55 50 -0.53 84 134
CREB1 0.035 0.041 -10000 0 -0.11 41 41
PGM1 0.027 0.34 0.55 45 -0.54 90 135
SMAD3 0.041 0.009 -10000 0 0 24 24
EDN1 0.035 0.21 0.46 4 -1 13 17
IGFBP1 0.04 0.34 0.55 48 -0.53 88 136
VEGFA -0.007 0.26 0.47 33 -0.48 71 104
HIF1A/JAB1 0.035 0.099 0.2 9 -0.15 75 84
CP -0.013 0.32 0.53 34 -0.55 88 122
CXCL12 -0.019 0.31 0.54 28 -0.53 94 122
COPS5 0.036 0.016 -10000 0 -0.001 87 87
SMAD3/SMAD4 0.052 0.034 -10000 0 -0.14 12 12
BNIP3 0.017 0.33 0.55 42 -0.54 90 132
EGLN3 -0.017 0.32 0.54 31 -0.55 96 127
CA9 -0.016 0.3 0.55 24 -0.53 88 112
TERT 0.022 0.32 0.54 42 -0.53 86 128
ENO1 0.035 0.34 0.55 49 -0.53 90 139
PFKL 0.037 0.34 0.55 47 -0.53 88 135
NCOA1 0.04 0.01 -10000 0 -0.001 29 29
ADM -0.001 0.32 0.54 26 -0.53 91 117
ARNT 0.031 0.098 0.2 39 -0.12 86 125
HNF4A 0.041 0.013 -10000 0 -10000 0 0
ADFP -0.002 0.32 0.54 36 -0.53 95 131
SLC2A1 0.005 0.28 0.49 24 -0.52 69 93
LEP 0.039 0.33 0.55 49 -0.53 86 135
HIF1A/ARNT/Cbp/p300 0.015 0.32 0.61 2 -0.61 54 56
EPO 0.03 0.28 0.51 24 -0.5 62 86
CREBBP 0.05 0.11 0.29 44 -0.22 14 58
HIF1A/ARNT/Cbp/p300/HDAC7 0.005 0.31 -10000 0 -0.6 57 57
PFKFB3 0.029 0.34 0.55 47 -0.54 89 136
NT5E -0.036 0.31 0.54 21 -0.55 98 119
Ephrin B reverse signaling

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
EFNB2 0.031 0.018 -10000 0 0 143 143
EPHB2 0.043 0.013 0.067 2 0 38 40
EFNB1 -0.001 0.024 0.029 210 -10000 0 210
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.077 0.066 0.23 1 -0.12 19 20
Ephrin B2/EPHB1-2 0.041 0.069 -10000 0 -0.1 77 77
neuron projection morphogenesis 0.052 0.052 -10000 0 -0.11 23 23
Ephrin B1/EPHB1-2/Tiam1 0.07 0.061 0.21 3 -0.11 29 32
DNM1 0.041 0.012 -10000 0 0 38 38
cell-cell signaling 0.003 0.006 0.024 2 -10000 0 2
MAP2K4 -0.13 0.21 0.23 3 -0.46 164 167
YES1 -0.2 0.33 -10000 0 -0.69 168 168
Ephrin B1/EPHB1-2/NCK2 0.08 0.052 0.21 3 -0.11 17 20
PI3K -0.1 0.22 -10000 0 -0.44 167 167
mol:GDP 0.068 0.06 0.2 3 -0.11 29 32
ITGA2B 0.04 0.009 -10000 0 0 30 30
endothelial cell proliferation 0.024 0.061 -10000 0 -0.11 83 83
FYN -0.2 0.33 -10000 0 -0.7 166 166
MAP3K7 -0.13 0.23 0.22 4 -0.48 160 164
FGR -0.19 0.32 -10000 0 -0.68 171 171
TIAM1 0.037 0.014 -10000 0 0 72 72
PIK3R1 0.034 0.017 -10000 0 0 108 108
RGS3 0.04 0.008 -10000 0 0 23 23
cell adhesion -0.11 0.21 -10000 0 -0.41 167 167
LYN -0.19 0.32 -10000 0 -0.69 163 163
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.3 -10000 0 -0.62 170 170
Ephrin B1/EPHB1-2 -0.14 0.24 -10000 0 -0.53 151 151
SRC -0.18 0.32 -10000 0 -0.68 166 166
ITGB3 0.033 0.017 -10000 0 0 121 121
EPHB1 0.04 0.014 -10000 0 0 59 59
EPHB4 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 34 34
Ephrin B2/EPHB4 0.025 0.061 -10000 0 -0.11 83 83
alphaIIb/beta3 Integrin 0.04 0.05 -10000 0 -0.14 34 34
BLK -0.19 0.32 -10000 0 -0.69 165 165
HCK -0.19 0.32 -10000 0 -0.68 165 165
regulation of stress fiber formation -0.077 0.051 0.11 17 -0.22 2 19
MAPK8 -0.14 0.21 0.24 1 -0.44 168 169
Ephrin B1/EPHB1-2/RGS3 0.08 0.052 0.21 4 -0.11 18 22
endothelial cell migration -0.11 0.18 0.19 5 -0.4 146 151
NCK2 0.042 0.004 -10000 0 0 6 6
PTPN13 0.022 0.022 -10000 0 0 276 276
regulation of focal adhesion formation -0.077 0.051 0.11 17 -0.22 2 19
chemotaxis -0.077 0.051 0.11 18 -0.2 4 22
PIK3CA 0.03 0.019 -10000 0 0 155 155
Rac1/GTP 0.066 0.059 0.2 1 -0.12 21 22
angiogenesis -0.14 0.24 -10000 0 -0.52 157 157
LCK -0.19 0.32 -10000 0 -0.68 170 170
Wnt signaling

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
Noncanonical Wnts/FZD -0.019 0.096 -9999 0 -0.2 94 94
FZD6 0.029 0.019 -9999 0 0 170 170
WNT6 0.041 0.006 -9999 0 0 13 13
WNT4 0.041 0.007 -9999 0 0 18 18
FZD3 0.029 0.019 -9999 0 0 168 168
WNT5A 0.035 0.015 -9999 0 0 91 91
WNT11 0.033 0.017 -9999 0 0 124 124
Osteopontin-mediated 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
IKK alpha homodimer -0.011 0.13 0.2 10 -0.22 121 131
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.18 0.28 1 -0.35 124 125
alphaV/beta3 Integrin/Osteopontin/Src -0.007 0.11 -10000 0 -0.16 155 155
AP1 -0.044 0.18 0.27 2 -0.28 154 156
ILK -0.027 0.11 0.19 11 -0.24 71 82
bone resorption -0.04 0.1 0.2 2 -0.25 59 61
PTK2B 0.033 0.017 -10000 0 0 118 118
PYK2/p130Cas 0.005 0.12 -10000 0 -0.19 88 88
ITGAV 0.026 0.033 -10000 0 -0.048 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.068 -10000 0 -0.14 68 68
alphaV/beta3 Integrin/Osteopontin 0.005 0.13 -10000 0 -0.17 163 163
MAP3K1 -0.027 0.1 0.19 11 -0.24 69 80
JUN 0.036 0.015 -10000 0 0 80 80
MAPK3 -0.047 0.14 0.19 13 -0.28 112 125
MAPK1 -0.046 0.14 0.19 13 -0.28 111 124
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 -0.032 0.1 0.17 13 -0.23 77 90
ITGB3 0.023 0.034 -10000 0 -0.048 76 76
NFKBIA -0.064 0.16 0.19 10 -0.36 110 120
FOS 0.027 0.021 -10000 0 0 207 207
CD44 0.035 0.016 -10000 0 0 96 96
CHUK 0.038 0.012 -10000 0 0 52 52
PLAU -0.18 0.42 -10000 0 -1 107 107
NF kappa B1 p50/RelA -0.032 0.2 -10000 0 -0.39 109 109
BCAR1 0.036 0.014 -10000 0 0 76 76
RELA 0.041 0.006 -10000 0 0 10 10
alphaV beta3 Integrin 0.004 0.091 -10000 0 -0.14 136 136
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.029 0.1 0.19 12 -0.23 72 84
VAV3 -0.039 0.1 0.17 11 -0.23 89 100
MAP3K14 -0.024 0.12 0.2 13 -0.23 108 121
ROCK2 0.037 0.013 -10000 0 0 65 65
SPP1 0.025 0.031 -10000 0 -0.05 51 51
RAC1 0.039 0.01 -10000 0 0 34 34
Rac1/GTP -0.034 0.11 0.18 11 -0.22 88 99
MMP2 -0.088 0.14 0.2 1 -0.31 131 132
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.021 0.081 -10000 0 -0.14 111 111
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.11 0.21 3 -0.22 72 75
AP1 -0.026 0.068 -10000 0 -0.12 172 172
mol:PIP3 -0.036 0.057 -10000 0 -0.13 126 126
AKT1 -0.002 0.094 0.24 18 -0.24 15 33
PTK2B -0.047 0.11 0.12 3 -0.19 183 186
RHOA 0.002 0.058 0.17 1 -0.3 8 9
PIK3CB 0.034 0.016 -10000 0 0 103 103
mol:Ca2+ -0.008 0.048 0.19 8 -0.14 19 27
MAGI3 0.04 0.009 -10000 0 0 30 30
RELA 0.041 0.006 -10000 0 0 10 10
apoptosis 0.002 0.069 0.072 123 -0.14 95 218
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
positive regulation of microtubule depolymerization -0.046 0.1 0.19 16 -0.2 125 141
NF kappa B1 p50/RelA -0.028 0.076 0.11 2 -0.16 113 115
endothelial cell migration -0.04 0.12 -10000 0 -0.3 99 99
ADCY4 -0.019 0.094 0.16 2 -0.2 99 101
ADCY5 -0.018 0.092 0.16 2 -0.19 103 105
ADCY6 -0.019 0.094 0.17 1 -0.2 103 104
ADCY7 -0.018 0.092 0.16 2 -0.19 100 102
ADCY1 -0.018 0.092 0.16 2 -0.2 99 101
ADCY2 -0.014 0.09 0.17 1 -0.2 90 91
ADCY3 -0.02 0.094 0.17 1 -0.2 105 106
ADCY8 -0.002 0.086 0.17 1 -0.19 77 78
ADCY9 -0.022 0.098 0.16 2 -0.2 107 109
GSK3B -0.046 0.11 0.21 15 -0.18 179 194
arachidonic acid secretion -0.029 0.098 0.14 2 -0.19 123 125
GNG2 0.039 0.01 -10000 0 0 34 34
TRIP6 0.012 0.052 -10000 0 -0.24 19 19
GNAO1 0.006 0.071 0.09 116 -0.14 92 208
HRAS 0.04 0.01 -10000 0 0 31 31
NFKBIA -0.03 0.091 0.17 9 -0.24 57 66
GAB1 0.038 0.012 -10000 0 0 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.26 -10000 0 -0.87 47 47
JUN 0.036 0.015 -10000 0 0 80 80
LPA/LPA2/NHERF2 0.015 0.037 -10000 0 -0.061 94 94
TIAM1 -0.037 0.3 -10000 0 -1 47 47
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 -0.004 0.044 0.19 8 -0.14 15 23
PLCB3 0.016 0.044 0.16 13 -0.062 91 104
FOS 0.026 0.02 -10000 0 0 207 207
positive regulation of mitosis -0.029 0.098 0.14 2 -0.19 123 125
LPA/LPA1-2-3 -0.017 0.049 -10000 0 -0.12 100 100
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 76 76
stress fiber formation -0.011 0.1 -10000 0 -0.25 46 46
GNAZ 0.008 0.073 0.091 122 -0.15 87 209
EGFR/PI3K-beta/Gab1 -0.025 0.066 -10000 0 -0.13 127 127
positive regulation of dendritic cell cytokine production -0.017 0.049 -10000 0 -0.12 100 100
LPA/LPA2/MAGI-3 0.016 0.037 -10000 0 -0.061 95 95
ARHGEF1 0.006 0.076 0.2 12 -0.13 94 106
GNAI2 0.006 0.076 0.091 126 -0.14 99 225
GNAI3 0.004 0.079 0.091 122 -0.15 98 220
GNAI1 0.003 0.079 0.091 119 -0.16 94 213
LPA/LPA3 -0.01 0.026 -10000 0 -0.065 100 100
LPA/LPA2 -0.01 0.025 -10000 0 -0.065 100 100
LPA/LPA1 -0.024 0.067 -10000 0 -0.17 100 100
HB-EGF/EGFR 0.023 0.052 -10000 0 -0.13 48 48
HBEGF -0.013 0.01 -10000 0 -10000 0 0
mol:DAG -0.004 0.044 0.19 8 -0.14 15 23
cAMP biosynthetic process -0.023 0.097 0.18 4 -0.2 97 101
NFKB1 0.036 0.015 -10000 0 0 84 84
SRC 0.039 0.01 -10000 0 0 36 36
GNB1 0.041 0.005 -10000 0 0 7 7
LYN -0.024 0.094 0.18 10 -0.23 60 70
GNAQ 0.009 0.032 0.043 124 -0.053 101 225
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.017 0.04 -10000 0 -0.1 100 100
IL8 -0.023 0.18 0.26 4 -0.37 91 95
PTK2 0.006 0.061 0.094 80 -0.13 75 155
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
CASP3 0.002 0.069 0.072 123 -0.14 95 218
EGFR 0.037 0.014 -10000 0 0 72 72
PLCG1 0.006 0.037 -10000 0 -0.098 30 30
PLD2 0.016 0.066 0.094 124 -0.12 90 214
G12/G13 0.023 0.078 -10000 0 -0.14 100 100
PI3K-beta -0.025 0.074 -10000 0 -0.21 42 42
cell migration -0.008 0.086 -10000 0 -0.24 46 46
SLC9A3R2 0.038 0.012 -10000 0 0 53 53
PXN -0.011 0.1 -10000 0 -0.25 46 46
HRAS/GTP -0.029 0.099 0.14 2 -0.2 121 123
RAC1 0.039 0.01 -10000 0 0 34 34
MMP9 0.029 0.02 -10000 0 0 178 178
PRKCE 0.039 0.01 -10000 0 0 36 36
PRKCD -0.016 0.054 0.18 11 -0.16 19 30
Gi(beta/gamma) -0.02 0.1 0.16 1 -0.19 119 120
mol:LPA -0.017 0.04 -10000 0 -0.1 100 100
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.099 0.19 1 -0.19 83 84
MAPKKK cascade -0.029 0.098 0.14 2 -0.19 123 125
contractile ring contraction involved in cytokinesis 0.002 0.061 0.17 1 -0.29 10 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.032 0.043 125 -0.052 107 232
GNA15 0.009 0.031 0.043 117 -0.054 93 210
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
MAPT -0.047 0.1 0.19 16 -0.2 127 143
GNA11 0.008 0.032 0.043 118 -0.054 97 215
Rac1/GTP -0.014 0.28 -10000 0 -0.93 47 47
MMP2 -0.04 0.12 -10000 0 -0.3 99 99
PDGFR-alpha signaling 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
PDGFRA 0.018 0.036 -10000 0 -0.054 79 79
PDGF/PDGFRA/CRKL 0.014 0.07 -10000 0 -0.1 126 126
positive regulation of JUN kinase activity 0.048 0.083 -10000 0 -0.11 99 99
CRKL 0.039 0.011 -10000 0 0 38 38
PDGF/PDGFRA/Caveolin-3 0.014 0.072 -10000 0 -0.1 129 129
AP1 -0.12 0.26 -10000 0 -0.65 99 99
mol:IP3 -0.015 0.045 0.065 39 -0.096 81 120
PLCG1 -0.015 0.045 0.065 39 -0.096 81 120
PDGF/PDGFRA/alphaV Integrin -0.007 0.09 -10000 0 -0.13 164 164
RAPGEF1 0.04 0.008 -10000 0 0 23 23
CRK 0.038 0.012 -10000 0 0 52 52
mol:Ca2+ -0.015 0.045 0.065 39 -0.096 81 120
CAV3 0.04 0.008 -10000 0 0 22 22
CAV1 0.036 0.015 -10000 0 0 80 80
SHC/Grb2/SOS1 0.05 0.084 -10000 0 -0.12 98 98
PDGF/PDGFRA/Shf 0.014 0.071 -10000 0 -0.1 125 125
FOS -0.12 0.26 0.32 1 -0.64 98 99
JUN -0.033 0.043 0.23 3 -0.2 11 14
oligodendrocyte development -0.007 0.09 -10000 0 -0.13 164 164
GRB2 0.041 0.007 -10000 0 0 17 17
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:DAG -0.015 0.045 0.065 39 -0.096 81 120
PDGF/PDGFRA 0.018 0.036 -10000 0 -0.054 79 79
actin cytoskeleton reorganization 0.015 0.071 -10000 0 -0.1 127 127
SRF -0.007 0.024 0.033 124 -10000 0 124
SHC1 0.04 0.01 -10000 0 0 31 31
PI3K 0.012 0.08 -10000 0 -0.14 96 96
PDGF/PDGFRA/Crk/C3G 0.036 0.072 -10000 0 -0.12 82 82
JAK1 -0.01 0.02 0.03 23 -10000 0 23
ELK1/SRF -0.025 0.064 0.15 18 -0.16 56 74
SHB 0.041 0.007 -10000 0 0 17 17
SHF 0.039 0.011 -10000 0 0 41 41
CSNK2A1 0.036 0.031 0.084 1 -0.028 60 61
GO:0007205 -0.025 0.072 0.088 21 -0.19 65 86
SOS1 0.038 0.013 -10000 0 0 56 56
Ras protein signal transduction 0.048 0.083 -10000 0 -0.11 99 99
PDGF/PDGFRA/SHB 0.015 0.071 -10000 0 -0.1 127 127
PDGF/PDGFRA/Caveolin-1 0.012 0.074 -10000 0 -0.11 116 116
ITGAV 0.033 0.017 -10000 0 0 117 117
ELK1 -0.025 0.08 0.2 17 -0.18 65 82
PIK3CA 0.03 0.019 -10000 0 0 155 155
PDGF/PDGFRA/Crk 0.014 0.07 -10000 0 -0.1 120 120
JAK-STAT cascade -0.01 0.02 0.03 23 -10000 0 23
cell proliferation 0.013 0.07 -10000 0 -0.1 125 125
Endothelins

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
AKT1 -0.004 0.14 0.23 31 -0.24 115 146
PTK2B 0.033 0.017 -10000 0 0 118 118
mol:Ca2+ -0.032 0.21 -10000 0 -0.55 36 36
EDN1 -0.005 0.1 0.22 8 -0.18 123 131
EDN3 0.036 0.014 -10000 0 0 77 77
EDN2 0.037 0.014 -10000 0 0 66 66
HRAS/GDP -0.051 0.19 0.27 2 -0.35 112 114
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.026 0.14 0.23 1 -0.26 101 102
ADCY4 0.01 0.14 0.21 66 -0.23 69 135
ADCY5 0.011 0.13 0.21 66 -0.23 68 134
ADCY6 0.008 0.14 0.21 70 -0.24 73 143
ADCY7 0.007 0.14 0.21 64 -0.24 72 136
ADCY1 0.009 0.14 0.21 68 -0.24 71 139
ADCY2 0.01 0.13 0.21 64 -0.23 61 125
ADCY3 0.009 0.14 0.21 69 -0.24 71 140
ADCY8 -0.002 0.11 0.22 33 -0.23 50 83
ADCY9 0.009 0.14 0.21 71 -0.23 74 145
arachidonic acid secretion -0.1 0.26 0.3 2 -0.49 136 138
ETB receptor/Endothelin-1/Gq/GTP 0 0.11 -10000 0 -0.24 60 60
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.01 -10000 0 0 31 31
ETA receptor/Endothelin-1/G12/GTP -0.006 0.13 0.35 7 -0.22 122 129
ETA receptor/Endothelin-1/Gs/GTP -0.004 0.12 0.32 7 -0.2 119 126
mol:GTP 0 0.006 -10000 0 -0.025 2 2
COL3A1 -0.057 0.16 0.27 7 -0.36 114 121
EDNRB 0.021 0.054 0.096 1 -0.089 96 97
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.003 0.14 0.26 11 -0.26 94 105
CYSLTR1 -0.015 0.15 0.27 8 -0.26 107 115
SLC9A1 -0.016 0.085 0.2 7 -0.17 88 95
mol:GDP -0.064 0.19 0.26 2 -0.37 112 114
SLC9A3 -0.022 0.19 -10000 0 -0.53 31 31
RAF1 -0.075 0.22 0.28 4 -0.41 135 139
JUN -0.073 0.3 -10000 0 -0.82 59 59
JAK2 -0.008 0.14 0.23 28 -0.24 114 142
mol:IP3 -0.023 0.14 0.22 1 -0.31 78 79
ETA receptor/Endothelin-1 -0.027 0.15 0.39 6 -0.28 127 133
PLCB1 0.033 0.017 -10000 0 0 114 114
PLCB2 0.037 0.014 -10000 0 -0.005 52 52
ETA receptor/Endothelin-3 0.015 0.084 0.19 7 -0.12 113 120
FOS -0.14 0.36 0.34 1 -0.83 111 112
Gai/GDP -0.032 0.24 -10000 0 -0.69 59 59
CRK 0.038 0.012 -10000 0 0 52 52
mol:Ca ++ -0.031 0.19 0.26 25 -0.34 108 133
BCAR1 0.036 0.014 -10000 0 0 76 76
PRKCB1 -0.027 0.14 0.26 4 -0.3 80 84
GNAQ 0.035 0.022 -10000 0 -0.038 31 31
GNAZ 0.039 0.011 -10000 0 0 42 42
GNAL 0.04 0.009 -10000 0 0 26 26
Gs family/GDP -0.05 0.18 0.27 1 -0.34 106 107
ETA receptor/Endothelin-1/Gq/GTP -0.015 0.14 0.22 5 -0.26 82 87
MAPK14 -0.017 0.11 0.27 3 -0.25 67 70
TRPC6 -0.034 0.21 -10000 0 -0.57 36 36
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.011 0.11 -10000 0 -0.24 68 68
ETB receptor/Endothelin-2 0.031 0.054 -10000 0 -0.071 91 91
ETB receptor/Endothelin-3 0.032 0.051 -10000 0 -0.067 81 81
ETB receptor/Endothelin-1 0.007 0.11 0.2 5 -0.19 99 104
MAPK3 -0.13 0.34 0.32 2 -0.75 116 118
MAPK1 -0.14 0.35 0.32 2 -0.75 120 122
Rac1/GDP -0.051 0.18 0.28 1 -0.35 109 110
cAMP biosynthetic process 0.044 0.13 0.24 68 -0.23 27 95
MAPK8 -0.053 0.24 -10000 0 -0.57 70 70
SRC 0.039 0.01 -10000 0 0 36 36
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.11 -10000 0 -0.27 61 61
p130Cas/CRK/Src/PYK2 -0.059 0.19 0.31 2 -0.41 87 89
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.05 0.19 0.28 1 -0.35 110 111
COL1A2 -0.075 0.21 0.27 5 -0.49 103 108
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.011 0.088 0.19 8 -0.13 127 135
mol:DAG -0.023 0.14 0.22 1 -0.31 78 79
MAP2K2 -0.099 0.27 0.29 4 -0.55 124 128
MAP2K1 -0.1 0.27 0.3 3 -0.56 124 127
EDNRA -0.003 0.1 0.22 8 -0.17 133 141
positive regulation of muscle contraction -0.014 0.12 0.2 29 -0.22 101 130
Gq family/GDP -0.013 0.19 -10000 0 -0.33 104 104
HRAS/GTP -0.053 0.18 0.25 2 -0.34 113 115
PRKCH -0.03 0.14 0.33 1 -0.3 87 88
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.031 0.15 0.26 3 -0.31 84 87
PRKCB -0.027 0.14 0.2 1 -0.29 88 89
PRKCE -0.028 0.14 0.3 4 -0.3 81 85
PRKCD -0.031 0.14 0.26 2 -0.31 81 83
PRKCG -0.034 0.15 -10000 0 -0.31 86 86
regulation of vascular smooth muscle contraction -0.18 0.44 -10000 0 -1 111 111
PRKCQ -0.03 0.15 0.29 7 -0.32 78 85
PLA2G4A -0.11 0.28 0.3 2 -0.54 136 138
GNA14 0.036 0.021 -10000 0 -0.038 32 32
GNA15 0.034 0.022 -10000 0 -0.036 28 28
GNA12 0.04 0.01 -10000 0 0 32 32
GNA11 0.034 0.021 -10000 0 -0.036 29 29
Rac1/GTP -0.006 0.13 0.35 6 -0.22 120 126
MMP1 0.02 0.12 0.35 16 -0.58 10 26
Syndecan-1-mediated signaling events

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
TGFB1 0.037 0.013 -10000 0 0 62 62
CCL5 0.03 0.019 -10000 0 0 161 161
SDCBP 0.036 0.014 -10000 0 0 75 75
FGFR/FGF2/Syndecan-1 -0.012 0.12 0.2 20 -0.33 42 62
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.013 0.13 0.23 15 -0.3 56 71
Syndecan-1/Syntenin -0.014 0.14 0.23 19 -0.29 67 86
MAPK3 -0.023 0.13 0.2 18 -0.28 60 78
HGF/MET 0.013 0.075 -10000 0 -0.14 105 105
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 62 62
BSG 0.037 0.014 -10000 0 0 71 71
keratinocyte migration -0.012 0.13 0.23 15 -0.3 56 71
Syndecan-1/RANTES -0.019 0.14 0.22 17 -0.29 76 93
Syndecan-1/CD147 -0.002 0.15 0.25 13 -0.29 61 74
Syndecan-1/Syntenin/PIP2 -0.016 0.14 0.22 18 -0.28 66 84
LAMA5 0.036 0.015 -10000 0 0 85 85
positive regulation of cell-cell adhesion -0.016 0.13 0.21 18 -0.28 66 84
MMP7 0.016 0.02 -10000 0 0 340 340
HGF 0.04 0.009 -10000 0 0 29 29
Syndecan-1/CASK -0.036 0.12 0.15 5 -0.29 63 68
Syndecan-1/HGF/MET -0.018 0.14 0.26 12 -0.28 74 86
regulation of cell adhesion -0.031 0.12 0.21 9 -0.29 55 64
HPSE 0.035 0.015 -10000 0 0 90 90
positive regulation of cell migration -0.012 0.12 0.2 20 -0.33 42 62
SDC1 -0.017 0.12 0.17 5 -0.34 37 42
Syndecan-1/Collagen -0.012 0.12 0.2 20 -0.33 42 62
PPIB 0.04 0.009 -10000 0 0 24 24
MET 0.027 0.02 -10000 0 0 198 198
PRKACA 0.035 0.015 -10000 0 0 89 89
MMP9 0.029 0.02 -10000 0 0 178 178
MAPK1 -0.022 0.13 0.21 16 -0.28 60 76
homophilic cell adhesion -0.012 0.13 0.2 28 -0.32 47 75
MMP1 0.03 0.019 -10000 0 0 159 159
Nectin adhesion pathway

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 93 93
PTK2 -0.045 0.14 -10000 0 -0.3 104 104
positive regulation of JNK cascade -0.032 0.14 -10000 0 -0.27 106 106
CDC42/GDP -0.039 0.2 -10000 0 -0.36 122 122
Rac1/GDP -0.041 0.19 -10000 0 -0.36 120 120
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.04 0.01 -10000 0 0 31 31
CDC42/GTP -0.037 0.18 -10000 0 -0.34 103 103
nectin-3/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
RAPGEF1 -0.056 0.18 -10000 0 -0.37 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.063 0.2 -10000 0 -0.4 127 127
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
TLN1 -0.039 0.085 0.19 2 -0.25 60 62
Rap1/GTP -0.044 0.14 -10000 0 -0.28 127 127
IQGAP1 0.037 0.014 -10000 0 0 69 69
Rap1/GTP/I-afadin 0.042 0.066 -10000 0 -0.11 69 69
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
PVR 0.04 0.009 -10000 0 0 27 27
Necl-5(dimer) 0.04 0.009 -10000 0 0 27 27
mol:GDP -0.067 0.22 -10000 0 -0.43 123 123
MLLT4 0.034 0.017 -10000 0 0 107 107
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.023 0.092 -10000 0 -0.13 100 100
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
positive regulation of lamellipodium assembly -0.041 0.16 -10000 0 -0.29 123 123
PVRL1 0.04 0.008 -10000 0 0 22 22
PVRL3 0.029 0.019 -10000 0 0 174 174
PVRL2 0.039 0.011 -10000 0 0 44 44
PIK3R1 0.034 0.017 -10000 0 0 108 108
CDH1 0.035 0.016 -10000 0 0 98 98
CLDN1 0.023 0.021 -10000 0 0 259 259
JAM-A/CLDN1 0.013 0.089 -10000 0 -0.12 125 125
SRC -0.083 0.21 -10000 0 -0.44 132 132
ITGB3 0.033 0.017 -10000 0 0 121 121
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
FARP2 -0.059 0.22 -10000 0 -0.44 100 100
RAC1 0.039 0.01 -10000 0 0 34 34
CTNNA1 0.039 0.011 -10000 0 0 38 38
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.023 0.079 -10000 0 -0.12 101 101
nectin-1/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
nectin-2/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.046 -10000 0 -0.11 42 42
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.078 -10000 0 -0.12 96 96
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.047 -10000 0 -0.11 42 42
F11R 0.04 0.01 -10000 0 0 32 32
positive regulation of filopodium formation -0.032 0.14 -10000 0 -0.27 106 106
alphaV/beta3 Integrin/Talin -0.031 0.11 0.26 2 -0.22 102 104
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
PIP5K1C -0.032 0.087 -10000 0 -0.17 121 121
VAV2 -0.075 0.24 -10000 0 -0.47 105 105
RAP1/GDP -0.039 0.18 -10000 0 -0.34 120 120
ITGAV 0.033 0.017 -10000 0 0 117 117
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.079 -10000 0 -0.12 102 102
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
Rac1/GTP -0.048 0.19 -10000 0 -0.35 123 123
PTPRM -0.029 0.097 -10000 0 -0.18 125 125
E-cadherin/beta catenin/alpha catenin 0.062 0.09 -10000 0 -0.13 58 58
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.04 0.009 -10000 0 0 24 24
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.006 0.085 -10000 0 -0.13 126 126
alphaM/beta2 Integrin/GPIbA 0.053 0.069 -10000 0 -0.12 60 60
alphaM/beta2 Integrin/proMMP-9 0.03 0.081 -10000 0 -0.13 83 83
PLAUR 0.036 0.014 -10000 0 0 77 77
HMGB1 0.041 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/Talin 0.047 0.076 -10000 0 -0.12 74 74
AGER 0.041 0.016 -10000 0 -0.054 10 10
RAP1A 0.039 0.01 -10000 0 0 35 35
SELPLG 0.04 0.009 -10000 0 0 27 27
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.082 0.083 -10000 0 -0.18 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.029 0.02 -10000 0 0 178 178
CYR61 0.03 0.019 -10000 0 0 157 157
TLN1 0.039 0.012 -10000 0 0 46 46
Rap1/GTP -0.061 0.17 -10000 0 -0.32 132 132
RHOA 0.041 0.007 -10000 0 0 14 14
P-selectin oligomer 0.039 0.011 -10000 0 0 38 38
MYH2 -0.081 0.17 0.2 2 -0.33 137 139
MST1R 0.039 0.011 -10000 0 0 42 42
leukocyte activation during inflammatory response 0.059 0.065 -10000 0 -0.1 51 51
APOB 0.041 0.007 -10000 0 0 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.021 -10000 0 0 273 273
JAM3 0.038 0.013 -10000 0 0 56 56
GP1BA 0.039 0.01 -10000 0 0 37 37
alphaM/beta2 Integrin/CTGF 0.035 0.081 -10000 0 -0.12 97 97
alphaM/beta2 Integrin -0.063 0.17 -10000 0 -0.34 122 122
JAM3 homodimer 0.038 0.013 -10000 0 0 56 56
ICAM2 0.039 0.011 -10000 0 0 41 41
ICAM1 0.026 0.02 -10000 0 0 207 207
phagocytosis triggered by activation of immune response cell surface activating receptor -0.063 0.17 -10000 0 -0.34 123 123
cell adhesion 0.052 0.069 -10000 0 -0.12 60 60
NFKB1 0.022 0.075 0.26 4 -0.22 24 28
THY1 0.025 0.021 -10000 0 0 221 221
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
Lipoprotein(a) 0.05 0.018 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.025 0.1 -10000 0 -0.13 138 138
IL6 -0.019 0.077 0.26 3 -0.43 10 13
ITGB2 0.034 0.022 -10000 0 -0.052 9 9
elevation of cytosolic calcium ion concentration 0.033 0.11 -10000 0 -0.16 105 105
alphaM/beta2 Integrin/JAM2/JAM3 0.067 0.075 -10000 0 -0.11 51 51
JAM2 0.038 0.013 -10000 0 0 57 57
alphaM/beta2 Integrin/ICAM1 0.052 0.1 -10000 0 -0.14 89 89
alphaM/beta2 Integrin/uPA/Plg 0.041 0.099 -10000 0 -0.14 102 102
RhoA/GTP -0.083 0.18 0.2 1 -0.34 142 143
positive regulation of phagocytosis -0.04 0.15 0.21 4 -0.3 100 104
Ron/MSP 0.054 0.029 -10000 0 -0.14 9 9
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.11 -10000 0 -0.16 105 105
alphaM/beta2 Integrin/uPAR 0.045 0.082 -10000 0 -0.15 68 68
PLAU 0.026 0.02 -10000 0 0 214 214
PLAT 0.026 0.02 -10000 0 0 213 213
actin filament polymerization -0.077 0.16 0.2 2 -0.32 135 137
MST1 0.041 0.007 -10000 0 0 15 15
alphaM/beta2 Integrin/lipoprotein(a) 0.065 0.069 -10000 0 -0.1 51 51
TNF -0.01 0.073 0.26 4 -0.32 9 13
RAP1B 0.038 0.013 -10000 0 0 59 59
alphaM/beta2 Integrin/uPA 0.018 0.094 -10000 0 -0.15 104 104
fibrinolysis 0.039 0.097 -10000 0 -0.14 102 102
HCK 0.036 0.015 -10000 0 0 80 80
dendritic cell antigen processing and presentation -0.063 0.17 -10000 0 -0.34 123 123
VTN 0.04 0.009 -10000 0 0 24 24
alphaM/beta2 Integrin/CYR61 0.024 0.085 -10000 0 -0.12 112 112
LPA 0.038 0.012 -10000 0 0 55 55
LRP1 0.036 0.014 -10000 0 0 75 75
cell migration 0.019 0.094 0.19 14 -0.13 126 140
FN1 0.021 0.021 -10000 0 0 277 277
alphaM/beta2 Integrin/Thy1 0.007 0.093 -10000 0 -0.12 155 155
MPO 0.041 0.008 -10000 0 0 19 19
KNG1 0.034 0.017 -10000 0 0 109 109
RAP1/GDP 0.039 0.049 -10000 0 -0.12 42 42
ROCK1 -0.083 0.17 0.26 2 -0.34 136 138
ELA2 0.037 0.013 -10000 0 0 64 64
PLG 0.038 0.012 -10000 0 0 49 49
CTGF 0.034 0.017 -10000 0 0 112 112
alphaM/beta2 Integrin/Hck 0.05 0.071 -10000 0 -0.13 49 49
ITGAM 0.042 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.073 0.076 -10000 0 -0.12 54 54
HP 0.01 0.018 -10000 0 0 429 429
leukocyte adhesion 0.019 0.11 -10000 0 -0.22 22 22
SELP 0.039 0.011 -10000 0 0 38 38
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.027 -10000 0 -0.046 42 42
CDKN2C 0.029 0.029 -10000 0 -0.043 51 51
CDKN2A 0.022 0.03 -10000 0 -0.039 61 61
CCND2 0.009 0.045 0.11 77 -0.12 2 79
RB1 -0.012 0.066 0.22 7 -0.14 86 93
CDK4 0.01 0.056 0.13 79 -0.12 19 98
CDK6 0.006 0.063 0.14 79 -0.12 43 122
G1/S progression 0.02 0.075 0.14 108 -0.23 8 116
TRAIL signaling pathway

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
TNFSF10 0.021 0.021 -10000 0 0 282 282
positive regulation of NF-kappaB transcription factor activity 0.002 0.067 -10000 0 -0.13 95 95
MAP2K4 -0.013 0.096 0.18 2 -0.27 39 41
IKBKB 0.039 0.011 -10000 0 0 44 44
TNFRSF10B 0.033 0.018 -10000 0 0 126 126
TNFRSF10A 0.031 0.018 -10000 0 0 141 141
SMPD1 -0.008 0.044 -10000 0 -0.1 92 92
IKBKG 0.042 0.003 -10000 0 0 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.018 -10000 0 0 137 137
TRAIL/TRAILR2 0.002 0.067 -10000 0 -0.13 96 96
TRAIL/TRAILR3 0.001 0.067 -10000 0 -0.13 100 100
TRAIL/TRAILR1 -0.001 0.069 -10000 0 -0.13 101 101
TRAIL/TRAILR4 0.002 0.067 -10000 0 -0.13 95 95
TRAIL/TRAILR1/DAP3/GTP 0.01 0.065 -10000 0 -0.1 99 99
IKK complex 0.02 0.091 -10000 0 -0.32 22 22
RIPK1 0.038 0.012 -10000 0 0 48 48
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.027 0.021 -10000 0 -0.13 9 9
MAPK3 -0.01 0.01 -10000 0 -10000 0 0
MAP3K1 -0.008 0.1 -10000 0 -0.28 39 39
TRAILR4 (trimer) 0.032 0.018 -10000 0 0 137 137
TRADD 0.036 0.014 -10000 0 0 76 76
TRAILR1 (trimer) 0.031 0.018 -10000 0 0 141 141
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.022 0.083 -10000 0 -0.18 95 95
CFLAR 0.04 0.008 -10000 0 0 21 21
MAPK1 -0.01 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.025 0.082 -10000 0 -0.11 87 87
mol:ceramide -0.007 0.044 -10000 0 -0.1 92 92
FADD 0.04 0.008 -10000 0 0 21 21
MAPK8 -0.022 0.1 0.2 5 -0.26 50 55
TRAF2 0.04 0.009 -10000 0 0 29 29
TRAILR3 (trimer) 0.032 0.018 -10000 0 0 134 134
CHUK 0.038 0.012 -10000 0 0 52 52
TRAIL/TRAILR1/FADD 0.01 0.07 -10000 0 -0.12 98 98
DAP3 0.039 0.011 -10000 0 0 40 40
CASP10 -0.006 0.1 0.16 82 -0.2 79 161
JNK cascade 0.002 0.067 -10000 0 -0.13 95 95
TRAIL (trimer) 0.021 0.021 -10000 0 0 282 282
TNFRSF10C 0.032 0.018 -10000 0 0 134 134
TRAIL/TRAILR1/DAP3/GTP/FADD 0.021 0.073 -10000 0 -0.11 95 95
TRAIL/TRAILR2/FADD 0.013 0.069 -10000 0 -0.11 94 94
cell death -0.007 0.044 -10000 0 -0.1 92 92
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.022 0.083 -10000 0 -0.18 92 92
TRAILR2 (trimer) 0.032 0.018 -10000 0 0 126 126
CASP8 -0.001 0.11 -10000 0 -0.65 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.028 0.082 -10000 0 -0.11 81 81
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.005 0 204 -10000 0 204
GNB1/GNG2 0.041 0.07 -10000 0 -0.11 89 89
regulation of S phase of mitotic cell cycle -0.012 0.076 -10000 0 -0.17 93 93
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.01 -10000 0 0 31 31
SHBG/T-DHT 0.026 0.007 -10000 0 -10000 0 0
PELP1 0.039 0.01 -10000 0 0 36 36
AKT1 -0.009 0.004 0.002 47 -10000 0 47
MAP2K1 -0.033 0.079 0.17 27 -0.17 78 105
T-DHT/AR 0.006 0.055 -10000 0 -0.13 79 79
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 103 103
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
mol:GDP -0.042 0.088 -10000 0 -0.24 82 82
cell proliferation -0.07 0.17 0.24 6 -0.39 107 113
PIK3CA 0.03 0.019 -10000 0 0 155 155
FOS -0.12 0.29 0.27 1 -0.7 105 106
mol:Ca2+ -0.006 0.021 -10000 0 -0.048 82 82
MAPK3 -0.052 0.13 0.22 7 -0.3 94 101
MAPK1 -0.042 0.14 -10000 0 -0.34 62 62
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 0 0.002 0.002 77 -0.004 103 180
cAMP biosynthetic process -0.001 0.024 0.16 6 -10000 0 6
GNG2 0.039 0.01 -10000 0 0 34 34
potassium channel inhibitor activity 0 0.002 0.002 77 -0.004 103 180
HRAS/GTP 0.025 0.078 -10000 0 -0.093 142 142
actin cytoskeleton reorganization 0.029 0.052 -10000 0 -0.11 46 46
SRC 0.039 0.01 -10000 0 0 36 36
voltage-gated calcium channel activity 0 0.002 0.002 77 -0.004 103 180
PI3K 0.023 0.052 -10000 0 -0.12 48 48
apoptosis 0.061 0.18 0.38 114 -0.22 5 119
T-DHT/AR/PELP1 0.025 0.058 -10000 0 -0.11 79 79
HRAS/GDP -0.006 0.11 0.15 1 -0.23 82 83
CREB1 -0.076 0.18 0.22 5 -0.41 114 119
RAC1-CDC42/GTP 0.038 0.059 -10000 0 -0.11 46 46
AR 0.033 0.017 -10000 0 0 122 122
GNB1 0.041 0.005 -10000 0 0 7 7
RAF1 -0.02 0.076 0.18 29 -0.18 17 46
RAC1-CDC42/GDP 0.016 0.12 0.19 3 -0.23 78 81
T-DHT/AR/PELP1/Src 0.039 0.066 -10000 0 -0.11 78 78
MAP2K2 -0.03 0.074 0.17 22 -0.17 68 90
T-DHT/AR/PELP1/Src/PI3K -0.012 0.077 -10000 0 -0.17 93 93
GNAZ 0.039 0.011 -10000 0 0 42 42
SHBG 0.039 0.01 -10000 0 0 35 35
Gi family/GNB1/GNG2/GDP -0.005 0.099 -10000 0 -0.3 34 34
mol:T-DHT 0 0.001 -10000 0 -0.004 27 27
RAC1 0.039 0.01 -10000 0 0 34 34
GNRH1 -0.008 0.004 0 125 -10000 0 125
Gi family/GTP -0.02 0.077 -10000 0 -0.18 72 72
CDC42 0.04 0.009 -10000 0 0 24 24
Thromboxane A2 receptor signaling

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
TGM2 0.033 0.017 -10000 0 0 114 114
GNB1/GNG2 -0.064 0.086 -10000 0 -0.18 190 190
AKT1 -0.027 0.14 0.25 2 -0.23 73 75
EGF 0.038 0.012 -10000 0 0 53 53
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.005 0.06 0.22 8 -0.18 2 10
mol:Ca2+ -0.052 0.19 0.3 2 -0.3 191 193
LYN 0.002 0.057 0.22 9 -0.17 4 13
RhoA/GTP -0.019 0.088 0.14 5 -0.13 179 184
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.21 0.32 1 -0.34 191 192
GNG2 0.039 0.01 -10000 0 0 34 34
ARRB2 0.039 0.011 -10000 0 0 44 44
TP alpha/Gq family/GDP/G beta5/gamma2 -0.024 0.16 -10000 0 -0.53 45 45
G beta5/gamma2 -0.073 0.12 -10000 0 -0.24 189 189
PRKCH -0.072 0.22 0.33 1 -0.35 189 190
DNM1 0.039 0.011 -10000 0 0 38 38
TXA2/TP beta/beta Arrestin3 0.029 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.041 0.006 -10000 0 0 12 12
G12 family/GTP -0.066 0.18 -10000 0 -0.3 188 188
ADRBK1 0.041 0.005 -10000 0 0 7 7
ADRBK2 0.036 0.015 -10000 0 0 84 84
RhoA/GTP/ROCK1 0.052 0.022 -10000 0 -0.11 8 8
mol:GDP 0.031 0.16 0.45 44 -0.24 1 45
mol:NADP 0.038 0.012 -10000 0 0 49 49
RAB11A 0.04 0.009 -10000 0 0 24 24
PRKG1 0.04 0.009 -10000 0 0 29 29
mol:IP3 -0.075 0.23 0.35 1 -0.37 193 194
cell morphogenesis 0.051 0.022 -10000 0 -0.11 8 8
PLCB2 -0.12 0.3 -10000 0 -0.5 192 192
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.002 0.053 0.24 6 -0.18 2 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.003 0.057 0.2 10 -0.18 3 13
RHOA 0.041 0.007 -10000 0 0 14 14
PTGIR 0.04 0.01 -10000 0 0 32 32
PRKCB1 -0.077 0.23 0.34 1 -0.38 188 189
GNAQ 0.038 0.012 -10000 0 0 49 49
mol:L-citrulline 0.038 0.012 -10000 0 0 49 49
TXA2/TXA2-R family -0.12 0.3 -10000 0 -0.52 191 191
LCK 0.004 0.058 0.22 8 -0.18 2 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.052 0.049 0.23 2 -0.15 8 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.1 -10000 0 -0.42 27 27
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.048 0.05 0.23 2 -0.15 8 10
MAPK14 -0.04 0.15 0.24 4 -0.23 181 185
TGM2/GTP -0.085 0.25 0.4 1 -0.41 170 171
MAPK11 -0.048 0.14 0.25 2 -0.22 188 190
ARHGEF1 -0.029 0.12 0.2 9 -0.18 183 192
GNAI2 0.041 0.007 -10000 0 0 15 15
JNK cascade -0.077 0.23 0.35 1 -0.38 191 192
RAB11/GDP 0.04 0.009 -10000 0 0 24 24
ICAM1 -0.058 0.2 0.28 5 -0.32 182 187
cAMP biosynthetic process -0.07 0.21 0.33 1 -0.34 179 180
Gq family/GTP/EBP50 0.01 0.05 0.25 2 -0.15 35 37
actin cytoskeleton reorganization 0.051 0.022 -10000 0 -0.11 8 8
SRC 0.003 0.058 0.22 7 -0.18 2 9
GNB5 0.04 0.009 -10000 0 0 29 29
GNB1 0.041 0.005 -10000 0 0 7 7
EGF/EGFR 0.002 0.075 0.22 11 -0.21 12 23
VCAM1 -0.062 0.21 0.28 4 -0.33 190 194
TP beta/Gq family/GDP/G beta5/gamma2 -0.024 0.16 -10000 0 -0.53 45 45
platelet activation -0.056 0.19 0.33 1 -0.3 189 190
PGI2/IP 0.028 0.016 -10000 0 -0.13 5 5
PRKACA 0.019 0.023 -10000 0 -0.16 7 7
Gq family/GDP/G beta5/gamma2 -0.015 0.13 -10000 0 -0.46 36 36
TXA2/TP beta/beta Arrestin2 0.013 0.062 -10000 0 -0.3 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.004 0.024 0.11 6 -0.15 7 13
mol:DAG -0.089 0.26 0.36 1 -0.42 189 190
EGFR 0.037 0.014 -10000 0 0 72 72
TXA2/TP alpha -0.1 0.28 0.38 1 -0.46 179 180
Gq family/GTP -0.008 0.065 -10000 0 -0.19 59 59
YES1 0.002 0.057 0.22 7 -0.18 2 9
GNAI2/GTP 0.027 0.046 -10000 0 -0.13 13 13
PGD2/DP 0.03 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.038 0.012 -10000 0 0 49 49
FYN 0.002 0.058 0.2 10 -0.16 8 18
mol:NO 0.038 0.012 -10000 0 0 49 49
GNA15 0.037 0.014 -10000 0 0 69 69
PGK/cGMP 0.049 0.019 -10000 0 -10000 0 0
RhoA/GDP 0.041 0.007 -10000 0 0 14 14
TP alpha/TGM2/GDP/G beta/gamma 0.06 0.063 0.26 1 -0.17 8 9
NOS3 0.038 0.012 -10000 0 0 49 49
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.072 0.22 0.32 3 -0.36 185 188
PRKCB -0.07 0.22 0.31 1 -0.35 190 191
PRKCE -0.071 0.22 0.32 5 -0.36 187 192
PRKCD -0.08 0.23 0.33 1 -0.38 188 189
PRKCG -0.08 0.24 0.34 1 -0.38 191 192
muscle contraction -0.11 0.28 0.38 1 -0.48 191 192
PRKCZ -0.07 0.21 0.3 2 -0.34 191 193
ARR3 0.042 0.002 -10000 0 0 1 1
TXA2/TP beta 0.045 0.052 0.24 1 -0.14 9 10
PRKCQ -0.072 0.22 0.36 3 -0.36 183 186
MAPKKK cascade -0.099 0.26 0.36 1 -0.44 188 189
SELE -0.051 0.18 0.28 3 -0.29 191 194
TP beta/GNAI2/GDP/G beta/gamma 0.071 0.059 0.26 1 -0.16 9 10
ROCK1 0.041 0.007 -10000 0 0 14 14
GNA14 0.039 0.01 -10000 0 0 33 33
chemotaxis -0.15 0.34 -10000 0 -0.6 191 191
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
Rac1/GTP 0.029 0.01 -10000 0 -0.13 1 1
BARD1 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
BARD1/CSTF1 0.039 0.053 -10000 0 -0.14 38 38
ATM 0.036 0.014 -10000 0 0 73 73
UBE2D3 0.038 0.012 -10000 0 0 48 48
PRKDC 0.039 0.011 -10000 0 0 44 44
ATR 0.035 0.016 -10000 0 0 93 93
UBE2L3 0.039 0.011 -10000 0 0 40 40
FANCD2 -0.004 0.089 -10000 0 -0.25 58 58
protein ubiquitination 0.013 0.1 -10000 0 -0.13 156 156
XRCC5 0.039 0.011 -10000 0 0 39 39
XRCC6 0.037 0.014 -10000 0 0 70 70
M/R/N Complex 0.048 0.071 -10000 0 -0.15 50 50
MRE11A 0.038 0.012 -10000 0 0 54 54
DNA-PK 0.054 0.066 -10000 0 -0.14 46 46
FA complex/FANCD2/Ubiquitin -0.007 0.13 -10000 0 -0.44 29 29
FANCF 0.04 0.009 -10000 0 0 28 28
BRCA1 0.034 0.016 -10000 0 0 106 106
CCNE1 0.028 0.02 -10000 0 0 189 189
CDK2/Cyclin E1 0.01 0.077 -10000 0 -0.14 104 104
FANCG 0.04 0.008 -10000 0 0 22 22
BRCA1/BACH1/BARD1 0.027 0.069 -10000 0 -0.14 74 74
FANCE 0.041 0.007 -10000 0 0 18 18
FANCC 0.04 0.009 -10000 0 0 29 29
NBN 0.035 0.016 -10000 0 0 96 96
FANCA 0.035 0.016 -10000 0 0 94 94
DNA repair -0.02 0.13 0.27 13 -0.37 38 51
BRCA1/BARD1/ubiquitin 0.027 0.069 -10000 0 -0.14 74 74
BARD1/DNA-PK 0.064 0.082 -10000 0 -0.14 60 60
FANCL 0.038 0.012 -10000 0 0 55 55
mRNA polyadenylation -0.038 0.053 0.14 38 -10000 0 38
BRCA1/BARD1/CTIP/M/R/N Complex -0.025 0.14 0.16 3 -0.29 80 83
BRCA1/BACH1/BARD1/TopBP1 0.037 0.077 -10000 0 -0.13 81 81
BRCA1/BARD1/P53 0.002 0.1 -10000 0 -0.13 190 190
BARD1/CSTF1/BRCA1 0.037 0.072 -10000 0 -0.12 75 75
BRCA1/BACH1 0.034 0.016 -10000 0 0 106 106
BARD1 0.037 0.014 -10000 0 0 66 66
PCNA 0.034 0.016 -10000 0 0 100 100
BRCA1/BARD1/UbcH5C 0.041 0.072 -10000 0 -0.12 75 75
BRCA1/BARD1/UbcH7 0.042 0.072 -10000 0 -0.12 73 73
BRCA1/BARD1/RAD51/PCNA 0.035 0.095 -10000 0 -0.13 115 115
BARD1/DNA-PK/P53 0.019 0.12 -10000 0 -0.13 179 179
BRCA1/BARD1/Ubiquitin 0.027 0.069 -10000 0 -0.14 74 74
BRCA1/BARD1/CTIP 0.014 0.086 0.18 9 -0.13 123 132
FA complex 0.012 0.087 -10000 0 -0.3 26 26
BARD1/EWS 0.042 0.05 -10000 0 -0.13 35 35
RBBP8 -0.015 0.009 -10000 0 -10000 0 0
TP53 0.026 0.02 -10000 0 0 213 213
TOPBP1 0.038 0.013 -10000 0 0 59 59
G1/S transition of mitotic cell cycle 0 0.1 0.13 190 -10000 0 190
BRCA1/BARD1 0.018 0.11 -10000 0 -0.13 150 150
CSTF1 0.037 0.014 -10000 0 0 68 68
BARD1/EWS-Fli1 0.02 0.038 -10000 0 -0.13 34 34
CDK2 0.038 0.013 -10000 0 0 59 59
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.016 -10000 0 0 93 93
RAD50 0.039 0.011 -10000 0 0 42 42
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.069 -10000 0 -0.14 74 74
EWSR1 0.038 0.012 -10000 0 0 54 54
TCGA08_rtk_signaling

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
PDGFRA 0.03 0.019 -10000 0 0 157 157
HRAS 0.04 0.01 -10000 0 0 31 31
EGFR 0.037 0.014 -10000 0 0 72 72
AKT 0.017 0.092 0.23 6 -0.18 38 44
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.039 0.01 -10000 0 0 37 37
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.03 0.019 -10000 0 0 155 155
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.027 0.02 -10000 0 0 198 198
PIK3CA 0.03 0.019 -10000 0 0 155 155
PIK3CB 0.034 0.016 -10000 0 0 103 103
NRAS 0.04 0.009 -10000 0 0 30 30
PIK3CG 0.033 0.017 -10000 0 0 118 118
PIK3R3 0.035 0.016 -10000 0 0 97 97
PIK3R2 0.037 0.013 -10000 0 0 63 63
NF1 0.034 0.016 -10000 0 0 101 101
RAS 0.005 0.078 0.15 35 -0.24 20 55
ERBB2 0.038 0.012 -10000 0 0 52 52
proliferation/survival/translation -0.017 0.086 0.21 32 -0.21 21 53
PI3K 0.003 0.088 0.17 28 -0.21 47 75
PIK3R1 0.034 0.017 -10000 0 0 108 108
KRAS 0.034 0.016 -10000 0 0 103 103
FOXO 0.038 0.054 0.17 24 -10000 0 24
AKT2 0.038 0.012 -10000 0 0 47 47
PTEN 0.039 0.011 -10000 0 0 38 38
Paxillin-dependent events mediated by a4b1

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
CRKL 0.039 0.011 -10000 0 0 38 38
Rac1/GDP 0.033 0.025 -10000 0 -0.024 66 66
DOCK1 0.037 0.013 -10000 0 0 62 62
ITGA4 0.035 0.015 -10000 0 0 88 88
RAC1 0.039 0.01 -10000 0 0 34 34
alpha4/beta7 Integrin 0.033 0.065 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 52 52
alpha4/beta1 Integrin 0.047 0.062 -10000 0 -0.12 49 49
alpha4/beta7 Integrin/Paxillin 0.052 0.069 0.18 55 -0.12 50 105
lamellipodium assembly -0.03 0.15 -10000 0 -0.36 75 75
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.024 0.061 -10000 0 -0.15 47 47
ARF6 0.041 0.008 -10000 0 0 19 19
TLN1 0.039 0.012 -10000 0 0 46 46
PXN -0.017 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.017 -10000 0 0 108 108
ARF6/GTP 0.062 0.071 -10000 0 -0.11 51 51
cell adhesion 0.061 0.077 0.2 47 -0.12 59 106
CRKL/CBL 0.055 0.021 -10000 0 -0.14 1 1
alpha4/beta1 Integrin/Paxillin 0.051 0.067 0.18 51 -0.11 48 99
ITGB1 0.039 0.011 -10000 0 0 38 38
ITGB7 0.039 0.011 -10000 0 0 40 40
ARF6/GDP 0.034 0.025 -10000 0 -0.024 66 66
alpha4/beta1 Integrin/Paxillin/VCAM1 0.025 0.094 0.2 28 -0.13 117 145
p130Cas/Crk/Dock1 0.055 0.054 -10000 0 -0.12 29 29
VCAM1 0.02 0.021 -10000 0 0 288 288
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.079 0.2 47 -0.12 59 106
alpha4/beta1 Integrin/Paxillin/GIT1 0.069 0.073 0.2 46 -0.11 48 94
BCAR1 0.036 0.014 -10000 0 0 76 76
mol:GDP -0.066 0.071 0.11 48 -0.2 46 94
CBL 0.04 0.008 -10000 0 0 23 23
PRKACA 0.035 0.015 -10000 0 0 89 89
GIT1 0.04 0.009 -10000 0 0 27 27
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.079 0.2 47 -0.12 59 106
Rac1/GTP -0.035 0.17 -10000 0 -0.4 75 75
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.065 0.18 -10000 0 -0.39 123 123
IHH 0.022 0.067 -10000 0 -0.099 128 128
SHH Np/Cholesterol/GAS1 0.027 0.027 -10000 0 -0.1 15 15
LRPAP1 0.036 0.015 -10000 0 0 78 78
dorsoventral neural tube patterning -0.027 0.027 0.1 15 -10000 0 15
SMO/beta Arrestin2 0.018 0.12 0.24 1 -0.2 99 100
SMO -0.002 0.11 -10000 0 -0.2 109 109
AKT1 -0.013 0.13 -10000 0 -0.39 36 36
ARRB2 0.039 0.011 -10000 0 0 44 44
BOC 0.036 0.015 -10000 0 0 85 85
ADRBK1 0.041 0.005 -10000 0 0 7 7
heart looping -0.001 0.11 0.19 3 -0.2 109 112
STIL 0 0.096 0.2 29 -0.17 103 132
DHH N/PTCH2 0.058 0.016 -10000 0 -10000 0 0
DHH N/PTCH1 0.003 0.11 -10000 0 -0.19 127 127
PIK3CA 0.03 0.019 -10000 0 0 155 155
DHH 0.041 0.006 -10000 0 0 13 13
PTHLH -0.032 0.17 -10000 0 -0.38 106 106
determination of left/right symmetry -0.001 0.11 0.19 3 -0.2 109 112
PIK3R1 0.034 0.017 -10000 0 0 108 108
skeletal system development -0.032 0.17 -10000 0 -0.38 106 106
IHH N/Hhip 0.035 0.055 -10000 0 -0.06 120 120
DHH N/Hhip 0.054 0.022 -10000 0 -0.14 1 1
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.001 0.11 0.19 3 -0.2 109 112
pancreas development 0.038 0.013 -10000 0 0 56 56
HHAT 0.04 0.008 -10000 0 0 23 23
PI3K 0.024 0.061 -10000 0 -0.15 47 47
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.037 0.014 -10000 0 0 68 68
somite specification -0.001 0.11 0.19 3 -0.2 109 112
SHH Np/Cholesterol/PTCH1 -0.006 0.085 -10000 0 -0.17 108 108
SHH Np/Cholesterol/PTCH2 0.032 0.017 -10000 0 -0.1 3 3
SHH Np/Cholesterol/Megalin 0.021 0.027 -10000 0 -0.1 14 14
SHH -0.018 0.007 -10000 0 -10000 0 0
catabolic process -0.036 0.096 -10000 0 -0.21 128 128
SMO/Vitamin D3 -0.006 0.1 0.2 19 -0.2 106 125
SHH Np/Cholesterol/Hhip 0.03 0.019 -10000 0 -0.1 4 4
LRP2 0.03 0.019 -10000 0 0 162 162
receptor-mediated endocytosis 0.002 0.1 0.19 21 -0.18 103 124
SHH Np/Cholesterol/BOC 0.025 0.029 -10000 0 -0.11 17 17
SHH Np/Cholesterol/CDO 0.023 0.035 -10000 0 -0.1 31 31
mesenchymal cell differentiation -0.03 0.019 0.1 4 -10000 0 4
mol:Vitamin D3 -0.012 0.089 0.2 26 -0.17 107 133
IHH N/PTCH2 0.039 0.054 -10000 0 -0.064 3 3
CDON 0.035 0.016 -10000 0 0 93 93
IHH N/PTCH1 -0.02 0.11 -10000 0 -0.21 128 128
Megalin/LRPAP1 0.029 0.053 -10000 0 -0.14 37 37
PTCH2 0.04 0.009 -10000 0 0 27 27
SHH Np/Cholesterol 0.034 0.047 0.2 42 -0.099 3 45
PTCH1 -0.036 0.096 -10000 0 -0.21 128 128
HHIP 0.038 0.013 -10000 0 0 56 56
IL1-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
UBC13/UEV1A 0.028 0.019 -10000 0 -0.13 8 8
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.14 -10000 0 -0.31 88 88
IRAK/TOLLIP 0.04 0.027 0.19 4 -0.1 11 15
IKBKB 0.039 0.011 -10000 0 0 44 44
IKBKG 0.042 0.003 -10000 0 0 2 2
IL1 alpha/IL1R2 0.047 0.039 -10000 0 -0.14 16 16
IL1A 0.04 0.01 -10000 0 0 31 31
IL1B -0.012 0.01 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.048 0.077 0.22 2 -0.12 60 62
IL1R2 0.036 0.015 -10000 0 0 85 85
IL1R1 0.031 0.019 -10000 0 0 148 148
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.14 -10000 0 -0.32 91 91
TOLLIP 0.04 0.009 -10000 0 0 29 29
TICAM2 0.038 0.013 -10000 0 0 58 58
MAP3K3 0.041 0.007 -10000 0 0 17 17
TAK1/TAB1/TAB2 0.062 0.054 -10000 0 -0.14 24 24
IKK complex/ELKS 0.014 0.089 0.26 3 -0.28 25 28
JUN -0.033 0.062 0.15 27 -0.2 16 43
MAP3K7 0.038 0.012 -10000 0 0 47 47
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.001 0.12 0.22 2 -0.17 138 140
IL1 alpha/IL1R1/IL1RAP/MYD88 0.038 0.086 -10000 0 -0.12 95 95
PIK3R1 0.034 0.017 -10000 0 0 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.038 0.1 -10000 0 -0.13 104 104
IL1 beta fragment/IL1R1/IL1RAP -0.012 0.096 0.18 4 -0.15 148 152
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 -0.025 0.057 0.17 24 -0.2 15 39
IRAK1 0.016 0.014 -10000 0 -0.11 6 6
IL1RN/IL1R1 0.022 0.072 -10000 0 -0.14 85 85
IRAK4 0.037 0.014 -10000 0 0 72 72
PRKCI 0.027 0.02 -10000 0 0 197 197
TRAF6 0.04 0.008 -10000 0 0 22 22
PI3K 0.024 0.061 -10000 0 -0.15 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.036 0.15 0.17 2 -0.3 103 105
CHUK 0.038 0.012 -10000 0 0 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.012 0.096 0.18 4 -0.15 148 152
IL1 beta/IL1R2 -0.004 0.089 0.24 2 -0.15 133 135
IRAK/TRAF6/TAK1/TAB1/TAB2 0.072 0.068 0.22 1 -0.14 33 34
NF kappa B1 p50/RelA -0.015 0.11 -10000 0 -0.18 124 124
IRAK3 0.035 0.016 -10000 0 0 97 97
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.003 0.12 0.22 2 -0.16 145 147
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.099 -10000 0 -0.2 104 104
IL1 alpha/IL1R1/IL1RAP 0.016 0.078 -10000 0 -0.13 95 95
RELA 0.041 0.006 -10000 0 0 10 10
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
SQSTM1 0.038 0.012 -10000 0 0 49 49
MYD88 0.041 0.007 -10000 0 0 14 14
IRAK/TRAF6/MEKK3 0.061 0.037 0.2 4 -0.11 17 21
IL1RAP 0.027 0.02 -10000 0 0 196 196
UBE2N 0.04 0.008 -10000 0 0 20 20
IRAK/TRAF6 -0.022 0.096 -10000 0 -0.17 136 136
CASP1 0.028 0.02 -10000 0 0 192 192
IL1RN/IL1R2 0.041 0.049 -10000 0 -0.14 31 31
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.002 0.1 0.2 4 -0.15 141 145
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.021 0.13 0.21 1 -0.29 88 89
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL1RN 0.039 0.011 -10000 0 0 39 39
TRAF6/TAK1/TAB1/TAB2 0.073 0.066 -10000 0 -0.14 29 29
MAP2K6 -0.021 0.059 0.19 24 -0.21 13 37
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.028 0.079 -10000 0 -0.13 91 91
PTK2 -0.011 0.13 0.23 9 -0.27 73 82
IGF1R 0.033 0.017 -10000 0 0 118 118
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.031 0.018 -10000 0 0 142 142
SRC 0.039 0.01 -10000 0 0 36 36
CDKN1B 0.002 0.089 -10000 0 -0.32 34 34
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.015 0.059 -10000 0 -0.27 15 15
ROCK1 0.041 0.007 -10000 0 0 14 14
AKT1 0.006 0.055 0.21 5 -0.26 14 19
PTK2B -0.014 0.06 0.19 13 -0.18 11 24
alphaV/beta3 Integrin/JAM-A 0.041 0.081 0.2 10 -0.12 87 97
CBL 0.04 0.008 -10000 0 0 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.03 0.079 -10000 0 -0.13 91 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.056 0.085 -10000 0 -0.12 88 88
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.084 -10000 0 -0.26 32 32
alphaV/beta3 Integrin/Syndecan-1 0.029 0.079 -10000 0 -0.13 92 92
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.019 0.1 -10000 0 -0.14 173 173
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 155 155
alphaV/beta3 Integrin/Osteopontin 0.005 0.099 -10000 0 -0.15 128 128
RPS6KB1 -0.034 0.1 0.28 10 -0.26 16 26
TLN1 0.039 0.012 -10000 0 0 46 46
MAPK3 -0.052 0.16 0.23 1 -0.33 122 123
GPR124 0.037 0.013 -10000 0 0 63 63
MAPK1 -0.049 0.16 0.23 1 -0.34 115 116
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 108 108
alphaV/beta3 Integrin/Tumstatin 0.031 0.08 -10000 0 -0.13 92 92
cell adhesion -0.001 0.1 -10000 0 -0.16 136 136
ANGPTL3 0.04 0.008 -10000 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.02 -10000 0 -0.11 2 2
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
TGFBR2 0.039 0.01 -10000 0 0 37 37
ITGB3 0.033 0.017 -10000 0 0 121 121
IGF1 0.036 0.015 -10000 0 0 84 84
RAC1 0.039 0.01 -10000 0 0 34 34
regulation of cell-matrix adhesion 0.029 0.076 -10000 0 -0.13 83 83
apoptosis 0.033 0.017 -10000 0 0 117 117
CD47 0.037 0.013 -10000 0 0 62 62
alphaV/beta3 Integrin/CD47 0.023 0.087 -10000 0 -0.14 103 103
VCL 0.039 0.01 -10000 0 0 36 36
alphaV/beta3 Integrin/Del1 0.005 0.082 -10000 0 -0.14 111 111
CSF1 0.035 0.015 -10000 0 0 89 89
PIK3C2A -0.005 0.1 -10000 0 -0.33 47 47
PI4 Kinase/Pyk2 0.006 0.055 -10000 0 -0.11 81 81
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.074 -10000 0 -0.12 94 94
FAK1/Vinculin 0.006 0.12 0.23 10 -0.22 79 89
alphaV beta3/Integrin/ppsTEM5 0.029 0.076 -10000 0 -0.13 83 83
RHOA 0.041 0.007 -10000 0 0 14 14
VTN 0.04 0.009 -10000 0 0 24 24
BCAR1 0.036 0.014 -10000 0 0 76 76
FGF2 0.039 0.011 -10000 0 0 45 45
F11R -0.018 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.008 0.088 -10000 0 -0.14 125 125
alphaV/beta3 Integrin/TGFBR2 0.027 0.084 -10000 0 -0.14 95 95
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.091 -10000 0 -0.13 96 96
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.026 0.077 -10000 0 -0.12 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.021 -10000 0 0 277 277
alphaV/beta3 Integrin/Pyk2 0.017 0.066 0.21 1 -0.11 87 88
SDC1 0.04 0.009 -10000 0 0 29 29
VAV3 -0.03 0.075 0.2 20 -0.21 38 58
PTPN11 0.04 0.009 -10000 0 0 27 27
IRS1 0.04 0.008 -10000 0 0 22 22
FAK1/Paxillin 0.009 0.12 0.23 9 -0.23 70 79
cell migration -0.002 0.11 0.21 9 -0.21 78 87
ITGAV 0.033 0.017 -10000 0 0 117 117
PI3K 0.028 0.091 -10000 0 -0.15 73 73
SPP1 0.03 0.019 -10000 0 0 154 154
KDR 0.04 0.009 -10000 0 0 30 30
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.017 -10000 0 0 117 117
COL4A3 0.041 0.005 -10000 0 0 7 7
angiogenesis -0.057 0.17 0.25 2 -0.37 118 120
Rac1/GTP -0.032 0.078 0.2 20 -0.2 38 58
EDIL3 0.027 0.02 -10000 0 0 202 202
cell proliferation 0.026 0.084 -10000 0 -0.14 95 95
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.015 0.15 -10000 0 -0.35 32 32
MAP3K8 0.04 0.009 -10000 0 0 21 21
FOS 0.014 0.11 -10000 0 -0.32 22 22
PRKCA 0.026 0.029 -10000 0 -0.015 169 169
PTPN7 0.031 0.032 -10000 0 -0.031 112 112
HRAS 0.039 0.01 -10000 0 0 31 31
PRKCB 0 0.007 0.01 94 -0.013 103 197
NRAS 0.04 0.01 -10000 0 0 30 30
RAS family/GTP 0.054 0.051 -10000 0 -0.11 29 29
MAPK3 0.03 0.081 -10000 0 -0.44 9 9
MAP2K1 0.001 0.096 0.16 3 -0.28 43 46
ELK1 0.028 0.032 -10000 0 -0.038 104 104
BRAF 0.001 0.072 -10000 0 -0.29 27 27
mol:GTP 0 0.002 0.002 86 -0.004 103 189
MAPK1 0.011 0.11 -10000 0 -0.38 33 33
RAF1 -0.002 0.078 -10000 0 -0.28 35 35
KRAS 0.034 0.016 -10000 0 0 103 103
IL6-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
BCL2L1 -0.089 0.35 -10000 0 -0.8 82 82
CRP -0.082 0.33 -10000 0 -0.79 73 73
cell cycle arrest -0.12 0.39 -10000 0 -0.89 90 90
TIMP1 -0.1 0.36 -10000 0 -0.76 112 112
IL6ST 0.024 0.036 -10000 0 -0.042 73 73
Rac1/GDP -0.011 0.17 0.28 6 -0.36 68 74
AP1 -0.029 0.21 -10000 0 -0.47 78 78
GAB2 0.033 0.02 -10000 0 -0.001 143 143
TNFSF11 -0.087 0.33 -10000 0 -0.78 77 77
HSP90B1 0.013 0.091 -10000 0 -1.1 2 2
GAB1 0.039 0.014 -10000 0 -0.002 55 55
MAPK14 -0.024 0.16 0.25 2 -0.5 39 41
AKT1 -0.01 0.15 0.31 4 -0.42 41 45
FOXO1 -0.011 0.14 0.3 4 -0.4 40 44
MAP2K6 -0.02 0.15 0.22 4 -0.37 57 61
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.032 0.21 0.3 8 -0.42 86 94
MITF -0.017 0.14 0.22 7 -0.32 68 75
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.037 0.014 -10000 0 0 66 66
A2M -0.12 0.4 -10000 0 -1.2 66 66
CEBPB 0.037 0.015 -10000 0 0 79 79
GRB2/SOS1/GAB family/SHP2 -0.01 0.16 0.29 4 -0.38 67 71
STAT3 -0.14 0.43 -10000 0 -0.99 90 90
STAT1 -0.069 0.28 -10000 0 -0.83 64 64
CEBPD -0.086 0.34 0.53 2 -0.8 78 80
PIK3CA 0.031 0.02 -10000 0 -0.001 158 158
PI3K 0.024 0.062 -10000 0 -0.15 49 49
JUN 0.036 0.015 -10000 0 0 80 80
PIAS3/MITF -0.006 0.15 0.24 4 -0.33 63 67
MAPK11 -0.023 0.16 0.25 2 -0.53 35 37
STAT3 (dimer)/FOXO1 -0.096 0.36 0.47 3 -0.74 103 106
GRB2/SOS1/GAB family 0.031 0.13 0.29 4 -0.27 36 40
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.008 0.11 0.2 3 -0.25 56 59
GRB2 0.042 0.01 -10000 0 -0.005 20 20
JAK2 0.035 0.016 -10000 0 0 92 92
LBP -0.031 0.27 0.44 1 -0.58 70 71
PIK3R1 0.034 0.018 -10000 0 -0.001 111 111
JAK1 0.034 0.028 -10000 0 -0.044 55 55
MYC -0.071 0.42 0.52 6 -0.88 99 105
FGG -0.086 0.33 -10000 0 -0.78 78 78
macrophage differentiation -0.12 0.39 -10000 0 -0.89 90 90
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.049 0.1 -10000 0 -0.17 49 49
JUNB -0.1 0.39 0.52 3 -0.86 96 99
FOS 0.026 0.02 -10000 0 0 207 207
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.009 0.16 0.23 5 -0.34 70 75
STAT1/PIAS1 -0.019 0.18 0.29 2 -0.38 74 76
GRB2/SOS1/GAB family/SHP2/PI3K -0.011 0.16 -10000 0 -0.4 49 49
STAT3 (dimer) -0.14 0.41 -10000 0 -0.96 90 90
PRKCD -0.06 0.26 0.34 4 -0.55 92 96
IL6R 0.032 0.027 -10000 0 -0.043 46 46
SOCS3 -0.035 0.21 0.34 1 -0.97 22 23
gp130 (dimer)/JAK1/JAK1/LMO4 0.044 0.089 -10000 0 -0.14 65 65
Rac1/GTP -0.017 0.18 0.29 6 -0.38 75 81
HCK 0.036 0.015 -10000 0 0 80 80
MAPKKK cascade -0.024 0.22 -10000 0 -0.5 80 80
bone resorption -0.079 0.31 -10000 0 -0.73 78 78
IRF1 -0.14 0.42 -10000 0 -0.93 111 111
mol:GDP -0.02 0.15 0.24 6 -0.35 66 72
SOS1 0.039 0.015 -10000 0 -0.002 59 59
VAV1 -0.021 0.15 0.23 5 -0.35 67 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.012 0.17 -10000 0 -0.44 58 58
PTPN11 0 0.16 -10000 0 -0.78 22 22
IL6/IL6RA 0.029 0.063 -10000 0 -0.14 42 42
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.066 -10000 0 -0.1 60 60
gp130 (dimer)/JAK2/JAK2/LMO4 0.043 0.075 -10000 0 -0.12 66 66
IL6 0.023 0.037 -10000 0 -0.043 74 74
PIAS3 0.04 0.008 -10000 0 0 23 23
PTPRE 0.027 0.038 0.1 9 -0.047 43 52
PIAS1 0.04 0.009 -10000 0 0 28 28
RAC1 0.04 0.01 -10000 0 0 34 34
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.095 0.16 2 -0.24 48 50
LMO4 0.028 0.037 -10000 0 -0.043 81 81
STAT3 (dimer)/PIAS3 -0.1 0.4 -10000 0 -0.9 89 89
MCL1 -0.012 0.16 0.36 1 -0.6 22 23
Syndecan-4-mediated 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
PTK2 -0.056 0.21 -10000 0 -0.36 144 144
Syndecan-4/Syndesmos -0.037 0.19 -10000 0 -0.42 77 77
positive regulation of JNK cascade -0.057 0.19 -10000 0 -0.41 84 84
Syndecan-4/ADAM12 -0.054 0.18 -10000 0 -0.46 61 61
CCL5 0.03 0.019 -10000 0 0 161 161
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DNM2 0.037 0.014 -10000 0 0 72 72
ITGA5 0.038 0.013 -10000 0 0 58 58
SDCBP 0.036 0.014 -10000 0 0 75 75
PLG 0.031 0.03 0.079 4 -0.042 62 66
ADAM12 0.03 0.019 -10000 0 0 163 163
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.04 0.01 -10000 0 0 32 32
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.04 0.19 -10000 0 -0.41 77 77
Syndecan-4/CXCL12/CXCR4 -0.06 0.2 -10000 0 -0.44 83 83
Syndecan-4/Laminin alpha3 -0.047 0.19 -10000 0 -0.43 76 76
MDK 0.04 0.009 -10000 0 0 24 24
Syndecan-4/FZD7 -0.041 0.19 -10000 0 -0.46 64 64
Syndecan-4/Midkine -0.039 0.2 -10000 0 -0.47 59 59
FZD7 0.037 0.013 -10000 0 0 65 65
Syndecan-4/FGFR1/FGF -0.025 0.18 -10000 0 -0.41 63 63
THBS1 0.027 0.02 -10000 0 0 199 199
integrin-mediated signaling pathway -0.055 0.18 -10000 0 -0.42 80 80
positive regulation of MAPKKK cascade -0.057 0.19 -10000 0 -0.41 84 84
Syndecan-4/TACI -0.037 0.19 -10000 0 -0.43 76 76
CXCR4 0.033 0.017 -10000 0 0 117 117
cell adhesion -0.032 0.097 0.22 4 -0.2 127 131
Syndecan-4/Dynamin -0.035 0.19 -10000 0 -0.42 70 70
Syndecan-4/TSP1 -0.058 0.19 -10000 0 -0.46 68 68
Syndecan-4/GIPC -0.037 0.18 -10000 0 -0.47 51 51
Syndecan-4/RANTES -0.05 0.2 -10000 0 -0.47 66 66
ITGB1 0.039 0.011 -10000 0 0 38 38
LAMA1 0.034 0.017 -10000 0 0 108 108
LAMA3 0.031 0.018 -10000 0 0 147 147
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA 0.002 0.12 0.87 8 -10000 0 8
Syndecan-4/alpha-Actinin -0.039 0.2 -10000 0 -0.43 76 76
TFPI 0.039 0.01 -10000 0 0 35 35
F2 0.038 0.026 0.085 2 -0.038 48 50
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
positive regulation of cell adhesion -0.056 0.17 -10000 0 -0.41 76 76
ACTN1 0.039 0.011 -10000 0 0 42 42
TNC 0.027 0.02 -10000 0 0 198 198
Syndecan-4/CXCL12 -0.057 0.2 -10000 0 -0.44 81 81
FGF6 0.036 0.014 -10000 0 0 73 73
RHOA 0.041 0.007 -10000 0 0 14 14
CXCL12 0.029 0.019 -10000 0 0 172 172
TNFRSF13B 0.039 0.011 -10000 0 0 42 42
FGF2 0.039 0.011 -10000 0 0 45 45
FGFR1 0.033 0.017 -10000 0 0 122 122
Syndecan-4/PI-4-5-P2 -0.06 0.18 -10000 0 -0.46 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.017 0.025 -10000 0 -0.039 28 28
cell migration -0.011 0.013 -10000 0 -10000 0 0
PRKCD 0.033 0.028 -10000 0 -0.041 51 51
vasculogenesis -0.056 0.18 -10000 0 -0.42 76 76
SDC4 -0.052 0.18 -10000 0 -0.5 53 53
Syndecan-4/Tenascin C -0.058 0.19 -10000 0 -0.46 68 68
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.039 0.19 -10000 0 -0.48 54 54
MMP9 0.027 0.024 -10000 0 -0.04 17 17
Rac1/GTP -0.033 0.099 0.22 4 -0.2 127 131
cytoskeleton organization -0.035 0.18 -10000 0 -0.4 77 77
GIPC1 0.035 0.015 -10000 0 0 89 89
Syndecan-4/TFPI -0.04 0.19 -10000 0 -0.42 77 77
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.037 0.013 -10000 0 0 62 62
LAT2 -0.018 0.1 0.19 3 -0.21 92 95
AP1 -0.031 0.18 -10000 0 -0.42 67 67
mol:PIP3 -0.032 0.13 0.26 13 -0.29 83 96
IKBKB -0.013 0.088 0.2 24 -0.19 63 87
AKT1 0.015 0.12 0.25 63 -0.22 11 74
IKBKG -0.02 0.084 0.19 12 -0.19 67 79
MS4A2 0.046 0.012 0.07 38 -0.004 10 48
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 155 155
MAP3K1 -0.033 0.13 0.22 3 -0.31 68 71
mol:Ca2+ -0.022 0.11 0.23 14 -0.23 80 94
LYN 0.036 0.019 0.091 2 -0.003 92 94
CBLB -0.014 0.095 0.2 5 -0.21 77 82
SHC1 0.04 0.01 -10000 0 0 31 31
RasGAP/p62DOK 0.021 0.073 -10000 0 -0.11 107 107
positive regulation of cell migration -0.01 0.002 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.01 0.081 0.3 21 -0.16 5 26
PTPN13 -0.055 0.2 -10000 0 -0.66 35 35
PTPN11 0.04 0.02 0.11 2 -0.033 23 25
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.006 0.13 0.31 21 -0.33 29 50
SYK 0.037 0.017 0.091 2 -0.003 77 79
GRB2 0.041 0.007 -10000 0 0 17 17
LAT/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 0.18 1 -0.27 99 100
LAT -0.017 0.095 -10000 0 -0.21 83 83
PAK2 -0.031 0.14 0.21 6 -0.32 74 80
NFATC2 0.004 0.054 -10000 0 -0.4 9 9
HRAS -0.027 0.14 0.22 5 -0.31 84 89
GAB2 0.031 0.018 -10000 0 0 141 141
PLA2G1B 0.01 0.15 -10000 0 -0.88 14 14
Fc epsilon R1 0.034 0.071 -10000 0 -0.094 112 112
Antigen/IgE/Fc epsilon R1 0.037 0.063 -10000 0 -0.081 102 102
mol:GDP -0.024 0.16 0.26 3 -0.38 66 69
JUN 0.036 0.015 -10000 0 0 80 80
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.017 -10000 0 0 108 108
FOS 0.026 0.02 -10000 0 0 207 207
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.1 0.14 5 -0.21 87 92
CHUK -0.021 0.085 0.2 10 -0.19 75 85
KLRG1 -0.015 0.079 0.16 5 -0.16 91 96
VAV1 -0.015 0.096 0.15 7 -0.22 77 84
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.097 0.2 3 -0.21 87 90
negative regulation of mast cell degranulation -0.02 0.073 0.13 1 -0.19 54 55
BTK -0.03 0.18 0.26 1 -0.51 50 51
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.2 123 123
GAB2/PI3K/SHP2 -0.039 0.055 -10000 0 -0.15 74 74
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.003 0.069 -10000 0 -0.15 86 86
RAF1 0.013 0.16 -10000 0 -0.97 14 14
Fc epsilon R1/FcgammaRIIB/SHIP 0.033 0.092 -10000 0 -0.12 124 124
FCER1G 0.027 0.02 0.066 1 0 201 202
FCER1A 0.039 0.015 0.1 1 -0.005 48 49
Antigen/IgE/Fc epsilon R1/Fyn 0.04 0.077 -10000 0 -0.094 104 104
MAPK3 0.011 0.15 -10000 0 -0.89 14 14
MAPK1 0.004 0.15 -10000 0 -0.9 14 14
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 -0.033 0.22 -10000 0 -0.59 52 52
DUSP1 0.027 0.02 -10000 0 0 206 206
NF-kappa-B/RelA 0.001 0.068 0.14 16 -0.14 66 82
actin cytoskeleton reorganization -0.049 0.2 -10000 0 -0.73 29 29
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.017 0.13 0.26 3 -0.28 78 81
FER -0.015 0.094 -10000 0 -0.21 79 79
RELA 0.041 0.006 -10000 0 0 10 10
ITK -0.002 0.058 -10000 0 -0.28 17 17
SOS1 0.038 0.013 -10000 0 0 56 56
PLCG1 -0.026 0.15 0.24 6 -0.34 80 86
cytokine secretion -0.003 0.047 0.084 9 -0.098 70 79
SPHK1 -0.017 0.097 0.21 2 -0.21 88 90
PTK2 -0.052 0.21 -10000 0 -0.78 29 29
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.14 -10000 0 -0.27 106 106
EDG1 -0.01 0.002 -10000 0 -10000 0 0
mol:DAG -0.033 0.14 0.26 12 -0.3 84 96
MAP2K2 0.003 0.15 -10000 0 -0.9 14 14
MAP2K1 0.004 0.15 -10000 0 -0.91 14 14
MAP2K7 0.039 0.011 -10000 0 0 43 43
KLRG1/SHP2 0.013 0.091 0.2 37 -0.18 55 92
MAP2K4 -0.072 0.32 -10000 0 -0.89 75 75
Fc epsilon R1/FcgammaRIIB 0.035 0.1 -10000 0 -0.13 124 124
mol:Choline -0.01 0.081 0.3 21 -0.16 5 26
SHC/Grb2/SOS1 0.023 0.13 -10000 0 -0.21 88 88
FYN 0.034 0.016 -10000 0 0 103 103
DOK1 0.04 0.009 -10000 0 0 24 24
PXN -0.052 0.19 -10000 0 -0.71 29 29
HCLS1 -0.01 0.099 0.19 7 -0.24 62 69
PRKCB -0.024 0.11 0.22 14 -0.23 84 98
FCGR2B 0.03 0.019 -10000 0 0 164 164
IGHE 0 0.007 0.048 2 -10000 0 2
KLRG1/SHIP -0.02 0.075 0.13 1 -0.19 54 55
LCP2 0.034 0.016 -10000 0 0 102 102
PLA2G4A -0.007 0.092 0.17 11 -0.22 65 76
RASA1 0.037 0.014 -10000 0 0 71 71
mol:Phosphatidic acid -0.01 0.081 0.3 21 -0.16 5 26
IKK complex -0.015 0.073 0.18 19 -0.16 51 70
WIPF1 0 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.16 0.61 -10000 0 -1.2 120 120
IL23A -0.11 0.55 -10000 0 -1.2 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.55 -10000 0 -1.1 100 100
positive regulation of T cell mediated cytotoxicity -0.13 0.61 0.68 1 -1.3 91 92
ITGA3 -0.16 0.58 -10000 0 -1.1 121 121
IL17F -0.042 0.36 0.5 11 -0.69 95 106
IL12B 0.034 0.074 0.16 11 -0.078 23 34
STAT1 (dimer) -0.15 0.58 -10000 0 -1.3 89 89
CD4 -0.11 0.57 0.72 2 -1.2 98 100
IL23 -0.1 0.53 -10000 0 -1.2 82 82
IL23R 0.039 0.14 -10000 0 -1.2 3 3
IL1B -0.13 0.59 -10000 0 -1.3 95 95
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.095 0.52 -10000 0 -1.1 85 85
TYK2 0.025 0.056 0.13 1 -10000 0 1
STAT4 0.04 0.009 -10000 0 0 29 29
STAT3 0.038 0.013 -10000 0 0 56 56
IL18RAP 0.042 0.007 -10000 0 -10000 0 0
IL12RB1 0.024 0.057 0.13 1 -0.066 2 3
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL12Rbeta1/TYK2 0.037 0.069 -10000 0 -10000 0 0
IL23R/JAK2 0.051 0.18 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.13 0.61 0.68 1 -1.3 91 92
natural killer cell activation -0.002 0.01 -10000 0 -10000 0 0
JAK2 0.032 0.07 0.16 11 -0.078 20 31
PIK3R1 0.034 0.017 -10000 0 0 108 108
NFKB1 0.037 0.016 -10000 0 0 84 84
RELA 0.043 0.008 -10000 0 0 10 10
positive regulation of dendritic cell antigen processing and presentation -0.091 0.5 -10000 0 -1.1 82 82
ALOX12B -0.098 0.52 -10000 0 -1.1 84 84
CXCL1 -0.13 0.57 -10000 0 -1.2 110 110
T cell proliferation -0.13 0.61 0.68 1 -1.3 91 92
NFKBIA 0.039 0.015 -10000 0 0 66 66
IL17A -0.03 0.29 0.43 10 -0.54 93 103
PI3K -0.15 0.53 -10000 0 -1.2 89 89
IFNG 0.007 0.04 0.1 5 -0.11 14 19
STAT3 (dimer) -0.13 0.51 -10000 0 -1.1 88 88
IL18R1 0.041 0.008 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.013 0.34 0.54 3 -0.65 76 79
IL18/IL18R 0.055 0.067 -10000 0 -0.11 62 62
macrophage activation -0.007 0.022 0.034 2 -0.045 80 82
TNF -0.11 0.55 -10000 0 -1.2 85 85
STAT3/STAT4 -0.12 0.56 -10000 0 -1.2 89 89
STAT4 (dimer) -0.13 0.58 -10000 0 -1.3 89 89
IL18 0.032 0.019 -10000 0 -10000 0 0
IL19 -0.095 0.52 -10000 0 -1.1 86 86
STAT5A (dimer) -0.13 0.58 -10000 0 -1.3 90 90
STAT1 0.034 0.017 -10000 0 0 108 108
SOCS3 0.037 0.014 -10000 0 0 67 67
CXCL9 -0.16 0.61 -10000 0 -1.2 124 124
MPO -0.096 0.52 -10000 0 -1.1 85 85
positive regulation of humoral immune response -0.13 0.61 0.68 1 -1.3 91 92
IL23/IL23R/JAK2/TYK2 -0.16 0.66 -10000 0 -1.5 90 90
IL6 -0.1 0.54 -10000 0 -1.2 90 90
STAT5A 0.038 0.012 -10000 0 0 51 51
IL2 0.039 0.017 -10000 0 -0.033 11 11
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.01 -10000 0 -10000 0 0
CD3E -0.11 0.54 -10000 0 -1.2 87 87
keratinocyte proliferation -0.13 0.61 0.68 1 -1.3 91 92
NOS2 -0.098 0.52 -10000 0 -1.1 92 92
Signaling events mediated by PRL

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
CCNE1 0.028 0.02 -10000 0 0 189 189
mol:Halofuginone 0.002 0.022 -10000 0 -0.17 9 9
ITGA1 0.033 0.017 -10000 0 0 124 124
CDKN1A 0.02 0.08 -10000 0 -0.36 18 18
PRL-3/alpha Tubulin 0.01 0.039 -10000 0 -0.13 36 36
mol:Ca2+ -0.003 0.071 0.26 35 -10000 0 35
AGT 0.039 0.011 -10000 0 0 44 44
CCNA2 -0.016 0.088 -10000 0 -0.62 7 7
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.007 0.043 -10000 0 -0.32 9 9
CDK2/Cyclin E1 0.025 0.097 -10000 0 -0.34 21 21
MAPK3 -0.012 0.01 0 236 -10000 0 236
PRL-2 /Rab GGTase beta 0.032 0.068 -10000 0 -0.14 72 72
MAPK1 -0.012 0.01 0 251 -10000 0 251
PTP4A1 -0.003 0.075 0.2 4 -0.61 7 11
PTP4A3 0.025 0.021 -10000 0 0 226 226
PTP4A2 0.04 0.01 -10000 0 0 31 31
ITGB1 -0.012 0.01 0 251 -10000 0 251
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 -0.008 0.11 -10000 0 -0.36 45 45
Rab GGTase beta/Rab GGTase alpha 0.035 0.063 -10000 0 -0.14 63 63
PRL-1/ATF-5 0.016 0.097 0.3 3 -0.54 9 12
RABGGTA 0.04 0.009 -10000 0 0 26 26
BCAR1 -0.003 0.068 0.26 32 -10000 0 32
RHOC -0.005 0.11 -10000 0 -0.36 42 42
RHOA -0.008 0.11 -10000 0 -0.36 46 46
cell motility 0.011 0.12 0.3 2 -0.34 44 46
PRL-1/alpha Tubulin -0.018 0.078 -10000 0 -0.54 9 9
PRL-3/alpha1 Integrin 0.011 0.067 -10000 0 -0.15 67 67
ROCK1 0.011 0.12 0.3 2 -0.34 44 46
RABGGTB 0.036 0.015 -10000 0 0 84 84
CDK2 0.038 0.013 -10000 0 0 59 59
mitosis -0.002 0.076 0.2 6 -0.61 7 13
ATF5 0.038 0.012 -10000 0 0 54 54
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.017 -10000 0 0 120 120
ANTXR2 0.035 0.015 -10000 0 0 91 91
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.011 -10000 0 -0.033 74 74
monocyte activation -0.076 0.17 -10000 0 -0.35 151 151
MAP2K2 -0.039 0.18 -10000 0 -0.58 56 56
MAP2K1 -0.011 0.011 0.007 39 -0.037 69 108
MAP2K7 -0.01 0.011 0.007 38 -0.037 68 106
MAP2K6 -0.009 0.012 0.007 34 -0.038 61 95
CYAA -0.022 0.032 -10000 0 -0.1 73 73
MAP2K4 -0.01 0.012 0.007 33 -0.038 68 101
IL1B -0.012 0.041 0.1 9 -0.09 82 91
Channel 0.023 0.056 -10000 0 -0.11 74 74
NLRP1 -0.006 0.01 -10000 0 -0.03 74 74
CALM1 0.04 0.01 -10000 0 0 31 31
negative regulation of phagocytosis 0.003 0.078 -10000 0 -0.42 17 17
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.011 0.033 74 -10000 0 74
MAPK3 -0.011 0.011 0.007 38 -0.037 72 110
MAPK1 -0.01 0.011 0.007 37 -0.037 66 103
PGR -0.008 0.011 0.007 36 -0.037 51 87
PA/Cellular Receptors 0.023 0.061 -10000 0 -0.12 73 73
apoptosis -0.006 0.011 -10000 0 -0.033 74 74
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.055 -10000 0 -0.11 74 74
macrophage activation -0.012 0.021 0.17 3 -0.11 1 4
TNF 0.04 0.009 -10000 0 0 26 26
VCAM1 -0.078 0.17 -10000 0 -0.35 149 149
platelet activation 0.003 0.078 -10000 0 -0.42 17 17
MAPKKK cascade 0.007 0.028 0.083 8 -0.087 6 14
IL18 -0.009 0.041 0.093 8 -0.093 73 81
negative regulation of macrophage activation -0.006 0.011 -10000 0 -0.033 74 74
LEF -0.006 0.011 -10000 0 -0.033 74 74
CASP1 0 0.012 0.018 34 -0.031 49 83
mol:cAMP 0 0.077 -10000 0 -0.43 17 17
necrosis -0.006 0.011 -10000 0 -0.033 74 74
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.053 -10000 0 -0.1 74 74
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.076 -10000 0 -0.14 104 104
CRKL -0.032 0.14 0.33 1 -0.43 43 44
mol:PIP3 0.007 0.079 -10000 0 -0.83 4 4
AKT1 0.001 0.081 0.38 2 -0.73 4 6
PTK2B 0.033 0.017 -10000 0 0 118 118
RAPGEF1 -0.034 0.14 0.31 1 -0.41 42 43
RANBP10 0.036 0.014 -10000 0 0 77 77
PIK3CA 0.03 0.019 -10000 0 0 155 155
HGF/MET/SHIP2 0.029 0.078 -10000 0 -0.12 102 102
MAP3K5 -0.024 0.14 0.28 2 -0.4 46 48
HGF/MET/CIN85/CBL/ENDOPHILINS 0.051 0.085 -10000 0 -0.11 105 105
AP1 -0.004 0.082 0.15 12 -0.14 106 118
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.04 0.01 -10000 0 0 31 31
apoptosis -0.16 0.36 -10000 0 -0.77 138 138
STAT3 (dimer) -0.01 0.11 0.19 4 -0.29 38 42
GAB1/CRKL/SHP2/PI3K -0.012 0.15 -10000 0 -0.39 46 46
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.01 0.15 0.29 3 -0.41 43 46
PTPN11 0.04 0.009 -10000 0 0 27 27
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.038 0.012 -10000 0 0 50 50
PTEN 0.039 0.011 -10000 0 0 38 38
ELK1 0.014 0.12 0.32 54 -10000 0 54
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.083 0.15 2 -0.22 49 51
PAK1 0.01 0.098 0.36 7 -0.69 4 11
HGF/MET/RANBP10 0.025 0.076 -10000 0 -0.12 104 104
HRAS -0.072 0.22 -10000 0 -0.48 119 119
DOCK1 -0.033 0.14 0.26 7 -0.42 43 50
GAB1 -0.029 0.15 0.25 1 -0.46 41 42
CRK -0.028 0.14 0.27 4 -0.42 43 47
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.056 0.19 -10000 0 -0.42 115 115
JUN 0.036 0.015 -10000 0 0 80 80
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.02 0.072 0.096 2 -0.16 103 105
PIK3R1 0.034 0.017 -10000 0 0 108 108
cell morphogenesis -0.009 0.15 0.26 34 -0.33 45 79
GRB2/SHC 0.018 0.096 0.19 3 -0.16 106 109
FOS 0.026 0.02 -10000 0 0 207 207
GLMN 0.005 0.007 0.069 7 -10000 0 7
cell motility 0.013 0.12 0.31 54 -10000 0 54
HGF/MET/MUC20 0.014 0.064 -10000 0 -0.11 105 105
cell migration 0.017 0.095 0.19 3 -0.16 106 109
GRB2 0.041 0.007 -10000 0 0 17 17
CBL 0.04 0.008 -10000 0 0 23 23
MET/RANBP10 0.01 0.073 -10000 0 -0.13 105 105
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.081 -10000 0 -0.18 81 81
MET/MUC20 -0.004 0.061 -10000 0 -0.13 107 107
RAP1B -0.034 0.13 0.27 2 -0.39 40 42
RAP1A -0.039 0.13 0.3 2 -0.4 43 45
HGF/MET/RANBP9 0.026 0.078 -10000 0 -0.12 102 102
RAF1 -0.072 0.21 -10000 0 -0.46 120 120
STAT3 -0.009 0.11 0.19 4 -0.3 34 38
cell proliferation -0.031 0.14 0.26 7 -0.3 81 88
RPS6KB1 -0.012 0.085 -10000 0 -0.32 30 30
MAPK3 -0.008 0.12 0.62 14 -10000 0 14
MAPK1 0.029 0.2 0.71 40 -10000 0 40
RANBP9 0.038 0.012 -10000 0 0 53 53
MAPK8 -0.022 0.15 -10000 0 -0.4 51 51
SRC -0.006 0.092 0.2 9 -0.18 83 92
PI3K 0 0.096 0.19 3 -0.18 96 99
MET/Glomulin 0.012 0.047 -10000 0 -0.12 47 47
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K1 -0.071 0.2 -10000 0 -0.44 119 119
MET 0.027 0.02 -10000 0 0 198 198
MAP4K1 -0.022 0.15 0.29 1 -0.43 44 45
PTK2 0.027 0.02 -10000 0 0 204 204
MAP2K2 -0.072 0.19 -10000 0 -0.43 120 120
BAD -0.003 0.079 0.34 2 -0.7 4 6
MAP2K4 -0.026 0.13 0.26 2 -0.37 46 48
SHP2/GRB2/SOS1/GAB1 -0.013 0.16 -10000 0 -0.36 54 54
INPPL1 0.04 0.009 -10000 0 0 30 30
PXN 0.041 0.007 -10000 0 0 14 14
SH3KBP1 0.041 0.007 -10000 0 0 16 16
HGS -0.026 0.071 0.084 2 -0.16 112 114
PLCgamma1/PKC 0.026 0.022 -10000 0 -0.13 10 10
HGF 0.04 0.009 -10000 0 0 29 29
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 80 80
PTPRJ 0.039 0.01 -10000 0 0 35 35
NCK/PLCgamma1 0.016 0.095 0.19 3 -0.17 97 100
PDPK1 0.002 0.076 -10000 0 -0.77 4 4
HGF/MET/SHIP 0.014 0.064 -10000 0 -0.11 105 105
Signaling events mediated by PTP1B

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
Jak2/Leptin Receptor -0.017 0.14 -10000 0 -0.38 56 56
PTP1B/AKT1 -0.034 0.11 -10000 0 -0.24 81 81
FYN 0.034 0.016 -10000 0 0 103 103
p210 bcr-abl/PTP1B -0.052 0.11 -10000 0 -0.26 86 86
EGFR 0.036 0.017 -10000 0 -0.004 83 83
EGF/EGFR -0.025 0.12 -10000 0 -0.24 84 84
CSF1 0.035 0.015 -10000 0 0 89 89
AKT1 0.039 0.011 -10000 0 0 37 37
INSR 0.038 0.012 -10000 0 0 53 53
PTP1B/N-cadherin -0.053 0.12 -10000 0 -0.25 119 119
Insulin Receptor/Insulin -0.008 0.11 -10000 0 -0.22 61 61
HCK 0.036 0.015 -10000 0 0 80 80
CRK 0.038 0.012 -10000 0 0 52 52
TYK2 -0.036 0.12 0.23 21 -0.26 67 88
EGF 0.037 0.017 -10000 0 -0.007 69 69
YES1 0.038 0.013 -10000 0 0 57 57
CAV1 -0.035 0.11 -10000 0 -0.24 72 72
TXN 0.038 0.012 -10000 0 0 49 49
PTP1B/IRS1/GRB2 -0.027 0.13 -10000 0 -0.25 89 89
cell migration 0.052 0.11 0.26 86 -10000 0 86
STAT3 0.038 0.013 -10000 0 0 56 56
PRLR 0.038 0.017 -10000 0 -10000 0 0
ITGA2B 0.039 0.009 -10000 0 0 30 30
CSF1R 0.035 0.016 -10000 0 0 98 98
Prolactin Receptor/Prolactin 0.055 0.029 -10000 0 -10000 0 0
FGR 0.041 0.007 -10000 0 0 17 17
PTP1B/p130 Cas -0.036 0.12 -10000 0 -0.25 84 84
Crk/p130 Cas -0.029 0.12 -10000 0 -0.25 79 79
DOK1 -0.037 0.11 -10000 0 -0.25 66 66
JAK2 -0.03 0.14 -10000 0 -0.39 58 58
Jak2/Leptin Receptor/Leptin -0.024 0.14 0.26 1 -0.28 69 70
PIK3R1 0.034 0.017 -10000 0 0 108 108
PTPN1 -0.052 0.12 -10000 0 -0.26 86 86
LYN 0.036 0.015 -10000 0 0 83 83
CDH2 0.02 0.021 -10000 0 0 299 299
SRC 0.01 0.083 -10000 0 -0.5 10 10
ITGB3 0.032 0.017 -10000 0 0 121 121
CAT1/PTP1B -0.037 0.13 0.25 5 -0.29 69 74
CAPN1 0.039 0.009 -10000 0 0 25 25
CSK 0.04 0.008 -10000 0 0 21 21
PI3K -0.01 0.11 -10000 0 -0.22 55 55
mol:H2O2 0.002 0.005 0.03 1 -10000 0 1
STAT3 (dimer) -0.02 0.13 0.25 1 -0.26 69 70
negative regulation of transcription -0.029 0.14 -10000 0 -0.39 58 58
FCGR2A 0.032 0.018 -10000 0 0 129 129
FER 0.037 0.012 -10000 0 0 55 55
alphaIIb/beta3 Integrin 0.038 0.05 -10000 0 -0.14 34 34
BLK 0.033 0.017 -10000 0 0 117 117
Insulin Receptor/Insulin/Shc 0.068 0.037 -10000 0 -0.12 5 5
RHOA 0.04 0.007 -10000 0 0 14 14
LEPR 0.039 0.012 -10000 0 0 45 45
BCAR1 0.036 0.014 -10000 0 0 76 76
p210 bcr-abl/Grb2 0.041 0.007 -10000 0 0 17 17
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.007 0.12 0.22 8 -0.29 47 55
PRL 0.042 0.012 -10000 0 -10000 0 0
SOCS3 -0.02 0.25 -10000 0 -1.1 26 26
SPRY2 0.023 0.021 -10000 0 0 247 247
Insulin Receptor/Insulin/IRS1 0.07 0.038 -10000 0 -0.12 8 8
CSF1/CSF1R -0.044 0.13 -10000 0 -0.27 90 90
Ras protein signal transduction 0.006 0.071 0.61 6 -10000 0 6
IRS1 0.04 0.008 -10000 0 0 22 22
INS 0.04 0.01 -10000 0 0 30 30
LEP 0.039 0.01 -10000 0 0 33 33
STAT5B -0.041 0.12 -10000 0 -0.28 80 80
STAT5A -0.043 0.12 -10000 0 -0.27 84 84
GRB2 0.041 0.007 -10000 0 0 17 17
PDGFB-D/PDGFRB -0.043 0.12 -10000 0 -0.25 87 87
CSN2 0.042 0.068 0.43 2 -10000 0 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
LAT -0.058 0.19 -10000 0 -0.48 87 87
YBX1 0.048 0.02 -10000 0 -0.28 1 1
LCK 0.04 0.009 -10000 0 0 29 29
SHC1 0.04 0.01 -10000 0 0 31 31
NOX4 0.021 0.021 -10000 0 0 281 281
Canonical Wnt signaling pathway

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
HDAC1 0.054 0.062 0.15 118 -0.033 29 147
AES 0.053 0.056 0.14 122 -0.032 14 136
FBXW11 0.04 0.009 -10000 0 0 25 25
mol:GTP 0.001 0.003 0.033 1 -10000 0 1
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 32 32
SMAD4 0.038 0.012 -10000 0 0 49 49
DKK2 0.039 0.012 -10000 0 0 47 47
TLE1 0.053 0.052 0.13 118 -0.033 12 130
MACF1 0.033 0.017 -10000 0 0 118 118
CTNNB1 0.033 0.12 0.29 27 -0.4 12 39
WIF1 0.04 0.01 -10000 0 -0.001 32 32
beta catenin/RanBP3 0.099 0.22 0.47 119 -0.43 7 126
KREMEN2 0.04 0.009 -10000 0 0 27 27
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.054 0.12 0.3 28 -0.38 11 39
FZD1 0.041 0.007 -10000 0 0 17 17
AXIN2 -0.047 0.22 0.68 7 -0.79 28 35
AXIN1 0.042 0.004 -10000 0 0 4 4
RAN 0.042 0.007 0.076 1 0 13 14
Axin1/APC/GSK3/beta catenin 0.047 0.087 0.41 1 -0.55 7 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.17 0.32 8 -0.41 61 69
Axin1/APC/GSK3 0.03 0.07 0.21 14 -0.24 11 25
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.088 0.28 13 -0.27 9 22
HNF1A 0.019 0.051 0.091 135 -10000 0 135
CTBP1 0.053 0.053 0.14 116 -0.033 12 128
MYC 0.043 0.55 0.63 163 -1.1 74 237
RANBP3 0.04 0.011 0.076 1 0 40 41
DKK2/LRP6/Kremen 2 0.057 0.054 -10000 0 -0.12 29 29
NKD1 0.038 0.012 -10000 0 0 49 49
TCF4 0.055 0.059 0.14 117 -0.033 13 130
TCF3 0.053 0.055 0.14 120 -0.034 13 133
WNT1/LRP6/FZD1/Axin1 0.08 0.061 -10000 0 -0.11 31 31
Ran/GTP 0.031 0.013 0.1 1 -0.12 3 4
CtBP/CBP/TCF/TLE1/AES 0.058 0.31 0.57 110 -0.36 35 145
LEF1 0.037 0.051 0.14 74 -0.033 13 87
DVL1 0.033 0.076 0.23 11 -0.3 13 24
CSNK2A1 0.038 0.013 -10000 0 0 54 54
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.066 0.19 -10000 0 -0.43 81 81
DKK1/LRP6/Kremen 2 0.056 0.054 -10000 0 -0.12 28 28
LRP6 0.034 0.017 -10000 0 0 107 107
CSNK1A1 0.059 0.065 0.15 130 -0.033 30 160
NLK 0.031 0.025 -10000 0 -0.024 83 83
CCND1 -0.18 0.51 0.71 17 -1.2 96 113
WNT1 0.041 0.006 -10000 0 0 13 13
GSK3A 0.039 0.011 0.065 1 0 38 39
GSK3B 0.04 0.009 -10000 0 0 26 26
FRAT1 0.04 0.009 -10000 0 -0.002 25 25
PPP2R5D 0.035 0.062 0.24 2 -0.29 12 14
APC -0.005 0.082 0.21 61 -10000 0 61
WNT1/LRP6/FZD1 0.019 0.062 0.18 2 -0.24 8 10
CREBBP 0.054 0.055 0.14 122 -0.033 15 137
IGF1 pathway

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
NCK2 0.042 0.004 -10000 0 0 6 6
PTK2 0.027 0.02 -10000 0 0 204 204
CRKL -0.022 0.052 0.12 13 -0.13 71 84
GRB2/SOS1/SHC 0.065 0.051 -10000 0 -0.13 26 26
HRAS 0.04 0.01 -10000 0 0 31 31
IRS1/Crk 0.011 0.057 -10000 0 -0.12 75 75
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.073 -10000 0 -0.12 75 75
AKT1 0 0.092 0.18 83 -0.18 14 97
BAD -0.007 0.085 0.16 79 -0.17 14 93
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.051 0.11 12 -0.13 66 78
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.069 0.2 4 -0.13 96 100
RAF1 0.016 0.12 0.28 9 -0.48 13 22
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.088 0.21 2 -0.13 96 98
YWHAZ 0.034 0.016 -10000 0 0 102 102
IGF-1R heterotetramer/IGF1/IRS1 0.018 0.068 0.18 2 -0.13 85 87
PIK3CA 0.03 0.019 -10000 0 0 155 155
RPS6KB1 0 0.096 0.18 89 -0.19 20 109
GNB2L1 0.041 0.005 -10000 0 0 7 7
positive regulation of MAPKKK cascade 0.014 0.11 0.28 13 -0.41 10 23
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 108 108
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
HRAS/GTP 0.014 0.068 -10000 0 -0.13 82 82
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.091 -10000 0 -0.12 85 85
IGF-1R heterotetramer 0.033 0.024 0.1 2 -0.052 16 18
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.076 0.2 2 -0.13 85 87
Crk/p130 Cas/Paxillin 0.043 0.082 0.25 9 -0.13 72 81
IGF1R 0.034 0.024 0.1 2 -0.052 16 18
IGF1 0.027 0.035 0.1 2 -0.053 70 72
IRS2/Crk 0.009 0.055 0.17 1 -0.13 62 63
PI3K 0.024 0.083 0.21 2 -0.12 95 97
apoptosis -0.002 0.09 0.18 6 -0.23 28 34
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
PRKCD -0.011 0.093 0.21 6 -0.21 69 75
RAF1/14-3-3 E 0.032 0.11 0.29 11 -0.41 13 24
BAD/14-3-3 0.002 0.093 0.23 28 -0.18 8 36
PRKCZ 0.001 0.095 0.18 92 -0.17 15 107
Crk/p130 Cas/Paxillin/FAK1 0.01 0.08 0.19 18 -0.16 42 60
PTPN1 0.038 0.012 -10000 0 0 54 54
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.011 0.094 -10000 0 -0.21 82 82
BCAR1 0.036 0.014 -10000 0 0 76 76
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.054 0.078 -10000 0 -0.11 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.038 0.013 -10000 0 0 56 56
IRS1/NCK2 0.025 0.069 0.14 16 -0.12 85 101
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 -0.021 0.052 0.11 13 -0.13 68 81
IRS1 0.004 0.062 0.13 17 -0.13 85 102
IRS2 -0.021 0.052 0.11 14 -0.13 71 85
IGF-1R heterotetramer/IGF1 0.02 0.076 0.16 2 -0.16 76 78
GRB2 0.041 0.007 -10000 0 0 17 17
PDPK1 0.008 0.099 0.19 90 -0.18 13 103
YWHAE 0.038 0.013 -10000 0 0 58 58
PRKD1 -0.012 0.097 0.2 8 -0.22 74 82
SHC1 0.04 0.01 -10000 0 0 31 31
Noncanonical Wnt signaling pathway

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
NFATC2 0.036 0.015 -10000 0 0 78 78
GNB1/GNG2 0.015 0.12 0.23 2 -0.26 46 48
mol:DAG -0.006 0.1 0.22 5 -0.25 42 47
PLCG1 -0.007 0.1 0.22 5 -0.26 42 47
YES1 -0.017 0.095 0.2 1 -0.27 44 45
FZD3 0.029 0.019 -10000 0 0 168 168
FZD6 0.029 0.019 -10000 0 0 170 170
G protein 0.029 0.13 0.25 40 -0.26 41 81
MAP3K7 -0.026 0.086 0.18 11 -0.23 40 51
mol:Ca2+ -0.006 0.1 0.21 5 -0.25 42 47
mol:IP3 -0.006 0.1 0.22 5 -0.25 42 47
NLK -0.032 0.27 -10000 0 -0.87 51 51
GNB1 0.041 0.005 -10000 0 0 7 7
CAMK2A -0.017 0.092 0.19 6 -0.24 40 46
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
Noncanonical Wnts/FZD -0.019 0.096 -10000 0 -0.2 94 94
CSNK1A1 0.04 0.009 -10000 0 0 26 26
GNAS -0.01 0.1 0.2 21 -0.2 86 107
GO:0007205 -0.013 0.096 0.2 6 -0.25 44 50
WNT6 0.041 0.006 -10000 0 0 13 13
WNT4 0.041 0.007 -10000 0 0 18 18
NFAT1/CK1 alpha 0.005 0.12 0.29 9 -0.27 41 50
GNG2 0.039 0.01 -10000 0 0 34 34
WNT5A 0.035 0.015 -10000 0 0 91 91
WNT11 0.033 0.017 -10000 0 0 124 124
CDC42 -0.019 0.095 0.19 7 -0.26 43 50
FoxO family signaling

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
G6PC -0.002 0.065 -10000 0 -10000 0 0
PLK1 -0.15 0.38 -10000 0 -0.86 93 93
CDKN1B -0.046 0.2 0.4 2 -0.38 81 83
FOXO3 -0.14 0.35 -10000 0 -0.57 179 179
KAT2B -0.008 0.028 0.043 4 -0.045 186 190
FOXO1/SIRT1 0.015 0.078 -10000 0 -0.23 16 16
CAT -0.16 0.4 0.65 1 -0.93 87 88
CTNNB1 0.04 0.01 -10000 0 0 31 31
AKT1 0.012 0.056 -10000 0 -0.064 155 155
FOXO1 -0.005 0.07 -10000 0 -0.24 12 12
MAPK10 0 0.047 0.19 7 -0.13 20 27
mol:GTP 0 0.003 -10000 0 -10000 0 0
FOXO4 -0.025 0.12 0.24 2 -0.32 49 51
response to oxidative stress -0.007 0.03 0.061 1 -0.052 105 106
FOXO3A/SIRT1 -0.13 0.34 0.41 1 -0.55 185 186
XPO1 0.039 0.011 -10000 0 0 39 39
EP300 0.038 0.015 -10000 0 -10000 0 0
BCL2L11 0.01 0.11 -10000 0 -0.93 6 6
FOXO1/SKP2 0.012 0.075 -10000 0 -0.24 17 17
mol:GDP -0.007 0.03 0.061 1 -0.052 105 106
RAN 0.041 0.007 -10000 0 0 13 13
GADD45A -0.077 0.28 -10000 0 -0.81 50 50
YWHAQ 0.04 0.009 -10000 0 0 28 28
FOXO1/14-3-3 family 0.014 0.13 0.27 2 -0.34 41 43
MST1 0.011 0.056 -10000 0 -0.063 191 191
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 57 57
FOXO4/14-3-3 family 0.002 0.14 -10000 0 -0.38 42 42
YWHAB 0.038 0.012 -10000 0 0 52 52
MAPK8 0.001 0.052 0.19 11 -0.13 21 32
MAPK9 -0.001 0.052 0.19 10 -0.14 20 30
YWHAG 0.04 0.009 -10000 0 0 25 25
YWHAE 0.038 0.013 -10000 0 0 58 58
YWHAZ 0.034 0.016 -10000 0 0 102 102
SIRT1 0.037 0.018 0.12 2 -0.035 24 26
SOD2 -0.12 0.3 -10000 0 -0.64 103 103
RBL2 -0.12 0.33 -10000 0 -0.77 78 78
RAL/GDP 0.031 0.056 -10000 0 -0.1 45 45
CHUK 0.012 0.054 -10000 0 -0.063 173 173
Ran/GTP 0.027 0.019 -10000 0 -0.13 3 3
CSNK1G2 0.037 0.013 -10000 0 0 64 64
RAL/GTP 0.031 0.057 -10000 0 -0.089 54 54
CSNK1G1 0.041 0.008 -10000 0 0 19 19
FASLG 0.017 0.065 -10000 0 -1.2 1 1
SKP2 0.036 0.014 -10000 0 0 73 73
USP7 0.038 0.012 -10000 0 0 50 50
IKBKB 0.011 0.054 -10000 0 -0.062 181 181
CCNB1 -0.18 0.43 -10000 0 -0.98 101 101
FOXO1-3a-4/beta catenin -0.06 0.2 -10000 0 -0.39 98 98
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.074 -10000 0 -0.24 17 17
CSNK1A1 0.04 0.009 -10000 0 0 26 26
SGK1 -0.008 0.028 0.043 4 -0.045 186 190
CSNK1G3 0.039 0.011 -10000 0 0 38 38
Ran/GTP/Exportin 1 0.046 0.038 -10000 0 -0.11 24 24
ZFAND5 -0.019 0.1 0.22 2 -0.27 49 51
SFN 0.036 0.015 -10000 0 0 86 86
CDK2 0.04 0.014 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.006 0.14 0.21 3 -0.33 59 62
CREBBP 0.04 0.013 -10000 0 -10000 0 0
FBXO32 -0.2 0.54 0.48 6 -1.1 144 150
BCL6 -0.13 0.35 -10000 0 -0.92 68 68
RALB 0.04 0.009 -10000 0 0 26 26
RALA 0.04 0.01 -10000 0 0 30 30
YWHAH 0.037 0.013 -10000 0 0 60 60
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.11 0.15 56 -0.28 41 97
adherens junction organization -0.026 0.13 0.18 6 -0.36 50 56
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.11 0.21 9 -0.28 31 40
FMN1 -0.023 0.12 0.16 6 -0.28 65 71
mol:IP3 0.003 0.098 0.16 60 -0.23 45 105
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.13 0.17 5 -0.29 65 70
CTNNB1 0.041 0.011 0.069 3 0 31 34
AKT1 -0.015 0.092 0.19 10 -0.25 44 54
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.15 -10000 0 -0.4 43 43
CTNND1 0.042 0.009 -10000 0 -0.002 18 18
mol:PI-4-5-P2 -0.02 0.12 0.2 4 -0.28 64 68
VASP -0.021 0.12 0.16 5 -0.28 64 69
ZYX -0.016 0.11 0.16 6 -0.29 51 57
JUB -0.022 0.12 0.16 6 -0.29 64 70
EGFR(dimer) -0.005 0.13 0.2 1 -0.31 56 57
E-cadherin/beta catenin-gamma catenin 0.05 0.06 -10000 0 -0.11 46 46
mol:PI-3-4-5-P3 -0.004 0.1 0.22 2 -0.26 45 47
PIK3CA 0.03 0.02 -10000 0 -0.001 159 159
PI3K -0.004 0.11 0.22 2 -0.27 45 47
FYN -0.012 0.12 0.2 8 -0.28 61 69
mol:Ca2+ 0.003 0.096 0.16 60 -0.22 45 105
JUP 0.038 0.014 -10000 0 0 67 67
PIK3R1 0.035 0.018 -10000 0 0 109 109
mol:DAG 0.003 0.098 0.16 60 -0.23 45 105
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP 0.013 0.11 0.22 12 -0.27 33 45
establishment of polarity of embryonic epithelium -0.02 0.12 0.2 3 -0.28 64 67
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 0.039 0.01 -10000 0 0 34 34
RHOA 0.041 0.007 -10000 0 0 14 14
EGFR 0.037 0.014 -10000 0 0 72 72
CASR -0.004 0.093 0.15 62 -0.24 35 97
RhoA/GTP 0.015 0.1 0.2 4 -0.24 35 39
AKT2 -0.016 0.092 0.18 8 -0.25 47 55
actin cable formation -0.025 0.11 0.21 7 -0.32 46 53
apoptosis 0.001 0.11 0.27 45 -0.17 64 109
CTNNA1 0.041 0.012 -10000 0 -0.001 39 39
mol:GDP -0.005 0.1 0.16 58 -0.27 35 93
PIP5K1A -0.022 0.12 0.16 5 -0.29 64 69
PLCG1 0.002 0.1 0.16 60 -0.23 45 105
Rac1/GTP 0.004 0.13 -10000 0 -0.3 54 54
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.019 -10000 0 0 143 143
ELF1 0.047 0.023 -10000 0 -0.27 2 2
CCNA2 0.032 0.018 -10000 0 0 135 135
PIK3CA 0.031 0.019 -10000 0 0 155 155
JAK3 0.038 0.013 -10000 0 -0.001 56 56
PIK3R1 0.034 0.017 -10000 0 -0.001 110 110
JAK1 0.04 0.011 -10000 0 -0.002 36 36
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.001 0.14 -10000 0 -0.33 47 47
SHC1 0.04 0.01 -10000 0 -0.001 32 32
SP1 0.044 0.043 -10000 0 -0.28 9 9
IL2RA 0.02 0.032 -10000 0 -0.49 2 2
IL2RB 0.037 0.015 -10000 0 -0.001 77 77
SOS1 0.038 0.013 -10000 0 -0.001 58 58
IL2RG 0.029 0.02 -10000 0 0 184 184
G1/S transition of mitotic cell cycle -0.039 0.18 0.29 4 -0.59 27 31
PTPN11 0.04 0.011 -10000 0 -0.004 31 31
CCND2 0.012 0.058 -10000 0 -0.49 7 7
LCK 0.04 0.011 -10000 0 -0.004 33 33
GRB2 0.041 0.009 -10000 0 -0.003 19 19
IL2 0.039 0.013 -10000 0 -0.002 49 49
CDK6 0.032 0.018 -10000 0 0 129 129
CCND3 0.004 0.14 -10000 0 -0.55 14 14
IL4-mediated signaling events

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
BCL2L1 -0.066 0.49 -10000 0 -1 69 69
STAT6 (cleaved dimer) -0.11 0.45 -10000 0 -0.95 86 86
IGHG1 0.034 0.23 0.45 4 -0.57 12 16
IGHG3 -0.069 0.45 -10000 0 -0.93 79 79
AKT1 -0.055 0.37 -10000 0 -0.81 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.044 0.36 -10000 0 -0.86 68 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.051 0.4 -10000 0 -0.93 65 65
THY1 -0.23 0.66 0.78 1 -1.2 157 158
MYB 0.034 0.017 -10000 0 0 111 111
HMGA1 0.037 0.014 -10000 0 0 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.37 0.53 2 -0.72 75 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.055 0.4 -10000 0 -0.92 67 67
SP1 0.022 0.073 -10000 0 -0.13 104 104
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.001 0.05 -10000 0 -0.086 2 2
STAT6 (dimer)/ETS1 -0.086 0.46 -10000 0 -0.96 80 80
SOCS1 -0.03 0.35 0.52 1 -0.66 68 69
SOCS3 -0.034 0.37 -10000 0 -0.88 51 51
FCER2 -0.032 0.39 -10000 0 -0.83 44 44
PARP14 0.033 0.019 -10000 0 -10000 0 0
CCL17 -0.062 0.47 -10000 0 -1 65 65
GRB2 0.041 0.007 -10000 0 0 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.011 0.3 -10000 0 -0.64 59 59
T cell proliferation -0.086 0.49 -10000 0 -1 82 82
IL4R/JAK1 -0.079 0.49 -10000 0 -1 80 80
EGR2 -0.059 0.48 -10000 0 -1 63 63
JAK2 0.033 0.073 0.17 4 -10000 0 4
JAK3 0.034 0.026 -10000 0 -0.038 44 44
PIK3R1 0.034 0.017 -10000 0 0 108 108
JAK1 0.041 0.041 0.11 4 -0.036 23 27
COL1A2 -0.15 0.56 -10000 0 -1.3 108 108
CCL26 -0.072 0.49 -10000 0 -1 69 69
IL4R -0.068 0.52 -10000 0 -1.1 75 75
PTPN6 0.006 0.043 -10000 0 -0.074 2 2
IL13RA2 -0.061 0.47 -10000 0 -1 67 67
IL13RA1 0.036 0.076 0.18 7 -10000 0 7
IRF4 0.058 0.15 -10000 0 -1.3 1 1
ARG1 0.05 0.19 -10000 0 -0.69 6 6
CBL -0.027 0.35 0.57 2 -0.68 74 76
GTF3A 0.013 0.08 -10000 0 -0.13 123 123
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL13RA1/JAK2 0.043 0.12 0.25 5 -0.18 25 30
IRF4/BCL6 0.043 0.14 -10000 0 -1.2 1 1
CD40LG 0.049 0.01 -10000 0 -0.12 1 1
MAPK14 -0.029 0.36 -10000 0 -0.72 73 73
mitosis -0.046 0.35 0.5 1 -0.76 71 72
STAT6 -0.064 0.54 0.78 2 -1.1 78 80
SPI1 0.045 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.34 -10000 0 -0.73 72 72
STAT6 (dimer) -0.062 0.54 0.78 2 -1.1 78 80
STAT6 (dimer)/PARP14 -0.1 0.48 -10000 0 -1 80 80
mast cell activation -0.004 0.019 -10000 0 -0.043 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.075 0.39 -10000 0 -0.88 73 73
FRAP1 -0.055 0.37 -10000 0 -0.81 71 71
LTA -0.06 0.47 -10000 0 -0.98 71 71
FES 0.04 0.008 -10000 0 0 22 22
T-helper 1 cell differentiation 0.058 0.53 1.1 78 -0.78 2 80
CCL11 -0.096 0.5 -10000 0 -1 83 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.048 0.38 -10000 0 -0.87 68 68
IL2RG 0.027 0.025 -10000 0 -0.04 19 19
IL10 -0.058 0.48 -10000 0 -1 66 66
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 33 33
IL4 0.038 0.23 -10000 0 -0.93 14 14
IL5 -0.063 0.47 -10000 0 -1 62 62
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.047 0.46 0.7 2 -0.89 81 83
COL1A1 -0.22 0.65 -10000 0 -1.3 143 143
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.085 0.49 -10000 0 -1.1 64 64
IL2R gamma/JAK3 0.02 0.074 -10000 0 -0.13 92 92
TFF3 -0.067 0.49 -10000 0 -1 75 75
ALOX15 -0.062 0.47 -10000 0 -1 64 64
MYBL1 0.036 0.014 -10000 0 0 73 73
T-helper 2 cell differentiation -0.1 0.47 -10000 0 -0.94 90 90
SHC1 0.04 0.01 -10000 0 0 31 31
CEBPB 0.04 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.052 0.4 -10000 0 -0.89 71 71
mol:PI-3-4-5-P3 -0.054 0.37 -10000 0 -0.81 71 71
PI3K -0.064 0.4 -10000 0 -0.89 71 71
DOK2 0.032 0.018 -10000 0 0 135 135
ETS1 0.001 0.047 -10000 0 -0.099 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.008 0.29 -10000 0 -0.61 64 64
ITGB3 -0.096 0.54 -10000 0 -1.1 85 85
PIGR -0.058 0.49 -10000 0 -1 67 67
IGHE -0.002 0.089 0.19 39 -0.19 23 62
MAPKKK cascade -0.007 0.29 -10000 0 -0.6 64 64
BCL6 0.03 0.018 -10000 0 0 146 146
OPRM1 -0.063 0.47 -10000 0 -1 58 58
RETNLB -0.056 0.48 -10000 0 -0.98 73 73
SELP -0.057 0.48 -10000 0 -1 63 63
AICDA -0.051 0.45 -10000 0 -0.97 62 62
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.1 -10000 0 -0.13 144 144
SMAD6-7/SMURF1 0.07 0.04 -10000 0 -0.15 8 8
NOG 0.038 0.012 -10000 0 0 50 50
SMAD9 0.006 0.12 -10000 0 -0.42 37 37
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD5 -0.002 0.098 0.22 2 -0.28 38 40
BMP7/USAG1 -0.02 0.084 -10000 0 -0.16 134 134
SMAD5/SKI 0.011 0.11 0.24 1 -0.28 40 41
SMAD1 0.003 0.096 -10000 0 -0.3 31 31
BMP2 0.038 0.012 -10000 0 0 49 49
SMAD1/SMAD1/SMAD4 0.027 0.1 -10000 0 -0.3 28 28
BMPR1A 0.037 0.013 -10000 0 0 65 65
BMPR1B 0.031 0.019 -10000 0 0 153 153
BMPR1A-1B/BAMBI 0.007 0.088 -10000 0 -0.14 121 121
AHSG 0.034 0.017 -10000 0 0 109 109
CER1 0.038 0.012 -10000 0 0 49 49
BMP2-4/CER1 0.06 0.045 -10000 0 -0.12 11 11
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.008 0.11 0.19 1 -0.26 58 59
BMP2-4 (homodimer) 0.047 0.036 -10000 0 -0.14 11 11
RGMB 0.039 0.011 -10000 0 0 42 42
BMP6/BMPR2/BMPR1A-1B 0.05 0.085 -10000 0 -0.13 82 82
RGMA 0.039 0.01 -10000 0 0 34 34
SMURF1 0.041 0.008 -10000 0 0 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.002 0.081 0.17 2 -0.24 34 36
BMP2-4/USAG1 0.022 0.07 -10000 0 -0.12 71 71
SMAD6/SMURF1/SMAD5 0.01 0.11 0.24 1 -0.28 40 41
SOSTDC1 0.023 0.021 -10000 0 0 255 255
BMP7/BMPR2/BMPR1A-1B 0.008 0.1 -10000 0 -0.14 154 154
SKI 0.042 0.003 -10000 0 0 3 3
BMP6 (homodimer) 0.037 0.013 -10000 0 0 63 63
HFE2 0.041 0.005 -10000 0 0 8 8
ZFYVE16 0.035 0.016 -10000 0 0 93 93
MAP3K7 0.038 0.012 -10000 0 0 47 47
BMP2-4/CHRD 0.052 0.046 -10000 0 -0.12 8 8
SMAD5/SMAD5/SMAD4 0.008 0.11 0.24 1 -0.28 39 40
MAPK1 0.039 0.012 -10000 0 0 46 46
TAK1/TAB family 0.032 0.12 -10000 0 -0.24 39 39
BMP7 (homodimer) 0.022 0.021 -10000 0 0 271 271
NUP214 0.039 0.01 -10000 0 0 33 33
BMP6/FETUA 0.045 0.028 -10000 0 -10000 0 0
SMAD1/SKI 0.023 0.1 -10000 0 -0.29 32 32
SMAD6 0.04 0.01 -10000 0 0 32 32
CTDSP2 0.039 0.011 -10000 0 0 42 42
BMP2-4/FETUA 0.053 0.045 -10000 0 -0.12 8 8
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
GREM1 0.035 0.016 -10000 0 0 98 98
BMPR2 (homodimer) 0.04 0.009 -10000 0 0 29 29
GADD34/PP1CA 0.057 0.056 -10000 0 -0.12 35 35
BMPR1A-1B (homodimer) 0.016 0.078 -10000 0 -0.15 90 90
CHRDL1 0.026 0.02 -10000 0 0 213 213
ENDOFIN/SMAD1 0.019 0.1 -10000 0 -0.29 31 31
SMAD6-7/SMURF1/SMAD1 0.049 0.11 -10000 0 -0.3 28 28
SMAD6/SMURF1 0.04 0.008 -10000 0 0 19 19
BAMBI 0.029 0.019 -10000 0 0 172 172
SMURF2 0.039 0.01 -10000 0 0 35 35
BMP2-4/CHRDL1 0.019 0.077 -10000 0 -0.12 102 102
BMP2-4/GREM1 0.052 0.049 -10000 0 -0.12 16 16
SMAD7 0.039 0.011 -10000 0 0 45 45
SMAD8A/SMAD8A/SMAD4 0.019 0.13 -10000 0 -0.4 44 44
SMAD1/SMAD6 0.023 0.1 -10000 0 -0.3 30 30
TAK1/SMAD6 0.052 0.036 -10000 0 -0.14 15 15
BMP7 0.022 0.021 -10000 0 0 271 271
BMP6 0.037 0.013 -10000 0 0 63 63
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.084 -10000 0 -0.24 35 35
PPM1A 0.041 0.007 -10000 0 0 16 16
SMAD1/SMURF2 0.021 0.1 -10000 0 -0.3 31 31
SMAD7/SMURF1 0.053 0.029 -10000 0 -0.14 8 8
CTDSPL 0.041 0.006 -10000 0 0 10 10
PPP1CA 0.041 0.006 -10000 0 0 13 13
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.041 0.006 -10000 0 0 13 13
PPP1R15A 0.039 0.011 -10000 0 0 44 44
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.001 0.087 -10000 0 -0.25 35 35
CHRD 0.033 0.017 -10000 0 0 116 116
BMPR2 0.04 0.009 -10000 0 0 29 29
BMP2-4/BMPR2/BMPR1A-1B/RGM 0 0.087 -10000 0 -0.26 31 31
BMP4 0.036 0.014 -10000 0 0 75 75
FST 0.033 0.017 -10000 0 0 120 120
BMP2-4/NOG 0.058 0.05 -10000 0 -0.12 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.017 0.11 -10000 0 -0.14 150 150
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.087 -10000 0 -0.14 68 68
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.039 0.011 -10000 0 0 38 38
STAT1 (dimer)/Cbp/p300 0.005 0.12 0.28 6 -0.22 81 87
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.081 -10000 0 -0.15 69 69
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.093 -10000 0 -0.2 85 85
CaM/Ca2+ 0.044 0.088 -10000 0 -0.14 65 65
RAP1A 0.039 0.01 -10000 0 0 35 35
STAT1 (dimer)/SHP2 0 0.093 0.19 19 -0.17 81 100
AKT1 0.005 0.1 0.19 71 -0.22 31 102
MAP2K1 -0.028 0.066 0.14 27 -0.18 34 61
MAP3K11 -0.022 0.072 0.16 34 -0.17 30 64
IFNGR1 0.035 0.021 0.083 2 -0.005 111 113
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.01 0.1 -10000 0 -0.29 42 42
Rap1/GTP -0.044 0.057 0.068 13 -0.17 46 59
CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.091 -10000 0 -0.14 62 62
CEBPB -0.029 0.16 0.28 1 -0.44 56 57
STAT3 0.038 0.013 -10000 0 0 56 56
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.048 0.16 -10000 0 -0.77 15 15
STAT1 -0.028 0.082 0.18 23 -0.2 50 73
CALM1 0.04 0.01 -10000 0 0 31 31
IFN-gamma (dimer) 0.032 0.025 0.085 2 -0.017 103 105
PIK3CA 0.03 0.019 -10000 0 0 155 155
STAT1 (dimer)/PIAS1 -0.009 0.093 0.23 8 -0.2 60 68
CEBPB/PTGES2/Cbp/p300 -0.011 0.12 -10000 0 -0.3 55 55
mol:Ca2+ 0.036 0.085 -10000 0 -0.14 68 68
MAPK3 -0.021 0.14 -10000 0 -0.65 15 15
STAT1 (dimer) -0.022 0.13 0.19 2 -0.28 81 83
MAPK1 -0.058 0.21 0.42 1 -0.74 42 43
JAK2 0.033 0.022 0.083 2 -0.007 114 116
PIK3R1 0.034 0.017 -10000 0 0 108 108
JAK1 0.036 0.022 0.082 1 -0.019 67 68
CAMK2D 0.036 0.015 -10000 0 0 82 82
DAPK1 -0.027 0.16 0.24 1 -0.48 48 49
SMAD7 -0.003 0.071 0.15 38 -0.13 50 88
CBL/CRKL/C3G 0.026 0.085 0.24 7 -0.17 33 40
PI3K 0.02 0.092 -10000 0 -0.17 63 63
IFNG 0.032 0.025 0.085 2 -0.017 103 105
apoptosis -0.022 0.15 -10000 0 -0.42 53 53
CAMK2G 0.04 0.008 -10000 0 0 23 23
STAT3 (dimer) 0.038 0.013 -10000 0 0 56 56
CAMK2A 0.041 0.006 -10000 0 0 12 12
CAMK2B 0.041 0.007 -10000 0 0 18 18
FRAP1 -0.004 0.098 0.16 78 -0.21 34 112
PRKCD 0.002 0.11 0.2 59 -0.23 33 92
RAP1B 0.038 0.013 -10000 0 0 59 59
negative regulation of cell growth -0.025 0.093 -10000 0 -0.2 85 85
PTPN2 0.04 0.008 -10000 0 0 20 20
EP300 0.036 0.014 -10000 0 0 73 73
IRF1 -0.046 0.097 0.22 7 -0.27 63 70
STAT1 (dimer)/PIASy -0.029 0.087 0.19 21 -0.22 40 61
SOCS1 0.003 0.18 -10000 0 -1.1 15 15
mol:GDP 0.023 0.081 0.22 7 -0.16 33 40
CASP1 -0.023 0.08 0.16 15 -0.17 97 112
PTGES2 0.04 0.009 -10000 0 0 27 27
IRF9 -0.008 0.052 0.11 8 -0.12 54 62
mol:PI-3-4-5-P3 0.006 0.082 -10000 0 -0.17 66 66
RAP1/GDP 0.015 0.086 0.2 2 -0.18 46 48
CBL -0.021 0.072 0.16 32 -0.18 26 58
MAP3K1 -0.02 0.07 0.16 28 -0.18 29 57
PIAS1 0.04 0.009 -10000 0 0 28 28
PIAS4 0.038 0.012 -10000 0 0 55 55
antigen processing and presentation of peptide antigen via MHC class II -0.025 0.093 -10000 0 -0.2 85 85
PTPN11 -0.015 0.074 0.17 34 -0.17 33 67
CREBBP 0.038 0.013 -10000 0 0 54 54
RAPGEF1 0.04 0.008 -10000 0 0 23 23
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 0.031 0.1 0.21 18 -0.26 24 42
TBX21 -0.029 0.28 -10000 0 -0.74 45 45
B2M 0.038 0.014 -10000 0 -10000 0 0
TYK2 0.025 0.044 -10000 0 -0.052 81 81
IL12RB1 0.024 0.045 -10000 0 -0.052 92 92
GADD45B -0.06 0.35 -10000 0 -0.95 56 56
IL12RB2 0.028 0.046 -10000 0 -0.051 89 89
GADD45G -0.031 0.3 -10000 0 -0.73 58 58
natural killer cell activation 0.002 0.021 0.048 10 -0.036 69 79
RELB 0.04 0.009 -10000 0 0 27 27
RELA 0.041 0.006 -10000 0 0 10 10
IL18 0.03 0.025 -10000 0 -0.042 20 20
IL2RA 0.039 0.011 -10000 0 0 45 45
IFNG 0.037 0.013 -10000 0 0 60 60
STAT3 (dimer) -0.027 0.29 -10000 0 -0.63 71 71
HLA-DRB5 0.02 0.028 -10000 0 -0.008 262 262
FASLG -0.026 0.28 0.53 1 -0.77 42 43
NF kappa B2 p52/RelB -0.015 0.29 -10000 0 -0.67 60 60
CD4 0.025 0.028 -10000 0 -0.012 189 189
SOCS1 0.038 0.012 -10000 0 0 50 50
EntrezGene:6955 -0.001 0.01 -10000 0 -0.026 59 59
CD3D 0.027 0.03 -10000 0 -0.039 65 65
CD3E 0.029 0.029 -10000 0 -0.037 67 67
CD3G 0.026 0.029 -10000 0 -0.04 57 57
IL12Rbeta2/JAK2 0.033 0.073 -10000 0 -0.15 27 27
CCL3 -0.046 0.33 -10000 0 -0.87 53 53
CCL4 -0.029 0.28 0.41 1 -0.66 60 61
HLA-A 0.038 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.061 0.082 -10000 0 -0.11 82 82
NOS2 -0.027 0.27 0.4 1 -0.59 71 72
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.1 0.21 17 -0.25 25 42
IL1R1 -0.11 0.43 -10000 0 -1 96 96
IL4 0.019 0.044 0.096 2 -0.061 18 20
JAK2 0.024 0.043 -10000 0 -0.052 79 79
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 42 42
TCR/CD3/MHC I/CD8 -0.012 0.12 -10000 0 -0.43 26 26
RAB7A -0.032 0.28 -10000 0 -0.61 75 75
lysosomal transport -0.028 0.26 0.39 1 -0.58 75 76
FOS -0.19 0.52 -10000 0 -1.1 126 126
STAT4 (dimer) -0.022 0.29 0.42 2 -0.66 66 68
STAT5A (dimer) -0.024 0.28 -10000 0 -0.66 59 59
GZMA -0.055 0.35 -10000 0 -0.96 52 52
GZMB -0.037 0.32 0.56 1 -0.88 46 47
HLX 0 0 -10000 0 -10000 0 0
LCK -0.036 0.29 0.42 2 -0.7 59 61
TCR/CD3/MHC II/CD4 -0.069 0.21 -10000 0 -0.38 132 132
IL2/IL2R 0.047 0.082 -10000 0 -0.11 94 94
MAPK14 -0.049 0.33 -10000 0 -0.74 74 74
CCR5 -0.021 0.25 0.36 2 -0.55 71 73
IL1B 0.023 0.042 -10000 0 -0.052 66 66
STAT6 0.012 0.14 -10000 0 -0.56 12 12
STAT4 0.04 0.009 -10000 0 0 29 29
STAT3 0.038 0.013 -10000 0 0 56 56
STAT1 0.034 0.017 -10000 0 0 108 108
NFKB1 0.036 0.015 -10000 0 0 84 84
NFKB2 0.04 0.009 -10000 0 0 24 24
IL12B 0.027 0.046 -10000 0 -0.051 91 91
CD8A 0.043 0.005 -10000 0 -10000 0 0
CD8B 0.001 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.1 0.25 24 -0.21 18 42
IL2RB 0.036 0.014 -10000 0 0 75 75
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.28 0.42 2 -0.61 66 68
IL2RG 0.028 0.02 -10000 0 0 183 183
IL12 0.024 0.072 -10000 0 -0.15 33 33
STAT5A 0.038 0.012 -10000 0 0 51 51
CD247 -0.001 0.009 -10000 0 -0.023 43 43
IL2 0.039 0.012 -10000 0 0 46 46
SPHK2 0.04 0.009 -10000 0 0 25 25
FRAP1 0.04 0.009 -10000 0 0 27 27
IL12A 0.019 0.041 -10000 0 -0.052 66 66
IL12/IL12R/TYK2/JAK2 -0.045 0.3 -10000 0 -0.74 59 59
MAP2K3 -0.053 0.34 -10000 0 -0.78 72 72
RIPK2 0.033 0.017 -10000 0 0 125 125
MAP2K6 -0.056 0.32 -10000 0 -0.72 76 76
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.024 0.029 -10000 0 -0.011 206 206
IL18RAP 0.04 0.019 -10000 0 -0.042 24 24
IL12Rbeta1/TYK2 0.039 0.058 -10000 0 -0.087 5 5
EOMES 0.005 0.076 -10000 0 -0.52 9 9
STAT1 (dimer) -0.043 0.29 -10000 0 -0.65 69 69
T cell proliferation -0.021 0.24 0.38 2 -0.5 75 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.04 0.019 -10000 0 -0.042 23 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.03 0.25 -10000 0 -0.56 71 71
ATF2 -0.048 0.3 -10000 0 -0.68 76 76
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.039 0.011 -9999 0 0 38 38
ITGB7 0.039 0.011 -9999 0 0 40 40
ITGA4 0.035 0.015 -9999 0 0 88 88
alpha4/beta7 Integrin 0.033 0.065 -9999 0 -0.14 65 65
alpha4/beta1 Integrin 0.033 0.064 -9999 0 -0.14 64 64
EPHB forward 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
Ephrin A5/EPHB2 0.035 0.048 -10000 0 -0.12 42 42
cell-cell adhesion 0.041 0.041 0.12 78 -10000 0 78
Ephrin B/EPHB2/RasGAP 0.053 0.096 -10000 0 -0.12 101 101
ITSN1 0.04 0.008 -10000 0 0 22 22
PIK3CA 0.03 0.019 -10000 0 0 155 155
SHC1 0.04 0.01 -10000 0 0 31 31
Ephrin B1/EPHB3 0.037 0.038 -10000 0 -0.11 22 22
Ephrin B1/EPHB1 0.048 0.024 -10000 0 -0.11 5 5
HRAS/GDP -0.019 0.11 -10000 0 -0.18 130 130
Ephrin B/EPHB1/GRB7 0.058 0.089 -10000 0 -0.12 82 82
Endophilin/SYNJ1 -0.025 0.059 0.19 12 -0.2 6 18
KRAS 0.034 0.016 -10000 0 0 103 103
Ephrin B/EPHB1/Src 0.061 0.087 -10000 0 -0.12 77 77
endothelial cell migration 0.021 0.076 -10000 0 -0.12 99 99
GRB2 0.041 0.007 -10000 0 0 17 17
GRB7 0.037 0.013 -10000 0 0 63 63
PAK1 -0.018 0.071 0.18 29 -0.2 9 38
HRAS 0.04 0.01 -10000 0 0 31 31
RRAS -0.025 0.058 0.19 9 -0.2 11 20
DNM1 0.039 0.011 -10000 0 0 38 38
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.011 0.071 0.19 34 -0.18 4 38
lamellipodium assembly -0.041 0.041 -10000 0 -0.12 78 78
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.072 -10000 0 -0.15 70 70
PIK3R1 0.034 0.017 -10000 0 0 108 108
EPHB2 0.039 0.011 -10000 0 0 38 38
EPHB3 0.032 0.018 -10000 0 0 135 135
EPHB1 0.038 0.013 -10000 0 0 59 59
EPHB4 0.04 0.009 -10000 0 0 29 29
mol:GDP -0.04 0.098 0.19 15 -0.23 70 85
Ephrin B/EPHB2 0.048 0.08 -10000 0 -0.11 96 96
Ephrin B/EPHB3 0.035 0.076 -10000 0 -0.11 88 88
JNK cascade -0.003 0.1 0.28 51 -0.18 3 54
Ephrin B/EPHB1 0.049 0.075 -10000 0 -0.11 81 81
RAP1/GDP -0.026 0.12 0.29 4 -0.22 81 85
EFNB2 0.031 0.018 -10000 0 0 143 143
EFNB3 0.037 0.014 -10000 0 0 71 71
EFNB1 0.041 0.007 -10000 0 0 16 16
Ephrin B2/EPHB1-2 0.036 0.067 -10000 0 -0.11 77 77
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.029 0.099 -10000 0 -0.16 84 84
Rap1/GTP -0.045 0.05 0.054 13 -0.19 16 29
axon guidance 0.035 0.047 -10000 0 -0.12 42 42
MAPK3 -0.003 0.069 0.2 6 -0.21 13 19
MAPK1 -0.001 0.068 0.2 6 -0.21 13 19
Rac1/GDP -0.03 0.11 0.26 7 -0.21 75 82
actin cytoskeleton reorganization -0.051 0.06 -10000 0 -0.16 72 72
CDC42/GDP -0.029 0.11 0.26 6 -0.22 77 83
PI3K 0.025 0.08 -10000 0 -0.12 99 99
EFNA5 0.034 0.016 -10000 0 0 103 103
Ephrin B2/EPHB4 0.023 0.061 -10000 0 -0.11 83 83
Ephrin B/EPHB2/Intersectin/N-WASP -0.001 0.08 -10000 0 -0.16 98 98
CDC42 0.04 0.009 -10000 0 0 24 24
RAS family/GTP -0.041 0.049 0.051 10 -0.19 14 24
PTK2 0.16 0.26 0.56 165 -10000 0 165
MAP4K4 -0.003 0.1 0.28 51 -0.19 3 54
SRC 0.039 0.01 -10000 0 0 36 36
KALRN 0.038 0.012 -10000 0 0 54 54
Intersectin/N-WASP 0.056 0.025 -10000 0 -0.14 6 6
neuron projection morphogenesis -0.017 0.094 0.28 24 -0.21 14 38
MAP2K1 -0.001 0.066 0.21 2 -0.22 12 14
WASL 0.04 0.009 -10000 0 0 24 24
Ephrin B1/EPHB1-2/NCK1 0.076 0.065 -10000 0 -0.12 40 40
cell migration -0.009 0.091 0.23 11 -0.24 21 32
NRAS 0.04 0.009 -10000 0 0 30 30
SYNJ1 -0.025 0.06 0.19 12 -0.2 6 18
PXN 0.041 0.007 -10000 0 0 14 14
TF -0.029 0.054 0.17 11 -0.2 6 17
HRAS/GTP 0.033 0.081 -10000 0 -0.12 86 86
Ephrin B1/EPHB1-2 0.062 0.043 -10000 0 -0.11 18 18
cell adhesion mediated by integrin 0.009 0.064 0.17 12 -0.22 14 26
RAC1 0.039 0.01 -10000 0 0 34 34
mol:GTP 0.037 0.083 -10000 0 -0.12 93 93
RAC1-CDC42/GTP -0.04 0.046 -10000 0 -0.19 10 10
RASA1 0.037 0.014 -10000 0 0 71 71
RAC1-CDC42/GDP -0.018 0.11 0.27 6 -0.21 74 80
ruffle organization -0.021 0.08 0.23 15 -0.24 2 17
NCK1 0.036 0.015 -10000 0 0 80 80
receptor internalization -0.03 0.055 0.17 11 -0.19 8 19
Ephrin B/EPHB2/KALRN 0.059 0.092 -10000 0 -0.12 88 88
ROCK1 0.02 0.089 0.19 111 -10000 0 111
RAS family/GDP -0.055 0.062 -10000 0 -0.16 107 107
Rac1/GTP -0.039 0.046 0.051 4 -0.12 78 82
Ephrin B/EPHB1/Src/Paxillin 0.004 0.072 -10000 0 -0.15 78 78
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.15 0.24 19 -0.33 61 80
FYN -0.029 0.18 0.23 18 -0.4 77 95
LAT/GRAP2/SLP76 -0.003 0.15 0.24 6 -0.33 69 75
IKBKB 0.039 0.011 -10000 0 0 44 44
AKT1 -0.014 0.14 0.21 13 -0.32 73 86
B2M 0.037 0.017 -10000 0 -0.003 76 76
IKBKG -0.002 0.05 0.12 11 -0.11 46 57
MAP3K8 0.04 0.008 -10000 0 0 21 21
mol:Ca2+ -0.013 0.016 0.051 11 -0.042 45 56
integrin-mediated signaling pathway 0.045 0.035 -10000 0 -0.11 22 22
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.026 0.18 0.24 11 -0.43 74 85
TRPV6 0.087 0.34 1.3 43 -10000 0 43
CD28 0.041 0.007 -10000 0 0 16 16
SHC1 -0.01 0.16 0.22 24 -0.39 61 85
receptor internalization -0.016 0.14 0.17 3 -0.34 72 75
PRF1 -0.009 0.21 -10000 0 -0.81 25 25
KRAS 0.034 0.016 -10000 0 0 103 103
GRB2 0.041 0.007 -10000 0 0 17 17
COT/AKT1 0.005 0.12 0.21 11 -0.26 70 81
LAT -0.017 0.16 0.23 10 -0.38 64 74
EntrezGene:6955 0.001 0.003 -10000 0 -0.023 3 3
CD3D 0.034 0.018 -10000 0 -0.001 111 111
CD3E 0.037 0.016 -10000 0 -0.001 80 80
CD3G 0.032 0.02 -10000 0 -0.002 136 136
RASGRP2 0.008 0.019 -10000 0 -0.14 2 2
RASGRP1 -0.021 0.15 0.22 11 -0.32 80 91
HLA-A 0.038 0.015 -10000 0 -0.002 67 67
RASSF5 0.039 0.01 -10000 0 0 34 34
RAP1A/GTP/RAPL 0.046 0.035 -10000 0 -0.11 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.061 0.14 24 -0.11 43 67
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.065 -10000 0 -0.16 71 71
PRKCA -0.008 0.083 0.17 19 -0.2 55 74
GRAP2 0.038 0.013 -10000 0 0 57 57
mol:IP3 -0.016 0.11 -10000 0 -0.27 66 66
EntrezGene:6957 0.001 0.004 -10000 0 -0.022 2 2
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.36 45 45
ORAI1 -0.082 0.28 -10000 0 -1.1 43 43
CSK -0.014 0.16 0.23 11 -0.39 61 72
B7 family/CD28 0.027 0.16 0.27 6 -0.36 63 69
CHUK 0.038 0.012 -10000 0 0 52 52
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.023 0.17 0.21 3 -0.4 70 73
PTPN6 -0.01 0.16 0.2 35 -0.36 66 101
VAV1 -0.018 0.16 0.21 12 -0.4 64 76
Monovalent TCR/CD3 -0.004 0.083 -10000 0 -0.21 65 65
CBL 0.04 0.008 -10000 0 0 23 23
LCK -0.018 0.18 0.23 19 -0.4 70 89
PAG1 -0.009 0.16 0.21 33 -0.4 58 91
RAP1A 0.039 0.01 -10000 0 0 35 35
TCR/CD3/MHC I/CD8/LCK -0.022 0.17 0.2 4 -0.37 79 83
CD80 0.04 0.01 -10000 0 0 35 35
CD86 0.035 0.016 -10000 0 0 102 102
PDK1/CARD11/BCL10/MALT1 -0.007 0.085 -10000 0 -0.2 66 66
HRAS 0.04 0.01 -10000 0 0 31 31
GO:0035030 -0.013 0.13 0.18 18 -0.3 68 86
CD8A 0.042 0.01 -10000 0 -0.015 15 15
CD8B 0.001 0.004 -10000 0 -0.022 4 4
PTPRC 0.025 0.021 -10000 0 0 228 228
PDK1/PKC theta -0.021 0.16 0.25 9 -0.37 69 78
CSK/PAG1 -0.008 0.16 0.23 22 -0.39 57 79
SOS1 0.038 0.013 -10000 0 0 56 56
peptide-MHC class I 0.038 0.07 -10000 0 -0.18 45 45
GRAP2/SLP76 0.001 0.17 0.25 6 -0.38 71 77
STIM1 -0.022 0.075 1.1 1 -10000 0 1
RAS family/GTP 0.011 0.078 0.16 13 -0.16 51 64
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.018 0.15 0.17 3 -0.36 72 75
mol:DAG -0.028 0.09 -10000 0 -0.24 70 70
RAP1A/GDP 0.011 0.033 0.073 17 -0.058 43 60
PLCG1 0.038 0.012 -10000 0 0 50 50
CD247 0.001 0.003 -10000 0 -0.023 3 3
cytotoxic T cell degranulation -0.007 0.2 -10000 0 -0.76 26 26
RAP1A/GTP 0.003 0.011 -10000 0 -0.037 17 17
mol:PI-3-4-5-P3 -0.018 0.16 0.22 13 -0.36 74 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.011 0.14 0.22 1 -0.34 61 62
NRAS 0.04 0.009 -10000 0 0 30 30
ZAP70 0.041 0.006 -10000 0 0 10 10
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
LAT/GRAP2/SLP76/VAV1 -0.012 0.14 0.24 5 -0.35 64 69
MALT1 0.036 0.014 -10000 0 0 76 76
TRAF6 0.04 0.008 -10000 0 0 22 22
CD8 heterodimer 0.031 0.012 -10000 0 -0.038 7 7
CARD11 0.038 0.013 -10000 0 0 56 56
PRKCB -0.028 0.062 -10000 0 -0.17 70 70
PRKCE -0.005 0.085 0.17 22 -0.2 52 74
PRKCQ -0.023 0.17 0.23 9 -0.4 71 80
LCP2 0.034 0.016 -10000 0 0 102 102
BCL10 0.041 0.006 -10000 0 0 11 11
regulation of survival gene product expression -0.009 0.12 0.2 15 -0.27 73 88
IKK complex 0.004 0.05 0.13 22 -0.095 23 45
RAS family/GDP -0.002 0.014 -10000 0 -0.035 40 40
MAP3K14 -0.002 0.094 0.16 15 -0.2 70 85
PDPK1 -0.015 0.13 0.21 15 -0.3 72 87
TCR/CD3/MHC I/CD8/Fyn -0.037 0.2 -10000 0 -0.48 69 69
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.049 0.064 -9999 0 -0.13 48 48
E-cadherin/beta catenin 0.04 0.052 -9999 0 -0.14 36 36
CTNNB1 0.04 0.01 -9999 0 0 31 31
JUP 0.037 0.014 -9999 0 0 67 67
CDH1 0.035 0.016 -9999 0 0 98 98
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.001 0.068 0.14 13 -0.19 56 69
CRKL 0.039 0.011 -10000 0 0 38 38
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DOCK1 0.037 0.013 -10000 0 0 62 62
ITGA4 0.035 0.015 -10000 0 0 88 88
alpha4/beta7 Integrin/MAdCAM1 0.067 0.074 -10000 0 -0.11 66 66
EPO 0.04 0.008 -10000 0 0 20 20
alpha4/beta7 Integrin 0.033 0.065 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 52 52
alpha4/beta1 Integrin 0.033 0.064 -10000 0 -0.14 64 64
EPO/EPOR (dimer) 0.052 0.025 -10000 0 -0.14 2 2
lamellipodium assembly 0.017 0.11 0.21 1 -0.34 20 21
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.024 0.061 -10000 0 -0.15 47 47
ARF6 0.041 0.008 -10000 0 0 19 19
JAK2 0.007 0.067 -10000 0 -0.18 53 53
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 108 108
MADCAM1 0.037 0.013 -10000 0 0 64 64
cell adhesion 0.065 0.072 -10000 0 -0.11 66 66
CRKL/CBL 0.055 0.021 -10000 0 -0.14 1 1
ITGB1 0.039 0.011 -10000 0 0 38 38
SRC -0.018 0.089 0.18 34 -0.19 40 74
ITGB7 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 34 34
alpha4/beta1 Integrin/VCAM1 -0.005 0.096 -10000 0 -0.14 153 153
p130Cas/Crk/Dock1 0.012 0.098 0.23 17 -0.18 44 61
VCAM1 0.02 0.021 -10000 0 0 288 288
RHOA 0.041 0.007 -10000 0 0 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 0.07 0.073 -10000 0 -0.11 63 63
BCAR1 -0.02 0.08 0.17 29 -0.18 40 69
EPOR 0.036 0.014 -10000 0 0 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.04 0.008 -10000 0 0 23 23
GIT1 0.04 0.009 -10000 0 0 27 27
Rac1/GTP 0.017 0.11 0.21 1 -0.36 20 21
FAS signaling pathway (CD95)

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
SPTAN1 -0.025 0.06 0.2 3 -0.22 35 38
RFC1 -0.023 0.06 0.22 1 -0.22 35 36
PRKDC -0.019 0.068 0.21 13 -0.21 38 51
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP7 0.002 0.12 -10000 0 -0.57 20 20
FASLG/FAS/FADD/FAF1 0.022 0.082 0.15 103 -0.18 38 141
MAP2K4 0.002 0.12 0.32 4 -0.32 38 42
mol:ceramide 0.018 0.094 -10000 0 -0.29 23 23
GSN -0.023 0.061 0.2 4 -0.22 37 41
FASLG/FAS/FADD/FAF1/Caspase 8 0.027 0.091 0.21 16 -0.25 18 34
FAS 0.035 0.018 -10000 0 -0.002 105 105
BID -0.034 0.024 0.23 2 -0.13 12 14
MAP3K1 -0.001 0.11 0.25 7 -0.36 30 37
MAP3K7 0.039 0.012 -10000 0 0 47 47
RB1 -0.025 0.061 0.18 2 -0.22 35 37
CFLAR 0.04 0.008 -10000 0 0 21 21
HGF/MET -0.014 0.092 -10000 0 -0.14 168 168
ARHGDIB -0.012 0.074 0.23 23 -0.22 25 48
FADD 0.041 0.012 -10000 0 -0.01 28 28
actin filament polymerization 0.023 0.06 0.21 37 -0.2 4 41
NFKB1 -0.05 0.24 -10000 0 -0.64 72 72
MAPK8 -0.002 0.12 0.34 3 -0.36 32 35
DFFA -0.021 0.064 0.2 7 -0.21 40 47
DNA fragmentation during apoptosis -0.021 0.062 0.22 5 -0.21 38 43
FAS/FADD/MET 0.017 0.09 -10000 0 -0.13 129 129
CFLAR/RIP1 0.052 0.031 -10000 0 -0.15 8 8
FAIM3 0.04 0.009 -10000 0 0 26 26
FAF1 0.041 0.013 -10000 0 -0.009 33 33
PARP1 -0.02 0.067 0.22 13 -0.21 36 49
DFFB -0.021 0.062 0.22 5 -0.21 38 43
CHUK -0.058 0.22 -10000 0 -0.61 71 71
FASLG 0.041 0.013 -10000 0 -0.012 29 29
FAS/FADD 0.036 0.062 -10000 0 -0.14 56 56
HGF 0.04 0.009 -10000 0 0 29 29
LMNA -0.019 0.068 0.19 17 -0.22 30 47
CASP6 -0.019 0.06 0.14 2 -0.24 26 28
CASP10 0.037 0.017 -10000 0 -0.004 75 75
CASP3 -0.022 0.064 0.16 4 -0.24 41 45
PTPN13 0.021 0.021 -10000 0 0 276 276
CASP8 -0.031 0.02 0.26 2 -10000 0 2
IL6 -0.043 0.24 -10000 0 -0.65 52 52
MET 0.027 0.02 -10000 0 0 198 198
ICAD/CAD -0.024 0.061 0.19 11 -0.2 40 51
FASLG/FAS/FADD/FAF1/Caspase 10 0.018 0.095 -10000 0 -0.3 23 23
activation of caspase activity by cytochrome c -0.034 0.024 0.23 2 -0.13 12 14
PAK2 -0.024 0.06 0.14 2 -0.22 39 41
BCL2 0.036 0.014 -10000 0 0 76 76
BCR signaling 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
JUN -0.052 0.14 -10000 0 -0.34 72 72
IKBKB 0.017 0.099 0.26 11 -0.27 19 30
AKT1 0.024 0.093 0.23 44 -0.18 8 52
IKBKG 0.02 0.077 0.23 1 -0.27 9 10
CALM1 -0.012 0.12 0.2 7 -0.35 37 44
PIK3CA 0.03 0.019 -10000 0 0 155 155
MAP3K1 -0.045 0.16 -10000 0 -0.42 59 59
MAP3K7 0.038 0.012 -10000 0 0 47 47
mol:Ca2+ -0.011 0.12 0.21 4 -0.36 44 48
DOK1 0.04 0.009 -10000 0 0 24 24
AP-1 -0.027 0.096 -10000 0 -0.21 71 71
LYN 0.036 0.015 -10000 0 0 83 83
BLNK 0.037 0.014 -10000 0 0 70 70
SHC1 0.04 0.01 -10000 0 0 31 31
BCR complex 0.053 0.025 -10000 0 -0.13 3 3
CD22 -0.011 0.088 -10000 0 -0.27 37 37
CAMK2G -0.015 0.11 0.2 14 -0.33 39 53
CSNK2A1 0.038 0.012 -10000 0 0 54 54
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.02 0.063 -10000 0 -0.13 59 59
GO:0007205 -0.013 0.13 0.21 4 -0.36 45 49
SYK 0.037 0.014 -10000 0 0 70 70
ELK1 -0.017 0.12 0.22 3 -0.35 43 46
NFATC1 -0.029 0.11 0.21 2 -0.29 49 51
B-cell antigen/BCR complex 0.053 0.025 -10000 0 -0.13 3 3
PAG1/CSK 0.053 0.027 -10000 0 -0.14 5 5
NFKBIB 0.012 0.066 0.13 1 -0.13 81 82
HRAS -0.011 0.1 0.25 3 -0.28 41 44
NFKBIA 0.014 0.061 0.13 1 -0.12 71 72
NF-kappa-B/RelA/I kappa B beta 0.02 0.059 0.13 1 -0.1 72 73
RasGAP/Csk 0.057 0.088 -10000 0 -0.11 84 84
mol:GDP -0.012 0.12 0.21 4 -0.35 46 50
PTEN 0.039 0.011 -10000 0 0 38 38
CD79B 0.04 0.008 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha 0.022 0.055 0.13 2 -0.1 64 66
GRB2 0.041 0.007 -10000 0 0 17 17
PI3K/BCAP/CD19 -0.027 0.15 -10000 0 -0.41 44 44
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 -0.008 0.12 0.21 4 -0.36 43 47
CSK 0.04 0.008 -10000 0 0 21 21
FOS -0.017 0.12 0.22 5 -0.33 48 53
CHUK -0.002 0.11 0.23 1 -0.29 53 54
IBTK 0.037 0.014 -10000 0 0 66 66
CARD11/BCL10/MALT1/TAK1 0.013 0.13 -10000 0 -0.32 39 39
PTPN6 -0.003 0.09 0.18 24 -0.27 28 52
RELA 0.041 0.006 -10000 0 0 10 10
BCL2A1 0.014 0.044 0.11 3 -0.079 67 70
VAV2 -0.022 0.12 -10000 0 -0.32 52 52
ubiquitin-dependent protein catabolic process 0.015 0.065 -10000 0 -0.12 81 81
BTK -0.037 0.25 -10000 0 -1.1 32 32
CD19 -0.019 0.095 -10000 0 -0.28 42 42
MAP4K1 0.039 0.012 -10000 0 0 46 46
CD72 0.04 0.008 -10000 0 0 20 20
PAG1 0.038 0.012 -10000 0 0 53 53
MAPK14 -0.038 0.14 0.26 3 -0.36 59 62
SH3BP5 0.04 0.008 -10000 0 0 23 23
PIK3AP1 -0.01 0.13 0.24 4 -0.39 36 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.17 -10000 0 -0.45 52 52
RAF1 -0.015 0.095 0.24 5 -0.28 38 43
RasGAP/p62DOK/SHIP 0.045 0.078 -10000 0 -0.11 88 88
CD79A 0.037 0.013 -10000 0 0 60 60
re-entry into mitotic cell cycle -0.027 0.095 -10000 0 -0.21 66 66
RASA1 0.037 0.014 -10000 0 0 71 71
MAPK3 -0.02 0.085 0.23 6 -0.26 35 41
MAPK1 -0.018 0.083 0.22 7 -0.25 33 40
CD72/SHP1 0.025 0.12 0.28 21 -0.26 28 49
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 -0.043 0.14 -10000 0 -0.36 58 58
actin cytoskeleton organization -0.024 0.11 0.25 3 -0.29 49 52
NF-kappa-B/RelA 0.033 0.12 0.24 1 -0.22 75 76
Calcineurin 0.012 0.12 -10000 0 -0.3 43 43
PI3K -0.011 0.075 -10000 0 -0.25 20 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.12 0.23 4 -0.36 41 45
SOS1 0.038 0.013 -10000 0 0 56 56
Bam32/HPK1 -0.051 0.25 -10000 0 -0.68 63 63
DAPP1 -0.075 0.27 -10000 0 -0.76 63 63
cytokine secretion -0.027 0.1 0.21 2 -0.27 49 51
mol:DAG -0.008 0.12 0.21 4 -0.36 43 47
PLCG2 0.035 0.015 -10000 0 0 87 87
MAP2K1 -0.018 0.091 0.24 6 -0.27 36 42
B-cell antigen/BCR complex/FcgammaRIIB 0.037 0.071 -10000 0 -0.12 75 75
mol:PI-3-4-5-P3 0.011 0.094 0.22 38 -0.22 13 51
ETS1 -0.013 0.11 0.25 8 -0.32 40 48
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.069 0.083 -10000 0 -0.12 61 61
B-cell antigen/BCR complex/LYN -0.013 0.1 -10000 0 -0.28 44 44
MALT1 0.036 0.014 -10000 0 0 76 76
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 -0.024 0.11 0.25 3 -0.3 51 54
B-cell antigen/BCR complex/LYN/SYK 0.054 0.11 0.34 14 -0.24 16 30
CARD11 -0.013 0.12 0.22 7 -0.36 41 48
FCGR2B 0.03 0.019 -10000 0 0 164 164
PPP3CA 0.037 0.013 -10000 0 0 61 61
BCL10 0.041 0.006 -10000 0 0 11 11
IKK complex 0.018 0.052 0.15 18 -0.12 13 31
PTPRC 0.025 0.021 -10000 0 0 228 228
PDPK1 0.015 0.083 0.2 46 -0.17 9 55
PPP3CB 0.04 0.01 -10000 0 0 31 31
PPP3CC 0.033 0.017 -10000 0 0 117 117
POU2F2 0.014 0.042 0.12 2 -0.076 70 72
Retinoic acid receptors-mediated 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
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC3 0.041 0.007 -10000 0 0 15 15
VDR 0.038 0.013 -10000 0 0 56 56
Cbp/p300/PCAF 0.04 0.044 -10000 0 -0.14 26 26
EP300 0.036 0.014 -10000 0 0 73 73
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.012 0.095 0.18 1 -0.26 47 48
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.009 -10000 0 0 28 28
AKT1 0.01 0.091 0.21 17 -0.21 26 43
RAR alpha/9cRA/Cyclin H -0.002 0.12 -10000 0 -0.24 73 73
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.079 -10000 0 -0.21 52 52
CDC2 0.026 0.024 -10000 0 -0.005 199 199
response to UV -0.001 0.008 -10000 0 -0.026 43 43
RAR alpha/Jnk1 0.017 0.068 -10000 0 -0.16 43 43
NCOR2 0.04 0.009 -10000 0 0 28 28
VDR/VDR/Vit D3 0.023 0.031 -10000 0 -0.13 22 22
RXRs/RARs/NRIP1/9cRA -0.037 0.19 -10000 0 -0.51 60 60
NCOA2 0.037 0.014 -10000 0 0 71 71
NCOA3 0.036 0.015 -10000 0 0 83 83
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.038 0.013 -10000 0 0 56 56
RARG 0.036 0.021 -10000 0 -0.018 68 68
RAR gamma1/9cRA 0.042 0.033 -10000 0 -0.11 14 14
MAPK3 0.036 0.022 -10000 0 -0.026 59 59
MAPK1 0.039 0.012 -10000 0 0 46 46
MAPK8 0.035 0.024 -10000 0 -0.025 70 70
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.013 0.14 -10000 0 -0.32 74 74
RARA 0.007 0.054 -10000 0 -0.16 42 42
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.083 -10000 0 -0.22 52 52
PRKCA 0.031 0.031 -10000 0 -0.072 34 34
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.044 0.2 -10000 0 -0.55 60 60
RXRG 0.016 0.057 -10000 0 -0.2 29 29
RXRA -0.027 0.097 -10000 0 -0.24 51 51
RXRB 0.013 0.059 -10000 0 -0.2 33 33
VDR/Vit D3/DNA 0.023 0.031 -10000 0 -0.13 22 22
RBP1 0.03 0.019 -10000 0 0 164 164
CRBP1/9-cic-RA 0.002 0.057 -10000 0 -0.13 89 89
RARB 0.032 0.026 -10000 0 -0.015 118 118
PRKCG 0.036 0.032 -10000 0 -0.071 44 44
MNAT1 0.04 0.008 -10000 0 0 22 22
RAR alpha/RXRs -0.015 0.16 0.27 2 -0.36 74 76
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.13 0.23 1 -0.3 60 61
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.1 0.18 1 -0.26 47 48
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.043 0.2 -10000 0 -0.55 60 60
positive regulation of DNA binding -0.009 0.11 -10000 0 -0.23 74 74
NRIP1 -0.079 0.32 -10000 0 -0.98 54 54
RXRs/RARs -0.027 0.17 -10000 0 -0.42 63 63
RXRs/RXRs/DNA/9cRA -0.03 0.13 -10000 0 -0.33 76 76
PRKACA 0.035 0.015 -10000 0 0 89 89
CDK7 0.035 0.016 -10000 0 0 98 98
TFIIH 0.06 0.054 -10000 0 -0.14 25 25
RAR alpha/9cRA 0.037 0.087 -10000 0 -0.23 19 19
CCNH 0.037 0.014 -10000 0 0 68 68
CREBBP 0.038 0.012 -10000 0 0 54 54
RAR gamma2/9cRA 0.044 0.061 -10000 0 -0.13 34 34
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.042 0.15 -10000 0 -0.34 100 100
KLHL20 -0.016 0.1 0.2 14 -0.23 51 65
CYFIP2 0.038 0.012 -10000 0 0 47 47
Rac1/GDP -0.012 0.11 0.28 4 -0.26 44 48
ENAH -0.038 0.14 -10000 0 -0.33 97 97
AP1M1 0.036 0.014 -10000 0 0 77 77
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.04 0.01 -10000 0 0 31 31
CDC42/GTP 0.003 0.079 0.16 4 -0.22 23 27
ABI1/Sra1/Nap1 -0.033 0.054 -10000 0 -0.16 64 64
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.068 -10000 0 -0.11 43 43
RAPGEF1 -0.035 0.13 0.28 3 -0.31 81 84
CTNND1 0.041 0.007 -10000 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.029 0.15 -10000 0 -0.34 102 102
CRK -0.033 0.13 0.25 1 -0.33 79 80
E-cadherin/gamma catenin/alpha catenin 0.05 0.065 -10000 0 -0.14 42 42
alphaE/beta7 Integrin 0.05 0.038 -10000 0 -0.14 17 17
IQGAP1 0.037 0.014 -10000 0 0 69 69
NCKAP1 0.04 0.01 -10000 0 0 31 31
Rap1/GTP/I-afadin 0.043 0.066 -10000 0 -0.11 69 69
DLG1 -0.044 0.15 -10000 0 -0.34 103 103
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.048 -10000 0 -0.15 55 55
MLLT4 0.034 0.017 -10000 0 0 107 107
ARF6/GTP/NME1/Tiam1 0.045 0.062 -10000 0 -0.11 58 58
PI3K -0.04 0.063 -10000 0 -0.21 40 40
ARF6 0.041 0.008 -10000 0 0 19 19
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.052 -10000 0 -0.15 30 30
TIAM1 0.037 0.014 -10000 0 0 72 72
E-cadherin(dimer)/Ca2+ 0.062 0.072 -10000 0 -0.13 51 51
AKT1 -0.008 0.063 0.16 15 -0.16 16 31
PIK3R1 0.034 0.017 -10000 0 0 108 108
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP -0.013 0.11 0.22 5 -0.26 47 52
actin cytoskeleton organization -0.01 0.077 0.16 15 -0.17 48 63
CDC42/GDP -0.012 0.11 0.28 4 -0.26 45 49
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.002 0.073 -10000 0 -0.2 55 55
ITGB7 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 34 34
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.067 0.078 -10000 0 -0.14 51 51
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.056 -10000 0 -0.11 48 48
mol:GDP -0.031 0.11 0.28 4 -0.29 47 51
CDC42/GTP/IQGAP1 0.04 0.047 -10000 0 -0.11 42 42
JUP 0.037 0.014 -10000 0 0 67 67
p120 catenin/RhoA/GDP -0.001 0.12 0.24 4 -0.27 45 49
RAC1/GTP/IQGAP1 0.038 0.046 -10000 0 -0.11 42 42
PIP5K1C/AP1M1 0.049 0.026 -10000 0 -0.14 1 1
RHOA 0.041 0.007 -10000 0 0 14 14
CDC42 0.04 0.009 -10000 0 0 24 24
CTNNA1 0.039 0.011 -10000 0 0 38 38
positive regulation of S phase of mitotic cell cycle -0.016 0.059 0.12 5 -0.12 94 99
NME1 0.035 0.015 -10000 0 0 91 91
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.039 0.15 -10000 0 -0.35 92 92
regulation of cell-cell adhesion -0.008 0.064 -10000 0 -0.18 27 27
WASF2 -0.007 0.043 0.11 13 -0.095 42 55
Rap1/GTP 0.002 0.087 0.2 9 -0.24 24 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.071 0.083 -10000 0 -0.12 48 48
CCND1 -0.02 0.072 0.14 5 -0.15 95 100
VAV2 -0.051 0.22 -10000 0 -0.62 49 49
RAP1/GDP 0 0.098 0.24 6 -0.27 26 32
adherens junction assembly -0.039 0.14 -10000 0 -0.34 93 93
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 26 26
PIP5K1C 0.038 0.012 -10000 0 0 54 54
regulation of heterotypic cell-cell adhesion 0.045 0.076 0.22 5 -0.13 60 65
E-cadherin/beta catenin 0.007 0.042 0.15 1 -0.23 14 15
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.037 0.14 -10000 0 -0.33 92 92
PIK3CA 0.03 0.019 -10000 0 0 155 155
Rac1/GTP -0.057 0.13 -10000 0 -0.36 61 61
E-cadherin/beta catenin/alpha catenin 0.052 0.066 -10000 0 -0.13 48 48
ITGAE 0.039 0.01 -10000 0 0 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.03 0.16 -10000 0 -0.34 102 102
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.007 0.051 -10000 0 -0.15 40 40
EPHB2 0.039 0.011 -10000 0 0 38 38
Syndecan-2/TACI 0.026 0.041 -10000 0 -0.11 39 39
LAMA1 0.034 0.017 -10000 0 0 108 108
Syndecan-2/alpha2 ITGB1 0.041 0.086 -10000 0 -0.12 81 81
HRAS 0.04 0.01 -10000 0 0 31 31
Syndecan-2/CASK 0.001 0.028 -10000 0 -0.099 40 40
ITGA5 0.038 0.013 -10000 0 0 58 58
BAX 0.02 0.064 -10000 0 -10000 0 0
EPB41 0.039 0.01 -10000 0 0 35 35
positive regulation of cell-cell adhesion 0.017 0.046 -10000 0 -0.098 67 67
LAMA3 0.031 0.018 -10000 0 0 147 147
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.033 0.017 -10000 0 0 114 114
Syndecan-2/MMP2 0.008 0.052 -10000 0 -0.16 40 40
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.035 0.057 -10000 0 -0.14 43 43
dendrite morphogenesis 0.025 0.043 -10000 0 -0.12 38 38
Syndecan-2/GM-CSF 0.027 0.041 -10000 0 -0.11 39 39
determination of left/right symmetry 0.01 0.007 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.024 0.041 -10000 0 -0.11 38 38
GNB2L1 0.041 0.005 -10000 0 0 7 7
MAPK3 0.009 0.074 0.2 63 -10000 0 63
MAPK1 0.01 0.074 0.2 63 -10000 0 63
Syndecan-2/RACK1 0.041 0.048 -10000 0 -0.096 44 44
NF1 0.034 0.016 -10000 0 0 101 101
FGFR/FGF/Syndecan-2 0.01 0.007 -10000 0 -10000 0 0
ITGA2 0.033 0.017 -10000 0 0 118 118
MAPK8 0 0.02 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.054 0.076 -10000 0 -0.11 51 51
Syndecan-2/Kininogen 0.022 0.039 -10000 0 -0.11 35 35
ITGB1 0.039 0.011 -10000 0 0 38 38
SRC 0.006 0.073 0.19 65 -0.17 1 66
Syndecan-2/CASK/Protein 4.1 0.023 0.038 -10000 0 -0.094 43 43
extracellular matrix organization 0.024 0.042 -10000 0 -0.11 36 36
actin cytoskeleton reorganization 0.007 0.051 -10000 0 -0.15 40 40
Syndecan-2/Caveolin-2/Ras 0.03 0.06 -10000 0 -0.11 64 64
Syndecan-2/Laminin alpha3 0.018 0.045 -10000 0 -0.13 34 34
Syndecan-2/RasGAP 0.063 0.069 -10000 0 -0.099 53 53
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
PRKCD 0.038 0.013 -10000 0 0 56 56
Syndecan-2 dimer 0.025 0.043 -10000 0 -0.12 38 38
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.059 0.2 1 -0.11 5 6
RHOA 0.041 0.007 -10000 0 0 14 14
SDCBP 0.036 0.014 -10000 0 0 75 75
TNFRSF13B 0.039 0.011 -10000 0 0 42 42
RASA1 0.037 0.014 -10000 0 0 71 71
alpha2/beta1 Integrin 0.035 0.057 -10000 0 -0.14 43 43
Syndecan-2/Synbindin 0.021 0.043 -10000 0 -0.12 39 39
TGFB1 0.037 0.013 -10000 0 0 62 62
CASP3 0.004 0.07 0.2 51 -0.18 1 52
FN1 0.021 0.021 -10000 0 0 277 277
Syndecan-2/IL8 0.018 0.044 -10000 0 -0.12 37 37
SDC2 0.01 0.007 -10000 0 -10000 0 0
KNG1 0.034 0.017 -10000 0 0 109 109
Syndecan-2/Neurofibromin 0.023 0.042 -10000 0 -0.12 35 35
TRAPPC4 0.034 0.016 -10000 0 0 102 102
CSF2 0.04 0.009 -10000 0 0 25 25
Syndecan-2/TGFB1 0.024 0.042 -10000 0 -0.11 36 36
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.046 -10000 0 -0.098 67 67
Syndecan-2/Ezrin 0.024 0.038 -10000 0 -0.095 42 42
PRKACA 0 0.069 0.2 43 -0.18 3 46
angiogenesis 0.018 0.044 -10000 0 -0.12 37 37
MMP2 0.022 0.021 -10000 0 0 273 273
IL8 0.032 0.018 -10000 0 0 139 139
calcineurin-NFAT signaling pathway 0.025 0.041 -10000 0 -0.11 39 39
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.067 0.066 -10000 0 -0.11 55 55
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.13 -10000 0 -0.32 63 63
AKT1 -0.09 0.27 -10000 0 -0.66 94 94
PIK3CA 0.03 0.019 -10000 0 0 155 155
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.089 0.28 -10000 0 -0.67 95 95
mol:Ca2+ -0.003 0.07 0.2 1 -0.28 21 22
IGF1R 0.033 0.017 -10000 0 0 118 118
E2/ER alpha (dimer)/Striatin 0.035 0.051 -10000 0 -0.11 52 52
SHC1 0.04 0.01 -10000 0 0 31 31
apoptosis 0.086 0.26 0.63 95 -10000 0 95
RhoA/GTP 0.014 0.049 -10000 0 -0.11 59 59
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.006 0.14 -10000 0 -0.29 73 73
regulation of stress fiber formation 0.014 0.072 0.16 15 -0.19 20 35
E2/ERA-ERB (dimer) 0.037 0.047 -10000 0 -0.11 44 44
KRAS 0.034 0.016 -10000 0 0 103 103
G13/GTP 0.033 0.046 -10000 0 -0.1 53 53
pseudopodium formation -0.014 0.072 0.19 20 -0.16 15 35
E2/ER alpha (dimer)/PELP1 0.036 0.047 -10000 0 -0.11 44 44
GRB2 0.041 0.007 -10000 0 0 17 17
GNG2 0.039 0.01 -10000 0 0 34 34
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.04 0.01 -10000 0 0 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.038 0.16 -10000 0 -0.38 80 80
E2/ER beta (dimer) 0.03 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.079 0.14 3 -0.22 55 58
mol:NADP -0.038 0.16 -10000 0 -0.38 80 80
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 -0.001 0.067 -10000 0 -0.29 21 21
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
PLCB1 0.005 0.064 -10000 0 -0.3 20 20
PLCB2 0.007 0.062 -10000 0 -0.28 21 21
IGF1 0.036 0.015 -10000 0 0 84 84
mol:L-citrulline -0.038 0.16 -10000 0 -0.38 80 80
RHOA 0.041 0.007 -10000 0 0 14 14
Gai/GDP -0.02 0.2 -10000 0 -0.59 58 58
JNK cascade 0.03 0.005 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 76 76
ESR2 0.041 0.007 -10000 0 0 18 18
GNAQ 0.038 0.012 -10000 0 0 49 49
ESR1 0.035 0.016 -10000 0 0 92 92
Gq family/GDP/Gbeta gamma -0.037 0.22 -10000 0 -0.62 67 67
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.11 -10000 0 -0.64 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.006 0.14 0.24 1 -0.29 71 72
GNAZ 0.039 0.011 -10000 0 0 42 42
E2/ER alpha (dimer) 0.016 0.043 -10000 0 -0.13 44 44
STRN 0.04 0.009 -10000 0 0 30 30
GNAL 0.04 0.009 -10000 0 0 26 26
PELP1 0.039 0.01 -10000 0 0 36 36
MAPK11 0.013 0.008 0.069 1 -10000 0 1
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
HBEGF -0.015 0.14 0.31 17 -0.33 50 67
cAMP biosynthetic process 0.032 0.039 -10000 0 -0.092 41 41
SRC -0.022 0.13 0.22 19 -0.33 50 69
PI3K 0.024 0.061 -10000 0 -0.15 47 47
GNB1 0.041 0.005 -10000 0 0 7 7
G13/GDP/Gbeta gamma 0.04 0.095 -10000 0 -0.2 56 56
SOS1 0.038 0.013 -10000 0 0 56 56
IGF-1R heterotetramer/IGF1 -0.038 0.1 -10000 0 -0.25 70 70
Gs family/GTP 0.041 0.044 -10000 0 -0.093 41 41
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.05 -10000 0 -0.11 29 29
vasodilation -0.036 0.16 -10000 0 -0.37 80 80
mol:DAG -0.001 0.067 -10000 0 -0.29 21 21
Gs family/GDP/Gbeta gamma 0.003 0.081 -10000 0 -0.21 51 51
MSN -0.017 0.073 0.17 39 -0.17 15 54
Gq family/GTP 0.019 0.067 -10000 0 -0.28 21 21
mol:PI-3-4-5-P3 -0.085 0.27 -10000 0 -0.63 102 102
NRAS 0.04 0.009 -10000 0 0 30 30
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.16 0.37 80 -10000 0 80
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
RhoA/GDP 0.014 0.09 -10000 0 -0.22 55 55
NOS3 -0.041 0.17 -10000 0 -0.4 80 80
GNA11 0.037 0.013 -10000 0 0 61 61
MAPKKK cascade -0.028 0.19 -10000 0 -0.47 77 77
E2/ER alpha (dimer)/PELP1/Src -0.011 0.14 0.24 4 -0.29 77 81
ruffle organization -0.014 0.072 0.19 20 -0.16 15 35
ROCK2 -0.008 0.083 0.22 22 -0.17 8 30
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA13 0.04 0.009 -10000 0 0 28 28
MMP9 -0.015 0.15 0.35 20 -0.32 52 72
MMP2 -0.019 0.13 0.24 5 -0.34 43 48
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.015 0.16 -10000 0 -0.44 55 55
HDAC1 0.043 0.025 0.083 115 -0.003 61 176
AES 0.039 0.016 0.08 17 0 68 85
FBXW11 0.04 0.009 -10000 0 0 25 25
DTX1 0.041 0.005 -10000 0 0 8 8
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 32 32
TLE1 0.04 0.015 0.077 15 -0.001 52 67
AP1 -0.005 0.083 0.15 1 -0.18 91 92
NCSTN 0.04 0.008 -10000 0 0 24 24
ADAM10 0.039 0.011 -10000 0 0 45 45
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.071 0.22 -10000 0 -0.59 60 60
NICD/RBPSUH -0.013 0.15 -10000 0 -0.44 55 55
WIF1 0.04 0.01 -10000 0 0 31 31
NOTCH1 -0.004 0.15 -10000 0 -0.46 52 52
PSENEN 0.035 0.016 -10000 0 0 92 92
KREMEN2 0.04 0.009 -10000 0 0 27 27
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.018 0.091 0.25 2 -0.34 12 14
APH1B 0.036 0.015 -10000 0 0 83 83
APH1A 0.041 0.006 -10000 0 0 10 10
AXIN1 0.002 0.067 -10000 0 -0.41 4 4
CtBP/CBP/TCF1/TLE1/AES 0.013 0.099 0.18 86 -0.18 53 139
PSEN1 0.039 0.01 -10000 0 0 35 35
FOS 0.026 0.02 -10000 0 0 207 207
JUN 0.036 0.015 -10000 0 0 80 80
MAP3K7 0.041 0.015 0.069 15 0 47 62
CTNNB1 0.001 0.085 0.23 3 -0.34 12 15
MAPK3 0.041 0.007 -10000 0 0 17 17
DKK2/LRP6/Kremen 2 0.056 0.054 -10000 0 -0.12 29 29
HNF1A 0.002 0.008 0.037 19 -10000 0 19
CTBP1 0.04 0.015 0.08 19 0 56 75
MYC -0.16 0.42 -10000 0 -1.2 76 76
NKD1 0.039 0.012 -10000 0 0 49 49
FZD1 0.041 0.007 -10000 0 0 17 17
NOTCH1 precursor/Deltex homolog 1 0.013 0.16 -10000 0 -0.44 55 55
apoptosis -0.005 0.082 0.15 1 -0.17 91 92
Delta 1/NOTCHprecursor 0.01 0.16 -10000 0 -0.44 55 55
DLL1 0.038 0.012 -10000 0 0 52 52
PPARD 0.008 0.076 -10000 0 -1 2 2
Gamma Secretase 0.072 0.086 -10000 0 -0.12 66 66
APC -0.021 0.12 -10000 0 -0.42 34 34
DVL1 0.018 0.058 -10000 0 -0.27 16 16
CSNK2A1 0.037 0.012 -10000 0 0 54 54
MAP3K7IP1 0.041 0.016 0.068 16 0 54 70
DKK1/LRP6/Kremen 2 0.055 0.053 -10000 0 -0.12 28 28
LRP6 0.034 0.016 -10000 0 0 107 107
CSNK1A1 0.039 0.009 -10000 0 0 26 26
NLK 0.027 0.043 -10000 0 -0.22 12 12
CCND1 -0.15 0.44 -10000 0 -1.2 82 82
WNT1 0.041 0.006 -10000 0 0 13 13
Axin1/APC/beta catenin 0.003 0.11 0.27 2 -0.36 19 21
DKK2 0.038 0.012 -10000 0 0 47 47
NOTCH1 precursor/DVL1 0.015 0.15 -10000 0 -0.39 52 52
GSK3B 0.041 0.009 -10000 0 0 26 26
FRAT1 0.041 0.009 -10000 0 0 24 24
NOTCH/Deltex homolog 1 0.019 0.16 -10000 0 -0.45 55 55
PPP2R5D 0.021 0.053 -10000 0 -0.29 11 11
MAPK1 0.039 0.012 -10000 0 0 46 46
WNT1/LRP6/FZD1 0.075 0.061 -10000 0 -0.11 31 31
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.03 0.024 -10000 0 -0.01 137 137
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.012 0.073 0.15 79 -0.18 6 85
DAPP1 -0.006 0.1 0.2 11 -0.26 39 50
Src family/SYK family/BLNK-LAT/BTK-ITK -0.011 0.14 -10000 0 -0.34 51 51
mol:DAG 0.006 0.076 0.18 20 -0.18 22 42
HRAS 0.041 0.014 0.079 3 -0.005 36 39
RAP1A 0.041 0.012 0.07 3 -0.001 36 39
ARF5/GDP 0.017 0.096 -10000 0 -0.24 34 34
PLCG2 0.035 0.015 -10000 0 0 87 87
PLCG1 0.038 0.012 -10000 0 0 50 50
ARF5 0.039 0.011 -10000 0 0 44 44
mol:GTP -0.012 0.067 0.14 80 -0.18 5 85
ARF1/GTP 0.001 0.064 0.14 85 -0.17 5 90
RHOA 0.041 0.007 -10000 0 0 14 14
YES1 0.038 0.013 -10000 0 0 57 57
RAP1A/GTP -0.008 0.076 0.16 80 -0.18 5 85
ADAP1 -0.014 0.061 0.13 74 -0.18 5 79
ARAP3 -0.012 0.066 0.14 80 -0.18 5 85
INPPL1 0.04 0.009 -10000 0 0 30 30
PREX1 0.037 0.013 -10000 0 0 64 64
ARHGEF6 0.037 0.013 -10000 0 0 65 65
ARHGEF7 0.04 0.009 -10000 0 0 27 27
ARF1 0.038 0.012 -10000 0 0 50 50
NRAS 0.042 0.011 0.069 3 0 30 33
FYN 0.034 0.016 -10000 0 0 103 103
ARF6 0.041 0.008 -10000 0 0 19 19
FGR 0.041 0.007 -10000 0 0 17 17
mol:Ca2+ 0.002 0.05 0.19 13 -0.12 4 17
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.037 0.014 -10000 0 0 72 72
ZAP70 0.041 0.006 -10000 0 0 10 10
mol:IP3 -0.002 0.062 0.23 12 -0.16 8 20
LYN 0.036 0.015 -10000 0 0 83 83
ARF1/GDP 0.018 0.096 -10000 0 -0.25 33 33
RhoA/GDP 0.036 0.083 0.19 47 -0.18 18 65
PDK1/Src/Hsp90 0.05 0.021 -10000 0 -0.11 3 3
BLNK 0.037 0.014 -10000 0 0 70 70
actin cytoskeleton reorganization 0.009 0.093 0.23 17 -0.27 18 35
SRC 0.039 0.01 -10000 0 0 36 36
PLEKHA2 -0.014 0.006 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 34 34
PTEN 0.031 0.028 -10000 0 -0.03 80 80
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.011 0.075 0.15 84 -0.18 5 89
RhoA/GTP -0.01 0.079 0.16 86 -0.18 6 92
Src family/SYK family/BLNK-LAT 0 0.098 0.18 6 -0.28 33 39
BLK 0.033 0.017 -10000 0 0 117 117
PDPK1 0.04 0.009 -10000 0 0 25 25
CYTH1 -0.014 0.061 0.13 74 -0.18 5 79
HCK 0.036 0.015 -10000 0 0 80 80
CYTH3 -0.014 0.061 0.13 74 -0.18 5 79
CYTH2 -0.014 0.061 0.13 74 -0.18 5 79
KRAS 0.034 0.018 0.091 1 -0.001 107 108
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.011 0.043 0.16 2 -0.16 7 9
SGK1 0.011 0.041 -10000 0 -0.16 8 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.093 0.18 1 -0.26 36 37
SOS1 0.038 0.013 -10000 0 0 56 56
SYK 0.037 0.014 -10000 0 0 70 70
ARF6/GDP 0.002 0.079 0.17 56 -0.17 16 72
mol:PI-3-4-5-P3 -0.014 0.065 0.14 74 -0.18 5 79
ARAP3/RAP1A/GTP -0.008 0.076 0.16 80 -0.18 5 85
VAV1 0.037 0.014 -10000 0 0 68 68
mol:PI-3-4-P2 -0.01 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.066 0.22 29 -0.12 39 68
PLEKHA1 -0.015 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.099 -10000 0 -0.25 35 35
LAT 0.041 0.006 -10000 0 0 13 13
Rac1/GTP -0.004 0.1 -10000 0 -0.27 47 47
ITK -0.014 0.065 0.13 76 -0.18 6 82
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0 0.092 0.22 14 -0.23 28 42
LCK 0.04 0.009 -10000 0 0 29 29
BTK -0.015 0.068 0.13 76 -0.2 9 85
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.028 0.2 -10000 0 -0.72 37 37
epithelial cell differentiation -0.027 0.19 -10000 0 -0.67 37 37
ITCH 0.039 0.037 0.1 8 -0.099 26 34
WWP1 -0.064 0.27 -10000 0 -1.1 33 33
FYN 0.034 0.016 -10000 0 0 103 103
EGFR 0.037 0.014 -10000 0 0 72 72
PRL 0.039 0.011 -10000 0 0 39 39
neuron projection morphogenesis -0.043 0.16 0.25 9 -0.57 35 44
PTPRZ1 0.039 0.01 -10000 0 0 36 36
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.004 0.18 0.29 1 -0.61 36 37
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.034 0.18 -10000 0 -0.65 38 38
ADAM17 0.038 0.035 0.11 4 -0.082 28 32
ErbB4/ErbB4 -0.05 0.21 -10000 0 -0.79 36 36
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.03 0.2 -10000 0 -0.71 37 37
NCOR1 0.037 0.013 -10000 0 0 61 61
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.18 -10000 0 -0.58 42 42
GRIN2B -0.035 0.16 0.25 4 -0.56 40 44
ErbB4/ErbB2/betacellulin -0.028 0.18 -10000 0 -0.64 38 38
STAT1 0.034 0.017 -10000 0 0 108 108
HBEGF 0.04 0.01 -10000 0 0 32 32
PRLR 0.035 0.015 -10000 0 0 88 88
E4ICDs/ETO2 -0.031 0.2 -10000 0 -0.72 37 37
axon guidance -0.056 0.23 -10000 0 -0.82 39 39
NEDD4 0.038 0.039 0.11 8 -0.084 38 46
Prolactin receptor/Prolactin receptor/Prolactin 0.049 0.025 -10000 0 -10000 0 0
CBFA2T3 0.036 0.015 -10000 0 0 81 81
ErbB4/ErbB2/HBEGF -0.022 0.18 -10000 0 -0.63 38 38
MAPK3 -0.023 0.16 0.27 7 -0.58 35 42
STAT1 (dimer) -0.034 0.21 -10000 0 -0.72 38 38
MAPK1 -0.024 0.16 0.27 7 -0.59 35 42
JAK2 0.035 0.016 -10000 0 0 92 92
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.17 -10000 0 -0.64 37 37
NRG1 -0.008 0.032 0.035 109 -0.11 20 129
NRG3 0.035 0.016 -10000 0 0 92 92
NRG2 0.041 0.007 -10000 0 0 14 14
NRG4 0.029 0.019 -10000 0 0 171 171
heart development -0.056 0.23 -10000 0 -0.82 39 39
neural crest cell migration -0.032 0.17 -10000 0 -0.63 37 37
ERBB2 -0.008 0.033 0.036 121 -0.1 24 145
WWOX/E4ICDs -0.03 0.2 -10000 0 -0.72 37 37
SHC1 0.04 0.01 -10000 0 0 31 31
ErbB4/EGFR/neuregulin 4 -0.037 0.2 -10000 0 -0.7 37 37
apoptosis 0.031 0.19 0.62 44 -10000 0 44
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.026 0.2 -10000 0 -0.72 37 37
ErbB4/ErbB2/epiregulin -0.02 0.18 -10000 0 -0.63 38 38
ErbB4/ErbB4/betacellulin/betacellulin -0.035 0.2 -10000 0 -0.73 37 37
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.2 -10000 0 -0.64 36 36
MDM2 -0.042 0.19 0.28 9 -0.77 30 39
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.02 0.16 -10000 0 -0.57 38 38
STAT5A -0.057 0.22 -10000 0 -0.8 38 38
ErbB4/EGFR/neuregulin 1 beta -0.027 0.18 -10000 0 -0.62 38 38
DLG4 0.039 0.01 -10000 0 0 34 34
GRB2/SHC 0.056 0.024 -10000 0 -0.14 5 5
E4ICDs/TAB2/NCoR1 -0.02 0.2 -10000 0 -0.7 38 38
STAT5A (dimer) -0.022 0.22 -10000 0 -0.75 37 37
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
STAT5B (dimer) -0.038 0.23 -10000 0 -0.81 38 38
LRIG1 0.033 0.017 -10000 0 0 119 119
EREG 0.039 0.011 -10000 0 0 45 45
BTC 0.034 0.017 -10000 0 0 111 111
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.06 0.23 -10000 0 -0.83 39 39
ERBB4 -0.048 0.2 -10000 0 -0.84 32 32
STAT5B 0.039 0.011 -10000 0 0 43 43
YAP1 0.007 0.1 -10000 0 -0.52 17 17
GRB2 0.041 0.007 -10000 0 0 17 17
ErbB4/ErbB2/neuregulin 4 -0.033 0.18 -10000 0 -0.64 38 38
glial cell differentiation 0.02 0.2 0.69 38 -10000 0 38
WWOX 0.037 0.014 -10000 0 0 71 71
cell proliferation -0.07 0.21 0.28 1 -0.6 60 61
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.012 0.17 -10000 0 -0.78 16 16
UGCG -0.008 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.02 0.18 0.29 3 -0.38 74 77
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.006 0.15 -10000 0 -0.68 22 22
mol:DAG -0.008 0.029 0.17 13 -10000 0 13
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.23 0.37 1 -0.5 78 79
FRAP1 -0.056 0.26 0.4 1 -0.59 77 78
FOXO3 -0.055 0.26 0.37 1 -0.53 94 95
AKT1 -0.064 0.28 -10000 0 -0.58 94 94
GAB2 0.03 0.02 -10000 0 -0.002 152 152
SMPD1 0 0.12 -10000 0 -0.59 19 19
SGMS1 -0.003 0.038 0.065 9 -0.078 79 88
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 -0.02 0.035 -10000 0 -0.12 52 52
CALM1 0.04 0.01 -10000 0 0 31 31
cell proliferation 0.003 0.18 0.24 16 -0.32 81 97
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.021 0.064 -10000 0 -0.14 54 54
RPS6KB1 -0.023 0.2 -10000 0 -0.83 29 29
mol:sphingomyelin -0.008 0.029 0.17 13 -10000 0 13
natural killer cell activation -0.001 0.004 -10000 0 -0.015 19 19
JAK3 0.035 0.022 -10000 0 -0.046 23 23
PIK3R1 0.031 0.023 -10000 0 -0.041 24 24
JAK1 0.037 0.02 -10000 0 -0.043 22 22
NFKB1 0.036 0.015 -10000 0 0 84 84
MYC -0.035 0.35 0.42 10 -0.82 78 88
MYB -0.041 0.29 -10000 0 -1.1 38 38
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.028 0.17 0.25 3 -0.36 90 93
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.005 0.19 -10000 0 -0.77 29 29
mol:PI-3-4-5-P3 -0.025 0.17 0.27 4 -0.35 90 94
Rac1/GDP 0.008 0.045 -10000 0 -0.11 48 48
T cell proliferation -0.029 0.16 0.25 5 -0.34 88 93
SHC1 0.037 0.016 -10000 0 -0.011 48 48
RAC1 0.039 0.01 -10000 0 0 34 34
positive regulation of cyclin-dependent protein kinase activity 0.002 0.02 0.032 46 -0.064 38 84
PRKCZ -0.031 0.17 0.25 5 -0.35 89 94
NF kappa B1 p50/RelA -0.03 0.24 0.4 1 -0.5 80 81
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.003 0.12 -10000 0 -0.34 40 40
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
IL2RA 0.036 0.017 -10000 0 -0.009 63 63
IL2RB 0.034 0.022 -10000 0 -0.045 22 22
TERT 0.037 0.014 -10000 0 0 68 68
E2F1 -0.001 0.12 -10000 0 -0.41 40 40
SOS1 0.035 0.018 -10000 0 -0.008 73 73
RPS6 0.039 0.011 -10000 0 0 41 41
mol:cAMP -0.001 0.01 0.032 35 -0.017 46 81
PTPN11 0.036 0.02 -10000 0 -0.018 62 62
IL2RG 0.026 0.026 -10000 0 -0.042 27 27
actin cytoskeleton organization -0.029 0.16 0.25 5 -0.34 88 93
GRB2 0.038 0.015 -10000 0 -0.017 36 36
IL2 0.035 0.023 -10000 0 -0.04 35 35
PIK3CA 0.028 0.024 -10000 0 -0.043 22 22
Rac1/GTP 0.031 0.062 -10000 0 -0.11 46 46
LCK 0.036 0.023 -10000 0 -0.04 36 36
BCL2 -0.032 0.2 0.4 1 -0.56 43 44
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.013 -10000 0 0 64 64
Caspase 8 (4 units) 0.036 0.094 -10000 0 -0.24 28 28
NEF 0.003 0.005 -10000 0 -0.1 1 1
NFKBIA 0.026 0.042 0.085 6 -0.068 78 84
BIRC3 -0.058 0.1 0.2 4 -0.28 89 93
CYCS -0.006 0.069 0.19 12 -0.25 19 31
RIPK1 0.038 0.012 -10000 0 0 48 48
CD247 0.003 0.005 -10000 0 -0.1 1 1
MAP2K7 -0.006 0.17 -10000 0 -0.55 36 36
protein ubiquitination -0.001 0.098 0.22 7 -0.27 34 41
CRADD 0.041 0.006 -10000 0 0 13 13
DAXX 0.041 0.008 -10000 0 0 19 19
FAS 0.035 0.016 -10000 0 0 99 99
BID 0.001 0.063 0.16 2 -0.26 16 18
NF-kappa-B/RelA/I kappa B alpha 0.029 0.12 -10000 0 -0.18 120 120
TRADD 0.036 0.014 -10000 0 0 76 76
MAP3K5 0.037 0.014 -10000 0 0 69 69
CFLAR 0.04 0.008 -10000 0 0 21 21
FADD 0.04 0.008 -10000 0 0 21 21
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.029 0.12 -10000 0 -0.18 120 120
MAPK8 -0.01 0.16 -10000 0 -0.53 34 34
APAF1 0.04 0.01 -10000 0 0 32 32
TRAF1 0.04 0.008 -10000 0 0 22 22
TRAF2 0.04 0.009 -10000 0 0 29 29
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.067 -10000 0 -0.17 51 51
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.005 0.11 -10000 0 -0.32 36 36
CHUK -0.002 0.1 0.24 6 -0.29 34 40
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.085 -10000 0 -0.13 60 60
TCRz/NEF 0.01 0.008 -10000 0 -0.17 1 1
TNF 0.04 0.009 -10000 0 0 26 26
FASLG 0.022 0.014 -10000 0 -0.3 1 1
NFKB1 0.027 0.041 0.085 6 -0.07 66 72
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
CASP6 -0.045 0.23 -10000 0 -0.54 85 85
CASP7 -0.046 0.2 0.29 6 -0.4 112 118
RELA 0.027 0.044 0.081 6 -0.066 97 103
CASP2 0.038 0.012 -10000 0 0 51 51
CASP3 -0.056 0.2 0.29 6 -0.41 116 122
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
CASP8 0.04 0.009 -10000 0 0 28 28
CASP9 0.04 0.009 -10000 0 0 26 26
MAP3K14 0.007 0.11 0.25 6 -0.31 31 37
APAF-1/Caspase 9 -0.028 0.11 0.19 1 -0.25 93 94
BCL2 -0.011 0.14 -10000 0 -0.49 32 32
Circadian rhythm pathway

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
chromatin modification -0.049 0.31 -10000 0 -1 49 49
CLOCK 0.032 0.032 -10000 0 -0.069 41 41
TIMELESS/CRY2 -0.051 0.31 -10000 0 -1 49 49
DEC1/BMAL1 0.044 0.047 -10000 0 -0.082 56 56
ATR 0.035 0.016 -10000 0 0 93 93
NR1D1 -0.016 0.12 -10000 0 -0.64 3 3
ARNTL 0.032 0.032 -10000 0 -0.068 43 43
TIMELESS -0.081 0.32 -10000 0 -1.1 49 49
NPAS2 0.027 0.031 -10000 0 -0.068 38 38
CRY2 0.042 0.004 -10000 0 0 5 5
mol:CO 0.001 0.041 0.13 49 -10000 0 49
CHEK1 0.033 0.017 -10000 0 0 120 120
mol:HEME -0.001 0.041 -10000 0 -0.13 49 49
PER1 0.039 0.011 -10000 0 0 42 42
BMAL/CLOCK/NPAS2 0.034 0.096 -10000 0 -0.14 112 112
BMAL1/CLOCK -0.04 0.2 -10000 0 -0.59 51 51
S phase of mitotic cell cycle -0.049 0.31 -10000 0 -1 49 49
TIMELESS/CHEK1/ATR -0.052 0.32 -10000 0 -1.1 49 49
mol:NADPH -0.001 0.041 -10000 0 -0.13 49 49
PER1/TIMELESS -0.053 0.31 -10000 0 -1 49 49
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.04 0.009 -10000 0 0 26 26
HIF-2-alpha transcription factor network

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
MMP14 -0.054 0.3 -10000 0 -0.88 64 64
oxygen homeostasis 0.003 0.011 0.032 19 -0.024 4 23
TCEB2 0.04 0.008 -10000 0 0 23 23
TCEB1 0.038 0.012 -10000 0 0 50 50
VHL/Elongin B/Elongin C/HIF2A 0.04 0.13 0.29 9 -0.22 59 68
EPO 0.026 0.18 0.36 10 -0.36 36 46
FIH (dimer) 0.04 0.023 0.089 2 -0.035 34 36
APEX1 0.033 0.034 -10000 0 -0.038 42 42
SERPINE1 -0.008 0.16 0.36 8 -0.34 47 55
FLT1 -0.043 0.26 -10000 0 -0.7 70 70
ADORA2A 0.005 0.17 0.34 16 -0.34 39 55
germ cell development 0.008 0.18 0.36 15 -0.34 51 66
SLC11A2 0.011 0.19 0.35 12 -0.37 47 59
BHLHE40 0.012 0.18 0.33 19 -0.31 64 83
HIF1AN 0.04 0.023 0.089 2 -0.035 34 36
HIF2A/ARNT/SIRT1 0.04 0.16 0.32 9 -0.26 58 67
ETS1 0.043 0.025 0.12 1 -0.11 5 6
CITED2 0.014 0.15 -10000 0 -0.63 25 25
KDR -0.035 0.25 -10000 0 -0.71 63 63
PGK1 0.012 0.19 0.36 15 -0.38 50 65
SIRT1 0.041 0.008 -10000 0 0 20 20
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.062 0.23 0.46 1 -0.39 40 41
EPAS1 0.005 0.11 0.22 16 -0.22 65 81
SP1 0.034 0.05 -10000 0 -0.11 56 56
ABCG2 0.012 0.18 0.35 13 -0.34 49 62
EFNA1 0.001 0.19 0.35 11 -0.38 57 68
FXN 0.006 0.17 0.34 16 -0.34 43 59
POU5F1 0.006 0.18 0.36 14 -0.36 51 65
neuron apoptosis -0.061 0.22 0.38 40 -0.46 1 41
EP300 0.036 0.014 -10000 0 0 73 73
EGLN3 0.028 0.027 0.085 1 -0.035 22 23
EGLN2 0.04 0.023 0.091 2 -0.033 31 33
EGLN1 0.039 0.024 0.089 2 -0.035 33 35
VHL/Elongin B/Elongin C 0.069 0.039 -10000 0 -0.12 11 11
VHL 0.04 0.009 -10000 0 0 28 28
ARNT 0.035 0.033 -10000 0 -0.039 41 41
SLC2A1 -0.012 0.18 0.35 10 -0.35 65 75
TWIST1 0.005 0.17 0.33 20 -0.33 46 66
ELK1 0.047 0.013 -10000 0 -0.088 3 3
HIF2A/ARNT/Cbp/p300 0.04 0.16 0.35 6 -0.27 50 56
VEGFA 0.012 0.18 0.33 19 -0.31 64 83
CREBBP 0.038 0.012 -10000 0 0 54 54
Aurora B 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
Condensin I complex -0.008 0.039 -10000 0 -0.11 62 62
STMN1 -0.011 0.016 0.029 13 -10000 0 13
Aurora B/RasGAP/Survivin 0.045 0.075 -10000 0 -0.16 52 52
Chromosomal passenger complex/Cul3 protein complex -0.006 0.092 -10000 0 -0.24 49 49
BIRC5 0.037 0.014 -10000 0 -0.002 63 63
DES -0.047 0.28 -10000 0 -0.8 63 63
Aurora C/Aurora B/INCENP 0.063 0.048 -10000 0 -0.12 28 28
Aurora B/TACC1 0.036 0.04 -10000 0 -0.1 29 29
Aurora B/PP2A 0.044 0.05 -10000 0 -0.14 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.011 0.063 -10000 0 -0.16 78 78
mitotic metaphase/anaphase transition 0.002 0.006 0.013 111 -10000 0 111
NDC80 -0.004 0.01 0.02 12 -10000 0 12
Cul3 protein complex 0.05 0.06 -10000 0 -0.12 42 42
KIF2C -0.058 0.19 -10000 0 -0.48 81 81
PEBP1 -0.001 0.003 -10000 0 -0.011 40 40
KIF20A 0.033 0.018 -10000 0 0 133 133
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.058 -10000 0 -0.14 45 45
SEPT1 0.041 0.007 -10000 0 0 16 16
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.041 0.2 0.25 1 -0.56 63 64
PSMA3 0.037 0.013 -10000 0 0 60 60
G2/M transition of mitotic cell cycle -0.001 0.003 0.009 37 -0.008 20 57
H3F3B 0.002 0.057 -10000 0 -0.2 40 40
AURKB 0.038 0.016 -10000 0 0 81 81
AURKC 0.042 0.002 -10000 0 0 1 1
CDCA8 0.036 0.016 -10000 0 -0.005 69 69
cytokinesis -0.032 0.18 0.18 2 -0.42 76 78
Aurora B/Septin1 -0.007 0.19 0.22 1 -0.38 87 88
AURKA -0.001 0.003 0.009 37 -0.008 20 57
INCENP 0.039 0.016 -10000 0 -0.03 27 27
KLHL13 0.033 0.017 -10000 0 0 121 121
BUB1 0.037 0.015 -10000 0 0 78 78
hSgo1/Aurora B/Survivin 0.04 0.079 -10000 0 -0.15 63 63
EVI5 0.039 0.01 -10000 0 0 35 35
RhoA/GTP 0.002 0.17 -10000 0 -0.34 76 76
SGOL1 0.036 0.014 -10000 0 0 74 74
CENPA -0.017 0.12 -10000 0 -0.29 62 62
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.032 0.066 -10000 0 -0.14 63 63
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.037 0.063 -10000 0 -0.14 55 55
RHOA 0.041 0.007 -10000 0 0 14 14
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.024 0.14 -10000 0 -0.34 75 75
RASA1 0.037 0.014 -10000 0 0 71 71
KLHL9 0.039 0.011 -10000 0 0 42 42
mitotic prometaphase -0.001 0.003 -10000 0 -0.011 40 40
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.066 -10000 0 -0.14 63 63
PPP1CC 0.039 0.01 -10000 0 0 36 36
Centraspindlin -0.011 0.17 -10000 0 -0.37 77 77
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
NSUN2 -0.012 0.12 -10000 0 -0.33 67 67
MYLK 0.001 0.057 -10000 0 -0.2 41 41
KIF23 0.035 0.016 -10000 0 0 98 98
VIM -0.01 0.016 0.034 12 -10000 0 12
RACGAP1 0.037 0.014 -10000 0 -0.004 54 54
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.028 0.12 -10000 0 -0.31 87 87
Chromosomal passenger complex -0.035 0.15 -10000 0 -0.32 80 80
Chromosomal passenger complex/EVI5 0.067 0.098 -10000 0 -0.17 57 57
TACC1 0.035 0.016 -10000 0 0 93 93
PPP2R5D 0.04 0.009 -10000 0 0 29 29
CUL3 0.04 0.008 -10000 0 0 21 21
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.013 0.14 0.26 4 -0.37 38 42
ACTA1 0.006 0.087 0.22 15 -0.24 17 32
NUMA1 -0.016 0.14 0.26 5 -0.37 35 40
SPTAN1 -0.001 0.087 0.24 11 -0.26 14 25
LIMK1 0.002 0.086 0.23 12 -0.26 13 25
BIRC3 0.026 0.02 -10000 0 0 218 218
BIRC2 0.036 0.014 -10000 0 0 75 75
BAX 0.04 0.008 -10000 0 0 22 22
CASP10 -0.011 0.025 0.058 54 -10000 0 54
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.034 0.17 0.26 5 -0.39 67 72
DIABLO 0.037 0.013 -10000 0 0 63 63
apoptotic nuclear changes -0.002 0.086 0.24 11 -0.25 14 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.041 0.006 -10000 0 0 13 13
GSN -0.001 0.087 0.22 15 -0.25 16 31
MADD 0.041 0.006 -10000 0 0 11 11
TFAP2A -0.031 0.21 -10000 0 -0.57 54 54
BID 0.007 0.035 0.13 23 -0.094 26 49
MAP3K1 -0.027 0.14 -10000 0 -0.38 68 68
TRADD 0.036 0.014 -10000 0 0 76 76
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.041 -10000 0 -0.15 19 19
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.11 0.24 45 -0.24 23 68
CASP9 0.04 0.009 -10000 0 0 26 26
DNA repair -0.013 0.081 0.26 24 -0.18 12 36
neuron apoptosis -0.037 0.2 -10000 0 -0.66 44 44
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.014 0.12 0.28 6 -0.35 24 30
APAF1 0.04 0.01 -10000 0 0 32 32
CASP6 -0.1 0.34 -10000 0 -0.85 91 91
TRAF2 0.04 0.009 -10000 0 0 29 29
ICAD/CAD 0 0.085 0.25 11 -0.25 11 22
CASP7 0.014 0.11 0.19 83 -0.27 25 108
KRT18 -0.016 0.15 -10000 0 -0.62 23 23
apoptosis -0.042 0.16 0.27 8 -0.38 74 82
DFFA 0.003 0.084 0.22 13 -0.25 13 26
DFFB 0.004 0.088 0.24 15 -0.26 12 27
PARP1 0.013 0.081 0.18 12 -0.27 24 36
actin filament polymerization 0.002 0.085 0.26 11 -0.24 13 24
TNF 0.04 0.009 -10000 0 0 26 26
CYCS 0.001 0.07 0.14 20 -0.21 36 56
SATB1 -0.11 0.32 -10000 0 -0.81 91 91
SLK -0.001 0.086 0.22 13 -0.25 16 29
p15 BID/BAX 0.032 0.05 0.16 3 -0.2 8 11
CASP2 0.005 0.089 0.24 20 -0.24 31 51
JNK cascade 0.026 0.14 0.37 68 -10000 0 68
CASP3 0.007 0.09 0.2 22 -0.24 17 39
LMNB2 -0.047 0.21 0.27 2 -0.46 82 84
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP4 0.034 0.017 -10000 0 0 107 107
Mammalian IAPs/DIABLO 0.012 0.089 -10000 0 -0.13 132 132
negative regulation of DNA binding -0.03 0.2 -10000 0 -0.56 54 54
stress fiber formation -0.002 0.086 0.22 13 -0.25 16 29
GZMB -0.016 0.009 0 133 -10000 0 133
CASP1 -0.012 0.07 -10000 0 -0.2 68 68
LMNB1 -0.048 0.2 0.27 5 -0.4 87 92
APP -0.037 0.2 -10000 0 -0.67 44 44
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.01 0.002 0 28 -10000 0 28
VIM -0.036 0.16 0.27 10 -0.38 79 89
LMNA -0.017 0.15 0.26 5 -0.34 71 76
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.085 -10000 0 -0.24 36 36
LRDD 0.039 0.01 -10000 0 0 35 35
SREBF1 0.001 0.085 0.22 12 -0.25 14 26
APAF-1/Caspase 9 0.028 0.15 -10000 0 -0.64 20 20
nuclear fragmentation during apoptosis -0.016 0.13 0.26 5 -0.36 35 40
CFL2 -0.003 0.086 0.25 13 -0.27 11 24
GAS2 0.005 0.089 0.23 20 -0.26 13 33
positive regulation of apoptosis -0.041 0.18 0.25 6 -0.39 96 102
PRF1 0.037 0.013 -10000 0 0 61 61
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.014 0.006 -10000 0 -10000 0 0
ADCY5 -0.014 0.006 0 86 -10000 0 86
ADCY6 -0.015 0.005 0 55 -10000 0 55
ADCY7 -0.014 0.006 0 77 -10000 0 77
ADCY1 -0.015 0.005 -10000 0 -10000 0 0
ADCY2 -0.014 0.006 0 95 -10000 0 95
ADCY3 -0.015 0.005 0 52 -10000 0 52
ADCY8 -0.008 0.008 -10000 0 -10000 0 0
PRKCE -0.01 0.003 0 36 -10000 0 36
ADCY9 -0.014 0.006 0 76 -10000 0 76
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.054 0.085 0.22 71 -0.2 4 75
Reelin signaling pathway

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
CDK5R1/CDK5 0.046 0.041 -10000 0 -0.14 20 20
VLDLR 0.032 0.018 -10000 0 0 129 129
CRKL 0.039 0.011 -10000 0 0 38 38
LRPAP1 0.036 0.015 -10000 0 0 78 78
FYN 0.034 0.016 -10000 0 0 103 103
ITGA3 0.034 0.016 -10000 0 0 104 104
RELN/VLDLR/Fyn 0.032 0.067 -10000 0 -0.13 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.095 0.061 -10000 0 -0.11 17 17
AKT1 0 0.075 -10000 0 -0.17 60 60
MAP2K7 0.039 0.011 -10000 0 0 43 43
RAPGEF1 0.04 0.008 -10000 0 0 23 23
DAB1 0.04 0.009 -10000 0 0 27 27
RELN/LRP8/DAB1 0.059 0.039 -10000 0 -0.11 5 5
LRPAP1/LRP8 0.041 0.053 -10000 0 -0.14 36 36
RELN/LRP8/DAB1/Fyn 0.066 0.056 -10000 0 -0.1 32 32
DAB1/alpha3/beta1 Integrin 0.029 0.082 -10000 0 -0.12 84 84
long-term memory 0.073 0.071 0.22 7 -0.11 28 35
DAB1/LIS1 0.058 0.082 -10000 0 -0.11 54 54
DAB1/CRLK/C3G 0.046 0.073 -10000 0 -0.12 52 52
PIK3CA 0.03 0.019 -10000 0 0 155 155
DAB1/NCK2 0.064 0.083 -10000 0 -0.12 55 55
ARHGEF2 0.039 0.01 -10000 0 0 37 37
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.034 0.017 -10000 0 0 111 111
CDK5R1 0.04 0.009 -10000 0 0 30 30
RELN 0.034 0.017 -10000 0 0 110 110
PIK3R1 0.034 0.017 -10000 0 0 108 108
RELN/LRP8/Fyn 0.045 0.057 -10000 0 -0.12 32 32
GRIN2A/RELN/LRP8/DAB1/Fyn 0.076 0.069 -10000 0 -0.11 31 31
MAPK8 0.04 0.009 -10000 0 0 30 30
RELN/VLDLR/DAB1 0.042 0.054 -10000 0 -0.11 37 37
ITGB1 0.039 0.011 -10000 0 0 38 38
MAP1B 0 0.066 0.22 25 -0.2 5 30
RELN/LRP8 0.049 0.055 -10000 0 -0.12 28 28
GRIN2B/RELN/LRP8/DAB1/Fyn 0.077 0.068 -10000 0 -0.11 26 26
PI3K 0.024 0.061 -10000 0 -0.15 47 47
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.066 -10000 0 -0.14 69 69
RAP1A -0.002 0.097 0.3 27 -0.18 2 29
PAFAH1B1 0.038 0.012 -10000 0 0 49 49
MAPK8IP1 0.04 0.009 -10000 0 0 30 30
CRLK/C3G 0.056 0.018 -10000 0 -10000 0 0
GRIN2B 0.037 0.014 -10000 0 0 71 71
NCK2 0.042 0.004 -10000 0 0 6 6
neuron differentiation 0.023 0.059 0.17 1 -0.22 9 10
neuron adhesion -0.011 0.1 0.28 33 -0.25 1 34
LRP8 0.039 0.011 -10000 0 0 39 39
GSK3B -0.005 0.076 0.18 8 -0.16 61 69
RELN/VLDLR/DAB1/Fyn 0.051 0.068 -10000 0 -0.12 50 50
MAP3K11 0.041 0.006 -10000 0 0 12 12
RELN/VLDLR/DAB1/P13K -0.004 0.068 -10000 0 -0.16 64 64
CDK5 0.036 0.015 -10000 0 0 83 83
MAPT -0.009 0.034 0.68 1 -10000 0 1
neuron migration 0.004 0.099 0.27 29 -0.24 16 45
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.022 0.057 0.17 1 -0.21 8 9
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 58 58
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.022 0.012 -10000 0 -0.1 1 1
ARNO/beta Arrestin1-2 0.043 0.032 -10000 0 -0.089 9 9
EGFR 0.037 0.014 -10000 0 0 72 72
EPHA2 0.039 0.01 -10000 0 0 35 35
USP6 0.039 0.01 -10000 0 0 36 36
IQSEC1 0.041 0.007 -10000 0 0 14 14
EGFR/EGFR/EGF/EGF 0.041 0.051 -10000 0 -0.13 37 37
ARRB2 0.016 0.017 -10000 0 -0.2 3 3
mol:GTP 0.001 0.014 -10000 0 -0.06 12 12
ARRB1 0.038 0.012 -10000 0 0 49 49
FBXO8 0.037 0.014 -10000 0 0 68 68
TSHR 0.038 0.013 -10000 0 0 60 60
EGF 0.038 0.012 -10000 0 0 53 53
somatostatin receptor activity 0 0 0 5 -0.001 40 45
ARAP2 0 0 0 10 0 34 44
mol:GDP 0.013 0.071 0.15 2 -0.19 31 33
mol:PI-3-4-5-P3 0 0 0 7 0 36 43
ITGA2B 0.04 0.009 -10000 0 0 30 30
ARF6 0.041 0.008 -10000 0 0 19 19
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.077 -10000 0 -0.12 61 61
ADAP1 0 0 0 7 0 22 29
KIF13B 0.034 0.017 -10000 0 0 112 112
HGF/MET 0.013 0.075 -10000 0 -0.14 105 105
PXN 0.041 0.007 -10000 0 0 14 14
ARF6/GTP 0.015 0.082 0.19 5 -0.22 37 42
EGFR/EGFR/EGF/EGF/ARFGEP100 0.06 0.055 -10000 0 -0.12 35 35
ADRB2 0.041 0.006 -10000 0 0 13 13
receptor agonist activity 0 0 0 8 0 34 42
actin filament binding 0 0 0 3 0 40 43
SRC 0.039 0.01 -10000 0 0 36 36
ITGB3 0.033 0.017 -10000 0 0 121 121
GNAQ 0.038 0.012 -10000 0 0 49 49
EFA6/PI-4-5-P2 0 0 0.001 11 -0.001 26 37
ARF6/GDP 0.01 0.077 0.19 8 -0.24 24 32
ARF6/GDP/GULP/ACAP1 0.029 0.084 -10000 0 -0.21 26 26
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.058 -10000 0 -0.11 34 34
ACAP1 0 0 0 4 0 1 5
ACAP2 0 0 0 6 0 34 40
LHCGR/beta Arrestin2 0.031 0.026 -10000 0 -0.063 32 32
EFNA1 0.034 0.017 -10000 0 0 107 107
HGF 0.04 0.009 -10000 0 0 29 29
CYTH3 0 0 0.001 10 -0.001 34 44
CYTH2 0 0.001 0.003 4 -0.004 37 41
NCK1 0.036 0.015 -10000 0 0 80 80
fibronectin binding 0 0 0 8 0 33 41
endosomal lumen acidification 0 0 0 10 0 20 30
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.032 0.018 -10000 0 0 129 129
GNAQ/ARNO 0.027 0.009 -10000 0 0 49 49
mol:Phosphatidic acid 0 0 0 6 0 34 40
PIP3-E 0.038 0.012 -10000 0 0 52 52
MET 0.027 0.02 -10000 0 0 198 198
GNA14 0.04 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GIT1 0.04 0.009 -10000 0 0 27 27
mol:PI-4-5-P2 0 0 0.001 13 -0.001 34 47
GNA11 0.037 0.013 -10000 0 0 61 61
LHCGR 0.04 0.009 -10000 0 0 25 25
AGTR1 0.037 0.014 -10000 0 0 68 68
desensitization of G-protein coupled receptor protein signaling pathway 0.031 0.026 -10000 0 -0.063 32 32
IPCEF1/ARNO 0.054 0.044 -10000 0 -0.087 35 35
alphaIIb/beta3 Integrin 0.04 0.05 -10000 0 -0.14 34 34
EPO signaling pathway

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
BCL2L1 0.029 0.14 0.36 1 -0.59 15 16
CRKL 0.025 0.085 0.18 114 -0.16 2 116
mol:DAG 0.044 0.073 0.22 4 -0.22 16 20
HRAS 0.018 0.097 0.25 40 -0.18 3 43
MAPK8 0.011 0.078 0.18 83 -0.13 6 89
RAP1A 0.024 0.085 0.18 114 -0.16 3 117
GAB1 0.023 0.083 0.18 107 -0.16 2 109
MAPK14 0.012 0.081 0.18 87 -0.13 6 93
EPO 0.045 0.015 0.083 5 -0.038 7 12
PLCG1 0.045 0.074 0.22 4 -0.22 16 20
EPOR/TRPC2/IP3 Receptors 0.04 0.019 0.082 4 -0.038 6 10
RAPGEF1 0.04 0.008 -10000 0 0 23 23
EPO/EPOR (dimer)/SOCS3 0.064 0.051 -10000 0 -0.13 16 16
GAB1/SHC/GRB2/SOS1 0.069 0.081 0.26 16 -0.16 6 22
EPO/EPOR (dimer) 0.057 0.033 -10000 0 -0.09 5 5
IRS2 0.024 0.084 0.18 111 -0.16 2 113
STAT1 0.036 0.096 0.24 4 -0.26 23 27
STAT5B 0.046 0.077 0.24 4 -0.21 20 24
cell proliferation 0.005 0.078 0.17 87 -0.14 7 94
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.061 0.16 3 -0.17 5 8
TEC 0.018 0.081 0.18 96 -0.18 8 104
SOCS3 0.037 0.014 -10000 0 0 67 67
STAT1 (dimer) 0.036 0.095 0.24 5 -0.26 23 28
JAK2 0.039 0.02 0.082 6 -0.037 4 10
PIK3R1 0.034 0.017 -10000 0 0 108 108
EPO/EPOR (dimer)/JAK2 0.07 0.07 0.24 34 -0.1 25 59
EPO/EPOR 0.057 0.033 -10000 0 -0.09 5 5
LYN 0.036 0.018 -10000 0 -0.037 9 9
TEC/VAV2 0.032 0.076 0.22 28 -0.17 11 39
elevation of cytosolic calcium ion concentration 0.04 0.019 0.082 4 -0.038 6 10
SHC1 0.04 0.01 -10000 0 0 31 31
EPO/EPOR (dimer)/LYN 0.062 0.062 -10000 0 -0.11 33 33
mol:IP3 0.044 0.073 0.22 4 -0.22 16 20
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.045 0.072 0.21 39 -0.14 4 43
SH2B3 0 0.008 0.032 11 -10000 0 11
NFKB1 0.008 0.076 0.18 70 -0.16 7 77
EPO/EPOR (dimer)/JAK2/SOCS3 0.016 0.047 0.21 2 -0.16 28 30
PTPN6 0.033 0.062 0.17 67 -0.12 7 74
TEC/VAV2/GRB2 0.051 0.086 0.23 33 -0.17 11 44
EPOR 0.04 0.019 0.083 4 -0.038 6 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.068 0.081 0.23 29 -0.16 6 35
SOS1 0.038 0.013 -10000 0 0 56 56
PLCG2 0.035 0.015 -10000 0 0 87 87
CRKL/CBL/C3G 0.072 0.077 0.23 44 -0.19 2 46
VAV2 0.022 0.083 0.18 105 -0.16 3 108
CBL 0.026 0.087 0.18 120 -0.19 2 122
SHC/Grb2/SOS1 0.038 0.057 0.17 2 -0.13 13 15
STAT5A 0.046 0.08 0.24 4 -0.22 22 26
GRB2 0.041 0.007 -10000 0 0 17 17
STAT5 (dimer) 0.063 0.092 0.28 4 -0.28 13 17
LYN/PLCgamma2 0.038 0.051 -10000 0 -0.13 36 36
PTPN11 0.04 0.009 -10000 0 0 27 27
BTK 0.024 0.085 0.18 113 -0.17 6 119
BCL2 0.028 0.12 0.36 1 -0.48 10 11
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.008 0.054 0.17 51 -0.092 3 54
BUB1B -0.024 0.082 0.12 1 -0.21 67 68
PLK1 -0.001 0.037 0.076 5 -0.099 42 47
PLK1S1 -0.001 0.021 0.044 8 -0.055 40 48
KIF2A -0.001 0.033 0.067 5 -0.09 41 46
regulation of mitotic centrosome separation -0.001 0.037 0.076 5 -0.1 41 46
GOLGA2 0.04 0.009 -10000 0 0 26 26
Hec1/SPC24 -0.01 0.025 -10000 0 -0.08 47 47
WEE1 -0.012 0.088 -10000 0 -0.33 29 29
cytokinesis -0.038 0.13 0.14 4 -0.27 111 115
PP2A-alpha B56 -0.008 0.25 -10000 0 -0.68 65 65
AURKA -0.001 0.023 0.05 9 -0.063 34 43
PICH/PLK1 -0.032 0.069 0.073 1 -0.16 106 107
CENPE -0.007 0.035 0.15 2 -0.13 20 22
RhoA/GTP 0.03 0.012 -10000 0 -0.13 3 3
positive regulation of microtubule depolymerization -0.001 0.033 0.067 5 -0.09 41 46
PPP2CA 0.04 0.009 -10000 0 0 26 26
FZR1 0.038 0.013 -10000 0 0 56 56
TPX2 -0.025 0.099 -10000 0 -0.25 89 89
PAK1 0.037 0.014 -10000 0 0 70 70
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.009 -10000 0 0 25 25
CLSPN 0.009 0.037 -10000 0 -0.26 7 7
GORASP1 0.041 0.006 -10000 0 0 10 10
metaphase 0 0.004 0.016 13 -0.013 26 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.001 0.021 0.044 8 -0.055 40 48
G2 phase of mitotic cell cycle -0.001 0.003 0.011 19 -10000 0 19
STAG2 0.039 0.01 -10000 0 0 35 35
GRASP65/GM130/RAB1/GTP 0.016 0.069 -10000 0 -0.62 5 5
spindle elongation -0.001 0.037 0.076 5 -0.1 41 46
ODF2 0.04 0.009 -10000 0 0 27 27
BUB1 -0.046 0.25 -10000 0 -0.72 65 65
TPT1 -0.002 0.051 -10000 0 -0.19 33 33
CDC25C -0.007 0.089 -10000 0 -0.33 37 37
CDC25B 0.024 0.03 -10000 0 -0.03 106 106
SGOL1 -0.008 0.054 0.093 3 -0.17 51 54
RHOA 0.041 0.007 -10000 0 0 14 14
CCNB1/CDK1 0.004 0.13 -10000 0 -0.21 122 122
CDC14B -0.01 0.005 0.011 30 -10000 0 30
CDC20 0.034 0.016 -10000 0 0 104 104
PLK1/PBIP1 -0.003 0.032 -10000 0 -0.1 33 33
mitosis -0.001 0.003 0.012 13 -0.011 7 20
FBXO5 -0.015 0.063 0.1 4 -0.16 64 68
CDC2 0.028 0.022 -10000 0 -0.029 16 16
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.054 -10000 0 -0.25 20 20
ERCC6L -0.03 0.098 -10000 0 -0.2 119 119
NLP/gamma Tubulin -0.001 0.032 0.066 3 -0.087 47 50
microtubule cytoskeleton organization -0.002 0.051 -10000 0 -0.19 33 33
G2/M transition DNA damage checkpoint 0 0.003 0.011 13 -10000 0 13
PPP1R12A 0.04 0.01 -10000 0 0 31 31
interphase 0 0.003 0.011 13 -10000 0 13
PLK1/PRC1-2 0.014 0.083 -10000 0 -0.16 84 84
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.06 -10000 0 -0.12 33 33
RAB1A 0.04 0.009 -10000 0 0 29 29
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.026 0.058 13 -0.067 39 52
mitotic prometaphase -0.001 0.004 0.019 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.066 -10000 0 -0.23 25 25
microtubule-based process 0.014 0.052 -10000 0 -0.14 36 36
Golgi organization -0.001 0.037 0.076 5 -0.1 41 46
Cohesin/SA2 0.014 0.047 0.11 1 -0.098 59 60
PPP1CB/MYPT1 0.05 0.042 -10000 0 -0.14 23 23
KIF20A 0.032 0.018 -10000 0 0 133 133
APC/C/CDC20 0.017 0.051 0.098 1 -0.13 39 40
PPP2R1A 0.039 0.011 -10000 0 0 42 42
chromosome segregation -0.003 0.032 -10000 0 -0.1 33 33
PRC1 0.036 0.015 -10000 0 0 82 82
ECT2 0.037 0.12 0.21 140 -0.16 44 184
C13orf34 0 0.029 0.065 8 -0.077 39 47
NUDC 0.002 0.054 -10000 0 -0.25 20 20
regulation of attachment of spindle microtubules to kinetochore -0.024 0.081 0.12 1 -0.21 67 68
spindle assembly -0.001 0.034 0.07 11 -0.092 39 50
spindle stabilization -0.001 0.021 0.043 8 -0.055 40 48
APC/C/HCDH1 0.032 0.012 -10000 0 -10000 0 0
MKLP2/PLK1 0.014 0.052 -10000 0 -0.14 36 36
CCNB1 0.026 0.027 -10000 0 -0.03 63 63
PPP1CB 0.04 0.01 -10000 0 0 33 33
BTRC 0.04 0.008 -10000 0 0 21 21
ROCK2 -0.006 0.095 -10000 0 -0.32 41 41
TUBG1 -0.002 0.054 -10000 0 -0.2 33 33
G2/M transition of mitotic cell cycle -0.035 0.1 0.13 16 -0.21 114 130
MLF1IP -0.008 0.007 0.011 50 -10000 0 50
INCENP 0.041 0.005 -10000 0 0 5 5
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.003 0.07 -10000 0 -0.19 53 53
epithelial cell differentiation 0.056 0.069 -10000 0 -0.13 51 51
CYFIP2 0.038 0.012 -10000 0 0 47 47
ENAH -0.033 0.071 0.22 13 -0.22 4 17
EGFR 0.037 0.014 -10000 0 0 72 72
EPHA2 0.039 0.01 -10000 0 0 35 35
MYO6 -0.03 0.048 0.18 7 -0.21 17 24
CTNNB1 0.04 0.01 -10000 0 0 31 31
ABI1/Sra1/Nap1 0.061 0.059 -10000 0 -0.12 41 41
AQP5 -0.076 0.14 0.18 4 -0.37 97 101
CTNND1 0.041 0.007 -10000 0 0 17 17
mol:PI-4-5-P2 -0.03 0.043 0.18 6 -0.2 12 18
regulation of calcium-dependent cell-cell adhesion -0.028 0.043 0.18 6 -0.2 12 18
EGF 0.038 0.012 -10000 0 0 53 53
NCKAP1 0.04 0.01 -10000 0 0 31 31
AQP3 -0.024 0.058 0.18 4 -0.29 15 19
cortical microtubule organization 0.056 0.069 -10000 0 -0.13 51 51
GO:0000145 -0.03 0.039 0.16 6 -0.19 12 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.072 -10000 0 -0.13 51 51
MLLT4 0.034 0.017 -10000 0 0 107 107
ARF6/GDP -0.05 0.046 -10000 0 -0.2 23 23
ARF6 0.041 0.008 -10000 0 0 19 19
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.077 -10000 0 -0.12 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.048 0.2 4 -0.21 15 19
PVRL2 0.039 0.011 -10000 0 0 44 44
ZYX -0.028 0.039 0.18 5 -0.2 8 13
ARF6/GTP 0.066 0.083 -10000 0 -0.12 62 62
CDH1 0.035 0.016 -10000 0 0 98 98
EGFR/EGFR/EGF/EGF 0.037 0.075 -10000 0 -0.13 66 66
RhoA/GDP 0.056 0.072 -10000 0 -0.13 50 50
actin cytoskeleton organization -0.032 0.048 0.16 6 -0.23 16 22
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
GIT1 0.04 0.009 -10000 0 0 27 27
IGF1R 0.033 0.017 -10000 0 0 118 118
IGF1 0.036 0.015 -10000 0 0 84 84
DIAPH1 -0.002 0.22 -10000 0 -0.57 63 63
Wnt receptor signaling pathway -0.056 0.069 0.13 51 -10000 0 51
RHOA 0.041 0.007 -10000 0 0 14 14
RhoA/GTP -0.049 0.045 -10000 0 -0.19 22 22
CTNNA1 0.039 0.011 -10000 0 0 38 38
VCL -0.033 0.049 0.16 6 -0.24 16 22
EFNA1 0.034 0.017 -10000 0 0 107 107
LPP -0.029 0.044 0.17 6 -0.2 14 20
Ephrin A1/EPHA2 0.032 0.077 -10000 0 -0.13 74 74
SEC6/SEC8 -0.045 0.043 -10000 0 -0.19 21 21
MGAT3 -0.029 0.044 0.18 6 -0.2 12 18
HGF/MET 0.016 0.087 -10000 0 -0.13 113 113
HGF 0.04 0.009 -10000 0 0 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.003 0.07 -10000 0 -0.19 53 53
actin cable formation 0.002 0.097 0.25 28 -0.25 14 42
KIAA1543 -0.033 0.043 0.17 6 -0.2 13 19
KIFC3 -0.032 0.041 0.18 5 -0.2 12 17
NCK1 0.036 0.015 -10000 0 0 80 80
EXOC3 0.041 0.005 -10000 0 0 8 8
ACTN1 -0.031 0.049 0.18 7 -0.22 16 23
NCK1/GIT1 0.044 0.047 -10000 0 -0.14 30 30
mol:GDP 0.056 0.069 -10000 0 -0.13 51 51
EXOC4 0.038 0.012 -10000 0 0 49 49
STX4 -0.029 0.034 -10000 0 -0.12 49 49
PIP5K1C -0.031 0.043 0.18 6 -0.2 12 18
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 26 26
ROCK1 -0.026 0.085 0.26 12 -0.23 4 16
adherens junction assembly -0.05 0.13 -10000 0 -0.4 42 42
IGF-1R heterotetramer/IGF1 0.023 0.083 -10000 0 -0.13 94 94
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
MET 0.027 0.02 -10000 0 0 198 198
PLEKHA7 -0.031 0.045 0.18 7 -0.2 14 21
mol:GTP 0.058 0.075 -10000 0 -0.12 61 61
establishment of epithelial cell apical/basal polarity -0.038 0.056 0.14 25 -0.2 16 41
cortical actin cytoskeleton stabilization 0.003 0.07 -10000 0 -0.19 53 53
regulation of cell-cell adhesion -0.032 0.048 0.16 6 -0.23 16 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.003 0.07 -10000 0 -0.19 53 53
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.038 0.012 -10000 0 0 54 54
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.04 0.008 -10000 0 0 23 23
TCEB1 0.038 0.012 -10000 0 0 50 50
HIF1A/p53 0 0.086 0.22 1 -0.25 41 42
HIF1A -0.001 0.072 0.16 3 -0.25 29 32
COPS5 0.036 0.015 -10000 0 0 86 86
VHL/Elongin B/Elongin C/RBX1/CUL2 0.086 0.071 -10000 0 -0.12 26 26
FIH (dimer) 0.04 0.009 -10000 0 0 25 25
CDKN2A 0.029 0.019 -10000 0 0 175 175
ARNT/IPAS 0.054 0.025 -10000 0 -0.14 4 4
HIF1AN 0.04 0.009 -10000 0 0 25 25
GNB2L1 0.041 0.005 -10000 0 0 7 7
HIF1A/ARNT 0.015 0.085 0.22 1 -0.24 35 36
CUL2 0.039 0.01 -10000 0 0 36 36
OS9 0.039 0.011 -10000 0 0 38 38
RACK1/Elongin B/Elongin C 0.071 0.038 -10000 0 -0.12 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.005 0.073 0.15 3 -0.26 27 30
PHD1-3/OS9 0.053 0.08 -10000 0 -0.11 86 86
HIF1A/RACK1/Elongin B/Elongin C 0.048 0.09 -10000 0 -0.26 27 27
VHL 0.04 0.009 -10000 0 0 28 28
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 0.012 0.08 0.22 1 -0.25 31 32
EGLN3 0.028 0.02 -10000 0 0 187 187
EGLN2 0.04 0.009 -10000 0 0 29 29
EGLN1 0.039 0.01 -10000 0 0 36 36
TP53 0.026 0.02 -10000 0 0 213 213
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.12 -10000 0 -0.53 24 24
ARNT 0.041 0.006 -10000 0 0 12 12
ARD1A 0.04 0.01 -10000 0 0 31 31
RBX1 0.037 0.014 -10000 0 0 71 71
HIF1A/p19ARF 0.004 0.085 -10000 0 -0.27 33 33
Regulation of Telomerase

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
Telomerase catalytic core complex -0.03 0.18 -10000 0 -0.51 26 26
RAD9A 0.042 0.004 -10000 0 0 6 6
AP1 0.002 0.084 -10000 0 -0.15 115 115
IFNAR2 0.03 0.027 -10000 0 -0.033 70 70
AKT1 0.013 0.038 -10000 0 -0.15 6 6
ER alpha/Oestrogen 0.013 0.044 -10000 0 -0.13 44 44
NFX1/SIN3/HDAC complex 0.001 0.084 0.17 5 -0.26 32 37
EGF 0.038 0.013 -10000 0 0 53 53
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.045 0.043 -10000 0 -0.13 6 6
TERT/c-Abl -0.019 0.18 -10000 0 -0.48 28 28
SAP18 0.039 0.01 -10000 0 0 34 34
MRN complex 0.048 0.071 -10000 0 -0.15 50 50
WT1 0.029 0.027 -10000 0 -0.033 68 68
WRN 0.033 0.017 -10000 0 0 124 124
SP1 0.032 0.031 -10000 0 -0.041 79 79
SP3 0.041 0.008 -10000 0 -0.002 14 14
TERF2IP 0.036 0.014 -10000 0 0 75 75
Telomerase/Nucleolin -0.018 0.18 -10000 0 -0.44 37 37
Mad/Max 0.055 0.024 -10000 0 -10000 0 0
TERT -0.032 0.18 -10000 0 -0.52 25 25
CCND1 -0.11 0.37 -10000 0 -0.97 81 81
MAX 0.04 0.009 -10000 0 -0.003 18 18
RBBP7 0.04 0.009 -10000 0 0 26 26
RBBP4 0.038 0.012 -10000 0 0 46 46
TERF2 0.035 0.021 0.095 44 0 79 123
PTGES3 0.038 0.013 -10000 0 0 56 56
SIN3A 0.04 0.009 -10000 0 0 28 28
Telomerase/911 0.024 0.081 -10000 0 -0.29 21 21
CDKN1B -0.002 0.083 0.2 4 -0.33 22 26
RAD1 0.038 0.013 -10000 0 0 57 57
XRCC5 0.039 0.011 -10000 0 0 39 39
XRCC6 0.037 0.014 -10000 0 0 70 70
SAP30 0.038 0.013 -10000 0 0 55 55
TRF2/PARP2 0.049 0.035 -10000 0 -0.13 9 9
UBE3A 0.041 0.006 -10000 0 0 7 7
JUN 0.036 0.015 -10000 0 0 81 81
E6 0 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.023 0.027 -10000 0 -0.051 30 30
FOS 0.026 0.021 -10000 0 0 210 210
IFN-gamma/IRF1 0.025 0.082 -10000 0 -0.16 81 81
PARP2 0.04 0.009 -10000 0 0 30 30
BLM 0.037 0.014 -10000 0 0 67 67
Telomerase 0.004 0.061 -10000 0 -0.26 18 18
IRF1 0.029 0.041 0.11 1 -0.14 21 22
ESR1 0.035 0.016 -10000 0 0 92 92
KU/TER 0.043 0.054 -10000 0 -0.16 31 31
ATM/TRF2 0.037 0.056 -10000 0 -0.14 41 41
ubiquitin-dependent protein catabolic process 0.004 0.084 0.18 5 -0.27 26 31
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.004 0.085 0.18 5 -0.28 25 30
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.03 0.03 -10000 0 -0.04 74 74
ATM 0.009 0.066 -10000 0 -0.24 32 32
SMAD3 -0.013 0.016 0.025 70 -10000 0 70
ABL1 0.039 0.011 -10000 0 0 41 41
MXD1 0.04 0.009 -10000 0 -0.002 19 19
MRE11A 0.038 0.012 -10000 0 0 54 54
HUS1 0.04 0.008 -10000 0 0 20 20
RPS6KB1 0.039 0.011 -10000 0 0 38 38
TERT/NF kappa B1/14-3-3 -0.008 0.19 -10000 0 -0.51 22 22
NR2F2 0.04 0.013 -10000 0 0 38 38
MAPK3 -0.016 0.015 0.022 51 -0.041 1 52
MAPK1 -0.015 0.015 0.022 47 -0.041 1 48
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 62 62
NFKB1 0.036 0.015 -10000 0 0 84 84
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.065 -10000 0 -0.24 32 32
NBN 0.035 0.016 -10000 0 0 96 96
EGFR 0.036 0.014 -10000 0 0 72 72
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.04 0.052 -10000 0 -0.14 37 37
MYC 0.022 0.021 -10000 0 0 268 268
IL2 0.03 0.031 -10000 0 -0.042 74 74
KU 0.043 0.054 -10000 0 -0.16 31 31
RAD50 0.039 0.011 -10000 0 0 42 42
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.037 0.013 -10000 0 0 62 62
TRF2/BLM 0.043 0.044 -10000 0 -0.13 21 21
FRAP1 0.04 0.009 -10000 0 0 27 27
KU/TERT -0.012 0.19 -10000 0 -0.48 29 29
SP1/HDAC2 0.043 0.05 -10000 0 -0.11 16 16
PINX1 0.033 0.017 -10000 0 0 123 123
Telomerase/EST1A -0.025 0.17 -10000 0 -0.44 34 34
Smad3/Myc 0.015 0.038 -10000 0 -0.15 19 19
911 complex 0.071 0.037 -10000 0 -0.12 9 9
IFNG 0.034 0.036 0.11 2 -0.11 26 28
Telomerase/PinX1 -0.025 0.17 -10000 0 -0.44 34 34
Telomerase/AKT1/mTOR/p70S6K -0.001 0.1 -10000 0 -0.31 32 32
SIN3B 0.037 0.013 -10000 0 0 65 65
YWHAE 0.038 0.013 -10000 0 0 58 58
Telomerase/EST1B -0.025 0.17 -10000 0 -0.44 34 34
response to DNA damage stimulus 0.001 0.035 0.063 3 -0.11 49 52
MRN complex/TRF2/Rap1 0.065 0.081 -10000 0 -0.14 38 38
TRF2/WRN 0.038 0.041 -10000 0 -0.11 21 21
Telomerase/hnRNP C1/C2 -0.025 0.17 -10000 0 -0.44 34 34
E2F1 0.031 0.027 -10000 0 -0.033 69 69
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.04 0.009 -10000 0 0 30 30
DKC1 0.04 0.008 -10000 0 0 20 20
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.007 -10000 0 -10000 0 0
SMARCC1 -0.014 0.18 -10000 0 -1.1 14 14
REL 0.04 0.008 -10000 0 0 20 20
HDAC7 -0.045 0.093 0.21 7 -0.22 66 73
JUN 0.036 0.015 -10000 0 0 80 80
EP300 0.037 0.014 -10000 0 0 73 73
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.012 0.022 0.063 15 -10000 0 15
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.002 0.12 0.28 6 -0.22 80 86
MAP2K6 0.029 0.025 -10000 0 -0.034 48 48
BRM/BAF57 0.032 0.059 -10000 0 -0.13 53 53
MAP2K4 0.032 0.024 -10000 0 -0.034 45 45
SMARCA2 0.032 0.018 -10000 0 0 135 135
PDE9A -0.081 0.32 -10000 0 -0.83 82 82
NCOA2 0.037 0.014 -10000 0 0 71 71
CEBPA 0.037 0.014 -10000 0 0 67 67
EHMT2 0.041 0.007 -10000 0 0 18 18
cell proliferation -0.014 0.12 0.29 12 -0.3 34 46
NR0B1 0.039 0.011 -10000 0 0 38 38
EGR1 0.028 0.02 -10000 0 0 194 194
RXRs/9cRA 0.064 0.035 -10000 0 -0.1 3 3
AR/RACK1/Src -0.013 0.094 0.21 31 -0.22 20 51
AR/GR -0.012 0.093 0.23 1 -0.19 85 86
GNB2L1 0.042 0.005 -10000 0 0 7 7
PKN1 0.035 0.016 -10000 0 0 99 99
RCHY1 0.037 0.014 -10000 0 0 72 72
epidermal growth factor receptor activity 0 0 0.003 1 -10000 0 1
MAPK8 -0.013 0.021 0.051 7 -0.059 1 8
T-DHT/AR/TIF2/CARM1 0.004 0.088 0.25 5 -0.21 23 28
SRC -0.015 0.068 0.17 45 -0.16 7 52
NR3C1 0.039 0.012 -10000 0 0 46 46
KLK3 0.005 0.072 -10000 0 -10000 0 0
APPBP2 0.031 0.026 -10000 0 -0.034 65 65
TRIM24 0.039 0.012 -10000 0 0 44 44
T-DHT/AR/TIP60 -0.035 0.059 0.088 4 -0.16 59 63
TMPRSS2 0.016 0.11 -10000 0 -0.58 11 11
RXRG 0.036 0.015 -10000 0 0 86 86
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.04 0.01 -10000 0 0 33 33
RXRB 0.041 0.007 -10000 0 0 17 17
CARM1 0.037 0.014 -10000 0 0 69 69
NR2C2 0.041 0.007 -10000 0 0 16 16
KLK2 0 0.077 0.26 1 -0.29 5 6
AR -0.019 0.079 0.15 12 -0.19 73 85
SENP1 0.039 0.01 -10000 0 0 35 35
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.038 0.01 -10000 0 0 35 35
SRY 0.041 0.002 -10000 0 0 2 2
GATA2 0.039 0.01 -10000 0 0 35 35
MYST2 0.04 0.009 -10000 0 0 27 27
HOXB13 0.04 0.011 -10000 0 0 38 38
T-DHT/AR/RACK1/Src -0.016 0.097 0.22 33 -0.23 22 55
positive regulation of transcription 0.039 0.01 -10000 0 0 35 35
DNAJA1 0.031 0.026 -10000 0 -0.034 64 64
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.089 0.17 21 -0.26 49 70
NCOA1 0.041 0.035 0.12 3 -0.18 12 15
SPDEF 0.038 0.015 -10000 0 0 72 72
T-DHT/AR/TIF2 -0.012 0.095 0.2 9 -0.25 43 52
T-DHT/AR/Hsp90 -0.035 0.059 0.088 4 -0.16 59 63
GSK3B 0.04 0.009 -10000 0 0 26 26
NR2C1 0.039 0.011 -10000 0 0 41 41
mol:T-DHT -0.023 0.052 0.19 13 -0.16 7 20
SIRT1 0.041 0.008 -10000 0 0 20 20
ZMIZ2 -0.001 0.001 -10000 0 -0.012 2 2
POU2F1 0.034 0.056 0.12 4 -0.1 73 77
T-DHT/AR/DAX-1 -0.02 0.082 0.2 16 -0.22 22 38
CREBBP 0.038 0.012 -10000 0 0 54 54
SMARCE1 0.039 0.011 -10000 0 0 43 43
Canonical NF-kappaB 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
FBXW11 0.036 0.028 0.091 2 -0.07 31 33
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.13 0.24 4 -0.28 61 65
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.015 0.041 -10000 0 -0.13 41 41
NFKBIA -0.036 0.067 0.25 3 -0.27 32 35
BIRC2 0.036 0.014 -10000 0 0 75 75
IKBKB 0.039 0.011 -10000 0 0 44 44
RIPK2 0.033 0.017 -10000 0 0 125 125
IKBKG -0.005 0.11 -10000 0 -0.3 48 48
IKK complex/A20 0.033 0.12 -10000 0 -0.32 29 29
NEMO/A20/RIP2 0.033 0.017 -10000 0 0 125 125
XPO1 0.039 0.011 -10000 0 0 39 39
NEMO/ATM 0.003 0.13 -10000 0 -0.35 39 39
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
Exportin 1/RanGTP 0.047 0.035 -10000 0 -0.11 24 24
IKK complex/ELKS 0.006 0.11 -10000 0 -0.32 36 36
BCL10/MALT1/TRAF6 0.065 0.047 -10000 0 -0.12 20 20
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.032 0.028 0.084 1 -0.072 26 27
RELA 0.036 0.028 0.097 1 -0.069 34 35
MALT1 0.036 0.014 -10000 0 0 76 76
cIAP1/UbcH5C 0.04 0.053 -10000 0 -0.14 38 38
ATM 0.036 0.014 -10000 0 0 73 73
TNF/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
TRAF6 0.04 0.008 -10000 0 0 22 22
PRKCA 0.035 0.015 -10000 0 0 90 90
CHUK 0.038 0.012 -10000 0 0 52 52
UBE2D3 0.038 0.012 -10000 0 0 48 48
TNF 0.04 0.009 -10000 0 0 26 26
NF kappa B1 p50/RelA 0.057 0.082 -10000 0 -0.15 62 62
BCL10 0.041 0.006 -10000 0 0 11 11
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.066 0.25 3 -0.27 32 35
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.028 0.087 3 -0.07 31 34
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
IKK complex 0.019 0.13 -10000 0 -0.34 35 35
CYLD 0.038 0.012 -10000 0 0 51 51
IKK complex/PKC alpha 0.023 0.13 -10000 0 -0.33 37 37
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.046 0.051 -10000 0 -0.14 35 35
Necdin/E2F1 0.045 0.041 -10000 0 -0.14 17 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.072 0.061 -10000 0 -0.11 42 42
NGF (dimer)/p75(NTR)/BEX1 0.022 0.053 -10000 0 -0.11 63 63
NT-4/5 (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
IKBKB 0.039 0.011 -10000 0 0 44 44
AKT1 0.016 0.09 0.19 101 -0.18 6 107
IKBKG 0.042 0.003 -10000 0 0 2 2
BDNF 0.04 0.008 -10000 0 0 23 23
MGDIs/NGR/p75(NTR)/LINGO1 0.049 0.022 -10000 0 -0.11 3 3
FURIN 0.04 0.01 -10000 0 0 32 32
proBDNF (dimer)/p75(NTR)/Sortilin 0.066 0.049 -10000 0 -0.12 26 26
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.02 0.071 -10000 0 -0.13 79 79
proBDNF (dimer) 0.04 0.008 -10000 0 0 23 23
NTRK1 0.039 0.01 -10000 0 0 35 35
RTN4R 0.038 0.012 -10000 0 0 54 54
neuron apoptosis -0.059 0.13 0.36 1 -0.38 46 47
IRAK1 0.041 0.007 -10000 0 0 18 18
SHC1 0.017 0.01 0.069 8 -0.11 1 9
ARHGDIA 0.038 0.012 -10000 0 0 55 55
RhoA/GTP 0.03 0.012 -10000 0 -0.13 3 3
Gamma Secretase 0.073 0.087 -10000 0 -0.12 66 66
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.055 0.058 -10000 0 -0.11 51 51
MAGEH1 0.039 0.011 -10000 0 0 45 45
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.054 0.054 -10000 0 -0.1 41 41
Mammalian IAPs/DIABLO 0.012 0.089 -10000 0 -0.13 132 132
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.04 0.009 -10000 0 0 26 26
APP 0.038 0.012 -10000 0 0 51 51
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.042 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.047 0.027 0.19 1 -0.11 7 8
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.041 0.2 3 -10000 0 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.062 -10000 0 -0.16 52 52
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.05 0.023 -10000 0 -0.11 7 7
NCSTN 0.04 0.009 -10000 0 0 24 24
mol:GTP 0.045 0.035 -10000 0 -0.11 23 23
PSENEN 0.035 0.016 -10000 0 0 92 92
mol:ceramide -0.021 0.028 0.19 3 -10000 0 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.091 -10000 0 -0.33 20 20
p75(NTR)/beta APP 0.047 0.045 -10000 0 -0.14 28 28
BEX1 0.027 0.02 -10000 0 0 205 205
mol:GDP -0.008 0.004 -10000 0 -0.1 1 1
NGF (dimer) -0.004 0.075 -10000 0 -0.1 173 173
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.064 0.037 -10000 0 -0.11 8 8
PIK3R1 0.034 0.017 -10000 0 0 108 108
RAC1/GTP 0.044 0.016 -10000 0 -0.06 2 2
MYD88 0.041 0.007 -10000 0 0 14 14
CHUK 0.038 0.012 -10000 0 0 52 52
NGF (dimer)/p75(NTR)/PKA 0.045 0.035 -10000 0 -0.11 23 23
RHOB 0.04 0.008 -10000 0 0 21 21
RHOA 0.041 0.007 -10000 0 0 14 14
MAGE-G1/E2F1 0.053 0.025 -10000 0 -0.14 2 2
NT3 (dimer) 0.031 0.018 -10000 0 0 147 147
TP53 -0.023 0.048 0.21 9 -0.18 13 22
PRDM4 -0.022 0.028 0.19 3 -10000 0 3
BDNF (dimer) 0.019 0.091 -10000 0 -0.11 166 166
PIK3CA 0.03 0.019 -10000 0 0 155 155
SORT1 0.039 0.012 -10000 0 0 46 46
activation of caspase activity 0.065 0.057 -10000 0 -0.11 42 42
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.062 0.049 -10000 0 -0.11 33 33
RHOC 0.041 0.006 -10000 0 0 12 12
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.016 0.057 0.24 5 -0.2 15 20
DIABLO 0.037 0.013 -10000 0 0 63 63
SMPD2 -0.021 0.028 0.19 3 -10000 0 3
APH1B 0.036 0.015 -10000 0 0 83 83
APH1A 0.041 0.006 -10000 0 0 10 10
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.038 -10000 0 -0.11 27 27
PSEN1 0.039 0.01 -10000 0 0 35 35
APAF-1/Pro-Caspase 9 0.051 0.041 -10000 0 -0.15 19 19
NT3 (dimer)/p75(NTR) 0.041 0.037 -10000 0 -0.14 10 10
MAPK8 -0.02 0.064 0.25 6 -0.23 13 19
MAPK9 -0.02 0.061 0.24 5 -0.23 10 15
APAF1 0.04 0.01 -10000 0 0 32 32
NTF3 0.031 0.018 -10000 0 0 147 147
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.036 0.014 -10000 0 0 77 77
RAC1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA-B-C/GDP 0.074 0.05 -10000 0 -0.1 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.075 0.076 -10000 0 -0.13 57 57
RhoA-B-C/GTP 0.044 0.034 -10000 0 -0.1 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.099 0.065 -10000 0 -0.11 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.084 0.059 -10000 0 -0.12 32 32
PRKACB 0.038 0.012 -10000 0 0 48 48
proBDNF (dimer)/p75 ECD 0.046 0.047 -10000 0 -0.14 31 31
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.02 -10000 0 0 218 218
BIRC2 0.036 0.014 -10000 0 0 75 75
neuron projection morphogenesis -0.019 0.05 0.15 4 -0.16 25 29
BAD -0.024 0.068 0.26 4 -0.21 26 30
RIPK2 0.033 0.017 -10000 0 0 125 125
NGFR 0.04 0.009 -10000 0 0 28 28
CYCS -0.026 0.033 0.19 2 -0.18 5 7
ADAM17 0.038 0.013 -10000 0 0 57 57
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.05 0.056 -10000 0 -0.1 45 45
BCL2L11 -0.025 0.068 0.26 4 -0.21 26 30
BDNF (dimer)/p75(NTR) 0.057 0.019 -10000 0 -0.14 1 1
PI3K 0.035 0.06 -10000 0 -0.12 48 48
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.061 0.047 -10000 0 -0.1 28 28
NDNL2 0.039 0.011 -10000 0 0 39 39
YWHAE 0.038 0.013 -10000 0 0 58 58
PRKCI 0.027 0.02 -10000 0 0 197 197
NGF (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.06 0.053 -10000 0 -0.11 40 40
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCZ 0.042 0 -10000 0 -10000 0 0
PLG 0.038 0.012 -10000 0 0 49 49
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.045 0.16 6 -0.16 26 32
SQSTM1 0.038 0.012 -10000 0 0 49 49
NGFRAP1 0.041 0.007 -10000 0 0 16 16
CASP3 -0.027 0.072 0.26 4 -0.23 28 32
E2F1 0.038 0.012 -10000 0 0 49 49
CASP9 0.04 0.009 -10000 0 0 26 26
IKK complex 0.046 0.099 -10000 0 -0.26 20 20
NGF (dimer)/TRKA 0.029 0.007 -10000 0 -10000 0 0
MMP7 0.016 0.02 -10000 0 0 340 340
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.054 -10000 0 -0.11 33 33
MMP3 0.038 0.013 -10000 0 0 59 59
APAF-1/Caspase 9 -0.056 0.061 -10000 0 -0.2 51 51
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.038 0.19 0.35 2 -0.98 21 23
VDR 0.038 0.013 -10000 0 0 56 56
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.023 0.091 -10000 0 -0.23 52 52
RXRs/LXRs/DNA/Oxysterols 0.016 0.13 -10000 0 -0.34 55 55
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.016 0.057 1 -0.047 50 51
RARs/THRs/DNA/Src-1 -0.004 0.095 -10000 0 -0.18 113 113
RXRs/NUR77 0.079 0.072 0.3 1 -0.11 38 39
RXRs/PPAR 0.026 0.056 -10000 0 -0.16 13 13
NCOR2 0.04 0.009 -10000 0 0 28 28
VDR/VDR/Vit D3 0.023 0.031 -10000 0 -0.13 22 22
RARs/VDR/DNA/Vit D3 0.064 0.069 -10000 0 -0.11 59 59
RARA 0.039 0.01 -10000 0 0 35 35
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.038 0.013 -10000 0 0 56 56
RARs/RARs/DNA/9cRA 0.052 0.053 -10000 0 -0.1 46 46
RARG 0.04 0.009 -10000 0 0 27 27
RPS6KB1 -0.018 0.1 0.56 5 -0.42 22 27
RARs/THRs/DNA/SMRT -0.003 0.09 -10000 0 -0.23 39 39
THRA 0.039 0.011 -10000 0 0 40 40
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.031 -10000 0 -0.13 22 22
RXRs/PPAR/9cRA/PGJ2/DNA 0.071 0.077 0.31 12 -0.15 33 45
NR1H4 0.041 0.007 -10000 0 0 16 16
RXRs/LXRs/DNA 0.095 0.1 0.32 1 -0.19 35 36
NR1H2 0.034 0.032 -10000 0 -0.059 52 52
NR1H3 0.035 0.034 -10000 0 -0.065 54 54
RXRs/VDR/DNA/Vit D3 0.072 0.071 0.28 1 -0.11 43 44
NR4A1 0.034 0.016 -10000 0 0 103 103
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.023 0.042 0.14 3 -0.14 9 12
RXRG 0.032 0.031 0.1 1 -0.055 44 45
RXR alpha/CCPG 0.026 0.022 -10000 0 -0.039 42 42
RXRA 0.035 0.031 0.1 1 -0.057 50 51
RXRB 0.036 0.034 0.1 1 -0.062 56 57
THRB 0.034 0.017 -10000 0 0 108 108
PPARG 0.039 0.01 -10000 0 0 37 37
PPARD 0.04 0.008 -10000 0 0 21 21
TNF 0.008 0.13 -10000 0 -0.5 10 10
mol:Oxysterols 0 0.015 0.027 1 -0.041 59 60
cholesterol transport 0.016 0.13 -10000 0 -0.34 55 55
PPARA 0.034 0.016 -10000 0 0 104 104
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.036 0.015 -10000 0 0 80 80
RXRs/NUR77/BCL2 0.021 0.047 -10000 0 -0.14 22 22
SREBF1 0.007 0.12 -10000 0 -0.51 9 9
RXRs/RXRs/DNA/9cRA 0.071 0.077 0.31 12 -0.15 33 45
ABCA1 -0.035 0.26 -10000 0 -0.79 56 56
RARs/THRs 0.07 0.092 -10000 0 -0.12 82 82
RXRs/FXR 0.088 0.068 0.3 1 -0.11 30 31
BCL2 0.036 0.014 -10000 0 0 76 76
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.049 0.023 -10000 0 -0.11 5 5
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.038 0.012 -10000 0 0 48 48
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.016 -10000 0 0 100 100
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.037 0.013 -10000 0 0 61 61
RAC1-CDC42/GTP/PAK family 0.007 0.049 -10000 0 -0.15 34 34
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.038 0.013 -10000 0 0 57 57
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.041 0.007 -10000 0 0 17 17
FYN 0.034 0.016 -10000 0 0 103 103
MAP3K12 0.041 0.007 -10000 0 0 14 14
FGR 0.041 0.007 -10000 0 0 17 17
p38 alpha/TAB1 0.002 0.12 0.2 1 -0.26 54 55
PRKG1 0.04 0.009 -10000 0 0 29 29
DUSP8 0.04 0.009 -10000 0 0 28 28
PGK/cGMP/p38 alpha -0.003 0.11 0.18 1 -0.26 55 56
apoptosis 0.001 0.11 0.19 1 -0.25 55 56
RAL/GTP 0.046 0.037 -10000 0 -0.12 25 25
LYN 0.036 0.015 -10000 0 0 83 83
DUSP1 0.027 0.02 -10000 0 0 206 206
PAK1 0.037 0.014 -10000 0 0 70 70
SRC 0.039 0.01 -10000 0 0 36 36
RAC1/OSM/MEKK3/MKK3 0.091 0.04 -10000 0 -0.11 1 1
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 0.039 0.01 -10000 0 0 34 34
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.041 0.007 -10000 0 0 17 17
RAC1-CDC42/GTP 0.05 0.023 -10000 0 -0.13 4 4
MAPK11 -0.028 0.12 0.2 2 -0.28 69 71
BLK 0.033 0.017 -10000 0 0 117 117
HCK 0.036 0.015 -10000 0 0 80 80
MAP2K3 0.038 0.012 -10000 0 0 47 47
DUSP16 0.036 0.015 -10000 0 0 86 86
DUSP10 0.034 0.017 -10000 0 0 109 109
TRAF6/MEKK3 0.049 0.021 -10000 0 -0.099 7 7
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
MAPK14 -0.011 0.12 0.19 3 -0.27 60 63
positive regulation of innate immune response -0.024 0.14 0.23 2 -0.33 62 64
LCK 0.04 0.009 -10000 0 0 29 29
p38alpha-beta/MKP7 -0.013 0.14 0.24 2 -0.32 56 58
p38alpha-beta/MKP5 -0.018 0.14 0.24 2 -0.32 61 63
PGK/cGMP 0.029 0.007 -10000 0 -10000 0 0
PAK2 0.04 0.009 -10000 0 0 25 25
p38alpha-beta/MKP1 -0.029 0.14 0.25 1 -0.32 64 65
CDC42 0.04 0.009 -10000 0 0 24 24
RALB 0.04 0.009 -10000 0 0 26 26
RALA 0.04 0.009 -10000 0 0 30 30
PAK3 0.037 0.013 -10000 0 0 62 62
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.013 0.01 0.016 28 -10000 0 28
RAS family/GTP 0.017 0.1 0.26 2 -0.22 29 31
NFATC4 -0.017 0.082 0.25 20 -0.18 4 24
ERBB2IP 0.036 0.015 -10000 0 -0.002 74 74
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.079 0.18 8 -0.16 58 66
JUN 0.009 0.086 0.21 5 -10000 0 5
HRAS 0.04 0.01 -10000 0 0 31 31
DOCK7 -0.024 0.082 0.24 12 -0.21 10 22
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.037 0.08 0.21 27 -0.12 70 97
AKT1 -0.005 0.012 0.021 29 -10000 0 29
BAD -0.015 0.007 0.012 13 -10000 0 13
MAPK10 -0.008 0.07 0.2 24 -0.14 4 28
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.085 0.2 2 -0.16 58 60
RAF1 0.008 0.11 0.26 26 -0.23 30 56
ErbB2/ErbB3/neuregulin 2 0.028 0.074 0.19 36 -0.12 76 112
STAT3 -0.027 0.25 -10000 0 -0.91 42 42
cell migration -0.008 0.073 0.22 24 -0.18 8 32
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.029 0.24 0.42 2 -0.56 54 56
FOS -0.033 0.22 0.36 5 -0.4 127 132
NRAS 0.04 0.01 -10000 0 0 30 30
mol:Ca2+ -0.001 0.079 0.18 8 -0.16 58 66
MAPK3 -0.01 0.19 0.36 5 -0.47 45 50
MAPK1 -0.024 0.2 0.37 4 -0.5 48 52
JAK2 -0.022 0.079 0.25 9 -0.24 6 15
NF2 0.004 0.075 -10000 0 -0.7 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.073 0.18 3 -0.17 69 72
NRG1 0.035 0.016 -10000 0 0 93 93
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
MAPK8 -0.019 0.11 0.22 5 -0.22 76 81
MAPK9 -0.011 0.071 0.2 23 -0.16 5 28
ERBB2 -0.024 0.041 0.26 10 -10000 0 10
ERBB3 0.033 0.018 -10000 0 0 124 124
SHC1 0.04 0.01 -10000 0 0 31 31
RAC1 0.039 0.01 -10000 0 0 34 34
apoptosis 0.005 0.027 0.18 1 -0.21 7 8
STAT3 (dimer) -0.023 0.25 -10000 0 -0.88 42 42
RNF41 -0.017 0.016 0.047 11 -0.12 3 14
FRAP1 -0.014 0.007 0.012 13 -10000 0 13
RAC1-CDC42/GTP -0.03 0.056 0.09 20 -0.14 41 61
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.015 0.017 4 -0.12 5 9
CHRNA1 0.006 0.15 0.36 4 -0.37 34 38
myelination -0.01 0.097 0.26 32 -0.2 4 36
PPP3CB -0.02 0.079 0.2 17 -0.19 5 22
KRAS 0.034 0.016 -10000 0 0 103 103
RAC1-CDC42/GDP 0.02 0.099 0.21 2 -0.17 67 69
NRG2 0.041 0.007 -10000 0 0 14 14
mol:GDP -0.001 0.073 0.18 3 -0.17 68 71
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K2 -0.006 0.11 0.25 23 -0.23 42 65
SRC 0.039 0.01 -10000 0 0 36 36
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.021 0.085 0.24 13 -0.21 9 22
MAP2K1 -0.017 0.19 0.38 1 -0.51 33 34
heart morphogenesis -0.001 0.079 0.18 8 -0.16 58 66
RAS family/GDP 0.025 0.1 0.27 2 -0.19 46 48
GRB2 0.041 0.007 -10000 0 0 17 17
PRKACA 0.008 0.084 -10000 0 -0.73 7 7
CHRNE 0.008 0.023 0.071 2 -10000 0 2
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.012 -10000 0 -0.021 29 29
nervous system development -0.001 0.079 0.18 8 -0.16 58 66
CDC42 0.04 0.009 -10000 0 0 24 24
EGFR-dependent Endothelin 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
HRAS 0.04 0.01 -10000 0 0 31 31
EGFR 0.037 0.014 -10000 0 0 72 72
EGF/EGFR 0.046 0.059 -10000 0 -0.099 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 0.081 0.077 -10000 0 -0.11 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.036 0.015 -10000 0 0 86 86
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.038 0.012 -10000 0 0 53 53
EGF/EGFR dimer/SHC 0.058 0.055 -10000 0 -0.12 33 33
mol:GDP 0.073 0.073 -10000 0 -0.11 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.035 0.016 -10000 0 0 99 99
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
HRAS/GTP 0.048 0.061 -10000 0 -0.11 49 49
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.069 0.073 -10000 0 -0.12 44 44
FRAP1 -0.016 0.073 0.2 40 -0.18 4 44
EGF/EGFR dimer 0.041 0.051 -10000 0 -0.13 37 37
SOS1 0.038 0.013 -10000 0 0 56 56
GRB2 0.041 0.007 -10000 0 0 17 17
ETA receptor/Endothelin-1 0.037 0.047 -10000 0 -0.14 25 25
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.039 0.011 -10000 0 0 38 38
RAS family/GTP/Tiam1 0.012 0.06 -10000 0 -0.16 38 38
NT3 (dimer)/TRKC 0.04 0.036 -10000 0 -0.14 8 8
NT3 (dimer)/TRKB 0.056 0.045 -10000 0 -0.12 10 10
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.08 -10000 0 -0.19 63 63
RAPGEF1 0.04 0.008 -10000 0 0 23 23
BDNF 0.04 0.008 -10000 0 0 23 23
PIK3CA 0.03 0.019 -10000 0 0 155 155
DYNLT1 0.036 0.015 -10000 0 0 81 81
NTRK1 0.039 0.01 -10000 0 0 35 35
NTRK2 0.039 0.01 -10000 0 0 36 36
NTRK3 0.038 0.012 -10000 0 0 49 49
NT-4/5 (dimer)/TRKB 0.051 0.018 -10000 0 -0.088 1 1
neuron apoptosis -0.03 0.1 0.25 33 -0.22 4 37
SHC 2-3/Grb2 0.031 0.11 0.24 3 -0.27 33 36
SHC1 0.04 0.01 -10000 0 0 31 31
SHC2 0.007 0.12 0.21 3 -0.37 41 44
SHC3 0.025 0.088 0.21 3 -0.38 17 20
STAT3 (dimer) 0.003 0.11 -10000 0 -0.27 75 75
NT3 (dimer)/TRKA 0.054 0.046 -10000 0 -0.12 10 10
RIN/GDP 0.047 0.086 0.23 23 -0.19 24 47
GIPC1 0.035 0.015 -10000 0 0 89 89
KRAS 0.034 0.016 -10000 0 0 103 103
DNAJA3 0.01 0.052 0.15 10 -0.15 13 23
RIN/GTP 0.029 0.008 -10000 0 -10000 0 0
CCND1 -0.048 0.17 -10000 0 -0.49 74 74
MAGED1 0.04 0.009 -10000 0 0 26 26
PTPN11 0.04 0.009 -10000 0 0 27 27
RICS 0.037 0.014 -10000 0 0 71 71
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.065 0.051 -10000 0 -0.13 26 26
GRB2 0.041 0.007 -10000 0 0 17 17
NGF (dimer)/TRKA/MATK 0.048 0.02 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.047 0.038 -10000 0 -0.14 15 15
ELMO1 0.035 0.015 -10000 0 0 87 87
RhoG/GTP/ELMO1/DOCK1 0.034 0.048 -10000 0 -0.11 44 44
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.04 0.01 -10000 0 0 31 31
DOCK1 0.037 0.013 -10000 0 0 62 62
GAB2 0.031 0.018 -10000 0 0 141 141
RIT2 0.039 0.01 -10000 0 0 37 37
RIT1 0.038 0.012 -10000 0 0 48 48
FRS2 0.039 0.011 -10000 0 0 40 40
DNM1 0.039 0.011 -10000 0 0 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 52 52
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.028 0.062 0.18 9 -0.15 15 24
mol:GDP 0.043 0.11 0.27 25 -0.27 25 50
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.03 -10000 0 -0.13 19 19
RIT1/GDP 0.043 0.084 0.23 17 -0.19 26 43
TIAM1 0.037 0.014 -10000 0 0 72 72
PIK3R1 0.034 0.017 -10000 0 0 108 108
BDNF (dimer)/TRKB 0.071 0.032 -10000 0 -0.12 1 1
KIDINS220/CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.048 0.038 -10000 0 -0.14 16 16
FRS2 family/SHP2 0.067 0.051 -10000 0 -0.12 29 29
SHC/GRB2/SOS1/GAB1 0.078 0.062 -10000 0 -0.12 32 32
RIT1/GTP 0.025 0.026 -10000 0 -0.13 15 15
NT3 (dimer) 0.031 0.018 -10000 0 0 147 147
RAP1/GDP 0.033 0.074 0.18 17 -0.17 28 45
KIDINS220/CRKL 0.039 0.011 -10000 0 0 38 38
BDNF (dimer) 0.04 0.008 -10000 0 0 23 23
ubiquitin-dependent protein catabolic process 0.042 0.033 -10000 0 -0.11 15 15
Schwann cell development -0.007 0.011 -10000 0 -0.044 11 11
EHD4 0.039 0.011 -10000 0 0 38 38
FRS2 family/GRB2/SOS1 0.081 0.062 -10000 0 -0.12 33 33
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.084 -10000 0 -0.24 27 27
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.069 0.053 0.21 1 -0.11 9 10
ABL1 0.039 0.011 -10000 0 0 41 41
SH2B family/GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
Rap1/GTP 0.007 0.11 -10000 0 -0.33 27 27
STAT3 0.004 0.11 -10000 0 -0.27 75 75
axon guidance 0.047 0.041 -10000 0 -0.11 9 9
MAPK3 -0.008 0.047 0.19 28 -10000 0 28
MAPK1 -0.007 0.046 0.19 27 -10000 0 27
CDC42/GDP 0.049 0.087 0.23 25 -0.19 23 48
NTF3 0.031 0.018 -10000 0 0 147 147
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.048 0.022 -10000 0 -0.11 2 2
PI3K 0.024 0.061 -10000 0 -0.15 47 47
FRS3 0.04 0.008 -10000 0 0 23 23
FAIM 0.038 0.012 -10000 0 0 52 52
GAB1 0.038 0.012 -10000 0 0 52 52
RASGRF1 0.01 0.053 0.15 10 -0.16 13 23
SOS1 0.038 0.013 -10000 0 0 56 56
MCF2L 0.005 0.061 0.18 41 -0.12 8 49
RGS19 0.036 0.015 -10000 0 0 78 78
CDC42 0.04 0.009 -10000 0 0 24 24
RAS family/GTP 0.035 0.12 0.3 3 -0.34 30 33
Rac1/GDP 0.048 0.087 0.23 26 -0.19 23 49
NGF (dimer)/TRKA/GRIT 0.042 0.036 -10000 0 -0.11 20 20
neuron projection morphogenesis -0.052 0.25 -10000 0 -0.84 43 43
NGF (dimer)/TRKA/NEDD4-2 0.043 0.033 -10000 0 -0.11 15 15
MAP2K1 -0.011 0.072 0.19 48 -0.19 3 51
NGFR 0.04 0.009 -10000 0 0 28 28
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.04 -10000 0 -0.14 25 25
RAS family/GTP/PI3K -0.004 0.072 -10000 0 -0.19 52 52
FRS2 family/SHP2/GRB2/SOS1 0.09 0.076 -10000 0 -0.13 43 43
NRAS 0.04 0.009 -10000 0 0 30 30
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
PRKCI 0.027 0.02 -10000 0 0 197 197
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.047 -10000 0 -0.5 2 2
RASA1 0.037 0.014 -10000 0 0 71 71
TRKA/c-Abl 0.052 0.033 -10000 0 -0.14 11 11
SQSTM1 0.038 0.012 -10000 0 0 49 49
BDNF (dimer)/TRKB/GIPC 0.071 0.059 -10000 0 -0.11 21 21
NGF (dimer)/TRKA/p62/Atypical PKCs 0.048 0.069 -10000 0 -0.11 52 52
MATK 0.038 0.013 -10000 0 0 59 59
NEDD4L 0.036 0.015 -10000 0 0 79 79
RAS family/GDP -0.009 0.038 -10000 0 -0.14 26 26
NGF (dimer)/TRKA 0.015 0.052 0.16 6 -0.16 14 20
Rac1/GTP -0.003 0.048 -10000 0 -0.14 25 25
FRS2 family/SHP2/CRK family 0.088 0.069 -10000 0 -0.11 26 26
Arf6 downstream 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
PLAUR -0.028 0.2 -10000 0 -0.81 35 35
regulation of axonogenesis -0.002 0.051 0.21 23 -10000 0 23
myoblast fusion -0.011 0.1 0.35 38 -10000 0 38
mol:GTP 0.017 0.067 -10000 0 -0.2 46 46
regulation of calcium-dependent cell-cell adhesion -0.034 0.089 0.2 43 -10000 0 43
ARF1/GTP 0.038 0.06 -10000 0 -0.16 42 42
mol:GM1 0.003 0.047 -10000 0 -0.15 46 46
mol:Choline 0.001 0.04 0.093 1 -0.16 28 29
lamellipodium assembly -0.013 0.12 -10000 0 -0.4 46 46
MAPK3 0.01 0.085 -10000 0 -0.28 41 41
ARF6/GTP/NME1/Tiam1 0.035 0.09 -10000 0 -0.2 43 43
ARF1 0.038 0.012 -10000 0 0 50 50
ARF6/GDP 0.011 0.1 -10000 0 -0.35 38 38
ARF1/GDP 0.014 0.1 -10000 0 -0.31 44 44
ARF6 0.042 0.046 -10000 0 -0.13 35 35
RAB11A 0.04 0.009 -10000 0 0 24 24
TIAM1 0.032 0.023 -10000 0 -0.046 29 29
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.079 -10000 0 -0.28 35 35
actin filament bundle formation -0.025 0.11 0.31 48 -10000 0 48
KALRN 0.003 0.075 -10000 0 -0.26 38 38
RAB11FIP3/RAB11A 0.058 0.023 -10000 0 -0.14 6 6
RhoA/GDP 0.026 0.11 -10000 0 -0.31 48 48
NME1 0.031 0.024 -10000 0 -0.012 121 121
Rac1/GDP 0.025 0.11 -10000 0 -0.31 47 47
substrate adhesion-dependent cell spreading 0.017 0.067 -10000 0 -0.2 46 46
cortical actin cytoskeleton organization -0.013 0.12 -10000 0 -0.41 46 46
RAC1 0.039 0.01 -10000 0 0 34 34
liver development 0.017 0.067 -10000 0 -0.2 46 46
ARF6/GTP 0.017 0.067 -10000 0 -0.2 46 46
RhoA/GTP 0.041 0.063 -10000 0 -0.16 46 46
mol:GDP -0.004 0.098 -10000 0 -0.35 39 39
ARF6/GTP/RAB11FIP3/RAB11A 0.061 0.067 -10000 0 -0.14 51 51
RHOA 0.041 0.007 -10000 0 0 14 14
PLD1 0.008 0.049 -10000 0 -0.17 32 32
RAB11FIP3 0.042 0.003 -10000 0 0 3 3
tube morphogenesis -0.013 0.12 -10000 0 -0.4 46 46
ruffle organization 0.002 0.051 -10000 0 -0.21 23 23
regulation of epithelial cell migration 0.017 0.067 -10000 0 -0.2 46 46
PLD2 0.015 0.049 -10000 0 -0.15 40 40
PIP5K1A 0.002 0.052 -10000 0 -0.21 23 23
mol:Phosphatidic acid 0.001 0.04 0.093 1 -0.16 28 29
Rac1/GTP -0.014 0.12 -10000 0 -0.41 46 46
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.025 0.12 0.25 3 -0.31 27 30
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
AKT1 0.039 0.01 -10000 0 0 37 37
AKT2 0.038 0.012 -10000 0 0 47 47
STXBP4 0.038 0.012 -10000 0 0 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.013 0.12 0.24 5 -0.32 28 33
YWHAZ 0.034 0.016 -10000 0 0 102 102
CALM1 0.04 0.01 -10000 0 0 31 31
YWHAQ 0.04 0.009 -10000 0 0 28 28
TBC1D4 -0.018 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.037 0.013 -10000 0 0 60 60
YWHAB 0.038 0.012 -10000 0 0 52 52
SNARE/Synip 0.045 0.029 -10000 0 -0.11 9 9
YWHAG 0.04 0.009 -10000 0 0 25 25
ASIP 0.037 0.013 -10000 0 0 60 60
PRKCI 0.027 0.02 -10000 0 0 197 197
AS160/CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
RHOQ 0.039 0.01 -10000 0 0 33 33
GYS1 0.009 0.029 0.25 4 -0.17 6 10
PRKCZ 0.042 0 -10000 0 -10000 0 0
TRIP10 0.038 0.012 -10000 0 0 47 47
TC10/GTP/CIP4/Exocyst 0.047 0.029 -10000 0 -0.11 12 12
AS160/14-3-3 0.021 0.081 0.21 1 -0.25 23 24
VAMP2 0.037 0.014 -10000 0 0 67 67
SLC2A4 0.011 0.13 0.24 4 -0.36 28 32
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.024 0.025 -10000 0 -0.2 6 6
SFN 0.036 0.015 -10000 0 0 86 86
LNPEP 0.036 0.015 -10000 0 0 86 86
YWHAE 0.038 0.013 -10000 0 0 58 58
mTOR signaling pathway

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
GBL 0.04 0.009 -10000 0 0 25 25
MKNK1 0.04 0.009 -10000 0 0 25 25
mol:PIP3 -0.013 0.038 0.2 1 -0.16 15 16
FRAP1 0.028 0.1 -10000 0 -0.43 22 22
AKT1 0.018 0.081 0.17 100 -0.17 10 110
INSR 0.038 0.012 -10000 0 0 53 53
Insulin Receptor/Insulin 0.048 0.023 -10000 0 -0.11 4 4
mol:GTP 0.051 0.088 0.23 28 -0.16 11 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.052 -10000 0 -0.19 29 29
TSC2 0.039 0.01 -10000 0 0 35 35
RHEB/GDP 0.029 0.068 0.16 6 -0.16 14 20
TSC1 0.04 0.009 -10000 0 0 28 28
Insulin Receptor/IRS1 0.034 0.033 -10000 0 -0.23 7 7
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.071 -10000 0 -0.22 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.11 0.25 17 -0.31 28 45
MAP3K5 -0.009 0.066 0.2 5 -0.22 46 51
PIK3R1 0.034 0.017 -10000 0 0 108 108
apoptosis -0.009 0.066 0.2 5 -0.22 46 51
mol:LY294002 0 0 0.001 4 -0.001 6 10
EIF4B 0.024 0.1 0.26 14 -0.29 28 42
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.098 0.23 14 -0.27 27 41
eIF4E/eIF4G1/eIF4A1 0.012 0.062 -10000 0 -0.27 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.053 -10000 0 -0.16 16 16
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.075 0.2 21 -0.18 24 45
FKBP1A 0.039 0.012 -10000 0 0 50 50
RHEB/GTP 0.052 0.084 0.22 18 -0.16 13 31
mol:Amino Acids 0 0 0.001 4 -0.001 6 10
FKBP12/Rapamycin 0.028 0.013 -10000 0 -0.13 2 2
PDPK1 0.006 0.075 0.16 91 -0.17 11 102
EIF4E 0.039 0.011 -10000 0 0 43 43
ASK1/PP5C 0.013 0.2 -10000 0 -0.56 52 52
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.12 -10000 0 -0.46 20 20
TSC1/TSC2 0.057 0.095 0.25 28 -0.18 10 38
tumor necrosis factor receptor activity 0 0 0.001 6 -0.001 4 10
RPS6 0.039 0.011 -10000 0 0 41 41
PPP5C 0.04 0.01 -10000 0 0 32 32
EIF4G1 0.032 0.018 -10000 0 0 129 129
IRS1 0.01 0.03 -10000 0 -0.24 7 7
INS 0.04 0.009 -10000 0 0 30 30
PTEN 0.039 0.011 -10000 0 0 38 38
PDK2 0.006 0.073 0.16 86 -0.17 10 96
EIF4EBP1 -0.053 0.3 -10000 0 -1.1 46 46
PIK3CA 0.03 0.019 -10000 0 0 155 155
PPP2R5D 0.03 0.1 0.28 6 -0.38 22 28
peptide biosynthetic process -0.014 0.032 0.19 11 -10000 0 11
RHEB 0.037 0.013 -10000 0 0 64 64
EIF4A1 0.039 0.011 -10000 0 0 39 39
mol:Rapamycin 0 0.001 0.004 39 -0.002 4 43
EEF2 -0.014 0.032 0.19 11 -10000 0 11
eIF4E/4E-BP1 -0.032 0.29 -10000 0 -0.98 46 46
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.015 0.058 14 -10000 0 14
SNTA1 0.039 0.011 -10000 0 0 44 44
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.018 0.016 0.058 14 -10000 0 14
MAPK12 -0.008 0.044 0.21 7 -0.16 17 24
CCND1 -0.038 0.13 -10000 0 -0.37 72 72
p38 gamma/SNTA1 0.023 0.071 0.22 12 -0.17 31 43
MAP2K3 0.038 0.012 -10000 0 0 47 47
PKN1 0.035 0.016 -10000 0 0 99 99
G2/M transition checkpoint -0.008 0.043 0.21 7 -0.16 17 24
MAP2K6 0.004 0.047 0.24 6 -0.17 22 28
MAPT 0 0.054 0.15 17 -0.19 16 33
MAPK13 -0.017 0.008 0 98 -10000 0 98
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.05 -10000 0 -0.2 32 32
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.053 -10000 0 -0.11 63 63
TRAF2/ASK1 0.044 0.035 -10000 0 -0.11 20 20
ATM 0.036 0.014 -10000 0 0 73 73
MAP2K3 -0.041 0.16 -10000 0 -0.32 105 105
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.043 0.14 0.21 2 -0.32 79 81
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.013 -10000 0 0 61 61
TXN 0.009 0.003 -10000 0 -10000 0 0
CALM1 0.04 0.01 -10000 0 0 31 31
GADD45A 0.036 0.014 -10000 0 0 73 73
GADD45B 0.035 0.016 -10000 0 0 99 99
MAP3K1 0.036 0.014 -10000 0 0 77 77
MAP3K6 0.04 0.008 -10000 0 0 22 22
MAP3K7 0.038 0.012 -10000 0 0 47 47
MAP3K4 0.038 0.012 -10000 0 0 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.048 0.041 -10000 0 -0.14 20 20
TAK1/TAB family 0.017 0.067 0.17 6 -0.25 24 30
RAC1/OSM/MEKK3 0.072 0.026 -10000 0 -0.11 1 1
TRAF2 0.04 0.009 -10000 0 0 29 29
RAC1/OSM/MEKK3/MKK3 -0.009 0.14 -10000 0 -0.28 92 92
TRAF6 0.01 0.041 -10000 0 -0.2 21 21
RAC1 0.039 0.01 -10000 0 0 34 34
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.041 0.007 -10000 0 0 18 18
CCM2 0.041 0.007 -10000 0 0 17 17
CaM/Ca2+/CAMKIIB 0.051 0.019 -10000 0 -0.11 3 3
MAPK11 0.031 0.018 -10000 0 0 142 142
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.062 0.044 -10000 0 -0.1 22 22
OSM/MEKK3 0.059 0.014 -10000 0 -10000 0 0
TAOK1 0.003 0.054 -10000 0 -0.2 38 38
TAOK2 0.004 0.053 -10000 0 -0.2 36 36
TAOK3 0 0.059 -10000 0 -0.2 46 46
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
MAPK14 0.04 0.009 -10000 0 0 28 28
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
MAP3K5 0.037 0.014 -10000 0 0 69 69
MAP3K10 0.039 0.011 -10000 0 0 41 41
MAP3K3 0.041 0.007 -10000 0 0 17 17
TRX/ASK1 0.023 0.046 0.11 1 -0.15 33 34
GADD45/MTK1/MTK1 0.055 0.069 -10000 0 -0.11 58 58
Aurora A signaling

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
Aurora A/GADD45A 0.042 0.041 0.17 3 -0.15 11 14
BIRC5 0.037 0.013 -10000 0 0 60 60
NFKBIA -0.004 0.028 0.25 1 -0.18 6 7
CPEB1 0.039 0.01 -10000 0 0 34 34
AKT1 -0.003 0.042 0.26 9 -0.18 7 16
NDEL1 0.039 0.011 -10000 0 0 38 38
Aurora A/BRCA1 0.027 0.05 0.15 3 -0.1 53 56
NDEL1/TACC3 0.045 0.051 0.17 2 -0.11 30 32
GADD45A 0.036 0.014 -10000 0 0 73 73
GSK3B 0.039 0.012 0.091 15 0 26 41
PAK1/Aurora A 0.042 0.042 0.17 3 -0.16 10 13
MDM2 0.039 0.01 -10000 0 0 35 35
JUB 0.037 0.013 -10000 0 0 60 60
TPX2 -0.015 0.009 -10000 0 -10000 0 0
TP53 -0.046 0.12 0.16 2 -0.24 142 144
DLG7 -0.002 0.025 0.25 1 -0.17 3 4
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.04 0.009 -10000 0 0 27 27
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.054 0.18 2 -0.12 30 32
G2/M transition of mitotic cell cycle 0.026 0.049 0.15 3 -0.1 53 56
AURKA 0.01 0.03 0.13 13 -0.2 7 20
AURKB 0 0.063 -10000 0 -0.2 45 45
CDC25B 0.005 0.045 -10000 0 -0.22 18 18
G2/M transition checkpoint 0.033 0.044 0.15 3 -0.11 31 34
mRNA polyadenylation 0.039 0.035 0.15 2 -0.14 10 12
Aurora A/CPEB 0.039 0.036 0.15 2 -0.14 10 12
Aurora A/TACC1/TRAP/chTOG 0.055 0.075 0.21 2 -0.18 14 16
BRCA1 0.034 0.016 -10000 0 0 106 106
centrosome duplication 0.042 0.041 0.17 3 -0.16 10 13
regulation of centrosome cycle 0.044 0.05 0.17 2 -0.11 30 32
spindle assembly 0.053 0.074 0.21 2 -0.17 14 16
TDRD7 0.035 0.016 -10000 0 0 92 92
Aurora A/RasGAP/Survivin 0.044 0.073 0.2 5 -0.14 13 18
CENPA 0.008 0.055 -10000 0 -0.33 12 12
Aurora A/PP2A 0.046 0.039 0.17 3 -0.15 10 13
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.013 0.06 0.15 9 -0.2 17 26
negative regulation of DNA binding -0.045 0.12 0.16 2 -0.24 142 144
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.057 0.018 -10000 0 -10000 0 0
RASA1 0.037 0.014 -10000 0 0 71 71
Ajuba/Aurora A 0.034 0.044 0.15 3 -0.11 31 34
mitotic prometaphase 0.003 0.025 0.074 62 -10000 0 62
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.03 0.13 13 -0.2 7 20
TACC1 0.035 0.016 -10000 0 0 93 93
TACC3 0.034 0.017 -10000 0 0 112 112
Aurora A/Antizyme1 0.029 0.044 0.15 2 -0.1 36 38
Aurora A/RasGAP 0.042 0.042 0.17 3 -0.16 10 13
OAZ1 0.034 0.017 -10000 0 0 107 107
RAN 0.041 0.006 -10000 0 0 13 13
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.034 0.017 0.091 14 0 89 103
GIT1 0.04 0.009 -10000 0 0 27 27
GIT1/beta-PIX/PAK1 0.066 0.044 -10000 0 -0.12 15 15
Importin alpha/Importin beta/TPX2 -0.015 0.009 -10000 0 -10000 0 0
PPP2R5D 0.04 0.009 -10000 0 0 29 29
Aurora A/TPX2 0.018 0.037 0.15 2 -0.19 9 11
PAK1 0.037 0.014 -10000 0 0 70 70
CKAP5 0.039 0.011 -10000 0 0 45 45
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.061 0.1 0.29 21 -0.31 9 30
PDGFB-D/PDGFRB/SLAP 0.032 0.038 -10000 0 -0.14 10 10
PDGFB-D/PDGFRB/APS/CBL 0.048 0.024 -10000 0 -0.11 4 4
AKT1 0.024 0.11 0.26 43 -0.18 1 44
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.094 0.27 18 -0.33 10 28
PIK3CA 0.03 0.019 -10000 0 0 155 155
FGR 0.023 0.092 0.26 11 -0.39 13 24
mol:Ca2+ 0.027 0.087 0.25 15 -0.36 10 25
MYC 0.004 0.28 0.4 9 -0.67 74 83
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.038 0.059 0.19 43 -0.11 17 60
LRP1/PDGFRB/PDGFB 0.055 0.057 -10000 0 -0.12 36 36
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 0.04 0.009 -10000 0 0 27 27
GO:0007205 0.026 0.088 0.26 14 -0.37 10 24
PTEN 0.039 0.011 -10000 0 0 38 38
GRB2 0.041 0.007 -10000 0 0 17 17
GRB7 0.037 0.013 -10000 0 0 63 63
PDGFB-D/PDGFRB/SHP2 0.047 0.043 -10000 0 -0.14 22 22
PDGFB-D/PDGFRB/GRB10 0.051 0.034 -10000 0 -0.15 9 9
cell cycle arrest 0.032 0.038 -10000 0 -0.14 10 10
HRAS 0.04 0.01 -10000 0 0 31 31
HIF1A 0.01 0.096 0.24 41 -0.2 6 47
GAB1 0.023 0.1 0.28 8 -0.3 15 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.11 0.29 20 -0.28 14 34
PDGFB-D/PDGFRB 0.057 0.052 -10000 0 -0.13 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.042 -10000 0 -0.14 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.054 0.12 0.33 15 -0.26 30 45
positive regulation of MAPKKK cascade 0.047 0.043 -10000 0 -0.14 22 22
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 0.027 0.088 0.26 14 -0.37 10 24
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.04 0.009 -10000 0 -0.003 23 23
PDGFB-D/PDGFRB/GRB7 0.047 0.034 -10000 0 -0.14 8 8
SHB 0.041 0.007 -10000 0 0 17 17
BLK -0.036 0.16 0.3 4 -0.36 96 100
PTPN2 0.039 0.015 -10000 0 -0.014 36 36
PDGFB-D/PDGFRB/SNX15 0.054 0.025 -10000 0 -0.14 3 3
BCAR1 0.036 0.014 -10000 0 0 76 76
VAV2 0.01 0.13 0.3 9 -0.34 37 46
CBL 0.04 0.008 -10000 0 0 23 23
PDGFB-D/PDGFRB/DEP1 0.047 0.04 -10000 0 -0.14 19 19
LCK 0.028 0.079 0.27 8 -0.38 6 14
PDGFRB 0.036 0.019 -10000 0 -0.007 81 81
ACP1 0.04 0.009 -10000 0 0 26 26
HCK 0.016 0.095 0.3 4 -0.46 13 17
ABL1 0.019 0.091 0.24 19 -0.25 14 33
PDGFB-D/PDGFRB/CBL 0.023 0.1 0.27 8 -0.37 11 19
PTPN1 0.036 0.017 -10000 0 -0.007 70 70
SNX15 0.041 0.005 -10000 0 0 7 7
STAT3 0.038 0.013 -10000 0 0 56 56
STAT1 0.034 0.017 -10000 0 0 108 108
cell proliferation 0.012 0.26 0.34 18 -0.6 74 92
SLA 0.027 0.02 -10000 0 0 206 206
actin cytoskeleton reorganization 0.01 0.095 0.22 78 -0.18 1 79
SRC 0.026 0.058 0.32 3 -10000 0 3
PI3K -0.027 0.036 -10000 0 -0.12 31 31
PDGFB-D/PDGFRB/GRB7/SHC 0.063 0.042 -10000 0 -0.12 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.28 18 -0.34 10 28
LYN 0.001 0.12 0.3 4 -0.44 31 35
LRP1 0.036 0.014 -10000 0 0 75 75
SOS1 0.038 0.013 -10000 0 0 56 56
STAT5B 0.039 0.011 -10000 0 0 43 43
STAT5A 0.038 0.012 -10000 0 0 51 51
NCK1-2/p130 Cas 0.075 0.075 -10000 0 -0.12 18 18
SPHK1 0.042 0.009 -10000 0 0 20 20
EDG1 0.042 0.007 -10000 0 0 12 12
mol:DAG 0.027 0.088 0.26 14 -0.37 10 24
PLCG1 0.027 0.09 0.26 14 -0.38 10 24
NHERF/PDGFRB 0.061 0.047 -10000 0 -0.12 17 17
YES1 0.003 0.12 0.26 5 -0.42 33 38
cell migration 0.059 0.047 -10000 0 -0.12 17 17
SHC/Grb2/SOS1 0.083 0.073 -10000 0 -0.13 24 24
SLC9A3R2 0.038 0.012 -10000 0 0 53 53
SLC9A3R1 0.038 0.012 -10000 0 0 49 49
NHERF1-2/PDGFRB/PTEN 0.079 0.057 -10000 0 -0.12 25 25
FYN -0.014 0.14 0.28 3 -0.38 55 58
DOK1 0.006 0.069 0.19 56 -10000 0 56
HRAS/GTP 0.029 0.01 -10000 0 -0.13 1 1
PDGFB 0.038 0.013 -10000 0 0 57 57
RAC1 -0.032 0.24 0.3 10 -0.56 72 82
PRKCD 0.004 0.068 0.2 51 -10000 0 51
FER 0.004 0.066 0.19 49 -10000 0 49
MAPKKK cascade -0.002 0.08 0.18 64 -0.18 4 68
RASA1 0.003 0.064 0.19 45 -0.2 1 46
NCK1 0.036 0.015 -10000 0 0 80 80
NCK2 0.042 0.004 -10000 0 0 6 6
p62DOK/Csk 0.056 0.056 0.2 58 -0.11 11 69
PDGFB-D/PDGFRB/SHB 0.053 0.026 -10000 0 -0.14 3 3
chemotaxis 0.02 0.09 0.24 19 -0.25 14 33
STAT1-3-5/STAT1-3-5 0.05 0.08 -10000 0 -0.14 22 22
Bovine Papilomavirus E5/PDGFRB 0.026 0.019 -10000 0 -0.077 6 6
PTPRJ 0.039 0.01 -10000 0 0 35 35
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.039 0.011 -10000 0 0 41 41
VLDLR 0.032 0.018 -10000 0 0 129 129
LRPAP1 0.036 0.015 -10000 0 0 78 78
NUDC 0.04 0.009 -10000 0 0 26 26
RELN/LRP8 0.049 0.055 -10000 0 -0.12 28 28
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
KATNA1 0.037 0.013 -10000 0 0 61 61
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.001 0.068 0.21 35 -0.19 1 36
IQGAP1/CaM 0.041 0.056 -10000 0 -0.14 45 45
DAB1 0.04 0.009 -10000 0 0 27 27
IQGAP1 0.037 0.014 -10000 0 0 69 69
PLA2G7 0.03 0.019 -10000 0 0 157 157
CALM1 0.04 0.01 -10000 0 0 31 31
DYNLT1 0.036 0.015 -10000 0 0 81 81
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.053 -10000 0 -0.14 36 36
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.04 0.009 -10000 0 0 30 30
LIS1/Poliovirus Protein 3A -0.015 0.013 -10000 0 -0.13 5 5
CDK5R2 0.041 0.006 -10000 0 0 11 11
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.043 0.059 -10000 0 -0.12 37 37
YWHAE 0.038 0.013 -10000 0 0 58 58
NDEL1/14-3-3 E 0.035 0.084 0.28 26 -0.17 7 33
MAP1B -0.002 0.049 0.18 3 -0.19 34 37
RAC1 0.012 0.043 0.12 25 -0.59 1 26
p35/CDK5 -0.006 0.071 0.19 37 -0.18 1 38
RELN 0.034 0.017 -10000 0 0 110 110
PAFAH/LIS1 0.024 0.027 -10000 0 -0.15 5 5
LIS1/CLIP170 -0.015 0.013 -10000 0 -0.13 5 5
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.024 0.079 0.2 16 -0.19 13 29
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.096 -10000 0 -0.2 85 85
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.007 0.081 0.21 51 -0.16 4 55
LIS1/IQGAP1 0.03 0.026 -10000 0 -0.15 5 5
RHOA 0.012 0.044 -10000 0 -0.45 2 2
PAFAH1B1 -0.017 0.008 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.016 -10000 0 0 92 92
PAFAH1B2 0.04 0.01 -10000 0 0 31 31
MAP1B/LIS1/Dynein heavy chain 0.012 0.061 0.18 1 -0.15 38 39
NDEL1/Katanin 60/Dynein heavy chain 0.043 0.093 0.29 24 -0.18 11 35
LRP8 0.039 0.011 -10000 0 0 39 39
NDEL1/Katanin 60 0.033 0.084 0.27 27 -0.17 11 38
P39/CDK5 -0.006 0.073 0.19 39 -0.18 1 40
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.025 -10000 0 -0.15 5 5
CDK5 -0.01 0.054 0.19 20 -0.19 1 21
PPP2R5D 0.04 0.009 -10000 0 0 29 29
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.012 0.011 -10000 0 -0.11 5 5
CSNK2A1 0.038 0.012 -10000 0 0 54 54
RELN/VLDLR/DAB1/LIS1 0.056 0.065 0.2 20 -0.11 33 53
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 58 58
CDC42 0.012 0.049 -10000 0 -0.45 3 3
ceramide signaling pathway

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
MAP4K4 -0.023 0.13 0.25 3 -0.36 46 49
BAG4 0.037 0.013 -10000 0 0 64 64
BAD -0.008 0.048 0.17 5 -0.14 31 36
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 218 218
BAX -0.007 0.047 0.14 8 -0.14 28 36
EnzymeConsortium:3.1.4.12 -0.003 0.032 0.074 3 -0.084 39 42
IKBKB -0.024 0.13 0.23 11 -0.35 43 54
MAP2K2 -0.01 0.04 0.15 3 -0.14 9 12
MAP2K1 -0.012 0.045 0.17 8 -0.15 9 17
SMPD1 -0.003 0.037 0.097 1 -0.1 38 39
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.014 0.14 0.25 10 -0.36 46 56
MAP2K4 -0.01 0.041 0.14 1 -0.13 25 26
protein ubiquitination -0.029 0.13 0.24 2 -0.36 46 48
EnzymeConsortium:2.7.1.37 -0.013 0.044 0.15 4 -0.15 9 13
response to UV 0 0 0.002 7 -0.002 4 11
RAF1 -0.01 0.044 0.14 5 -0.13 23 28
CRADD 0.041 0.006 -10000 0 0 13 13
mol:ceramide -0.004 0.047 0.12 2 -0.13 38 40
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.044 -10000 0 -0.11 37 37
MADD 0.041 0.006 -10000 0 0 11 11
MAP3K1 -0.008 0.044 0.11 2 -0.13 39 41
TRADD 0.036 0.014 -10000 0 0 76 76
RELA/p50 0.041 0.006 -10000 0 0 10 10
MAPK3 -0.008 0.045 0.17 3 -0.16 11 14
MAPK1 -0.012 0.052 0.16 4 -0.16 24 28
p50/RELA/I-kappa-B-alpha 0.045 0.051 -10000 0 -0.14 37 37
FADD -0.018 0.14 0.24 10 -0.36 45 55
KSR1 -0.007 0.042 0.12 1 -0.13 26 27
MAPK8 -0.016 0.043 0.17 3 -0.14 12 15
TRAF2 0.04 0.009 -10000 0 0 29 29
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.032 0.13 0.23 3 -0.35 48 51
TNF R/SODD 0.044 0.038 -10000 0 -0.13 14 14
TNF 0.04 0.009 -10000 0 0 26 26
CYCS -0.007 0.049 0.14 4 -0.14 22 26
IKBKG -0.03 0.13 0.23 3 -0.36 42 45
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.018 0.14 -10000 0 -0.38 45 45
RELA 0.041 0.006 -10000 0 0 10 10
RIPK1 0.038 0.012 -10000 0 0 48 48
AIFM1 -0.006 0.047 0.12 8 -0.14 22 30
TNF/TNF R/SODD 0.059 0.046 -10000 0 -0.12 15 15
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.13 -10000 0 -0.65 19 19
NSMAF -0.015 0.14 0.25 15 -0.37 43 58
response to hydrogen peroxide 0 0 0.002 7 -0.002 4 11
BCL2 0.036 0.014 -10000 0 0 76 76
Syndecan-3-mediated signaling events

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
CTTN 0.039 0.01 -9999 0 0 34 34
Syndecan-3/Src/Cortactin 0.026 0.094 -9999 0 -0.38 13 13
Syndecan-3/Neurocan 0.002 0.066 -9999 0 -0.42 13 13
POMC 0.041 0.007 -9999 0 0 17 17
EGFR 0.037 0.014 -9999 0 0 72 72
Syndecan-3/EGFR 0.03 0.074 -9999 0 -0.42 13 13
AGRP 0.036 0.014 -9999 0 0 76 76
NCSTN 0.04 0.009 -9999 0 0 24 24
PSENEN 0.035 0.016 -9999 0 0 92 92
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.036 0.015 -9999 0 0 83 83
APH1A 0.041 0.006 -9999 0 0 10 10
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.038 0.081 -9999 0 -0.39 13 13
Syndecan-3/IL8 0.023 0.074 -9999 0 -0.42 13 13
PSEN1 0.039 0.01 -9999 0 0 35 35
Src/Cortactin 0.052 0.032 -9999 0 -0.14 10 10
FYN 0.034 0.016 -9999 0 0 103 103
limb bud formation 0.003 0.068 -9999 0 -0.43 13 13
MC4R 0 0 -9999 0 -10000 0 0
SRC 0.039 0.01 -9999 0 0 36 36
PTN 0.023 0.021 -9999 0 0 253 253
FGFR/FGF/Syndecan-3 0.003 0.069 -9999 0 -0.43 13 13
neuron projection morphogenesis -0.013 0.072 -9999 0 -0.37 13 13
Syndecan-3/AgRP 0.03 0.074 -9999 0 -0.42 13 13
Syndecan-3/AgRP/MC4R 0.028 0.071 -9999 0 -0.41 13 13
Fyn/Cortactin 0.037 0.055 -9999 0 -0.14 44 44
SDC3 0.003 0.07 -9999 0 -0.44 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.023 0.073 -9999 0 -0.42 13 13
IL8 0.032 0.018 -9999 0 0 139 139
Syndecan-3/Fyn/Cortactin 0.04 0.082 -9999 0 -0.4 13 13
Syndecan-3/CASK 0.002 0.066 -9999 0 -0.42 13 13
alpha-MSH/MC4R 0.03 0.005 -9999 0 -10000 0 0
Gamma Secretase 0.073 0.087 -9999 0 -0.12 66 66
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.037 0.016 0.079 1 -0.057 3 4
HSPA8 0.039 0.01 -10000 0 0 34 34
SMAD3/SMAD4/ER alpha 0.065 0.092 0.26 11 -0.15 29 40
AKT1 0.04 0.017 -10000 0 -0.098 5 5
GSC 0.008 0.096 -10000 0 -0.95 3 3
NKX2-5 0.039 0.017 -10000 0 -0.018 38 38
muscle cell differentiation -0.04 0.11 0.25 28 -10000 0 28
SMAD2-3/SMAD4/SP1 0.072 0.12 -10000 0 -0.19 15 15
SMAD4 0.036 0.046 -10000 0 -0.096 18 18
CBFB 0.036 0.015 -10000 0 0 82 82
SAP18 0.039 0.01 -10000 0 0 34 34
Cbp/p300/MSG1 0.06 0.056 -10000 0 -0.14 26 26
SMAD3/SMAD4/VDR 0.074 0.1 -10000 0 -0.2 16 16
MYC 0.021 0.022 0.12 4 -0.044 2 6
CDKN2B -0.044 0.16 -10000 0 -0.92 9 9
AP1 0.004 0.092 -10000 0 -0.23 38 38
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.001 0.13 0.2 3 -0.31 54 57
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.063 -10000 0 -0.2 35 35
SP3 0.037 0.024 0.08 2 -0.038 47 49
CREB1 0.041 0.008 -10000 0 0 19 19
FOXH1 0.041 0.019 -10000 0 -0.059 17 17
SMAD3/SMAD4/GR 0.054 0.079 -10000 0 -0.14 35 35
GATA3 0.042 0.012 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.004 0.096 0.17 6 -0.27 37 43
MEF2C/TIF2 0.023 0.068 0.26 6 -0.21 17 23
endothelial cell migration -0.031 0.1 0.91 5 -10000 0 5
MAX 0.029 0.027 0.098 3 -0.036 78 81
RBBP7 0.04 0.009 -10000 0 0 26 26
RBBP4 0.038 0.012 -10000 0 0 46 46
RUNX2 0.039 0.011 -10000 0 0 45 45
RUNX3 0.039 0.01 -10000 0 0 33 33
RUNX1 0.039 0.01 -10000 0 0 33 33
CTBP1 0.038 0.013 -10000 0 0 56 56
NR3C1 0.027 0.028 0.098 3 -0.036 78 81
VDR 0.038 0.013 -10000 0 0 56 56
CDKN1A 0.012 0.076 -10000 0 -0.61 3 3
KAT2B 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.081 0.06 -10000 0 -0.18 5 5
DCP1A 0.04 0.008 -10000 0 0 20 20
SKI 0.042 0.003 -10000 0 0 3 3
SERPINE1 0.03 0.1 -10000 0 -0.92 5 5
SMAD3/SMAD4/ATF2 0.064 0.075 -10000 0 -0.14 23 23
SMAD3/SMAD4/ATF3 0.061 0.068 -10000 0 -0.13 17 17
SAP30 0.038 0.012 -10000 0 0 55 55
Cbp/p300/PIAS3 0.061 0.059 -10000 0 -0.14 29 29
JUN -0.002 0.087 0.19 3 -0.24 36 39
SMAD3/SMAD4/IRF7 0.071 0.071 -10000 0 -0.14 9 9
TFE3 0.038 0.033 0.11 1 -0.081 37 38
COL1A2 -0.091 0.26 -10000 0 -0.62 103 103
mesenchymal cell differentiation -0.064 0.07 0.13 16 -10000 0 16
DLX1 0.041 0.008 -10000 0 0 19 19
TCF3 0.037 0.014 -10000 0 0 71 71
FOS 0.025 0.029 -10000 0 -0.051 28 28
SMAD3/SMAD4/Max 0.063 0.068 -10000 0 -0.13 11 11
Cbp/p300/SNIP1 0.058 0.057 -10000 0 -0.14 27 27
ZBTB17 0.039 0.012 0.1 4 -0.042 4 8
LAMC1 0.009 0.073 -10000 0 -0.26 25 25
TGIF2/HDAC complex/SMAD3/SMAD4 0.062 0.075 -10000 0 -0.14 24 24
IRF7 0.041 0.012 0.087 1 -10000 0 1
ESR1 0.046 0.036 0.12 91 0 92 183
HNF4A 0.038 0.012 -10000 0 0 47 47
MEF2C -0.003 0.061 0.22 13 -0.23 16 29
SMAD2-3/SMAD4 0.071 0.074 -10000 0 -0.13 14 14
Cbp/p300/Src-1 0.058 0.062 -10000 0 -0.14 36 36
IGHV3OR16-13 0.009 0.061 -10000 0 -0.43 10 10
TGIF2/HDAC complex 0.038 0.012 -10000 0 0 54 54
CREBBP 0.038 0.014 -10000 0 -0.002 56 56
SKIL 0.025 0.021 -10000 0 0 228 228
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.038 0.012 -10000 0 0 47 47
SNIP1 0.039 0.011 -10000 0 0 38 38
GCN5L2 0.039 0.013 -10000 0 -0.045 3 3
SMAD3/SMAD4/TFE3 0.078 0.083 -10000 0 -0.16 27 27
MSG1/HSC70 0.053 0.027 -10000 0 -0.14 5 5
SMAD2 0.039 0.025 -10000 0 -0.064 20 20
SMAD3 0.035 0.046 -10000 0 -0.092 22 22
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.066 0.18 1 -0.19 21 22
SMAD2/SMAD2/SMAD4 -0.01 0.061 0.17 7 -0.17 44 51
NCOR1 0.037 0.013 -10000 0 0 61 61
NCOA2 0.037 0.014 -10000 0 0 71 71
NCOA1 0.04 0.009 -10000 0 0 28 28
MYOD/E2A 0.052 0.024 -10000 0 -0.14 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.082 0.12 -10000 0 -0.2 7 7
IFNB1 0.012 0.052 0.27 3 -0.15 3 6
SMAD3/SMAD4/MEF2C 0.052 0.084 0.28 2 -0.22 16 18
CITED1 0.039 0.01 -10000 0 0 35 35
SMAD2-3/SMAD4/ARC105 0.068 0.068 -10000 0 -0.12 13 13
RBL1 0.037 0.013 -10000 0 0 61 61
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.074 -10000 0 -0.4 7 7
RUNX1-3/PEBPB2 0.064 0.044 -10000 0 -0.11 14 14
SMAD7 -0.003 0.14 -10000 0 -0.38 30 30
MYC/MIZ-1 0.017 0.059 0.2 4 -0.14 52 56
SMAD3/SMAD4 -0.006 0.1 0.26 1 -0.33 30 31
IL10 0.022 0.061 0.22 18 -0.15 1 19
PIASy/HDAC complex 0.037 0.014 -10000 0 -0.037 5 5
PIAS3 0.04 0.01 -10000 0 -0.004 26 26
CDK2 0.038 0.015 -10000 0 -0.002 62 62
IL5 0.022 0.06 0.23 14 -10000 0 14
CDK4 0.038 0.015 -10000 0 -0.002 63 63
PIAS4 0.037 0.015 -10000 0 -0.037 5 5
ATF3 0.037 0.014 -10000 0 0 69 69
SMAD3/SMAD4/SP1 0.054 0.11 -10000 0 -0.17 36 36
FOXG1 -0.001 0.001 -10000 0 -10000 0 0
FOXO3 0.01 0.012 -10000 0 -0.11 5 5
FOXO1 0.01 0.012 -10000 0 -0.11 5 5
FOXO4 0.01 0.012 -10000 0 -0.11 5 5
heart looping -0.003 0.061 0.22 13 -0.22 16 29
CEBPB 0.036 0.018 -10000 0 -0.061 5 5
SMAD3/SMAD4/DLX1 0.068 0.067 -10000 0 -0.13 10 10
MYOD1 0.04 0.008 -10000 0 0 20 20
SMAD3/SMAD4/HNF4 0.065 0.068 -10000 0 -0.12 14 14
SMAD3/SMAD4/GATA3 0.078 0.071 -10000 0 -0.13 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.021 -10000 0 0 228 228
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.085 0.085 -10000 0 -0.14 4 4
SMAD3/SMAD4/SP1-3 0.07 0.12 -10000 0 -0.2 33 33
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.067 -10000 0 -0.1 121 121
SIN3B 0.037 0.013 -10000 0 0 65 65
SIN3A 0.04 0.009 -10000 0 0 28 28
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.1 0.073 -10000 0 -0.17 12 12
ITGB5 -0.006 0.094 0.21 13 -0.26 35 48
TGIF/SIN3/HDAC complex/CtBP 0.007 0.089 -10000 0 -0.26 33 33
SMAD3/SMAD4/AR 0.042 0.091 -10000 0 -0.14 60 60
AR 0.033 0.017 -10000 0 0 122 122
negative regulation of cell growth 0.018 0.074 0.19 1 -0.22 28 29
SMAD3/SMAD4/MYOD 0.068 0.068 -10000 0 -0.13 13 13
E2F5 0.037 0.014 -10000 0 0 71 71
E2F4 0.036 0.015 -10000 0 0 79 79
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.098 0.081 -10000 0 -0.14 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.052 -10000 0 -0.29 7 7
TFDP1 0.038 0.012 -10000 0 0 52 52
SMAD3/SMAD4/AP1 0.033 0.11 0.26 3 -0.23 38 41
SMAD3/SMAD4/RUNX2 0.065 0.07 -10000 0 -0.13 17 17
TGIF2 0.038 0.012 -10000 0 0 54 54
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.04 0.01 -10000 0 0 31 31
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.009 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.064 0.063 0.18 81 -0.11 18 99
CDKN1B 0.017 0.092 0.21 39 -0.3 27 66
CDKN1A 0.009 0.084 0.21 14 -0.3 30 44
FRAP1 0.04 0.009 -10000 0 0 27 27
PRKDC 0.039 0.011 -10000 0 0 44 44
FOXO3 0.006 0.079 -10000 0 -0.29 33 33
AKT1 0.007 0.08 -10000 0 -0.31 30 30
BAD 0.041 0.005 -10000 0 0 9 9
AKT3 0.005 0.043 -10000 0 -0.2 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.079 -10000 0 -0.29 33 33
AKT1/ASK1 0.028 0.088 -10000 0 -0.28 35 35
BAD/YWHAZ 0.056 0.044 -10000 0 -0.12 7 7
RICTOR 0.037 0.014 -10000 0 0 68 68
RAF1 0.04 0.008 -10000 0 0 21 21
JNK cascade -0.026 0.086 0.28 35 -10000 0 35
TSC1 0.003 0.078 0.23 2 -0.3 30 32
YWHAZ 0.034 0.016 -10000 0 0 102 102
AKT1/RAF1 0.035 0.093 -10000 0 -0.3 33 33
EP300 0.036 0.014 -10000 0 0 73 73
mol:GDP 0.006 0.081 -10000 0 -0.3 33 33
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.001 0.08 -10000 0 -0.3 34 34
YWHAQ 0.04 0.009 -10000 0 0 28 28
TBC1D4 0.007 0.028 0.24 5 -0.17 3 8
MAP3K5 0.037 0.014 -10000 0 0 69 69
MAPKAP1 0.04 0.009 -10000 0 0 27 27
negative regulation of cell cycle -0.027 0.083 0.3 13 -0.21 3 16
YWHAH 0.037 0.013 -10000 0 0 60 60
AKT1S1 0.008 0.081 0.22 11 -0.3 27 38
CASP9 0.002 0.079 -10000 0 -0.3 31 31
YWHAB 0.038 0.012 -10000 0 0 52 52
p27Kip1/KPNA1 0.037 0.11 0.27 10 -0.3 32 42
GBL 0.04 0.009 -10000 0 0 25 25
PDK1/Src/Hsp90 0.05 0.021 -10000 0 -0.11 3 3
YWHAE 0.038 0.013 -10000 0 0 58 58
SRC 0.039 0.01 -10000 0 0 36 36
AKT2/p21CIP1 0.012 0.075 0.21 14 -0.26 27 41
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.091 -10000 0 -0.35 26 26
CHUK 0.001 0.08 -10000 0 -0.31 31 31
BAD/BCL-XL 0.028 0.086 -10000 0 -0.3 28 28
mTORC2 0.078 0.062 -10000 0 -0.12 33 33
AKT2 0.016 0.017 -10000 0 -0.2 3 3
FOXO1-3a-4/14-3-3 family 0.028 0.1 0.24 2 -0.37 13 15
PDPK1 0.04 0.009 -10000 0 0 25 25
MDM2 0.006 0.087 0.2 13 -0.3 33 46
MAPKKK cascade -0.034 0.092 0.3 33 -10000 0 33
MDM2/Cbp/p300 0.039 0.1 0.32 3 -0.3 33 36
TSC1/TSC2 -0.003 0.082 0.29 4 -0.29 33 37
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.31 3 -0.29 33 36
glucose import -0.003 0.034 0.21 11 -0.16 3 14
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.023 0.087 0.28 1 -0.28 16 17
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.003 0.032 0.21 10 -0.16 3 13
GSK3A 0.005 0.078 0.22 3 -0.3 29 32
FOXO1 0.006 0.079 -10000 0 -0.29 33 33
GSK3B 0.007 0.088 0.21 16 -0.3 33 49
SFN 0.036 0.015 -10000 0 0 86 86
G1/S transition of mitotic cell cycle 0.007 0.094 0.3 10 -0.3 32 42
p27Kip1/14-3-3 family 0.023 0.078 -10000 0 -0.3 13 13
PRKACA 0.035 0.015 -10000 0 0 89 89
KPNA1 0.039 0.01 -10000 0 0 33 33
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.04 0.009 -10000 0 0 25 25
RHEB 0.037 0.013 -10000 0 0 64 64
CREBBP 0.038 0.012 -10000 0 0 54 54
Atypical NF-kappaB pathway

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
BCL3/RelA 0.055 0.027 -10000 0 -0.16 5 5
FBXW11 0.04 0.009 -10000 0 0 25 25
NF kappa B1 p50/c-Rel 0.027 0.038 -10000 0 -0.12 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.076 -10000 0 -0.21 23 23
NFKBIA 0.006 0.062 -10000 0 -0.15 51 51
MAPK14 0.04 0.009 -10000 0 0 28 28
NF kappa B1 p105/p50 0.026 0.04 -10000 0 -0.12 30 30
ARRB2 0.014 0.028 -10000 0 -0.2 9 9
REL 0.04 0.008 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.04 -10000 0 -0.12 31 31
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.04 -10000 0 -0.12 32 32
PIK3CA 0.03 0.019 -10000 0 0 155 155
NF kappa B1 p50 dimer 0.019 0.041 -10000 0 -0.14 31 31
PIK3R1 0.034 0.017 -10000 0 0 108 108
NFKB1 -0.016 0.009 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.051 0.14 2 -0.14 35 37
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.082 -10000 0 -0.23 21 21
SRC 0.039 0.01 -10000 0 0 36 36
PI3K 0.024 0.061 -10000 0 -0.15 47 47
NF kappa B1 p50/RelA 0.013 0.052 0.14 2 -0.14 35 37
IKBKB 0.039 0.011 -10000 0 0 44 44
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -10000 0 0 25 25
SYK 0.037 0.014 -10000 0 0 70 70
I kappa B alpha/PIK3R1 0.018 0.068 0.19 1 -0.15 49 50
cell death 0.02 0.077 -10000 0 -0.22 22 22
NF kappa B1 p105/c-Rel 0.027 0.038 -10000 0 -0.12 30 30
LCK 0.04 0.009 -10000 0 0 29 29
BCL3 0.039 0.011 -10000 0 0 40 40
S1P3 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
PDGFRB 0.037 0.013 -10000 0 0 64 64
mol:S1P 0.001 0.007 -10000 0 -0.028 24 24
S1P1/S1P/Gi 0.007 0.081 -10000 0 -0.18 59 59
GNAO1 0.033 0.024 -10000 0 -0.05 20 20
S1P/S1P3/G12/G13 0.047 0.032 -10000 0 -0.066 25 25
AKT1 0.015 0.1 -10000 0 -0.45 21 21
AKT3 -0.02 0.23 -10000 0 -0.97 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
GNAI2 0.04 0.02 -10000 0 -0.049 22 22
GNAI3 0.038 0.021 -10000 0 -0.047 20 20
GNAI1 0.034 0.022 -10000 0 -0.046 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.007 -10000 0 -0.03 24 24
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.006 -10000 0 0 12 12
mol:Ca2+ -0.001 0.1 0.16 1 -0.27 49 50
MAPK3 -0.009 0.096 0.21 1 -0.26 50 51
MAPK1 -0.004 0.089 -10000 0 -0.27 38 38
JAK2 -0.018 0.11 0.18 6 -0.3 52 58
CXCR4 -0.01 0.099 0.19 3 -0.27 49 52
FLT1 0.04 0.023 -10000 0 -0.059 20 20
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC -0.002 0.099 0.22 15 -0.27 42 57
S1P/S1P3/Gi 0 0.1 0.16 1 -0.27 48 49
RAC1 0.039 0.01 -10000 0 0 34 34
RhoA/GTP 0.01 0.11 -10000 0 -0.26 47 47
VEGFA 0.003 0.011 0.018 97 -0.038 23 120
S1P/S1P2/Gi -0.002 0.089 0.14 1 -0.24 42 43
VEGFR1 homodimer/VEGFA homodimer 0.036 0.032 -10000 0 -0.088 25 25
RHOA 0.041 0.007 -10000 0 0 14 14
S1P/S1P3/Gq 0.018 0.037 -10000 0 -0.14 25 25
GNAQ 0.038 0.012 -10000 0 0 49 49
GNAZ 0.038 0.021 -10000 0 -0.047 21 21
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
Rac1/GTP 0.009 0.1 -10000 0 -0.26 47 47
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.039 0.01 0 34 -9999 0 34
PI3K Class IB/PDE3B 0.039 0.01 -9999 0 0 34 34
PDE3B 0.039 0.01 -9999 0 0 34 34
Regulation of cytoplasmic and 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
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD2 0.008 0.054 0.19 8 -0.23 6 14
SMAD3 0.014 0.054 0.22 2 -0.3 4 6
SMAD3/SMAD4 -0.017 0.16 -10000 0 -0.39 79 79
SMAD4/Ubc9/PIASy 0.066 0.042 -10000 0 -0.13 11 11
SMAD2/SMAD2/SMAD4 0.046 0.086 0.28 1 -0.21 5 6
PPM1A 0.041 0.007 -10000 0 0 16 16
CALM1 0.04 0.01 -10000 0 0 31 31
SMAD2/SMAD4 0.026 0.054 0.22 3 -0.19 8 11
MAP3K1 0.036 0.014 -10000 0 0 77 77
TRAP-1/SMAD4 0.049 0.044 -10000 0 -0.14 24 24
MAPK3 0.041 0.007 -10000 0 0 17 17
MAPK1 0.039 0.012 -10000 0 0 46 46
NUP214 0.039 0.01 -10000 0 0 33 33
CTDSP1 0.041 0.006 -10000 0 0 13 13
CTDSP2 0.039 0.011 -10000 0 0 42 42
CTDSPL 0.041 0.006 -10000 0 0 10 10
KPNB1 0.04 0.01 -10000 0 0 31 31
TGFBRAP1 0.04 0.008 -10000 0 0 20 20
UBE2I 0.04 0.009 -10000 0 0 27 27
NUP153 0.037 0.014 -10000 0 0 67 67
KPNA2 0.036 0.015 -10000 0 0 86 86
PIAS4 0.038 0.012 -10000 0 0 55 55
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.07 0.067 -10000 0 -0.11 45 45
MAP4K1 0.039 0.012 -10000 0 0 46 46
MAP3K8 0.04 0.008 -10000 0 0 21 21
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.041 0.007 -10000 0 0 17 17
CRKL 0.039 0.011 -10000 0 0 38 38
MAP3K1 0.004 0.062 -10000 0 -0.23 18 18
JUN -0.007 0.11 0.24 1 -0.51 23 24
MAP3K7 0.005 0.064 0.21 5 -0.21 21 26
GRAP2 0.038 0.013 -10000 0 0 57 57
CRK 0.038 0.012 -10000 0 0 52 52
MAP2K4 -0.005 0.078 0.23 1 -0.28 24 25
LAT 0.041 0.006 -10000 0 0 13 13
LCP2 0.034 0.016 -10000 0 0 102 102
MAPK8 -0.003 0.12 -10000 0 -0.55 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.067 -10000 0 -0.21 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.079 0.077 -10000 0 -0.11 45 45
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.038 0.012 -10000 0 0 47 47
GNB1/GNG2 0.071 0.042 -10000 0 -0.12 18 18
forebrain development 0.014 0.11 -10000 0 -0.38 30 30
GNAO1 0.035 0.016 -10000 0 0 101 101
SMO/beta Arrestin2 0.054 0.026 -10000 0 -0.14 4 4
SMO 0.04 0.01 -10000 0 -0.001 33 33
ARRB2 0.039 0.011 -10000 0 0 44 44
GLI3/SPOP 0.02 0.13 -10000 0 -0.36 30 30
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.04 0.009 -10000 0 0 26 26
GNAI2 0.041 0.007 -10000 0 0 15 15
SIN3/HDAC complex 0.076 0.054 -10000 0 -0.12 10 10
GNAI1 0.035 0.016 -10000 0 0 95 95
XPO1 0.039 0.012 -10000 0 -0.002 42 42
GLI1/Su(fu) 0.02 0.11 -10000 0 -0.41 25 25
SAP30 0.038 0.012 -10000 0 0 55 55
mol:GDP 0.04 0.01 -10000 0 -0.001 33 33
MIM/GLI2A 0.032 0.026 -10000 0 -0.12 2 2
IFT88 0.037 0.014 -10000 0 0 70 70
GNAI3 0.039 0.011 -10000 0 0 45 45
GLI2 0.016 0.073 0.19 6 -0.24 15 21
GLI3 0.003 0.12 0.22 3 -0.36 30 33
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 57 57
SAP18 0.039 0.01 -10000 0 0 34 34
embryonic digit morphogenesis 0.037 0.014 -10000 0 0 70 70
GNG2 0.039 0.01 -10000 0 0 34 34
Gi family/GTP 0.002 0.076 -10000 0 -0.24 29 29
SIN3B 0.037 0.013 -10000 0 0 65 65
SIN3A 0.04 0.009 -10000 0 0 28 28
GLI3/Su(fu) 0.017 0.12 0.23 3 -0.32 36 39
GLI2/Su(fu) 0.024 0.083 0.19 5 -0.25 21 26
FOXA2 0.025 0.094 -10000 0 -0.58 11 11
neural tube patterning 0.014 0.11 -10000 0 -0.38 30 30
SPOP 0.04 0.009 -10000 0 0 27 27
Su(fu)/PIAS1 0.04 0.06 0.21 1 -0.18 27 28
GNB1 0.041 0.005 -10000 0 0 7 7
CSNK1G2 0.037 0.013 -10000 0 0 64 64
CSNK1G3 0.039 0.011 -10000 0 0 38 38
MTSS1 0.032 0.026 -10000 0 -0.12 2 2
embryonic limb morphogenesis 0.014 0.11 -10000 0 -0.38 30 30
SUFU 0.023 0.039 -10000 0 -0.24 10 10
LGALS3 0.037 0.014 -10000 0 0 70 70
catabolic process 0.026 0.13 -10000 0 -0.35 31 31
GLI3A/CBP 0.047 0.015 -10000 0 -10000 0 0
KIF3A 0.038 0.012 -10000 0 0 51 51
GLI1 0.013 0.11 -10000 0 -0.38 30 30
RAB23 0.041 0.007 -10000 0 0 15 15
CSNK1A1 0.04 0.009 -10000 0 0 26 26
IFT172 0.04 0.009 -10000 0 0 28 28
RBBP7 0.04 0.009 -10000 0 0 26 26
Su(fu)/Galectin3 0.037 0.058 0.21 1 -0.18 25 26
GNAZ 0.039 0.011 -10000 0 0 42 42
RBBP4 0.038 0.012 -10000 0 0 46 46
CSNK1G1 0.041 0.008 -10000 0 0 19 19
PIAS1 0.04 0.009 -10000 0 0 28 28
PRKACA 0.035 0.015 -10000 0 0 89 89
GLI2/SPOP 0.034 0.08 0.21 1 -0.24 17 18
STK36 0.04 0.011 -10000 0 -0.003 33 33
Gi family/GNB1/GNG2/GDP 0 0.086 -10000 0 -0.26 33 33
PTCH1 0.014 0.1 -10000 0 -0.35 30 30
MIM/GLI1 0.026 0.099 -10000 0 -0.35 21 21
CREBBP 0.047 0.015 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.004 0.11 0.18 7 -0.31 38 45
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.034 0.25 0.49 2 -0.56 56 58
PCK1 -0.092 0.4 -10000 0 -1.1 72 72
HNF4A -0.067 0.34 0.57 5 -0.76 86 91
KCNJ11 -0.003 0.23 0.53 1 -0.54 30 31
AKT1 0.006 0.17 -10000 0 -0.35 26 26
response to starvation -0.015 0.045 -10000 0 -0.12 79 79
DLK1 0.006 0.24 0.64 3 -0.55 27 30
NKX2-1 -0.002 0.15 0.36 3 -0.32 26 29
ACADM -0.049 0.27 0.54 1 -0.6 66 67
TAT -0.023 0.19 -10000 0 -0.52 22 22
CEBPB 0.039 0.017 -10000 0 -0.064 2 2
CEBPA 0.042 0.016 -10000 0 -0.066 1 1
TTR 0.042 0.17 0.52 2 -0.92 4 6
PKLR -0.021 0.25 0.45 3 -0.56 42 45
APOA1 -0.12 0.47 -10000 0 -1.1 94 94
CPT1C -0.026 0.24 0.49 1 -0.58 42 43
ALAS1 -0.005 0.18 -10000 0 -0.79 5 5
TFRC -0.054 0.38 -10000 0 -0.94 69 69
FOXF1 0.035 0.015 -10000 0 -10000 0 0
NF1 0.039 0.02 -10000 0 -0.16 1 1
HNF1A (dimer) 0.009 0.001 -10000 0 -10000 0 0
CPT1A -0.04 0.27 0.53 1 -0.59 61 62
HMGCS1 -0.032 0.26 0.47 6 -0.58 62 68
NR3C1 0.048 0.015 -10000 0 -10000 0 0
CPT1B -0.033 0.24 -10000 0 -0.56 48 48
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.006 -10000 0 -10000 0 0
GCK -0.029 0.24 0.48 3 -0.57 44 47
CREB1 0.021 0.095 -10000 0 -0.21 74 74
IGFBP1 -0.001 0.15 -10000 0 -0.52 3 3
PDX1 0.014 0.14 0.4 1 -0.29 25 26
UCP2 -0.055 0.3 0.49 8 -0.65 81 89
ALDOB -0.003 0.23 -10000 0 -0.53 31 31
AFP 0.015 0.049 -10000 0 -10000 0 0
BDH1 -0.053 0.27 -10000 0 -0.59 72 72
HADH -0.003 0.23 -10000 0 -0.48 51 51
F2 -0.029 0.31 -10000 0 -0.73 38 38
HNF1A 0.009 0.001 -10000 0 -10000 0 0
G6PC 0.028 0.088 -10000 0 -10000 0 0
SLC2A2 0.034 0.16 -10000 0 -0.42 2 2
INS 0.03 0.013 0.18 1 -10000 0 1
FOXA1 0.056 0.016 -10000 0 -10000 0 0
FOXA3 0.022 0.12 -10000 0 -0.2 110 110
FOXA2 0.016 0.29 -10000 0 -0.59 37 37
ABCC8 -0.003 0.23 0.53 1 -0.55 24 25
ALB 0.016 0.05 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.051 0.093 -10000 0 -0.21 34 34
Ran/GTP/Exportin 1/HDAC1 -0.03 0.032 -10000 0 -0.12 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.1 0.24 1 -0.29 30 31
SUMO1 0.041 0.006 -10000 0 0 13 13
ZFPM1 0.036 0.015 -10000 0 0 86 86
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.035 -10000 0 -0.15 25 25
FKBP3 0.039 0.01 -10000 0 0 34 34
Histones 0.069 0.087 0.24 1 -0.22 19 20
YY1/LSF 0.012 0.083 -10000 0 -0.22 45 45
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
I kappa B alpha/HDAC3 0.016 0.061 -10000 0 -0.18 39 39
I kappa B alpha/HDAC1 0.031 0.09 0.22 1 -0.23 48 49
SAP18 0.039 0.01 -10000 0 0 34 34
RELA 0.017 0.086 0.22 3 -0.37 13 16
HDAC1/Smad7 0.062 0.053 -10000 0 -0.12 33 33
RANGAP1 0.038 0.013 -10000 0 0 57 57
HDAC3/TR2 0.047 0.061 0.22 1 -0.2 19 20
NuRD/MBD3 Complex 0.01 0.098 0.17 5 -0.29 32 37
NF kappa B1 p50/RelA 0.023 0.1 0.25 1 -0.26 37 38
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.039 0.01 -10000 0 0 35 35
GATA1 0.042 0.002 -10000 0 0 1 1
Mad/Max 0.059 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.005 0.1 -10000 0 -0.27 38 38
RBBP7 0.04 0.009 -10000 0 0 26 26
NPC 0.02 0.022 -10000 0 -0.085 23 23
RBBP4 0.039 0.012 -10000 0 0 46 46
MAX 0.041 0.007 -10000 0 0 16 16
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.009 -10000 0 0 25 25
NFKBIA 0.009 0.071 -10000 0 -0.27 30 30
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.006 0.091 -10000 0 -0.28 30 30
SIN3 complex 0.076 0.054 -10000 0 -0.12 10 10
SMURF1 0.041 0.008 -10000 0 0 19 19
CHD3 0.038 0.012 -10000 0 0 55 55
SAP30 0.038 0.012 -10000 0 0 55 55
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.037 0.013 -10000 0 0 61 61
YY1/HDAC3 0.016 0.078 -10000 0 -0.24 30 30
YY1/HDAC2 0.015 0.077 -10000 0 -0.21 41 41
YY1/HDAC1 0.012 0.079 -10000 0 -0.22 41 41
NuRD/MBD2 Complex (MeCP1) 0.011 0.097 0.17 5 -0.29 29 34
PPARG 0.031 0.067 0.2 6 -0.2 24 30
HDAC8/hEST1B 0.042 0.036 -10000 0 -0.11 20 20
UBE2I 0.04 0.009 -10000 0 0 27 27
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -10000 0 0 25 25
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
HDAC3/SMRT (N-CoR2) 0.048 0.06 0.22 1 -0.19 20 21
MBD3L2 0.039 0.011 -10000 0 0 40 40
ubiquitin-dependent protein catabolic process 0.061 0.053 -10000 0 -0.12 33 33
CREBBP 0.038 0.012 -10000 0 0 54 54
NuRD/MBD3/MBD3L2 Complex 0.008 0.1 0.19 8 -0.27 42 50
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC3 0.022 0.038 -10000 0 -0.29 5 5
HDAC2 0.038 0.012 -10000 0 0 47 47
YY1 0.005 0.057 -10000 0 -0.24 25 25
HDAC8 0.04 0.009 -10000 0 0 26 26
SMAD7 0.039 0.011 -10000 0 0 45 45
NCOR2 0.04 0.009 -10000 0 0 28 28
MXD1 0.041 0.007 -10000 0 0 18 18
STAT3 0.009 0.066 -10000 0 -0.24 33 33
NFKB1 0.036 0.015 -10000 0 0 84 84
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
YY1/LSF/HDAC1 0.022 0.092 -10000 0 -0.21 48 48
YY1/SAP30/HDAC1 0.025 0.085 -10000 0 -0.2 42 42
EP300 0.036 0.014 -10000 0 0 73 73
STAT3 (dimer non-phopshorylated) 0.009 0.066 -10000 0 -0.24 33 33
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.071 -10000 0 -0.27 30 30
histone deacetylation 0.011 0.096 0.17 5 -0.29 29 34
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.084 -10000 0 -0.28 22 22
nuclear export -0.041 0.036 0.11 20 -10000 0 20
PRKACA 0.035 0.015 -10000 0 0 89 89
GATAD2B 0.038 0.012 -10000 0 0 52 52
GATAD2A 0.038 0.013 -10000 0 0 59 59
GATA2/HDAC3 0.048 0.059 0.22 1 -0.19 20 21
GATA1/HDAC1 0.049 0.044 -10000 0 -0.14 27 27
GATA1/HDAC3 0.051 0.06 0.22 1 -0.2 20 21
CHD4 0.036 0.015 -10000 0 0 79 79
TNF-alpha/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
SIN3/HDAC complex/Mad/Max 0.01 0.092 -10000 0 -0.3 26 26
NuRD Complex 0.004 0.1 0.19 8 -0.28 39 47
positive regulation of chromatin silencing 0.065 0.085 0.23 1 -0.21 19 20
SIN3B 0.037 0.013 -10000 0 0 65 65
MTA2 0.041 0.005 -10000 0 0 9 9
SIN3A 0.04 0.009 -10000 0 0 28 28
XPO1 0.039 0.011 -10000 0 0 39 39
SUMO1/HDAC1 0.037 0.065 -10000 0 -0.18 25 25
HDAC complex 0.072 0.078 -10000 0 -0.14 55 55
GATA1/Fog1 0.053 0.022 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.057 0.062 -10000 0 -0.13 44 44
TNF 0.04 0.009 -10000 0 0 26 26
negative regulation of cell growth 0.01 0.091 -10000 0 -0.29 26 26
NuRD/MBD2/PRMT5 Complex 0.011 0.097 0.17 5 -0.29 29 34
Ran/GTP/Exportin 1 0.038 0.071 0.18 1 -0.2 26 27
NF kappa B/RelA/I kappa B alpha 0.016 0.083 -10000 0 -0.28 27 27
SIN3/HDAC complex/NCoR1 -0.001 0.096 0.17 1 -0.25 45 46
TFCP2 0.039 0.01 -10000 0 0 37 37
NR2C1 0.039 0.011 -10000 0 0 41 41
MBD3 0.037 0.014 -10000 0 0 67 67
MBD2 0.039 0.011 -10000 0 0 42 42
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
CDC42/GTP 0.007 0.085 -10000 0 -0.23 36 36
PLCG1 -0.013 0.072 -10000 0 -0.18 69 69
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
cell migration 0.007 0.084 -10000 0 -0.22 36 36
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.073 -10000 0 -0.18 68 68
MAPK1 -0.006 0.063 -10000 0 -0.16 58 58
S1P/S1P5/Gi -0.005 0.079 -10000 0 -0.18 70 70
GNAI1 0.035 0.016 -10000 0 0 95 95
CDC42/GDP 0.029 0.014 -10000 0 -0.13 4 4
S1P/S1P5/G12 0.027 0.007 -10000 0 -10000 0 0
RHOA -0.012 0.038 0.18 17 -0.17 1 18
S1P/S1P4/Gi -0.005 0.079 -10000 0 -0.18 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.011 -10000 0 0 42 42
S1P/S1P4/G12/G13 0.047 0.024 -10000 0 -0.099 9 9
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
CDC42 0.04 0.009 -10000 0 0 24 24
Ephrin A reverse signaling

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
MAPKKK cascade 0.037 0.041 -10000 0 -0.11 31 31
EFNA5 0.034 0.016 -10000 0 0 103 103
FYN -0.013 0.036 0.18 7 -10000 0 7
neuron projection morphogenesis 0.037 0.041 -10000 0 -0.11 31 31
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.038 0.042 -10000 0 -0.11 31 31
EPHA5 0.04 0.009 -10000 0 0 26 26
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.085 0.22 36 -10000 0 36
GNAI2 0.041 0.007 -10000 0 0 15 15
S1P/S1P5/G12 0.027 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
RhoA/GTP 0.007 0.086 -10000 0 -0.23 36 36
negative regulation of cAMP metabolic process -0.005 0.078 -10000 0 -0.18 70 70
GNAZ 0.039 0.011 -10000 0 0 42 42
GNAI3 0.039 0.011 -10000 0 0 45 45
GNA12 0.04 0.01 -10000 0 0 32 32
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.079 -10000 0 -0.18 70 70
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
RHOA 0.041 0.007 -10000 0 0 14 14
GNAI1 0.035 0.016 -10000 0 0 95 95
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.038 0.012 -10000 0 0 51 51
NFATC1 0.019 0.1 0.25 3 -0.33 17 20
NFATC2 0.027 0.058 0.17 9 -0.22 10 19
NFATC3 0.026 0.016 -10000 0 -10000 0 0
YWHAE 0.038 0.013 -10000 0 0 58 58
Calcineurin A alpha-beta B1/CABIN1 -0.003 0.086 0.18 1 -0.26 27 28
Exportin 1/Ran/NUP214 0.067 0.052 -10000 0 -0.12 33 33
mol:DAG 0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.028 0.097 -10000 0 -0.24 21 21
BCL2/BAX 0.051 0.026 -10000 0 -0.14 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.019 -10000 0 -0.13 5 5
CaM/Ca2+ 0.029 0.019 -10000 0 -0.13 5 5
BAX 0.04 0.008 -10000 0 0 22 22
MAPK14 0.04 0.009 -10000 0 0 28 28
BAD 0.041 0.005 -10000 0 0 9 9
CABIN1/MEF2D 0.013 0.09 -10000 0 -0.25 25 25
Calcineurin A alpha-beta B1/BCL2 0.036 0.014 -10000 0 0 76 76
FKBP8 0.036 0.014 -10000 0 0 74 74
activation-induced cell death of T cells -0.013 0.089 0.25 25 -10000 0 25
KPNB1 0.04 0.01 -10000 0 0 31 31
KPNA2 0.036 0.015 -10000 0 0 86 86
XPO1 0.039 0.011 -10000 0 0 39 39
SFN 0.036 0.015 -10000 0 0 86 86
MAP3K8 0.041 0.008 -10000 0 0 21 21
NFAT4/CK1 alpha 0.028 0.045 0.19 2 -0.16 9 11
MEF2D/NFAT1/Cbp/p300 0.071 0.091 0.25 1 -0.22 8 9
CABIN1 -0.003 0.086 0.18 1 -0.27 27 28
CALM1 0.04 0.01 -10000 0 0 31 31
RAN 0.041 0.006 -10000 0 0 13 13
MAP3K1 0.036 0.014 -10000 0 0 77 77
CAMK4 0.037 0.013 -10000 0 0 64 64
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.041 0.007 -10000 0 0 17 17
YWHAH 0.037 0.013 -10000 0 0 60 60
Calcineurin A alpha-beta B1/AKAP79/PKA 0.051 0.027 -10000 0 -0.14 2 2
YWHAB 0.038 0.012 -10000 0 0 52 52
MAPK8 0.04 0.01 -10000 0 0 30 30
MAPK9 0.039 0.011 -10000 0 0 39 39
YWHAG 0.04 0.009 -10000 0 0 25 25
FKBP1A 0.038 0.012 -10000 0 0 50 50
NFAT1-c-4/YWHAQ 0.035 0.11 0.27 2 -0.31 17 19
PRKCH 0.039 0.011 -10000 0 0 41 41
CABIN1/Cbp/p300 0.044 0.052 -10000 0 -0.16 26 26
CASP3 0.037 0.014 -10000 0 0 67 67
PIM1 0.039 0.011 -10000 0 0 45 45
Calcineurin A alpha-beta B1/FKBP12/FK506 0.026 0.012 -10000 0 -0.1 2 2
apoptosis 0.019 0.037 -10000 0 -0.2 11 11
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.076 -10000 0 -0.27 17 17
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.039 0.01 -10000 0 0 36 36
JNK2/NFAT4 0.026 0.068 -10000 0 -0.14 68 68
BAD/BCL-XL 0.053 0.032 -10000 0 -0.14 11 11
PRKCD 0.038 0.013 -10000 0 0 56 56
NUP214 0.04 0.01 -10000 0 0 33 33
PRKCZ 0.043 0.002 -10000 0 -10000 0 0
PRKCA 0.035 0.015 -10000 0 0 90 90
PRKCG 0.041 0.005 -10000 0 0 7 7
PRKCQ 0.035 0.016 -10000 0 0 92 92
FKBP38/BCL2 0.046 0.03 -10000 0 -0.14 3 3
EP300 0.037 0.015 -10000 0 0 73 73
PRKCB1 0.038 0.012 -10000 0 0 48 48
CSNK2A1 0.038 0.012 -10000 0 0 54 54
NFATc/JNK1 0.032 0.11 0.26 2 -0.32 17 19
CaM/Ca2+/FKBP38 0.047 0.027 -10000 0 -0.13 4 4
FKBP12/FK506 0.028 0.013 -10000 0 -0.13 2 2
CSNK1A1 0.017 0.017 0.093 6 -0.11 3 9
CaM/Ca2+/CAMK IV 0.048 0.028 -10000 0 -0.11 7 7
NFATc/ERK1 0.035 0.11 0.26 3 -0.32 15 18
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.025 0.099 -10000 0 -0.24 24 24
NR4A1 0.017 0.075 0.19 22 -0.23 19 41
GSK3B 0.041 0.009 -10000 0 0 26 26
positive T cell selection 0.026 0.016 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.023 0.047 0.12 7 -0.18 11 18
RCH1/ KPNB1 0.035 0.064 -10000 0 -0.14 60 60
YWHAQ 0.04 0.009 -10000 0 0 28 28
PRKACA 0.036 0.016 -10000 0 0 89 89
AKAP5 0.041 0.008 -10000 0 0 19 19
MEF2D 0.041 0.01 -10000 0 0 28 28
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.034 0.016 -10000 0 0 102 102
NFATc/p38 alpha 0.034 0.11 0.26 3 -0.31 17 20
CREBBP 0.039 0.013 -10000 0 0 54 54
BCL2 0.036 0.014 -10000 0 0 76 76
Coregulation of Androgen receptor activity

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
NRIP1 0.037 0.015 -9999 0 -10000 0 0
SVIL 0.037 0.015 -9999 0 -10000 0 0
ZNF318 0.037 0.01 -9999 0 -0.035 2 2
JMJD2C 0.043 0.015 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.037 0.062 -9999 0 -0.1 77 77
CARM1 0.037 0.014 -9999 0 0 69 69
PRDX1 0.039 0.01 -9999 0 0 36 36
PELP1 0.039 0.01 -9999 0 0 36 36
CTNNB1 0.04 0.01 -9999 0 -10000 0 0
AKT1 0.039 0.01 -9999 0 0 37 37
PTK2B 0.034 0.017 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.033 0.015 -9999 0 -0.034 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.041 0.01 -9999 0 -10000 0 0
GSN 0.04 0.012 -9999 0 -10000 0 0
NCOA2 0.037 0.014 -9999 0 0 71 71
NCOA6 0.04 0.012 -9999 0 -10000 0 0
DNA-PK 0.052 0.066 -9999 0 -0.14 46 46
NCOA4 0.04 0.008 -9999 0 0 23 23
PIAS3 0.041 0.009 -9999 0 -10000 0 0
cell proliferation 0.018 0.048 -9999 0 -0.42 6 6
XRCC5 0.039 0.011 -9999 0 0 39 39
UBE3A 0.043 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.038 0.063 -9999 0 -0.11 79 79
FHL2 0.025 0.069 -9999 0 -0.61 5 5
RANBP9 0.039 0.013 -9999 0 -10000 0 0
JMJD1A 0.052 0.019 -9999 0 -0.14 1 1
CDK6 0.032 0.018 -9999 0 0 129 129
TGFB1I1 0.042 0.006 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.013 0.079 -9999 0 -0.12 129 129
XRCC6 0.036 0.014 -9999 0 0 70 70
T-DHT/AR 0.036 0.057 -9999 0 -0.1 71 71
CTDSP1 0.041 0.006 -9999 0 0 13 13
CTDSP2 0.037 0.011 -9999 0 -10000 0 0
BRCA1 0.035 0.017 -9999 0 -10000 0 0
TCF4 0.036 0.013 -9999 0 0 59 59
CDKN2A 0.028 0.019 -9999 0 0 175 175
SRF 0.043 0.021 -9999 0 -0.14 4 4
NKX3-1 0.014 0.082 -9999 0 -0.3 30 30
KLK3 0.004 0.048 -9999 0 -10000 0 0
TMF1 0.039 0.011 -9999 0 0 38 38
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.041 0.009 -9999 0 -10000 0 0
APPL1 -0.011 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.033 0.065 -9999 0 -0.11 89 89
AR 0.037 0.02 -9999 0 -0.043 1 1
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.041 0.007 -9999 0 0 18 18
PRKDC 0.038 0.011 -9999 0 0 44 44
PA2G4 0.039 0.008 -9999 0 0 25 25
UBE2I 0.04 0.009 -9999 0 0 27 27
T-DHT/AR/Cyclin D3/CDK11 p58 0.034 0.058 -9999 0 -0.095 81 81
RPS6KA3 0.038 0.014 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.035 0.066 -9999 0 -0.11 90 90
LATS2 0.039 0.009 -9999 0 0 28 28
T-DHT/AR/PRX1 0.031 0.06 -9999 0 -0.095 90 90
Cyclin D3/CDK11 p58 0.028 0.016 -9999 0 -0.13 5 5
VAV3 0.034 0.017 -9999 0 -10000 0 0
KLK2 0.021 0.065 -9999 0 -0.3 17 17
CASP8 0.04 0.009 -9999 0 0 28 28
T-DHT/AR/TIF2/CARM1 0.045 0.071 -9999 0 -0.11 72 72
TMPRSS2 0.013 0.09 -9999 0 -0.31 33 33
CCND1 0.031 0.018 -9999 0 0 144 144
PIAS1 0.041 0.01 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.032 3 3
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.04 0.013 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.017 0.076 -9999 0 -0.12 119 119
CMTM2 0.036 0.014 -9999 0 0 75 75
SNURF 0.041 0.006 -9999 0 0 10 10
ZMIZ1 0.005 0.005 -9999 0 -0.032 3 3
CCND3 0.039 0.01 -9999 0 0 33 33
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.037 0.016 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.056 0.05 -10000 0 -0.11 21 21
fibroblast growth factor receptor signaling pathway 0.055 0.049 -10000 0 -0.11 21 21
LAMA1 0.034 0.017 -10000 0 0 108 108
PRNP 0.036 0.014 -10000 0 0 77 77
GPC1/SLIT2 0.018 0.072 -10000 0 -0.14 91 91
SMAD2 -0.021 0.035 0.2 7 -0.19 1 8
GPC1/PrPc/Cu2+ 0.039 0.043 -10000 0 -0.11 35 35
GPC1/Laminin alpha1 0.046 0.032 -10000 0 -0.14 6 6
TDGF1 0.041 0.006 -10000 0 0 12 12
CRIPTO/GPC1 0.058 0.017 -10000 0 -0.14 1 1
APP/GPC1 0.047 0.046 -10000 0 -0.14 29 29
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.025 0.19 5 -0.12 1 6
FLT1 0.04 0.01 -10000 0 0 31 31
GPC1/TGFB/TGFBR1/TGFBR2 0.069 0.043 -10000 0 -0.12 17 17
SERPINC1 0.04 0.008 -10000 0 0 23 23
FYN -0.016 0.026 0.19 5 -0.12 1 6
FGR -0.019 0.025 0.1 18 -0.12 1 19
positive regulation of MAPKKK cascade 0.005 0.072 0.21 15 -0.2 15 30
SLIT2 0.028 0.02 -10000 0 0 184 184
GPC1/NRG 0.049 0.026 -10000 0 -0.14 1 1
NRG1 0.035 0.016 -10000 0 0 93 93
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.023 -10000 0 -0.11 6 6
LYN -0.017 0.025 0.19 5 -0.12 1 6
mol:Spermine -0.01 0.002 -10000 0 -10000 0 0
cell growth 0.055 0.049 -10000 0 -0.11 21 21
BMP signaling pathway -0.04 0.009 0 26 -10000 0 26
SRC -0.019 0.025 0.1 17 -0.12 1 18
TGFBR1 0.04 0.009 -10000 0 0 25 25
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.037 0.014 -10000 0 0 69 69
GPC1 0.04 0.009 -10000 0 0 26 26
TGFBR1 (dimer) 0.04 0.009 -10000 0 0 25 25
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.016 0.024 0.19 4 -0.12 1 5
HCK -0.017 0.025 0.1 17 -10000 0 17
FGF2 0.039 0.011 -10000 0 0 45 45
FGFR1 0.033 0.017 -10000 0 0 122 122
VEGFR1 homodimer 0.04 0.01 -10000 0 0 31 31
TGFBR2 0.039 0.01 -10000 0 0 37 37
cell death 0.046 0.046 -10000 0 -0.14 29 29
ATIII/GPC1 0.057 0.019 -10000 0 -0.14 1 1
PLA2G2A/GPC1 0.051 0.026 -10000 0 -0.14 3 3
LCK -0.019 0.025 0.19 5 -10000 0 5
neuron differentiation 0.049 0.026 -10000 0 -0.14 1 1
PrPc/Cu2+ 0.019 0.038 -10000 0 -0.13 34 34
APP 0.038 0.012 -10000 0 0 51 51
TGFBR2 (dimer) 0.039 0.01 -10000 0 0 37 37
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.04 0.009 -10000 0 0 25 25
SPHK1 0.04 0.008 -10000 0 0 20 20
GNAI2 0.041 0.007 -10000 0 0 15 15
mol:S1P 0.015 0.029 -10000 0 -0.17 12 12
GNAO1 0.034 0.016 -10000 0 0 101 101
mol:Sphinganine-1-P -0.019 0.006 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.048 0.19 1 -0.15 13 14
GNAI3 0.039 0.011 -10000 0 0 45 45
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.006 -10000 0 0 12 12
S1P1/S1P 0.037 0.042 0.19 1 -0.15 12 13
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.035 0.016 -10000 0 0 95 95
S1P/S1P5/G12 0.032 0.038 -10000 0 -0.14 12 12
S1P/S1P3/Gq 0.015 0.079 -10000 0 -0.26 36 36
S1P/S1P4/Gi -0.009 0.09 -10000 0 -0.2 71 71
GNAQ 0.038 0.012 -10000 0 0 49 49
GNAZ 0.039 0.011 -10000 0 0 42 42
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
ABCC1 0.04 0.009 -10000 0 0 26 26
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.017 0.085 -10000 0 -0.38 21 21
Crk/p130 Cas/Paxillin 0.005 0.039 -10000 0 -0.18 5 5
JUN 0.003 0.062 0.19 4 -0.23 11 15
HRAS 0.04 0.01 -10000 0 0 31 31
RET51/GFRalpha1/GDNF/GRB10 0.09 0.04 -10000 0 -0.11 5 5
RAP1A 0.039 0.01 -10000 0 0 35 35
FRS2 0.039 0.011 -10000 0 0 40 40
RAP1A/GDP 0.024 0.03 -10000 0 -0.13 21 21
RET51/GFRalpha1/GDNF/DOK1 0.09 0.04 -10000 0 -0.11 5 5
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 52 52
RET9/GFRalpha1/GDNF/Enigma 0.063 0.035 -10000 0 -0.11 2 2
RHOA 0.041 0.007 -10000 0 0 14 14
RAP1A/GTP 0.075 0.051 -10000 0 -0.1 15 15
GRB7 0.037 0.013 -10000 0 0 63 63
RET51/GFRalpha1/GDNF 0.078 0.047 -10000 0 -0.11 3 3
MAPKKK cascade 0.048 0.046 -10000 0 -0.15 4 4
BCAR1 0.036 0.014 -10000 0 0 76 76
RET9/GFRalpha1/GDNF/IRS1 0.063 0.036 -10000 0 -0.11 5 5
lamellipodium assembly 0.03 0.051 0.14 2 -0.18 4 6
RET51/GFRalpha1/GDNF/SHC 0.089 0.039 -10000 0 -0.11 2 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
RET9/GFRalpha1/GDNF/SHC 0.063 0.035 -10000 0 -0.11 2 2
RET9/GFRalpha1/GDNF/Shank3 0.066 0.031 -10000 0 -0.11 1 1
MAPK3 -0.008 0.066 0.18 43 -10000 0 43
DOK1 0.04 0.009 -10000 0 0 24 24
DOK6 0.037 0.013 -10000 0 0 61 61
PXN 0.041 0.007 -10000 0 0 14 14
neurite development 0.001 0.06 0.22 11 -0.2 5 16
DOK5 0.022 0.021 -10000 0 0 269 269
GFRA1 0.037 0.013 -10000 0 0 62 62
MAPK8 0.012 0.06 -10000 0 -0.24 8 8
HRAS/GTP 0.081 0.048 -10000 0 -0.15 4 4
tube development 0.064 0.03 0.24 5 -0.1 2 7
MAPK1 -0.009 0.062 0.18 40 -10000 0 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.046 -10000 0 -0.16 28 28
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC 0.039 0.01 -10000 0 0 36 36
PDLIM7 0.039 0.01 -10000 0 0 36 36
RET51/GFRalpha1/GDNF/Dok6 0.092 0.055 -10000 0 -0.11 1 1
SHC1 0.04 0.01 -10000 0 0 31 31
RET51/GFRalpha1/GDNF/Dok4 0.086 0.041 -10000 0 -0.11 1 1
RET51/GFRalpha1/GDNF/Dok5 0.041 0.079 -10000 0 -0.11 85 85
PRKCA 0.035 0.015 -10000 0 0 90 90
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
CREB1 0.036 0.063 -10000 0 -0.21 20 20
PIK3R1 0.034 0.017 -10000 0 0 108 108
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.035 -10000 0 -0.14 12 12
RET51/GFRalpha1/GDNF/Grb7 0.085 0.043 -10000 0 -0.11 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.041 0.007 -10000 0 0 17 17
DOK4 0.038 0.012 -10000 0 0 52 52
JNK cascade 0.003 0.061 0.19 4 -0.23 11 15
RET9/GFRalpha1/GDNF/FRS2 0.06 0.041 -10000 0 -0.11 12 12
SHANK3 0.042 0.002 -10000 0 0 1 1
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 80 80
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.038 -10000 0 -0.14 25 25
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.027 0.049 -10000 0 -0.16 27 27
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.058 -10000 0 -0.16 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.043 -10000 0 -0.15 22 22
PI3K 0.043 0.064 0.22 7 -0.24 3 10
SOS1 0.038 0.013 -10000 0 0 56 56
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.086 0.034 -10000 0 -0.1 2 2
GRB10 0.04 0.008 -10000 0 0 23 23
activation of MAPKK activity 0.029 0.053 0.16 1 -0.26 7 8
RET51/GFRalpha1/GDNF/FRS2 0.086 0.047 -10000 0 -0.11 12 12
GAB1 0.038 0.012 -10000 0 0 52 52
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 33 33
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.03 0.037 -10000 0 -0.15 11 11
RET51/GFRalpha1/GDNF/PKC alpha 0.078 0.056 -10000 0 -0.11 27 27
GRB2 0.041 0.007 -10000 0 0 17 17
PRKACA 0.035 0.015 -10000 0 0 89 89
GDNF 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 34 34
RET51/GFRalpha1/GDNF/IRS1 0.091 0.039 -10000 0 -0.11 5 5
Rac1/GTP 0.042 0.064 0.2 4 -0.21 4 8
RET9/GFRalpha1/GDNF 0.047 0.022 -10000 0 -0.11 1 1
GFRalpha1/GDNF 0.051 0.025 -10000 0 -0.14 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 93 93
AKT1 0.013 0.11 0.3 9 -0.31 18 27
PTK2B -0.012 0.077 0.2 14 -0.32 7 21
VEGFR2 homodimer/Frs2 0.033 0.057 -10000 0 -0.37 4 4
CAV1 0.036 0.015 -10000 0 0 80 80
CALM1 0.04 0.01 -10000 0 0 31 31
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.058 -10000 0 -0.36 4 4
endothelial cell proliferation 0.035 0.098 0.29 15 -0.29 9 24
mol:Ca2+ 0.019 0.063 0.26 2 -0.28 8 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.046 0.078 -10000 0 -0.21 20 20
RP11-342D11.1 -0.006 0.057 0.17 22 -0.33 5 27
CDH5 0.036 0.015 -10000 0 0 78 78
VEGFA homodimer 0.065 0.049 -10000 0 -0.11 33 33
SHC1 0.04 0.01 -10000 0 0 31 31
SHC2 0.037 0.013 -10000 0 0 64 64
HRAS/GDP 0.039 0.069 -10000 0 -0.24 11 11
SH2D2A 0.039 0.01 -10000 0 0 33 33
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.051 0.085 0.29 2 -0.32 10 12
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.035 0.053 -10000 0 -0.28 5 5
VEGFR1 homodimer 0.04 0.01 -10000 0 0 31 31
SHC/GRB2/SOS1 0.072 0.085 -10000 0 -0.25 11 11
GRB10 0.019 0.069 0.28 1 -0.34 9 10
PTPN11 0.04 0.009 -10000 0 0 27 27
GRB2 0.041 0.007 -10000 0 0 17 17
PAK1 0.037 0.014 -10000 0 0 70 70
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.089 -10000 0 -0.21 22 22
HRAS 0.04 0.01 -10000 0 0 31 31
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.11 -10000 0 -0.26 76 76
HIF1A 0.039 0.011 -10000 0 0 42 42
FRS2 0.039 0.011 -10000 0 0 40 40
oxygen and reactive oxygen species metabolic process 0.044 0.077 -10000 0 -0.21 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.04 0.008 -10000 0 0 21 21
Nck/Pak 0.036 0.056 -10000 0 -0.14 43 43
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.023 0.062 -10000 0 -0.27 7 7
mol:GDP 0.056 0.076 -10000 0 -0.24 11 11
mol:NADP 0.038 0.082 0.29 7 -0.29 12 19
eNOS/Hsp90 0.035 0.077 0.27 7 -0.28 12 19
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 0.019 0.064 0.26 2 -0.28 8 10
HIF1A/ARNT 0.05 0.045 -10000 0 -0.14 25 25
SHB 0.041 0.007 -10000 0 0 17 17
VEGFA 0.002 0.004 -10000 0 -0.037 6 6
VEGFC 0.036 0.015 -10000 0 0 80 80
FAK1/Vinculin 0.012 0.13 0.28 7 -0.29 43 50
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.088 -10000 0 -0.21 33 33
PTPN6 0.037 0.014 -10000 0 0 67 67
EPAS1 0.043 0.031 -10000 0 -0.27 3 3
mol:L-citrulline 0.038 0.082 0.29 7 -0.29 12 19
ITGAV 0.033 0.017 -10000 0 0 117 117
PIK3CA 0.03 0.019 -10000 0 0 155 155
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.054 0.07 -10000 0 -0.29 6 6
VEGFR2 homodimer/VEGFA homodimer 0.043 0.062 -10000 0 -0.29 8 8
VEGFR2/3 heterodimer 0.034 0.058 -10000 0 -0.33 5 5
VEGFB 0.039 0.011 -10000 0 0 42 42
MAPK11 -0.004 0.069 0.26 5 -0.31 9 14
VEGFR2 homodimer 0.022 0.044 -10000 0 -0.38 5 5
FLT1 0.04 0.01 -10000 0 0 31 31
NEDD4 0.041 0.014 -10000 0 -0.054 5 5
MAPK3 -0.002 0.073 0.26 10 -0.29 7 17
MAPK1 -0.002 0.074 0.27 9 -0.3 7 16
VEGFA145/NRP2 0.016 0.045 -10000 0 -0.12 49 49
VEGFR1/2 heterodimer 0.034 0.058 -10000 0 -0.29 7 7
KDR 0.022 0.044 -10000 0 -0.38 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.033 0.073 -10000 0 -0.21 20 20
SRC 0.039 0.01 -10000 0 0 36 36
platelet activating factor biosynthetic process 0 0.077 0.27 9 -0.3 7 16
PI3K 0.012 0.082 0.26 3 -0.32 9 12
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.025 0.063 -10000 0 -0.25 10 10
FES 0.02 0.065 0.26 3 -0.27 8 11
GAB1 0.019 0.083 0.26 5 -0.31 16 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.053 -10000 0 -0.28 5 5
CTNNB1 0.04 0.01 -10000 0 0 31 31
SOS1 0.038 0.013 -10000 0 0 56 56
ARNT 0.041 0.006 -10000 0 0 12 12
eNOS/Caveolin-1 0.044 0.084 0.31 4 -0.3 12 16
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.062 -10000 0 -0.27 8 8
PI3K/GAB1 0.024 0.11 0.27 5 -0.31 20 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.084 -10000 0 -0.21 12 12
PRKACA 0.035 0.015 -10000 0 0 89 89
VEGFR2/3 heterodimer/VEGFC homodimer 0.05 0.068 -10000 0 -0.29 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.019 0.064 0.26 2 -0.34 5 7
actin cytoskeleton reorganization 0.034 0.053 -10000 0 -0.28 5 5
PTK2 -0.005 0.11 0.25 2 -0.3 38 40
EDG1 0.02 0.062 0.24 2 -0.33 5 7
mol:DAG 0.019 0.064 0.26 2 -0.28 8 10
CaM/Ca2+ 0.033 0.066 0.25 2 -0.27 8 10
MAP2K3 -0.008 0.059 0.19 21 -0.33 5 26
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.073 0.24 5 -0.34 9 14
PLCG1 0.019 0.064 0.26 2 -0.29 8 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.059 0.064 -10000 0 -0.27 5 5
IQGAP1 0.037 0.014 -10000 0 0 69 69
YES1 0.038 0.013 -10000 0 0 57 57
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.061 -10000 0 -0.28 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.033 0.053 -10000 0 -0.31 5 5
cell migration 0 0.13 0.26 8 -0.34 35 43
mol:PI-3-4-5-P3 0.012 0.078 0.25 3 -0.27 13 16
FYN 0.034 0.016 -10000 0 0 103 103
VEGFB/NRP1 0.026 0.062 0.24 3 -0.24 10 13
mol:NO 0.038 0.082 0.29 7 -0.29 12 19
PXN 0.041 0.007 -10000 0 0 14 14
HRAS/GTP 0.017 0.057 -10000 0 -0.24 11 11
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.026 0.062 -10000 0 -0.34 9 9
VHL 0.04 0.009 -10000 0 0 28 28
ITGB3 0.033 0.017 -10000 0 0 121 121
NOS3 0.038 0.087 0.3 6 -0.32 12 18
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.056 -10000 0 -0.32 5 5
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.008 0.065 0.19 23 -0.34 5 28
PRKCB -0.007 0.06 0.18 24 -0.33 5 29
VCL 0.039 0.01 -10000 0 0 36 36
VEGFA165/NRP1 0.01 0.055 0.17 19 -0.26 8 27
VEGFR1/2 heterodimer/VEGFA homodimer 0.034 0.057 -10000 0 -0.28 7 7
VEGFA165/NRP2 0.016 0.045 -10000 0 -0.12 49 49
MAPKKK cascade -0.023 0.07 0.19 24 -0.34 7 31
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFC homodimer 0.036 0.015 -10000 0 0 80 80
NCK1 0.036 0.015 -10000 0 0 80 80
ROCK1 0.041 0.007 -10000 0 0 14 14
FAK1/Paxillin 0.015 0.12 0.28 7 -0.29 39 46
MAP3K13 0.014 0.062 0.26 3 -0.27 9 12
PDPK1 -0.003 0.067 0.24 3 -0.28 7 10
Ceramide signaling pathway

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
SPHK2 -0.019 0.005 -10000 0 -10000 0 0
MAP4K4 -0.002 0.081 0.2 2 -0.24 31 33
BAG4 0.037 0.013 -10000 0 0 64 64
PKC zeta/ceramide 0.032 0.031 -10000 0 -0.18 8 8
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 218 218
BAX 0.012 0.058 -10000 0 -0.34 14 14
RIPK1 0.038 0.012 -10000 0 0 48 48
AKT1 0.001 0.12 0.67 17 -10000 0 17
BAD 0.001 0.03 0.18 4 -0.18 8 12
SMPD1 0.01 0.06 0.16 17 -0.17 25 42
RB1 -0.006 0.038 0.22 2 -0.18 8 10
FADD/Caspase 8 -0.004 0.11 0.25 8 -0.3 40 48
MAP2K4 -0.006 0.028 -10000 0 -0.18 7 7
NSMAF 0.038 0.012 -10000 0 0 54 54
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.033 0.18 7 -0.18 8 15
EGF 0.038 0.012 -10000 0 0 53 53
mol:ceramide 0.006 0.027 -10000 0 -0.19 8 8
MADD 0.041 0.006 -10000 0 0 11 11
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.009 -10000 0 -10000 0 0
ASAH1 0.032 0.018 -10000 0 0 128 128
negative regulation of cell cycle -0.006 0.038 0.22 2 -0.18 8 10
cell proliferation 0.026 0.051 0.2 5 -0.18 7 12
BID 0.02 0.095 -10000 0 -0.5 7 7
MAP3K1 -0.001 0.027 -10000 0 -0.18 7 7
EIF2A 0.009 0.079 0.18 74 -0.2 9 83
TRADD 0.036 0.014 -10000 0 0 76 76
CRADD 0.041 0.006 -10000 0 0 13 13
MAPK3 -0.003 0.037 0.17 6 -0.19 7 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.044 0.17 6 -0.17 7 13
Cathepsin D/ceramide 0.03 0.032 -10000 0 -0.17 9 9
FADD -0.001 0.084 0.21 6 -0.25 29 35
KSR1 -0.001 0.026 -10000 0 -0.18 8 8
MAPK8 0.008 0.048 -10000 0 -0.21 14 14
PRKRA 0.004 0.044 0.2 17 -0.18 7 24
PDGFA 0.041 0.007 -10000 0 0 18 18
TRAF2 0.04 0.009 -10000 0 0 29 29
IGF1 0.036 0.015 -10000 0 0 84 84
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.006 0.027 -10000 0 -0.19 8 8
CTSD 0.038 0.012 -10000 0 0 54 54
regulation of nitric oxide biosynthetic process 0.043 0.05 -10000 0 -0.14 36 36
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.029 0.054 0.21 5 -0.2 7 12
PRKCD 0.038 0.013 -10000 0 0 56 56
PRKCZ 0.042 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.043 0.05 -10000 0 -0.14 36 36
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.041 0.007 -10000 0 0 18 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.005 0.086 -10000 0 -0.26 30 30
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
mol:Sphingosine-1-phosphate -0.019 0.005 -10000 0 -10000 0 0
MAP2K1 -0.009 0.036 0.17 11 -0.18 6 17
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
CYCS 0.009 0.05 0.14 3 -0.19 11 14
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
NFKB1 0.036 0.015 -10000 0 0 84 84
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
EIF2AK2 -0.001 0.057 0.19 30 -0.17 11 41
TNF-alpha/TNFR1A/FAN 0.059 0.052 -10000 0 -0.14 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.14 -10000 0 -0.37 55 55
MAP2K2 -0.008 0.033 0.17 6 -0.18 7 13
SMPD3 -0.004 0.1 0.19 6 -0.29 54 60
TNF 0.04 0.009 -10000 0 0 26 26
PKC zeta/PAR4 0.06 0.016 -10000 0 -0.14 2 2
mol:PHOSPHOCHOLINE 0.004 0.035 0.12 3 -0.14 8 11
NF kappa B1/RelA/I kappa B alpha 0.081 0.083 -10000 0 -0.12 62 62
AIFM1 0.01 0.042 0.12 5 -0.17 11 16
BCL2 0.036 0.014 -10000 0 0 76 76
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.047 0.045 -9999 0 -0.14 27 27
FBXW11 0.04 0.009 -9999 0 0 25 25
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -9999 0 0 25 25
CHUK 0.038 0.012 -9999 0 0 52 52
NF kappa B2 p100/RelB 0.094 0.067 -9999 0 -0.12 30 30
NFKB1 0.036 0.015 -9999 0 0 84 84
MAP3K14 0.04 0.009 -9999 0 0 29 29
NF kappa B1 p50/RelB 0.042 0.05 -9999 0 -0.14 35 35
RELB 0.04 0.009 -9999 0 0 27 27
NFKB2 0.04 0.009 -9999 0 0 24 24
NF kappa B2 p52/RelB 0.051 0.022 -9999 0 -0.13 4 4
regulation of B cell activation 0.05 0.022 -9999 0 -0.13 4 4
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.045 0.15 18 -10000 0 18
KIRREL 0.041 0.017 0.084 2 -0.037 2 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.045 -10000 0 -0.15 18 18
PLCG1 0.038 0.012 -10000 0 0 50 50
ARRB2 0.039 0.011 -10000 0 0 44 44
WASL 0.04 0.009 -10000 0 0 24 24
Nephrin/NEPH1/podocin/CD2AP 0.073 0.071 -10000 0 -0.12 41 41
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.057 -10000 0 -0.15 15 15
FYN 0.003 0.065 0.17 60 -0.18 3 63
mol:Ca2+ 0.075 0.064 -10000 0 -0.13 25 25
mol:DAG 0.077 0.065 -10000 0 -0.13 25 25
NPHS2 0.043 0.02 -10000 0 -0.043 19 19
mol:IP3 0.077 0.065 -10000 0 -0.13 25 25
regulation of endocytosis 0.053 0.059 -10000 0 -0.12 20 20
Nephrin/NEPH1/podocin/Cholesterol 0.064 0.048 0.18 1 -0.11 18 19
establishment of cell polarity 0.049 0.045 -10000 0 -0.15 18 18
Nephrin/NEPH1/podocin/NCK1-2 0.086 0.078 -10000 0 -0.12 31 31
Nephrin/NEPH1/beta Arrestin2 0.056 0.06 -10000 0 -0.12 20 20
NPHS1 0.04 0.022 -10000 0 -0.044 17 17
Nephrin/NEPH1/podocin 0.055 0.056 0.22 1 -0.12 19 20
TJP1 0.037 0.013 -10000 0 0 64 64
NCK1 0.036 0.015 -10000 0 0 80 80
NCK2 0.042 0.004 -10000 0 0 6 6
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.078 0.066 -10000 0 -0.13 25 25
CD2AP 0.037 0.014 -10000 0 0 67 67
Nephrin/NEPH1/podocin/GRB2 0.085 0.059 -10000 0 -0.12 18 18
GRB2 0.041 0.007 -10000 0 0 17 17
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.005 0.071 0.17 68 -0.12 3 71
cytoskeleton organization 0.013 0.054 0.25 4 -0.16 13 17
Nephrin/NEPH1 0.042 0.034 -10000 0 -0.096 18 18
Nephrin/NEPH1/ZO-1 0.055 0.062 -10000 0 -0.13 37 37
Insulin Pathway

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
CBL/APS/CAP 0.06 0.041 -10000 0 -0.11 9 9
TC10/GTP 0.05 0.036 -10000 0 -0.1 10 10
Insulin Receptor/Insulin/IRS1/Shp2 0.089 0.058 -10000 0 -0.12 23 23
HRAS 0.04 0.01 -10000 0 0 31 31
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.038 0.012 -10000 0 0 53 53
FOXO3 -0.005 0.009 0.022 10 -0.037 5 15
AKT1 0.016 0.098 0.24 33 -0.18 3 36
INSR 0.042 0.016 0.082 13 -10000 0 13
Insulin Receptor/Insulin 0.081 0.053 0.24 28 -0.1 3 31
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.04 0.008 -10000 0 0 23 23
SORBS1 0.039 0.011 -10000 0 0 40 40
CRK 0.038 0.012 -10000 0 0 52 52
PTPN1 -0.005 0.042 0.15 36 -10000 0 36
CAV1 -0.007 0.042 0.17 18 -10000 0 18
CBL/APS/CAP/Crk-II/C3G 0.08 0.043 -10000 0 -0.11 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.096 0.046 -10000 0 -0.11 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.064 -10000 0 -0.11 45 45
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.097 0.22 1 -0.31 36 37
RPS6KB1 0.005 0.09 0.2 42 -0.18 8 50
PARD6A 0.036 0.015 -10000 0 0 81 81
CBL 0.04 0.008 -10000 0 0 23 23
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.081 -10000 0 -0.69 7 7
PIK3R1 0.034 0.017 -10000 0 0 108 108
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.082 0.2 20 -0.17 14 34
HRAS/GTP -0.026 0.033 0.049 1 -0.11 21 22
Insulin Receptor 0.042 0.016 0.082 13 -10000 0 13
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.1 0.062 -10000 0 -0.11 11 11
PRKCI -0.006 0.13 -10000 0 -0.39 51 51
Insulin Receptor/Insulin/GRB14/PDK1 0.02 0.053 -10000 0 -0.12 44 44
SHC1 0.04 0.01 -10000 0 0 31 31
negative regulation of MAPKKK cascade 0.046 0.084 -10000 0 -0.56 7 7
PI3K 0.051 0.073 -10000 0 -0.11 43 43
NCK2 0.042 0.004 -10000 0 0 6 6
RHOQ 0.039 0.01 -10000 0 0 33 33
mol:H2O2 -0.001 0.005 0.035 3 -10000 0 3
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
AKT2 0.015 0.095 0.22 37 -0.18 3 40
PRKCZ 0.036 0.09 -10000 0 -0.32 26 26
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.007 0.041 0.15 18 -10000 0 18
F2RL2 0.036 0.014 -10000 0 0 73 73
TRIP10 0.038 0.012 -10000 0 0 47 47
Insulin Receptor/Insulin/Shc 0.07 0.037 -10000 0 -0.098 5 5
TC10/GTP/CIP4/Exocyst 0.047 0.029 -10000 0 -0.11 12 12
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.093 0.071 -10000 0 -0.12 25 25
RAPGEF1 0.04 0.008 -10000 0 0 23 23
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 80 80
CBL/APS/CAP/Crk-II 0.065 0.036 -10000 0 -0.12 6 6
TC10/GDP 0.027 0.02 -10000 0 -0.13 8 8
Insulin Receptor/Insulin/SHC/GRB10 0.088 0.053 -10000 0 -0.11 11 11
INPP5D -0.012 0.019 0.045 27 -0.094 7 34
SOS1 0.038 0.013 -10000 0 0 56 56
SGK1 -0.004 0.004 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 27 27
IRS1 0.04 0.008 -10000 0 0 22 22
p62DOK/RasGAP 0.047 0.085 -10000 0 -0.56 7 7
INS 0.044 0.014 0.083 18 -10000 0 18
mol:PI-3-4-P2 -0.012 0.019 0.045 27 -0.094 7 34
GRB2 0.041 0.007 -10000 0 0 17 17
EIF4EBP1 0.003 0.08 0.18 33 -0.17 2 35
PTPRA 0.042 0.014 0.082 5 -10000 0 5
PIK3CA 0.03 0.019 -10000 0 0 155 155
TC10/GTP/CIP4 0.047 0.029 -10000 0 -0.11 12 12
PDPK1 0.04 0.009 -10000 0 0 25 25
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.029 0.059 0.16 1 -0.15 30 31
Insulin Receptor/Insulin/IRS1 0.071 0.038 -10000 0 -0.099 8 8
Insulin Receptor/Insulin/IRS3 0.059 0.03 -10000 0 -0.14 3 3
Par3/Par6 0.067 0.051 -10000 0 -0.1 14 14
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.09 0.05 -10000 0 -0.11 20 20
HDAC3 0.041 0.007 -10000 0 0 15 15
Ran/GTP/Exportin 1/HDAC4 -0.027 0.024 -10000 0 -0.12 33 33
GATA1/HDAC4 0.06 0.01 -10000 0 -10000 0 0
GATA1/HDAC5 0.059 0.015 -10000 0 -10000 0 0
GATA2/HDAC5 0.055 0.02 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.051 0.059 -10000 0 -0.12 36 36
HDAC9 0.035 0.015 -10000 0 0 88 88
Glucocorticoid receptor/Hsp90/HDAC6 0.045 0.039 -10000 0 -0.11 30 30
HDAC4/ANKRA2 0.049 0.033 -10000 0 -0.14 9 9
HDAC5/YWHAB 0.051 0.03 -10000 0 -0.14 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.035 -10000 0 -0.15 25 25
GATA2 0.039 0.01 -10000 0 0 35 35
HDAC4/RFXANK 0.047 0.041 -10000 0 -0.14 20 20
BCOR 0.041 0.005 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.018 -10000 0 0 141 141
HDAC5 0.04 0.01 -10000 0 0 32 32
GNB1/GNG2 0.053 0.038 -10000 0 -0.14 19 19
Histones -0.006 0.071 -10000 0 -0.19 39 39
ADRBK1 0.041 0.005 -10000 0 0 7 7
HDAC4 0.041 0.007 -10000 0 0 15 15
XPO1 0.039 0.011 -10000 0 0 39 39
HDAC5/ANKRA2 0.048 0.033 -10000 0 -0.13 9 9
HDAC4/Ubc9 0.057 0.018 -10000 0 -0.14 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.052 0.03 -10000 0 -0.14 8 8
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.041 0.007 -10000 0 0 15 15
HDAC5/RFXANK 0.046 0.042 -10000 0 -0.14 21 21
CAMK4 0.037 0.013 -10000 0 0 64 64
Tubulin/HDAC6 0.05 0.018 -10000 0 -10000 0 0
SUMO1 0.041 0.006 -10000 0 0 13 13
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.038 0.012 -10000 0 0 52 52
GATA1 0.042 0.002 -10000 0 0 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.038 0.013 -10000 0 0 58 58
NR3C1 0.039 0.012 -10000 0 0 46 46
SUMO1/HDAC4 0.041 0.062 -10000 0 -0.18 18 18
SRF 0.039 0.011 -10000 0 0 42 42
HDAC4/YWHAB 0.053 0.029 -10000 0 -0.14 7 7
Tubulin 0.028 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.052 0.03 -10000 0 -0.14 8 8
GNB1 0.041 0.005 -10000 0 0 7 7
RANGAP1 0.038 0.013 -10000 0 0 57 57
BCL6/BCoR 0.036 0.053 -10000 0 -0.14 36 36
HDAC4/HDAC3/SMRT (N-CoR2) 0.075 0.033 -10000 0 -0.12 7 7
HDAC4/SRF 0.068 0.034 -10000 0 -0.12 1 1
HDAC4/ER alpha 0.04 0.054 -10000 0 -0.14 43 43
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.006 0.07 -10000 0 -0.19 39 39
cell motility 0.05 0.017 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.04 0.009 -10000 0 0 27 27
HDAC7/HDAC3 0.029 0.012 -10000 0 -0.13 3 3
BCL6 0.031 0.018 -10000 0 0 146 146
HDAC4/CaMK II delta B 0.041 0.007 -10000 0 0 15 15
Hsp90/HDAC6 0.03 0.005 -10000 0 -10000 0 0
ESR1 0.035 0.016 -10000 0 0 92 92
HDAC6/HDAC11 0.056 0.026 -10000 0 -0.14 7 7
Ran/GTP/Exportin 1 0.038 0.071 0.18 1 -0.2 26 27
NPC 0.02 0.022 -10000 0 -0.085 23 23
MEF2C 0.036 0.014 -10000 0 0 75 75
RAN 0.041 0.006 -10000 0 0 13 13
HDAC4/MEF2C 0.094 0.063 -10000 0 -0.12 18 18
GNG2 0.039 0.01 -10000 0 0 34 34
NCOR2 0.04 0.009 -10000 0 0 28 28
TUBB2A 0.038 0.012 -10000 0 0 47 47
HDAC11 0.04 0.008 -10000 0 0 23 23
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
ANKRA2 0.035 0.015 -10000 0 0 87 87
RFXANK 0.036 0.014 -10000 0 0 77 77
nuclear import -0.036 0.041 0.18 14 -10000 0 14
IL27-mediated signaling events

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
TGFB1 0.037 0.013 -10000 0 0 62 62
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.11 0.53 9 -10000 0 9
IL27/IL27R/JAK1 0.08 0.12 -10000 0 -0.91 3 3
TBX21 0.004 0.1 0.36 5 -0.57 3 8
IL12B 0.042 0.008 -10000 0 0 20 20
IL12A -0.006 0.006 0.013 26 -10000 0 26
IL6ST 0.036 0.018 -10000 0 -0.032 2 2
IL27RA/JAK1 0.049 0.11 -10000 0 -1.1 3 3
IL27 0.043 0.009 -10000 0 -0.036 3 3
TYK2 0.039 0.016 -10000 0 -0.036 3 3
T-helper cell lineage commitment 0.006 0.061 0.2 20 -0.18 31 51
T-helper 2 cell differentiation -0.003 0.11 0.53 9 -10000 0 9
T cell proliferation during immune response -0.003 0.11 0.53 9 -10000 0 9
MAPKKK cascade 0.003 0.11 -10000 0 -0.53 9 9
STAT3 0.038 0.013 -10000 0 0 56 56
STAT2 0.039 0.011 -10000 0 0 43 43
STAT1 0.034 0.017 -10000 0 0 108 108
IL12RB1 0.039 0.012 -10000 0 0 49 49
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.002 0.1 0.36 2 -0.55 3 5
IL27/IL27R/JAK2/TYK2 0.003 0.12 -10000 0 -0.54 9 9
positive regulation of T cell mediated cytotoxicity 0.003 0.11 -10000 0 -0.53 9 9
STAT1 (dimer) 0.063 0.13 -10000 0 -0.81 3 3
JAK2 0.037 0.018 -10000 0 -0.037 1 1
JAK1 0.039 0.01 -10000 0 0 34 34
STAT2 (dimer) 0.02 0.13 -10000 0 -0.49 11 11
T cell proliferation 0.005 0.11 0.34 2 -0.51 9 11
IL12/IL12R/TYK2/JAK2 0.015 0.17 -10000 0 -0.7 26 26
IL17A 0.008 0.056 0.2 18 -0.18 26 44
mast cell activation -0.003 0.11 0.53 9 -10000 0 9
IFNG 0.013 0.03 0.1 1 -0.098 6 7
T cell differentiation -0.001 0.003 0.014 1 -0.022 3 4
STAT3 (dimer) 0.025 0.13 -10000 0 -0.43 14 14
STAT5A (dimer) 0.025 0.13 -10000 0 -0.52 9 9
STAT4 (dimer) 0.024 0.13 -10000 0 -0.51 9 9
STAT4 0.04 0.009 -10000 0 0 29 29
T cell activation -0.008 0.011 0.12 1 -0.046 33 34
IL27R/JAK2/TYK2 0.053 0.1 -10000 0 -0.94 3 3
GATA3 0.015 0.12 0.63 19 -10000 0 19
IL18 -0.006 0.006 0.002 178 -10000 0 178
positive regulation of mast cell cytokine production 0.025 0.13 -10000 0 -0.42 14 14
IL27/EBI3 0.059 0.022 -10000 0 -10000 0 0
IL27RA 0.024 0.12 -10000 0 -1.1 3 3
IL6 0.034 0.017 -10000 0 0 111 111
STAT5A 0.038 0.012 -10000 0 0 51 51
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.008 0.042 0.48 3 -10000 0 3
IL1B -0.007 0.006 0.002 149 -10000 0 149
EBI3 0.039 0.014 -10000 0 -0.037 1 1
TNF -0.008 0.005 0.006 65 -10000 0 65
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.015 0.17 -10000 0 -0.68 14 14
NCK1/PAK1/Dok-R -0.029 0.072 -10000 0 -0.33 15 15
NCK1/Dok-R 0.05 0.098 -10000 0 -0.88 2 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
mol:beta2-estradiol -0.008 0.008 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
SHC1 0.04 0.01 -10000 0 0 31 31
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
F2 0.01 0.038 -10000 0 -0.079 4 4
TNIP2 0.038 0.012 -10000 0 0 49 49
NF kappa B/RelA 0.076 0.1 -10000 0 -0.84 2 2
FN1 0.021 0.021 -10000 0 0 277 277
PLD2 0.033 0.077 -10000 0 -0.9 2 2
PTPN11 0.04 0.009 -10000 0 0 27 27
GRB14 0.038 0.012 -10000 0 0 53 53
ELK1 0.032 0.078 -10000 0 -0.85 2 2
GRB7 0.037 0.013 -10000 0 0 63 63
PAK1 0.037 0.014 -10000 0 0 70 70
Tie2/Ang1/alpha5/beta1 Integrin 0.037 0.12 -10000 0 -0.86 2 2
CDKN1A 0.014 0.19 -10000 0 -0.62 39 39
ITGA5 0.038 0.013 -10000 0 0 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.054 0.096 -10000 0 -0.88 2 2
CRK 0.038 0.012 -10000 0 0 52 52
mol:NO 0.03 0.15 0.37 1 -0.51 15 16
PLG 0.031 0.076 -10000 0 -0.9 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.027 0.14 -10000 0 -0.75 6 6
GRB2 0.041 0.007 -10000 0 0 17 17
PIK3R1 0.034 0.017 -10000 0 0 108 108
ANGPT2 -0.045 0.29 -10000 0 -1 38 38
BMX 0.032 0.077 -10000 0 -0.9 2 2
ANGPT1 0.03 0.054 -10000 0 -10000 0 0
tube development -0.002 0.21 -10000 0 -0.7 39 39
ANGPT4 0.035 0.021 -10000 0 -0.012 82 82
response to hypoxia 0.001 0.008 0.033 1 -0.062 2 3
Tie2/Ang1/GRB14 0.054 0.089 -10000 0 -0.91 2 2
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
FGF2 0.039 0.012 -10000 0 0 45 45
STAT5A (dimer) 0.015 0.24 -10000 0 -0.8 39 39
mol:L-citrulline 0.03 0.15 0.37 1 -0.51 15 16
AGTR1 0.033 0.025 -10000 0 -0.047 35 35
MAPK14 0.041 0.12 -10000 0 -1 4 4
Tie2/SHP2 0.038 0.11 -10000 0 -0.65 4 4
TEK 0.03 0.11 -10000 0 -0.69 4 4
RPS6KB1 0.016 0.16 -10000 0 -0.66 11 11
Angiotensin II/AT1 0.025 0.024 -10000 0 -0.057 35 35
Tie2/Ang1/GRB2 0.058 0.091 -10000 0 -0.91 2 2
MAPK3 0.028 0.075 -10000 0 -0.85 2 2
MAPK1 0.027 0.074 -10000 0 -0.85 2 2
Tie2/Ang1/GRB7 0.054 0.09 -10000 0 -0.91 2 2
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 0.031 0.08 -10000 0 -0.9 2 2
PI3K 0.017 0.16 -10000 0 -0.82 8 8
FES 0.043 0.11 -10000 0 -1 2 2
Crk/Dok-R 0.056 0.095 -10000 0 -0.88 2 2
Tie2/Ang1/ABIN2 0.056 0.091 -10000 0 -0.91 2 2
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.019 0.16 -10000 0 -0.61 15 15
STAT5A 0.038 0.012 -10000 0 0 51 51
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.061 0.18 -10000 0 -0.67 8 8
Tie2/Ang2 -0.013 0.27 -10000 0 -0.95 39 39
Tie2/Ang1 0.043 0.082 -10000 0 -0.94 2 2
FOXO1 0.015 0.18 -10000 0 -0.6 39 39
ELF1 0.047 0.019 -10000 0 -0.13 2 2
ELF2 0.04 0.079 -10000 0 -0.9 2 2
mol:Choline 0.033 0.076 -10000 0 -0.87 2 2
cell migration -0.017 0.047 -10000 0 -0.18 15 15
FYN -0.01 0.23 -10000 0 -0.8 39 39
DOK2 0.032 0.018 -10000 0 0 135 135
negative regulation of cell cycle 0.017 0.18 -10000 0 -0.56 39 39
ETS1 0.043 0.021 -10000 0 -10000 0 0
PXN 0.061 0.17 0.4 1 -0.57 8 9
ITGB1 0.039 0.011 -10000 0 0 38 38
NOS3 0.026 0.16 -10000 0 -0.58 14 14
RAC1 0.039 0.01 -10000 0 0 34 34
TNF 0.049 0.014 -10000 0 -10000 0 0
MAPKKK cascade 0.033 0.076 -10000 0 -0.87 2 2
RASA1 0.037 0.014 -10000 0 0 71 71
Tie2/Ang1/Shc 0.059 0.091 -10000 0 -0.91 2 2
NCK1 0.036 0.015 -10000 0 0 80 80
vasculogenesis 0.031 0.14 0.36 3 -0.42 24 27
mol:Phosphatidic acid 0.033 0.076 -10000 0 -0.87 2 2
mol:Angiotensin II 0 0.008 -10000 0 -0.033 30 30
mol:NADP 0.03 0.15 0.37 1 -0.51 15 16
Rac1/GTP 0.029 0.15 -10000 0 -0.67 8 8
MMP2 0.033 0.087 -10000 0 -0.9 2 2
Glucocorticoid receptor regulatory network

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
PCK2 -0.02 0.075 -10000 0 -0.47 5 5
SMARCC2 0.04 0.009 -10000 0 0 25 25
SMARCC1 0.04 0.008 -10000 0 0 21 21
TBX21 0.04 0.058 0.41 1 -10000 0 1
SUMO2 0.037 0.015 -10000 0 -0.03 20 20
STAT1 (dimer) 0.022 0.064 -10000 0 -0.18 46 46
FKBP4 0.036 0.015 -10000 0 0 86 86
FKBP5 0.031 0.018 -10000 0 0 147 147
GR alpha/HSP90/FKBP51/HSP90 -0.035 0.074 0.2 2 -0.21 19 21
PRL 0.049 0.068 0.39 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.059 0.12 0.38 3 -0.35 1 4
RELA 0.013 0.097 -10000 0 -0.16 126 126
FGG -0.055 0.11 0.33 3 -0.32 1 4
GR beta/TIF2 -0.033 0.079 0.22 2 -0.24 7 9
IFNG 0.047 0.1 -10000 0 -10000 0 0
apoptosis -0.055 0.17 -10000 0 -0.46 37 37
CREB1 0.049 0.009 -10000 0 -10000 0 0
histone acetylation 0.022 0.083 0.29 10 -0.39 6 16
BGLAP 0.045 0.091 -10000 0 -0.89 3 3
GR/PKAc 0.032 0.085 -10000 0 -0.16 24 24
NF kappa B1 p50/RelA 0.01 0.17 -10000 0 -0.3 115 115
SMARCD1 0.041 0.008 -10000 0 0 19 19
MDM2 -0.013 0.047 0.14 4 -0.24 7 11
GATA3 0.05 0.014 -10000 0 -10000 0 0
AKT1 0.035 0.016 0.17 2 -0.052 7 9
CSF2 0.012 0.054 -10000 0 -10000 0 0
GSK3B 0.037 0.015 -10000 0 -0.03 17 17
NR1I3 -0.043 0.16 -10000 0 -0.5 6 6
CSN2 -0.05 0.097 0.28 3 -0.31 1 4
BRG1/BAF155/BAF170/BAF60A 0.077 0.065 -10000 0 -0.13 32 32
NFATC1 0.043 0.017 -10000 0 -10000 0 0
POU2F1 0.046 0.01 -10000 0 -10000 0 0
CDKN1A -0.041 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.005 -10000 0 -10000 0 0
SFN 0.036 0.015 -10000 0 0 86 86
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.025 0.082 0.22 1 -0.2 28 29
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.28 -10000 0 -0.7 92 92
JUN 0.041 0.098 0.34 9 -0.28 3 12
IL4 0.042 0.057 -10000 0 -10000 0 0
CDK5R1 0.039 0.01 -10000 0 0 30 30
PRKACA 0.035 0.015 -10000 0 0 89 89
cortisol/GR alpha (monomer)/AP-1 -0.041 0.07 0.2 13 -0.22 25 38
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.017 0.081 0.22 1 -0.2 20 21
cortisol/GR alpha (monomer) -0.071 0.13 0.4 4 -0.4 1 5
NCOA2 0.037 0.014 -10000 0 0 71 71
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.032 0.054 -10000 0 -0.12 30 30
AP-1/NFAT1-c-4 0.039 0.14 -10000 0 -0.37 20 20
AFP 0.03 0.095 -10000 0 -10000 0 0
SUV420H1 0.04 0.009 -10000 0 0 30 30
IRF1 -0.1 0.22 -10000 0 -0.58 83 83
TP53 0.036 0.028 -10000 0 -10000 0 0
PPP5C 0.04 0.01 -10000 0 0 32 32
KRT17 0.029 0.16 -10000 0 -0.72 12 12
KRT14 0.026 0.17 0.5 8 -1.1 10 18
TBP 0.044 0.032 -10000 0 -0.34 3 3
CREBBP 0.029 0.051 0.34 11 -10000 0 11
HDAC1 0.033 0.012 -10000 0 -0.059 2 2
HDAC2 0.037 0.011 -10000 0 -10000 0 0
AP-1 0.038 0.14 -10000 0 -0.38 20 20
MAPK14 0.037 0.016 -10000 0 -0.03 19 19
MAPK10 0.033 0.021 -10000 0 -0.03 30 30
MAPK11 0.029 0.021 -10000 0 -0.03 16 16
KRT5 -0.006 0.26 -10000 0 -0.83 44 44
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.041 0.012 -10000 0 -0.068 2 2
STAT1 0.022 0.064 -10000 0 -0.18 46 46
CGA 0.046 0.064 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.061 0.11 0.31 2 -0.36 36 38
MAPK3 0.036 0.019 -10000 0 -0.03 34 34
MAPK1 0.035 0.018 -10000 0 -0.03 21 21
ICAM1 -0.076 0.32 -10000 0 -0.77 93 93
NFKB1 0.006 0.11 -10000 0 -0.2 112 112
MAPK8 0.049 0.083 0.57 1 -0.23 4 5
MAPK9 0.036 0.017 -10000 0 -0.031 22 22
cortisol/GR alpha (dimer) -0.057 0.18 -10000 0 -0.48 37 37
BAX -0.048 0.12 -10000 0 -10000 0 0
POMC 0.056 0.094 0.51 1 -10000 0 1
EP300 0.027 0.047 0.33 9 -0.06 44 53
cortisol/GR alpha (dimer)/p53 -0.078 0.12 0.38 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.047 0.25 5 -0.22 7 12
SGK1 -0.025 0.11 0.34 9 -0.29 50 59
IL13 0.049 0.092 -10000 0 -0.46 1 1
IL6 0.013 0.16 -10000 0 -0.62 18 18
PRKACG 0.041 0.005 -10000 0 0 9 9
IL5 0.048 0.096 -10000 0 -10000 0 0
IL2 0.038 0.12 -10000 0 -0.53 5 5
CDK5 0.035 0.015 -10000 0 0 83 83
PRKACB 0.038 0.012 -10000 0 0 48 48
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.013 0.23 -10000 0 -0.79 37 37
CDK5R1/CDK5 0.045 0.041 -10000 0 -0.13 20 20
NF kappa B1 p50/RelA/PKAc 0.043 0.15 -10000 0 -0.22 93 93
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.36 4 -0.32 1 5
SMARCA4 0.035 0.015 -10000 0 0 90 90
chromatin remodeling -0.03 0.092 0.28 2 -0.36 10 12
NF kappa B1 p50/RelA/Cbp 0.024 0.16 0.42 6 -0.25 107 113
JUN (dimer) 0.04 0.098 0.34 9 -0.28 3 12
YWHAH 0.037 0.013 -10000 0 0 60 60
VIPR1 0.041 0.057 0.4 1 -10000 0 1
NR3C1 -0.047 0.092 0.27 2 -0.32 6 8
NR4A1 0.038 0.018 -10000 0 -10000 0 0
TIF2/SUV420H1 0.042 0.052 -10000 0 -0.14 36 36
MAPKKK cascade -0.055 0.17 -10000 0 -0.46 37 37
cortisol/GR alpha (dimer)/Src-1 -0.055 0.12 0.38 4 -10000 0 4
PBX1 0.044 0.013 -10000 0 -10000 0 0
POU1F1 0.046 0.009 -10000 0 -10000 0 0
SELE 0.022 0.12 -10000 0 -0.37 4 4
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.031 0.092 0.28 2 -0.36 10 12
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.36 4 -0.32 1 5
mol:cortisol -0.043 0.066 0.21 3 -10000 0 3
MMP1 0.009 0.18 -10000 0 -0.8 21 21
Signaling events mediated by HDAC Class III

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
EP300 0.036 0.014 -10000 0 0 73 73
HDAC4 0.041 0.007 -10000 0 0 15 15
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.013 0.004 -10000 0 -10000 0 0
CDKN1A 0.024 0.066 0.29 19 -10000 0 19
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.04 0.008 -10000 0 0 22 22
FOXO3 0.002 0.042 0.25 15 -10000 0 15
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.035 -10000 0 -0.18 19 19
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.037 0.014 -10000 0 0 70 70
TAT 0.036 0.014 -10000 0 0 75 75
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.01 0.002 -10000 0 -10000 0 0
PPARGC1A 0.038 0.012 -10000 0 0 55 55
FHL2 0.04 0.008 -10000 0 0 20 20
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.046 0.041 -10000 0 -0.17 15 15
HIST2H4A -0.013 0.004 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.036 0.048 0.15 58 -0.21 6 64
SIRT1 0.037 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.072 0.034 -10000 0 -0.12 8 8
SIRT1/Histone H1b 0.005 0.091 -10000 0 -0.2 68 68
apoptosis -0.064 0.045 0.14 15 -10000 0 15
SIRT1/PGC1A 0.046 0.026 -10000 0 -0.11 8 8
p53/SIRT1 -0.01 0.09 -10000 0 -0.15 163 163
SIRT1/FOXO4 0.009 0.075 -10000 0 -0.15 84 84
FOXO1/FHL2/SIRT1 0.046 0.025 -10000 0 -0.1 12 12
HIST1H1E -0.005 0.07 -10000 0 -0.21 53 53
SIRT1/p300 0.044 0.042 -10000 0 -0.14 23 23
muscle cell differentiation -0.018 0.023 0.11 9 -0.21 2 11
TP53 0.024 0.019 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.065 0.046 -10000 0 -0.14 15 15
CREBBP 0.038 0.012 -10000 0 0 54 54
MEF2D 0.04 0.009 -10000 0 0 28 28
HIV-1 Tat/SIRT1 0.048 0.031 -10000 0 -0.13 8 8
ACSS2 -0.021 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.018 0.024 0.21 2 -0.11 9 11
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.02 0.024 0.21 3 -0.11 2 5
NFATC2 0.021 0.024 0.22 3 -0.11 3 6
NFATC3 0.021 0.024 0.2 3 -0.11 2 5
CD40LG 0.034 0.1 0.31 16 -0.24 1 17
PTGS2 0.014 0.09 0.34 8 -0.27 5 13
JUNB 0.03 0.019 -10000 0 0 160 160
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.017 -10000 0 -0.13 3 3
CaM/Ca2+ 0.032 0.017 -10000 0 -0.13 3 3
CALM1 0.042 0.011 -10000 0 -0.001 32 32
JUN 0.038 0.016 0.099 1 0 81 82
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.027 0.012 -10000 0 -0.1 2 2
FOSL1 0.041 0.007 -10000 0 0 15 15
CREM 0.04 0.008 -10000 0 0 20 20
Jun/NFAT1-c-4/p21SNFT 0.056 0.069 0.24 8 -10000 0 8
FOS 0.028 0.022 0.099 1 0 207 208
IFNG 0.024 0.097 0.32 13 -0.24 1 14
AP-1/NFAT1-c-4 0.084 0.12 -10000 0 -0.23 3 3
FASLG 0.031 0.1 0.32 14 -0.24 2 16
NFAT1-c-4/ICER1 0.053 0.058 0.22 7 -10000 0 7
IL2RA 0.031 0.1 0.33 14 -0.25 2 16
FKBP12/FK506 0.028 0.013 -10000 0 -0.13 2 2
CSF2 0.033 0.1 0.32 15 -0.24 1 16
JunB/Fra1/NFAT1-c-4 0.048 0.074 0.23 4 -0.18 3 7
IL4 0.032 0.1 0.3 19 -0.24 1 20
IL2 -0.039 0.23 -10000 0 -0.86 41 41
IL3 0.026 0.12 -10000 0 -0.58 21 21
FKBP1A 0.038 0.012 -10000 0 0 50 50
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.046 0.01 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.015 0.12 -10000 0 -0.85 9 9
MKNK1 0.04 0.009 -10000 0 0 25 25
MAPK14 0.042 0.053 0.17 1 -0.14 32 33
ATF2/c-Jun -0.02 0.1 -10000 0 -0.31 43 43
MAPK11 0.031 0.054 -10000 0 -0.14 31 31
MITF 0.019 0.061 -10000 0 -0.28 16 16
MAPKAPK5 0.019 0.058 -10000 0 -0.26 17 17
KRT8 0.016 0.061 -10000 0 -0.23 24 24
MAPKAPK3 0.041 0.006 -10000 0 0 13 13
MAPKAPK2 0.04 0.008 -10000 0 0 23 23
p38alpha-beta/CK2 0.042 0.078 -10000 0 -0.31 14 14
CEBPB 0.021 0.053 -10000 0 -0.28 10 10
SLC9A1 0.02 0.056 -10000 0 -0.28 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.014 0.074 0.23 1 -0.24 28 29
p38alpha-beta/MNK1 0.053 0.077 -10000 0 -0.26 14 14
JUN -0.023 0.1 -10000 0 -0.31 43 43
PPARGC1A 0.022 0.054 -10000 0 -0.28 12 12
USF1 0.018 0.058 -10000 0 -0.26 17 17
RAB5/GDP/GDI1 0.005 0.077 -10000 0 -0.19 30 30
NOS2 0.014 0.055 -10000 0 -0.28 14 14
DDIT3 0.016 0.061 -10000 0 -0.22 25 25
RAB5A 0.041 0.006 -10000 0 0 13 13
HSPB1 0.002 0.05 0.28 2 -0.23 16 18
p38alpha-beta/HBP1 0.045 0.084 -10000 0 -0.21 25 25
CREB1 -0.005 0.098 -10000 0 -0.3 19 19
RAB5/GDP 0.03 0.012 -10000 0 -0.13 3 3
EIF4E -0.007 0.064 0.19 22 -0.3 9 31
RPS6KA4 0.02 0.056 -10000 0 -0.28 14 14
PLA2G4A -0.01 0.06 0.2 11 -0.31 11 22
GDI1 0.017 0.062 -10000 0 -0.25 22 22
TP53 0.002 0.064 0.2 1 -0.36 12 13
RPS6KA5 0.018 0.059 -10000 0 -0.25 19 19
ESR1 0.007 0.075 -10000 0 -0.22 44 44
HBP1 0.038 0.012 -10000 0 0 50 50
MEF2C 0.015 0.068 -10000 0 -0.28 21 21
MEF2A 0.017 0.058 -10000 0 -0.25 18 18
EIF4EBP1 -0.001 0.092 -10000 0 -0.2 82 82
KRT19 0.007 0.08 -10000 0 -0.22 47 47
ELK4 0.019 0.057 -10000 0 -0.27 15 15
ATF6 0.018 0.056 -10000 0 -0.26 16 16
ATF1 -0.005 0.098 -10000 0 -0.2 95 95
p38alpha-beta/MAPKAPK2 0.053 0.077 -10000 0 -0.24 16 16
p38alpha-beta/MAPKAPK3 0.055 0.076 -10000 0 -0.25 14 14
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.054 -10000 0 -0.4 5 5
VEGFR1 homodimer/NRP1 0.008 0.046 -10000 0 -0.4 5 5
mol:DAG -0.024 0.039 0.19 1 -0.31 6 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.042 -10000 0 -0.36 5 5
CaM/Ca2+ 0.025 0.053 0.2 1 -0.28 7 8
HIF1A 0.045 0.033 -10000 0 -0.28 5 5
GAB1 0.038 0.012 -10000 0 0 52 52
AKT1 0.001 0.09 0.22 7 -0.27 16 23
PLCG1 -0.024 0.04 0.2 1 -0.31 6 7
NOS3 0.026 0.071 0.3 4 -0.27 9 13
CBL 0.04 0.008 -10000 0 0 23 23
mol:NO 0.028 0.072 0.27 6 -0.26 9 15
FLT1 0.019 0.044 -10000 0 -0.49 4 4
PGF 0.04 0.009 -10000 0 0 27 27
VEGFR1 homodimer/NRP2/VEGFR121 0.018 0.062 -10000 0 -0.31 8 8
CALM1 0.04 0.01 -10000 0 0 31 31
PIK3CA 0.03 0.019 -10000 0 0 155 155
eNOS/Hsp90 0.021 0.069 0.28 4 -0.25 9 13
endothelial cell proliferation -0.003 0.066 0.24 4 -0.29 11 15
mol:Ca2+ -0.023 0.039 0.19 1 -0.31 6 7
MAPK3 -0.027 0.056 0.16 17 -0.25 9 26
MAPK1 -0.026 0.054 0.16 14 -0.25 9 23
PIK3R1 0.034 0.017 -10000 0 0 108 108
PLGF homodimer 0.04 0.009 -10000 0 0 27 27
PRKACA 0.035 0.015 -10000 0 0 89 89
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.036 0.015 -10000 0 0 80 80
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.008 0.046 -10000 0 -0.4 5 5
platelet activating factor biosynthetic process -0.027 0.058 0.15 24 -0.3 5 29
PI3K 0.039 0.08 -10000 0 -0.24 16 16
PRKCA -0.021 0.046 0.22 4 -0.27 8 12
PRKCB -0.022 0.036 0.18 1 -0.29 6 7
VEGFR1 homodimer/PLGF homodimer 0.035 0.054 -10000 0 -0.4 5 5
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.039 0.011 -10000 0 0 42 42
mol:IP3 -0.024 0.039 0.19 1 -0.31 6 7
RASA1 -0.021 0.045 0.2 2 -0.34 6 8
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFR1 homodimer 0.019 0.044 -10000 0 -0.49 4 4
VEGFB homodimer 0.039 0.011 -10000 0 0 42 42
NCK1 0.036 0.015 -10000 0 0 80 80
eNOS/Caveolin-1 0.043 0.082 0.3 4 -0.26 10 14
PTPN11 0.04 0.009 -10000 0 0 27 27
mol:PI-3-4-5-P3 0.037 0.079 -10000 0 -0.24 16 16
mol:L-citrulline 0.028 0.072 0.27 6 -0.26 9 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.066 -10000 0 -0.27 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.058 -10000 0 -0.28 10 10
CD2AP 0.037 0.014 -10000 0 0 67 67
PI3K/GAB1 0.044 0.088 -10000 0 -0.24 17 17
PDPK1 0.001 0.091 0.22 8 -0.31 7 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.056 -10000 0 -0.28 10 10
mol:NADP 0.028 0.072 0.27 6 -0.26 9 15
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.065 -10000 0 -0.26 10 10
VEGFR1 homodimer/NRP2 0.028 0.058 -10000 0 -0.34 8 8
Arf1 pathway

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
coatomer protein complex 0.022 0.047 0.15 65 -0.12 1 66
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.013 0.031 0.12 1 -0.14 4 5
AP2 0.038 0.045 -10000 0 -0.14 22 22
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.052 0.019 -10000 0 -0.12 1 1
CLTB 0.04 0.009 -10000 0 0 27 27
coatomer protein complex/ARF1/GTP/ER cargo protein 0.019 0.03 -10000 0 -0.15 14 14
CD4 0.032 0.018 -10000 0 0 132 132
CLTA 0.04 0.008 -10000 0 0 20 20
mol:GTP -0.003 0.003 0.012 6 -0.02 1 7
ARFGAP1 -0.009 0.004 0 77 -10000 0 77
mol:PI-4-5-P2 0.01 0.016 0.079 25 -10000 0 25
ARF1/GTP 0.023 0.012 0.079 1 -0.14 1 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.025 0.055 0.17 59 -0.17 4 63
mol:Choline 0.01 0.016 0.079 25 -10000 0 25
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.039 0.012 -10000 0 0 50 50
DDEF1 0.005 0.012 0.08 12 -10000 0 12
ARF1/GDP 0.006 0.011 0.06 1 -0.07 5 6
AP2M1 0.032 0.018 -10000 0 0 137 137
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.016 0.05 16 -0.1 2 18
Rac/GTP 0.029 0.011 -10000 0 -0.13 1 1
ARF1/GTP/GGA3/ARF-GAP1 0.044 0.026 -10000 0 -0.1 1 1
ARFIP2 0.035 0.019 -10000 0 -0.041 28 28
COPA 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 34 34
ARF1/GTP/coatomer protein complex 0.013 0.04 0.13 2 -0.16 19 21
ARF1/GTP/ARHGAP10 0.024 0.01 -10000 0 -0.11 1 1
GGA3 0.041 0.008 -10000 0 0 19 19
ARF1/GTP/Membrin 0.023 0.05 -10000 0 -0.22 21 21
AP2A1 0.039 0.011 -10000 0 0 43 43
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.033 -10000 0 -0.16 14 14
ARF1/GDP/Membrin 0.025 0.057 -10000 0 -0.25 21 21
Arfaptin 2/Rac/GDP 0.051 0.019 -10000 0 -0.11 1 1
CYTH2 -0.003 0.003 0.012 6 -0.02 1 7
ARF1/GTP/GGA3 0.049 0.021 -10000 0 -0.12 2 2
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
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 0.008 0.055 -10000 0 -0.34 6 6
PLD2 0.01 0.016 0.08 25 -10000 0 25
ARF-GAP1/v-SNARE -0.009 0.004 0 77 -10000 0 77
PIP5K1A 0.01 0.016 0.079 25 -10000 0 25
ARF1/GTP/Membrin/GBF1/p115 0.018 0.025 -10000 0 -0.075 17 17
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.01 0.016 0.079 25 -10000 0 25
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.004 0 77 -10000 0 77
GOSR2 0.011 0.052 -10000 0 -0.31 14 14
USO1 0.004 0.008 0.041 25 -0.029 1 26
GBF1 0.005 0.07 -10000 0 -0.34 22 22
ARF1/GTP/Arfaptin 2 0.05 0.02 -10000 0 -0.12 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.038 0.061 -10000 0 -0.13 38 38
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.038 0.013 -10000 0 0 56 56
Ran/GTP/Exportin 1/HDAC4 -0.029 0.033 -10000 0 -0.16 24 24
MDM2/SUMO1 0.039 0.062 -10000 0 -0.18 18 18
HDAC4 0.041 0.007 -10000 0 0 15 15
Ran/GTP/Exportin 1/HDAC1 -0.031 0.04 -10000 0 -0.17 30 30
SUMO1 0.041 0.006 -10000 0 0 13 13
NPC/RanGAP1/SUMO1 0.008 0.033 -10000 0 -0.14 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.001 0.039 -10000 0 -0.17 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
SUMO1/HDAC4 0.041 0.062 -10000 0 -0.18 18 18
SUMO1/HDAC1 0.037 0.065 -10000 0 -0.18 25 25
RANGAP1 0.038 0.013 -10000 0 0 57 57
MDM2/SUMO1/SUMO1 0.083 0.056 -10000 0 -0.12 20 20
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.035 -10000 0 -0.15 25 25
Ran/GTP 0.023 0.058 0.17 1 -0.15 36 37
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.039 0.01 -10000 0 0 35 35
UBE2I 0.04 0.009 -10000 0 0 27 27
Ran/GTP/Exportin 1 0.019 0.068 0.2 13 -0.2 26 39
NPC 0.02 0.022 -10000 0 -0.085 23 23
PIAS2 0.038 0.012 -10000 0 0 51 51
PIAS1 0.04 0.009 -10000 0 0 28 28
EntrezGene:9972 0 0 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.017 -10000 0 -0.13 3 3
PDGFRB 0.037 0.014 -10000 0 0 64 64
SPHK1 0.014 0.073 -10000 0 -0.61 7 7
mol:S1P 0.013 0.067 -10000 0 -0.51 7 7
S1P1/S1P/Gi 0.022 0.09 -10000 0 -0.32 23 23
GNAO1 0.034 0.018 -10000 0 -0.002 108 108
PDGFB-D/PDGFRB/PLCgamma1 0.011 0.11 0.26 4 -0.29 32 36
PLCG1 0.006 0.097 0.21 12 -0.3 29 41
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.014 -10000 0 0 64 64
GNAI2 0.041 0.012 -10000 0 -0.013 24 24
GNAI3 0.039 0.015 -10000 0 -0.005 53 53
GNAI1 0.035 0.018 -10000 0 -0.002 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.026 0.024 0.2 6 -0.12 3 9
S1P1/S1P 0.023 0.061 -10000 0 -0.32 8 8
negative regulation of cAMP metabolic process 0.022 0.089 -10000 0 -0.32 23 23
MAPK3 0.009 0.1 -10000 0 -0.43 18 18
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
KDR 0.044 0.011 -10000 0 -10000 0 0
PLCB2 0.017 0.059 -10000 0 -0.29 8 8
RAC1 0.039 0.01 -10000 0 0 34 34
RhoA/GTP 0.024 0.056 -10000 0 -0.27 9 9
receptor internalization 0.021 0.058 -10000 0 -0.3 8 8
PTGS2 -0.001 0.15 -10000 0 -0.75 13 13
Rac1/GTP 0.022 0.055 -10000 0 -0.28 8 8
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFA 0.004 0.002 -10000 0 -10000 0 0
negative regulation of T cell proliferation 0.022 0.089 -10000 0 -0.32 23 23
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.015 -10000 0 -0.006 51 51
MAPK1 0.01 0.11 -10000 0 -0.49 15 15
S1P1/S1P/PDGFB-D/PDGFRB 0.034 0.072 -10000 0 -0.26 9 9
ABCC1 0.041 0.009 -10000 0 0 26 26
Effects of Botulinum toxin

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
STX1A -0.01 0.002 0 13 -10000 0 13
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.057 0.019 -10000 0 -0.14 2 2
STXBP1 0.039 0.011 -10000 0 0 41 41
ACh/CHRNA1 0.029 0.025 0.092 2 -0.049 36 38
RAB3GAP2/RIMS1/UNC13B 0.071 0.04 -10000 0 -0.12 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.041 0.007 -10000 0 0 15 15
mol:ACh 0.004 0.025 0.073 35 -0.085 5 40
RAB3GAP2 0.039 0.01 -10000 0 0 37 37
STX1A/SNAP25/VAMP2 0.056 0.058 0.18 2 -0.13 5 7
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.029 0.025 0.092 2 -0.049 36 38
UNC13B 0.04 0.009 -10000 0 0 25 25
CHRNA1 0.038 0.013 -10000 0 0 59 59
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.03 0.026 0.092 2 -0.049 37 39
SNAP25 0.006 0.002 -10000 0 0 71 71
VAMP2 0.005 0.002 -10000 0 0 67 67
SYT1 0.038 0.012 -10000 0 0 47 47
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.034 0.011 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.056 0.058 0.18 2 -0.13 5 7
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.063 0.035 -9999 0 -0.098 17 17
MAPK9 0.009 0.002 -9999 0 0 39 39
adrenocorticotropin secretion -0.01 0.003 0 44 -10000 0 44
GNB1/GNG2 0.049 0.032 -9999 0 -0.11 19 19
GNB1 0.041 0.005 -9999 0 0 7 7
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.009 0.002 -9999 0 0 28 28
Gs family/GTP 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.002 0 -9999 0 -10000 0 0
GNAL 0.04 0.009 -9999 0 0 26 26
GNG2 0.039 0.01 -9999 0 0 34 34
CRH 0.039 0.011 -9999 0 0 44 44
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.009 0.002 -9999 0 0 30 30
MAPK11 0.007 0.004 -9999 0 0 142 142
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.012 -10000 0 -0.072 4 4
NFATC2 0.048 0.18 0.41 5 -0.39 35 40
NFATC3 0.069 0.067 0.29 26 -0.26 2 28
CD40LG 0.083 0.15 0.49 5 -0.5 2 7
ITCH 0.021 0.057 0.2 6 -0.23 20 26
CBLB 0.019 0.061 0.2 6 -0.25 22 28
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.047 0.14 0.38 2 -0.52 7 9
JUNB 0.03 0.019 -10000 0 0 160 160
CaM/Ca2+/Calcineurin A alpha-beta B1 0.043 0.051 -10000 0 -0.18 24 24
T cell anergy 0.002 0.071 0.27 6 -0.29 20 26
TLE4 0.01 0.16 0.28 4 -0.41 47 51
Jun/NFAT1-c-4/p21SNFT 0.082 0.15 -10000 0 -0.48 1 1
AP-1/NFAT1-c-4 0.092 0.19 -10000 0 -0.56 1 1
IKZF1 0.023 0.11 0.22 19 -0.26 35 54
T-helper 2 cell differentiation 0.035 0.14 0.45 2 -0.49 1 3
AP-1/NFAT1 0.038 0.14 0.32 2 -0.27 28 30
CALM1 0.042 0.036 -10000 0 -0.12 21 21
EGR2 0.06 0.16 0.57 8 -1 2 10
EGR3 0.053 0.14 0.57 6 -0.53 1 7
NFAT1/FOXP3 0.059 0.14 0.33 3 -0.28 32 35
EGR1 0.028 0.021 -10000 0 -0.035 2 2
JUN 0.04 0.026 0.14 2 -0.045 10 12
EGR4 0.041 0.009 -10000 0 -0.035 2 2
mol:Ca2+ 0.005 0.022 -10000 0 -0.1 23 23
GBP3 -0.019 0.21 0.3 9 -0.46 91 100
FOSL1 0.041 0.007 -10000 0 0 15 15
NFAT1-c-4/MAF/IRF4 0.095 0.15 -10000 0 -0.47 2 2
DGKA 0.026 0.12 0.3 7 -0.31 30 37
CREM 0.04 0.008 -10000 0 -0.002 21 21
NFAT1-c-4/PPARG 0.084 0.14 -10000 0 -0.5 2 2
CTLA4 0.027 0.1 0.23 1 -0.24 31 32
NFAT1-c-4 (dimer)/EGR1 0.062 0.15 -10000 0 -0.54 2 2
NFAT1-c-4 (dimer)/EGR4 0.091 0.15 -10000 0 -0.5 2 2
FOS 0.029 0.029 0.14 2 -0.042 8 10
IFNG 0.036 0.13 -10000 0 -0.49 6 6
T cell activation 0.054 0.12 0.6 1 -10000 0 1
MAF 0.036 0.015 -10000 0 0 84 84
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.06 0.13 0.57 3 -0.51 22 25
TNF 0.047 0.13 0.46 2 -0.52 2 4
FASLG 0.05 0.17 0.7 1 -1 3 4
TBX21 0.047 0.013 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.037 0.018 -10000 0 -0.12 1 1
PTPN1 0.027 0.12 0.32 3 -0.29 28 31
NFAT1-c-4/ICER1 0.085 0.14 -10000 0 -0.5 2 2
GATA3 0.042 0.011 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.039 0.13 -10000 0 -0.48 6 6
IL2RA 0.05 0.15 0.39 1 -0.47 9 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.022 0.12 0.27 2 -0.32 28 30
E2F1 0.032 0.05 -10000 0 -0.18 27 27
PPARG 0.039 0.01 -10000 0 0 37 37
SLC3A2 0.025 0.13 0.29 5 -0.32 30 35
IRF4 0.041 0.008 -10000 0 0 19 19
PTGS2 0.056 0.14 0.68 1 -0.51 3 4
CSF2 0.078 0.15 0.49 5 -0.5 2 7
JunB/Fra1/NFAT1-c-4 0.077 0.15 -10000 0 -0.48 2 2
IL4 0.034 0.14 0.45 2 -0.51 1 3
IL5 0.078 0.15 0.48 4 -0.5 2 6
IL2 0.054 0.12 0.6 1 -10000 0 1
IL3 0.037 0.079 -10000 0 -0.42 10 10
RNF128 0.023 0.045 0.2 7 -0.16 22 29
NFATC1 0.06 0.13 0.52 21 -0.57 3 24
CDK4 -0.078 0.28 -10000 0 -1.2 28 28
PTPRK 0.013 0.15 0.28 5 -0.39 45 50
IL8 0.048 0.14 0.55 4 -0.49 2 6
POU2F1 0.046 0.01 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.01 0.068 0.27 6 -0.4 2 8
CRKL 0.014 0.065 0.29 3 -0.42 2 5
HRAS 0.029 0.081 0.25 1 -0.28 9 10
mol:PIP3 0.023 0.089 0.36 1 -0.33 9 10
SPRED1 0.035 0.015 -10000 0 0 90 90
SPRED2 0.04 0.009 -10000 0 0 24 24
GAB1 0.018 0.061 0.22 1 -0.44 2 3
FOXO3 0.021 0.091 0.35 1 -0.38 11 12
AKT1 0.022 0.096 0.37 1 -0.41 11 12
BAD 0.017 0.092 0.35 1 -0.38 11 12
megakaryocyte differentiation 0.023 0.059 0.24 3 -0.3 1 4
GSK3B 0.021 0.098 0.32 8 -0.38 11 19
RAF1 0.021 0.076 0.26 6 -0.25 8 14
SHC1 0.04 0.01 -10000 0 0 31 31
STAT3 0.018 0.061 0.26 3 -0.44 2 5
STAT1 0.032 0.11 -10000 0 -0.87 3 3
HRAS/SPRED1 0.033 0.083 0.26 3 -0.29 5 8
cell proliferation 0.018 0.062 0.24 3 -0.43 2 5
PIK3CA 0.03 0.019 -10000 0 0 155 155
TEC 0.033 0.017 -10000 0 0 115 115
RPS6KB1 0.021 0.099 0.3 1 -0.38 11 12
HRAS/SPRED2 0.04 0.084 0.26 3 -0.27 6 9
LYN/TEC/p62DOK 0.041 0.097 -10000 0 -0.34 4 4
MAPK3 0.016 0.065 0.22 7 -0.24 5 12
STAP1 0.023 0.061 0.24 3 -0.43 2 5
GRAP2 0.038 0.013 -10000 0 0 57 57
JAK2 0.029 0.11 -10000 0 -0.66 4 4
STAT1 (dimer) 0.031 0.12 -10000 0 -0.85 3 3
mol:Gleevec -0.002 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.062 0.092 0.3 1 -0.34 4 5
actin filament polymerization 0.024 0.061 0.25 2 -0.42 2 4
LYN 0.036 0.015 -10000 0 0 83 83
STAP1/STAT5A (dimer) 0.017 0.099 0.3 1 -0.5 5 6
PIK3R1 0.034 0.017 -10000 0 0 108 108
CBL/CRKL/GRB2 0.044 0.083 0.42 1 -0.43 2 3
PI3K 0.023 0.1 0.32 1 -0.35 12 13
PTEN 0.039 0.011 -10000 0 0 38 38
SCF/KIT/EPO/EPOR 0.061 0.14 -10000 0 -1.3 2 2
MAPK8 0.018 0.063 0.24 3 -0.44 2 5
STAT3 (dimer) 0.02 0.063 0.25 4 -0.43 2 6
positive regulation of transcription 0.016 0.058 0.2 8 -0.2 5 13
mol:GDP 0.036 0.086 0.27 1 -0.29 6 7
PIK3C2B 0.019 0.066 0.25 4 -0.44 2 6
CBL/CRKL 0.03 0.077 0.42 1 -0.44 2 3
FER 0.018 0.061 0.24 2 -0.44 2 4
SH2B3 0.023 0.061 0.24 3 -0.43 2 5
PDPK1 0.022 0.087 0.29 4 -0.3 8 12
SNAI2 0.023 0.068 0.25 4 -0.51 2 6
positive regulation of cell proliferation 0.02 0.11 -10000 0 -0.7 3 3
KITLG 0.044 0.015 -10000 0 -0.041 3 3
cell motility 0.02 0.11 -10000 0 -0.7 3 3
PTPN6 0.033 0.017 -10000 0 -0.005 80 80
EPOR 0.01 0.17 -10000 0 -0.57 27 27
STAT5A (dimer) 0.021 0.1 0.31 1 -0.51 5 6
SOCS1 0.038 0.012 -10000 0 0 50 50
cell migration -0.017 0.06 0.43 2 -0.26 1 3
SOS1 0.038 0.013 -10000 0 0 56 56
EPO 0.043 0.011 -10000 0 -0.035 3 3
VAV1 0.037 0.014 -10000 0 0 68 68
GRB10 0.018 0.063 0.26 1 -0.44 2 3
PTPN11 0.038 0.011 -10000 0 -0.004 31 31
SCF/KIT 0.027 0.065 0.25 3 -0.45 2 5
GO:0007205 -0.002 0.004 -10000 0 -10000 0 0
MAP2K1 0.014 0.067 0.22 11 -0.24 3 14
CBL 0.04 0.008 -10000 0 0 23 23
KIT 0.017 0.16 -10000 0 -0.63 10 10
MAP2K2 0.013 0.063 0.22 6 -0.23 4 10
SHC/Grb2/SOS1 0.065 0.094 0.3 1 -0.33 4 5
STAT5A 0.023 0.1 -10000 0 -0.53 5 5
GRB2 0.041 0.007 -10000 0 0 17 17
response to radiation 0.027 0.071 0.26 6 -0.5 2 8
SHC/GRAP2 0.053 0.024 -10000 0 -0.14 1 1
PTPRO 0.02 0.056 0.24 3 -0.3 1 4
SH2B2 0.023 0.061 0.24 3 -0.43 2 5
DOK1 0.04 0.009 -10000 0 0 24 24
MATK 0.018 0.06 0.26 1 -0.44 2 3
CREBBP 0.059 0.029 0.15 2 -0.15 3 5
BCL2 -0.021 0.23 -10000 0 -0.66 34 34
Aurora C signaling

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
INCENP 0.042 0.004 -9999 0 0 5 5
Aurora C/Aurora B/INCENP 0.063 0.046 -9999 0 -0.11 28 28
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.005 0.065 -9999 0 -0.39 14 14
AURKB 0.036 0.015 -9999 0 0 81 81
AURKC 0.042 0.002 -9999 0 0 1 1
Glypican 2 network

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
MDK 0.04 0.009 -9999 0 0 24 24
GPC2 0.04 0.008 -9999 0 0 22 22
GPC2/Midkine 0.055 0.032 -9999 0 -0.14 13 13
neuron projection morphogenesis 0.054 0.032 -9999 0 -0.14 13 13
Arf6 trafficking events

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
SLC2A4 0.039 0.01 -10000 0 0 33 33
CLTC 0.015 0.089 0.23 1 -0.48 11 12
calcium ion-dependent exocytosis 0.017 0.045 0.18 2 -0.19 6 8
Dynamin 2/GTP 0.021 0.042 -10000 0 -0.11 45 45
EXOC4 0.038 0.012 -10000 0 0 49 49
CD59 0.01 0.062 -10000 0 -0.36 11 11
CPE 0.012 0.013 -10000 0 -0.11 4 4
CTNNB1 0.04 0.01 -10000 0 0 31 31
membrane fusion 0.004 0.035 -10000 0 -0.2 5 5
CTNND1 -0.006 0.072 0.18 57 -0.2 3 60
DNM2 0.037 0.014 -10000 0 0 72 72
mol:PI-4-5-P2 0.017 0.056 0.2 3 -0.24 12 15
TSHR 0.014 0.015 -10000 0 -0.11 7 7
INS 0.006 0.1 -10000 0 -0.44 26 26
BIN1 0.041 0.007 -10000 0 0 18 18
mol:Choline 0.004 0.035 -10000 0 -0.2 5 5
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.014 -10000 0 -0.11 5 5
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.041 0.008 -10000 0 0 19 19
mol:Ca2+ 0.021 0.042 -10000 0 -0.11 45 45
JUP 0.008 0.064 -10000 0 -0.36 11 11
ASAP2/amphiphysin II 0.048 0.024 -10000 0 -0.098 11 11
ARF6/GTP 0.028 0.019 -10000 0 -0.13 8 8
CDH1 0.007 0.064 -10000 0 -0.38 10 10
clathrin-independent pinocytosis 0.028 0.019 -10000 0 -0.13 8 8
MAPK8IP3 0.04 0.009 -10000 0 0 27 27
positive regulation of endocytosis 0.028 0.019 -10000 0 -0.13 8 8
EXOC2 0.041 0.006 -10000 0 0 13 13
substrate adhesion-dependent cell spreading 0.009 0.1 -10000 0 -0.36 27 27
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.039 0.011 -10000 0 0 42 42
regulation of calcium-dependent cell-cell adhesion -0.035 0.086 0.35 12 -10000 0 12
positive regulation of phagocytosis 0.015 0.015 -10000 0 -0.11 7 7
ARF6/GTP/JIP3 0.05 0.024 -10000 0 -0.11 8 8
ACAP1 0.005 0.034 -10000 0 -0.18 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.061 -10000 0 -0.34 11 11
clathrin heavy chain/ACAP1 0.015 0.078 0.26 2 -0.38 11 13
JIP4/KLC1 0.045 0.03 -10000 0 -0.098 18 18
EXOC1 0.038 0.012 -10000 0 0 47 47
exocyst 0.008 0.1 -10000 0 -0.37 27 27
RALA/GTP 0.027 0.021 -10000 0 -0.13 9 9
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.047 0.032 -10000 0 -0.11 18 18
receptor recycling 0.028 0.019 -10000 0 -0.13 8 8
CTNNA1 -0.006 0.071 0.18 55 -0.2 3 58
NME1 0.014 0.014 -10000 0 -0.11 5 5
clathrin coat assembly 0.015 0.089 0.23 1 -0.47 11 12
IL2RA 0.013 0.061 0.22 1 -0.35 10 11
VAMP3 0.015 0.015 -10000 0 -0.11 7 7
GLUT4/clathrin heavy chain/ACAP1 0.038 0.081 -10000 0 -0.35 11 11
EXOC6 0.038 0.012 -10000 0 0 55 55
PLD1 0 0.05 -10000 0 -0.2 29 29
PLD2 0.014 0.029 -10000 0 -0.19 5 5
EXOC5 0.04 0.009 -10000 0 0 27 27
PIP5K1C 0.012 0.05 0.18 2 -0.24 10 12
SDC1 0.01 0.061 -10000 0 -0.36 10 10
ARF6/GDP 0.025 0.04 -10000 0 -0.12 38 38
EXOC7 0.041 0.006 -10000 0 0 12 12
E-cadherin/beta catenin 0.038 0.089 -10000 0 -0.36 12 12
mol:Phosphatidic acid 0.004 0.035 -10000 0 -0.2 5 5
endocytosis -0.047 0.023 0.098 11 -10000 0 11
SCAMP2 0.04 0.008 -10000 0 0 23 23
ADRB2 0.008 0.087 -10000 0 -0.43 12 12
EXOC3 0.041 0.005 -10000 0 0 8 8
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.046 0.19 5 -0.11 45 50
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.008 0.086 -10000 0 -0.43 12 12
RALA 0.04 0.009 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.091 -10000 0 -0.4 11 11
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.062 0.028 -10000 0 -0.098 1 1
RGS9BP 0.037 0.013 -10000 0 0 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.05 0.017 -10000 0 -10000 0 0
mol:ADP -0.01 0.003 -10000 0 -10000 0 0
GNAT2 0.041 0.005 -10000 0 0 8 8
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.05 0.018 -10000 0 -10000 0 0
GRK7 0.038 0.012 -10000 0 0 51 51
CNGB3 0.038 0.012 -10000 0 0 53 53
Cone Metarhodopsin II/X-Arrestin 0.031 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.057 0.19 43 -10000 0 43
Cone PDE6 0.088 0.057 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0.024 0.008 -10000 0 -10000 0 0
Na + (4 Units) 0.066 0.03 -10000 0 -10000 0 0
GNAT2/GDP 0.08 0.039 -10000 0 -0.1 1 1
GNB5 0.04 0.009 -10000 0 0 29 29
mol:GMP (4 units) -0.002 0.06 0.19 49 -10000 0 49
Cone Transducin 0.067 0.031 -10000 0 -0.11 1 1
SLC24A2 0.039 0.011 -10000 0 0 41 41
GNB3/GNGT2 0.052 0.024 -10000 0 -0.14 1 1
GNB3 0.037 0.014 -10000 0 0 66 66
GNAT2/GTP 0.031 0.004 -10000 0 -10000 0 0
CNGA3 0.041 0.005 -10000 0 0 7 7
ARR3 0.042 0.002 -10000 0 0 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.051 0.018 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
Cone CNG Channel 0.079 0.046 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.039 0.011 -10000 0 0 41 41
RGS9 0.039 0.011 -10000 0 0 39 39
PDE6C 0.04 0.009 -10000 0 0 24 24
GNGT2 0.04 0.009 -10000 0 0 25 25
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.038 0.013 -10000 0 0 59 59
Visual signal transduction: Rods

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
mol:K + 0.04 0.008 -10000 0 0 20 20
GNAT1/GTP 0.03 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.053 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.049 0.021 -10000 0 -0.11 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.041 0.007 -10000 0 0 15 15
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.069 0.037 -10000 0 -0.11 2 2
mol:Na + 0.07 0.042 -10000 0 -0.11 1 1
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.086 0.05 -10000 0 -0.11 1 1
CNGB1 0.038 0.012 -10000 0 0 49 49
RDH5 0.037 0.014 -10000 0 0 72 72
SAG 0.041 0.006 -10000 0 0 10 10
mol:Ca2+ -0.018 0.082 0.33 21 -10000 0 21
Na + (4 Units) 0.056 0.038 -10000 0 -0.11 1 1
RGS9 0.039 0.011 -10000 0 0 39 39
GNB1/GNGT1 0.057 0.023 -10000 0 -0.14 5 5
GNAT1/GDP 0.079 0.039 -10000 0 -0.1 1 1
GUCY2D 0.039 0.01 -10000 0 0 37 37
GNGT1 0.04 0.009 -10000 0 0 29 29
GUCY2F 0.042 0.002 -10000 0 0 1 1
GNB5 0.04 0.009 -10000 0 0 29 29
mol:GMP (4 units) 0.04 0.025 0.17 13 -0.1 2 15
mol:11-cis-retinal 0.037 0.014 -10000 0 0 72 72
mol:cGMP 0.077 0.034 0.2 2 -0.11 1 3
GNB1 0.041 0.005 -10000 0 0 7 7
Rhodopsin 0.05 0.031 -10000 0 -0.14 7 7
SLC24A1 0.04 0.008 -10000 0 0 20 20
CNGA1 0.041 0.008 -10000 0 0 19 19
Metarhodopsin II 0.026 0.005 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.093 0.038 -10000 0 -0.11 1 1
RGS9BP 0.037 0.013 -10000 0 0 62 62
Metarhodopsin II/Transducin 0.025 0.019 -10000 0 -0.14 6 6
GCAP Family/Ca ++ 0.073 0.024 -10000 0 -0.11 1 1
PDE6A/B 0.059 0.013 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.073 0.027 -10000 0 -0.11 5 5
PDE6B 0.041 0.005 -10000 0 0 7 7
PDE6A 0.041 0.008 -10000 0 0 19 19
PDE6G 0.038 0.013 -10000 0 0 58 58
RHO 0.04 0.008 -10000 0 0 23 23
PDE6 0.096 0.054 -10000 0 -0.15 2 2
GUCA1A 0.04 0.009 -10000 0 0 25 25
GC2/GCAP Family 0.098 0.031 -10000 0 -0.11 1 1
GUCA1C 0.04 0.009 -10000 0 0 28 28
GUCA1B 0.04 0.008 -10000 0 0 23 23
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 = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/2008725/1.GetReducedSegments.Finished/OV.RS.tsv

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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