Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 101 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
HIF-1-alpha transcription factor network 124
FOXM1 transcription factor network 102
Angiopoietin receptor Tie2-mediated signaling 87
Endothelins 83
TCGA08_p53 76
TCGA08_rtk_signaling 76
HIF-2-alpha transcription factor network 75
Thromboxane A2 receptor signaling 73
Ceramide signaling pathway 73
PDGFR-alpha signaling pathway 72
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 124 9473 76 -0.07 0.11 1000 -1000 -0.014 -1000
FOXM1 transcription factor network 102 5219 51 -0.3 0.056 1000 -1000 -0.043 -1000
Angiopoietin receptor Tie2-mediated signaling 87 7697 88 -0.29 0.053 1000 -1000 -0.049 -1000
Endothelins 83 7982 96 -0.12 0.037 1000 -1000 -0.023 -1000
TCGA08_p53 76 534 7 -0.002 0.033 1000 -1000 -0.011 -1000
TCGA08_rtk_signaling 76 1998 26 -0.033 0.1 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 75 3261 43 -0.081 0.048 1000 -1000 -0.041 -1000
Thromboxane A2 receptor signaling 73 7669 105 -0.07 0.045 1000 -1000 -0.021 -1000
Ceramide signaling pathway 73 5589 76 -0.087 0.072 1000 -1000 -0.019 -1000
PDGFR-alpha signaling pathway 72 3182 44 -0.096 0.037 1000 -1000 -0.025 -1000
Effects of Botulinum toxin 70 1836 26 -0.008 0.053 1000 -1000 -0.011 -1000
Syndecan-3-mediated signaling events 69 2441 35 -0.063 0.08 1000 -1000 -0.012 -1000
Canonical Wnt signaling pathway 66 3403 51 -0.1 0.068 1000 -1000 -0.021 -1000
Wnt signaling 66 468 7 -0.005 0.038 1000 -1000 0 -1000
PLK2 and PLK4 events 65 197 3 -0.019 0.036 1000 -1000 -0.02 -1000
Ras signaling in the CD4+ TCR pathway 65 1117 17 0 0.042 1000 -1000 0 -1000
Arf6 signaling events 64 4020 62 -0.004 0.094 1000 -1000 -0.002 -1000
TCGA08_retinoblastoma 63 505 8 -0.049 0.059 1000 -1000 -0.004 -1000
LPA receptor mediated events 62 6324 102 -0.12 0.037 1000 -1000 -0.033 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 62 2073 33 -0.048 0.069 1000 -1000 -0.008 -1000
Syndecan-1-mediated signaling events 61 2090 34 -0.009 0.036 1000 -1000 -0.014 -1000
EGFR-dependent Endothelin signaling events 61 1289 21 -0.017 0.036 1000 -1000 -0.024 -1000
Syndecan-4-mediated signaling events 59 4013 67 -0.15 0.037 1000 -1000 -0.031 -1000
S1P4 pathway 59 1478 25 -0.016 0.037 1000 -1000 -0.009 -1000
S1P5 pathway 58 996 17 -0.012 0.037 1000 -1000 -0.012 -1000
Nongenotropic Androgen signaling 57 2986 52 -0.087 0.06 1000 -1000 -0.024 -1000
Signaling events mediated by VEGFR1 and VEGFR2 53 6738 125 -0.058 0.05 1000 -1000 -0.04 -1000
amb2 Integrin signaling 52 4289 82 -0.017 0.076 1000 -1000 -0.021 -1000
Glypican 2 network 52 210 4 0 0.008 1000 -1000 0 -1000
IL2 signaling events mediated by STAT5 52 1147 22 -0.072 0.039 1000 -1000 -0.017 -1000
IL23-mediated signaling events 52 3137 60 -0.061 0.15 1000 -1000 -0.042 -1000
IL2 signaling events mediated by PI3K 51 2967 58 -0.19 0.047 1000 -1000 -0.029 -1000
Fc-epsilon receptor I signaling in mast cells 50 4915 97 -0.1 0.05 1000 -1000 -0.042 -1000
Syndecan-2-mediated signaling events 48 3329 69 -0.025 0.038 1000 -1000 -0.033 -1000
Osteopontin-mediated events 47 1821 38 -0.068 0.051 1000 -1000 -0.015 -1000
FoxO family signaling 47 3062 64 -0.17 0.053 1000 -1000 -0.018 -1000
Arf6 downstream pathway 46 1988 43 -0.026 0.05 1000 -1000 -0.03 -1000
Ephrin B reverse signaling 46 2212 48 -0.065 0.067 1000 -1000 -0.047 -1000
S1P1 pathway 46 1673 36 -0.026 0.038 1000 -1000 -0.019 -1000
BCR signaling pathway 46 4651 99 -0.049 0.052 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 44 753 17 -0.12 0.064 1000 -1000 -0.012 -1000
Presenilin action in Notch and Wnt signaling 44 2708 61 -0.081 0.08 1000 -1000 -0.039 -1000
Glypican 1 network 44 2144 48 -0.033 0.054 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 43 2811 65 -0.042 0.037 1000 -1000 -0.046 -1000
Regulation of nuclear SMAD2/3 signaling 43 5873 136 -0.21 0.2 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 43 2956 68 -0.099 0.048 1000 -1000 -0.027 -1000
Signaling events mediated by PTP1B 42 3260 76 -0.034 0.061 1000 -1000 -0.023 -1000
mTOR signaling pathway 42 2264 53 -0.038 0.047 1000 -1000 -0.026 -1000
EPHB forward signaling 42 3620 85 -0.053 0.082 1000 -1000 -0.042 -1000
IL12-mediated signaling events 41 3595 87 -0.11 0.1 1000 -1000 -0.014 -1000
Noncanonical Wnt signaling pathway 41 1086 26 -0.031 0.038 1000 -1000 -0.02 -1000
E-cadherin signaling in keratinocytes 41 1791 43 -0.041 0.064 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 40 2204 54 -0.035 0.078 1000 -1000 -0.025 -1000
Reelin signaling pathway 40 2279 56 -0.015 0.073 1000 -1000 -0.014 -1000
FAS signaling pathway (CD95) 40 1909 47 -0.14 0.049 1000 -1000 -0.023 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 2968 74 -0.11 0.078 1000 -1000 -0.05 -1000
Class I PI3K signaling events 40 2938 73 -0.046 0.066 1000 -1000 -0.02 -1000
BMP receptor signaling 39 3204 81 -0.029 0.059 1000 -1000 -0.007 -1000
Class I PI3K signaling events mediated by Akt 39 2703 68 -0.033 0.066 1000 -1000 -0.019 -1000
Paxillin-dependent events mediated by a4b1 39 1432 36 -0.055 0.057 1000 -1000 -0.043 -1000
Signaling events mediated by PRL 39 1341 34 -0.029 0.048 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 38 1411 37 -0.034 0.085 1000 -1000 -0.016 -1000
Sphingosine 1-phosphate (S1P) pathway 37 1039 28 -0.02 0.037 1000 -1000 -0.02 -1000
PLK1 signaling events 37 3221 85 -0.037 0.062 1000 -1000 -0.021 -1000
Integrins in angiogenesis 37 3121 84 -0.042 0.071 1000 -1000 -0.019 -1000
Plasma membrane estrogen receptor signaling 37 3203 86 -0.069 0.053 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 37 1651 44 -0.003 0.043 1000 -1000 -0.008 -1000
IL1-mediated signaling events 36 2263 62 -0.039 0.075 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 36 1986 54 -0.035 0.048 1000 -1000 -0.034 -1000
IL6-mediated signaling events 36 2729 75 -0.081 0.098 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 36 4320 120 -0.04 0.091 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 36 3507 97 -0.053 0.066 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 35 2984 85 -0.13 0.12 1000 -1000 -0.035 -1000
IFN-gamma pathway 35 2394 68 -0.04 0.066 1000 -1000 -0.037 -1000
IGF1 pathway 35 2025 57 -0.049 0.067 1000 -1000 -0.027 -1000
EPO signaling pathway 34 1880 55 -0.006 0.069 1000 -1000 -0.021 -1000
Aurora B signaling 34 2297 67 -0.031 0.062 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 33 2512 74 -0.068 0.064 1000 -1000 -0.024 -1000
Signaling events regulated by Ret tyrosine kinase 33 2724 82 -0.051 0.069 1000 -1000 -0.025 -1000
E-cadherin signaling in the nascent adherens junction 33 2514 76 -0.044 0.091 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 32 2104 65 -0.016 0.074 1000 -1000 -0.021 -1000
p75(NTR)-mediated signaling 32 4010 125 -0.025 0.084 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 32 1284 40 -0.051 0.052 1000 -1000 -0.046 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 31 714 23 -0.022 0.057 1000 -1000 -0.005 -1000
Signaling mediated by p38-gamma and p38-delta 31 470 15 -0.026 0.037 1000 -1000 -0.019 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 31 1406 45 -0.027 0.077 1000 -1000 -0.018 -1000
S1P3 pathway 31 1322 42 -0.029 0.037 1000 -1000 -0.017 -1000
ErbB4 signaling events 30 2104 69 -0.071 0.064 1000 -1000 -0.02 -1000
IL4-mediated signaling events 30 2753 91 -0.31 0.058 1000 -1000 -0.059 -1000
Retinoic acid receptors-mediated signaling 30 1752 58 -0.047 0.06 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 30 398 13 0 0.069 1000 -1000 0 -1000
TCR signaling in naïve CD8+ T cells 29 2773 93 -0.33 0.38 1000 -1000 -0.025 -1000
Insulin Pathway 29 2167 74 -0.053 0.085 1000 -1000 -0.031 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 29 2272 78 -0.023 0.076 1000 -1000 -0.034 -1000
Visual signal transduction: Cones 28 1067 38 -0.013 0.06 1000 -1000 -0.014 -1000
a4b1 and a4b7 Integrin signaling 28 144 5 0.029 0.053 1000 -1000 0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 28 2356 83 -0.031 0.07 1000 -1000 -0.016 -1000
LPA4-mediated signaling events 27 331 12 -0.018 0.016 1000 -1000 -0.015 -1000
BARD1 signaling events 27 1543 57 -0.065 0.084 1000 -1000 -0.055 -1000
Aurora A signaling 27 1633 60 -0.017 0.059 1000 -1000 -0.019 -1000
Regulation of Telomerase 27 2834 102 -0.026 0.079 1000 -1000 -0.031 -1000
Nectin adhesion pathway 26 1700 63 -0.011 0.085 1000 -1000 -0.022 -1000
VEGFR1 specific signals 26 1471 56 -0.034 0.043 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 25 823 32 -0.019 0.044 1000 -1000 -0.019 -1000
Circadian rhythm pathway 24 545 22 -0.01 0.056 1000 -1000 -0.019 -1000
Glucocorticoid receptor regulatory network 24 2825 114 -0.13 0.065 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class I 24 2523 104 -0.048 0.066 1000 -1000 -0.036 -1000
TRAIL signaling pathway 23 1141 48 -0.022 0.088 1000 -1000 -0.019 -1000
Regulation of Androgen receptor activity 23 1628 70 -0.032 0.068 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 22 1175 52 -0.046 0.11 1000 -1000 -0.021 -1000
Calcium signaling in the CD4+ TCR pathway 22 701 31 -0.022 0.074 1000 -1000 -0.025 -1000
E-cadherin signaling events 22 114 5 0.034 0.064 1000 -1000 0.034 -1000
Arf6 trafficking events 21 1510 71 -0.037 0.049 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 20 1529 76 -0.028 0.068 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 20 1572 75 -0.03 0.094 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 19 763 39 -0.033 0.066 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 19 606 31 -0.023 0.038 1000 -1000 -0.019 -1000
ceramide signaling pathway 18 905 49 -0.016 0.055 1000 -1000 -0.015 -1000
Signaling mediated by p38-alpha and p38-beta 18 819 44 -0.014 0.074 1000 -1000 -0.013 -1000
Arf1 pathway 18 1016 54 -0.054 0.045 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 17 459 27 -0.033 0.075 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 16 630 39 -0.074 0.037 1000 -1000 -0.01 -1000
Rapid glucocorticoid signaling 16 329 20 -0.011 0.037 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 15 535 34 -0.056 0.098 1000 -1000 -0.041 -1000
Signaling events mediated by the Hedgehog family 15 813 52 -0.016 0.089 1000 -1000 -0.02 -1000
Aurora C signaling 15 110 7 0 0.061 1000 -1000 -0.006 -1000
FOXA2 and FOXA3 transcription factor networks 11 519 46 0 0.11 1000 -1000 -0.036 -1000
IL27-mediated signaling events 11 570 51 -0.023 0.069 1000 -1000 -0.036 -1000
Class IB PI3K non-lipid kinase events 11 33 3 -0.037 0.037 1000 -1000 -0.034 -1000
Visual signal transduction: Rods 8 463 52 -0.035 0.087 1000 -1000 -0.009 -1000
Ephrin A reverse signaling 2 20 7 -0.019 0.049 1000 -1000 -0.013 -1000
Total 5247 294883 7203 -7.1 8.6 131000 -131000 -3 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.04 0.45 0.6 99 -0.73 83 182
HDAC7 -0.003 0.009 -10000 0 -0.043 14 14
HIF1A/ARNT/Cbp/p300/Src-1 -0.031 0.38 0.58 32 -0.71 73 105
SMAD4 0.034 0.014 0.081 12 0 58 70
ID2 0.061 0.46 0.64 96 -0.72 83 179
AP1 0.014 0.081 -10000 0 -0.17 73 73
ABCG2 0.027 0.46 0.62 97 -0.73 85 182
HIF1A 0.045 0.13 0.24 74 -0.16 60 134
TFF3 0.057 0.46 0.65 89 -0.72 81 170
GATA2 0.04 0.014 0.077 22 -0.091 2 24
AKT1 0.056 0.14 0.26 84 -0.2 36 120
response to hypoxia 0.017 0.096 0.18 87 -0.12 40 127
MCL1 0.068 0.46 0.64 97 -0.72 83 180
NDRG1 0.011 0.44 0.6 81 -0.73 87 168
SERPINE1 -0.053 0.38 0.56 41 -0.75 76 117
FECH 0.053 0.46 0.64 90 -0.72 83 173
FURIN 0.065 0.46 0.64 98 -0.72 83 181
NCOA2 0.038 0.006 -10000 0 -10000 0 0
EP300 0.079 0.2 0.39 92 -0.3 31 123
HMOX1 -0.003 0.45 0.64 70 -0.75 86 156
BHLHE40 -0.049 0.39 0.54 74 -0.69 89 163
BHLHE41 -0.049 0.39 0.54 74 -0.69 89 163
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.069 0.18 0.36 35 -0.23 37 72
ENG 0.034 0.16 0.32 50 -0.26 18 68
JUN 0.036 0.013 0.066 2 -0.001 45 47
RORA 0.037 0.45 0.63 83 -0.72 84 167
ABCB1 -0.049 0.2 -10000 0 -0.84 25 25
TFRC 0.045 0.46 0.64 89 -0.73 83 172
CXCR4 0.029 0.46 0.64 81 -0.74 86 167
TF -0.065 0.4 0.65 38 -0.72 88 126
CITED2 0.027 0.45 0.61 92 -0.72 86 178
HIF1A/ARNT -0.061 0.43 0.66 21 -0.84 73 94
LDHA -0.065 0.28 -10000 0 -0.98 40 40
ETS1 0.072 0.47 0.64 101 -0.72 83 184
PGK1 0.062 0.47 0.64 98 -0.73 84 182
NOS2 -0.049 0.39 0.54 74 -0.69 89 163
ITGB2 0.02 0.45 0.63 78 -0.74 86 164
ALDOA 0.071 0.47 0.64 101 -0.73 82 183
Cbp/p300/CITED2 -0.025 0.44 0.62 59 -0.78 84 143
FOS 0.026 0.019 -10000 0 0 167 167
HK2 0.073 0.47 0.64 102 -0.73 82 184
SP1 0.033 0.059 0.11 28 -0.15 39 67
GCK 0.11 0.26 0.63 48 -0.53 6 54
HK1 0.017 0.44 0.64 74 -0.72 83 157
NPM1 0.067 0.46 0.64 98 -0.72 82 180
EGLN1 0.065 0.46 0.62 109 -0.72 83 192
CREB1 0.033 0.034 -10000 0 -0.099 30 30
PGM1 0.066 0.47 0.63 111 -0.73 82 193
SMAD3 0.038 0.009 0.081 12 -10000 0 12
EDN1 0.059 0.22 0.48 34 -0.54 18 52
IGFBP1 0.007 0.41 0.61 68 -0.74 71 139
VEGFA -0.017 0.38 0.57 56 -0.65 84 140
HIF1A/JAB1 0.046 0.1 0.2 44 -0.19 17 61
CP -0.02 0.43 0.63 62 -0.74 88 150
CXCL12 -0.019 0.41 0.61 53 -0.72 80 133
COPS5 0.038 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.052 0.14 6 -0.14 34 40
BNIP3 0.005 0.44 0.65 68 -0.73 82 150
EGLN3 0.017 0.44 0.61 85 -0.72 82 167
CA9 -0.006 0.42 0.61 57 -0.73 79 136
TERT 0.065 0.46 0.65 98 -0.72 83 181
ENO1 0.06 0.47 0.63 111 -0.73 82 193
PFKL 0.069 0.47 0.65 99 -0.72 83 182
NCOA1 0.034 0.011 -10000 0 0 49 49
ADM -0.006 0.44 0.64 67 -0.74 89 156
ARNT 0.048 0.12 0.23 78 -0.14 67 145
HNF4A 0.038 0.012 -10000 0 -10000 0 0
ADFP -0.049 0.39 0.54 74 -0.69 89 163
SLC2A1 0.016 0.39 0.59 73 -0.63 81 154
LEP 0.024 0.42 0.61 81 -0.74 70 151
HIF1A/ARNT/Cbp/p300 -0.045 0.38 0.58 29 -0.72 73 102
EPO 0.029 0.31 0.56 49 -0.6 38 87
CREBBP 0.084 0.19 0.39 95 -0.27 28 123
HIF1A/ARNT/Cbp/p300/HDAC7 -0.07 0.37 0.56 20 -0.73 78 98
PFKFB3 0.023 0.45 0.65 77 -0.73 82 159
NT5E -0.014 0.43 0.64 58 -0.72 89 147
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 -0.093 0.63 0.96 28 -1.2 101 129
PLK1 0.055 0.14 0.62 10 -0.77 5 15
BIRC5 -0.073 0.43 0.62 10 -1.2 59 69
HSPA1B -0.093 0.63 0.9 33 -1.2 103 136
MAP2K1 0.042 0.095 0.25 44 -10000 0 44
BRCA2 -0.09 0.63 1 26 -1.2 98 124
FOXM1 -0.22 0.9 1.1 26 -1.8 102 128
XRCC1 -0.087 0.64 1 27 -1.2 100 127
FOXM1B/p19 -0.3 0.55 -10000 0 -1.3 101 101
Cyclin D1/CDK4 -0.11 0.56 0.87 20 -1.1 104 124
CDC2 -0.1 0.68 1 34 -1.3 102 136
TGFA -0.069 0.56 0.84 35 -1 103 138
SKP2 -0.091 0.63 0.98 28 -1.2 100 128
CCNE1 0.024 0.037 0.1 15 -0.035 110 125
CKS1B -0.1 0.66 1 28 -1.2 105 133
RB1 -0.08 0.36 0.46 13 -0.99 51 64
FOXM1C/SP1 -0.19 0.71 0.85 18 -1.4 103 121
AURKB 0.056 0.13 0.67 9 -0.88 2 11
CENPF -0.12 0.69 1 30 -1.2 113 143
CDK4 0.024 0.049 0.15 23 -10000 0 23
MYC -0.11 0.54 0.78 26 -1 105 131
CHEK2 0.031 0.082 0.21 34 -10000 0 34
ONECUT1 -0.092 0.61 0.87 35 -1.1 104 139
CDKN2A 0.004 0.018 0.078 1 -0.16 3 4
LAMA4 -0.095 0.64 0.94 31 -1.2 103 134
FOXM1B/HNF6 -0.17 0.74 0.91 28 -1.4 104 132
FOS -0.15 0.68 0.95 30 -1.2 129 159
SP1 0.034 0.019 -10000 0 -0.044 24 24
CDC25B -0.09 0.65 1 29 -1.2 103 132
response to radiation 0.021 0.063 0.14 67 -10000 0 67
CENPB -0.083 0.65 0.97 33 -1.2 104 137
CENPA -0.095 0.64 1 28 -1.2 101 129
NEK2 -0.086 0.64 1.1 28 -1.2 101 129
HIST1H2BA -0.093 0.63 0.9 33 -1.2 103 136
CCNA2 0.023 0.031 0.09 5 -0.035 76 81
EP300 0.034 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 -0.18 0.8 1.1 26 -1.5 109 135
CCNB2 -0.11 0.67 1 30 -1.3 101 131
CCNB1 -0.13 0.72 1.1 28 -1.3 109 137
ETV5 -0.12 0.67 0.98 27 -1.2 123 150
ESR1 -0.094 0.63 0.96 28 -1.2 101 129
CCND1 -0.12 0.58 0.89 28 -1.1 105 133
GSK3A 0.034 0.08 0.2 42 -10000 0 42
Cyclin A-E1/CDK1-2 0.043 0.098 0.24 18 -0.16 42 60
CDK2 0.024 0.037 0.1 12 -0.035 117 129
G2/M transition of mitotic cell cycle 0.023 0.075 0.17 63 -10000 0 63
FOXM1B/Cbp/p300 -0.16 0.66 0.78 17 -1.3 103 120
GAS1 -0.096 0.65 0.97 30 -1.2 104 134
MMP2 -0.12 0.67 0.94 31 -1.2 117 148
RB1/FOXM1C -0.16 0.58 0.85 17 -1.2 104 121
CREBBP 0.037 0.004 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.23 0.41 -10000 0 -0.83 138 138
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.38 129 129
NCK1/Dok-R -0.14 0.35 -10000 0 -0.85 96 96
PIK3CA 0.032 0.013 -10000 0 0 74 74
mol:beta2-estradiol 0.031 0.097 0.23 96 -10000 0 96
RELA 0.037 0.005 -10000 0 0 10 10
SHC1 0.033 0.011 -10000 0 0 53 53
Rac/GDP 0.018 0.019 -10000 0 -0.13 5 5
F2 0.053 0.11 0.28 87 -0.11 8 95
TNIP2 0.037 0.005 -10000 0 0 11 11
NF kappa B/RelA -0.11 0.36 -10000 0 -0.83 96 96
FN1 0.035 0.009 -10000 0 0 31 31
PLD2 -0.15 0.36 -10000 0 -0.88 96 96
PTPN11 0.037 0.006 -10000 0 0 12 12
GRB14 0.032 0.013 -10000 0 0 71 71
ELK1 -0.14 0.33 -10000 0 -0.82 96 96
GRB7 0.037 0.007 -10000 0 0 16 16
PAK1 0.036 0.007 -10000 0 0 18 18
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 95 95
CDKN1A -0.19 0.35 -10000 0 -0.66 167 167
ITGA5 0.033 0.012 -10000 0 0 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.35 -10000 0 -0.86 96 96
CRK 0.036 0.008 -10000 0 0 25 25
mol:NO -0.12 0.32 0.42 2 -0.59 134 136
PLG -0.15 0.36 -10000 0 -0.88 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.74 124 124
GRB2 0.036 0.007 -10000 0 0 19 19
PIK3R1 0.032 0.013 -10000 0 0 67 67
ANGPT2 -0.22 0.45 -10000 0 -1 112 112
BMX -0.15 0.36 -10000 0 -0.88 96 96
ANGPT1 -0.16 0.42 -10000 0 -1 95 95
tube development -0.21 0.36 -10000 0 -0.7 164 164
ANGPT4 0.023 0.029 -10000 0 -0.026 126 126
response to hypoxia -0.013 0.026 -10000 0 -0.063 96 96
Tie2/Ang1/GRB14 -0.14 0.37 -10000 0 -0.89 96 96
alpha5/beta1 Integrin 0.032 0.043 -10000 0 -0.14 21 21
FGF2 0.036 0.017 -10000 0 -0.013 44 44
STAT5A (dimer) -0.23 0.44 -10000 0 -0.81 172 172
mol:L-citrulline -0.12 0.32 0.42 2 -0.59 134 136
AGTR1 0.022 0.034 -10000 0 -0.039 114 114
MAPK14 -0.16 0.37 -10000 0 -0.89 97 97
Tie2/SHP2 -0.078 0.24 -10000 0 -0.85 33 33
TEK -0.088 0.25 -10000 0 -0.96 31 31
RPS6KB1 -0.2 0.37 -10000 0 -0.77 134 134
Angiotensin II/AT1 0.015 0.036 -10000 0 -0.057 88 88
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.9 96 96
MAPK3 -0.15 0.34 -10000 0 -0.84 96 96
MAPK1 -0.15 0.33 -10000 0 -0.84 96 96
Tie2/Ang1/GRB7 -0.14 0.37 -10000 0 -0.9 96 96
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 -0.15 0.36 -10000 0 -0.88 96 96
PI3K -0.24 0.44 -10000 0 -0.92 130 130
FES -0.16 0.38 -10000 0 -0.9 97 97
Crk/Dok-R -0.14 0.36 -10000 0 -0.86 96 96
Tie2/Ang1/ABIN2 -0.14 0.37 -10000 0 -0.9 96 96
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.2 0.36 -10000 0 -0.74 140 140
STAT5A 0.037 0.005 -10000 0 0 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.77 132 132
Tie2/Ang2 -0.29 0.5 -10000 0 -0.97 163 163
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 96 96
FOXO1 -0.22 0.39 -10000 0 -0.76 166 166
ELF1 0.028 0.036 0.1 3 -0.046 80 83
ELF2 -0.14 0.35 -10000 0 -0.86 96 96
mol:Choline -0.15 0.35 -10000 0 -0.86 96 96
cell migration -0.066 0.097 -10000 0 -0.22 130 130
FYN -0.24 0.41 -10000 0 -0.8 164 164
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.32 0.39 2 -0.59 171 173
ETS1 0 0.12 -10000 0 -0.25 91 91
PXN -0.17 0.31 -10000 0 -0.65 133 133
ITGB1 0.029 0.016 -10000 0 0 117 117
NOS3 -0.15 0.35 0.47 1 -0.67 133 134
RAC1 0.026 0.017 -10000 0 0 156 156
TNF -0.003 0.12 -10000 0 -0.25 93 93
MAPKKK cascade -0.15 0.35 -10000 0 -0.86 96 96
RASA1 0.035 0.01 -10000 0 0 35 35
Tie2/Ang1/Shc -0.15 0.37 -10000 0 -0.9 96 96
NCK1 0.036 0.009 -10000 0 0 28 28
vasculogenesis -0.11 0.29 0.4 3 -0.53 134 137
mol:Phosphatidic acid -0.15 0.35 -10000 0 -0.86 96 96
mol:Angiotensin II -0.004 0.013 -10000 0 -0.032 75 75
mol:NADP -0.12 0.32 0.42 2 -0.59 134 136
Rac1/GTP -0.18 0.34 -10000 0 -0.7 129 129
MMP2 -0.15 0.36 -10000 0 -0.89 96 96
Endothelins

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
AKT1 -0.022 0.14 0.21 74 -0.26 87 161
PTK2B 0.037 0.006 -10000 0 0 15 15
mol:Ca2+ -0.084 0.24 0.39 1 -0.54 67 68
EDN1 0.003 0.091 0.16 4 -0.16 103 107
EDN3 0.034 0.012 -10000 0 0 56 56
EDN2 0.037 0.006 -10000 0 0 15 15
HRAS/GDP -0.015 0.18 0.3 20 -0.36 64 84
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.001 0.12 0.18 19 -0.25 60 79
ADCY4 -0.037 0.095 0.14 34 -0.2 96 130
ADCY5 -0.037 0.095 0.14 34 -0.2 96 130
ADCY6 -0.008 0.13 0.22 48 -0.24 62 110
ADCY7 -0.011 0.13 0.22 50 -0.24 65 115
ADCY1 0 0.11 0.22 35 -0.25 40 75
ADCY2 -0.006 0.13 0.22 47 -0.24 63 110
ADCY3 -0.037 0.095 0.14 34 -0.2 96 130
ADCY8 -0.009 0.13 0.22 45 -0.24 54 99
ADCY9 -0.008 0.13 0.22 51 -0.24 64 115
arachidonic acid secretion -0.078 0.26 0.34 23 -0.51 103 126
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.11 0.17 13 -0.22 70 83
GNAO1 0.031 0.014 -10000 0 0 87 87
HRAS 0.035 0.01 -10000 0 0 37 37
ETA receptor/Endothelin-1/G12/GTP 0.005 0.12 -10000 0 -0.23 69 69
ETA receptor/Endothelin-1/Gs/GTP 0.002 0.12 -10000 0 -0.21 98 98
mol:GTP 0 0.007 0.026 3 -0.025 4 7
COL3A1 -0.076 0.15 0.19 9 -0.36 103 112
EDNRB 0.024 0.045 0.098 62 -0.084 45 107
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.02 0.14 0.21 69 -0.28 64 133
CYSLTR1 -0.041 0.12 0.18 35 -0.24 96 131
SLC9A1 -0.016 0.087 0.13 4 -0.19 67 71
mol:GDP -0.024 0.17 0.3 21 -0.38 62 83
SLC9A3 -0.12 0.29 -10000 0 -0.65 85 85
RAF1 -0.035 0.21 0.3 31 -0.41 88 119
JUN -0.12 0.32 0.47 1 -0.76 74 75
JAK2 -0.023 0.14 0.21 64 -0.25 87 151
mol:IP3 -0.005 0.12 0.21 16 -0.27 52 68
ETA receptor/Endothelin-1 -0.028 0.14 -10000 0 -0.28 109 109
PLCB1 0.033 0.014 -10000 0 -0.003 59 59
PLCB2 0.03 0.023 -10000 0 -0.024 73 73
ETA receptor/Endothelin-3 0.007 0.087 -10000 0 -0.15 99 99
FOS -0.097 0.35 0.4 20 -0.84 83 103
Gai/GDP -0.073 0.28 -10000 0 -0.72 71 71
CRK 0.036 0.008 -10000 0 0 25 25
mol:Ca ++ -0.021 0.17 0.26 54 -0.33 83 137
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.007 0.12 0.21 19 -0.28 55 74
GNAQ 0.028 0.027 -10000 0 -0.035 67 67
GNAZ 0.032 0.014 -10000 0 0 81 81
GNAL 0.036 0.007 -10000 0 0 17 17
Gs family/GDP -0.014 0.16 0.29 18 -0.35 62 80
ETA receptor/Endothelin-1/Gq/GTP -0.009 0.12 0.19 11 -0.26 67 78
MAPK14 -0.012 0.098 0.18 6 -0.25 45 51
TRPC6 -0.089 0.25 -10000 0 -0.57 66 66
GNAI2 0.034 0.011 -10000 0 0 46 46
GNAI3 0.037 0.007 -10000 0 0 16 16
GNAI1 0.019 0.019 -10000 0 0 255 255
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.003 0.1 0.17 18 -0.24 50 68
ETB receptor/Endothelin-2 0.019 0.07 -10000 0 -0.11 98 98
ETB receptor/Endothelin-3 0.016 0.069 -10000 0 -0.11 93 93
ETB receptor/Endothelin-1 0 0.1 0.17 28 -0.16 115 143
MAPK3 -0.078 0.32 0.39 21 -0.73 84 105
MAPK1 -0.093 0.34 0.38 23 -0.77 89 112
Rac1/GDP -0.015 0.15 0.31 13 -0.37 45 58
cAMP biosynthetic process 0.019 0.12 0.23 50 -0.22 39 89
MAPK8 -0.12 0.3 0.35 4 -0.57 125 129
SRC 0.036 0.009 -10000 0 0 31 31
ETB receptor/Endothelin-1/Gi/GTP -0.032 0.14 0.15 4 -0.34 60 64
p130Cas/CRK/Src/PYK2 -0.021 0.19 0.37 15 -0.47 47 62
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.018 0.15 0.31 11 -0.38 47 58
COL1A2 -0.055 0.17 0.22 1 -0.47 60 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.006 0.091 -10000 0 -0.15 108 108
mol:DAG -0.005 0.12 0.21 16 -0.27 53 69
MAP2K2 -0.056 0.26 0.37 29 -0.56 85 114
MAP2K1 -0.062 0.26 0.33 25 -0.57 87 112
EDNRA -0.007 0.1 0.16 1 -0.19 98 99
positive regulation of muscle contraction 0.019 0.14 0.22 126 -0.26 46 172
Gq family/GDP 0.001 0.16 0.31 4 -0.34 63 67
HRAS/GTP -0.015 0.17 0.29 25 -0.35 64 89
PRKCH -0.007 0.12 0.24 16 -0.29 48 64
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCA -0.012 0.13 0.21 18 -0.28 54 72
PRKCB -0.007 0.12 0.21 20 -0.27 56 76
PRKCE -0.013 0.12 0.21 15 -0.29 51 66
PRKCD -0.007 0.13 0.25 22 -0.28 52 74
PRKCG -0.013 0.13 0.22 17 -0.28 55 72
regulation of vascular smooth muscle contraction -0.12 0.42 0.45 14 -1 83 97
PRKCQ -0.005 0.12 0.24 19 -0.28 42 61
PLA2G4A -0.088 0.28 0.35 23 -0.56 103 126
GNA14 0.028 0.027 -10000 0 -0.035 67 67
GNA15 0.031 0.02 -10000 0 -0.035 27 27
GNA12 0.024 0.018 -10000 0 0 180 180
GNA11 0.033 0.017 -10000 0 -0.037 17 17
Rac1/GTP 0.007 0.11 -10000 0 -0.23 65 65
MMP1 0.021 0.073 0.22 13 -10000 0 13
TCGA08_p53

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
CDKN2A -0.002 0.004 0 444 -10000 0 444
TP53 0.005 0.034 -10000 0 -0.26 6 6
Senescence 0.004 0.036 -10000 0 -0.24 8 8
Apoptosis 0.004 0.036 -10000 0 -0.24 8 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.002 0.035 0.3 7 -10000 0 7
MDM4 0.033 0.012 -10000 0 0 61 61
TCGA08_rtk_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
PDGFRA 0.025 0.018 -10000 0 0 165 165
HRAS 0.035 0.01 -10000 0 0 37 37
EGFR 0.01 0.017 -10000 0 0 373 373
AKT 0.087 0.12 0.25 113 -0.18 10 123
FOXO3 0.033 0.012 -10000 0 0 61 61
AKT1 0.033 0.012 -10000 0 0 58 58
FOXO1 0.031 0.015 -10000 0 0 95 95
AKT3 0.036 0.008 -10000 0 0 22 22
FOXO4 0.038 0.002 -10000 0 0 2 2
MET 0.024 0.018 -10000 0 0 184 184
PIK3CA 0.032 0.013 -10000 0 0 74 74
PIK3CB 0.036 0.007 -10000 0 0 18 18
NRAS 0.033 0.013 -10000 0 0 66 66
PIK3CG 0.026 0.017 -10000 0 0 157 157
PIK3R3 0.036 0.007 -10000 0 0 17 17
PIK3R2 0.036 0.007 -10000 0 0 20 20
NF1 0.037 0.003 -10000 0 0 4 4
RAS -0.003 0.056 -10000 0 -0.26 11 11
ERBB2 0.037 0.004 -10000 0 0 7 7
proliferation/survival/translation -0.033 0.096 0.34 18 -0.26 7 25
PI3K 0.036 0.087 0.21 65 -0.15 11 76
PIK3R1 0.033 0.013 -10000 0 0 67 67
KRAS 0.035 0.009 -10000 0 0 34 34
FOXO 0.1 0.1 0.24 122 -0.1 4 126
AKT2 0.036 0.007 -10000 0 0 18 18
PTEN 0.026 0.017 -10000 0 0 158 158
HIF-2-alpha transcription factor network

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
MMP14 -0.017 0.16 -10000 0 -0.63 30 30
oxygen homeostasis 0.006 0.027 0.06 65 -0.027 17 82
TCEB2 0.037 0.004 -10000 0 0 6 6
TCEB1 0.036 0.008 -10000 0 0 22 22
VHL/Elongin B/Elongin C/HIF2A 0.012 0.15 0.32 34 -0.26 40 74
EPO -0.044 0.23 0.42 29 -0.46 62 91
FIH (dimer) 0.017 0.044 0.12 24 -0.042 60 84
APEX1 0.014 0.045 0.13 6 -0.054 38 44
SERPINE1 -0.078 0.22 0.38 14 -0.49 85 99
FLT1 -0.014 0.17 -10000 0 -0.71 23 23
ADORA2A -0.038 0.26 0.46 44 -0.47 71 115
germ cell development -0.046 0.24 0.4 44 -0.44 83 127
SLC11A2 -0.038 0.27 0.48 42 -0.46 82 124
BHLHE40 -0.05 0.25 0.39 43 -0.45 84 127
HIF1AN 0.017 0.044 0.12 24 -0.042 60 84
HIF2A/ARNT/SIRT1 -0.018 0.17 0.33 32 -0.32 56 88
ETS1 0.048 0.032 0.12 41 -0.11 11 52
CITED2 -0.06 0.26 -10000 0 -0.79 52 52
KDR -0.005 0.16 -10000 0 -0.86 16 16
PGK1 -0.042 0.28 0.45 50 -0.48 87 137
SIRT1 0.027 0.017 -10000 0 0 149 149
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.042 0.28 0.49 10 -0.51 83 93
EPAS1 0.005 0.15 0.32 48 -0.27 39 87
SP1 0.042 0.011 0.11 8 -10000 0 8
ABCG2 -0.048 0.28 0.48 40 -0.47 94 134
EFNA1 -0.044 0.27 0.46 38 -0.47 85 123
FXN -0.038 0.26 0.46 44 -0.47 70 114
POU5F1 -0.05 0.25 0.39 43 -0.45 84 127
neuron apoptosis 0.042 0.28 0.5 83 -0.48 9 92
EP300 0.034 0.011 -10000 0 0 49 49
EGLN3 0.019 0.044 0.12 21 -0.042 66 87
EGLN2 0.024 0.047 0.12 29 -0.042 66 95
EGLN1 0.024 0.046 0.12 28 -0.043 45 73
VHL/Elongin B/Elongin C 0.046 0.023 -10000 0 -0.11 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.014 0.045 0.12 6 -0.053 38 44
SLC2A1 -0.063 0.24 0.41 30 -0.46 87 117
TWIST1 -0.07 0.22 0.42 17 -0.45 92 109
ELK1 0.039 0.035 0.11 29 -0.095 25 54
HIF2A/ARNT/Cbp/p300 -0.002 0.2 0.36 37 -0.33 56 93
VEGFA -0.081 0.25 0.42 18 -0.48 102 120
CREBBP 0.037 0.004 -10000 0 0 7 7
Thromboxane A2 receptor signaling

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
TGM2 0.035 0.011 -10000 0 0 43 43
GNB1/GNG2 -0.045 0.077 -10000 0 -0.17 130 130
AKT1 -0.007 0.16 0.28 35 -0.3 44 79
EGF 0.036 0.008 -10000 0 0 25 25
mol:TXA2 0 0.001 0.003 2 -10000 0 2
FGR -0.021 0.063 0.31 12 -0.16 3 15
mol:Ca2+ -0.003 0.18 0.35 23 -0.27 132 155
LYN -0.02 0.068 0.31 14 -0.16 8 22
RhoA/GTP 0 0.082 0.16 20 -0.13 93 113
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.018 0.2 0.38 23 -0.32 127 150
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.036 0.008 -10000 0 0 27 27
TP alpha/Gq family/GDP/G beta5/gamma2 0.004 0.077 -10000 0 -0.25 32 32
G beta5/gamma2 -0.053 0.1 -10000 0 -0.23 129 129
PRKCH -0.017 0.2 0.36 23 -0.32 129 152
DNM1 0.036 0.008 -10000 0 0 26 26
TXA2/TP beta/beta Arrestin3 0.015 0.019 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.005 55 -0.002 5 60
PTGDR 0.036 0.009 -10000 0 0 29 29
G12 family/GTP -0.044 0.14 -10000 0 -0.29 102 102
ADRBK1 0.037 0.006 -10000 0 0 13 13
ADRBK2 0.035 0.009 -10000 0 0 32 32
RhoA/GTP/ROCK1 0.045 0.027 -10000 0 -0.12 10 10
mol:GDP -0.005 0.13 0.41 16 -0.26 20 36
mol:NADP 0.026 0.018 -10000 0 0 160 160
RAB11A 0.036 0.007 -10000 0 0 17 17
PRKG1 0.028 0.016 -10000 0 0 127 127
mol:IP3 -0.015 0.22 0.38 22 -0.33 132 154
cell morphogenesis 0.045 0.026 -10000 0 -0.12 10 10
PLCB2 -0.039 0.27 0.45 12 -0.44 132 144
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.018 0.067 0.3 16 -10000 0 16
mol:PDG2 0 0 0.003 1 -10000 0 1
HCK -0.024 0.051 0.29 6 -0.17 10 16
RHOA 0.036 0.007 -10000 0 0 20 20
PTGIR 0.036 0.008 -10000 0 0 27 27
PRKCB1 -0.021 0.21 0.36 22 -0.34 132 154
GNAQ 0.035 0.01 -10000 0 0 35 35
mol:L-citrulline 0.026 0.018 -10000 0 0 160 160
TXA2/TXA2-R family -0.05 0.28 0.42 19 -0.48 130 149
LCK -0.019 0.066 0.3 15 -10000 0 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.033 0.039 0.2 2 -0.13 3 5
TXA2-R family/G12 family/GDP/G beta/gamma -0.033 0.16 -10000 0 -0.46 61 61
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.03 0.041 0.2 2 -0.13 3 5
MAPK14 -0.006 0.15 0.29 31 -0.22 125 156
TGM2/GTP -0.019 0.23 0.4 18 -0.37 122 140
MAPK11 -0.008 0.15 0.29 29 -0.22 125 154
ARHGEF1 0.007 0.12 0.22 40 -0.18 94 134
GNAI2 0.034 0.011 -10000 0 0 46 46
JNK cascade -0.024 0.22 0.38 22 -0.35 130 152
RAB11/GDP 0.035 0.01 -10000 0 -0.009 23 23
ICAM1 -0.006 0.18 0.32 32 -0.27 126 158
cAMP biosynthetic process -0.016 0.2 0.35 22 -0.31 126 148
Gq family/GTP/EBP50 0.014 0.055 0.25 8 -0.16 32 40
actin cytoskeleton reorganization 0.045 0.026 -10000 0 -0.12 10 10
SRC -0.025 0.049 0.27 7 -10000 0 7
GNB5 0.036 0.007 -10000 0 0 18 18
GNB1 0.034 0.011 -10000 0 0 47 47
EGF/EGFR -0.013 0.11 0.31 17 -0.22 47 64
VCAM1 -0.024 0.2 0.32 33 -0.33 135 168
TP beta/Gq family/GDP/G beta5/gamma2 0.004 0.077 -10000 0 -0.25 32 32
platelet activation -0.011 0.19 0.37 23 -0.28 127 150
PGI2/IP 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.014 0.024 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.008 0.067 -10000 0 -0.22 30 30
TXA2/TP beta/beta Arrestin2 0.005 0.048 -10000 0 -0.3 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.02 -10000 0 -10000 0 0
mol:DAG -0.024 0.23 0.39 22 -0.38 129 151
EGFR 0.01 0.017 -10000 0 0 373 373
TXA2/TP alpha -0.032 0.25 0.45 13 -0.42 126 139
Gq family/GTP 0.008 0.041 0.21 6 -0.12 28 34
YES1 -0.02 0.065 0.29 14 -0.16 3 17
GNAI2/GTP 0.008 0.049 -10000 0 -0.14 4 4
PGD2/DP 0.026 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.035 0.01 -10000 0 0 35 35
FYN -0.019 0.067 0.29 14 -0.16 7 21
mol:NO 0.026 0.018 -10000 0 0 160 160
GNA15 0.034 0.011 -10000 0 0 45 45
PGK/cGMP 0.03 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.035 0.011 -10000 0 -0.008 26 26
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.043 0.18 1 -0.13 3 4
NOS3 0.026 0.018 -10000 0 0 160 160
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCA -0.017 0.2 0.36 22 -0.32 127 149
PRKCB -0.018 0.2 0.35 23 -0.32 132 155
PRKCE -0.019 0.2 0.36 23 -0.33 132 155
PRKCD -0.022 0.22 0.36 24 -0.35 129 153
PRKCG -0.023 0.22 0.37 22 -0.35 132 154
muscle contraction -0.044 0.26 0.41 19 -0.44 130 149
PRKCZ -0.018 0.2 0.35 24 -0.32 130 154
ARR3 0.038 0.002 -10000 0 0 2 2
TXA2/TP beta 0.037 0.039 0.19 1 -0.13 4 5
PRKCQ -0.026 0.2 0.35 24 -0.32 127 151
MAPKKK cascade -0.034 0.24 0.39 21 -0.4 130 151
SELE -0.012 0.18 0.33 25 -0.27 134 159
TP beta/GNAI2/GDP/G beta/gamma 0.026 0.054 0.19 2 -0.16 16 18
ROCK1 0.037 0.007 -10000 0 0 16 16
GNA14 0.035 0.009 -10000 0 0 34 34
chemotaxis -0.07 0.31 0.49 10 -0.56 135 145
GNA12 0.024 0.018 -10000 0 0 180 180
GNA13 0.036 0.008 -10000 0 0 21 21
GNA11 0.034 0.011 -10000 0 0 46 46
Rac1/GTP 0.018 0.02 -10000 0 -0.13 5 5
Ceramide 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
SPHK2 -0.012 0.012 0 247 -10000 0 247
MAP4K4 0.002 0.057 -10000 0 -0.23 13 13
BAG4 0.037 0.005 -10000 0 0 10 10
PKC zeta/ceramide -0.054 0.12 -10000 0 -0.2 158 158
NFKBIA 0.034 0.012 -10000 0 0 54 54
BIRC3 0.031 0.014 -10000 0 0 84 84
BAX -0.024 0.094 -10000 0 -0.36 29 29
RIPK1 0.036 0.007 -10000 0 0 19 19
AKT1 -0.001 0.078 0.63 6 -10000 0 6
BAD -0.06 0.12 0.22 2 -0.21 157 159
SMPD1 -0.003 0.054 0.18 2 -0.21 16 18
RB1 -0.061 0.12 0.21 1 -0.21 158 159
FADD/Caspase 8 0.013 0.054 -10000 0 -0.26 5 5
MAP2K4 -0.06 0.12 0.19 5 -0.21 149 154
NSMAF 0.036 0.008 -10000 0 0 27 27
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.064 0.12 0.2 5 -0.21 155 160
EGF 0.036 0.008 -10000 0 0 25 25
mol:ceramide -0.056 0.13 -10000 0 -0.22 158 158
MADD 0.036 0.007 -10000 0 0 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.012 0.012 0 244 -10000 0 244
ASAH1 0.037 0.007 -10000 0 0 16 16
negative regulation of cell cycle -0.06 0.12 0.21 1 -0.21 158 159
cell proliferation -0.036 0.11 -10000 0 -0.19 140 140
BID -0.042 0.21 -10000 0 -0.65 49 49
MAP3K1 -0.058 0.12 0.17 2 -0.21 149 151
EIF2A -0.062 0.11 0.2 2 -0.2 155 157
TRADD 0.037 0.005 -10000 0 0 8 8
CRADD 0.037 0.007 -10000 0 0 16 16
MAPK3 -0.059 0.1 0.19 4 -0.2 147 151
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.068 0.11 0.19 4 -0.21 154 158
Cathepsin D/ceramide -0.043 0.13 -10000 0 -0.21 156 156
FADD 0.008 0.049 -10000 0 -0.22 6 6
KSR1 -0.06 0.12 0.2 1 -0.21 158 159
MAPK8 -0.087 0.15 0.16 2 -0.25 190 192
PRKRA -0.063 0.12 -10000 0 -0.21 157 157
PDGFA 0.02 0.019 -10000 0 0 241 241
TRAF2 0.036 0.007 -10000 0 0 19 19
IGF1 0.036 0.008 -10000 0 0 25 25
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.056 0.12 -10000 0 -0.21 158 158
CTSD 0.033 0.012 -10000 0 0 58 58
regulation of nitric oxide biosynthetic process 0.051 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.12 -10000 0 -0.2 140 140
PRKCD 0.035 0.01 -10000 0 0 42 42
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.012 0.012 0 244 -10000 0 244
RelA/NF kappa B1 0.051 0.025 -10000 0 -0.14 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.036 0.007 -10000 0 0 18 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.058 -10000 0 -0.25 9 9
TNFR1A/BAG4/TNF-alpha 0.055 0.056 -10000 0 -0.12 41 41
mol:Sphingosine-1-phosphate -0.012 0.012 0 247 -10000 0 247
MAP2K1 -0.068 0.11 0.18 5 -0.21 154 159
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.037 0.005 -10000 0 0 10 10
CYCS -0.014 0.07 -10000 0 -0.27 22 22
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
NFKB1 0.036 0.007 -10000 0 0 18 18
TNFR1A/BAG4 0.036 0.054 -10000 0 -0.14 42 42
EIF2AK2 -0.065 0.12 0.21 2 -0.21 155 157
TNF-alpha/TNFR1A/FAN 0.049 0.066 -10000 0 -0.13 54 54
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.032 0.058 -10000 0 -0.31 7 7
MAP2K2 -0.063 0.1 0.18 8 -0.2 150 158
SMPD3 0.005 0.057 0.16 1 -0.27 8 9
TNF 0.037 0.004 -10000 0 0 6 6
PKC zeta/PAR4 0.027 0.005 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.03 0.074 0.13 6 -0.13 134 140
NF kappa B1/RelA/I kappa B alpha 0.072 0.048 -10000 0 -0.12 19 19
AIFM1 -0.039 0.087 -10000 0 -0.29 26 26
BCL2 0.036 0.007 -10000 0 0 17 17
PDGFR-alpha signaling pathway

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
PDGFRA 0.018 0.033 0.092 4 -0.056 53 57
PDGF/PDGFRA/CRKL 0.009 0.068 -10000 0 -0.14 67 67
positive regulation of JUN kinase activity 0.026 0.062 -10000 0 -0.11 65 65
CRKL 0.036 0.009 -10000 0 0 29 29
PDGF/PDGFRA/Caveolin-3 0.01 0.068 -10000 0 -0.14 68 68
AP1 -0.096 0.22 0.29 2 -0.6 75 77
mol:IP3 -0.017 0.04 0.052 46 -0.095 59 105
PLCG1 -0.017 0.04 0.052 46 -0.096 59 105
PDGF/PDGFRA/alphaV Integrin 0.006 0.075 -10000 0 -0.15 77 77
RAPGEF1 0.036 0.008 -10000 0 0 21 21
CRK 0.036 0.008 -10000 0 0 25 25
mol:Ca2+ -0.017 0.04 0.052 45 -0.095 59 104
CAV3 0.037 0.005 -10000 0 0 11 11
CAV1 0.016 0.019 -10000 0 0 287 287
SHC/Grb2/SOS1 0.028 0.063 -10000 0 -0.11 65 65
PDGF/PDGFRA/Shf -0.003 0.053 0.082 1 -0.088 117 118
FOS -0.091 0.22 0.22 1 -0.62 69 70
JUN -0.025 0.056 0.22 9 -0.2 16 25
oligodendrocyte development 0.005 0.075 -10000 0 -0.15 77 77
GRB2 0.036 0.007 -10000 0 0 19 19
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:DAG -0.017 0.04 0.052 46 -0.095 59 105
PDGF/PDGFRA 0.018 0.033 0.092 4 -0.056 53 57
actin cytoskeleton reorganization 0.008 0.066 -10000 0 -0.14 66 66
SRF -0.015 0.021 0.034 67 -10000 0 67
SHC1 0.034 0.012 -10000 0 0 53 53
PI3K 0.009 0.091 -10000 0 -0.15 110 110
PDGF/PDGFRA/Crk/C3G 0.028 0.073 -10000 0 -0.13 76 76
JAK1 -0.011 0.02 0.025 70 -10000 0 70
ELK1/SRF -0.017 0.083 0.14 72 -0.16 55 127
SHB 0.034 0.011 -10000 0 0 52 52
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.035 -10000 0 -0.032 108 108
GO:0007205 -0.028 0.067 0.1 18 -0.2 53 71
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.026 0.062 -10000 0 -0.11 65 65
PDGF/PDGFRA/SHB 0.008 0.066 -10000 0 -0.14 66 66
PDGF/PDGFRA/Caveolin-1 -0.013 0.075 -10000 0 -0.16 85 85
ITGAV 0.035 0.009 -10000 0 0 34 34
ELK1 -0.032 0.068 0.14 7 -0.15 85 92
PIK3CA 0.032 0.013 -10000 0 0 74 74
PDGF/PDGFRA/Crk 0.007 0.073 -10000 0 -0.14 77 77
JAK-STAT cascade -0.011 0.02 0.025 70 -10000 0 70
cell proliferation -0.003 0.053 0.082 1 -0.088 117 118
Effects of Botulinum toxin

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
STX1A -0.008 0.006 0 166 -10000 0 166
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.041 0.04 -10000 0 -0.14 19 19
STXBP1 0.03 0.015 -10000 0 0 106 106
ACh/CHRNA1 0.027 0.054 0.097 54 -0.075 93 147
RAB3GAP2/RIMS1/UNC13B 0.053 0.051 -10000 0 -0.13 26 26
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 0.036 0.008 -10000 0 0 24 24
mol:ACh 0.016 0.065 0.098 140 -0.088 92 232
RAB3GAP2 0.036 0.008 -10000 0 0 27 27
STX1A/SNAP25/VAMP2 0.022 0.1 0.18 16 -0.15 83 99
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.027 0.054 0.097 54 -0.075 93 147
UNC13B 0.032 0.013 -10000 0 0 73 73
CHRNA1 0.036 0.007 -10000 0 0 18 18
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.013 0.042 0.1 20 -0.084 41 61
SNAP25 0.002 0.003 -10000 0 0 275 275
VAMP2 0.004 0.001 -10000 0 0 50 50
SYT1 0.018 0.019 -10000 0 0 266 266
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.016 0.086 1 -10000 0 1
STX1A/SNAP25 fragment 1/VAMP2 0.022 0.1 0.18 16 -0.15 83 99
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.037 0.006 -10000 0 0 13 13
Syndecan-3/Src/Cortactin -0.022 0.18 -10000 0 -0.45 71 71
Syndecan-3/Neurocan -0.057 0.2 -10000 0 -0.53 74 74
POMC 0.037 0.006 -10000 0 0 13 13
EGFR 0.01 0.017 -10000 0 0 373 373
Syndecan-3/EGFR -0.053 0.16 -10000 0 -0.42 72 72
AGRP 0.037 0.005 -10000 0 0 8 8
NCSTN 0.036 0.009 -10000 0 0 29 29
PSENEN 0.035 0.009 -10000 0 0 33 33
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.037 0.006 -10000 0 0 14 14
APH1A 0.036 0.007 -10000 0 0 17 17
NCAN 0.024 0.018 -10000 0 0 189 189
long-term memory -0.029 0.2 -10000 0 -0.49 76 76
Syndecan-3/IL8 -0.052 0.18 -10000 0 -0.47 74 74
PSEN1 0.034 0.011 -10000 0 0 48 48
Src/Cortactin 0.051 0.018 -10000 0 -0.14 1 1
FYN 0.031 0.015 -10000 0 0 93 93
limb bud formation -0.061 0.18 -10000 0 -0.49 74 74
MC4R 0.036 0.007 -10000 0 0 19 19
SRC 0.035 0.009 -10000 0 0 31 31
PTN 0.023 0.018 -10000 0 0 197 197
FGFR/FGF/Syndecan-3 -0.062 0.18 -10000 0 -0.5 74 74
neuron projection morphogenesis -0.033 0.2 0.33 6 -0.49 71 77
Syndecan-3/AgRP -0.04 0.19 -10000 0 -0.48 74 74
Syndecan-3/AgRP/MC4R -0.021 0.19 -10000 0 -0.48 74 74
Fyn/Cortactin 0.03 0.061 -10000 0 -0.14 53 53
SDC3 -0.063 0.18 -10000 0 -0.5 74 74
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.052 0.18 -10000 0 -0.46 74 74
IL8 0.02 0.019 -10000 0 0 244 244
Syndecan-3/Fyn/Cortactin -0.03 0.2 -10000 0 -0.5 76 76
Syndecan-3/CASK -0.062 0.17 -10000 0 -0.48 74 74
alpha-MSH/MC4R 0.053 0.013 -10000 0 -10000 0 0
Gamma Secretase 0.08 0.073 -10000 0 -0.15 28 28
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.046 0.12 68 -0.039 84 152
AES 0.032 0.043 0.11 66 -0.036 85 151
FBXW11 0.036 0.008 -10000 0 0 24 24
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.027 -10000 0 -10000 0 0
SMAD4 0.033 0.012 -10000 0 0 58 58
DKK2 0.035 0.009 -10000 0 0 31 31
TLE1 0.032 0.042 0.11 66 -0.036 84 150
MACF1 0.034 0.012 -10000 0 0 52 52
CTNNB1 0.043 0.11 0.28 28 -0.35 15 43
WIF1 0.029 0.015 -10000 0 0 110 110
beta catenin/RanBP3 0.068 0.16 0.42 64 -0.35 9 73
KREMEN2 0.037 0.004 -10000 0 0 6 6
DKK1 0.019 0.019 -10000 0 0 258 258
beta catenin/beta TrCP1 0.059 0.12 0.29 27 -0.34 16 43
FZD1 0.026 0.018 -10000 0 0 162 162
AXIN2 -0.025 0.094 0.12 2 -0.24 69 71
AXIN1 0.038 0.004 -10000 0 0 6 6
RAN 0.037 0.006 -10000 0 0 13 13
Axin1/APC/GSK3/beta catenin 0.013 0.16 -10000 0 -0.6 30 30
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.025 0.13 0.25 10 -0.41 20 30
Axin1/APC/GSK3 0.004 0.096 0.26 8 -0.36 20 28
Axin1/APC/GSK3/beta catenin/Macf1 0.026 0.13 0.29 9 -0.38 30 39
HNF1A 0.034 0.044 0.11 71 -0.036 89 160
CTBP1 0.032 0.042 0.11 62 -0.037 84 146
MYC -0.1 0.41 0.74 14 -1.2 51 65
RANBP3 0.037 0.007 -10000 0 0 16 16
DKK2/LRP6/Kremen 2 0.066 0.028 -10000 0 -0.12 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.031 0.04 0.11 62 -0.037 68 130
TCF3 0.033 0.043 0.11 67 -0.036 87 154
WNT1/LRP6/FZD1/Axin1 0.063 0.046 -10000 0 -10000 0 0
Ran/GTP 0.026 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.038 0.19 0.46 67 -0.35 19 86
LEF1 0.035 0.045 0.12 73 -0.037 85 158
DVL1 0.006 0.1 -10000 0 -0.41 19 19
CSNK2A1 0.034 0.011 -10000 0 0 50 50
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.011 0.16 0.25 10 -0.5 30 40
DKK1/LRP6/Kremen 2 0.035 0.038 -10000 0 -10000 0 0
LRP6 0.035 0.011 -10000 0 0 44 44
CSNK1A1 0.035 0.047 0.12 70 -0.039 86 156
NLK 0.027 0.024 -10000 0 -0.033 58 58
CCND1 -0.083 0.35 0.8 3 -1.2 39 42
WNT1 0.037 0.007 -10000 0 0 18 18
GSK3A 0.036 0.008 0.058 1 0 25 26
GSK3B 0.035 0.01 -10000 0 0 37 37
FRAT1 0.027 0.017 -10000 0 0 138 138
PPP2R5D 0.018 0.057 -10000 0 -0.26 14 14
APC 0.035 0.11 0.19 146 -10000 0 146
WNT1/LRP6/FZD1 0.003 0.045 -10000 0 -0.26 9 9
CREBBP 0.034 0.043 0.11 67 -0.036 88 155
Wnt signaling

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
Noncanonical Wnts/FZD -0.005 0.087 -9999 0 -0.17 88 88
FZD6 0.028 0.017 -9999 0 0 132 132
WNT6 0.038 0.002 -9999 0 0 2 2
WNT4 0.036 0.008 -9999 0 0 21 21
FZD3 0.03 0.015 -9999 0 0 108 108
WNT5A 0.03 0.015 -9999 0 0 101 101
WNT11 0.037 0.007 -9999 0 0 16 16
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.031 0.014 -9999 0 0 84 84
PLK4 0.036 0.007 -9999 0 0 18 18
regulation of centriole replication -0.019 0.009 0 95 -9999 0 95
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.003 0.13 0.32 1 -0.27 63 64
MAP3K8 0.024 0.018 -10000 0 0 176 176
FOS 0.02 0.11 0.23 6 -0.28 28 34
PRKCA 0.029 0.026 -10000 0 -0.03 79 79
PTPN7 0.029 0.03 0.068 53 -0.03 92 145
HRAS 0.035 0.01 -10000 0 0 37 37
PRKCB 0 0.008 0.017 61 -0.012 78 139
NRAS 0.033 0.013 -10000 0 0 66 66
RAS family/GTP 0.042 0.067 -10000 0 -0.13 54 54
MAPK3 0.036 0.051 -10000 0 -0.33 2 2
MAP2K1 0.008 0.056 0.18 1 -0.22 12 13
ELK1 0.027 0.029 -10000 0 -0.04 82 82
BRAF 0.007 0.022 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.003 61 -0.004 80 141
MAPK1 0.009 0.13 -10000 0 -0.42 34 34
RAF1 0 0.067 -10000 0 -0.34 17 17
KRAS 0.035 0.01 -10000 0 0 34 34
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.014 0.034 -10000 0 -0.1 38 38
ARNO/beta Arrestin1-2 0.042 0.026 -10000 0 -0.094 7 7
EGFR 0.01 0.017 -10000 0 0 373 373
EPHA2 0.034 0.012 -10000 0 0 56 56
USP6 0.036 0.007 -10000 0 0 20 20
IQSEC1 0.037 0.007 -10000 0 0 17 17
EGFR/EGFR/EGF/EGF -0.004 0.057 -10000 0 -0.14 65 65
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
mol:GTP 0.002 0.014 0.12 2 -0.067 3 5
ARRB1 0.037 0.005 -10000 0 0 11 11
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.034 0.011 -10000 0 0 51 51
EGF 0.036 0.008 -10000 0 0 25 25
somatostatin receptor activity 0 0 0.001 136 0 10 146
ARAP2 0 0 0 115 0 6 121
mol:GDP 0.063 0.07 0.16 125 -0.16 7 132
mol:PI-3-4-5-P3 0 0 0 128 0 9 137
ITGA2B 0.037 0.003 -10000 0 0 4 4
ARF6 0.036 0.009 -10000 0 0 31 31
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
ADAP1 0 0 0 59 0 4 63
KIF13B 0.033 0.012 -10000 0 0 62 62
HGF/MET 0.034 0.027 -10000 0 -10000 0 0
PXN 0.037 0.005 -10000 0 0 9 9
ARF6/GTP 0.078 0.094 0.2 127 -0.21 9 136
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.057 -10000 0 -0.12 64 64
ADRB2 0.035 0.01 -10000 0 0 41 41
receptor agonist activity 0 0 0 129 0 10 139
actin filament binding 0 0 0 129 0 10 139
SRC 0.036 0.009 -10000 0 0 31 31
ITGB3 0.037 0.004 -10000 0 0 6 6
GNAQ 0.035 0.01 -10000 0 0 35 35
EFA6/PI-4-5-P2 0.001 0.001 0.001 149 -0.001 7 156
ARF6/GDP 0.033 0.073 0.17 15 -0.21 25 40
ARF6/GDP/GULP/ACAP1 0.053 0.075 0.2 27 -0.18 5 32
alphaIIb/beta3 Integrin/paxillin/GIT1 0.094 0.016 -10000 0 -10000 0 0
ACAP1 0 0 0 58 -10000 0 58
ACAP2 0 0 0 99 0 5 104
LHCGR/beta Arrestin2 0.031 0.025 -10000 0 -0.14 7 7
EFNA1 0.034 0.012 -10000 0 0 53 53
HGF 0.026 0.018 -10000 0 0 163 163
CYTH3 0 0 0.001 132 -0.001 9 141
CYTH2 0 0.001 0.003 3 -0.004 10 13
NCK1 0.036 0.009 -10000 0 0 28 28
fibronectin binding 0 0 0 129 0 10 139
endosomal lumen acidification 0 0 0 125 0 11 136
microtubule-based process 0 0 -10000 0 0 4 4
GULP1 0.025 0.018 -10000 0 0 169 169
GNAQ/ARNO 0.027 0.008 0.042 7 0 35 42
mol:Phosphatidic acid 0 0 0 99 0 5 104
PIP3-E 0 0 0 59 0 20 79
MET 0.024 0.018 -10000 0 0 184 184
GNA14 0.035 0.009 -10000 0 0 34 34
GNA15 0.034 0.011 -10000 0 0 45 45
GIT1 0.037 0.004 -10000 0 0 7 7
mol:PI-4-5-P2 0 0 0.001 137 -0.001 8 145
GNA11 0.034 0.011 -10000 0 0 46 46
LHCGR 0.038 0.002 -10000 0 0 1 1
AGTR1 0.036 0.008 -10000 0 0 22 22
desensitization of G-protein coupled receptor protein signaling pathway 0.031 0.025 -10000 0 -0.14 7 7
IPCEF1/ARNO 0.001 0.038 -10000 0 -0.084 65 65
alphaIIb/beta3 Integrin 0.055 0.006 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.027 -10000 0 -0.054 53 53
CDKN2C -0.007 0.023 -10000 0 -0.034 122 122
CDKN2A 0.006 0.016 0.087 1 -10000 0 1
CCND2 -0.002 0.019 0.11 6 -10000 0 6
RB1 -0.049 0.091 0.17 1 -0.19 143 144
CDK4 -0.002 0.021 0.13 6 -10000 0 6
CDK6 -0.001 0.02 0.13 6 -10000 0 6
G1/S progression 0.059 0.099 0.19 165 -0.16 2 167
LPA receptor mediated events

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
GNB1/GNG2 0.005 0.057 -10000 0 -0.14 61 61
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.097 0.22 11 -0.2 45 56
AP1 -0.01 0.073 0.09 3 -0.14 94 97
mol:PIP3 -0.024 0.05 -10000 0 -0.13 77 77
AKT1 0.002 0.096 0.21 21 -0.25 24 45
PTK2B -0.002 0.058 0.12 6 -0.15 58 64
RHOA 0.019 0.08 0.17 18 -0.36 12 30
PIK3CB 0.036 0.008 -10000 0 -0.003 20 20
mol:Ca2+ -0.009 0.04 0.17 5 -0.14 19 24
MAGI3 0 0 -10000 0 -0.005 2 2
RELA 0.037 0.005 -10000 0 0 10 10
apoptosis 0.002 0.062 0.1 36 -0.16 54 90
HRAS/GDP 0.022 0.028 -10000 0 -0.13 16 16
positive regulation of microtubule depolymerization -0.021 0.073 0.18 9 -0.21 37 46
NF kappa B1 p50/RelA -0.021 0.067 0.078 64 -0.16 56 120
endothelial cell migration -0.016 0.097 -10000 0 -0.3 54 54
ADCY4 -0.007 0.09 0.16 13 -0.25 39 52
ADCY5 -0.007 0.09 0.16 13 -0.25 39 52
ADCY6 -0.004 0.09 0.17 12 -0.25 37 49
ADCY7 -0.007 0.094 0.17 12 -0.24 43 55
ADCY1 -0.013 0.082 0.16 5 -0.25 37 42
ADCY2 -0.006 0.092 0.17 12 -0.24 40 52
ADCY3 -0.007 0.09 0.16 13 -0.25 39 52
ADCY8 -0.006 0.088 0.16 13 -0.24 39 52
ADCY9 -0.005 0.091 0.17 13 -0.24 40 53
GSK3B -0.01 0.064 0.18 6 -0.16 57 63
arachidonic acid secretion -0.022 0.11 0.15 9 -0.24 69 78
GNG2 0 0.001 0.002 1 -0.004 16 17
TRIP6 -0.013 0.081 -10000 0 -0.25 52 52
GNAO1 0.004 0.058 0.13 25 -0.16 48 73
HRAS 0.035 0.01 -10000 0 0 37 37
NFKBIA -0.017 0.084 0.18 14 -0.22 38 52
GAB1 0.034 0.012 -10000 0 0 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.002 0.2 -10000 0 -0.82 29 29
JUN 0.034 0.011 -10000 0 0 44 44
LPA/LPA2/NHERF2 0.02 0.029 -10000 0 -0.061 54 54
TIAM1 -0.01 0.24 -10000 0 -1 29 29
PIK3R1 0.033 0.013 -10000 0 0 68 68
mol:IP3 -0.009 0.038 0.2 3 -0.14 19 22
PLCB3 0.007 0.035 0.2 4 -10000 0 4
FOS 0.025 0.018 -10000 0 0 166 166
positive regulation of mitosis -0.022 0.11 0.15 9 -0.24 69 78
LPA/LPA1-2-3 -0.008 0.04 -10000 0 -0.12 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -0.002 2 2
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.01 0.066 0.15 1 -0.27 10 11
GNAZ 0.003 0.063 0.13 28 -0.17 48 76
EGFR/PI3K-beta/Gab1 -0.02 0.054 -10000 0 -0.13 77 77
positive regulation of dendritic cell cytokine production -0.008 0.04 -10000 0 -0.12 54 54
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.05 56 56
ARHGEF1 0.034 0.12 0.2 143 -0.16 37 180
GNAI2 0.004 0.069 0.13 39 -0.17 54 93
GNAI3 0.007 0.063 0.13 39 -0.15 54 93
GNAI1 0.001 0.049 0.13 17 -0.16 32 49
LPA/LPA3 -0.006 0.021 -10000 0 -0.066 54 54
LPA/LPA2 -0.005 0.021 -10000 0 -0.065 54 54
LPA/LPA1 -0.012 0.054 -10000 0 -0.17 54 54
HB-EGF/EGFR -0.005 0.052 0.1 11 -0.14 51 62
HBEGF -0.01 0.012 0 291 -10000 0 291
mol:DAG -0.009 0.038 0.2 3 -0.14 19 22
cAMP biosynthetic process -0.001 0.11 0.19 34 -0.26 47 81
NFKB1 0.036 0.007 -10000 0 0 18 18
SRC 0.035 0.009 -10000 0 0 31 31
GNB1 0.034 0.011 -10000 0 0 47 47
LYN -0.024 0.095 0.18 18 -0.22 65 83
GNAQ 0.009 0.026 0.058 38 -0.057 57 95
LPAR2 0 0.001 0.002 1 -0.005 4 5
LPAR3 0 0.001 -10000 0 -0.002 5 5
LPAR1 -0.009 0.033 -10000 0 -0.1 54 54
IL8 -0.12 0.2 0.29 14 -0.39 161 175
PTK2 0.014 0.058 0.13 38 -0.13 53 91
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
CASP3 0.002 0.063 0.1 36 -0.16 54 90
EGFR 0.01 0.017 -10000 0 0 373 373
PLCG1 0.005 0.038 0.062 25 -0.082 57 82
PLD2 0.016 0.054 0.13 38 -0.12 55 93
G12/G13 0.016 0.062 -10000 0 -0.15 48 48
PI3K-beta -0.013 0.068 -10000 0 -0.25 24 24
cell migration 0.001 0.072 -10000 0 -0.25 29 29
SLC9A3R2 0.037 0.004 -10000 0 0 7 7
PXN 0.01 0.067 -10000 0 -0.28 10 10
HRAS/GTP -0.022 0.11 0.16 9 -0.26 65 74
RAC1 0.026 0.017 -10000 0 0 156 156
MMP9 0.017 0.019 -10000 0 0 281 281
PRKCE 0.037 0.004 -10000 0 -0.011 3 3
PRKCD -0.005 0.055 0.2 13 -0.2 3 16
Gi(beta/gamma) -0.013 0.11 0.15 14 -0.26 61 75
mol:LPA -0.009 0.033 -10000 0 -0.1 54 54
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.08 0.13 1 -0.21 45 46
MAPKKK cascade -0.022 0.11 0.15 9 -0.24 69 78
contractile ring contraction involved in cytokinesis 0.019 0.081 0.18 17 -0.35 12 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.009 0.026 0.058 37 -0.057 57 94
GNA15 0.008 0.026 0.058 35 -0.056 55 90
GNA12 0.024 0.018 -10000 0 0 180 180
GNA13 0.036 0.007 -10000 0 0 21 21
MAPT -0.021 0.074 0.18 9 -0.21 38 47
GNA11 0.011 0.023 0.058 39 -0.056 38 77
Rac1/GTP -0.003 0.22 -10000 0 -0.86 29 29
MMP2 -0.016 0.097 -10000 0 -0.3 54 54
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.009 -10000 0 0 34 34
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.037 0.004 -10000 0 0 6 6
TCEB1 0.036 0.008 -10000 0 0 22 22
HIF1A/p53 -0.04 0.13 0.2 2 -0.28 98 100
HIF1A -0.033 0.11 -10000 0 -0.28 78 78
COPS5 0.037 0.006 -10000 0 0 13 13
VHL/Elongin B/Elongin C/RBX1/CUL2 0.052 0.061 -10000 0 -0.12 23 23
FIH (dimer) 0.028 0.016 -10000 0 0 131 131
CDKN2A 0.005 0.013 -10000 0 0 444 444
ARNT/IPAS 0.051 0.016 -10000 0 -10000 0 0
HIF1AN 0.028 0.016 -10000 0 0 131 131
GNB2L1 0.037 0.005 -10000 0 0 10 10
HIF1A/ARNT -0.039 0.13 -10000 0 -0.28 97 97
CUL2 0.028 0.017 -10000 0 0 133 133
OS9 0.031 0.015 -10000 0 0 93 93
RACK1/Elongin B/Elongin C 0.069 0.032 -10000 0 -0.13 9 9
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.038 0.13 0.2 2 -0.28 101 103
PHD1-3/OS9 0.056 0.065 -10000 0 -0.14 30 30
HIF1A/RACK1/Elongin B/Elongin C -0.02 0.15 -10000 0 -0.28 101 101
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.035 0.01 -10000 0 0 35 35
HIF1A/JAB1 -0.04 0.13 0.23 1 -0.28 101 102
EGLN3 0.031 0.015 -10000 0 0 96 96
EGLN2 0.036 0.008 -10000 0 0 21 21
EGLN1 0.035 0.009 -10000 0 0 32 32
TP53 0.032 0.013 -10000 0 0 71 71
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.006 0.1 -10000 0 -0.62 12 12
ARNT 0.037 0.005 -10000 0 0 11 11
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.034 0.011 -10000 0 0 45 45
HIF1A/p19ARF -0.048 0.11 -10000 0 -0.27 90 90
Syndecan-1-mediated signaling events

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
TGFB1 0.033 0.012 -10000 0 0 57 57
CCL5 0.034 0.012 -10000 0 0 55 55
SDCBP 0.036 0.007 -10000 0 0 20 20
FGFR/FGF2/Syndecan-1 0.011 0.096 0.17 40 -0.23 11 51
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 0.016 0.1 0.21 21 -0.24 16 37
Syndecan-1/Syntenin 0.026 0.11 0.22 33 -0.24 18 51
MAPK3 0.003 0.1 0.19 25 -0.22 22 47
HGF/MET 0.034 0.027 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.033 0.012 -10000 0 0 57 57
BSG 0.033 0.012 -10000 0 0 57 57
keratinocyte migration 0.015 0.1 0.21 21 -0.23 16 37
Syndecan-1/RANTES 0.02 0.1 0.22 24 -0.24 14 38
Syndecan-1/CD147 0.024 0.12 0.23 15 -0.23 22 37
Syndecan-1/Syntenin/PIP2 0.023 0.11 0.2 33 -0.23 18 51
LAMA5 0.032 0.013 -10000 0 0 72 72
positive regulation of cell-cell adhesion 0.022 0.1 0.2 33 -0.23 18 51
MMP7 0.027 0.017 -10000 0 0 140 140
HGF 0.026 0.018 -10000 0 0 163 163
Syndecan-1/CASK -0.009 0.081 0.16 4 -0.23 15 19
Syndecan-1/HGF/MET 0.023 0.093 0.24 10 -0.24 10 20
regulation of cell adhesion -0.005 0.11 0.23 30 -0.23 22 52
HPSE 0.033 0.012 -10000 0 0 59 59
positive regulation of cell migration 0.011 0.096 0.17 40 -0.23 11 51
SDC1 0.008 0.089 0.15 33 -0.15 86 119
Syndecan-1/Collagen 0.011 0.096 0.17 40 -0.23 11 51
PPIB 0.035 0.01 -10000 0 0 35 35
MET 0.024 0.018 -10000 0 0 184 184
PRKACA 0.036 0.007 -10000 0 0 17 17
MMP9 0.017 0.019 -10000 0 0 281 281
MAPK1 0.002 0.1 0.18 23 -0.22 22 45
homophilic cell adhesion 0.015 0.1 0.19 49 -0.23 13 62
MMP1 0.032 0.013 -10000 0 0 74 74
EGFR-dependent Endothelin 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
HRAS 0.035 0.01 -10000 0 0 37 37
EGFR 0.01 0.017 -10000 0 0 373 373
EGF/EGFR 0.001 0.053 -10000 0 -0.11 66 66
EGF/EGFR dimer/SHC/GRB2/SOS1 0.007 0.059 -10000 0 -0.11 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.029 0.016 -10000 0 0 123 123
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.036 0.008 -10000 0 0 25 25
EGF/EGFR dimer/SHC 0.001 0.057 -10000 0 -0.12 63 63
mol:GDP 0.005 0.056 -10000 0 -0.11 63 63
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.034 0.012 -10000 0 0 54 54
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
HRAS/GTP -0.004 0.052 -10000 0 -0.11 71 71
SHC1 0.034 0.012 -10000 0 0 53 53
HRAS/GDP 0 0.059 -10000 0 -0.12 71 71
FRAP1 -0.017 0.039 0.055 20 -0.11 63 83
EGF/EGFR dimer -0.004 0.057 -10000 0 -0.14 65 65
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.036 0.007 -10000 0 0 19 19
ETA receptor/Endothelin-1 0.024 0.06 -10000 0 -0.14 52 52
Syndecan-4-mediated signaling events

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
PTK2 -0.032 0.16 -10000 0 -0.46 43 43
Syndecan-4/Syndesmos -0.14 0.29 -10000 0 -0.76 66 66
positive regulation of JNK cascade -0.13 0.26 -10000 0 -0.64 78 78
Syndecan-4/ADAM12 -0.14 0.29 -10000 0 -0.76 66 66
CCL5 0.034 0.012 -10000 0 0 55 55
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
DNM2 0.036 0.007 -10000 0 0 20 20
ITGA5 0.033 0.012 -10000 0 0 62 62
SDCBP 0.036 0.007 -10000 0 0 20 20
PLG 0.028 0.025 -10000 0 -0.044 41 41
ADAM12 0.026 0.017 -10000 0 0 154 154
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.024 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.29 -10000 0 -0.76 66 66
Syndecan-4/CXCL12/CXCR4 -0.14 0.29 -10000 0 -0.69 78 78
Syndecan-4/Laminin alpha3 -0.13 0.3 -10000 0 -0.75 66 66
MDK 0.031 0.015 -10000 0 0 96 96
Syndecan-4/FZD7 -0.14 0.3 -10000 0 -0.67 90 90
Syndecan-4/Midkine -0.14 0.3 -10000 0 -0.69 83 83
FZD7 0.027 0.017 -10000 0 0 144 144
Syndecan-4/FGFR1/FGF -0.1 0.29 -10000 0 -0.72 63 63
THBS1 0.031 0.014 -10000 0 0 90 90
integrin-mediated signaling pathway -0.13 0.29 -10000 0 -0.64 86 86
positive regulation of MAPKKK cascade -0.13 0.26 -10000 0 -0.64 78 78
Syndecan-4/TACI -0.13 0.3 -10000 0 -0.76 66 66
CXCR4 0.03 0.015 -10000 0 0 104 104
cell adhesion -0.009 0.056 0.21 3 -0.24 20 23
Syndecan-4/Dynamin -0.13 0.3 -10000 0 -0.76 66 66
Syndecan-4/TSP1 -0.14 0.29 -10000 0 -0.76 65 65
Syndecan-4/GIPC -0.13 0.3 -10000 0 -0.76 66 66
Syndecan-4/RANTES -0.13 0.29 -10000 0 -0.76 66 66
ITGB1 0.029 0.016 -10000 0 0 117 117
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.034 0.011 -10000 0 0 48 48
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCA 0 0.11 1.1 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.14 0.3 -10000 0 -0.68 84 84
TFPI 0.03 0.015 -10000 0 0 105 105
F2 0.01 0.043 -10000 0 -0.046 171 171
alpha5/beta1 Integrin 0.032 0.043 -10000 0 -0.14 21 21
positive regulation of cell adhesion -0.13 0.28 -10000 0 -0.72 66 66
ACTN1 0.029 0.016 -10000 0 0 124 124
TNC 0.028 0.016 -10000 0 0 125 125
Syndecan-4/CXCL12 -0.14 0.29 -10000 0 -0.76 65 65
FGF6 0.036 0.009 -10000 0 0 28 28
RHOA 0.036 0.007 -10000 0 0 20 20
CXCL12 0.024 0.018 -10000 0 0 186 186
TNFRSF13B 0.037 0.005 -10000 0 0 10 10
FGF2 0.036 0.008 -10000 0 0 25 25
FGFR1 0.037 0.004 -10000 0 0 7 7
Syndecan-4/PI-4-5-P2 -0.14 0.29 -10000 0 -0.76 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.029 0.025 -10000 0 -0.044 41 41
cell migration -0.01 0.016 -10000 0 -10000 0 0
PRKCD 0.029 0.025 -10000 0 -0.044 38 38
vasculogenesis -0.13 0.28 -10000 0 -0.72 65 65
SDC4 -0.15 0.31 -10000 0 -0.82 65 65
Syndecan-4/Tenascin C -0.14 0.3 -10000 0 -0.68 86 86
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.3 -10000 0 -0.76 67 67
MMP9 0.012 0.024 -10000 0 -0.044 36 36
Rac1/GTP -0.009 0.057 0.21 3 -0.25 20 23
cytoskeleton organization -0.14 0.27 -10000 0 -0.71 66 66
GIPC1 0.036 0.007 -10000 0 0 18 18
Syndecan-4/TFPI -0.14 0.3 -10000 0 -0.72 73 73
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
CDC42/GTP 0.004 0.1 -10000 0 -0.24 51 51
PLCG1 -0.016 0.094 0.11 1 -0.2 85 86
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.011 -10000 0 0 46 46
GNAI3 0.037 0.007 -10000 0 0 16 16
G12/G13 0.027 0.048 -10000 0 -0.14 29 29
cell migration 0.003 0.1 -10000 0 -0.23 51 51
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.016 0.097 0.11 1 -0.2 91 92
MAPK1 -0.01 0.091 -10000 0 -0.19 82 82
S1P/S1P5/Gi -0.012 0.098 -10000 0 -0.2 84 84
GNAI1 0.019 0.019 -10000 0 0 255 255
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.1 29 29
RHOA 0.037 0.1 0.19 146 -0.18 3 149
S1P/S1P4/Gi -0.012 0.098 -10000 0 -0.2 84 84
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.014 -10000 0 0 81 81
S1P/S1P4/G12/G13 0.025 0.038 -10000 0 -0.1 29 29
GNA12 0.024 0.018 -10000 0 0 180 180
GNA13 0.036 0.008 -10000 0 0 21 21
CDC42 0.036 0.008 -10000 0 0 26 26
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.004 0.1 0.24 53 -10000 0 53
GNAI2 0.034 0.011 -10000 0 0 46 46
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.1 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
RhoA/GTP 0.004 0.11 -10000 0 -0.24 53 53
negative regulation of cAMP metabolic process -0.012 0.098 -10000 0 -0.2 85 85
GNAZ 0.032 0.014 -10000 0 0 81 81
GNAI3 0.037 0.007 -10000 0 0 16 16
GNA12 0.024 0.018 -10000 0 0 180 180
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.012 0.098 -10000 0 -0.2 84 84
RhoA/GDP 0.025 0.019 -10000 0 -0.13 7 7
RHOA 0.036 0.007 -10000 0 0 20 20
GNAI1 0.019 0.019 -10000 0 0 255 255
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 33 -10000 0 33
GNB1/GNG2 0.038 0.032 -10000 0 -0.1 20 20
regulation of S phase of mitotic cell cycle -0.005 0.08 -10000 0 -0.18 72 72
GNAO1 0.031 0.014 -10000 0 0 87 87
HRAS 0.035 0.01 -10000 0 0 37 37
SHBG/T-DHT 0.025 0.005 -10000 0 -10000 0 0
PELP1 0.036 0.007 -10000 0 0 19 19
AKT1 -0.011 0.004 0 58 -10000 0 58
MAP2K1 -0.031 0.081 0.17 28 -0.18 66 94
T-DHT/AR 0.026 0.008 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 9 -0.006 77 86
GNAI2 0.034 0.011 -10000 0 0 46 46
GNAI3 0.036 0.007 -10000 0 0 16 16
GNAI1 0.019 0.019 -10000 0 0 255 255
mol:GDP -0.021 0.034 -10000 0 -0.15 12 12
cell proliferation -0.057 0.18 0.26 15 -0.42 85 100
PIK3CA 0.032 0.013 -10000 0 0 74 74
FOS -0.087 0.28 0.36 3 -0.69 84 87
mol:Ca2+ -0.004 0.02 0.027 2 -0.053 58 60
MAPK3 -0.04 0.13 0.24 17 -0.31 77 94
MAPK1 -0.038 0.16 0.24 3 -0.4 55 58
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:IP3 0 0.002 0.003 59 -0.004 75 134
cAMP biosynthetic process -0.003 0.013 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 0.003 59 -0.004 75 134
HRAS/GTP 0.042 0.066 -10000 0 -0.096 69 69
actin cytoskeleton reorganization 0.02 0.055 -10000 0 -0.12 47 47
SRC 0.035 0.009 -10000 0 0 31 31
voltage-gated calcium channel activity 0 0.002 0.003 59 -0.004 75 134
PI3K 0.02 0.063 -10000 0 -0.13 75 75
apoptosis 0.046 0.19 0.42 85 -0.24 12 97
T-DHT/AR/PELP1 0.044 0.025 -10000 0 -0.12 7 7
HRAS/GDP 0.01 0.06 -10000 0 -0.18 16 16
CREB1 -0.066 0.19 0.24 12 -0.46 85 97
RAC1-CDC42/GTP 0.029 0.061 -10000 0 -0.12 47 47
AR 0.036 0.008 -10000 0 0 23 23
GNB1 0.034 0.011 -10000 0 0 47 47
RAF1 -0.021 0.076 0.19 27 -0.22 13 40
RAC1-CDC42/GDP 0.022 0.054 -10000 0 -0.16 13 13
T-DHT/AR/PELP1/Src 0.06 0.033 -10000 0 -0.12 7 7
MAP2K2 -0.034 0.075 0.17 20 -0.17 65 85
T-DHT/AR/PELP1/Src/PI3K -0.004 0.08 -10000 0 -0.18 71 71
GNAZ 0.032 0.014 -10000 0 0 81 81
SHBG 0.036 0.007 -10000 0 0 17 17
Gi family/GNB1/GNG2/GDP -0.044 0.17 -10000 0 -0.44 60 60
mol:T-DHT 0 0.001 0.002 1 -0.004 23 24
RAC1 0.026 0.017 -10000 0 0 156 156
GNRH1 -0.012 0.002 0 11 -10000 0 11
Gi family/GTP -0.008 0.081 0.12 1 -0.19 61 62
CDC42 0.036 0.008 -10000 0 0 26 26
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.045 0.042 -10000 0 -0.14 24 24
AKT1 -0.058 0.21 0.31 15 -0.38 107 122
PTK2B -0.013 0.12 0.22 53 -0.35 16 69
VEGFR2 homodimer/Frs2 0.023 0.072 0.16 3 -0.3 16 19
CAV1 0.016 0.019 -10000 0 0 287 287
CALM1 0.033 0.012 -10000 0 0 60 60
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.009 0.1 -10000 0 -0.26 33 33
endothelial cell proliferation -0.016 0.17 0.31 27 -0.35 53 80
mol:Ca2+ -0.005 0.13 0.24 69 -0.27 31 100
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.012 0.11 -10000 0 -0.24 40 40
RP11-342D11.1 -0.026 0.098 0.17 40 -0.25 37 77
CDH5 0.031 0.014 -10000 0 0 91 91
VEGFA homodimer 0.018 0.077 -10000 0 -0.12 107 107
SHC1 0.034 0.012 -10000 0 0 53 53
SHC2 0.033 0.012 -10000 0 0 57 57
HRAS/GDP -0.006 0.097 -10000 0 -0.24 45 45
SH2D2A 0.037 0.006 -10000 0 0 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.003 0.13 0.29 2 -0.36 22 24
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.009 0.1 -10000 0 -0.27 30 30
VEGFR1 homodimer 0.035 0.01 -10000 0 0 37 37
SHC/GRB2/SOS1 0.021 0.11 -10000 0 -0.25 40 40
GRB10 -0.025 0.1 0.2 23 -0.31 37 60
PTPN11 0.037 0.006 -10000 0 0 12 12
GRB2 0.036 0.007 -10000 0 0 19 19
PAK1 0.036 0.007 -10000 0 0 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.016 0.14 0.27 1 -0.27 50 51
HRAS 0.035 0.01 -10000 0 0 37 37
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.13 0.2 4 -0.35 42 46
HIF1A 0.034 0.011 -10000 0 0 47 47
FRS2 0.036 0.008 -10000 0 0 24 24
oxygen and reactive oxygen species metabolic process 0.011 0.1 -10000 0 -0.24 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.037 0.005 -10000 0 0 10 10
Nck/Pak 0.05 0.025 -10000 0 -0.14 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.004 0.12 -10000 0 -0.26 44 44
mol:GDP 0.01 0.1 -10000 0 -0.24 43 43
mol:NADP 0.015 0.14 0.34 19 -0.34 17 36
eNOS/Hsp90 0.026 0.14 0.34 17 -0.33 17 34
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:IP3 -0.005 0.13 0.24 69 -0.28 31 100
HIF1A/ARNT 0.047 0.032 -10000 0 -0.14 11 11
SHB 0.034 0.011 -10000 0 0 52 52
VEGFA 0.024 0.024 0.08 11 -0.053 14 25
VEGFC 0.034 0.011 -10000 0 0 51 51
FAK1/Vinculin -0.025 0.16 0.26 16 -0.4 44 60
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.036 0.007 -10000 0 0 20 20
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.025 0.12 0.23 1 -0.26 37 38
PTPN6 0.034 0.012 -10000 0 0 55 55
EPAS1 0.03 0.057 0.13 2 -0.19 20 22
mol:L-citrulline 0.015 0.14 0.34 19 -0.34 17 36
ITGAV 0.035 0.009 -10000 0 0 34 34
PIK3CA 0.032 0.013 -10000 0 0 74 74
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.029 0.12 0.23 1 -0.26 34 35
VEGFR2 homodimer/VEGFA homodimer 0.01 0.12 -10000 0 -0.26 42 42
VEGFR2/3 heterodimer 0.022 0.073 0.16 3 -0.29 17 20
VEGFB 0.037 0.005 -10000 0 0 9 9
MAPK11 -0.009 0.14 0.28 45 -0.3 35 80
VEGFR2 homodimer 0.001 0.072 0.16 14 -0.38 11 25
FLT1 0.035 0.01 -10000 0 0 37 37
NEDD4 0.032 0.028 0.082 28 -0.05 38 66
MAPK3 0.008 0.14 0.28 51 -0.26 25 76
MAPK1 0.006 0.14 0.28 53 -0.26 30 83
VEGFA145/NRP2 0.004 0.08 -10000 0 -0.14 107 107
VEGFR1/2 heterodimer 0.02 0.072 0.16 3 -0.29 17 20
KDR 0.001 0.072 0.16 14 -0.38 11 25
VEGFA165/NRP1/VEGFR2 homodimer 0.015 0.11 0.23 5 -0.24 40 45
SRC 0.035 0.009 -10000 0 0 31 31
platelet activating factor biosynthetic process 0.007 0.14 0.28 53 -0.26 30 83
PI3K -0.036 0.17 0.26 9 -0.3 104 113
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.008 0.11 -10000 0 -0.2 57 57
FES -0.006 0.14 0.24 72 -0.26 37 109
GAB1 -0.025 0.16 0.25 11 -0.29 102 113
VEGFR2 homodimer/VEGFA homodimer/Src 0.008 0.1 -10000 0 -0.26 31 31
CTNNB1 0.036 0.007 -10000 0 0 17 17
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.037 0.005 -10000 0 0 11 11
eNOS/Caveolin-1 -0.007 0.11 0.33 4 -0.36 15 19
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.11 -10000 0 -0.25 41 41
PI3K/GAB1 -0.045 0.2 0.3 11 -0.37 100 111
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.041 0.12 0.26 3 -0.24 30 33
PRKACA 0.036 0.007 -10000 0 0 17 17
VEGFR2/3 heterodimer/VEGFC homodimer 0.045 0.074 0.2 1 -0.27 15 16
HSP90AA1 0.035 0.01 -10000 0 0 35 35
CDC42 -0.006 0.13 0.24 70 -0.26 37 107
actin cytoskeleton reorganization 0.009 0.1 -10000 0 -0.26 30 30
PTK2 -0.024 0.17 0.25 29 -0.42 42 71
EDG1 -0.026 0.098 0.17 40 -0.25 37 77
mol:DAG -0.005 0.13 0.24 69 -0.28 31 100
CaM/Ca2+ -0.013 0.12 0.21 61 -0.28 31 92
MAP2K3 -0.013 0.13 0.24 60 -0.27 31 91
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.028 0.14 0.25 68 -0.31 38 106
PLCG1 -0.006 0.13 0.24 69 -0.28 31 100
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.025 0.11 0.23 1 -0.25 30 31
IQGAP1 0.034 0.011 -10000 0 0 47 47
YES1 0.035 0.01 -10000 0 0 43 43
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.008 0.11 -10000 0 -0.26 35 35
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.006 0.1 -10000 0 -0.26 33 33
cell migration -0.029 0.17 0.28 18 -0.39 54 72
mol:PI-3-4-5-P3 -0.032 0.16 0.26 10 -0.29 104 114
FYN 0.031 0.015 -10000 0 0 93 93
VEGFB/NRP1 -0.01 0.12 0.2 65 -0.26 31 96
mol:NO 0.015 0.14 0.34 19 -0.34 17 36
PXN 0.037 0.005 -10000 0 0 9 9
HRAS/GTP -0.052 0.073 -10000 0 -0.25 42 42
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.011 0.12 -10000 0 -0.31 38 38
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.037 0.004 -10000 0 0 6 6
NOS3 0.012 0.14 0.35 17 -0.38 17 34
VEGFR2 homodimer/VEGFA homodimer/Sck 0.002 0.11 -10000 0 -0.27 38 38
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCA -0.011 0.13 0.24 59 -0.27 31 90
PRKCB -0.007 0.12 0.24 59 -0.26 31 90
VCL 0.028 0.016 -10000 0 0 128 128
VEGFA165/NRP1 -0.009 0.1 0.19 28 -0.26 37 65
VEGFR1/2 heterodimer/VEGFA homodimer 0.006 0.1 -10000 0 -0.26 32 32
VEGFA165/NRP2 0.004 0.08 -10000 0 -0.14 107 107
MAPKKK cascade -0.018 0.11 0.25 13 -0.32 30 43
NRP2 0.037 0.005 -10000 0 0 8 8
VEGFC homodimer 0.034 0.011 -10000 0 0 51 51
NCK1 0.036 0.009 -10000 0 0 28 28
ROCK1 0.037 0.007 -10000 0 0 16 16
FAK1/Paxillin -0.01 0.17 0.27 19 -0.4 43 62
MAP3K13 -0.007 0.13 0.24 68 -0.26 37 105
PDPK1 -0.044 0.15 0.24 27 -0.27 103 130
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.03 0.087 -10000 0 -0.14 92 92
alphaM/beta2 Integrin/GPIbA 0.05 0.071 -10000 0 -0.12 62 62
alphaM/beta2 Integrin/proMMP-9 -0.008 0.089 -10000 0 -0.13 144 144
PLAUR 0.031 0.014 -10000 0 0 90 90
HMGB1 0.04 0.014 0.087 1 -10000 0 1
alphaM/beta2 Integrin/Talin 0.039 0.073 -10000 0 -0.13 58 58
AGER 0.042 0.01 0.085 2 -10000 0 2
RAP1A 0.037 0.005 -10000 0 0 10 10
SELPLG 0.037 0.006 -10000 0 0 12 12
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.075 0.087 -10000 0 -0.13 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.019 -10000 0 0 281 281
CYR61 0.025 0.018 -10000 0 0 167 167
TLN1 0.03 0.015 -10000 0 0 104 104
Rap1/GTP 0.025 0.071 -10000 0 -0.21 20 20
RHOA 0.036 0.007 -10000 0 0 20 20
P-selectin oligomer 0.037 0.006 -10000 0 0 14 14
MYH2 0.019 0.066 -10000 0 -0.23 13 13
MST1R 0.036 0.008 -10000 0 0 22 22
leukocyte activation during inflammatory response 0.053 0.067 -10000 0 -0.1 59 59
APOB 0.037 0.006 -10000 0 0 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.03 0.015 -10000 0 0 104 104
JAM3 0.034 0.012 -10000 0 0 55 55
GP1BA 0.037 0.006 -10000 0 0 12 12
alphaM/beta2 Integrin/CTGF 0.021 0.087 -10000 0 -0.13 105 105
alphaM/beta2 Integrin 0.021 0.075 -10000 0 -0.24 19 19
JAM3 homodimer 0.034 0.012 -10000 0 0 55 55
ICAM2 0.035 0.009 -10000 0 0 30 30
ICAM1 0.032 0.014 -10000 0 0 78 78
phagocytosis triggered by activation of immune response cell surface activating receptor 0.021 0.075 0.14 2 -0.23 19 21
cell adhesion 0.049 0.07 -10000 0 -0.12 62 62
NFKB1 -0.003 0.081 0.21 22 -10000 0 22
THY1 0.032 0.014 -10000 0 0 83 83
RhoA/GDP 0.025 0.019 -10000 0 -0.13 7 7
Lipoprotein(a) 0.046 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.036 0.1 -10000 0 -0.14 103 103
IL6 -0.017 0.037 -10000 0 -10000 0 0
ITGB2 0.033 0.02 0.083 1 -10000 0 1
elevation of cytosolic calcium ion concentration 0.026 0.087 -10000 0 -0.14 72 72
alphaM/beta2 Integrin/JAM2/JAM3 0.05 0.1 -10000 0 -0.15 88 88
JAM2 0.034 0.012 -10000 0 0 55 55
alphaM/beta2 Integrin/ICAM1 0.076 0.078 -10000 0 -0.12 49 49
alphaM/beta2 Integrin/uPA/Plg 0.039 0.084 -10000 0 -0.13 66 66
RhoA/GTP 0.024 0.068 -10000 0 -0.24 13 13
positive regulation of phagocytosis 0.012 0.1 0.17 1 -0.23 56 57
Ron/MSP 0.052 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.09 -10000 0 -0.14 72 72
alphaM/beta2 Integrin/uPAR 0.038 0.079 -10000 0 -0.14 69 69
PLAU 0.022 0.019 -10000 0 0 215 215
PLAT 0.028 0.016 -10000 0 0 131 131
actin filament polymerization 0.02 0.066 0.19 2 -0.22 13 15
MST1 0.036 0.008 -10000 0 0 27 27
alphaM/beta2 Integrin/lipoprotein(a) 0.062 0.07 -10000 0 -0.11 59 59
TNF 0.003 0.089 0.22 20 -10000 0 20
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.075 -10000 0 -0.14 68 68
fibrinolysis 0.034 0.081 -10000 0 -0.13 66 66
HCK 0.027 0.017 -10000 0 0 145 145
dendritic cell antigen processing and presentation 0.021 0.075 0.14 2 -0.23 19 21
VTN 0.037 0.004 -10000 0 0 7 7
alphaM/beta2 Integrin/CYR61 0.012 0.094 -10000 0 -0.14 123 123
LPA 0.035 0.01 -10000 0 0 35 35
LRP1 0.032 0.013 -10000 0 0 73 73
cell migration -0.001 0.1 0.15 4 -0.14 146 150
FN1 0.035 0.009 -10000 0 0 31 31
alphaM/beta2 Integrin/Thy1 0.032 0.085 -10000 0 -0.13 87 87
MPO 0.037 0.004 -10000 0 0 6 6
KNG1 0.037 0.007 -10000 0 0 16 16
RAP1/GDP 0.025 0.007 -10000 0 -0.1 1 1
ROCK1 0.019 0.068 0.21 2 -0.24 14 16
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.035 0.01 -10000 0 0 37 37
CTGF 0.027 0.017 -10000 0 0 143 143
alphaM/beta2 Integrin/Hck 0.03 0.091 -10000 0 -0.17 70 70
ITGAM 0.043 0.01 0.085 2 -10000 0 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.074 -10000 0 -0.12 57 57
HP 0.028 0.017 -10000 0 0 136 136
leukocyte adhesion 0.02 0.12 -10000 0 -0.26 32 32
SELP 0.037 0.006 -10000 0 0 14 14
Glypican 2 network

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
MDK 0.031 0.015 -9999 0 0 96 96
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.008 0.049 -9999 0 -0.13 57 57
neuron projection morphogenesis 0.008 0.049 -9999 0 -0.13 57 57
IL2 signaling events mediated by STAT5

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
GAB2 0.033 0.014 -10000 0 -0.004 59 59
ELF1 0.039 0.017 -10000 0 -10000 0 0
CCNA2 0.029 0.016 -10000 0 0 119 119
PIK3CA 0.032 0.015 -10000 0 -0.003 81 81
JAK3 0.036 0.01 -10000 0 -0.007 26 26
PIK3R1 0.033 0.014 -10000 0 -0.001 70 70
JAK1 0.034 0.012 -10000 0 -0.003 48 48
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.02 0.18 0.24 1 -0.48 45 46
SHC1 0.033 0.014 -10000 0 -0.004 60 60
SP1 -0.014 0.12 -10000 0 -0.27 89 89
IL2RA 0.012 0.011 -10000 0 -10000 0 0
IL2RB 0.034 0.013 -10000 0 -0.003 55 55
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.036 0.01 -10000 0 -0.004 29 29
G1/S transition of mitotic cell cycle -0.07 0.27 0.31 9 -0.6 91 100
PTPN11 0.037 0.009 -10000 0 -0.009 17 17
CCND2 -0.072 0.19 -10000 0 -0.49 88 88
LCK 0.036 0.01 -10000 0 -0.006 26 26
GRB2 0.036 0.01 -10000 0 -0.006 24 24
IL2 0.037 0.009 -10000 0 -0.011 14 14
CDK6 0.025 0.018 -10000 0 0 165 165
CCND3 -0.025 0.2 0.34 3 -0.72 28 31
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.061 0.6 0.72 42 -1 129 171
IL23A 0.089 0.37 0.77 20 -0.97 22 42
NF kappa B1 p50/RelA/I kappa B alpha 0.088 0.35 0.61 31 -0.84 27 58
positive regulation of T cell mediated cytotoxicity 0.095 0.4 0.75 40 -0.95 26 66
ITGA3 0.091 0.36 0.72 26 -0.92 20 46
IL17F 0.037 0.27 0.49 41 -0.6 28 69
IL12B 0.061 0.08 0.2 71 -10000 0 71
STAT1 (dimer) 0.072 0.37 0.64 36 -0.92 26 62
CD4 0.074 0.42 0.72 36 -1.1 33 69
IL23 0.095 0.36 0.72 18 -0.95 21 39
IL23R 0.068 0.14 0.27 103 -0.15 10 113
IL1B 0.084 0.4 0.75 30 -1.2 22 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.09 0.36 0.68 34 -0.91 19 53
TYK2 0.043 0.06 0.15 49 -10000 0 49
STAT4 0.035 0.009 -10000 0 0 31 31
STAT3 0.035 0.01 -10000 0 0 40 40
IL18RAP 0.036 0.008 -10000 0 -0.032 3 3
IL12RB1 0.045 0.06 0.15 52 -10000 0 52
PIK3CA 0.032 0.013 -10000 0 0 74 74
IL12Rbeta1/TYK2 0.055 0.076 0.19 37 -0.13 12 49
IL23R/JAK2 0.1 0.16 0.35 97 -0.2 11 108
positive regulation of chronic inflammatory response 0.095 0.4 0.75 40 -0.95 26 66
natural killer cell activation -0.005 0.011 -10000 0 -0.03 42 42
JAK2 0.057 0.08 0.2 69 -10000 0 69
PIK3R1 0.033 0.013 -10000 0 0 67 67
NFKB1 0.04 0.01 0.067 3 0 18 21
RELA 0.04 0.008 0.067 3 0 10 13
positive regulation of dendritic cell antigen processing and presentation 0.097 0.35 0.71 19 -0.91 21 40
ALOX12B 0.087 0.36 0.68 37 -0.86 24 61
CXCL1 0.096 0.37 0.73 39 -0.91 20 59
T cell proliferation 0.095 0.4 0.75 40 -0.95 26 66
NFKBIA 0.037 0.014 0.068 2 0 54 56
IL17A 0.069 0.25 0.46 54 -0.48 26 80
PI3K 0.051 0.35 0.62 28 -0.9 26 54
IFNG 0.019 0.033 0.097 26 -0.087 3 29
STAT3 (dimer) 0.054 0.35 0.62 28 -0.86 27 55
IL18R1 0.036 0.008 -10000 0 -0.033 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.096 0.27 0.55 52 -0.51 21 73
IL18/IL18R 0.062 0.037 -10000 0 -0.12 7 7
macrophage activation -0.002 0.016 0.038 1 -0.043 15 16
TNF 0.091 0.37 0.76 20 -0.98 18 38
STAT3/STAT4 0.071 0.36 0.61 28 -0.88 27 55
STAT4 (dimer) 0.073 0.36 0.63 31 -0.92 26 57
IL18 0.032 0.013 -10000 0 -10000 0 0
IL19 0.091 0.36 0.67 37 -0.89 21 58
STAT5A (dimer) 0.085 0.37 0.64 36 -0.9 27 63
STAT1 0.035 0.01 -10000 0 0 41 41
SOCS3 0.037 0.004 -10000 0 0 6 6
CXCL9 0.1 0.37 0.76 26 -0.91 20 46
MPO 0.088 0.36 0.69 31 -0.91 19 50
positive regulation of humoral immune response 0.095 0.4 0.75 40 -0.95 26 66
IL23/IL23R/JAK2/TYK2 0.078 0.39 0.73 33 -0.98 26 59
IL6 0.15 0.37 0.73 48 -0.91 18 66
STAT5A 0.037 0.005 -10000 0 0 8 8
IL2 0.023 0.03 -10000 0 -0.037 98 98
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.03 42 42
CD3E 0.088 0.36 0.68 34 -0.9 20 54
keratinocyte proliferation 0.095 0.4 0.75 40 -0.95 26 66
NOS2 0.089 0.36 0.66 41 -0.83 28 69
IL2 signaling events mediated by PI3K

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
BCL2L1 0.007 0.095 0.32 3 -0.39 3 6
UGCG -0.025 0.19 -10000 0 -0.73 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.15 0.27 6 -0.34 44 50
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.023 0.18 -10000 0 -0.72 30 30
mol:DAG -0.19 0.36 -10000 0 -0.82 125 125
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.18 0.28 5 -0.42 58 63
FRAP1 -0.027 0.2 0.3 6 -0.47 59 65
FOXO3 -0.037 0.2 0.28 8 -0.47 66 74
AKT1 -0.037 0.21 0.3 4 -0.5 64 68
GAB2 0.03 0.02 -10000 0 -0.012 84 84
SMPD1 0.002 0.1 -10000 0 -0.52 15 15
SGMS1 -0.13 0.27 -10000 0 -0.6 122 122
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 -0.03 0.043 -10000 0 -0.12 75 75
CALM1 0.033 0.012 -10000 0 0 60 60
cell proliferation -0.093 0.24 0.29 7 -0.42 122 129
EIF3A 0.026 0.017 -10000 0 0 153 153
PI3K 0.018 0.078 -10000 0 -0.15 75 75
RPS6KB1 0.029 0.042 -10000 0 -0.7 1 1
mol:sphingomyelin -0.19 0.36 -10000 0 -0.82 125 125
natural killer cell activation 0 0.004 0.007 26 -0.01 47 73
JAK3 0.035 0.017 -10000 0 -0.029 25 25
PIK3R1 0.032 0.02 -10000 0 -0.031 24 24
JAK1 0.033 0.019 -10000 0 -0.029 25 25
NFKB1 0.036 0.007 -10000 0 0 18 18
MYC -0.065 0.29 0.42 7 -0.83 57 64
MYB 0.034 0.042 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.16 0.25 6 -0.39 50 56
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.047 0.055 -10000 0 -0.64 1 1
mol:PI-3-4-5-P3 -0.022 0.16 0.24 6 -0.38 50 56
Rac1/GDP 0.004 0.05 0.11 4 -0.13 48 52
T cell proliferation -0.02 0.15 0.24 7 -0.35 50 57
SHC1 0.03 0.02 -10000 0 -0.011 86 86
RAC1 0.026 0.017 -10000 0 0 156 156
positive regulation of cyclin-dependent protein kinase activity 0.005 0.011 0.056 24 -10000 0 24
PRKCZ -0.023 0.15 0.23 6 -0.36 50 56
NF kappa B1 p50/RelA -0.001 0.19 0.31 5 -0.42 59 64
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.007 0.092 0.2 3 -0.29 21 24
HSP90AA1 0.035 0.01 -10000 0 0 35 35
RELA 0.037 0.005 -10000 0 0 10 10
IL2RA 0.023 0.022 -10000 0 -0.005 180 180
IL2RB 0.033 0.019 -10000 0 -0.029 24 24
TERT 0.036 0.007 -10000 0 0 17 17
E2F1 0.031 0.02 -10000 0 -10000 0 0
SOS1 0 0.003 0.008 30 -0.009 46 76
RPS6 0.032 0.013 -10000 0 0 71 71
mol:cAMP -0.003 0.007 -10000 0 -0.031 25 25
PTPN11 0.034 0.017 -10000 0 -0.022 42 42
IL2RG 0.035 0.017 -10000 0 -0.031 23 23
actin cytoskeleton organization -0.02 0.15 0.24 7 -0.35 50 57
GRB2 0.034 0.016 -10000 0 -0.017 44 44
IL2 0.036 0.016 -10000 0 -0.031 23 23
PIK3CA 0.031 0.021 -10000 0 -0.03 28 28
Rac1/GTP 0.027 0.065 0.16 5 -0.12 48 53
LCK 0.035 0.017 -10000 0 -0.031 22 22
BCL2 -0.015 0.16 0.42 1 -0.46 25 26
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.033 0.013 -10000 0 0 65 65
LAT2 -0.017 0.093 -10000 0 -0.28 46 46
AP1 -0.051 0.18 -10000 0 -0.4 66 66
mol:PIP3 0.016 0.14 0.27 35 -0.31 37 72
IKBKB 0.008 0.096 0.21 33 -0.19 37 70
AKT1 -0.055 0.1 0.29 9 -0.28 40 49
IKBKG 0.008 0.095 0.21 32 -0.19 37 69
MS4A2 0.04 0.008 0.068 5 0 7 12
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.013 -10000 0 0 74 74
MAP3K1 -0.022 0.12 0.25 15 -0.32 49 64
mol:Ca2+ 0.018 0.12 0.24 36 -0.24 35 71
LYN 0.031 0.016 0.09 1 -0.034 7 8
CBLB -0.023 0.11 0.18 1 -0.28 65 66
SHC1 0.034 0.012 -10000 0 0 53 53
RasGAP/p62DOK 0.05 0.052 -10000 0 -0.12 36 36
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.032 0.072 0.29 12 -0.17 10 22
PTPN13 -0.035 0.19 0.34 1 -0.59 38 39
PTPN11 0.031 0.023 -10000 0 -0.036 48 48
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.035 0.12 0.34 7 -0.31 40 47
SYK 0.031 0.015 -10000 0 -0.034 7 7
GRB2 0.037 0.007 -10000 0 0 19 19
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.12 0.21 7 -0.28 55 62
LAT -0.023 0.11 0.18 1 -0.28 64 65
PAK2 -0.022 0.13 0.25 14 -0.34 52 66
NFATC2 -0.013 0.013 -10000 0 -0.043 69 69
HRAS -0.023 0.14 0.24 8 -0.35 54 62
GAB2 0.034 0.011 -10000 0 0 51 51
PLA2G1B -0.007 0.19 -10000 0 -0.9 20 20
Fc epsilon R1 0.042 0.067 -10000 0 -0.11 70 70
Antigen/IgE/Fc epsilon R1 0.043 0.06 -10000 0 -0.094 69 69
mol:GDP -0.016 0.14 0.23 5 -0.36 50 55
JUN 0.034 0.011 -10000 0 0 44 44
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.033 0.013 -10000 0 0 67 67
FOS 0.025 0.018 -10000 0 0 166 166
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.12 -10000 0 -0.28 67 67
CHUK 0.008 0.094 0.21 31 -0.19 38 69
KLRG1 -0.02 0.095 0.12 2 -0.27 48 50
VAV1 -0.025 0.11 0.15 3 -0.29 61 64
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.023 0.11 0.18 1 -0.28 64 65
negative regulation of mast cell degranulation -0.024 0.089 -10000 0 -0.25 50 50
BTK -0.014 0.13 -10000 0 -0.37 46 46
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.19 121 121
GAB2/PI3K/SHP2 -0.07 0.072 -10000 0 -0.21 71 71
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.079 -10000 0 -0.21 53 53
RAF1 -0.006 0.2 -10000 0 -0.97 20 20
Fc epsilon R1/FcgammaRIIB/SHIP 0.024 0.095 -10000 0 -0.13 128 128
FCER1G 0.03 0.016 -10000 0 0 111 111
FCER1A 0.034 0.013 -10000 0 -0.032 9 9
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.082 -10000 0 -0.11 97 97
MAPK3 -0.006 0.18 -10000 0 -0.89 20 20
MAPK1 -0.015 0.2 -10000 0 -0.94 20 20
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 -0.1 0.28 -10000 0 -0.56 128 128
DUSP1 0.032 0.014 -10000 0 0 78 78
NF-kappa-B/RelA 0.017 0.068 0.16 23 -0.13 38 61
actin cytoskeleton reorganization -0.026 0.19 0.36 1 -0.59 37 38
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.014 0.15 0.26 3 -0.35 57 60
FER -0.023 0.11 0.18 1 -0.28 67 68
RELA 0.037 0.005 -10000 0 0 10 10
ITK 0.002 0.037 -10000 0 -0.23 4 4
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.005 0.14 0.27 15 -0.35 46 61
cytokine secretion 0.008 0.045 0.088 22 -0.094 40 62
SPHK1 -0.019 0.11 0.16 2 -0.28 64 66
PTK2 -0.028 0.2 0.36 1 -0.63 36 37
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.027 0.13 0.24 17 -0.29 46 63
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.15 0.27 27 -0.34 43 70
MAP2K2 -0.009 0.19 -10000 0 -0.9 20 20
MAP2K1 -0.016 0.18 -10000 0 -0.92 20 20
MAP2K7 0.036 0.007 -10000 0 0 18 18
KLRG1/SHP2 0.001 0.096 0.2 7 -0.25 46 53
MAP2K4 0.026 0.14 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.026 0.1 -10000 0 -0.14 128 128
mol:Choline -0.032 0.072 0.29 12 -0.17 10 22
SHC/Grb2/SOS1 0.013 0.13 0.2 1 -0.27 67 68
FYN 0.031 0.015 -10000 0 0 93 93
DOK1 0.038 0.002 -10000 0 0 2 2
PXN -0.029 0.19 0.42 3 -0.58 36 39
HCLS1 -0.026 0.12 0.16 6 -0.31 66 72
PRKCB 0.01 0.12 0.23 32 -0.25 41 73
FCGR2B 0.021 0.019 -10000 0 0 223 223
IGHE -0.001 0.005 0.029 5 -10000 0 5
KLRG1/SHIP -0.024 0.091 -10000 0 -0.26 50 50
LCP2 0.032 0.014 -10000 0 0 77 77
PLA2G4A -0.016 0.12 0.16 6 -0.3 59 65
RASA1 0.035 0.01 -10000 0 0 35 35
mol:Phosphatidic acid -0.032 0.072 0.29 12 -0.17 10 22
IKK complex 0.005 0.084 0.23 21 -0.16 24 45
WIPF1 0.036 0.007 -10000 0 0 19 19
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.015 0.06 -10000 0 -0.13 67 67
EPHB2 0.035 0.01 -10000 0 0 39 39
Syndecan-2/TACI 0.018 0.054 -10000 0 -0.12 64 64
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.022 0.073 -10000 0 -0.12 64 64
HRAS 0.035 0.01 -10000 0 0 37 37
Syndecan-2/CASK -0.008 0.04 -10000 0 -0.11 68 68
ITGA5 0.033 0.012 -10000 0 0 62 62
BAX -0.01 0.071 -10000 0 -0.89 3 3
EPB41 0.037 0.006 -10000 0 0 13 13
positive regulation of cell-cell adhesion 0.014 0.053 -10000 0 -0.11 72 72
LAMA3 0.034 0.011 -10000 0 0 48 48
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.019 -10000 0 0 237 237
Syndecan-2/MMP2 0.01 0.061 -10000 0 -0.14 65 65
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.022 0.054 -10000 0 -0.14 41 41
dendrite morphogenesis 0.017 0.052 -10000 0 -0.12 60 60
Syndecan-2/GM-CSF 0.018 0.054 -10000 0 -0.12 64 64
determination of left/right symmetry 0.007 0.023 -10000 0 -0.23 4 4
Syndecan-2/PKC delta 0.017 0.053 -10000 0 -0.12 61 61
GNB2L1 0.037 0.005 -10000 0 0 10 10
MAPK3 -0.023 0.051 0.18 10 -0.19 4 14
MAPK1 -0.02 0.049 0.12 31 -0.21 4 35
Syndecan-2/RACK1 0.031 0.063 -10000 0 -0.11 75 75
NF1 0.037 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.023 -10000 0 -0.23 4 4
ITGA2 0.029 0.016 -10000 0 0 114 114
MAPK8 -0.005 0.038 -10000 0 -0.39 3 3
Syndecan-2/alpha2/beta1 Integrin 0.01 0.063 -10000 0 -0.11 90 90
Syndecan-2/Kininogen 0.018 0.054 -10000 0 -0.12 63 63
ITGB1 0.029 0.016 -10000 0 0 117 117
SRC -0.025 0.052 0.17 12 -0.19 8 20
Syndecan-2/CASK/Protein 4.1 0.016 0.049 -10000 0 -0.1 66 66
extracellular matrix organization 0.015 0.053 -10000 0 -0.12 61 61
actin cytoskeleton reorganization 0.015 0.059 -10000 0 -0.13 67 67
Syndecan-2/Caveolin-2/Ras 0.008 0.067 -10000 0 -0.13 77 77
Syndecan-2/Laminin alpha3 0.016 0.052 -10000 0 -0.12 61 61
Syndecan-2/RasGAP 0.038 0.078 -10000 0 -0.12 80 80
alpha5/beta1 Integrin 0.032 0.043 -10000 0 -0.14 21 21
PRKCD 0.035 0.01 -10000 0 0 42 42
Syndecan-2 dimer 0.017 0.052 -10000 0 -0.12 60 60
GO:0007205 0.001 0.01 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.015 0.066 0.19 3 -0.19 17 20
RHOA 0.036 0.007 -10000 0 0 20 20
SDCBP 0.036 0.007 -10000 0 0 20 20
TNFRSF13B 0.037 0.005 -10000 0 0 10 10
RASA1 0.035 0.01 -10000 0 0 35 35
alpha2/beta1 Integrin 0.022 0.054 -10000 0 -0.14 41 41
Syndecan-2/Synbindin 0.017 0.058 -10000 0 -0.12 64 64
TGFB1 0.033 0.012 -10000 0 0 57 57
CASP3 -0.017 0.05 0.18 7 -0.19 4 11
FN1 0.035 0.009 -10000 0 0 31 31
Syndecan-2/IL8 -0.003 0.068 -10000 0 -0.17 61 61
SDC2 0.007 0.023 -10000 0 -0.23 4 4
KNG1 0.037 0.007 -10000 0 0 16 16
Syndecan-2/Neurofibromin 0.018 0.055 -10000 0 -0.12 67 67
TRAPPC4 0.036 0.007 -10000 0 0 17 17
CSF2 0.037 0.005 -10000 0 0 8 8
Syndecan-2/TGFB1 0.015 0.053 -10000 0 -0.12 61 61
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.054 -10000 0 -0.11 72 72
Syndecan-2/Ezrin 0.015 0.052 -10000 0 -0.11 69 69
PRKACA -0.022 0.052 0.18 11 -0.19 4 15
angiogenesis -0.003 0.068 -10000 0 -0.17 61 61
MMP2 0.03 0.015 -10000 0 0 104 104
IL8 0.02 0.019 -10000 0 0 244 244
calcineurin-NFAT signaling pathway 0.018 0.054 -10000 0 -0.12 64 64
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.005 0.079 0.19 3 -0.19 38 41
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.13 0.28 3 -0.32 44 47
alphaV/beta3 Integrin/Osteopontin/Src 0.028 0.08 -10000 0 -0.15 76 76
AP1 -0.012 0.14 0.28 4 -0.28 79 83
ILK -0.031 0.072 0.19 3 -0.23 33 36
bone resorption -0.04 0.082 0.18 6 -0.25 25 31
PTK2B 0.037 0.006 -10000 0 0 15 15
PYK2/p130Cas 0.046 0.09 -10000 0 -0.18 41 41
ITGAV 0.031 0.027 -10000 0 -0.056 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.022 0.068 -10000 0 -0.14 73 73
alphaV/beta3 Integrin/Osteopontin 0.051 0.093 -10000 0 -0.16 71 71
MAP3K1 -0.029 0.065 0.19 3 -0.2 27 30
JUN 0.035 0.011 -10000 0 0 44 44
MAPK3 -0.032 0.085 0.18 7 -0.24 41 48
MAPK1 -0.029 0.086 0.17 12 -0.25 39 51
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 -0.028 0.061 0.2 2 -0.21 23 25
ITGB3 0.033 0.027 -10000 0 -0.055 40 40
NFKBIA -0.036 0.11 0.19 7 -0.32 46 53
FOS 0.026 0.018 -10000 0 0 166 166
CD44 0.029 0.016 -10000 0 0 113 113
CHUK 0.027 0.017 -10000 0 0 139 139
PLAU -0.068 0.26 -10000 0 -0.99 32 32
NF kappa B1 p50/RelA 0.005 0.13 0.25 1 -0.33 40 41
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.037 0.005 -10000 0 0 10 10
alphaV beta3 Integrin 0.041 0.058 -10000 0 -0.11 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.031 0.065 0.18 3 -0.23 29 32
VAV3 -0.034 0.063 0.18 2 -0.23 31 33
MAP3K14 -0.028 0.075 0.18 6 -0.22 29 35
ROCK2 0.036 0.007 -10000 0 0 19 19
SPP1 0.031 0.026 -10000 0 -0.058 30 30
RAC1 0.026 0.017 -10000 0 0 156 156
Rac1/GTP -0.022 0.07 0.15 4 -0.22 28 32
MMP2 -0.061 0.12 0.24 2 -0.32 62 64
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 -0.013 0.076 -10000 0 -0.38 6 6
PLK1 -0.067 0.21 -10000 0 -0.68 23 23
CDKN1B -0.11 0.22 0.41 4 -0.37 137 141
FOXO3 -0.07 0.23 0.32 3 -0.49 89 92
KAT2B -0.001 0.021 0.048 15 -0.041 82 97
FOXO1/SIRT1 0.004 0.081 -10000 0 -0.27 27 27
CAT -0.08 0.26 -10000 0 -0.82 33 33
CTNNB1 0.036 0.007 -10000 0 0 17 17
AKT1 0.021 0.044 0.11 1 -0.061 72 73
FOXO1 -0.012 0.085 0.27 2 -0.3 23 25
MAPK10 0.044 0.092 0.19 125 -0.15 19 144
mol:GTP -0.001 0.005 -10000 0 -10000 0 0
FOXO4 -0.028 0.21 0.33 9 -0.5 54 63
response to oxidative stress 0 0.023 0.053 13 -0.043 61 74
FOXO3A/SIRT1 -0.068 0.23 -10000 0 -0.48 89 89
XPO1 0.037 0.004 -10000 0 0 4 4
EP300 0.035 0.012 -10000 0 -10000 0 0
BCL2L11 0.024 0.034 -10000 0 -10000 0 0
FOXO1/SKP2 0.007 0.086 0.24 2 -0.28 22 24
mol:GDP 0 0.023 0.053 13 -0.043 61 74
RAN 0.035 0.012 -10000 0 -0.014 24 24
GADD45A -0.14 0.33 0.42 1 -0.88 68 69
YWHAQ 0.037 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.003 0.15 -10000 0 -0.5 25 25
MST1 0.022 0.043 0.11 2 -0.059 87 89
CSNK1D 0.036 0.007 -10000 0 0 20 20
CSNK1E 0.033 0.013 -10000 0 0 65 65
FOXO4/14-3-3 family -0.003 0.15 -10000 0 -0.5 26 26
YWHAB 0.034 0.011 -10000 0 0 44 44
MAPK8 0.023 0.077 0.18 70 -0.14 16 86
MAPK9 0.053 0.097 0.19 146 -0.15 15 161
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.036 0.009 -10000 0 0 29 29
YWHAZ 0.036 0.008 -10000 0 0 21 21
SIRT1 0.022 0.023 -10000 0 -0.035 31 31
SOD2 -0.14 0.36 0.43 7 -0.76 106 113
RBL2 -0.073 0.29 -10000 0 -0.92 37 37
RAL/GDP 0.02 0.05 -10000 0 -0.14 20 20
CHUK 0.013 0.04 0.1 1 -0.059 79 80
Ran/GTP 0.02 0.026 -10000 0 -0.12 6 6
CSNK1G2 0.036 0.007 -10000 0 0 20 20
RAL/GTP 0.023 0.051 0.15 3 -0.12 23 26
CSNK1G1 0.037 0.005 -10000 0 0 10 10
FASLG 0.021 0.042 -10000 0 -0.59 1 1
SKP2 0.036 0.007 -10000 0 0 20 20
USP7 0.036 0.011 -10000 0 -0.011 21 21
IKBKB 0.024 0.044 0.11 2 -0.059 92 94
CCNB1 -0.17 0.42 0.53 2 -1 89 91
FOXO1-3a-4/beta catenin -0.042 0.22 0.42 7 -0.39 85 92
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.085 0.24 2 -0.28 22 24
CSNK1A1 0.037 0.006 -10000 0 0 13 13
SGK1 -0.001 0.021 0.048 15 -0.041 82 97
CSNK1G3 0.037 0.006 -10000 0 0 12 12
Ran/GTP/Exportin 1 0.041 0.037 -10000 0 -0.12 8 8
ZFAND5 -0.016 0.18 0.42 6 -0.54 31 37
SFN 0.032 0.014 -10000 0 0 80 80
CDK2 0.037 0.012 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.014 0.16 -10000 0 -0.43 36 36
CREBBP 0.039 0.006 -10000 0 -0.032 1 1
FBXO32 -0.066 0.21 0.35 1 -0.45 89 90
BCL6 -0.093 0.33 -10000 0 -1 46 46
RALB 0.034 0.014 -10000 0 -0.016 33 33
RALA 0.025 0.019 -10000 0 -0.001 177 177
YWHAH 0.032 0.013 -10000 0 0 73 73
Arf6 downstream pathway

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
PLAUR -0.017 0.2 -10000 0 -0.82 26 26
regulation of axonogenesis 0.005 0.069 0.22 41 -10000 0 41
myoblast fusion -0.015 0.098 0.36 28 -0.17 2 30
mol:GTP 0.013 0.07 -10000 0 -0.18 54 54
regulation of calcium-dependent cell-cell adhesion -0.026 0.075 0.15 68 -10000 0 68
ARF1/GTP 0.033 0.065 -10000 0 -0.14 56 56
mol:GM1 0.001 0.05 -10000 0 -0.14 54 54
mol:Choline -0.017 0.042 0.063 1 -0.13 48 49
lamellipodium assembly -0.012 0.11 -10000 0 -0.38 39 39
MAPK3 0.01 0.085 0.14 38 -0.21 51 89
ARF6/GTP/NME1/Tiam1 0.027 0.076 0.15 1 -0.15 68 69
ARF1 0.036 0.008 -10000 0 0 23 23
ARF6/GDP 0.015 0.098 0.17 2 -0.36 28 30
ARF1/GDP 0.012 0.11 -10000 0 -0.28 52 52
ARF6 0.04 0.042 -10000 0 -0.13 25 25
RAB11A 0.036 0.007 -10000 0 0 17 17
TIAM1 0.03 0.022 -10000 0 -0.046 31 31
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.083 0.14 37 -0.23 40 77
actin filament bundle formation -0.017 0.11 0.29 54 -10000 0 54
KALRN 0.002 0.08 0.12 3 -0.26 37 40
RAB11FIP3/RAB11A 0.049 0.034 -10000 0 -0.16 12 12
RhoA/GDP 0.018 0.11 -10000 0 -0.29 54 54
NME1 -0.001 0.008 -10000 0 -0.03 26 26
Rac1/GDP 0.012 0.097 -10000 0 -0.29 39 39
substrate adhesion-dependent cell spreading 0.013 0.07 -10000 0 -0.18 54 54
cortical actin cytoskeleton organization -0.013 0.11 -10000 0 -0.38 39 39
RAC1 0.026 0.017 -10000 0 0 156 156
liver development 0.013 0.07 -10000 0 -0.18 54 54
ARF6/GTP 0.013 0.07 -10000 0 -0.18 54 54
RhoA/GTP 0.033 0.067 -10000 0 -0.15 57 57
mol:GDP -0.008 0.11 0.17 2 -0.3 51 53
ARF6/GTP/RAB11FIP3/RAB11A 0.05 0.072 -10000 0 -0.13 61 61
RHOA 0.036 0.007 -10000 0 0 20 20
PLD1 0.011 0.055 -10000 0 -0.14 53 53
RAB11FIP3 0.036 0.007 -10000 0 0 19 19
tube morphogenesis -0.012 0.11 -10000 0 -0.38 39 39
ruffle organization -0.005 0.069 -10000 0 -0.22 41 41
regulation of epithelial cell migration 0.013 0.07 -10000 0 -0.18 54 54
PLD2 0.012 0.055 -10000 0 -0.14 50 50
PIP5K1A -0.005 0.069 -10000 0 -0.22 41 41
mol:Phosphatidic acid -0.017 0.042 0.063 1 -0.13 48 49
Rac1/GTP -0.013 0.11 -10000 0 -0.38 39 39
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.029 0.016 -10000 0 0 115 115
EPHB2 0.035 0.011 0.062 1 0 39 40
EFNB1 -0.018 0.016 0.024 58 -10000 0 58
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.051 0.053 -10000 0 -0.14 9 9
Ephrin B2/EPHB1-2 0.034 0.056 -10000 0 -0.1 50 50
neuron projection morphogenesis 0.035 0.041 -10000 0 -0.12 14 14
Ephrin B1/EPHB1-2/Tiam1 0.058 0.048 0.18 1 -0.1 27 28
DNM1 0.036 0.009 -10000 0 0 26 26
cell-cell signaling 0 0.004 0.023 2 -10000 0 2
MAP2K4 -0.052 0.16 0.2 1 -0.51 51 52
YES1 -0.052 0.23 -10000 0 -0.74 51 51
Ephrin B1/EPHB1-2/NCK2 0.062 0.044 0.18 1 -0.1 19 20
PI3K -0.017 0.19 -10000 0 -0.55 52 52
mol:GDP 0.056 0.047 0.18 1 -0.1 27 28
ITGA2B 0.037 0.003 -10000 0 0 4 4
endothelial cell proliferation 0.018 0.046 -10000 0 -0.11 42 42
FYN -0.063 0.24 -10000 0 -0.76 51 51
MAP3K7 -0.048 0.16 -10000 0 -0.54 49 49
FGR -0.049 0.22 -10000 0 -0.72 51 51
TIAM1 0.034 0.011 -10000 0 0 44 44
PIK3R1 0.033 0.013 -10000 0 0 67 67
RGS3 0.036 0.008 -10000 0 0 24 24
cell adhesion -0.031 0.17 -10000 0 -0.52 52 52
LYN -0.058 0.23 -10000 0 -0.73 51 51
Ephrin B1/EPHB1-2/Src Family Kinases -0.054 0.21 -10000 0 -0.67 51 51
Ephrin B1/EPHB1-2 -0.045 0.17 -10000 0 -0.57 49 49
SRC -0.048 0.22 -10000 0 -0.71 51 51
ITGB3 0.037 0.004 -10000 0 0 6 6
EPHB1 0.031 0.015 -10000 0 0 95 95
EPHB4 0.026 0.017 -10000 0 0 157 157
RAC1 0.026 0.017 -10000 0 0 156 156
Ephrin B2/EPHB4 0.018 0.046 -10000 0 -0.11 42 42
alphaIIb/beta3 Integrin 0.055 0.006 -10000 0 -10000 0 0
BLK -0.051 0.22 -10000 0 -0.71 52 52
HCK -0.063 0.23 -10000 0 -0.73 51 51
regulation of stress fiber formation -0.06 0.043 0.1 19 -10000 0 19
MAPK8 -0.055 0.15 0.22 1 -0.49 51 52
Ephrin B1/EPHB1-2/RGS3 0.067 0.034 -10000 0 -0.11 5 5
endothelial cell migration 0.004 0.16 0.19 112 -0.44 43 155
NCK2 0.036 0.007 -10000 0 0 19 19
PTPN13 0.035 0.014 -10000 0 0 63 63
regulation of focal adhesion formation -0.06 0.043 0.1 19 -10000 0 19
chemotaxis -0.065 0.033 0.11 5 -10000 0 5
PIK3CA 0.032 0.013 -10000 0 0 74 74
Rac1/GTP 0.043 0.047 -10000 0 -0.13 10 10
angiogenesis -0.045 0.17 -10000 0 -0.56 50 50
LCK -0.047 0.22 -10000 0 -0.71 51 51
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.001 0.078 -10000 0 -0.14 105 105
PDGFRB 0.037 0.009 0.059 1 0 25 26
SPHK1 0.018 0.021 -10000 0 -10000 0 0
mol:S1P 0.019 0.028 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.004 0.12 0.21 24 -0.38 27 51
GNAO1 0.033 0.016 -10000 0 0 87 87
PDGFB-D/PDGFRB/PLCgamma1 0.026 0.13 0.24 35 -0.34 27 62
PLCG1 -0.009 0.12 0.22 16 -0.36 27 43
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.009 0.059 1 0 25 26
GNAI2 0.037 0.012 -10000 0 0 46 46
GNAI3 0.038 0.008 -10000 0 0 16 16
GNAI1 0.02 0.02 -10000 0 0 255 255
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.026 0.051 0.078 25 -0.12 105 130
S1P1/S1P 0 0.052 0.22 2 -0.22 1 3
negative regulation of cAMP metabolic process -0.003 0.12 0.21 24 -0.37 27 51
MAPK3 -0.004 0.13 0.27 17 -0.39 23 40
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
RhoA/GDP 0.025 0.019 -10000 0 -0.13 7 7
KDR 0.032 0.015 -10000 0 0 90 90
PLCB2 0.029 0.081 0.21 30 -0.21 1 31
RAC1 0.026 0.017 -10000 0 0 156 156
RhoA/GTP -0.001 0.049 0.15 1 -0.2 3 4
receptor internalization -0.001 0.049 0.21 2 -0.21 1 3
PTGS2 0.027 0.14 0.34 11 -0.47 11 22
Rac1/GTP -0.003 0.041 -10000 0 -0.19 2 2
RHOA 0.036 0.007 -10000 0 0 20 20
VEGFA 0.025 0.019 -10000 0 0 181 181
negative regulation of T cell proliferation -0.003 0.12 0.21 24 -0.37 27 51
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.015 -10000 0 0 81 81
MAPK1 -0.001 0.13 0.28 16 -0.4 21 37
S1P1/S1P/PDGFB-D/PDGFRB 0.03 0.087 0.24 19 -0.22 4 23
ABCC1 0.038 0.008 -10000 0 0 19 19
BCR signaling pathway

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
JUN -0.006 0.12 0.34 4 -0.31 34 38
IKBKB 0.018 0.081 0.3 7 -0.28 8 15
AKT1 0.006 0.093 0.23 36 -0.18 13 49
IKBKG 0.011 0.077 0.31 4 -0.24 13 17
CALM1 -0.024 0.12 0.21 6 -0.37 41 47
PIK3CA 0.032 0.013 -10000 0 0 74 74
MAP3K1 0.023 0.14 0.29 16 -0.34 37 53
MAP3K7 0.034 0.011 -10000 0 0 45 45
mol:Ca2+ -0.022 0.13 0.22 5 -0.38 41 46
DOK1 0.038 0.002 -10000 0 0 2 2
AP-1 -0.013 0.098 0.22 13 -0.22 45 58
LYN 0.032 0.013 -10000 0 0 72 72
BLNK 0.021 0.019 -10000 0 0 226 226
SHC1 0.034 0.012 -10000 0 0 53 53
BCR complex 0.052 0.015 -10000 0 -10000 0 0
CD22 -0.015 0.091 -10000 0 -0.29 36 36
CAMK2G -0.017 0.12 0.22 8 -0.35 42 50
CSNK2A1 0.034 0.011 -10000 0 0 50 50
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.036 0.056 -10000 0 -0.19 24 24
GO:0007205 -0.023 0.14 0.23 6 -0.39 42 48
SYK 0.032 0.013 -10000 0 0 76 76
ELK1 -0.028 0.13 0.22 5 -0.37 42 47
NFATC1 -0.02 0.098 0.3 6 -0.26 37 43
B-cell antigen/BCR complex 0.052 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.024 0.022 -10000 0 -0.13 10 10
NFKBIB 0.022 0.045 0.18 3 -0.13 20 23
HRAS -0.024 0.12 0.2 12 -0.33 43 55
NFKBIA 0.023 0.041 0.18 3 -0.12 15 18
NF-kappa-B/RelA/I kappa B beta 0.027 0.04 0.17 4 -0.1 20 24
RasGAP/Csk 0.044 0.096 -10000 0 -0.12 118 118
mol:GDP -0.021 0.13 0.22 6 -0.37 42 48
PTEN 0.026 0.017 -10000 0 0 158 158
CD79B 0.037 0.005 -10000 0 0 10 10
NF-kappa-B/RelA/I kappa B alpha 0.028 0.038 0.17 4 -0.1 13 17
GRB2 0.036 0.007 -10000 0 0 19 19
PI3K/BCAP/CD19 -0.033 0.16 0.38 4 -0.42 49 53
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:IP3 -0.022 0.13 0.23 4 -0.4 40 44
CSK 0.036 0.007 -10000 0 0 20 20
FOS -0.026 0.13 0.2 10 -0.36 44 54
CHUK -0.049 0.14 0.3 4 -0.26 119 123
IBTK 0.035 0.009 -10000 0 0 31 31
CARD11/BCL10/MALT1/TAK1 0.003 0.13 0.25 2 -0.34 40 42
PTPN6 -0.024 0.09 0.16 12 -0.3 35 47
RELA 0.037 0.005 -10000 0 0 10 10
BCL2A1 0.018 0.035 0.099 14 -0.091 23 37
VAV2 -0.019 0.1 -10000 0 -0.3 44 44
ubiquitin-dependent protein catabolic process 0.024 0.045 0.18 3 -0.13 20 23
BTK 0.019 0.012 -10000 0 -10000 0 0
CD19 -0.015 0.094 -10000 0 -0.29 38 38
MAP4K1 0.036 0.008 -10000 0 0 21 21
CD72 0.033 0.012 -10000 0 0 58 58
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.019 0.12 0.28 14 -0.3 37 51
SH3BP5 0.034 0.011 -10000 0 0 52 52
PIK3AP1 -0.021 0.14 0.24 4 -0.41 39 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.032 0.18 -10000 0 -0.5 52 52
RAF1 -0.03 0.11 0.19 8 -0.31 45 53
RasGAP/p62DOK/SHIP 0.036 0.084 -10000 0 -0.11 115 115
CD79A 0.035 0.009 -10000 0 0 31 31
re-entry into mitotic cell cycle -0.014 0.097 0.21 13 -0.22 44 57
RASA1 0.035 0.01 -10000 0 0 35 35
MAPK3 -0.036 0.098 0.22 6 -0.28 44 50
MAPK1 -0.034 0.1 0.2 6 -0.29 42 48
CD72/SHP1 0.001 0.11 0.25 16 -0.28 37 53
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 0.019 0.12 0.28 17 -0.3 37 54
actin cytoskeleton organization 0.028 0.12 0.24 27 -0.28 29 56
NF-kappa-B/RelA 0.046 0.092 0.32 3 -0.25 24 27
Calcineurin -0.002 0.13 0.23 3 -0.33 42 45
PI3K -0.032 0.088 -10000 0 -0.25 43 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.14 0.22 8 -0.38 49 57
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.017 0.15 -10000 0 -0.56 13 13
DAPP1 -0.004 0.15 -10000 0 -0.65 11 11
cytokine secretion -0.018 0.094 0.3 6 -0.25 37 43
mol:DAG -0.022 0.13 0.23 4 -0.4 40 44
PLCG2 0.033 0.013 -10000 0 0 65 65
MAP2K1 -0.033 0.1 0.2 5 -0.3 45 50
B-cell antigen/BCR complex/FcgammaRIIB 0.017 0.075 -10000 0 -0.12 99 99
mol:PI-3-4-5-P3 -0.02 0.072 0.2 19 -0.22 17 36
ETS1 -0.026 0.12 0.21 7 -0.33 41 48
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.039 0.092 -10000 0 -0.15 63 63
B-cell antigen/BCR complex/LYN -0.009 0.097 -10000 0 -0.3 38 38
MALT1 0.035 0.009 -10000 0 0 30 30
TRAF6 0.037 0.006 -10000 0 0 14 14
RAC1 0.025 0.12 0.24 23 -0.29 28 51
B-cell antigen/BCR complex/LYN/SYK 0.032 0.1 0.24 9 -0.25 44 53
CARD11 -0.022 0.13 0.21 7 -0.37 42 49
FCGR2B 0.021 0.019 -10000 0 0 223 223
PPP3CA 0.035 0.01 -10000 0 0 37 37
BCL10 0.036 0.007 -10000 0 0 20 20
IKK complex 0.006 0.048 0.18 9 -0.12 15 24
PTPRC 0.03 0.016 -10000 0 0 110 110
PDPK1 -0.015 0.063 0.18 23 -0.17 12 35
PPP3CB 0.028 0.017 -10000 0 0 133 133
PPP3CC 0.037 0.006 -10000 0 0 12 12
POU2F2 0.017 0.032 0.11 7 -0.084 22 29
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.069 0.06 -10000 0 -0.12 32 32
MAP4K1 0.036 0.008 -10000 0 0 21 21
MAP3K8 0.025 0.018 -10000 0 0 176 176
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.036 0.009 -10000 0 0 29 29
MAP3K1 -0.001 0.054 -10000 0 -0.24 7 7
JUN -0.12 0.23 0.24 2 -0.52 121 123
MAP3K7 -0.001 0.054 -10000 0 -0.24 9 9
GRAP2 0.035 0.01 -10000 0 0 36 36
CRK 0.036 0.008 -10000 0 0 25 25
MAP2K4 -0.01 0.07 0.16 4 -0.25 19 23
LAT 0.037 0.005 -10000 0 0 9 9
LCP2 0.032 0.014 -10000 0 0 77 77
MAPK8 -0.11 0.24 -10000 0 -0.54 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.011 0.057 -10000 0 -0.16 33 33
LAT/GRAP2/SLP76/HPK1/HIP-55 0.064 0.055 -10000 0 -0.11 32 32
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.03 0.17 -10000 0 -0.47 62 62
HDAC1 0.028 0.034 0.098 14 -0.039 84 98
AES 0.036 0.013 0.072 12 -0.003 35 47
FBXW11 0.036 0.008 -10000 0 0 24 24
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.027 -10000 0 -10000 0 0
TLE1 0.035 0.013 0.072 9 -0.006 35 44
AP1 -0.012 0.076 -10000 0 -0.21 58 58
NCSTN 0.036 0.009 -10000 0 0 29 29
ADAM10 0.034 0.012 -10000 0 0 56 56
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.011 0.13 -10000 0 -0.48 15 15
NICD/RBPSUH -0.011 0.18 -10000 0 -0.48 61 61
WIF1 0.03 0.016 -10000 0 0 110 110
NOTCH1 -0.031 0.17 -10000 0 -0.49 61 61
PSENEN 0.035 0.009 -10000 0 0 33 33
KREMEN2 0.037 0.004 -10000 0 0 6 6
DKK1 0.019 0.019 -10000 0 0 258 258
beta catenin/beta TrCP1 0.054 0.097 0.24 23 -0.28 12 35
APH1B 0.037 0.006 -10000 0 0 14 14
APH1A 0.036 0.007 -10000 0 0 17 17
AXIN1 0.012 0.068 0.26 3 -0.47 1 4
CtBP/CBP/TCF1/TLE1/AES 0.016 0.075 0.18 47 -0.21 9 56
PSEN1 0.034 0.011 -10000 0 0 48 48
FOS 0.025 0.018 -10000 0 0 166 166
JUN 0.034 0.011 -10000 0 0 44 44
MAP3K7 0.033 0.018 0.064 7 -0.009 62 69
CTNNB1 0.039 0.094 0.22 33 -0.28 9 42
MAPK3 0.037 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.065 0.028 -10000 0 -0.12 1 1
HNF1A 0.037 0.01 0.072 10 -0.018 11 21
CTBP1 0.035 0.013 0.074 9 -0.006 33 42
MYC -0.081 0.37 -10000 0 -1.2 52 52
NKD1 0 0.003 -10000 0 -10000 0 0
FZD1 0.026 0.018 -10000 0 0 162 162
NOTCH1 precursor/Deltex homolog 1 -0.035 0.16 -10000 0 -0.47 62 62
apoptosis -0.012 0.076 -10000 0 -0.21 59 59
Delta 1/NOTCHprecursor -0.035 0.16 -10000 0 -0.47 62 62
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.021 0.068 -10000 0 -0.72 3 3
Gamma Secretase 0.08 0.073 -10000 0 -0.15 29 29
APC -0.023 0.17 0.28 1 -0.65 29 30
DVL1 0.012 0.1 -10000 0 -0.34 28 28
CSNK2A1 0.034 0.012 -10000 0 -0.001 51 51
MAP3K7IP1 0 0.008 0.026 9 -10000 0 9
DKK1/LRP6/Kremen 2 0.034 0.038 -10000 0 -10000 0 0
LRP6 0.034 0.011 -10000 0 0 44 44
CSNK1A1 0.037 0.007 -10000 0 -0.002 14 14
NLK 0.006 0.041 -10000 0 -0.21 14 14
CCND1 -0.052 0.34 -10000 0 -1.1 44 44
WNT1 0.036 0.007 -10000 0 0 18 18
Axin1/APC/beta catenin 0.009 0.14 0.27 5 -0.42 30 35
DKK2 0.035 0.009 -10000 0 0 31 31
NOTCH1 precursor/DVL1 -0.015 0.19 0.31 1 -0.49 57 58
GSK3B 0.035 0.01 -10000 0 0 37 37
FRAT1 0.028 0.017 -10000 0 0 138 138
NOTCH/Deltex homolog 1 -0.03 0.17 -10000 0 -0.47 62 62
PPP2R5D 0.021 0.047 -10000 0 -0.28 7 7
MAPK1 0.034 0.011 -10000 0 0 47 47
WNT1/LRP6/FZD1 0.06 0.045 -10000 0 -10000 0 0
RBPJ 0.036 0.008 -10000 0 0 21 21
CREBBP 0.033 0.022 0.072 4 -0.019 62 66
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.054 0.056 -10000 0 -0.13 35 35
fibroblast growth factor receptor signaling pathway 0.054 0.055 -10000 0 -0.13 35 35
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.032 0.013 -10000 0 0 74 74
GPC1/SLIT2 0.033 0.045 -10000 0 -0.14 24 24
SMAD2 -0.023 0.054 0.21 12 -0.2 3 15
GPC1/PrPc/Cu2+ 0.026 0.057 -10000 0 -0.13 49 49
GPC1/Laminin alpha1 0.015 0.04 -10000 0 -0.13 35 35
TDGF1 0.036 0.007 -10000 0 0 20 20
CRIPTO/GPC1 0.039 0.047 -10000 0 -0.14 29 29
APP/GPC1 0.037 0.056 -10000 0 -0.15 36 36
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.024 0.033 0.09 21 -0.12 23 44
FLT1 0.035 0.01 -10000 0 0 37 37
GPC1/TGFB/TGFBR1/TGFBR2 0.054 0.053 -10000 0 -0.12 34 34
SERPINC1 0.037 0.005 -10000 0 0 11 11
FYN -0.018 0.029 0.09 24 -0.12 8 32
FGR -0.022 0.033 0.09 22 -0.12 21 43
positive regulation of MAPKKK cascade -0.029 0.12 0.2 22 -0.28 58 80
SLIT2 0.03 0.015 -10000 0 0 100 100
GPC1/NRG 0.039 0.05 -10000 0 -0.14 34 34
NRG1 0.037 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.008 0.087 -10000 0 -0.13 122 122
LYN -0.022 0.034 0.09 23 -0.12 23 46
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.054 0.055 -10000 0 -0.13 35 35
BMP signaling pathway -0.033 0.012 0 64 -10000 0 64
SRC -0.025 0.035 0.09 23 -0.12 28 51
TGFBR1 0.036 0.007 -10000 0 0 17 17
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.018 0.019 -10000 0 0 266 266
GPC1 0.033 0.013 -10000 0 0 64 64
TGFBR1 (dimer) 0.036 0.007 -10000 0 0 17 17
VEGFA 0.024 0.018 -10000 0 0 181 181
BLK -0.025 0.035 0.09 25 -0.12 26 51
HCK -0.018 0.031 0.09 19 -0.12 16 35
FGF2 0.036 0.008 -10000 0 0 25 25
FGFR1 0.037 0.004 -10000 0 0 7 7
VEGFR1 homodimer 0.035 0.01 -10000 0 0 37 37
TGFBR2 0.035 0.009 -10000 0 0 30 30
cell death 0.037 0.055 -10000 0 -0.15 36 36
ATIII/GPC1 0.039 0.049 -10000 0 -0.14 32 32
PLA2G2A/GPC1 -0.003 0.073 -10000 0 -0.15 92 92
LCK -0.025 0.034 0.09 23 -0.12 25 48
neuron differentiation 0.039 0.05 -10000 0 -0.14 34 34
PrPc/Cu2+ 0.016 0.037 -10000 0 -0.13 29 29
APP 0.036 0.007 -10000 0 0 19 19
TGFBR2 (dimer) 0.035 0.009 -10000 0 0 30 30
ErbB2/ErbB3 signaling events

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
USP8 -0.016 0.01 0.014 17 -10000 0 17
RAS family/GTP 0.013 0.11 0.22 1 -0.2 38 39
NFATC4 -0.027 0.065 0.2 12 -0.2 5 17
ERBB2IP 0.035 0.011 -10000 0 -0.001 40 40
HSP90 (dimer) 0.035 0.01 -10000 0 0 35 35
mammary gland morphogenesis -0.037 0.071 0.16 5 -0.18 15 20
JUN -0.003 0.088 0.23 9 -0.35 7 16
HRAS 0.035 0.01 -10000 0 0 37 37
DOCK7 -0.039 0.065 0.15 7 -0.18 17 24
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.079 0.21 15 -0.13 84 99
AKT1 -0.01 0.009 0.015 35 -10000 0 35
BAD -0.017 0.007 0.015 3 -10000 0 3
MAPK10 0.003 0.074 0.16 43 -0.15 12 55
mol:GTP 0 0.002 0.003 2 -0.006 24 26
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.077 0.19 7 -0.2 14 21
RAF1 -0.016 0.11 0.32 11 -0.24 30 41
ErbB2/ErbB3/neuregulin 2 0.001 0.073 0.21 15 -0.13 91 106
STAT3 -0.028 0.25 -10000 0 -0.9 38 38
cell migration -0.008 0.072 0.18 28 -0.16 22 50
mol:PI-3-4-5-P3 -0.001 0.002 0.004 17 -0.004 76 93
cell proliferation -0.039 0.24 0.49 3 -0.62 49 52
FOS -0.03 0.2 0.36 11 -0.42 90 101
NRAS 0.033 0.013 -10000 0 0 66 66
mol:Ca2+ -0.037 0.071 0.16 5 -0.18 15 20
MAPK3 -0.016 0.18 0.42 5 -0.48 38 43
MAPK1 -0.042 0.22 0.42 5 -0.58 51 56
JAK2 -0.03 0.076 0.17 18 -0.18 16 34
NF2 0.012 0.014 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.007 0.078 0.14 11 -0.16 89 100
NRG1 0.037 0.005 -10000 0 0 9 9
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
MAPK8 -0.017 0.085 0.18 2 -0.22 49 51
MAPK9 0.009 0.078 0.17 55 -0.14 5 60
ERBB2 -0.016 0.07 0.26 31 -10000 0 31
ERBB3 0.018 0.019 -10000 0 0 260 260
SHC1 0.034 0.012 -10000 0 0 53 53
RAC1 0.026 0.017 -10000 0 0 156 156
apoptosis 0.013 0.03 0.19 11 -0.069 2 13
STAT3 (dimer) -0.025 0.24 -10000 0 -0.88 38 38
RNF41 -0.021 0.016 0.077 5 -0.12 2 7
FRAP1 -0.008 0.005 0.002 78 -10000 0 78
RAC1-CDC42/GTP -0.024 0.045 -10000 0 -0.13 52 52
ErbB2/ErbB2/HSP90 (dimer) -0.018 0.058 0.2 31 -0.14 1 32
CHRNA1 -0.006 0.15 0.37 7 -0.37 39 46
myelination -0.028 0.084 0.26 18 -0.2 5 23
PPP3CB -0.026 0.067 0.17 12 -0.18 14 26
KRAS 0.035 0.009 -10000 0 0 34 34
RAC1-CDC42/GDP 0.022 0.074 0.22 1 -0.16 49 50
NRG2 0.037 0.005 -10000 0 0 8 8
mol:GDP -0.007 0.078 0.14 11 -0.16 89 100
SOS1 0 0.001 -10000 0 -0.004 8 8
MAP2K2 -0.026 0.11 0.28 12 -0.24 35 47
SRC 0.035 0.009 -10000 0 0 31 31
mol:cAMP -0.001 0.001 0.003 7 -0.004 1 8
PTPN11 -0.034 0.08 0.17 16 -0.23 5 21
MAP2K1 -0.034 0.2 0.46 3 -0.59 32 35
heart morphogenesis -0.037 0.071 0.16 5 -0.18 15 20
RAS family/GDP 0.019 0.11 0.24 1 -0.18 73 74
GRB2 0.036 0.007 -10000 0 0 19 19
PRKACA 0.019 0.009 -10000 0 -10000 0 0
CHRNE 0.002 0.026 0.086 6 -0.12 7 13
HSP90AA1 0.035 0.01 -10000 0 0 35 35
activation of caspase activity 0.01 0.009 -10000 0 -0.015 35 35
nervous system development -0.037 0.071 0.16 5 -0.18 15 20
CDC42 0.036 0.008 -10000 0 0 26 26
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.039 -10000 0 -0.056 96 96
HSPA8 0.037 0.009 -10000 0 0 27 27
SMAD3/SMAD4/ER alpha 0.046 0.087 0.23 9 -0.16 18 27
AKT1 0.031 0.019 -10000 0 -0.034 24 24
GSC 0.004 0.033 0.11 20 -0.063 3 23
NKX2-5 0.034 0.017 0.074 7 -0.056 12 19
muscle cell differentiation -0.017 0.13 0.31 52 -10000 0 52
SMAD2-3/SMAD4/SP1 0.052 0.14 0.33 5 -0.25 48 53
SMAD4 0.023 0.056 0.14 1 -0.13 31 32
CBFB 0.037 0.006 -10000 0 0 13 13
SAP18 0.035 0.011 -10000 0 0 46 46
Cbp/p300/MSG1 0.009 0.087 -10000 0 -0.11 149 149
SMAD3/SMAD4/VDR 0.046 0.12 -10000 0 -0.2 32 32
MYC 0.029 0.015 -10000 0 -10000 0 0
CDKN2B -0.21 0.2 -10000 0 -0.53 50 50
AP1 -0.003 0.099 0.22 2 -0.26 40 42
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.015 0.13 -10000 0 -0.37 41 41
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.042 0.15 0.21 2 -0.41 53 55
SP3 0.036 0.016 0.081 14 -0.053 10 24
CREB1 0.037 0.005 -10000 0 0 8 8
FOXH1 0.036 0.015 0.076 10 -0.053 9 19
SMAD3/SMAD4/GR 0.042 0.093 0.24 2 -0.18 22 24
GATA3 0.029 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.008 0.098 -10000 0 -0.3 32 32
MEF2C/TIF2 -0.02 0.075 0.26 10 -0.22 17 27
endothelial cell migration 0.2 0.49 1.1 106 -10000 0 106
MAX 0.027 0.043 0.085 87 -0.053 88 175
RBBP7 0.037 0.005 -10000 0 0 10 10
RBBP4 0.034 0.012 -10000 0 0 61 61
RUNX2 0.037 0.004 -10000 0 0 7 7
RUNX3 0.035 0.009 -10000 0 0 34 34
RUNX1 0.037 0.006 -10000 0 0 13 13
CTBP1 0.036 0.008 -10000 0 0 27 27
NR3C1 0.028 0.043 0.086 89 -0.053 89 178
VDR 0.036 0.008 -10000 0 0 23 23
CDKN1A -0.097 0.35 0.38 2 -1.1 58 60
KAT2B -0.003 0.008 -10000 0 -0.027 9 9
SMAD2/SMAD2/SMAD4/FOXH1 0.049 0.078 0.2 3 -0.16 36 39
DCP1A 0.036 0.008 -10000 0 0 26 26
SKI 0.036 0.009 -10000 0 0 27 27
SERPINE1 -0.2 0.5 -10000 0 -1.2 106 106
SMAD3/SMAD4/ATF2 0.042 0.087 0.22 1 -0.16 29 30
SMAD3/SMAD4/ATF3 0.018 0.1 -10000 0 -0.19 56 56
SAP30 0.037 0.007 -10000 0 0 19 19
Cbp/p300/PIAS3 0.042 0.075 -10000 0 -0.095 96 96
JUN -0.015 0.097 0.2 8 -0.26 38 46
SMAD3/SMAD4/IRF7 0.045 0.09 -10000 0 -0.17 31 31
TFE3 0.017 0.061 0.11 8 -0.096 103 111
COL1A2 -0.06 0.2 -10000 0 -0.63 56 56
mesenchymal cell differentiation -0.042 0.087 0.16 33 -0.22 1 34
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.036 0.007 -10000 0 0 18 18
FOS 0.02 0.03 0.13 1 -0.049 29 30
SMAD3/SMAD4/Max 0.042 0.088 0.24 2 -0.17 16 18
Cbp/p300/SNIP1 0.044 0.058 -10000 0 -0.082 29 29
ZBTB17 0.036 0.006 -10000 0 -10000 0 0
LAMC1 -0.034 0.099 0.17 7 -0.31 39 46
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.085 0.22 1 -0.16 30 31
IRF7 0.035 0.01 -10000 0 -10000 0 0
ESR1 0.043 0.033 0.12 67 -0.002 34 101
HNF4A 0.035 0.01 -10000 0 0 37 37
MEF2C -0.026 0.071 0.24 14 -0.22 19 33
SMAD2-3/SMAD4 0.043 0.096 0.24 1 -0.2 31 32
Cbp/p300/Src-1 0.032 0.076 -10000 0 -0.1 90 90
IGHV3OR16-13 0.005 0.055 -10000 0 -0.48 6 6
TGIF2/HDAC complex 0.034 0.011 -10000 0 0 45 45
CREBBP 0.022 0.035 -10000 0 -0.046 103 103
SKIL 0.037 0.006 -10000 0 0 12 12
HDAC1 0.036 0.008 -10000 0 0 24 24
HDAC2 0.033 0.012 -10000 0 0 61 61
SNIP1 0.037 0.007 -10000 0 0 14 14
GCN5L2 -0.003 0.013 -10000 0 -0.027 92 92
SMAD3/SMAD4/TFE3 0.032 0.12 0.27 3 -0.23 47 50
MSG1/HSC70 0.01 0.079 -10000 0 -0.14 102 102
SMAD2 0.036 0.018 0.092 4 -0.051 13 17
SMAD3 0.02 0.059 0.14 2 -0.13 38 40
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.075 -10000 0 -0.2 36 36
SMAD2/SMAD2/SMAD4 -0.015 0.067 0.17 5 -0.19 45 50
NCOR1 0.036 0.009 -10000 0 0 27 27
NCOA2 0.037 0.005 -10000 0 0 11 11
NCOA1 0.034 0.011 -10000 0 0 49 49
MYOD/E2A 0.053 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.061 0.15 0.34 4 -0.25 40 44
IFNB1 -0.006 0.06 0.17 8 -0.18 7 15
SMAD3/SMAD4/MEF2C 0.028 0.093 0.24 1 -0.23 20 21
CITED1 0.026 0.017 -10000 0 0 153 153
SMAD2-3/SMAD4/ARC105 0.057 0.098 0.26 1 -0.18 27 28
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.022 0.14 -10000 0 -0.43 38 38
RUNX1-3/PEBPB2 0.068 0.024 -10000 0 -10000 0 0
SMAD7 -0.043 0.18 0.28 1 -0.44 61 62
MYC/MIZ-1 0.029 0.058 -10000 0 -0.14 49 49
SMAD3/SMAD4 -0.08 0.23 0.2 2 -0.46 115 117
IL10 -0.012 0.063 0.18 9 -0.19 4 13
PIASy/HDAC complex 0.03 0.031 0.073 16 -0.031 87 103
PIAS3 0.024 0.029 -10000 0 -0.031 108 108
CDK2 0.022 0.033 -10000 0 -0.043 92 92
IL5 -0.011 0.065 0.19 10 -0.19 2 12
CDK4 0.021 0.031 -10000 0 -0.046 69 69
PIAS4 0.03 0.031 0.074 14 -0.031 87 101
ATF3 0.028 0.016 -10000 0 0 129 129
SMAD3/SMAD4/SP1 0.03 0.14 0.31 1 -0.25 53 54
FOXG1 0.027 0.021 0.068 3 -0.004 146 149
FOXO3 -0.017 0.013 -10000 0 -0.065 1 1
FOXO1 -0.016 0.012 -10000 0 -10000 0 0
FOXO4 -0.019 0.011 -10000 0 -10000 0 0
heart looping -0.026 0.07 0.24 14 -0.22 19 33
CEBPB 0.032 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.025 0.073 0.19 1 -0.14 48 49
MYOD1 0.037 0.005 -10000 0 0 10 10
SMAD3/SMAD4/HNF4 0.04 0.086 0.22 1 -0.16 28 29
SMAD3/SMAD4/GATA3 0.036 0.087 -10000 0 -0.17 24 24
SnoN/SIN3/HDAC complex/NCoR1 0.037 0.006 -10000 0 0 12 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.095 -10000 0 -0.16 13 13
SMAD3/SMAD4/SP1-3 0.047 0.14 0.32 1 -0.25 48 49
MED15 0.035 0.009 -10000 0 0 31 31
SP1 0.016 0.075 0.12 20 -0.12 107 127
SIN3B 0.036 0.009 -10000 0 0 27 27
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.069 0.085 0.25 1 -0.16 38 39
ITGB5 -0.031 0.11 0.26 11 -0.28 32 43
TGIF/SIN3/HDAC complex/CtBP -0.015 0.12 -10000 0 -0.35 34 34
SMAD3/SMAD4/AR 0.041 0.086 0.22 1 -0.16 29 30
AR 0.036 0.008 -10000 0 0 23 23
negative regulation of cell growth -0.015 0.12 0.18 1 -0.29 59 60
SMAD3/SMAD4/MYOD 0.043 0.087 0.22 1 -0.16 37 38
E2F5 0.037 0.005 -10000 0 0 9 9
E2F4 0.037 0.005 -10000 0 0 8 8
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.061 0.099 0.24 1 -0.17 34 35
SMAD2-3/SMAD4/FOXO1-3a-4 -0.025 0.13 0.22 2 -0.41 38 40
TFDP1 0.034 0.012 -10000 0 0 56 56
SMAD3/SMAD4/AP1 0.019 0.12 0.25 2 -0.26 39 41
SMAD3/SMAD4/RUNX2 0.043 0.087 0.22 1 -0.16 32 33
TGIF2 0.034 0.011 -10000 0 0 45 45
TGIF1 0.033 0.013 -10000 0 0 67 67
ATF2 0.037 0.005 -10000 0 0 11 11
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.043 0.011 -10000 0 -10000 0 0
NFATC2 0.024 0.16 0.29 5 -0.37 37 42
NFATC3 0.017 0.13 0.28 20 -0.24 73 93
CD40LG -0.011 0.34 0.5 44 -0.69 71 115
ITCH 0.034 0.048 0.19 8 -10000 0 8
CBLB 0.036 0.049 0.2 11 -0.12 1 12
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.045 0.26 0.38 15 -0.63 53 68
JUNB 0.032 0.014 -10000 0 0 77 77
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.029 -10000 0 -0.13 7 7
T cell anergy 0.016 0.067 0.21 23 -0.21 2 25
TLE4 0.014 0.11 -10000 0 -0.32 19 19
Jun/NFAT1-c-4/p21SNFT -0.014 0.33 0.45 3 -0.73 71 74
AP-1/NFAT1-c-4 -0.041 0.34 -10000 0 -0.78 67 67
IKZF1 0.023 0.094 0.39 5 -0.31 12 17
T-helper 2 cell differentiation -0.069 0.23 -10000 0 -0.61 43 43
AP-1/NFAT1 0.02 0.15 0.29 18 -0.29 43 61
CALM1 0.046 0.024 0.13 1 -10000 0 1
EGR2 -0.069 0.42 0.5 13 -0.97 75 88
EGR3 -0.053 0.42 0.47 28 -0.96 74 102
NFAT1/FOXP3 0.048 0.13 0.26 3 -0.29 24 27
EGR1 0.03 0.016 0.073 1 -10000 0 1
JUN 0.033 0.043 0.12 34 -0.05 13 47
EGR4 0.038 0.004 0.073 1 -10000 0 1
mol:Ca2+ 0.005 0.004 -10000 0 -10000 0 0
GBP3 0.011 0.1 0.18 3 -0.24 37 40
FOSL1 0.034 0.012 -10000 0 0 56 56
NFAT1-c-4/MAF/IRF4 0.014 0.34 0.43 6 -0.72 74 80
DGKA 0.016 0.1 -10000 0 -0.31 18 18
CREM 0.028 0.016 -10000 0 0 120 120
NFAT1-c-4/PPARG -0.001 0.33 0.43 5 -0.73 74 79
CTLA4 0.012 0.093 -10000 0 -0.27 19 19
NFAT1-c-4 (dimer)/EGR1 -0.023 0.34 0.43 2 -0.76 76 78
NFAT1-c-4 (dimer)/EGR4 0.007 0.34 0.43 6 -0.74 74 80
FOS 0.024 0.039 0.11 20 -0.052 10 30
IFNG -0.001 0.13 -10000 0 -0.44 11 11
T cell activation -0.01 0.22 0.43 5 -0.54 33 38
MAF 0.035 0.01 -10000 0 0 36 36
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.6 73 -0.44 28 101
TNF -0.036 0.31 0.39 18 -0.7 75 93
FASLG -0.093 0.46 0.55 3 -1.1 76 79
TBX21 0.041 0.007 0.11 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.028 0.018 -10000 0 -10000 0 0
PTPN1 0.014 0.12 0.43 2 -0.36 22 24
NFAT1-c-4/ICER1 -0.023 0.32 0.42 6 -0.74 74 80
GATA3 0.029 0.017 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.012 0.14 -10000 0 -0.43 11 11
IL2RA -0.054 0.25 0.33 11 -0.6 59 70
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.012 0.11 -10000 0 -0.36 21 21
E2F1 0.036 0.05 -10000 0 -0.25 12 12
PPARG 0.036 0.008 -10000 0 0 25 25
SLC3A2 0.012 0.12 0.24 1 -0.38 26 27
IRF4 0.037 0.005 -10000 0 0 10 10
PTGS2 -0.07 0.28 0.44 3 -0.69 68 71
CSF2 -0.01 0.34 0.5 44 -0.69 70 114
JunB/Fra1/NFAT1-c-4 -0.013 0.32 -10000 0 -0.72 72 72
IL4 -0.072 0.23 -10000 0 -0.64 42 42
IL5 -0.011 0.34 0.5 44 -0.69 70 114
IL2 -0.01 0.22 0.43 5 -0.56 31 36
IL3 0.007 0.087 -10000 0 -0.53 8 8
RNF128 0.013 0.023 0.18 1 -10000 0 1
NFATC1 -0.006 0.28 0.44 28 -0.6 73 101
CDK4 -0.014 0.27 0.56 38 -1 14 52
PTPRK 0.002 0.14 -10000 0 -0.43 36 36
IL8 -0.099 0.29 0.46 7 -0.74 66 73
POU2F1 0.04 0.009 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.036 0.008 -10000 0 0 25 25
Jak2/Leptin Receptor 0.001 0.13 -10000 0 -0.35 40 40
PTP1B/AKT1 0.002 0.12 0.21 3 -0.25 56 59
FYN 0.031 0.015 -10000 0 0 93 93
p210 bcr-abl/PTP1B -0.01 0.11 0.22 3 -0.27 48 51
EGFR 0.01 0.017 -10000 0 -0.031 4 4
EGF/EGFR -0.034 0.095 -10000 0 -0.29 41 41
CSF1 0.037 0.005 -10000 0 0 9 9
AKT1 0.034 0.012 -10000 0 0 58 58
INSR 0.036 0.007 -10000 0 -0.002 16 16
PTP1B/N-cadherin -0.005 0.12 0.21 2 -0.27 58 60
Insulin Receptor/Insulin 0.02 0.12 -10000 0 -0.26 38 38
HCK 0.027 0.017 -10000 0 0 145 145
CRK 0.036 0.008 -10000 0 0 25 25
TYK2 -0.012 0.12 0.28 20 -0.29 44 64
EGF 0.028 0.025 -10000 0 -0.023 93 93
YES1 0.035 0.01 -10000 0 0 43 43
CAV1 0.004 0.15 0.24 29 -0.29 57 86
TXN 0.035 0.011 -10000 0 -0.001 42 42
PTP1B/IRS1/GRB2 0.007 0.13 0.22 1 -0.27 51 52
cell migration 0.01 0.11 0.27 48 -0.22 3 51
STAT3 0.035 0.01 -10000 0 0 40 40
PRLR 0.039 0.006 -10000 0 -10000 0 0
ITGA2B 0.037 0.003 -10000 0 0 4 4
CSF1R 0.028 0.017 -10000 0 0 132 132
Prolactin Receptor/Prolactin 0.058 0.013 -10000 0 -10000 0 0
FGR 0.033 0.012 -10000 0 0 58 58
PTP1B/p130 Cas -0.012 0.11 0.19 3 -0.26 50 53
Crk/p130 Cas -0.001 0.12 0.2 3 -0.26 52 55
DOK1 -0.009 0.11 0.2 5 -0.3 35 40
JAK2 -0.01 0.13 0.26 1 -0.36 42 43
Jak2/Leptin Receptor/Leptin -0.012 0.12 -10000 0 -0.32 32 32
PIK3R1 0.033 0.013 -10000 0 0 67 67
PTPN1 -0.01 0.11 0.22 3 -0.27 48 51
LYN 0.032 0.013 -10000 0 0 72 72
CDH2 0.033 0.012 -10000 0 0 57 57
SRC 0.015 0.1 -10000 0 -0.48 17 17
ITGB3 0.037 0.004 -10000 0 0 6 6
CAT1/PTP1B -0.007 0.18 0.28 31 -0.37 63 94
CAPN1 0.036 0.006 -10000 0 -0.003 9 9
CSK 0.036 0.007 -10000 0 0 20 20
PI3K 0.009 0.13 -10000 0 -0.3 44 44
mol:H2O2 0.003 0.005 0.027 3 -10000 0 3
STAT3 (dimer) -0.01 0.11 -10000 0 -0.29 32 32
negative regulation of transcription -0.01 0.13 0.26 1 -0.35 42 43
FCGR2A 0.029 0.016 -10000 0 0 114 114
FER 0.037 0.009 -10000 0 -0.003 19 19
alphaIIb/beta3 Integrin 0.054 0.006 -10000 0 -10000 0 0
BLK 0.037 0.007 -10000 0 0 16 16
Insulin Receptor/Insulin/Shc 0.061 0.036 -10000 0 -0.13 8 8
RHOA 0.036 0.007 -10000 0 0 20 20
LEPR 0.036 0.008 -10000 0 0 22 22
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.036 0.007 -10000 0 0 19 19
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.004 0.16 0.22 19 -0.36 60 79
PRL 0.039 0.007 -10000 0 -10000 0 0
SOCS3 0.024 0.016 -10000 0 -10000 0 0
SPRY2 0.03 0.019 -10000 0 0 140 140
Insulin Receptor/Insulin/IRS1 0.058 0.046 -10000 0 -0.12 22 22
CSF1/CSF1R -0.003 0.13 0.22 1 -0.28 54 55
Ras protein signal transduction -0.005 0.091 0.58 10 -10000 0 10
IRS1 0.034 0.011 -10000 0 0 52 52
INS 0.036 0.008 -10000 0 -0.001 21 21
LEP 0.026 0.017 -10000 0 0 158 158
STAT5B -0.003 0.11 0.25 2 -0.3 30 32
STAT5A -0.003 0.11 0.25 2 -0.29 33 35
GRB2 0.036 0.007 -10000 0 0 19 19
PDGFB-D/PDGFRB 0.002 0.12 0.22 3 -0.27 47 50
CSN2 0.013 0.04 -10000 0 -10000 0 0
PIK3CA 0.032 0.013 -10000 0 0 74 74
LAT -0.027 0.18 -10000 0 -0.46 64 64
YBX1 0.041 0.04 -10000 0 -0.29 7 7
LCK 0.036 0.008 -10000 0 0 21 21
SHC1 0.034 0.012 -10000 0 0 53 53
NOX4 0.035 0.016 -10000 0 0 83 83
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.035 0.01 -10000 0 0 39 39
mol:PIP3 -0.021 0.054 0.091 3 -0.22 22 25
FRAP1 0.025 0.1 0.24 3 -0.48 13 16
AKT1 0.009 0.1 0.17 104 -0.24 31 135
INSR 0.037 0.006 -10000 0 0 15 15
Insulin Receptor/Insulin 0.047 0.013 -10000 0 -10000 0 0
mol:GTP 0.036 0.11 0.2 69 -0.25 31 100
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.054 -10000 0 -0.19 25 25
TSC2 0.036 0.008 -10000 0 0 26 26
RHEB/GDP -0.02 0.072 0.11 35 -0.24 26 61
TSC1 0.035 0.01 -10000 0 0 41 41
Insulin Receptor/IRS1 0.023 0.06 -10000 0 -0.25 22 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.026 0.075 0.17 3 -0.2 21 24
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.017 -10000 0 0 153 153
RPS6KB1 0.035 0.088 0.25 12 -0.29 7 19
MAP3K5 -0.025 0.084 0.16 1 -0.22 73 74
PIK3R1 0.033 0.013 -10000 0 0 67 67
apoptosis -0.025 0.083 0.16 1 -0.22 73 74
mol:LY294002 0 0 0.001 13 -0.001 21 34
EIF4B 0.03 0.087 0.24 17 -0.29 7 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.071 0.27 2 -0.24 9 11
eIF4E/eIF4G1/eIF4A1 0.01 0.073 -10000 0 -0.3 16 16
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.083 0.18 1 -0.23 32 33
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.06 0.18 20 -0.16 18 38
FKBP1A 0.033 0.013 -10000 0 0 63 63
RHEB/GTP 0.017 0.087 0.24 6 -0.23 28 34
mol:Amino Acids 0 0 0.001 13 -0.001 21 34
FKBP12/Rapamycin 0.022 0.024 -10000 0 -0.13 10 10
PDPK1 -0.024 0.056 0.16 9 -0.21 21 30
EIF4E 0.035 0.01 -10000 0 0 37 37
ASK1/PP5C -0.038 0.23 -10000 0 -0.56 81 81
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.08 -10000 0 -0.3 29 29
TSC1/TSC2 0.04 0.12 0.22 70 -0.27 31 101
tumor necrosis factor receptor activity 0 0 0.001 21 -0.001 13 34
RPS6 0.032 0.013 -10000 0 0 71 71
PPP5C 0.035 0.009 -10000 0 0 32 32
EIF4G1 0.034 0.011 -10000 0 0 46 46
IRS1 0.001 0.058 -10000 0 -0.26 23 23
INS 0.036 0.007 -10000 0 0 20 20
PTEN 0.026 0.017 -10000 0 0 158 158
PDK2 -0.024 0.056 0.16 9 -0.22 20 29
EIF4EBP1 -0.024 0.25 -10000 0 -1.1 26 26
PIK3CA 0.033 0.014 -10000 0 0 74 74
PPP2R5D 0.019 0.092 0.26 3 -0.43 13 16
peptide biosynthetic process -0.022 0.017 0.18 3 -10000 0 3
RHEB 0.026 0.018 -10000 0 0 159 159
EIF4A1 0.036 0.007 -10000 0 0 20 20
mol:Rapamycin 0 0.001 0.004 20 -0.003 13 33
EEF2 -0.022 0.017 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.007 0.25 -10000 0 -1.1 26 26
EPHB forward signaling

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
Ephrin A5/EPHB2 0.046 0.015 -10000 0 -10000 0 0
cell-cell adhesion 0.031 0.04 0.19 13 -10000 0 13
Ephrin B/EPHB2/RasGAP 0.062 0.089 -10000 0 -0.13 73 73
ITSN1 0.036 0.007 -10000 0 0 17 17
PIK3CA 0.032 0.013 -10000 0 0 74 74
SHC1 0.034 0.012 -10000 0 0 53 53
Ephrin B1/EPHB3 0.046 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.04 0.026 -10000 0 -0.11 6 6
HRAS/GDP 0.004 0.081 -10000 0 -0.21 41 41
Ephrin B/EPHB1/GRB7 0.069 0.074 -10000 0 -0.12 45 45
Endophilin/SYNJ1 -0.026 0.058 0.19 15 -0.18 2 17
KRAS 0.035 0.009 -10000 0 0 34 34
Ephrin B/EPHB1/Src 0.064 0.076 -10000 0 -0.12 50 50
endothelial cell migration 0.022 0.072 -10000 0 -0.14 63 63
GRB2 0.036 0.007 -10000 0 0 19 19
GRB7 0.037 0.007 -10000 0 0 16 16
PAK1 -0.029 0.064 0.2 18 -10000 0 18
HRAS 0.035 0.01 -10000 0 0 37 37
RRAS -0.025 0.061 0.21 13 -0.18 10 23
DNM1 0.036 0.008 -10000 0 0 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.019 0.066 0.19 18 -0.18 11 29
lamellipodium assembly -0.031 0.04 -10000 0 -0.19 13 13
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.012 0.071 -10000 0 -0.28 14 14
PIK3R1 0.033 0.013 -10000 0 0 67 67
EPHB2 0.035 0.01 -10000 0 0 39 39
EPHB3 0.034 0.011 -10000 0 0 47 47
EPHB1 0.031 0.015 -10000 0 0 95 95
EPHB4 0.026 0.017 -10000 0 0 157 157
mol:GDP 0.018 0.11 0.2 99 -0.23 33 132
Ephrin B/EPHB2 0.053 0.068 -10000 0 -0.11 63 63
Ephrin B/EPHB3 0.053 0.067 -10000 0 -0.11 62 62
JNK cascade -0.006 0.072 0.23 23 -0.19 4 27
Ephrin B/EPHB1 0.053 0.065 -10000 0 -0.11 52 52
RAP1/GDP 0.024 0.12 0.2 106 -0.22 33 139
EFNB2 0.029 0.016 -10000 0 0 115 115
EFNB3 0.036 0.008 -10000 0 0 25 25
EFNB1 0.038 0.002 -10000 0 0 2 2
Ephrin B2/EPHB1-2 0.034 0.058 -10000 0 -0.11 50 50
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.037 0.005 -10000 0 0 10 10
CDC42/GTP 0.046 0.082 -10000 0 -0.19 31 31
Rap1/GTP -0.045 0.051 0.053 7 -0.2 21 28
axon guidance 0.046 0.014 -10000 0 -10000 0 0
MAPK3 -0.004 0.07 0.16 5 -0.28 14 19
MAPK1 -0.004 0.072 0.18 1 -0.28 17 18
Rac1/GDP -0.009 0.091 0.23 22 -0.24 31 53
actin cytoskeleton reorganization -0.042 0.06 -10000 0 -0.2 37 37
CDC42/GDP 0.029 0.13 0.22 107 -0.23 33 140
PI3K 0.026 0.076 -10000 0 -0.14 63 63
EFNA5 0.037 0.005 -10000 0 0 9 9
Ephrin B2/EPHB4 0.018 0.046 -10000 0 -0.11 42 42
Ephrin B/EPHB2/Intersectin/N-WASP 0.004 0.06 -10000 0 -0.17 42 42
CDC42 0.036 0.008 -10000 0 0 26 26
RAS family/GTP -0.053 0.06 -10000 0 -0.24 24 24
PTK2 -0.013 0.087 0.54 11 -0.2 15 26
MAP4K4 -0.006 0.073 0.23 23 -0.19 4 27
SRC 0.035 0.009 -10000 0 0 31 31
KALRN 0.036 0.008 -10000 0 0 22 22
Intersectin/N-WASP 0.035 0.033 -10000 0 -0.14 7 7
neuron projection morphogenesis 0.055 0.17 0.34 112 -0.22 12 124
MAP2K1 0.001 0.07 0.2 1 -0.28 15 16
WASL 0.026 0.017 -10000 0 0 157 157
Ephrin B1/EPHB1-2/NCK1 0.082 0.039 -10000 0 -0.12 10 10
cell migration -0.01 0.086 0.2 5 -0.28 19 24
NRAS 0.033 0.013 -10000 0 0 66 66
SYNJ1 -0.027 0.058 0.19 15 -0.18 2 17
PXN 0.037 0.005 -10000 0 0 9 9
TF -0.022 0.051 0.18 7 -0.18 20 27
HRAS/GTP 0.036 0.079 -10000 0 -0.14 59 59
Ephrin B1/EPHB1-2 0.054 0.035 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.019 0.049 0.15 5 -0.23 7 12
RAC1 0.026 0.017 -10000 0 0 156 156
mol:GTP 0.044 0.076 -10000 0 -0.13 60 60
RAC1-CDC42/GTP -0.032 0.046 -10000 0 -0.2 14 14
RASA1 0.035 0.01 -10000 0 0 35 35
RAC1-CDC42/GDP 0.012 0.094 0.24 20 -0.24 31 51
ruffle organization 0.066 0.17 0.32 130 -0.25 7 137
NCK1 0.036 0.009 -10000 0 0 28 28
receptor internalization -0.032 0.054 0.18 14 -0.18 2 16
Ephrin B/EPHB2/KALRN 0.068 0.079 -10000 0 -0.12 60 60
ROCK1 -0.009 0.048 0.18 21 -10000 0 21
RAS family/GDP -0.044 0.063 -10000 0 -0.21 42 42
Rac1/GTP -0.029 0.045 -10000 0 -0.2 13 13
Ephrin B/EPHB1/Src/Paxillin 0.01 0.062 -10000 0 -0.15 52 52
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.044 0.091 0.23 35 -0.2 8 43
TBX21 0.076 0.2 0.55 10 -0.57 8 18
B2M 0.036 0.007 -10000 0 0 20 20
TYK2 0.039 0.041 0.12 18 -0.056 10 28
IL12RB1 0.039 0.042 0.12 18 -0.056 12 30
GADD45B 0.067 0.3 0.53 20 -0.98 26 46
IL12RB2 0.041 0.042 0.12 22 -0.053 23 45
GADD45G 0.1 0.2 0.52 16 -0.54 6 22
natural killer cell activation 0.013 0.025 0.058 78 -0.037 12 90
RELB 0.035 0.009 -10000 0 0 30 30
RELA 0.037 0.005 -10000 0 0 10 10
IL18 0.034 0.025 0.091 2 -0.039 27 29
IL2RA 0.026 0.017 -10000 0 0 152 152
IFNG 0.035 0.01 -10000 0 0 35 35
STAT3 (dimer) 0.07 0.23 0.44 38 -0.51 32 70
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 41 41
FASLG 0.08 0.2 0.53 13 -0.57 8 21
NF kappa B2 p52/RelB 0.062 0.19 0.44 14 -0.47 18 32
CD4 0.025 0.027 -10000 0 -0.017 132 132
SOCS1 0.037 0.004 -10000 0 0 7 7
EntrezGene:6955 -0.001 0.01 -10000 0 -0.026 56 56
CD3D 0.025 0.029 -10000 0 -0.025 113 113
CD3E 0.028 0.028 -10000 0 -0.035 78 78
CD3G 0.027 0.03 -10000 0 -0.043 70 70
IL12Rbeta2/JAK2 0.057 0.062 0.19 19 -10000 0 19
CCL3 0.079 0.2 0.46 37 -0.48 18 55
CCL4 0.047 0.33 0.54 28 -1 32 60
HLA-A 0.037 0.006 -10000 0 0 15 15
IL18/IL18R 0.097 0.074 0.24 18 -0.13 6 24
NOS2 0.082 0.2 0.45 40 -0.44 17 57
IL12/IL12R/TYK2/JAK2/SPHK2 0.041 0.091 0.22 32 -0.22 10 42
IL1R1 0.079 0.21 0.58 11 -0.59 7 18
IL4 0.002 0.05 -10000 0 -0.08 76 76
JAK2 0.035 0.04 0.12 16 -0.057 10 26
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 41 41
TCR/CD3/MHC I/CD8 0.012 0.048 -10000 0 -0.25 7 7
RAB7A 0.083 0.27 0.55 13 -0.78 26 39
lysosomal transport 0.085 0.26 0.54 15 -0.73 26 41
FOS -0.11 0.48 0.49 17 -1 100 117
STAT4 (dimer) 0.096 0.22 0.48 36 -0.52 17 53
STAT5A (dimer) 0.081 0.2 0.43 17 -0.48 17 34
GZMA 0.075 0.21 0.52 24 -0.57 8 32
GZMB 0.073 0.2 0.58 12 -0.58 7 19
HLX 0.035 0.009 -10000 0 0 30 30
LCK 0.069 0.21 0.46 34 -0.51 17 51
TCR/CD3/MHC II/CD4 -0.02 0.12 0.16 19 -0.24 83 102
IL2/IL2R 0.064 0.049 -10000 0 -10000 0 0
MAPK14 0.098 0.25 0.53 20 -0.71 22 42
CCR5 0.091 0.21 0.55 17 -0.78 5 22
IL1B 0.03 0.039 0.12 8 -0.051 29 37
STAT6 0.051 0.1 0.3 17 -0.41 4 21
STAT4 0.035 0.009 -10000 0 0 31 31
STAT3 0.035 0.01 -10000 0 0 40 40
STAT1 0.035 0.01 -10000 0 0 41 41
NFKB1 0.036 0.007 -10000 0 0 18 18
NFKB2 0.028 0.017 -10000 0 0 132 132
IL12B 0.042 0.042 0.12 23 -0.056 15 38
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.037 0.004 -10000 0 0 7 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.043 0.091 0.2 8 -0.23 35 43
IL2RB 0.034 0.011 -10000 0 0 49 49
proteasomal ubiquitin-dependent protein catabolic process 0.097 0.21 0.47 38 -0.49 17 55
IL2RG 0.036 0.008 -10000 0 0 25 25
IL12 0.064 0.063 0.19 23 -10000 0 23
STAT5A 0.037 0.005 -10000 0 0 8 8
CD247 0.028 0.028 -10000 0 -0.041 66 66
IL2 0.037 0.005 -10000 0 0 9 9
SPHK2 0.036 0.009 -10000 0 0 29 29
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.04 0.042 0.12 17 -0.057 12 29
IL12/IL12R/TYK2/JAK2 0.074 0.22 0.5 35 -0.52 18 53
MAP2K3 0.094 0.24 0.52 20 -0.67 22 42
RIPK2 0.037 0.006 -10000 0 0 14 14
MAP2K6 0.098 0.24 0.5 25 -0.62 22 47
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.021 0.028 -10000 0 -0.012 186 186
IL18RAP 0.04 0.023 0.091 3 -0.038 33 36
IL12Rbeta1/TYK2 0.052 0.065 0.18 10 -0.15 15 25
EOMES -0.019 0.04 0.1 1 -0.11 46 47
STAT1 (dimer) 0.085 0.2 0.46 30 -0.47 15 45
T cell proliferation 0.085 0.19 0.43 38 -0.43 20 58
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.04 0.023 0.091 3 -0.038 33 36
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.053 0.18 0.41 3 -0.49 21 24
ATF2 0.09 0.24 0.51 19 -0.67 22 41
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.004 0.097 -10000 0 -0.25 28 28
mol:DAG -0.011 0.086 0.2 4 -0.24 27 31
PLCG1 -0.012 0.088 0.2 4 -0.25 27 31
YES1 -0.015 0.082 0.13 1 -0.17 82 83
FZD3 0.03 0.015 -10000 0 0 108 108
FZD6 0.028 0.017 -10000 0 0 132 132
G protein 0.004 0.1 0.2 26 -0.27 27 53
MAP3K7 -0.031 0.078 0.2 9 -0.23 31 40
mol:Ca2+ -0.011 0.084 0.18 5 -0.24 27 32
mol:IP3 -0.011 0.086 0.2 4 -0.24 27 31
NLK -0.011 0.16 -10000 0 -0.83 18 18
GNB1 0.034 0.011 -10000 0 0 47 47
CAMK2A -0.027 0.08 0.22 9 -0.23 26 35
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.005 0.087 -10000 0 -0.17 88 88
CSNK1A1 0.037 0.006 -10000 0 0 13 13
GNAS -0.015 0.079 -10000 0 -0.17 83 83
GO:0007205 -0.016 0.087 0.24 8 -0.25 26 34
WNT6 0.038 0.002 -10000 0 0 2 2
WNT4 0.036 0.008 -10000 0 0 21 21
NFAT1/CK1 alpha -0.004 0.097 0.22 3 -0.26 29 32
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.03 0.015 -10000 0 0 101 101
WNT11 0.037 0.007 -10000 0 0 16 16
CDC42 -0.025 0.08 0.17 4 -0.26 23 27
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.02 0.11 0.2 3 -0.37 29 32
adherens junction organization -0.001 0.077 -10000 0 -0.3 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.11 0.19 48 -0.29 23 71
FMN1 0.008 0.064 0.14 4 -0.25 17 21
mol:IP3 -0.009 0.078 0.14 2 -0.25 32 34
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.013 0.068 0.15 3 -0.27 17 20
CTNNB1 0.036 0.007 -10000 0 0 17 17
AKT1 -0.004 0.091 0.15 2 -0.34 24 26
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.071 -10000 0 -0.41 6 6
CTNND1 0.036 0.01 -10000 0 0 36 36
mol:PI-4-5-P2 0.003 0.066 0.14 3 -0.26 19 22
VASP 0.001 0.065 0.14 4 -0.26 18 22
ZYX 0.006 0.059 0.15 3 -0.33 9 12
JUB 0.008 0.064 0.14 4 -0.25 17 21
EGFR(dimer) 0 0.066 -10000 0 -0.31 14 14
E-cadherin/beta catenin-gamma catenin 0.064 0.031 -10000 0 -0.11 3 3
mol:PI-3-4-5-P3 0.025 0.097 0.22 1 -0.29 24 25
PIK3CA 0.032 0.015 -10000 0 -0.002 78 78
PI3K 0.025 0.099 0.22 1 -0.3 24 25
FYN -0.041 0.13 0.17 5 -0.32 71 76
mol:Ca2+ -0.009 0.077 0.14 2 -0.25 32 34
JUP 0.034 0.012 -10000 0 0 52 52
PIK3R1 0.033 0.016 -10000 0 -0.004 75 75
mol:DAG -0.009 0.078 0.14 2 -0.25 32 34
CDH1 0.035 0.01 -10000 0 0 39 39
RhoA/GDP 0.052 0.12 0.19 86 -0.28 24 110
establishment of polarity of embryonic epithelium 0.001 0.064 0.14 4 -0.26 18 22
SRC 0.035 0.009 -10000 0 0 31 31
RAC1 0.026 0.017 -10000 0 0 156 156
RHOA 0.036 0.007 -10000 0 0 20 20
EGFR 0.01 0.017 -10000 0 0 373 373
CASR -0.025 0.074 0.15 14 -0.28 24 38
RhoA/GTP 0.007 0.085 -10000 0 -0.27 25 25
AKT2 -0.003 0.082 0.17 1 -0.29 24 25
actin cable formation -0.002 0.064 0.13 4 -0.26 19 23
apoptosis 0.008 0.1 0.34 28 -0.17 12 40
CTNNA1 0.037 0.008 -10000 0 -0.002 20 20
mol:GDP -0.022 0.073 0.17 2 -0.29 23 25
PIP5K1A 0.002 0.067 -10000 0 -0.26 19 19
PLCG1 -0.009 0.08 0.14 2 -0.26 32 34
Rac1/GTP -0.004 0.071 -10000 0 -0.31 14 14
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.011 -10000 0 0 50 50
VLDLR 0.028 0.016 -10000 0 0 129 129
LRPAP1 0.037 0.007 -10000 0 0 16 16
NUDC 0.035 0.009 -10000 0 0 30 30
RELN/LRP8 0.042 0.045 -10000 0 -0.13 11 11
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 14 14
KATNA1 0.034 0.011 -10000 0 0 46 46
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.033 0.1 0.19 128 -0.21 6 134
IQGAP1/CaM 0.032 0.059 -10000 0 -0.14 46 46
DAB1 0.037 0.006 -10000 0 0 12 12
IQGAP1 0.034 0.011 -10000 0 0 47 47
PLA2G7 0.034 0.012 -10000 0 0 56 56
CALM1 0.033 0.012 -10000 0 0 60 60
DYNLT1 0.035 0.01 -10000 0 0 42 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.046 0.036 -10000 0 -0.15 14 14
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.036 0.008 -10000 0 0 26 26
CDK5R1 0.036 0.008 -10000 0 0 25 25
LIS1/Poliovirus Protein 3A -0.023 0.028 -10000 0 -0.14 24 24
CDK5R2 0.036 0.007 -10000 0 0 17 17
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.034 0.049 -10000 0 -0.12 20 20
YWHAE 0.036 0.009 -10000 0 0 29 29
NDEL1/14-3-3 E 0.058 0.17 0.32 127 -0.27 17 144
MAP1B -0.013 0.066 -10000 0 -0.2 50 50
RAC1 -0.003 0.051 -10000 0 -0.25 13 13
p35/CDK5 -0.026 0.055 0.18 6 -0.21 12 18
RELN 0.024 0.018 -10000 0 0 181 181
PAFAH/LIS1 0.022 0.039 -10000 0 -0.15 21 21
LIS1/CLIP170 0.022 0.042 -10000 0 -0.15 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.035 0.08 0.14 10 -0.28 25 35
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.012 0.086 -10000 0 -0.23 51 51
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.05 0.16 0.3 121 -0.27 15 136
LIS1/IQGAP1 0.02 0.048 -10000 0 -0.18 24 24
RHOA -0.006 0.064 -10000 0 -0.32 13 13
PAFAH1B1 -0.02 0.008 -10000 0 -10000 0 0
PAFAH1B3 0.032 0.013 -10000 0 0 75 75
PAFAH1B2 0.037 0.005 -10000 0 0 8 8
MAP1B/LIS1/Dynein heavy chain 0.006 0.079 -10000 0 -0.2 53 53
NDEL1/Katanin 60/Dynein heavy chain 0.078 0.15 0.34 100 -0.26 22 122
LRP8 0.035 0.01 -10000 0 0 37 37
NDEL1/Katanin 60 0.05 0.16 0.32 116 -0.27 18 134
P39/CDK5 -0.025 0.056 0.18 7 -0.21 12 19
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.051 -10000 0 -0.19 24 24
CDK5 -0.014 0.043 0.17 7 -0.22 6 13
PPP2R5D 0.037 0.005 -10000 0 0 10 10
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.036 -10000 0 -0.12 26 26
CSNK2A1 0.034 0.011 -10000 0 0 50 50
RELN/VLDLR/DAB1/LIS1 0.033 0.06 -10000 0 -0.13 33 33
RELN/VLDLR 0.046 0.06 -10000 0 -0.12 26 26
CDC42 -0.002 0.042 -10000 0 -0.18 16 16
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.03 0.042 -10000 0 -0.14 18 18
VLDLR 0.028 0.016 -10000 0 0 129 129
CRKL 0.036 0.009 -10000 0 0 29 29
LRPAP1 0.037 0.007 -10000 0 0 16 16
FYN 0.031 0.015 -10000 0 0 93 93
ITGA3 0.033 0.012 -10000 0 0 59 59
RELN/VLDLR/Fyn 0.02 0.062 -10000 0 -0.13 52 52
MAPK8IP1/MKK7/MAP3K11/JNK1 0.073 0.062 -10000 0 -0.11 5 5
AKT1 -0.015 0.071 -10000 0 -0.2 53 53
MAP2K7 0.036 0.007 -10000 0 0 18 18
RAPGEF1 0.036 0.008 -10000 0 0 21 21
DAB1 0.037 0.006 -10000 0 0 12 12
RELN/LRP8/DAB1 0.043 0.037 -10000 0 -0.11 3 3
LRPAP1/LRP8 0.046 0.036 -10000 0 -0.15 14 14
RELN/LRP8/DAB1/Fyn 0.043 0.06 -10000 0 -0.12 33 33
DAB1/alpha3/beta1 Integrin 0.033 0.059 -10000 0 -0.12 23 23
long-term memory 0.042 0.064 -10000 0 -0.12 33 33
DAB1/LIS1 0.05 0.073 -10000 0 -0.13 31 31
DAB1/CRLK/C3G 0.04 0.06 -10000 0 -0.19 1 1
PIK3CA 0.032 0.013 -10000 0 0 74 74
DAB1/NCK2 0.052 0.073 -10000 0 -0.13 29 29
ARHGEF2 0.036 0.007 -10000 0 0 20 20
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.037 0.006 -10000 0 0 14 14
CDK5R1 0.036 0.008 -10000 0 0 25 25
RELN 0.024 0.018 -10000 0 0 181 181
PIK3R1 0.033 0.013 -10000 0 0 67 67
RELN/LRP8/Fyn 0.031 0.057 -10000 0 -0.13 34 34
GRIN2A/RELN/LRP8/DAB1/Fyn 0.054 0.072 -10000 0 -0.12 33 33
MAPK8 0.029 0.016 -10000 0 0 122 122
RELN/VLDLR/DAB1 0.032 0.046 -10000 0 -0.11 20 20
ITGB1 0.029 0.016 -10000 0 0 117 117
MAP1B 0.019 0.081 0.16 95 -0.2 3 98
RELN/LRP8 0.042 0.045 -10000 0 -0.13 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn 0.053 0.072 -10000 0 -0.12 33 33
PI3K 0.02 0.075 -10000 0 -0.15 75 75
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.027 -10000 0 -0.14 1 1
RAP1A 0.029 0.11 0.27 42 -10000 0 42
PAFAH1B1 0.036 0.008 -10000 0 0 27 27
MAPK8IP1 0.036 0.009 -10000 0 0 28 28
CRLK/C3G 0.051 0.016 -10000 0 -10000 0 0
GRIN2B 0.036 0.008 -10000 0 0 24 24
NCK2 0.036 0.007 -10000 0 0 19 19
neuron differentiation 0.009 0.066 -10000 0 -0.24 15 15
neuron adhesion 0.03 0.12 0.27 43 -10000 0 43
LRP8 0.035 0.01 -10000 0 0 37 37
GSK3B -0.013 0.078 -10000 0 -0.3 19 19
RELN/VLDLR/DAB1/Fyn 0.032 0.065 -10000 0 -0.11 52 52
MAP3K11 0.037 0.005 -10000 0 0 11 11
RELN/VLDLR/DAB1/P13K -0.007 0.073 -10000 0 -0.19 57 57
CDK5 0.025 0.018 -10000 0 0 178 178
MAPT -0.012 0.067 0.7 1 -10000 0 1
neuron migration -0.004 0.11 0.2 61 -0.29 27 88
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.009 0.067 -10000 0 -0.24 15 15
RELN/VLDLR 0.046 0.06 -10000 0 -0.12 26 26
FAS signaling pathway (CD95)

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
SPTAN1 -0.019 0.057 0.22 7 -0.22 22 29
RFC1 -0.021 0.05 0.19 2 -0.22 24 26
PRKDC -0.018 0.053 0.18 3 -0.22 22 25
RIPK1 0.034 0.012 -10000 0 -0.012 30 30
CASP7 -0.14 0.27 -10000 0 -0.58 138 138
FASLG/FAS/FADD/FAF1 -0.007 0.084 0.16 31 -0.18 42 73
MAP2K4 -0.034 0.14 0.28 4 -0.32 48 52
mol:ceramide 0.009 0.091 0.18 4 -0.24 20 24
GSN -0.009 0.061 0.19 12 -0.23 19 31
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.096 0.18 13 -0.25 27 40
FAS 0.023 0.02 -10000 0 0 219 219
BID -0.031 0.032 -10000 0 -0.13 13 13
MAP3K1 -0.082 0.19 0.42 1 -0.37 142 143
MAP3K7 0.035 0.011 -10000 0 0 45 45
RB1 -0.017 0.045 0.23 1 -0.22 22 23
CFLAR 0.035 0.011 -10000 0 -0.018 19 19
HGF/MET 0.036 0.051 -10000 0 -0.12 24 24
ARHGDIB -0.016 0.058 0.22 7 -0.23 20 27
FADD 0.039 0.008 -10000 0 0 13 13
actin filament polymerization 0.008 0.061 0.23 19 -0.19 12 31
NFKB1 0.03 0.11 -10000 0 -0.64 11 11
MAPK8 -0.026 0.14 0.45 2 -0.32 37 39
DFFA -0.018 0.05 0.22 3 -0.22 23 26
DNA fragmentation during apoptosis -0.016 0.047 0.22 2 -0.21 22 24
FAS/FADD/MET 0.026 0.053 -10000 0 -0.12 27 27
CFLAR/RIP1 0.049 0.02 -10000 0 -0.13 2 2
FAIM3 0.036 0.007 -10000 0 0 17 17
FAF1 0.039 0.011 -10000 0 0 31 31
PARP1 -0.02 0.05 0.22 2 -0.22 25 27
DFFB -0.017 0.047 0.22 2 -0.22 22 24
CHUK 0.017 0.098 -10000 0 -0.61 10 10
FASLG 0.04 0.008 -10000 0 0 11 11
FAS/FADD 0.025 0.054 -10000 0 -0.14 35 35
HGF 0.026 0.018 -10000 0 0 163 163
LMNA -0.022 0.048 0.2 3 -0.2 22 25
CASP6 -0.018 0.048 0.18 3 -0.21 23 26
CASP10 0.04 0.005 -10000 0 0 1 1
CASP3 -0.012 0.051 -10000 0 -0.23 24 24
PTPN13 0.033 0.012 -10000 0 0 60 60
CASP8 -0.032 0.008 -10000 0 -10000 0 0
IL6 0.022 0.14 -10000 0 -0.58 8 8
MET 0.024 0.018 -10000 0 0 184 184
ICAD/CAD -0.022 0.05 0.25 4 -0.21 22 26
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.092 0.18 4 -0.25 20 24
activation of caspase activity by cytochrome c -0.031 0.032 -10000 0 -0.13 13 13
PAK2 -0.012 0.054 0.21 7 -0.21 22 29
BCL2 0.036 0.007 -10000 0 0 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.001 0.085 -10000 0 -0.21 55 55
epithelial cell differentiation 0.063 0.053 -10000 0 -0.13 26 26
CYFIP2 0.032 0.013 -10000 0 0 76 76
ENAH -0.042 0.072 0.26 11 -0.27 6 17
EGFR 0.01 0.017 -10000 0 0 373 373
EPHA2 0.034 0.012 -10000 0 0 56 56
MYO6 -0.03 0.049 0.18 9 -0.21 12 21
CTNNB1 0.036 0.007 -10000 0 0 17 17
ABI1/Sra1/Nap1 0.033 0.066 -10000 0 -0.13 57 57
AQP5 -0.018 0.079 0.25 1 -0.36 20 21
CTNND1 0.035 0.01 -10000 0 0 36 36
mol:PI-4-5-P2 -0.032 0.045 0.17 7 -0.2 14 21
regulation of calcium-dependent cell-cell adhesion -0.028 0.045 0.18 9 -0.19 8 17
EGF 0.036 0.008 -10000 0 0 25 25
NCKAP1 0.038 0.003 -10000 0 0 3 3
AQP3 -0.033 0.093 -10000 0 -0.33 39 39
cortical microtubule organization 0.063 0.053 -10000 0 -0.13 26 26
GO:0000145 -0.031 0.041 0.16 7 -0.19 14 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.07 0.055 -10000 0 -0.13 26 26
MLLT4 0.035 0.01 -10000 0 0 36 36
ARF6/GDP -0.053 0.039 -10000 0 -0.22 12 12
ARF6 0.035 0.009 -10000 0 0 31 31
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.03 0.083 0.16 1 -0.31 32 33
PVRL2 0.035 0.009 -10000 0 0 31 31
ZYX -0.024 0.045 0.18 4 -0.21 17 21
ARF6/GTP 0.078 0.062 -10000 0 -0.13 24 24
CDH1 0.035 0.01 -10000 0 0 39 39
EGFR/EGFR/EGF/EGF 0 0.061 -10000 0 -0.13 67 67
RhoA/GDP 0.064 0.058 -10000 0 -0.14 30 30
actin cytoskeleton organization -0.027 0.046 0.17 6 -0.22 13 19
IGF-1R heterotetramer 0.034 0.011 -10000 0 0 51 51
GIT1 0.037 0.004 -10000 0 0 7 7
IGF1R 0.034 0.011 -10000 0 0 51 51
IGF1 0.036 0.008 -10000 0 0 25 25
DIAPH1 -0.11 0.27 -10000 0 -0.51 142 142
Wnt receptor signaling pathway -0.063 0.053 0.13 26 -10000 0 26
RHOA 0.036 0.007 -10000 0 0 20 20
RhoA/GTP -0.054 0.041 -10000 0 -0.23 13 13
CTNNA1 0.036 0.007 -10000 0 0 19 19
VCL -0.027 0.047 0.17 6 -0.22 13 19
EFNA1 0.034 0.012 -10000 0 0 53 53
LPP -0.031 0.049 0.18 5 -0.22 16 21
Ephrin A1/EPHA2 0.046 0.063 -10000 0 -0.14 41 41
SEC6/SEC8 -0.045 0.028 -10000 0 -0.14 24 24
MGAT3 -0.029 0.046 0.18 9 -0.19 8 17
HGF/MET 0.036 0.052 -10000 0 -0.14 19 19
HGF 0.026 0.018 -10000 0 0 163 163
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.085 -10000 0 -0.21 55 55
actin cable formation -0.039 0.11 0.35 11 -0.31 33 44
KIAA1543 -0.026 0.035 0.16 6 -0.18 8 14
KIFC3 -0.032 0.042 0.19 5 -0.19 8 13
NCK1 0.036 0.009 -10000 0 0 28 28
EXOC3 0.036 0.007 -10000 0 0 20 20
ACTN1 -0.027 0.051 0.19 7 -0.21 18 25
NCK1/GIT1 0.051 0.024 -10000 0 -0.14 6 6
mol:GDP 0.063 0.053 -10000 0 -0.13 26 26
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.032 0.047 0.19 7 -0.22 11 18
PIP5K1C -0.032 0.046 0.18 7 -0.2 14 21
LIMA1 0.032 0.013 -10000 0 0 72 72
ABI1 0.028 0.017 -10000 0 0 136 136
ROCK1 -0.034 0.091 0.33 16 -0.29 5 21
adherens junction assembly -0.024 0.067 0.23 6 -0.3 14 20
IGF-1R heterotetramer/IGF1 0.049 0.063 -10000 0 -0.14 39 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.049 0.023 -10000 0 -0.14 3 3
MET 0.024 0.018 -10000 0 0 184 184
PLEKHA7 -0.029 0.03 0.055 20 -0.13 26 46
mol:GTP 0.072 0.054 -10000 0 -0.13 25 25
establishment of epithelial cell apical/basal polarity -0.039 0.058 0.19 4 -0.24 7 11
cortical actin cytoskeleton stabilization -0.001 0.085 -10000 0 -0.21 55 55
regulation of cell-cell adhesion -0.027 0.046 0.17 6 -0.22 13 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.085 -10000 0 -0.21 55 55
Class I PI3K signaling events

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
ARF5/GTP -0.027 0.048 0.17 7 -0.22 10 17
DAPP1 -0.022 0.13 0.2 4 -0.29 65 69
Src family/SYK family/BLNK-LAT/BTK-ITK -0.043 0.19 0.29 3 -0.47 59 62
mol:DAG -0.007 0.092 0.2 25 -0.2 45 70
HRAS 0.036 0.02 0.089 3 -0.032 24 27
RAP1A 0.039 0.014 0.064 7 -0.019 20 27
ARF5/GDP -0.001 0.098 -10000 0 -0.34 30 30
PLCG2 0.033 0.013 -10000 0 0 65 65
PLCG1 0.035 0.01 -10000 0 0 43 43
ARF5 0.026 0.018 -10000 0 0 164 164
mol:GTP -0.026 0.053 0.18 13 -0.19 10 23
ARF1/GTP -0.018 0.049 0.15 14 -0.2 12 26
RHOA 0.036 0.007 -10000 0 0 20 20
YES1 0.035 0.01 -10000 0 0 43 43
RAP1A/GTP -0.026 0.048 0.16 13 -0.19 10 23
ADAP1 -0.025 0.05 0.17 13 -0.18 10 23
ARAP3 -0.025 0.052 0.18 13 -0.19 10 23
INPPL1 0.037 0.006 -10000 0 0 13 13
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.034 0.011 -10000 0 0 51 51
ARHGEF7 0.033 0.012 -10000 0 0 58 58
ARF1 0.036 0.008 -10000 0 0 23 23
NRAS 0.035 0.019 -10000 0 -0.033 11 11
FYN 0.031 0.015 -10000 0 0 93 93
ARF6 0.035 0.009 -10000 0 0 31 31
FGR 0.033 0.012 -10000 0 0 58 58
mol:Ca2+ 0.005 0.062 0.15 44 -0.12 17 61
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.034 0.011 -10000 0 0 44 44
ZAP70 0.037 0.003 -10000 0 0 4 4
mol:IP3 -0.008 0.066 0.18 26 -0.16 22 48
LYN 0.032 0.013 -10000 0 0 72 72
ARF1/GDP 0.01 0.11 0.24 1 -0.35 34 35
RhoA/GDP 0.028 0.091 0.2 16 -0.21 32 48
PDK1/Src/Hsp90 0.066 0.028 -10000 0 -0.12 2 2
BLNK 0.021 0.019 -10000 0 0 226 226
actin cytoskeleton reorganization 0.009 0.11 0.22 29 -0.29 27 56
SRC 0.035 0.009 -10000 0 0 31 31
PLEKHA2 -0.017 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.017 -10000 0 0 156 156
PTEN 0.027 0.022 -10000 0 -0.037 13 13
HSP90AA1 0.035 0.01 -10000 0 0 35 35
ARF6/GTP -0.027 0.056 0.18 15 -0.2 10 25
RhoA/GTP -0.028 0.058 0.19 15 -0.2 11 26
Src family/SYK family/BLNK-LAT -0.046 0.15 -10000 0 -0.34 81 81
BLK 0.037 0.007 -10000 0 0 16 16
PDPK1 0.037 0.004 -10000 0 0 6 6
CYTH1 -0.025 0.05 0.17 13 -0.18 10 23
HCK 0.027 0.017 -10000 0 0 145 145
CYTH3 -0.025 0.05 0.17 13 -0.18 10 23
CYTH2 -0.025 0.05 0.17 13 -0.18 10 23
KRAS 0.035 0.021 0.086 1 -0.033 30 31
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.043 0.24 2 -0.2 12 14
SGK1 0 0.04 -10000 0 -0.19 13 13
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.11 0.22 3 -0.35 35 38
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.032 0.013 -10000 0 0 76 76
ARF6/GDP -0.027 0.067 0.2 12 -0.22 24 36
mol:PI-3-4-5-P3 -0.026 0.051 0.17 12 -0.19 10 22
ARAP3/RAP1A/GTP -0.026 0.049 0.16 13 -0.19 10 23
VAV1 0.036 0.008 -10000 0 0 26 26
mol:PI-3-4-P2 -0.012 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.063 0.093 0.21 108 -0.14 41 149
PLEKHA1 -0.012 0.009 -10000 0 -10000 0 0
Rac1/GDP 0 0.1 0.24 1 -0.32 33 34
LAT 0.037 0.005 -10000 0 0 9 9
Rac1/GTP -0.006 0.15 0.16 1 -0.44 39 40
ITK -0.028 0.051 0.16 14 -0.19 10 24
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.02 0.11 0.24 13 -0.27 51 64
LCK 0.036 0.008 -10000 0 0 21 21
BTK -0.027 0.054 0.16 16 -0.19 10 26
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.067 0.065 -10000 0 -0.12 12 12
SMAD6-7/SMURF1 0.047 0.039 -10000 0 -0.12 3 3
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.024 0.16 -10000 0 -0.47 52 52
SMAD4 0.033 0.012 -10000 0 0 58 58
SMAD5 -0.024 0.097 -10000 0 -0.31 42 42
BMP7/USAG1 0.034 0.027 -10000 0 -10000 0 0
SMAD5/SKI -0.019 0.11 -10000 0 -0.31 47 47
SMAD1 -0.029 0.15 -10000 0 -0.42 44 44
BMP2 0.028 0.016 -10000 0 0 128 128
SMAD1/SMAD1/SMAD4 -0.01 0.13 -10000 0 -0.4 36 36
BMPR1A 0.027 0.017 -10000 0 0 149 149
BMPR1B 0.037 0.006 -10000 0 0 12 12
BMPR1A-1B/BAMBI 0.022 0.063 -10000 0 -0.12 56 56
AHSG 0.036 0.007 -10000 0 0 19 19
CER1 0.033 0.012 -10000 0 0 60 60
BMP2-4/CER1 0.04 0.056 -10000 0 -0.12 35 35
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.01 0.079 -10000 0 -0.24 32 32
BMP2-4 (homodimer) 0.029 0.051 -10000 0 -0.14 35 35
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.059 0.058 -10000 0 -0.12 12 12
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.026 0.017 -10000 0 0 157 157
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.017 0.067 -10000 0 -0.17 60 60
BMP2-4/USAG1 0.033 0.047 -10000 0 -0.12 17 17
SMAD6/SMURF1/SMAD5 -0.012 0.098 -10000 0 -0.3 40 40
SOSTDC1 0.025 0.018 -10000 0 0 177 177
BMP7/BMPR2/BMPR1A-1B 0.059 0.058 -10000 0 -0.12 14 14
SKI 0.036 0.008 -10000 0 0 27 27
BMP6 (homodimer) 0.036 0.009 -10000 0 0 28 28
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.035 0.01 -10000 0 0 38 38
MAP3K7 0.034 0.011 -10000 0 0 45 45
BMP2-4/CHRD 0.042 0.055 -10000 0 -0.12 34 34
SMAD5/SMAD5/SMAD4 -0.022 0.11 -10000 0 -0.31 51 51
MAPK1 0.034 0.011 -10000 0 0 47 47
TAK1/TAB family 0.008 0.065 -10000 0 -0.18 26 26
BMP7 (homodimer) 0.034 0.011 -10000 0 0 47 47
NUP214 0.036 0.008 -10000 0 0 22 22
BMP6/FETUA 0.051 0.016 -10000 0 -10000 0 0
SMAD1/SKI -0.013 0.15 -10000 0 -0.41 44 44
SMAD6 0.037 0.005 -10000 0 0 10 10
CTDSP2 0.032 0.014 -10000 0 0 81 81
BMP2-4/FETUA 0.042 0.056 -10000 0 -0.12 35 35
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.033 0.013 -10000 0 0 66 66
BMPR2 (homodimer) 0.037 0.005 -10000 0 0 11 11
GADD34/PP1CA 0.053 0.053 -10000 0 -0.13 31 31
BMPR1A-1B (homodimer) 0.037 0.032 -10000 0 -0.14 6 6
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.015 0.16 0.3 1 -0.41 47 48
SMAD6-7/SMURF1/SMAD1 0.004 0.14 -10000 0 -0.46 27 27
SMAD6/SMURF1 0.026 0.017 -10000 0 0 157 157
BAMBI 0.02 0.019 -10000 0 0 242 242
SMURF2 0.036 0.007 -10000 0 0 19 19
BMP2-4/CHRDL1 0.027 0.044 -10000 0 -0.11 35 35
BMP2-4/GREM1 0.037 0.055 -10000 0 -0.12 34 34
SMAD7 0.035 0.01 -10000 0 0 43 43
SMAD8A/SMAD8A/SMAD4 -0.014 0.16 -10000 0 -0.44 61 61
SMAD1/SMAD6 -0.014 0.14 -10000 0 -0.42 37 37
TAK1/SMAD6 0.034 0.036 -10000 0 -0.14 10 10
BMP7 0.034 0.011 -10000 0 0 47 47
BMP6 0.036 0.009 -10000 0 0 28 28
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.001 0.055 -10000 0 -0.22 17 17
PPM1A 0.035 0.01 -10000 0 0 35 35
SMAD1/SMURF2 -0.013 0.16 0.3 1 -0.41 46 47
SMAD7/SMURF1 0.034 0.03 -10000 0 -0.14 3 3
CTDSPL 0.037 0.006 -10000 0 0 14 14
PPP1CA 0.036 0.008 -10000 0 0 22 22
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.037 0.007 -10000 0 0 16 16
PPP1R15A 0.034 0.011 -10000 0 0 51 51
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.011 0.069 -10000 0 -0.21 30 30
CHRD 0.036 0.007 -10000 0 0 19 19
BMPR2 0.037 0.005 -10000 0 0 11 11
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.016 0.069 -10000 0 -0.17 56 56
BMP4 0.034 0.012 -10000 0 0 54 54
FST 0.034 0.011 -10000 0 0 50 50
BMP2-4/NOG 0.027 0.044 -10000 0 -0.11 35 35
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.057 0.063 -10000 0 -0.11 10 10
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.021 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.049 0.033 -10000 0 -0.12 10 10
CDKN1B -0.026 0.13 0.2 6 -0.34 62 68
CDKN1A -0.026 0.13 -10000 0 -0.34 63 63
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.035 0.01 -10000 0 0 42 42
FOXO3 -0.021 0.12 0.2 4 -0.36 54 58
AKT1 -0.02 0.13 -10000 0 -0.34 63 63
BAD 0.037 0.007 -10000 0 0 16 16
AKT3 0.015 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.028 0.12 -10000 0 -0.33 66 66
AKT1/ASK1 -0.011 0.13 -10000 0 -0.33 67 67
BAD/YWHAZ 0.066 0.037 -10000 0 -0.13 12 12
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.036 0.008 -10000 0 0 27 27
JNK cascade 0.011 0.13 0.32 67 -10000 0 67
TSC1 -0.029 0.13 0.2 1 -0.35 64 65
YWHAZ 0.036 0.008 -10000 0 0 21 21
AKT1/RAF1 -0.004 0.14 -10000 0 -0.35 68 68
EP300 0.034 0.011 -10000 0 0 49 49
mol:GDP -0.02 0.13 -10000 0 -0.34 63 63
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.03 0.13 -10000 0 -0.34 67 67
YWHAQ 0.037 0.005 -10000 0 0 8 8
TBC1D4 -0.001 0.025 0.14 14 -10000 0 14
MAP3K5 0.031 0.014 -10000 0 0 91 91
MAPKAP1 0.035 0.009 -10000 0 0 32 32
negative regulation of cell cycle 0.006 0.11 0.34 28 -0.17 1 29
YWHAH 0.032 0.013 -10000 0 0 73 73
AKT1S1 -0.023 0.12 -10000 0 -0.32 68 68
CASP9 -0.023 0.12 -10000 0 -0.34 62 62
YWHAB 0.034 0.011 -10000 0 0 44 44
p27Kip1/KPNA1 -0.009 0.14 0.29 4 -0.33 66 70
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.066 0.028 -10000 0 -0.12 2 2
YWHAE 0.036 0.009 -10000 0 0 29 29
SRC 0.035 0.009 -10000 0 0 31 31
AKT2/p21CIP1 -0.027 0.12 0.24 1 -0.3 64 65
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0 0.039 -10000 0 -10000 0 0
CHUK -0.021 0.11 -10000 0 -0.34 48 48
BAD/BCL-XL -0.002 0.13 -10000 0 -0.33 65 65
mTORC2 0.022 0.014 -10000 0 -0.093 6 6
AKT2 0.015 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.017 0.14 -10000 0 -0.44 32 32
PDPK1 0.037 0.004 -10000 0 0 6 6
MDM2 -0.011 0.13 0.2 35 -0.33 59 94
MAPKKK cascade 0.004 0.14 0.34 68 -10000 0 68
MDM2/Cbp/p300 0.021 0.14 0.27 4 -0.32 60 64
TSC1/TSC2 -0.033 0.13 0.24 10 -0.35 66 76
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.14 0.26 4 -0.31 60 64
glucose import -0.008 0.024 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.001 0.076 -10000 0 -0.19 63 63
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.024 0.2 4 -10000 0 4
GSK3A -0.024 0.12 0.2 4 -0.33 60 64
FOXO1 -0.023 0.13 -10000 0 -0.35 57 57
GSK3B -0.029 0.13 0.2 3 -0.35 66 69
SFN 0.032 0.014 -10000 0 0 80 80
G1/S transition of mitotic cell cycle -0.031 0.14 0.26 9 -0.35 65 74
p27Kip1/14-3-3 family 0.008 0.11 -10000 0 -0.51 14 14
PRKACA 0.036 0.007 -10000 0 0 17 17
KPNA1 0.036 0.008 -10000 0 0 23 23
HSP90AA1 0.035 0.01 -10000 0 0 35 35
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.026 0.017 -10000 0 0 159 159
CREBBP 0.037 0.004 -10000 0 0 7 7
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.036 0.009 -9999 0 0 29 29
Rac1/GDP 0.027 0.02 -9999 0 -0.025 7 7
DOCK1 0.026 0.017 -9999 0 0 159 159
ITGA4 0.037 0.006 -9999 0 0 13 13
RAC1 0.026 0.017 -9999 0 0 156 156
alpha4/beta7 Integrin 0.053 0.012 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.036 0.008 -9999 0 0 25 25
alpha4/beta1 Integrin 0.057 0.033 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.054 0.016 -9999 0 -10000 0 0
lamellipodium assembly -0.044 0.14 -9999 0 -0.36 74 74
PIK3CA 0.032 0.013 -9999 0 0 74 74
PI3K 0.02 0.075 -9999 0 -0.15 75 75
ARF6 0.035 0.009 -9999 0 0 31 31
TLN1 0.03 0.015 -9999 0 0 104 104
PXN -0.022 0.005 -9999 0 -10000 0 0
PIK3R1 0.033 0.013 -9999 0 0 67 67
ARF6/GTP 0.053 0.048 -9999 0 -0.11 1 1
cell adhesion 0.046 0.05 -9999 0 -0.12 12 12
CRKL/CBL 0.052 0.014 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.043 0.026 -9999 0 -10000 0 0
ITGB1 0.029 0.016 -9999 0 0 117 117
ITGB7 0.037 0.006 -9999 0 0 14 14
ARF6/GDP 0.036 0.015 -9999 0 -0.026 10 10
alpha4/beta1 Integrin/Paxillin/VCAM1 0.012 0.08 -9999 0 -0.11 119 119
p130Cas/Crk/Dock1 0.03 0.036 -9999 0 -0.11 18 18
VCAM1 0.023 0.018 -9999 0 0 196 196
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.051 -9999 0 -0.12 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.046 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.055 0.045 -9999 0 -10000 0 0
CBL 0.037 0.005 -9999 0 0 9 9
PRKACA 0.036 0.007 -9999 0 0 17 17
GIT1 0.037 0.004 -9999 0 0 7 7
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.051 -9999 0 -0.12 12 12
Rac1/GTP -0.05 0.16 -9999 0 -0.4 74 74
Signaling events mediated by PRL

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
CCNE1 0.033 0.012 -10000 0 0 60 60
mol:Halofuginone -0.002 0.03 -10000 0 -0.17 15 15
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.025 0.15 -10000 0 -0.4 59 59
PRL-3/alpha Tubulin 0.041 0.042 -10000 0 -0.14 22 22
mol:Ca2+ -0.018 0.044 0.26 11 -10000 0 11
AGT 0.03 0.015 -10000 0 0 106 106
CCNA2 -0.026 0.11 0.18 22 -0.58 14 36
TUBA1B 0.037 0.007 -10000 0 0 16 16
EGR1 0.002 0.058 0.11 4 -0.34 14 18
CDK2/Cyclin E1 -0.003 0.15 -10000 0 -0.36 59 59
MAPK3 -0.02 0.009 0 78 -10000 0 78
PRL-2 /Rab GGTase beta 0.048 0.035 -10000 0 -0.16 12 12
MAPK1 -0.018 0.01 0 116 -10000 0 116
PTP4A1 -0.023 0.1 -10000 0 -0.6 14 14
PTP4A3 0.032 0.013 -10000 0 0 74 74
PTP4A2 0.036 0.007 -10000 0 0 20 20
ITGB1 -0.015 0.011 0 175 -10000 0 175
SRC 0.035 0.009 -10000 0 0 31 31
RAC1 0 0.085 -10000 0 -0.38 20 20
Rab GGTase beta/Rab GGTase alpha 0.046 0.032 -10000 0 -0.14 11 11
PRL-1/ATF-5 -0.029 0.11 0.33 1 -0.54 15 16
RABGGTA 0.035 0.01 -10000 0 0 40 40
BCAR1 -0.009 0.054 0.25 21 -10000 0 21
RHOC -0.003 0.11 -10000 0 -0.39 34 34
RHOA -0.006 0.13 -10000 0 -0.43 34 34
cell motility -0.002 0.12 0.26 1 -0.4 30 31
PRL-1/alpha Tubulin -0.028 0.11 0.2 24 -0.55 15 39
PRL-3/alpha1 Integrin 0.018 0.032 -10000 0 -0.13 21 21
ROCK1 -0.001 0.12 0.26 1 -0.36 38 39
RABGGTB 0.036 0.008 -10000 0 0 25 25
CDK2 0.035 0.01 -10000 0 0 43 43
mitosis -0.023 0.099 -10000 0 -0.59 14 14
ATF5 0.035 0.009 -10000 0 0 31 31
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.038 -10000 0 -10000 0 0
CRKL 0.036 0.009 -10000 0 0 29 29
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
DOCK1 0.026 0.017 -10000 0 0 159 159
ITGA4 0.037 0.006 -10000 0 0 13 13
alpha4/beta7 Integrin/MAdCAM1 0.085 0.037 -10000 0 -0.12 6 6
EPO 0.026 0.017 -10000 0 0 157 157
alpha4/beta7 Integrin 0.053 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.036 0.008 -10000 0 0 25 25
alpha4/beta1 Integrin 0.042 0.024 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.038 0.026 -10000 0 -10000 0 0
lamellipodium assembly -0.018 0.11 -10000 0 -0.39 23 23
PIK3CA 0.032 0.013 -10000 0 0 74 74
PI3K 0.02 0.075 -10000 0 -0.15 75 75
ARF6 0.035 0.009 -10000 0 0 31 31
JAK2 0.012 0.027 -10000 0 -10000 0 0
PXN 0.037 0.005 -10000 0 0 9 9
PIK3R1 0.033 0.013 -10000 0 0 67 67
MADCAM1 0.036 0.008 -10000 0 0 25 25
cell adhesion 0.082 0.036 -10000 0 -0.12 6 6
CRKL/CBL 0.052 0.014 -10000 0 -10000 0 0
ITGB1 0.029 0.016 -10000 0 0 117 117
SRC -0.034 0.059 0.2 4 -10000 0 4
ITGB7 0.037 0.006 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
alpha4/beta1 Integrin/VCAM1 0.006 0.079 -10000 0 -0.12 125 125
p130Cas/Crk/Dock1 -0.033 0.064 0.21 4 -0.19 8 12
VCAM1 0.023 0.018 -10000 0 0 196 196
RHOA 0.036 0.007 -10000 0 0 20 20
alpha4/beta1 Integrin/Paxillin/GIT1 0.069 0.049 -10000 0 -10000 0 0
BCAR1 -0.031 0.059 0.27 5 -10000 0 5
EPOR 0.036 0.007 -10000 0 0 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.037 0.005 -10000 0 0 9 9
GIT1 0.037 0.004 -10000 0 0 7 7
Rac1/GTP -0.018 0.11 -10000 0 -0.4 23 23
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.036 0.009 -10000 0 0 29 29
SPHK1 0.034 0.011 -10000 0 0 49 49
GNAI2 0.034 0.011 -10000 0 0 46 46
mol:S1P 0.018 0.014 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
mol:Sphinganine-1-P -0.02 0.008 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.045 -10000 0 -0.17 2 2
GNAI3 0.037 0.007 -10000 0 0 16 16
G12/G13 0.027 0.048 -10000 0 -0.14 29 29
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.02 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 0 255 255
S1P/S1P5/G12 0.018 0.036 -10000 0 -0.18 2 2
S1P/S1P3/Gq 0.027 0.043 0.17 9 -0.24 8 17
S1P/S1P4/Gi -0.007 0.1 0.15 2 -0.28 44 46
GNAQ 0.035 0.01 -10000 0 0 35 35
GNAZ 0.032 0.014 -10000 0 0 81 81
GNA14 0.035 0.009 -10000 0 0 34 34
GNA15 0.034 0.011 -10000 0 0 45 45
GNA12 0.024 0.018 -10000 0 0 180 180
GNA13 0.036 0.008 -10000 0 0 21 21
GNA11 0.034 0.011 -10000 0 0 46 46
ABCC1 0.036 0.007 -10000 0 0 19 19
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.002 0.01 -10000 0 -0.035 23 23
BUB1B -0.012 0.082 0.11 22 -0.21 59 81
PLK1 0.009 0.028 0.093 21 -0.07 4 25
PLK1S1 0.004 0.016 0.055 22 -0.039 3 25
KIF2A -0.005 0.044 0.17 10 -0.12 16 26
regulation of mitotic centrosome separation 0.009 0.028 0.093 21 -0.07 4 25
GOLGA2 0.036 0.009 -10000 0 0 28 28
Hec1/SPC24 0.015 0.042 0.11 4 -0.099 43 47
WEE1 -0.017 0.13 -10000 0 -0.43 39 39
cytokinesis -0.018 0.12 0.16 13 -0.3 61 74
PP2A-alpha B56 0.062 0.08 -10000 0 -0.5 7 7
AURKA 0.006 0.037 0.11 2 -0.2 13 15
PICH/PLK1 -0.028 0.068 0.12 12 -0.15 89 101
CENPE 0.007 0.05 0.15 33 -0.13 4 37
RhoA/GTP 0.025 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization -0.005 0.044 0.17 10 -0.12 16 26
PPP2CA 0.036 0.008 -10000 0 0 22 22
FZR1 0.036 0.007 -10000 0 0 18 18
TPX2 -0.022 0.09 0.11 4 -0.22 84 88
PAK1 0.037 0.007 -10000 0 0 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.036 0.008 -10000 0 0 24 24
CLSPN 0.012 0.031 0.12 1 -0.21 7 8
GORASP1 0.035 0.009 -10000 0 0 34 34
metaphase 0.001 0.003 0.016 8 -0.011 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.016 0.055 22 -0.039 3 25
G2 phase of mitotic cell cycle -0.001 0.003 0.014 2 -0.011 1 3
STAG2 0.036 0.008 -10000 0 0 23 23
GRASP65/GM130/RAB1/GTP -0.015 0.15 -10000 0 -0.6 27 27
spindle elongation 0.009 0.028 0.093 21 -0.07 4 25
ODF2 0.036 0.009 -10000 0 0 29 29
BUB1 0.029 0.067 -10000 0 -0.55 6 6
TPT1 -0.001 0.053 0.097 1 -0.18 38 39
CDC25C 0.015 0.03 -10000 0 -0.22 6 6
CDC25B 0.025 0.026 -10000 0 -0.03 72 72
SGOL1 0.002 0.01 0.035 23 -10000 0 23
RHOA 0.036 0.007 -10000 0 0 20 20
CCNB1/CDK1 0 0.1 -10000 0 -0.21 90 90
CDC14B -0.011 0.005 0.01 17 -10000 0 17
CDC20 0.028 0.016 -10000 0 0 129 129
PLK1/PBIP1 -0.008 0.039 0.084 8 -0.09 75 83
mitosis -0.002 0.006 0.029 15 -10000 0 15
FBXO5 -0.009 0.06 0.11 24 -0.16 48 72
CDC2 0 0.005 -10000 0 -0.012 69 69
NDC80 0.03 0.015 -10000 0 0 98 98
metaphase plate congression 0.005 0.06 -10000 0 -0.26 23 23
ERCC6L -0.019 0.091 0.15 1 -0.2 90 91
NLP/gamma Tubulin 0.003 0.028 0.074 14 -0.099 21 35
microtubule cytoskeleton organization -0.001 0.052 0.097 1 -0.18 38 39
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 4 -10000 0 4
PPP1R12A 0.036 0.008 -10000 0 0 26 26
interphase -0.001 0.002 0.012 4 -10000 0 4
PLK1/PRC1-2 0.012 0.078 0.15 2 -0.14 90 92
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.054 -10000 0 -0.12 29 29
RAB1A 0.036 0.007 -10000 0 0 18 18
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.027 0.075 40 -0.064 10 50
mitotic prometaphase 0 0.005 0.021 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.097 0.17 2 -0.22 76 78
microtubule-based process 0.024 0.027 0.11 7 -0.066 2 9
Golgi organization 0.009 0.028 0.093 21 -0.07 4 25
Cohesin/SA2 0.024 0.033 0.1 5 -0.095 18 23
PPP1CB/MYPT1 0.048 0.036 -10000 0 -0.15 15 15
KIF20A 0.029 0.016 -10000 0 0 111 111
APC/C/CDC20 0.024 0.026 0.11 5 -0.066 1 6
PPP2R1A 0.034 0.012 -10000 0 0 56 56
chromosome segregation -0.008 0.039 0.083 8 -0.089 75 83
PRC1 0.029 0.016 -10000 0 0 124 124
ECT2 0.004 0.06 0.15 41 -0.12 17 58
C13orf34 0.007 0.024 0.07 36 -0.058 3 39
NUDC 0.005 0.06 -10000 0 -0.26 23 23
regulation of attachment of spindle microtubules to kinetochore -0.012 0.082 0.11 22 -0.21 59 81
spindle assembly 0.005 0.028 0.086 22 -0.076 14 36
spindle stabilization 0.004 0.016 0.055 22 -0.039 3 25
APC/C/HCDH1 0.025 0.027 0.084 1 -0.12 16 17
MKLP2/PLK1 0.024 0.027 0.11 7 -0.066 2 9
CCNB1 0.028 0.02 -10000 0 -0.031 15 15
PPP1CB 0.037 0.006 -10000 0 0 13 13
BTRC 0.028 0.016 -10000 0 0 130 130
ROCK2 0.019 0.031 -10000 0 -0.21 3 3
TUBG1 0.004 0.051 -10000 0 -0.22 23 23
G2/M transition of mitotic cell cycle -0.027 0.087 0.1 1 -0.2 90 91
MLF1IP -0.008 0.006 0.011 6 -10000 0 6
INCENP 0.037 0.005 -10000 0 0 8 8
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.001 0.078 -10000 0 -0.14 105 105
alphaV beta3 Integrin 0.061 0.048 -10000 0 -0.13 26 26
PTK2 -0.028 0.13 0.26 7 -0.35 33 40
IGF1R 0.034 0.011 -10000 0 0 51 51
PI4KB 0.037 0.006 -10000 0 0 13 13
MFGE8 0.037 0.006 -10000 0 0 15 15
SRC 0.035 0.009 -10000 0 0 31 31
CDKN1B 0 0.094 -10000 0 -0.31 40 40
VEGFA 0.024 0.018 -10000 0 0 181 181
ILK 0.013 0.07 -10000 0 -0.3 22 22
ROCK1 0.037 0.007 -10000 0 0 16 16
AKT1 -0.003 0.068 0.2 1 -0.31 21 22
PTK2B -0.015 0.092 0.18 45 -0.2 15 60
alphaV/beta3 Integrin/JAM-A 0.071 0.047 -10000 0 -0.11 20 20
CBL 0.037 0.005 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.063 0.044 -10000 0 -0.12 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.071 0.067 -10000 0 -0.13 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.1 -10000 0 -0.31 28 28
alphaV/beta3 Integrin/Syndecan-1 0.056 0.044 -10000 0 -0.12 16 16
PI4KA 0.033 0.013 -10000 0 0 68 68
IGF-1R heterotetramer/IGF1/IRS1 0.05 0.083 -10000 0 -0.14 67 67
PI4 Kinase 0.038 0.051 -10000 0 -0.14 34 34
PIK3CA 0.032 0.013 -10000 0 0 74 74
alphaV/beta3 Integrin/Osteopontin 0.049 0.07 -10000 0 -0.14 56 56
RPS6KB1 -0.042 0.075 0.32 6 -0.21 18 24
TLN1 0.03 0.015 -10000 0 0 104 104
MAPK3 0.002 0.086 -10000 0 -0.33 27 27
GPR124 0.036 0.008 -10000 0 0 22 22
MAPK1 -0.001 0.085 -10000 0 -0.34 24 24
PXN 0.037 0.005 -10000 0 0 9 9
PIK3R1 0.033 0.013 -10000 0 0 67 67
alphaV/beta3 Integrin/Tumstatin 0.065 0.044 -10000 0 -0.12 24 24
cell adhesion 0.048 0.054 -10000 0 -0.16 26 26
ANGPTL3 0.037 0.006 -10000 0 0 12 12
VEGFR2 homodimer/VEGFA homodimer/Src 0.012 0.077 -10000 0 -0.13 101 101
IGF-1R heterotetramer 0.034 0.011 -10000 0 0 51 51
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
TGFBR2 0.035 0.009 -10000 0 0 30 30
ITGB3 0.037 0.004 -10000 0 0 6 6
IGF1 0.036 0.008 -10000 0 0 25 25
RAC1 0.026 0.017 -10000 0 0 156 156
regulation of cell-matrix adhesion 0.061 0.045 -10000 0 -0.12 24 24
apoptosis 0.035 0.009 -10000 0 0 34 34
CD47 0.036 0.008 -10000 0 0 26 26
alphaV/beta3 Integrin/CD47 0.061 0.048 -10000 0 -0.13 26 26
VCL 0.028 0.016 -10000 0 0 128 128
alphaV/beta3 Integrin/Del1 0.064 0.043 -10000 0 -0.12 23 23
CSF1 0.037 0.005 -10000 0 0 9 9
PIK3C2A 0.01 0.018 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.006 0.093 -10000 0 -0.22 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.031 0.092 -10000 0 -0.13 113 113
FAK1/Vinculin -0.02 0.12 0.27 5 -0.32 26 31
alphaV beta3/Integrin/ppsTEM5 0.062 0.045 -10000 0 -0.12 24 24
RHOA 0.036 0.007 -10000 0 0 20 20
VTN 0.037 0.004 -10000 0 0 7 7
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.036 0.008 -10000 0 0 25 25
F11R -0.02 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.063 0.046 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.06 0.048 -10000 0 -0.12 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.061 0.041 -10000 0 -0.11 24 24
HSP90AA1 0.035 0.01 -10000 0 0 35 35
alphaV/beta3 Integrin/Talin 0.047 0.051 -10000 0 -0.12 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.009 -10000 0 0 31 31
alphaV/beta3 Integrin/Pyk2 0.035 0.098 0.2 37 -0.13 112 149
SDC1 0.032 0.014 -10000 0 0 82 82
VAV3 -0.027 0.028 0.18 1 -0.18 5 6
PTPN11 0.037 0.006 -10000 0 0 12 12
IRS1 0.034 0.011 -10000 0 0 52 52
FAK1/Paxillin -0.009 0.12 0.25 7 -0.32 26 33
cell migration -0.027 0.1 0.25 5 -0.29 26 31
ITGAV 0.035 0.009 -10000 0 0 34 34
PI3K 0.056 0.085 -10000 0 -0.2 14 14
SPP1 0.034 0.012 -10000 0 0 54 54
KDR 0.031 0.014 -10000 0 0 90 90
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.035 0.009 -10000 0 0 34 34
COL4A3 0.038 0.002 -10000 0 0 1 1
angiogenesis -0.001 0.094 -10000 0 -0.37 25 25
Rac1/GTP -0.027 0.033 -10000 0 -0.18 6 6
EDIL3 0.037 0.005 -10000 0 0 8 8
cell proliferation 0.06 0.047 -10000 0 -0.12 27 27
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.05 0.04 -10000 0 -0.098 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.047 0.18 -10000 0 -0.47 54 54
AKT1 -0.053 0.23 -10000 0 -0.63 60 60
PIK3CA 0.032 0.013 -10000 0 0 74 74
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.047 0.24 -10000 0 -0.65 59 59
mol:Ca2+ 0.007 0.051 0.17 19 -0.21 3 22
IGF1R 0.034 0.011 -10000 0 0 51 51
E2/ER alpha (dimer)/Striatin 0.048 0.013 -10000 0 -10000 0 0
SHC1 0.034 0.012 -10000 0 0 53 53
apoptosis 0.053 0.22 0.6 61 -10000 0 61
RhoA/GTP -0.044 0.036 -10000 0 -0.13 51 51
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.15 -10000 0 -0.39 51 51
regulation of stress fiber formation 0.039 0.059 0.18 22 -0.14 27 49
E2/ERA-ERB (dimer) 0.046 0.016 -10000 0 -10000 0 0
KRAS 0.035 0.009 -10000 0 0 34 34
G13/GTP 0.044 0.014 -10000 0 -10000 0 0
pseudopodium formation -0.039 0.059 0.14 27 -0.18 22 49
E2/ER alpha (dimer)/PELP1 0.045 0.023 -10000 0 -0.11 7 7
GRB2 0.036 0.007 -10000 0 0 19 19
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
HRAS 0.035 0.01 -10000 0 0 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.019 0.17 0.28 2 -0.44 49 51
E2/ER beta (dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.004 0.059 -10000 0 -0.19 24 24
mol:NADP -0.019 0.17 0.28 2 -0.44 49 51
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:IP3 0.007 0.051 0.18 19 -0.22 3 22
IGF-1R heterotetramer 0.034 0.011 -10000 0 0 51 51
PLCB1 0.01 0.037 -10000 0 -0.2 1 1
PLCB2 0.009 0.037 -10000 0 -0.2 1 1
IGF1 0.036 0.008 -10000 0 0 25 25
mol:L-citrulline -0.019 0.17 0.28 2 -0.44 49 51
RHOA 0.036 0.007 -10000 0 0 20 20
Gai/GDP -0.069 0.24 -10000 0 -0.64 71 71
JNK cascade 0.026 0.007 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.035 0.009 -10000 0 0 34 34
GNAQ 0.035 0.01 -10000 0 0 35 35
ESR1 0.035 0.009 -10000 0 0 32 32
Gq family/GDP/Gbeta gamma -0.01 0.15 -10000 0 -0.46 39 39
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.14 -10000 0 -0.69 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.003 0.16 0.26 9 -0.39 49 58
GNAZ 0.032 0.014 -10000 0 0 81 81
E2/ER alpha (dimer) 0.026 0.007 -10000 0 -10000 0 0
STRN 0.038 0.002 -10000 0 0 2 2
GNAL 0.036 0.007 -10000 0 0 17 17
PELP1 0.036 0.007 -10000 0 0 19 19
MAPK11 -0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.034 0.011 -10000 0 0 46 46
GNAI3 0.037 0.007 -10000 0 0 16 16
GNAI1 0.019 0.019 -10000 0 0 255 255
HBEGF -0.02 0.19 0.34 25 -0.44 52 77
cAMP biosynthetic process 0.038 0.017 -10000 0 -10000 0 0
SRC -0.049 0.17 0.21 6 -0.44 56 62
PI3K 0.02 0.075 -10000 0 -0.15 75 75
GNB1 0.034 0.011 -10000 0 0 47 47
G13/GDP/Gbeta gamma 0.02 0.068 -10000 0 -0.18 29 29
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.12 -10000 0 -0.33 48 48
Gs family/GTP 0.048 0.021 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.065 -10000 0 -0.13 54 54
vasodilation -0.017 0.16 0.28 2 -0.42 49 51
mol:DAG 0.007 0.051 0.18 19 -0.22 3 22
Gs family/GDP/Gbeta gamma 0.002 0.061 -10000 0 -0.18 29 29
MSN -0.039 0.061 0.14 27 -0.19 22 49
Gq family/GTP 0.024 0.04 -10000 0 -0.21 1 1
mol:PI-3-4-5-P3 -0.045 0.23 -10000 0 -0.62 59 59
NRAS 0.033 0.013 -10000 0 0 66 66
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.16 0.42 49 -0.28 2 51
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
RhoA/GDP 0.019 0.069 -10000 0 -0.19 26 26
NOS3 -0.022 0.18 0.29 2 -0.47 49 51
GNA11 0.034 0.011 -10000 0 0 46 46
MAPKKK cascade -0.001 0.16 0.31 1 -0.48 38 39
E2/ER alpha (dimer)/PELP1/Src -0.007 0.17 0.25 15 -0.4 51 66
ruffle organization -0.039 0.059 0.14 27 -0.18 22 49
ROCK2 -0.034 0.065 0.17 30 -0.19 13 43
GNA14 0.035 0.009 -10000 0 0 34 34
GNA15 0.034 0.011 -10000 0 0 45 45
GNA13 0.036 0.008 -10000 0 0 21 21
MMP9 -0.034 0.18 0.35 6 -0.41 61 67
MMP2 -0.032 0.18 0.25 12 -0.44 54 66
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.016 0.035 -10000 0 -0.095 41 41
TRAF2/ASK1 0.032 0.044 -10000 0 -0.11 36 36
ATM 0.035 0.01 -10000 0 0 38 38
MAP2K3 0.018 0.083 0.22 4 -0.28 17 21
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.014 0.086 0.23 6 -0.26 22 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.033 0.013 -10000 0 0 68 68
TXN 0.007 0.002 -10000 0 0 41 41
CALM1 0.033 0.012 -10000 0 0 60 60
GADD45A 0.032 0.014 -10000 0 0 79 79
GADD45B 0.032 0.014 -10000 0 0 79 79
MAP3K1 0.036 0.008 -10000 0 0 23 23
MAP3K6 0.036 0.008 -10000 0 0 24 24
MAP3K7 0.034 0.011 -10000 0 0 45 45
MAP3K4 0.033 0.013 -10000 0 0 66 66
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.034 0.052 -10000 0 -0.14 37 37
TAK1/TAB family -0.003 0.029 0.067 36 -0.14 13 49
RAC1/OSM/MEKK3 0.032 0.026 -10000 0 -0.1 5 5
TRAF2 0.036 0.007 -10000 0 0 19 19
RAC1/OSM/MEKK3/MKK3 0.012 0.066 -10000 0 -0.23 17 17
TRAF6 0.008 0.001 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.018 0.019 -10000 0 0 262 262
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.009 0.056 -10000 0 -0.13 57 57
MAPK11 0.034 0.011 -10000 0 0 49 49
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.011 0.069 -10000 0 -0.13 70 70
OSM/MEKK3 0.028 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 38 38
TAOK2 0.012 0.023 -10000 0 -0.2 6 6
TAOK3 0.007 0.041 -10000 0 -0.2 19 19
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.037 0.005 -10000 0 0 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.031 0.014 -10000 0 0 91 91
MAP3K10 0.036 0.007 -10000 0 0 19 19
MAP3K3 0.037 0.004 -10000 0 0 6 6
TRX/ASK1 0.023 0.034 -10000 0 -0.17 12 12
GADD45/MTK1/MTK1 0.043 0.076 -10000 0 -0.13 68 68
IL1-mediated signaling events

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
UBC13/UEV1A 0.025 0.019 -10000 0 -0.13 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.033 0.012 -10000 0 0 58 58
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.11 -10000 0 -0.28 58 58
IRAK/TOLLIP 0.03 0.036 0.18 4 -0.12 22 26
IKBKB 0.037 0.003 -10000 0 0 4 4
IKBKG 0.037 0.003 -10000 0 0 4 4
IL1 alpha/IL1R2 0.044 0.023 -10000 0 -10000 0 0
IL1A 0.036 0.008 -10000 0 0 23 23
IL1B -0.015 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.052 0.19 4 -0.13 29 33
IL1R2 0.031 0.014 -10000 0 0 89 89
IL1R1 0.037 0.006 -10000 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.1 -10000 0 -0.3 36 36
TOLLIP 0.035 0.009 -10000 0 0 34 34
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.037 0.004 -10000 0 0 6 6
TAK1/TAB1/TAB2 0.02 0.022 -10000 0 -0.1 14 14
IKK complex/ELKS -0.038 0.12 -10000 0 -0.3 38 38
JUN -0.032 0.034 0.14 4 -0.18 5 9
MAP3K7 0.034 0.011 -10000 0 0 45 45
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.029 0.11 -10000 0 -0.14 107 107
IL1 alpha/IL1R1/IL1RAP/MYD88 0.066 0.069 -10000 0 -0.12 50 50
PIK3R1 0.033 0.013 -10000 0 0 67 67
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.075 0.075 -10000 0 -0.12 49 49
IL1 beta fragment/IL1R1/IL1RAP 0.024 0.08 -10000 0 -0.14 84 84
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 -0.025 0.029 0.16 5 -0.17 3 8
IRAK1 -0.019 0.01 -10000 0 -0.11 5 5
IL1RN/IL1R1 0.054 0.01 -10000 0 -10000 0 0
IRAK4 0.036 0.008 -10000 0 0 22 22
PRKCI 0.036 0.008 -10000 0 0 25 25
TRAF6 0.037 0.006 -10000 0 0 14 14
PI3K 0.02 0.075 -10000 0 -0.15 75 75
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.11 -10000 0 -0.26 66 66
CHUK 0.027 0.017 -10000 0 0 139 139
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.024 0.08 -10000 0 -0.14 84 84
IL1 beta/IL1R2 0.019 0.071 -10000 0 -0.13 69 69
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.045 0.16 4 -0.11 32 36
NF kappa B1 p50/RelA 0.014 0.098 -10000 0 -0.2 40 40
IRAK3 0.036 0.009 -10000 0 0 29 29
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.039 0.082 -10000 0 -0.13 81 81
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.073 -10000 0 -0.28 14 14
IL1 alpha/IL1R1/IL1RAP 0.051 0.054 -10000 0 -0.12 34 34
RELA 0.037 0.005 -10000 0 0 10 10
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.035 0.01 -10000 0 0 36 36
MYD88 0.035 0.01 -10000 0 0 37 37
IRAK/TRAF6/MEKK3 0.052 0.04 0.19 4 -0.12 22 26
IL1RAP 0.031 0.014 -10000 0 0 86 86
UBE2N 0.037 0.006 -10000 0 0 15 15
IRAK/TRAF6 -0.039 0.062 0.063 70 -0.19 24 94
CASP1 0.03 0.015 -10000 0 0 109 109
IL1RN/IL1R2 0.046 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.038 0.095 -10000 0 -0.14 92 92
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.097 -10000 0 -0.31 35 35
PIK3CA 0.032 0.013 -10000 0 0 74 74
IL1RN 0.037 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.044 0.035 -10000 0 -0.11 19 19
MAP2K6 -0.025 0.032 0.18 8 -0.17 3 11
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.048 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.036 0.007 -10000 0 0 19 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.037 0.004 -10000 0 0 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.036 0.007 -10000 0 0 20 20
RAC1-CDC42/GTP/PAK family 0.001 0.046 -10000 0 -0.14 44 44
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.035 0.01 -10000 0 0 43 43
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.037 0.004 -10000 0 0 6 6
FYN 0.031 0.015 -10000 0 0 93 93
MAP3K12 0.037 0.005 -10000 0 0 11 11
FGR 0.033 0.012 -10000 0 0 58 58
p38 alpha/TAB1 -0.035 0.078 -10000 0 -0.24 48 48
PRKG1 0.028 0.016 -10000 0 0 127 127
DUSP8 0.035 0.01 -10000 0 0 42 42
PGK/cGMP/p38 alpha 0.004 0.1 0.18 2 -0.25 42 44
apoptosis -0.034 0.075 -10000 0 -0.24 48 48
RAL/GTP 0.028 0.038 -10000 0 -0.12 20 20
LYN 0.032 0.013 -10000 0 0 72 72
DUSP1 0.032 0.014 -10000 0 0 78 78
PAK1 0.036 0.007 -10000 0 0 18 18
SRC 0.035 0.009 -10000 0 0 31 31
RAC1/OSM/MEKK3/MKK3 0.048 0.037 -10000 0 -0.11 5 5
TRAF6 0.037 0.006 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
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 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.028 -10000 0 -0.11 5 5
MAPK11 0 0.13 0.23 13 -0.31 45 58
BLK 0.037 0.007 -10000 0 0 16 16
HCK 0.027 0.017 -10000 0 0 145 145
MAP2K3 0.037 0.005 -10000 0 0 11 11
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.034 0.011 -10000 0 0 48 48
TRAF6/MEKK3 0.046 0.011 -10000 0 -0.1 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.11 0.19 15 -0.28 42 57
positive regulation of innate immune response 0.002 0.14 0.24 12 -0.34 47 59
LCK 0.036 0.008 -10000 0 0 21 21
p38alpha-beta/MKP7 0 0.14 0.23 12 -0.33 47 59
p38alpha-beta/MKP5 0.015 0.14 0.25 11 -0.34 42 53
PGK/cGMP 0.021 0.012 -10000 0 -10000 0 0
PAK2 0.035 0.009 -10000 0 0 33 33
p38alpha-beta/MKP1 0.006 0.15 0.26 12 -0.34 49 61
CDC42 0.036 0.008 -10000 0 0 26 26
RALB 0.036 0.007 -10000 0 0 17 17
RALA 0.025 0.018 -10000 0 0 173 173
PAK3 0.027 0.017 -10000 0 0 139 139
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.066 0.28 0.6 14 -0.74 23 37
CRP 0.056 0.27 0.59 10 -0.74 22 32
cell cycle arrest 0.049 0.3 0.54 17 -0.77 33 50
TIMP1 0.003 0.37 0.57 14 -0.79 73 87
IL6ST 0.029 0.034 -10000 0 -0.051 29 29
Rac1/GDP 0.04 0.11 0.3 14 -0.32 11 25
AP1 0.013 0.2 -10000 0 -0.55 38 38
GAB2 0.035 0.013 -10000 0 -0.042 1 1
TNFSF11 0.054 0.26 0.57 9 -0.74 23 32
HSP90B1 -0.002 0.28 -10000 0 -0.95 37 37
GAB1 0.034 0.013 -10000 0 -0.042 1 1
MAPK14 0.026 0.065 -10000 0 -0.27 4 4
AKT1 -0.013 0.17 -10000 0 -0.58 29 29
FOXO1 -0.019 0.17 0.32 1 -0.55 33 34
MAP2K6 0.029 0.071 0.21 2 -0.27 7 9
mol:GTP 0 0.004 -10000 0 -0.022 1 1
MAP2K4 0.034 0.14 0.36 24 -0.37 18 42
MITF 0.031 0.084 0.23 11 -0.28 11 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.035 0.01 -10000 0 0 42 42
A2M -0.081 0.35 -10000 0 -1.2 46 46
CEBPB 0.033 0.023 0.12 1 -0.11 7 8
GRB2/SOS1/GAB family/SHP2 0.02 0.13 0.27 2 -0.45 27 29
STAT3 0.031 0.31 0.55 14 -0.83 33 47
STAT1 0.021 0.064 -10000 0 -0.7 3 3
CEBPD 0.022 0.34 0.57 10 -0.88 45 55
PIK3CA 0.033 0.014 -10000 0 -0.042 1 1
PI3K 0.021 0.076 -10000 0 -0.15 75 75
JUN 0.035 0.011 -10000 0 0 44 44
PIAS3/MITF 0.075 0.11 0.27 21 -0.28 12 33
MAPK11 0.023 0.063 -10000 0 -0.28 3 3
STAT3 (dimer)/FOXO1 -0.023 0.27 0.45 11 -0.63 54 65
GRB2/SOS1/GAB family 0.042 0.12 0.23 2 -0.31 30 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.005 0.1 0.18 9 -0.28 37 46
GRB2 0.037 0.009 -10000 0 -0.042 1 1
JAK2 0.032 0.013 -10000 0 0 74 74
LBP 0.064 0.27 0.51 21 -0.61 36 57
PIK3R1 0.033 0.013 -10000 0 -0.042 1 1
JAK1 0.03 0.026 -10000 0 -0.041 47 47
MYC 0.011 0.37 0.61 11 -0.87 60 71
FGG 0.055 0.26 0.57 9 -0.74 22 31
macrophage differentiation 0.049 0.3 0.54 17 -0.77 33 50
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.057 0.075 -10000 0 -0.17 7 7
JUNB 0.048 0.3 0.55 17 -0.85 29 46
FOS 0.025 0.018 -10000 0 0 166 166
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.031 0.085 0.22 16 -0.28 11 27
STAT1/PIAS1 0.073 0.13 0.3 14 -0.32 11 25
GRB2/SOS1/GAB family/SHP2/PI3K 0 0.17 -10000 0 -0.51 34 34
STAT3 (dimer) 0.036 0.3 0.55 15 -0.82 33 48
PRKCD 0.098 0.22 0.41 88 -0.45 24 112
IL6R 0.031 0.028 -10000 0 -0.041 62 62
SOCS3 0.057 0.092 0.49 5 -10000 0 5
gp130 (dimer)/JAK1/JAK1/LMO4 0.045 0.088 0.19 1 -0.17 43 44
Rac1/GTP 0.038 0.12 0.31 15 -0.34 12 27
HCK 0.027 0.017 -10000 0 0 145 145
MAPKKK cascade 0.014 0.19 0.33 3 -0.59 35 38
bone resorption 0.057 0.26 0.54 12 -0.69 23 35
IRF1 0.048 0.3 0.57 14 -0.83 29 43
mol:GDP 0.03 0.093 0.25 16 -0.27 13 29
SOS1 0.001 0.005 0.025 12 -0.022 1 13
VAV1 0.028 0.091 0.24 14 -0.28 13 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.012 0.075 -10000 0 -0.32 15 15
PTPN11 0.02 0.085 -10000 0 -0.7 6 6
IL6/IL6RA 0.025 0.039 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.075 -10000 0 -0.15 43 43
gp130 (dimer)/JAK2/JAK2/LMO4 0.05 0.064 -10000 0 -0.12 33 33
IL6 0.016 0.028 -10000 0 -0.048 9 9
PIAS3 0.036 0.007 -10000 0 0 17 17
PTPRE 0.01 0.031 -10000 0 -0.06 28 28
PIAS1 0.036 0.008 -10000 0 0 26 26
RAC1 0.027 0.018 -10000 0 0 157 157
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.026 0.058 0.17 8 -0.24 5 13
LMO4 0.03 0.034 -10000 0 -0.051 26 26
STAT3 (dimer)/PIAS3 0.027 0.28 0.49 3 -0.76 33 36
MCL1 -0.01 0.17 0.4 1 -0.74 15 16
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.036 0.009 -10000 0 0 29 29
RAS family/GTP/Tiam1 -0.005 0.084 -10000 0 -0.2 64 64
NT3 (dimer)/TRKC 0.048 0.026 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.027 0.07 -10000 0 -0.12 75 75
SHC/Grb2/SOS1/GAB1/PI3K -0.007 0.093 -10000 0 -0.2 75 75
RAPGEF1 0.036 0.008 -10000 0 0 21 21
BDNF 0.033 0.013 -10000 0 0 69 69
PIK3CA 0.032 0.013 -10000 0 0 74 74
DYNLT1 0.035 0.01 -10000 0 0 42 42
NTRK1 0.037 0.006 -10000 0 0 13 13
NTRK2 0.027 0.017 -10000 0 0 139 139
NTRK3 0.035 0.01 -10000 0 0 35 35
NT-4/5 (dimer)/TRKB 0.013 0.059 -10000 0 -0.11 80 80
neuron apoptosis -0.003 0.12 0.31 45 -0.26 1 46
SHC 2-3/Grb2 0.002 0.13 0.27 1 -0.33 45 46
SHC1 0.034 0.012 -10000 0 0 53 53
SHC2 -0.012 0.12 -10000 0 -0.44 28 28
SHC3 -0.013 0.12 -10000 0 -0.42 30 30
STAT3 (dimer) 0.013 0.085 -10000 0 -0.28 37 37
NT3 (dimer)/TRKA 0.061 0.031 -10000 0 -10000 0 0
RIN/GDP 0.003 0.074 0.19 7 -0.22 25 32
GIPC1 0.036 0.007 -10000 0 0 18 18
KRAS 0.035 0.009 -10000 0 0 34 34
DNAJA3 -0.007 0.038 0.14 3 -0.16 3 6
RIN/GTP 0.012 0.036 -10000 0 -0.13 27 27
CCND1 -0.011 0.11 -10000 0 -0.49 26 26
MAGED1 0.036 0.008 -10000 0 0 27 27
PTPN11 0.037 0.006 -10000 0 0 12 12
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.041 0.032 -10000 0 -0.12 14 14
GRB2 0.036 0.007 -10000 0 0 19 19
NGF (dimer)/TRKA/MATK 0.048 0.013 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.05 0.019 -10000 0 -0.14 1 1
ELMO1 0.019 0.019 -10000 0 0 251 251
RhoG/GTP/ELMO1/DOCK1 0.011 0.047 -10000 0 -0.12 46 46
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.035 0.01 -10000 0 0 37 37
DOCK1 0.026 0.017 -10000 0 0 159 159
GAB2 0.034 0.011 -10000 0 0 51 51
RIT2 0.025 0.018 -10000 0 0 168 168
RIT1 0.033 0.012 -10000 0 0 60 60
FRS2 0.036 0.008 -10000 0 0 24 24
DNM1 0.036 0.008 -10000 0 0 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.036 0.008 -10000 0 0 25 25
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.047 0.16 2 -0.17 11 13
mol:GDP 0.003 0.11 0.27 13 -0.3 28 41
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.003 0.043 -10000 0 -0.13 45 45
RIT1/GDP 0.011 0.083 0.21 11 -0.22 25 36
TIAM1 0.034 0.011 -10000 0 0 44 44
PIK3R1 0.033 0.013 -10000 0 0 67 67
BDNF (dimer)/TRKB 0.028 0.071 -10000 0 -0.12 74 74
KIDINS220/CRKL/C3G 0.051 0.016 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.051 -10000 0 -0.15 31 31
FRS2 family/SHP2 0.07 0.027 -10000 0 -0.12 6 6
SHC/GRB2/SOS1/GAB1 0.05 0.046 -10000 0 -0.11 25 25
RIT1/GTP 0.015 0.04 -10000 0 -0.13 36 36
NT3 (dimer) 0.036 0.008 -10000 0 0 26 26
RAP1/GDP 0 0.059 -10000 0 -0.17 28 28
KIDINS220/CRKL 0.036 0.009 -10000 0 0 29 29
BDNF (dimer) 0.033 0.013 -10000 0 0 69 69
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -0.11 1 1
Schwann cell development -0.011 0.016 -10000 0 -0.055 37 37
EHD4 0.035 0.01 -10000 0 0 36 36
FRS2 family/GRB2/SOS1 0.065 0.029 -10000 0 -0.11 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.01 0.069 -10000 0 -0.24 22 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.037 0.005 -10000 0 0 10 10
CDC42/GTP 0.018 0.08 -10000 0 -0.15 73 73
ABL1 0.032 0.013 -10000 0 0 71 71
SH2B family/GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
Rap1/GTP 0.005 0.07 -10000 0 -0.24 11 11
STAT3 0.013 0.085 -10000 0 -0.28 37 37
axon guidance 0.005 0.07 -10000 0 -0.14 80 80
MAPK3 -0.013 0.046 0.18 25 -10000 0 25
MAPK1 -0.013 0.042 0.18 20 -10000 0 20
CDC42/GDP 0.011 0.078 0.18 11 -0.21 24 35
NTF3 0.036 0.008 -10000 0 0 26 26
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.045 0.025 -10000 0 -0.11 9 9
PI3K 0.02 0.075 -10000 0 -0.15 75 75
FRS3 0.037 0.003 -10000 0 0 4 4
FAIM 0.035 0.009 -10000 0 0 30 30
GAB1 0.034 0.012 -10000 0 0 55 55
RASGRF1 -0.007 0.038 0.14 2 -0.13 4 6
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.019 0.021 0.09 10 -0.12 2 12
RGS19 0.034 0.012 -10000 0 0 55 55
CDC42 0.036 0.008 -10000 0 0 26 26
RAS family/GTP 0.011 0.099 0.23 2 -0.38 19 21
Rac1/GDP 0.01 0.071 0.22 7 -0.23 18 25
NGF (dimer)/TRKA/GRIT 0.025 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.04 0.24 -10000 0 -0.85 38 38
NGF (dimer)/TRKA/NEDD4-2 0.045 0.017 -10000 0 -0.11 1 1
MAP2K1 -0.009 0.063 0.19 24 -0.18 6 30
NGFR 0.032 0.013 -10000 0 0 72 72
NGF (dimer)/TRKA/GIPC/GAIP 0.013 0.046 -10000 0 -0.2 14 14
RAS family/GTP/PI3K -0.025 0.11 -10000 0 -0.2 105 105
FRS2 family/SHP2/GRB2/SOS1 0.079 0.039 -10000 0 -0.14 10 10
NRAS 0.033 0.013 -10000 0 0 66 66
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
PRKCI 0.036 0.008 -10000 0 0 25 25
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.088 -10000 0 -0.48 13 13
RASA1 0.035 0.01 -10000 0 0 35 35
TRKA/c-Abl 0.033 0.059 -10000 0 -0.14 50 50
SQSTM1 0.035 0.01 -10000 0 0 36 36
BDNF (dimer)/TRKB/GIPC 0.049 0.076 -10000 0 -0.12 69 69
NGF (dimer)/TRKA/p62/Atypical PKCs 0.055 0.034 -10000 0 -0.1 15 15
MATK 0.036 0.007 -10000 0 0 20 20
NEDD4L 0.034 0.011 -10000 0 0 45 45
RAS family/GDP -0.019 0.056 -10000 0 -0.16 48 48
NGF (dimer)/TRKA 0.009 0.039 0.15 4 -0.13 4 8
Rac1/GTP -0.013 0.057 -10000 0 -0.2 26 26
FRS2 family/SHP2/CRK family 0.091 0.056 -10000 0 -0.12 17 17
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.022 0.1 0.27 26 -0.3 20 46
PDGFB-D/PDGFRB/SLAP 0.02 0.072 -10000 0 -0.15 71 71
PDGFB-D/PDGFRB/APS/CBL 0.046 0.022 -10000 0 -0.11 7 7
AKT1 -0.027 0.094 0.29 14 -0.24 16 30
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.025 0.11 0.28 20 -0.33 19 39
PIK3CA 0.032 0.013 -10000 0 0 74 74
FGR 0.008 0.092 0.26 5 -0.44 12 17
mol:Ca2+ 0.017 0.11 0.27 17 -0.37 19 36
MYC 0.008 0.26 0.39 35 -0.67 52 87
SHC1 0.034 0.012 -10000 0 0 53 53
HRAS/GDP 0.016 0.068 0.18 33 -0.16 17 50
LRP1/PDGFRB/PDGFB 0.051 0.055 -10000 0 -0.13 32 32
GRB10 0.022 0.019 -10000 0 0 213 213
PTPN11 0.037 0.006 -10000 0 0 12 12
GO:0007205 0.017 0.11 0.28 16 -0.37 19 35
PTEN 0.026 0.017 -10000 0 0 158 158
GRB2 0.036 0.007 -10000 0 0 19 19
GRB7 0.037 0.007 -10000 0 0 16 16
PDGFB-D/PDGFRB/SHP2 0.049 0.033 -10000 0 -0.14 13 13
PDGFB-D/PDGFRB/GRB10 0.022 0.051 -10000 0 -0.14 34 34
cell cycle arrest 0.019 0.072 -10000 0 -0.15 71 71
HRAS 0.035 0.01 -10000 0 0 37 37
HIF1A -0.032 0.087 0.26 14 -0.25 15 29
GAB1 0.012 0.13 0.31 16 -0.37 28 44
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.012 0.13 0.32 24 -0.33 26 50
PDGFB-D/PDGFRB 0.054 0.053 -10000 0 -0.14 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.045 0.04 -10000 0 -0.14 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.005 0.1 0.23 4 -0.28 34 38
positive regulation of MAPKKK cascade 0.049 0.033 -10000 0 -0.14 13 13
PIK3R1 0.033 0.013 -10000 0 0 67 67
mol:IP3 0.017 0.11 0.28 16 -0.38 19 35
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.034 0.013 -10000 0 -0.013 32 32
PDGFB-D/PDGFRB/GRB7 0.051 0.022 -10000 0 -0.14 4 4
SHB 0.034 0.011 -10000 0 0 52 52
BLK 0.015 0.076 0.26 5 -0.39 7 12
PTPN2 0.035 0.016 0.065 1 -0.015 42 43
PDGFB-D/PDGFRB/SNX15 0.051 0.025 -10000 0 -0.14 7 7
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0 0.16 0.32 19 -0.4 44 63
CBL 0.037 0.005 -10000 0 0 9 9
PDGFB-D/PDGFRB/DEP1 0.05 0.026 -10000 0 -0.14 7 7
LCK 0.018 0.065 0.31 2 -0.34 4 6
PDGFRB 0.032 0.022 0.069 2 -0.02 71 73
ACP1 0.036 0.009 -10000 0 0 29 29
HCK -0.046 0.17 -10000 0 -0.48 60 60
ABL1 0.008 0.12 0.25 24 -0.34 27 51
PDGFB-D/PDGFRB/CBL 0.012 0.13 0.32 10 -0.41 28 38
PTPN1 0.033 0.017 -10000 0 -0.009 64 64
SNX15 0.037 0.004 -10000 0 0 7 7
STAT3 0.035 0.01 -10000 0 0 40 40
STAT1 0.035 0.01 -10000 0 0 41 41
cell proliferation 0.016 0.24 0.37 41 -0.6 52 93
SLA 0.028 0.016 -10000 0 0 131 131
actin cytoskeleton reorganization -0.015 0.075 0.2 40 -0.19 7 47
SRC 0.014 0.057 0.36 1 -0.44 2 3
PI3K -0.05 0.044 -10000 0 -0.17 33 33
PDGFB-D/PDGFRB/GRB7/SHC 0.062 0.038 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.026 0.11 0.28 20 -0.34 19 39
LYN -0.033 0.16 0.22 1 -0.46 52 53
LRP1 0.032 0.013 -10000 0 0 73 73
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.037 0.005 -10000 0 0 8 8
STAT5A 0.037 0.005 -10000 0 0 8 8
NCK1-2/p130 Cas 0.065 0.065 -10000 0 -0.14 23 23
SPHK1 0.035 0.012 0.06 4 0 49 53
EDG1 0 0.004 0.024 4 -10000 0 4
mol:DAG 0.017 0.11 0.28 16 -0.38 19 35
PLCG1 0.017 0.11 0.28 16 -0.38 19 35
NHERF/PDGFRB 0.065 0.036 -10000 0 -0.12 11 11
YES1 -0.009 0.14 0.24 1 -0.56 26 27
cell migration 0.064 0.036 -10000 0 -0.12 11 11
SHC/Grb2/SOS1 0.066 0.061 -10000 0 -0.13 19 19
SLC9A3R2 0.037 0.004 -10000 0 0 7 7
SLC9A3R1 0.035 0.01 -10000 0 0 35 35
NHERF1-2/PDGFRB/PTEN 0.057 0.058 -10000 0 -0.11 14 14
FYN -0.053 0.18 -10000 0 -0.45 80 80
DOK1 -0.014 0.059 0.18 36 -10000 0 36
HRAS/GTP 0.022 0.028 -10000 0 -0.13 16 16
PDGFB 0.035 0.01 -10000 0 0 35 35
RAC1 0.03 0.19 0.36 43 -0.42 48 91
PRKCD -0.011 0.062 0.18 37 -0.14 1 38
FER -0.012 0.062 0.18 36 -0.14 1 37
MAPKKK cascade -0.006 0.075 0.17 57 -0.17 5 62
RASA1 -0.012 0.063 0.18 36 -0.18 5 41
NCK1 0.036 0.009 -10000 0 0 28 28
NCK2 0.036 0.007 -10000 0 0 19 19
p62DOK/Csk -0.013 0.063 0.17 34 -0.19 3 37
PDGFB-D/PDGFRB/SHB 0.047 0.027 -10000 0 -0.14 5 5
chemotaxis 0.008 0.12 0.24 27 -0.33 27 54
STAT1-3-5/STAT1-3-5 0.063 0.071 -10000 0 -0.14 36 36
Bovine Papilomavirus E5/PDGFRB 0.021 0.024 -10000 0 -0.11 9 9
PTPRJ 0.037 0.006 -10000 0 0 15 15
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.035 -10000 0 -0.14 9 9
CRKL 0.043 0.11 0.28 6 -0.4 16 22
mol:PIP3 0.002 0.053 0.29 1 -0.54 2 3
AKT1 -0.011 0.051 -10000 0 -0.54 1 1
PTK2B 0.037 0.006 -10000 0 0 15 15
RAPGEF1 0.04 0.11 0.3 15 -0.37 16 31
RANBP10 0.037 0.005 -10000 0 0 9 9
PIK3CA 0.032 0.013 -10000 0 0 74 74
HGF/MET/SHIP2 0.045 0.039 -10000 0 -0.12 2 2
MAP3K5 0.042 0.1 0.26 5 -0.37 15 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.043 0.036 -10000 0 -10000 0 0
AP1 0.034 0.079 0.15 90 -0.15 42 132
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.034 0.012 -10000 0 0 53 53
apoptosis -0.13 0.36 -10000 0 -0.77 115 115
STAT3 (dimer) 0.01 0.061 -10000 0 -0.27 13 13
GAB1/CRKL/SHP2/PI3K 0.061 0.12 0.3 2 -0.42 14 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.059 0.11 0.29 4 -0.39 16 20
PTPN11 0.037 0.006 -10000 0 0 12 12
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.035 0.01 -10000 0 0 43 43
PTEN 0.026 0.017 -10000 0 0 158 158
ELK1 0.11 0.18 0.35 176 -10000 0 176
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.011 0.034 0.16 1 -0.14 14 15
PAK1 -0.014 0.053 -10000 0 -0.52 1 1
HGF/MET/RANBP10 0.046 0.038 -10000 0 -10000 0 0
HRAS 0.008 0.084 -10000 0 -0.47 11 11
DOCK1 0.031 0.1 0.29 7 -0.39 15 22
GAB1 0.041 0.1 0.22 2 -0.42 15 17
CRK 0.042 0.11 0.28 4 -0.4 16 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.068 -10000 0 -0.42 10 10
JUN 0.034 0.011 -10000 0 0 44 44
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.017 -10000 0 -0.12 1 1
PIK3R1 0.033 0.013 -10000 0 0 67 67
cell morphogenesis 0.025 0.11 0.28 27 -0.32 14 41
GRB2/SHC 0.071 0.064 0.17 91 -0.12 2 93
FOS 0.025 0.018 -10000 0 0 166 166
GLMN 0.004 0.004 0.068 2 -10000 0 2
cell motility 0.11 0.18 0.35 176 -10000 0 176
HGF/MET/MUC20 0.031 0.025 -10000 0 -10000 0 0
cell migration 0.069 0.063 0.16 91 -0.12 2 93
GRB2 0.036 0.007 -10000 0 0 19 19
CBL 0.037 0.005 -10000 0 0 9 9
MET/RANBP10 0.035 0.027 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.048 -10000 0 -0.26 7 7
MET/MUC20 0.018 0.013 -10000 0 -10000 0 0
RAP1B 0.04 0.1 0.28 15 -0.35 16 31
RAP1A 0.035 0.1 0.31 16 -0.36 15 31
HGF/MET/RANBP9 0.043 0.043 -10000 0 -0.12 9 9
RAF1 0.028 0.1 0.3 1 -0.45 13 14
STAT3 0.008 0.058 -10000 0 -0.29 12 12
cell proliferation 0.03 0.078 0.26 8 -0.28 10 18
RPS6KB1 0.014 0.019 -10000 0 -10000 0 0
MAPK3 0.079 0.16 0.33 119 -10000 0 119
MAPK1 0.12 0.22 0.41 142 -10000 0 142
RANBP9 0.036 0.007 -10000 0 0 18 18
MAPK8 -0.035 0.15 0.26 4 -0.35 53 57
SRC 0.006 0.047 -10000 0 -0.25 7 7
PI3K 0.056 0.073 0.17 78 -0.15 8 86
MET/Glomulin 0.016 0.028 -10000 0 -0.088 21 21
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.022 0.1 0.27 2 -0.43 14 16
MET 0.024 0.018 -10000 0 0 184 184
MAP4K1 0.051 0.11 0.29 5 -0.39 15 20
PTK2 0.035 0.009 -10000 0 0 33 33
MAP2K2 0.028 0.1 0.31 8 -0.44 11 19
BAD -0.017 0.052 -10000 0 -0.41 2 2
MAP2K4 0.036 0.1 0.26 8 -0.35 14 22
SHP2/GRB2/SOS1/GAB1 0.02 0.079 -10000 0 -0.34 16 16
INPPL1 0.037 0.006 -10000 0 0 13 13
PXN 0.037 0.005 -10000 0 0 9 9
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.001 0.017 0.09 1 -0.12 1 2
PLCgamma1/PKC 0.025 0.014 -10000 0 -0.13 3 3
HGF 0.026 0.018 -10000 0 0 163 163
RASA1 0.035 0.01 -10000 0 0 35 35
NCK1 0.036 0.009 -10000 0 0 28 28
PTPRJ 0.037 0.006 -10000 0 0 15 15
NCK/PLCgamma1 0.074 0.058 0.17 97 -0.12 1 98
PDPK1 -0.002 0.048 0.27 2 -0.56 1 3
HGF/MET/SHIP 0.031 0.025 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.052 0.075 -10000 0 -0.12 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.036 0.009 -10000 0 0 29 29
STAT1 (dimer)/Cbp/p300 0.025 0.089 0.29 8 -0.22 20 28
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.063 0.17 1 -0.14 39 40
antigen processing and presentation of peptide antigen via MHC class I -0.026 0.079 -10000 0 -0.19 59 59
CaM/Ca2+ 0.048 0.08 -10000 0 -0.14 41 41
RAP1A 0.037 0.005 -10000 0 0 10 10
STAT1 (dimer)/SHP2 -0.023 0.062 0.17 19 -0.19 9 28
AKT1 -0.032 0.092 0.31 10 -0.23 31 41
MAP2K1 -0.027 0.063 0.17 24 -0.2 8 32
MAP3K11 -0.02 0.071 0.23 17 -0.18 6 23
IFNGR1 0.032 0.02 0.095 3 -0.037 19 22
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.12 -10000 0 -0.3 61 61
Rap1/GTP -0.04 0.036 -10000 0 -0.16 6 6
CRKL/C3G 0.051 0.016 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.066 0.078 -10000 0 -0.13 35 35
CEBPB -0.002 0.13 0.37 9 -0.43 22 31
STAT3 0.035 0.01 -10000 0 0 40 40
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.063 0.096 -10000 0 -0.74 4 4
STAT1 -0.023 0.069 0.27 11 -0.19 9 20
CALM1 0.033 0.012 -10000 0 0 60 60
IFN-gamma (dimer) 0.03 0.022 -10000 0 -0.037 39 39
PIK3CA 0.032 0.013 -10000 0 0 74 74
STAT1 (dimer)/PIAS1 -0.024 0.078 0.21 23 -0.21 15 38
CEBPB/PTGES2/Cbp/p300 0.007 0.11 -10000 0 -0.32 28 28
mol:Ca2+ 0.048 0.072 -10000 0 -0.12 39 39
MAPK3 0.011 0.084 0.42 3 -0.59 2 5
STAT1 (dimer) -0.026 0.11 0.18 5 -0.26 57 62
MAPK1 -0.038 0.21 0.45 3 -0.74 37 40
JAK2 0.028 0.023 0.087 2 -0.038 36 38
PIK3R1 0.033 0.013 -10000 0 0 67 67
JAK1 0.034 0.018 0.076 1 -0.037 17 18
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.006 0.11 0.36 8 -0.42 10 18
SMAD7 -0.009 0.065 0.17 24 -0.14 17 41
CBL/CRKL/C3G 0.022 0.078 0.29 9 -0.19 3 12
PI3K 0.029 0.096 -10000 0 -0.19 34 34
IFNG 0.03 0.022 -10000 0 -0.037 39 39
apoptosis 0.018 0.099 0.37 6 -0.44 8 14
CAMK2G 0.026 0.018 -10000 0 0 159 159
STAT3 (dimer) 0.035 0.01 -10000 0 0 40 40
CAMK2A 0.037 0.005 -10000 0 0 8 8
CAMK2B 0.018 0.019 -10000 0 0 262 262
FRAP1 -0.033 0.084 0.29 10 -0.21 32 42
PRKCD -0.031 0.09 0.32 11 -0.22 20 31
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.026 0.079 -10000 0 -0.19 59 59
PTPN2 0.036 0.008 -10000 0 0 22 22
EP300 0.035 0.011 -10000 0 0 49 49
IRF1 -0.034 0.072 0.32 7 -0.28 13 20
STAT1 (dimer)/PIASy -0.025 0.07 0.26 10 -0.19 5 15
SOCS1 0.018 0.095 -10000 0 -1 4 4
mol:GDP -0.019 0.074 0.2 22 -0.18 3 25
CASP1 -0.018 0.079 0.23 14 -0.17 60 74
PTGES2 0.036 0.008 -10000 0 0 21 21
IRF9 0.004 0.064 0.21 11 -0.17 27 38
mol:PI-3-4-5-P3 0.015 0.084 -10000 0 -0.16 50 50
RAP1/GDP -0.031 0.053 0.11 18 -0.18 4 22
CBL -0.019 0.071 0.25 14 -0.19 4 18
MAP3K1 -0.021 0.064 0.23 11 -0.18 6 17
PIAS1 0.036 0.008 -10000 0 0 26 26
PIAS4 0.036 0.007 -10000 0 0 16 16
antigen processing and presentation of peptide antigen via MHC class II -0.026 0.079 -10000 0 -0.19 59 59
PTPN11 -0.016 0.065 0.18 28 -0.18 6 34
CREBBP 0.038 0.005 -10000 0 0 7 7
RAPGEF1 0.036 0.008 -10000 0 0 21 21
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.036 0.007 -10000 0 0 19 19
PTK2 0.035 0.009 -10000 0 0 33 33
CRKL -0.018 0.044 0.1 27 -0.15 24 51
GRB2/SOS1/SHC 0.041 0.032 -10000 0 -0.12 14 14
HRAS 0.035 0.01 -10000 0 0 37 37
IRS1/Crk 0.017 0.046 -10000 0 -0.13 39 39
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.056 -10000 0 -0.14 28 28
AKT1 -0.036 0.073 0.16 22 -0.22 30 52
BAD -0.041 0.07 0.15 21 -0.22 28 49
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.043 0.1 27 -0.15 22 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.026 0.048 -10000 0 -0.14 29 29
RAF1 -0.036 0.14 0.26 3 -0.54 30 33
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.046 0.054 -10000 0 -0.13 29 29
YWHAZ 0.036 0.008 -10000 0 0 21 21
IGF-1R heterotetramer/IGF1/IRS1 0.035 0.048 -10000 0 -0.15 24 24
PIK3CA 0.032 0.013 -10000 0 0 74 74
RPS6KB1 -0.034 0.071 0.16 28 -0.2 23 51
GNB2L1 0.037 0.005 -10000 0 0 10 10
positive regulation of MAPKKK cascade -0.034 0.12 0.25 6 -0.42 30 36
PXN 0.037 0.005 -10000 0 0 9 9
PIK3R1 0.033 0.013 -10000 0 0 67 67
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
HRAS/GTP 0.017 0.052 -10000 0 -0.13 42 42
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.067 0.056 -10000 0 -0.12 33 33
IGF-1R heterotetramer 0.038 0.014 0.1 1 -0.035 1 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.048 0.06 -10000 0 -0.14 35 35
Crk/p130 Cas/Paxillin 0.038 0.055 0.22 1 -0.13 36 37
IGF1R 0.038 0.014 0.1 1 -0.036 1 2
IGF1 0.034 0.025 -10000 0 -0.059 28 28
IRS2/Crk -0.029 0.055 0.1 20 -0.18 30 50
PI3K 0.041 0.087 -10000 0 -0.14 78 78
apoptosis 0.039 0.078 0.21 30 -0.18 20 50
HRAS/GDP 0.022 0.028 -10000 0 -0.13 16 16
PRKCD 0.005 0.06 0.2 5 -0.21 23 28
RAF1/14-3-3 E -0.012 0.13 0.29 4 -0.47 30 34
BAD/14-3-3 -0.04 0.081 0.19 20 -0.22 30 50
PRKCZ -0.029 0.069 0.16 29 -0.19 23 52
Crk/p130 Cas/Paxillin/FAK1 -0.049 0.07 0.13 20 -0.22 31 51
PTPN1 0.034 0.011 -10000 0 0 45 45
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.007 0.058 -10000 0 -0.22 25 25
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.04 0.071 -10000 0 -0.14 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.028 0.05 0.13 4 -0.14 34 38
GRB10 0.022 0.019 -10000 0 0 213 213
PTPN11 -0.018 0.044 0.1 27 -0.15 23 50
IRS1 0.011 0.041 0.12 4 -0.15 24 28
IRS2 -0.014 0.039 0.1 22 -0.17 12 34
IGF-1R heterotetramer/IGF1 0.041 0.051 -10000 0 -0.17 24 24
GRB2 0.036 0.007 -10000 0 0 19 19
PDPK1 -0.028 0.075 0.18 29 -0.2 22 51
YWHAE 0.036 0.009 -10000 0 0 29 29
PRKD1 0.002 0.058 0.2 1 -0.23 22 23
SHC1 0.034 0.012 -10000 0 0 53 53
EPO signaling pathway

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
BCL2L1 0.035 0.089 0.36 3 -10000 0 3
CRKL 0.032 0.1 0.26 37 -0.17 1 38
mol:DAG 0.011 0.07 0.24 3 -0.21 31 34
HRAS 0.032 0.11 0.25 54 -0.2 12 66
MAPK8 0.008 0.078 0.17 78 -10000 0 78
RAP1A 0.033 0.1 0.24 39 -0.18 2 41
GAB1 0.028 0.097 0.26 31 -0.18 2 33
MAPK14 0.026 0.1 0.18 138 -10000 0 138
EPO 0.025 0.024 -10000 0 -0.036 26 26
PLCG1 0.011 0.071 0.24 3 -0.21 31 34
EPOR/TRPC2/IP3 Receptors 0.039 0.022 0.1 3 -0.036 27 30
RAPGEF1 0.036 0.008 -10000 0 0 21 21
EPO/EPOR (dimer)/SOCS3 0.054 0.038 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.049 0.082 0.25 19 -0.19 11 30
EPO/EPOR (dimer) 0.037 0.035 -10000 0 -10000 0 0
IRS2 0.024 0.097 0.25 30 -0.18 11 41
STAT1 0.012 0.075 0.26 3 -0.24 18 21
STAT5B 0.012 0.075 0.24 4 -0.22 22 26
cell proliferation 0.004 0.077 0.16 79 -10000 0 79
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.078 0.14 5 -0.19 19 24
TEC 0.034 0.1 0.26 39 -0.17 1 40
SOCS3 0.037 0.004 -10000 0 0 6 6
STAT1 (dimer) 0.013 0.074 0.26 3 -0.23 18 21
JAK2 0.034 0.023 0.094 3 -0.036 23 26
PIK3R1 0.033 0.013 -10000 0 0 67 67
EPO/EPOR (dimer)/JAK2 0.053 0.072 0.25 5 -0.17 1 6
EPO/EPOR 0.037 0.035 -10000 0 -10000 0 0
LYN 0.034 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.09 0.21 35 -0.17 1 36
elevation of cytosolic calcium ion concentration 0.039 0.022 0.1 3 -0.036 27 30
SHC1 0.034 0.012 -10000 0 0 53 53
EPO/EPOR (dimer)/LYN 0.042 0.06 -10000 0 -0.13 30 30
mol:IP3 0.011 0.07 0.24 3 -0.21 31 34
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.011 0.1 0.24 27 -0.19 21 48
SH2B3 0.039 0.017 -10000 0 -0.034 2 2
NFKB1 0.026 0.1 0.17 139 -0.21 1 140
EPO/EPOR (dimer)/JAK2/SOCS3 0.021 0.035 0.17 22 -10000 0 22
PTPN6 0.031 0.094 0.18 113 -0.17 1 114
TEC/VAV2/GRB2 0.069 0.085 0.26 25 -0.2 4 29
EPOR 0.039 0.022 0.1 3 -0.036 27 30
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.094 0.23 24 -0.19 11 35
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.033 0.013 -10000 0 0 65 65
CRKL/CBL/C3G 0.068 0.082 0.25 25 -0.17 1 26
VAV2 0.03 0.098 0.25 34 -0.17 1 35
CBL 0.035 0.1 0.26 39 -0.17 1 40
SHC/Grb2/SOS1 0.024 0.053 -10000 0 -0.19 10 10
STAT5A 0.012 0.074 0.26 3 -0.21 33 36
GRB2 0.036 0.007 -10000 0 0 19 19
STAT5 (dimer) 0.029 0.083 0.28 6 -0.23 9 15
LYN/PLCgamma2 0.028 0.071 -10000 0 -0.17 53 53
PTPN11 0.037 0.006 -10000 0 0 12 12
BTK 0.032 0.1 0.26 35 -0.17 1 36
BCL2 0.036 0.091 0.36 1 -10000 0 1
Aurora B signaling

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
Condensin I complex -0.011 0.1 -10000 0 -0.23 72 72
STMN1 -0.021 0.009 0.019 1 -10000 0 1
Aurora B/RasGAP/Survivin 0.035 0.075 -10000 0 -0.14 73 73
Chromosomal passenger complex/Cul3 protein complex -0.031 0.076 -10000 0 -0.19 66 66
BIRC5 0.03 0.016 0.067 2 0 109 111
DES 0.025 0.092 -10000 0 -0.6 10 10
Aurora C/Aurora B/INCENP 0.059 0.027 -10000 0 -10000 0 0
Aurora B/TACC1 0.043 0.026 -10000 0 -0.11 9 9
Aurora B/PP2A 0.05 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.003 0.051 -10000 0 -0.19 31 31
mitotic metaphase/anaphase transition -0.001 0.003 0.022 1 -10000 0 1
NDC80 -0.019 0.01 0.027 1 -10000 0 1
Cul3 protein complex 0.029 0.033 -10000 0 -0.14 8 8
KIF2C -0.019 0.12 -10000 0 -0.43 36 36
PEBP1 0.036 0.008 -10000 0 0 20 20
KIF20A 0.029 0.016 -10000 0 0 111 111
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.045 -10000 0 -0.14 25 25
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.033 0.013 -10000 0 0 64 64
SMC4 0.033 0.013 -10000 0 0 67 67
NSUN2/NPM1/Nucleolin -0.004 0.084 -10000 0 -0.5 10 10
PSMA3 0.035 0.01 -10000 0 0 40 40
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.01 0.031 -10000 0 -0.2 11 11
AURKB 0.033 0.014 -10000 0 -0.007 52 52
AURKC 0.034 0.011 -10000 0 0 48 48
CDCA8 0.033 0.015 -10000 0 -0.004 63 63
cytokinesis -0.027 0.14 0.17 1 -0.43 49 50
Aurora B/Septin1 -0.014 0.14 0.2 2 -0.41 47 49
AURKA 0.033 0.013 -10000 0 0 65 65
INCENP 0.035 0.016 0.064 4 -0.024 30 34
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.037 0.006 0.062 1 0 12 13
hSgo1/Aurora B/Survivin 0.023 0.05 -10000 0 -0.11 57 57
EVI5 0.037 0.007 -10000 0 0 18 18
RhoA/GTP 0.01 0.13 -10000 0 -0.32 54 54
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.003 0.1 -10000 0 -0.34 33 33
NCAPG 0.031 0.014 -10000 0 0 88 88
Aurora B/HC8 Proteasome 0.045 0.031 -10000 0 -0.14 9 9
NCAPD2 0.032 0.014 -10000 0 0 78 78
Aurora B/PP1-gamma 0.048 0.027 -10000 0 -0.14 6 6
RHOA 0.036 0.007 -10000 0 0 20 20
NCAPH 0.036 0.009 -10000 0 0 29 29
NPM1 0.003 0.083 -10000 0 -0.38 17 17
RASA1 0.035 0.01 -10000 0 0 35 35
KLHL9 0.023 0.018 -10000 0 0 199 199
mitotic prometaphase -0.001 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.031 -10000 0 -0.14 9 9
PPP1CC 0.037 0.006 -10000 0 0 14 14
Centraspindlin 0.003 0.13 -10000 0 -0.35 52 52
RhoA/GDP 0.025 0.019 -10000 0 -0.13 7 7
NSUN2 0.002 0.041 -10000 0 -0.28 9 9
MYLK -0.014 0.069 -10000 0 -0.2 62 62
KIF23 0.029 0.018 -10000 0 -0.006 102 102
VIM -0.016 0.012 0.023 2 -10000 0 2
RACGAP1 0.032 0.016 -10000 0 -0.003 84 84
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.063 -10000 0 -0.28 22 22
Chromosomal passenger complex -0.014 0.1 0.14 4 -0.27 55 59
Chromosomal passenger complex/EVI5 0.062 0.086 -10000 0 -0.15 56 56
TACC1 0.036 0.008 -10000 0 0 22 22
PPP2R5D 0.037 0.005 -10000 0 0 10 10
CUL3 0.038 0.003 -10000 0 0 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.008 0.1 0.3 1 -0.3 34 35
ACTA1 -0.032 0.092 0.24 3 -0.29 32 35
NUMA1 0 0.092 0.3 1 -0.32 25 26
SPTAN1 -0.041 0.094 0.22 9 -0.29 36 45
LIMK1 0.01 0.11 0.19 76 -0.34 16 92
BIRC3 0.032 0.014 -10000 0 0 84 84
BIRC2 0.037 0.006 -10000 0 0 14 14
BAX 0.035 0.01 -10000 0 0 41 41
CASP10 -0.01 0.032 0.084 47 -10000 0 47
CRMA 0 0 -10000 0 -0.001 4 4
XIAP 0 0 0.001 3 -0.001 11 14
PTK2 -0.007 0.096 0.3 1 -0.29 37 38
DIABLO 0.037 0.005 -10000 0 0 10 10
apoptotic nuclear changes -0.04 0.093 0.22 9 -0.29 36 45
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.037 0.007 -10000 0 0 16 16
GSN -0.032 0.098 0.22 9 -0.32 29 38
MADD 0.036 0.007 -10000 0 0 19 19
TFAP2A 0.041 0.089 -10000 0 -0.64 7 7
BID -0.002 0.04 -10000 0 -0.18 20 20
MAP3K1 -0.002 0.055 -10000 0 -0.39 6 6
TRADD 0.037 0.005 -10000 0 0 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.018 -10000 0 -0.14 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.037 0.098 0.21 12 -0.3 35 47
CASP9 0.035 0.009 -10000 0 0 30 30
DNA repair 0.028 0.067 0.19 39 -10000 0 39
neuron apoptosis 0.02 0.11 -10000 0 -0.62 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.021 0.094 0.32 2 -0.32 28 30
APAF1 0.037 0.005 -10000 0 0 8 8
CASP6 0.026 0.12 0.37 1 -0.86 7 8
TRAF2 0.036 0.007 -10000 0 0 19 19
ICAD/CAD -0.042 0.09 0.39 3 -0.31 27 30
CASP7 -0.068 0.1 -10000 0 -0.22 133 133
KRT18 0.025 0.057 -10000 0 -0.47 5 5
apoptosis -0.033 0.098 0.6 1 -0.34 26 27
DFFA -0.039 0.088 0.26 3 -0.31 29 32
DFFB -0.037 0.087 0.3 2 -0.32 27 29
PARP1 -0.028 0.068 -10000 0 -0.2 39 39
actin filament polymerization -0.016 0.1 0.32 16 -0.18 76 92
TNF 0.037 0.004 -10000 0 0 6 6
CYCS 0.011 0.04 0.2 3 -0.24 3 6
SATB1 0.018 0.11 0.35 1 -0.75 7 8
SLK -0.025 0.086 0.29 2 -0.3 29 31
p15 BID/BAX 0 0.074 0.18 3 -0.18 52 55
CASP2 0.052 0.096 0.21 113 -0.24 5 118
JNK cascade 0.002 0.055 0.39 6 -10000 0 6
CASP3 -0.036 0.09 0.24 1 -0.31 32 33
LMNB2 0.061 0.089 0.26 13 -0.31 3 16
RIPK1 0.036 0.007 -10000 0 0 19 19
CASP4 0.031 0.015 -10000 0 0 93 93
Mammalian IAPs/DIABLO 0.057 0.036 -10000 0 -0.15 6 6
negative regulation of DNA binding 0.041 0.088 -10000 0 -0.63 7 7
stress fiber formation -0.035 0.086 0.29 2 -0.3 29 31
GZMB -0.015 0.012 0 193 -10000 0 193
CASP1 -0.01 0.066 -10000 0 -0.2 55 55
LMNB1 0.041 0.13 0.27 13 -0.35 16 29
APP 0.02 0.11 -10000 0 -0.63 13 13
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
response to stress 0 0 0.001 8 -0.001 27 35
CASP8 -0.011 0.002 0 14 -10000 0 14
VIM -0.031 0.099 0.43 1 -0.34 27 28
LMNA 0.064 0.089 0.27 13 -0.3 4 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.016 0.053 -10000 0 -0.22 10 10
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.038 0.087 0.2 2 -0.31 29 31
APAF-1/Caspase 9 0.018 0.084 -10000 0 -0.61 8 8
nuclear fragmentation during apoptosis 0 0.09 0.3 1 -0.31 25 26
CFL2 0.016 0.11 0.18 76 -0.32 17 93
GAS2 -0.03 0.09 0.18 5 -0.3 29 34
positive regulation of apoptosis 0.06 0.1 0.24 23 -0.34 6 29
PRF1 0.025 0.018 -10000 0 0 169 169
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.006 0.098 -10000 0 -0.39 29 29
Crk/p130 Cas/Paxillin -0.051 0.093 -10000 0 -0.2 109 109
JUN -0.017 0.049 -10000 0 -0.24 13 13
HRAS 0.035 0.01 -10000 0 0 37 37
RET51/GFRalpha1/GDNF/GRB10 0.043 0.062 -10000 0 -0.11 31 31
RAP1A 0.037 0.005 -10000 0 0 10 10
FRS2 0.036 0.008 -10000 0 0 24 24
RAP1A/GDP 0.027 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.069 0.045 -10000 0 -10000 0 0
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.037 0.006 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.036 0.008 -10000 0 0 25 25
RET9/GFRalpha1/GDNF/Enigma 0.052 0.033 -10000 0 -10000 0 0
RHOA 0.036 0.007 -10000 0 0 20 20
RAP1A/GTP 0.061 0.049 -10000 0 -0.11 1 1
GRB7 0.037 0.007 -10000 0 0 16 16
RET51/GFRalpha1/GDNF 0.068 0.045 -10000 0 -10000 0 0
MAPKKK cascade 0 0.074 -10000 0 -0.12 97 97
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.043 0.046 -10000 0 -0.1 23 23
lamellipodium assembly -0.02 0.082 -10000 0 -0.21 52 52
RET51/GFRalpha1/GDNF/SHC 0.063 0.05 -10000 0 -0.12 8 8
PIK3CA 0.032 0.013 -10000 0 0 74 74
RET9/GFRalpha1/GDNF/SHC 0.045 0.039 -10000 0 -0.11 8 8
RET9/GFRalpha1/GDNF/Shank3 0.035 0.022 -10000 0 -10000 0 0
MAPK3 -0.028 0.039 0.2 9 -10000 0 9
DOK1 0.038 0.002 -10000 0 0 2 2
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.037 0.005 -10000 0 0 9 9
neurite development -0.022 0.04 0.2 7 -0.21 8 15
DOK5 0.029 0.016 -10000 0 0 111 111
GFRA1 0.027 0.017 -10000 0 0 138 138
MAPK8 0 0.046 -10000 0 -0.17 24 24
HRAS/GTP 0.031 0.093 -10000 0 -0.12 106 106
tube development 0.029 0.031 0.21 6 -0.1 8 14
MAPK1 -0.024 0.051 0.25 10 -10000 0 10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.06 -10000 0 -0.21 13 13
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
SRC 0.035 0.009 -10000 0 0 31 31
PDLIM7 0.037 0.005 -10000 0 0 9 9
RET51/GFRalpha1/GDNF/Dok6 0.062 0.044 -10000 0 -10000 0 0
SHC1 0.034 0.012 -10000 0 0 53 53
RET51/GFRalpha1/GDNF/Dok4 0.068 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.044 0.074 -10000 0 -0.11 66 66
PRKCA 0.037 0.004 -10000 0 0 6 6
HRAS/GDP 0.022 0.028 -10000 0 -0.13 16 16
CREB1 -0.024 0.095 -10000 0 -0.19 108 108
PIK3R1 0.033 0.013 -10000 0 0 67 67
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.005 0.063 -10000 0 -0.17 27 27
RET51/GFRalpha1/GDNF/Grb7 0.068 0.045 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.029 0.016 -10000 0 0 121 121
DOK4 0.037 0.006 -10000 0 0 12 12
JNK cascade -0.018 0.049 -10000 0 -0.23 15 15
RET9/GFRalpha1/GDNF/FRS2 0.051 0.033 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.035 0.01 -10000 0 0 35 35
NCK1 0.036 0.009 -10000 0 0 28 28
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.008 0.056 -10000 0 -0.17 16 16
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.091 -10000 0 -0.19 103 103
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.026 0.097 -10000 0 -0.19 119 119
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.012 0.044 -10000 0 -0.18 16 16
PI3K -0.049 0.13 0.18 1 -0.26 98 99
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.042 0.039 -10000 0 -0.1 8 8
GRB10 0.022 0.019 -10000 0 0 213 213
activation of MAPKK activity 0.014 0.046 -10000 0 -0.25 12 12
RET51/GFRalpha1/GDNF/FRS2 0.067 0.046 -10000 0 -10000 0 0
GAB1 0.034 0.012 -10000 0 0 55 55
IRS1 0.034 0.011 -10000 0 0 52 52
IRS2 0.031 0.015 -10000 0 0 94 94
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.051 -10000 0 -0.17 23 23
RET51/GFRalpha1/GDNF/PKC alpha 0.068 0.045 -10000 0 -10000 0 0
GRB2 0.036 0.007 -10000 0 0 19 19
PRKACA 0.036 0.007 -10000 0 0 17 17
GDNF 0.037 0.005 -10000 0 0 8 8
RAC1 0.026 0.017 -10000 0 0 156 156
RET51/GFRalpha1/GDNF/IRS1 0.06 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.022 0.096 -10000 0 -0.24 52 52
RET9/GFRalpha1/GDNF 0.037 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.04 0.025 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.005 0.076 -10000 0 -0.29 26 26
KLHL20 0.045 0.097 0.22 66 -0.19 23 89
CYFIP2 0.032 0.013 -10000 0 0 76 76
Rac1/GDP 0.007 0.065 0.22 4 -0.28 11 15
ENAH 0.005 0.078 -10000 0 -0.31 23 23
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 56 0 5 61
RAP1A 0.037 0.005 -10000 0 0 10 10
CTNNB1 0.037 0.007 -10000 0 0 17 17
CDC42/GTP -0.026 0.056 0.12 22 -0.22 16 38
ABI1/Sra1/Nap1 -0.017 0.036 -10000 0 -0.14 32 32
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.084 0.04 -10000 0 -0.13 8 8
RAPGEF1 -0.004 0.08 0.23 2 -0.28 22 24
CTNND1 0.035 0.01 -10000 0 0 36 36
regulation of calcium-dependent cell-cell adhesion 0.018 0.08 -10000 0 -0.29 26 26
CRK 0.003 0.082 0.18 22 -0.29 23 45
E-cadherin/gamma catenin/alpha catenin 0.063 0.036 -10000 0 -0.12 9 9
alphaE/beta7 Integrin 0.051 0.024 -10000 0 -0.14 6 6
IQGAP1 0.034 0.011 -10000 0 0 47 47
NCKAP1 0.038 0.003 -10000 0 0 3 3
Rap1/GTP/I-afadin 0.044 0.015 -10000 0 -0.099 1 1
DLG1 0.004 0.079 -10000 0 -0.3 26 26
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.036 0.044 -10000 0 -0.18 31 31
MLLT4 0.035 0.01 -10000 0 0 36 36
ARF6/GTP/NME1/Tiam1 0.038 0.032 -10000 0 -0.1 22 22
PI3K -0.044 0.058 0.063 2 -0.23 31 33
ARF6 0.035 0.009 -10000 0 0 31 31
mol:Ca2+ 0 0 0.001 67 0 29 96
E-cadherin/gamma catenin 0.049 0.019 -10000 0 -10000 0 0
TIAM1 0.035 0.011 -10000 0 0 44 44
E-cadherin(dimer)/Ca2+ 0.071 0.055 -10000 0 -0.13 26 26
AKT1 -0.022 0.058 0.15 16 -0.19 21 37
PIK3R1 0.033 0.013 -10000 0 0 67 67
CDH1 0.035 0.01 -10000 0 0 39 39
RhoA/GDP 0.013 0.079 0.24 9 -0.26 12 21
actin cytoskeleton organization 0.038 0.079 0.18 66 -0.14 23 89
CDC42/GDP 0.011 0.075 0.22 9 -0.26 12 21
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.052 -10000 0 -0.19 25 25
ITGB7 0.037 0.006 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.077 0.06 -10000 0 -0.14 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin 0.056 0.033 -10000 0 -0.11 11 11
mol:GDP -0.004 0.082 0.24 10 -0.29 13 23
CDC42/GTP/IQGAP1 0.037 0.042 -10000 0 -0.11 34 34
JUP 0.034 0.011 -10000 0 0 52 52
p120 catenin/RhoA/GDP 0.027 0.085 0.24 9 -0.25 17 26
RAC1/GTP/IQGAP1 0.025 0.043 -10000 0 -0.12 32 32
PIP5K1C/AP1M1 0.021 0.03 -10000 0 -0.13 19 19
RHOA 0.036 0.007 -10000 0 0 20 20
CDC42 0.036 0.008 -10000 0 0 26 26
CTNNA1 0.036 0.007 -10000 0 0 19 19
positive regulation of S phase of mitotic cell cycle 0.013 0.048 0.13 16 -0.12 32 48
NME1 0 0 -10000 0 0 31 31
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.007 0.076 -10000 0 -0.3 23 23
regulation of cell-cell adhesion -0.029 0.04 -10000 0 -0.17 25 25
WASF2 -0.009 0.019 -10000 0 -0.074 33 33
Rap1/GTP -0.022 0.066 0.16 29 -0.25 15 44
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.091 0.053 -10000 0 -0.13 13 13
CCND1 0.015 0.057 0.14 16 -0.15 32 48
VAV2 0.016 0.13 -10000 0 -0.56 14 14
RAP1/GDP -0.01 0.071 0.17 28 -0.25 15 43
adherens junction assembly 0.007 0.074 -10000 0 -0.29 23 23
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.028 0.017 -10000 0 0 136 136
PIP5K1C 0.035 0.01 -10000 0 0 42 42
regulation of heterotypic cell-cell adhesion 0.063 0.049 0.2 2 -0.13 15 17
E-cadherin/beta catenin 0.008 0.02 -10000 0 -0.097 5 5
mol:GTP 0 0 0.001 63 0 31 94
SRC 0.004 0.073 -10000 0 -0.29 24 24
PIK3CA 0.032 0.013 -10000 0 0 74 74
Rac1/GTP -0.008 0.077 0.18 2 -0.29 24 26
E-cadherin/beta catenin/alpha catenin 0.064 0.038 -10000 0 -0.13 11 11
ITGAE 0.036 0.007 -10000 0 0 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.018 0.082 -10000 0 -0.3 26 26
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.036 0.008 -10000 0 0 24 24
HDAC2 0.033 0.012 -10000 0 0 61 61
GNB1/GNG2 0.029 0.035 -10000 0 -0.11 15 15
forebrain development 0.051 0.084 0.35 14 -0.4 3 17
GNAO1 0.032 0.015 -10000 0 0 87 87
SMO/beta Arrestin2 0.037 0.032 -10000 0 -0.14 4 4
SMO 0.027 0.018 -10000 0 -10000 0 0
ARRB2 0.036 0.009 -10000 0 0 27 27
GLI3/SPOP -0.001 0.11 -10000 0 -0.31 37 37
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.035 0.01 -10000 0 0 37 37
GNAI2 0.035 0.011 -10000 0 0 46 46
SIN3/HDAC complex 0.056 0.042 -10000 0 -0.12 18 18
GNAI1 0.019 0.019 -10000 0 0 255 255
XPO1 0.04 0.008 0.089 4 -10000 0 4
GLI1/Su(fu) 0.021 0.059 0.3 7 -0.39 2 9
SAP30 0.036 0.007 -10000 0 0 19 19
mol:GDP 0.027 0.018 -10000 0 -10000 0 0
MIM/GLI2A 0.042 0.013 0.12 11 -10000 0 11
IFT88 0.035 0.01 -10000 0 0 35 35
GNAI3 0.037 0.007 -10000 0 0 16 16
GLI2 0.001 0.088 0.16 1 -0.32 23 24
GLI3 -0.016 0.099 -10000 0 -0.3 35 35
CSNK1D 0.036 0.007 -10000 0 0 20 20
CSNK1E 0.033 0.013 -10000 0 0 65 65
SAP18 0.034 0.011 -10000 0 0 46 46
embryonic digit morphogenesis 0.035 0.01 -10000 0 0 35 35
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.008 0.089 0.14 1 -0.26 36 37
SIN3B 0.035 0.008 -10000 0 0 27 27
SIN3A 0 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) -0.014 0.075 -10000 0 -0.26 29 29
GLI2/Su(fu) -0.003 0.073 -10000 0 -0.3 20 20
FOXA2 0.048 0.044 -10000 0 -0.5 2 2
neural tube patterning 0.051 0.084 0.35 14 -0.4 3 17
SPOP 0.036 0.008 -10000 0 0 25 25
Su(fu)/PIAS1 0.047 0.038 0.099 141 -0.078 11 152
GNB1 0.034 0.011 -10000 0 0 47 47
CSNK1G2 0.036 0.007 -10000 0 0 20 20
CSNK1G3 0.037 0.006 -10000 0 0 12 12
MTSS1 0.042 0.013 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.051 0.084 0.35 14 -0.4 3 17
SUFU 0.003 0.011 0.048 2 -0.1 4 6
LGALS3 0.029 0.016 -10000 0 0 118 118
catabolic process 0.01 0.14 -10000 0 -0.4 38 38
GLI3A/CBP 0.045 0.01 -10000 0 -10000 0 0
KIF3A 0.034 0.012 -10000 0 0 53 53
GLI1 0.049 0.084 0.37 12 -0.41 3 15
RAB23 0.035 0.009 -10000 0 0 33 33
CSNK1A1 0.037 0.006 -10000 0 0 13 13
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.037 0.005 -10000 0 0 10 10
Su(fu)/Galectin3 0.038 0.041 0.099 117 -0.11 9 126
GNAZ 0.032 0.014 -10000 0 0 81 81
RBBP4 0.033 0.012 -10000 0 0 61 61
CSNK1G1 0.037 0.005 -10000 0 0 10 10
PIAS1 0.036 0.008 -10000 0 0 26 26
PRKACA 0.036 0.007 -10000 0 0 17 17
GLI2/SPOP 0.017 0.096 -10000 0 -0.31 27 27
STK36 0.003 0.007 0.033 19 -10000 0 19
Gi family/GNB1/GNG2/GDP -0.016 0.1 -10000 0 -0.35 31 31
PTCH1 0.052 0.095 0.48 10 -0.54 1 11
MIM/GLI1 0.074 0.086 0.38 11 -0.43 2 13
CREBBP 0.045 0.01 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.002 0.097 0.17 2 -0.3 31 33
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.051 0.024 -10000 0 -0.14 6 6
Necdin/E2F1 -0.015 0.082 -10000 0 -0.14 146 146
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.073 0.048 -10000 0 -0.12 23 23
NGF (dimer)/p75(NTR)/BEX1 0.012 0.063 -10000 0 -0.11 95 95
NT-4/5 (dimer)/p75(NTR) 0.024 0.01 -10000 0 -10000 0 0
IKBKB 0.037 0.003 -10000 0 0 4 4
AKT1 -0.018 0.078 0.2 24 -0.2 24 48
IKBKG 0.037 0.003 -10000 0 0 4 4
BDNF 0.033 0.013 -10000 0 0 69 69
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.009 -10000 0 -10000 0 0
FURIN 0.037 0.005 -10000 0 0 11 11
proBDNF (dimer)/p75(NTR)/Sortilin 0.056 0.035 -10000 0 -0.12 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.022 0.068 -10000 0 -0.16 47 47
proBDNF (dimer) 0.033 0.013 -10000 0 0 69 69
NTRK1 0.037 0.006 -10000 0 0 13 13
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.002 0.13 0.27 3 -0.36 42 45
IRAK1 0.036 0.008 -10000 0 0 22 22
SHC1 -0.003 0.036 0.093 60 -10000 0 60
ARHGDIA 0.036 0.007 -10000 0 0 20 20
RhoA/GTP 0.025 0.019 -10000 0 -0.13 7 7
Gamma Secretase 0.08 0.073 -10000 0 -0.15 28 28
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.058 -10000 0 -0.11 52 52
MAGEH1 0.032 0.013 -10000 0 0 71 71
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.001 0.074 -10000 0 -0.11 143 143
Mammalian IAPs/DIABLO 0.057 0.036 -10000 0 -0.15 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.036 0.008 -10000 0 0 27 27
APP 0.036 0.007 -10000 0 0 19 19
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.032 0.013 -10000 0 0 73 73
RhoA/GDP/RHOGDI 0.051 0.03 0.18 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.004 0.055 0.22 8 -10000 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.057 -10000 0 -0.18 33 33
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.02 -10000 0 -0.11 1 1
NCSTN 0.036 0.009 -10000 0 0 29 29
mol:GTP 0.032 0.04 -10000 0 -0.11 29 29
PSENEN 0.035 0.009 -10000 0 0 33 33
mol:ceramide -0.007 0.045 0.1 65 -10000 0 65
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.052 -10000 0 -0.26 10 10
p75(NTR)/beta APP 0.044 0.031 -10000 0 -0.14 8 8
BEX1 0.029 0.016 -10000 0 0 116 116
mol:GDP -0.008 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.047 0.035 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.041 0.018 -10000 0 -10000 0 0
PIK3R1 0.033 0.013 -10000 0 0 67 67
RAC1/GTP 0.026 0.025 -10000 0 -0.094 5 5
MYD88 0.035 0.01 -10000 0 0 37 37
CHUK 0.027 0.017 -10000 0 0 139 139
NGF (dimer)/p75(NTR)/PKA 0.033 0.041 -10000 0 -0.11 29 29
RHOB 0.032 0.013 -10000 0 0 75 75
RHOA 0.036 0.007 -10000 0 0 20 20
MAGE-G1/E2F1 0.026 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.036 0.008 -10000 0 0 26 26
TP53 -0.007 0.077 0.2 40 -0.2 6 46
PRDM4 -0.007 0.047 0.1 71 -10000 0 71
BDNF (dimer) 0.076 0.036 -10000 0 -10000 0 0
PIK3CA 0.032 0.013 -10000 0 0 74 74
SORT1 0.037 0.006 -10000 0 0 15 15
activation of caspase activity 0.066 0.046 -10000 0 -0.12 23 23
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.058 0.032 -10000 0 -0.11 5 5
RHOC 0.036 0.007 -10000 0 0 20 20
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.016 0.11 0.24 44 -0.3 18 62
DIABLO 0.037 0.005 -10000 0 0 10 10
SMPD2 -0.007 0.045 0.1 65 -10000 0 65
APH1B 0.037 0.006 -10000 0 0 14 14
APH1A 0.036 0.007 -10000 0 0 17 17
proNGF (dimer)/p75(NTR)/Sortilin 0.042 0.023 -10000 0 -0.11 4 4
PSEN1 0.034 0.011 -10000 0 0 48 48
APAF-1/Pro-Caspase 9 0.051 0.018 -10000 0 -0.14 2 2
NT3 (dimer)/p75(NTR) 0.046 0.022 -10000 0 -10000 0 0
MAPK8 0.001 0.076 0.23 18 -0.26 7 25
MAPK9 0.029 0.1 0.24 49 -0.26 10 59
APAF1 0.037 0.005 -10000 0 0 8 8
NTF3 0.036 0.008 -10000 0 0 26 26
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.019 -10000 0 0 264 264
RAC1/GDP 0.018 0.019 -10000 0 -0.13 5 5
RhoA-B-C/GDP 0.049 0.073 -10000 0 -0.14 53 53
p75 CTF/Sortilin/TRAF6/NRIF 0.072 0.059 -10000 0 -0.12 31 31
RhoA-B-C/GTP 0.032 0.04 -10000 0 -0.11 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.08 0.062 -10000 0 -0.12 24 24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.084 0.031 -10000 0 -0.12 2 2
PRKACB 0.034 0.011 -10000 0 0 50 50
proBDNF (dimer)/p75 ECD 0.047 0.02 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.031 0.014 -10000 0 0 84 84
BIRC2 0.037 0.006 -10000 0 0 14 14
neuron projection morphogenesis -0.016 0.066 0.13 26 -0.16 27 53
BAD 0.014 0.1 0.25 34 -0.28 14 48
RIPK2 0.037 0.006 -10000 0 0 14 14
NGFR 0.032 0.013 -10000 0 0 72 72
CYCS -0.012 0.043 0.19 5 -0.18 3 8
ADAM17 0.037 0.006 -10000 0 0 13 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.058 0.031 -10000 0 -0.11 3 3
BCL2L11 0.014 0.1 0.25 34 -0.29 13 47
BDNF (dimer)/p75(NTR) 0.042 0.024 -10000 0 -10000 0 0
PI3K 0.029 0.069 -10000 0 -0.12 73 73
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.04 0.022 -10000 0 -0.1 4 4
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.036 0.009 -10000 0 0 29 29
PRKCI 0.036 0.008 -10000 0 0 25 25
NGF (dimer)/p75(NTR) 0.024 0.01 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.051 0.047 -10000 0 -0.11 27 27
TRAF6 0.037 0.006 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.035 0.01 -10000 0 0 37 37
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.031 0.035 0.14 15 -0.15 2 17
SQSTM1 0.035 0.01 -10000 0 0 36 36
NGFRAP1 0.037 0.006 -10000 0 0 14 14
CASP3 0.014 0.1 0.24 34 -0.28 15 49
E2F1 0.035 0.01 -10000 0 0 36 36
CASP9 0.035 0.009 -10000 0 0 30 30
IKK complex 0.04 0.069 -10000 0 -0.26 8 8
NGF (dimer)/TRKA 0.027 0.004 -10000 0 -10000 0 0
MMP7 0.027 0.017 -10000 0 0 140 140
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.065 0.054 -10000 0 -0.11 30 30
MMP3 0.036 0.008 -10000 0 0 23 23
APAF-1/Caspase 9 -0.025 0.041 -10000 0 -0.2 7 7
Signaling events mediated by HDAC Class III

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
EP300 0.034 0.011 -10000 0 0 49 49
HDAC4 0.035 0.009 -10000 0 0 31 31
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.001 0.037 -10000 0 -0.12 39 39
CDKN1A -0.032 0.11 -10000 0 -0.47 28 28
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.01 -10000 0 0 41 41
FOXO3 -0.004 0.022 0.25 2 -0.1 1 3
FOXO1 0.031 0.015 -10000 0 0 95 95
FOXO4 0.011 0.024 -10000 0 -0.18 8 8
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.035 0.01 -10000 0 0 41 41
TAT 0.037 0.006 -10000 0 0 12 12
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.012 0.002 -10000 0 -10000 0 0
PPARGC1A 0.032 0.014 -10000 0 0 78 78
FHL2 0.028 0.016 -10000 0 0 127 127
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.042 0.046 0.16 30 -0.16 6 36
HIST2H4A 0.001 0.037 0.12 39 -10000 0 39
SIRT1/FOXO3a 0.023 0.043 0.15 32 -0.096 13 45
SIRT1 0.035 0.046 0.18 39 -10000 0 39
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.055 0.17 25 -0.12 17 42
SIRT1/Histone H1b 0.03 0.044 0.15 29 -0.16 7 36
apoptosis -0.051 0.052 0.13 10 -0.17 25 35
SIRT1/PGC1A 0.032 0.043 0.14 31 -0.11 14 45
p53/SIRT1 0.041 0.083 0.34 28 -0.15 20 48
SIRT1/FOXO4 0.03 0.044 0.16 2 -0.17 7 9
FOXO1/FHL2/SIRT1 0.027 0.055 0.16 13 -0.11 34 47
HIST1H1E 0.013 0.024 -10000 0 -0.18 7 7
SIRT1/p300 0.041 0.05 0.16 31 -0.15 12 43
muscle cell differentiation 0.005 0.037 0.12 5 -0.11 39 44
TP53 0.042 0.046 0.18 43 -10000 0 43
KU70/SIRT1/BAX 0.052 0.052 0.17 25 -0.13 10 35
CREBBP 0.037 0.004 -10000 0 0 7 7
MEF2D 0.037 0.006 -10000 0 0 13 13
HIV-1 Tat/SIRT1 0.043 0.044 0.16 31 -0.14 5 36
ACSS2 0.001 0.037 0.12 39 -10000 0 39
SIRT1/PCAF/MYOD -0.005 0.038 0.12 39 -0.12 5 44
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.033 0.012 -10000 0 0 58 58
SMAD2 -0.022 0.068 0.17 2 -0.22 34 36
SMAD3 0.011 0.064 0.27 1 -0.33 7 8
SMAD3/SMAD4 -0.008 0.17 -10000 0 -0.48 47 47
SMAD4/Ubc9/PIASy 0.057 0.052 -10000 0 -0.12 34 34
SMAD2/SMAD2/SMAD4 0.021 0.11 -10000 0 -0.26 28 28
PPM1A 0.035 0.01 -10000 0 0 35 35
CALM1 0.033 0.012 -10000 0 0 60 60
SMAD2/SMAD4 -0.004 0.07 -10000 0 -0.2 37 37
MAP3K1 0.036 0.008 -10000 0 0 23 23
TRAP-1/SMAD4 0.039 0.052 -10000 0 -0.14 38 38
MAPK3 0.037 0.003 -10000 0 0 4 4
MAPK1 0.034 0.011 -10000 0 0 47 47
NUP214 0.036 0.008 -10000 0 0 22 22
CTDSP1 0.037 0.007 -10000 0 0 16 16
CTDSP2 0.032 0.014 -10000 0 0 81 81
CTDSPL 0.037 0.006 -10000 0 0 14 14
KPNB1 0.036 0.008 -10000 0 0 23 23
TGFBRAP1 0.037 0.005 -10000 0 0 11 11
UBE2I 0.037 0.004 -10000 0 0 5 5
NUP153 0.035 0.009 -10000 0 0 32 32
KPNA2 0.035 0.01 -10000 0 0 39 39
PIAS4 0.037 0.007 -10000 0 0 16 16
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.005 0 47 -10000 0 47
SNTA1 0.032 0.014 -10000 0 0 78 78
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.034 0.084 51 -10000 0 51
MAPK12 -0.011 0.03 0.2 3 -0.17 10 13
CCND1 -0.023 0.11 -10000 0 -0.37 43 43
p38 gamma/SNTA1 -0.012 0.036 0.2 4 -0.16 11 15
MAP2K3 0.037 0.005 -10000 0 0 11 11
PKN1 0.034 0.011 -10000 0 0 45 45
G2/M transition checkpoint -0.011 0.03 0.2 3 -0.16 10 13
MAP2K6 -0.006 0.035 0.22 6 -0.18 11 17
MAPT -0.026 0.078 0.17 4 -0.2 75 79
MAPK13 -0.021 0.007 0 47 -10000 0 47
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.031 -10000 0 -0.2 11 11
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.005 -10000 0 0 10 10
Caspase 8 (4 units) -0.004 0.095 -10000 0 -0.24 22 22
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.04 0.019 0.079 64 -10000 0 64
BIRC3 -0.025 0.03 0.18 3 -0.2 2 5
CYCS -0.002 0.08 0.18 47 -0.26 12 59
RIPK1 0.036 0.007 -10000 0 0 19 19
CD247 0.039 0.007 -10000 0 -10000 0 0
MAP2K7 -0.009 0.11 -10000 0 -0.38 13 13
protein ubiquitination 0.012 0.069 0.2 4 -0.26 9 13
CRADD 0.037 0.007 -10000 0 0 16 16
DAXX 0.037 0.005 -10000 0 0 8 8
FAS 0.021 0.019 -10000 0 0 219 219
BID -0.014 0.061 -10000 0 -0.27 8 8
NF-kappa-B/RelA/I kappa B alpha 0.077 0.053 -10000 0 -0.13 16 16
TRADD 0.037 0.005 -10000 0 0 8 8
MAP3K5 0.031 0.014 -10000 0 0 91 91
CFLAR 0.037 0.005 -10000 0 0 9 9
FADD 0.037 0.006 -10000 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.077 0.054 -10000 0 -0.13 16 16
MAPK8 -0.006 0.1 0.55 1 -0.36 13 14
APAF1 0.037 0.005 -10000 0 0 8 8
TRAF1 0.036 0.009 -10000 0 0 28 28
TRAF2 0.036 0.007 -10000 0 0 19 19
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.059 0.18 1 -0.28 8 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.028 0.078 -10000 0 -0.29 11 11
CHUK 0.013 0.07 0.21 4 -0.28 8 12
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.045 0.084 -10000 0 -0.12 59 59
TCRz/NEF 0.034 0.006 -10000 0 -10000 0 0
TNF 0.037 0.004 -10000 0 0 6 6
FASLG 0.019 0.01 -10000 0 -10000 0 0
NFKB1 0.043 0.017 0.08 72 -10000 0 72
TNFR1A/BAG4/TNF-alpha 0.055 0.056 -10000 0 -0.12 41 41
CASP6 0.01 0.11 -10000 0 -0.57 6 6
CASP7 -0.027 0.14 0.27 5 -0.3 48 53
RELA 0.044 0.016 0.081 74 -10000 0 74
CASP2 0.026 0.018 -10000 0 0 160 160
CASP3 0.002 0.11 0.28 6 -0.34 17 23
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
TNFR1A/BAG4 0.036 0.054 -10000 0 -0.14 42 42
CASP8 0.037 0.006 -10000 0 0 14 14
CASP9 0.035 0.009 -10000 0 0 30 30
MAP3K14 0.024 0.079 0.2 3 -0.27 12 15
APAF-1/Caspase 9 -0.01 0.082 0.17 5 -0.23 13 18
BCL2 -0.014 0.098 0.39 2 -0.34 15 17
S1P3 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
PDGFRB 0.036 0.008 -10000 0 0 25 25
mol:S1P 0.001 0.002 0.019 4 -10000 0 4
S1P1/S1P/Gi -0.015 0.09 -10000 0 -0.2 75 75
GNAO1 0.032 0.015 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.026 0.039 -10000 0 -0.1 29 29
AKT1 -0.018 0.16 -10000 0 -0.46 53 53
AKT3 -0.029 0.13 -10000 0 -0.5 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.036 0.008 -10000 0 0 25 25
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.037 0.007 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.02 4 -10000 0 4
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.099 0.2 1 -0.29 35 36
MAPK3 -0.012 0.098 0.19 1 -0.28 38 39
MAPK1 -0.006 0.092 0.19 1 -0.27 32 33
JAK2 -0.012 0.11 0.2 8 -0.31 40 48
CXCR4 -0.009 0.099 0.19 1 -0.28 40 41
FLT1 0.036 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.018 0.019 -10000 0 -0.13 5 5
SRC -0.013 0.095 -10000 0 -0.28 36 36
S1P/S1P3/Gi -0.007 0.099 0.2 1 -0.29 35 36
RAC1 0.026 0.017 -10000 0 0 156 156
RhoA/GTP 0.009 0.11 0.19 1 -0.27 40 41
VEGFA 0.025 0.019 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.009 0.098 0.16 1 -0.26 47 48
VEGFR1 homodimer/VEGFA homodimer 0.007 0.079 -10000 0 -0.14 107 107
RHOA 0.036 0.007 -10000 0 0 20 20
S1P/S1P3/Gq 0.016 0.039 -10000 0 -0.15 26 26
GNAQ 0.035 0.01 -10000 0 0 35 35
GNAZ 0.032 0.014 -10000 0 -10000 0 0
G12/G13 0.027 0.048 -10000 0 -0.14 29 29
GNA14 0.035 0.009 -10000 0 0 34 34
GNA15 0.034 0.011 -10000 0 0 45 45
GNA12 0.024 0.018 -10000 0 0 180 180
GNA13 0.036 0.008 -10000 0 0 21 21
GNA11 0.034 0.011 -10000 0 0 46 46
Rac1/GTP 0 0.092 -10000 0 -0.3 25 25
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.13 -10000 0 -0.63 18 18
epithelial cell differentiation -0.004 0.14 -10000 0 -0.65 18 18
ITCH 0.03 0.032 0.11 1 -0.1 23 24
WWP1 -0.023 0.22 -10000 0 -1.1 18 18
FYN 0.031 0.015 -10000 0 0 93 93
EGFR 0.01 0.017 -10000 0 0 373 373
PRL 0.036 0.007 -10000 0 0 17 17
neuron projection morphogenesis -0.028 0.11 0.28 6 -0.49 19 25
PTPRZ1 0.024 0.018 -10000 0 0 186 186
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.054 0.12 -10000 0 -0.53 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.11 -10000 0 -0.57 18 18
ADAM17 0.031 0.031 -10000 0 -0.099 23 23
ErbB4/ErbB4 -0.003 0.13 -10000 0 -0.68 18 18
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.12 -10000 0 -0.62 18 18
NCOR1 0.036 0.008 -10000 0 0 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.12 -10000 0 -0.58 18 18
GRIN2B -0.01 0.11 0.21 2 -0.55 18 20
ErbB4/ErbB2/betacellulin 0.027 0.11 0.22 1 -0.55 18 19
STAT1 0.035 0.01 -10000 0 0 41 41
HBEGF 0.036 0.008 -10000 0 0 22 22
PRLR 0.037 0.005 -10000 0 0 10 10
E4ICDs/ETO2 0.022 0.13 -10000 0 -0.63 18 18
axon guidance -0.025 0.16 0.33 1 -0.79 18 19
NEDD4 0.03 0.031 0.11 1 -0.11 21 22
Prolactin receptor/Prolactin receptor/Prolactin 0.053 0.012 -10000 0 -10000 0 0
CBFA2T3 0.036 0.009 -10000 0 0 28 28
ErbB4/ErbB2/HBEGF 0.026 0.11 0.22 1 -0.55 18 19
MAPK3 -0.018 0.11 0.29 6 -0.51 18 24
STAT1 (dimer) 0.021 0.13 -10000 0 -0.63 18 18
MAPK1 -0.02 0.11 0.33 5 -0.5 19 24
JAK2 0.032 0.013 -10000 0 0 74 74
ErbB4/ErbB2/neuregulin 1 beta 0.004 0.11 0.21 1 -0.55 18 19
NRG1 -0.023 0.017 -10000 0 -0.084 18 18
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.037 0.005 -10000 0 0 8 8
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.025 0.16 0.33 1 -0.79 18 19
neural crest cell migration 0.005 0.11 0.21 1 -0.54 18 19
ERBB2 -0.023 0.019 0.047 11 -0.084 18 29
WWOX/E4ICDs 0.024 0.13 -10000 0 -0.63 18 18
SHC1 0.034 0.012 -10000 0 0 53 53
ErbB4/EGFR/neuregulin 4 -0.013 0.099 -10000 0 -0.47 18 18
apoptosis -0.006 0.12 0.58 18 -10000 0 18
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.025 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB2/epiregulin 0.026 0.11 -10000 0 -0.55 18 18
ErbB4/ErbB4/betacellulin/betacellulin 0.024 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.064 0.13 -10000 0 -0.57 18 18
MDM2 0.009 0.14 0.27 41 -0.6 18 59
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.02 0.1 -10000 0 -0.51 18 18
STAT5A -0.033 0.15 0.29 1 -0.77 18 19
ErbB4/EGFR/neuregulin 1 beta -0.003 0.089 -10000 0 -0.43 18 18
DLG4 0.037 0.006 -10000 0 0 14 14
GRB2/SHC 0.044 0.037 -10000 0 -0.15 14 14
E4ICDs/TAB2/NCoR1 0.017 0.12 -10000 0 -0.61 18 18
STAT5A (dimer) 0.004 0.16 -10000 0 -0.72 18 18
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.012 0.16 0.29 2 -0.77 18 20
LRIG1 0.031 0.014 -10000 0 0 87 87
EREG 0.036 0.008 -10000 0 0 22 22
BTC 0.037 0.005 -10000 0 0 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.16 0.33 1 -0.8 18 19
ERBB4 -0.003 0.13 -10000 0 -0.69 18 18
STAT5B 0.037 0.005 -10000 0 0 8 8
YAP1 -0.071 0.2 -10000 0 -0.48 93 93
GRB2 0.036 0.007 -10000 0 0 19 19
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.54 18 18
glial cell differentiation -0.017 0.12 0.6 18 -10000 0 18
WWOX 0.036 0.007 -10000 0 0 17 17
cell proliferation -0.011 0.11 -10000 0 -0.57 18 18
IL4-mediated signaling events

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.042 0.38 0.83 1 -1 22 23
STAT6 (cleaved dimer) -0.067 0.35 -10000 0 -0.95 29 29
IGHG1 -0.01 0.26 0.43 21 -0.78 23 44
IGHG3 -0.058 0.36 0.63 1 -0.94 29 30
AKT1 -0.018 0.27 0.52 6 -0.72 29 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.018 0.19 0.46 5 -0.55 8 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.004 0.26 0.51 3 -0.74 19 22
THY1 -0.12 0.5 0.78 2 -1.2 61 63
MYB 0.033 0.012 -10000 0 0 60 60
HMGA1 0.037 0.006 -10000 0 0 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.001 0.26 0.55 7 -0.59 17 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.004 0.25 0.5 3 -0.77 16 19
SP1 0.028 0.077 0.12 88 -0.14 73 161
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.046 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.047 0.36 -10000 0 -0.97 26 26
SOCS1 -0.035 0.3 0.52 3 -0.67 30 33
SOCS3 -0.001 0.22 -10000 0 -0.69 2 2
FCER2 -0.024 0.32 0.66 2 -0.79 17 19
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.056 0.38 0.79 2 -1 22 24
GRB2 0.036 0.007 -10000 0 0 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.006 0.22 0.44 10 -0.57 19 29
T cell proliferation -0.064 0.37 0.66 1 -1 26 27
IL4R/JAK1 -0.066 0.38 0.66 1 -1 27 28
EGR2 -0.11 0.5 0.8 2 -1.3 53 55
JAK2 0.019 0.067 0.15 18 -10000 0 18
JAK3 0.035 0.018 -10000 0 -0.039 17 17
PIK3R1 0.033 0.013 -10000 0 0 67 67
JAK1 0.027 0.04 0.11 6 -10000 0 6
COL1A2 -0.11 0.47 0.54 3 -1.2 76 79
CCL26 -0.055 0.38 0.72 1 -0.97 29 30
IL4R -0.052 0.41 0.81 3 -1.1 23 26
PTPN6 0.016 0.037 -10000 0 -0.06 4 4
IL13RA2 -0.31 0.65 0.76 3 -1.1 175 178
IL13RA1 0.024 0.068 0.16 18 -10000 0 18
IRF4 0.044 0.12 -10000 0 -0.52 2 2
ARG1 0.006 0.21 0.52 2 -0.79 9 11
CBL -0.007 0.24 0.49 4 -0.56 17 21
GTF3A 0.049 0.035 0.12 70 -0.15 3 73
PIK3CA 0.032 0.013 -10000 0 0 74 74
IL13RA1/JAK2 0.024 0.1 0.23 10 -0.17 10 20
IRF4/BCL6 0.04 0.12 -10000 0 -0.45 2 2
CD40LG 0.042 0.005 0.14 1 -10000 0 1
MAPK14 -0.004 0.24 0.53 1 -0.58 12 13
mitosis -0.015 0.26 0.51 6 -0.68 29 35
STAT6 -0.06 0.42 0.82 4 -1.1 27 31
SPI1 0.038 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.018 0.25 0.49 6 -0.66 29 35
STAT6 (dimer) -0.06 0.42 0.82 4 -1.1 27 31
STAT6 (dimer)/PARP14 -0.077 0.37 -10000 0 -1 27 27
mast cell activation -0.002 0.016 -10000 0 -0.041 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.009 0.21 0.49 3 -0.6 5 8
FRAP1 -0.018 0.27 0.52 6 -0.72 29 35
LTA -0.057 0.38 0.72 1 -1 23 24
FES 0.037 0.007 -10000 0 0 16 16
T-helper 1 cell differentiation 0.058 0.42 1.1 27 -0.82 4 31
CCL11 -0.059 0.36 -10000 0 -0.99 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.013 0.21 0.51 4 -0.6 6 10
IL2RG 0.035 0.018 -10000 0 -0.039 13 13
IL10 -0.052 0.38 0.75 4 -1 22 26
IRS1 0.034 0.011 -10000 0 0 52 52
IRS2 0.031 0.015 -10000 0 0 94 94
IL4 0.027 0.17 0.57 1 -0.9 5 6
IL5 -0.057 0.38 -10000 0 -1.1 20 20
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.053 0.38 0.7 6 -0.92 35 41
COL1A1 0.019 0.26 0.56 13 -0.89 12 25
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.071 0.38 -10000 0 -1.1 23 23
IL2R gamma/JAK3 0.055 0.02 -10000 0 -0.08 1 1
TFF3 -0.051 0.38 0.79 2 -1 21 23
ALOX15 -0.057 0.38 0.72 1 -1.1 21 22
MYBL1 0.031 0.015 -10000 0 0 97 97
T-helper 2 cell differentiation -0.04 0.34 0.63 4 -0.81 30 34
SHC1 0.034 0.012 -10000 0 0 53 53
CEBPB 0.035 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.013 0.26 0.51 5 -0.78 19 24
mol:PI-3-4-5-P3 -0.018 0.27 0.52 6 -0.72 29 35
PI3K -0.023 0.28 0.53 5 -0.77 29 34
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.004 0.047 -10000 0 -0.091 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.007 0.21 0.43 10 -0.56 22 32
ITGB3 -0.056 0.38 0.72 1 -1 22 23
PIGR -0.052 0.38 0.77 3 -1 23 26
IGHE -0.004 0.08 0.17 41 -0.18 16 57
MAPKKK cascade 0.009 0.21 0.44 11 -0.55 22 33
BCL6 0.032 0.013 -10000 0 0 70 70
OPRM1 -0.056 0.38 0.72 1 -1.1 21 22
RETNLB -0.055 0.38 0.72 1 -0.97 29 30
SELP -0.054 0.38 0.79 2 -1 22 24
AICDA -0.056 0.36 0.7 2 -1 21 23
Retinoic acid receptors-mediated signaling

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
HDAC1 0.036 0.008 -10000 0 0 24 24
HDAC3 0.037 0.005 -10000 0 0 8 8
VDR 0.036 0.008 -10000 0 0 23 23
Cbp/p300/PCAF 0.044 0.025 -10000 0 -0.11 8 8
EP300 0.034 0.011 -10000 0 0 49 49
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.058 -10000 0 -0.23 14 14
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.037 0.005 -10000 0 0 8 8
AKT1 0.007 0.08 0.16 58 -0.22 13 71
RAR alpha/9cRA/Cyclin H 0.001 0.11 0.38 1 -0.24 48 49
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.06 -10000 0 -0.21 25 25
CDC2 -0.001 0.004 -10000 0 -10000 0 0
response to UV -0.001 0.007 0.03 1 -0.025 33 34
RAR alpha/Jnk1 0.019 0.041 0.16 1 -0.35 2 3
NCOR2 0.037 0.004 -10000 0 0 6 6
VDR/VDR/Vit D3 0.027 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.022 0.15 0.41 3 -0.5 37 40
NCOA2 0.037 0.005 -10000 0 0 11 11
NCOA3 0.034 0.011 -10000 0 0 45 45
NCOA1 0.034 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.036 0.008 -10000 0 0 23 23
RARG 0.033 0.018 -10000 0 -0.024 44 44
RAR gamma1/9cRA 0.048 0.012 -10000 0 -10000 0 0
MAPK3 0.033 0.019 -10000 0 -0.033 37 37
MAPK1 0.034 0.011 -10000 0 0 47 47
MAPK8 0.025 0.023 -10000 0 -0.007 146 146
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0 0.11 -10000 0 -0.3 49 49
RARA 0.007 0.036 -10000 0 -0.2 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.048 0.23 1 -0.19 15 16
PRKCA 0.032 0.029 0.084 5 -0.074 33 38
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.023 0.16 0.48 2 -0.55 38 40
RXRG 0.017 0.029 -10000 0 -10000 0 0
RXRA -0.017 0.064 -10000 0 -0.19 33 33
RXRB 0.018 0.028 0.13 1 -10000 0 1
VDR/Vit D3/DNA 0.027 0.006 -10000 0 -10000 0 0
RBP1 0.027 0.017 -10000 0 0 143 143
CRBP1/9-cic-RA -0.003 0.059 -10000 0 -0.13 91 91
RARB 0.033 0.022 0.077 1 -0.035 44 45
PRKCG 0.03 0.029 0.084 5 -0.073 33 38
MNAT1 0.034 0.011 -10000 0 0 44 44
RAR alpha/RXRs -0.006 0.12 0.25 1 -0.37 34 35
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.001 0.095 0.35 2 -0.28 31 33
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.067 0.23 2 -0.2 24 26
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.023 0.16 0.45 2 -0.55 38 40
positive regulation of DNA binding -0.006 0.1 -10000 0 -0.23 48 48
NRIP1 -0.047 0.27 0.53 2 -1 33 35
RXRs/RARs -0.008 0.12 -10000 0 -0.38 41 41
RXRs/RXRs/DNA/9cRA -0.016 0.1 -10000 0 -0.3 50 50
PRKACA 0.036 0.007 -10000 0 0 17 17
CDK7 0.036 0.008 -10000 0 0 26 26
TFIIH 0.06 0.051 -10000 0 -0.16 19 19
RAR alpha/9cRA 0.024 0.092 -10000 0 -0.19 25 25
CCNH 0.036 0.008 -10000 0 0 21 21
CREBBP 0.037 0.004 -10000 0 0 7 7
RAR gamma2/9cRA 0.057 0.052 -10000 0 -0.15 18 18
Alternative 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
IKK alpha homodimer 0.04 0.027 -9999 0 -0.14 2 2
FBXW11 0.036 0.008 -9999 0 0 24 24
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.008 -9999 0 0 24 24
CHUK 0.027 0.017 -9999 0 0 139 139
NF kappa B2 p100/RelB 0.069 0.064 -9999 0 -0.12 12 12
NFKB1 0.036 0.007 -9999 0 0 18 18
MAP3K14 0.037 0.006 -9999 0 0 13 13
NF kappa B1 p50/RelB 0.05 0.023 -9999 0 -0.14 4 4
RELB 0.035 0.009 -9999 0 0 30 30
NFKB2 0.028 0.017 -9999 0 0 132 132
NF kappa B2 p52/RelB 0.036 0.023 -9999 0 -10000 0 0
regulation of B cell activation 0.036 0.023 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.035 0.077 0.22 16 -0.28 10 26
FYN -0.003 0.11 0.26 9 -0.32 26 35
LAT/GRAP2/SLP76 0.028 0.077 0.27 4 -0.3 10 14
IKBKB 0.037 0.003 -10000 0 0 4 4
AKT1 0.009 0.091 0.24 16 -0.26 20 36
B2M 0.038 0.009 -10000 0 0 20 20
IKBKG -0.001 0.035 0.1 14 -0.1 8 22
MAP3K8 0.025 0.018 -10000 0 0 176 176
mol:Ca2+ -0.01 0.01 -10000 0 -0.04 4 4
integrin-mediated signaling pathway 0.024 0.007 -10000 0 -0.1 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.014 0.11 0.28 15 -0.33 19 34
TRPV6 0.38 0.59 1.3 155 -10000 0 155
CD28 0.038 0.002 -10000 0 0 1 1
SHC1 0.026 0.083 0.24 19 -0.33 9 28
receptor internalization 0.027 0.066 0.21 4 -0.44 5 9
PRF1 -0.1 0.29 -10000 0 -0.6 123 123
KRAS 0.035 0.009 -10000 0 0 34 34
GRB2 0.036 0.007 -10000 0 0 19 19
COT/AKT1 0.009 0.069 0.24 3 -0.22 19 22
LAT 0.02 0.076 0.25 7 -0.32 10 17
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.036 0.012 -10000 0 0 46 46
CD3E 0.039 0.007 -10000 0 0 10 10
CD3G 0.038 0.008 -10000 0 -10000 0 0
RASGRP2 0.006 0.02 -10000 0 -0.15 5 5
RASGRP1 -0.015 0.13 0.24 26 -0.24 83 109
HLA-A 0.038 0.008 -10000 0 0 15 15
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.025 0.007 -10000 0 -0.1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.058 0.15 36 -0.11 15 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.038 -10000 0 -0.14 21 21
PRKCA 0.006 0.063 0.18 27 -0.19 5 32
GRAP2 0.035 0.01 -10000 0 0 36 36
mol:IP3 0.007 0.056 -10000 0 -0.23 11 11
EntrezGene:6957 0.002 0.004 0.022 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.024 0.051 0.16 7 -0.32 4 11
ORAI1 -0.33 0.5 -10000 0 -1.1 155 155
CSK 0.02 0.073 0.23 6 -0.32 10 16
B7 family/CD28 0.066 0.096 0.28 16 -0.3 9 25
CHUK 0.027 0.017 -10000 0 0 139 139
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.024 0.078 0.22 7 -0.34 10 17
PTPN6 0.02 0.083 0.22 23 -0.33 10 33
VAV1 0.026 0.083 0.24 21 -0.32 10 31
Monovalent TCR/CD3 0.027 0.018 0.12 1 -10000 0 1
CBL 0.037 0.005 -10000 0 0 9 9
LCK 0.011 0.092 0.24 12 -0.35 12 24
PAG1 0.023 0.073 0.21 9 -0.31 10 19
RAP1A 0.037 0.005 -10000 0 0 10 10
TCR/CD3/MHC I/CD8/LCK 0.024 0.079 0.22 9 -0.34 10 19
CD80 0.037 0.006 -10000 0 0 13 13
CD86 0.034 0.013 -10000 0 0 63 63
PDK1/CARD11/BCL10/MALT1 0.004 0.048 -10000 0 -0.16 21 21
HRAS 0.035 0.01 -10000 0 0 37 37
GO:0035030 0.014 0.073 0.2 21 -0.27 9 30
CD8A 0.002 0.004 0.024 1 -10000 0 1
CD8B 0.039 0.006 -10000 0 -10000 0 0
PTPRC 0.03 0.016 -10000 0 0 110 110
PDK1/PKC theta 0.012 0.099 0.29 16 -0.32 13 29
CSK/PAG1 0.018 0.072 0.23 6 -0.3 10 16
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.051 0.036 -10000 0 -0.14 14 14
GRAP2/SLP76 0.038 0.086 0.26 4 -0.34 10 14
STIM1 -0.065 0.12 1.1 2 -10000 0 2
RAS family/GTP 0.009 0.076 0.19 19 -0.18 27 46
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.027 0.068 0.21 4 -0.46 5 9
mol:DAG -0.005 0.043 -10000 0 -0.21 11 11
RAP1A/GDP 0.011 0.028 0.075 28 -0.056 10 38
PLCG1 0.034 0.01 -10000 0 0 43 43
CD247 0.038 0.008 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.098 0.28 0.37 1 -0.58 123 124
RAP1A/GTP 0.004 0.008 -10000 0 -0.056 5 5
mol:PI-3-4-5-P3 0.015 0.096 0.26 16 -0.3 17 33
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.07 -10000 0 -0.29 10 10
NRAS 0.033 0.013 -10000 0 0 66 66
ZAP70 0.038 0.003 -10000 0 0 4 4
GRB2/SOS1 0.025 0.02 -10000 0 -0.13 8 8
LAT/GRAP2/SLP76/VAV1 0.018 0.07 0.2 1 -0.3 9 10
MALT1 0.035 0.009 -10000 0 0 30 30
TRAF6 0.037 0.006 -10000 0 0 14 14
CD8 heterodimer 0.03 0.009 -10000 0 -10000 0 0
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.014 0.029 -10000 0 -0.16 11 11
PRKCE 0.005 0.063 0.18 27 -0.18 7 34
PRKCQ 0.015 0.1 0.28 19 -0.34 13 32
LCP2 0.032 0.013 -10000 0 0 77 77
BCL10 0.036 0.007 -10000 0 0 20 20
regulation of survival gene product expression 0.009 0.083 0.23 16 -0.23 20 36
IKK complex 0.004 0.044 0.14 21 -0.098 2 23
RAS family/GDP -0.003 0.015 -10000 0 -0.041 33 33
MAP3K14 0.009 0.066 0.19 20 -0.18 19 39
PDPK1 0.011 0.086 0.25 16 -0.26 16 32
TCR/CD3/MHC I/CD8/Fyn 0.019 0.069 0.27 1 -0.38 7 8
Insulin Pathway

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
CBL/APS/CAP 0.036 0.049 -10000 0 -0.11 22 22
TC10/GTP 0.03 0.048 -10000 0 -0.12 21 21
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.06 -10000 0 -0.13 28 28
HRAS 0.035 0.01 -10000 0 0 37 37
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.032 0.013 -10000 0 0 71 71
FOXO3 -0.053 0.21 -10000 0 -0.65 52 52
AKT1 -0.027 0.088 0.25 13 -0.21 26 39
INSR 0.034 0.022 -10000 0 -0.039 34 34
Insulin Receptor/Insulin 0.057 0.063 0.23 4 -0.14 34 38
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.019 -10000 0 0 213 213
SORBS1 0.028 0.017 -10000 0 0 133 133
CRK 0.036 0.008 -10000 0 0 25 25
PTPN1 -0.027 0.039 0.14 7 -0.25 7 14
CAV1 -0.012 0.038 0.2 5 -0.19 8 13
CBL/APS/CAP/Crk-II/C3G 0.054 0.055 -10000 0 -0.1 14 14
Insulin Receptor/Insulin/IRS1/NCK2 0.075 0.064 -10000 0 -0.14 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.08 -10000 0 -0.13 81 81
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.069 -10000 0 -0.32 11 11
RPS6KB1 -0.033 0.081 0.22 14 -0.2 26 40
PARD6A 0.036 0.007 -10000 0 0 19 19
CBL 0.037 0.005 -10000 0 0 9 9
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.019 -10000 0 -10000 0 0
PIK3R1 0.033 0.013 -10000 0 0 67 67
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.036 0.085 0.17 19 -0.22 26 45
HRAS/GTP -0.035 0.033 0.035 18 -0.12 41 59
Insulin Receptor 0.034 0.022 -10000 0 -0.039 34 34
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.085 0.069 -10000 0 -0.13 32 32
PRKCI 0.028 0.087 -10000 0 -0.43 16 16
Insulin Receptor/Insulin/GRB14/PDK1 0.015 0.068 -10000 0 -0.13 77 77
SHC1 0.034 0.012 -10000 0 0 53 53
negative regulation of MAPKKK cascade 0.035 0.055 -10000 0 -10000 0 0
PI3K 0.048 0.088 -10000 0 -0.13 81 81
NCK2 0.036 0.007 -10000 0 0 19 19
RHOQ 0.037 0.006 -10000 0 0 15 15
mol:H2O2 -0.005 0.005 -10000 0 -0.033 7 7
HRAS/GDP 0.022 0.028 -10000 0 -0.13 16 16
AKT2 -0.028 0.082 0.25 13 -0.2 8 21
PRKCZ 0.006 0.075 -10000 0 -0.4 15 15
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.016 0.049 0.17 16 -0.15 4 20
F2RL2 0.037 0.005 -10000 0 0 10 10
TRIP10 0.036 0.008 -10000 0 0 26 26
Insulin Receptor/Insulin/Shc 0.059 0.039 -10000 0 -0.12 8 8
TC10/GTP/CIP4/Exocyst 0.044 0.029 -10000 0 -0.11 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.048 -10000 0 -0.12 14 14
RAPGEF1 0.036 0.008 -10000 0 0 21 21
RASA1 0.035 0.01 -10000 0 0 35 35
NCK1 0.036 0.009 -10000 0 0 28 28
CBL/APS/CAP/Crk-II 0.048 0.041 -10000 0 -0.11 14 14
TC10/GDP 0.024 0.024 -10000 0 -0.13 12 12
Insulin Receptor/Insulin/SHC/GRB10 0.045 0.067 -10000 0 -0.13 34 34
INPP5D -0.022 0.025 0.047 22 -0.11 22 44
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.006 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.037 0.006 -10000 0 0 12 12
IRS1 0.034 0.011 -10000 0 0 52 52
p62DOK/RasGAP 0.035 0.055 -10000 0 -10000 0 0
INS 0.036 0.024 0.098 11 -0.039 33 44
mol:PI-3-4-P2 -0.022 0.024 0.046 22 -0.11 22 44
GRB2 0.036 0.007 -10000 0 0 19 19
EIF4EBP1 -0.037 0.081 0.23 13 -0.21 25 38
PTPRA 0.033 0.016 -10000 0 -0.052 6 6
PIK3CA 0.032 0.013 -10000 0 0 74 74
TC10/GTP/CIP4 0.044 0.029 -10000 0 -0.11 14 14
PDPK1 0.037 0.004 -10000 0 0 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.015 0.052 -10000 0 -0.16 32 32
Insulin Receptor/Insulin/IRS1 0.057 0.047 -10000 0 -0.12 22 22
Insulin Receptor/Insulin/IRS3 0.05 0.033 -10000 0 -0.069 6 6
Par3/Par6 0.077 0.041 -10000 0 -0.11 16 16
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.018 0.11 0.28 14 -0.39 20 34
CRKL 0.017 0.1 0.24 7 -0.41 21 28
HRAS 0.031 0.099 0.25 3 -0.33 20 23
mol:PIP3 0.061 0.13 0.31 36 -0.38 16 52
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.037 0.004 -10000 0 0 5 5
GAB1 0.024 0.11 0.24 8 -0.42 21 29
FOXO3 0.042 0.17 0.32 27 -0.39 40 67
AKT1 0.049 0.17 0.32 26 -0.39 40 66
BAD 0.042 0.16 0.31 28 -0.37 40 68
megakaryocyte differentiation 0.025 0.1 0.23 8 -0.41 19 27
GSK3B 0.041 0.17 0.32 26 -0.38 43 69
RAF1 0.02 0.087 0.25 5 -0.28 21 26
SHC1 0.034 0.012 -10000 0 0 53 53
STAT3 0.017 0.1 0.24 2 -0.42 21 23
STAT1 0.016 0.19 -10000 0 -0.86 20 20
HRAS/SPRED1 0.023 0.086 0.21 3 -0.27 21 24
cell proliferation 0.012 0.095 0.24 2 -0.4 21 23
PIK3CA 0.033 0.013 -10000 0 0 74 74
TEC 0.037 0.006 -10000 0 0 13 13
RPS6KB1 0.052 0.12 0.27 15 -0.38 21 36
HRAS/SPRED2 0.043 0.096 0.26 5 -0.27 20 25
LYN/TEC/p62DOK 0.063 0.12 -10000 0 -0.41 21 21
MAPK3 0.016 0.079 0.24 11 -0.21 22 33
STAP1 0.021 0.1 0.28 3 -0.41 21 24
GRAP2 0.035 0.01 -10000 0 0 36 36
JAK2 0.017 0.17 -10000 0 -0.72 21 21
STAT1 (dimer) 0.022 0.19 -10000 0 -0.84 20 20
mol:Gleevec -0.002 0.006 -10000 0 -0.022 1 1
GRB2/SOCS1/VAV1 0.076 0.11 0.29 1 -0.39 21 22
actin filament polymerization 0.026 0.1 0.25 2 -0.4 21 23
LYN 0.032 0.013 -10000 0 0 72 72
STAP1/STAT5A (dimer) 0.022 0.13 0.34 1 -0.54 21 22
PIK3R1 0.033 0.013 -10000 0 0 67 67
CBL/CRKL/GRB2 0.052 0.11 0.28 6 -0.38 21 27
PI3K 0.063 0.13 0.31 11 -0.4 19 30
PTEN 0.026 0.017 -10000 0 0 158 158
SCF/KIT/EPO/EPOR 0.029 0.22 -10000 0 -0.98 20 20
MAPK8 0.011 0.096 0.24 2 -0.4 21 23
STAT3 (dimer) 0.019 0.1 0.27 3 -0.41 21 24
positive regulation of transcription 0.017 0.069 0.21 12 -0.18 18 30
mol:GDP 0.041 0.097 0.22 1 -0.33 21 22
PIK3C2B 0.018 0.1 0.28 5 -0.41 21 26
CBL/CRKL 0.04 0.11 0.27 7 -0.39 21 28
FER 0.023 0.1 0.25 4 -0.42 20 24
SH2B3 0.019 0.1 0.26 1 -0.42 20 21
PDPK1 0.055 0.12 0.29 34 -0.33 19 53
SNAI2 0.026 0.11 0.24 8 -0.42 20 28
positive regulation of cell proliferation 0.027 0.16 -10000 0 -0.66 21 21
KITLG 0.039 0.021 -10000 0 -0.051 20 20
cell motility 0.027 0.16 -10000 0 -0.66 21 21
PTPN6 0.024 0.025 -10000 0 -0.033 64 64
EPOR 0.05 0.084 -10000 0 -0.5 2 2
STAT5A (dimer) 0.033 0.14 0.3 1 -0.54 21 22
SOCS1 0.037 0.004 -10000 0 0 7 7
cell migration -0.023 0.1 0.4 20 -0.24 2 22
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.027 0.022 -10000 0 -0.036 13 13
VAV1 0.036 0.008 -10000 0 0 26 26
GRB10 0.013 0.089 0.27 5 -0.43 13 18
PTPN11 0.029 0.021 -10000 0 -0.032 51 51
SCF/KIT 0.029 0.11 0.26 2 -0.43 21 23
GO:0007205 -0.002 0.006 0.021 16 -10000 0 16
MAP2K1 0.011 0.077 0.21 5 -0.23 22 27
CBL 0.037 0.005 -10000 0 0 9 9
KIT 0.009 0.24 -10000 0 -1.1 22 22
MAP2K2 0.015 0.082 0.29 10 -0.23 20 30
SHC/Grb2/SOS1 0.053 0.11 -10000 0 -0.38 21 21
STAT5A 0.033 0.14 -10000 0 -0.55 21 21
GRB2 0.036 0.007 -10000 0 0 19 19
response to radiation 0.028 0.11 0.24 8 -0.41 20 28
SHC/GRAP2 0.044 0.031 -10000 0 -0.14 8 8
PTPRO 0.024 0.1 0.23 8 -0.42 19 27
SH2B2 0.025 0.1 0.25 2 -0.41 21 23
DOK1 0.038 0.002 -10000 0 0 2 2
MATK 0.021 0.1 0.24 2 -0.41 20 22
CREBBP 0.053 0.044 0.15 1 -0.12 20 21
BCL2 0.041 0.13 -10000 0 -0.85 5 5
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.042 0.01 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.011 0.06 -10000 0 -0.11 87 87
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.037 0.005 -10000 0 0 9 9
RGS9-1/Gbeta5/R9AP 0.047 0.015 -10000 0 -0.11 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.048 0.013 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.037 0.005 -10000 0 0 9 9
Cone Metarhodopsin II/X-Arrestin 0.028 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.058 0.096 82 -10000 0 82
Cone PDE6 0.058 0.048 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.017 0.064 -10000 0 -0.11 86 86
GNAT2/GDP 0.06 0.021 -10000 0 -0.1 1 1
GNB5 0.036 0.007 -10000 0 0 18 18
mol:GMP (4 units) -0.013 0.036 0.2 12 -10000 0 12
Cone Transducin 0.046 0.011 -10000 0 -10000 0 0
SLC24A2 0.031 0.015 -10000 0 0 95 95
GNB3/GNGT2 0.027 0.006 -10000 0 -10000 0 0
GNB3 0.036 0.008 -10000 0 0 22 22
GNAT2/GTP 0.027 0.004 -10000 0 -10000 0 0
CNGA3 0.023 0.018 -10000 0 0 200 200
ARR3 0.038 0.002 -10000 0 0 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.011 0.06 -10000 0 -0.11 87 87
mol:Pi 0.047 0.015 -10000 0 -0.11 1 1
Cone CNG Channel 0.031 0.076 -10000 0 -0.11 82 82
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.031 0.015 -10000 0 0 95 95
RGS9 0.036 0.007 -10000 0 0 18 18
PDE6C 0.028 0.017 -10000 0 0 132 132
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.036 0.008 -10000 0 0 27 27
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.029 0.016 -9999 0 0 117 117
ITGB7 0.037 0.006 -9999 0 0 14 14
ITGA4 0.037 0.006 -9999 0 0 13 13
alpha4/beta7 Integrin 0.053 0.012 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.042 0.024 -9999 0 -9999 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.034 0.011 -10000 0 0 50 50
NFATC1 0.001 0.11 0.24 1 -0.39 25 26
NFATC2 -0.031 0.084 0.16 2 -0.17 102 104
NFATC3 0.009 0.019 -10000 0 -0.1 14 14
YWHAE 0.036 0.009 -10000 0 0 29 29
Calcineurin A alpha-beta B1/CABIN1 -0.013 0.073 0.16 3 -0.21 39 42
Exportin 1/Ran/NUP214 0.07 0.03 -10000 0 -0.15 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.02 0.089 -10000 0 -0.21 27 27
BCL2/BAX 0.049 0.024 -10000 0 -0.14 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.026 -10000 0 -0.13 14 14
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 14 14
BAX 0.035 0.01 -10000 0 0 41 41
MAPK14 0.037 0.005 -10000 0 0 8 8
BAD 0.037 0.007 -10000 0 0 16 16
CABIN1/MEF2D 0.004 0.079 -10000 0 -0.21 37 37
Calcineurin A alpha-beta B1/BCL2 0.036 0.007 -10000 0 0 17 17
FKBP8 0.036 0.008 -10000 0 0 24 24
activation-induced cell death of T cells -0.004 0.079 0.2 37 -10000 0 37
KPNB1 0.036 0.008 -10000 0 0 23 23
KPNA2 0.035 0.01 -10000 0 0 39 39
XPO1 0.037 0.003 -10000 0 0 4 4
SFN 0.032 0.014 -10000 0 0 80 80
MAP3K8 0.025 0.018 -10000 0 0 176 176
NFAT4/CK1 alpha 0.024 0.044 -10000 0 -0.17 16 16
MEF2D/NFAT1/Cbp/p300 0.018 0.11 0.23 1 -0.22 37 38
CABIN1 -0.013 0.073 0.16 3 -0.21 39 42
CALM1 0.033 0.012 -10000 0 0 60 60
RAN 0.037 0.006 -10000 0 0 13 13
MAP3K1 0.036 0.008 -10000 0 0 23 23
CAMK4 0.037 0.005 -10000 0 0 10 10
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.037 0.003 -10000 0 0 4 4
YWHAH 0.032 0.013 -10000 0 0 73 73
Calcineurin A alpha-beta B1/AKAP79/PKA 0.05 0.017 -10000 0 -10000 0 0
YWHAB 0.034 0.011 -10000 0 0 44 44
MAPK8 0.029 0.016 -10000 0 0 122 122
MAPK9 0.037 0.006 -10000 0 0 14 14
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.033 0.012 -10000 0 0 63 63
NFAT1-c-4/YWHAQ 0.002 0.11 -10000 0 -0.36 24 24
PRKCH 0.034 0.011 -10000 0 0 46 46
CABIN1/Cbp/p300 0.048 0.029 -10000 0 -0.14 8 8
CASP3 0.035 0.009 -10000 0 0 31 31
PIM1 0.037 0.005 -10000 0 0 11 11
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.019 -10000 0 -0.1 10 10
apoptosis 0.02 0.035 -10000 0 -0.16 13 13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.097 -10000 0 -0.3 29 29
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.038 0.002 -10000 0 0 2 2
JNK2/NFAT4 0.026 0.037 -10000 0 -0.12 20 20
BAD/BCL-XL 0.048 0.026 -10000 0 -0.14 5 5
PRKCD 0.035 0.01 -10000 0 0 42 42
NUP214 0.036 0.008 -10000 0 0 22 22
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.037 0.004 -10000 0 0 6 6
PRKCG 0.035 0.009 -10000 0 0 31 31
PRKCQ 0.027 0.017 -10000 0 0 143 143
FKBP38/BCL2 0.052 0.015 -10000 0 -10000 0 0
EP300 0.034 0.011 -10000 0 0 49 49
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.034 0.011 -10000 0 0 50 50
NFATc/JNK1 0.01 0.1 -10000 0 -0.37 25 25
CaM/Ca2+/FKBP38 0.04 0.031 -10000 0 -0.11 14 14
FKBP12/FK506 0.022 0.023 -10000 0 -0.13 10 10
CSNK1A1 -0.016 0.021 0.088 12 -0.11 9 21
CaM/Ca2+/CAMK IV 0.041 0.03 -10000 0 -0.11 14 14
NFATc/ERK1 0.02 0.11 -10000 0 -0.37 25 25
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.02 0.09 -10000 0 -0.21 27 27
NR4A1 -0.022 0.079 0.17 5 -0.21 34 39
GSK3B 0.035 0.01 -10000 0 0 37 37
positive T cell selection 0.009 0.019 -10000 0 -0.1 14 14
NFAT1/CK1 alpha -0.018 0.072 0.14 1 -0.18 46 47
RCH1/ KPNB1 0.037 0.058 -10000 0 -0.15 44 44
YWHAQ 0.037 0.005 -10000 0 0 8 8
PRKACA 0.036 0.007 -10000 0 0 17 17
AKAP5 0.035 0.009 -10000 0 0 34 34
MEF2D 0.037 0.006 -10000 0 0 13 13
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.036 0.008 -10000 0 0 21 21
NFATc/p38 alpha 0.02 0.11 0.25 1 -0.37 25 26
CREBBP 0.037 0.004 -10000 0 0 7 7
BCL2 0.036 0.007 -10000 0 0 17 17
LPA4-mediated signaling events

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
ADCY4 -0.009 0.001 0 2 -9999 0 2
ADCY5 -0.009 0.001 0 2 -9999 0 2
ADCY6 -0.018 0.003 0 18 -9999 0 18
ADCY7 -0.017 0.005 0 37 -9999 0 37
ADCY1 -0.013 0.009 0 152 -9999 0 152
ADCY2 -0.018 0.003 0 18 -9999 0 18
ADCY3 -0.009 0.001 0 2 -9999 0 2
ADCY8 -0.016 0.007 0 72 -9999 0 72
PRKCE -0.012 0.001 0 2 -9999 0 2
ADCY9 -0.018 0.003 0 13 -9999 0 13
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.016 0.047 0.18 13 -9999 0 13
BARD1 signaling events

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
BARD1/CSTF1 0.044 0.039 -10000 0 -0.14 19 19
ATM 0.035 0.01 -10000 0 0 38 38
UBE2D3 0.037 0.006 -10000 0 0 12 12
PRKDC 0.035 0.01 -10000 0 0 42 42
ATR 0.036 0.008 -10000 0 0 27 27
UBE2L3 0.035 0.009 -10000 0 0 33 33
FANCD2 0.009 0.035 -10000 0 -0.2 14 14
protein ubiquitination 0.077 0.057 -10000 0 -0.12 21 21
XRCC5 0.037 0.005 -10000 0 0 10 10
XRCC6 0.035 0.01 -10000 0 0 41 41
M/R/N Complex 0.071 0.025 -10000 0 -0.12 4 4
MRE11A 0.037 0.005 -10000 0 0 10 10
DNA-PK 0.059 0.05 -10000 0 -0.14 22 22
FA complex/FANCD2/Ubiquitin 0.003 0.085 -10000 0 -0.29 27 27
FANCF 0.036 0.008 -10000 0 0 25 25
BRCA1 0.037 0.006 -10000 0 0 14 14
CCNE1 0.033 0.012 -10000 0 0 60 60
CDK2/Cyclin E1 0.046 0.024 -10000 0 -0.14 2 2
FANCG 0.031 0.014 -10000 0 0 86 86
BRCA1/BACH1/BARD1 0.047 0.038 -10000 0 -0.14 19 19
FANCE 0.037 0.004 -10000 0 0 7 7
FANCC 0.036 0.007 -10000 0 0 19 19
NBN 0.037 0.006 -10000 0 0 13 13
FANCA 0.036 0.007 -10000 0 0 20 20
DNA repair -0.014 0.084 0.24 9 -0.29 15 24
BRCA1/BARD1/ubiquitin 0.047 0.038 -10000 0 -0.14 19 19
BARD1/DNA-PK 0.07 0.067 -10000 0 -0.14 35 35
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.039 0.14 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.065 -10000 0 -0.22 27 27
BRCA1/BACH1/BARD1/TopBP1 0.053 0.062 -10000 0 -0.13 47 47
BRCA1/BARD1/P53 0.068 0.068 -10000 0 -0.13 46 46
BARD1/CSTF1/BRCA1 0.061 0.043 -10000 0 -0.12 19 19
BRCA1/BACH1 0.037 0.006 -10000 0 0 14 14
BARD1 0.036 0.008 -10000 0 0 23 23
PCNA 0.033 0.012 -10000 0 0 63 63
BRCA1/BARD1/UbcH5C 0.065 0.043 -10000 0 -0.13 20 20
BRCA1/BARD1/UbcH7 0.061 0.047 -10000 0 -0.13 23 23
BRCA1/BARD1/RAD51/PCNA 0.071 0.062 -10000 0 -0.13 33 33
BARD1/DNA-PK/P53 0.069 0.084 -10000 0 -0.13 57 57
BRCA1/BARD1/Ubiquitin 0.047 0.038 -10000 0 -0.14 19 19
BRCA1/BARD1/CTIP 0.041 0.058 -10000 0 -0.13 44 44
FA complex 0.012 0.058 -10000 0 -0.18 35 35
BARD1/EWS 0.044 0.039 -10000 0 -0.14 19 19
RBBP8 -0.02 0.009 -10000 0 -10000 0 0
TP53 0.032 0.013 -10000 0 0 71 71
TOPBP1 0.034 0.011 -10000 0 0 50 50
G1/S transition of mitotic cell cycle -0.065 0.067 0.13 46 -10000 0 46
BRCA1/BARD1 0.084 0.06 -10000 0 -0.13 21 21
CSTF1 0.035 0.01 -10000 0 0 39 39
BARD1/EWS-Fli1 0.022 0.03 -10000 0 -0.13 19 19
CDK2 0.035 0.01 -10000 0 0 43 43
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.036 0.007 -10000 0 0 17 17
RAD50 0.037 0.006 -10000 0 0 13 13
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.047 0.038 -10000 0 -0.14 19 19
EWSR1 0.035 0.009 -10000 0 0 34 34
Aurora A 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
Aurora A/GADD45A 0.024 0.067 0.16 1 -0.22 26 27
BIRC5 0.03 0.015 -10000 0 0 109 109
NFKBIA -0.009 0.045 0.23 4 -0.18 18 22
CPEB1 0.034 0.012 -10000 0 0 56 56
AKT1 -0.006 0.036 0.25 2 -0.18 9 11
NDEL1 0.036 0.008 -10000 0 0 21 21
Aurora A/BRCA1 0.028 0.052 -10000 0 -0.17 23 23
NDEL1/TACC3 0.038 0.068 -10000 0 -0.18 29 29
GADD45A 0.032 0.014 -10000 0 0 79 79
GSK3B 0.036 0.015 0.089 26 0 37 63
PAK1/Aurora A 0.032 0.057 0.16 1 -0.18 23 24
MDM2 0.034 0.012 -10000 0 0 54 54
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.017 0.011 -10000 0 -10000 0 0
TP53 0.006 0.064 -10000 0 -0.24 25 25
DLG7 0.002 0.04 0.1 17 -0.17 21 38
AURKAIP1 0.036 0.009 -10000 0 0 29 29
ARHGEF7 0.033 0.012 -10000 0 0 58 58
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.04 0.072 -10000 0 -0.2 29 29
G2/M transition of mitotic cell cycle 0.028 0.051 -10000 0 -0.17 23 23
AURKA 0.011 0.051 0.14 15 -0.21 21 36
AURKB 0.009 0.032 -10000 0 -0.13 21 21
CDC25B 0.003 0.073 -10000 0 -0.27 28 28
G2/M transition checkpoint 0.002 0.041 -10000 0 -0.16 23 23
mRNA polyadenylation 0.021 0.056 -10000 0 -0.17 23 23
Aurora A/CPEB 0.022 0.056 -10000 0 -0.17 23 23
Aurora A/TACC1/TRAP/chTOG 0.051 0.086 -10000 0 -0.22 25 25
BRCA1 0.037 0.006 -10000 0 0 14 14
centrosome duplication 0.031 0.057 0.16 1 -0.18 23 24
regulation of centrosome cycle 0.037 0.067 -10000 0 -0.18 29 29
spindle assembly 0.049 0.084 -10000 0 -0.22 25 25
TDRD7 0.034 0.011 -10000 0 0 44 44
Aurora A/RasGAP/Survivin 0.037 0.083 -10000 0 -0.2 30 30
CENPA 0 0.079 -10000 0 -0.32 26 26
Aurora A/PP2A 0.033 0.057 -10000 0 -0.19 23 23
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.056 0.15 2 -0.21 21 23
negative regulation of DNA binding 0.004 0.073 0.16 1 -0.26 27 28
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.042 0.045 -10000 0 -0.14 27 27
RASA1 0.035 0.01 -10000 0 0 35 35
Ajuba/Aurora A 0.002 0.041 -10000 0 -0.16 23 23
mitotic prometaphase -0.004 0.011 0.069 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.051 0.14 15 -0.21 21 36
TACC1 0.036 0.008 -10000 0 0 22 22
TACC3 0.033 0.012 -10000 0 0 57 57
Aurora A/Antizyme1 0.047 0.062 -10000 0 -0.18 23 23
Aurora A/RasGAP 0.029 0.067 -10000 0 -0.24 23 23
OAZ1 0.036 0.008 -10000 0 0 23 23
RAN 0.037 0.006 -10000 0 0 13 13
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.037 0.014 0.089 26 0 17 43
GIT1 0.037 0.004 -10000 0 0 7 7
GIT1/beta-PIX/PAK1 0.059 0.048 -10000 0 -0.12 26 26
Importin alpha/Importin beta/TPX2 -0.017 0.011 -10000 0 -10000 0 0
PPP2R5D 0.037 0.005 -10000 0 0 10 10
Aurora A/TPX2 -0.006 0.069 -10000 0 -0.22 31 31
PAK1 0.036 0.007 -10000 0 0 18 18
CKAP5 0.035 0.01 -10000 0 0 40 40
Regulation of Telomerase

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
Telomerase catalytic core complex 0.024 0.16 -10000 0 -0.56 11 11
RAD9A 0.037 0.006 -10000 0 0 12 12
AP1 0.01 0.081 -10000 0 -0.17 73 73
IFNAR2 0.034 0.021 -10000 0 -0.036 37 37
AKT1 0.012 0.056 -10000 0 -0.25 19 19
ER alpha/Oestrogen 0.024 0.015 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.007 0.086 -10000 0 -0.26 36 36
EGF 0.034 0.015 -10000 0 -0.033 18 18
SMG5 0.037 0.006 -10000 0 0 13 13
SMG6 0.036 0.008 -10000 0 0 21 21
SP3/HDAC2 0.039 0.053 -10000 0 -0.16 22 22
TERT/c-Abl 0.03 0.17 -10000 0 -0.54 16 16
SAP18 0.035 0.011 -10000 0 0 46 46
MRN complex 0.071 0.025 -10000 0 -0.12 4 4
WT1 0.033 0.021 -10000 0 -0.035 37 37
WRN 0.036 0.008 -10000 0 0 27 27
SP1 0.034 0.024 -10000 0 -0.043 39 39
SP3 0.034 0.016 -10000 0 -0.031 25 25
TERF2IP 0.035 0.01 -10000 0 0 38 38
Telomerase/Nucleolin 0.046 0.16 -10000 0 -0.54 14 14
Mad/Max 0.048 0.028 -10000 0 -10000 0 0
TERT 0.02 0.16 -10000 0 -0.57 11 11
CCND1 -0.018 0.29 -10000 0 -0.95 40 40
MAX 0.032 0.018 -10000 0 -0.031 29 29
RBBP7 0.037 0.005 -10000 0 0 10 10
RBBP4 0.033 0.012 -10000 0 0 61 61
TERF2 0.029 0.011 0.085 6 0 51 57
PTGES3 0.036 0.008 -10000 0 0 27 27
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.044 0.11 -10000 0 -0.47 13 13
CDKN1B -0.026 0.082 0.14 4 -0.34 26 30
RAD1 0.036 0.008 -10000 0 0 23 23
XRCC5 0.037 0.005 -10000 0 0 10 10
XRCC6 0.035 0.01 -10000 0 0 41 41
SAP30 0.037 0.007 -10000 0 0 19 19
TRF2/PARP2 0.031 0.057 -10000 0 -0.14 46 46
UBE3A 0.036 0.011 -10000 0 -0.03 9 9
JUN 0.033 0.017 -10000 0 -0.031 19 19
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.025 0.021 -10000 0 -0.044 24 24
FOS 0.024 0.021 -10000 0 -0.031 17 17
IFN-gamma/IRF1 0.035 0.069 -10000 0 -0.18 38 38
PARP2 0.034 0.011 -10000 0 0 52 52
BLM 0.03 0.015 -10000 0 0 107 107
Telomerase 0.007 0.09 -10000 0 -0.26 35 35
IRF1 0.027 0.039 -10000 0 -0.12 29 29
ESR1 0.036 0.009 -10000 0 0 32 32
KU/TER 0.048 0.029 -10000 0 -0.14 9 9
ATM/TRF2 0.045 0.028 -10000 0 -0.1 9 9
ubiquitin-dependent protein catabolic process 0.001 0.084 -10000 0 -0.26 29 29
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.086 -10000 0 -0.27 29 29
HDAC1 0.036 0.008 -10000 0 0 24 24
HDAC2 0.031 0.024 -10000 0 -0.042 34 34
ATM 0.022 0.037 0.13 37 -0.18 5 42
SMAD3 -0.019 0.013 0.022 24 -10000 0 24
ABL1 0.032 0.013 -10000 0 0 71 71
MXD1 0.035 0.016 -10000 0 -0.031 29 29
MRE11A 0.037 0.005 -10000 0 0 10 10
HUS1 0.026 0.017 -10000 0 0 154 154
RPS6KB1 0.037 0.005 -10000 0 0 9 9
TERT/NF kappa B1/14-3-3 0.041 0.18 -10000 0 -0.56 15 15
NR2F2 0.023 0.023 -10000 0 -0.03 49 49
MAPK3 -0.018 0.016 0.021 61 -10000 0 61
MAPK1 -0.016 0.016 0.021 58 -10000 0 58
TGFB1/TGF beta receptor Type II 0.033 0.012 -10000 0 0 57 57
NFKB1 0.036 0.007 -10000 0 0 18 18
HNRNPC 0.035 0.009 -10000 0 0 31 31
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.022 0.037 0.13 37 -0.18 5 42
NBN 0.037 0.006 -10000 0 0 13 13
EGFR 0.01 0.017 -10000 0 -0.031 1 1
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.003 0.057 -10000 0 -0.14 65 65
MYC 0.029 0.02 -10000 0 -0.03 21 21
IL2 0.035 0.023 -10000 0 -0.043 37 37
KU 0.048 0.029 -10000 0 -0.14 9 9
RAD50 0.037 0.006 -10000 0 0 13 13
HSP90AA1 0.035 0.01 -10000 0 0 35 35
TGFB1 0.033 0.012 -10000 0 0 57 57
TRF2/BLM 0.013 0.077 -10000 0 -0.14 92 92
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.047 0.17 -10000 0 -0.56 11 11
SP1/HDAC2 0.043 0.047 -10000 0 -0.14 14 14
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.043 0.16 -10000 0 -0.51 14 14
Smad3/Myc 0.014 0.049 -10000 0 -0.12 41 41
911 complex 0.049 0.04 -10000 0 -0.12 5 5
IFNG 0.028 0.04 -10000 0 -0.12 31 31
Telomerase/PinX1 0.035 0.15 -10000 0 -0.51 13 13
Telomerase/AKT1/mTOR/p70S6K 0.013 0.12 -10000 0 -0.38 26 26
SIN3B 0.036 0.009 -10000 0 0 27 27
YWHAE 0.036 0.009 -10000 0 0 29 29
Telomerase/EST1B 0.047 0.16 -10000 0 -0.52 12 12
response to DNA damage stimulus 0.008 0.019 -10000 0 -0.086 12 12
MRN complex/TRF2/Rap1 0.079 0.072 -10000 0 -0.14 39 39
TRF2/WRN 0.036 0.045 -10000 0 -0.11 39 39
Telomerase/hnRNP C1/C2 0.045 0.16 -10000 0 -0.52 14 14
E2F1 0.032 0.021 -10000 0 -0.035 34 34
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.036 0.007 -10000 0 0 18 18
DKC1 0.036 0.008 -10000 0 0 21 21
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.036 0.008 -10000 0 0 25 25
alphaV beta3 Integrin 0.045 0.042 -10000 0 -0.14 24 24
PTK2 0.011 0.11 -10000 0 -0.28 49 49
positive regulation of JNK cascade 0.023 0.09 -10000 0 -0.26 33 33
CDC42/GDP 0.038 0.13 0.31 1 -0.35 35 36
Rac1/GDP 0.027 0.11 0.3 1 -0.35 21 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.037 0.005 -10000 0 0 10 10
CTNNB1 0.036 0.007 -10000 0 0 17 17
CDC42/GTP 0.031 0.11 -10000 0 -0.32 33 33
nectin-3/I-afadin 0.045 0.027 -10000 0 -0.14 5 5
RAPGEF1 0.006 0.12 0.28 4 -0.36 39 43
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.13 -10000 0 -0.39 39 39
PDGFB-D/PDGFRB 0.036 0.008 -10000 0 0 25 25
TLN1 -0.009 0.056 0.16 15 -0.22 16 31
Rap1/GTP 0 0.086 -10000 0 -0.27 39 39
IQGAP1 0.034 0.011 -10000 0 0 47 47
Rap1/GTP/I-afadin 0.044 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.045 0.027 -10000 0 -0.14 5 5
PVR 0.036 0.009 -10000 0 0 28 28
Necl-5(dimer) 0.036 0.009 -10000 0 0 28 28
mol:GDP 0.024 0.14 0.31 1 -0.42 36 37
MLLT4 0.035 0.01 -10000 0 0 36 36
PIK3CA 0.032 0.013 -10000 0 0 74 74
PI3K 0.059 0.089 -10000 0 -0.13 73 73
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.051 0.016 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.018 0.085 -10000 0 -0.3 19 19
PVRL1 0.037 0.005 -10000 0 0 9 9
PVRL3 0.033 0.012 -10000 0 0 60 60
PVRL2 0.035 0.009 -10000 0 0 31 31
PIK3R1 0.033 0.013 -10000 0 0 67 67
CDH1 0.035 0.01 -10000 0 0 39 39
CLDN1 0.036 0.008 -10000 0 0 27 27
JAM-A/CLDN1 0.076 0.045 -10000 0 -0.11 8 8
SRC 0.01 0.14 -10000 0 -0.42 39 39
ITGB3 0.037 0.004 -10000 0 0 6 6
nectin-1(dimer)/I-afadin/I-afadin 0.051 0.016 -10000 0 -10000 0 0
FARP2 0.029 0.14 -10000 0 -0.43 24 24
RAC1 0.026 0.017 -10000 0 0 156 156
CTNNA1 0.036 0.007 -10000 0 0 19 19
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.06 0.035 -10000 0 -0.12 5 5
nectin-1/I-afadin 0.051 0.016 -10000 0 -10000 0 0
nectin-2/I-afadin 0.049 0.023 -10000 0 -0.14 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.043 -10000 0 -0.12 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.061 0.034 -10000 0 -0.12 5 5
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.042 -10000 0 -0.11 34 34
F11R 0.034 0.011 -10000 0 0 52 52
positive regulation of filopodium formation 0.023 0.09 -10000 0 -0.26 33 33
alphaV/beta3 Integrin/Talin 0.029 0.089 0.22 29 -0.2 34 63
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.049 0.023 -10000 0 -0.14 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.049 0.023 -10000 0 -0.14 3 3
PIP5K1C -0.011 0.039 0.093 4 -0.2 15 19
VAV2 0.025 0.15 -10000 0 -0.49 25 25
RAP1/GDP 0.027 0.11 0.27 1 -0.32 37 38
ITGAV 0.035 0.009 -10000 0 0 34 34
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.058 0.038 -10000 0 -0.13 7 7
nectin-3(dimer)/I-afadin/I-afadin 0.045 0.027 -10000 0 -0.14 5 5
Rac1/GTP 0.024 0.1 -10000 0 -0.36 19 19
PTPRM 0.008 0.043 -10000 0 -0.22 16 16
E-cadherin/beta catenin/alpha catenin 0.085 0.06 -10000 0 -0.12 14 14
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.036 0.008 -10000 0 0 26 26
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.027 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.014 0.015 -10000 0 -10000 0 0
mol:DAG -0.018 0.033 0.19 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.003 0.06 -10000 0 -0.19 8 8
CaM/Ca2+ -0.022 0.043 0.17 4 -0.19 2 6
HIF1A 0.041 0.013 -10000 0 -10000 0 0
GAB1 0.034 0.012 -10000 0 0 55 55
AKT1 -0.034 0.086 0.2 4 -0.31 24 28
PLCG1 -0.018 0.034 0.19 2 -10000 0 2
NOS3 0.003 0.071 -10000 0 -0.33 7 7
CBL 0.037 0.005 -10000 0 0 9 9
mol:NO 0.011 0.076 -10000 0 -0.32 7 7
FLT1 0.016 0.007 -10000 0 -10000 0 0
PGF 0.032 0.013 -10000 0 0 73 73
VEGFR1 homodimer/NRP2/VEGFR121 0.009 0.073 -10000 0 -0.2 8 8
CALM1 0.033 0.012 -10000 0 0 60 60
PIK3CA 0.032 0.013 -10000 0 0 74 74
eNOS/Hsp90 0.031 0.089 -10000 0 -0.32 7 7
endothelial cell proliferation -0.002 0.052 0.2 1 -0.25 3 4
mol:Ca2+ -0.018 0.033 0.19 2 -10000 0 2
MAPK3 -0.027 0.033 0.15 2 -10000 0 2
MAPK1 -0.026 0.035 0.15 2 -0.19 1 3
PIK3R1 0.033 0.013 -10000 0 0 67 67
PLGF homodimer 0.032 0.013 -10000 0 0 73 73
PRKACA 0.036 0.007 -10000 0 0 17 17
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.019 -10000 0 0 287 287
VEGFA homodimer 0.024 0.018 -10000 0 0 181 181
VEGFR1 homodimer/VEGFA homodimer 0.02 0.038 -10000 0 -0.21 8 8
platelet activating factor biosynthetic process -0.023 0.051 -10000 0 -10000 0 0
PI3K 0.038 0.079 -10000 0 -0.2 16 16
PRKCA -0.023 0.033 0.17 2 -10000 0 2
PRKCB -0.016 0.031 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.03 0.028 -10000 0 -10000 0 0
VEGFA 0.024 0.018 -10000 0 0 181 181
VEGFB 0.037 0.005 -10000 0 0 9 9
mol:IP3 -0.018 0.033 0.19 2 -10000 0 2
RASA1 -0.026 0.029 0.16 4 -0.2 6 10
NRP2 0.037 0.005 -10000 0 0 8 8
VEGFR1 homodimer 0.016 0.007 -10000 0 -10000 0 0
VEGFB homodimer 0.037 0.005 -10000 0 0 9 9
NCK1 0.036 0.009 -10000 0 0 28 28
eNOS/Caveolin-1 0 0.073 -10000 0 -0.33 8 8
PTPN11 0.037 0.006 -10000 0 0 12 12
mol:PI-3-4-5-P3 0.036 0.078 -10000 0 -0.2 16 16
mol:L-citrulline 0.011 0.076 -10000 0 -0.32 7 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.024 0.085 -10000 0 -0.2 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.009 0.073 -10000 0 -0.21 9 9
CD2AP 0.034 0.011 -10000 0 0 47 47
PI3K/GAB1 0.043 0.089 -10000 0 -0.2 23 23
PDPK1 -0.033 0.063 0.17 16 -0.26 3 19
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.008 0.075 -10000 0 -0.21 11 11
mol:NADP 0.011 0.076 -10000 0 -0.32 7 7
HSP90AA1 0.035 0.01 -10000 0 0 35 35
ubiquitin-dependent protein catabolic process 0.023 0.083 -10000 0 -0.2 10 10
VEGFR1 homodimer/NRP2 0.033 0.027 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.016 0.1 -10000 0 -0.25 42 42
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 14 14
AKT1 0.033 0.012 -10000 0 0 58 58
AKT2 0.036 0.007 -10000 0 0 18 18
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.005 0.095 0.18 2 -0.26 45 47
YWHAZ 0.036 0.008 -10000 0 0 21 21
CALM1 0.033 0.012 -10000 0 0 60 60
YWHAQ 0.037 0.005 -10000 0 0 8 8
TBC1D4 -0.019 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.032 0.013 -10000 0 0 73 73
YWHAB 0.034 0.011 -10000 0 0 44 44
SNARE/Synip 0.04 0.036 -10000 0 -0.12 19 19
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.035 0.01 -10000 0 0 35 35
PRKCI 0.036 0.008 -10000 0 0 25 25
AS160/CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 14 14
RHOQ 0.037 0.006 -10000 0 0 15 15
GYS1 0 0.035 -10000 0 -0.2 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.036 0.008 -10000 0 0 26 26
TC10/GTP/CIP4/Exocyst 0.044 0.029 -10000 0 -0.11 14 14
AS160/14-3-3 -0.006 0.098 -10000 0 -0.38 21 21
VAMP2 0.034 0.011 -10000 0 0 50 50
SLC2A4 -0.007 0.1 0.19 2 -0.28 46 48
STX4 0.037 0.007 -10000 0 0 16 16
GSK3B 0.003 0.078 -10000 0 -0.3 29 29
SFN 0.032 0.014 -10000 0 0 80 80
LNPEP 0.037 0.005 -10000 0 0 10 10
YWHAE 0.036 0.009 -10000 0 0 29 29
Circadian rhythm 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
chromatin modification 0.032 0.15 -10000 0 -0.98 10 10
CLOCK 0.035 0.019 -10000 0 -0.067 10 10
TIMELESS/CRY2 0.025 0.16 -10000 0 -1 10 10
DEC1/BMAL1 0.035 0.056 -10000 0 -0.14 42 42
ATR 0.036 0.008 -10000 0 0 27 27
NR1D1 0.01 0.058 -10000 0 -0.38 2 2
ARNTL 0.033 0.02 -10000 0 -0.07 8 8
TIMELESS -0.007 0.15 -10000 0 -1.1 10 10
NPAS2 0.038 0.017 -10000 0 -0.067 10 10
CRY2 0.036 0.008 -10000 0 0 25 25
mol:CO -0.01 0.027 0.13 10 -0.069 47 57
CHEK1 0.034 0.011 -10000 0 0 52 52
mol:HEME 0.01 0.027 0.069 47 -0.13 10 57
PER1 0.034 0.012 -10000 0 0 53 53
BMAL/CLOCK/NPAS2 0.056 0.076 0.23 1 -0.14 50 51
BMAL1/CLOCK 0.009 0.12 -10000 0 -0.51 18 18
S phase of mitotic cell cycle 0.032 0.15 -10000 0 -0.98 10 10
TIMELESS/CHEK1/ATR 0.032 0.16 -10000 0 -1 10 10
mol:NADPH 0.01 0.027 0.069 47 -0.13 10 57
PER1/TIMELESS 0.024 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.037 0.007 -10000 0 0 16 16
Glucocorticoid receptor regulatory network

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
PCK2 -0.024 0.1 -10000 0 -0.59 10 10
SMARCC2 0.034 0.011 -10000 0 0 52 52
SMARCC1 0.035 0.01 -10000 0 0 35 35
TBX21 0.03 0.055 0.34 1 -10000 0 1
SUMO2 0.035 0.018 -10000 0 -0.031 31 31
STAT1 (dimer) 0.037 0.038 0.1 5 -0.17 13 18
FKBP4 0.035 0.01 -10000 0 0 36 36
FKBP5 0.029 0.016 -10000 0 0 121 121
GR alpha/HSP90/FKBP51/HSP90 -0.008 0.078 -10000 0 -0.21 8 8
PRL 0.038 0.05 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.04 0.12 -10000 0 -0.32 1 1
RELA 0.016 0.11 0.17 32 -0.16 125 157
FGG -0.048 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.023 0.076 -10000 0 -0.24 1 1
IFNG 0.034 0.078 -10000 0 -10000 0 0
apoptosis -0.018 0.2 0.45 20 -0.52 29 49
CREB1 0.044 0.009 -10000 0 -10000 0 0
histone acetylation 0.021 0.052 -10000 0 -10000 0 0
BGLAP 0.039 0.06 -10000 0 -10000 0 0
GR/PKAc 0.023 0.091 -10000 0 -0.18 19 19
NF kappa B1 p50/RelA 0.027 0.18 0.29 27 -0.26 121 148
SMARCD1 0.036 0.007 -10000 0 0 18 18
MDM2 -0.008 0.035 -10000 0 -10000 0 0
GATA3 0.034 0.021 -10000 0 -10000 0 0
AKT1 0.029 0.029 0.16 8 -0.086 17 25
CSF2 0.004 0.032 -10000 0 -10000 0 0
GSK3B 0.033 0.019 -10000 0 -0.031 27 27
NR1I3 -0.013 0.18 0.45 16 -0.5 17 33
CSN2 -0.045 0.087 -10000 0 -0.29 2 2
BRG1/BAF155/BAF170/BAF60A 0.065 0.075 -10000 0 -0.16 40 40
NFATC1 0.042 0.008 -10000 0 -10000 0 0
POU2F1 0.041 0.012 -10000 0 -10000 0 0
CDKN1A -0.12 0.41 -10000 0 -1.2 59 59
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 0.028 25 -10000 0 25
SFN 0.032 0.014 -10000 0 0 80 80
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.024 0.08 -10000 0 -0.2 4 4
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.068 0.27 0.42 15 -0.66 70 85
JUN 0.025 0.054 0.35 3 -10000 0 3
IL4 0.035 0.051 -10000 0 -10000 0 0
CDK5R1 0.036 0.009 -10000 0 0 25 25
PRKACA 0.036 0.007 -10000 0 0 17 17
cortisol/GR alpha (monomer)/AP-1 -0.048 0.053 -10000 0 -0.25 7 7
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.02 0.087 -10000 0 -0.18 13 13
cortisol/GR alpha (monomer) -0.054 0.12 -10000 0 -0.37 2 2
NCOA2 0.037 0.005 -10000 0 0 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.039 0.032 0.17 5 -10000 0 5
AP-1/NFAT1-c-4 0.051 0.073 0.42 2 -10000 0 2
AFP 0.025 0.069 -10000 0 -10000 0 0
SUV420H1 0.034 0.012 -10000 0 0 56 56
IRF1 -0.029 0.12 -10000 0 -0.63 15 15
TP53 -0.014 0.17 -10000 0 -0.48 58 58
PPP5C 0.035 0.009 -10000 0 0 32 32
KRT17 0.039 0.078 0.43 1 -10000 0 1
KRT14 0.03 0.066 0.35 1 -10000 0 1
TBP 0.043 0.017 -10000 0 -10000 0 0
CREBBP 0.03 0.018 -10000 0 -0.092 10 10
HDAC1 0.033 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.012 -10000 0 -10000 0 0
AP-1 0.051 0.073 0.43 2 -10000 0 2
MAPK14 0.035 0.018 -10000 0 -0.031 29 29
MAPK10 0.03 0.021 -10000 0 -0.031 27 27
MAPK11 0.032 0.02 -10000 0 -0.031 28 28
KRT5 0.038 0.076 0.43 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.033 0.019 0.097 2 -0.067 10 12
STAT1 0.037 0.038 0.1 4 -0.17 13 17
CGA 0.036 0.054 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.035 0.071 -10000 0 -0.36 9 9
MAPK3 0.034 0.02 0.078 1 -0.031 38 39
MAPK1 0.032 0.02 -10000 0 -0.031 28 28
ICAM1 0.017 0.12 -10000 0 -10000 0 0
NFKB1 0.016 0.11 0.17 30 -0.16 123 153
MAPK8 0.034 0.058 0.33 1 -10000 0 1
MAPK9 0.035 0.018 -10000 0 -0.031 27 27
cortisol/GR alpha (dimer) -0.022 0.2 0.45 20 -0.54 29 49
BAX -0.032 0.17 -10000 0 -0.93 8 8
POMC 0.03 0.072 0.47 1 -10000 0 1
EP300 0.027 0.019 -10000 0 -0.092 10 10
cortisol/GR alpha (dimer)/p53 -0.069 0.13 -10000 0 -0.42 17 17
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.069 0.24 32 -10000 0 32
SGK1 -0.017 0.061 -10000 0 -0.25 14 14
IL13 0.029 0.064 -10000 0 -10000 0 0
IL6 0.019 0.11 0.3 4 -10000 0 4
PRKACG 0.036 0.007 -10000 0 0 20 20
IL5 0.014 0.079 -10000 0 -10000 0 0
IL2 0.039 0.074 -10000 0 -10000 0 0
CDK5 0.025 0.019 -10000 0 0 178 178
PRKACB 0.034 0.011 -10000 0 0 50 50
HSP90AA1 0.035 0.01 -10000 0 0 35 35
IL8 -0.13 0.39 0.32 2 -0.78 127 129
CDK5R1/CDK5 0.031 0.043 -10000 0 -0.14 18 18
NF kappa B1 p50/RelA/PKAc 0.055 0.16 0.3 22 -0.21 111 133
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.04 0.11 -10000 0 -0.45 1 1
SMARCA4 0.033 0.012 -10000 0 0 61 61
chromatin remodeling -0.036 0.11 -10000 0 -0.37 25 25
NF kappa B1 p50/RelA/Cbp 0.044 0.16 -10000 0 -0.22 115 115
JUN (dimer) 0.025 0.054 0.35 3 -10000 0 3
YWHAH 0.032 0.013 -10000 0 0 73 73
VIPR1 0.033 0.061 0.36 4 -10000 0 4
NR3C1 -0.038 0.085 -10000 0 -0.34 1 1
NR4A1 0.04 0.009 -10000 0 -10000 0 0
TIF2/SUV420H1 0.037 0.054 -10000 0 -0.14 42 42
MAPKKK cascade -0.018 0.2 0.45 20 -0.52 29 49
cortisol/GR alpha (dimer)/Src-1 -0.046 0.12 -10000 0 -0.39 2 2
PBX1 0.041 0.011 -10000 0 -10000 0 0
POU1F1 0.042 0.011 -10000 0 -10000 0 0
SELE 0.022 0.13 -10000 0 -10000 0 0
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.036 0.11 -10000 0 -0.37 25 25
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.04 0.11 -10000 0 -0.45 1 1
mol:cortisol -0.034 0.059 -10000 0 -0.2 1 1
MMP1 0.034 0.076 0.34 1 -0.46 5 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.053 0.097 -10000 0 -0.21 46 46
Ran/GTP/Exportin 1/HDAC1 -0.029 0.022 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.11 -10000 0 -0.27 47 47
SUMO1 0.037 0.004 -10000 0 0 5 5
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.001 0.041 -10000 0 -0.14 21 21
FKBP3 0.035 0.01 -10000 0 0 39 39
Histones 0.035 0.075 -10000 0 -0.23 22 22
YY1/LSF 0.014 0.066 -10000 0 -0.22 21 21
SMG5 0.037 0.006 -10000 0 0 13 13
RAN 0.037 0.006 -10000 0 0 13 13
I kappa B alpha/HDAC3 0.002 0.076 -10000 0 -0.2 51 51
I kappa B alpha/HDAC1 0.01 0.095 -10000 0 -0.23 54 54
SAP18 0.034 0.011 -10000 0 0 46 46
RELA -0.003 0.083 0.19 1 -0.28 20 21
HDAC1/Smad7 0.045 0.042 -10000 0 -0.12 7 7
RANGAP1 0.034 0.011 -10000 0 0 44 44
HDAC3/TR2 0.026 0.071 -10000 0 -0.25 21 21
NuRD/MBD3 Complex -0.011 0.12 -10000 0 -0.32 43 43
NF kappa B1 p50/RelA 0.011 0.092 -10000 0 -0.31 19 19
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.037 0.007 -10000 0 0 16 16
GATA1 0.038 0.002 -10000 0 0 2 2
Mad/Max 0.052 0.015 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.01 0.11 -10000 0 -0.32 41 41
RBBP7 0.037 0.005 -10000 0 0 10 10
NPC 0.018 0.02 -10000 0 -0.086 18 18
RBBP4 0.033 0.012 -10000 0 0 61 61
MAX 0.035 0.01 -10000 0 0 36 36
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.036 0.008 -10000 0 0 24 24
NFKBIA 0 0.08 -10000 0 -0.32 26 26
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.089 -10000 0 -0.28 31 31
SIN3 complex 0.057 0.042 -10000 0 -0.12 18 18
SMURF1 0.026 0.017 -10000 0 0 157 157
CHD3 0.037 0.006 -10000 0 0 13 13
SAP30 0.036 0.007 -10000 0 0 19 19
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.036 0.008 -10000 0 0 27 27
YY1/HDAC3 -0.002 0.078 -10000 0 -0.24 31 31
YY1/HDAC2 0.014 0.063 -10000 0 -0.22 21 21
YY1/HDAC1 0.016 0.065 -10000 0 -0.22 21 21
NuRD/MBD2 Complex (MeCP1) -0.006 0.097 -10000 0 -0.27 40 40
PPARG 0.001 0.078 -10000 0 -0.21 54 54
HDAC8/hEST1B 0.048 0.012 -10000 0 -10000 0 0
UBE2I 0.037 0.004 -10000 0 0 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.008 -10000 0 0 24 24
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
HDAC3/SMRT (N-CoR2) 0.026 0.071 -10000 0 -0.25 21 21
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.041 -10000 0 -0.12 7 7
CREBBP 0.037 0.004 -10000 0 0 7 7
NuRD/MBD3/MBD3L2 Complex -0.006 0.11 -10000 0 -0.29 44 44
HDAC1 0.036 0.008 -10000 0 0 24 24
HDAC3 0.007 0.062 -10000 0 -0.29 15 15
HDAC2 0.033 0.012 -10000 0 0 61 61
YY1 0.01 0.033 -10000 0 -0.23 8 8
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.035 0.01 -10000 0 0 43 43
NCOR2 0.037 0.004 -10000 0 0 6 6
MXD1 0.038 0.002 -10000 0 0 2 2
STAT3 0.006 0.062 -10000 0 -0.22 34 34
NFKB1 0.036 0.007 -10000 0 0 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.008 -10000 0 0 24 24
YY1/LSF/HDAC1 0.03 0.073 -10000 0 -0.21 21 21
YY1/SAP30/HDAC1 0.031 0.072 -10000 0 -0.21 21 21
EP300 0.034 0.011 -10000 0 0 49 49
STAT3 (dimer non-phopshorylated) 0.006 0.062 -10000 0 -0.22 34 34
proteasomal ubiquitin-dependent protein catabolic process 0 0.08 -10000 0 -0.32 26 26
histone deacetylation -0.006 0.096 -10000 0 -0.27 41 41
STAT3 (dimer non-phopshorylated)/HDAC3 0.001 0.094 -10000 0 -0.31 28 28
nuclear export -0.048 0.011 -10000 0 -10000 0 0
PRKACA 0.036 0.007 -10000 0 0 17 17
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.034 0.011 -10000 0 0 50 50
GATA2/HDAC3 0.026 0.071 -10000 0 -0.25 20 20
GATA1/HDAC1 0.051 0.024 -10000 0 -0.14 6 6
GATA1/HDAC3 0.027 0.071 -10000 0 -0.25 21 21
CHD4 0.035 0.01 -10000 0 0 41 41
TNF-alpha/TNFR1A 0.036 0.055 -10000 0 -0.14 43 43
SIN3/HDAC complex/Mad/Max -0.007 0.088 -10000 0 -0.28 31 31
NuRD Complex -0.005 0.11 0.16 2 -0.3 42 44
positive regulation of chromatin silencing 0.033 0.074 -10000 0 -0.23 22 22
SIN3B 0.036 0.008 -10000 0 0 27 27
MTA2 0.037 0.005 -10000 0 0 9 9
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.037 0.003 -10000 0 0 4 4
SUMO1/HDAC1 0.037 0.055 -10000 0 -0.22 5 5
HDAC complex 0.066 0.073 -10000 0 -0.15 42 42
GATA1/Fog1 0.028 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.055 0.05 -10000 0 -0.14 22 22
TNF 0.037 0.004 -10000 0 0 6 6
negative regulation of cell growth -0.007 0.088 -10000 0 -0.28 32 32
NuRD/MBD2/PRMT5 Complex -0.006 0.097 -10000 0 -0.27 40 40
Ran/GTP/Exportin 1 0.037 0.059 -10000 0 -0.16 21 21
NF kappa B/RelA/I kappa B alpha -0.007 0.097 -10000 0 -0.26 52 52
SIN3/HDAC complex/NCoR1 -0.005 0.094 -10000 0 -0.3 30 30
TFCP2 0.036 0.008 -10000 0 0 26 26
NR2C1 0.037 0.005 -10000 0 0 8 8
MBD3 0.035 0.01 -10000 0 0 35 35
MBD2 0.037 0.007 -10000 0 0 16 16
TRAIL 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
TNFSF10 0.03 0.015 -10000 0 0 103 103
positive regulation of NF-kappaB transcription factor activity 0.037 0.045 -10000 0 -0.14 25 25
MAP2K4 0.015 0.053 0.21 2 -0.22 7 9
IKBKB 0.037 0.003 -10000 0 0 4 4
TNFRSF10B 0.036 0.008 -10000 0 0 23 23
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.028 -10000 0 -0.1 21 21
IKBKG 0.037 0.003 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.037 0.005 -10000 0 0 10 10
TRAIL/TRAILR2 0.037 0.045 -10000 0 -0.14 24 24
TRAIL/TRAILR3 0.037 0.045 -10000 0 -0.14 25 25
TRAIL/TRAILR1 0.016 0.035 -10000 0 -0.13 26 26
TRAIL/TRAILR4 0.037 0.045 -10000 0 -0.14 25 25
TRAIL/TRAILR1/DAP3/GTP 0.03 0.04 -10000 0 -0.1 33 33
IKK complex -0.022 0.11 -10000 0 -0.22 111 111
RIPK1 0.036 0.007 -10000 0 0 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.024 -10000 0 -0.13 12 12
MAPK3 -0.019 0.01 -10000 0 -10000 0 0
MAP3K1 0.022 0.05 -10000 0 -0.21 6 6
TRAILR4 (trimer) 0.037 0.005 -10000 0 0 10 10
TRADD 0.037 0.005 -10000 0 0 8 8
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.018 0.047 -10000 0 -0.16 24 24
CFLAR 0.037 0.005 -10000 0 0 9 9
MAPK1 -0.017 0.011 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.048 -10000 0 -0.11 26 26
mol:ceramide 0.014 0.028 -10000 0 -0.1 21 21
FADD 0.037 0.006 -10000 0 0 13 13
MAPK8 0.007 0.042 0.19 1 -0.23 5 6
TRAF2 0.036 0.007 -10000 0 0 19 19
TRAILR3 (trimer) 0.037 0.006 -10000 0 0 12 12
CHUK 0.027 0.017 -10000 0 0 139 139
TRAIL/TRAILR1/FADD 0.034 0.039 -10000 0 -0.11 26 26
DAP3 0.036 0.008 -10000 0 0 23 23
CASP10 -0.006 0.051 0.14 14 -0.16 23 37
JNK cascade 0.037 0.045 -10000 0 -0.14 25 25
TRAIL (trimer) 0.03 0.015 -10000 0 0 103 103
TNFRSF10C 0.037 0.006 -10000 0 0 12 12
TRAIL/TRAILR1/DAP3/GTP/FADD 0.044 0.047 -10000 0 -0.1 33 33
TRAIL/TRAILR2/FADD 0.052 0.049 -10000 0 -0.12 24 24
cell death 0.014 0.028 -10000 0 -0.1 21 21
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.024 0.049 -10000 0 -0.16 23 23
TRAILR2 (trimer) 0.036 0.008 -10000 0 0 23 23
CASP8 0.016 0.027 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.088 0.057 -10000 0 -0.11 24 24
Regulation of Androgen receptor activity

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
HDAC1 -0.011 0.003 0 25 -10000 0 25
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.037 0.004 -10000 0 -0.01 3 3
HDAC7 -0.032 0.054 0.18 2 -0.24 9 11
JUN 0.035 0.011 -10000 0 0 44 44
EP300 0.034 0.011 -10000 0 0 49 49
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.018 0.018 0.038 22 -10000 0 22
FOXO1 0.031 0.015 -10000 0 0 95 95
T-DHT/AR 0.02 0.076 0.25 1 -0.23 16 17
MAP2K6 0.036 0.012 -10000 0 -0.035 10 10
BRM/BAF57 0.049 0.024 -10000 0 -0.14 3 3
MAP2K4 0.036 0.013 0.075 1 -0.035 11 12
SMARCA2 0.034 0.012 -10000 0 -10000 0 0
PDE9A -0.013 0.2 -10000 0 -0.8 28 28
NCOA2 0.037 0.006 -10000 0 0 11 11
CEBPA 0.029 0.016 -10000 0 0 121 121
EHMT2 0.038 0.003 -10000 0 0 4 4
cell proliferation -0.011 0.095 0.34 7 -0.33 10 17
NR0B1 0.031 0.014 -10000 0 0 90 90
EGR1 0.03 0.016 -10000 0 0 107 107
RXRs/9cRA 0.068 0.021 -10000 0 -0.11 1 1
AR/RACK1/Src -0.015 0.062 0.2 11 -0.22 2 13
AR/GR 0.004 0.062 0.19 1 -0.21 25 26
GNB2L1 0.037 0.005 -10000 0 0 10 10
PKN1 0.034 0.011 -10000 0 0 45 45
RCHY1 0.037 0.006 -10000 0 0 15 15
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.014 0.017 0.032 14 -10000 0 14
T-DHT/AR/TIF2/CARM1 0.017 0.057 0.23 6 -0.2 4 10
SRC -0.022 0.038 0.19 10 -10000 0 10
NR3C1 0.036 0.008 -10000 0 0 23 23
KLK3 -0.028 0.084 0.4 1 -0.62 1 2
APPBP2 0.035 0.015 -10000 0 -0.034 16 16
TRIM24 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.024 0.028 0.09 3 -0.16 7 10
TMPRSS2 0.014 0.089 -10000 0 -0.58 9 9
RXRG 0.037 0.006 -10000 0 0 13 13
mol:9cRA 0 0 0.003 1 -10000 0 1
RXRA 0.036 0.008 -10000 0 0 25 25
RXRB 0.038 0.003 -10000 0 0 3 3
CARM1 0.036 0.008 -10000 0 0 21 21
NR2C2 0.037 0.005 -10000 0 0 8 8
KLK2 -0.006 0.049 0.23 2 -10000 0 2
AR -0.005 0.046 0.16 6 -0.19 21 27
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.035 0.01 -10000 0 0 35 35
MDM2 0.033 0.012 -10000 0 -0.001 55 55
SRY -0.001 0.001 -10000 0 -0.017 1 1
GATA2 0.037 0.007 -10000 0 0 16 16
MYST2 0 0 -10000 0 -0.003 1 1
HOXB13 0.038 0.004 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.017 0.064 0.2 17 -0.23 2 19
positive regulation of transcription 0.036 0.007 -10000 0 0 16 16
DNAJA1 0.032 0.017 -10000 0 -0.034 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.036 -10000 0 -0.26 8 8
NCOA1 0.04 0.024 0.13 5 -0.18 2 7
SPDEF 0.038 0.004 -10000 0 0 4 4
T-DHT/AR/TIF2 -0.028 0.085 0.25 2 -0.24 44 46
T-DHT/AR/Hsp90 -0.022 0.045 0.2 6 -0.21 3 9
GSK3B 0.035 0.01 -10000 0 0 37 37
NR2C1 0.037 0.005 -10000 0 0 8 8
mol:T-DHT -0.02 0.036 0.14 13 -0.12 4 17
SIRT1 0.027 0.017 -10000 0 0 149 149
ZMIZ2 0.026 0.017 -10000 0 0 152 152
POU2F1 0.038 0.035 0.12 13 -0.11 21 34
T-DHT/AR/DAX-1 -0.021 0.04 0.22 3 -0.19 2 5
CREBBP 0.037 0.004 -10000 0 0 7 7
SMARCE1 0.037 0.005 -10000 0 0 9 9
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.018 0.14 0.32 14 -1 8 22
VDR 0.036 0.008 -10000 0 0 23 23
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.1 0.25 2 -0.28 42 44
RXRs/LXRs/DNA/Oxysterols 0.004 0.14 0.3 2 -0.41 45 47
MED1 0.035 0.01 -10000 0 0 40 40
mol:9cRA 0 0.016 0.043 4 -0.048 43 47
RARs/THRs/DNA/Src-1 0.016 0.056 -10000 0 -0.16 44 44
RXRs/NUR77 0.078 0.068 0.22 1 -0.14 6 7
RXRs/PPAR 0.018 0.049 -10000 0 -0.18 4 4
NCOR2 0.037 0.004 -10000 0 0 6 6
VDR/VDR/Vit D3 0.027 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.082 0.026 -10000 0 -10000 0 0
RARA 0.037 0.004 -10000 0 0 6 6
NCOA1 0.034 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.036 0.008 -10000 0 0 23 23
RARs/RARs/DNA/9cRA 0.057 0.033 -10000 0 -10000 0 0
RARG 0.037 0.005 -10000 0 0 11 11
RPS6KB1 -0.006 0.08 0.5 6 -0.4 8 14
RARs/THRs/DNA/SMRT 0.029 0.031 -10000 0 -0.18 9 9
THRA 0.037 0.006 -10000 0 0 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.027 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.058 0.075 0.29 3 -0.16 41 44
NR1H4 0.037 0.005 -10000 0 0 8 8
RXRs/LXRs/DNA 0.084 0.11 0.31 2 -0.22 40 42
NR1H2 0.03 0.032 0.09 2 -0.062 48 50
NR1H3 0.031 0.033 -10000 0 -0.069 43 43
RXRs/VDR/DNA/Vit D3 0.071 0.064 0.21 1 -0.11 32 33
NR4A1 0.036 0.007 -10000 0 0 17 17
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.008 0.063 -10000 0 -0.21 18 18
RXRG 0.031 0.03 0.09 1 -0.059 46 47
RXR alpha/CCPG 0.023 0.022 -10000 0 -0.059 8 8
RXRA 0.03 0.031 0.09 1 -0.061 46 47
RXRB 0.032 0.033 -10000 0 -0.067 48 48
THRB 0.037 0.005 -10000 0 0 8 8
PPARG 0.036 0.008 -10000 0 0 25 25
PPARD 0.038 0.003 -10000 0 0 3 3
TNF -0.001 0.13 -10000 0 -0.52 13 13
mol:Oxysterols 0 0.015 0.043 4 -0.041 48 52
cholesterol transport 0.004 0.14 0.3 2 -0.41 45 47
PPARA 0.034 0.011 -10000 0 0 44 44
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.037 0.005 -10000 0 0 11 11
RXRs/NUR77/BCL2 0.02 0.032 -10000 0 -0.17 2 2
SREBF1 -0.012 0.17 -10000 0 -0.49 42 42
RXRs/RXRs/DNA/9cRA 0.058 0.075 0.28 3 -0.16 41 44
ABCA1 -0.046 0.26 -10000 0 -0.85 45 45
RARs/THRs 0.11 0.029 -10000 0 -0.12 1 1
RXRs/FXR 0.079 0.068 0.22 1 -0.15 5 6
BCL2 0.036 0.007 -10000 0 0 17 17
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.002 0.039 0.098 27 -0.12 6 33
NFATC2 -0.001 0.028 0.084 17 -0.095 11 28
NFATC3 -0.003 0.039 0.098 27 -0.12 7 34
CD40LG 0.013 0.12 0.29 39 -10000 0 39
PTGS2 -0.022 0.07 0.27 4 -10000 0 4
JUNB 0.032 0.014 -10000 0 0 77 77
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.027 -10000 0 -0.12 13 13
CaM/Ca2+ 0.026 0.027 -10000 0 -0.12 13 13
CALM1 0.036 0.014 -10000 0 -10000 0 0
JUN 0.037 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.02 -10000 0 -0.1 10 10
FOSL1 0.034 0.012 -10000 0 0 56 56
CREM 0.029 0.016 -10000 0 0 120 120
Jun/NFAT1-c-4/p21SNFT 0.056 0.072 0.27 13 -0.18 4 17
FOS 0.028 0.02 -10000 0 -10000 0 0
IFNG 0.008 0.11 0.3 29 -10000 0 29
AP-1/NFAT1-c-4 0.074 0.11 -10000 0 -0.26 3 3
FASLG 0.011 0.12 0.29 36 -10000 0 36
NFAT1-c-4/ICER1 0.041 0.054 0.22 10 -10000 0 10
IL2RA 0.001 0.09 0.25 17 -10000 0 17
FKBP12/FK506 0.022 0.023 -10000 0 -0.13 10 10
CSF2 0.013 0.12 0.3 33 -10000 0 33
JunB/Fra1/NFAT1-c-4 0.046 0.059 0.22 5 -0.18 1 6
IL4 0.013 0.12 0.29 38 -10000 0 38
IL2 0.014 0.084 -10000 0 -0.81 5 5
IL3 0.031 0.081 -10000 0 -0.61 7 7
FKBP1A 0.033 0.012 -10000 0 0 63 63
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.04 0.009 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.064 0.031 -9999 0 -0.12 3 3
E-cadherin/beta catenin 0.049 0.022 -9999 0 -0.14 3 3
CTNNB1 0.036 0.007 -9999 0 0 17 17
JUP 0.034 0.011 -9999 0 0 52 52
CDH1 0.035 0.01 -9999 0 0 39 39
Arf6 trafficking 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
SLC2A4 0.037 0.006 -10000 0 0 14 14
CLTC 0.007 0.097 -10000 0 -0.34 31 31
calcium ion-dependent exocytosis 0.015 0.067 0.13 1 -0.22 19 20
Dynamin 2/GTP 0.027 0.011 -10000 0 -0.1 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.002 0.084 -10000 0 -0.29 30 30
CPE -0.015 0.009 -10000 0 -0.11 1 1
CTNNB1 0.036 0.007 -10000 0 0 17 17
membrane fusion 0.019 0.065 -10000 0 -0.22 15 15
CTNND1 -0.02 0.011 0.089 1 -0.18 1 2
DNM2 0.036 0.007 -10000 0 0 20 20
mol:PI-4-5-P2 0.007 0.069 0.15 4 -0.23 23 27
TSHR -0.017 0.009 0.093 1 -0.11 1 2
INS 0.006 0.095 -10000 0 -0.46 19 19
BIN1 0.032 0.013 -10000 0 0 76 76
mol:Choline 0.019 0.065 -10000 0 -0.22 15 15
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.005 -10000 0 -0.1 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.009 -10000 0 0 31 31
mol:Ca2+ 0.026 0.01 -10000 0 -0.1 1 1
JUP 0.01 0.075 -10000 0 -0.28 25 25
ASAP2/amphiphysin II 0.029 0.045 -10000 0 -0.1 48 48
ARF6/GTP 0.026 0.01 -10000 0 -0.13 1 1
CDH1 0.007 0.076 -10000 0 -0.28 27 27
clathrin-independent pinocytosis 0.026 0.009 -10000 0 -0.13 1 1
MAPK8IP3 0.037 0.004 -10000 0 0 6 6
positive regulation of endocytosis 0.026 0.009 -10000 0 -0.13 1 1
EXOC2 0.036 0.008 -10000 0 0 23 23
substrate adhesion-dependent cell spreading 0 0.056 -10000 0 -0.27 10 10
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.035 0.01 -10000 0 0 36 36
regulation of calcium-dependent cell-cell adhesion -0.037 0.084 0.28 26 -10000 0 26
positive regulation of phagocytosis -0.015 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.047 0.015 -10000 0 -0.11 1 1
ACAP1 0.02 0.061 -10000 0 -0.22 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.001 0.071 -10000 0 -0.29 22 22
clathrin heavy chain/ACAP1 0.011 0.09 0.2 7 -0.25 35 42
JIP4/KLC1 0.049 0.061 -10000 0 -0.15 38 38
EXOC1 0.034 0.011 -10000 0 0 47 47
exocyst 0 0.056 -10000 0 -0.27 10 10
RALA/GTP 0.014 0.029 -10000 0 -0.13 17 17
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.039 0.039 -10000 0 -0.12 26 26
receptor recycling 0.026 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.02 0.011 0.089 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.1 1 1
clathrin coat assembly 0.008 0.096 -10000 0 -0.33 31 31
IL2RA 0.004 0.072 -10000 0 -0.34 17 17
VAMP3 -0.015 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.029 0.09 -10000 0 -0.24 35 35
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.042 -10000 0 -0.21 14 14
PLD2 0 0.042 -10000 0 -0.21 14 14
EXOC5 0.031 0.014 -10000 0 0 91 91
PIP5K1C 0.006 0.066 -10000 0 -0.24 20 20
SDC1 0.011 0.078 -10000 0 -0.28 27 27
ARF6/GDP 0.026 0.007 -10000 0 0 31 31
EXOC7 0.037 0.004 -10000 0 0 7 7
E-cadherin/beta catenin 0.039 0.087 -10000 0 -0.29 26 26
mol:Phosphatidic acid 0.019 0.065 -10000 0 -0.22 15 15
endocytosis -0.028 0.044 0.1 48 -10000 0 48
SCAMP2 0.036 0.009 -10000 0 0 29 29
ADRB2 0.006 0.095 0.27 1 -0.33 30 31
EXOC3 0.036 0.007 -10000 0 0 20 20
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.024 0.01 0.09 1 -0.1 1 2
KLC1 0.033 0.013 -10000 0 0 64 64
AVPR2 0.001 0.093 0.21 3 -0.32 31 34
RALA 0.025 0.018 -10000 0 0 173 173
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.09 0.22 1 -0.27 31 32
Coregulation of Androgen receptor activity

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
NRIP1 0.035 0.012 -10000 0 -10000 0 0
SVIL 0.026 0.018 -10000 0 -10000 0 0
ZNF318 0.035 0.006 -10000 0 -0.046 1 1
JMJD2C 0.004 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.052 0.04 -10000 0 -0.094 3 3
CARM1 0.036 0.008 -10000 0 0 21 21
PRDX1 0.036 0.008 -10000 0 0 24 24
PELP1 0.036 0.007 -10000 0 0 19 19
CTNNB1 0.037 0.007 -10000 0 -10000 0 0
AKT1 0.033 0.012 -10000 0 -0.001 59 59
PTK2B 0.037 0.006 -10000 0 -10000 0 0
MED1 0.034 0.01 -10000 0 0 40 40
MAK 0.034 0.009 -10000 0 -0.046 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.023 0.019 -10000 0 -10000 0 0
GSN 0.033 0.014 -10000 0 -10000 0 0
NCOA2 0.037 0.006 -10000 0 0 11 11
NCOA6 0.034 0.013 -10000 0 -10000 0 0
DNA-PK 0.057 0.05 -10000 0 -0.14 22 22
NCOA4 0.029 0.016 -10000 0 0 125 125
PIAS3 0.037 0.007 -10000 0 -10000 0 0
cell proliferation 0.013 0.049 -10000 0 -0.43 5 5
XRCC5 0.037 0.005 -10000 0 0 10 10
UBE3A 0.038 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.031 0.031 -10000 0 -0.073 18 18
FHL2 -0.028 0.17 -10000 0 -0.66 33 33
RANBP9 0.037 0.007 -10000 0 -10000 0 0
JMJD1A 0.01 0.005 -10000 0 -10000 0 0
CDK6 0.025 0.018 -10000 0 0 165 165
TGFB1I1 0.034 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.034 0.056 -10000 0 -0.11 32 32
XRCC6 0.034 0.01 -10000 0 0 41 41
T-DHT/AR 0.044 0.073 -10000 0 -0.14 15 15
CTDSP1 0.037 0.007 -10000 0 -10000 0 0
CTDSP2 0.031 0.014 -10000 0 -0.04 1 1
BRCA1 0.037 0.006 -10000 0 -10000 0 0
TCF4 0.032 0.012 -10000 0 -0.034 1 1
CDKN2A 0.005 0.012 -10000 0 0 444 444
SRF 0.04 0.055 0.1 73 -0.15 33 106
NKX3-1 0.013 0.034 -10000 0 -0.3 1 1
KLK3 0.018 0.046 -10000 0 -10000 0 0
TMF1 0.036 0.007 -10000 0 0 19 19
HNRNPA1 0.036 0.007 -10000 0 -10000 0 0
AOF2 0.001 0.001 -10000 0 -10000 0 0
APPL1 -0.021 0.009 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.05 0.04 -10000 0 -0.094 3 3
AR 0.036 0.03 -10000 0 -0.065 33 33
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.035 0.009 -10000 0 -10000 0 0
PAWR 0.037 0.007 -10000 0 0 18 18
PRKDC 0.034 0.01 -10000 0 0 42 42
PA2G4 0.035 0.009 -10000 0 -0.034 1 1
UBE2I 0.037 0.004 -10000 0 0 5 5
T-DHT/AR/Cyclin D3/CDK11 p58 0.045 0.043 -10000 0 -0.083 28 28
RPS6KA3 0.037 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.041 0.046 -10000 0 -0.1 7 7
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.046 0.042 -10000 0 -0.11 10 10
Cyclin D3/CDK11 p58 0.022 0.028 -10000 0 -0.13 16 16
VAV3 0.03 0.016 -10000 0 -10000 0 0
KLK2 0.009 0.039 -10000 0 -0.32 3 3
CASP8 0.036 0.006 -10000 0 0 14 14
T-DHT/AR/TIF2/CARM1 0.068 0.048 -10000 0 -0.11 1 1
TMPRSS2 0.012 0.033 -10000 0 -0.32 1 1
CCND1 0.03 0.016 -10000 0 -10000 0 0
PIAS1 0.037 0.009 -10000 0 -10000 0 0
mol:T-DHT 0.003 0.016 0.045 1 -0.05 18 19
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.038 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.038 0.04 -10000 0 -0.1 1 1
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.027 0.029 -10000 0 -0.069 15 15
CCND3 0.036 0.009 -10000 0 0 28 28
TGIF1 0.032 0.013 -10000 0 0 67 67
FKBP4 0.036 0.01 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.059 0.041 -10000 0 -0.11 20 20
HDAC3 0.037 0.005 -10000 0 0 8 8
Ran/GTP/Exportin 1/HDAC4 -0.03 0.022 -10000 0 -0.1 35 35
GATA1/HDAC4 0.048 0.034 -10000 0 -0.14 15 15
GATA1/HDAC5 0.054 0.013 -10000 0 -0.14 1 1
GATA2/HDAC5 0.052 0.016 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.054 0.051 -10000 0 -0.12 28 28
HDAC9 0.023 0.018 -10000 0 0 202 202
Glucocorticoid receptor/Hsp90/HDAC6 0.064 0.04 -10000 0 -0.13 16 16
HDAC4/ANKRA2 0.046 0.04 -10000 0 -0.14 19 19
HDAC5/YWHAB 0.047 0.029 -10000 0 -0.16 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.001 0.041 -10000 0 -0.14 21 21
GATA2 0.037 0.007 -10000 0 0 16 16
HDAC4/RFXANK 0.04 0.049 -10000 0 -0.15 30 30
BCOR 0.035 0.01 -10000 0 0 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.037 0.007 -10000 0 0 16 16
GNB1/GNG2 0.02 0.031 -10000 0 -0.13 20 20
Histones 0.022 0.066 -10000 0 -0.16 39 39
ADRBK1 0.037 0.006 -10000 0 0 13 13
HDAC4 0.035 0.009 -10000 0 0 31 31
XPO1 0.037 0.003 -10000 0 0 4 4
HDAC5/ANKRA2 0.051 0.025 -10000 0 -0.14 7 7
HDAC4/Ubc9 0.048 0.034 -10000 0 -0.14 15 15
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.049 0.031 -10000 0 -0.14 11 11
TUBA1B 0.037 0.007 -10000 0 0 16 16
HDAC6 0.038 0.002 -10000 0 0 2 2
HDAC5/RFXANK 0.045 0.038 -10000 0 -0.14 18 18
CAMK4 0.037 0.005 -10000 0 0 10 10
Tubulin/HDAC6 0.059 0.053 -10000 0 -0.12 36 36
SUMO1 0.037 0.004 -10000 0 0 5 5
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.034 0.011 -10000 0 0 44 44
GATA1 0.038 0.002 -10000 0 0 2 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.036 0.009 -10000 0 0 29 29
NR3C1 0.036 0.008 -10000 0 0 23 23
SUMO1/HDAC4 0.035 0.057 -10000 0 -0.24 5 5
SRF 0.037 0.004 -10000 0 0 6 6
HDAC4/YWHAB 0.042 0.043 -10000 0 -0.15 20 20
Tubulin 0.039 0.052 -10000 0 -0.14 36 36
HDAC4/14-3-3 E 0.043 0.044 -10000 0 -0.14 24 24
GNB1 0.034 0.011 -10000 0 0 47 47
RANGAP1 0.034 0.011 -10000 0 0 44 44
BCL6/BCoR 0.038 0.047 -10000 0 -0.14 28 28
HDAC4/HDAC3/SMRT (N-CoR2) 0.067 0.037 -10000 0 -0.12 15 15
HDAC4/SRF 0.067 0.035 -10000 0 -0.12 13 13
HDAC4/ER alpha 0.046 0.035 -10000 0 -0.14 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.022 0.065 -10000 0 -0.16 39 39
cell motility 0.058 0.053 -10000 0 -0.12 36 36
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.037 0.004 -10000 0 0 5 5
HDAC7/HDAC3 0.027 0.008 -10000 0 -0.13 1 1
BCL6 0.033 0.013 -10000 0 0 70 70
HDAC4/CaMK II delta B 0.035 0.009 -10000 0 0 31 31
Hsp90/HDAC6 0.051 0.019 -10000 0 -0.14 2 2
ESR1 0.035 0.009 -10000 0 0 32 32
HDAC6/HDAC11 0.055 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.059 -10000 0 -0.16 21 21
NPC 0.018 0.02 -10000 0 -0.086 18 18
MEF2C 0.035 0.009 -10000 0 0 31 31
RAN 0.037 0.006 -10000 0 0 13 13
HDAC4/MEF2C 0.094 0.055 -10000 0 -0.12 25 25
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.037 0.004 -10000 0 0 6 6
TUBB2A 0.034 0.011 -10000 0 0 47 47
HDAC11 0.037 0.005 -10000 0 0 8 8
HSP90AA1 0.035 0.01 -10000 0 0 35 35
RANBP2 0.036 0.008 -10000 0 0 24 24
ANKRA2 0.037 0.007 -10000 0 0 16 16
RFXANK 0.035 0.01 -10000 0 0 36 36
nuclear import -0.028 0.058 0.21 26 -10000 0 26
Canonical NF-kappaB pathway

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
FBXW11 0.035 0.019 0.082 8 -0.073 11 19
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.085 0.23 4 -0.26 22 26
ERC1 0.033 0.012 -10000 0 0 58 58
RIP2/NOD2 0.052 0.018 -10000 0 -0.14 2 2
NFKBIA -0.033 0.045 0.2 2 -0.27 13 15
BIRC2 0.037 0.006 -10000 0 0 14 14
IKBKB 0.037 0.003 -10000 0 0 4 4
RIPK2 0.037 0.006 -10000 0 0 14 14
IKBKG 0.023 0.055 -10000 0 -0.34 8 8
IKK complex/A20 0.063 0.079 -10000 0 -0.33 8 8
NEMO/A20/RIP2 0.037 0.006 -10000 0 0 14 14
XPO1 0.037 0.003 -10000 0 0 4 4
NEMO/ATM 0.043 0.063 -10000 0 -0.34 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.037 0.006 -10000 0 0 13 13
Exportin 1/RanGTP 0.048 0.022 -10000 0 -0.14 6 6
IKK complex/ELKS 0.038 0.07 -10000 0 -0.31 9 9
BCL10/MALT1/TRAF6 0.065 0.035 -10000 0 -0.12 10 10
NOD2 0.036 0.007 -10000 0 0 20 20
NFKB1 0.035 0.019 0.082 9 -0.072 12 21
RELA 0.035 0.019 0.082 9 -0.07 12 21
MALT1 0.035 0.009 -10000 0 0 30 30
cIAP1/UbcH5C 0.051 0.027 -10000 0 -0.18 6 6
ATM 0.035 0.01 -10000 0 0 38 38
TNF/TNFR1A 0.036 0.055 -10000 0 -0.14 43 43
TRAF6 0.037 0.006 -10000 0 0 14 14
PRKCA 0.037 0.004 -10000 0 0 6 6
CHUK 0.027 0.017 -10000 0 0 139 139
UBE2D3 0.037 0.006 -10000 0 0 12 12
TNF 0.037 0.004 -10000 0 0 6 6
NF kappa B1 p50/RelA 0.066 0.059 -10000 0 -0.16 26 26
BCL10 0.036 0.007 -10000 0 0 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.033 0.044 0.2 2 -0.27 13 15
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.019 0.082 8 -0.073 11 19
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
IKK complex 0.047 0.067 -10000 0 -0.32 8 8
CYLD 0.037 0.006 -10000 0 0 12 12
IKK complex/PKC alpha 0.057 0.074 -10000 0 -0.32 8 8
Atypical NF-kappaB 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
BCL3/RelA 0.051 0.019 -10000 0 -0.14 2 2
FBXW11 0.036 0.008 -10000 0 0 24 24
NF kappa B1 p50/c-Rel 0.034 0.017 -10000 0 -0.12 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.072 0.2 2 -0.26 16 18
NFKBIA 0.005 0.056 -10000 0 -0.19 24 24
MAPK14 0.037 0.005 -10000 0 0 8 8
NF kappa B1 p105/p50 0.032 0.02 -10000 0 -0.14 5 5
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
REL 0.038 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.033 0.017 -10000 0 -0.12 4 4
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.018 -10000 0 -0.12 5 5
PIK3CA 0.032 0.013 -10000 0 0 74 74
NF kappa B1 p50 dimer -0.021 0.026 0.18 6 -0.14 5 11
PIK3R1 0.033 0.013 -10000 0 0 67 67
NFKB1 -0.023 0.005 -10000 0 -10000 0 0
RELA 0.037 0.005 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.014 0.041 0.14 1 -0.21 5 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.027 0.075 0.19 2 -0.26 16 18
SRC 0.035 0.009 -10000 0 0 31 31
PI3K 0.02 0.075 -10000 0 -0.15 75 75
NF kappa B1 p50/RelA 0.013 0.041 -10000 0 -0.21 5 5
IKBKB 0.037 0.003 -10000 0 0 4 4
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.008 -10000 0 0 24 24
SYK 0.032 0.013 -10000 0 0 76 76
I kappa B alpha/PIK3R1 0.018 0.074 0.19 4 -0.24 25 29
cell death 0.027 0.072 0.18 2 -0.25 17 19
NF kappa B1 p105/c-Rel 0.034 0.017 -10000 0 -0.12 5 5
LCK 0.036 0.008 -10000 0 0 21 21
BCL3 0.036 0.008 -10000 0 0 27 27
ceramide signaling pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.003 0.086 -10000 0 -0.3 21 21
BAG4 0.037 0.005 -10000 0 0 10 10
BAD -0.004 0.034 0.12 4 -0.14 10 14
NFKBIA 0.034 0.012 -10000 0 0 54 54
BIRC3 0.031 0.014 -10000 0 0 84 84
BAX 0 0.045 0.19 13 -0.15 9 22
EnzymeConsortium:3.1.4.12 0.003 0.023 0.081 2 -0.084 10 12
IKBKB -0.007 0.086 0.24 1 -0.31 17 18
MAP2K2 -0.011 0.05 0.18 19 -0.16 8 27
MAP2K1 -0.015 0.041 0.17 6 -0.16 10 16
SMPD1 0.002 0.03 0.12 3 -0.12 14 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.01 0.083 -10000 0 -0.35 10 10
MAP2K4 -0.007 0.038 0.18 4 -0.15 6 10
protein ubiquitination -0.007 0.089 0.52 1 -0.33 15 16
EnzymeConsortium:2.7.1.37 -0.016 0.047 0.18 6 -0.17 7 13
response to UV 0 0 0.002 8 -0.002 1 9
RAF1 -0.011 0.039 0.17 6 -0.15 11 17
CRADD 0.036 0.007 -10000 0 0 16 16
mol:ceramide 0.002 0.034 0.12 3 -0.13 12 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.031 -10000 0 -0.11 16 16
MADD 0.036 0.007 -10000 0 0 19 19
MAP3K1 -0.002 0.036 0.17 5 -0.15 7 12
TRADD 0.037 0.005 -10000 0 0 8 8
RELA/p50 0.037 0.005 -10000 0 0 10 10
MAPK3 -0.008 0.045 0.18 7 -0.16 5 12
MAPK1 -0.015 0.056 0.18 6 -0.2 16 22
p50/RELA/I-kappa-B-alpha 0.045 0.036 -10000 0 -0.14 16 16
FADD 0.007 0.079 -10000 0 -0.32 11 11
KSR1 -0.004 0.034 0.13 4 -0.15 8 12
MAPK8 -0.01 0.035 0.19 5 -0.15 4 9
TRAF2 0.036 0.007 -10000 0 0 19 19
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.01 0.081 0.21 1 -0.32 15 16
TNF R/SODD 0.036 0.054 -10000 0 -0.14 42 42
TNF 0.037 0.004 -10000 0 0 6 6
CYCS 0.015 0.052 0.15 20 -0.15 5 25
IKBKG -0.007 0.085 0.21 2 -0.31 17 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.012 0.088 -10000 0 -0.34 13 13
RELA 0.037 0.005 -10000 0 0 10 10
RIPK1 0.036 0.007 -10000 0 0 19 19
AIFM1 -0.005 0.042 0.14 14 -0.15 8 22
TNF/TNF R/SODD 0.055 0.056 -10000 0 -0.12 41 41
TNFRSF1A 0.033 0.013 -10000 0 0 66 66
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.035 0.089 -10000 0 -0.64 8 8
NSMAF 0.005 0.086 0.22 4 -0.3 19 23
response to hydrogen peroxide 0 0 0.002 8 -0.002 1 9
BCL2 0.036 0.007 -10000 0 0 17 17
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.045 0.063 0.31 1 -10000 0 1
MKNK1 0.035 0.01 -10000 0 0 39 39
MAPK14 0.047 0.036 0.17 3 -0.082 22 25
ATF2/c-Jun 0.001 0.091 -10000 0 -0.31 31 31
MAPK11 0.044 0.038 0.17 3 -0.082 22 25
MITF 0.032 0.048 0.18 3 -0.2 7 10
MAPKAPK5 0.034 0.038 0.18 3 -10000 0 3
KRT8 0.035 0.038 0.21 2 -10000 0 2
MAPKAPK3 0.036 0.008 -10000 0 0 21 21
MAPKAPK2 0.036 0.007 -10000 0 0 17 17
p38alpha-beta/CK2 0.063 0.056 0.24 3 -10000 0 3
CEBPB 0.024 0.067 0.2 3 -0.2 26 29
SLC9A1 0.032 0.04 0.16 1 -0.25 2 3
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.033 0.054 0.27 4 -0.26 1 5
p38alpha-beta/MNK1 0.065 0.068 -10000 0 -0.14 17 17
JUN -0.003 0.088 -10000 0 -0.32 29 29
PPARGC1A 0.033 0.055 0.19 5 -0.2 13 18
USF1 0.028 0.037 0.18 3 -10000 0 3
RAB5/GDP/GDI1 0.014 0.076 -10000 0 -0.21 26 26
NOS2 0.028 0.036 0.18 3 -10000 0 3
DDIT3 0.024 0.057 0.23 1 -0.2 17 18
RAB5A 0.035 0.009 -10000 0 0 33 33
HSPB1 0.074 0.13 0.28 123 -0.15 5 128
p38alpha-beta/HBP1 0.056 0.058 0.24 2 -10000 0 2
CREB1 0.025 0.067 0.23 1 -0.18 32 33
RAB5/GDP 0.02 0.033 -10000 0 -0.13 24 24
EIF4E -0.014 0.06 0.22 10 -0.19 7 17
RPS6KA4 0.034 0.038 0.18 3 -10000 0 3
PLA2G4A -0.014 0.055 0.23 6 -0.19 11 17
GDI1 0.024 0.06 0.2 2 -0.23 18 20
TP53 0.009 0.049 0.17 9 -10000 0 9
RPS6KA5 0.035 0.041 0.18 3 -0.19 1 4
ESR1 0.033 0.037 0.23 1 -10000 0 1
HBP1 0.026 0.017 -10000 0 0 157 157
MEF2C 0.032 0.048 0.18 3 -0.22 7 10
MEF2A 0.031 0.048 0.2 2 -0.22 7 9
EIF4EBP1 0.021 0.073 0.23 1 -0.26 6 7
KRT19 0.036 0.039 0.19 3 -10000 0 3
ELK4 0.033 0.038 0.18 3 -10000 0 3
ATF6 0.034 0.038 0.23 1 -10000 0 1
ATF1 0.019 0.071 0.23 1 -0.31 3 4
p38alpha-beta/MAPKAPK2 0.074 0.056 0.27 1 -10000 0 1
p38alpha-beta/MAPKAPK3 0.074 0.057 0.23 3 -0.13 2 5
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 0.008 0.035 0.13 30 -0.18 3 33
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.002 0.046 0.14 4 -0.17 11 15
AP2 0.022 0.027 -10000 0 -0.13 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.036 -10000 0 -0.12 16 16
CLTB 0.037 0.005 -10000 0 0 9 9
coatomer protein complex/ARF1/GTP/ER cargo protein 0.011 0.037 -10000 0 -0.18 10 10
CD4 0.032 0.013 -10000 0 0 76 76
CLTA 0.034 0.011 -10000 0 0 44 44
mol:GTP -0.003 0.002 0.007 1 -0.019 6 7
ARFGAP1 -0.011 0.003 0 45 -10000 0 45
mol:PI-4-5-P2 0.008 0.018 0.096 15 -0.064 4 19
ARF1/GTP 0.019 0.017 -10000 0 -0.11 6 6
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.031 -10000 0 -0.18 9 9
mol:Choline 0.007 0.018 0.099 15 -10000 0 15
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.036 0.008 -10000 0 0 23 23
DDEF1 0.006 0.018 0.098 15 -10000 0 15
ARF1/GDP 0.006 0.013 -10000 0 -0.082 7 7
AP2M1 0.035 0.009 -10000 0 0 32 32
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.017 0.066 1 -0.11 9 10
Rac/GTP 0.018 0.02 -10000 0 -0.14 5 5
ARF1/GTP/GGA3/ARF-GAP1 0.042 0.025 -10000 0 -0.1 8 8
ARFIP2 0.032 0.016 -10000 0 -0.037 17 17
COPA 0.037 0.006 -10000 0 0 14 14
RAC1 0.026 0.017 -10000 0 0 156 156
ARF1/GTP/coatomer protein complex 0.006 0.044 -10000 0 -0.18 11 11
ARF1/GTP/ARHGAP10 0.022 0.015 -10000 0 -0.11 6 6
GGA3 0.037 0.005 -10000 0 0 9 9
ARF1/GTP/Membrin 0.028 0.026 -10000 0 -0.25 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.037 -10000 0 -0.19 12 12
ARF1/GDP/Membrin 0.032 0.029 -10000 0 -0.28 3 3
Arfaptin 2/Rac/GDP 0.029 0.036 -10000 0 -0.12 16 16
CYTH2 -0.003 0.002 0.007 1 -0.019 6 7
ARF1/GTP/GGA3 0.045 0.021 -10000 0 -0.12 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.019 -10000 0 -0.13 5 5
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.005 0.058 -10000 0 -0.26 14 14
PLD2 0.007 0.018 0.099 15 -10000 0 15
ARF-GAP1/v-SNARE -0.011 0.003 0 45 -10000 0 45
PIP5K1A 0.008 0.018 0.097 15 -0.064 4 19
ARF1/GTP/Membrin/GBF1/p115 0.006 0.036 -10000 0 -0.1 12 12
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.018 0.099 15 -10000 0 15
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.003 0 45 -10000 0 45
GOSR2 0.016 0.018 -10000 0 -0.32 1 1
USO1 0.013 0.034 -10000 0 -0.29 6 6
GBF1 -0.054 0.14 -10000 0 -0.31 108 108
ARF1/GTP/Arfaptin 2 0.043 0.033 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.032 0.046 -10000 0 -0.12 35 35
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 0.036 0.008 -9999 0 0 24 24
Ran/GTP/Exportin 1/HDAC4 -0.033 0.03 -9999 0 -0.12 35 35
MDM2/SUMO1 0.035 0.053 -9999 0 -0.21 5 5
HDAC4 0.035 0.009 -9999 0 0 31 31
Ran/GTP/Exportin 1/HDAC1 -0.032 0.029 -9999 0 -0.14 25 25
SUMO1 0.037 0.004 -9999 0 0 5 5
NPC/RanGAP1/SUMO1 0.005 0.033 -9999 0 -0.15 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.008 0.04 -9999 0 -0.15 21 21
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.037 0.006 -9999 0 0 13 13
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.036 0.008 -9999 0 0 24 24
SUMO1/HDAC4 0.035 0.057 -9999 0 -0.24 5 5
SUMO1/HDAC1 0.037 0.055 -9999 0 -0.22 5 5
RANGAP1 0.034 0.011 -9999 0 0 44 44
MDM2/SUMO1/SUMO1 0.075 0.051 -9999 0 -0.12 16 16
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.001 0.041 -9999 0 -0.14 21 21
Ran/GTP 0.02 0.049 -9999 0 -0.14 21 21
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.034 0.012 -9999 0 0 54 54
UBE2I 0.037 0.004 -9999 0 0 5 5
Ran/GTP/Exportin 1 0.013 0.05 -9999 0 -0.16 21 21
NPC 0.018 0.02 -9999 0 -0.086 18 18
PIAS2 0.036 0.007 -9999 0 0 19 19
PIAS1 0.036 0.008 -9999 0 0 26 26
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.036 0.007 -10000 0 0 17 17
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -10000 0 0
monocyte activation -0.074 0.16 -10000 0 -0.34 138 138
MAP2K2 0.019 0.038 -10000 0 -0.59 2 2
MAP2K1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K7 -0.009 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.002 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -10000 0 0
MAP2K4 -0.009 0.002 -10000 0 -10000 0 0
IL1B -0.004 0.044 0.084 71 -0.086 9 80
Channel 0.023 0.004 -10000 0 -10000 0 0
NLRP1 -0.009 0.002 -10000 0 -10000 0 0
CALM1 0.033 0.012 -10000 0 0 60 60
negative regulation of phagocytosis -0.022 0.12 -10000 0 -0.41 46 46
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 -10000 0 -10000 0 0
MAPK3 -0.009 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.003 -10000 0 -10000 0 0
PGR -0.009 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.002 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.004 -10000 0 -10000 0 0
macrophage activation -0.012 0.013 0.071 9 -10000 0 9
TNF 0.037 0.004 -10000 0 0 6 6
VCAM1 -0.074 0.16 -10000 0 -0.34 136 136
platelet activation -0.022 0.12 -10000 0 -0.41 46 46
MAPKKK cascade 0.004 0.018 0.064 3 -0.067 24 27
IL18 -0.009 0.036 0.1 5 -10000 0 5
negative regulation of macrophage activation -0.002 0 -10000 0 -10000 0 0
LEF -0.002 0 -10000 0 -10000 0 0
CASP1 -0.001 0.004 0.022 12 -10000 0 12
mol:cAMP -0.022 0.12 -10000 0 -0.41 46 46
necrosis -0.002 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.004 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.036 0.029 -9999 0 -0.094 20 20
MAPK9 0.008 0.001 -9999 0 0 14 14
adrenocorticotropin secretion -0.011 0.002 0 16 -10000 0 16
GNB1/GNG2 0.019 0.026 -9999 0 -0.1 20 20
GNB1 0.034 0.011 -9999 0 0 47 47
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 0.008 0.001 -9999 0 0 8 8
Gs family/GTP 0.023 0.004 -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 0.003 0 -9999 0 -10000 0 0
GNAL 0.036 0.007 -9999 0 0 17 17
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.037 0.007 -9999 0 0 16 16
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 122 122
MAPK11 0.007 0.002 -9999 0 0 49 49
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.056 0.019 -10000 0 -10000 0 0
KIRREL 0.04 0.01 0.083 2 -0.042 1 3
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.056 0.019 -10000 0 -10000 0 0
PLCG1 0.035 0.01 -10000 0 0 43 43
ARRB2 0.036 0.008 -10000 0 0 27 27
WASL 0.026 0.017 -10000 0 0 157 157
Nephrin/NEPH1/podocin/CD2AP 0.084 0.051 0.21 1 -0.12 17 18
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.015 0.039 -10000 0 -0.21 8 8
FYN -0.009 0.043 0.17 24 -10000 0 24
mol:Ca2+ 0.084 0.041 0.2 1 -0.12 3 4
mol:DAG 0.086 0.042 0.2 1 -0.12 3 4
NPHS2 0.041 0.009 0.09 1 -0.042 1 2
mol:IP3 0.086 0.042 0.2 1 -0.12 3 4
regulation of endocytosis 0.053 0.05 -10000 0 -0.13 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.072 0.028 0.18 1 -10000 0 1
establishment of cell polarity 0.056 0.019 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.098 0.059 -10000 0 -0.14 16 16
Nephrin/NEPH1/beta Arrestin2 0.056 0.052 -10000 0 -0.13 4 4
NPHS1 0.039 0.011 0.078 6 -10000 0 6
Nephrin/NEPH1/podocin 0.055 0.044 0.21 1 -0.11 1 2
TJP1 0.035 0.009 -10000 0 0 33 33
NCK1 0.036 0.009 -10000 0 0 28 28
NCK2 0.036 0.007 -10000 0 0 19 19
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.088 0.042 0.21 1 -0.12 3 4
CD2AP 0.034 0.011 -10000 0 0 47 47
Nephrin/NEPH1/podocin/GRB2 0.089 0.043 0.21 1 -0.12 7 8
GRB2 0.036 0.007 -10000 0 0 19 19
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.053 0.18 30 -10000 0 30
cytoskeleton organization -0.01 0.04 0.22 7 -0.2 4 11
Nephrin/NEPH1 0.047 0.016 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.066 0.038 -10000 0 -0.14 9 9
Signaling events mediated by the Hedgehog family

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
TGFB2 0.039 0.044 0.31 2 -10000 0 2
IHH 0.054 0.023 0.18 5 -10000 0 5
SHH Np/Cholesterol/GAS1 0.015 0.027 -10000 0 -0.11 15 15
LRPAP1 0.037 0.007 -10000 0 0 16 16
dorsoventral neural tube patterning -0.015 0.027 0.11 15 -10000 0 15
SMO/beta Arrestin2 0.089 0.066 0.27 15 -10000 0 15
SMO 0.03 0.041 0.25 3 -10000 0 3
AKT1 -0.009 0.14 -10000 0 -0.46 30 30
ARRB2 0.036 0.008 -10000 0 0 27 27
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.037 0.006 -10000 0 0 13 13
heart looping 0.031 0.042 0.25 4 -10000 0 4
STIL 0.044 0.095 0.19 132 -10000 0 132
DHH N/PTCH2 0.027 0.004 -10000 0 -10000 0 0
DHH N/PTCH1 0.029 0.022 -10000 0 -10000 0 0
PIK3CA 0.032 0.013 -10000 0 0 74 74
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.035 0.045 -10000 0 -10000 0 0
determination of left/right symmetry 0.031 0.042 0.25 4 -10000 0 4
PIK3R1 0.033 0.013 -10000 0 0 67 67
skeletal system development 0.035 0.045 0.3 2 -10000 0 2
IHH N/Hhip 0.035 0.014 0.12 4 -10000 0 4
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.031 0.042 0.25 4 -10000 0 4
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.036 0.007 -10000 0 0 18 18
PI3K 0.02 0.075 -10000 0 -0.15 75 75
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.031 0.014 -10000 0 0 89 89
somite specification 0.031 0.042 0.25 4 -10000 0 4
SHH Np/Cholesterol/PTCH1 0.026 0.028 0.18 1 -10000 0 1
SHH Np/Cholesterol/PTCH2 0.022 0.016 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.021 0.016 -10000 0 -10000 0 0
SHH -0.016 0.011 -10000 0 -10000 0 0
catabolic process 0.041 0.034 0.19 2 -10000 0 2
SMO/Vitamin D3 0.029 0.04 0.27 3 -10000 0 3
SHH Np/Cholesterol/Hhip -0.011 0.008 -10000 0 -10000 0 0
LRP2 0.037 0.006 -10000 0 0 13 13
receptor-mediated endocytosis 0.028 0.04 0.23 4 -10000 0 4
SHH Np/Cholesterol/BOC -0.011 0.008 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.022 0.016 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.011 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.08 0.086 0.21 140 -10000 0 140
IHH N/PTCH2 0.063 0.017 0.16 3 -10000 0 3
CDON 0.037 0.004 -10000 0 0 7 7
IHH N/PTCH1 0.055 0.032 -10000 0 -10000 0 0
Megalin/LRPAP1 0.05 0.029 -10000 0 -0.14 10 10
PTCH2 0.037 0.005 -10000 0 0 10 10
SHH Np/Cholesterol 0.012 0.009 -10000 0 -10000 0 0
PTCH1 0.041 0.034 0.19 2 -10000 0 2
HHIP 0 0 -10000 0 -10000 0 0
Aurora C signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.037 0.005 -9999 0 0 8 8
Aurora C/Aurora B/INCENP 0.061 0.027 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.005 0.062 -9999 0 -0.39 12 12
AURKB 0.035 0.01 -9999 0 0 42 42
AURKC 0.034 0.011 -9999 0 0 48 48
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.047 0.2 0.6 1 -0.68 19 20
PCK1 0.048 0.12 0.43 2 -0.62 3 5
HNF4A 0.069 0.18 0.74 2 -0.69 8 10
KCNJ11 0.074 0.19 0.47 3 -0.6 16 19
AKT1 0.064 0.14 0.42 1 -0.42 16 17
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.085 0.2 0.58 3 -0.67 11 14
NKX2-1 0.042 0.11 -10000 0 -0.72 1 1
ACADM 0.056 0.18 0.52 3 -0.72 11 14
TAT 0.052 0.14 0.62 1 -0.66 5 6
CEBPB 0.034 0.016 0.12 1 -10000 0 1
CEBPA 0.032 0.018 0.093 1 -10000 0 1
TTR 0.035 0.19 0.6 4 -0.64 13 17
PKLR 0.061 0.17 0.56 2 -0.67 9 11
APOA1 0.087 0.22 0.77 2 -0.82 9 11
CPT1C 0.06 0.17 0.47 3 -0.58 14 17
ALAS1 0.036 0.25 0.44 1 -1.2 15 16
TFRC 0.026 0.29 0.51 6 -0.96 34 40
FOXF1 0.029 0.013 -10000 0 -0.089 1 1
NF1 0.035 0.036 -10000 0 -0.17 15 15
HNF1A (dimer) 0.048 0.007 0.15 1 -10000 0 1
CPT1A 0.058 0.17 0.6 1 -0.68 8 9
HMGCS1 0.061 0.17 0.5 5 -0.69 8 13
NR3C1 0.048 0.019 -10000 0 -10000 0 0
CPT1B 0.048 0.16 0.6 1 -0.67 9 10
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.04 0.006 -10000 0 -10000 0 0
GCK 0.1 0.2 0.53 24 -0.67 8 32
CREB1 0.045 0.013 0.15 1 -10000 0 1
IGFBP1 0.055 0.13 -10000 0 -0.58 7 7
PDX1 0.063 0.12 -10000 0 -10000 0 0
UCP2 0.03 0.24 0.53 3 -0.68 41 44
ALDOB 0.075 0.19 0.57 2 -0.7 10 12
AFP 0.013 0.029 -10000 0 -10000 0 0
BDH1 0.051 0.2 0.56 2 -0.68 18 20
HADH 0.067 0.21 0.55 1 -0.7 17 18
F2 0.085 0.22 0.97 1 -0.86 8 9
HNF1A 0.048 0.007 0.15 1 -10000 0 1
G6PC 0.012 0.082 0.42 1 -0.34 1 2
SLC2A2 0.079 0.13 -10000 0 -10000 0 0
INS 0.026 0.042 0.19 14 -0.094 34 48
FOXA1 0.01 0.015 0.16 1 -10000 0 1
FOXA3 0.019 0.057 0.21 3 -0.19 24 27
FOXA2 0.11 0.23 0.64 2 -0.72 14 16
ABCC8 0.073 0.19 0.57 2 -0.7 10 12
ALB 0.014 0.03 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.037 0.013 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.001 0.06 0.38 3 -10000 0 3
IL27/IL27R/JAK1 0.039 0.063 -10000 0 -10000 0 0
TBX21 -0.021 0.086 0.34 13 -10000 0 13
IL12B 0.038 0.005 -10000 0 0 8 8
IL12A -0.011 0.002 0.013 2 -10000 0 2
IL6ST 0.035 0.011 -10000 0 -0.033 1 1
IL27RA/JAK1 0.025 0.043 -10000 0 -10000 0 0
IL27 -0.001 0.003 -10000 0 -10000 0 0
TYK2 0.035 0.011 -10000 0 -0.033 1 1
T-helper cell lineage commitment 0.069 0.079 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.001 0.06 0.38 3 -10000 0 3
T cell proliferation during immune response -0.001 0.06 0.38 3 -10000 0 3
MAPKKK cascade 0.001 0.06 -10000 0 -0.38 3 3
STAT3 0.035 0.01 -10000 0 0 40 40
STAT2 0.036 0.008 -10000 0 0 21 21
STAT1 0.034 0.01 -10000 0 0 41 41
IL12RB1 0.036 0.008 -10000 0 0 22 22
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.023 0.082 0.34 11 -10000 0 11
IL27/IL27R/JAK2/TYK2 0.001 0.06 -10000 0 -0.38 3 3
positive regulation of T cell mediated cytotoxicity 0.001 0.06 -10000 0 -0.38 3 3
STAT1 (dimer) 0.044 0.081 -10000 0 -10000 0 0
JAK2 0.032 0.014 -10000 0 -0.032 1 1
JAK1 0.034 0.011 -10000 0 0 44 44
STAT2 (dimer) 0.014 0.093 -10000 0 -0.32 12 12
T cell proliferation 0.009 0.054 -10000 0 -0.3 1 1
IL12/IL12R/TYK2/JAK2 0.009 0.18 -10000 0 -0.76 26 26
IL17A 0.067 0.079 -10000 0 -10000 0 0
mast cell activation -0.001 0.06 0.38 3 -10000 0 3
IFNG 0.003 0.028 -10000 0 -0.089 21 21
T cell differentiation -0.002 0.003 -10000 0 -0.017 10 10
STAT3 (dimer) 0.011 0.1 -10000 0 -0.36 13 13
STAT5A (dimer) 0.015 0.095 -10000 0 -0.32 12 12
STAT4 (dimer) 0.014 0.092 -10000 0 -0.34 8 8
STAT4 0.035 0.009 -10000 0 0 31 31
T cell activation -0.005 0.005 -10000 0 -0.084 1 1
IL27R/JAK2/TYK2 0.038 0.064 -10000 0 -10000 0 0
GATA3 0.003 0.07 0.62 6 -10000 0 6
IL18 -0.01 0.004 0 74 -10000 0 74
positive regulation of mast cell cytokine production 0.011 0.1 -10000 0 -0.36 13 13
IL27/EBI3 0.025 0.011 -10000 0 -10000 0 0
IL27RA 0.002 0.029 -10000 0 -10000 0 0
IL6 0.023 0.021 -10000 0 -10000 0 0
STAT5A 0.037 0.005 -10000 0 0 8 8
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.008 0.028 -10000 0 -10000 0 0
IL1B -0.009 0.005 0 101 -10000 0 101
EBI3 0.036 0.011 -10000 0 -0.033 1 1
TNF -0.012 0.001 0 6 -10000 0 6
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.037 0.005 0 11 -9999 0 11
PI3K Class IB/PDE3B 0.037 0.005 -9999 0 0 11 11
PDE3B 0.037 0.005 -9999 0 0 11 11
Visual signal transduction: Rods

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
mol:K + 0.037 0.005 -10000 0 0 10 10
GNAT1/GTP 0.027 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.049 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.049 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.037 0.006 -10000 0 0 14 14
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.07 0.025 -10000 0 -10000 0 0
mol:Na + 0.044 0.017 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.047 0.015 -10000 0 -0.11 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.055 0.02 -10000 0 -10000 0 0
CNGB1 0.037 0.005 -10000 0 0 11 11
RDH5 0.036 0.008 -10000 0 0 25 25
SAG 0.037 0.005 -10000 0 0 11 11
mol:Ca2+ -0.035 0.026 0.16 8 -10000 0 8
Na + (4 Units) 0.042 0.019 -10000 0 -10000 0 0
RGS9 0.036 0.007 -10000 0 0 18 18
GNB1/GNGT1 0.032 0.038 -10000 0 -0.14 13 13
GNAT1/GDP 0.06 0.022 -10000 0 -0.1 1 1
GUCY2D 0.037 0.006 -10000 0 0 12 12
GNGT1 0.026 0.017 -10000 0 0 158 158
GUCY2F 0.038 0.002 -10000 0 0 1 1
GNB5 0.036 0.007 -10000 0 0 18 18
mol:GMP (4 units) 0.029 0.009 -10000 0 -10000 0 0
mol:11-cis-retinal 0.036 0.008 -10000 0 0 25 25
mol:cGMP 0.029 0.007 -10000 0 -10000 0 0
GNB1 0.034 0.011 -10000 0 0 47 47
Rhodopsin 0.052 0.015 -10000 0 -10000 0 0
SLC24A1 0.037 0.005 -10000 0 0 10 10
CNGA1 0.037 0.005 -10000 0 0 9 9
Metarhodopsin II 0.024 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.047 0.009 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.006 0.037 -10000 0 -0.16 15 15
GCAP Family/Ca ++ 0.024 0.003 -10000 0 -10000 0 0
PDE6A/B 0.054 0.01 -10000 0 -10000 0 0
mol:Pi 0.047 0.015 -10000 0 -0.11 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.042 0.042 -10000 0 -0.11 13 13
PDE6B 0.037 0.005 -10000 0 0 11 11
PDE6A 0.037 0.004 -10000 0 0 7 7
PDE6G 0.037 0.003 -10000 0 0 4 4
RHO 0.037 0.006 -10000 0 0 13 13
PDE6 0.087 0.027 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.048 0.006 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.037 0.004 -10000 0 0 6 6
Ephrin A reverse signaling

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
MAPKKK cascade 0.049 0.009 -10000 0 -9999 0 0
EFNA5 0.037 0.005 -10000 0 0 9 9
FYN -0.019 0.016 0.18 2 -9999 0 2
neuron projection morphogenesis 0.049 0.009 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.049 0.009 -10000 0 -9999 0 0
EPHA5 0.037 0.005 -10000 0 0 9 9
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 509 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.34 0.025 -0.28 0.039
47_PPARGC1A 0.038 0.038 0.038 0
105_BMP4 0.038 0.038 0 0.038
105_BMP6 0.038 0.038 0 0.038
105_BMP7 0.038 0.038 0 0.038
105_BMP2 0.038 0.038 0 0.038
131_RELN/VLDLR 0 0.077 0.097 0.097
30_TGFB1/TGF beta receptor Type II 0 0.037 0 0
84_STAT5B 0.17 0.14 -0.28 0.062
84_STAT5A 0.17 0.14 -0.28 0.056
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/2540041/2.GDAC_MergeDataFiles.Finished/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/GBM-TP/2541655/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

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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