Ovarian Serous Cystadenocarcinoma: Paradigm Report
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

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

Summary

There were 91 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 118
FOXM1 transcription factor network 110
PLK2 and PLK4 events 108
Wnt signaling 105
TCGA08_p53 103
Syndecan-1-mediated signaling events 94
TCGA08_retinoblastoma 94
IGF1 pathway 88
LPA receptor mediated events 87
Canonical Wnt signaling pathway 82
Results

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 118 9001 76 -0.078 0.063 1000 -1000 0 -1000
FOXM1 transcription factor network 110 5634 51 -0.47 0.035 1000 -1000 -0.021 -1000
PLK2 and PLK4 events 108 326 3 -0.025 0.035 1000 -1000 -0.02 -1000
Wnt signaling 105 740 7 -0.037 0.036 1000 -1000 0 -1000
TCGA08_p53 103 724 7 -0.079 0.036 1000 -1000 -0.008 -1000
Syndecan-1-mediated signaling events 94 3226 34 -0.073 0.049 1000 -1000 -0.008 -1000
TCGA08_retinoblastoma 94 753 8 -0.03 0.035 1000 -1000 -0.009 -1000
IGF1 pathway 88 5017 57 -0.058 0.044 1000 -1000 -0.025 -1000
LPA receptor mediated events 87 8946 102 -0.06 0.036 1000 -1000 -0.032 -1000
Canonical Wnt signaling pathway 82 4202 51 -0.36 0.16 1000 -1000 -0.016 -1000
Osteopontin-mediated events 79 3039 38 -0.17 0.036 1000 -1000 -0.013 -1000
amb2 Integrin signaling 78 6457 82 -0.064 0.059 1000 -1000 -0.014 -1000
Glypican 2 network 77 309 4 -0.012 -0.012 1000 -1000 0 -1000
Syndecan-4-mediated signaling events 77 5160 67 -0.12 0.047 1000 -1000 -0.028 -1000
Endothelins 76 7314 96 -0.22 0.036 1000 -1000 -0.022 -1000
Ras signaling in the CD4+ TCR pathway 71 1211 17 -0.001 0.034 1000 -1000 -0.004 -1000
Fc-epsilon receptor I signaling in mast cells 70 6809 97 -0.079 0.04 1000 -1000 -0.042 -1000
TRAIL signaling pathway 70 3382 48 -0.038 0.037 1000 -1000 -0.021 -1000
Nectin adhesion pathway 68 4338 63 -0.091 0.063 1000 -1000 -0.024 -1000
Noncanonical Wnt signaling pathway 66 1740 26 -0.038 0.036 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 65 6825 105 -0.12 0.047 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 65 3143 48 -0.15 0.077 1000 -1000 -0.044 -1000
Syndecan-2-mediated signaling events 61 4219 69 -0.028 0.048 1000 -1000 -0.033 -1000
Nongenotropic Androgen signaling 61 3223 52 -0.15 0.076 1000 -1000 -0.019 -1000
EPHB forward signaling 60 5149 85 -0.07 0.13 1000 -1000 -0.037 -1000
IL23-mediated signaling events 60 3634 60 -0.23 0.069 1000 -1000 -0.023 -1000
Class I PI3K signaling events 59 4327 73 -0.037 0.046 1000 -1000 -0.018 -1000
IL2 signaling events mediated by PI3K 57 3347 58 -0.089 0.036 1000 -1000 -0.019 -1000
PDGFR-alpha signaling pathway 56 2496 44 -0.16 0.044 1000 -1000 -0.022 -1000
BCR signaling pathway 56 5614 99 -0.046 0.049 1000 -1000 -0.037 -1000
FOXA2 and FOXA3 transcription factor networks 52 2411 46 -0.31 0.037 1000 -1000 -0.031 -1000
Integrins in angiogenesis 51 4286 84 -0.059 0.05 1000 -1000 -0.019 -1000
IL2 signaling events mediated by STAT5 51 1135 22 -0.036 0.045 1000 -1000 -0.012 -1000
IL6-mediated signaling events 49 3701 75 -0.17 0.066 1000 -1000 -0.039 -1000
mTOR signaling pathway 48 2585 53 -0.12 0.044 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 48 3712 76 -0.062 0.063 1000 -1000 -0.03 -1000
Arf6 downstream pathway 47 2037 43 -0.066 0.047 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 47 1240 26 -0.053 0.058 1000 -1000 -0.012 -1000
BARD1 signaling events 45 2619 57 -0.038 0.061 1000 -1000 -0.054 -1000
Signaling events mediated by PTP1B 45 3470 76 -0.055 0.063 1000 -1000 -0.02 -1000
EPO signaling pathway 45 2494 55 0 0.073 1000 -1000 -0.014 -1000
Paxillin-independent events mediated by a4b1 and a4b7 45 1667 37 -0.029 0.086 1000 -1000 -0.007 -1000
ErbB2/ErbB3 signaling events 44 2898 65 -0.061 0.036 1000 -1000 -0.045 -1000
FoxO family signaling 44 2859 64 -0.13 0.037 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 44 1516 34 -0.057 0.042 1000 -1000 -0.026 -1000
Presenilin action in Notch and Wnt signaling 43 2623 61 -0.3 0.076 1000 -1000 -0.028 -1000
IL1-mediated signaling events 43 2674 62 -0.033 0.068 1000 -1000 -0.021 -1000
Reelin signaling pathway 41 2297 56 -0.015 0.091 1000 -1000 -0.008 -1000
HIF-2-alpha transcription factor network 41 1789 43 -0.052 0.047 1000 -1000 -0.055 -1000
Syndecan-3-mediated signaling events 41 1435 35 -0.037 0.07 1000 -1000 -0.016 -1000
Aurora A signaling 40 2432 60 -0.044 0.063 1000 -1000 -0.019 -1000
Regulation of nuclear SMAD2/3 signaling 39 5377 136 -0.11 0.068 1000 -1000 -0.045 -1000
IFN-gamma pathway 39 2702 68 -0.05 0.067 1000 -1000 -0.03 -1000
Aurora B signaling 39 2619 67 -0.056 0.055 1000 -1000 -0.015 -1000
p75(NTR)-mediated signaling 38 4783 125 -0.055 0.089 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 38 1221 32 -0.021 0.04 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 38 576 15 -0.085 0.035 1000 -1000 -0.022 -1000
E-cadherin signaling in keratinocytes 38 1635 43 -0.021 0.047 1000 -1000 -0.01 -1000
E-cadherin signaling events 38 192 5 0.032 0.047 1000 -1000 0.033 -1000
IL4-mediated signaling events 37 3371 91 -0.18 0.062 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 37 1776 47 -0.032 0.052 1000 -1000 -0.023 -1000
Retinoic acid receptors-mediated signaling 37 2194 58 -0.097 0.043 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 37 2754 74 -0.053 0.061 1000 -1000 -0.047 -1000
Regulation of Telomerase 36 3680 102 -0.23 0.065 1000 -1000 -0.023 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 35 809 23 -0.032 0.039 1000 -1000 -0.006 -1000
PDGFR-beta signaling pathway 35 3444 97 -0.085 0.064 1000 -1000 -0.035 -1000
IL12-mediated signaling events 34 2975 87 -0.2 0.081 1000 -1000 -0.022 -1000
Class I PI3K signaling events mediated by Akt 34 2350 68 -0.022 0.063 1000 -1000 -0.018 -1000
Circadian rhythm pathway 33 740 22 -0.071 0.059 1000 -1000 -0.028 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 33 1814 54 -0.021 0.051 1000 -1000 -0.019 -1000
BMP receptor signaling 33 2712 81 -0.017 0.07 1000 -1000 -0.007 -1000
TCR signaling in naïve CD8+ T cells 33 3091 93 -0.068 0.075 1000 -1000 -0.024 -1000
Plasma membrane estrogen receptor signaling 33 2909 86 -0.054 0.054 1000 -1000 -0.023 -1000
ErbB4 signaling events 32 2250 69 -0.05 0.048 1000 -1000 -0.018 -1000
Paxillin-dependent events mediated by a4b1 32 1164 36 -0.082 0.086 1000 -1000 -0.047 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 32 1470 45 -0.049 0.075 1000 -1000 -0.027 -1000
Insulin Pathway 32 2398 74 -0.023 0.078 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 32 1057 33 0 0.066 1000 -1000 -0.013 -1000
Neurotrophic factor-mediated Trk receptor signaling 32 3903 120 -0.13 0.086 1000 -1000 -0.025 -1000
Caspase cascade in apoptosis 31 2328 74 -0.048 0.052 1000 -1000 -0.026 -1000
PLK1 signaling events 31 2669 85 -0.046 0.057 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 31 1250 40 -0.056 0.057 1000 -1000 -0.046 -1000
Regulation of p38-alpha and p38-beta 30 1645 54 -0.026 0.06 1000 -1000 -0.007 -1000
JNK signaling in the CD4+ TCR pathway 29 503 17 0 0.06 1000 -1000 -0.006 -1000
S1P5 pathway 29 493 17 -0.002 0.036 1000 -1000 -0.011 -1000
Atypical NF-kappaB pathway 29 917 31 -0.019 0.036 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class II 28 2146 75 -0.028 0.082 1000 -1000 -0.022 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 28 2438 85 -0.18 0.064 1000 -1000 -0.035 -1000
Glucocorticoid receptor regulatory network 27 3168 114 -0.12 0.058 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 27 2244 83 -0.018 0.062 1000 -1000 -0.006 -1000
Sumoylation by RanBP2 regulates transcriptional repression 27 738 27 -0.03 0.076 1000 -1000 -0.023 -1000
Ceramide signaling pathway 26 2025 76 -0.062 0.063 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 25 1013 39 -0.031 0.057 1000 -1000 -0.022 -1000
ceramide signaling pathway 25 1263 49 -0.016 0.053 1000 -1000 -0.021 -1000
Regulation of Androgen receptor activity 24 1736 70 -0.088 0.065 1000 -1000 -0.034 -1000
Arf6 signaling events 23 1436 62 0 0.088 1000 -1000 0 -1000
Glypican 1 network 23 1139 48 -0.035 0.066 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 23 1953 82 -0.018 0.086 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class I 23 2464 104 -0.027 0.057 1000 -1000 -0.022 -1000
S1P4 pathway 23 578 25 -0.01 0.05 1000 -1000 -0.006 -1000
p38 MAPK signaling pathway 23 1026 44 -0.001 0.063 1000 -1000 -0.006 -1000
Coregulation of Androgen receptor activity 22 1678 76 -0.07 0.046 1000 -1000 -0.01 -1000
Hedgehog signaling events mediated by Gli proteins 22 1472 65 -0.001 0.054 1000 -1000 -0.011 -1000
Sphingosine 1-phosphate (S1P) pathway 20 574 28 -0.013 0.05 1000 -1000 -0.024 -1000
Aurora C signaling 18 131 7 0 0.057 1000 -1000 -0.006 -1000
Effects of Botulinum toxin 18 475 26 -0.008 0.061 1000 -1000 -0.008 -1000
Signaling events mediated by the Hedgehog family 17 908 52 -0.015 0.058 1000 -1000 -0.019 -1000
Signaling events mediated by VEGFR1 and VEGFR2 17 2217 125 -0.009 0.067 1000 -1000 -0.018 -1000
EGFR-dependent Endothelin signaling events 17 367 21 -0.009 0.074 1000 -1000 -0.003 -1000
Alternative NF-kappaB pathway 17 224 13 0 0.089 1000 -1000 0 -1000
S1P3 pathway 16 689 42 -0.013 0.05 1000 -1000 -0.017 -1000
Arf1 pathway 16 896 54 -0.008 0.043 1000 -1000 -0.009 -1000
Nephrin/Neph1 signaling in the kidney podocyte 15 510 34 -0.048 0.083 1000 -1000 -0.036 -1000
Cellular roles of Anthrax toxin 15 614 39 -0.091 0.036 1000 -1000 -0.015 -1000
RXR and RAR heterodimerization with other nuclear receptor 15 818 52 -0.003 0.1 1000 -1000 -0.009 -1000
S1P1 pathway 15 552 36 0 0.039 1000 -1000 -0.014 -1000
IL27-mediated signaling events 13 675 51 -0.011 0.065 1000 -1000 -0.037 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 13 898 68 -0.08 0.11 1000 -1000 -0.031 -1000
VEGFR1 specific signals 13 772 56 -0.022 0.049 1000 -1000 -0.026 -1000
Angiopoietin receptor Tie2-mediated signaling 13 1205 88 -0.019 0.074 1000 -1000 -0.046 -1000
LPA4-mediated signaling events 12 154 12 -0.015 0.046 1000 -1000 -0.015 -1000
Arf6 trafficking events 12 877 71 -0.039 0.046 1000 -1000 -0.031 -1000
Class IB PI3K non-lipid kinase events 12 36 3 -0.036 0.036 1000 -1000 -0.034 -1000
Calcium signaling in the CD4+ TCR pathway 11 342 31 -0.021 0.053 1000 -1000 -0.02 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 11 912 78 -0.02 0.069 1000 -1000 -0.024 -1000
Visual signal transduction: Cones 9 349 38 -0.001 0.073 1000 -1000 -0.01 -1000
Visual signal transduction: Rods 9 473 52 -0.014 0.077 1000 -1000 -0.004 -1000
Signaling mediated by p38-alpha and p38-beta 8 372 44 -0.024 0.051 1000 -1000 -0.007 -1000
Ephrin A reverse signaling 7 52 7 -0.011 0.045 1000 -1000 -0.01 -1000
Rapid glucocorticoid signaling 7 146 20 -0.008 0.036 1000 -1000 -0.008 -1000
a4b1 and a4b7 Integrin signaling 6 30 5 0.036 0.053 1000 -1000 0.033 -1000
Total 5262 292741 7203 -8.2 7.6 131000 -131000 -2.7 -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 -0.007 0.44 0.55 59 -0.7 108 167
HDAC7 -0.002 0.007 -10000 0 -0.043 11 11
HIF1A/ARNT/Cbp/p300/Src-1 -0.023 0.37 0.56 11 -0.66 84 95
SMAD4 0.031 0.014 -10000 0 0 94 94
ID2 -0.015 0.45 0.56 61 -0.7 112 173
AP1 -0.022 0.11 -10000 0 -0.21 130 130
ABCG2 0.001 0.44 0.55 63 -0.7 106 169
HIF1A 0.025 0.12 0.21 42 -0.15 84 126
TFF3 -0.022 0.42 0.56 48 -0.69 106 154
GATA2 0.038 0.01 -10000 0 0 26 26
AKT1 0.029 0.12 0.21 47 -0.16 81 128
response to hypoxia 0.003 0.085 0.15 57 -0.12 84 141
MCL1 -0.013 0.43 0.55 55 -0.7 104 159
NDRG1 -0.051 0.4 0.54 37 -0.71 99 136
SERPINE1 -0.047 0.41 0.55 36 -0.69 106 142
FECH -0.003 0.44 0.56 63 -0.69 108 171
FURIN 0.005 0.44 0.56 64 -0.69 106 170
NCOA2 0.036 0.01 -10000 0 -10000 0 0
EP300 0.043 0.15 0.29 63 -0.28 32 95
HMOX1 -0.035 0.43 0.55 43 -0.7 112 155
BHLHE40 -0.062 0.4 0.5 59 -0.69 108 167
BHLHE41 -0.062 0.4 0.5 59 -0.69 108 167
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.062 0.17 0.34 15 -0.24 35 50
ENG 0.028 0.14 0.27 27 -0.24 24 51
JUN 0.034 0.013 -10000 0 0 62 62
RORA -0.019 0.43 0.55 51 -0.7 106 157
ABCB1 -0.006 0.084 -10000 0 -0.48 1 1
TFRC -0.042 0.42 0.56 44 -0.7 106 150
CXCR4 -0.035 0.44 0.56 54 -0.7 115 169
TF -0.005 0.43 0.56 58 -0.69 105 163
CITED2 -0.027 0.44 0.55 56 -0.71 108 164
HIF1A/ARNT -0.077 0.45 -10000 0 -0.86 85 85
LDHA -0.034 0.23 -10000 0 -0.98 25 25
ETS1 0.003 0.44 0.55 65 -0.69 105 170
PGK1 -0.008 0.46 0.56 64 -0.73 109 173
NOS2 -0.062 0.4 0.5 59 -0.69 108 167
ITGB2 -0.049 0.44 0.55 44 -0.72 116 160
ALDOA 0.007 0.44 0.56 67 -0.69 108 175
Cbp/p300/CITED2 -0.043 0.44 0.56 38 -0.78 94 132
FOS 0.021 0.019 -10000 0 0 231 231
HK2 0.004 0.44 0.56 66 -0.69 107 173
SP1 0.043 0.006 -10000 0 -10000 0 0
GCK 0.063 0.19 0.56 6 -0.54 2 8
HK1 0.003 0.44 0.56 64 -0.7 106 170
NPM1 0.005 0.44 0.56 65 -0.69 108 173
EGLN1 -0.007 0.44 0.55 62 -0.7 105 167
CREB1 0.038 0.023 -10000 0 -0.099 12 12
PGM1 -0.011 0.45 0.56 65 -0.72 110 175
SMAD3 0.036 0.006 -10000 0 -10000 0 0
EDN1 0.045 0.16 0.45 6 -0.47 6 12
IGFBP1 0.003 0.44 0.55 64 -0.69 108 172
VEGFA -0.037 0.32 0.47 47 -0.58 90 137
HIF1A/JAB1 0.038 0.097 0.2 10 -0.21 20 30
CP -0.057 0.43 0.56 41 -0.72 109 150
CXCL12 -0.078 0.41 0.56 32 -0.7 113 145
COPS5 0.035 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.073 -10000 0 -0.19 49 49
BNIP3 -0.028 0.44 0.54 52 -0.72 105 157
EGLN3 -0.026 0.42 0.55 45 -0.7 104 149
CA9 -0.033 0.42 0.54 48 -0.7 103 151
TERT -0.007 0.43 0.55 61 -0.7 102 163
ENO1 0.002 0.44 0.56 62 -0.71 105 167
PFKL 0.002 0.44 0.56 62 -0.69 107 169
NCOA1 0.035 0.009 -10000 0 0 31 31
ADM -0.063 0.43 0.55 35 -0.73 113 148
ARNT 0.023 0.11 0.2 39 -0.14 79 118
HNF4A 0.038 0.01 -10000 0 -10000 0 0
ADFP -0.048 0.43 0.55 45 -0.71 113 158
SLC2A1 -0.027 0.36 0.49 42 -0.61 100 142
LEP 0.005 0.44 0.56 64 -0.69 106 170
HIF1A/ARNT/Cbp/p300 -0.035 0.37 0.56 11 -0.67 86 97
EPO 0.044 0.31 0.54 20 -0.64 34 54
CREBBP 0.05 0.14 0.28 71 -0.26 20 91
HIF1A/ARNT/Cbp/p300/HDAC7 -0.051 0.36 0.53 6 -0.68 86 92
PFKFB3 -0.027 0.44 0.54 56 -0.71 112 168
NT5E -0.069 0.41 0.56 34 -0.71 108 142
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 -0.29 0.6 -10000 0 -1.2 134 134
PLK1 0.013 0.17 -10000 0 -1.2 8 8
BIRC5 -0.11 0.44 -10000 0 -1.4 54 54
HSPA1B -0.29 0.6 0.67 1 -1.1 146 147
MAP2K1 0.009 0.068 0.19 1 -10000 0 1
BRCA2 -0.29 0.6 -10000 0 -1.2 125 125
FOXM1 -0.47 0.93 0.74 1 -1.7 146 147
XRCC1 -0.29 0.6 0.76 2 -1.2 131 133
FOXM1B/p19 -0.39 0.65 -10000 0 -1.3 157 157
Cyclin D1/CDK4 -0.34 0.58 -10000 0 -1.1 164 164
CDC2 -0.34 0.67 -10000 0 -1.3 136 136
TGFA -0.28 0.53 0.62 1 -0.98 149 150
SKP2 -0.28 0.6 -10000 0 -1.2 126 126
CCNE1 -0.012 0.093 -10000 0 -0.13 121 121
CKS1B -0.31 0.62 -10000 0 -1.2 139 139
RB1 -0.25 0.44 -10000 0 -0.98 109 109
FOXM1C/SP1 -0.39 0.72 -10000 0 -1.4 153 153
AURKB -0.073 0.36 -10000 0 -1.2 46 46
CENPF -0.32 0.63 -10000 0 -1.2 142 142
CDK4 -0.001 0.067 -10000 0 -0.3 15 15
MYC -0.3 0.49 0.62 1 -0.96 151 152
CHEK2 0.003 0.077 0.19 1 -0.33 9 10
ONECUT1 -0.32 0.59 0.65 1 -1.1 154 155
CDKN2A 0.02 0.035 -10000 0 -0.1 19 19
LAMA4 -0.29 0.6 -10000 0 -1.2 132 132
FOXM1B/HNF6 -0.41 0.73 -10000 0 -1.4 155 155
FOS -0.4 0.68 -10000 0 -1.2 197 197
SP1 0.029 0.026 -10000 0 -0.048 49 49
CDC25B -0.32 0.64 -10000 0 -1.2 149 149
response to radiation -0.002 0.037 0.081 15 -10000 0 15
CENPB -0.28 0.6 -10000 0 -1.2 128 128
CENPA -0.3 0.61 -10000 0 -1.2 132 132
NEK2 -0.3 0.6 -10000 0 -1.2 128 128
HIST1H2BA -0.29 0.6 0.67 1 -1.1 146 147
CCNA2 -0.008 0.095 -10000 0 -0.12 132 132
EP300 0.033 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 -0.41 0.78 -10000 0 -1.6 133 133
CCNB2 -0.31 0.62 -10000 0 -1.2 135 135
CCNB1 -0.33 0.67 -10000 0 -1.3 132 132
ETV5 -0.26 0.62 0.82 2 -1.2 130 132
ESR1 -0.29 0.6 -10000 0 -1.2 125 125
CCND1 -0.36 0.58 -10000 0 -1.1 164 164
GSK3A 0.008 0.059 0.15 1 -10000 0 1
Cyclin A-E1/CDK1-2 -0.016 0.12 -10000 0 -0.2 110 110
CDK2 0.021 0.031 -10000 0 -0.03 127 127
G2/M transition of mitotic cell cycle -0.003 0.044 0.092 16 -10000 0 16
FOXM1B/Cbp/p300 -0.34 0.66 -10000 0 -1.3 146 146
GAS1 -0.34 0.64 -10000 0 -1.2 153 153
MMP2 -0.39 0.67 -10000 0 -1.2 189 189
RB1/FOXM1C -0.37 0.6 -10000 0 -1.1 164 164
CREBBP 0.035 0.009 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.017 -10000 0 0 172 172
PLK4 0.035 0.009 -10000 0 0 31 31
regulation of centriole replication -0.025 0.064 0.06 66 -0.19 57 123
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.037 0.12 -9999 0 -0.25 104 104
FZD6 0.024 0.018 -9999 0 0 185 185
WNT6 0.036 0.005 -9999 0 0 8 8
WNT4 0.035 0.007 -9999 0 0 22 22
FZD3 0.025 0.017 -9999 0 0 169 169
WNT5A 0.025 0.017 -9999 0 0 164 164
WNT11 0.031 0.014 -9999 0 0 88 88
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 -0.006 0.004 0 151 -10000 0 151
TP53 -0.075 0.12 -10000 0 -0.26 137 137
Senescence -0.079 0.12 -10000 0 -0.26 149 149
Apoptosis -0.079 0.12 -10000 0 -0.26 149 149
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.089 0.18 124 -10000 0 124
MDM4 0.036 0.006 -10000 0 0 14 14
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.01 -10000 0 0 39 39
CCL5 0.023 0.018 -10000 0 0 196 196
SDCBP 0.034 0.01 -10000 0 0 45 45
FGFR/FGF2/Syndecan-1 -0.051 0.15 0.2 5 -0.36 74 79
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 -0.053 0.16 0.24 12 -0.33 89 101
Syndecan-1/Syntenin -0.048 0.17 0.24 19 -0.34 88 107
MAPK3 -0.061 0.16 0.22 18 -0.31 100 118
HGF/MET 0.049 0.017 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.034 0.01 -10000 0 0 39 39
BSG 0.029 0.015 -10000 0 0 109 109
keratinocyte migration -0.053 0.16 0.24 14 -0.33 89 103
Syndecan-1/RANTES -0.068 0.17 0.23 14 -0.34 113 127
Syndecan-1/CD147 -0.049 0.18 0.27 15 -0.32 101 116
Syndecan-1/Syntenin/PIP2 -0.048 0.16 0.21 18 -0.33 87 105
LAMA5 0.031 0.014 -10000 0 0 89 89
positive regulation of cell-cell adhesion -0.048 0.16 0.22 15 -0.32 87 102
MMP7 0.016 0.018 -10000 0 0 300 300
HGF 0.036 0.006 -10000 0 0 15 15
Syndecan-1/CASK -0.073 0.15 -10000 0 -0.33 90 90
Syndecan-1/HGF/MET -0.033 0.17 0.26 18 -0.33 82 100
regulation of cell adhesion -0.066 0.15 0.21 11 -0.31 97 108
HPSE 0.029 0.015 -10000 0 0 116 116
positive regulation of cell migration -0.051 0.15 0.2 5 -0.36 74 79
SDC1 -0.045 0.15 0.16 5 -0.38 61 66
Syndecan-1/Collagen -0.051 0.15 0.2 5 -0.36 74 79
PPIB 0.034 0.01 -10000 0 0 40 40
MET 0.034 0.01 -10000 0 0 43 43
PRKACA 0.031 0.013 -10000 0 0 79 79
MMP9 0.019 0.018 -10000 0 0 257 257
MAPK1 -0.06 0.16 0.21 16 -0.31 101 117
homophilic cell adhesion -0.049 0.16 0.21 14 -0.35 76 90
MMP1 0.025 0.017 -10000 0 0 172 172
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.021 -10000 0 -10000 0 0
CDKN2C 0.015 0.062 -10000 0 -0.22 28 28
CDKN2A -0.029 0.11 -10000 0 -0.26 92 92
CCND2 0.021 0.067 0.14 107 -0.12 5 112
RB1 -0.03 0.089 0.21 9 -0.17 121 130
CDK4 0.024 0.083 0.17 109 -0.13 18 127
CDK6 0.028 0.078 0.17 111 -0.12 5 116
G1/S progression 0.035 0.092 0.17 139 -0.21 9 148
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.036 0.006 -10000 0 0 13 13
PTK2 0.025 0.017 -10000 0 0 174 174
CRKL -0.027 0.093 0.18 2 -0.18 126 128
GRB2/SOS1/SHC 0.044 0.026 -10000 0 -0.16 6 6
HRAS 0.034 0.01 -10000 0 0 38 38
IRS1/Crk -0.024 0.096 -10000 0 -0.18 132 132
IGF-1R heterotetramer/IGF1/PTP1B -0.001 0.1 -10000 0 -0.17 131 131
AKT1 -0.012 0.12 0.18 82 -0.25 48 130
BAD -0.018 0.12 0.17 82 -0.24 49 131
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.093 0.18 3 -0.18 123 126
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.023 0.1 0.2 5 -0.18 133 138
RAF1 -0.002 0.14 0.27 12 -0.4 24 36
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.1 0.18 2 -0.16 137 139
YWHAZ 0.029 0.015 -10000 0 0 105 105
IGF-1R heterotetramer/IGF1/IRS1 -0.024 0.11 0.17 2 -0.19 136 138
PIK3CA 0.026 0.017 -10000 0 0 158 158
RPS6KB1 -0.011 0.12 0.18 89 -0.24 46 135
GNB2L1 0.035 0.008 -10000 0 0 27 27
positive regulation of MAPKKK cascade 0.002 0.13 0.27 17 -0.34 22 39
PXN 0.037 0.004 -10000 0 0 5 5
PIK3R1 0.031 0.014 -10000 0 0 90 90
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
HRAS/GTP -0.02 0.087 -10000 0 -0.16 128 128
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.02 0.096 -10000 0 -0.14 128 128
IGF-1R heterotetramer 0.021 0.044 0.096 3 -0.077 54 57
IGF-1R heterotetramer/IGF1/IRS/Nck -0.008 0.11 0.18 2 -0.18 140 142
Crk/p130 Cas/Paxillin -0.006 0.1 0.23 4 -0.16 132 136
IGF1R 0.021 0.044 0.096 3 -0.077 54 57
IGF1 0.015 0.046 0.091 3 -0.083 60 63
IRS2/Crk -0.032 0.11 0.17 3 -0.19 144 147
PI3K -0.012 0.11 -10000 0 -0.18 123 123
apoptosis 0.009 0.11 0.23 39 -0.19 68 107
HRAS/GDP 0.025 0.015 -10000 0 -0.19 2 2
PRKCD -0.058 0.14 0.2 2 -0.28 120 122
RAF1/14-3-3 E 0.011 0.13 0.28 11 -0.34 25 36
BAD/14-3-3 -0.01 0.12 0.19 68 -0.24 40 108
PRKCZ -0.01 0.12 0.18 90 -0.2 77 167
Crk/p130 Cas/Paxillin/FAK1 -0.021 0.091 0.14 41 -0.25 32 73
PTPN1 0.033 0.012 -10000 0 0 58 58
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.054 0.14 -10000 0 -0.27 132 132
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.02 0.1 -10000 0 -0.15 124 124
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.018 0.1 0.16 1 -0.18 140 141
GRB10 0.035 0.008 -10000 0 0 29 29
PTPN11 -0.029 0.095 0.18 3 -0.18 133 136
IRS1 -0.031 0.099 0.13 8 -0.19 133 141
IRS2 -0.036 0.11 0.18 3 -0.2 128 131
IGF-1R heterotetramer/IGF1 -0.021 0.12 -10000 0 -0.23 119 119
GRB2 0.035 0.007 -10000 0 0 22 22
PDPK1 -0.006 0.13 0.19 86 -0.21 77 163
YWHAE 0.033 0.011 -10000 0 0 53 53
PRKD1 -0.054 0.14 0.2 2 -0.28 119 121
SHC1 0.035 0.008 -10000 0 0 27 27
LPA receptor mediated events

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
GNB1/GNG2 -0.015 0.075 -10000 0 -0.16 107 107
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.1 0.21 2 -0.25 46 48
AP1 -0.047 0.093 -10000 0 -0.16 175 175
mol:PIP3 -0.032 0.056 -10000 0 -0.14 103 103
AKT1 -0.013 0.11 0.22 11 -0.25 52 63
PTK2B -0.046 0.1 0.12 3 -0.18 166 169
RHOA -0.028 0.11 -10000 0 -0.35 42 42
PIK3CB 0.034 0.01 -10000 0 0 37 37
mol:Ca2+ -0.007 0.045 0.18 8 -0.14 23 31
MAGI3 0 0 -10000 0 -0.003 2 2
RELA 0.036 0.004 -10000 0 0 7 7
apoptosis -0.006 0.076 0.067 103 -0.16 91 194
HRAS/GDP 0.025 0.015 -10000 0 -0.19 2 2
positive regulation of microtubule depolymerization -0.046 0.1 0.19 15 -0.2 112 127
NF kappa B1 p50/RelA -0.033 0.081 -10000 0 -0.17 108 108
endothelial cell migration -0.06 0.15 -10000 0 -0.38 98 98
ADCY4 -0.03 0.1 0.14 6 -0.22 107 113
ADCY5 -0.03 0.1 0.14 6 -0.22 107 113
ADCY6 -0.027 0.1 0.16 4 -0.22 103 107
ADCY7 -0.03 0.11 0.16 4 -0.22 107 111
ADCY1 -0.028 0.1 0.16 4 -0.22 104 108
ADCY2 -0.024 0.099 0.15 5 -0.21 100 105
ADCY3 -0.03 0.1 0.14 6 -0.22 107 113
ADCY8 -0.019 0.096 0.16 2 -0.2 95 97
ADCY9 -0.028 0.1 0.16 4 -0.22 102 106
GSK3B -0.046 0.11 0.2 13 -0.19 163 176
arachidonic acid secretion -0.034 0.1 0.14 3 -0.21 121 124
GNG2 0 0.001 0.002 2 -0.003 21 23
TRIP6 0.002 0.069 -10000 0 -0.28 26 26
GNAO1 -0.006 0.086 0.084 104 -0.17 101 205
HRAS 0.034 0.01 -10000 0 0 38 38
NFKBIA -0.032 0.09 0.16 6 -0.25 44 50
GAB1 0.034 0.01 -10000 0 0 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.028 0.18 -10000 0 -0.9 18 18
JUN 0.033 0.012 -10000 0 0 62 62
LPA/LPA2/NHERF2 0.01 0.04 -10000 0 -0.069 97 97
TIAM1 0.009 0.2 -10000 0 -1.1 18 18
PIK3R1 0.031 0.014 -10000 0 -10000 0 0
mol:IP3 -0.006 0.043 0.18 8 -0.15 17 25
PLCB3 0.009 0.042 0.18 6 -0.068 94 100
FOS 0.021 0.018 -10000 0 0 231 231
positive regulation of mitosis -0.034 0.1 0.14 3 -0.21 121 124
LPA/LPA1-2-3 -0.025 0.062 -10000 0 -0.14 110 110
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.015 0.098 -10000 0 -0.26 34 34
GNAZ -0.005 0.083 0.084 99 -0.17 97 196
EGFR/PI3K-beta/Gab1 -0.021 0.065 -10000 0 -0.14 103 103
positive regulation of dendritic cell cytokine production -0.025 0.062 -10000 0 -0.14 110 110
LPA/LPA2/MAGI-3 -0.011 0.025 -10000 0 -0.059 110 110
ARHGEF1 -0.001 0.078 0.21 7 -0.16 86 93
GNAI2 -0.006 0.089 0.084 104 -0.17 105 209
GNAI3 -0.007 0.088 0.084 102 -0.17 107 209
GNAI1 -0.009 0.09 0.084 96 -0.18 100 196
LPA/LPA3 -0.014 0.032 -10000 0 -0.074 110 110
LPA/LPA2 -0.014 0.032 -10000 0 -0.074 110 110
LPA/LPA1 -0.034 0.084 -10000 0 -0.2 102 102
HB-EGF/EGFR 0 0.086 -10000 0 -0.16 106 106
HBEGF -0.034 0.085 0.06 110 -0.19 102 212
mol:DAG -0.006 0.043 0.18 8 -0.15 17 25
cAMP biosynthetic process -0.033 0.1 0.17 7 -0.21 107 114
NFKB1 0.033 0.011 -10000 0 0 51 51
SRC 0.035 0.008 -10000 0 0 25 25
GNB1 0.034 0.01 -10000 0 0 37 37
LYN -0.042 0.11 0.17 8 -0.26 81 89
GNAQ 0.003 0.036 0.04 100 -0.063 107 207
LPAR2 0 0.001 -10000 0 -0.002 8 8
LPAR3 0 0.001 -10000 0 -0.002 10 10
LPAR1 -0.022 0.05 -10000 0 -0.12 99 99
IL8 -0.045 0.19 0.27 5 -0.43 76 81
PTK2 -0.002 0.07 0.086 71 -0.14 83 154
Rac1/GDP 0.025 0.011 -10000 0 -0.19 1 1
CASP3 -0.006 0.076 0.067 103 -0.16 91 194
EGFR 0.036 0.005 -10000 0 0 11 11
PLCG1 0.007 0.029 -10000 0 -0.057 68 68
PLD2 0.006 0.073 0.086 102 -0.14 94 196
G12/G13 0.011 0.086 -10000 0 -0.16 104 104
PI3K-beta -0.043 0.093 -10000 0 -0.25 62 62
cell migration -0.004 0.068 -10000 0 -0.24 23 23
SLC9A3R2 0.035 0.008 -10000 0 0 24 24
PXN -0.016 0.1 -10000 0 -0.27 33 33
HRAS/GTP -0.034 0.11 0.14 3 -0.21 119 122
RAC1 0.035 0.008 -10000 0 0 28 28
MMP9 0.019 0.018 -10000 0 0 257 257
PRKCE 0.036 0.006 -10000 0 0 12 12
PRKCD -0.019 0.054 0.17 8 -0.16 20 28
Gi(beta/gamma) -0.027 0.11 0.15 3 -0.21 113 116
mol:LPA -0.022 0.05 -10000 0 -0.12 99 99
TRIP6/p130 Cas/FAK1/Paxillin -0.024 0.1 -10000 0 -0.24 60 60
MAPKKK cascade -0.034 0.1 0.14 3 -0.21 121 124
contractile ring contraction involved in cytokinesis -0.029 0.11 -10000 0 -0.35 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.004 0.036 0.042 19 -0.063 106 125
GNA15 0.005 0.033 0.04 95 -0.065 82 177
GNA12 0.034 0.009 -10000 0 0 36 36
GNA13 0.036 0.006 -10000 0 0 14 14
MAPT -0.047 0.11 0.19 15 -0.2 130 145
GNA11 0.005 0.033 0.04 94 -0.065 84 178
Rac1/GTP 0.028 0.19 -10000 0 -0.96 18 18
MMP2 -0.06 0.15 -10000 0 -0.38 98 98
Canonical Wnt 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
HDAC1 0.07 0.082 0.15 186 -0.048 28 214
AES 0.057 0.068 0.13 168 -0.047 27 195
FBXW11 0.036 0.007 -10000 0 0 17 17
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
LRP6/FZD1 0.044 0.032 -10000 0 -0.19 6 6
SMAD4 0.03 0.014 -10000 0 0 94 94
DKK2 0.033 0.012 -10000 0 0 62 62
TLE1 0.063 0.071 0.14 179 -0.051 23 202
MACF1 0.032 0.013 -10000 0 0 75 75
CTNNB1 0.04 0.095 0.26 31 -0.27 6 37
WIF1 0.035 0.009 -10000 0 0 34 34
beta catenin/RanBP3 0.13 0.22 0.44 153 -0.27 5 158
KREMEN2 0.035 0.009 -10000 0 0 33 33
DKK1 0.035 0.008 -10000 0 0 27 27
beta catenin/beta TrCP1 0.06 0.097 0.28 30 -0.27 4 34
FZD1 0.035 0.008 -10000 0 0 27 27
AXIN2 -0.11 0.24 0.12 4 -0.36 168 172
AXIN1 0.035 0.01 -10000 0 0 36 36
RAN 0.035 0.01 -10000 0 0 37 37
Axin1/APC/GSK3/beta catenin 0.01 0.17 -10000 0 -0.5 43 43
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.022 0.18 0.3 16 -0.42 53 69
Axin1/APC/GSK3 0.023 0.083 0.2 16 -0.26 19 35
Axin1/APC/GSK3/beta catenin/Macf1 0.016 0.1 0.28 11 -0.33 22 33
HNF1A 0.034 0.066 0.098 195 -10000 0 195
CTBP1 0.061 0.074 0.15 157 -0.05 24 181
MYC -0.095 0.62 0.63 111 -1.2 99 210
RANBP3 0.035 0.011 -10000 0 0 43 43
DKK2/LRP6/Kremen 2 0.059 0.037 -10000 0 -0.16 6 6
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.056 0.079 0.14 156 -0.08 25 181
TCF3 0.058 0.066 0.13 167 -0.029 21 188
WNT1/LRP6/FZD1/Axin1 0.075 0.044 -10000 0 -0.15 6 6
Ran/GTP 0.021 0.04 -10000 0 -0.18 20 20
CtBP/CBP/TCF/TLE1/AES 0.16 0.38 0.62 159 -0.35 24 183
LEF1 0.064 0.069 0.14 174 -0.028 22 196
DVL1 0.027 0.084 0.2 13 -0.25 21 34
CSNK2A1 0.032 0.013 -10000 0 0 71 71
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.088 0.21 -10000 0 -0.43 98 98
DKK1/LRP6/Kremen 2 0.061 0.035 -10000 0 -0.16 6 6
LRP6 0.033 0.011 -10000 0 0 56 56
CSNK1A1 0.071 0.077 0.15 190 -0.029 30 220
NLK 0.018 0.03 -10000 0 -0.033 120 120
CCND1 -0.36 0.65 0.67 11 -1.4 146 157
WNT1 0.036 0.004 -10000 0 0 7 7
GSK3A 0.034 0.01 -10000 0 0 38 38
GSK3B 0.034 0.01 -10000 0 0 41 41
FRAT1 0.035 0.007 -10000 0 -0.004 16 16
PPP2R5D 0.028 0.057 0.17 2 -0.29 6 8
APC 0.001 0.07 0.19 53 -10000 0 53
WNT1/LRP6/FZD1 0.022 0.058 0.18 5 -0.18 20 25
CREBBP 0.065 0.07 0.14 182 -0.029 21 203
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.016 0.12 0.2 7 -0.2 126 133
NF kappa B1 p50/RelA/I kappa B alpha -0.042 0.17 0.25 2 -0.35 100 102
alphaV/beta3 Integrin/Osteopontin/Src -0.009 0.12 -10000 0 -0.22 106 106
AP1 -0.069 0.2 0.31 1 -0.33 144 145
ILK -0.026 0.1 0.2 6 -0.21 97 103
bone resorption -0.036 0.1 -10000 0 -0.25 59 59
PTK2B 0.031 0.014 -10000 0 0 87 87
PYK2/p130Cas -0.005 0.11 -10000 0 -0.18 123 123
ITGAV 0.012 0.072 -10000 0 -0.11 88 88
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.033 0.062 -10000 0 -0.19 34 34
alphaV/beta3 Integrin/Osteopontin 0.013 0.13 -10000 0 -0.2 122 122
MAP3K1 -0.026 0.1 0.2 6 -0.2 97 103
JUN 0.026 0.047 -10000 0 -0.049 65 65
MAPK3 -0.051 0.12 0.2 8 -0.29 83 91
MAPK1 -0.051 0.13 0.2 7 -0.29 87 94
Rac1/GDP 0.025 0.011 -10000 0 -0.19 1 1
NFKB1 0.033 0.011 -10000 0 0 51 51
MAPK8 -0.041 0.097 0.19 6 -0.24 58 64
ITGB3 0.025 0.033 -10000 0 -0.047 82 82
NFKBIA -0.064 0.16 0.2 8 -0.35 98 106
FOS 0 0.081 -10000 0 -0.045 232 232
CD44 0.032 0.013 -10000 0 0 76 76
CHUK 0.035 0.009 -10000 0 0 33 33
PLAU -0.17 0.42 -10000 0 -1.1 85 85
NF kappa B1 p50/RelA -0.025 0.19 0.27 3 -0.38 96 99
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
alphaV beta3 Integrin 0.019 0.084 -10000 0 -0.19 56 56
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.029 0.1 0.19 7 -0.21 100 107
VAV3 -0.056 0.12 0.18 2 -0.28 83 85
MAP3K14 -0.027 0.11 0.2 8 -0.2 126 134
ROCK2 0.036 0.006 -10000 0 0 14 14
SPP1 0.002 0.092 -10000 0 -0.17 85 85
RAC1 0.035 0.008 -10000 0 0 28 28
Rac1/GTP -0.059 0.12 0.19 4 -0.27 91 95
MMP2 -0.11 0.17 0.2 2 -0.36 142 144
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.014 0.12 -10000 0 -0.18 148 148
alphaM/beta2 Integrin/GPIbA 0.029 0.089 -10000 0 -0.16 87 87
alphaM/beta2 Integrin/proMMP-9 -0.018 0.12 -10000 0 -0.19 146 146
PLAUR 0.029 0.015 -10000 0 0 108 108
HMGB1 0.039 0.009 0.079 1 -10000 0 1
alphaM/beta2 Integrin/Talin 0.029 0.092 -10000 0 -0.16 88 88
AGER 0.039 0.007 -10000 0 -10000 0 0
RAP1A 0.036 0.007 -10000 0 0 17 17
SELPLG 0.036 0.004 -10000 0 0 7 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.059 0.096 -10000 0 -0.15 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.019 0.018 -10000 0 0 257 257
CYR61 0.024 0.018 -10000 0 0 184 184
TLN1 0.036 0.007 -10000 0 0 19 19
Rap1/GTP -0.05 0.16 -10000 0 -0.33 98 98
RHOA 0.034 0.01 -10000 0 0 43 43
P-selectin oligomer 0.036 0.007 -10000 0 0 18 18
MYH2 -0.053 0.16 0.2 2 -0.37 82 84
MST1R 0.035 0.009 -10000 0 0 33 33
leukocyte activation during inflammatory response 0.036 0.079 -10000 0 -0.14 79 79
APOB 0.036 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 0.019 0.018 -10000 0 0 246 246
JAM3 0.032 0.013 -10000 0 0 74 74
GP1BA 0.034 0.01 -10000 0 0 37 37
alphaM/beta2 Integrin/CTGF -0.017 0.12 -10000 0 -0.18 162 162
alphaM/beta2 Integrin -0.04 0.16 -10000 0 -0.37 82 82
JAM3 homodimer 0.032 0.013 -10000 0 0 74 74
ICAM2 0.034 0.01 -10000 0 0 41 41
ICAM1 0.027 0.016 -10000 0 0 133 133
phagocytosis triggered by activation of immune response cell surface activating receptor -0.038 0.16 -10000 0 -0.36 83 83
cell adhesion 0.028 0.088 -10000 0 -0.16 87 87
NFKB1 0.014 0.078 -10000 0 -0.26 12 12
THY1 0.024 0.018 -10000 0 0 177 177
RhoA/GDP 0.012 0.054 -10000 0 -0.19 36 36
Lipoprotein(a) 0.043 0.018 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.005 0.12 -10000 0 -0.18 135 135
IL6 -0.016 0.067 -10000 0 -10000 0 0
ITGB2 0.028 0.019 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.003 0.14 -10000 0 -0.24 105 105
alphaM/beta2 Integrin/JAM2/JAM3 0.04 0.093 -10000 0 -0.15 80 80
JAM2 0.033 0.011 -10000 0 0 51 51
alphaM/beta2 Integrin/ICAM1 0.043 0.1 -10000 0 -0.19 64 64
alphaM/beta2 Integrin/uPA/Plg 0.017 0.12 -10000 0 -0.2 110 110
RhoA/GTP -0.064 0.17 -10000 0 -0.37 96 96
positive regulation of phagocytosis -0.036 0.15 0.26 1 -0.31 93 94
Ron/MSP 0.046 0.028 -10000 0 -0.18 5 5
alphaM/beta2 Integrin/uPAR/uPA 0.005 0.14 -10000 0 -0.24 105 105
alphaM/beta2 Integrin/uPAR 0.015 0.11 -10000 0 -0.21 91 91
PLAU 0.023 0.018 -10000 0 0 194 194
PLAT 0.022 0.018 -10000 0 0 207 207
actin filament polymerization -0.05 0.16 0.2 2 -0.35 82 84
MST1 0.034 0.01 -10000 0 0 40 40
alphaM/beta2 Integrin/lipoprotein(a) 0.041 0.083 -10000 0 -0.14 79 79
TNF -0.015 0.067 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.001 0.12 -10000 0 -0.21 113 113
fibrinolysis 0.015 0.12 -10000 0 -0.2 110 110
HCK 0.031 0.014 -10000 0 0 88 88
dendritic cell antigen processing and presentation -0.038 0.16 -10000 0 -0.36 83 83
VTN 0.035 0.007 -10000 0 0 22 22
alphaM/beta2 Integrin/CYR61 -0.014 0.11 -10000 0 -0.17 166 166
LPA 0.032 0.012 -10000 0 0 65 65
LRP1 0.036 0.006 -10000 0 0 15 15
cell migration -0.032 0.13 0.18 1 -0.2 160 161
FN1 0.028 0.016 -10000 0 0 126 126
alphaM/beta2 Integrin/Thy1 -0.013 0.12 -10000 0 -0.18 154 154
MPO 0.036 0.006 -10000 0 0 12 12
KNG1 0.03 0.014 -10000 0 0 96 96
RAP1/GDP 0.023 0.018 -10000 0 -0.15 5 5
ROCK1 -0.056 0.16 0.23 3 -0.36 91 94
ELA2 0.032 0.012 -10000 0 0 64 64
PLG 0.035 0.009 -10000 0 0 34 34
CTGF 0.022 0.018 -10000 0 0 206 206
alphaM/beta2 Integrin/Hck 0.027 0.087 -10000 0 -0.16 77 77
ITGAM 0.04 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.049 0.091 -10000 0 -0.15 82 82
HP 0.015 0.018 -10000 0 0 313 313
leukocyte adhesion -0.004 0.12 -10000 0 -0.22 64 64
SELP 0.036 0.007 -10000 0 0 18 18
Glypican 2 network

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
MDK 0.028 0.016 -9999 0 0 129 129
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.012 0.08 -9999 0 -0.19 90 90
neuron projection morphogenesis -0.012 0.08 -9999 0 -0.19 90 90
Syndecan-4-mediated signaling events

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
PTK2 -0.065 0.23 -10000 0 -0.47 97 97
Syndecan-4/Syndesmos -0.1 0.23 -10000 0 -0.44 127 127
positive regulation of JNK cascade -0.12 0.24 -10000 0 -0.5 103 103
Syndecan-4/ADAM12 -0.085 0.24 -10000 0 -0.53 76 76
CCL5 0.023 0.018 -10000 0 0 196 196
Rac1/GDP 0.025 0.011 -10000 0 -0.19 1 1
DNM2 0.033 0.012 -10000 0 0 60 60
ITGA5 0.034 0.01 -10000 0 0 40 40
SDCBP 0.034 0.01 -10000 0 0 45 45
PLG 0.03 0.024 -10000 0 -0.084 2 2
ADAM12 0.036 0.007 -10000 0 0 19 19
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 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.1 0.23 -10000 0 -0.44 127 127
Syndecan-4/CXCL12/CXCR4 -0.12 0.25 -10000 0 -0.54 101 101
Syndecan-4/Laminin alpha3 -0.11 0.24 -10000 0 -0.5 107 107
MDK 0.028 0.016 -10000 0 0 129 129
Syndecan-4/FZD7 -0.096 0.25 -10000 0 -0.47 120 120
Syndecan-4/Midkine -0.1 0.25 -10000 0 -0.47 127 127
FZD7 0.029 0.015 -10000 0 0 112 112
Syndecan-4/FGFR1/FGF -0.065 0.23 -10000 0 -0.54 58 58
THBS1 0.03 0.014 -10000 0 0 94 94
integrin-mediated signaling pathway -0.11 0.23 -10000 0 -0.46 123 123
positive regulation of MAPKKK cascade -0.12 0.24 -10000 0 -0.5 103 103
Syndecan-4/TACI -0.086 0.24 -10000 0 -0.52 77 77
CXCR4 0.027 0.016 -10000 0 0 135 135
cell adhesion -0.014 0.082 0.21 3 -0.22 67 70
Syndecan-4/Dynamin -0.083 0.24 -10000 0 -0.45 116 116
Syndecan-4/TSP1 -0.096 0.24 -10000 0 -0.46 124 124
Syndecan-4/GIPC -0.082 0.23 -10000 0 -0.53 67 67
Syndecan-4/RANTES -0.11 0.25 -10000 0 -0.48 124 124
ITGB1 0.036 0.006 -10000 0 0 15 15
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.016 0.018 -10000 0 0 294 294
RAC1 0.035 0.008 -10000 0 0 28 28
PRKCA 0.008 0.095 0.9 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.088 0.25 -10000 0 -0.46 123 123
TFPI 0.035 0.008 -10000 0 0 23 23
F2 0.024 0.032 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.047 0.029 -10000 0 -0.19 5 5
positive regulation of cell adhesion -0.12 0.23 -10000 0 -0.48 107 107
ACTN1 0.034 0.01 -10000 0 0 44 44
TNC 0.022 0.018 -10000 0 0 206 206
Syndecan-4/CXCL12 -0.11 0.25 -10000 0 -0.55 86 86
FGF6 0.034 0.011 -10000 0 0 47 47
RHOA 0.034 0.01 -10000 0 0 43 43
CXCL12 0.023 0.018 -10000 0 0 196 196
TNFRSF13B 0.033 0.011 -10000 0 0 50 50
FGF2 0.035 0.008 -10000 0 0 29 29
FGFR1 0.033 0.012 -10000 0 0 61 61
Syndecan-4/PI-4-5-P2 -0.1 0.23 -10000 0 -0.44 127 127
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.001 0.089 -10000 0 -0.26 50 50
cell migration -0.01 0.014 0.014 1 -10000 0 1
PRKCD 0.021 0.057 -10000 0 -0.25 18 18
vasculogenesis -0.091 0.23 -10000 0 -0.44 124 124
SDC4 -0.1 0.25 -10000 0 -0.47 126 126
Syndecan-4/Tenascin C -0.11 0.25 -10000 0 -0.48 123 123
Syndecan-4/PI-4-5-P2/PKC alpha -0.02 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.083 0.24 -10000 0 -0.45 123 123
MMP9 -0.021 0.1 -10000 0 -0.28 70 70
Rac1/GTP -0.014 0.084 0.21 3 -0.22 67 70
cytoskeleton organization -0.1 0.22 -10000 0 -0.42 127 127
GIPC1 0.031 0.014 -10000 0 0 84 84
Syndecan-4/TFPI -0.084 0.24 -10000 0 -0.53 75 75
Endothelins

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
AKT1 -0.033 0.14 0.18 13 -0.27 112 125
PTK2B 0.031 0.014 -10000 0 0 87 87
mol:Ca2+ -0.026 0.18 -10000 0 -0.54 24 24
EDN1 -0.019 0.1 -10000 0 -0.2 116 116
EDN3 0.033 0.011 -10000 0 0 51 51
EDN2 0.033 0.011 -10000 0 0 52 52
HRAS/GDP -0.049 0.17 0.26 1 -0.34 96 97
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.024 0.13 -10000 0 -0.27 74 74
ADCY4 -0.052 0.097 -10000 0 -0.22 110 110
ADCY5 -0.052 0.097 -10000 0 -0.22 110 110
ADCY6 -0.011 0.13 0.2 38 -0.24 101 139
ADCY7 -0.016 0.13 0.2 33 -0.24 105 138
ADCY1 -0.012 0.13 0.2 38 -0.24 102 140
ADCY2 -0.011 0.13 0.2 34 -0.23 92 126
ADCY3 -0.052 0.097 -10000 0 -0.22 110 110
ADCY8 -0.013 0.1 0.2 20 -0.23 64 84
ADCY9 -0.012 0.13 0.2 38 -0.24 103 141
arachidonic acid secretion -0.11 0.26 0.29 1 -0.48 139 140
ETB receptor/Endothelin-1/Gq/GTP -0.01 0.1 -10000 0 -0.23 65 65
GNAO1 0.034 0.011 -10000 0 0 47 47
HRAS 0.034 0.01 -10000 0 0 38 38
ETA receptor/Endothelin-1/G12/GTP -0.025 0.13 -10000 0 -0.25 115 115
ETA receptor/Endothelin-1/Gs/GTP -0.023 0.12 -10000 0 -0.23 115 115
mol:GTP -0.001 0.006 -10000 0 -0.023 9 9
COL3A1 -0.087 0.2 -10000 0 -0.44 118 118
EDNRB 0.015 0.05 -10000 0 -0.091 85 85
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.027 0.14 -10000 0 -0.29 97 97
CYSLTR1 -0.056 0.12 -10000 0 -0.26 118 118
SLC9A1 -0.025 0.086 -10000 0 -0.19 84 84
mol:GDP -0.063 0.17 0.25 1 -0.36 97 98
SLC9A3 -0.026 0.17 -10000 0 -0.54 22 22
RAF1 -0.082 0.22 0.26 6 -0.4 137 143
JUN -0.067 0.29 -10000 0 -0.95 40 40
JAK2 -0.034 0.14 0.18 10 -0.27 109 119
mol:IP3 -0.019 0.13 -10000 0 -0.3 61 61
ETA receptor/Endothelin-1 -0.049 0.16 -10000 0 -0.32 119 119
PLCB1 0.034 0.009 -10000 0 -10000 0 0
PLCB2 0.032 0.015 -10000 0 -0.013 48 48
ETA receptor/Endothelin-3 0.003 0.075 -10000 0 -0.14 97 97
FOS -0.18 0.4 -10000 0 -0.9 119 119
Gai/GDP -0.035 0.23 -10000 0 -0.7 52 52
CRK 0.033 0.011 -10000 0 0 55 55
mol:Ca ++ -0.042 0.18 0.23 13 -0.36 108 121
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.026 0.13 0.2 3 -0.3 64 67
GNAQ 0.031 0.02 -10000 0 -0.033 39 39
GNAZ 0.034 0.01 -10000 0 0 46 46
GNAL 0.036 0.006 -10000 0 0 13 13
Gs family/GDP -0.049 0.16 0.24 1 -0.33 93 94
ETA receptor/Endothelin-1/Gq/GTP -0.027 0.13 -10000 0 -0.25 92 92
MAPK14 -0.014 0.1 0.23 3 -0.25 50 53
TRPC6 -0.028 0.18 -10000 0 -0.58 22 22
GNAI2 0.036 0.007 -10000 0 0 20 20
GNAI3 0.036 0.007 -10000 0 0 20 20
GNAI1 0.031 0.014 -10000 0 0 83 83
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.01 0.1 -10000 0 -0.25 54 54
ETB receptor/Endothelin-2 0.027 0.045 -10000 0 -0.079 13 13
ETB receptor/Endothelin-3 0.028 0.045 -10000 0 -0.078 13 13
ETB receptor/Endothelin-1 -0.005 0.1 -10000 0 -0.2 101 101
MAPK3 -0.16 0.36 0.33 1 -0.78 122 123
MAPK1 -0.17 0.38 -10000 0 -0.81 125 125
Rac1/GDP -0.051 0.17 0.26 1 -0.35 93 94
cAMP biosynthetic process 0.003 0.12 0.22 35 -0.22 71 106
MAPK8 -0.041 0.21 -10000 0 -0.51 62 62
SRC 0.035 0.008 -10000 0 0 25 25
ETB receptor/Endothelin-1/Gi/GTP -0.013 0.097 -10000 0 -0.27 39 39
p130Cas/CRK/Src/PYK2 -0.055 0.18 0.28 3 -0.4 75 78
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.051 0.17 0.26 1 -0.35 92 93
COL1A2 -0.091 0.25 -10000 0 -0.6 94 94
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.002 0.076 -10000 0 -0.14 98 98
mol:DAG -0.019 0.13 -10000 0 -0.3 61 61
MAP2K2 -0.12 0.28 0.31 1 -0.57 126 127
MAP2K1 -0.12 0.28 0.29 2 -0.58 127 129
EDNRA -0.022 0.098 -10000 0 -0.19 126 126
positive regulation of muscle contraction -0.034 0.12 0.21 7 -0.25 101 108
Gq family/GDP -0.021 0.17 -10000 0 -0.31 94 94
HRAS/GTP -0.055 0.17 0.24 2 -0.33 102 104
PRKCH -0.026 0.13 0.2 1 -0.3 63 64
RAC1 0.035 0.008 -10000 0 0 28 28
PRKCA -0.028 0.13 0.22 3 -0.3 67 70
PRKCB -0.023 0.13 -10000 0 -0.3 66 66
PRKCE -0.027 0.13 0.23 3 -0.3 67 70
PRKCD -0.03 0.13 0.24 2 -0.3 67 69
PRKCG -0.026 0.14 0.22 6 -0.31 64 70
regulation of vascular smooth muscle contraction -0.22 0.48 -10000 0 -1.1 119 119
PRKCQ -0.033 0.14 0.24 6 -0.29 82 88
PLA2G4A -0.12 0.28 0.29 1 -0.52 139 140
GNA14 0.031 0.02 -10000 0 -0.034 38 38
GNA15 0.029 0.019 -10000 0 -0.033 27 27
GNA12 0.034 0.009 -10000 0 0 36 36
GNA11 0.03 0.019 -10000 0 -0.032 28 28
Rac1/GTP -0.026 0.13 -10000 0 -0.25 116 116
MMP1 0.034 0.096 0.33 20 -10000 0 20
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 -0.001 0.16 -10000 0 -0.28 85 85
MAP3K8 0.028 0.036 -10000 0 -0.025 68 68
FOS 0.009 0.11 -10000 0 -0.36 11 11
PRKCA 0.023 0.029 -10000 0 -0.029 113 113
PTPN7 0.024 0.033 -10000 0 -0.036 111 111
HRAS 0.034 0.01 -10000 0 0 38 38
PRKCB -0.001 0.008 0.009 107 -0.015 118 225
NRAS 0.029 0.027 -10000 0 -0.01 88 88
RAS family/GTP 0.031 0.071 -10000 0 -0.16 52 52
MAPK3 0.031 0.058 -10000 0 -0.33 3 3
MAP2K1 0.009 0.071 0.18 1 -0.24 17 18
ELK1 0.021 0.033 -10000 0 -0.039 117 117
BRAF 0.005 0.032 -10000 0 -0.25 3 3
mol:GTP -0.001 0.002 0.002 23 -0.005 118 141
MAPK1 0.002 0.13 -10000 0 -0.41 35 35
RAF1 0 0.056 -10000 0 -0.33 11 11
KRAS 0.03 0.014 -10000 0 0 92 92
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.031 0.013 -10000 0 0 77 77
LAT2 -0.038 0.12 0.19 2 -0.26 102 104
AP1 -0.033 0.16 0.29 1 -0.37 59 60
mol:PIP3 -0.029 0.13 0.25 11 -0.27 84 95
IKBKB -0.009 0.092 0.2 26 -0.18 59 85
AKT1 0 0.13 0.24 54 -0.25 31 85
IKBKG -0.018 0.085 0.19 10 -0.18 61 71
MS4A2 0.04 0.013 0.063 63 -0.018 12 75
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.017 -10000 0 0 158 158
MAP3K1 -0.005 0.14 0.24 51 -0.29 52 103
mol:Ca2+ -0.02 0.11 0.23 11 -0.22 78 89
LYN 0.03 0.016 0.073 1 0 106 107
CBLB -0.036 0.12 0.2 3 -0.26 98 101
SHC1 0.035 0.008 -10000 0 0 27 27
RasGAP/p62DOK 0.039 0.068 -10000 0 -0.15 50 50
positive regulation of cell migration -0.008 0.001 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.024 0.085 0.29 14 -0.2 15 29
PTPN13 -0.078 0.21 -10000 0 -0.67 37 37
PTPN11 0.029 0.027 0.075 4 -0.031 78 82
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.019 0.14 0.29 12 -0.33 30 42
SYK 0.032 0.015 0.073 1 0 83 84
GRB2 0.035 0.007 -10000 0 0 22 22
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.12 0.18 1 -0.26 91 92
LAT -0.037 0.12 0.19 2 -0.26 101 103
PAK2 -0.004 0.15 0.24 57 -0.3 61 118
NFATC2 -0.015 0.02 -10000 0 -0.054 102 102
HRAS -0.03 0.14 0.24 4 -0.3 84 88
GAB2 0.029 0.015 -10000 0 0 106 106
PLA2G1B 0.007 0.15 -10000 0 -0.94 12 12
Fc epsilon R1 0.021 0.088 -10000 0 -0.14 108 108
Antigen/IgE/Fc epsilon R1 0.024 0.078 -10000 0 -0.12 106 106
mol:GDP -0.026 0.14 0.23 2 -0.33 67 69
JUN 0.033 0.012 -10000 0 0 62 62
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.014 -10000 0 0 90 90
FOS 0.02 0.018 -10000 0 0 231 231
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.033 0.13 -10000 0 -0.26 105 105
CHUK -0.019 0.087 0.2 11 -0.18 61 72
KLRG1 -0.034 0.11 -10000 0 -0.2 119 119
VAV1 -0.036 0.12 0.2 2 -0.26 99 101
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.037 0.12 0.19 2 -0.26 98 100
negative regulation of mast cell degranulation -0.035 0.099 -10000 0 -0.22 88 88
BTK -0.025 0.14 -10000 0 -0.34 56 56
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.14 -10000 0 -0.25 141 141
GAB2/PI3K/SHP2 -0.05 0.074 -10000 0 -0.2 74 74
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.036 0.12 -10000 0 -0.22 120 120
RAF1 0.011 0.16 -10000 0 -1 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.12 -10000 0 -0.21 126 126
FCER1G 0.021 0.036 -10000 0 -0.009 178 178
FCER1A 0.035 0.01 -10000 0 -0.001 32 32
Antigen/IgE/Fc epsilon R1/Fyn 0.019 0.095 -10000 0 -0.14 118 118
MAPK3 0.009 0.15 -10000 0 -0.94 12 12
MAPK1 -0.002 0.16 -10000 0 -0.96 12 12
NFKB1 0.033 0.011 -10000 0 0 51 51
MAPK8 -0.021 0.2 -10000 0 -0.57 41 41
DUSP1 0.03 0.015 -10000 0 0 104 104
NF-kappa-B/RelA 0 0.069 0.14 17 -0.13 57 74
actin cytoskeleton reorganization -0.065 0.21 -10000 0 -0.72 29 29
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.032 0.14 0.24 6 -0.29 86 92
FER -0.035 0.12 0.17 2 -0.26 95 97
RELA 0.036 0.004 -10000 0 0 7 7
ITK -0.004 0.048 -10000 0 -0.27 8 8
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.024 0.14 0.3 5 -0.29 84 89
cytokine secretion -0.004 0.046 0.083 4 -0.096 63 67
SPHK1 -0.034 0.12 0.19 2 -0.26 96 98
PTK2 -0.069 0.22 -10000 0 -0.78 28 28
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.13 0.19 1 -0.27 95 96
EDG1 -0.008 0.001 -10000 0 -10000 0 0
mol:DAG -0.034 0.14 0.26 10 -0.29 89 99
MAP2K2 -0.001 0.15 -10000 0 -0.96 12 12
MAP2K1 0.002 0.15 -10000 0 -0.97 12 12
MAP2K7 0.034 0.01 -10000 0 0 38 38
KLRG1/SHP2 -0.008 0.11 0.2 28 -0.24 60 88
MAP2K4 -0.079 0.33 -10000 0 -0.9 71 71
Fc epsilon R1/FcgammaRIIB 0 0.13 -10000 0 -0.22 126 126
mol:Choline -0.024 0.085 0.29 14 -0.2 15 29
SHC/Grb2/SOS1 -0.006 0.14 0.2 1 -0.25 100 101
FYN 0.028 0.016 -10000 0 0 131 131
DOK1 0.036 0.005 -10000 0 0 9 9
PXN -0.066 0.2 -10000 0 -0.69 29 29
HCLS1 -0.051 0.15 0.19 1 -0.33 97 98
PRKCB -0.022 0.11 0.23 10 -0.22 85 95
FCGR2B 0.02 0.018 -10000 0 0 231 231
IGHE 0 0.006 0.025 3 -10000 0 3
KLRG1/SHIP -0.036 0.1 -10000 0 -0.22 88 88
LCP2 0.031 0.013 -10000 0 0 80 80
PLA2G4A -0.041 0.13 0.16 3 -0.27 98 101
RASA1 0.032 0.012 -10000 0 0 64 64
mol:Phosphatidic acid -0.024 0.085 0.29 14 -0.2 15 29
IKK complex -0.011 0.077 0.19 21 -0.16 37 58
WIPF1 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.019 0.018 -10000 0 0 250 250
positive regulation of NF-kappaB transcription factor activity -0.008 0.085 -10000 0 -0.19 89 89
MAP2K4 -0.018 0.096 -10000 0 -0.29 32 32
IKBKB 0.034 0.01 -10000 0 0 40 40
TNFRSF10B 0.03 0.015 -10000 0 0 99 99
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 -0.012 0.055 -10000 0 -0.13 87 87
IKBKG 0.037 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.03 0.014 -10000 0 0 98 98
TRAIL/TRAILR2 -0.008 0.085 -10000 0 -0.19 89 89
TRAIL/TRAILR3 -0.008 0.085 -10000 0 -0.19 89 89
TRAIL/TRAILR1 -0.018 0.077 -10000 0 -0.19 89 89
TRAIL/TRAILR4 -0.008 0.085 -10000 0 -0.19 89 89
TRAIL/TRAILR1/DAP3/GTP 0 0.067 -10000 0 -0.14 86 86
IKK complex 0.018 0.08 -10000 0 -0.32 13 13
RIPK1 0.035 0.008 -10000 0 0 26 26
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.017 -10000 0 -0.19 3 3
MAPK3 -0.038 0.073 0.06 33 -0.19 89 122
MAP3K1 -0.022 0.095 -10000 0 -0.22 75 75
TRAILR4 (trimer) 0.03 0.014 -10000 0 0 98 98
TRADD 0.033 0.012 -10000 0 0 57 57
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.016 0.081 -10000 0 -0.19 87 87
CFLAR 0.035 0.008 -10000 0 0 24 24
MAPK1 -0.034 0.071 0.06 36 -0.19 81 117
TRAIL/TRAILR1/FADD/TRADD/RIP 0.021 0.081 -10000 0 -0.14 83 83
mol:ceramide -0.012 0.054 -10000 0 -0.13 87 87
FADD 0.035 0.008 -10000 0 0 23 23
MAPK8 -0.021 0.1 0.2 4 -0.28 34 38
TRAF2 0.035 0.009 -10000 0 0 30 30
TRAILR3 (trimer) 0.03 0.014 -10000 0 0 98 98
CHUK 0.035 0.009 -10000 0 0 33 33
TRAIL/TRAILR1/FADD -0.002 0.074 -10000 0 -0.16 86 86
DAP3 0.035 0.009 -10000 0 0 33 33
CASP10 -0.002 0.098 0.16 82 -0.2 68 150
JNK cascade -0.008 0.085 -10000 0 -0.19 89 89
TRAIL (trimer) 0.019 0.018 -10000 0 0 250 250
TNFRSF10C 0.03 0.014 -10000 0 0 98 98
TRAIL/TRAILR1/DAP3/GTP/FADD 0.012 0.073 -10000 0 -0.14 82 82
TRAIL/TRAILR2/FADD 0.007 0.082 -10000 0 -0.16 86 86
cell death -0.012 0.054 -10000 0 -0.13 87 87
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.023 0.088 -10000 0 -0.2 84 84
TRAILR2 (trimer) 0.03 0.014 -10000 0 0 99 99
CASP8 0.016 0.076 -10000 0 -0.62 5 5
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.024 0.088 -10000 0 -0.14 82 82
Nectin adhesion pathway

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
PDGFRB 0.035 0.009 -10000 0 0 32 32
alphaV beta3 Integrin 0.029 0.071 -10000 0 -0.19 48 48
PTK2 -0.057 0.14 -10000 0 -0.34 83 83
positive regulation of JNK cascade -0.036 0.14 -10000 0 -0.28 110 110
CDC42/GDP -0.042 0.2 -10000 0 -0.36 119 119
Rac1/GDP -0.044 0.19 -10000 0 -0.36 120 120
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.007 -10000 0 0 17 17
CTNNB1 0.035 0.007 -10000 0 0 22 22
CDC42/GTP -0.042 0.18 -10000 0 -0.34 109 109
nectin-3/I-afadin -0.002 0.091 -10000 0 -0.19 94 94
RAPGEF1 -0.063 0.18 -10000 0 -0.38 121 121
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.073 0.2 -10000 0 -0.42 121 121
PDGFB-D/PDGFRB 0.035 0.009 -10000 0 0 32 32
TLN1 -0.041 0.088 0.19 1 -0.27 48 49
Rap1/GTP -0.061 0.13 -10000 0 -0.28 120 120
IQGAP1 0.033 0.011 -10000 0 0 53 53
Rap1/GTP/I-afadin 0.04 0.023 -10000 0 -0.14 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.002 0.091 -10000 0 -0.19 94 94
PVR 0.034 0.01 -10000 0 0 38 38
Necl-5(dimer) 0.034 0.01 -10000 0 0 38 38
mol:GDP -0.07 0.22 -10000 0 -0.44 120 120
MLLT4 0.033 0.011 -10000 0 0 53 53
PIK3CA 0.026 0.017 -10000 0 0 158 158
PI3K 0.015 0.1 -10000 0 -0.16 96 96
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.048 0.018 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.04 0.15 -10000 0 -0.29 115 115
PVRL1 0.036 0.007 -10000 0 0 18 18
PVRL3 0.024 0.018 -10000 0 0 179 179
PVRL2 0.033 0.011 -10000 0 0 56 56
PIK3R1 0.031 0.014 -10000 0 0 90 90
CDH1 0.032 0.012 -10000 0 0 66 66
CLDN1 0.023 0.018 -10000 0 0 191 191
JAM-A/CLDN1 0.012 0.099 -10000 0 -0.16 106 106
SRC -0.091 0.21 -10000 0 -0.45 124 124
ITGB3 0.036 0.007 -10000 0 0 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.048 0.018 -10000 0 -10000 0 0
FARP2 -0.068 0.22 -10000 0 -0.46 88 88
RAC1 0.035 0.008 -10000 0 0 28 28
CTNNA1 0.036 0.007 -10000 0 0 19 19
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.018 0.088 -10000 0 -0.16 92 92
nectin-1/I-afadin 0.048 0.018 -10000 0 -10000 0 0
nectin-2/I-afadin 0.039 0.044 -10000 0 -0.19 15 15
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.05 -10000 0 -0.16 31 31
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.02 0.088 -10000 0 -0.16 92 92
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.049 -10000 0 -0.16 30 30
F11R 0.034 0.01 -10000 0 0 44 44
positive regulation of filopodium formation -0.036 0.14 -10000 0 -0.28 110 110
alphaV/beta3 Integrin/Talin -0.028 0.12 0.22 3 -0.26 66 69
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.044 -10000 0 -0.19 15 15
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.044 -10000 0 -0.19 15 15
PIP5K1C -0.035 0.094 -10000 0 -0.19 112 112
VAV2 -0.072 0.23 -10000 0 -0.48 88 88
RAP1/GDP -0.046 0.17 -10000 0 -0.34 122 122
ITGAV 0.032 0.012 -10000 0 0 65 65
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.013 0.094 -10000 0 -0.17 100 100
nectin-3(dimer)/I-afadin/I-afadin -0.002 0.091 -10000 0 -0.19 94 94
Rac1/GTP -0.047 0.18 -10000 0 -0.35 114 114
PTPRM -0.039 0.11 -10000 0 -0.2 132 132
E-cadherin/beta catenin/alpha catenin 0.063 0.08 -10000 0 -0.16 33 33
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.036 0.006 -10000 0 0 15 15
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.023 0.13 -10000 0 -0.31 55 55
mol:DAG -0.023 0.12 0.19 7 -0.3 52 59
PLCG1 -0.024 0.12 0.19 7 -0.3 52 59
YES1 -0.035 0.12 -10000 0 -0.25 99 99
FZD3 0.025 0.017 -10000 0 0 169 169
FZD6 0.024 0.018 -10000 0 0 185 185
G protein -0.015 0.13 0.2 19 -0.3 52 71
MAP3K7 -0.035 0.11 0.18 10 -0.27 54 64
mol:Ca2+ -0.022 0.12 0.19 7 -0.29 52 59
mol:IP3 -0.023 0.12 0.19 7 -0.3 52 59
NLK -0.038 0.26 -10000 0 -0.81 50 50
GNB1 0.034 0.01 -10000 0 0 37 37
CAMK2A -0.028 0.11 0.2 10 -0.28 52 62
MAP3K7IP1 0.034 0.011 -10000 0 0 48 48
Noncanonical Wnts/FZD -0.037 0.12 -10000 0 -0.25 104 104
CSNK1A1 0.036 0.006 -10000 0 0 13 13
GNAS -0.031 0.12 -10000 0 -0.24 94 94
GO:0007205 -0.026 0.12 0.2 10 -0.29 53 63
WNT6 0.036 0.005 -10000 0 0 8 8
WNT4 0.035 0.007 -10000 0 0 22 22
NFAT1/CK1 alpha -0.03 0.13 0.21 2 -0.3 57 59
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.025 0.017 -10000 0 0 164 164
WNT11 0.031 0.014 -10000 0 0 88 88
CDC42 -0.036 0.12 0.19 1 -0.32 48 49
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.034 0.01 -10000 0 0 42 42
GNB1/GNG2 -0.055 0.082 -10000 0 -0.18 155 155
AKT1 -0.024 0.14 0.24 4 -0.25 68 72
EGF 0.035 0.008 -10000 0 0 26 26
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.008 0.053 0.18 11 -10000 0 11
mol:Ca2+ -0.039 0.18 0.29 3 -0.29 162 165
LYN -0.001 0.056 0.19 10 -0.2 6 16
RhoA/GTP -0.018 0.083 0.13 5 -0.14 147 152
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.062 0.19 0.3 2 -0.33 157 159
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.034 0.01 -10000 0 0 43 43
TP alpha/Gq family/GDP/G beta5/gamma2 -0.024 0.16 -10000 0 -0.53 46 46
G beta5/gamma2 -0.066 0.11 -10000 0 -0.23 154 154
PRKCH -0.054 0.2 0.3 2 -0.34 153 155
DNM1 0.036 0.007 -10000 0 0 19 19
TXA2/TP beta/beta Arrestin3 0.028 0.022 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.004 19 -0.002 44 63
PTGDR 0.036 0.004 -10000 0 0 6 6
G12 family/GTP -0.055 0.17 -10000 0 -0.3 156 156
ADRBK1 0.037 0.004 -10000 0 0 5 5
ADRBK2 0.033 0.011 -10000 0 0 51 51
RhoA/GTP/ROCK1 0.033 0.055 -10000 0 -0.16 37 37
mol:GDP 0.018 0.14 0.45 28 -0.24 2 30
mol:NADP 0.033 0.011 -10000 0 0 50 50
RAB11A 0.036 0.007 -10000 0 0 18 18
PRKG1 0.036 0.005 -10000 0 0 10 10
mol:IP3 -0.058 0.22 0.33 2 -0.36 162 164
cell morphogenesis 0.032 0.055 -10000 0 -0.16 37 37
PLCB2 -0.093 0.28 0.36 1 -0.48 162 163
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.048 0.18 12 -10000 0 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.048 0.17 10 -10000 0 10
RHOA 0.034 0.01 -10000 0 0 43 43
PTGIR 0.035 0.008 -10000 0 0 23 23
PRKCB1 -0.061 0.21 0.3 2 -0.36 157 159
GNAQ 0.036 0.007 -10000 0 0 17 17
mol:L-citrulline 0.033 0.011 -10000 0 0 50 50
TXA2/TXA2-R family -0.099 0.28 0.36 1 -0.51 156 157
LCK 0.009 0.053 0.18 12 -10000 0 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.047 0.04 -10000 0 -0.18 1 1
TXA2-R family/G12 family/GDP/G beta/gamma -0.014 0.13 -10000 0 -0.41 50 50
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.044 0.04 -10000 0 -0.16 1 1
MAPK14 -0.036 0.14 0.26 6 -0.22 155 161
TGM2/GTP -0.064 0.23 0.35 1 -0.4 148 149
MAPK11 -0.041 0.13 0.23 4 -0.22 153 157
ARHGEF1 -0.022 0.11 0.18 8 -0.18 147 155
GNAI2 0.036 0.007 -10000 0 0 20 20
JNK cascade -0.062 0.22 0.33 2 -0.38 156 158
RAB11/GDP 0.035 0.007 -10000 0 -10000 0 0
ICAM1 -0.043 0.18 0.27 5 -0.3 153 158
cAMP biosynthetic process -0.055 0.2 0.31 2 -0.33 157 159
Gq family/GTP/EBP50 0.012 0.045 0.26 2 -0.17 25 27
actin cytoskeleton reorganization 0.032 0.055 -10000 0 -0.16 37 37
SRC 0.007 0.052 0.18 12 -10000 0 12
GNB5 0.035 0.009 -10000 0 0 33 33
GNB1 0.034 0.01 -10000 0 0 37 37
EGF/EGFR 0.003 0.077 0.2 15 -0.22 14 29
VCAM1 -0.061 0.21 0.26 6 -0.36 156 162
TP beta/Gq family/GDP/G beta5/gamma2 -0.024 0.16 -10000 0 -0.53 46 46
platelet activation -0.047 0.18 0.34 3 -0.29 157 160
PGI2/IP 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.019 0.009 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 -0.015 0.13 -10000 0 -0.44 40 40
TXA2/TP beta/beta Arrestin2 0.011 0.055 -10000 0 -0.35 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.005 0.011 -10000 0 -10000 0 0
mol:DAG -0.07 0.24 0.33 2 -0.41 157 159
EGFR 0.036 0.005 -10000 0 0 11 11
TXA2/TP alpha -0.081 0.26 0.37 1 -0.44 156 157
Gq family/GTP -0.009 0.061 -10000 0 -0.19 54 54
YES1 0.007 0.054 0.18 12 -0.2 3 15
GNAI2/GTP 0.017 0.037 -10000 0 -0.13 4 4
PGD2/DP 0.027 0.003 -10000 0 -10000 0 0
SLC9A3R1 0.033 0.011 -10000 0 0 55 55
FYN 0.001 0.054 0.18 12 -0.21 4 16
mol:NO 0.033 0.011 -10000 0 0 50 50
GNA15 0.032 0.012 -10000 0 0 63 63
PGK/cGMP 0.044 0.016 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.01 -10000 0 0 43 43
TP alpha/TGM2/GDP/G beta/gamma 0.043 0.042 -10000 0 -0.17 1 1
NOS3 0.033 0.011 -10000 0 0 50 50
RAC1 0.035 0.008 -10000 0 0 28 28
PRKCA -0.055 0.2 0.3 3 -0.34 154 157
PRKCB -0.055 0.2 0.3 2 -0.34 156 158
PRKCE -0.055 0.21 0.32 4 -0.35 151 155
PRKCD -0.066 0.22 0.31 2 -0.38 154 156
PRKCG -0.063 0.22 0.35 2 -0.38 153 155
muscle contraction -0.092 0.26 0.36 1 -0.47 156 157
PRKCZ -0.053 0.2 0.31 2 -0.33 156 158
ARR3 0.037 0 -10000 0 -10000 0 0
TXA2/TP beta 0.047 0.039 -10000 0 -10000 0 0
PRKCQ -0.06 0.2 0.31 3 -0.35 154 157
MAPKKK cascade -0.079 0.24 0.33 2 -0.43 158 160
SELE -0.042 0.17 0.26 4 -0.29 156 160
TP beta/GNAI2/GDP/G beta/gamma 0.044 0.047 -10000 0 -0.2 2 2
ROCK1 0.036 0.007 -10000 0 0 17 17
GNA14 0.036 0.006 -10000 0 0 16 16
chemotaxis -0.12 0.32 -10000 0 -0.6 156 156
GNA12 0.034 0.009 -10000 0 0 36 36
GNA13 0.036 0.006 -10000 0 0 14 14
GNA11 0.033 0.012 -10000 0 0 57 57
Rac1/GTP 0.025 0.011 -10000 0 -0.19 1 1
Ephrin B reverse signaling

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
EFNB2 0.024 0.018 -10000 0 0 179 179
EPHB2 0.037 0.009 -10000 0 0 19 19
EFNB1 -0.002 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.076 0.049 -10000 0 -0.14 11 11
Ephrin B2/EPHB1-2 0.02 0.086 -10000 0 -0.14 106 106
neuron projection morphogenesis 0.052 0.038 -10000 0 -0.13 11 11
Ephrin B1/EPHB1-2/Tiam1 0.071 0.043 -10000 0 -0.14 10 10
DNM1 0.037 0.008 -10000 0 0 19 19
cell-cell signaling 0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.1 0.2 0.21 1 -0.48 113 114
YES1 -0.14 0.31 -10000 0 -0.72 113 113
Ephrin B1/EPHB1-2/NCK2 0.074 0.038 -10000 0 -0.14 6 6
PI3K -0.08 0.21 -10000 0 -0.47 111 111
mol:GDP 0.069 0.042 -10000 0 -0.14 10 10
ITGA2B 0.035 0.007 -10000 0 0 21 21
endothelial cell proliferation -0.001 0.083 -10000 0 -0.16 109 109
FYN -0.15 0.31 -10000 0 -0.73 113 113
MAP3K7 -0.1 0.22 0.23 3 -0.51 111 114
FGR -0.14 0.31 -10000 0 -0.71 115 115
TIAM1 0.034 0.011 -10000 0 0 47 47
PIK3R1 0.031 0.014 -10000 0 0 90 90
RGS3 0.036 0.006 -10000 0 0 15 15
cell adhesion -0.082 0.2 -10000 0 -0.44 110 110
LYN -0.15 0.31 -10000 0 -0.73 111 111
Ephrin B1/EPHB1-2/Src Family Kinases -0.14 0.28 -10000 0 -0.66 115 115
Ephrin B1/EPHB1-2 -0.11 0.23 -10000 0 -0.56 108 108
SRC -0.14 0.3 -10000 0 -0.71 112 112
ITGB3 0.036 0.007 -10000 0 0 18 18
EPHB1 0.037 0.009 -10000 0 0 27 27
EPHB4 0.036 0.005 -10000 0 0 10 10
RAC1 0.035 0.008 -10000 0 0 28 28
Ephrin B2/EPHB4 0 0.083 -10000 0 -0.16 109 109
alphaIIb/beta3 Integrin 0.052 0.012 -10000 0 -10000 0 0
BLK -0.15 0.3 -10000 0 -0.72 113 113
HCK -0.14 0.3 -10000 0 -0.72 110 110
regulation of stress fiber formation -0.072 0.037 0.14 6 -10000 0 6
MAPK8 -0.1 0.2 0.21 2 -0.46 113 115
Ephrin B1/EPHB1-2/RGS3 0.077 0.029 -10000 0 -10000 0 0
endothelial cell migration -0.1 0.18 0.19 7 -0.45 107 114
NCK2 0.036 0.006 -10000 0 0 13 13
PTPN13 0.024 0.019 -10000 0 0 192 192
regulation of focal adhesion formation -0.072 0.037 0.14 6 -10000 0 6
chemotaxis -0.074 0.028 -10000 0 -10000 0 0
PIK3CA 0.026 0.017 -10000 0 0 158 158
Rac1/GTP 0.066 0.044 -10000 0 -0.13 11 11
angiogenesis -0.11 0.23 -10000 0 -0.55 109 109
LCK -0.14 0.31 -10000 0 -0.71 115 115
Syndecan-2-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
Syndecan-2/Fibronectin -0.011 0.087 -10000 0 -0.18 100 100
EPHB2 0.036 0.007 -10000 0 0 19 19
Syndecan-2/TACI 0.011 0.062 -10000 0 -0.15 61 61
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.002 0.1 -10000 0 -0.16 113 113
HRAS 0.034 0.01 -10000 0 0 38 38
Syndecan-2/CASK -0.011 0.05 -10000 0 -0.15 61 61
ITGA5 0.034 0.01 -10000 0 0 40 40
BAX -0.013 0.047 -10000 0 -10000 0 0
EPB41 0.036 0.005 -10000 0 0 9 9
positive regulation of cell-cell adhesion 0.009 0.061 -10000 0 -0.14 65 65
LAMA3 0.016 0.018 -10000 0 0 294 294
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.032 0.013 -10000 0 0 76 76
Syndecan-2/MMP2 -0.024 0.096 -10000 0 -0.2 110 110
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.048 0.018 -10000 0 -10000 0 0
dendrite morphogenesis 0.012 0.062 -10000 0 -0.15 60 60
Syndecan-2/GM-CSF 0.013 0.063 -10000 0 -0.15 60 60
determination of left/right symmetry 0.009 0.008 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.006 0.068 -10000 0 -0.16 73 73
GNB2L1 0.035 0.008 -10000 0 0 27 27
MAPK3 0.023 0.083 0.2 61 -0.14 59 120
MAPK1 0.02 0.081 0.2 56 -0.15 52 108
Syndecan-2/RACK1 0.023 0.064 -10000 0 -0.13 65 65
NF1 0.034 0.011 -10000 0 0 47 47
FGFR/FGF/Syndecan-2 0.009 0.008 -10000 0 -10000 0 0
ITGA2 0.033 0.011 -10000 0 0 52 52
MAPK8 -0.006 0.056 -10000 0 -0.15 60 60
Syndecan-2/alpha2/beta1 Integrin 0.025 0.061 -10000 0 -0.13 56 56
Syndecan-2/Kininogen 0.01 0.059 -10000 0 -0.15 54 54
ITGB1 0.036 0.006 -10000 0 0 15 15
SRC 0.006 0.086 0.19 66 -10000 0 66
Syndecan-2/CASK/Protein 4.1 0.012 0.057 -10000 0 -0.14 61 61
extracellular matrix organization 0.011 0.062 -10000 0 -0.15 59 59
actin cytoskeleton reorganization -0.011 0.087 -10000 0 -0.18 100 100
Syndecan-2/Caveolin-2/Ras 0.014 0.078 -10000 0 -0.16 76 76
Syndecan-2/Laminin alpha3 -0.028 0.088 -10000 0 -0.18 115 115
Syndecan-2/RasGAP 0.026 0.078 -10000 0 -0.14 80 80
alpha5/beta1 Integrin 0.047 0.029 -10000 0 -0.19 5 5
PRKCD 0.033 0.011 -10000 0 0 53 53
Syndecan-2 dimer 0.012 0.063 -10000 0 -0.15 60 60
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.01 0.068 0.19 3 -0.14 65 68
RHOA 0.034 0.01 -10000 0 0 43 43
SDCBP 0.034 0.01 -10000 0 0 45 45
TNFRSF13B 0.033 0.011 -10000 0 0 50 50
RASA1 0.032 0.012 -10000 0 0 64 64
alpha2/beta1 Integrin 0.048 0.018 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.008 0.07 -10000 0 -0.16 69 69
TGFB1 0.034 0.01 -10000 0 0 39 39
CASP3 0.017 0.084 0.2 55 -0.15 60 115
FN1 0.028 0.016 -10000 0 0 126 126
Syndecan-2/IL8 -0.004 0.077 -10000 0 -0.17 79 79
SDC2 0.009 0.008 -10000 0 -10000 0 0
KNG1 0.03 0.014 -10000 0 0 96 96
Syndecan-2/Neurofibromin 0.011 0.062 -10000 0 -0.15 61 61
TRAPPC4 0.034 0.009 -10000 0 0 36 36
CSF2 0.036 0.007 -10000 0 0 18 18
Syndecan-2/TGFB1 0.011 0.062 -10000 0 -0.15 59 59
Syndecan-2/Syntenin/PI-4-5-P2 0.009 0.062 -10000 0 -0.14 65 65
Syndecan-2/Ezrin 0.003 0.07 -10000 0 -0.15 84 84
PRKACA 0.02 0.077 0.2 53 -0.14 49 102
angiogenesis -0.004 0.077 -10000 0 -0.17 79 79
MMP2 0.019 0.018 -10000 0 0 246 246
IL8 0.026 0.017 -10000 0 0 156 156
calcineurin-NFAT signaling pathway 0.011 0.062 -10000 0 -0.15 61 61
Nongenotropic Androgen signaling

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
PTK2 -0.005 0.005 0.001 189 -10000 0 189
GNB1/GNG2 0.024 0.052 -10000 0 -0.14 42 42
regulation of S phase of mitotic cell cycle -0.006 0.074 -10000 0 -0.19 61 61
GNAO1 0.034 0.011 -10000 0 0 47 47
HRAS 0.033 0.017 -10000 0 -0.007 38 38
SHBG/T-DHT 0.023 0.006 -10000 0 -10000 0 0
PELP1 0.033 0.01 -10000 0 0 43 43
AKT1 -0.007 0.004 0.003 68 -10000 0 68
MAP2K1 -0.029 0.082 0.18 20 -0.17 54 74
T-DHT/AR 0.01 0.052 -10000 0 -0.19 32 32
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 1 -0.007 118 119
GNAI2 0.035 0.007 -10000 0 0 20 20
GNAI3 0.035 0.007 -10000 0 0 20 20
GNAI1 0.031 0.014 -10000 0 0 83 83
mol:GDP -0.027 0.076 -10000 0 -0.28 34 34
cell proliferation -0.081 0.19 0.25 9 -0.41 118 127
PIK3CA 0.026 0.017 -10000 0 0 158 158
FOS -0.15 0.33 0.33 2 -0.74 119 121
mol:Ca2+ -0.005 0.022 -10000 0 -0.057 55 55
MAPK3 -0.054 0.14 0.23 9 -0.29 108 117
MAPK1 -0.055 0.16 0.21 1 -0.41 53 54
PIK3R1 0.031 0.014 -10000 0 0 90 90
mol:IP3 -0.001 0.002 0.002 10 -0.004 117 127
cAMP biosynthetic process -0.003 0.021 0.24 2 -10000 0 2
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 0.002 10 -0.004 117 127
HRAS/GTP 0.025 0.072 -10000 0 -0.14 35 35
actin cytoskeleton reorganization 0.02 0.057 -10000 0 -0.14 46 46
SRC 0.035 0.008 -10000 0 0 25 25
voltage-gated calcium channel activity -0.001 0.002 0.002 10 -0.004 117 127
PI3K 0.014 0.061 -10000 0 -0.16 46 46
apoptosis 0.076 0.2 0.41 123 -0.23 6 129
T-DHT/AR/PELP1 0.026 0.051 -10000 0 -0.16 32 32
HRAS/GDP 0.008 0.094 -10000 0 -0.27 35 35
CREB1 -0.096 0.21 0.23 6 -0.44 123 129
RAC1-CDC42/GTP 0.028 0.063 -10000 0 -0.14 46 46
AR 0.025 0.041 -10000 0 -0.024 96 96
GNB1 0.034 0.01 -10000 0 0 37 37
RAF1 -0.016 0.077 0.19 20 -0.2 14 34
RAC1-CDC42/GDP 0.032 0.099 -10000 0 -0.27 33 33
T-DHT/AR/PELP1/Src 0.045 0.055 -10000 0 -0.15 31 31
MAP2K2 -0.026 0.08 0.18 19 -0.17 58 77
T-DHT/AR/PELP1/Src/PI3K -0.006 0.074 -10000 0 -0.19 61 61
GNAZ 0.034 0.01 -10000 0 0 46 46
SHBG 0.035 0.009 -10000 0 0 33 33
Gi family/GNB1/GNG2/GDP -0.011 0.11 -10000 0 -0.33 37 37
mol:T-DHT 0 0.001 -10000 0 -0.003 40 40
RAC1 0.035 0.008 -10000 0 0 28 28
GNRH1 -0.007 0.004 0.001 109 -10000 0 109
Gi family/GTP -0.009 0.071 -10000 0 -0.19 48 48
CDC42 0.036 0.006 -10000 0 0 15 15
EPHB forward signaling

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
Ephrin A5/EPHB2 0.046 0.014 -10000 0 -10000 0 0
cell-cell adhesion 0.048 0.055 0.14 101 -10000 0 101
Ephrin B/EPHB2/RasGAP 0.029 0.11 -10000 0 -0.16 125 125
ITSN1 0.037 0.004 -10000 0 0 6 6
PIK3CA 0.026 0.017 -10000 0 0 158 158
SHC1 0.035 0.008 -10000 0 0 27 27
Ephrin B1/EPHB3 0.023 0.054 -10000 0 -0.16 36 36
Ephrin B1/EPHB1 0.047 0.011 -10000 0 -10000 0 0
HRAS/GDP -0.041 0.12 -10000 0 -0.22 109 109
Ephrin B/EPHB1/GRB7 0.033 0.1 -10000 0 -0.15 112 112
Endophilin/SYNJ1 -0.034 0.064 0.18 8 -10000 0 8
KRAS 0.03 0.014 -10000 0 0 92 92
Ephrin B/EPHB1/Src 0.038 0.1 -10000 0 -0.15 105 105
endothelial cell migration 0.001 0.092 -10000 0 -0.15 116 116
GRB2 0.035 0.007 -10000 0 0 22 22
GRB7 0.033 0.012 -10000 0 0 60 60
PAK1 -0.033 0.069 0.18 17 -10000 0 17
HRAS 0.034 0.01 -10000 0 0 38 38
RRAS -0.035 0.067 0.18 7 -0.25 8 15
DNM1 0.036 0.007 -10000 0 0 19 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.074 0.18 25 -0.25 2 27
lamellipodium assembly -0.048 0.055 -10000 0 -0.14 101 101
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.011 0.087 -10000 0 -0.17 105 105
PIK3R1 0.031 0.014 -10000 0 0 90 90
EPHB2 0.036 0.007 -10000 0 0 19 19
EPHB3 0.025 0.017 -10000 0 0 165 165
EPHB1 0.035 0.008 -10000 0 0 27 27
EPHB4 0.036 0.005 -10000 0 0 10 10
mol:GDP -0.06 0.11 0.18 5 -0.26 86 91
Ephrin B/EPHB2 0.029 0.092 -10000 0 -0.14 110 110
Ephrin B/EPHB3 0.008 0.097 -10000 0 -0.16 117 117
JNK cascade -0.005 0.085 0.28 35 -10000 0 35
Ephrin B/EPHB1 0.027 0.091 -10000 0 -0.14 108 108
RAP1/GDP -0.054 0.11 0.26 1 -0.23 97 98
EFNB2 0.024 0.018 -10000 0 0 179 179
EFNB3 0.034 0.01 -10000 0 0 38 38
EFNB1 0.037 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.018 0.086 -10000 0 -0.15 106 106
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.007 -10000 0 0 17 17
CDC42/GTP 0.008 0.11 -10000 0 -0.19 99 99
Rap1/GTP -0.049 0.059 -10000 0 -0.15 101 101
axon guidance 0.045 0.014 -10000 0 -10000 0 0
MAPK3 -0.018 0.08 0.23 2 -0.27 8 10
MAPK1 -0.015 0.081 0.21 6 -0.27 10 16
Rac1/GDP -0.051 0.12 0.28 2 -0.24 94 96
actin cytoskeleton reorganization -0.064 0.074 -10000 0 -0.19 82 82
CDC42/GDP -0.051 0.12 0.28 2 -0.24 94 96
PI3K 0.005 0.095 -10000 0 -0.15 116 116
EFNA5 0.035 0.008 -10000 0 0 28 28
Ephrin B2/EPHB4 -0.001 0.083 -10000 0 -0.16 109 109
Ephrin B/EPHB2/Intersectin/N-WASP -0.012 0.086 -10000 0 -0.22 10 10
CDC42 0.036 0.006 -10000 0 0 15 15
RAS family/GTP -0.053 0.07 -10000 0 -0.16 111 111
PTK2 0.13 0.26 0.56 142 -0.27 20 162
MAP4K4 -0.005 0.086 0.28 35 -10000 0 35
SRC 0.035 0.008 -10000 0 0 25 25
KALRN 0.036 0.007 -10000 0 0 17 17
Intersectin/N-WASP 0.053 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.087 0.27 11 -0.24 12 23
MAP2K1 -0.016 0.08 -10000 0 -0.28 8 8
WASL 0.036 0.006 -10000 0 0 16 16
Ephrin B1/EPHB1-2/NCK1 0.079 0.048 -10000 0 -0.15 15 15
cell migration -0.026 0.1 0.26 4 -0.25 25 29
NRAS 0.031 0.014 -10000 0 0 88 88
SYNJ1 -0.035 0.065 0.18 8 -10000 0 8
PXN 0.037 0.004 -10000 0 0 5 5
TF -0.037 0.059 0.16 7 -10000 0 7
HRAS/GTP 0.012 0.094 -10000 0 -0.15 115 115
Ephrin B1/EPHB1-2 0.066 0.018 -10000 0 -10000 0 0
cell adhesion mediated by integrin 0.021 0.081 0.16 78 -0.19 19 97
RAC1 0.035 0.008 -10000 0 0 28 28
mol:GTP 0.017 0.097 -10000 0 -0.15 119 119
RAC1-CDC42/GTP -0.051 0.066 -10000 0 -0.16 101 101
RASA1 0.032 0.012 -10000 0 0 64 64
RAC1-CDC42/GDP -0.04 0.12 0.29 2 -0.24 91 93
ruffle organization -0.036 0.078 0.23 4 -0.25 10 14
NCK1 0.033 0.011 -10000 0 0 53 53
receptor internalization -0.038 0.06 0.16 8 -10000 0 8
Ephrin B/EPHB2/KALRN 0.041 0.1 -10000 0 -0.15 105 105
ROCK1 0.016 0.09 0.19 95 -0.15 34 129
RAS family/GDP -0.07 0.079 -10000 0 -0.21 84 84
Rac1/GTP -0.048 0.059 -10000 0 -0.15 97 97
Ephrin B/EPHB1/Src/Paxillin -0.012 0.085 -10000 0 -0.17 106 106
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.61 0.64 2 -1.2 125 127
IL23A -0.057 0.42 0.67 1 -0.96 46 47
NF kappa B1 p50/RelA/I kappa B alpha -0.069 0.43 0.58 1 -0.84 91 92
positive regulation of T cell mediated cytotoxicity -0.068 0.46 0.6 4 -0.87 93 97
ITGA3 -0.07 0.43 -10000 0 -0.97 54 54
IL17F -0.04 0.31 0.45 20 -0.58 83 103
IL12B 0.029 0.068 0.16 9 -0.079 1 10
STAT1 (dimer) -0.088 0.44 0.57 2 -0.86 93 95
CD4 -0.043 0.41 0.68 2 -0.82 74 76
IL23 -0.064 0.4 -10000 0 -0.92 48 48
IL23R 0.017 0.11 0.21 36 -0.14 73 109
IL1B -0.06 0.43 0.67 1 -0.86 77 78
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.057 0.41 -10000 0 -0.83 74 74
TYK2 0.017 0.062 0.13 2 -0.31 6 8
STAT4 0.036 0.007 -10000 0 0 17 17
STAT3 0.034 0.01 -10000 0 0 41 41
IL18RAP 0.037 0.005 -10000 0 -10000 0 0
IL12RB1 0.021 0.053 0.13 3 -10000 0 3
PIK3CA 0.026 0.017 -10000 0 0 158 158
IL12Rbeta1/TYK2 0.028 0.069 0.17 1 -0.2 9 10
IL23R/JAK2 0.034 0.14 0.29 24 -0.19 66 90
positive regulation of chronic inflammatory response -0.068 0.46 0.6 4 -0.87 93 97
natural killer cell activation -0.001 0.01 -10000 0 -0.027 3 3
JAK2 0.026 0.067 0.16 6 -10000 0 6
PIK3R1 0.031 0.014 -10000 0 0 90 90
NFKB1 0.029 0.048 -10000 0 -0.29 11 11
RELA 0.038 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.059 0.39 -10000 0 -0.86 52 52
ALOX12B -0.058 0.41 0.61 1 -0.82 78 79
CXCL1 -0.14 0.57 0.65 2 -1.1 100 102
T cell proliferation -0.068 0.46 0.6 4 -0.87 93 97
NFKBIA 0.027 0.053 -10000 0 -0.29 14 14
IL17A -0.022 0.27 0.4 21 -0.47 82 103
PI3K -0.11 0.4 0.57 1 -0.84 82 83
IFNG 0.011 0.029 0.1 4 -0.089 11 15
STAT3 (dimer) -0.1 0.39 0.55 2 -0.82 83 85
IL18R1 0.037 0.005 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.001 0.29 0.47 11 -0.5 81 92
IL18/IL18R 0.069 0.033 -10000 0 -0.16 7 7
macrophage activation -0.007 0.019 -10000 0 -0.042 41 41
TNF -0.058 0.42 0.66 2 -0.92 56 58
STAT3/STAT4 -0.064 0.43 0.57 1 -0.83 92 93
STAT4 (dimer) -0.068 0.44 0.57 2 -0.84 93 95
IL18 0.032 0.013 -10000 0 -10000 0 0
IL19 -0.056 0.41 0.65 1 -0.82 75 76
STAT5A (dimer) -0.067 0.44 0.57 2 -0.85 92 94
STAT1 0.031 0.014 -10000 0 0 84 84
SOCS3 0.036 0.007 -10000 0 0 19 19
CXCL9 -0.23 0.64 0.64 3 -1.1 157 160
MPO -0.057 0.41 0.61 1 -0.82 76 77
positive regulation of humoral immune response -0.068 0.46 0.6 4 -0.87 93 97
IL23/IL23R/JAK2/TYK2 -0.085 0.46 0.62 2 -0.9 92 94
IL6 -0.053 0.41 0.63 2 -0.82 78 80
STAT5A 0.035 0.008 -10000 0 0 27 27
IL2 0.034 0.015 -10000 0 -0.037 1 1
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.01 -10000 0 -0.027 3 3
CD3E -0.056 0.41 -10000 0 -0.84 68 68
keratinocyte proliferation -0.068 0.46 0.6 4 -0.87 93 97
NOS2 -0.058 0.41 0.57 4 -0.78 93 97
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.089 0.16 92 -0.25 5 97
DAPP1 -0.014 0.11 0.25 3 -0.28 36 39
Src family/SYK family/BLNK-LAT/BTK-ITK -0.037 0.16 -10000 0 -0.4 47 47
mol:DAG -0.004 0.087 0.2 13 -0.18 36 49
HRAS 0.032 0.021 0.073 3 -0.015 77 80
RAP1A 0.037 0.012 0.065 4 -0.009 22 26
ARF5/GDP 0.022 0.075 -10000 0 -0.22 26 26
PLCG2 0.03 0.015 -10000 0 0 100 100
PLCG1 0.035 0.008 -10000 0 0 25 25
ARF5 0.035 0.009 -10000 0 0 31 31
mol:GTP -0.002 0.085 0.15 95 -0.16 40 135
ARF1/GTP 0.005 0.08 0.14 92 -0.16 41 133
RHOA 0.034 0.01 -10000 0 0 43 43
YES1 0.034 0.01 -10000 0 0 42 42
RAP1A/GTP 0.003 0.091 0.17 94 -0.16 40 134
ADAP1 -0.004 0.079 0.14 91 -0.16 40 131
ARAP3 -0.002 0.085 0.15 95 -0.16 40 135
INPPL1 0.035 0.008 -10000 0 0 25 25
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.034 0.01 -10000 0 0 39 39
ARHGEF7 0.035 0.008 -10000 0 0 23 23
ARF1 0.035 0.009 -10000 0 0 31 31
NRAS 0.032 0.018 0.067 1 -0.003 98 99
FYN 0.028 0.016 -10000 0 0 131 131
ARF6 0.036 0.005 -10000 0 0 11 11
FGR 0.035 0.009 -10000 0 0 30 30
mol:Ca2+ -0.003 0.052 0.16 16 -0.12 12 28
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.034 0.011 -10000 0 0 47 47
ZAP70 0.036 0.004 -10000 0 0 7 7
mol:IP3 -0.008 0.067 0.19 16 -0.16 15 31
LYN 0.029 0.015 -10000 0 0 106 106
ARF1/GDP 0.022 0.074 -10000 0 -0.22 25 25
RhoA/GDP 0.029 0.099 0.19 37 -0.17 50 87
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
BLNK 0.029 0.015 -10000 0 0 107 107
actin cytoskeleton reorganization 0.005 0.094 0.22 16 -0.22 26 42
SRC 0.035 0.008 -10000 0 0 25 25
PLEKHA2 -0.011 0.017 0.056 15 -0.16 3 18
RAC1 0.035 0.008 -10000 0 0 28 28
PTEN 0.027 0.025 -10000 0 -0.027 67 67
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.09 0.16 95 -0.25 6 101
RhoA/GTP -0.006 0.099 0.16 94 -0.26 12 106
Src family/SYK family/BLNK-LAT -0.031 0.12 -10000 0 -0.34 48 48
BLK 0.029 0.015 -10000 0 0 105 105
PDPK1 0.035 0.007 -10000 0 0 21 21
CYTH1 -0.004 0.079 0.14 91 -0.16 40 131
HCK 0.031 0.014 -10000 0 0 88 88
CYTH3 -0.004 0.079 0.14 91 -0.16 40 131
CYTH2 -0.004 0.079 0.14 91 -0.16 40 131
KRAS 0.028 0.02 0.085 1 -0.007 118 119
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.013 0.053 0.17 8 -0.14 14 22
SGK1 0.013 0.05 0.13 5 -0.14 13 18
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.071 -10000 0 -0.25 20 20
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.014 -10000 0 0 83 83
ARF6/GDP 0.006 0.087 0.16 80 -0.21 13 93
mol:PI-3-4-5-P3 -0.005 0.08 0.14 89 -0.16 40 129
ARAP3/RAP1A/GTP 0.003 0.092 0.17 94 -0.16 40 134
VAV1 0.033 0.011 -10000 0 0 50 50
mol:PI-3-4-P2 -0.008 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.034 0.08 0.21 37 -0.16 48 85
PLEKHA1 -0.017 0.029 0.056 8 -0.16 19 27
Rac1/GDP 0.024 0.075 -10000 0 -0.22 25 25
LAT 0.036 0.005 -10000 0 0 8 8
Rac1/GTP 0.006 0.082 -10000 0 -0.26 34 34
ITK -0.005 0.08 0.14 91 -0.16 37 128
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.012 0.11 0.23 12 -0.25 37 49
LCK 0.035 0.008 -10000 0 0 26 26
BTK -0.005 0.084 0.14 95 -0.16 40 135
IL2 signaling events mediated by PI3K

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
BCL2L1 0.016 0.089 -10000 0 -0.37 1 1
UGCG -0.042 0.22 -10000 0 -0.74 42 42
AKT1/mTOR/p70S6K/Hsp90/TERT -0.028 0.2 0.27 5 -0.39 94 99
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.039 0.21 -10000 0 -0.73 42 42
mol:DAG -0.006 0.026 0.16 11 -10000 0 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.052 0.26 0.3 5 -0.49 108 113
FRAP1 -0.077 0.3 0.31 5 -0.59 108 113
FOXO3 -0.075 0.3 0.31 4 -0.57 112 116
AKT1 -0.089 0.34 0.32 4 -0.63 112 116
GAB2 0.014 0.063 -10000 0 -0.047 142 142
SMPD1 -0.001 0.13 -10000 0 -0.75 13 13
SGMS1 -0.004 0.04 0.059 12 -0.077 96 108
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 -0.022 0.047 -10000 0 -0.16 46 46
CALM1 0.036 0.006 -10000 0 0 16 16
cell proliferation -0.028 0.23 0.24 14 -0.36 117 131
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.011 0.073 -10000 0 -0.2 46 46
RPS6KB1 0.004 0.13 -10000 0 -0.99 6 6
mol:sphingomyelin -0.006 0.026 0.16 11 -10000 0 11
natural killer cell activation -0.002 0.005 0.005 17 -0.012 100 117
JAK3 0.03 0.019 -10000 0 -0.029 30 30
PIK3R1 0.024 0.035 -10000 0 -0.05 47 47
JAK1 0.029 0.036 -10000 0 -0.062 38 38
NFKB1 0.033 0.011 -10000 0 0 51 51
MYC -0.083 0.41 0.4 14 -0.87 102 116
MYB -0.058 0.34 -10000 0 -1.2 45 45
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.18 0.31 3 -0.37 84 87
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.12 -10000 0 -0.9 6 6
mol:PI-3-4-5-P3 -0.021 0.18 0.29 5 -0.36 82 87
Rac1/GDP -0.001 0.054 -10000 0 -0.15 46 46
T cell proliferation -0.019 0.17 0.28 5 -0.34 80 85
SHC1 0.029 0.02 -10000 0 -0.018 73 73
RAC1 0.035 0.008 -10000 0 0 28 28
positive regulation of cyclin-dependent protein kinase activity 0.002 0.023 0.031 72 -0.065 45 117
PRKCZ -0.021 0.17 0.28 5 -0.36 80 85
NF kappa B1 p50/RelA -0.044 0.27 0.32 5 -0.51 107 112
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.012 0.088 -10000 0 -0.3 16 16
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
IL2RA 0.029 0.021 -10000 0 -0.019 76 76
IL2RB 0.028 0.02 -10000 0 -0.029 27 27
TERT 0.034 0.011 -10000 0 0 48 48
E2F1 0 0.13 -10000 0 -0.42 45 45
SOS1 -0.001 0.005 0.006 22 -0.011 100 122
RPS6 0.035 0.008 -10000 0 0 27 27
mol:cAMP -0.001 0.011 0.031 43 -0.017 76 119
PTPN11 0.028 0.023 -10000 0 -0.029 68 68
IL2RG 0.028 0.022 -10000 0 -0.029 44 44
actin cytoskeleton organization -0.019 0.17 0.28 5 -0.34 80 85
GRB2 0.029 0.025 -10000 0 -0.024 72 72
IL2 0.031 0.021 -10000 0 -0.029 46 46
PIK3CA 0.019 0.042 -10000 0 -0.077 37 37
Rac1/GTP 0.021 0.068 -10000 0 -0.14 46 46
LCK 0.03 0.022 -10000 0 -0.029 51 51
BCL2 -0.043 0.23 -10000 0 -0.52 69 69
PDGFR-alpha signaling pathway

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
PDGFRA 0.01 0.059 -10000 0 -0.077 111 111
PDGF/PDGFRA/CRKL 0.016 0.069 -10000 0 -0.19 38 38
positive regulation of JUN kinase activity 0.041 0.061 -10000 0 -0.14 45 45
CRKL 0.034 0.009 -10000 0 0 35 35
PDGF/PDGFRA/Caveolin-3 0.016 0.071 -10000 0 -0.19 40 40
AP1 -0.16 0.31 -10000 0 -0.71 116 116
mol:IP3 -0.026 0.065 0.094 5 -0.21 37 42
PLCG1 -0.026 0.065 0.094 5 -0.21 37 42
PDGF/PDGFRA/alphaV Integrin -0.003 0.096 -10000 0 -0.21 82 82
RAPGEF1 0.035 0.008 -10000 0 0 23 23
CRK 0.033 0.011 -10000 0 0 55 55
mol:Ca2+ -0.026 0.065 0.094 5 -0.21 37 42
CAV3 0.036 0.006 -10000 0 0 13 13
CAV1 0.027 0.016 -10000 0 0 140 140
SHC/Grb2/SOS1 0.043 0.062 -10000 0 -0.14 45 45
PDGF/PDGFRA/Shf -0.001 0.059 -10000 0 -0.19 40 40
FOS -0.15 0.32 0.31 9 -0.7 116 125
JUN -0.027 0.08 0.27 20 -0.23 25 45
oligodendrocyte development -0.003 0.096 -10000 0 -0.21 82 82
GRB2 0.035 0.007 -10000 0 0 22 22
PIK3R1 0.031 0.014 -10000 0 0 90 90
mol:DAG -0.026 0.065 0.094 5 -0.21 37 42
PDGF/PDGFRA 0.01 0.059 -10000 0 -0.077 111 111
actin cytoskeleton reorganization 0.016 0.071 -10000 0 -0.19 40 40
SRF -0.011 0.043 0.066 3 -0.18 24 27
SHC1 0.035 0.008 -10000 0 0 27 27
PI3K 0.014 0.087 -10000 0 -0.19 68 68
PDGF/PDGFRA/Crk/C3G 0.044 0.066 -10000 0 -0.16 40 40
JAK1 -0.03 0.063 -10000 0 -0.2 56 56
ELK1/SRF -0.023 0.063 0.15 20 -0.18 38 58
SHB 0.036 0.006 -10000 0 0 15 15
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.029 0.079 82 -0.026 45 127
GO:0007205 -0.026 0.07 0.12 2 -0.24 37 39
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.041 0.061 -10000 0 -0.14 45 45
PDGF/PDGFRA/SHB 0.016 0.071 -10000 0 -0.19 40 40
PDGF/PDGFRA/Caveolin-1 -0.011 0.1 -10000 0 -0.22 90 90
ITGAV 0.032 0.012 -10000 0 0 65 65
ELK1 -0.032 0.07 0.14 2 -0.22 37 39
PIK3CA 0.026 0.017 -10000 0 0 158 158
PDGF/PDGFRA/Crk 0.014 0.071 -10000 0 -0.2 40 40
JAK-STAT cascade -0.029 0.063 -10000 0 -0.2 56 56
cell proliferation -0.001 0.059 -10000 0 -0.19 40 40
BCR signaling pathway

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
JUN -0.035 0.14 0.29 1 -0.32 64 65
IKBKB 0.017 0.089 0.25 6 -0.24 13 19
AKT1 0.022 0.11 0.25 48 -0.19 28 76
IKBKG 0.016 0.078 0.22 2 -0.24 10 12
CALM1 -0.025 0.12 0.24 5 -0.31 52 57
PIK3CA 0.026 0.017 -10000 0 0 158 158
MAP3K1 -0.024 0.16 -10000 0 -0.4 54 54
MAP3K7 0.034 0.01 -10000 0 0 46 46
mol:Ca2+ -0.022 0.13 0.22 6 -0.3 62 68
DOK1 0.036 0.005 -10000 0 0 9 9
AP-1 -0.028 0.1 0.2 2 -0.22 63 65
LYN 0.029 0.015 -10000 0 0 106 106
BLNK 0.029 0.015 -10000 0 0 107 107
SHC1 0.035 0.008 -10000 0 0 27 27
BCR complex 0.049 0.017 -10000 0 -10000 0 0
CD22 -0.02 0.11 -10000 0 -0.3 60 60
CAMK2G -0.023 0.12 0.21 13 -0.32 45 58
CSNK2A1 0.032 0.013 -10000 0 0 71 71
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.084 -10000 0 -0.17 90 90
GO:0007205 -0.024 0.13 0.22 6 -0.31 65 71
SYK 0.031 0.014 -10000 0 0 83 83
ELK1 -0.028 0.12 0.24 3 -0.33 49 52
NFATC1 -0.035 0.12 0.21 2 -0.31 54 56
B-cell antigen/BCR complex 0.049 0.017 -10000 0 -10000 0 0
PAG1/CSK 0.022 0.03 -10000 0 -0.19 10 10
NFKBIB 0.017 0.057 0.14 2 -0.13 47 49
HRAS -0.024 0.11 0.23 4 -0.28 56 60
NFKBIA 0.019 0.053 0.14 2 -0.13 39 41
NF-kappa-B/RelA/I kappa B beta 0.023 0.052 0.14 2 -0.11 37 39
RasGAP/Csk 0.023 0.11 -10000 0 -0.15 120 120
mol:GDP -0.023 0.13 0.22 5 -0.33 50 55
PTEN 0.033 0.012 -10000 0 0 61 61
CD79B 0.036 0.006 -10000 0 0 15 15
NF-kappa-B/RelA/I kappa B alpha 0.024 0.05 0.14 2 -0.11 28 30
GRB2 0.035 0.007 -10000 0 0 22 22
PI3K/BCAP/CD19 -0.046 0.18 -10000 0 -0.42 64 64
PIK3R1 0.031 0.014 -10000 0 0 90 90
mol:IP3 -0.021 0.13 0.22 6 -0.31 60 66
CSK 0.035 0.009 -10000 0 0 31 31
FOS -0.041 0.14 0.22 7 -0.32 66 73
CHUK 0.001 0.1 0.21 3 -0.26 41 44
IBTK 0.035 0.008 -10000 0 0 25 25
CARD11/BCL10/MALT1/TAK1 -0.006 0.13 0.22 2 -0.29 55 57
PTPN6 -0.019 0.11 0.18 8 -0.35 37 45
RELA 0.036 0.004 -10000 0 0 7 7
BCL2A1 0.016 0.04 0.11 2 -0.079 46 48
VAV2 -0.026 0.13 -10000 0 -0.38 49 49
ubiquitin-dependent protein catabolic process 0.02 0.056 0.14 2 -0.12 47 49
BTK 0.022 0.01 -10000 0 -10000 0 0
CD19 -0.02 0.12 -10000 0 -0.3 62 62
MAP4K1 0.031 0.013 -10000 0 0 79 79
CD72 0.036 0.005 -10000 0 0 9 9
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.14 0.31 3 -0.35 53 56
SH3BP5 0.033 0.011 -10000 0 0 53 53
PIK3AP1 -0.024 0.14 0.23 6 -0.33 65 71
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.04 0.18 -10000 0 -0.34 103 103
RAF1 -0.026 0.11 0.22 7 -0.27 55 62
RasGAP/p62DOK/SHIP 0.019 0.094 -10000 0 -0.14 116 116
CD79A 0.034 0.01 -10000 0 0 41 41
re-entry into mitotic cell cycle -0.028 0.1 0.2 2 -0.22 61 63
RASA1 0.032 0.012 -10000 0 0 64 64
MAPK3 -0.028 0.096 0.24 4 -0.26 42 46
MAPK1 -0.026 0.097 0.24 7 -0.25 44 51
CD72/SHP1 0.018 0.14 0.28 25 -0.33 40 65
NFKB1 0.033 0.011 -10000 0 0 51 51
MAPK8 -0.021 0.14 0.27 1 -0.35 52 53
actin cytoskeleton organization -0.024 0.12 0.27 1 -0.34 49 50
NF-kappa-B/RelA 0.039 0.11 0.26 2 -0.24 44 46
Calcineurin -0.011 0.13 0.26 3 -0.3 50 53
PI3K -0.035 0.095 -10000 0 -0.28 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.023 0.14 0.2 16 -0.35 62 78
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.021 0.21 -10000 0 -0.56 56 56
DAPP1 -0.043 0.23 -10000 0 -0.62 58 58
cytokine secretion -0.033 0.11 0.21 2 -0.29 53 55
mol:DAG -0.021 0.13 0.22 6 -0.31 60 66
PLCG2 0.03 0.015 -10000 0 0 100 100
MAP2K1 -0.027 0.1 0.23 6 -0.27 46 52
B-cell antigen/BCR complex/FcgammaRIIB 0.015 0.091 -10000 0 -0.16 102 102
mol:PI-3-4-5-P3 0.003 0.11 0.22 31 -0.24 30 61
ETS1 -0.02 0.11 0.24 8 -0.31 38 46
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.031 0.11 -10000 0 -0.18 94 94
B-cell antigen/BCR complex/LYN -0.021 0.12 -10000 0 -0.31 65 65
MALT1 0.033 0.011 -10000 0 0 56 56
TRAF6 0.036 0.005 -10000 0 0 9 9
RAC1 -0.026 0.13 0.27 1 -0.36 48 49
B-cell antigen/BCR complex/LYN/SYK 0.015 0.14 0.32 6 -0.3 42 48
CARD11 -0.024 0.12 0.21 6 -0.29 65 71
FCGR2B 0.02 0.018 -10000 0 0 231 231
PPP3CA 0.032 0.012 -10000 0 0 66 66
BCL10 0.035 0.009 -10000 0 0 31 31
IKK complex 0.019 0.051 0.14 25 -0.1 5 30
PTPRC 0.027 0.016 -10000 0 0 142 142
PDPK1 0.017 0.1 0.21 57 -0.17 28 85
PPP3CB 0.035 0.008 -10000 0 0 27 27
PPP3CC 0.03 0.014 -10000 0 0 93 93
POU2F2 0.016 0.039 0.12 8 -0.082 37 45
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.32 0.46 1 -0.67 96 97
PCK1 -0.3 0.56 -10000 0 -1.2 143 143
HNF4A -0.2 0.43 0.55 2 -0.82 145 147
KCNJ11 -0.074 0.27 -10000 0 -0.59 62 62
AKT1 -0.045 0.18 -10000 0 -0.36 57 57
response to starvation -0.027 0.052 -10000 0 -0.11 122 122
DLK1 -0.061 0.27 0.59 1 -0.68 35 36
NKX2-1 -0.034 0.15 -10000 0 -0.32 49 49
ACADM -0.13 0.32 -10000 0 -0.66 96 96
TAT -0.091 0.22 -10000 0 -0.57 39 39
CEBPB 0.036 0.013 -10000 0 -10000 0 0
CEBPA 0.035 0.015 -10000 0 -10000 0 0
TTR -0.031 0.18 0.47 1 -0.77 6 7
PKLR -0.1 0.3 0.48 5 -0.62 79 84
APOA1 -0.31 0.61 -10000 0 -1.2 158 158
CPT1C -0.11 0.29 -10000 0 -0.6 97 97
ALAS1 -0.053 0.26 -10000 0 -1.3 14 14
TFRC -0.12 0.36 -10000 0 -0.91 63 63
FOXF1 0.031 0.014 -10000 0 -10000 0 0
NF1 0.033 0.034 -10000 0 -0.16 13 13
HNF1A (dimer) 0.008 0.001 -10000 0 -10000 0 0
CPT1A -0.11 0.3 -10000 0 -0.64 77 77
HMGCS1 -0.1 0.3 0.49 2 -0.63 81 83
NR3C1 0.043 0.015 -10000 0 -10000 0 0
CPT1B -0.12 0.28 -10000 0 -0.63 77 77
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.037 0.004 -10000 0 -10000 0 0
GCK -0.11 0.3 -10000 0 -0.62 84 84
CREB1 -0.017 0.12 -10000 0 -0.21 144 144
IGFBP1 -0.053 0.18 -10000 0 -0.61 9 9
PDX1 -0.027 0.15 0.3 1 -0.32 43 44
UCP2 -0.13 0.34 0.48 4 -0.7 97 101
ALDOB -0.072 0.27 -10000 0 -0.66 43 43
AFP -0.004 0.05 -10000 0 -10000 0 0
BDH1 -0.11 0.35 0.49 10 -0.7 97 107
HADH -0.074 0.27 -10000 0 -0.59 62 62
F2 -0.14 0.38 -10000 0 -0.81 76 76
HNF1A 0.008 0.001 -10000 0 -10000 0 0
G6PC -0.01 0.11 -10000 0 -10000 0 0
SLC2A2 -0.024 0.18 -10000 0 -0.47 1 1
INS 0.027 0.028 0.19 8 -10000 0 8
FOXA1 0.016 0.003 -10000 0 -10000 0 0
FOXA3 -0.03 0.11 -10000 0 -0.2 106 106
FOXA2 -0.075 0.33 -10000 0 -0.68 62 62
ABCC8 -0.074 0.27 -10000 0 -0.66 43 43
ALB -0.004 0.05 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.069 -10000 0 -0.16 48 48
PTK2 0 0.12 0.29 4 -0.31 41 45
IGF1R 0.029 0.015 -10000 0 0 116 116
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.028 0.016 -10000 0 0 129 129
SRC 0.035 0.008 -10000 0 0 25 25
CDKN1B -0.02 0.12 -10000 0 -0.37 55 55
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.019 0.046 -10000 0 -0.34 5 5
ROCK1 0.036 0.007 -10000 0 0 17 17
AKT1 0.004 0.058 0.21 6 -0.26 14 20
PTK2B -0.019 0.049 0.18 13 -0.14 34 47
alphaV/beta3 Integrin/JAM-A 0.045 0.081 -10000 0 -0.15 65 65
CBL 0.036 0.007 -10000 0 0 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.049 0.069 -10000 0 -0.16 47 47
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.004 0.12 -10000 0 -0.19 126 126
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.01 0.083 -10000 0 -0.32 18 18
alphaV/beta3 Integrin/Syndecan-1 0.016 0.1 -10000 0 -0.18 109 109
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.036 0.13 -10000 0 -0.2 165 165
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.017 -10000 0 0 158 158
alphaV/beta3 Integrin/Osteopontin 0.021 0.1 -10000 0 -0.18 99 99
RPS6KB1 -0.059 0.12 0.3 12 -0.26 73 85
TLN1 0.036 0.007 -10000 0 0 19 19
MAPK3 -0.04 0.15 0.32 1 -0.39 64 65
GPR124 0.032 0.012 -10000 0 0 66 66
MAPK1 -0.042 0.15 0.32 1 -0.4 63 64
PXN 0.037 0.004 -10000 0 0 5 5
PIK3R1 0.031 0.014 -10000 0 0 90 90
alphaV/beta3 Integrin/Tumstatin 0.05 0.069 -10000 0 -0.16 47 47
cell adhesion 0.005 0.1 -10000 0 -0.18 110 110
ANGPTL3 0.036 0.006 -10000 0 0 12 12
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.029 0.015 -10000 0 0 116 116
Rac1/GDP 0.025 0.011 -10000 0 -0.19 1 1
TGFBR2 0.036 0.007 -10000 0 0 20 20
ITGB3 0.036 0.007 -10000 0 0 18 18
IGF1 0.025 0.017 -10000 0 0 164 164
RAC1 0.035 0.008 -10000 0 0 28 28
regulation of cell-matrix adhesion 0.045 0.065 -10000 0 -0.16 42 42
apoptosis 0.032 0.012 -10000 0 0 65 65
CD47 0.033 0.012 -10000 0 0 58 58
alphaV/beta3 Integrin/CD47 0.037 0.085 -10000 0 -0.18 62 62
VCL 0.036 0.007 -10000 0 0 20 20
alphaV/beta3 Integrin/Del1 0.045 0.07 -10000 0 -0.16 48 48
CSF1 0.037 0.004 -10000 0 0 6 6
PIK3C2A 0.005 0.033 -10000 0 -0.33 2 2
PI4 Kinase/Pyk2 0.015 0.049 -10000 0 -0.13 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.063 -10000 0 -0.14 48 48
FAK1/Vinculin 0.017 0.11 0.25 6 -0.27 39 45
alphaV beta3/Integrin/ppsTEM5 0.046 0.065 -10000 0 -0.16 42 42
RHOA 0.034 0.01 -10000 0 0 43 43
VTN 0.035 0.007 -10000 0 0 22 22
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.035 0.008 -10000 0 0 29 29
F11R -0.022 0.037 0.06 7 -0.19 22 29
alphaV/beta3 Integrin/Lactadherin 0.019 0.097 -10000 0 -0.17 104 104
alphaV/beta3 Integrin/TGFBR2 0.046 0.073 -10000 0 -0.16 53 53
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.064 -10000 0 -0.15 47 47
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.045 0.066 -10000 0 -0.14 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.028 0.016 -10000 0 0 126 126
alphaV/beta3 Integrin/Pyk2 0.033 0.059 0.2 1 -0.14 46 47
SDC1 0.027 0.016 -10000 0 0 137 137
VAV3 -0.023 0.066 0.21 7 -0.22 40 47
PTPN11 0.036 0.005 -10000 0 0 8 8
IRS1 0.029 0.015 -10000 0 0 115 115
FAK1/Paxillin 0.018 0.11 0.28 4 -0.26 40 44
cell migration 0.008 0.098 0.24 6 -0.25 39 45
ITGAV 0.032 0.012 -10000 0 0 65 65
PI3K 0.023 0.094 -10000 0 -0.17 72 72
SPP1 0.03 0.015 -10000 0 0 104 104
KDR 0.035 0.007 -10000 0 0 21 21
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.032 0.012 -10000 0 0 65 65
COL4A3 0.037 0.004 -10000 0 0 5 5
angiogenesis -0.041 0.16 0.31 2 -0.42 64 66
Rac1/GTP -0.027 0.086 0.21 7 -0.16 140 147
EDIL3 0.034 0.01 -10000 0 0 38 38
cell proliferation 0.046 0.072 -10000 0 -0.16 53 53
IL2 signaling events mediated by STAT5

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
GAB2 0.025 0.033 -10000 0 -0.014 129 129
ELF1 0.039 0.028 -10000 0 -0.28 3 3
CCNA2 0.028 0.016 -10000 0 0 131 131
PIK3CA 0.022 0.031 -10000 0 -0.008 178 178
JAK3 0.031 0.016 -10000 0 -0.028 20 20
PIK3R1 0.026 0.033 -10000 0 -0.015 107 107
JAK1 0.027 0.044 -10000 0 -0.1 32 32
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.01 0.18 0.24 3 -0.45 50 53
SHC1 0.032 0.016 -10000 0 -0.014 53 53
SP1 0.045 0.009 -10000 0 -10000 0 0
IL2RA 0.009 0.045 -10000 0 -0.19 23 23
IL2RB 0.028 0.018 -10000 0 -0.005 113 113
SOS1 0 0.003 -10000 0 -10000 0 0
IL2RG 0.03 0.018 -10000 0 -0.009 84 84
G1/S transition of mitotic cell cycle 0.007 0.11 0.3 2 -0.34 5 7
PTPN11 0.034 0.015 -10000 0 -0.023 32 32
CCND2 0.018 0.009 -10000 0 -10000 0 0
LCK 0.032 0.016 -10000 0 -0.03 24 24
GRB2 0.033 0.015 -10000 0 -0.014 43 43
IL2 0.033 0.016 -10000 0 -0.013 49 49
CDK6 0.036 0.005 -10000 0 0 11 11
CCND3 -0.036 0.26 0.37 3 -0.88 40 43
IL6-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
BCL2L1 -0.098 0.35 -10000 0 -0.82 79 79
CRP -0.1 0.35 -10000 0 -0.83 78 78
cell cycle arrest -0.14 0.43 -10000 0 -0.95 92 92
TIMP1 -0.099 0.35 -10000 0 -0.75 94 94
IL6ST 0.022 0.033 -10000 0 -0.046 2 2
Rac1/GDP 0.005 0.13 0.29 4 -0.29 40 44
AP1 -0.017 0.17 -10000 0 -0.45 51 51
GAB2 0.031 0.017 -10000 0 0 106 106
TNFSF11 -0.11 0.35 -10000 0 -0.82 81 81
HSP90B1 -0.019 0.2 -10000 0 -1 16 16
GAB1 0.036 0.011 -10000 0 0 38 38
MAPK14 0.001 0.072 -10000 0 -0.27 9 9
AKT1 0.007 0.11 0.27 3 -0.35 21 24
FOXO1 0.01 0.11 0.27 2 -0.34 21 23
MAP2K6 0.001 0.088 -10000 0 -0.26 26 26
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.17 0.33 3 -0.35 80 83
MITF -0.002 0.1 0.23 1 -0.28 32 33
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.031 0.013 -10000 0 0 78 78
A2M -0.14 0.44 -10000 0 -1.3 65 65
CEBPB 0.033 0.012 -10000 0 0 57 57
GRB2/SOS1/GAB family/SHP2 0.009 0.13 0.25 3 -0.37 39 42
STAT3 -0.17 0.48 -10000 0 -1.1 92 92
STAT1 -0.047 0.26 -10000 0 -0.92 40 40
CEBPD -0.12 0.38 -10000 0 -0.89 83 83
PIK3CA 0.026 0.017 -10000 0 -10000 0 0
PI3K 0.015 0.072 -10000 0 -0.2 46 46
JUN 0.033 0.012 -10000 0 0 62 62
PIAS3/MITF 0.009 0.11 0.25 3 -0.28 28 31
MAPK11 0.001 0.061 -10000 0 -0.28 7 7
STAT3 (dimer)/FOXO1 -0.11 0.37 0.44 2 -0.77 99 101
GRB2/SOS1/GAB family 0.038 0.096 0.24 1 -0.24 17 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.015 0.077 -10000 0 -0.22 30 30
GRB2 0.037 0.009 -10000 0 -10000 0 0
JAK2 0.033 0.011 -10000 0 0 52 52
LBP -0.055 0.28 -10000 0 -0.62 77 77
PIK3R1 0.031 0.014 -10000 0 -10000 0 0
JAK1 0.022 0.058 -10000 0 -0.097 61 61
MYC -0.13 0.47 0.51 1 -0.93 119 120
FGG -0.11 0.35 -10000 0 -0.83 78 78
macrophage differentiation -0.14 0.43 -10000 0 -0.95 92 92
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.066 0.077 -10000 0 -0.16 11 11
JUNB -0.11 0.39 -10000 0 -0.88 86 86
FOS 0.021 0.018 -10000 0 0 231 231
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.001 0.11 0.21 1 -0.29 36 37
STAT1/PIAS1 -0.009 0.17 0.31 1 -0.32 83 84
GRB2/SOS1/GAB family/SHP2/PI3K 0.006 0.11 -10000 0 -0.37 23 23
STAT3 (dimer) -0.17 0.46 -10000 0 -1 92 92
PRKCD -0.056 0.23 0.38 3 -0.49 90 93
IL6R 0.029 0.024 -10000 0 -0.035 54 54
SOCS3 0.011 0.063 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.08 -10000 0 -0.18 35 35
Rac1/GTP -0.004 0.15 0.28 2 -0.3 61 63
HCK 0.031 0.014 -10000 0 0 88 88
MAPKKK cascade 0 0.17 -10000 0 -0.46 49 49
bone resorption -0.1 0.33 -10000 0 -0.76 83 83
IRF1 -0.16 0.44 -10000 0 -0.97 105 105
mol:GDP -0.006 0.11 0.23 1 -0.29 36 37
SOS1 0.002 0.006 0.026 24 -10000 0 24
VAV1 -0.006 0.11 0.23 1 -0.29 36 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.02 0.086 -10000 0 -0.32 25 25
PTPN11 0.025 0.066 -10000 0 -0.76 3 3
IL6/IL6RA 0.035 0.039 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.047 0.062 -10000 0 -0.18 20 20
gp130 (dimer)/JAK2/JAK2/LMO4 0.051 0.054 -10000 0 -0.17 12 12
IL6 0.019 0.032 -10000 0 -0.036 63 63
PIAS3 0.033 0.012 -10000 0 0 62 62
PTPRE 0.026 0.034 -10000 0 -0.28 1 1
PIAS1 0.036 0.007 -10000 0 0 18 18
RAC1 0.034 0.016 -10000 0 -0.01 28 28
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.067 -10000 0 -0.21 25 25
LMO4 0.019 0.049 -10000 0 -0.23 9 9
STAT3 (dimer)/PIAS3 -0.13 0.42 -10000 0 -0.94 89 89
MCL1 0.021 0.12 -10000 0 -0.46 3 3
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.035 0.009 -10000 0 0 34 34
MKNK1 0.035 0.008 -10000 0 0 28 28
mol:PIP3 -0.022 0.081 0.18 18 -0.23 44 62
FRAP1 0.028 0.11 0.3 2 -0.48 17 19
AKT1 0.012 0.11 0.18 112 -0.23 39 151
INSR 0.034 0.01 -10000 0 0 39 39
Insulin Receptor/Insulin 0.044 0.016 -10000 0 -10000 0 0
mol:GTP 0.034 0.11 0.21 48 -0.21 36 84
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.009 0.049 -10000 0 -0.19 15 15
TSC2 0.033 0.011 -10000 0 0 53 53
RHEB/GDP 0.016 0.085 -10000 0 -0.19 35 35
TSC1 0.035 0.009 -10000 0 0 32 32
Insulin Receptor/IRS1 0.005 0.091 -10000 0 -0.27 51 51
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.07 0.16 1 -0.23 13 14
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.038 0.1 0.26 21 -0.3 12 33
MAP3K5 0.001 0.047 0.18 5 -0.21 20 25
PIK3R1 0.031 0.014 -10000 0 0 90 90
apoptosis 0.001 0.047 0.18 5 -0.21 20 25
mol:LY294002 0 0 0.001 6 -0.001 51 57
EIF4B 0.034 0.095 0.25 19 -0.28 11 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.089 0.24 17 -0.26 12 29
eIF4E/eIF4G1/eIF4A1 0 0.072 -10000 0 -0.3 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0 0.093 -10000 0 -0.2 76 76
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.075 0.21 17 -0.18 7 24
FKBP1A 0.034 0.011 -10000 0 0 48 48
RHEB/GTP 0.038 0.1 0.23 15 -0.19 34 49
mol:Amino Acids 0 0 0.001 6 -0.001 51 57
FKBP12/Rapamycin 0.023 0.029 -10000 0 -0.19 9 9
PDPK1 0.005 0.11 0.18 104 -0.23 38 142
EIF4E 0.033 0.011 -10000 0 0 51 51
ASK1/PP5C 0.032 0.16 -10000 0 -0.52 33 33
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.003 0.11 -10000 0 -0.39 26 26
TSC1/TSC2 0.04 0.12 0.24 50 -0.22 36 86
tumor necrosis factor receptor activity 0 0 0.001 51 -0.001 6 57
RPS6 0.035 0.008 -10000 0 0 27 27
PPP5C 0.035 0.009 -10000 0 0 32 32
EIF4G1 0.028 0.016 -10000 0 0 126 126
IRS1 -0.015 0.09 -10000 0 -0.28 52 52
INS 0.035 0.008 -10000 0 0 26 26
PTEN 0.032 0.012 -10000 0 0 61 61
PDK2 0.005 0.11 0.18 105 -0.23 38 143
EIF4EBP1 -0.12 0.4 -10000 0 -1.2 63 63
PIK3CA 0.026 0.017 -10000 0 0 158 158
PPP2R5D 0.029 0.11 0.27 5 -0.42 17 22
peptide biosynthetic process -0.012 0.026 0.19 8 -10000 0 8
RHEB 0.035 0.009 -10000 0 0 34 34
EIF4A1 0.034 0.01 -10000 0 0 37 37
mol:Rapamycin 0.001 0.002 0.003 132 -0.003 11 143
EEF2 -0.012 0.026 0.19 8 -10000 0 8
eIF4E/4E-BP1 -0.096 0.38 -10000 0 -1.1 63 63
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.024 0.12 -10000 0 -0.31 71 71
KLHL20 -0.012 0.1 0.2 12 -0.22 42 54
CYFIP2 0.033 0.011 -10000 0 0 51 51
Rac1/GDP 0 0.092 0.24 1 -0.24 32 33
ENAH -0.026 0.12 -10000 0 -0.32 68 68
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 17 0 113 130
RAP1A 0.036 0.007 -10000 0 0 17 17
CTNNB1 0.035 0.007 -10000 0 0 22 22
CDC42/GTP -0.004 0.059 0.12 15 -0.17 34 49
ABI1/Sra1/Nap1 -0.034 0.053 -10000 0 -0.15 53 53
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.073 -10000 0 -0.17 36 36
RAPGEF1 -0.021 0.11 0.23 1 -0.3 54 55
CTNND1 0.035 0.007 -10000 0 0 20 20
regulation of calcium-dependent cell-cell adhesion -0.014 0.13 -10000 0 -0.32 72 72
CRK -0.017 0.12 -10000 0 -0.31 57 57
E-cadherin/gamma catenin/alpha catenin 0.049 0.063 -10000 0 -0.18 31 31
alphaE/beta7 Integrin 0.037 0.053 -10000 0 -0.19 23 23
IQGAP1 0.033 0.011 -10000 0 0 53 53
NCKAP1 0.036 0.005 -10000 0 0 11 11
Rap1/GTP/I-afadin 0.04 0.023 -10000 0 -0.14 5 5
DLG1 -0.017 0.11 -10000 0 -0.32 55 55
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.037 -10000 0 -0.15 21 21
MLLT4 0.033 0.011 -10000 0 0 53 53
ARF6/GTP/NME1/Tiam1 0.037 0.035 -10000 0 -0.14 16 16
PI3K -0.025 0.048 -10000 0 -0.19 21 21
ARF6 0.036 0.005 -10000 0 0 11 11
mol:Ca2+ 0 0 0 84 0 119 203
E-cadherin/gamma catenin 0.035 0.058 -10000 0 -0.2 25 25
TIAM1 0.034 0.011 -10000 0 0 47 47
E-cadherin(dimer)/Ca2+ 0.058 0.069 -10000 0 -0.16 37 37
AKT1 0.008 0.067 0.16 45 -0.16 11 56
PIK3R1 0.031 0.014 -10000 0 0 90 90
CDH1 0.032 0.012 -10000 0 0 66 66
RhoA/GDP -0.002 0.099 0.23 1 -0.26 37 38
actin cytoskeleton organization -0.006 0.079 0.16 14 -0.16 40 54
CDC42/GDP 0.004 0.091 0.23 1 -0.24 28 29
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.001 0.074 -10000 0 -0.2 53 53
ITGB7 0.037 0.003 -10000 0 0 4 4
RAC1 0.035 0.008 -10000 0 0 28 28
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.063 0.074 -10000 0 -0.17 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.05 -10000 0 -0.15 26 26
mol:GDP -0.016 0.094 0.23 1 -0.27 31 32
CDC42/GTP/IQGAP1 0.035 0.049 -10000 0 -0.16 30 30
JUP 0.034 0.011 -10000 0 0 48 48
p120 catenin/RhoA/GDP 0.005 0.11 0.24 1 -0.27 34 35
RAC1/GTP/IQGAP1 0.033 0.05 -10000 0 -0.16 31 31
PIP5K1C/AP1M1 0.024 0.008 -10000 0 -10000 0 0
RHOA 0.034 0.01 -10000 0 0 43 43
CDC42 0.036 0.006 -10000 0 0 15 15
CTNNA1 0.036 0.007 -10000 0 0 19 19
positive regulation of S phase of mitotic cell cycle -0.03 0.071 -10000 0 -0.14 141 141
NME1 0 0 -10000 0 -0.001 123 123
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.022 0.12 -10000 0 -0.32 65 65
regulation of cell-cell adhesion -0.01 0.046 -10000 0 -0.15 34 34
WASF2 -0.019 0.029 -10000 0 -0.082 53 53
Rap1/GTP -0.005 0.066 0.16 23 -0.19 31 54
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.063 0.086 -10000 0 -0.16 52 52
CCND1 -0.037 0.086 -10000 0 -0.17 141 141
VAV2 -0.02 0.18 -10000 0 -0.56 32 32
RAP1/GDP -0.002 0.074 0.19 4 -0.23 17 21
adherens junction assembly -0.022 0.12 -10000 0 -0.31 67 67
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 0 27 27
PIP5K1C 0.033 0.011 -10000 0 0 54 54
regulation of heterotypic cell-cell adhesion 0.039 0.08 0.21 1 -0.17 52 53
E-cadherin/beta catenin 0.008 0.038 -10000 0 -0.24 10 10
mol:GTP 0 0 0 74 -0.001 123 197
SRC -0.023 0.12 -10000 0 -0.32 69 69
PIK3CA 0.026 0.017 -10000 0 0 158 158
Rac1/GTP -0.062 0.12 -10000 0 -0.35 48 48
E-cadherin/beta catenin/alpha catenin 0.052 0.059 -10000 0 -0.18 26 26
ITGAE 0.031 0.013 -10000 0 0 81 81
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.13 -10000 0 -0.32 72 72
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 -0.066 0.27 -10000 0 -0.89 50 50
regulation of axonogenesis 0.005 0.056 0.19 32 -10000 0 32
myoblast fusion 0.011 0.14 0.38 55 -10000 0 55
mol:GTP 0.005 0.082 -10000 0 -0.22 54 54
regulation of calcium-dependent cell-cell adhesion -0.015 0.09 0.21 64 -10000 0 64
ARF1/GTP 0.025 0.076 -10000 0 -0.19 52 52
mol:GM1 -0.004 0.059 -10000 0 -0.17 51 51
mol:Choline -0.005 0.045 -10000 0 -0.15 40 40
lamellipodium assembly -0.028 0.15 -10000 0 -0.43 57 57
MAPK3 -0.004 0.11 -10000 0 -0.32 54 54
ARF6/GTP/NME1/Tiam1 0.016 0.091 -10000 0 -0.21 64 64
ARF1 0.035 0.009 -10000 0 0 31 31
ARF6/GDP -0.011 0.14 -10000 0 -0.39 55 55
ARF1/GDP -0.002 0.13 -10000 0 -0.37 54 54
ARF6 0.03 0.054 -10000 0 -0.13 51 51
RAB11A 0.036 0.007 -10000 0 0 18 18
TIAM1 0.025 0.035 -10000 0 -0.059 50 50
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.11 -10000 0 -0.33 48 48
actin filament bundle formation 0.006 0.14 0.38 57 -10000 0 57
KALRN -0.014 0.1 -10000 0 -0.29 56 56
RAB11FIP3/RAB11A 0.047 0.03 -10000 0 -0.19 6 6
RhoA/GDP -0.006 0.14 -10000 0 -0.38 57 57
NME1 -0.003 0.01 0.023 1 -0.031 51 52
Rac1/GDP 0.003 0.13 -10000 0 -0.36 57 57
substrate adhesion-dependent cell spreading 0.005 0.082 -10000 0 -0.22 54 54
cortical actin cytoskeleton organization -0.029 0.15 -10000 0 -0.44 57 57
RAC1 0.035 0.008 -10000 0 0 28 28
liver development 0.005 0.082 -10000 0 -0.22 54 54
ARF6/GTP 0.005 0.082 -10000 0 -0.22 54 54
RhoA/GTP 0.015 0.09 -10000 0 -0.19 78 78
mol:GDP -0.021 0.13 -10000 0 -0.4 49 49
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.076 -10000 0 -0.16 51 51
RHOA 0.034 0.01 -10000 0 0 43 43
PLD1 0.004 0.055 -10000 0 -0.16 45 45
RAB11FIP3 0.034 0.009 -10000 0 0 36 36
tube morphogenesis -0.028 0.15 -10000 0 -0.43 57 57
ruffle organization -0.005 0.056 -10000 0 -0.19 32 32
regulation of epithelial cell migration 0.005 0.082 -10000 0 -0.22 54 54
PLD2 0.006 0.062 -10000 0 -0.17 51 51
PIP5K1A -0.005 0.056 -10000 0 -0.19 32 32
mol:Phosphatidic acid -0.005 0.045 -10000 0 -0.15 40 40
Rac1/GTP -0.029 0.15 -10000 0 -0.44 57 57
TCGA08_rtk_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
PDGFRA 0.031 0.014 -10000 0 0 83 83
HRAS 0.034 0.01 -10000 0 0 38 38
EGFR 0.036 0.005 -10000 0 0 11 11
AKT 0.05 0.081 0.22 9 -0.19 12 21
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.034 0.01 -10000 0 0 46 46
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.009 -10000 0 0 31 31
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.034 0.01 -10000 0 0 43 43
PIK3CA 0.026 0.017 -10000 0 0 158 158
PIK3CB 0.034 0.01 -10000 0 0 37 37
NRAS 0.031 0.014 -10000 0 0 88 88
PIK3CG 0.036 0.006 -10000 0 0 14 14
PIK3R3 0.034 0.01 -10000 0 0 38 38
PIK3R2 0.034 0.011 -10000 0 0 48 48
NF1 0.034 0.011 -10000 0 0 47 47
RAS 0.017 0.063 0.16 9 -0.12 56 65
ERBB2 0.034 0.009 -10000 0 0 36 36
proliferation/survival/translation -0.053 0.071 0.17 7 -0.21 38 45
PI3K 0.036 0.069 0.18 36 -0.16 11 47
PIK3R1 0.031 0.014 -10000 0 0 90 90
KRAS 0.03 0.014 -10000 0 0 92 92
FOXO 0.058 0.052 0.15 50 -10000 0 50
AKT2 0.033 0.011 -10000 0 0 51 51
PTEN 0.033 0.012 -10000 0 0 61 61
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.038 0.052 -10000 0 -0.19 23 23
ATM 0.034 0.01 -10000 0 0 39 39
UBE2D3 0.035 0.009 -10000 0 0 34 34
PRKDC 0.033 0.011 -10000 0 0 53 53
ATR 0.033 0.011 -10000 0 0 49 49
UBE2L3 0.034 0.01 -10000 0 0 37 37
FANCD2 0.01 0.036 -10000 0 -0.23 11 11
protein ubiquitination 0.026 0.093 -10000 0 -0.16 86 86
XRCC5 0.035 0.008 -10000 0 0 24 24
XRCC6 0.033 0.011 -10000 0 0 52 52
M/R/N Complex 0.057 0.043 -10000 0 -0.16 11 11
MRE11A 0.035 0.008 -10000 0 0 27 27
DNA-PK 0.047 0.066 -10000 0 -0.18 34 34
FA complex/FANCD2/Ubiquitin -0.008 0.12 -10000 0 -0.36 39 39
FANCF 0.034 0.01 -10000 0 0 40 40
BRCA1 0.035 0.008 -10000 0 0 25 25
CCNE1 0.023 0.018 -10000 0 0 198 198
CDK2/Cyclin E1 0.001 0.088 -10000 0 -0.19 84 84
FANCG 0.033 0.011 -10000 0 0 51 51
BRCA1/BACH1/BARD1 0.042 0.046 -10000 0 -0.19 17 17
FANCE 0.035 0.007 -10000 0 0 21 21
FANCC 0.036 0.007 -10000 0 0 19 19
NBN 0.032 0.012 -10000 0 0 63 63
FANCA 0.031 0.013 -10000 0 0 80 80
DNA repair -0.011 0.11 0.26 15 -0.31 31 46
BRCA1/BARD1/ubiquitin 0.042 0.046 -10000 0 -0.19 17 17
BARD1/DNA-PK 0.058 0.08 -10000 0 -0.18 41 41
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.052 0.19 23 -10000 0 23
BRCA1/BARD1/CTIP/M/R/N Complex 0.013 0.066 0.16 1 -0.22 22 23
BRCA1/BACH1/BARD1/TopBP1 0.049 0.067 -10000 0 -0.17 37 37
BRCA1/BARD1/P53 0.015 0.11 -10000 0 -0.16 125 125
BARD1/CSTF1/BRCA1 0.053 0.054 -10000 0 -0.16 23 23
BRCA1/BACH1 0.035 0.008 -10000 0 0 25 25
BARD1 0.035 0.009 -10000 0 0 32 32
PCNA 0.033 0.012 -10000 0 0 62 62
BRCA1/BARD1/UbcH5C 0.056 0.053 -10000 0 -0.16 24 24
BRCA1/BARD1/UbcH7 0.058 0.047 -10000 0 -0.16 17 17
BRCA1/BARD1/RAD51/PCNA 0.061 0.072 -10000 0 -0.17 37 37
BARD1/DNA-PK/P53 0.012 0.12 -10000 0 -0.16 145 145
BRCA1/BARD1/Ubiquitin 0.042 0.046 -10000 0 -0.19 17 17
BRCA1/BARD1/CTIP 0.031 0.067 -10000 0 -0.17 44 44
FA complex 0.008 0.076 -10000 0 -0.19 55 55
BARD1/EWS 0.04 0.046 -10000 0 -0.19 17 17
RBBP8 -0.025 0.048 -10000 0 -0.19 36 36
TP53 0.023 0.018 -10000 0 0 192 192
TOPBP1 0.033 0.011 -10000 0 0 51 51
G1/S transition of mitotic cell cycle -0.014 0.1 0.16 125 -10000 0 125
BRCA1/BARD1 0.031 0.098 -10000 0 -0.16 86 86
CSTF1 0.033 0.011 -10000 0 0 53 53
BARD1/EWS-Fli1 0.02 0.038 -10000 0 -0.19 17 17
CDK2 0.035 0.008 -10000 0 0 25 25
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.008 -10000 0 0 28 28
RAD50 0.036 0.007 -10000 0 0 18 18
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.042 0.046 -10000 0 -0.19 17 17
EWSR1 0.034 0.01 -10000 0 0 44 44
Signaling events mediated by PTP1B

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
PDGFRB 0.035 0.009 -10000 0 0 32 32
Jak2/Leptin Receptor 0.015 0.1 -10000 0 -0.37 21 21
PTP1B/AKT1 -0.015 0.1 -10000 0 -0.25 43 43
FYN 0.028 0.016 -10000 0 0 131 131
p210 bcr-abl/PTP1B -0.028 0.098 -10000 0 -0.28 37 37
EGFR 0.036 0.011 -10000 0 -0.013 21 21
EGF/EGFR 0.003 0.1 -10000 0 -0.25 31 31
CSF1 0.037 0.004 -10000 0 0 6 6
AKT1 0.034 0.011 -10000 0 -0.001 47 47
INSR 0.034 0.01 -10000 0 -0.001 40 40
PTP1B/N-cadherin -0.03 0.11 -10000 0 -0.26 69 69
Insulin Receptor/Insulin 0.005 0.11 -10000 0 -0.25 36 36
HCK 0.031 0.014 -10000 0 0 88 88
CRK 0.033 0.011 -10000 0 0 55 55
TYK2 -0.014 0.11 0.22 30 -0.28 34 64
EGF 0.036 0.01 -10000 0 -0.002 28 28
YES1 0.034 0.01 -10000 0 0 42 42
CAV1 -0.028 0.11 0.18 1 -0.25 60 61
TXN 0.034 0.009 -10000 0 0 30 30
PTP1B/IRS1/GRB2 -0.019 0.12 -10000 0 -0.27 53 53
cell migration 0.028 0.098 0.28 37 -10000 0 37
STAT3 0.034 0.01 -10000 0 0 41 41
PRLR 0.037 0.01 -10000 0 -10000 0 0
ITGA2B 0.035 0.007 -10000 0 0 21 21
CSF1R 0.03 0.014 -10000 0 0 96 96
Prolactin Receptor/Prolactin 0.053 0.02 -10000 0 -10000 0 0
FGR 0.035 0.009 -10000 0 0 30 30
PTP1B/p130 Cas -0.028 0.092 -10000 0 -0.26 38 38
Crk/p130 Cas -0.017 0.099 -10000 0 -0.27 35 35
DOK1 -0.019 0.093 0.22 3 -0.26 32 35
JAK2 0.003 0.1 -10000 0 -0.39 21 21
Jak2/Leptin Receptor/Leptin 0.007 0.12 -10000 0 -0.28 26 26
PIK3R1 0.031 0.014 -10000 0 0 90 90
PTPN1 -0.028 0.099 -10000 0 -0.28 37 37
LYN 0.029 0.015 -10000 0 0 106 106
CDH2 0.025 0.017 -10000 0 0 165 165
SRC 0 0.12 -10000 0 -0.48 25 25
ITGB3 0.035 0.007 -10000 0 0 18 18
CAT1/PTP1B -0.029 0.13 0.23 10 -0.32 50 60
CAPN1 0.034 0.008 -10000 0 0 23 23
CSK 0.035 0.009 -10000 0 0 31 31
PI3K -0.005 0.1 -10000 0 -0.25 36 36
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.009 0.11 -10000 0 -0.26 23 23
negative regulation of transcription 0.003 0.1 -10000 0 -0.38 21 21
FCGR2A 0.027 0.017 -10000 0 0 144 144
FER 0.034 0.01 -10000 0 0 40 40
alphaIIb/beta3 Integrin 0.051 0.012 -10000 0 -10000 0 0
BLK 0.029 0.015 -10000 0 0 105 105
Insulin Receptor/Insulin/Shc 0.063 0.029 -10000 0 -0.17 1 1
RHOA 0.033 0.01 -10000 0 0 43 43
LEPR 0.035 0.008 -10000 0 0 24 24
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.007 -10000 0 0 22 22
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.023 0.13 0.22 4 -0.33 44 48
PRL 0.037 0.01 -10000 0 -10000 0 0
SOCS3 0.009 0.15 -10000 0 -1.1 9 9
SPRY2 0.02 0.018 -10000 0 0 220 220
Insulin Receptor/Insulin/IRS1 0.04 0.071 -10000 0 -0.17 49 49
CSF1/CSF1R -0.015 0.12 -10000 0 -0.27 48 48
Ras protein signal transduction 0.005 0.091 0.6 10 -0.23 1 11
IRS1 0.029 0.015 -10000 0 0 115 115
INS 0.035 0.008 -10000 0 0 26 26
LEP 0.036 0.007 -10000 0 0 20 20
STAT5B -0.013 0.11 0.18 1 -0.27 45 46
STAT5A -0.013 0.11 0.18 1 -0.27 45 46
GRB2 0.035 0.007 -10000 0 0 22 22
PDGFB-D/PDGFRB -0.016 0.1 -10000 0 -0.27 35 35
CSN2 0.031 0.059 -10000 0 -10000 0 0
PIK3CA 0.026 0.017 -10000 0 0 158 158
LAT -0.055 0.19 -10000 0 -0.46 86 86
YBX1 0.038 0.045 -10000 0 -0.32 7 7
LCK 0.035 0.008 -10000 0 0 26 26
SHC1 0.035 0.008 -10000 0 0 27 27
NOX4 0.027 0.017 -10000 0 0 142 142
EPO signaling 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
BCL2L1 0.034 0.11 0.36 2 -0.36 11 13
CRKL 0.044 0.073 0.17 112 -10000 0 112
mol:DAG 0.028 0.078 0.22 2 -0.2 35 37
HRAS 0.028 0.093 0.27 32 -10000 0 32
MAPK8 0.007 0.09 0.19 74 -0.16 37 111
RAP1A 0.045 0.074 0.17 114 -10000 0 114
GAB1 0.042 0.072 0.17 105 -10000 0 105
MAPK14 0.008 0.091 0.19 76 -0.15 40 116
EPO 0.042 0.01 0.077 9 -10000 0 9
PLCG1 0.028 0.079 0.22 2 -0.2 35 37
EPOR/TRPC2/IP3 Receptors 0.036 0.015 0.077 1 -10000 0 1
RAPGEF1 0.035 0.008 -10000 0 0 23 23
EPO/EPOR (dimer)/SOCS3 0.067 0.032 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.063 0.06 0.21 31 -0.13 3 34
EPO/EPOR (dimer) 0.053 0.024 -10000 0 -10000 0 0
IRS2 0.036 0.069 0.17 92 -0.22 1 93
STAT1 0.021 0.097 0.26 1 -0.23 50 51
STAT5B 0.032 0.079 0.25 1 -0.2 34 35
cell proliferation 0.003 0.088 0.18 75 -0.15 33 108
GAB1/SHIP/PIK3R1/SHP2/SHC 0.039 0.051 -10000 0 -0.13 16 16
TEC 0.045 0.074 0.17 115 -10000 0 115
SOCS3 0.036 0.007 -10000 0 0 19 19
STAT1 (dimer) 0.021 0.096 0.26 1 -0.23 50 51
JAK2 0.038 0.015 0.076 8 -10000 0 8
PIK3R1 0.031 0.014 -10000 0 0 90 90
EPO/EPOR (dimer)/JAK2 0.068 0.052 0.22 27 -0.1 5 32
EPO/EPOR 0.053 0.024 -10000 0 -10000 0 0
LYN 0.03 0.015 -10000 0 -10000 0 0
TEC/VAV2 0.058 0.063 0.22 36 -10000 0 36
elevation of cytosolic calcium ion concentration 0.036 0.015 0.077 1 -10000 0 1
SHC1 0.035 0.008 -10000 0 0 27 27
EPO/EPOR (dimer)/LYN 0.046 0.076 -10000 0 -0.16 48 48
mol:IP3 0.028 0.078 0.22 2 -0.2 35 37
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.03 0.081 0.22 28 -0.13 44 72
SH2B3 0 0.007 0.024 31 -10000 0 31
NFKB1 0.004 0.093 0.19 70 -0.18 38 108
EPO/EPOR (dimer)/JAK2/SOCS3 0.022 0.027 -10000 0 -0.19 2 2
PTPN6 0.039 0.056 0.17 73 -10000 0 73
TEC/VAV2/GRB2 0.073 0.066 0.23 34 -0.13 3 37
EPOR 0.036 0.015 0.077 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.062 0.06 0.21 31 -0.13 3 34
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.015 -10000 0 0 100 100
CRKL/CBL/C3G 0.073 0.065 0.23 35 -10000 0 35
VAV2 0.042 0.073 0.17 106 -10000 0 106
CBL 0.045 0.075 0.17 114 -10000 0 114
SHC/Grb2/SOS1 0.031 0.031 -10000 0 -0.13 3 3
STAT5A 0.031 0.079 0.25 1 -0.2 34 35
GRB2 0.035 0.007 -10000 0 0 22 22
STAT5 (dimer) 0.051 0.082 0.27 1 -0.22 3 4
LYN/PLCgamma2 0.014 0.081 -10000 0 -0.2 60 60
PTPN11 0.036 0.005 -10000 0 0 8 8
BTK 0.046 0.075 0.17 118 -10000 0 118
BCL2 0.028 0.12 0.36 2 -0.36 18 20
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.016 0.044 -10000 0 -0.17 19 19
CRKL 0.034 0.009 -10000 0 0 35 35
Rac1/GDP 0.025 0.011 -10000 0 -0.19 1 1
DOCK1 0.035 0.009 -10000 0 0 31 31
ITGA4 0.036 0.005 -10000 0 0 11 11
alpha4/beta7 Integrin/MAdCAM1 0.064 0.067 -10000 0 -0.15 35 35
EPO 0.036 0.006 -10000 0 0 12 12
alpha4/beta7 Integrin 0.053 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.011 -10000 0 0 55 55
alpha4/beta1 Integrin 0.052 0.012 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.047 0.019 -10000 0 -10000 0 0
lamellipodium assembly 0.017 0.1 -10000 0 -0.39 10 10
PIK3CA 0.026 0.017 -10000 0 0 158 158
PI3K 0.014 0.072 -10000 0 -0.2 46 46
ARF6 0.036 0.005 -10000 0 0 11 11
JAK2 0.025 0.019 -10000 0 -10000 0 0
PXN 0.037 0.004 -10000 0 0 5 5
PIK3R1 0.031 0.014 -10000 0 0 90 90
MADCAM1 0.032 0.012 -10000 0 0 67 67
cell adhesion 0.061 0.065 -10000 0 -0.15 35 35
CRKL/CBL 0.05 0.016 -10000 0 -10000 0 0
ITGB1 0.036 0.006 -10000 0 0 15 15
SRC -0.029 0.088 0.2 21 -0.15 131 152
ITGB7 0.037 0.003 -10000 0 0 4 4
RAC1 0.035 0.008 -10000 0 0 28 28
alpha4/beta1 Integrin/VCAM1 0 0.1 -10000 0 -0.16 143 143
p130Cas/Crk/Dock1 0.007 0.094 0.21 17 -0.14 125 142
VCAM1 0.019 0.018 -10000 0 0 253 253
RHOA 0.034 0.01 -10000 0 0 43 43
alpha4/beta1 Integrin/Paxillin/GIT1 0.086 0.028 -10000 0 -10000 0 0
BCAR1 -0.029 0.08 0.19 21 -0.14 131 152
EPOR 0.032 0.012 -10000 0 0 65 65
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.007 -10000 0 0 17 17
GIT1 0.035 0.008 -10000 0 0 23 23
Rac1/GTP 0.017 0.1 -10000 0 -0.43 9 9
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.032 0.063 3 -0.16 21 24
RAS family/GTP 0.003 0.11 0.21 1 -0.21 65 66
NFATC4 -0.011 0.096 0.26 30 -0.19 17 47
ERBB2IP 0.032 0.013 -10000 0 -0.003 60 60
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.006 0.085 0.2 10 -0.19 59 69
JUN 0.005 0.086 0.25 4 -10000 0 4
HRAS 0.034 0.01 -10000 0 0 38 38
DOCK7 -0.03 0.072 0.14 24 -0.19 52 76
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.031 0.083 0.2 20 -0.16 58 78
AKT1 -0.004 0.011 0.021 35 -10000 0 35
BAD -0.014 0.027 0.056 9 -0.16 14 23
MAPK10 0.001 0.082 0.21 38 -0.15 10 48
mol:GTP 0 0.002 -10000 0 -0.005 40 40
ErbB2/ErbB3/neuregulin 1 beta -0.004 0.091 0.21 10 -0.2 59 69
RAF1 -0.002 0.12 0.25 18 -0.24 48 66
ErbB2/ErbB3/neuregulin 2 0.011 0.075 0.22 9 -0.16 66 75
STAT3 -0.032 0.26 -10000 0 -0.93 39 39
cell migration 0.003 0.083 0.21 38 -0.15 12 50
mol:PI-3-4-5-P3 -0.001 0.002 0.005 29 -0.004 56 85
cell proliferation -0.055 0.24 -10000 0 -0.59 52 52
FOS -0.061 0.24 0.33 5 -0.43 134 139
NRAS 0.029 0.027 -10000 0 -0.28 3 3
mol:Ca2+ -0.006 0.085 0.2 10 -0.19 59 69
MAPK3 -0.027 0.19 -10000 0 -0.48 41 41
MAPK1 -0.05 0.21 -10000 0 -0.52 50 50
JAK2 -0.021 0.085 0.2 20 -0.2 39 59
NF2 0.005 0.062 -10000 0 -0.67 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.002 0.073 0.19 3 -0.2 53 56
NRG1 0.032 0.013 0.056 1 0 66 67
GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
MAPK8 -0.016 0.1 0.22 7 -0.23 63 70
MAPK9 -0.003 0.081 0.21 35 -0.15 11 46
ERBB2 -0.018 0.05 0.29 13 -10000 0 13
ERBB3 0.027 0.017 -10000 0 0 146 146
SHC1 0.035 0.008 -10000 0 0 27 27
RAC1 0.035 0.008 -10000 0 0 28 28
apoptosis 0.01 0.038 0.23 11 -0.21 2 13
STAT3 (dimer) -0.03 0.25 -10000 0 -0.91 39 39
RNF41 -0.019 0.031 0.064 3 -0.15 23 26
FRAP1 -0.014 0.025 0.059 5 -0.16 12 17
RAC1-CDC42/GTP -0.034 0.048 0.058 1 -0.15 57 58
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.01 0.026 2 -10000 0 2
CHRNA1 -0.014 0.16 -10000 0 -0.38 26 26
myelination -0.004 0.11 0.27 42 -0.22 9 51
PPP3CB -0.021 0.086 0.19 27 -0.19 43 70
KRAS 0.029 0.024 -10000 0 -0.006 92 92
RAC1-CDC42/GDP 0.02 0.098 0.2 3 -0.19 61 64
NRG2 0.036 0.005 -10000 0 0 10 10
mol:GDP -0.002 0.073 0.19 3 -0.19 53 56
SOS1 0 0.001 -10000 0 -0.004 7 7
MAP2K2 -0.015 0.12 0.24 16 -0.25 54 70
SRC 0.035 0.008 -10000 0 0 25 25
mol:cAMP -0.001 0.001 0.004 16 -0.004 8 24
PTPN11 -0.022 0.089 0.2 25 -0.2 44 69
MAP2K1 -0.033 0.2 -10000 0 -0.55 29 29
heart morphogenesis -0.006 0.085 0.2 10 -0.19 59 69
RAS family/GDP 0.013 0.11 0.23 1 -0.21 63 64
GRB2 0.035 0.007 -10000 0 0 22 22
PRKACA 0.009 0.064 -10000 0 -0.7 4 4
CHRNE 0.007 0.023 0.091 4 -10000 0 4
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.014 0.19 1 -0.021 35 36
nervous system development -0.006 0.085 0.2 10 -0.19 59 69
CDC42 0.036 0.006 -10000 0 0 15 15
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.007 0.045 -10000 0 -10000 0 0
PLK1 -0.041 0.23 -10000 0 -0.82 20 20
CDKN1B -0.051 0.21 0.35 3 -0.41 99 102
FOXO3 -0.039 0.22 -10000 0 -0.49 83 83
KAT2B -0.002 0.02 -10000 0 -0.044 83 83
FOXO1/SIRT1 0.019 0.058 0.2 1 -0.2 5 6
CAT -0.072 0.33 0.46 1 -1 40 41
CTNNB1 0.035 0.007 -10000 0 0 22 22
AKT1 0.02 0.051 -10000 0 -0.1 31 31
FOXO1 0.008 0.052 0.23 1 -0.24 1 2
MAPK10 -0.001 0.05 0.2 4 -0.15 29 33
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
FOXO4 -0.033 0.13 0.22 1 -0.32 64 65
response to oxidative stress -0.001 0.022 -10000 0 -0.044 78 78
FOXO3A/SIRT1 -0.043 0.22 -10000 0 -0.47 88 88
XPO1 0.036 0.006 -10000 0 0 13 13
EP300 0.034 0.012 -10000 0 -10000 0 0
BCL2L11 0.023 0.066 -10000 0 -0.64 4 4
FOXO1/SKP2 0.023 0.052 -10000 0 -0.22 1 1
mol:GDP -0.001 0.022 -10000 0 -0.044 78 78
RAN 0.033 0.022 -10000 0 -0.015 37 37
GADD45A -0.067 0.28 -10000 0 -0.81 52 52
YWHAQ 0.036 0.007 -10000 0 0 19 19
FOXO1/14-3-3 family -0.03 0.19 -10000 0 -0.45 62 62
MST1 0.022 0.042 -10000 0 -0.062 76 76
CSNK1D 0.035 0.009 -10000 0 0 32 32
CSNK1E 0.033 0.012 -10000 0 0 59 59
FOXO4/14-3-3 family -0.064 0.22 -10000 0 -0.49 75 75
YWHAB 0.034 0.01 -10000 0 0 42 42
MAPK8 -0.002 0.053 0.2 4 -0.15 31 35
MAPK9 -0.003 0.055 0.2 4 -0.16 32 36
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.033 0.011 -10000 0 0 53 53
YWHAZ 0.029 0.015 -10000 0 0 105 105
SIRT1 0.026 0.028 -10000 0 -0.04 55 55
SOD2 -0.12 0.34 -10000 0 -0.81 85 85
RBL2 -0.079 0.3 -10000 0 -0.82 56 56
RAL/GDP 0.024 0.063 -10000 0 -0.17 31 31
CHUK 0.02 0.05 -10000 0 -0.075 76 76
Ran/GTP 0.014 0.043 -10000 0 -0.19 20 20
CSNK1G2 0.033 0.012 -10000 0 0 62 62
RAL/GTP 0.024 0.062 -10000 0 -0.14 36 36
CSNK1G1 0.036 0.006 -10000 0 0 12 12
FASLG 0.027 0.032 -10000 0 -10000 0 0
SKP2 0.034 0.01 -10000 0 0 42 42
USP7 0.035 0.008 -10000 0 0 25 25
IKBKB 0.022 0.039 -10000 0 -0.059 72 72
CCNB1 -0.13 0.42 -10000 0 -1.1 71 71
FOXO1-3a-4/beta catenin -0.045 0.2 -10000 0 -0.38 90 90
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.052 -10000 0 -0.22 1 1
CSNK1A1 0.036 0.006 -10000 0 0 13 13
SGK1 -0.002 0.02 -10000 0 -0.044 83 83
CSNK1G3 0.034 0.01 -10000 0 0 45 45
Ran/GTP/Exportin 1 0.036 0.045 -10000 0 -0.16 20 20
ZFAND5 -0.025 0.11 0.21 1 -0.26 64 65
SFN 0.026 0.017 -10000 0 0 148 148
CDK2 0.037 0.009 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.053 0.21 -10000 0 -0.45 76 76
CREBBP 0.036 0.01 -10000 0 -10000 0 0
FBXO32 -0.036 0.2 -10000 0 -0.45 83 83
BCL6 -0.071 0.3 -10000 0 -0.94 42 42
RALB 0.033 0.029 -10000 0 -0.053 22 22
RALA 0.034 0.022 -10000 0 -0.2 3 3
YWHAH 0.03 0.014 -10000 0 0 92 92
Signaling events mediated by PRL

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
CCNE1 0.023 0.018 -10000 0 0 198 198
mol:Halofuginone -0.002 0.036 -10000 0 -0.19 18 18
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.005 0.14 -10000 0 -0.53 24 24
PRL-3/alpha Tubulin -0.002 0.061 -10000 0 -0.19 50 50
mol:Ca2+ 0.012 0.093 0.29 50 -10000 0 50
AGT 0.033 0.011 -10000 0 0 55 55
CCNA2 -0.036 0.15 -10000 0 -0.7 19 19
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.001 0.068 -10000 0 -0.35 18 18
CDK2/Cyclin E1 -0.011 0.14 -10000 0 -0.48 29 29
MAPK3 -0.026 0.056 -10000 0 -0.19 49 49
PRL-2 /Rab GGTase beta 0.039 0.06 -10000 0 -0.22 24 24
MAPK1 -0.024 0.057 -10000 0 -0.19 49 49
PTP4A1 -0.04 0.14 -10000 0 -0.71 18 18
PTP4A3 0.021 0.018 -10000 0 0 223 223
PTP4A2 0.035 0.009 -10000 0 0 30 30
ITGB1 -0.026 0.056 -10000 0 -0.19 49 49
SRC 0.035 0.008 -10000 0 0 25 25
RAC1 -0.033 0.16 -10000 0 -0.43 57 57
Rab GGTase beta/Rab GGTase alpha 0.042 0.049 -10000 0 -0.2 19 19
PRL-1/ATF-5 -0.007 0.15 -10000 0 -0.67 18 18
RABGGTA 0.035 0.008 -10000 0 0 24 24
BCAR1 0.014 0.087 0.28 50 -10000 0 50
RHOC -0.034 0.16 -10000 0 -0.46 54 54
RHOA -0.057 0.2 -10000 0 -0.47 77 77
cell motility -0.038 0.18 -10000 0 -0.46 61 61
PRL-1/alpha Tubulin -0.038 0.13 -10000 0 -0.67 18 18
PRL-3/alpha1 Integrin -0.002 0.061 -10000 0 -0.19 50 50
ROCK1 -0.036 0.18 -10000 0 -0.45 62 62
RABGGTB 0.035 0.008 -10000 0 0 28 28
CDK2 0.035 0.008 -10000 0 0 25 25
mitosis -0.039 0.14 -10000 0 -0.7 18 18
ATF5 0.035 0.008 -10000 0 0 27 27
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.093 -10000 0 -0.42 19 19
HDAC1 0.045 0.034 0.084 125 -0.077 11 136
AES 0.036 0.017 0.073 31 0 66 97
FBXW11 0.036 0.007 -10000 0 0 17 17
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.044 0.032 -10000 0 -0.19 6 6
TLE1 0.038 0.012 0.071 27 0 24 51
AP1 -0.04 0.099 -10000 0 -0.21 120 120
NCSTN 0.035 0.009 -10000 0 0 30 30
ADAM10 0.035 0.009 -10000 0 0 29 29
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.096 0.21 -10000 0 -0.56 47 47
NICD/RBPSUH 0.006 0.092 -10000 0 -0.42 20 20
WIF1 0.034 0.009 -10000 0 0 34 34
NOTCH1 0.023 0.09 -10000 0 -0.44 18 18
PSENEN 0.031 0.013 -10000 0 0 83 83
KREMEN2 0.035 0.009 -10000 0 0 33 33
DKK1 0.035 0.008 -10000 0 0 27 27
beta catenin/beta TrCP1 0 0.096 -10000 0 -0.31 22 22
APH1B 0.035 0.007 -10000 0 0 21 21
APH1A 0.034 0.01 -10000 0 0 43 43
AXIN1 -0.004 0.12 0.23 1 -0.44 25 26
CtBP/CBP/TCF1/TLE1/AES 0.031 0.1 0.19 107 -0.21 22 129
PSEN1 0.035 0.007 -10000 0 0 19 19
FOS 0.02 0.018 -10000 0 0 231 231
JUN 0.033 0.012 -10000 0 0 62 62
MAP3K7 0.038 0.015 0.062 33 0 46 79
CTNNB1 -0.013 0.091 -10000 0 -0.32 22 22
MAPK3 0.036 0.004 -10000 0 0 7 7
DKK2/LRP6/Kremen 2 0.058 0.037 -10000 0 -0.16 6 6
HNF1A 0.004 0.01 0.036 35 -10000 0 35
CTBP1 0.037 0.016 0.074 33 0 55 88
MYC -0.25 0.52 -10000 0 -1.3 100 100
NKD1 0.001 0.003 -10000 0 -10000 0 0
FZD1 0.035 0.008 -10000 0 0 27 27
NOTCH1 precursor/Deltex homolog 1 0.006 0.092 -10000 0 -0.42 20 20
apoptosis -0.04 0.099 -10000 0 -0.21 120 120
Delta 1/NOTCHprecursor 0.006 0.092 -10000 0 -0.42 20 20
DLL1 0 0 -10000 0 -10000 0 0
PPARD -0.003 0.074 -10000 0 -0.87 2 2
Gamma Secretase 0.068 0.072 -10000 0 -0.16 30 30
APC -0.002 0.12 0.23 1 -0.46 23 24
DVL1 0.002 0.085 -10000 0 -0.32 31 31
CSNK2A1 0.031 0.012 -10000 0 0 71 71
MAP3K7IP1 0.038 0.016 0.065 9 0 48 57
DKK1/LRP6/Kremen 2 0.061 0.035 -10000 0 -0.16 6 6
LRP6 0.033 0.011 -10000 0 0 56 56
CSNK1A1 0.035 0.006 -10000 0 0 13 13
NLK 0.03 0.042 -10000 0 -0.21 9 9
CCND1 -0.3 0.57 -10000 0 -1.3 131 131
WNT1 0.036 0.004 -10000 0 0 7 7
Axin1/APC/beta catenin -0.005 0.12 0.28 4 -0.42 20 24
DKK2 0.033 0.012 -10000 0 0 62 62
NOTCH1 precursor/DVL1 0.015 0.13 -10000 0 -0.46 20 20
GSK3B 0.035 0.01 -10000 0 0 41 41
FRAT1 0.038 0.008 -10000 0 0 14 14
NOTCH/Deltex homolog 1 0.011 0.093 -10000 0 -0.42 19 19
PPP2R5D 0.008 0.052 -10000 0 -0.36 5 5
MAPK1 0.033 0.012 -10000 0 0 62 62
WNT1/LRP6/FZD1 0.076 0.041 -10000 0 -0.15 6 6
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.022 0.024 -10000 0 -0.015 89 89
IL1-mediated signaling events

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
UBC13/UEV1A 0.02 0.037 -10000 0 -0.19 16 16
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.034 0.01 -10000 0 0 37 37
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.1 -10000 0 -0.31 42 42
IRAK/TOLLIP 0.02 0.057 0.18 3 -0.14 54 57
IKBKB 0.034 0.01 -10000 0 0 40 40
IKBKG 0.037 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.046 0.02 -10000 0 -10000 0 0
IL1A 0.036 0.006 -10000 0 0 14 14
IL1B -0.033 0.07 -10000 0 -0.19 75 75
IRAK/TRAF6/p62/Atypical PKCs 0.021 0.075 0.19 2 -0.15 66 68
IL1R2 0.032 0.013 -10000 0 0 72 72
IL1R1 0.036 0.006 -10000 0 0 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.097 -10000 0 -0.31 31 31
TOLLIP 0.035 0.009 -10000 0 0 34 34
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.006 -10000 0 0 16 16
TAK1/TAB1/TAB2 0.057 0.049 -10000 0 -0.18 16 16
IKK complex/ELKS 0.01 0.078 -10000 0 -0.27 16 16
JUN -0.033 0.055 0.16 16 -0.23 6 22
MAP3K7 0.034 0.01 -10000 0 0 46 46
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.015 0.1 -10000 0 -0.17 92 92
IL1 alpha/IL1R1/IL1RAP/MYD88 0.058 0.07 -10000 0 -0.16 34 34
PIK3R1 0.031 0.014 -10000 0 0 90 90
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.068 0.074 -10000 0 -0.16 31 31
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.081 -10000 0 -0.16 77 77
NFKB1 0.033 0.011 -10000 0 0 51 51
MAPK8 -0.026 0.052 0.17 18 -0.23 4 22
IRAK1 0.01 0.029 -10000 0 -0.16 15 15
IL1RN/IL1R1 0.052 0.015 -10000 0 -0.19 1 1
IRAK4 0.036 0.006 -10000 0 0 16 16
PRKCI 0.025 0.017 -10000 0 0 168 168
TRAF6 0.036 0.005 -10000 0 0 9 9
PI3K 0.014 0.072 -10000 0 -0.2 46 46
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.002 0.11 0.17 2 -0.29 47 49
CHUK 0.035 0.009 -10000 0 0 33 33
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.081 -10000 0 -0.16 77 77
IL1 beta/IL1R2 0.008 0.078 0.24 1 -0.17 76 77
IRAK/TRAF6/TAK1/TAB1/TAB2 0.051 0.08 0.21 2 -0.15 56 58
NF kappa B1 p50/RelA 0.001 0.1 -10000 0 -0.18 85 85
IRAK3 0.036 0.006 -10000 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.03 0.082 -10000 0 -0.16 65 65
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.062 -10000 0 -0.19 32 32
IL1 alpha/IL1R1/IL1RAP 0.049 0.054 -10000 0 -0.16 22 22
RELA 0.036 0.004 -10000 0 0 7 7
MAP3K7IP1 0.034 0.011 -10000 0 0 48 48
SQSTM1 0.033 0.011 -10000 0 0 50 50
MYD88 0.035 0.009 -10000 0 0 31 31
IRAK/TRAF6/MEKK3 0.04 0.063 0.2 3 -0.14 50 53
IL1RAP 0.028 0.016 -10000 0 0 131 131
UBE2N 0.035 0.008 -10000 0 0 24 24
IRAK/TRAF6 -0.004 0.078 -10000 0 -0.16 83 83
CASP1 0.027 0.016 -10000 0 0 140 140
IL1RN/IL1R2 0.047 0.019 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.028 0.098 -10000 0 -0.18 74 74
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.1 -10000 0 -0.31 33 33
PIK3CA 0.026 0.017 -10000 0 0 158 158
IL1RN 0.036 0.005 -10000 0 0 10 10
TRAF6/TAK1/TAB1/TAB2 0.064 0.064 -10000 0 -0.16 29 29
MAP2K6 -0.02 0.055 0.19 18 -0.24 4 22
Reelin 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
CDK5R1/CDK5 0.04 0.043 -10000 0 -0.19 14 14
VLDLR 0.028 0.016 -10000 0 0 131 131
CRKL 0.034 0.009 -10000 0 0 35 35
LRPAP1 0.033 0.012 -10000 0 0 58 58
FYN 0.028 0.016 -10000 0 0 131 131
ITGA3 0.034 0.011 -10000 0 0 48 48
RELN/VLDLR/Fyn 0.021 0.086 -10000 0 -0.16 84 84
MAPK8IP1/MKK7/MAP3K11/JNK1 0.091 0.043 -10000 0 -0.15 1 1
AKT1 -0.015 0.073 -10000 0 -0.2 57 57
MAP2K7 0.034 0.01 -10000 0 0 38 38
RAPGEF1 0.035 0.008 -10000 0 0 23 23
DAB1 0.036 0.007 -10000 0 0 18 18
RELN/LRP8/DAB1 0.058 0.034 -10000 0 -0.13 11 11
LRPAP1/LRP8 0.032 0.057 -10000 0 -0.19 27 27
RELN/LRP8/DAB1/Fyn 0.05 0.069 -10000 0 -0.15 39 39
DAB1/alpha3/beta1 Integrin 0.034 0.08 -10000 0 -0.16 52 52
long-term memory 0.057 0.076 -10000 0 -0.15 31 31
DAB1/LIS1 0.049 0.085 -10000 0 -0.15 52 52
DAB1/CRLK/C3G 0.037 0.076 -10000 0 -0.16 45 45
PIK3CA 0.026 0.017 -10000 0 0 158 158
DAB1/NCK2 0.051 0.089 -10000 0 -0.16 58 58
ARHGEF2 0.035 0.009 -10000 0 0 31 31
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.035 0.009 -10000 0 0 30 30
CDK5R1 0.034 0.01 -10000 0 0 38 38
RELN 0.032 0.013 -10000 0 0 70 70
PIK3R1 0.031 0.014 -10000 0 0 90 90
RELN/LRP8/Fyn 0.038 0.07 -10000 0 -0.15 55 55
GRIN2A/RELN/LRP8/DAB1/Fyn 0.063 0.079 -10000 0 -0.15 37 37
MAPK8 0.036 0.005 -10000 0 0 10 10
RELN/VLDLR/DAB1 0.041 0.06 -10000 0 -0.14 43 43
ITGB1 0.036 0.006 -10000 0 0 15 15
MAP1B -0.005 0.07 0.2 18 -0.26 10 28
RELN/LRP8 0.051 0.053 -10000 0 -0.15 27 27
GRIN2B/RELN/LRP8/DAB1/Fyn 0.061 0.077 -10000 0 -0.16 33 33
PI3K 0.014 0.072 -10000 0 -0.2 46 46
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.044 0.039 -10000 0 -0.19 11 11
RAP1A -0.006 0.092 0.32 14 -0.25 4 18
PAFAH1B1 0.034 0.011 -10000 0 0 48 48
MAPK8IP1 0.037 0.004 -10000 0 0 5 5
CRLK/C3G 0.049 0.016 -10000 0 -10000 0 0
GRIN2B 0.033 0.011 -10000 0 0 50 50
NCK2 0.036 0.006 -10000 0 0 13 13
neuron differentiation 0.02 0.063 0.16 2 -0.22 11 13
neuron adhesion -0.007 0.099 0.35 14 -0.25 5 19
LRP8 0.032 0.012 -10000 0 0 65 65
GSK3B -0.011 0.085 0.18 6 -0.2 56 62
RELN/VLDLR/DAB1/Fyn 0.033 0.083 -10000 0 -0.14 80 80
MAP3K11 0.036 0.006 -10000 0 0 12 12
RELN/VLDLR/DAB1/P13K -0.011 0.079 -10000 0 -0.2 66 66
CDK5 0.033 0.012 -10000 0 0 57 57
MAPT -0.004 0.058 0.74 3 -10000 0 3
neuron migration -0.01 0.1 0.27 11 -0.27 27 38
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.019 0.062 -10000 0 -0.22 11 11
RELN/VLDLR 0.043 0.082 -10000 0 -0.15 62 62
HIF-2-alpha transcription factor network

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
MMP14 0.032 0.073 -10000 0 -0.54 5 5
oxygen homeostasis 0.002 0.015 0.033 38 -0.024 39 77
TCEB2 0.035 0.007 -10000 0 0 21 21
TCEB1 0.034 0.01 -10000 0 0 37 37
VHL/Elongin B/Elongin C/HIF2A 0.04 0.1 0.28 6 -0.25 15 21
EPO 0.023 0.19 0.44 3 -0.41 35 38
FIH (dimer) 0.03 0.03 0.098 3 -0.035 76 79
APEX1 0.017 0.053 -10000 0 -0.18 14 14
SERPINE1 0.001 0.18 0.37 7 -0.41 42 49
FLT1 0.008 0.15 -10000 0 -0.61 22 22
ADORA2A 0.021 0.19 0.35 28 -0.4 41 69
germ cell development 0.01 0.18 0.32 17 -0.39 43 60
SLC11A2 0.024 0.2 0.36 20 -0.42 45 65
BHLHE40 0.009 0.18 0.33 17 -0.41 43 60
HIF1AN 0.03 0.03 0.098 3 -0.035 76 79
HIF2A/ARNT/SIRT1 0.041 0.14 0.35 4 -0.31 24 28
ETS1 0.045 0.012 -10000 0 -10000 0 0
CITED2 -0.052 0.29 -10000 0 -0.91 49 49
KDR 0.013 0.13 -10000 0 -0.62 16 16
PGK1 0.012 0.22 0.35 21 -0.47 56 77
SIRT1 0.035 0.008 -10000 0 0 23 23
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.04 0.22 -10000 0 -0.46 42 42
EPAS1 0.023 0.097 0.22 23 -0.24 17 40
SP1 0.042 0.005 -10000 0 -10000 0 0
ABCG2 0.027 0.2 0.36 22 -0.41 41 63
EFNA1 0.013 0.2 0.34 17 -0.43 46 63
FXN 0.017 0.19 0.34 28 -0.4 42 70
POU5F1 0.009 0.18 0.33 17 -0.41 43 60
neuron apoptosis -0.038 0.22 0.45 42 -10000 0 42
EP300 0.033 0.011 -10000 0 0 52 52
EGLN3 0.027 0.03 0.11 1 -0.05 5 6
EGLN2 0.029 0.03 0.11 1 -0.039 34 35
EGLN1 0.025 0.049 0.095 4 -0.064 69 73
VHL/Elongin B/Elongin C 0.042 0.028 -10000 0 -0.16 7 7
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.02 0.037 -10000 0 -0.075 1 1
SLC2A1 -0.011 0.21 0.34 21 -0.42 71 92
TWIST1 -0.027 0.2 0.33 15 -0.4 78 93
ELK1 0.033 0.041 -10000 0 -0.11 38 38
HIF2A/ARNT/Cbp/p300 0.047 0.15 0.34 9 -0.3 22 31
VEGFA 0.009 0.18 0.33 17 -0.41 43 60
CREBBP 0.035 0.009 -10000 0 0 32 32
Syndecan-3-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
CTTN 0.036 0.007 -9999 0 0 20 20
Syndecan-3/Src/Cortactin -0.008 0.13 -9999 0 -0.43 26 26
Syndecan-3/Neurocan -0.018 0.11 -9999 0 -0.45 31 31
POMC 0.036 0.006 -9999 0 0 13 13
EGFR 0.036 0.005 -9999 0 0 11 11
Syndecan-3/EGFR 0.014 0.12 -9999 0 -0.45 31 31
AGRP 0.033 0.011 -9999 0 0 52 52
NCSTN 0.035 0.009 -9999 0 0 30 30
PSENEN 0.031 0.014 -9999 0 0 83 83
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.035 0.007 -9999 0 0 21 21
APH1A 0.034 0.01 -9999 0 0 43 43
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.011 0.12 -9999 0 -0.42 31 31
Syndecan-3/IL8 0.001 0.12 -9999 0 -0.47 31 31
PSEN1 0.036 0.007 -9999 0 0 19 19
Src/Cortactin 0.05 0.021 -9999 0 -0.19 2 2
FYN 0.028 0.016 -9999 0 0 131 131
limb bud formation -0.016 0.12 -9999 0 -0.49 28 28
MC4R 0.033 0.012 -9999 0 0 60 60
SRC 0.035 0.008 -9999 0 0 25 25
PTN 0.018 0.018 -9999 0 0 271 271
FGFR/FGF/Syndecan-3 -0.016 0.12 -9999 0 -0.5 28 28
neuron projection morphogenesis -0.037 0.11 -9999 0 -0.42 26 26
Syndecan-3/AgRP 0.011 0.12 -9999 0 -0.46 31 31
Syndecan-3/AgRP/MC4R 0.026 0.12 -9999 0 -0.44 31 31
Fyn/Cortactin 0.02 0.075 -9999 0 -0.19 53 53
SDC3 -0.016 0.12 -9999 0 -0.5 28 28
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.001 0.12 -9999 0 -0.46 31 31
IL8 0.026 0.017 -9999 0 0 156 156
Syndecan-3/Fyn/Cortactin 0.012 0.13 -9999 0 -0.43 31 31
Syndecan-3/CASK -0.018 0.11 -9999 0 -0.45 31 31
alpha-MSH/MC4R 0.047 0.019 -9999 0 -10000 0 0
Gamma Secretase 0.07 0.072 -9999 0 -0.16 30 30
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.035 0.055 0.17 4 -0.17 23 27
BIRC5 0.031 0.014 -10000 0 0 90 90
NFKBIA -0.007 0.055 0.23 4 -0.18 29 33
CPEB1 0.035 0.009 -10000 0 0 31 31
AKT1 -0.003 0.055 0.29 6 -0.19 22 28
NDEL1 0.034 0.01 -10000 0 0 43 43
Aurora A/BRCA1 0.023 0.044 0.15 3 -0.15 22 25
NDEL1/TACC3 0.038 0.064 0.17 2 -0.18 27 29
GADD45A 0.032 0.012 -10000 0 0 66 66
GSK3B 0.036 0.017 0.088 37 0 41 78
PAK1/Aurora A 0.037 0.054 0.17 4 -0.17 21 25
MDM2 0.035 0.007 -10000 0 0 21 21
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.04 0.065 0.06 12 -0.19 77 89
TP53 -0.04 0.12 0.16 3 -0.26 113 116
DLG7 -0.013 0.05 0.25 1 -0.17 41 42
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.035 0.008 -10000 0 0 23 23
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.04 0.068 0.18 2 -0.18 31 33
G2/M transition of mitotic cell cycle 0.023 0.044 0.15 3 -0.15 22 25
AURKA 0.01 0.051 0.13 32 -0.24 14 46
AURKB -0.002 0.071 -10000 0 -0.23 34 34
CDC25B -0.012 0.092 0.12 1 -0.27 52 53
G2/M transition checkpoint 0.004 0.036 0.078 23 -0.14 22 45
mRNA polyadenylation 0.022 0.044 0.15 2 -0.15 21 23
Aurora A/CPEB 0.022 0.044 0.15 2 -0.15 21 23
Aurora A/TACC1/TRAP/chTOG 0.051 0.081 -10000 0 -0.17 43 43
BRCA1 0.035 0.008 -10000 0 0 25 25
centrosome duplication 0.037 0.054 0.17 4 -0.17 21 25
regulation of centrosome cycle 0.037 0.063 0.16 2 -0.18 27 29
spindle assembly 0.049 0.08 -10000 0 -0.17 43 43
TDRD7 0.031 0.014 -10000 0 0 83 83
Aurora A/RasGAP/Survivin 0.038 0.079 -10000 0 -0.15 51 51
CENPA -0.009 0.089 -10000 0 -0.32 36 36
Aurora A/PP2A 0.039 0.053 0.17 4 -0.16 21 25
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.016 0.07 0.18 3 -0.23 29 32
negative regulation of DNA binding -0.044 0.12 0.16 3 -0.26 122 125
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.05 0.015 -10000 0 -10000 0 0
RASA1 0.032 0.012 -10000 0 0 64 64
Ajuba/Aurora A 0.004 0.037 0.079 23 -0.14 22 45
mitotic prometaphase 0.002 0.022 0.069 48 -10000 0 48
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.05 0.13 32 -0.24 14 46
TACC1 0.032 0.013 -10000 0 0 74 74
TACC3 0.031 0.013 -10000 0 0 78 78
Aurora A/Antizyme1 0.021 0.044 0.15 2 -0.15 21 23
Aurora A/RasGAP 0.035 0.057 0.17 4 -0.18 21 25
OAZ1 0.033 0.012 -10000 0 0 57 57
RAN 0.034 0.01 -10000 0 0 37 37
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.02 0.087 37 0 79 116
GIT1 0.035 0.008 -10000 0 0 23 23
GIT1/beta-PIX/PAK1 0.063 0.027 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.04 0.065 0.06 12 -0.19 77 89
PPP2R5D 0.035 0.007 -10000 0 0 22 22
Aurora A/TPX2 -0.007 0.063 0.15 1 -0.18 56 57
PAK1 0.033 0.011 -10000 0 0 49 49
CKAP5 0.036 0.006 -10000 0 0 14 14
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.012 -10000 0 -10000 0 0
HSPA8 0.031 0.013 -10000 0 0 75 75
SMAD3/SMAD4/ER alpha 0.054 0.098 0.24 13 -0.18 36 49
AKT1 0.035 0.012 -10000 0 -0.031 1 1
GSC 0.013 0.037 0.076 116 -0.072 5 121
NKX2-5 0.037 0.007 0.077 1 -10000 0 1
muscle cell differentiation -0.005 0.12 0.34 35 -10000 0 35
SMAD2-3/SMAD4/SP1 0.036 0.13 -10000 0 -0.23 44 44
SMAD4 0.012 0.074 -10000 0 -0.22 26 26
CBFB 0.033 0.012 -10000 0 0 61 61
SAP18 0.036 0.007 -10000 0 0 18 18
Cbp/p300/MSG1 0.065 0.035 -10000 0 -0.16 5 5
SMAD3/SMAD4/VDR 0.055 0.11 -10000 0 -0.2 26 26
MYC 0.017 0.017 -10000 0 -10000 0 0
CDKN2B -0.039 0.12 -10000 0 -0.45 16 16
AP1 -0.035 0.12 -10000 0 -0.28 66 66
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.002 0.12 -10000 0 -0.33 38 38
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.081 -10000 0 -0.24 35 35
SP3 0.034 0.022 0.072 1 -0.079 13 14
CREB1 0.036 0.006 -10000 0 0 15 15
FOXH1 0.026 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.013 0.11 -10000 0 -0.19 79 79
GATA3 0.038 0.01 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0 0.086 -10000 0 -0.28 27 27
MEF2C/TIF2 0.059 0.096 0.25 26 -0.23 5 31
endothelial cell migration -0.043 0.056 0.58 2 -10000 0 2
MAX 0.026 0.023 -10000 0 -0.032 70 70
RBBP7 0.036 0.007 -10000 0 0 18 18
RBBP4 0.033 0.012 -10000 0 0 58 58
RUNX2 0.036 0.007 -10000 0 0 19 19
RUNX3 0.026 0.017 -10000 0 0 152 152
RUNX1 0.036 0.004 -10000 0 0 7 7
CTBP1 0.033 0.011 -10000 0 0 55 55
NR3C1 0.023 0.024 -10000 0 -0.032 70 70
VDR 0.036 0.005 -10000 0 0 10 10
CDKN1A -0.038 0.23 -10000 0 -1.2 17 17
KAT2B 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.033 0.07 -10000 0 -0.18 29 29
DCP1A 0.035 0.008 -10000 0 0 25 25
SKI 0.035 0.008 -10000 0 0 25 25
SERPINE1 0.043 0.056 -10000 0 -0.58 2 2
SMAD3/SMAD4/ATF2 0.033 0.094 -10000 0 -0.18 45 45
SMAD3/SMAD4/ATF3 -0.002 0.12 -10000 0 -0.2 102 102
SAP30 0.034 0.01 -10000 0 0 44 44
Cbp/p300/PIAS3 0.06 0.044 -10000 0 -0.18 8 8
JUN -0.035 0.12 0.2 2 -0.28 66 68
SMAD3/SMAD4/IRF7 0.009 0.12 -10000 0 -0.19 95 95
TFE3 0.033 0.031 -10000 0 -0.086 25 25
COL1A2 -0.11 0.28 -10000 0 -0.69 97 97
mesenchymal cell differentiation -0.033 0.093 0.18 47 -10000 0 47
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.032 0.013 -10000 0 0 71 71
FOS 0.003 0.07 -10000 0 -0.12 72 72
SMAD3/SMAD4/Max 0.029 0.093 -10000 0 -0.18 47 47
Cbp/p300/SNIP1 0.061 0.036 -10000 0 -0.16 5 5
ZBTB17 0.034 0.006 -10000 0 -10000 0 0
LAMC1 -0.01 0.097 -10000 0 -0.32 30 30
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.11 -10000 0 -0.2 63 63
IRF7 0.028 0.017 -10000 0 -10000 0 0
ESR1 0.045 0.031 0.11 89 -10000 0 89
HNF4A 0.035 0.009 -10000 0 0 33 33
MEF2C 0.044 0.1 0.21 98 -0.25 4 102
SMAD2-3/SMAD4 0.035 0.1 -10000 0 -0.2 41 41
Cbp/p300/Src-1 0.056 0.055 -10000 0 -0.18 21 21
IGHV3OR16-13 0.001 0.072 -10000 0 -0.51 9 9
TGIF2/HDAC complex 0.033 0.012 -10000 0 0 60 60
CREBBP 0.036 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.016 -10000 0 0 136 136
HDAC1 0.035 0.008 -10000 0 0 23 23
HDAC2 0.034 0.01 -10000 0 0 41 41
SNIP1 0.035 0.008 -10000 0 0 26 26
GCN5L2 0.036 0.009 -10000 0 0 30 30
SMAD3/SMAD4/TFE3 0.044 0.11 -10000 0 -0.2 56 56
MSG1/HSC70 0.028 0.071 -10000 0 -0.19 48 48
SMAD2 0.034 0.02 -10000 0 -0.055 11 11
SMAD3 0.015 0.055 -10000 0 -0.12 26 26
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.003 0.081 -10000 0 -0.21 50 50
SMAD2/SMAD2/SMAD4 -0.02 0.08 0.16 5 -0.21 62 67
NCOR1 0.034 0.01 -10000 0 0 45 45
NCOA2 0.035 0.009 -10000 0 0 34 34
NCOA1 0.035 0.009 -10000 0 0 31 31
MYOD/E2A 0.046 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.047 0.14 -10000 0 -0.24 33 33
IFNB1 -0.02 0.085 0.2 1 -0.21 37 38
SMAD3/SMAD4/MEF2C 0.068 0.11 0.3 11 -0.26 7 18
CITED1 0.036 0.006 -10000 0 0 13 13
SMAD2-3/SMAD4/ARC105 0.036 0.09 -10000 0 -0.18 41 41
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.091 -10000 0 -0.29 22 22
RUNX1-3/PEBPB2 0.042 0.066 -10000 0 -0.16 43 43
SMAD7 -0.067 0.21 -10000 0 -0.48 75 75
MYC/MIZ-1 -0.001 0.078 -10000 0 -0.2 66 66
SMAD3/SMAD4 0.001 0.092 -10000 0 -0.33 20 20
IL10 0.005 0.075 0.24 12 -0.23 10 22
PIASy/HDAC complex 0.032 0.011 -10000 0 -10000 0 0
PIAS3 0.033 0.012 -10000 0 0 62 62
CDK2 0.036 0.008 -10000 0 -10000 0 0
IL5 0.005 0.075 0.24 12 -0.23 10 22
CDK4 0.036 0.01 -10000 0 0 34 34
PIAS4 0.032 0.011 -10000 0 -10000 0 0
ATF3 0.024 0.018 -10000 0 0 181 181
SMAD3/SMAD4/SP1 0.018 0.13 -10000 0 -0.22 63 63
FOXG1 -0.001 0.003 0.021 3 -10000 0 3
FOXO3 0.009 0.006 -10000 0 -0.034 1 1
FOXO1 0.009 0.006 -10000 0 -0.028 1 1
FOXO4 0.009 0.006 -10000 0 -0.028 1 1
heart looping 0.044 0.1 0.2 98 -0.25 4 102
CEBPB 0.034 0.012 -10000 0 0 57 57
SMAD3/SMAD4/DLX1 0.015 0.083 -10000 0 -0.17 51 51
MYOD1 0.036 0.006 -10000 0 0 12 12
SMAD3/SMAD4/HNF4 0.032 0.093 -10000 0 -0.18 45 45
SMAD3/SMAD4/GATA3 0.045 0.095 -10000 0 -0.18 37 37
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.016 -10000 0 0 136 136
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.042 0.11 -10000 0 -0.18 45 45
SMAD3/SMAD4/SP1-3 0.034 0.14 -10000 0 -0.24 47 47
MED15 0 0 -10000 0 -10000 0 0
SP1 0.01 0.066 -10000 0 -0.11 112 112
SIN3B 0.032 0.012 -10000 0 0 68 68
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.049 0.076 -10000 0 -0.16 27 27
ITGB5 -0.023 0.1 0.21 10 -0.28 36 46
TGIF/SIN3/HDAC complex/CtBP 0 0.087 -10000 0 -0.32 22 22
SMAD3/SMAD4/AR 0.018 0.1 -10000 0 -0.18 69 69
AR 0.03 0.014 -10000 0 0 96 96
negative regulation of cell growth -0.028 0.12 -10000 0 -0.29 67 67
SMAD3/SMAD4/MYOD 0.034 0.094 -10000 0 -0.18 48 48
E2F5 0.034 0.01 -10000 0 0 42 42
E2F4 0.033 0.012 -10000 0 0 57 57
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.048 0.081 -10000 0 -0.16 27 27
SMAD2-3/SMAD4/FOXO1-3a-4 -0.002 0.085 -10000 0 -0.27 28 28
TFDP1 0.033 0.011 -10000 0 0 51 51
SMAD3/SMAD4/AP1 -0.01 0.14 -10000 0 -0.28 66 66
SMAD3/SMAD4/RUNX2 0.033 0.093 -10000 0 -0.18 47 47
TGIF2 0.033 0.012 -10000 0 0 60 60
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.006 -10000 0 0 13 13
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.08 0.23 1 -0.16 41 42
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.009 -10000 0 0 35 35
STAT1 (dimer)/Cbp/p300 0.01 0.12 0.26 12 -0.25 62 74
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.071 -10000 0 -0.18 41 41
antigen processing and presentation of peptide antigen via MHC class I -0.033 0.095 -10000 0 -0.21 91 91
CaM/Ca2+ 0.047 0.08 0.22 1 -0.16 40 41
RAP1A 0.036 0.007 -10000 0 0 17 17
STAT1 (dimer)/SHP2 0.006 0.091 0.22 11 -0.18 67 78
AKT1 0.009 0.11 0.22 34 -0.23 23 57
MAP2K1 -0.019 0.064 0.17 17 -0.18 14 31
MAP3K11 -0.016 0.071 0.17 39 -0.19 15 54
IFNGR1 0.032 0.023 0.076 1 -0.052 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.018 0.054 -10000 0 -0.25 9 9
Rap1/GTP -0.036 0.039 -10000 0 -0.15 34 34
CRKL/C3G 0.049 0.016 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.067 0.079 -10000 0 -0.16 41 41
CEBPB 0.001 0.12 0.28 3 -0.38 18 21
STAT3 0.034 0.01 -10000 0 0 41 41
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.051 0.14 -10000 0 -0.73 12 12
STAT1 -0.025 0.082 0.2 16 -0.23 27 43
CALM1 0.036 0.006 -10000 0 0 16 16
IFN-gamma (dimer) 0.032 0.022 0.075 1 -0.037 41 42
PIK3CA 0.026 0.017 -10000 0 0 158 158
STAT1 (dimer)/PIAS1 0.001 0.094 0.22 15 -0.2 48 63
CEBPB/PTGES2/Cbp/p300 0.005 0.092 -10000 0 -0.26 21 21
mol:Ca2+ 0.041 0.078 0.22 1 -0.16 41 42
MAPK3 0.005 0.091 -10000 0 -0.61 5 5
STAT1 (dimer) -0.024 0.14 -10000 0 -0.29 89 89
MAPK1 -0.05 0.22 -10000 0 -0.78 40 40
JAK2 0.029 0.022 -10000 0 -0.037 38 38
PIK3R1 0.031 0.014 -10000 0 0 90 90
JAK1 0.033 0.023 0.076 1 -0.048 23 24
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.009 0.092 0.27 2 -0.37 7 9
SMAD7 -0.003 0.083 0.17 20 -0.15 75 95
CBL/CRKL/C3G 0.034 0.078 0.24 7 -0.17 17 24
PI3K 0.016 0.087 -10000 0 -0.17 59 59
IFNG 0.032 0.022 0.076 1 -0.037 41 42
apoptosis 0.015 0.083 0.28 1 -0.33 4 5
CAMK2G 0.035 0.008 -10000 0 0 23 23
STAT3 (dimer) 0.034 0.01 -10000 0 0 41 41
CAMK2A 0.036 0.005 -10000 0 0 11 11
CAMK2B 0.036 0.005 -10000 0 0 10 10
FRAP1 0.003 0.1 0.18 51 -0.22 23 74
PRKCD 0.008 0.11 0.23 34 -0.23 24 58
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.033 0.095 -10000 0 -0.21 91 91
PTPN2 0.036 0.007 -10000 0 0 17 17
EP300 0.033 0.011 -10000 0 -10000 0 0
IRF1 -0.048 0.12 0.25 4 -0.32 63 67
STAT1 (dimer)/PIASy -0.002 0.09 0.22 14 -0.23 27 41
SOCS1 0.003 0.17 -10000 0 -1.1 12 12
mol:GDP 0.029 0.075 0.24 6 -0.18 14 20
CASP1 -0.016 0.093 0.16 13 -0.19 88 101
PTGES2 0.036 0.007 -10000 0 0 17 17
IRF9 0 0.043 0.11 13 -0.11 17 30
mol:PI-3-4-5-P3 0.006 0.077 -10000 0 -0.16 59 59
RAP1/GDP 0.016 0.064 -10000 0 -0.15 34 34
CBL -0.016 0.071 0.19 17 -0.19 13 30
MAP3K1 -0.016 0.067 0.19 13 -0.19 14 27
PIAS1 0.036 0.007 -10000 0 0 18 18
PIAS4 0.033 0.011 -10000 0 0 55 55
antigen processing and presentation of peptide antigen via MHC class II -0.033 0.095 -10000 0 -0.21 91 91
PTPN11 -0.013 0.073 0.17 42 -0.16 36 78
CREBBP 0.034 0.009 -10000 0 0 32 32
RAPGEF1 0.035 0.008 -10000 0 0 23 23
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.007 0.035 -10000 0 -0.11 48 48
STMN1 -0.018 0.044 -10000 0 -0.2 24 24
Aurora B/RasGAP/Survivin 0.025 0.095 -10000 0 -0.19 73 73
Chromosomal passenger complex/Cul3 protein complex -0.019 0.11 -10000 0 -0.27 64 64
BIRC5 0.024 0.048 -10000 0 -0.034 93 93
DES -0.042 0.26 -10000 0 -0.82 49 49
Aurora C/Aurora B/INCENP 0.055 0.042 -10000 0 -0.16 13 13
Aurora B/TACC1 0.034 0.035 -10000 0 -0.14 13 13
Aurora B/PP2A 0.041 0.043 -10000 0 -0.2 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.003 0.049 -10000 0 -0.16 40 40
mitotic metaphase/anaphase transition 0 0.004 0.01 47 -0.01 8 55
NDC80 -0.007 0.027 0.017 3 -0.2 9 12
Cul3 protein complex 0.043 0.031 -10000 0 -0.16 10 10
KIF2C -0.054 0.19 -10000 0 -0.53 62 62
PEBP1 -0.002 0.004 0.008 2 -0.012 37 39
KIF20A 0.023 0.046 -10000 0 -0.025 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.027 0.067 -10000 0 -0.2 40 40
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.051 0.2 -10000 0 -0.59 51 51
PSMA3 0.036 0.007 -10000 0 0 18 18
G2/M transition of mitotic cell cycle 0 0.003 0.009 33 -0.008 5 38
H3F3B 0.006 0.047 -10000 0 -0.24 19 19
AURKB 0.025 0.046 -10000 0 -0.038 84 84
AURKC 0.034 0.01 -10000 0 0 38 38
CDCA8 0.025 0.05 -10000 0 -0.042 81 81
cytokinesis -0.056 0.22 -10000 0 -0.52 74 74
Aurora B/Septin1 -0.049 0.21 -10000 0 -0.48 76 76
AURKA 0 0.003 0.009 33 -0.008 5 38
INCENP 0.033 0.017 -10000 0 -0.029 35 35
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.037 0.006 0.057 4 0 8 12
hSgo1/Aurora B/Survivin 0.017 0.068 -10000 0 -0.18 49 49
EVI5 0.036 0.005 -10000 0 0 8 8
RhoA/GTP -0.03 0.2 -10000 0 -0.42 79 79
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.033 0.14 -10000 0 -0.32 74 74
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.037 0.056 -10000 0 -0.2 25 25
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.041 0.049 -10000 0 -0.21 17 17
RHOA 0.034 0.01 -10000 0 0 43 43
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.027 0.15 -10000 0 -0.39 56 56
RASA1 0.032 0.012 -10000 0 0 64 64
KLHL9 0.034 0.01 -10000 0 0 40 40
mitotic prometaphase -0.002 0.004 0.008 2 -0.012 37 39
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.055 -10000 0 -0.2 25 25
PPP1CC 0.036 0.005 -10000 0 0 8 8
Centraspindlin -0.035 0.2 -10000 0 -0.45 75 75
RhoA/GDP 0.012 0.054 -10000 0 -0.19 36 36
NSUN2 -0.024 0.11 -10000 0 -0.35 48 48
MYLK -0.02 0.087 -10000 0 -0.24 70 70
KIF23 0.016 0.068 -10000 0 -0.064 106 106
VIM -0.031 0.062 -10000 0 -0.2 59 59
RACGAP1 0.021 0.062 -10000 0 -0.083 69 69
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.027 0.13 -10000 0 -0.35 66 66
Chromosomal passenger complex -0.042 0.15 -10000 0 -0.36 75 75
Chromosomal passenger complex/EVI5 0.046 0.12 -10000 0 -0.24 62 62
TACC1 0.032 0.013 -10000 0 0 74 74
PPP2R5D 0.035 0.007 -10000 0 0 22 22
CUL3 0.037 0.004 -10000 0 0 5 5
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.053 0.015 -10000 0 -0.19 1 1
Necdin/E2F1 -0.004 0.089 -10000 0 -0.19 88 88
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.07 0.05 -10000 0 -0.16 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.001 0.071 -10000 0 -0.16 81 81
NT-4/5 (dimer)/p75(NTR) 0.026 0.005 -10000 0 -10000 0 0
IKBKB 0.034 0.01 -10000 0 0 40 40
AKT1 0.021 0.098 0.19 112 -0.16 35 147
IKBKG 0.037 0 -10000 0 -10000 0 0
BDNF 0.035 0.008 -10000 0 0 26 26
MGDIs/NGR/p75(NTR)/LINGO1 0.024 0.005 -10000 0 -10000 0 0
FURIN 0.036 0.006 -10000 0 0 16 16
proBDNF (dimer)/p75(NTR)/Sortilin 0.069 0.02 -10000 0 -0.16 1 1
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.022 0.058 -10000 0 -0.16 38 38
proBDNF (dimer) 0.035 0.008 -10000 0 0 26 26
NTRK1 0.036 0.006 -10000 0 0 15 15
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.055 0.14 0.23 2 -0.44 39 41
IRAK1 0.034 0.011 -10000 0 0 48 48
SHC1 0.016 0.006 0.065 4 -10000 0 4
ARHGDIA 0.035 0.008 -10000 0 0 23 23
RhoA/GTP 0.012 0.054 -10000 0 -0.19 36 36
Gamma Secretase 0.07 0.072 -10000 0 -0.16 30 30
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.064 -10000 0 -0.15 49 49
MAGEH1 0.032 0.012 -10000 0 0 64 64
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.02 0.082 -10000 0 -0.15 96 96
Mammalian IAPs/DIABLO 0.032 0.077 -10000 0 -0.15 71 71
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.035 0.008 -10000 0 0 23 23
APP 0.034 0.009 -10000 0 0 35 35
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.012 -10000 0 0 57 57
RhoA/GDP/RHOGDI 0.036 0.048 0.18 4 -0.14 33 37
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.002 0.045 0.21 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.003 0.082 -10000 0 -0.23 46 46
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.047 0.012 -10000 0 -10000 0 0
NCSTN 0.035 0.009 -10000 0 0 30 30
mol:GTP 0.029 0.056 -10000 0 -0.16 42 42
PSENEN 0.031 0.014 -10000 0 0 83 83
mol:ceramide -0.012 0.03 0.19 10 -0.15 1 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.008 0.069 -10000 0 -0.18 56 56
p75(NTR)/beta APP 0.042 0.047 -10000 0 -0.19 18 18
BEX1 0.019 0.018 -10000 0 0 259 259
mol:GDP -0.007 0.001 -10000 0 -10000 0 0
NGF (dimer) -0.004 0.092 -10000 0 -0.14 148 148
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.044 0.012 -10000 0 -10000 0 0
PIK3R1 0.031 0.014 -10000 0 0 90 90
RAC1/GTP 0.039 0.015 -10000 0 -0.13 1 1
MYD88 0.035 0.009 -10000 0 0 31 31
CHUK 0.035 0.009 -10000 0 0 33 33
NGF (dimer)/p75(NTR)/PKA 0.03 0.057 -10000 0 -0.16 42 42
RHOB 0.03 0.015 -10000 0 0 104 104
RHOA 0.034 0.01 -10000 0 0 43 43
MAGE-G1/E2F1 0.026 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.028 0.016 -10000 0 0 127 127
TP53 -0.042 0.067 0.19 11 -0.25 4 15
PRDM4 -0.013 0.028 0.19 8 -0.15 1 9
BDNF (dimer) 0.008 0.1 -10000 0 -0.15 146 146
PIK3CA 0.026 0.017 -10000 0 0 158 158
SORT1 0.036 0.005 -10000 0 0 9 9
activation of caspase activity 0.063 0.047 -10000 0 -0.15 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.066 0.019 -10000 0 -0.15 1 1
RHOC 0.036 0.007 -10000 0 0 18 18
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.005 0.056 0.22 8 -0.21 7 15
DIABLO 0.035 0.008 -10000 0 0 26 26
SMPD2 -0.012 0.03 0.19 10 -0.15 1 11
APH1B 0.035 0.007 -10000 0 0 21 21
APH1A 0.034 0.01 -10000 0 0 43 43
proNGF (dimer)/p75(NTR)/Sortilin 0.047 0.015 -10000 0 -0.16 1 1
PSEN1 0.036 0.007 -10000 0 0 19 19
APAF-1/Pro-Caspase 9 0.052 0.016 -10000 0 -0.19 1 1
NT3 (dimer)/p75(NTR) 0.039 0.025 -10000 0 -10000 0 0
MAPK8 -0.007 0.057 0.24 6 -0.23 7 13
MAPK9 -0.008 0.06 0.24 6 -0.25 7 13
APAF1 0.037 0.004 -10000 0 0 6 6
NTF3 0.028 0.016 -10000 0 0 127 127
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.018 -10000 0 0 232 232
RAC1/GDP 0.025 0.011 -10000 0 -0.19 1 1
RhoA-B-C/GDP 0.021 0.1 -10000 0 -0.16 114 114
p75 CTF/Sortilin/TRAF6/NRIF 0.077 0.049 -10000 0 -0.15 14 14
RhoA-B-C/GTP 0.029 0.056 -10000 0 -0.16 42 42
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.089 0.052 -10000 0 -0.15 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.087 0.026 -10000 0 -0.15 1 1
PRKACB 0.032 0.012 -10000 0 0 63 63
proBDNF (dimer)/p75 ECD 0.05 0.015 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.017 -10000 0 0 151 151
BIRC2 0.034 0.01 -10000 0 0 41 41
neuron projection morphogenesis -0.025 0.076 0.15 13 -0.18 52 65
BAD -0.009 0.065 0.26 4 -0.24 9 13
RIPK2 0.032 0.012 -10000 0 0 67 67
NGFR 0.035 0.007 -10000 0 0 22 22
CYCS -0.019 0.036 0.19 7 -0.14 16 23
ADAM17 0.036 0.006 -10000 0 0 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.058 0.032 -10000 0 -0.15 5 5
BCL2L11 -0.009 0.065 0.26 4 -0.24 9 13
BDNF (dimer)/p75(NTR) 0.05 0.016 -10000 0 -10000 0 0
PI3K 0.028 0.064 -10000 0 -0.15 45 45
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.044 0.014 -10000 0 -0.14 1 1
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.033 0.011 -10000 0 0 53 53
PRKCI 0.025 0.017 -10000 0 0 168 168
NGF (dimer)/p75(NTR) 0.026 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.06 0.042 -10000 0 -0.15 18 18
TRAF6 0.036 0.005 -10000 0 0 9 9
RAC1 0.035 0.008 -10000 0 0 28 28
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.035 0.009 -10000 0 0 34 34
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.021 0.025 0.16 2 -0.16 7 9
SQSTM1 0.033 0.011 -10000 0 0 50 50
NGFRAP1 0.036 0.006 -10000 0 0 15 15
CASP3 -0.011 0.069 0.24 5 -0.23 18 23
E2F1 0.035 0.009 -10000 0 0 32 32
CASP9 0.036 0.007 -10000 0 0 20 20
IKK complex 0.044 0.091 -10000 0 -0.24 15 15
NGF (dimer)/TRKA 0.027 0.005 -10000 0 -10000 0 0
MMP7 0.016 0.018 -10000 0 0 300 300
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.072 0.044 -10000 0 -0.14 13 13
MMP3 0.034 0.01 -10000 0 0 38 38
APAF-1/Caspase 9 -0.044 0.051 -10000 0 -0.15 71 71
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.006 0.12 -10000 0 -0.27 54 54
CaM/Ca2+ 0.026 0.01 -10000 0 -0.19 1 1
AKT1 0.034 0.01 -10000 0 0 46 46
AKT2 0.033 0.011 -10000 0 0 51 51
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.015 0.12 0.18 3 -0.29 57 60
YWHAZ 0.029 0.015 -10000 0 0 105 105
CALM1 0.036 0.006 -10000 0 0 16 16
YWHAQ 0.036 0.007 -10000 0 0 19 19
TBC1D4 -0.018 0.028 0.06 11 -0.19 11 22
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.03 0.014 -10000 0 0 92 92
YWHAB 0.034 0.01 -10000 0 0 42 42
SNARE/Synip 0.023 0.006 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.035 0.009 -10000 0 0 32 32
PRKCI 0.025 0.017 -10000 0 0 168 168
AS160/CaM/Ca2+ 0.026 0.01 -10000 0 -0.19 1 1
RHOQ 0.035 0.008 -10000 0 0 26 26
GYS1 -0.002 0.052 -10000 0 -0.21 26 26
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.011 -10000 0 0 51 51
TC10/GTP/CIP4/Exocyst 0.04 0.032 -10000 0 -0.16 10 10
AS160/14-3-3 -0.021 0.13 -10000 0 -0.34 46 46
VAMP2 0.034 0.01 -10000 0 0 37 37
SLC2A4 -0.018 0.13 0.19 3 -0.32 57 60
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.01 0.058 -10000 0 -0.24 25 25
SFN 0.026 0.017 -10000 0 0 148 148
LNPEP 0.035 0.009 -10000 0 0 30 30
YWHAE 0.033 0.011 -10000 0 0 53 53
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.039 0.056 30 -0.16 30 60
SNTA1 0.035 0.009 -10000 0 0 31 31
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.027 0.049 -10000 0 -0.16 50 50
MAPK12 -0.005 0.031 0.21 4 -0.19 9 13
CCND1 -0.085 0.17 -10000 0 -0.38 122 122
p38 gamma/SNTA1 0.032 0.051 0.22 6 -0.17 14 20
MAP2K3 0.034 0.01 -10000 0 0 43 43
PKN1 0.03 0.015 -10000 0 0 99 99
G2/M transition checkpoint -0.005 0.031 0.21 4 -0.18 9 13
MAP2K6 0 0.038 0.24 2 -0.2 15 17
MAPT -0.001 0.056 0.14 8 -0.18 25 33
MAPK13 -0.021 0.046 0.06 30 -0.19 30 60
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.041 -10000 0 -0.23 15 15
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.002 0.096 0.21 7 -0.27 29 36
adherens junction organization -0.012 0.11 0.18 2 -0.31 39 41
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.1 0.22 12 -0.25 20 32
FMN1 -0.007 0.1 0.18 2 -0.26 51 53
mol:IP3 -0.011 0.069 -10000 0 -0.24 23 23
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.004 0.11 0.18 2 -0.27 51 53
CTNNB1 0.037 0.009 0.061 5 0 22 27
AKT1 -0.012 0.076 -10000 0 -0.25 28 28
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.12 -10000 0 -0.35 31 31
CTNND1 0.037 0.008 -10000 0 0 20 20
mol:PI-4-5-P2 -0.009 0.094 0.17 1 -0.26 43 44
VASP -0.011 0.1 0.17 2 -0.27 47 49
ZYX -0.014 0.1 0.17 2 -0.29 46 48
JUB -0.007 0.1 0.18 2 -0.26 51 53
EGFR(dimer) 0.009 0.11 -10000 0 -0.26 51 51
E-cadherin/beta catenin-gamma catenin 0.047 0.061 -10000 0 -0.15 36 36
mol:PI-3-4-5-P3 0.001 0.089 -10000 0 -0.26 25 25
PIK3CA 0.026 0.017 -10000 0 -10000 0 0
PI3K 0.001 0.09 -10000 0 -0.26 25 25
FYN -0.021 0.13 0.22 6 -0.31 59 65
mol:Ca2+ 0.005 0.085 -10000 0 -0.24 20 20
JUP 0.034 0.011 0.063 1 0 48 49
PIK3R1 0.031 0.016 -10000 0 -0.002 95 95
mol:DAG -0.011 0.069 -10000 0 -0.24 23 23
CDH1 0.033 0.013 0.062 1 0 66 67
RhoA/GDP 0.017 0.11 0.23 13 -0.26 27 40
establishment of polarity of embryonic epithelium -0.011 0.098 0.17 2 -0.26 47 49
SRC 0.035 0.008 -10000 0 0 25 25
RAC1 0.035 0.008 -10000 0 0 28 28
RHOA 0.034 0.01 -10000 0 0 43 43
EGFR 0.036 0.005 -10000 0 0 11 11
CASR 0.003 0.086 0.16 67 -0.24 18 85
RhoA/GTP 0.012 0.098 0.21 6 -0.24 28 34
AKT2 -0.012 0.074 -10000 0 -0.24 25 25
actin cable formation -0.012 0.098 0.19 5 -0.26 45 50
apoptosis -0.006 0.097 0.25 31 -0.23 9 40
CTNNA1 0.037 0.008 -10000 0 0 19 19
mol:GDP 0.004 0.093 0.16 68 -0.26 19 87
PIP5K1A -0.01 0.095 0.18 1 -0.27 43 44
PLCG1 -0.012 0.071 -10000 0 -0.24 23 23
Rac1/GTP 0.018 0.11 -10000 0 -0.27 38 38
homophilic cell adhesion 0.001 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.047 0.065 -9999 0 -0.17 36 36
E-cadherin/beta catenin 0.038 0.05 -9999 0 -0.19 20 20
CTNNB1 0.035 0.007 -9999 0 0 22 22
JUP 0.034 0.011 -9999 0 0 48 48
CDH1 0.032 0.012 -9999 0 0 66 66
IL4-mediated signaling events

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
BCL2L1 0 0.4 0.73 1 -0.94 39 40
STAT6 (cleaved dimer) -0.032 0.37 -10000 0 -0.86 52 52
IGHG1 0.032 0.23 0.39 2 -0.66 18 20
IGHG3 -0.021 0.38 -10000 0 -0.86 51 51
AKT1 0.011 0.27 -10000 0 -0.66 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.047 0.2 -10000 0 -0.61 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 0.02 0.27 -10000 0 -0.7 24 24
THY1 -0.18 0.64 -10000 0 -1.2 122 122
MYB 0.027 0.016 -10000 0 0 134 134
HMGA1 0.036 0.006 -10000 0 0 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.041 0.27 0.48 2 -0.55 30 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.031 0.26 -10000 0 -0.71 20 20
SP1 0.013 0.07 -10000 0 -0.13 97 97
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.001 0.046 -10000 0 -0.29 2 2
STAT6 (dimer)/ETS1 -0.008 0.38 -10000 0 -0.9 44 44
SOCS1 0.008 0.3 -10000 0 -0.64 43 43
SOCS3 0.041 0.23 -10000 0 -0.64 6 6
FCER2 0.005 0.34 -10000 0 -0.86 20 20
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.015 0.4 -10000 0 -0.96 38 38
GRB2 0.035 0.007 -10000 0 0 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.042 0.21 -10000 0 -0.6 13 13
T cell proliferation -0.025 0.4 -10000 0 -0.94 49 49
IL4R/JAK1 -0.029 0.42 -10000 0 -0.98 48 48
EGR2 -0.02 0.43 -10000 0 -1 47 47
JAK2 0.034 0.064 0.15 1 -10000 0 1
JAK3 0.034 0.016 -10000 0 -10000 0 0
PIK3R1 0.031 0.014 -10000 0 0 90 90
JAK1 0.035 0.046 -10000 0 -0.24 6 6
COL1A2 -0.16 0.57 -10000 0 -1.3 99 99
CCL26 -0.015 0.4 -10000 0 -0.88 51 51
IL4R -0.017 0.44 -10000 0 -1 44 44
PTPN6 0.005 0.041 -10000 0 -0.28 2 2
IL13RA2 -0.013 0.4 -10000 0 -0.95 39 39
IL13RA1 0.017 0.098 0.15 1 -0.31 27 28
IRF4 0.062 0.13 -10000 0 -0.8 2 2
ARG1 0.048 0.17 -10000 0 -0.54 9 9
CBL 0.034 0.25 -10000 0 -0.51 32 32
GTF3A 0.018 0.071 -10000 0 -0.13 91 91
PIK3CA 0.026 0.017 -10000 0 0 158 158
IL13RA1/JAK2 0.038 0.11 0.22 3 -0.21 31 34
IRF4/BCL6 0.041 0.12 -10000 0 -0.76 2 2
CD40LG 0.043 0.002 -10000 0 -10000 0 0
MAPK14 0.039 0.25 0.55 1 -0.57 17 18
mitosis 0.014 0.26 -10000 0 -0.63 28 28
STAT6 -0.015 0.44 0.69 1 -0.99 50 51
SPI1 0.041 0.007 -10000 0 -10000 0 0
RPS6KB1 0.012 0.25 -10000 0 -0.62 26 26
STAT6 (dimer) -0.012 0.44 0.69 1 -0.99 50 51
STAT6 (dimer)/PARP14 -0.035 0.4 -10000 0 -0.93 50 50
mast cell activation -0.006 0.016 -10000 0 -0.042 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.04 0.23 -10000 0 -0.6 15 15
FRAP1 0.011 0.27 -10000 0 -0.66 29 29
LTA -0.013 0.4 -10000 0 -0.95 39 39
FES 0.035 0.007 -10000 0 0 21 21
T-helper 1 cell differentiation 0.009 0.44 0.97 50 -0.69 1 51
CCL11 -0.014 0.38 -10000 0 -0.92 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.045 0.23 -10000 0 -0.6 15 15
IL2RG 0.033 0.018 -10000 0 -0.051 2 2
IL10 -0.013 0.4 -10000 0 -0.96 38 38
IRS1 0.029 0.015 -10000 0 0 115 115
IRS2 0.029 0.015 -10000 0 0 118 118
IL4 0.045 0.19 -10000 0 -0.8 10 10
IL5 -0.014 0.4 -10000 0 -0.96 38 38
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.008 0.4 0.62 1 -0.84 56 57
COL1A1 -0.16 0.61 -10000 0 -1.4 101 101
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.035 0.42 -10000 0 -1 43 43
IL2R gamma/JAK3 0.048 0.026 -10000 0 -10000 0 0
TFF3 -0.007 0.4 -10000 0 -0.96 38 38
ALOX15 -0.013 0.4 -10000 0 -0.96 38 38
MYBL1 0.033 0.012 -10000 0 0 62 62
T-helper 2 cell differentiation -0.04 0.36 -10000 0 -0.78 58 58
SHC1 0.035 0.008 -10000 0 0 27 27
CEBPB 0.037 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.023 0.26 -10000 0 -0.67 26 26
mol:PI-3-4-5-P3 0.012 0.27 -10000 0 -0.67 28 28
PI3K 0.008 0.28 -10000 0 -0.71 28 28
DOK2 0 0 -10000 0 -10000 0 0
ETS1 -0.005 0.043 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.044 0.21 -10000 0 -0.56 14 14
ITGB3 -0.015 0.4 -10000 0 -0.96 38 38
PIGR -0.012 0.4 -10000 0 -0.96 37 37
IGHE -0.011 0.079 0.18 24 -0.21 19 43
MAPKKK cascade 0.044 0.2 -10000 0 -0.55 14 14
BCL6 0.027 0.015 -10000 0 0 125 125
OPRM1 -0.015 0.4 -10000 0 -0.96 38 38
RETNLB -0.015 0.4 -10000 0 -0.88 51 51
SELP -0.011 0.4 -10000 0 -0.95 38 38
AICDA -0.005 0.38 -10000 0 -0.91 38 38
FAS signaling pathway (CD95)

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
SPTAN1 -0.023 0.052 0.23 1 -0.2 32 33
RFC1 -0.02 0.051 0.22 2 -0.2 32 34
PRKDC -0.018 0.069 0.22 15 -0.2 33 48
RIPK1 0.035 0.008 -10000 0 0 26 26
CASP7 -0.005 0.15 -10000 0 -0.62 25 25
FASLG/FAS/FADD/FAF1 0.018 0.083 0.17 70 -0.2 32 102
MAP2K4 0.021 0.1 0.23 7 -0.35 19 26
mol:ceramide 0.026 0.076 -10000 0 -0.27 17 17
GSN -0.022 0.054 0.22 1 -0.2 31 32
FASLG/FAS/FADD/FAF1/Caspase 8 0.023 0.087 0.2 7 -0.26 20 27
FAS 0.033 0.013 -10000 0 0 71 71
BID -0.032 0.043 -10000 0 -0.18 34 34
MAP3K1 0.019 0.12 0.24 9 -0.41 23 32
MAP3K7 0.034 0.011 -10000 0 0 46 46
RB1 -0.018 0.049 0.22 4 -0.19 30 34
CFLAR 0.035 0.008 -10000 0 0 24 24
HGF/MET 0.024 0.087 -10000 0 -0.16 87 87
ARHGDIB -0.016 0.075 0.22 23 -0.2 24 47
FADD 0.037 0.008 -10000 0 0 23 23
actin filament polymerization 0.022 0.056 0.2 32 -0.22 1 33
NFKB1 -0.016 0.19 -10000 0 -0.63 43 43
MAPK8 0.021 0.1 0.23 3 -0.36 15 18
DFFA -0.024 0.056 0.22 2 -0.2 35 37
DNA fragmentation during apoptosis -0.019 0.048 0.22 1 -0.19 33 34
FAS/FADD/MET 0.052 0.064 -10000 0 -0.18 32 32
CFLAR/RIP1 0.047 0.03 -10000 0 -0.19 6 6
FAIM3 0.036 0.006 -10000 0 0 15 15
FAF1 0.036 0.009 -10000 0 0 31 31
PARP1 -0.017 0.06 0.22 11 -0.2 35 46
DFFB -0.02 0.048 0.22 1 -0.19 33 34
CHUK -0.026 0.18 -10000 0 -0.6 42 42
FASLG 0.038 0.007 -10000 0 -10000 0 0
FAS/FADD 0.033 0.067 -10000 0 -0.21 35 35
HGF 0.036 0.006 -10000 0 0 15 15
LMNA -0.015 0.065 0.19 20 -0.2 27 47
CASP6 -0.017 0.046 -10000 0 -0.2 25 25
CASP10 0.037 0.006 -10000 0 -10000 0 0
CASP3 -0.018 0.055 -10000 0 -0.22 36 36
PTPN13 0.023 0.018 -10000 0 0 190 190
CASP8 -0.03 0.017 -10000 0 -0.2 4 4
IL6 0.002 0.17 -10000 0 -0.57 25 25
MET 0.034 0.01 -10000 0 0 43 43
ICAD/CAD -0.025 0.052 0.19 3 -0.19 25 28
FASLG/FAS/FADD/FAF1/Caspase 10 0.025 0.076 -10000 0 -0.27 17 17
activation of caspase activity by cytochrome c -0.032 0.043 -10000 0 -0.18 34 34
PAK2 0.009 0.093 0.22 66 -0.2 30 96
BCL2 0.034 0.01 -10000 0 0 42 42
Retinoic acid receptors-mediated signaling

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
HDAC1 0.035 0.008 -10000 0 0 23 23
HDAC3 0.036 0.006 -10000 0 0 16 16
VDR 0.036 0.005 -10000 0 0 10 10
Cbp/p300/PCAF 0.042 0.026 -10000 0 -0.16 5 5
EP300 0.033 0.011 -10000 0 0 52 52
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.006 0.064 -10000 0 -0.29 12 12
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.006 -10000 0 0 13 13
AKT1 0.02 0.083 0.18 65 -0.24 8 73
RAR alpha/9cRA/Cyclin H -0.005 0.12 -10000 0 -0.3 34 34
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.004 0.063 -10000 0 -0.2 25 25
CDC2 0.02 0.045 -10000 0 -0.066 58 58
response to UV -0.002 0.009 -10000 0 -0.026 59 59
RAR alpha/Jnk1 0.019 0.054 -10000 0 -0.18 15 15
NCOR2 0.036 0.006 -10000 0 0 14 14
VDR/VDR/Vit D3 0.027 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.033 0.2 -10000 0 -0.53 64 64
NCOA2 0.035 0.009 -10000 0 0 34 34
NCOA3 0.033 0.012 -10000 0 0 59 59
NCOA1 0.035 0.009 -10000 0 0 31 31
VDR/VDR/DNA 0.036 0.005 -10000 0 0 10 10
RARG 0.03 0.021 -10000 0 -0.025 62 62
RAR gamma1/9cRA 0.041 0.018 -10000 0 -10000 0 0
MAPK3 0.029 0.023 -10000 0 -0.03 67 67
MAPK1 0.033 0.012 -10000 0 0 62 62
MAPK8 0.028 0.026 -10000 0 -0.041 61 61
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.007 0.14 -10000 0 -0.33 58 58
RARA 0.012 0.036 -10000 0 -0.21 4 4
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.008 0.056 -10000 0 -0.2 22 22
PRKCA 0.026 0.036 -10000 0 -0.07 59 59
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.039 0.21 -10000 0 -0.59 63 63
RXRG 0.017 0.036 -10000 0 -10000 0 0
RXRA -0.019 0.088 0.16 2 -0.26 24 26
RXRB 0.017 0.035 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.027 0.004 -10000 0 -10000 0 0
RBP1 0.027 0.016 -10000 0 0 137 137
CRBP1/9-cic-RA -0.007 0.074 -10000 0 -0.19 75 75
RARB 0.029 0.026 -10000 0 -0.043 59 59
PRKCG 0.027 0.035 -10000 0 -0.069 57 57
MNAT1 0.036 0.006 -10000 0 0 15 15
RAR alpha/RXRs -0.009 0.15 0.27 2 -0.38 56 58
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.004 0.12 0.26 1 -0.32 25 26
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.072 -10000 0 -0.28 14 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.04 0.22 -10000 0 -0.59 64 64
positive regulation of DNA binding -0.011 0.11 -10000 0 -0.24 61 61
NRIP1 -0.097 0.38 -10000 0 -1.1 61 61
RXRs/RARs -0.014 0.16 -10000 0 -0.41 64 64
RXRs/RXRs/DNA/9cRA -0.026 0.13 -10000 0 -0.34 60 60
PRKACA 0.031 0.013 -10000 0 0 79 79
CDK7 0.031 0.013 -10000 0 0 82 82
TFIIH 0.043 0.08 -10000 0 -0.21 41 41
RAR alpha/9cRA 0.028 0.087 -10000 0 -0.23 23 23
CCNH 0.033 0.012 -10000 0 0 57 57
CREBBP 0.035 0.009 -10000 0 0 32 32
RAR gamma2/9cRA 0.035 0.071 -10000 0 -0.18 38 38
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.062 -10000 0 -0.2 39 39
epithelial cell differentiation 0.052 0.066 -10000 0 -0.16 37 37
CYFIP2 0.033 0.011 -10000 0 0 51 51
ENAH -0.037 0.08 0.2 10 -0.23 28 38
EGFR 0.036 0.005 -10000 0 0 11 11
EPHA2 0.033 0.011 -10000 0 0 53 53
MYO6 -0.026 0.054 0.18 8 -0.26 14 22
CTNNB1 0.035 0.007 -10000 0 0 22 22
ABI1/Sra1/Nap1 0.054 0.059 -10000 0 -0.16 31 31
AQP5 -0.013 0.044 -10000 0 -0.24 7 7
CTNND1 0.036 0.007 -10000 0 0 20 20
mol:PI-4-5-P2 -0.024 0.046 0.18 9 -0.25 6 15
regulation of calcium-dependent cell-cell adhesion -0.025 0.045 0.18 7 -0.25 6 13
EGF 0.035 0.008 -10000 0 0 26 26
NCKAP1 0.036 0.005 -10000 0 0 11 11
AQP3 -0.014 0.045 0.17 1 -0.24 8 9
cortical microtubule organization 0.052 0.066 -10000 0 -0.16 37 37
GO:0000145 -0.024 0.043 0.16 9 -0.24 6 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.058 0.069 -10000 0 -0.16 37 37
MLLT4 0.033 0.011 -10000 0 0 53 53
ARF6/GDP -0.048 0.056 -10000 0 -0.17 64 64
ARF6 0.036 0.005 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.079 -10000 0 -0.16 48 48
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.024 0.073 0.17 5 -0.26 32 37
PVRL2 0.033 0.011 -10000 0 0 56 56
ZYX -0.024 0.049 0.18 8 -0.26 9 17
ARF6/GTP 0.061 0.083 -10000 0 -0.16 47 47
CDH1 0.032 0.012 -10000 0 0 66 66
EGFR/EGFR/EGF/EGF 0.045 0.064 -10000 0 -0.16 36 36
RhoA/GDP 0.041 0.085 -10000 0 -0.16 64 64
actin cytoskeleton organization -0.034 0.057 0.16 8 -0.27 14 22
IGF-1R heterotetramer 0.029 0.015 -10000 0 0 116 116
GIT1 0.035 0.008 -10000 0 0 23 23
IGF1R 0.029 0.015 -10000 0 0 116 116
IGF1 0.025 0.017 -10000 0 0 164 164
DIAPH1 0.02 0.18 -10000 0 -0.59 34 34
Wnt receptor signaling pathway -0.052 0.066 0.16 37 -10000 0 37
RHOA 0.034 0.01 -10000 0 0 43 43
RhoA/GTP -0.053 0.065 -10000 0 -0.18 78 78
CTNNA1 0.036 0.007 -10000 0 0 19 19
VCL -0.035 0.058 0.16 8 -0.27 14 22
EFNA1 0.032 0.013 -10000 0 0 69 69
LPP -0.031 0.051 0.17 6 -0.27 8 14
Ephrin A1/EPHA2 0.029 0.08 -10000 0 -0.16 64 64
SEC6/SEC8 -0.034 0.043 -10000 0 -0.17 35 35
MGAT3 -0.025 0.046 0.18 7 -0.25 6 13
HGF/MET 0.045 0.06 -10000 0 -0.16 27 27
HGF 0.036 0.006 -10000 0 0 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.062 -10000 0 -0.2 39 39
actin cable formation -0.007 0.11 0.26 16 -0.29 23 39
KIAA1543 -0.023 0.042 0.15 8 -0.24 6 14
KIFC3 -0.027 0.048 0.18 9 -0.25 6 15
NCK1 0.033 0.011 -10000 0 0 53 53
EXOC3 0.033 0.011 -10000 0 0 49 49
ACTN1 -0.026 0.056 0.18 10 -0.29 10 20
NCK1/GIT1 0.041 0.044 -10000 0 -0.19 15 15
mol:GDP 0.052 0.066 -10000 0 -0.16 37 37
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.027 0.037 -10000 0 -0.15 37 37
PIP5K1C -0.024 0.047 0.18 9 -0.25 6 15
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 0 27 27
ROCK1 -0.031 0.091 0.24 12 -0.26 23 35
adherens junction assembly -0.039 0.11 0.18 1 -0.42 23 24
IGF-1R heterotetramer/IGF1 -0.007 0.1 -10000 0 -0.16 130 130
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.044 -10000 0 -0.19 15 15
MET 0.034 0.01 -10000 0 0 43 43
PLEKHA7 -0.027 0.037 -10000 0 -0.15 37 37
mol:GTP 0.052 0.078 -10000 0 -0.16 48 48
establishment of epithelial cell apical/basal polarity -0.021 0.065 0.14 48 -0.25 10 58
cortical actin cytoskeleton stabilization 0.005 0.062 -10000 0 -0.2 39 39
regulation of cell-cell adhesion -0.034 0.057 0.16 8 -0.27 14 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.062 -10000 0 -0.2 39 39
Regulation of Telomerase

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
Telomerase catalytic core complex -0.08 0.22 -10000 0 -0.53 39 39
RAD9A 0.036 0.006 -10000 0 0 12 12
AP1 -0.031 0.11 -10000 0 -0.21 130 130
IFNAR2 0.022 0.033 -10000 0 -0.032 124 124
AKT1 0.009 0.05 -10000 0 -0.28 11 11
ER alpha/Oestrogen 0.018 0.019 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.006 0.076 -10000 0 -0.27 27 27
EGF 0.034 0.009 -10000 0 -0.002 28 28
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.024 0.061 -10000 0 -0.2 19 19
TERT/c-Abl -0.072 0.22 -10000 0 -0.51 47 47
SAP18 0.035 0.007 -10000 0 0 18 18
MRN complex 0.057 0.043 -10000 0 -0.16 11 11
WT1 0.012 0.052 -10000 0 -0.054 117 117
WRN 0.031 0.014 -10000 0 0 89 89
SP1 0.021 0.034 -10000 0 -0.038 129 129
SP3 0.031 0.03 -10000 0 -0.11 12 12
TERF2IP 0.032 0.012 -10000 0 0 63 63
Telomerase/Nucleolin -0.068 0.21 -10000 0 -0.47 56 56
Mad/Max 0.041 0.033 -10000 0 -10000 0 0
TERT -0.085 0.22 -10000 0 -0.56 33 33
CCND1 -0.23 0.48 -10000 0 -1 130 130
MAX 0.034 0.011 -10000 0 -0.027 11 11
RBBP7 0.035 0.007 -10000 0 0 18 18
RBBP4 0.032 0.012 -10000 0 0 58 58
TERF2 0.019 0.049 -10000 0 -0.22 19 19
PTGES3 0.035 0.008 -10000 0 0 24 24
SIN3A 0 0.002 -10000 0 -10000 0 0
Telomerase/911 0.008 0.1 -10000 0 -0.37 22 22
CDKN1B -0.048 0.14 -10000 0 -0.3 100 100
RAD1 0.033 0.011 -10000 0 0 52 52
XRCC5 0.035 0.008 -10000 0 0 24 24
XRCC6 0.033 0.011 -10000 0 0 52 52
SAP30 0.033 0.01 -10000 0 0 44 44
TRF2/PARP2 0.029 0.059 -10000 0 -0.17 36 36
UBE3A 0.033 0.011 -10000 0 -0.027 4 4
JUN 0.026 0.043 -10000 0 -0.04 69 69
E6 -0.001 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.022 -10000 0 -10000 0 0
FOS -0.002 0.082 -10000 0 -0.24 46 46
IFN-gamma/IRF1 -0.004 0.11 -10000 0 -0.22 108 108
PARP2 0.034 0.01 -10000 0 0 45 45
BLM 0.033 0.011 -10000 0 0 53 53
Telomerase 0.005 0.067 0.15 4 -0.3 13 17
IRF1 0.008 0.077 -10000 0 -0.19 58 58
ESR1 0.034 0.009 -10000 0 -10000 0 0
KU/TER 0.042 0.043 -10000 0 -0.2 13 13
ATM/TRF2 0.039 0.038 -10000 0 -0.094 22 22
ubiquitin-dependent protein catabolic process -0.007 0.078 0.18 1 -0.27 25 26
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.008 0.079 -10000 0 -0.27 25 25
HDAC1 0.035 0.008 -10000 0 0 23 23
HDAC2 0.017 0.043 -10000 0 -0.045 123 123
ATM 0.022 0.039 0.15 19 -0.24 4 23
SMAD3 -0.007 0.019 0.07 1 -10000 0 1
ABL1 0.033 0.011 -10000 0 0 55 55
MXD1 0.034 0.01 -10000 0 -0.027 8 8
MRE11A 0.035 0.008 -10000 0 0 27 27
HUS1 0.036 0.005 -10000 0 0 10 10
RPS6KB1 0.036 0.006 -10000 0 0 16 16
TERT/NF kappa B1/14-3-3 -0.052 0.22 -10000 0 -0.53 30 30
NR2F2 0.032 0.022 0.058 12 -0.003 87 99
MAPK3 -0.011 0.018 -10000 0 -10000 0 0
MAPK1 -0.014 0.035 0.065 4 -0.2 13 17
TGFB1/TGF beta receptor Type II 0.035 0.01 -10000 0 0 39 39
NFKB1 0.033 0.011 -10000 0 0 51 51
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.022 0.039 0.15 19 -0.24 4 23
NBN 0.032 0.012 -10000 0 0 63 63
EGFR 0.035 0.006 -10000 0 -10000 0 0
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.047 0.02 -10000 0 -10000 0 0
MYC 0.007 0.057 -10000 0 -0.19 26 26
IL2 0.02 0.034 -10000 0 -0.039 121 121
KU 0.042 0.043 -10000 0 -0.2 13 13
RAD50 0.036 0.007 -10000 0 0 18 18
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.01 -10000 0 0 39 39
TRF2/BLM 0.028 0.061 -10000 0 -0.18 35 35
FRAP1 0.036 0.006 -10000 0 0 14 14
KU/TERT -0.064 0.22 -10000 0 -0.5 47 47
SP1/HDAC2 0.027 0.059 -10000 0 -0.2 11 11
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.074 0.2 -10000 0 -0.46 52 52
Smad3/Myc -0.002 0.063 -10000 0 -0.16 63 63
911 complex 0.06 0.045 -10000 0 -0.16 15 15
IFNG 0.019 0.055 -10000 0 -0.14 56 56
Telomerase/PinX1 -0.074 0.2 -10000 0 -0.46 52 52
Telomerase/AKT1/mTOR/p70S6K -0.009 0.11 -10000 0 -0.36 25 25
SIN3B 0.032 0.012 -10000 0 0 68 68
YWHAE 0.033 0.011 -10000 0 0 53 53
Telomerase/EST1B -0.074 0.2 -10000 0 -0.46 52 52
response to DNA damage stimulus 0.009 0.024 0.13 2 -0.099 14 16
MRN complex/TRF2/Rap1 0.065 0.068 -10000 0 -0.15 24 24
TRF2/WRN 0.031 0.049 -10000 0 -0.17 23 23
Telomerase/hnRNP C1/C2 -0.074 0.2 -10000 0 -0.46 52 52
E2F1 0.021 0.029 -10000 0 -0.03 117 117
ZNFX1 0 0.002 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.007 -10000 0 0 22 22
DKC1 0.036 0.007 -10000 0 0 17 17
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.03 0.014 -10000 0 0 94 94
SMAD2 0.006 0.056 0.19 6 -0.19 14 20
SMAD3 0.014 0.051 0.28 1 -0.18 16 17
SMAD3/SMAD4 -0.032 0.18 -10000 0 -0.45 70 70
SMAD4/Ubc9/PIASy 0.039 0.071 -10000 0 -0.16 48 48
SMAD2/SMAD2/SMAD4 0.027 0.11 0.26 1 -0.25 30 31
PPM1A 0.036 0.005 -10000 0 0 8 8
CALM1 0.036 0.006 -10000 0 0 16 16
SMAD2/SMAD4 0.016 0.066 0.22 2 -0.21 24 26
MAP3K1 0.033 0.011 -10000 0 0 53 53
TRAP-1/SMAD4 0.026 0.073 -10000 0 -0.19 49 49
MAPK3 0.036 0.004 -10000 0 0 7 7
MAPK1 0.033 0.012 -10000 0 0 62 62
NUP214 0.035 0.009 -10000 0 0 30 30
CTDSP1 0.036 0.006 -10000 0 0 13 13
CTDSP2 0.036 0.006 -10000 0 0 15 15
CTDSPL 0.036 0.006 -10000 0 0 14 14
KPNB1 0.035 0.008 -10000 0 0 29 29
TGFBRAP1 0.037 0.004 -10000 0 0 5 5
UBE2I 0.035 0.008 -10000 0 0 25 25
NUP153 0.032 0.012 -10000 0 0 63 63
KPNA2 0.033 0.012 -10000 0 0 59 59
PIAS4 0.033 0.011 -10000 0 0 55 55
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.042 0.11 0.29 19 -0.28 10 29
PDGFB-D/PDGFRB/SLAP 0.03 0.037 -10000 0 -0.19 7 7
PDGFB-D/PDGFRB/APS/CBL 0.045 0.015 -10000 0 -10000 0 0
AKT1 0.013 0.11 0.25 36 -0.26 7 43
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.097 0.27 18 -0.28 13 31
PIK3CA 0.026 0.017 -10000 0 0 158 158
FGR 0.014 0.09 0.26 4 -0.42 9 13
mol:Ca2+ 0.018 0.091 0.25 13 -0.3 14 27
MYC -0.054 0.34 0.34 26 -0.71 100 126
SHC1 0.035 0.008 -10000 0 0 27 27
HRAS/GDP 0.025 0.068 0.18 40 -0.16 30 70
LRP1/PDGFRB/PDGFB 0.064 0.025 -10000 0 -10000 0 0
GRB10 0.035 0.008 -10000 0 0 29 29
PTPN11 0.036 0.005 -10000 0 0 8 8
GO:0007205 0.017 0.092 0.26 11 -0.31 14 25
PTEN 0.033 0.012 -10000 0 0 61 61
GRB2 0.035 0.007 -10000 0 0 22 22
GRB7 0.033 0.012 -10000 0 0 60 60
PDGFB-D/PDGFRB/SHP2 0.05 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.046 0.031 -10000 0 -0.2 6 6
cell cycle arrest 0.03 0.037 -10000 0 -0.19 7 7
HRAS 0.034 0.01 -10000 0 0 38 38
HIF1A 0.007 0.1 0.22 39 -0.24 7 46
GAB1 0.006 0.12 0.29 7 -0.31 25 32
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.01 0.12 0.3 18 -0.28 26 44
PDGFB-D/PDGFRB 0.046 0.056 -10000 0 -0.16 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.042 0.047 -10000 0 -0.19 18 18
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.028 0.13 0.31 12 -0.28 37 49
positive regulation of MAPKKK cascade 0.05 0.015 -10000 0 -10000 0 0
PIK3R1 0.031 0.014 -10000 0 0 90 90
mol:IP3 0.018 0.092 0.26 11 -0.31 13 24
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.031 4 4
PDGFB-D/PDGFRB/GRB7 0.041 0.04 -10000 0 -0.17 14 14
SHB 0.036 0.006 -10000 0 0 15 15
BLK -0.049 0.16 0.33 1 -0.38 85 86
PTPN2 0.033 0.016 -10000 0 -0.017 45 45
PDGFB-D/PDGFRB/SNX15 0.051 0.015 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.016 0.16 0.29 10 -0.37 56 66
CBL 0.036 0.007 -10000 0 0 17 17
PDGFB-D/PDGFRB/DEP1 0.051 0.015 -10000 0 -10000 0 0
LCK 0.018 0.077 0.25 5 -0.38 5 10
PDGFRB 0.032 0.019 0.063 1 -0.014 64 65
ACP1 0.034 0.009 -10000 0 0 36 36
HCK 0.013 0.069 0.33 1 -0.41 3 4
ABL1 0.003 0.1 0.25 15 -0.27 24 39
PDGFB-D/PDGFRB/CBL 0.004 0.12 0.36 2 -0.38 18 20
PTPN1 0.029 0.018 -10000 0 -0.009 86 86
SNX15 0.037 0.004 -10000 0 0 6 6
STAT3 0.034 0.01 -10000 0 0 41 41
STAT1 0.031 0.014 -10000 0 0 84 84
cell proliferation -0.039 0.31 0.33 30 -0.63 100 130
SLA 0.024 0.018 -10000 0 0 186 186
actin cytoskeleton reorganization 0.034 0.087 0.22 58 -0.19 10 68
SRC 0.017 0.059 0.33 1 -10000 0 1
PI3K -0.035 0.052 -10000 0 -0.15 62 62
PDGFB-D/PDGFRB/GRB7/SHC 0.058 0.042 -10000 0 -0.15 13 13
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.032 0.099 0.27 18 -0.29 13 31
LYN -0.038 0.16 0.22 1 -0.46 58 59
LRP1 0.036 0.006 -10000 0 0 15 15
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.035 0.008 -10000 0 0 25 25
STAT5A 0.035 0.008 -10000 0 0 27 27
NCK1-2/p130 Cas 0.057 0.066 -10000 0 -0.16 20 20
SPHK1 0.035 0.01 0.057 1 0 35 36
EDG1 0.037 0.006 0.057 1 0 10 11
mol:DAG 0.018 0.092 0.26 11 -0.31 13 24
PLCG1 0.017 0.093 0.27 9 -0.32 13 22
NHERF/PDGFRB 0.056 0.052 -10000 0 -0.16 23 23
YES1 -0.004 0.13 0.27 3 -0.5 26 29
cell migration 0.055 0.052 -10000 0 -0.16 23 23
SHC/Grb2/SOS1 0.061 0.059 -10000 0 -0.15 13 13
SLC9A3R2 0.035 0.008 -10000 0 0 24 24
SLC9A3R1 0.033 0.011 -10000 0 0 55 55
NHERF1-2/PDGFRB/PTEN 0.055 0.081 -10000 0 -0.16 58 58
FYN -0.044 0.17 0.32 1 -0.45 67 68
DOK1 0.003 0.065 0.18 48 -0.16 8 56
HRAS/GTP 0.025 0.015 -10000 0 -0.19 2 2
PDGFB 0.033 0.011 -10000 0 0 49 49
RAC1 -0.085 0.31 0.3 9 -0.62 104 113
PRKCD 0.001 0.072 0.19 49 -0.17 17 66
FER 0.004 0.066 0.19 49 -0.16 6 55
MAPKKK cascade 0.004 0.079 0.19 65 -0.22 1 66
RASA1 -0.001 0.071 0.19 45 -0.18 19 64
NCK1 0.033 0.011 -10000 0 0 53 53
NCK2 0.036 0.006 -10000 0 0 13 13
p62DOK/Csk 0.045 0.059 0.19 48 -0.16 15 63
PDGFB-D/PDGFRB/SHB 0.05 0.016 -10000 0 -10000 0 0
chemotaxis 0.004 0.1 0.24 16 -0.26 24 40
STAT1-3-5/STAT1-3-5 0.046 0.079 -10000 0 -0.16 38 38
Bovine Papilomavirus E5/PDGFRB 0.021 0.018 -10000 0 -10000 0 0
PTPRJ 0.037 0.004 -10000 0 0 6 6
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.081 0.23 7 -0.21 8 15
TBX21 0.027 0.22 -10000 0 -0.67 9 9
B2M 0.033 0.011 -10000 0 0 50 50
TYK2 0.022 0.05 -10000 0 -0.095 30 30
IL12RB1 0.025 0.04 -10000 0 -0.058 2 2
GADD45B 0.021 0.23 -10000 0 -0.68 21 21
IL12RB2 0.028 0.042 -10000 0 -0.076 2 2
GADD45G 0.044 0.19 -10000 0 -0.62 11 11
natural killer cell activation 0.005 0.021 0.042 31 -0.036 59 90
RELB 0.035 0.008 -10000 0 0 28 28
RELA 0.036 0.004 -10000 0 0 7 7
IL18 0.032 0.028 -10000 0 -0.18 5 5
IL2RA 0.035 0.008 -10000 0 0 26 26
IFNG 0.036 0.007 -10000 0 0 18 18
STAT3 (dimer) 0.039 0.23 0.4 1 -0.58 32 33
HLA-DRB5 -0.003 0.01 -10000 0 -0.024 74 74
FASLG 0.029 0.22 -10000 0 -0.68 8 8
NF kappa B2 p52/RelB 0.039 0.22 -10000 0 -0.52 40 40
CD4 0.02 0.03 -10000 0 -0.021 166 166
SOCS1 0.036 0.007 -10000 0 0 20 20
EntrezGene:6955 -0.004 0.012 -10000 0 -0.026 108 108
CD3D 0.018 0.032 -10000 0 -0.039 100 100
CD3E 0.022 0.031 -10000 0 -0.031 130 130
CD3G 0.021 0.032 -10000 0 -0.031 139 139
IL12Rbeta2/JAK2 0.04 0.059 -10000 0 -10000 0 0
CCL3 0.026 0.22 0.4 2 -0.51 43 45
CCL4 -0.078 0.45 -10000 0 -1.1 78 78
HLA-A 0.034 0.01 -10000 0 0 45 45
IL18/IL18R 0.081 0.043 -10000 0 -0.18 7 7
NOS2 0.033 0.2 0.38 3 -0.45 42 45
IL12/IL12R/TYK2/JAK2/SPHK2 0.04 0.084 0.23 7 -0.22 9 16
IL1R1 0.027 0.23 -10000 0 -0.73 9 9
IL4 0.013 0.041 -10000 0 -10000 0 0
JAK2 0.025 0.04 -10000 0 -0.067 3 3
EntrezGene:6957 -0.003 0.01 -10000 0 -0.024 74 74
TCR/CD3/MHC I/CD8 -0.011 0.074 -10000 0 -0.21 48 48
RAB7A 0.041 0.19 -10000 0 -0.52 22 22
lysosomal transport 0.043 0.19 -10000 0 -0.5 22 22
FOS -0.2 0.55 -10000 0 -1.2 120 120
STAT4 (dimer) 0.05 0.21 0.43 2 -0.55 21 23
STAT5A (dimer) 0.041 0.22 -10000 0 -0.51 40 40
GZMA 0.027 0.22 -10000 0 -0.67 9 9
GZMB 0.029 0.22 -10000 0 -0.66 10 10
HLX 0 0 -10000 0 -10000 0 0
LCK 0.019 0.22 0.53 2 -0.54 39 41
TCR/CD3/MHC II/CD4 -0.043 0.12 0.14 4 -0.21 159 163
IL2/IL2R 0.071 0.04 -10000 0 -0.13 1 1
MAPK14 0.04 0.22 -10000 0 -0.61 22 22
CCR5 0.04 0.18 0.36 2 -0.42 31 33
IL1B 0.022 0.047 -10000 0 -0.19 6 6
STAT6 0.032 0.1 -10000 0 -0.5 5 5
STAT4 0.036 0.007 -10000 0 0 17 17
STAT3 0.034 0.01 -10000 0 0 41 41
STAT1 0.031 0.014 -10000 0 0 84 84
NFKB1 0.033 0.011 -10000 0 0 51 51
NFKB2 0.036 0.006 -10000 0 0 13 13
IL12B 0.028 0.042 -10000 0 -0.076 2 2
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.041 0.081 0.21 8 -0.23 7 15
IL2RB 0.03 0.014 -10000 0 0 93 93
proteasomal ubiquitin-dependent protein catabolic process 0.052 0.2 0.41 3 -0.51 21 24
IL2RG 0.033 0.012 -10000 0 0 60 60
IL12 0.038 0.058 -10000 0 -10000 0 0
STAT5A 0.035 0.008 -10000 0 0 27 27
CD247 -0.003 0.01 -10000 0 -0.024 74 74
IL2 0.035 0.008 -10000 0 0 28 28
SPHK2 0.036 0.007 -10000 0 0 18 18
FRAP1 0.036 0.006 -10000 0 0 14 14
IL12A 0.023 0.04 -10000 0 -0.06 7 7
IL12/IL12R/TYK2/JAK2 0.011 0.23 -10000 0 -0.56 43 43
MAP2K3 0.028 0.22 -10000 0 -0.66 19 19
RIPK2 0.032 0.012 -10000 0 0 67 67
MAP2K6 0.041 0.21 -10000 0 -0.63 18 18
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.006 0.087 -10000 0 -0.13 106 106
IL18RAP 0.039 0.007 -10000 0 -0.036 1 1
IL12Rbeta1/TYK2 0.034 0.06 -10000 0 -0.21 9 9
EOMES -0.016 0.032 0.079 7 -0.09 19 26
STAT1 (dimer) 0.026 0.23 0.39 2 -0.58 37 39
T cell proliferation 0.044 0.18 0.37 4 -0.45 18 22
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.007 -10000 0 -0.036 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.17 -10000 0 -0.5 14 14
ATF2 0.038 0.21 0.44 1 -0.56 22 23
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.014 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.044 -10000 0 -0.16 16 16
CDKN1B -0.009 0.12 0.2 28 -0.39 36 64
CDKN1A -0.01 0.11 0.2 7 -0.34 43 50
FRAP1 0.036 0.006 -10000 0 0 14 14
PRKDC 0.033 0.011 -10000 0 0 53 53
FOXO3 -0.01 0.1 -10000 0 -0.33 45 45
AKT1 -0.008 0.11 -10000 0 -0.35 43 43
BAD 0.036 0.006 -10000 0 0 13 13
AKT3 0.016 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.01 0.1 -10000 0 -0.33 45 45
AKT1/ASK1 0.011 0.11 -10000 0 -0.32 46 46
BAD/YWHAZ 0.044 0.052 -10000 0 -0.17 17 17
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.035 0.007 -10000 0 0 22 22
JNK cascade -0.01 0.11 0.32 46 -10000 0 46
TSC1 -0.011 0.1 0.25 1 -0.35 41 42
YWHAZ 0.029 0.015 -10000 0 0 105 105
AKT1/RAF1 0.014 0.12 -10000 0 -0.34 44 44
EP300 0.033 0.011 -10000 0 0 52 52
mol:GDP -0.008 0.11 -10000 0 -0.35 43 43
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.016 0.11 -10000 0 -0.34 45 45
YWHAQ 0.036 0.007 -10000 0 0 19 19
TBC1D4 0.007 0.022 0.24 4 -10000 0 4
MAP3K5 0.034 0.01 -10000 0 0 42 42
MAPKAP1 0.036 0.006 -10000 0 0 16 16
negative regulation of cell cycle 0.017 0.12 0.3 56 -0.17 2 58
YWHAH 0.03 0.014 -10000 0 0 92 92
AKT1S1 -0.01 0.1 -10000 0 -0.33 45 45
CASP9 -0.012 0.1 0.25 1 -0.34 43 44
YWHAB 0.034 0.01 -10000 0 0 42 42
p27Kip1/KPNA1 0.008 0.13 0.25 5 -0.36 39 44
GBL 0.035 0.009 -10000 0 0 34 34
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
YWHAE 0.033 0.011 -10000 0 0 53 53
SRC 0.035 0.008 -10000 0 0 25 25
AKT2/p21CIP1 -0.004 0.097 0.2 7 -0.29 43 50
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.082 -10000 0 -0.36 18 18
CHUK -0.016 0.11 -10000 0 -0.34 45 45
BAD/BCL-XL 0.01 0.11 -10000 0 -0.33 41 41
mTORC2 0.063 0.026 -10000 0 -0.14 3 3
AKT2 0.015 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.022 0.15 -10000 0 -0.38 51 51
PDPK1 0.035 0.007 -10000 0 0 21 21
MDM2 -0.007 0.11 0.2 13 -0.34 42 55
MAPKKK cascade -0.014 0.11 0.34 44 -10000 0 44
MDM2/Cbp/p300 0.028 0.12 0.3 2 -0.32 41 43
TSC1/TSC2 -0.018 0.11 0.27 4 -0.33 45 49
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.11 0.29 2 -0.31 41 43
glucose import -0.001 0.03 0.21 10 -10000 0 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.082 -10000 0 -0.31 7 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.001 0.027 0.21 8 -10000 0 8
GSK3A -0.007 0.11 0.22 12 -0.34 40 52
FOXO1 -0.01 0.1 -10000 0 -0.33 45 45
GSK3B -0.011 0.11 0.22 13 -0.35 43 56
SFN 0.026 0.017 -10000 0 0 148 148
G1/S transition of mitotic cell cycle -0.008 0.12 0.29 10 -0.35 41 51
p27Kip1/14-3-3 family -0.013 0.12 -10000 0 -0.43 25 25
PRKACA 0.031 0.013 -10000 0 0 79 79
KPNA1 0.036 0.007 -10000 0 0 17 17
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.035 0.009 -10000 0 0 34 34
CREBBP 0.035 0.009 -10000 0 0 32 32
Circadian rhythm pathway

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
chromatin modification -0.033 0.3 -10000 0 -1.1 39 39
CLOCK 0.03 0.032 -10000 0 -0.074 36 36
TIMELESS/CRY2 -0.037 0.31 -10000 0 -1.1 39 39
DEC1/BMAL1 0.046 0.029 -10000 0 -10000 0 0
ATR 0.033 0.011 -10000 0 0 49 49
NR1D1 -0.006 0.11 -10000 0 -0.67 1 1
ARNTL 0.031 0.028 -10000 0 -0.067 36 36
TIMELESS -0.071 0.32 -10000 0 -1.2 39 39
NPAS2 0.031 0.028 -10000 0 -0.066 38 38
CRY2 0.037 0.003 -10000 0 0 4 4
mol:CO 0 0.039 0.13 39 -10000 0 39
CHEK1 0.031 0.013 -10000 0 0 82 82
mol:HEME 0 0.039 -10000 0 -0.13 39 39
PER1 0.034 0.01 -10000 0 0 44 44
BMAL/CLOCK/NPAS2 0.059 0.074 -10000 0 -0.16 45 45
BMAL1/CLOCK -0.016 0.18 -10000 0 -0.59 39 39
S phase of mitotic cell cycle -0.033 0.3 -10000 0 -1.1 39 39
TIMELESS/CHEK1/ATR -0.035 0.31 -10000 0 -1.1 39 39
mol:NADPH 0 0.039 -10000 0 -0.13 39 39
PER1/TIMELESS -0.04 0.31 -10000 0 -1.1 39 39
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.036 0.006 -10000 0 0 15 15
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.035 0.007 -10000 0 0 22 22
VLDLR 0.028 0.016 -10000 0 0 131 131
LRPAP1 0.033 0.012 -10000 0 0 58 58
NUDC 0.035 0.008 -10000 0 0 25 25
RELN/LRP8 0.051 0.053 -10000 0 -0.15 27 27
CaM/Ca2+ 0.026 0.01 -10000 0 -0.19 1 1
KATNA1 0.034 0.01 -10000 0 0 42 42
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.004 0.061 0.19 20 -0.16 20 40
IQGAP1/CaM 0.037 0.058 -10000 0 -0.19 29 29
DAB1 0.036 0.007 -10000 0 0 18 18
IQGAP1 0.033 0.011 -10000 0 0 53 53
PLA2G7 0.032 0.012 -10000 0 0 68 68
CALM1 0.036 0.006 -10000 0 0 16 16
DYNLT1 0.034 0.01 -10000 0 0 45 45
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.057 -10000 0 -0.19 27 27
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.034 0.01 -10000 0 0 38 38
LIS1/Poliovirus Protein 3A -0.018 0.031 -10000 0 -0.16 24 24
CDK5R2 0.036 0.005 -10000 0 0 8 8
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.042 0.066 -10000 0 -0.16 43 43
YWHAE 0.033 0.011 -10000 0 0 53 53
NDEL1/14-3-3 E 0.02 0.086 0.26 14 -0.23 11 25
MAP1B -0.019 0.077 -10000 0 -0.22 64 64
RAC1 0.002 0.045 -10000 0 -0.28 7 7
p35/CDK5 -0.015 0.067 0.19 13 -0.22 3 16
RELN 0.032 0.013 -10000 0 0 70 70
PAFAH/LIS1 0.019 0.043 -10000 0 -0.16 24 24
LIS1/CLIP170 -0.018 0.031 -10000 0 -0.16 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.009 0.085 0.18 2 -0.25 18 20
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.003 0.095 -10000 0 -0.22 55 55
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.006 0.079 0.22 21 -0.23 10 31
LIS1/IQGAP1 0.014 0.058 -10000 0 -0.17 42 42
RHOA -0.019 0.11 -10000 0 -0.4 34 34
PAFAH1B1 -0.021 0.039 0.06 10 -0.19 23 33
PAFAH1B3 0.032 0.013 -10000 0 0 75 75
PAFAH1B2 0.035 0.007 -10000 0 0 21 21
MAP1B/LIS1/Dynein heavy chain -0.007 0.084 0.18 1 -0.19 71 72
NDEL1/Katanin 60/Dynein heavy chain 0.026 0.093 0.25 11 -0.23 15 26
LRP8 0.032 0.012 -10000 0 0 65 65
NDEL1/Katanin 60 0.016 0.087 0.24 13 -0.23 14 27
P39/CDK5 -0.015 0.07 0.2 16 -0.22 3 19
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.05 -10000 0 -0.17 29 29
CDK5 -0.017 0.063 0.19 15 -0.23 3 18
PPP2R5D 0.035 0.007 -10000 0 0 22 22
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.015 0.026 -10000 0 -0.13 24 24
CSNK2A1 0.032 0.013 -10000 0 0 71 71
RELN/VLDLR/DAB1/LIS1 0.042 0.078 -10000 0 -0.15 52 52
RELN/VLDLR 0.043 0.082 -10000 0 -0.15 62 62
CDC42 0.005 0.032 -10000 0 -0.12 18 18
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS 0.064 0.071 -9999 0 -0.16 24 24
SMAD6-7/SMURF1 0.055 0.056 -9999 0 -0.16 28 28
NOG 0 0 -9999 0 -10000 0 0
SMAD9 0.018 0.087 -9999 0 -0.39 21 21
SMAD4 0.03 0.014 -9999 0 0 94 94
SMAD5 0.011 0.067 -9999 0 -0.27 11 11
BMP7/USAG1 0.034 0.026 -9999 0 -10000 0 0
SMAD5/SKI 0.027 0.074 -9999 0 -0.25 12 12
SMAD1 -0.017 0.12 -9999 0 -0.32 59 59
BMP2 0.034 0.01 -9999 0 0 41 41
SMAD1/SMAD1/SMAD4 -0.011 0.13 -9999 0 -0.31 60 60
BMPR1A 0.035 0.009 -9999 0 0 33 33
BMPR1B 0.034 0.01 -9999 0 0 39 39
BMPR1A-1B/BAMBI 0.056 0.044 -9999 0 -0.16 14 14
AHSG 0.03 0.014 -9999 0 0 97 97
CER1 0.035 0.009 -9999 0 0 33 33
BMP2-4/CER1 0.063 0.025 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.006 0.067 -9999 0 -0.24 13 13
BMP2-4 (homodimer) 0.045 0.021 -9999 0 -10000 0 0
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.063 0.068 -9999 0 -0.16 32 32
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.036 0.005 -9999 0 0 9 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.009 0.051 -9999 0 -0.15 33 33
BMP2-4/USAG1 0.058 0.026 -9999 0 -10000 0 0
SMAD6/SMURF1/SMAD5 0.027 0.076 -9999 0 -0.26 12 12
SOSTDC1 0.027 0.017 -9999 0 0 145 145
BMP7/BMPR2/BMPR1A-1B 0.06 0.068 -9999 0 -0.17 30 30
SKI 0.035 0.008 -9999 0 0 25 25
BMP6 (homodimer) 0.033 0.011 -9999 0 0 52 52
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.034 0.01 -9999 0 0 46 46
MAP3K7 0.034 0.01 -9999 0 0 46 46
BMP2-4/CHRD 0.055 0.032 -9999 0 -10000 0 0
SMAD5/SMAD5/SMAD4 0.02 0.078 -9999 0 -0.26 18 18
MAPK1 0.033 0.012 -9999 0 0 62 62
TAK1/TAB family 0.05 0.084 -9999 0 -0.24 10 10
BMP7 (homodimer) 0.032 0.013 -9999 0 0 73 73
NUP214 0.035 0.009 -9999 0 0 30 30
BMP6/FETUA 0.04 0.024 -9999 0 -10000 0 0
SMAD1/SKI 0.001 0.13 -9999 0 -0.31 59 59
SMAD6 0.036 0.005 -9999 0 0 9 9
CTDSP2 0.036 0.006 -9999 0 0 15 15
BMP2-4/FETUA 0.055 0.031 -9999 0 -10000 0 0
MAP3K7IP1 0.034 0.011 -9999 0 0 48 48
GREM1 0.028 0.016 -9999 0 0 122 122
BMPR2 (homodimer) 0.034 0.01 -9999 0 0 41 41
GADD34/PP1CA 0.059 0.044 -9999 0 -0.16 14 14
BMPR1A-1B (homodimer) 0.042 0.044 -9999 0 -0.19 15 15
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.001 0.13 -9999 0 -0.3 58 58
SMAD6-7/SMURF1/SMAD1 0.018 0.14 -9999 0 -0.32 57 57
SMAD6/SMURF1 0.036 0.005 -9999 0 0 9 9
BAMBI 0.029 0.015 -9999 0 0 110 110
SMURF2 0.035 0.008 -9999 0 0 24 24
BMP2-4/CHRDL1 0.041 0.019 -9999 0 -10000 0 0
BMP2-4/GREM1 0.059 0.026 -9999 0 -10000 0 0
SMAD7 0.032 0.013 -9999 0 0 74 74
SMAD8A/SMAD8A/SMAD4 0.024 0.095 -9999 0 -0.35 28 28
SMAD1/SMAD6 0.001 0.13 -9999 0 -0.31 58 58
TAK1/SMAD6 0.045 0.039 -9999 0 -0.19 12 12
BMP7 0.032 0.013 -9999 0 0 73 73
BMP6 0.033 0.011 -9999 0 0 52 52
MAP3K7IP2 0.034 0.01 -9999 0 0 37 37
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.071 -9999 0 -0.28 16 16
PPM1A 0.036 0.005 -9999 0 0 8 8
SMAD1/SMURF2 -0.001 0.13 -9999 0 -0.31 60 60
SMAD7/SMURF1 0.036 0.057 -9999 0 -0.19 28 28
CTDSPL 0.036 0.006 -9999 0 0 14 14
PPP1CA 0.036 0.007 -9999 0 0 19 19
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.036 0.006 -9999 0 0 13 13
PPP1R15A 0.034 0.01 -9999 0 0 39 39
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.013 0.052 -9999 0 -0.16 30 30
CHRD 0.03 0.015 -9999 0 0 101 101
BMPR2 0.034 0.01 -9999 0 0 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.008 0.05 -9999 0 -0.16 34 34
BMP4 0.033 0.011 -9999 0 0 54 54
FST 0.029 0.015 -9999 0 0 108 108
BMP2-4/NOG 0.041 0.019 -9999 0 -10000 0 0
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.07 0.073 -9999 0 -0.16 30 30
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.096 0.21 14 -0.25 34 48
FYN -0.011 0.13 0.23 10 -0.32 50 60
LAT/GRAP2/SLP76 0.013 0.099 0.28 2 -0.26 38 40
IKBKB 0.034 0.01 -10000 0 0 40 40
AKT1 0.002 0.095 0.2 9 -0.26 36 45
B2M 0.035 0.012 -10000 0 0 50 50
IKBKG 0.003 0.038 0.11 8 -0.097 26 34
MAP3K8 0.032 0.012 -10000 0 0 68 68
mol:Ca2+ -0.012 0.009 0.019 2 -0.037 21 23
integrin-mediated signaling pathway 0.022 0.018 -10000 0 -0.15 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.001 0.12 0.24 6 -0.32 38 44
TRPV6 0.075 0.32 1.3 35 -10000 0 35
CD28 0.037 0.005 -10000 0 0 10 10
SHC1 0.009 0.1 0.22 20 -0.28 35 55
receptor internalization 0.006 0.089 0.16 1 -0.28 31 32
PRF1 0.019 0.12 -10000 0 -0.73 8 8
KRAS 0.03 0.014 -10000 0 0 92 92
GRB2 0.035 0.007 -10000 0 0 22 22
COT/AKT1 0.012 0.087 0.2 6 -0.23 31 37
LAT 0.004 0.1 0.23 7 -0.29 38 45
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.032 0.014 -10000 0 -10000 0 0
CD3E 0.037 0.007 -10000 0 -10000 0 0
CD3G 0.036 0.009 -10000 0 0 32 32
RASGRP2 0.009 0.017 0.097 1 -0.16 1 2
RASGRP1 -0.016 0.13 0.22 8 -0.28 64 72
HLA-A 0.035 0.011 -10000 0 -10000 0 0
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.023 0.018 -10000 0 -0.15 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.05 0.12 22 -0.1 29 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.012 0.047 -10000 0 -0.14 43 43
PRKCA 0.004 0.065 0.18 15 -0.16 22 37
GRAP2 0.033 0.011 -10000 0 0 49 49
mol:IP3 0.001 0.072 -10000 0 -0.21 37 37
EntrezGene:6957 0.001 0.002 0.009 8 -10000 0 8
TCR/CD3/MHC I/CD8 0.007 0.067 -10000 0 -0.27 17 17
ORAI1 -0.068 0.27 0.37 4 -1.1 35 39
CSK 0.003 0.1 0.24 6 -0.3 35 41
B7 family/CD28 0.05 0.1 0.32 1 -0.28 20 21
CHUK 0.035 0.009 -10000 0 0 33 33
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.002 0.1 -10000 0 -0.3 40 40
PTPN6 0.006 0.1 0.19 25 -0.29 36 61
VAV1 0.007 0.1 0.22 10 -0.29 37 47
Monovalent TCR/CD3 0.02 0.025 -10000 0 -0.18 7 7
CBL 0.036 0.007 -10000 0 0 17 17
LCK 0.001 0.12 0.24 9 -0.31 44 53
PAG1 0.005 0.1 0.23 5 -0.29 38 43
RAP1A 0.036 0.007 -10000 0 0 17 17
TCR/CD3/MHC I/CD8/LCK 0.002 0.1 0.19 1 -0.3 40 41
CD80 0.036 0.007 -10000 0 0 17 17
CD86 0.034 0.01 -10000 0 0 40 40
PDK1/CARD11/BCL10/MALT1 -0.006 0.059 -10000 0 -0.17 39 39
HRAS 0.034 0.01 -10000 0 0 38 38
GO:0035030 0.007 0.077 0.2 5 -0.25 20 25
CD8A 0.001 0.002 0.01 9 -10000 0 9
CD8B 0.001 0.003 0.01 13 -10000 0 13
PTPRC 0.027 0.017 -10000 0 0 142 142
PDK1/PKC theta -0.003 0.11 0.25 6 -0.29 35 41
CSK/PAG1 0.001 0.097 0.22 4 -0.29 36 40
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.029 0.087 -10000 0 -0.25 43 43
GRAP2/SLP76 0.018 0.11 0.25 5 -0.29 40 45
STIM1 -0.01 0.12 1.3 4 -10000 0 4
RAS family/GTP 0.003 0.072 0.15 11 -0.15 49 60
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.005 0.09 0.16 1 -0.3 30 31
mol:DAG -0.012 0.059 -10000 0 -0.19 38 38
RAP1A/GDP 0.01 0.026 0.066 14 -0.052 25 39
PLCG1 0.035 0.008 -10000 0 0 25 25
CD247 0.001 0.002 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.019 0.12 -10000 0 -0.7 8 8
RAP1A/GTP 0.004 0.008 -10000 0 -0.045 5 5
mol:PI-3-4-5-P3 0.002 0.1 0.22 7 -0.28 37 44
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.009 0.091 -10000 0 -0.25 36 36
NRAS 0.031 0.014 -10000 0 0 88 88
ZAP70 0.036 0.004 -10000 0 0 7 7
GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
LAT/GRAP2/SLP76/VAV1 0.007 0.093 0.24 3 -0.26 37 40
MALT1 0.033 0.011 -10000 0 0 56 56
TRAF6 0.036 0.005 -10000 0 0 9 9
CD8 heterodimer 0.002 0.005 0.016 28 -10000 0 28
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.017 0.041 -10000 0 -0.14 38 38
PRKCE 0.004 0.065 0.18 14 -0.16 21 35
PRKCQ -0.003 0.11 0.24 5 -0.31 37 42
LCP2 0.031 0.013 -10000 0 0 80 80
BCL10 0.035 0.009 -10000 0 0 31 31
regulation of survival gene product expression 0.004 0.085 0.19 9 -0.22 36 45
IKK complex 0.013 0.042 0.14 18 -0.093 3 21
RAS family/GDP -0.004 0.015 -10000 0 -0.035 60 60
MAP3K14 0.008 0.068 0.16 6 -0.18 30 36
PDPK1 0.002 0.089 0.2 9 -0.24 36 45
TCR/CD3/MHC I/CD8/Fyn -0.014 0.11 -10000 0 -0.36 37 37
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.054 0.035 -10000 0 -0.14 10 10
ER alpha/Gai/GDP/Gbeta gamma -0.012 0.13 -10000 0 -0.43 28 28
AKT1 -0.035 0.2 -10000 0 -0.62 46 46
PIK3CA 0.026 0.017 -10000 0 0 158 158
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.033 0.2 -10000 0 -0.61 49 49
mol:Ca2+ 0.015 0.04 0.18 13 -0.29 4 17
IGF1R 0.029 0.015 -10000 0 0 116 116
E2/ER alpha (dimer)/Striatin 0.046 0.013 -10000 0 -10000 0 0
SHC1 0.035 0.008 -10000 0 0 27 27
apoptosis 0.034 0.19 0.58 47 -10000 0 47
RhoA/GTP 0 0.068 -10000 0 -0.16 71 71
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.002 0.11 -10000 0 -0.34 30 30
regulation of stress fiber formation 0.021 0.089 0.22 21 -0.19 20 41
E2/ERA-ERB (dimer) 0.046 0.014 -10000 0 -10000 0 0
KRAS 0.03 0.014 -10000 0 0 92 92
G13/GTP 0.043 0.013 -10000 0 -10000 0 0
pseudopodium formation -0.021 0.089 0.19 20 -0.22 21 41
E2/ER alpha (dimer)/PELP1 0.043 0.017 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 22 22
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.011 -10000 0 0 47 47
HRAS 0.034 0.01 -10000 0 0 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.009 0.13 -10000 0 -0.41 33 33
E2/ER beta (dimer) 0.027 0.004 -10000 0 -10000 0 0
mol:GDP 0.007 0.048 -10000 0 -0.18 16 16
mol:NADP -0.009 0.13 -10000 0 -0.41 33 33
PIK3R1 0.031 0.014 -10000 0 0 90 90
mol:IP3 0.015 0.041 0.18 13 -0.3 4 17
IGF-1R heterotetramer 0.029 0.015 -10000 0 0 116 116
PLCB1 0.021 0.026 -10000 0 -0.31 2 2
PLCB2 0.02 0.027 -10000 0 -0.27 3 3
IGF1 0.025 0.017 -10000 0 0 164 164
mol:L-citrulline -0.009 0.13 -10000 0 -0.41 33 33
RHOA 0.034 0.01 -10000 0 0 43 43
Gai/GDP -0.018 0.2 -10000 0 -0.6 51 51
JNK cascade 0.027 0.004 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.036 0.006 -10000 0 0 12 12
GNAQ 0.036 0.007 -10000 0 0 17 17
ESR1 0.035 0.009 -10000 0 0 33 33
Gq family/GDP/Gbeta gamma -0.054 0.24 -10000 0 -0.64 68 68
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.022 0.13 -10000 0 -0.74 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.015 0.12 0.26 1 -0.34 29 30
GNAZ 0.034 0.01 -10000 0 0 46 46
E2/ER alpha (dimer) 0.026 0.007 -10000 0 -10000 0 0
STRN 0.037 0.004 -10000 0 0 5 5
GNAL 0.036 0.006 -10000 0 0 13 13
PELP1 0.034 0.01 -10000 0 0 43 43
MAPK11 0.012 0.008 -10000 0 -10000 0 0
GNAI2 0.036 0.007 -10000 0 0 20 20
GNAI3 0.036 0.007 -10000 0 0 20 20
GNAI1 0.031 0.014 -10000 0 0 83 83
HBEGF -0.014 0.15 0.3 19 -0.38 45 64
cAMP biosynthetic process 0.039 0.013 -10000 0 -10000 0 0
SRC -0.009 0.13 0.21 18 -0.41 28 46
PI3K 0.014 0.072 -10000 0 -0.2 46 46
GNB1 0.034 0.01 -10000 0 0 37 37
G13/GDP/Gbeta gamma 0.023 0.058 -10000 0 -0.17 13 13
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.038 0.098 -10000 0 -0.28 45 45
Gs family/GTP 0.049 0.017 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.033 0.07 -10000 0 -0.16 52 52
vasodilation -0.008 0.12 -10000 0 -0.39 33 33
mol:DAG 0.015 0.041 0.18 13 -0.3 4 17
Gs family/GDP/Gbeta gamma 0.006 0.05 -10000 0 -0.17 14 14
MSN -0.024 0.092 0.2 18 -0.23 21 39
Gq family/GTP 0.033 0.03 -10000 0 -0.28 3 3
mol:PI-3-4-5-P3 -0.031 0.19 -10000 0 -0.59 49 49
NRAS 0.031 0.014 -10000 0 0 88 88
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.008 0.12 0.39 33 -10000 0 33
GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
RhoA/GDP 0.013 0.068 -10000 0 -0.19 23 23
NOS3 -0.01 0.14 -10000 0 -0.43 33 33
GNA11 0.033 0.012 -10000 0 0 57 57
MAPKKK cascade 0.014 0.13 -10000 0 -0.51 24 24
E2/ER alpha (dimer)/PELP1/Src 0.011 0.12 0.24 5 -0.35 29 34
ruffle organization -0.021 0.089 0.19 20 -0.22 21 41
ROCK2 -0.009 0.095 0.22 21 -0.24 13 34
GNA14 0.036 0.006 -10000 0 0 16 16
GNA15 0.032 0.012 -10000 0 0 63 63
GNA13 0.036 0.006 -10000 0 0 14 14
MMP9 -0.018 0.15 0.36 13 -0.37 46 59
MMP2 -0.017 0.14 0.22 4 -0.37 39 43
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.003 0.17 -10000 0 -0.69 26 26
epithelial cell differentiation -0.016 0.16 -10000 0 -0.61 28 28
ITCH 0.032 0.038 0.097 4 -0.1 29 33
WWP1 -0.05 0.28 -10000 0 -1.2 26 26
FYN 0.028 0.016 -10000 0 0 131 131
EGFR 0.036 0.005 -10000 0 0 11 11
PRL 0.035 0.009 -10000 0 0 33 33
neuron projection morphogenesis -0.023 0.13 0.29 4 -0.51 26 30
PTPRZ1 0.035 0.009 -10000 0 0 33 33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.023 0.15 -10000 0 -0.55 26 26
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.015 0.15 -10000 0 -0.61 26 26
ADAM17 0.033 0.037 0.097 4 -0.095 31 35
ErbB4/ErbB4 -0.029 0.18 -10000 0 -0.75 26 26
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.037 0.16 -10000 0 -0.68 26 26
NCOR1 0.034 0.01 -10000 0 0 45 45
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.016 0.15 -10000 0 -0.58 27 27
GRIN2B -0.023 0.13 0.21 1 -0.53 27 28
ErbB4/ErbB2/betacellulin 0.002 0.14 -10000 0 -0.58 26 26
STAT1 0.031 0.014 -10000 0 0 84 84
HBEGF 0.036 0.006 -10000 0 0 12 12
PRLR 0.034 0.009 -10000 0 0 35 35
E4ICDs/ETO2 -0.009 0.17 -10000 0 -0.69 26 26
axon guidance -0.045 0.19 -10000 0 -0.75 29 29
NEDD4 0.031 0.037 0.1 2 -0.093 32 34
Prolactin receptor/Prolactin receptor/Prolactin 0.048 0.018 -10000 0 -10000 0 0
CBFA2T3 0.031 0.013 -10000 0 0 79 79
ErbB4/ErbB2/HBEGF 0.003 0.15 -10000 0 -0.59 26 26
MAPK3 -0.004 0.14 0.34 2 -0.52 26 28
STAT1 (dimer) -0.012 0.17 -10000 0 -0.64 30 30
MAPK1 -0.005 0.14 0.34 2 -0.52 26 28
JAK2 0.033 0.011 -10000 0 0 52 52
ErbB4/ErbB2/neuregulin 1 beta -0.013 0.14 -10000 0 -0.58 26 26
NRG1 -0.007 0.026 0.074 1 -10000 0 1
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.005 -10000 0 0 10 10
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.045 0.19 -10000 0 -0.75 29 29
neural crest cell migration -0.013 0.14 -10000 0 -0.57 26 26
ERBB2 -0.008 0.026 0.074 1 -10000 0 1
WWOX/E4ICDs -0.009 0.16 -10000 0 -0.65 26 26
SHC1 0.035 0.008 -10000 0 0 27 27
ErbB4/EGFR/neuregulin 4 -0.005 0.16 -10000 0 -0.65 26 26
apoptosis 0.015 0.15 0.64 26 -10000 0 26
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.003 0.17 -10000 0 -0.69 26 26
ErbB4/ErbB2/epiregulin 0.001 0.15 -10000 0 -0.59 26 26
ErbB4/ErbB4/betacellulin/betacellulin -0.005 0.17 -10000 0 -0.68 26 26
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.03 0.16 -10000 0 -0.57 26 26
MDM2 -0.028 0.16 0.27 11 -0.68 26 37
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.003 0.13 -10000 0 -0.54 26 26
STAT5A -0.047 0.18 -10000 0 -0.72 29 29
ErbB4/EGFR/neuregulin 1 beta -0.001 0.15 -10000 0 -0.59 26 26
DLG4 0.034 0.009 -10000 0 0 36 36
GRB2/SHC 0.048 0.03 -10000 0 -0.19 6 6
E4ICDs/TAB2/NCoR1 0.005 0.17 -10000 0 -0.64 27 27
STAT5A (dimer) -0.011 0.18 -10000 0 -0.68 28 28
MAP3K7IP2 0.034 0.01 -10000 0 0 37 37
STAT5B (dimer) -0.027 0.19 -10000 0 -0.73 29 29
LRIG1 0.026 0.017 -10000 0 0 149 149
EREG 0.034 0.01 -10000 0 0 37 37
BTC 0.034 0.01 -10000 0 0 39 39
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.047 0.19 -10000 0 -0.76 29 29
ERBB4 -0.03 0.18 -10000 0 -0.75 26 26
STAT5B 0.035 0.008 -10000 0 0 25 25
YAP1 -0.023 0.14 -10000 0 -0.53 33 33
GRB2 0.035 0.007 -10000 0 0 22 22
ErbB4/ErbB2/neuregulin 4 -0.016 0.14 -10000 0 -0.58 26 26
glial cell differentiation -0.005 0.17 0.63 27 -10000 0 27
WWOX 0.027 0.017 -10000 0 0 146 146
cell proliferation -0.019 0.15 0.28 2 -0.59 27 29
Paxillin-dependent events mediated by a4b1

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
CRKL 0.034 0.009 -9999 0 0 35 35
Rac1/GDP 0.026 0.026 -9999 0 -0.27 1 1
DOCK1 0.035 0.009 -9999 0 0 31 31
ITGA4 0.036 0.005 -9999 0 0 11 11
RAC1 0.035 0.008 -9999 0 0 28 28
alpha4/beta7 Integrin 0.053 0.009 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.033 0.011 -9999 0 0 55 55
alpha4/beta1 Integrin 0.061 0.029 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.048 0.023 -9999 0 -10000 0 0
lamellipodium assembly -0.021 0.13 -9999 0 -0.31 73 73
PIK3CA 0.026 0.017 -9999 0 0 158 158
PI3K 0.014 0.072 -9999 0 -0.2 46 46
ARF6 0.036 0.005 -9999 0 0 11 11
TLN1 0.036 0.007 -9999 0 0 19 19
PXN -0.014 0.006 -9999 0 -10000 0 0
PIK3R1 0.031 0.014 -9999 0 0 90 90
ARF6/GTP 0.078 0.043 -9999 0 -0.14 3 3
cell adhesion 0.083 0.048 -9999 0 -0.15 4 4
CRKL/CBL 0.05 0.016 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.048 0.024 -9999 0 -10000 0 0
ITGB1 0.036 0.006 -9999 0 0 15 15
ITGB7 0.037 0.003 -9999 0 0 4 4
ARF6/GDP 0.026 0.035 -9999 0 -0.28 4 4
alpha4/beta1 Integrin/Paxillin/VCAM1 0.023 0.1 -9999 0 -0.15 115 115
p130Cas/Crk/Dock1 0.04 0.031 -9999 0 -0.16 9 9
VCAM1 0.019 0.018 -9999 0 0 253 253
alpha4/beta1 Integrin/Paxillin/Talin 0.086 0.049 -9999 0 -0.15 4 4
alpha4/beta1 Integrin/Paxillin/GIT1 0.085 0.045 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.082 0.044 -9999 0 -10000 0 0
CBL 0.036 0.007 -9999 0 0 17 17
PRKACA 0.031 0.013 -9999 0 0 79 79
GIT1 0.035 0.008 -9999 0 0 23 23
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.086 0.049 -9999 0 -0.15 4 4
Rac1/GTP -0.025 0.14 -9999 0 -0.34 72 72
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.033 0.012 -10000 0 0 60 60
Caspase 8 (4 units) 0.043 0.083 -10000 0 -0.29 15 15
NEF 0.003 0 -10000 0 -10000 0 0
NFKBIA 0.022 0.065 0.073 6 -0.14 51 57
BIRC3 -0.049 0.11 0.19 5 -0.36 49 54
CYCS -0.002 0.068 0.18 3 -0.29 15 18
RIPK1 0.035 0.008 -10000 0 0 26 26
CD247 0.003 0 -10000 0 -10000 0 0
MAP2K7 0.004 0.16 -10000 0 -0.62 27 27
protein ubiquitination 0.008 0.09 0.22 2 -0.27 23 25
CRADD 0.037 0.004 -10000 0 0 6 6
DAXX 0.036 0.006 -10000 0 0 14 14
FAS 0.032 0.013 -10000 0 0 71 71
BID 0.006 0.066 0.14 1 -0.22 28 29
NF-kappa-B/RelA/I kappa B alpha 0.038 0.11 -10000 0 -0.21 71 71
TRADD 0.033 0.012 -10000 0 0 57 57
MAP3K5 0.034 0.01 -10000 0 0 42 42
CFLAR 0.035 0.008 -10000 0 0 24 24
FADD 0.035 0.008 -10000 0 0 23 23
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.038 0.11 -10000 0 -0.22 71 71
MAPK8 0.002 0.15 -10000 0 -0.58 27 27
APAF1 0.037 0.004 -10000 0 0 6 6
TRAF1 0.036 0.006 -10000 0 0 15 15
TRAF2 0.035 0.009 -10000 0 0 30 30
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.061 -10000 0 -0.19 30 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.015 0.1 -10000 0 -0.34 25 25
CHUK 0.006 0.095 0.22 2 -0.29 24 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.077 -10000 0 -0.17 35 35
TCRz/NEF 0.009 0.001 -10000 0 -10000 0 0
TNF 0.033 0.011 -10000 0 0 51 51
FASLG 0.021 0.004 -10000 0 -10000 0 0
NFKB1 0.026 0.049 -10000 0 -0.11 44 44
TNFR1A/BAG4/TNF-alpha 0.053 0.044 -10000 0 -0.16 11 11
CASP6 0.01 0.17 -10000 0 -0.54 38 38
CASP7 -0.017 0.18 0.26 6 -0.46 58 64
RELA 0.03 0.036 0.073 6 -0.075 51 57
CASP2 0.035 0.009 -10000 0 0 33 33
CASP3 -0.021 0.17 0.26 5 -0.42 62 67
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
TNFR1A/BAG4 0.038 0.042 -10000 0 -0.19 12 12
CASP8 0.036 0.007 -10000 0 0 19 19
CASP9 0.036 0.007 -10000 0 0 20 20
MAP3K14 0.014 0.099 -10000 0 -0.32 22 22
APAF-1/Caspase 9 -0.012 0.11 0.18 1 -0.28 57 58
BCL2 0.001 0.14 -10000 0 -0.53 26 26
Insulin Pathway

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
CBL/APS/CAP 0.038 0.062 -10000 0 -0.14 48 48
TC10/GTP 0.045 0.035 -10000 0 -0.14 10 10
Insulin Receptor/Insulin/IRS1/Shp2 0.06 0.079 -10000 0 -0.16 48 48
HRAS 0.034 0.01 -10000 0 0 38 38
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.033 0.011 -10000 0 0 49 49
FOXO3 -0.005 0.013 0.022 7 -0.037 54 61
AKT1 0.017 0.11 0.22 48 -0.24 9 57
INSR 0.036 0.018 0.077 11 -0.047 11 22
Insulin Receptor/Insulin 0.069 0.071 0.23 32 -0.26 11 43
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.035 0.008 -10000 0 0 29 29
SORBS1 0.036 0.005 -10000 0 0 11 11
CRK 0.033 0.011 -10000 0 0 55 55
PTPN1 -0.008 0.053 0.15 26 -0.33 7 33
CAV1 -0.014 0.067 0.17 14 -0.18 47 61
CBL/APS/CAP/Crk-II/C3G 0.074 0.035 -10000 0 -0.14 3 3
Insulin Receptor/Insulin/IRS1/NCK2 0.059 0.084 -10000 0 -0.16 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.015 0.078 -10000 0 -0.15 71 71
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.008 0.1 -10000 0 -0.31 37 37
RPS6KB1 0.009 0.099 0.2 47 -0.23 9 56
PARD6A 0.033 0.011 -10000 0 0 54 54
CBL 0.036 0.007 -10000 0 0 17 17
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.028 0.012 -10000 0 -10000 0 0
PIK3R1 0.031 0.014 -10000 0 0 90 90
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.032 0.093 0.22 10 -0.22 13 23
HRAS/GTP -0.023 0.042 -10000 0 -0.14 45 45
Insulin Receptor 0.036 0.018 0.077 11 -0.047 11 22
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.067 0.085 -10000 0 -0.15 49 49
PRKCI -0.008 0.13 -10000 0 -0.39 46 46
Insulin Receptor/Insulin/GRB14/PDK1 0.001 0.066 -10000 0 -0.15 64 64
SHC1 0.035 0.008 -10000 0 0 27 27
negative regulation of MAPKKK cascade 0.046 0.054 -10000 0 -10000 0 0
PI3K 0.023 0.085 -10000 0 -0.15 71 71
NCK2 0.036 0.006 -10000 0 0 13 13
RHOQ 0.035 0.008 -10000 0 0 26 26
mol:H2O2 -0.001 0.006 0.017 1 -0.041 7 8
HRAS/GDP 0.025 0.015 -10000 0 -0.19 2 2
AKT2 0.015 0.1 0.21 43 -0.24 7 50
PRKCZ -0.01 0.091 -10000 0 -0.32 37 37
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.01 0.056 0.16 12 -0.14 43 55
F2RL2 0.034 0.01 -10000 0 0 45 45
TRIP10 0.033 0.011 -10000 0 0 51 51
Insulin Receptor/Insulin/Shc 0.063 0.034 -10000 0 -0.18 1 1
TC10/GTP/CIP4/Exocyst 0.04 0.032 -10000 0 -0.16 10 10
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.073 0.045 -10000 0 -0.15 5 5
RAPGEF1 0.035 0.008 -10000 0 0 23 23
RASA1 0.032 0.012 -10000 0 0 64 64
NCK1 0.033 0.011 -10000 0 0 53 53
CBL/APS/CAP/Crk-II 0.061 0.028 -10000 0 -0.15 3 3
TC10/GDP 0.023 0.028 -10000 0 -0.19 9 9
Insulin Receptor/Insulin/SHC/GRB10 0.078 0.049 -10000 0 -0.16 7 7
INPP5D -0.016 0.045 0.072 7 -0.14 49 56
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.004 0.006 -10000 0 -0.026 7 7
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 8 8
IRS1 0.029 0.015 -10000 0 0 115 115
p62DOK/RasGAP 0.047 0.055 -10000 0 -10000 0 0
INS 0.038 0.018 0.086 3 -0.047 11 14
mol:PI-3-4-P2 -0.016 0.045 0.071 7 -0.14 49 56
GRB2 0.035 0.007 -10000 0 0 22 22
EIF4EBP1 0.001 0.096 0.2 41 -0.23 12 53
PTPRA 0.036 0.022 0.08 2 -0.091 7 9
PIK3CA 0.026 0.017 -10000 0 0 158 158
TC10/GTP/CIP4 0.04 0.032 -10000 0 -0.16 10 10
PDPK1 0.035 0.007 -10000 0 0 21 21
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.068 -10000 0 -0.17 54 54
Insulin Receptor/Insulin/IRS1 0.042 0.069 -10000 0 -0.15 49 49
Insulin Receptor/Insulin/IRS3 0.052 0.029 -10000 0 -0.082 1 1
Par3/Par6 0.063 0.046 -10000 0 -0.14 10 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.009 -9999 0 0 31 31
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.035 0.007 -9999 0 0 21 21
TCEB1 0.034 0.01 -9999 0 0 37 37
HIF1A/p53 0.009 0.073 -9999 0 -0.29 16 16
HIF1A 0.008 0.061 -9999 0 -0.3 11 11
COPS5 0.033 0.011 -9999 0 0 49 49
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.06 -9999 0 -0.16 23 23
FIH (dimer) 0.036 0.006 -9999 0 0 16 16
CDKN2A 0.026 0.017 -9999 0 0 151 151
ARNT/IPAS 0.047 0.019 -9999 0 -10000 0 0
HIF1AN 0.036 0.006 -9999 0 0 16 16
GNB2L1 0.035 0.008 -9999 0 0 27 27
HIF1A/ARNT 0.024 0.067 -9999 0 -0.3 12 12
CUL2 0.035 0.009 -9999 0 0 32 32
OS9 0.035 0.008 -9999 0 0 23 23
RACK1/Elongin B/Elongin C 0.06 0.043 -9999 0 -0.16 12 12
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.004 0.06 -9999 0 -0.29 12 12
PHD1-3/OS9 0.066 0.061 -9999 0 -0.16 24 24
HIF1A/RACK1/Elongin B/Elongin C 0.047 0.077 -9999 0 -0.3 10 10
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.024 0.07 -9999 0 -0.31 13 13
EGLN3 0.032 0.012 -9999 0 0 65 65
EGLN2 0.034 0.01 -9999 0 0 41 41
EGLN1 0.033 0.011 -9999 0 0 54 54
TP53 0.023 0.018 -9999 0 0 192 192
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.014 0.095 -9999 0 -0.6 10 10
ARNT 0.034 0.01 -9999 0 0 46 46
ARD1A 0.034 0.01 -9999 0 0 38 38
RBX1 0.033 0.012 -9999 0 0 58 58
HIF1A/p19ARF 0.013 0.076 -9999 0 -0.31 17 17
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.034 0.009 -10000 0 0 35 35
RAS family/GTP/Tiam1 0 0.078 -10000 0 -0.19 59 59
NT3 (dimer)/TRKC 0.04 0.024 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.061 0.025 -10000 0 -10000 0 0
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.064 -10000 0 -0.18 50 50
RAPGEF1 0.035 0.008 -10000 0 0 23 23
BDNF 0.035 0.008 -10000 0 0 26 26
PIK3CA 0.026 0.017 -10000 0 0 158 158
DYNLT1 0.034 0.01 -10000 0 0 45 45
NTRK1 0.036 0.006 -10000 0 0 15 15
NTRK2 0.036 0.007 -10000 0 0 17 17
NTRK3 0.036 0.006 -10000 0 0 12 12
NT-4/5 (dimer)/TRKB 0.047 0.012 -10000 0 -10000 0 0
neuron apoptosis -0.025 0.1 0.27 17 -0.23 2 19
SHC 2-3/Grb2 0.025 0.11 0.24 1 -0.29 17 18
SHC1 0.035 0.008 -10000 0 0 27 27
SHC2 -0.001 0.12 0.22 2 -0.35 49 51
SHC3 0.027 0.082 0.22 2 -0.38 12 14
STAT3 (dimer) -0.041 0.15 -10000 0 -0.3 126 126
NT3 (dimer)/TRKA 0.061 0.026 -10000 0 -10000 0 0
RIN/GDP 0.044 0.072 0.2 20 -0.22 10 30
GIPC1 0.031 0.014 -10000 0 0 84 84
KRAS 0.03 0.014 -10000 0 0 92 92
DNAJA3 0.012 0.057 0.18 11 -0.16 6 17
RIN/GTP 0.026 0.007 -10000 0 -10000 0 0
CCND1 -0.13 0.25 -10000 0 -0.54 136 136
MAGED1 0.035 0.008 -10000 0 0 23 23
PTPN11 0.036 0.005 -10000 0 0 8 8
RICS 0.033 0.012 -10000 0 0 59 59
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.044 0.026 -10000 0 -0.16 6 6
GRB2 0.035 0.007 -10000 0 0 22 22
NGF (dimer)/TRKA/MATK 0.044 0.016 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.049 0.017 -10000 0 -10000 0 0
ELMO1 0.034 0.009 -10000 0 0 36 36
RhoG/GTP/ELMO1/DOCK1 0.042 0.026 -10000 0 -0.15 6 6
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.01 -10000 0 0 38 38
DOCK1 0.035 0.009 -10000 0 0 31 31
GAB2 0.029 0.015 -10000 0 0 106 106
RIT2 0.035 0.009 -10000 0 0 33 33
RIT1 0.031 0.014 -10000 0 0 88 88
FRS2 0.035 0.008 -10000 0 0 25 25
DNM1 0.036 0.007 -10000 0 0 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.011 -10000 0 0 55 55
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.032 0.062 0.19 12 -0.17 5 17
mol:GDP 0.042 0.092 0.24 19 -0.31 12 31
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.007 -10000 0 -10000 0 0
RIT1/GDP 0.035 0.071 0.19 16 -0.24 9 25
TIAM1 0.034 0.011 -10000 0 0 47 47
PIK3R1 0.031 0.014 -10000 0 0 90 90
BDNF (dimer)/TRKB 0.065 0.03 -10000 0 -0.16 4 4
KIDINS220/CRKL/C3G 0.049 0.016 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.056 -10000 0 -0.19 27 27
FRS2 family/SHP2 0.068 0.022 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.059 0.033 -10000 0 -0.15 6 6
RIT1/GTP 0.012 0.05 -10000 0 -0.19 31 31
NT3 (dimer) 0.028 0.016 -10000 0 0 127 127
RAP1/GDP 0.017 0.049 -10000 0 -0.17 16 16
KIDINS220/CRKL 0.034 0.009 -10000 0 0 35 35
BDNF (dimer) 0.035 0.008 -10000 0 0 26 26
ubiquitin-dependent protein catabolic process 0.044 0.016 -10000 0 -10000 0 0
Schwann cell development -0.007 0.012 -10000 0 -0.049 10 10
EHD4 0.034 0.01 -10000 0 0 38 38
FRS2 family/GRB2/SOS1 0.061 0.03 -10000 0 -0.15 5 5
FRS2 family/SHP2/CRK family/C3G/GAB2 0.009 0.078 -10000 0 -0.22 25 25
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.007 -10000 0 0 17 17
CDC42/GTP 0.064 0.043 0.19 1 -0.14 2 3
ABL1 0.033 0.011 -10000 0 0 55 55
SH2B family/GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
Rap1/GTP 0.011 0.08 -10000 0 -0.26 22 22
STAT3 -0.041 0.15 -10000 0 -0.3 126 126
axon guidance 0.039 0.029 -10000 0 -0.14 2 2
MAPK3 -0.011 0.03 0.19 11 -10000 0 11
MAPK1 -0.009 0.031 0.19 12 -10000 0 12
CDC42/GDP 0.046 0.073 0.2 22 -0.22 10 32
NTF3 0.028 0.016 -10000 0 0 127 127
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.033 0.048 -10000 0 -0.16 28 28
PI3K 0.014 0.072 -10000 0 -0.2 46 46
FRS3 0.036 0.007 -10000 0 0 20 20
FAIM 0.031 0.013 -10000 0 0 78 78
GAB1 0.034 0.01 -10000 0 0 38 38
RASGRF1 0.012 0.057 0.18 12 -0.16 6 18
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.004 0.029 0.065 72 -10000 0 72
RGS19 0.033 0.012 -10000 0 0 60 60
CDC42 0.036 0.006 -10000 0 0 15 15
RAS family/GTP 0.026 0.1 0.28 2 -0.32 26 28
Rac1/GDP 0.045 0.073 0.2 22 -0.22 10 32
NGF (dimer)/TRKA/GRIT 0.041 0.027 -10000 0 -0.16 6 6
neuron projection morphogenesis -0.083 0.26 -10000 0 -0.88 39 39
NGF (dimer)/TRKA/NEDD4-2 0.044 0.016 -10000 0 -10000 0 0
MAP2K1 0 0.068 0.2 51 -0.14 6 57
NGFR 0.035 0.007 -10000 0 0 22 22
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.039 -10000 0 -0.18 15 15
RAS family/GTP/PI3K -0.016 0.085 -10000 0 -0.21 69 69
FRS2 family/SHP2/GRB2/SOS1 0.075 0.036 -10000 0 -0.14 5 5
NRAS 0.031 0.014 -10000 0 0 88 88
GRB2/SOS1 0.024 0.021 -10000 0 -0.19 5 5
PRKCI 0.025 0.017 -10000 0 0 168 168
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.035 0.008 -10000 0 0 28 28
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.11 -10000 0 -0.44 27 27
RASA1 0.032 0.012 -10000 0 0 64 64
TRKA/c-Abl 0.036 0.059 -10000 0 -0.19 31 31
SQSTM1 0.033 0.011 -10000 0 0 50 50
BDNF (dimer)/TRKB/GIPC 0.068 0.049 -10000 0 -0.15 9 9
NGF (dimer)/TRKA/p62/Atypical PKCs 0.032 0.056 -10000 0 -0.14 35 35
MATK 0.033 0.011 -10000 0 0 52 52
NEDD4L 0.034 0.01 -10000 0 0 44 44
RAS family/GDP -0.013 0.04 -10000 0 -0.14 29 29
NGF (dimer)/TRKA 0.003 0.047 0.18 11 -0.17 6 17
Rac1/GTP -0.01 0.053 -10000 0 -0.18 25 25
FRS2 family/SHP2/CRK family 0.086 0.047 -10000 0 -0.15 2 2
Caspase cascade in apoptosis

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
TOP1 0.014 0.11 0.27 3 -0.39 16 19
ACTA1 0.012 0.077 0.19 29 -0.21 8 37
NUMA1 0.02 0.1 0.27 3 -0.39 15 18
SPTAN1 0.005 0.078 0.22 11 -0.21 7 18
LIMK1 0.009 0.075 0.21 12 -0.21 5 17
BIRC3 0.026 0.017 -10000 0 0 151 151
BIRC2 0.034 0.01 -10000 0 0 41 41
BAX 0.034 0.009 -10000 0 0 36 36
CASP10 -0.011 0.021 0.055 42 -10000 0 42
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.002 0.14 0.26 4 -0.47 25 29
DIABLO 0.035 0.008 -10000 0 0 26 26
apoptotic nuclear changes 0.005 0.078 0.22 11 -0.21 7 18
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.037 0.004 -10000 0 0 6 6
GSN 0.005 0.077 0.2 16 -0.22 8 24
MADD 0.037 0.003 -10000 0 0 4 4
TFAP2A 0.028 0.12 -10000 0 -0.84 7 7
BID -0.005 0.053 -10000 0 -0.2 32 32
MAP3K1 -0.01 0.12 -10000 0 -0.37 45 45
TRADD 0.033 0.012 -10000 0 0 57 57
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.052 0.016 -10000 0 -0.19 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.008 0.096 0.23 38 -0.22 17 55
CASP9 0.035 0.007 -10000 0 0 20 20
DNA repair -0.013 0.063 0.26 8 -0.15 33 41
neuron apoptosis -0.007 0.17 -10000 0 -0.65 29 29
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.014 0.093 0.28 3 -0.34 14 17
APAF1 0.036 0.004 -10000 0 0 6 6
CASP6 -0.018 0.24 -10000 0 -0.9 34 34
TRAF2 0.035 0.009 -10000 0 0 30 30
ICAD/CAD 0.003 0.076 0.24 7 -0.24 3 10
CASP7 -0.01 0.12 0.2 39 -0.32 32 71
KRT18 -0.004 0.14 -10000 0 -0.55 25 25
apoptosis -0.012 0.13 0.32 10 -0.4 30 40
DFFA 0.007 0.079 0.24 8 -0.24 4 12
DFFB 0.01 0.074 0.2 16 -0.21 5 21
PARP1 0.013 0.063 0.15 33 -0.27 8 41
actin filament polymerization -0.009 0.071 0.2 5 -0.19 12 17
TNF 0.033 0.011 -10000 0 0 51 51
CYCS 0.004 0.065 0.15 14 -0.23 22 36
SATB1 -0.032 0.23 -10000 0 -0.85 34 34
SLK 0.006 0.078 0.2 23 -0.2 8 31
p15 BID/BAX 0.014 0.072 0.15 5 -0.16 61 66
CASP2 0.014 0.091 0.23 20 -0.29 22 42
JNK cascade 0.01 0.12 0.36 45 -10000 0 45
CASP3 0.014 0.08 0.2 28 -0.21 7 35
LMNB2 -0.017 0.19 0.24 6 -0.44 66 72
RIPK1 0.035 0.008 -10000 0 0 26 26
CASP4 0.03 0.014 -10000 0 0 94 94
Mammalian IAPs/DIABLO 0.032 0.077 -10000 0 -0.15 71 71
negative regulation of DNA binding 0.029 0.12 -10000 0 -0.82 7 7
stress fiber formation 0.006 0.078 0.2 25 -0.2 8 33
GZMB -0.009 0.022 0.06 43 -10000 0 43
CASP1 -0.048 0.15 -10000 0 -0.35 89 89
LMNB1 -0.009 0.17 0.28 2 -0.49 36 38
APP -0.007 0.17 -10000 0 -0.66 29 29
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.008 0.002 0.001 23 -10000 0 23
VIM -0.006 0.14 0.31 10 -0.41 32 42
LMNA 0.01 0.14 0.27 3 -0.46 26 29
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.086 -10000 0 -0.3 23 23
LRDD 0.035 0.008 -10000 0 0 29 29
SREBF1 0.011 0.076 0.22 14 -0.2 5 19
APAF-1/Caspase 9 0.024 0.12 0.31 2 -0.68 13 15
nuclear fragmentation during apoptosis 0.02 0.099 0.27 3 -0.38 15 18
CFL2 0.009 0.072 0.2 11 -0.2 5 16
GAS2 0.011 0.077 0.22 15 -0.21 5 20
positive regulation of apoptosis -0.007 0.16 0.25 4 -0.48 41 45
PRF1 0.034 0.01 -10000 0 0 46 46
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.008 0.027 6 -0.03 6 12
BUB1B -0.025 0.086 0.095 1 -0.24 58 59
PLK1 0.005 0.022 0.077 4 -0.071 7 11
PLK1S1 0.002 0.013 0.044 6 -0.04 6 12
KIF2A 0.005 0.019 0.068 4 -0.064 7 11
regulation of mitotic centrosome separation 0.005 0.022 0.077 4 -0.071 7 11
GOLGA2 0.035 0.009 -10000 0 0 34 34
Hec1/SPC24 -0.004 0.011 -10000 0 -0.058 9 9
WEE1 -0.01 0.091 -10000 0 -0.41 19 19
cytokinesis -0.035 0.13 -10000 0 -0.34 73 73
PP2A-alpha B56 0.057 0.079 -10000 0 -0.61 4 4
AURKA 0.002 0.015 0.05 6 -0.044 8 14
PICH/PLK1 -0.034 0.092 -10000 0 -0.2 103 103
CENPE 0.001 0.025 0.14 3 -0.14 1 4
RhoA/GTP 0.012 0.054 -10000 0 -0.19 36 36
positive regulation of microtubule depolymerization 0.005 0.019 0.067 4 -0.064 7 11
PPP2CA 0.035 0.009 -10000 0 0 30 30
FZR1 0.033 0.011 -10000 0 0 55 55
TPX2 -0.023 0.091 -10000 0 -0.24 77 77
PAK1 0.033 0.011 -10000 0 0 49 49
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.036 0.007 -10000 0 0 17 17
CLSPN 0.014 0.016 -10000 0 -0.19 1 1
GORASP1 0.036 0.006 -10000 0 0 16 16
metaphase 0 0.002 0.014 6 -0.014 5 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.044 6 -0.04 6 12
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.036 0.005 -10000 0 0 9 9
GRASP65/GM130/RAB1/GTP -0.003 0.11 -10000 0 -0.62 12 12
spindle elongation 0.005 0.022 0.077 4 -0.071 7 11
ODF2 0.035 0.008 -10000 0 0 26 26
BUB1 0.026 0.065 -10000 0 -0.65 4 4
TPT1 0.003 0.042 -10000 0 -0.18 23 23
CDC25C 0.012 0.034 -10000 0 -0.26 7 7
CDC25B 0.02 0.032 -10000 0 -0.034 76 76
SGOL1 0 0.008 0.03 6 -0.027 6 12
RHOA 0.034 0.01 -10000 0 0 43 43
CCNB1/CDK1 -0.009 0.14 -10000 0 -0.26 113 113
CDC14B -0.009 0.004 0.01 19 -10000 0 19
CDC20 0.03 0.015 -10000 0 0 100 100
PLK1/PBIP1 -0.01 0.046 -10000 0 -0.13 60 60
mitosis -0.001 0.003 0.011 6 -10000 0 6
FBXO5 -0.013 0.061 0.11 4 -0.19 39 43
CDC2 0.022 0.031 -10000 0 -0.034 67 67
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.003 0.055 -10000 0 -0.26 21 21
ERCC6L -0.04 0.12 -10000 0 -0.25 113 113
NLP/gamma Tubulin 0.001 0.028 0.062 3 -0.095 30 33
microtubule cytoskeleton organization 0.003 0.042 -10000 0 -0.18 23 23
G2/M transition DNA damage checkpoint -0.001 0.001 0.016 1 -10000 0 1
PPP1R12A 0.036 0.006 -10000 0 0 13 13
interphase -0.001 0.001 0.016 1 -10000 0 1
PLK1/PRC1-2 0.003 0.095 -10000 0 -0.18 95 95
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.058 -10000 0 -0.14 33 33
RAB1A 0.035 0.009 -10000 0 0 32 32
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.018 0.057 11 -0.05 6 17
mitotic prometaphase -0.001 0.004 0.019 21 -10000 0 21
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.072 -10000 0 -0.39 9 9
microtubule-based process 0.019 0.038 0.096 1 -0.16 13 14
Golgi organization 0.005 0.022 0.077 4 -0.071 7 11
Cohesin/SA2 0.021 0.03 -10000 0 -0.11 11 11
PPP1CB/MYPT1 0.048 0.034 -10000 0 -0.22 7 7
KIF20A 0.029 0.015 -10000 0 0 113 113
APC/C/CDC20 0.02 0.039 0.096 1 -0.16 13 14
PPP2R1A 0.035 0.009 -10000 0 0 33 33
chromosome segregation -0.01 0.045 -10000 0 -0.13 60 60
PRC1 0.03 0.014 -10000 0 0 94 94
ECT2 0.038 0.11 0.22 126 -0.14 57 183
C13orf34 0.004 0.019 0.065 7 -0.055 7 14
NUDC 0.003 0.055 -10000 0 -0.26 21 21
regulation of attachment of spindle microtubules to kinetochore -0.025 0.085 0.095 1 -0.24 58 59
spindle assembly 0.003 0.023 0.07 5 -0.078 14 19
spindle stabilization 0.002 0.013 0.044 6 -0.04 6 12
APC/C/HCDH1 0.028 0.011 -10000 0 -10000 0 0
MKLP2/PLK1 0.019 0.038 0.096 1 -0.17 13 14
CCNB1 0.023 0.031 -10000 0 -0.038 54 54
PPP1CB 0.036 0.007 -10000 0 0 20 20
BTRC 0.036 0.006 -10000 0 0 14 14
ROCK2 0.009 0.052 -10000 0 -0.27 3 3
TUBG1 -0.001 0.056 -10000 0 -0.21 32 32
G2/M transition of mitotic cell cycle -0.046 0.12 0.14 2 -0.25 113 115
MLF1IP -0.007 0.015 0.013 2 -0.19 3 5
INCENP 0.036 0.004 -10000 0 0 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.033 0.011 -10000 0 0 52 52
HDAC4 0.033 0.011 -10000 0 0 51 51
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.006 0.024 -10000 0 -0.13 15 15
CDKN1A 0.003 0.1 0.32 4 -0.53 13 17
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.034 0.009 -10000 0 0 36 36
FOXO3 -0.001 0.034 0.28 6 -10000 0 6
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.021 -10000 0 -0.21 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.011 -10000 0 0 52 52
TAT 0.033 0.012 -10000 0 0 59 59
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.001 -10000 0 -10000 0 0
PPARGC1A 0.035 0.009 -10000 0 0 30 30
FHL2 0.029 0.015 -10000 0 0 107 107
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.041 0.049 0.17 11 -0.2 16 27
HIST2H4A -0.006 0.024 0.13 15 -10000 0 15
SIRT1/FOXO3a 0.034 0.042 0.16 29 -0.2 1 30
SIRT1 0.03 0.053 0.2 13 -0.28 11 24
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.056 0.059 0.18 11 -0.18 24 35
SIRT1/Histone H1b 0.021 0.065 0.16 11 -0.22 18 29
apoptosis -0.056 0.05 0.17 16 -0.18 11 27
SIRT1/PGC1A 0.04 0.04 0.15 10 -0.16 15 25
p53/SIRT1 -0.019 0.12 0.36 11 -0.2 134 145
SIRT1/FOXO4 0.015 0.061 0.15 11 -0.2 21 32
FOXO1/FHL2/SIRT1 0.015 0.071 0.14 12 -0.15 76 88
HIST1H1E 0.013 0.022 -10000 0 -0.2 5 5
SIRT1/p300 0.04 0.054 0.17 11 -0.2 19 30
muscle cell differentiation -0.016 0.038 0.16 15 -0.14 15 30
TP53 -0.04 0.14 0.2 12 -0.28 119 131
KU70/SIRT1/BAX 0.057 0.05 0.18 11 -0.17 16 27
CREBBP 0.035 0.009 -10000 0 0 32 32
MEF2D 0.036 0.007 -10000 0 0 18 18
HIV-1 Tat/SIRT1 0.041 0.048 0.17 10 -0.2 15 25
ACSS2 -0.006 0.024 0.13 15 -10000 0 15
SIRT1/PCAF/MYOD 0.016 0.038 0.14 15 -0.16 15 30
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.046 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.008 -10000 0 0 26 26
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.006 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.033 0.012 -10000 0 0 60 60
RAC1-CDC42/GTP/PAK family 0.014 0.022 -10000 0 -0.17 5 5
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.01 -10000 0 0 42 42
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.006 -10000 0 0 16 16
FYN 0.028 0.016 -10000 0 0 131 131
MAP3K12 0.036 0.005 -10000 0 0 8 8
FGR 0.035 0.009 -10000 0 0 30 30
p38 alpha/TAB1 -0.001 0.11 0.19 2 -0.27 38 40
PRKG1 0.036 0.005 -10000 0 0 10 10
DUSP8 0.035 0.009 -10000 0 0 31 31
PGK/cGMP/p38 alpha -0.002 0.11 0.18 1 -0.27 38 39
apoptosis -0.001 0.1 0.18 2 -0.26 38 40
RAL/GTP 0.036 0.05 -10000 0 -0.16 31 31
LYN 0.029 0.015 -10000 0 0 106 106
DUSP1 0.03 0.015 -10000 0 0 104 104
PAK1 0.033 0.011 -10000 0 0 49 49
SRC 0.035 0.008 -10000 0 0 25 25
RAC1/OSM/MEKK3/MKK3 0.06 0.028 -10000 0 -0.15 2 2
TRAF6 0.036 0.005 -10000 0 0 9 9
RAC1 0.035 0.008 -10000 0 0 28 28
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 0.046 0.016 -10000 0 -0.16 1 1
MAPK11 -0.026 0.12 -10000 0 -0.3 40 40
BLK 0.029 0.015 -10000 0 0 105 105
HCK 0.031 0.014 -10000 0 0 88 88
MAP2K3 0.034 0.01 -10000 0 0 43 43
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.033 0.012 -10000 0 0 60 60
TRAF6/MEKK3 0.045 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0.034 0.011 -10000 0 0 48 48
MAPK14 -0.011 0.11 0.19 2 -0.29 42 44
positive regulation of innate immune response -0.022 0.13 -10000 0 -0.34 41 41
LCK 0.035 0.008 -10000 0 0 26 26
p38alpha-beta/MKP7 -0.024 0.12 -10000 0 -0.33 41 41
p38alpha-beta/MKP5 -0.014 0.13 -10000 0 -0.34 39 39
PGK/cGMP 0.027 0.004 -10000 0 -10000 0 0
PAK2 0.03 0.014 -10000 0 0 97 97
p38alpha-beta/MKP1 -0.019 0.13 -10000 0 -0.34 42 42
CDC42 0.036 0.006 -10000 0 0 15 15
RALB 0.035 0.007 -10000 0 0 21 21
RALA 0.035 0.008 -10000 0 0 28 28
PAK3 0.035 0.007 -10000 0 0 22 22
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.065 0.053 -10000 0 -0.14 15 15
MAP4K1 0.031 0.013 -10000 0 0 79 79
MAP3K8 0.032 0.012 -10000 0 0 68 68
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.009 -10000 0 0 35 35
MAP3K1 0.012 0.051 -10000 0 -0.19 18 18
JUN 0.004 0.076 0.22 2 -0.52 7 9
MAP3K7 0.014 0.054 0.19 5 -0.17 18 23
GRAP2 0.033 0.011 -10000 0 0 49 49
CRK 0.033 0.011 -10000 0 0 55 55
MAP2K4 0.005 0.076 0.19 2 -0.29 15 17
LAT 0.036 0.005 -10000 0 0 8 8
LCP2 0.031 0.013 -10000 0 0 80 80
MAPK8 0.014 0.069 -10000 0 -0.53 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.053 -10000 0 -0.17 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 0.06 0.049 -10000 0 -0.13 15 15
S1P5 pathway

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.002 0.088 0.24 35 -10000 0 35
GNAI2 0.036 0.007 -10000 0 0 20 20
S1P/S1P5/G12 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.011 -10000 0 0 47 47
RhoA/GTP 0.003 0.09 -10000 0 -0.24 35 35
negative regulation of cAMP metabolic process 0 0.072 -10000 0 -0.2 46 46
GNAZ 0.034 0.01 -10000 0 0 46 46
GNAI3 0.036 0.007 -10000 0 0 20 20
GNA12 0.034 0.009 -10000 0 0 36 36
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0 0.072 -10000 0 -0.2 46 46
RhoA/GDP 0.012 0.054 -10000 0 -0.19 36 36
RHOA 0.034 0.01 -10000 0 0 43 43
GNAI1 0.031 0.014 -10000 0 0 83 83
Atypical NF-kappaB pathway

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
BCL3/RelA 0.05 0.016 -10000 0 -10000 0 0
FBXW11 0.036 0.007 -10000 0 0 17 17
NF kappa B1 p50/c-Rel 0.027 0.036 -10000 0 -0.16 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.079 0.26 1 -0.26 15 16
NFKBIA 0.003 0.067 -10000 0 -0.17 53 53
MAPK14 0.036 0.006 -10000 0 0 13 13
NF kappa B1 p105/p50 0.027 0.037 -10000 0 -0.16 16 16
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL 0.036 0.005 -10000 0 0 11 11
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.034 -10000 0 -0.16 13 13
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.037 -10000 0 -0.16 16 16
PIK3CA 0.026 0.017 -10000 0 0 158 158
NF kappa B1 p50 dimer 0.018 0.039 -10000 0 -0.19 16 16
PIK3R1 0.031 0.014 -10000 0 0 90 90
NFKB1 -0.019 0.033 -10000 0 -0.19 16 16
RELA 0.036 0.004 -10000 0 0 7 7
positive regulation of anti-apoptosis 0.009 0.054 -10000 0 -0.15 40 40
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.015 0.081 0.22 1 -0.26 16 17
SRC 0.035 0.008 -10000 0 0 25 25
PI3K 0.014 0.072 -10000 0 -0.2 46 46
NF kappa B1 p50/RelA 0.009 0.054 -10000 0 -0.15 40 40
IKBKB 0.034 0.01 -10000 0 0 40 40
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.007 -10000 0 0 17 17
SYK 0.031 0.014 -10000 0 0 83 83
I kappa B alpha/PIK3R1 0.011 0.076 0.26 1 -0.18 54 55
cell death 0.015 0.078 0.22 1 -0.25 16 17
NF kappa B1 p105/c-Rel 0.027 0.036 -10000 0 -0.16 15 15
LCK 0.035 0.008 -10000 0 0 26 26
BCL3 0.034 0.01 -10000 0 0 39 39
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.036 -10000 0 -0.15 10 10
HDAC3 0.036 0.006 -10000 0 0 16 16
Ran/GTP/Exportin 1/HDAC4 -0.028 0.037 -10000 0 -0.14 50 50
GATA1/HDAC4 0.045 0.041 -10000 0 -0.19 13 13
GATA1/HDAC5 0.052 0.013 -10000 0 -10000 0 0
GATA2/HDAC5 0.049 0.017 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.044 0.061 -10000 0 -0.17 30 30
HDAC9 0.028 0.016 -10000 0 0 119 119
Glucocorticoid receptor/Hsp90/HDAC6 0.032 0.056 -10000 0 -0.16 41 41
HDAC4/ANKRA2 0.036 0.049 -10000 0 -0.19 19 19
HDAC5/YWHAB 0.045 0.031 -10000 0 -0.19 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.04 -10000 0 -0.16 27 27
GATA2 0.035 0.008 -10000 0 0 26 26
HDAC4/RFXANK 0.027 0.068 -10000 0 -0.2 40 40
BCOR 0.036 0.007 -10000 0 0 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.035 0.008 -10000 0 0 29 29
GNB1/GNG2 0.022 0.03 -10000 0 -0.19 10 10
Histones 0.005 0.059 -10000 0 -0.16 45 45
ADRBK1 0.037 0.004 -10000 0 0 5 5
HDAC4 0.033 0.011 -10000 0 0 51 51
XPO1 0.036 0.006 -10000 0 0 13 13
HDAC5/ANKRA2 0.043 0.032 -10000 0 -0.19 6 6
HDAC4/Ubc9 0.043 0.041 -10000 0 -0.19 13 13
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.027 -10000 0 -0.17 4 4
TUBA1B 0 0 </