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

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

Summary

There were 35 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
IL4-mediated signaling events 47
Signaling events mediated by the Hedgehog family 40
Signaling mediated by p38-alpha and p38-beta 39
Endothelins 34
FOXA2 and FOXA3 transcription factor networks 33
IL23-mediated signaling events 30
TCGA08_retinoblastoma 28
EGFR-dependent Endothelin signaling events 27
HIF-1-alpha transcription factor network 25
p75(NTR)-mediated signaling 24
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
IL4-mediated signaling events 47 4350 91 -0.65 0.58 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 40 2092 52 -0.12 0.08 1000 -1000 -0.034 -1000
Signaling mediated by p38-alpha and p38-beta 39 1725 44 -0.12 0.028 1000 -1000 -0.033 -1000
Endothelins 34 3332 96 -0.12 0.044 1000 -1000 -0.063 -1000
FOXA2 and FOXA3 transcription factor networks 33 1518 46 -0.32 0.037 1000 -1000 -0.13 -1000
IL23-mediated signaling events 30 1850 60 -0.3 0.028 1000 -1000 -0.12 -1000
TCGA08_retinoblastoma 28 230 8 -0.035 0.048 1000 -1000 -0.005 -1000
EGFR-dependent Endothelin signaling events 27 580 21 -0.059 0.04 1000 -1000 -0.04 -1000
HIF-1-alpha transcription factor network 25 1902 76 -0.24 0.036 1000 -1000 -0.12 -1000
p75(NTR)-mediated signaling 24 3108 125 -0.088 0.064 1000 -1000 -0.068 -1000
Fc-epsilon receptor I signaling in mast cells 23 2298 97 -0.09 0.037 1000 -1000 -0.057 -1000
Wnt signaling 23 165 7 -0.058 0.02 1000 -1000 -0.015 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 23 1567 68 -0.2 0.063 1000 -1000 -0.099 -1000
Visual signal transduction: Rods 23 1196 52 -0.083 0.027 1000 -1000 -0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 22 756 34 -0.023 0.028 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 22 779 34 -0.085 0.027 1000 -1000 -0.04 -1000
Osteopontin-mediated events 22 846 38 -0.087 0.033 1000 -1000 -0.034 -1000
Glucocorticoid receptor regulatory network 22 2580 114 -0.28 0.12 1000 -1000 -0.047 -1000
Signaling events regulated by Ret tyrosine kinase 22 1825 82 -0.058 0.028 1000 -1000 -0.048 -1000
Noncanonical Wnt signaling pathway 21 564 26 -0.061 0.027 1000 -1000 -0.038 -1000
BMP receptor signaling 21 1722 81 -0.076 0.051 1000 -1000 -0.042 -1000
Calcium signaling in the CD4+ TCR pathway 21 674 31 -0.16 0.027 1000 -1000 -0.045 -1000
FOXM1 transcription factor network 21 1095 51 -0.16 0.03 1000 -1000 -0.16 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 21 1714 78 -0.1 0.044 1000 -1000 -0.062 -1000
Arf6 signaling events 20 1293 62 -0.059 0.043 1000 -1000 -0.038 -1000
LPA receptor mediated events 20 2065 102 -0.074 0.039 1000 -1000 -0.088 -1000
Visual signal transduction: Cones 19 759 38 -0.088 0.031 1000 -1000 -0.012 -1000
amb2 Integrin signaling 19 1603 82 -0.11 0.034 1000 -1000 -0.036 -1000
Glypican 2 network 19 79 4 -0.003 -0.001 1000 -1000 0.01 -1000
IL12-mediated signaling events 18 1645 87 -0.11 0.03 1000 -1000 -0.072 -1000
Ephrin B reverse signaling 18 871 48 -0.073 0.028 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 18 1701 93 -0.026 0.04 1000 -1000 -0.049 -1000
Effects of Botulinum toxin 18 481 26 -0.043 0.026 1000 -1000 -0.004 -1000
Syndecan-4-mediated signaling events 18 1211 67 -0.074 0.035 1000 -1000 -0.039 -1000
Neurotrophic factor-mediated Trk receptor signaling 18 2205 120 -0.1 0.084 1000 -1000 -0.047 -1000
Thromboxane A2 receptor signaling 17 1821 105 -0.059 0.035 1000 -1000 -0.048 -1000
Glypican 1 network 17 838 48 -0.052 0.039 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 17 1484 86 -0.077 0.072 1000 -1000 -0.053 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 16 1416 85 -0.047 0.028 1000 -1000 -0.051 -1000
RXR and RAR heterodimerization with other nuclear receptor 16 834 52 -0.066 0.051 1000 -1000 -0.037 -1000
S1P1 pathway 16 576 36 -0.13 0.027 1000 -1000 -0.045 -1000
EPHB forward signaling 16 1434 85 -0.078 0.074 1000 -1000 -0.059 -1000
BCR signaling pathway 16 1673 99 -0.086 0.045 1000 -1000 -0.063 -1000
Reelin signaling pathway 15 840 56 -0.055 0.053 1000 -1000 -0.041 -1000
Canonical Wnt signaling pathway 15 773 51 -0.11 0.067 1000 -1000 -0.053 -1000
IL27-mediated signaling events 15 790 51 -0.12 0.065 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 14 754 52 -0.038 0.044 1000 -1000 -0.034 -1000
Angiopoietin receptor Tie2-mediated signaling 14 1268 88 -0.064 0.035 1000 -1000 -0.062 -1000
Aurora B signaling 14 997 67 -0.14 0.028 1000 -1000 -0.029 -1000
ErbB2/ErbB3 signaling events 13 888 65 -0.057 0.039 1000 -1000 -0.059 -1000
Ephrin A reverse signaling 13 95 7 -0.013 0.013 1000 -1000 -0.007 -1000
Syndecan-2-mediated signaling events 13 909 69 -0.054 0.042 1000 -1000 -0.041 -1000
Signaling events mediated by PTP1B 13 1003 76 -0.059 0.033 1000 -1000 -0.045 -1000
Nectin adhesion pathway 13 835 63 -0.05 0.057 1000 -1000 -0.062 -1000
IL6-mediated signaling events 13 1021 75 -0.32 0.053 1000 -1000 -0.064 -1000
FAS signaling pathway (CD95) 12 573 47 -0.051 0.041 1000 -1000 -0.038 -1000
Regulation of Androgen receptor activity 12 885 70 -0.12 0.034 1000 -1000 -0.046 -1000
Presenilin action in Notch and Wnt signaling 11 707 61 -0.11 0.06 1000 -1000 -0.047 -1000
Ceramide signaling pathway 11 864 76 -0.059 0.062 1000 -1000 -0.044 -1000
IL1-mediated signaling events 11 688 62 -0.044 0.055 1000 -1000 -0.045 -1000
TCGA08_p53 11 82 7 -0.022 0.024 1000 -1000 -0.011 -1000
Integrins in angiogenesis 11 970 84 -0.051 0.056 1000 -1000 -0.046 -1000
Caspase cascade in apoptosis 10 789 74 -0.061 0.049 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 577 54 -0.057 0.039 1000 -1000 -0.043 -1000
PLK1 signaling events 10 853 85 -0.028 0.042 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 10 781 74 -0.098 0.055 1000 -1000 -0.067 -1000
LPA4-mediated signaling events 9 110 12 -0.037 0.027 1000 -1000 -0.025 -1000
Coregulation of Androgen receptor activity 9 719 76 -0.098 0.048 1000 -1000 -0.025 -1000
IFN-gamma pathway 9 652 68 -0.032 0.039 1000 -1000 -0.049 -1000
HIF-2-alpha transcription factor network 9 420 43 -0.036 0.047 1000 -1000 -0.067 -1000
Signaling mediated by p38-gamma and p38-delta 9 135 15 -0.014 0.026 1000 -1000 -0.033 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 424 45 -0.021 0.059 1000 -1000 -0.056 -1000
IGF1 pathway 9 542 57 -0.023 0.054 1000 -1000 -0.035 -1000
S1P4 pathway 9 229 25 -0.019 0.039 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 8 326 39 -0.034 0.031 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 8 522 65 -0.18 0.063 1000 -1000 -0.049 -1000
Regulation of p38-alpha and p38-beta 8 484 54 -0.051 0.056 1000 -1000 -0.05 -1000
ErbB4 signaling events 7 504 69 -0.11 0.04 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 7 209 28 -0.018 0.036 1000 -1000 -0.024 -1000
JNK signaling in the CD4+ TCR pathway 7 122 17 0.001 0.048 1000 -1000 -0.036 -1000
S1P5 pathway 7 122 17 -0.017 0.027 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 7 903 125 -0.011 0.053 1000 -1000 -0.044 -1000
Class I PI3K signaling events 7 517 73 -0.052 0.052 1000 -1000 -0.043 -1000
Regulation of Telomerase 7 780 102 -0.1 0.065 1000 -1000 -0.055 -1000
Aurora C signaling 6 48 7 0 0.014 1000 -1000 -0.023 -1000
mTOR signaling pathway 6 353 53 -0.067 0.032 1000 -1000 -0.035 -1000
ceramide signaling pathway 6 342 49 -0.011 0.034 1000 -1000 -0.046 -1000
IL2 signaling events mediated by PI3K 6 371 58 -0.023 0.045 1000 -1000 -0.048 -1000
Insulin Pathway 6 505 74 -0.051 0.057 1000 -1000 -0.047 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 199 33 -0.05 0.067 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 6 637 97 -0.099 0.067 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 6 18 3 -0.016 0.016 1000 -1000 -0.012 -1000
Ras signaling in the CD4+ TCR pathway 6 114 17 0 0.044 1000 -1000 -0.027 -1000
Regulation of nuclear SMAD2/3 signaling 5 695 136 -0.15 0.066 1000 -1000 -0.055 -1000
a4b1 and a4b7 Integrin signaling 5 25 5 0.019 0.035 1000 -1000 0.011 -1000
Aurora A signaling 5 331 60 -0.02 0.05 1000 -1000 -0.023 -1000
Arf6 downstream pathway 5 238 43 -0.038 0.044 1000 -1000 -0.026 -1000
EPO signaling pathway 5 298 55 0.007 0.061 1000 -1000 -0.04 -1000
PDGFR-alpha signaling pathway 5 261 44 -0.041 0.049 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 5 203 40 -0.051 0.052 1000 -1000 -0.026 -1000
Retinoic acid receptors-mediated signaling 5 297 58 -0.039 0.053 1000 -1000 -0.052 -1000
TCGA08_rtk_signaling 5 144 26 -0.029 0.052 1000 -1000 -0.011 -1000
IL2 signaling events mediated by STAT5 5 115 22 -0.018 0.028 1000 -1000 -0.048 -1000
S1P3 pathway 5 249 42 -0.016 0.045 1000 -1000 -0.049 -1000
Signaling events mediated by PRL 5 187 34 -0.044 0.04 1000 -1000 -0.037 -1000
PLK2 and PLK4 events 4 12 3 0.005 -1000 1000 -1000 -0.01 -1000
TRAIL signaling pathway 4 234 48 0 0.055 1000 -1000 -0.033 -1000
FoxO family signaling 4 305 64 -0.039 0.056 1000 -1000 -0.07 -1000
Syndecan-3-mediated signaling events 4 146 35 -0.021 0.06 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 4 348 76 -0.014 0.06 1000 -1000 -0.058 -1000
VEGFR1 specific signals 4 234 56 -0.021 0.056 1000 -1000 -0.045 -1000
E-cadherin signaling in keratinocytes 4 175 43 -0.018 0.045 1000 -1000 -0.036 -1000
BARD1 signaling events 3 197 57 -0.053 0.06 1000 -1000 -0.046 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 142 37 -0.02 0.062 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 3 284 83 -0.009 0.053 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class I 3 399 104 -0.044 0.062 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 3 119 36 -0.049 0.051 1000 -1000 -0.032 -1000
Rapid glucocorticoid signaling 3 60 20 -0.006 0.033 1000 -1000 -0.004 -1000
E-cadherin signaling events 3 19 5 0.02 0.045 1000 -1000 0.01 -1000
p38 MAPK signaling pathway 3 165 44 -0.03 0.045 1000 -1000 -0.025 -1000
Canonical NF-kappaB pathway 2 110 39 -0.011 0.059 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class II 2 186 75 -0.031 0.068 1000 -1000 -0.034 -1000
Circadian rhythm pathway 2 54 22 -0.007 0.045 1000 -1000 -0.057 -1000
Class I PI3K signaling events mediated by Akt 2 201 68 -0.041 0.064 1000 -1000 -0.036 -1000
Arf6 trafficking events 2 175 71 -0.043 0.049 1000 -1000 -0.029 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 31 23 0.005 0.047 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 1 54 32 0 0.05 1000 -1000 -0.038 -1000
Atypical NF-kappaB pathway 1 57 31 0 0.038 1000 -1000 -0.022 -1000
Arf1 pathway 1 72 54 -0.001 0.042 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 5 27 0 0.057 1000 -1000 -0.032 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.073 1000 -1000 0 -1000
Total 1579 97533 7203 -8.7 -990 131000 -131000 -5.5 -131000
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.56 -10000 0 -1.3 89 89
STAT6 (cleaved dimer) -0.51 0.58 -10000 0 -1.3 98 98
IGHG1 -0.16 0.2 -10000 0 -0.48 42 42
IGHG3 -0.48 0.53 -10000 0 -1.2 107 107
AKT1 -0.24 0.31 -10000 0 -0.97 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.33 -10000 0 -1.1 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.25 0.34 -10000 0 -1 35 35
THY1 -0.51 0.57 -10000 0 -1.3 88 88
MYB 0.014 0.065 -10000 0 -0.26 14 14
HMGA1 0.021 0.044 -10000 0 -0.22 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.29 0.36 -10000 0 -0.83 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.34 -10000 0 -1 34 34
SP1 0.028 0.02 -10000 0 -10000 0 0
INPP5D 0.017 0.072 -10000 0 -0.48 7 7
SOCS5 0.039 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.57 -10000 0 -1.3 94 94
SOCS1 -0.31 0.33 -10000 0 -0.77 88 88
SOCS3 -0.24 0.29 -10000 0 -0.88 27 27
FCER2 -0.46 0.56 -10000 0 -1.4 79 79
PARP14 0.023 0.04 -10000 0 -0.48 2 2
CCL17 -0.57 0.63 -10000 0 -1.4 101 101
GRB2 0.027 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.26 -10000 0 -0.76 32 32
T cell proliferation -0.5 0.58 -10000 0 -1.3 95 95
IL4R/JAK1 -0.5 0.56 -10000 0 -1.3 92 92
EGR2 -0.52 0.58 -10000 0 -1.4 92 92
JAK2 -0.023 0.043 -10000 0 -10000 0 0
JAK3 0.027 0.029 -10000 0 -0.46 1 1
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
JAK1 0 0.036 -10000 0 -0.48 1 1
COL1A2 -0.15 0.25 -10000 0 -1.4 9 9
CCL26 -0.58 0.62 -10000 0 -1.4 110 110
IL4R -0.54 0.6 -10000 0 -1.4 92 92
PTPN6 0.035 0.031 -10000 0 -0.47 1 1
IL13RA2 -0.58 0.64 -10000 0 -1.4 108 108
IL13RA1 -0.023 0.046 -10000 0 -10000 0 0
IRF4 -0.17 0.4 -10000 0 -1.3 31 31
ARG1 -0.14 0.2 -10000 0 -0.75 18 18
CBL -0.28 0.33 -10000 0 -0.78 65 65
GTF3A 0.023 0.029 -10000 0 -0.16 1 1
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.026 0.059 -10000 0 -10000 0 0
IRF4/BCL6 -0.15 0.36 -10000 0 -1.2 31 31
CD40LG -0.016 0.14 -10000 0 -0.49 26 26
MAPK14 -0.27 0.33 -10000 0 -0.82 54 54
mitosis -0.22 0.29 -10000 0 -0.89 33 33
STAT6 -0.62 0.79 -10000 0 -1.6 104 104
SPI1 0.016 0.077 -10000 0 -0.48 8 8
RPS6KB1 -0.22 0.28 -10000 0 -0.87 31 31
STAT6 (dimer) -0.62 0.8 -10000 0 -1.6 104 104
STAT6 (dimer)/PARP14 -0.56 0.65 -10000 0 -1.4 107 107
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.36 -10000 0 -1 44 44
FRAP1 -0.24 0.31 -10000 0 -0.97 33 33
LTA -0.51 0.58 -10000 0 -1.3 90 90
FES 0.022 0.054 -10000 0 -0.48 4 4
T-helper 1 cell differentiation 0.58 0.68 1.5 104 -10000 0 104
CCL11 -0.55 0.6 -10000 0 -1.4 108 108
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.35 -10000 0 -1.1 34 34
IL2RG 0.015 0.081 -10000 0 -0.47 9 9
IL10 -0.5 0.58 -10000 0 -1.4 88 88
IRS1 0.015 0.081 -10000 0 -0.48 9 9
IRS2 0.015 0.061 -10000 0 -0.22 16 16
IL4 -0.11 0.11 -10000 0 -0.24 82 82
IL5 -0.5 0.56 -10000 0 -1.2 106 106
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.46 -10000 0 -1 98 98
COL1A1 -0.22 0.36 -10000 0 -1.4 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.59 -10000 0 -1.4 92 92
IL2R gamma/JAK3 0.027 0.068 -10000 0 -0.36 9 9
TFF3 -0.65 0.67 -10000 0 -1.5 125 125
ALOX15 -0.62 0.66 -10000 0 -1.5 116 116
MYBL1 0.022 0.022 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.42 0.47 -10000 0 -1 99 99
SHC1 0.023 0.013 -10000 0 -10000 0 0
CEBPB 0.027 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.33 -10000 0 -1 31 31
mol:PI-3-4-5-P3 -0.24 0.31 -10000 0 -0.97 33 33
PI3K -0.26 0.35 -10000 0 -1.1 33 33
DOK2 0.015 0.067 -10000 0 -0.48 6 6
ETS1 0.035 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.24 -10000 0 -0.74 27 27
ITGB3 -0.52 0.58 -10000 0 -1.4 91 91
PIGR -0.6 0.67 -10000 0 -1.5 111 111
IGHE 0.03 0.059 0.22 13 -10000 0 13
MAPKKK cascade -0.17 0.24 -10000 0 -0.71 27 27
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.5 0.56 -10000 0 -1.2 106 106
RETNLB -0.5 0.56 -10000 0 -1.2 106 106
SELP -0.52 0.61 -10000 0 -1.4 91 91
AICDA -0.51 0.56 -10000 0 -1.3 95 95
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.064 0.19 -10000 0 -0.55 37 37
IHH -0.045 0.16 -10000 0 -0.5 30 30
SHH Np/Cholesterol/GAS1 -0.037 0.12 -10000 0 -0.3 55 55
LRPAP1 0.026 0.028 -10000 0 -0.48 1 1
dorsoventral neural tube patterning 0.037 0.12 0.3 55 -10000 0 55
SMO/beta Arrestin2 -0.047 0.18 -10000 0 -0.46 38 38
SMO -0.063 0.18 -10000 0 -0.47 42 42
AKT1 -0.021 0.14 -10000 0 -0.5 16 16
ARRB2 0.026 0.008 -10000 0 -10000 0 0
BOC 0.019 0.062 -10000 0 -0.48 5 5
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.057 0.18 -10000 0 -0.47 41 41
STIL -0.062 0.16 -10000 0 -0.38 43 43
DHH N/PTCH2 0.012 0.1 -10000 0 -0.36 22 22
DHH N/PTCH1 -0.04 0.15 -10000 0 -0.32 63 63
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DHH 0.008 0.094 -10000 0 -0.48 12 12
PTHLH -0.085 0.25 -10000 0 -0.71 39 39
determination of left/right symmetry -0.057 0.18 -10000 0 -0.47 41 41
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
skeletal system development -0.084 0.24 -10000 0 -0.7 39 39
IHH N/Hhip -0.09 0.19 -10000 0 -0.42 77 77
DHH N/Hhip -0.058 0.16 -10000 0 -0.36 70 70
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.057 0.18 -10000 0 -0.47 41 41
pancreas development -0.083 0.19 -10000 0 -0.48 61 61
HHAT 0.008 0.093 -10000 0 -0.48 12 12
PI3K 0.038 0.012 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.005 0.093 -10000 0 -0.48 11 11
somite specification -0.057 0.18 -10000 0 -0.47 41 41
SHH Np/Cholesterol/PTCH1 -0.074 0.16 -10000 0 -0.32 85 85
SHH Np/Cholesterol/PTCH2 -0.034 0.12 -10000 0 -0.28 57 57
SHH Np/Cholesterol/Megalin -0.093 0.16 -10000 0 -0.32 100 100
SHH -0.051 0.13 -10000 0 -0.36 52 52
catabolic process -0.048 0.15 -10000 0 -0.36 55 55
SMO/Vitamin D3 -0.07 0.18 -10000 0 -0.45 41 41
SHH Np/Cholesterol/Hhip -0.08 0.15 -10000 0 -0.33 85 85
LRP2 -0.11 0.2 -10000 0 -0.48 75 75
receptor-mediated endocytosis -0.12 0.21 -10000 0 -0.51 53 53
SHH Np/Cholesterol/BOC -0.029 0.11 -10000 0 -0.29 51 51
SHH Np/Cholesterol/CDO -0.032 0.12 -10000 0 -0.29 53 53
mesenchymal cell differentiation 0.08 0.15 0.32 85 -10000 0 85
mol:Vitamin D3 -0.06 0.17 -10000 0 -0.36 55 55
IHH N/PTCH2 -0.019 0.12 -10000 0 -0.34 37 37
CDON 0.013 0.075 -10000 0 -0.48 7 7
IHH N/PTCH1 -0.039 0.15 -10000 0 -0.36 56 56
Megalin/LRPAP1 -0.062 0.16 -10000 0 -0.35 74 74
PTCH2 0.009 0.091 -10000 0 -0.48 11 11
SHH Np/Cholesterol -0.034 0.1 -10000 0 -0.28 52 52
PTCH1 -0.049 0.15 -10000 0 -0.36 55 55
HHIP -0.083 0.19 -10000 0 -0.48 61 61
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.34 -10000 0 -1 41 41
MKNK1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.023 0.12 -10000 0 -0.31 48 48
ATF2/c-Jun -0.026 0.11 -10000 0 -0.51 7 7
MAPK11 -0.023 0.12 -10000 0 -0.33 45 45
MITF -0.038 0.15 -10000 0 -0.38 52 52
MAPKAPK5 -0.034 0.14 -10000 0 -0.37 50 50
KRT8 -0.036 0.14 -10000 0 -0.36 52 52
MAPKAPK3 0.026 0.028 -10000 0 -0.48 1 1
MAPKAPK2 0.025 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.038 0.18 -10000 0 -0.45 50 50
CEBPB -0.035 0.14 -10000 0 -0.38 49 49
SLC9A1 -0.036 0.14 -10000 0 -0.37 51 51
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.033 0.14 -10000 0 -0.37 50 50
p38alpha-beta/MNK1 -0.015 0.15 -10000 0 -0.38 43 43
JUN -0.024 0.11 -10000 0 -0.51 7 7
PPARGC1A -0.076 0.19 -10000 0 -0.41 73 73
USF1 -0.031 0.13 -10000 0 -0.36 46 46
RAB5/GDP/GDI1 -0.021 0.11 -10000 0 -0.27 46 46
NOS2 -0.06 0.22 -10000 0 -0.83 19 19
DDIT3 -0.035 0.14 -10000 0 -0.36 50 50
RAB5A 0.027 0.005 -10000 0 -10000 0 0
HSPB1 -0.029 0.12 0.28 7 -0.31 46 53
p38alpha-beta/HBP1 -0.016 0.15 -10000 0 -0.38 43 43
CREB1 -0.036 0.15 -10000 0 -0.38 50 50
RAB5/GDP 0.02 0.004 -10000 0 -10000 0 0
EIF4E -0.034 0.13 -10000 0 -0.35 42 42
RPS6KA4 -0.036 0.14 -10000 0 -0.36 52 52
PLA2G4A -0.055 0.14 -10000 0 -0.37 51 51
GDI1 -0.032 0.14 -10000 0 -0.37 48 48
TP53 -0.055 0.16 -10000 0 -0.46 47 47
RPS6KA5 -0.036 0.14 -10000 0 -0.36 52 52
ESR1 -0.059 0.17 -10000 0 -0.41 61 61
HBP1 0.027 0.006 -10000 0 -10000 0 0
MEF2C -0.039 0.15 -10000 0 -0.38 52 52
MEF2A -0.034 0.14 -10000 0 -0.36 50 50
EIF4EBP1 -0.044 0.16 -10000 0 -0.41 52 52
KRT19 -0.047 0.16 -10000 0 -0.39 58 58
ELK4 -0.032 0.13 -10000 0 -0.36 47 47
ATF6 -0.032 0.13 -10000 0 -0.36 47 47
ATF1 -0.037 0.15 -10000 0 -0.38 52 52
p38alpha-beta/MAPKAPK2 -0.016 0.15 -10000 0 -0.38 42 42
p38alpha-beta/MAPKAPK3 -0.017 0.15 -10000 0 -0.38 46 46
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.005 0.15 0.27 34 -0.31 38 72
PTK2B 0.019 0.048 -10000 0 -0.49 3 3
mol:Ca2+ -0.065 0.29 0.51 1 -0.88 31 32
EDN1 0.01 0.15 0.24 35 -0.42 25 60
EDN3 0.01 0.041 -10000 0 -10000 0 0
EDN2 -0.049 0.16 -10000 0 -0.48 38 38
HRAS/GDP -0.05 0.22 0.29 5 -0.51 47 52
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.18 0.23 3 -0.44 43 46
ADCY4 0 0.12 0.29 5 -0.3 27 32
ADCY5 -0.024 0.16 0.31 4 -0.35 44 48
ADCY6 0.002 0.13 0.29 5 -0.31 28 33
ADCY7 -0.001 0.13 0.3 5 -0.3 29 34
ADCY1 -0.007 0.14 0.29 5 -0.32 35 40
ADCY2 -0.024 0.14 0.29 2 -0.32 39 41
ADCY3 0.002 0.13 0.3 6 -0.3 29 35
ADCY8 -0.002 0.12 0.32 5 -0.3 23 28
ADCY9 -0.002 0.13 0.3 6 -0.3 33 39
arachidonic acid secretion -0.066 0.22 0.24 1 -0.55 42 43
ETB receptor/Endothelin-1/Gq/GTP -0.027 0.15 0.19 2 -0.36 46 48
GNAO1 0.007 0.092 -10000 0 -0.33 20 20
HRAS 0.027 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.044 0.16 0.37 30 -0.32 24 54
ETA receptor/Endothelin-1/Gs/GTP 0.037 0.16 0.36 34 -0.29 41 75
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.005 0.18 0.27 33 -0.43 32 65
EDNRB 0.009 0.087 -10000 0 -0.5 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.008 0.18 0.28 28 -0.47 31 59
CYSLTR1 -0.002 0.17 0.27 34 -0.44 26 60
SLC9A1 0.011 0.099 0.2 34 -0.23 26 60
mol:GDP -0.067 0.23 0.29 5 -0.54 49 54
SLC9A3 -0.066 0.27 0.46 1 -0.75 37 38
RAF1 -0.07 0.22 0.28 2 -0.51 50 52
JUN -0.045 0.24 -10000 0 -0.77 22 22
JAK2 0.008 0.14 0.28 32 -0.33 29 61
mol:IP3 -0.047 0.2 0.28 1 -0.48 48 49
ETA receptor/Endothelin-1 0.041 0.2 0.44 35 -0.36 41 76
PLCB1 0.002 0.11 -10000 0 -0.45 18 18
PLCB2 0.013 0.081 -10000 0 -0.49 9 9
ETA receptor/Endothelin-3 0.026 0.082 0.3 2 -0.28 7 9
FOS -0.061 0.22 -10000 0 -0.78 20 20
Gai/GDP -0.047 0.24 -10000 0 -0.81 28 28
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.042 0.22 0.23 23 -0.53 43 66
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
PRKCB1 -0.047 0.19 0.27 1 -0.48 46 47
GNAQ 0.023 0.03 -10000 0 -0.49 1 1
GNAZ -0.017 0.14 -10000 0 -0.48 26 26
GNAL 0.007 0.089 -10000 0 -0.3 21 21
Gs family/GDP -0.057 0.21 0.27 3 -0.47 52 55
ETA receptor/Endothelin-1/Gq/GTP -0.017 0.17 0.21 26 -0.45 33 59
MAPK14 -0.043 0.16 0.24 3 -0.42 40 43
TRPC6 -0.073 0.31 0.52 1 -1 28 29
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.056 -10000 0 -0.48 4 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.039 0.17 0.18 1 -0.4 46 47
ETB receptor/Endothelin-2 -0.031 0.14 -10000 0 -0.38 43 43
ETB receptor/Endothelin-3 0.011 0.073 -10000 0 -0.34 10 10
ETB receptor/Endothelin-1 0.014 0.13 0.32 2 -0.36 30 32
MAPK3 -0.067 0.23 0.29 1 -0.71 27 28
MAPK1 -0.071 0.24 0.29 1 -0.71 29 30
Rac1/GDP -0.049 0.21 0.29 3 -0.51 42 45
cAMP biosynthetic process 0 0.16 0.27 22 -0.39 27 49
MAPK8 -0.057 0.27 0.37 1 -0.76 33 34
SRC 0.027 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.022 0.13 0.17 3 -0.4 23 26
p130Cas/CRK/Src/PYK2 -0.083 0.25 0.36 2 -0.61 48 50
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.048 0.21 0.28 4 -0.51 42 46
COL1A2 -0.004 0.19 0.29 18 -0.5 29 47
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.016 0.14 0.31 1 -0.34 46 47
mol:DAG -0.047 0.2 0.28 1 -0.48 48 49
MAP2K2 -0.067 0.21 0.29 1 -0.57 38 39
MAP2K1 -0.068 0.22 0.28 2 -0.56 39 41
EDNRA 0.031 0.11 0.24 35 -0.35 10 45
positive regulation of muscle contraction 0.021 0.14 0.24 54 -0.31 24 78
Gq family/GDP -0.039 0.22 0.27 1 -0.54 40 41
HRAS/GTP -0.069 0.22 0.29 2 -0.51 51 53
PRKCH -0.048 0.19 0.29 2 -0.49 43 45
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA -0.052 0.2 0.28 5 -0.5 44 49
PRKCB -0.055 0.2 0.24 2 -0.5 49 51
PRKCE -0.05 0.2 0.26 1 -0.5 43 44
PRKCD -0.048 0.19 0.27 1 -0.5 42 43
PRKCG -0.054 0.2 0.24 2 -0.48 46 48
regulation of vascular smooth muscle contraction -0.076 0.26 -10000 0 -0.94 20 20
PRKCQ -0.061 0.21 0.26 3 -0.5 51 54
PLA2G4A -0.075 0.24 0.25 1 -0.62 42 43
GNA14 -0.011 0.13 -10000 0 -0.49 25 25
GNA15 0.018 0.062 -10000 0 -0.49 5 5
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA11 0.022 0.04 -10000 0 -0.49 2 2
Rac1/GTP 0.043 0.16 0.37 30 -0.32 25 55
MMP1 -0.12 0.3 0.55 3 -0.85 48 51
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.3 -10000 0 -0.87 37 37
PCK1 -0.19 0.27 -10000 0 -0.89 26 26
HNF4A -0.31 0.38 -10000 0 -1 56 56
KCNJ11 -0.29 0.38 -10000 0 -1 50 50
AKT1 -0.1 0.16 -10000 0 -0.48 16 16
response to starvation -0.003 0.014 -10000 0 -10000 0 0
DLK1 -0.29 0.38 -10000 0 -1 54 54
NKX2-1 -0.25 0.48 -10000 0 -1.4 45 45
ACADM -0.24 0.3 -10000 0 -0.86 39 39
TAT -0.24 0.35 -10000 0 -1 42 42
CEBPB 0.023 0.017 -10000 0 -10000 0 0
CEBPA -0.003 0.11 -10000 0 -0.48 16 16
TTR -0.22 0.33 -10000 0 -1 38 38
PKLR -0.22 0.31 -10000 0 -0.86 39 39
APOA1 -0.32 0.41 -10000 0 -1.2 42 42
CPT1C -0.26 0.32 -10000 0 -0.91 42 42
ALAS1 -0.12 0.17 -10000 0 -0.83 2 2
TFRC -0.24 0.32 -10000 0 -1 32 32
FOXF1 0.037 0.079 0.22 15 -0.49 4 19
NF1 0.029 0.039 -10000 0 -0.48 2 2
HNF1A (dimer) -0.036 0.098 -10000 0 -0.24 33 33
CPT1A -0.24 0.31 -10000 0 -0.9 35 35
HMGCS1 -0.22 0.3 -10000 0 -0.86 34 34
NR3C1 -0.004 0.072 -10000 0 -0.23 17 17
CPT1B -0.26 0.34 -10000 0 -0.93 47 47
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.005 0.07 -10000 0 -0.21 21 21
GCK -0.24 0.33 -10000 0 -0.96 38 38
CREB1 0.017 0.031 -10000 0 -0.19 3 3
IGFBP1 -0.19 0.35 -10000 0 -1.4 24 24
PDX1 -0.3 0.47 -10000 0 -1.4 49 49
UCP2 -0.24 0.31 -10000 0 -0.86 43 43
ALDOB -0.29 0.38 -10000 0 -0.98 59 59
AFP -0.067 0.16 -10000 0 -0.63 13 13
BDH1 -0.24 0.32 -10000 0 -0.91 40 40
HADH -0.25 0.32 -10000 0 -0.89 41 41
F2 -0.32 0.39 -10000 0 -1.1 38 38
HNF1A -0.036 0.098 -10000 0 -0.24 33 33
G6PC -0.069 0.12 -10000 0 -0.28 63 63
SLC2A2 -0.18 0.21 -10000 0 -0.53 53 53
INS 0.009 0.042 0.19 11 -10000 0 11
FOXA1 0 0.11 0.25 3 -0.36 18 21
FOXA3 -0.11 0.2 -10000 0 -0.44 78 78
FOXA2 -0.29 0.37 -10000 0 -0.97 47 47
ABCC8 -0.29 0.36 -10000 0 -0.94 56 56
ALB -0.09 0.22 -10000 0 -0.76 24 24
IL23-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
CCL2 -0.22 0.46 -10000 0 -1.2 44 44
IL23A -0.23 0.48 -10000 0 -1.3 44 44
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.48 -10000 0 -1.2 46 46
positive regulation of T cell mediated cytotoxicity -0.26 0.55 -10000 0 -1.4 51 51
ITGA3 -0.24 0.49 -10000 0 -1.2 55 55
IL17F -0.15 0.29 -10000 0 -0.72 51 51
IL12B -0.023 0.13 -10000 0 -0.51 20 20
STAT1 (dimer) -0.24 0.52 -10000 0 -1.3 51 51
CD4 -0.22 0.46 -10000 0 -1.2 42 42
IL23 -0.22 0.47 -10000 0 -1.2 46 46
IL23R -0.036 0.21 -10000 0 -1.1 11 11
IL1B -0.25 0.51 -10000 0 -1.3 51 51
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.23 0.48 -10000 0 -1.2 54 54
TYK2 0.008 0.035 -10000 0 -10000 0 0
STAT4 0.013 0.086 -10000 0 -0.45 11 11
STAT3 0.028 0.004 -10000 0 -10000 0 0
IL18RAP -0.003 0.1 -10000 0 -0.49 14 14
IL12RB1 -0.005 0.09 -10000 0 -0.52 9 9
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.007 0.075 -10000 0 -0.38 8 8
IL23R/JAK2 -0.027 0.21 -10000 0 -1 11 11
positive regulation of chronic inflammatory response -0.26 0.55 -10000 0 -1.4 51 51
natural killer cell activation 0.003 0.009 0.08 2 -10000 0 2
JAK2 0.009 0.041 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.2 0.44 -10000 0 -1.1 46 46
ALOX12B -0.28 0.51 -10000 0 -1.2 63 63
CXCL1 -0.27 0.51 -10000 0 -1.3 59 59
T cell proliferation -0.26 0.55 -10000 0 -1.4 51 51
NFKBIA 0.023 0.011 -10000 0 -10000 0 0
IL17A -0.099 0.24 -10000 0 -0.57 37 37
PI3K -0.22 0.5 -10000 0 -1.2 51 51
IFNG -0.016 0.046 0.12 3 -0.13 36 39
STAT3 (dimer) -0.21 0.47 -10000 0 -1.2 51 51
IL18R1 0.011 0.075 -10000 0 -0.38 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.36 -10000 0 -1 34 34
IL18/IL18R 0.004 0.12 -10000 0 -0.34 29 29
macrophage activation -0.011 0.019 -10000 0 -0.045 40 40
TNF -0.24 0.51 -10000 0 -1.4 48 48
STAT3/STAT4 -0.23 0.5 -10000 0 -1.3 52 52
STAT4 (dimer) -0.25 0.53 -10000 0 -1.3 52 52
IL18 0 0.1 -10000 0 -0.48 15 15
IL19 -0.21 0.45 -10000 0 -1.2 41 41
STAT5A (dimer) -0.25 0.53 -10000 0 -1.3 51 51
STAT1 0.028 0.003 -10000 0 -10000 0 0
SOCS3 0.025 0.03 -10000 0 -0.48 1 1
CXCL9 -0.28 0.53 -10000 0 -1.3 61 61
MPO -0.23 0.46 -10000 0 -1.2 43 43
positive regulation of humoral immune response -0.26 0.55 -10000 0 -1.4 51 51
IL23/IL23R/JAK2/TYK2 -0.3 0.69 -10000 0 -1.7 51 51
IL6 -0.23 0.49 -10000 0 -1.3 51 51
STAT5A 0.026 0.028 -10000 0 -0.48 1 1
IL2 0.01 0.031 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.08 2 -10000 0 2
CD3E -0.23 0.47 -10000 0 -1.3 44 44
keratinocyte proliferation -0.26 0.55 -10000 0 -1.4 51 51
NOS2 -0.24 0.48 -10000 0 -1.2 53 53
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 0.015 0.049 -10000 0 -0.33 5 5
CDKN2C 0.024 0.021 -10000 0 -10000 0 0
CDKN2A -0.019 0.11 -10000 0 -0.44 16 16
CCND2 0.008 0.045 0.18 19 -0.11 1 20
RB1 -0.035 0.082 -10000 0 -0.22 52 52
CDK4 0.017 0.064 0.23 27 -10000 0 27
CDK6 0.015 0.066 0.23 26 -0.13 4 30
G1/S progression 0.048 0.093 0.21 79 -0.28 1 80
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.027 0.005 -9999 0 -10000 0 0
EGFR 0.008 0.089 -9999 0 -0.48 11 11
EGF/EGFR -0.026 0.13 -9999 0 -0.27 74 74
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.002 0.13 -9999 0 -0.27 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.019 0.062 -9999 0 -0.48 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.059 0.19 -9999 0 -0.48 56 56
EGF/EGFR dimer/SHC -0.022 0.13 -9999 0 -0.31 56 56
mol:GDP -0.005 0.12 -9999 0 -0.27 55 55
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.001 0.11 -9999 0 -0.42 22 22
GRB2/SOS1 0.04 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.014 0.11 -9999 0 -0.25 54 54
SHC1 0.023 0.013 -9999 0 -10000 0 0
HRAS/GDP -0.004 0.12 -9999 0 -0.26 54 54
FRAP1 -0.051 0.092 -9999 0 -0.26 55 55
EGF/EGFR dimer -0.038 0.15 -9999 0 -0.36 60 60
SOS1 0.028 0.003 -9999 0 -10000 0 0
GRB2 0.027 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.012 0.097 -9999 0 -0.35 23 23
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.37 -10000 0 -0.98 32 32
HDAC7 0.027 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.33 -10000 0 -0.96 22 22
SMAD4 0.026 0.009 -10000 0 -10000 0 0
ID2 -0.18 0.37 -10000 0 -0.98 32 32
AP1 0.017 0.079 -10000 0 -0.35 13 13
ABCG2 -0.18 0.38 -10000 0 -0.98 36 36
HIF1A -0.033 0.083 -10000 0 -0.24 7 7
TFF3 -0.23 0.41 -10000 0 -0.95 56 56
GATA2 0.002 0.11 -10000 0 -0.49 16 16
AKT1 -0.036 0.09 -10000 0 -0.24 21 21
response to hypoxia -0.05 0.085 -10000 0 -0.23 34 34
MCL1 -0.18 0.35 -10000 0 -0.98 31 31
NDRG1 -0.17 0.36 -10000 0 -0.97 33 33
SERPINE1 -0.18 0.38 -10000 0 -1 32 32
FECH -0.18 0.37 -10000 0 -0.98 32 32
FURIN -0.18 0.37 -10000 0 -1 31 31
NCOA2 0.014 0.077 -10000 0 -0.48 8 8
EP300 -0.04 0.12 -10000 0 -0.35 26 26
HMOX1 -0.18 0.37 -10000 0 -1 31 31
BHLHE40 -0.18 0.37 -10000 0 -0.99 32 32
BHLHE41 -0.18 0.38 -10000 0 -1 34 34
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.009 0.1 -10000 0 -10000 0 0
ENG 0.007 0.1 0.29 6 -0.47 1 7
JUN 0.022 0.042 -10000 0 -0.5 2 2
RORA -0.18 0.37 -10000 0 -1 32 32
ABCB1 -0.054 0.18 -10000 0 -1.1 8 8
TFRC -0.18 0.37 -10000 0 -0.99 33 33
CXCR4 -0.18 0.37 -10000 0 -0.99 32 32
TF -0.22 0.41 -10000 0 -0.94 59 59
CITED2 -0.18 0.37 -10000 0 -1 31 31
HIF1A/ARNT -0.19 0.46 -10000 0 -1.2 30 30
LDHA -0.017 0.12 -10000 0 -0.73 7 7
ETS1 -0.18 0.37 -10000 0 -0.98 32 32
PGK1 -0.18 0.37 -10000 0 -0.99 32 32
NOS2 -0.19 0.38 -10000 0 -0.97 36 36
ITGB2 -0.18 0.38 -10000 0 -1 33 33
ALDOA -0.18 0.37 -10000 0 -1 31 31
Cbp/p300/CITED2 -0.18 0.4 -10000 0 -1.2 27 27
FOS 0.002 0.095 -10000 0 -0.49 11 11
HK2 -0.18 0.38 -10000 0 -0.98 35 35
SP1 0.028 0.024 -10000 0 -10000 0 0
GCK -0.11 0.31 -10000 0 -1.5 13 13
HK1 -0.18 0.37 -10000 0 -0.99 31 31
NPM1 -0.18 0.37 -10000 0 -0.99 31 31
EGLN1 -0.18 0.36 -10000 0 -0.98 32 32
CREB1 0.032 0.005 -10000 0 -10000 0 0
PGM1 -0.18 0.37 -10000 0 -1 31 31
SMAD3 0.026 0.028 -10000 0 -0.48 1 1
EDN1 -0.1 0.32 -10000 0 -1 30 30
IGFBP1 -0.2 0.38 -10000 0 -0.96 41 41
VEGFA -0.12 0.29 0.4 1 -0.84 20 21
HIF1A/JAB1 -0.004 0.063 -10000 0 -10000 0 0
CP -0.21 0.41 -10000 0 -0.97 51 51
CXCL12 -0.19 0.38 -10000 0 -1 36 36
COPS5 0.025 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.025 -10000 0 -0.35 1 1
BNIP3 -0.18 0.37 -10000 0 -0.98 33 33
EGLN3 -0.19 0.39 -10000 0 -1 35 35
CA9 -0.24 0.41 -10000 0 -0.96 53 53
TERT -0.19 0.36 -10000 0 -1 30 30
ENO1 -0.18 0.37 -10000 0 -0.99 32 32
PFKL -0.18 0.37 -10000 0 -0.98 32 32
NCOA1 0.027 0.027 -10000 0 -0.48 1 1
ADM -0.19 0.38 -10000 0 -0.98 36 36
ARNT -0.021 0.068 -10000 0 -0.36 1 1
HNF4A -0.065 0.16 -10000 0 -0.46 38 38
ADFP -0.2 0.35 -10000 0 -0.91 41 41
SLC2A1 -0.13 0.3 0.4 1 -0.86 23 24
LEP -0.19 0.37 -10000 0 -1 34 34
HIF1A/ARNT/Cbp/p300 -0.14 0.34 -10000 0 -1 22 22
EPO -0.09 0.23 -10000 0 -0.74 12 12
CREBBP -0.038 0.11 -10000 0 -0.3 28 28
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.34 -10000 0 -1 19 19
PFKFB3 -0.18 0.37 -10000 0 -0.99 32 32
NT5E -0.2 0.38 -10000 0 -0.96 43 43
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.037 0.031 -10000 0 -0.35 2 2
Necdin/E2F1 0.03 0.053 -10000 0 -0.35 6 6
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.015 0.14 -10000 0 -0.29 56 56
NGF (dimer)/p75(NTR)/BEX1 -0.049 0.14 -10000 0 -0.33 59 59
NT-4/5 (dimer)/p75(NTR) -0.019 0.14 -10000 0 -0.36 43 43
IKBKB 0.024 0.01 -10000 0 -10000 0 0
AKT1 -0.051 0.097 0.2 7 -0.27 46 53
IKBKG 0.024 0.039 -10000 0 -0.48 2 2
BDNF -0.027 0.14 -10000 0 -0.29 61 61
MGDIs/NGR/p75(NTR)/LINGO1 0 0.12 -10000 0 -0.32 35 35
FURIN 0.022 0.03 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.01 0.13 -10000 0 -0.33 42 42
LINGO1 0.001 0.087 -10000 0 -0.48 8 8
Sortilin/TRAF6/NRIF 0.026 0.024 -10000 0 -0.24 1 1
proBDNF (dimer) -0.027 0.14 -10000 0 -0.29 61 61
NTRK1 0.003 0.095 -10000 0 -0.34 20 20
RTN4R 0.012 0.085 -10000 0 -0.48 10 10
neuron apoptosis -0.06 0.16 0.4 3 -0.47 24 27
IRAK1 0.027 0.006 -10000 0 -10000 0 0
SHC1 -0.04 0.1 -10000 0 -0.31 40 40
ARHGDIA 0.026 0.028 -10000 0 -0.48 1 1
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.06 0.038 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.016 0.13 -10000 0 -0.3 52 52
MAGEH1 0.023 0.048 -10000 0 -0.48 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.019 0.14 -10000 0 -0.3 53 53
Mammalian IAPs/DIABLO 0.049 0.072 -10000 0 -0.27 14 14
proNGF (dimer) -0.047 0.15 -10000 0 -0.48 31 31
MAGED1 0.027 0.01 -10000 0 -0.13 1 1
APP 0.026 0.007 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.015 0.14 -10000 0 -0.48 26 26
ZNF274 0.027 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.027 0.11 -10000 0 -0.27 50 50
NGF -0.047 0.15 -10000 0 -0.48 31 31
cell cycle arrest -0.048 0.097 0.26 6 -0.25 45 51
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.093 -10000 0 -0.25 44 44
NT-4/5 (dimer)/p75(NTR)/TRAF6 0 0.12 -10000 0 -0.31 43 43
NCSTN 0.024 0.01 -10000 0 -10000 0 0
mol:GTP -0.029 0.13 -10000 0 -0.32 50 50
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide -0.043 0.11 0.18 4 -0.28 50 54
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.013 0.081 -10000 0 -0.34 6 6
p75(NTR)/beta APP 0.012 0.089 -10000 0 -0.35 18 18
BEX1 -0.012 0.11 -10000 0 -0.21 57 57
mol:GDP -0.062 0.1 -10000 0 -0.31 49 49
NGF (dimer) -0.046 0.13 -10000 0 -0.3 60 60
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.12 -10000 0 -0.3 34 34
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
RAC1/GTP -0.018 0.1 -10000 0 -0.27 43 43
MYD88 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.028 0.13 -10000 0 -0.32 50 50
RHOB 0.028 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.035 0.032 -10000 0 -0.35 2 2
NT3 (dimer) -0.017 0.13 -10000 0 -0.36 39 39
TP53 -0.045 0.1 0.41 3 -0.28 38 41
PRDM4 -0.043 0.11 -10000 0 -0.28 50 50
BDNF (dimer) -0.088 0.17 -10000 0 -0.33 94 94
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
SORT1 0.024 0.039 -10000 0 -0.48 2 2
activation of caspase activity -0.019 0.13 -10000 0 -0.29 56 56
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.013 0.13 -10000 0 -0.29 50 50
RHOC 0.026 0.01 -10000 0 -10000 0 0
XIAP 0.028 0.003 -10000 0 -10000 0 0
MAPK10 -0.055 0.15 0.35 7 -0.4 32 39
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 -0.044 0.11 0.18 4 -0.29 50 54
APH1B 0.026 0.028 -10000 0 -0.48 1 1
APH1A 0.023 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.027 0.13 -10000 0 -0.32 50 50
PSEN1 0.027 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.013 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.02 0.14 -10000 0 -0.35 47 47
MAPK8 -0.041 0.13 0.35 7 -0.35 25 32
MAPK9 -0.041 0.13 0.36 6 -0.35 23 29
APAF1 0.027 0.005 -10000 0 -10000 0 0
NTF3 -0.017 0.13 -10000 0 -0.36 39 39
NTF4 -0.015 0.14 -10000 0 -0.48 26 26
NDN 0.018 0.062 -10000 0 -0.38 7 7
RAC1/GDP 0.018 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.007 0.12 -10000 0 -0.26 46 46
p75 CTF/Sortilin/TRAF6/NRIF 0.064 0.033 -10000 0 -0.28 2 2
RhoA-B-C/GTP -0.029 0.13 -10000 0 -0.32 50 50
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.014 0.12 -10000 0 -0.28 42 42
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.004 0.13 -10000 0 -0.3 42 42
PRKACB 0.023 0.041 -10000 0 -0.48 2 2
proBDNF (dimer)/p75 ECD -0.001 0.11 -10000 0 -0.35 26 26
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.003 0.1 -10000 0 -0.48 14 14
BIRC2 0.027 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.051 0.12 0.34 2 -0.31 47 49
BAD -0.049 0.14 0.38 7 -0.36 30 37
RIPK2 0.025 0.009 -10000 0 -10000 0 0
NGFR -0.008 0.12 -10000 0 -0.48 19 19
CYCS -0.05 0.097 0.25 5 -0.28 42 47
ADAM17 0.028 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.012 0.12 -10000 0 -0.29 47 47
BCL2L11 -0.049 0.14 0.36 7 -0.37 28 35
BDNF (dimer)/p75(NTR) -0.026 0.14 -10000 0 -0.36 44 44
PI3K -0.012 0.12 -10000 0 -0.28 49 49
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.014 0.13 -10000 0 -0.29 50 50
NDNL2 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.011 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.044 0.14 -10000 0 -0.37 49 49
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.014 0.13 -10000 0 -0.29 50 50
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCZ 0.022 0.044 -10000 0 -0.48 2 2
PLG 0 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.062 0.13 -10000 0 -0.3 71 71
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
NGFRAP1 0.012 0.089 -10000 0 -0.48 11 11
CASP3 -0.045 0.14 0.36 7 -0.34 31 38
E2F1 0.023 0.04 -10000 0 -0.48 2 2
CASP9 0.027 0.01 -10000 0 -0.13 1 1
IKK complex 0.003 0.12 -10000 0 -0.32 27 27
NGF (dimer)/TRKA -0.032 0.12 -10000 0 -0.35 40 40
MMP7 -0.046 0.16 -10000 0 -0.48 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.005 0.13 -10000 0 -0.28 49 49
MMP3 -0.077 0.18 -10000 0 -0.3 110 110
APAF-1/Caspase 9 -0.059 0.08 -10000 0 -0.29 16 16
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.016 -10000 0 -10000 0 0
LAT2 -0.042 0.13 -10000 0 -0.39 32 32
AP1 -0.023 0.2 -10000 0 -0.58 28 28
mol:PIP3 -0.035 0.19 0.32 16 -0.49 30 46
IKBKB 0.002 0.12 0.26 29 -0.29 16 45
AKT1 -0.019 0.16 0.32 39 -0.38 13 52
IKBKG -0.009 0.12 0.24 23 -0.27 23 46
MS4A2 -0.029 0.15 -10000 0 -0.48 33 33
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.021 0.15 0.26 11 -0.44 21 32
mol:Ca2+ -0.02 0.15 0.24 30 -0.36 30 60
LYN 0.022 0.041 -10000 0 -0.49 2 2
CBLB -0.038 0.12 -10000 0 -0.36 31 31
SHC1 0.023 0.013 -10000 0 -10000 0 0
RasGAP/p62DOK 0.037 0.057 -10000 0 -0.27 10 10
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.017 0.072 -10000 0 -0.48 7 7
PLD2 -0.03 0.16 0.34 32 -0.3 52 84
PTPN13 -0.047 0.17 -10000 0 -0.54 21 21
PTPN11 0.022 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.011 0.13 0.29 16 -0.33 14 30
SYK 0.021 0.057 -10000 0 -0.5 4 4
GRB2 0.027 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.051 0.17 -10000 0 -0.49 31 31
LAT -0.04 0.12 -10000 0 -0.37 31 31
PAK2 -0.025 0.16 0.28 10 -0.48 24 34
NFATC2 -0.046 0.14 -10000 0 -0.57 22 22
HRAS -0.029 0.18 0.26 8 -0.5 28 36
GAB2 0.021 0.055 -10000 0 -0.48 4 4
PLA2G1B -0.023 0.16 -10000 0 -0.91 11 11
Fc epsilon R1 -0.042 0.16 -10000 0 -0.36 59 59
Antigen/IgE/Fc epsilon R1 -0.036 0.14 -10000 0 -0.32 59 59
mol:GDP -0.048 0.18 -10000 0 -0.56 28 28
JUN 0.024 0.04 -10000 0 -0.48 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
FOS 0.004 0.094 -10000 0 -0.48 11 11
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.038 0.13 -10000 0 -0.38 32 32
CHUK -0.012 0.11 0.23 21 -0.27 24 45
KLRG1 -0.038 0.12 -10000 0 -0.4 21 21
VAV1 -0.043 0.14 -10000 0 -0.4 32 32
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.038 0.12 -10000 0 -0.36 31 31
negative regulation of mast cell degranulation -0.026 0.14 -10000 0 -0.46 19 19
BTK -0.054 0.2 -10000 0 -0.63 29 29
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.055 0.17 -10000 0 -0.4 48 48
GAB2/PI3K/SHP2 -0.064 0.1 -10000 0 -0.32 38 38
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.036 0.13 -10000 0 -0.41 24 24
RAF1 -0.01 0.18 -10000 0 -0.96 11 11
Fc epsilon R1/FcgammaRIIB/SHIP -0.026 0.17 -10000 0 -0.34 63 63
FCER1G 0.016 0.068 -10000 0 -0.49 6 6
FCER1A -0.059 0.17 -10000 0 -0.5 42 42
Antigen/IgE/Fc epsilon R1/Fyn -0.027 0.14 -10000 0 -0.31 59 59
MAPK3 -0.007 0.16 -10000 0 -0.88 11 11
MAPK1 -0.01 0.16 -10000 0 -0.89 11 11
NFKB1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 -0.043 0.23 -10000 0 -0.71 27 27
DUSP1 0.014 0.073 -10000 0 -0.36 11 11
NF-kappa-B/RelA 0 0.067 0.14 8 -0.18 12 20
actin cytoskeleton reorganization -0.027 0.16 -10000 0 -0.54 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.02 0.16 -10000 0 -0.45 25 25
FER -0.039 0.12 -10000 0 -0.36 31 31
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.025 0.1 -10000 0 -0.37 23 23
SOS1 0.028 0.003 -10000 0 -10000 0 0
PLCG1 -0.041 0.19 0.29 3 -0.56 28 31
cytokine secretion -0.008 0.041 -10000 0 -0.16 3 3
SPHK1 -0.048 0.13 -10000 0 -0.36 37 37
PTK2 -0.029 0.16 -10000 0 -0.58 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.049 0.18 0.24 1 -0.48 36 37
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.031 0.18 0.29 21 -0.47 31 52
MAP2K2 -0.014 0.16 -10000 0 -0.89 11 11
MAP2K1 -0.012 0.16 -10000 0 -0.9 11 11
MAP2K7 0.026 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.027 0.11 0.19 1 -0.38 19 20
MAP2K4 -0.09 0.33 -10000 0 -0.91 48 48
Fc epsilon R1/FcgammaRIIB -0.035 0.16 -10000 0 -0.34 63 63
mol:Choline -0.03 0.16 0.34 32 -0.3 52 84
SHC/Grb2/SOS1 -0.003 0.13 -10000 0 -0.4 17 17
FYN 0.023 0.039 -10000 0 -0.48 2 2
DOK1 0.025 0.039 -10000 0 -0.48 2 2
PXN -0.027 0.15 0.34 2 -0.54 14 16
HCLS1 -0.042 0.14 -10000 0 -0.4 32 32
PRKCB -0.021 0.15 0.26 21 -0.37 27 48
FCGR2B 0.009 0.083 -10000 0 -0.48 9 9
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.027 0.14 -10000 0 -0.47 19 19
LCP2 0.017 0.067 -10000 0 -0.49 6 6
PLA2G4A -0.056 0.14 -10000 0 -0.37 40 40
RASA1 0.025 0.028 -10000 0 -0.48 1 1
mol:Phosphatidic acid -0.03 0.16 0.34 32 -0.3 52 84
IKK complex 0.007 0.11 0.24 31 -0.22 12 43
WIPF1 0.025 0.039 -10000 0 -0.48 2 2
Wnt 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
Noncanonical Wnts/FZD -0.058 0.16 -9999 0 -0.32 72 72
FZD6 0.02 0.048 -9999 0 -0.48 3 3
WNT6 -0.001 0.1 -9999 0 -0.48 13 13
WNT4 -0.044 0.16 -9999 0 -0.48 40 40
FZD3 0.019 0.049 -9999 0 -0.48 3 3
WNT5A 0.005 0.1 -9999 0 -0.48 15 15
WNT11 -0.011 0.12 -9999 0 -0.48 19 19
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.002 0.12 -10000 0 -0.48 16 16
NFATC2 -0.037 0.22 -10000 0 -0.63 28 28
NFATC3 -0.002 0.071 -10000 0 -0.28 5 5
CD40LG -0.18 0.34 -10000 0 -0.95 40 40
ITCH -0.019 0.097 -10000 0 -0.35 1 1
CBLB -0.022 0.1 -10000 0 -0.24 25 25
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.17 0.39 -10000 0 -1.1 40 40
JUNB 0.021 0.048 -10000 0 -0.48 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.12 -10000 0 -0.28 65 65
T cell anergy -0.057 0.17 0.29 3 -0.4 62 65
TLE4 -0.037 0.19 -10000 0 -0.66 20 20
Jun/NFAT1-c-4/p21SNFT -0.089 0.31 -10000 0 -1 24 24
AP-1/NFAT1-c-4 -0.16 0.39 -10000 0 -1.1 35 35
IKZF1 -0.027 0.16 -10000 0 -0.68 12 12
T-helper 2 cell differentiation -0.061 0.23 0.32 1 -0.63 37 38
AP-1/NFAT1 -0.042 0.18 -10000 0 -0.49 25 25
CALM1 -0.006 0.08 -10000 0 -0.23 1 1
EGR2 -0.081 0.3 -10000 0 -1.2 18 18
EGR3 -0.099 0.35 -10000 0 -1.4 19 19
NFAT1/FOXP3 -0.027 0.21 -10000 0 -0.54 35 35
EGR1 0.01 0.076 -10000 0 -0.44 8 8
JUN -0.004 0.053 -10000 0 -0.48 2 2
EGR4 -0.03 0.13 -10000 0 -0.46 26 26
mol:Ca2+ -0.026 0.068 -10000 0 -0.17 66 66
GBP3 -0.067 0.25 -10000 0 -0.73 36 36
FOSL1 -0.026 0.13 -10000 0 -0.48 24 24
NFAT1-c-4/MAF/IRF4 -0.064 0.3 -10000 0 -0.95 24 24
DGKA -0.027 0.16 -10000 0 -0.58 15 15
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.089 0.31 -10000 0 -1 24 24
CTLA4 -0.057 0.22 -10000 0 -0.7 30 30
NFAT1-c-4 (dimer)/EGR1 -0.074 0.31 -10000 0 -1.1 22 22
NFAT1-c-4 (dimer)/EGR4 -0.093 0.31 -10000 0 -1 24 24
FOS -0.023 0.099 -10000 0 -0.48 12 12
IFNG -0.16 0.39 -10000 0 -1 51 51
T cell activation -0.058 0.18 -10000 0 -0.93 4 4
MAF 0.024 0.039 -10000 0 -0.48 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.063 0.24 0.93 17 -10000 0 17
TNF -0.13 0.3 -10000 0 -0.9 34 34
FASLG -0.15 0.45 -10000 0 -1.4 34 34
TBX21 -0.008 0.099 -10000 0 -0.32 21 21
BATF3 0.015 0.065 -10000 0 -0.48 5 5
PRKCQ -0.004 0.11 -10000 0 -0.5 17 17
PTPN1 -0.029 0.16 -10000 0 -0.61 13 13
NFAT1-c-4/ICER1 -0.065 0.28 -10000 0 -0.95 23 23
GATA3 0.023 0.024 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.16 0.38 -10000 0 -0.99 51 51
IL2RA -0.14 0.35 -10000 0 -0.96 43 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.028 0.16 -10000 0 -0.57 16 16
E2F1 0.026 0.04 -10000 0 -0.48 2 2
PPARG -0.021 0.15 -10000 0 -0.48 32 32
SLC3A2 -0.027 0.15 -10000 0 -0.53 17 17
IRF4 0 0.1 -10000 0 -0.48 13 13
PTGS2 -0.19 0.33 -10000 0 -0.88 48 48
CSF2 -0.2 0.34 -10000 0 -0.92 45 45
JunB/Fra1/NFAT1-c-4 -0.077 0.29 -10000 0 -0.98 22 22
IL4 -0.064 0.24 0.32 1 -0.66 37 38
IL5 -0.18 0.3 -10000 0 -0.92 35 35
IL2 -0.059 0.18 -10000 0 -0.96 4 4
IL3 -0.027 0.076 -10000 0 -0.73 2 2
RNF128 -0.09 0.23 -10000 0 -0.57 66 66
NFATC1 -0.063 0.24 -10000 0 -0.94 17 17
CDK4 0.051 0.16 0.7 9 -10000 0 9
PTPRK -0.027 0.16 -10000 0 -0.59 14 14
IL8 -0.18 0.32 -10000 0 -0.9 42 42
POU2F1 0.022 0.039 -10000 0 -0.48 2 2
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.014 0.007 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.01 0.045 -10000 0 -0.29 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0 0 -10000 0 -10000 0 0
GRK1 0.011 0.045 -10000 0 -0.48 1 1
CNG Channel -0.06 0.14 -10000 0 -0.28 81 81
mol:Na + -0.076 0.14 -10000 0 -0.29 96 96
mol:ADP 0.011 0.045 -10000 0 -0.48 1 1
RGS9-1/Gbeta5/R9AP 0.025 0.089 -10000 0 -0.3 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.074 0.15 -10000 0 -0.29 96 96
CNGB1 -0.06 0.18 -10000 0 -0.48 49 49
RDH5 0.016 0.057 -10000 0 -0.48 3 3
SAG 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.083 0.15 0.3 15 -0.28 93 108
Na + (4 Units) -0.074 0.14 -10000 0 -0.27 95 95
RGS9 0.004 0.1 -10000 0 -0.48 15 15
GNB1/GNGT1 -0.003 0.11 -10000 0 -0.35 32 32
GNAT1/GDP 0.022 0.075 -10000 0 -0.25 23 23
GUCY2D -0.01 0.12 -10000 0 -0.48 19 19
GNGT1 -0.029 0.15 -10000 0 -0.48 33 33
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.01 0.087 -10000 0 -0.28 30 30
mol:11-cis-retinal 0.016 0.057 -10000 0 -0.48 3 3
mol:cGMP -0.022 0.11 -10000 0 -0.28 51 51
GNB1 0.027 0.005 -10000 0 -10000 0 0
Rhodopsin 0.027 0.046 -10000 0 -0.37 3 3
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 -0.016 0.12 -10000 0 -0.24 57 57
Metarhodopsin II 0.02 0.029 -10000 0 -0.27 1 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family -0.016 0.12 -10000 0 -0.29 51 51
RGS9BP 0.01 0.08 -10000 0 -0.3 17 17
Metarhodopsin II/Transducin -0.014 0.073 -10000 0 -0.24 32 32
GCAP Family/Ca ++ -0.005 0.098 -10000 0 -0.28 35 35
PDE6A/B 0 0.1 -10000 0 -0.36 25 25
mol:Pi 0.024 0.088 -10000 0 -0.3 23 23
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.001 0.087 -10000 0 -0.27 32 32
PDE6B 0.003 0.11 -10000 0 -0.48 16 16
PDE6A -0.001 0.094 -10000 0 -0.48 10 10
PDE6G 0.014 0.075 -10000 0 -0.48 7 7
RHO 0.021 0.013 -10000 0 -10000 0 0
PDE6 0.018 0.13 -10000 0 -0.29 45 45
GUCA1A -0.019 0.13 -10000 0 -0.48 24 24
GC2/GCAP Family -0.005 0.098 -10000 0 -0.28 35 35
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.006 0.098 -10000 0 -0.4 17 17
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.012 0.13 0.41 30 -10000 0 30
KIRREL 0.001 0.1 -10000 0 -0.5 14 14
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.012 0.13 -10000 0 -0.41 30 30
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARRB2 0.026 0.008 -10000 0 -10000 0 0
WASL 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.006 0.1 -10000 0 -0.31 29 29
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.012 0.093 -10000 0 -0.3 29 29
FYN -0.001 0.11 0.15 42 -0.3 30 72
mol:Ca2+ 0.004 0.1 -10000 0 -0.3 30 30
mol:DAG 0.005 0.11 -10000 0 -0.31 30 30
NPHS2 -0.005 0.017 -10000 0 -10000 0 0
mol:IP3 0.005 0.11 -10000 0 -0.31 30 30
regulation of endocytosis 0.004 0.096 -10000 0 -0.28 30 30
Nephrin/NEPH1/podocin/Cholesterol -0.005 0.1 -10000 0 -0.3 30 30
establishment of cell polarity -0.012 0.13 -10000 0 -0.41 30 30
Nephrin/NEPH1/podocin/NCK1-2 0.017 0.11 -10000 0 -0.29 30 30
Nephrin/NEPH1/beta Arrestin2 0.005 0.098 -10000 0 -0.28 30 30
NPHS1 -0.021 0.14 -10000 0 -0.32 46 46
Nephrin/NEPH1/podocin -0.006 0.096 -10000 0 -0.3 30 30
TJP1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.028 0.004 -10000 0 -10000 0 0
NCK2 0.026 0.027 -10000 0 -0.48 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.006 0.11 -10000 0 -0.31 30 30
CD2AP 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.006 0.11 -10000 0 -0.31 30 30
GRB2 0.027 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.12 0.16 38 -0.28 42 80
cytoskeleton organization -0.023 0.11 0.2 6 -0.36 29 35
Nephrin/NEPH1 -0.005 0.095 -10000 0 -0.29 30 30
Nephrin/NEPH1/ZO-1 0.003 0.11 -10000 0 -0.33 30 30
Syndecan-1-mediated signaling events

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
TGFB1 0.023 0.047 -10000 0 -0.48 3 3
CCL5 0.015 0.066 -10000 0 -0.24 16 16
SDCBP 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.075 0.17 -10000 0 -0.5 33 33
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 -0.065 0.18 -10000 0 -0.51 32 32
Syndecan-1/Syntenin -0.058 0.17 -10000 0 -0.49 29 29
MAPK3 -0.061 0.16 0.3 1 -0.49 28 29
HGF/MET -0.022 0.14 -10000 0 -0.36 48 48
TGFB1/TGF beta receptor Type II 0.023 0.047 -10000 0 -0.48 3 3
BSG 0.024 0.028 -10000 0 -0.48 1 1
keratinocyte migration -0.064 0.18 -10000 0 -0.5 32 32
Syndecan-1/RANTES -0.065 0.18 0.32 1 -0.5 34 35
Syndecan-1/CD147 -0.047 0.18 0.32 1 -0.51 28 29
Syndecan-1/Syntenin/PIP2 -0.057 0.16 -10000 0 -0.47 29 29
LAMA5 0.013 0.081 -10000 0 -0.48 9 9
positive regulation of cell-cell adhesion -0.056 0.16 -10000 0 -0.46 29 29
MMP7 -0.046 0.16 -10000 0 -0.48 36 36
HGF 0 0.11 -10000 0 -0.48 16 16
Syndecan-1/CASK -0.076 0.16 -10000 0 -0.48 33 33
Syndecan-1/HGF/MET -0.085 0.2 0.32 1 -0.52 42 43
regulation of cell adhesion -0.064 0.15 0.29 1 -0.48 26 27
HPSE 0.018 0.067 -10000 0 -0.48 6 6
positive regulation of cell migration -0.075 0.17 -10000 0 -0.5 33 33
SDC1 -0.07 0.17 -10000 0 -0.51 32 32
Syndecan-1/Collagen -0.075 0.17 -10000 0 -0.5 33 33
PPIB 0.027 0.01 -10000 0 -10000 0 0
MET -0.029 0.15 -10000 0 -0.48 34 34
PRKACA 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.01 0.12 -10000 0 -0.48 20 20
MAPK1 -0.061 0.16 0.3 1 -0.49 26 27
homophilic cell adhesion -0.074 0.17 0.2 3 -0.5 33 36
MMP1 -0.061 0.17 -10000 0 -0.48 46 46
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.03 0.13 -10000 0 -0.32 46 46
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.14 0.33 4 -0.48 16 20
alphaV/beta3 Integrin/Osteopontin/Src -0.017 0.13 -10000 0 -0.36 41 41
AP1 -0.032 0.16 -10000 0 -0.52 20 20
ILK -0.038 0.13 -10000 0 -0.32 46 46
bone resorption -0.038 0.13 0.32 1 -0.43 20 21
PTK2B 0.019 0.048 -10000 0 -0.48 3 3
PYK2/p130Cas -0.008 0.14 -10000 0 -0.3 52 52
ITGAV 0.027 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.033 0.055 -10000 0 -0.35 7 7
alphaV/beta3 Integrin/Osteopontin -0.016 0.15 -10000 0 -0.36 46 46
MAP3K1 -0.038 0.13 -10000 0 -0.33 45 45
JUN 0.024 0.04 -10000 0 -0.48 2 2
MAPK3 -0.051 0.13 -10000 0 -0.34 47 47
MAPK1 -0.048 0.12 -10000 0 -0.33 43 43
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 -0.044 0.12 0.19 6 -0.32 43 49
ITGB3 -0.004 0.1 -10000 0 -0.49 12 12
NFKBIA -0.048 0.13 -10000 0 -0.5 17 17
FOS 0.004 0.094 -10000 0 -0.49 11 11
CD44 0.023 0.047 -10000 0 -0.48 3 3
CHUK 0.028 0.004 -10000 0 -10000 0 0
PLAU -0.087 0.28 -10000 0 -1 24 24
NF kappa B1 p50/RelA -0.021 0.15 -10000 0 -0.47 20 20
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.016 0.081 -10000 0 -0.36 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.13 -10000 0 -0.33 47 47
VAV3 -0.05 0.13 0.19 6 -0.34 45 51
MAP3K14 -0.042 0.13 -10000 0 -0.34 46 46
ROCK2 0.022 0.054 -10000 0 -0.48 4 4
SPP1 -0.047 0.17 -10000 0 -0.49 41 41
RAC1 0.025 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.04 0.12 -10000 0 -0.32 44 44
MMP2 -0.048 0.14 -10000 0 -0.48 22 22
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.036 0.08 -10000 0 -10000 0 0
SMARCC2 0.028 0.008 -10000 0 -10000 0 0
SMARCC1 0.028 0.007 -10000 0 -10000 0 0
TBX21 -0.058 0.18 0.38 3 -0.72 15 18
SUMO2 0.027 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.003 -10000 0 -10000 0 0
FKBP4 0.026 0.007 -10000 0 -10000 0 0
FKBP5 0.017 0.064 -10000 0 -0.29 11 11
GR alpha/HSP90/FKBP51/HSP90 0.062 0.11 0.28 21 -0.26 4 25
PRL -0.029 0.093 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.083 0.22 0.5 42 -0.41 3 45
RELA 0.003 0.087 -10000 0 -0.2 28 28
FGG -0.059 0.31 0.45 28 -0.5 89 117
GR beta/TIF2 0.046 0.12 0.29 24 -0.33 7 31
IFNG -0.21 0.37 -10000 0 -0.87 62 62
apoptosis 0.008 0.14 0.5 8 -0.71 3 11
CREB1 0.017 0.042 -10000 0 -0.38 2 2
histone acetylation 0.034 0.14 0.35 28 -0.31 9 37
BGLAP -0.028 0.16 -10000 0 -0.92 6 6
GR/PKAc 0.062 0.1 0.28 16 -0.36 1 17
NF kappa B1 p50/RelA 0.001 0.14 -10000 0 -0.33 37 37
SMARCD1 0.028 0.007 -10000 0 -10000 0 0
MDM2 0.041 0.081 0.21 34 -10000 0 34
GATA3 0.023 0.028 -10000 0 -10000 0 0
AKT1 0.023 0.005 -10000 0 -10000 0 0
CSF2 -0.18 0.44 -10000 0 -1.2 54 54
GSK3B 0.027 0.01 -10000 0 -10000 0 0
NR1I3 0.028 0.17 0.48 9 -0.74 6 15
CSN2 0.054 0.16 0.33 51 -0.24 28 79
BRG1/BAF155/BAF170/BAF60A 0.061 0.056 -10000 0 -0.27 8 8
NFATC1 0.021 0.048 -10000 0 -0.48 3 3
POU2F1 0.021 0.041 -10000 0 -0.48 2 2
CDKN1A -0.003 0.14 -10000 0 -1.4 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.011 0.09 -10000 0 -0.48 11 11
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.064 0.12 0.3 16 -0.24 13 29
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.005 0.16 0.44 9 -0.74 8 17
JUN -0.13 0.18 0.36 2 -0.45 51 53
IL4 -0.038 0.12 -10000 0 -0.31 34 34
CDK5R1 0.024 0.032 -10000 0 -0.49 1 1
PRKACA 0.026 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.12 0.16 0.21 21 -0.36 70 91
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.07 0.1 0.3 13 -0.26 3 16
cortisol/GR alpha (monomer) 0.12 0.27 0.57 56 -0.35 9 65
NCOA2 0.013 0.077 -10000 0 -0.48 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.057 0.11 -10000 0 -0.37 22 22
AP-1/NFAT1-c-4 -0.22 0.29 -10000 0 -0.6 103 103
AFP -0.11 0.21 -10000 0 -1.1 7 7
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.067 0.13 0.4 13 -10000 0 13
TP53 0.026 0.086 -10000 0 -0.58 6 6
PPP5C 0.027 0.006 -10000 0 -10000 0 0
KRT17 -0.24 0.42 -10000 0 -1.1 62 62
KRT14 -0.23 0.44 -10000 0 -1.3 50 50
TBP 0.026 0.042 -10000 0 -0.36 4 4
CREBBP 0.084 0.1 0.32 46 -0.21 1 47
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC2 0.039 0.033 -10000 0 -10000 0 0
AP-1 -0.22 0.29 -10000 0 -0.6 103 103
MAPK14 0.026 0.011 -10000 0 -10000 0 0
MAPK10 -0.011 0.13 -10000 0 -0.48 22 22
MAPK11 0.023 0.04 -10000 0 -0.48 2 2
KRT5 -0.28 0.46 -10000 0 -1.1 71 71
interleukin-1 receptor activity 0.013 0.031 -10000 0 -10000 0 0
NCOA1 0.027 0.03 -10000 0 -0.35 2 2
STAT1 0.033 0.003 -10000 0 -10000 0 0
CGA -0.047 0.14 -10000 0 -0.8 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.2 0.46 69 -10000 0 69
MAPK3 0.027 0.01 -10000 0 -10000 0 0
MAPK1 0.026 0.011 -10000 0 -10000 0 0
ICAM1 -0.083 0.25 -10000 0 -0.79 29 29
NFKB1 0.003 0.087 -10000 0 -0.24 10 10
MAPK8 -0.089 0.15 0.34 1 -0.37 45 46
MAPK9 0.026 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.007 0.14 0.5 8 -0.75 3 11
BAX -0.001 0.072 -10000 0 -10000 0 0
POMC -0.1 0.31 -10000 0 -1.5 13 13
EP300 0.084 0.1 0.32 45 -0.21 1 46
cortisol/GR alpha (dimer)/p53 0.094 0.22 0.5 44 -0.54 1 45
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.073 0.23 18 -10000 0 18
SGK1 0.074 0.15 0.47 2 -1.3 1 3
IL13 -0.12 0.19 -10000 0 -0.65 16 16
IL6 -0.087 0.27 -10000 0 -0.9 26 26
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.1 0.15 -10000 0 -0.38 55 55
IL2 -0.14 0.22 -10000 0 -0.64 27 27
CDK5 0.027 0.007 -10000 0 -10000 0 0
PRKACB 0.023 0.041 -10000 0 -0.48 2 2
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
IL8 -0.11 0.3 -10000 0 -0.86 39 39
CDK5R1/CDK5 0.037 0.027 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA/PKAc 0.029 0.12 -10000 0 -0.3 16 16
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.1 0.22 0.48 50 -10000 0 50
SMARCA4 0.017 0.072 -10000 0 -0.48 7 7
chromatin remodeling 0.061 0.14 0.33 28 -0.46 2 30
NF kappa B1 p50/RelA/Cbp 0.089 0.16 0.34 62 -0.34 8 70
JUN (dimer) -0.13 0.18 0.36 2 -0.44 51 53
YWHAH 0.027 0.006 -10000 0 -10000 0 0
VIPR1 -0.094 0.25 -10000 0 -0.8 32 32
NR3C1 0.071 0.17 0.39 41 -10000 0 41
NR4A1 -0.014 0.13 -10000 0 -0.52 21 21
TIF2/SUV420H1 0.027 0.06 -10000 0 -0.35 8 8
MAPKKK cascade 0.008 0.14 0.5 8 -0.71 3 11
cortisol/GR alpha (dimer)/Src-1 0.11 0.23 0.5 54 -10000 0 54
PBX1 0.008 0.087 -10000 0 -0.48 10 10
POU1F1 0 0.007 -10000 0 -10000 0 0
SELE -0.083 0.26 -10000 0 -0.94 22 22
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.061 0.14 0.33 28 -0.47 2 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.1 0.22 0.48 50 -10000 0 50
mol:cortisol 0.058 0.16 0.33 55 -0.19 24 79
MMP1 -0.22 0.44 -10000 0 -1.2 52 52
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.003 0.041 -10000 0 -0.32 2 2
Crk/p130 Cas/Paxillin -0.044 0.097 -10000 0 -0.28 35 35
JUN -0.029 0.11 -10000 0 -0.34 18 18
HRAS 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.024 0.13 -10000 0 -0.32 41 41
RAP1A 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.023 0.13 -10000 0 -0.33 41 41
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.011 0.1 -10000 0 -0.28 38 38
RHOA 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.022 0.11 -10000 0 -0.29 42 42
GRB7 0.021 0.055 -10000 0 -0.48 4 4
RET51/GFRalpha1/GDNF -0.024 0.13 -10000 0 -0.32 42 42
MAPKKK cascade -0.03 0.11 -10000 0 -0.3 38 38
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
RET9/GFRalpha1/GDNF/IRS1 -0.016 0.11 -10000 0 -0.28 43 43
lamellipodium assembly -0.028 0.093 -10000 0 -0.26 34 34
RET51/GFRalpha1/GDNF/SHC -0.021 0.12 -10000 0 -0.31 36 36
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.092 -10000 0 -0.28 29 29
RET9/GFRalpha1/GDNF/Shank3 -0.011 0.1 -10000 0 -0.27 38 38
MAPK3 -0.033 0.12 0.51 1 -0.28 41 42
DOK1 0.025 0.039 -10000 0 -0.48 2 2
DOK6 0.008 0.084 -10000 0 -0.48 9 9
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.027 0.11 0.57 1 -0.33 18 19
DOK5 -0.025 0.14 -10000 0 -0.48 26 26
GFRA1 -0.058 0.18 -10000 0 -0.34 81 81
MAPK8 -0.037 0.1 -10000 0 -0.28 42 42
HRAS/GTP -0.013 0.13 -10000 0 -0.34 40 40
tube development -0.007 0.097 0.21 7 -0.26 36 43
MAPK1 -0.031 0.11 0.51 1 -0.27 38 39
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.016 0.077 -10000 0 -0.24 33 33
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
PDLIM7 0.025 0.029 -10000 0 -0.48 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.021 0.13 -10000 0 -0.32 43 43
SHC1 0.023 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.024 0.13 -10000 0 -0.32 42 42
RET51/GFRalpha1/GDNF/Dok5 -0.05 0.15 -10000 0 -0.32 64 64
PRKCA 0.015 0.073 -10000 0 -0.36 11 11
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
CREB1 -0.022 0.097 -10000 0 -0.29 33 33
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.074 -10000 0 -0.24 29 29
RET51/GFRalpha1/GDNF/Grb7 -0.026 0.13 -10000 0 -0.33 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.016 0.11 -10000 0 -0.21 66 66
DOK4 0.021 0.044 -10000 0 -0.48 2 2
JNK cascade -0.028 0.1 0.18 1 -0.34 18 19
RET9/GFRalpha1/GDNF/FRS2 -0.01 0.097 -10000 0 -0.28 34 34
SHANK3 0.024 0.028 -10000 0 -0.48 1 1
RASA1 0.025 0.028 -10000 0 -0.48 1 1
NCK1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.014 0.073 -10000 0 -0.24 29 29
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.026 0.093 -10000 0 -0.26 40 40
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.033 0.11 -10000 0 -0.29 44 44
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.027 0.1 -10000 0 -0.28 38 38
PI3K -0.035 0.14 -10000 0 -0.38 39 39
SOS1 0.028 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.001 0.099 -10000 0 -0.26 36 36
GRB10 0.014 0.077 -10000 0 -0.48 8 8
activation of MAPKK activity -0.013 0.091 -10000 0 -0.24 36 36
RET51/GFRalpha1/GDNF/FRS2 -0.023 0.12 -10000 0 -0.31 41 41
GAB1 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.015 0.081 -10000 0 -0.48 9 9
IRS2 0.015 0.061 -10000 0 -0.22 16 16
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.028 0.1 -10000 0 -0.28 36 36
RET51/GFRalpha1/GDNF/PKC alpha -0.028 0.13 -10000 0 -0.32 46 46
GRB2 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.026 0.007 -10000 0 -10000 0 0
GDNF 0.014 0.029 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.029 0.13 -10000 0 -0.32 49 49
Rac1/GTP -0.026 0.11 -10000 0 -0.31 33 33
RET9/GFRalpha1/GDNF -0.022 0.1 -10000 0 -0.3 37 37
GFRalpha1/GDNF -0.029 0.12 -10000 0 -0.36 37 37
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 -0.006 0.12 -10000 0 -0.48 22 22
GNB1/GNG2 -0.033 0.16 -10000 0 -0.44 27 27
mol:DAG -0.048 0.14 -10000 0 -0.43 23 23
PLCG1 -0.049 0.14 -10000 0 -0.45 23 23
YES1 -0.061 0.14 -10000 0 -0.42 30 30
FZD3 0.019 0.049 -10000 0 -0.48 3 3
FZD6 0.02 0.048 -10000 0 -0.48 3 3
G protein -0.028 0.16 0.26 2 -0.46 22 24
MAP3K7 -0.049 0.12 0.24 1 -0.37 24 25
mol:Ca2+ -0.046 0.13 -10000 0 -0.42 23 23
mol:IP3 -0.048 0.14 -10000 0 -0.43 23 23
NLK 0.005 0.079 -10000 0 -0.84 3 3
GNB1 0.027 0.005 -10000 0 -10000 0 0
CAMK2A -0.05 0.14 0.24 1 -0.39 27 28
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.058 0.16 -10000 0 -0.32 72 72
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.061 0.14 -10000 0 -0.31 68 68
GO:0007205 -0.051 0.13 -10000 0 -0.42 23 23
WNT6 -0.001 0.1 -10000 0 -0.48 13 13
WNT4 -0.044 0.16 -10000 0 -0.48 40 40
NFAT1/CK1 alpha -0.047 0.16 -10000 0 -0.45 29 29
GNG2 0.024 0.039 -10000 0 -0.48 2 2
WNT5A 0.005 0.1 -10000 0 -0.48 15 15
WNT11 -0.011 0.12 -10000 0 -0.48 19 19
CDC42 -0.055 0.14 -10000 0 -0.44 26 26
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS -0.045 0.15 -10000 0 -0.29 79 79
SMAD6-7/SMURF1 0.043 0.042 -10000 0 -0.3 4 4
NOG -0.034 0.15 -10000 0 -0.33 60 60
SMAD9 -0.06 0.2 -10000 0 -0.54 45 45
SMAD4 0.025 0.009 -10000 0 -10000 0 0
SMAD5 -0.05 0.14 -10000 0 -0.46 19 19
BMP7/USAG1 -0.076 0.16 -10000 0 -0.35 74 74
SMAD5/SKI -0.037 0.14 0.24 1 -0.43 20 21
SMAD1 0.016 0.055 -10000 0 -0.42 1 1
BMP2 -0.015 0.13 -10000 0 -0.48 25 25
SMAD1/SMAD1/SMAD4 0.021 0.059 -10000 0 -0.33 2 2
BMPR1A 0.028 0.004 -10000 0 -10000 0 0
BMPR1B -0.046 0.18 -10000 0 -0.48 47 47
BMPR1A-1B/BAMBI -0.029 0.14 -10000 0 -0.32 63 63
AHSG 0.011 0.04 -10000 0 -10000 0 0
CER1 0 0 -10000 0 -10000 0 0
BMP2-4/CER1 -0.017 0.12 -10000 0 -0.32 44 44
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.043 0.14 -10000 0 -0.42 24 24
BMP2-4 (homodimer) -0.022 0.14 -10000 0 -0.37 44 44
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.004 0.13 -10000 0 -0.3 53 53
RGMA 0.001 0.099 -10000 0 -0.48 12 12
SMURF1 0.027 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.044 0.12 -10000 0 -0.37 24 24
BMP2-4/USAG1 -0.063 0.16 -10000 0 -0.34 72 72
SMAD6/SMURF1/SMAD5 -0.033 0.14 0.24 1 -0.45 17 18
SOSTDC1 -0.064 0.17 -10000 0 -0.48 43 43
BMP7/BMPR2/BMPR1A-1B -0.031 0.14 -10000 0 -0.29 72 72
SKI 0.027 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.006 0.097 -10000 0 -0.48 10 10
HFE2 0.018 0.028 -10000 0 -10000 0 0
ZFYVE16 0.027 0.007 -10000 0 -10000 0 0
MAP3K7 0.025 0.008 -10000 0 -10000 0 0
BMP2-4/CHRD -0.019 0.14 -10000 0 -0.36 48 48
SMAD5/SMAD5/SMAD4 -0.035 0.14 0.24 1 -0.43 19 20
MAPK1 0.027 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.024 0.12 -10000 0 -0.36 18 18
BMP7 (homodimer) -0.046 0.15 -10000 0 -0.48 33 33
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.077 -10000 0 -0.34 10 10
SMAD1/SKI 0.028 0.062 -10000 0 -0.41 1 1
SMAD6 0.023 0.047 -10000 0 -0.48 3 3
CTDSP2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/FETUA -0.012 0.12 -10000 0 -0.32 40 40
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.062 0.19 -10000 0 -0.48 55 55
BMPR2 (homodimer) 0.028 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.051 0.018 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.017 0.13 -10000 0 -0.35 47 47
CHRDL1 -0.04 0.16 -10000 0 -0.38 58 58
ENDOFIN/SMAD1 0.028 0.058 -10000 0 -0.39 1 1
SMAD6-7/SMURF1/SMAD1 0.037 0.074 -10000 0 -0.35 2 2
SMAD6/SMURF1 0.027 0.007 -10000 0 -10000 0 0
BAMBI -0.018 0.12 -10000 0 -0.48 20 20
SMURF2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.045 0.18 -10000 0 -0.37 69 69
BMP2-4/GREM1 -0.062 0.17 -10000 0 -0.33 90 90
SMAD7 0.024 0.029 -10000 0 -0.48 1 1
SMAD8A/SMAD8A/SMAD4 -0.046 0.19 -10000 0 -0.54 39 39
SMAD1/SMAD6 0.025 0.063 -10000 0 -0.41 1 1
TAK1/SMAD6 0.036 0.015 -10000 0 -10000 0 0
BMP7 -0.046 0.15 -10000 0 -0.48 33 33
BMP6 -0.006 0.097 -10000 0 -0.48 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.042 0.13 -10000 0 -0.4 28 28
PPM1A 0.027 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.026 0.063 -10000 0 -0.41 1 1
SMAD7/SMURF1 0.034 0.026 -10000 0 -0.35 1 1
CTDSPL 0.027 0.005 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.003 -10000 0 -10000 0 0
CTDSP1 0.028 0.003 -10000 0 -10000 0 0
PPP1R15A 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.065 0.15 -10000 0 -0.45 31 31
CHRD -0.005 0.11 -10000 0 -0.48 16 16
BMPR2 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.053 0.13 -10000 0 -0.4 27 27
BMP4 -0.012 0.13 -10000 0 -0.48 23 23
FST -0.015 0.11 -10000 0 -0.48 14 14
BMP2-4/NOG -0.042 0.17 -10000 0 -0.37 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.019 0.14 -10000 0 -0.28 64 64
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.015 0.044 -10000 0 -0.29 4 4
NFATC2 -0.031 0.083 -10000 0 -0.33 22 22
NFATC3 -0.012 0.033 -10000 0 -10000 0 0
CD40LG -0.14 0.23 0.34 1 -0.58 55 56
PTGS2 -0.15 0.23 -10000 0 -0.57 64 64
JUNB 0.021 0.048 -10000 0 -0.4 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.027 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.027 -10000 0 -10000 0 0
CALM1 0.01 0.026 -10000 0 -10000 0 0
JUN 0.006 0.047 -10000 0 -0.49 2 2
mol:Ca2+ -0.008 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.014 -10000 0 -10000 0 0
FOSL1 -0.026 0.13 -10000 0 -0.48 24 24
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.056 0.15 -10000 0 -0.37 42 42
FOS -0.012 0.096 -10000 0 -0.5 11 11
IFNG -0.15 0.23 0.34 1 -0.53 71 72
AP-1/NFAT1-c-4 -0.13 0.25 -10000 0 -0.6 54 54
FASLG -0.13 0.22 0.34 1 -0.55 51 52
NFAT1-c-4/ICER1 -0.045 0.1 -10000 0 -0.32 23 23
IL2RA -0.14 0.22 0.34 1 -0.55 54 55
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.16 0.25 0.33 1 -0.56 76 77
JunB/Fra1/NFAT1-c-4 -0.056 0.13 -10000 0 -0.35 32 32
IL4 -0.13 0.2 -10000 0 -0.47 65 65
IL2 0.002 0.12 -10000 0 -0.88 6 6
IL3 -0.008 0.069 -10000 0 -0.85 2 2
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
BATF3 0.015 0.065 -10000 0 -0.48 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.022 0.039 -10000 0 -0.48 2 2
FOXM1 transcription factor network

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
NFATC3 -0.077 0.41 -9999 0 -1.2 23 23
PLK1 -0.033 0.32 -9999 0 -1.3 19 19
BIRC5 -0.096 0.43 -9999 0 -1.4 33 33
HSPA1B -0.076 0.41 -9999 0 -1.2 24 24
MAP2K1 0.022 0.043 -9999 0 -10000 0 0
BRCA2 -0.083 0.42 -9999 0 -1.2 25 25
FOXM1 -0.14 0.62 -9999 0 -1.8 28 28
XRCC1 -0.074 0.41 -9999 0 -1.2 22 22
FOXM1B/p19 -0.12 0.4 -9999 0 -1.2 25 25
Cyclin D1/CDK4 -0.12 0.41 -9999 0 -1.1 29 29
CDC2 -0.086 0.43 -9999 0 -1.2 33 33
TGFA -0.13 0.42 -9999 0 -1 35 35
SKP2 -0.05 0.42 -9999 0 -1.2 24 24
CCNE1 0.009 0.085 -9999 0 -0.5 9 9
CKS1B -0.053 0.41 -9999 0 -1.2 22 22
RB1 -0.066 0.3 -9999 0 -0.94 26 26
FOXM1C/SP1 -0.1 0.48 -9999 0 -1.4 28 28
AURKB -0.098 0.41 -9999 0 -1.1 42 42
CENPF -0.091 0.45 -9999 0 -1.2 30 30
CDK4 0.016 0.028 -9999 0 -10000 0 0
MYC -0.075 0.36 -9999 0 -1 26 26
CHEK2 0.021 0.045 -9999 0 -10000 0 0
ONECUT1 -0.12 0.43 -9999 0 -1.1 31 31
CDKN2A -0.022 0.11 -9999 0 -0.48 15 15
LAMA4 -0.082 0.42 -9999 0 -1.2 24 24
FOXM1B/HNF6 -0.16 0.52 -9999 0 -1.5 30 30
FOS -0.099 0.44 -9999 0 -1.2 32 32
SP1 0.028 0.006 -9999 0 -10000 0 0
CDC25B -0.076 0.41 -9999 0 -1.2 21 21
response to radiation 0.004 0.024 -9999 0 -10000 0 0
CENPB -0.076 0.41 -9999 0 -1.2 23 23
CENPA -0.12 0.49 -9999 0 -1.3 38 38
NEK2 -0.095 0.47 -9999 0 -1.4 31 31
HIST1H2BA -0.079 0.41 -9999 0 -1.1 33 33
CCNA2 0.012 0.081 -9999 0 -0.5 8 8
EP300 0.027 0.005 -9999 0 -10000 0 0
CCNB1/CDK1 -0.11 0.49 -9999 0 -1.5 27 27
CCNB2 -0.089 0.44 -9999 0 -1.4 24 24
CCNB1 -0.088 0.44 -9999 0 -1.3 27 27
ETV5 -0.083 0.42 -9999 0 -1.2 27 27
ESR1 -0.12 0.46 -9999 0 -1.2 38 38
CCND1 -0.12 0.42 -9999 0 -1.1 29 29
GSK3A 0.02 0.039 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.03 0.1 -9999 0 -0.41 13 13
CDK2 0.024 0.018 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.004 0.028 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.082 0.45 -9999 0 -1.3 32 32
GAS1 -0.1 0.44 -9999 0 -1.2 32 32
MMP2 -0.09 0.44 -9999 0 -1.3 27 27
RB1/FOXM1C -0.12 0.43 -9999 0 -1.2 30 30
CREBBP 0.027 0.005 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.028 0.14 0.36 2 -0.41 30 32
CRKL -0.033 0.13 -10000 0 -0.43 31 31
HRAS -0.017 0.13 -10000 0 -0.4 24 24
mol:PIP3 -0.019 0.15 0.32 1 -0.44 27 28
SPRED1 0.027 0.006 -10000 0 -10000 0 0
SPRED2 0.028 0.002 -10000 0 -10000 0 0
GAB1 -0.034 0.14 -10000 0 -0.44 33 33
FOXO3 -0.021 0.15 0.48 1 -0.43 31 32
AKT1 -0.021 0.16 0.32 1 -0.45 33 34
BAD -0.02 0.15 0.31 1 -0.42 33 34
megakaryocyte differentiation -0.043 0.15 -10000 0 -0.44 36 36
GSK3B -0.018 0.15 0.31 1 -0.42 32 33
RAF1 -0.003 0.11 0.24 4 -0.34 20 24
SHC1 0.023 0.013 -10000 0 -10000 0 0
STAT3 -0.036 0.14 -10000 0 -0.45 34 34
STAT1 -0.095 0.33 -10000 0 -1 35 35
HRAS/SPRED1 0.002 0.12 -10000 0 -0.36 14 14
cell proliferation -0.034 0.14 -10000 0 -0.44 32 32
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
TEC 0.026 0.028 -10000 0 -0.48 1 1
RPS6KB1 -0.023 0.16 0.25 1 -0.45 35 36
HRAS/SPRED2 0.002 0.12 -10000 0 -0.33 22 22
LYN/TEC/p62DOK 0.001 0.15 -10000 0 -0.45 28 28
MAPK3 0.003 0.089 0.21 6 -0.26 10 16
STAP1 -0.055 0.17 -10000 0 -0.48 40 40
GRAP2 0.014 0.081 -10000 0 -0.48 9 9
JAK2 -0.079 0.29 -10000 0 -0.88 36 36
STAT1 (dimer) -0.09 0.32 -10000 0 -0.99 36 36
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.004 0.16 -10000 0 -0.43 31 31
actin filament polymerization -0.036 0.13 -10000 0 -0.42 31 31
LYN 0.022 0.039 -10000 0 -0.48 2 2
STAP1/STAT5A (dimer) -0.075 0.22 -10000 0 -0.62 41 41
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.003 0.13 0.39 1 -0.4 24 25
PI3K 0 0.16 0.28 1 -0.45 29 30
PTEN 0.027 0.005 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.089 0.38 -10000 0 -1.2 33 33
MAPK8 -0.035 0.14 -10000 0 -0.45 32 32
STAT3 (dimer) -0.035 0.14 -10000 0 -0.44 34 34
positive regulation of transcription 0.005 0.077 0.19 7 -0.22 8 15
mol:GDP -0.015 0.13 -10000 0 -0.41 26 26
PIK3C2B -0.037 0.15 0.36 1 -0.47 30 31
CBL/CRKL -0.016 0.13 0.4 1 -0.42 27 28
FER -0.035 0.14 -10000 0 -0.44 33 33
SH2B3 -0.037 0.15 -10000 0 -0.45 35 35
PDPK1 -0.017 0.14 0.31 3 -0.42 25 28
SNAI2 -0.039 0.15 -10000 0 -0.46 32 32
positive regulation of cell proliferation -0.067 0.25 -10000 0 -0.73 37 37
KITLG 0.01 0.087 -10000 0 -0.51 9 9
cell motility -0.067 0.25 -10000 0 -0.73 37 37
PTPN6 0.026 0.029 -10000 0 -0.48 1 1
EPOR -0.033 0.21 -10000 0 -0.82 14 14
STAT5A (dimer) -0.05 0.21 -10000 0 -0.6 37 37
SOCS1 0.025 0.029 -10000 0 -0.31 2 2
cell migration 0.044 0.15 0.44 38 -10000 0 38
SOS1 0.028 0.003 -10000 0 -10000 0 0
EPO 0.015 0.026 -10000 0 -0.15 2 2
VAV1 0.015 0.077 -10000 0 -0.48 8 8
GRB10 -0.038 0.14 0.36 1 -0.46 29 30
PTPN11 0.028 0.008 -10000 0 -10000 0 0
SCF/KIT -0.035 0.15 -10000 0 -0.46 35 35
GO:0007205 0.002 0.007 -10000 0 -10000 0 0
MAP2K1 -0.001 0.094 0.21 7 -0.28 12 19
CBL 0.027 0.006 -10000 0 -10000 0 0
KIT -0.1 0.39 -10000 0 -1.3 33 33
MAP2K2 0.001 0.093 0.21 7 -0.28 13 20
SHC/Grb2/SOS1 0.001 0.14 -10000 0 -0.44 25 25
STAT5A -0.05 0.21 -10000 0 -0.62 37 37
GRB2 0.027 0.006 -10000 0 -10000 0 0
response to radiation -0.038 0.14 0.27 1 -0.46 32 33
SHC/GRAP2 0.027 0.051 -10000 0 -0.35 5 5
PTPRO -0.044 0.15 -10000 0 -0.45 36 36
SH2B2 -0.037 0.14 -10000 0 -0.43 31 31
DOK1 0.025 0.039 -10000 0 -0.48 2 2
MATK -0.044 0.15 -10000 0 -0.45 38 38
CREBBP 0.02 0.048 -10000 0 -0.18 1 1
BCL2 -0.065 0.27 -10000 0 -1.1 17 17
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.055 -10000 0 -0.29 9 9
ARNO/beta Arrestin1-2 -0.014 0.18 -10000 0 -0.78 16 16
EGFR 0.008 0.09 -10000 0 -0.48 11 11
EPHA2 0.011 0.086 -10000 0 -0.48 10 10
USP6 0.026 0.008 -10000 0 -10000 0 0
IQSEC1 0.026 0.028 -10000 0 -0.49 1 1
EGFR/EGFR/EGF/EGF -0.038 0.15 -10000 0 -0.36 60 60
ARRB2 -0.006 0.069 -10000 0 -0.34 14 14
mol:GTP 0.007 0.049 0.19 2 -0.19 10 12
ARRB1 0.024 0.039 -10000 0 -0.48 2 2
FBXO8 0.027 0.005 -10000 0 -10000 0 0
TSHR -0.011 0.12 -10000 0 -0.48 20 20
EGF -0.059 0.19 -10000 0 -0.48 56 56
somatostatin receptor activity 0 0 0.001 15 -0.001 45 60
ARAP2 0.013 0.085 -10000 0 -0.48 10 10
mol:GDP -0.043 0.14 0.18 5 -0.34 48 53
mol:PI-3-4-5-P3 0 0 0.001 5 -0.001 22 27
ITGA2B -0.017 0.13 -10000 0 -0.48 21 21
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.069 -10000 0 -0.28 12 12
ADAP1 0.014 0.068 -10000 0 -0.48 6 6
KIF13B 0.017 0.055 -10000 0 -0.48 4 4
HGF/MET -0.023 0.14 -10000 0 -0.36 48 48
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.04 0.13 0.22 12 -0.29 46 58
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.02 0.14 -10000 0 -0.31 60 60
ADRB2 0.003 0.11 -10000 0 -0.45 18 18
receptor agonist activity 0 0 0 5 0 37 42
actin filament binding 0 0 0 14 -0.001 46 60
SRC 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.003 0.1 -10000 0 -0.48 12 12
GNAQ 0.025 0.028 -10000 0 -0.49 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 21 -0.001 33 54
ARF6/GDP -0.023 0.16 0.45 1 -0.51 23 24
ARF6/GDP/GULP/ACAP1 -0.026 0.15 0.21 2 -0.41 30 32
alphaIIb/beta3 Integrin/paxillin/GIT1 0.014 0.11 -10000 0 -0.29 31 31
ACAP1 0.017 0.067 -10000 0 -0.48 6 6
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.007 0.09 -10000 0 -0.42 14 14
EFNA1 0.018 0.055 -10000 0 -0.48 4 4
HGF 0 0.11 -10000 0 -0.48 16 16
CYTH3 0.006 0.005 -10000 0 -10000 0 0
CYTH2 -0.022 0.2 -10000 0 -1 14 14
NCK1 0.028 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0 14 0 42 56
endosomal lumen acidification 0 0 0 15 0 39 54
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.012 0.087 -10000 0 -0.48 10 10
GNAQ/ARNO -0.005 0.19 -10000 0 -0.94 14 14
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 4 0 14 18
MET -0.029 0.15 -10000 0 -0.48 34 34
GNA14 -0.01 0.13 -10000 0 -0.49 25 25
GNA15 0.019 0.061 -10000 0 -0.48 5 5
GIT1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 18 -0.001 36 54
GNA11 0.023 0.039 -10000 0 -0.48 2 2
LHCGR -0.01 0.1 -10000 0 -0.48 14 14
AGTR1 -0.017 0.13 -10000 0 -0.32 45 45
desensitization of G-protein coupled receptor protein signaling pathway -0.007 0.09 -10000 0 -0.42 14 14
IPCEF1/ARNO -0.042 0.2 -10000 0 -0.85 15 15
alphaIIb/beta3 Integrin -0.017 0.12 -10000 0 -0.37 31 31
LPA receptor mediated 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
GNB1/GNG2 0.038 0.07 -10000 0 -0.28 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.13 0.23 3 -0.38 20 23
AP1 -0.026 0.11 -10000 0 -0.25 54 54
mol:PIP3 -0.031 0.089 -10000 0 -0.25 40 40
AKT1 0.013 0.077 0.25 3 -0.31 5 8
PTK2B -0.05 0.15 0.26 1 -0.44 30 31
RHOA 0 0.075 0.19 2 -0.36 10 12
PIK3CB 0.024 0.039 -10000 0 -0.48 2 2
mol:Ca2+ -0.046 0.12 0.25 5 -0.3 46 51
MAGI3 0.023 0.04 -10000 0 -0.48 2 2
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.03 0.1 -10000 0 -0.27 49 49
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.057 0.14 0.26 4 -0.45 26 30
NF kappa B1 p50/RelA -0.045 0.13 -10000 0 -0.33 48 48
endothelial cell migration -0.002 0.1 -10000 0 -0.47 14 14
ADCY4 -0.015 0.094 0.24 1 -0.37 14 15
ADCY5 -0.033 0.12 0.24 1 -0.41 26 27
ADCY6 -0.017 0.098 0.24 1 -0.38 16 17
ADCY7 -0.017 0.095 -10000 0 -0.4 13 13
ADCY1 -0.021 0.1 0.24 1 -0.37 17 18
ADCY2 -0.029 0.11 0.24 1 -0.39 21 22
ADCY3 -0.015 0.096 0.24 1 -0.37 15 16
ADCY8 -0.018 0.093 -10000 0 -0.39 13 13
ADCY9 -0.019 0.1 0.24 1 -0.4 15 16
GSK3B -0.048 0.14 0.21 3 -0.46 25 28
arachidonic acid secretion -0.022 0.1 -10000 0 -0.36 19 19
GNG2 0.024 0.039 -10000 0 -0.48 2 2
TRIP6 0.006 0.07 -10000 0 -0.38 11 11
GNAO1 -0.007 0.083 -10000 0 -0.3 24 24
HRAS 0.027 0.005 -10000 0 -10000 0 0
NFKBIA -0.04 0.14 0.27 4 -0.36 41 45
GAB1 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.21 -10000 0 -0.92 17 17
JUN 0.024 0.04 -10000 0 -0.48 2 2
LPA/LPA2/NHERF2 0.028 0.048 -10000 0 -0.3 6 6
TIAM1 -0.023 0.25 -10000 0 -1.1 18 18
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 -0.042 0.12 0.25 5 -0.29 44 49
PLCB3 0.011 0.046 0.18 6 -0.27 6 12
FOS 0.004 0.094 -10000 0 -0.48 11 11
positive regulation of mitosis -0.022 0.1 -10000 0 -0.36 19 19
LPA/LPA1-2-3 -0.007 0.11 -10000 0 -0.27 49 49
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
stress fiber formation -0.035 0.12 0.25 1 -0.37 25 26
GNAZ -0.02 0.1 0.15 1 -0.3 37 38
EGFR/PI3K-beta/Gab1 -0.023 0.097 -10000 0 -0.26 40 40
positive regulation of dendritic cell cytokine production -0.008 0.11 -10000 0 -0.26 49 49
LPA/LPA2/MAGI-3 0.031 0.034 -10000 0 -0.3 2 2
ARHGEF1 0.025 0.076 0.2 24 -0.24 11 35
GNAI2 0.005 0.061 -10000 0 -0.29 13 13
GNAI3 0.005 0.06 -10000 0 -0.28 14 14
GNAI1 0.003 0.069 -10000 0 -0.33 13 13
LPA/LPA3 -0.033 0.11 -10000 0 -0.31 43 43
LPA/LPA2 0.019 0.019 -10000 0 -10000 0 0
LPA/LPA1 0.011 0.072 -10000 0 -0.33 14 14
HB-EGF/EGFR -0.009 0.099 -10000 0 -0.33 27 27
HBEGF -0.016 0.09 -10000 0 -0.37 20 20
mol:DAG -0.042 0.12 0.25 5 -0.29 44 49
cAMP biosynthetic process -0.023 0.11 0.28 3 -0.37 18 21
NFKB1 0.028 0.004 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
GNB1 0.027 0.005 -10000 0 -10000 0 0
LYN -0.043 0.14 0.3 3 -0.36 41 44
GNAQ -0.025 0.093 -10000 0 -0.28 36 36
LPAR2 0.026 0.007 -10000 0 -10000 0 0
LPAR3 -0.048 0.16 -10000 0 -0.28 85 85
LPAR1 0.015 0.077 -10000 0 -0.33 13 13
IL8 -0.074 0.17 0.34 2 -0.44 49 51
PTK2 -0.025 0.09 0.18 5 -0.26 38 43
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
CASP3 -0.03 0.1 -10000 0 -0.27 49 49
EGFR 0.008 0.089 -10000 0 -0.48 11 11
PLCG1 -0.031 0.11 0.16 5 -0.31 40 45
PLD2 -0.028 0.099 0.21 6 -0.26 45 51
G12/G13 0.039 0.055 -10000 0 -0.25 9 9
PI3K-beta 0.001 0.068 -10000 0 -0.34 6 6
cell migration -0.009 0.077 -10000 0 -0.27 14 14
SLC9A3R2 0.018 0.067 -10000 0 -0.48 6 6
PXN -0.035 0.13 0.25 1 -0.38 25 26
HRAS/GTP -0.023 0.1 -10000 0 -0.37 19 19
RAC1 0.025 0.009 -10000 0 -10000 0 0
MMP9 -0.01 0.12 -10000 0 -0.48 20 20
PRKCE 0.026 0.028 -10000 0 -0.49 1 1
PRKCD -0.045 0.11 0.28 3 -0.39 15 18
Gi(beta/gamma) -0.012 0.094 -10000 0 -0.38 13 13
mol:LPA -0.002 0.025 -10000 0 -0.17 7 7
TRIP6/p130 Cas/FAK1/Paxillin -0.029 0.13 -10000 0 -0.4 18 18
MAPKKK cascade -0.022 0.1 -10000 0 -0.36 19 19
contractile ring contraction involved in cytokinesis 0.002 0.075 0.19 2 -0.35 10 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.044 0.12 -10000 0 -0.31 55 55
GNA15 -0.028 0.096 -10000 0 -0.28 40 40
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.058 0.15 0.26 4 -0.46 26 30
GNA11 -0.025 0.09 -10000 0 -0.27 38 38
Rac1/GTP -0.006 0.23 -10000 0 -0.98 17 17
MMP2 -0.002 0.1 -10000 0 -0.47 14 14
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.023 0.075 -10000 0 -0.27 19 19
RGS9BP 0.01 0.08 -10000 0 -0.3 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.011 0.045 -10000 0 -0.48 1 1
mol:Na + -0.07 0.14 -10000 0 -0.32 78 78
mol:ADP -0.012 0.031 -10000 0 -0.35 1 1
GNAT2 0.024 0.016 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.025 0.089 -10000 0 -0.3 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.016 0.01 -10000 0 -10000 0 0
GRK7 0.023 0.015 -10000 0 -10000 0 0
CNGB3 -0.034 0.14 -10000 0 -0.48 28 28
Cone Metarhodopsin II/X-Arrestin 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.079 0.14 0.18 9 -0.31 81 90
Cone PDE6 0.022 0.075 -10000 0 -0.25 23 23
Cone Metarhodopsin II 0.021 0.029 -10000 0 -0.27 1 1
Na + (4 Units) -0.069 0.15 -10000 0 -0.31 81 81
GNAT2/GDP 0.031 0.082 -10000 0 -0.26 23 23
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.004 0.006 -10000 0 -10000 0 0
Cone Transducin 0.025 0.08 -10000 0 -0.29 19 19
SLC24A2 0 0.09 -10000 0 -0.26 28 28
GNB3/GNGT2 0.013 0.094 -10000 0 -0.37 19 19
GNB3 0.005 0.098 -10000 0 -0.4 17 17
GNAT2/GTP 0.018 0.011 -10000 0 -10000 0 0
CNGA3 -0.088 0.19 -10000 0 -0.48 58 58
ARR3 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.07 0.14 -10000 0 -0.32 78 78
mol:Pi 0.024 0.088 -10000 0 -0.3 23 23
Cone CNG Channel -0.054 0.12 -10000 0 -0.26 78 78
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0.09 -10000 0 -0.26 28 28
RGS9 0.004 0.1 -10000 0 -0.48 15 15
PDE6C 0 0 -10000 0 -10000 0 0
GNGT2 0.015 0.073 -10000 0 -0.36 11 11
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.009 0.14 -10000 0 -0.47 21 21
alphaM/beta2 Integrin/GPIbA -0.001 0.14 -10000 0 -0.4 30 30
alphaM/beta2 Integrin/proMMP-9 -0.003 0.14 -10000 0 -0.42 30 30
PLAUR 0.019 0.061 -10000 0 -0.48 5 5
HMGB1 0.018 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.017 0.12 -10000 0 -0.49 16 16
AGER -0.082 0.18 -10000 0 -0.33 101 101
RAP1A 0.027 0.006 -10000 0 -10000 0 0
SELPLG 0.017 0.072 -10000 0 -0.48 7 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.038 0.18 -10000 0 -0.34 72 72
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.01 0.12 -10000 0 -0.48 20 20
CYR61 0.022 0.048 -10000 0 -0.4 4 4
TLN1 0.025 0.028 -10000 0 -0.48 1 1
Rap1/GTP -0.048 0.16 -10000 0 -0.44 30 30
RHOA 0.027 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.006 0.12 -10000 0 -0.48 21 21
MYH2 -0.084 0.16 -10000 0 -0.45 32 32
MST1R 0.019 0.062 -10000 0 -0.48 5 5
leukocyte activation during inflammatory response -0.017 0.13 -10000 0 -0.34 36 36
APOB -0.027 0.13 -10000 0 -0.48 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.014 0.077 -10000 0 -0.48 8 8
JAM3 0.024 0.023 -10000 0 -10000 0 0
GP1BA 0 0.11 -10000 0 -0.48 16 16
alphaM/beta2 Integrin/CTGF 0.008 0.12 -10000 0 -0.41 23 23
alphaM/beta2 Integrin -0.073 0.18 -10000 0 -0.5 32 32
JAM3 homodimer 0.023 0.023 -10000 0 -10000 0 0
ICAM2 0.026 0.028 -10000 0 -0.48 1 1
ICAM1 0.009 0.09 -10000 0 -0.48 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.071 0.17 -10000 0 -0.49 32 32
cell adhesion -0.001 0.14 -10000 0 -0.4 30 30
NFKB1 -0.088 0.2 0.38 1 -0.46 53 54
THY1 0.017 0.067 -10000 0 -0.48 6 6
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.009 0.086 -10000 0 -0.29 24 24
alphaM/beta2 Integrin/LRP/tPA 0.001 0.14 -10000 0 -0.47 19 19
IL6 -0.098 0.22 -10000 0 -0.68 31 31
ITGB2 0.003 0.096 -10000 0 -0.51 11 11
elevation of cytosolic calcium ion concentration 0.003 0.15 -10000 0 -0.44 29 29
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.12 -10000 0 -0.43 17 17
JAM2 0.022 0.048 -10000 0 -0.48 3 3
alphaM/beta2 Integrin/ICAM1 0.023 0.15 -10000 0 -0.39 31 31
alphaM/beta2 Integrin/uPA/Plg -0.004 0.14 -10000 0 -0.42 29 29
RhoA/GTP -0.084 0.17 -10000 0 -0.46 34 34
positive regulation of phagocytosis -0.046 0.17 -10000 0 -0.55 23 23
Ron/MSP 0.022 0.076 -10000 0 -0.36 12 12
alphaM/beta2 Integrin/uPAR/uPA 0.005 0.15 -10000 0 -0.45 29 29
alphaM/beta2 Integrin/uPAR 0.013 0.13 -10000 0 -0.45 20 20
PLAU -0.013 0.12 -10000 0 -0.27 48 48
PLAT -0.006 0.083 -10000 0 -0.48 6 6
actin filament polymerization -0.081 0.15 -10000 0 -0.43 32 32
MST1 0.012 0.077 -10000 0 -0.48 7 7
alphaM/beta2 Integrin/lipoprotein(a) -0.014 0.13 -10000 0 -0.34 36 36
TNF -0.11 0.24 -10000 0 -0.76 32 32
RAP1B 0.026 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.006 0.15 -10000 0 -0.46 29 29
fibrinolysis -0.005 0.14 -10000 0 -0.42 29 29
HCK 0.014 0.077 -10000 0 -0.48 8 8
dendritic cell antigen processing and presentation -0.071 0.17 -10000 0 -0.49 32 32
VTN -0.007 0.11 -10000 0 -0.48 15 15
alphaM/beta2 Integrin/CYR61 0.015 0.12 -10000 0 -0.45 19 19
LPA 0.014 0.028 -10000 0 -10000 0 0
LRP1 0.02 0.061 -10000 0 -0.48 5 5
cell migration -0.016 0.14 -10000 0 -0.41 33 33
FN1 0.009 0.089 -10000 0 -0.48 10 10
alphaM/beta2 Integrin/Thy1 0.011 0.13 -10000 0 -0.48 19 19
MPO 0.011 0.074 -10000 0 -0.48 6 6
KNG1 0.008 0.044 -10000 0 -0.13 31 31
RAP1/GDP 0.034 0.012 -10000 0 -10000 0 0
ROCK1 -0.078 0.16 -10000 0 -0.44 33 33
ELA2 0 0 -10000 0 -10000 0 0
PLG 0 0 -10000 0 -10000 0 0
CTGF 0.013 0.078 -10000 0 -0.48 8 8
alphaM/beta2 Integrin/Hck 0.014 0.14 -10000 0 -0.57 15 15
ITGAM -0.003 0.11 -10000 0 -0.52 13 13
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.007 0.15 -10000 0 -0.4 33 33
HP -0.11 0.2 -10000 0 -0.48 74 74
leukocyte adhesion -0.044 0.16 -10000 0 -0.42 30 30
SELP -0.006 0.12 -10000 0 -0.48 21 21
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.002 0.11 -9999 0 -0.48 17 17
GPC2 -0.003 0.1 -9999 0 -0.48 12 12
GPC2/Midkine -0.001 0.11 -9999 0 -0.39 25 25
neuron projection morphogenesis -0.001 0.11 -9999 0 -0.38 25 25
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.025 0.14 -10000 0 -0.41 28 28
TBX21 -0.099 0.37 -10000 0 -1.2 29 29
B2M 0.026 0.014 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.006 0.09 -10000 0 -0.52 9 9
GADD45B -0.079 0.32 -10000 0 -0.88 34 34
IL12RB2 -0.008 0.099 -10000 0 -0.49 10 10
GADD45G -0.1 0.37 -10000 0 -1 40 40
natural killer cell activation 0.001 0.016 -10000 0 -10000 0 0
RELB 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.003 0.1 -10000 0 -0.49 15 15
IL2RA 0.002 0.1 -10000 0 -0.48 15 15
IFNG -0.033 0.14 -10000 0 -0.28 67 67
STAT3 (dimer) -0.073 0.29 -10000 0 -0.75 41 41
HLA-DRB5 -0.015 0.12 -10000 0 -0.3 44 44
FASLG -0.1 0.4 -10000 0 -1.2 34 34
NF kappa B2 p52/RelB -0.079 0.35 -10000 0 -0.94 36 36
CD4 0.015 0.072 -10000 0 -0.48 7 7
SOCS1 0.025 0.029 -10000 0 -0.31 2 2
EntrezGene:6955 -0.001 0.008 -10000 0 -10000 0 0
CD3D 0.009 0.085 -10000 0 -0.49 9 9
CD3E 0.011 0.083 -10000 0 -0.49 9 9
CD3G -0.002 0.11 -10000 0 -0.49 17 17
IL12Rbeta2/JAK2 0.01 0.083 -10000 0 -0.36 10 10
CCL3 -0.11 0.39 -10000 0 -1.2 32 32
CCL4 -0.091 0.35 -10000 0 -1.1 27 27
HLA-A 0.022 0.048 -10000 0 -0.48 3 3
IL18/IL18R 0.023 0.13 -10000 0 -0.36 29 29
NOS2 -0.1 0.39 -10000 0 -1.2 34 34
IL12/IL12R/TYK2/JAK2/SPHK2 -0.03 0.14 -10000 0 -0.41 29 29
IL1R1 -0.09 0.35 -10000 0 -1.1 27 27
IL4 -0.001 0.016 -10000 0 -10000 0 0
JAK2 0.018 0.03 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.045 0.27 -10000 0 -1 20 20
RAB7A -0.068 0.28 -10000 0 -0.76 32 32
lysosomal transport -0.062 0.26 -10000 0 -0.71 32 32
FOS -0.077 0.33 -10000 0 -1.1 26 26
STAT4 (dimer) -0.081 0.34 -10000 0 -0.87 40 40
STAT5A (dimer) -0.1 0.35 -10000 0 -0.9 43 43
GZMA -0.11 0.39 -10000 0 -1.2 30 30
GZMB -0.11 0.39 -10000 0 -1.2 32 32
HLX 0.02 0.055 -10000 0 -0.48 4 4
LCK -0.1 0.38 -10000 0 -1.1 36 36
TCR/CD3/MHC II/CD4 -0.033 0.18 -10000 0 -0.53 29 29
IL2/IL2R 0.03 0.11 -10000 0 -0.37 19 19
MAPK14 -0.093 0.35 -10000 0 -0.85 48 48
CCR5 -0.079 0.34 -10000 0 -1 28 28
IL1B -0.017 0.13 -10000 0 -0.49 23 23
STAT6 -0.004 0.12 -10000 0 -0.88 2 2
STAT4 0.013 0.086 -10000 0 -0.45 11 11
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.004 -10000 0 -10000 0 0
NFKB2 0.028 0.004 -10000 0 -10000 0 0
IL12B -0.011 0.12 -10000 0 -0.49 20 20
CD8A 0.008 0.092 -10000 0 -0.5 10 10
CD8B 0.001 0.1 -10000 0 -0.3 29 29
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.025 0.14 0.41 28 -10000 0 28
IL2RB 0.017 0.067 -10000 0 -0.48 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.3 -10000 0 -0.77 41 41
IL2RG 0.013 0.082 -10000 0 -0.48 9 9
IL12 -0.001 0.11 -10000 0 -0.36 25 25
STAT5A 0.026 0.028 -10000 0 -0.48 1 1
CD247 0.02 0.043 -10000 0 -0.49 2 2
IL2 0.021 0.019 -10000 0 -10000 0 0
SPHK2 0.023 0.047 -10000 0 -0.48 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.089 -10000 0 -0.5 9 9
IL12/IL12R/TYK2/JAK2 -0.11 0.43 -10000 0 -1.1 38 38
MAP2K3 -0.096 0.35 -10000 0 -0.82 51 51
RIPK2 0.025 0.009 -10000 0 -10000 0 0
MAP2K6 -0.1 0.36 -10000 0 -0.86 50 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.11 -10000 0 -0.46 18 18
IL18RAP 0.001 0.1 -10000 0 -0.49 14 14
IL12Rbeta1/TYK2 0.02 0.075 -10000 0 -0.39 8 8
EOMES -0.04 0.25 -10000 0 -1.2 13 13
STAT1 (dimer) -0.098 0.31 -10000 0 -0.79 41 41
T cell proliferation -0.046 0.24 -10000 0 -0.62 39 39
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.076 -10000 0 -0.38 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.062 0.27 -10000 0 -0.68 40 40
ATF2 -0.082 0.32 -10000 0 -0.77 48 48
Ephrin B reverse signaling

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
EFNB2 0.021 0.049 -10000 0 -0.48 3 3
EPHB2 0.007 0.096 -10000 0 -0.49 12 12
EFNB1 -0.005 0.06 -10000 0 -0.36 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.12 -10000 0 -0.35 23 23
Ephrin B2/EPHB1-2 0.01 0.097 -10000 0 -0.31 23 23
neuron projection morphogenesis -0.003 0.1 -10000 0 -0.33 23 23
Ephrin B1/EPHB1-2/Tiam1 0.003 0.12 -10000 0 -0.35 27 27
DNM1 0.013 0.082 -10000 0 -0.49 9 9
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.046 0.17 -10000 0 -0.62 27 27
YES1 -0.054 0.23 -10000 0 -0.85 27 27
Ephrin B1/EPHB1-2/NCK2 0.01 0.11 -10000 0 -0.36 22 22
PI3K -0.012 0.18 -10000 0 -0.62 27 27
mol:GDP 0.002 0.12 -10000 0 -0.35 27 27
ITGA2B -0.017 0.13 -10000 0 -0.48 21 21
endothelial cell proliferation 0.028 0.041 -10000 0 -0.3 5 5
FYN -0.06 0.24 -10000 0 -0.86 27 27
MAP3K7 -0.048 0.18 -10000 0 -0.65 27 27
FGR -0.052 0.24 -10000 0 -0.85 28 28
TIAM1 0.015 0.073 -10000 0 -0.48 7 7
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
RGS3 0.027 0.006 -10000 0 -10000 0 0
cell adhesion -0.054 0.19 -10000 0 -0.64 27 27
LYN -0.051 0.23 -10000 0 -0.85 27 27
Ephrin B1/EPHB1-2/Src Family Kinases -0.053 0.21 -10000 0 -0.79 27 27
Ephrin B1/EPHB1-2 -0.049 0.19 -10000 0 -0.71 26 26
SRC -0.05 0.23 -10000 0 -0.85 27 27
ITGB3 -0.003 0.1 -10000 0 -0.48 12 12
EPHB1 -0.009 0.1 -10000 0 -0.48 11 11
EPHB4 0.024 0.039 -10000 0 -0.48 2 2
RAC1 0.025 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.042 -10000 0 -0.3 5 5
alphaIIb/beta3 Integrin -0.017 0.12 -10000 0 -0.37 31 31
BLK -0.073 0.24 -10000 0 -0.87 28 28
HCK -0.054 0.24 -10000 0 -0.86 27 27
regulation of stress fiber formation -0.009 0.11 0.36 22 -10000 0 22
MAPK8 -0.044 0.16 -10000 0 -0.59 27 27
Ephrin B1/EPHB1-2/RGS3 0.012 0.11 -10000 0 -0.35 22 22
endothelial cell migration -0.038 0.15 0.38 1 -0.53 27 28
NCK2 0.026 0.027 -10000 0 -0.48 1 1
PTPN13 -0.026 0.16 -10000 0 -0.61 25 25
regulation of focal adhesion formation -0.009 0.11 0.36 22 -10000 0 22
chemotaxis -0.011 0.11 0.34 22 -10000 0 22
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.11 -10000 0 -0.34 23 23
angiogenesis -0.05 0.19 -10000 0 -0.7 27 27
LCK -0.054 0.23 -10000 0 -0.84 28 28
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.034 0.16 0.28 27 -0.49 20 47
FYN -0.006 0.2 0.28 10 -0.66 21 31
LAT/GRAP2/SLP76 0.008 0.17 0.27 5 -0.56 22 27
IKBKB 0.024 0.01 -10000 0 -10000 0 0
AKT1 0.001 0.14 0.23 14 -0.42 24 38
B2M 0.027 0.008 -10000 0 -10000 0 0
IKBKG 0.006 0.05 0.094 29 -0.15 11 40
MAP3K8 0.024 0.039 -10000 0 -0.48 2 2
mol:Ca2+ -0.02 0.022 0.086 2 -0.081 20 22
integrin-mediated signaling pathway 0.03 0.033 -10000 0 -0.3 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.011 0.19 0.26 9 -0.64 23 32
TRPV6 -0.014 0.27 1.1 14 -0.48 23 37
CD28 0.008 0.1 -10000 0 -0.49 14 14
SHC1 0.011 0.19 0.28 31 -0.63 20 51
receptor internalization -0.019 0.2 0.22 1 -0.6 29 30
PRF1 -0.011 0.22 -10000 0 -0.87 16 16
KRAS 0.026 0.008 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
COT/AKT1 0.014 0.12 0.21 14 -0.35 21 35
LAT -0.01 0.19 0.29 7 -0.68 21 28
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.012 0.084 -10000 0 -0.49 9 9
CD3E 0.013 0.084 -10000 0 -0.5 9 9
CD3G 0 0.11 -10000 0 -0.49 17 17
RASGRP2 0.001 0.033 0.066 2 -0.17 10 12
RASGRP1 -0.01 0.15 0.26 8 -0.48 22 30
HLA-A 0.023 0.048 -10000 0 -0.49 3 3
RASSF5 0.021 0.048 -10000 0 -0.48 3 3
RAP1A/GTP/RAPL 0.03 0.033 -10000 0 -0.3 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.062 0.14 39 -0.14 14 53
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.016 0.062 -10000 0 -0.22 20 20
PRKCA -0.003 0.084 0.16 6 -0.27 21 27
GRAP2 0.014 0.081 -10000 0 -0.48 9 9
mol:IP3 0.004 0.13 0.23 14 -0.42 20 34
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.019 0.18 -10000 0 -0.7 17 17
ORAI1 -0.007 0.21 0.41 4 -0.96 14 18
CSK -0.008 0.19 0.29 4 -0.66 21 25
B7 family/CD28 0.008 0.21 0.27 3 -0.7 22 25
CHUK 0.028 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.019 0.22 -10000 0 -0.76 22 22
PTPN6 -0.013 0.19 0.26 4 -0.69 19 23
VAV1 -0.016 0.19 0.26 3 -0.7 20 23
Monovalent TCR/CD3 -0.009 0.13 -10000 0 -0.47 20 20
CBL 0.027 0.006 -10000 0 -10000 0 0
LCK -0.005 0.2 0.28 8 -0.69 21 29
PAG1 -0.004 0.19 0.27 9 -0.65 21 30
RAP1A 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.017 0.21 0.22 1 -0.8 19 20
CD80 0.007 0.1 -10000 0 -0.49 14 14
CD86 0.016 0.078 -10000 0 -0.49 8 8
PDK1/CARD11/BCL10/MALT1 -0.01 0.078 -10000 0 -0.26 21 21
HRAS 0.027 0.005 -10000 0 -10000 0 0
GO:0035030 -0.016 0.16 0.22 6 -0.57 22 28
CD8A 0.009 0.091 -10000 0 -0.49 10 10
CD8B 0.003 0.1 -10000 0 -0.29 29 29
PTPRC 0.011 0.086 -10000 0 -0.49 10 10
PDK1/PKC theta -0.007 0.17 0.28 13 -0.54 22 35
CSK/PAG1 -0.002 0.19 0.26 11 -0.62 21 32
SOS1 0.028 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.036 0.039 -10000 0 -0.36 3 3
GRAP2/SLP76 0.008 0.2 0.25 2 -0.67 21 23
STIM1 0.008 0.081 1.2 1 -10000 0 1
RAS family/GTP 0.022 0.075 0.16 26 -0.18 15 41
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.023 0.22 -10000 0 -0.66 29 29
mol:DAG -0.02 0.1 0.12 1 -0.37 21 22
RAP1A/GDP 0.015 0.029 0.078 24 -0.065 8 32
PLCG1 0.027 0.006 -10000 0 -10000 0 0
CD247 0.022 0.041 -10000 0 -0.49 2 2
cytotoxic T cell degranulation -0.008 0.2 -10000 0 -0.82 16 16
RAP1A/GTP 0.001 0.012 -10000 0 -0.064 10 10
mol:PI-3-4-5-P3 -0.003 0.16 0.24 12 -0.51 23 35
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.006 0.17 0.25 13 -0.56 20 33
NRAS 0.027 0.006 -10000 0 -10000 0 0
ZAP70 0.003 0.1 -10000 0 -0.49 15 15
GRB2/SOS1 0.04 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.006 0.16 0.29 2 -0.54 22 24
MALT1 0.024 0.015 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.011 0.12 -10000 0 -0.41 21 21
CARD11 -0.003 0.12 -10000 0 -0.48 19 19
PRKCB -0.004 0.089 0.14 4 -0.3 20 24
PRKCE 0 0.082 0.16 6 -0.27 19 25
PRKCQ -0.013 0.19 0.26 9 -0.63 22 31
LCP2 0.017 0.067 -10000 0 -0.48 6 6
BCL10 0.027 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression 0.005 0.12 0.21 16 -0.36 23 39
IKK complex 0.016 0.059 0.14 29 -0.12 11 40
RAS family/GDP 0 0.01 -10000 0 -10000 0 0
MAP3K14 0.009 0.09 0.17 15 -0.28 19 34
PDPK1 0.002 0.13 0.24 16 -0.42 21 37
TCR/CD3/MHC I/CD8/Fyn -0.026 0.22 -10000 0 -0.87 18 18
Effects of Botulinum toxin

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
STX1A -0.001 0.047 -10000 0 -0.35 6 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.015 0.12 -10000 0 -0.35 36 36
STXBP1 0.018 0.063 -10000 0 -0.33 9 9
ACh/CHRNA1 -0.032 0.11 -10000 0 -0.28 46 46
RAB3GAP2/RIMS1/UNC13B 0.002 0.1 -10000 0 -0.3 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.04 0.15 -10000 0 -0.48 34 34
mol:ACh -0.005 0.035 0.082 16 -0.1 20 36
RAB3GAP2 0.026 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.011 0.097 -10000 0 -0.24 41 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.032 0.11 -10000 0 -0.28 46 46
UNC13B 0.025 0.029 -10000 0 -0.48 1 1
CHRNA1 -0.043 0.16 -10000 0 -0.32 72 72
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.028 0.098 -10000 0 -0.3 34 34
SNAP25 -0.005 0.043 -10000 0 -0.28 8 8
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.039 0.15 -10000 0 -0.48 31 31
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.012 0.056 -10000 0 -0.3 10 10
STX1A/SNAP25 fragment 1/VAMP2 -0.011 0.097 -10000 0 -0.24 41 41
Syndecan-4-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
PTK2 -0.003 0.14 -10000 0 -0.54 18 18
Syndecan-4/Syndesmos -0.029 0.19 -10000 0 -0.59 30 30
positive regulation of JNK cascade -0.018 0.19 -10000 0 -0.57 31 31
Syndecan-4/ADAM12 -0.053 0.22 -10000 0 -0.67 33 33
CCL5 0.015 0.066 -10000 0 -0.24 16 16
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
DNM2 0.026 0.007 -10000 0 -10000 0 0
ITGA5 0.022 0.044 -10000 0 -0.22 8 8
SDCBP 0.025 0.009 -10000 0 -10000 0 0
PLG 0 0.009 0.043 2 -0.048 2 4
ADAM12 -0.028 0.15 -10000 0 -0.48 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.014 -10000 0 -0.064 9 9
Syndecan-4/Laminin alpha1 -0.042 0.2 -10000 0 -0.61 32 32
Syndecan-4/CXCL12/CXCR4 -0.02 0.2 -10000 0 -0.61 31 31
Syndecan-4/Laminin alpha3 -0.056 0.2 -10000 0 -0.6 34 34
MDK 0.002 0.11 -10000 0 -0.48 17 17
Syndecan-4/FZD7 -0.03 0.19 -10000 0 -0.61 29 29
Syndecan-4/Midkine -0.04 0.2 -10000 0 -0.62 30 30
FZD7 0.022 0.055 -10000 0 -0.48 4 4
Syndecan-4/FGFR1/FGF -0.025 0.18 -10000 0 -0.56 31 31
THBS1 0.011 0.083 -10000 0 -0.48 9 9
integrin-mediated signaling pathway -0.053 0.21 -10000 0 -0.62 32 32
positive regulation of MAPKKK cascade -0.018 0.19 -10000 0 -0.57 31 31
Syndecan-4/TACI -0.054 0.2 -10000 0 -0.61 33 33
CXCR4 0.026 0.029 -10000 0 -0.48 1 1
cell adhesion 0.004 0.073 0.2 7 -0.34 11 18
Syndecan-4/Dynamin -0.029 0.19 -10000 0 -0.59 30 30
Syndecan-4/TSP1 -0.036 0.2 -10000 0 -0.62 31 31
Syndecan-4/GIPC -0.029 0.19 -10000 0 -0.59 30 30
Syndecan-4/RANTES -0.034 0.19 -10000 0 -0.61 29 29
ITGB1 0.027 0.01 -10000 0 -10000 0 0
LAMA1 -0.01 0.11 -10000 0 -0.48 15 15
LAMA3 -0.035 0.15 -10000 0 -0.48 35 35
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA 0.011 0.16 0.82 11 -0.42 7 18
Syndecan-4/alpha-Actinin -0.03 0.19 -10000 0 -0.6 31 31
TFPI -0.001 0.11 -10000 0 -0.33 28 28
F2 -0.007 0.065 -10000 0 -0.39 3 3
alpha5/beta1 Integrin 0.035 0.036 -10000 0 -0.29 3 3
positive regulation of cell adhesion -0.074 0.2 -10000 0 -0.6 36 36
ACTN1 0.026 0.028 -10000 0 -0.48 1 1
TNC -0.038 0.16 -10000 0 -0.39 55 55
Syndecan-4/CXCL12 -0.037 0.2 -10000 0 -0.63 30 30
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
CXCL12 0.007 0.1 -10000 0 -0.48 14 14
TNFRSF13B -0.032 0.15 -10000 0 -0.48 31 31
FGF2 0.012 0.08 -10000 0 -0.48 8 8
FGFR1 0.02 0.042 -10000 0 -0.48 2 2
Syndecan-4/PI-4-5-P2 -0.045 0.18 -10000 0 -0.59 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.007 0.088 -10000 0 -0.45 11 11
cell migration -0.016 0.01 -10000 0 -0.065 1 1
PRKCD 0.025 0.016 -10000 0 -10000 0 0
vasculogenesis -0.034 0.19 -10000 0 -0.59 31 31
SDC4 -0.044 0.2 -10000 0 -0.63 30 30
Syndecan-4/Tenascin C -0.056 0.22 -10000 0 -0.66 32 32
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.011 -10000 0 -0.058 1 1
Syndecan-4/Syntenin -0.03 0.19 -10000 0 -0.6 28 28
MMP9 -0.011 0.12 -10000 0 -0.48 20 20
Rac1/GTP 0.004 0.075 0.2 7 -0.35 11 18
cytoskeleton organization -0.027 0.18 -10000 0 -0.56 30 30
GIPC1 0.025 0.028 -10000 0 -0.48 1 1
Syndecan-4/TFPI -0.04 0.2 -10000 0 -0.62 31 31
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.01 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.016 0.087 -10000 0 -0.3 17 17
NT3 (dimer)/TRKC -0.027 0.14 -10000 0 -0.36 49 49
NT3 (dimer)/TRKB -0.033 0.15 -10000 0 -0.33 64 64
SHC/Grb2/SOS1/GAB1/PI3K 0.023 0.02 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.027 0.14 -10000 0 -0.29 61 61
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DYNLT1 0.025 0.012 -10000 0 -10000 0 0
NTRK1 0.003 0.095 -10000 0 -0.34 20 20
NTRK2 -0.02 0.14 -10000 0 -0.48 25 25
NTRK3 -0.023 0.14 -10000 0 -0.48 30 30
NT-4/5 (dimer)/TRKB -0.031 0.16 -10000 0 -0.34 62 62
neuron apoptosis 0.084 0.19 0.42 59 -10000 0 59
SHC 2-3/Grb2 -0.092 0.21 -10000 0 -0.47 59 59
SHC1 0.023 0.013 -10000 0 -10000 0 0
SHC2 -0.083 0.2 -10000 0 -0.52 47 47
SHC3 -0.1 0.22 -10000 0 -0.55 57 57
STAT3 (dimer) 0.02 0.069 -10000 0 -0.34 12 12
NT3 (dimer)/TRKA -0.012 0.12 -10000 0 -0.32 41 41
RIN/GDP 0.003 0.09 0.23 10 -0.24 11 21
GIPC1 0.025 0.028 -10000 0 -0.48 1 1
KRAS 0.026 0.008 -10000 0 -10000 0 0
DNAJA3 -0.044 0.098 -10000 0 -0.26 54 54
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.01 0.14 -10000 0 -0.76 12 12
MAGED1 0.027 0.01 -10000 0 -0.13 1 1
PTPN11 0.027 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.015 0.14 -10000 0 -0.48 26 26
SHC/GRB2/SOS1 0.046 0.024 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.028 0.13 -10000 0 -0.33 49 49
TRKA/NEDD4-2 0.016 0.073 -10000 0 -0.35 12 12
ELMO1 0.022 0.041 -10000 0 -0.48 2 2
RhoG/GTP/ELMO1/DOCK1 0.03 0.034 -10000 0 -0.3 3 3
NGF -0.047 0.15 -10000 0 -0.48 31 31
HRAS 0.027 0.005 -10000 0 -10000 0 0
DOCK1 0.026 0.028 -10000 0 -0.48 1 1
GAB2 0.021 0.055 -10000 0 -0.48 4 4
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.024 0.01 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
DNM1 0.013 0.082 -10000 0 -0.48 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.026 0.1 -10000 0 -0.26 47 47
mol:GDP 0.001 0.12 0.3 9 -0.36 11 20
NGF (dimer) -0.047 0.15 -10000 0 -0.48 31 31
RhoG/GDP 0.016 0.029 -10000 0 -0.35 2 2
RIT1/GDP 0.001 0.077 0.18 2 -0.24 9 11
TIAM1 0.015 0.073 -10000 0 -0.48 7 7
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.018 0.13 -10000 0 -0.33 48 48
KIDINS220/CRKL/C3G 0.039 0.012 -10000 0 -10000 0 0
SHC/RasGAP 0.032 0.027 -10000 0 -0.35 1 1
FRS2 family/SHP2 0.05 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.057 0.03 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.017 0.13 -10000 0 -0.36 39 39
RAP1/GDP 0.002 0.071 0.14 2 -0.21 8 10
KIDINS220/CRKL 0.027 0.01 -10000 0 -10000 0 0
BDNF (dimer) -0.027 0.14 -10000 0 -0.29 61 61
ubiquitin-dependent protein catabolic process -0.018 0.11 -10000 0 -0.3 39 39
Schwann cell development -0.025 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.027 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.021 0.043 -10000 0 -0.22 1 1
RAP1B 0.026 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.058 0.16 -10000 0 -0.33 71 71
ABL1 0.027 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.097 -10000 0 -0.39 12 12
STAT3 0.02 0.069 -10000 0 -0.34 12 12
axon guidance -0.063 0.15 -10000 0 -0.32 71 71
MAPK3 -0.032 0.12 0.18 19 -0.3 48 67
MAPK1 -0.03 0.12 0.18 20 -0.3 47 67
CDC42/GDP 0.012 0.095 0.24 10 -0.24 10 20
NTF3 -0.017 0.13 -10000 0 -0.36 39 39
NTF4 -0.015 0.14 -10000 0 -0.48 26 26
NGF (dimer)/TRKA/FAIM -0.015 0.11 -10000 0 -0.3 38 38
PI3K 0.038 0.012 -10000 0 -10000 0 0
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.028 0.004 -10000 0 -10000 0 0
GAB1 0.028 0.004 -10000 0 -10000 0 0
RASGRF1 -0.08 0.14 -10000 0 -0.32 80 80
SOS1 0.028 0.003 -10000 0 -10000 0 0
MCF2L -0.045 0.12 -10000 0 -0.33 52 52
RGS19 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.095 -10000 0 -0.41 6 6
Rac1/GDP 0.007 0.086 0.22 5 -0.25 9 14
NGF (dimer)/TRKA/GRIT -0.025 0.11 -10000 0 -0.3 40 40
neuron projection morphogenesis -0.026 0.14 -10000 0 -0.7 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.018 0.11 -10000 0 -0.3 39 39
MAP2K1 0.025 0.088 0.2 63 -10000 0 63
NGFR -0.008 0.12 -10000 0 -0.48 19 19
NGF (dimer)/TRKA/GIPC/GAIP -0.028 0.1 -10000 0 -0.28 42 42
RAS family/GTP/PI3K 0.021 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.069 0.032 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.011 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCZ 0.022 0.044 -10000 0 -0.48 2 2
MAPKKK cascade -0.089 0.23 -10000 0 -0.58 57 57
RASA1 0.025 0.028 -10000 0 -0.48 1 1
TRKA/c-Abl 0.019 0.074 -10000 0 -0.35 12 12
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.008 0.13 -10000 0 -0.3 49 49
NGF (dimer)/TRKA/p62/Atypical PKCs 0 0.11 -10000 0 -0.27 37 37
MATK 0.007 0.097 -10000 0 -0.48 13 13
NEDD4L 0.024 0.017 -10000 0 -10000 0 0
RAS family/GDP -0.023 0.049 -10000 0 -0.19 10 10
NGF (dimer)/TRKA -0.042 0.1 -10000 0 -0.27 55 55
Rac1/GTP -0.059 0.1 -10000 0 -0.28 41 41
FRS2 family/SHP2/CRK family 0.065 0.036 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.068 -10000 0 -0.49 6 6
GNB1/GNG2 -0.029 0.062 -10000 0 -0.2 36 36
AKT1 -0.008 0.095 0.21 3 -0.25 20 23
EGF -0.059 0.19 -10000 0 -0.48 56 56
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.002 0.067 -10000 0 -0.35 6 6
mol:Ca2+ -0.023 0.13 0.22 1 -0.32 41 42
LYN 0.003 0.052 -10000 0 -0.26 5 5
RhoA/GTP -0.007 0.052 -10000 0 -0.14 27 27
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.029 0.14 -10000 0 -0.37 37 37
GNG2 0.024 0.039 -10000 0 -0.49 2 2
ARRB2 0.026 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.028 0.16 -10000 0 -0.62 21 21
G beta5/gamma2 -0.026 0.086 -10000 0 -0.26 35 35
PRKCH -0.029 0.14 0.24 1 -0.37 38 39
DNM1 0.013 0.082 -10000 0 -0.48 9 9
TXA2/TP beta/beta Arrestin3 -0.004 0.04 0.095 2 -0.21 10 12
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.014 0.074 -10000 0 -0.49 7 7
G12 family/GTP -0.025 0.11 -10000 0 -0.32 34 34
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.026 0.028 -10000 0 -0.48 1 1
RhoA/GTP/ROCK1 0.035 0.01 -10000 0 -10000 0 0
mol:GDP 0.014 0.11 0.37 17 -10000 0 17
mol:NADP 0.004 0.088 -10000 0 -0.48 9 9
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.002 0.12 -10000 0 -0.49 20 20
mol:IP3 -0.033 0.16 -10000 0 -0.41 41 41
cell morphogenesis 0.035 0.01 -10000 0 -10000 0 0
PLCB2 -0.053 0.21 -10000 0 -0.57 41 41
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.021 0.088 -10000 0 -0.28 17 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.002 0.063 -10000 0 -0.31 6 6
RHOA 0.027 0.005 -10000 0 -10000 0 0
PTGIR 0.019 0.061 -10000 0 -0.49 5 5
PRKCB1 -0.032 0.15 -10000 0 -0.4 39 39
GNAQ 0.025 0.028 -10000 0 -0.48 1 1
mol:L-citrulline 0.004 0.088 -10000 0 -0.48 9 9
TXA2/TXA2-R family -0.049 0.2 -10000 0 -0.56 37 37
LCK 0.001 0.066 -10000 0 -0.32 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.057 -10000 0 -0.27 11 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.067 -10000 0 -0.44 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.021 0.063 -10000 0 -0.37 4 4
MAPK14 -0.012 0.096 0.24 4 -0.24 34 38
TGM2/GTP -0.04 0.17 -10000 0 -0.45 42 42
MAPK11 -0.018 0.092 0.18 1 -0.25 35 36
ARHGEF1 -0.013 0.07 -10000 0 -0.19 33 33
GNAI2 0.027 0.005 -10000 0 -10000 0 0
JNK cascade -0.031 0.15 -10000 0 -0.4 37 37
RAB11/GDP 0.027 0.005 -10000 0 -10000 0 0
ICAM1 -0.022 0.12 0.2 1 -0.33 36 37
cAMP biosynthetic process -0.034 0.14 -10000 0 -0.37 42 42
Gq family/GTP/EBP50 -0.01 0.087 -10000 0 -0.25 31 31
actin cytoskeleton reorganization 0.035 0.01 -10000 0 -10000 0 0
SRC 0.005 0.053 -10000 0 -0.27 4 4
GNB5 0.027 0.005 -10000 0 -10000 0 0
GNB1 0.027 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.029 0.095 0.22 4 -0.33 12 16
VCAM1 -0.023 0.12 -10000 0 -0.33 35 35
TP beta/Gq family/GDP/G beta5/gamma2 -0.028 0.16 -10000 0 -0.62 21 21
platelet activation -0.018 0.12 0.28 3 -0.32 37 40
PGI2/IP 0.014 0.044 -10000 0 -0.35 5 5
PRKACA 0.007 0.059 -10000 0 -0.3 11 11
Gq family/GDP/G beta5/gamma2 -0.023 0.15 -10000 0 -0.56 21 21
TXA2/TP beta/beta Arrestin2 -0.011 0.1 -10000 0 -0.48 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0 0.056 -10000 0 -0.3 10 10
mol:DAG -0.037 0.17 -10000 0 -0.45 40 40
EGFR 0.008 0.089 -10000 0 -0.48 11 11
TXA2/TP alpha -0.049 0.2 -10000 0 -0.52 42 42
Gq family/GTP -0.028 0.11 0.22 1 -0.26 53 54
YES1 0.006 0.056 -10000 0 -0.28 3 3
GNAI2/GTP 0.012 0.054 -10000 0 -0.3 4 4
PGD2/DP 0.011 0.053 -10000 0 -0.35 7 7
SLC9A3R1 0.026 0.013 -10000 0 -0.13 2 2
FYN 0.004 0.056 -10000 0 -0.34 3 3
mol:NO 0.004 0.088 -10000 0 -0.48 9 9
GNA15 0.019 0.061 -10000 0 -0.48 5 5
PGK/cGMP 0.003 0.093 -10000 0 -0.31 26 26
RhoA/GDP 0.027 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.028 0.079 -10000 0 -0.35 8 8
NOS3 0.004 0.088 -10000 0 -0.49 9 9
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA -0.03 0.15 0.26 3 -0.38 40 43
PRKCB -0.031 0.14 -10000 0 -0.39 38 38
PRKCE -0.028 0.14 -10000 0 -0.38 38 38
PRKCD -0.03 0.14 -10000 0 -0.39 37 37
PRKCG -0.035 0.15 0.25 1 -0.41 39 40
muscle contraction -0.046 0.19 -10000 0 -0.52 38 38
PRKCZ -0.028 0.13 -10000 0 -0.36 36 36
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta 0.024 0.064 -10000 0 -0.28 8 8
PRKCQ -0.036 0.15 -10000 0 -0.4 39 39
MAPKKK cascade -0.044 0.18 -10000 0 -0.49 40 40
SELE -0.024 0.12 -10000 0 -0.34 35 35
TP beta/GNAI2/GDP/G beta/gamma 0.033 0.07 -10000 0 -0.36 5 5
ROCK1 0.027 0.006 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.48 25 25
chemotaxis -0.053 0.21 -10000 0 -0.62 36 36
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.023 0.039 -10000 0 -0.48 2 2
Rac1/GTP 0.018 0.007 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.023 0.097 -10000 0 -0.36 17 17
fibroblast growth factor receptor signaling pathway 0.022 0.096 -10000 0 -0.36 17 17
LAMA1 -0.01 0.11 -10000 0 -0.48 15 15
PRNP 0.021 0.055 -10000 0 -0.48 4 4
GPC1/SLIT2 0.001 0.12 -10000 0 -0.36 31 31
SMAD2 0.002 0.056 0.18 2 -0.27 13 15
GPC1/PrPc/Cu2+ 0.02 0.074 -10000 0 -0.34 13 13
GPC1/Laminin alpha1 -0.003 0.11 -10000 0 -0.36 27 27
TDGF1 -0.008 0.1 -10000 0 -0.48 13 13
CRIPTO/GPC1 -0.002 0.11 -10000 0 -0.36 24 24
APP/GPC1 0.024 0.072 -10000 0 -0.35 12 12
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.083 -10000 0 -0.31 23 23
FLT1 0.022 0.048 -10000 0 -0.48 3 3
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.07 -10000 0 -0.3 13 13
SERPINC1 0.018 0.028 -10000 0 -10000 0 0
FYN -0.021 0.091 -10000 0 -0.32 25 25
FGR -0.024 0.093 -10000 0 -0.32 28 28
positive regulation of MAPKKK cascade -0.048 0.14 0.27 1 -0.39 35 36
SLIT2 -0.007 0.13 -10000 0 -0.48 23 23
GPC1/NRG -0.009 0.12 -10000 0 -0.37 31 31
NRG1 -0.017 0.12 -10000 0 -0.48 21 21
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.033 0.076 -10000 0 -0.3 16 16
LYN -0.016 0.079 -10000 0 -0.31 20 20
mol:Spermine -0.006 0.065 -10000 0 -0.35 12 12
cell growth 0.022 0.096 -10000 0 -0.36 17 17
BMP signaling pathway -0.009 0.094 0.41 15 -10000 0 15
SRC -0.019 0.082 -10000 0 -0.3 24 24
TGFBR1 0.026 0.013 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.052 0.17 -10000 0 -0.31 83 83
GPC1 0.009 0.094 -10000 0 -0.41 15 15
TGFBR1 (dimer) 0.026 0.013 -10000 0 -10000 0 0
VEGFA 0.025 0.029 -10000 0 -0.31 2 2
BLK -0.052 0.12 -10000 0 -0.31 56 56
HCK -0.025 0.093 -10000 0 -0.31 30 30
FGF2 0.012 0.08 -10000 0 -0.48 8 8
FGFR1 0.02 0.042 -10000 0 -0.48 2 2
VEGFR1 homodimer 0.022 0.047 -10000 0 -0.48 3 3
TGFBR2 0.026 0.028 -10000 0 -0.48 1 1
cell death 0.024 0.072 -10000 0 -0.35 12 12
ATIII/GPC1 0.017 0.075 -10000 0 -0.36 12 12
PLA2G2A/GPC1 -0.035 0.14 -10000 0 -0.36 52 52
LCK -0.025 0.094 -10000 0 -0.31 31 31
neuron differentiation -0.009 0.12 -10000 0 -0.37 31 31
PrPc/Cu2+ 0.015 0.04 -10000 0 -0.35 4 4
APP 0.026 0.007 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.026 0.028 -10000 0 -0.48 1 1
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.03 0.079 -10000 0 -0.27 16 16
ER alpha/Gai/GDP/Gbeta gamma -0.047 0.17 -10000 0 -0.53 28 28
AKT1 -0.077 0.27 -10000 0 -0.73 49 49
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.074 0.28 -10000 0 -0.74 49 49
mol:Ca2+ -0.045 0.15 -10000 0 -0.42 38 38
IGF1R 0.022 0.049 -10000 0 -0.48 3 3
E2/ER alpha (dimer)/Striatin 0.009 0.075 -10000 0 -0.3 16 16
SHC1 0.023 0.013 -10000 0 -10000 0 0
apoptosis 0.072 0.26 0.69 49 -10000 0 49
RhoA/GTP 0.005 0.054 -10000 0 -0.23 13 13
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.026 0.16 -10000 0 -0.45 27 27
regulation of stress fiber formation 0.013 0.073 0.34 4 -0.18 7 11
E2/ERA-ERB (dimer) 0.008 0.077 -10000 0 -0.3 17 17
KRAS 0.026 0.008 -10000 0 -10000 0 0
G13/GTP 0.011 0.064 -10000 0 -0.27 14 14
pseudopodium formation -0.013 0.073 0.18 7 -0.34 4 11
E2/ER alpha (dimer)/PELP1 0.009 0.071 -10000 0 -0.29 15 15
GRB2 0.027 0.006 -10000 0 -10000 0 0
GNG2 0.024 0.039 -10000 0 -0.48 2 2
GNAO1 0.007 0.092 -10000 0 -0.33 20 20
HRAS 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.053 0.19 0.23 2 -0.48 47 49
E2/ER beta (dimer) 0.018 0.028 -10000 0 -0.35 2 2
mol:GDP -0.014 0.094 -10000 0 -0.33 22 22
mol:NADP -0.053 0.19 0.23 2 -0.48 47 49
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:IP3 -0.048 0.15 -10000 0 -0.44 36 36
IGF-1R heterotetramer 0.022 0.049 -10000 0 -0.48 3 3
PLCB1 -0.041 0.15 -10000 0 -0.45 35 35
PLCB2 -0.036 0.15 -10000 0 -0.44 36 36
IGF1 0.003 0.1 -10000 0 -0.48 13 13
mol:L-citrulline -0.053 0.19 0.23 2 -0.48 47 49
RHOA 0.027 0.005 -10000 0 -10000 0 0
Gai/GDP -0.038 0.21 -10000 0 -0.72 27 27
JNK cascade 0.018 0.028 -10000 0 -0.35 2 2
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
ESR2 0.024 0.039 -10000 0 -0.48 2 2
GNAQ 0.025 0.028 -10000 0 -0.48 1 1
ESR1 -0.009 0.11 -10000 0 -0.48 15 15
Gq family/GDP/Gbeta gamma -0.059 0.24 -10000 0 -0.75 34 34
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.008 0.092 -10000 0 -0.49 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.022 0.14 -10000 0 -0.45 22 22
GNAZ -0.017 0.14 -10000 0 -0.48 26 26
E2/ER alpha (dimer) -0.005 0.078 -10000 0 -0.35 15 15
STRN 0.025 0.039 -10000 0 -0.48 2 2
GNAL 0.007 0.089 -10000 0 -0.3 21 21
PELP1 0.026 0.008 -10000 0 -10000 0 0
MAPK11 0.009 0.033 -10000 0 -0.29 4 4
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.056 -10000 0 -0.48 4 4
HBEGF -0.049 0.18 0.4 5 -0.5 29 34
cAMP biosynthetic process -0.002 0.077 -10000 0 -0.26 23 23
SRC -0.045 0.16 -10000 0 -0.51 26 26
PI3K 0.038 0.012 -10000 0 -10000 0 0
GNB1 0.027 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.01 0.097 -10000 0 -0.35 14 14
SOS1 0.028 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.04 0.12 -10000 0 -0.41 21 21
Gs family/GTP 0.003 0.081 -10000 0 -0.27 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.019 -10000 0 -10000 0 0
vasodilation -0.05 0.18 0.23 2 -0.46 47 49
mol:DAG -0.048 0.15 -10000 0 -0.44 36 36
Gs family/GDP/Gbeta gamma -0.014 0.095 -10000 0 -0.35 16 16
MSN -0.014 0.077 0.31 1 -0.37 4 5
Gq family/GTP -0.027 0.15 -10000 0 -0.45 35 35
mol:PI-3-4-5-P3 -0.07 0.27 -10000 0 -0.71 49 49
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.05 0.18 0.46 47 -0.23 2 49
GRB2/SOS1 0.04 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.002 0.098 -10000 0 -0.34 19 19
NOS3 -0.057 0.2 0.24 1 -0.5 47 48
GNA11 0.023 0.039 -10000 0 -0.48 2 2
MAPKKK cascade -0.042 0.2 0.35 2 -0.51 43 45
E2/ER alpha (dimer)/PELP1/Src -0.029 0.16 0.26 2 -0.47 26 28
ruffle organization -0.013 0.073 0.18 7 -0.34 4 11
ROCK2 -0.009 0.075 0.32 1 -0.28 1 2
GNA14 -0.01 0.13 -10000 0 -0.48 25 25
GNA15 0.019 0.061 -10000 0 -0.48 5 5
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.058 0.17 0.37 1 -0.48 31 32
MMP2 -0.046 0.16 0.28 4 -0.49 27 31
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.002 0.11 -10000 0 -0.35 31 31
CRKL -0.012 0.11 0.28 4 -0.38 13 17
mol:PIP3 0.004 0.009 -10000 0 -10000 0 0
AKT1 0.005 0.039 -10000 0 -10000 0 0
PTK2B 0.019 0.048 -10000 0 -0.48 3 3
RAPGEF1 -0.012 0.11 0.27 4 -0.39 8 12
RANBP10 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.002 0.12 -10000 0 -0.31 44 44
MAP3K5 -0.011 0.12 0.28 4 -0.41 11 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.01 0.12 -10000 0 -0.28 44 44
AP1 0.002 0.082 -10000 0 -0.3 14 14
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.023 0.013 -10000 0 -10000 0 0
apoptosis -0.041 0.22 -10000 0 -0.77 29 29
STAT3 (dimer) -0.027 0.12 -10000 0 -0.4 16 16
GAB1/CRKL/SHP2/PI3K 0.02 0.12 0.27 3 -0.4 8 11
INPP5D 0.017 0.072 -10000 0 -0.48 7 7
CBL/CRK 0.001 0.11 0.36 2 -0.36 12 14
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.005 -10000 0 -10000 0 0
ELK1 -0.012 0.11 0.29 26 -0.2 4 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.067 -10000 0 -0.27 8 8
PAK1 0.01 0.056 0.39 2 -10000 0 2
HGF/MET/RANBP10 -0.003 0.12 -10000 0 -0.31 46 46
HRAS -0.047 0.19 -10000 0 -0.59 37 37
DOCK1 -0.014 0.11 0.27 5 -0.37 13 18
GAB1 -0.014 0.11 0.23 1 -0.38 14 15
CRK -0.013 0.11 0.38 2 -0.37 13 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.046 0.19 -10000 0 -0.51 48 48
JUN 0.024 0.04 -10000 0 -0.48 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.024 0.09 -10000 0 -0.25 47 47
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
cell morphogenesis -0.018 0.13 0.35 8 -0.42 12 20
GRB2/SHC 0.006 0.09 -10000 0 -0.24 30 30
FOS 0.004 0.094 -10000 0 -0.48 11 11
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility -0.012 0.11 0.29 26 -0.2 5 31
HGF/MET/MUC20 -0.017 0.12 -10000 0 -0.31 47 47
cell migration 0.004 0.087 -10000 0 -0.24 30 30
GRB2 0.027 0.006 -10000 0 -10000 0 0
CBL 0.027 0.006 -10000 0 -10000 0 0
MET/RANBP10 -0.004 0.12 -10000 0 -0.35 34 34
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.11 -10000 0 -0.3 36 36
MET/MUC20 -0.02 0.11 -10000 0 -0.35 34 34
RAP1B -0.003 0.11 0.27 6 -0.39 7 13
RAP1A -0.013 0.1 0.25 5 -0.39 7 12
HGF/MET/RANBP9 -0.002 0.12 -10000 0 -0.31 43 43
RAF1 -0.041 0.19 -10000 0 -0.56 37 37
STAT3 -0.028 0.12 -10000 0 -0.41 16 16
cell proliferation -0.017 0.16 0.32 11 -0.39 38 49
RPS6KB1 0 0.04 -10000 0 -0.2 2 2
MAPK3 -0.022 0.092 0.36 8 -10000 0 8
MAPK1 -0.004 0.14 0.64 11 -10000 0 11
RANBP9 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.001 0.11 0.28 4 -0.4 7 11
SRC -0.03 0.097 -10000 0 -0.38 13 13
PI3K 0.009 0.096 -10000 0 -0.24 36 36
MET/Glomulin -0.015 0.098 -10000 0 -0.3 34 34
SOS1 0.028 0.003 -10000 0 -10000 0 0
MAP2K1 -0.037 0.17 -10000 0 -0.52 37 37
MET -0.029 0.15 -10000 0 -0.48 34 34
MAP4K1 -0.011 0.12 0.3 4 -0.42 13 17
PTK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K2 -0.038 0.17 -10000 0 -0.52 37 37
BAD 0.002 0.044 0.4 1 -10000 0 1
MAP2K4 -0.01 0.11 0.27 4 -0.37 11 15
SHP2/GRB2/SOS1/GAB1 -0.002 0.13 -10000 0 -0.35 37 37
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.027 0.006 -10000 0 -10000 0 0
HGS -0.026 0.085 -10000 0 -0.24 45 45
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF 0 0.11 -10000 0 -0.48 16 16
RASA1 0.025 0.028 -10000 0 -0.48 1 1
NCK1 0.028 0.004 -10000 0 -10000 0 0
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.005 0.097 -10000 0 -0.23 45 45
PDPK1 0.003 0.027 -10000 0 -10000 0 0
HGF/MET/SHIP -0.009 0.14 -10000 0 -0.34 48 48
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.006 0.15 1 2 -1.2 3 5
VDR 0.021 0.056 -10000 0 -0.48 4 4
FAM120B 0.025 0.008 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.021 0.11 -10000 0 -0.28 24 24
RXRs/LXRs/DNA/Oxysterols -0.023 0.14 -10000 0 -0.45 22 22
MED1 0.027 0.005 -10000 0 -10000 0 0
mol:9cRA -0.001 0.016 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.002 0.086 -10000 0 -0.24 32 32
RXRs/NUR77 -0.011 0.13 -10000 0 -0.28 51 51
RXRs/PPAR -0.039 0.12 -10000 0 -0.27 70 70
NCOR2 0.026 0.028 -10000 0 -0.48 1 1
VDR/VDR/Vit D3 0.016 0.04 -10000 0 -0.35 4 4
RARs/VDR/DNA/Vit D3 0.051 0.053 -10000 0 -0.26 8 8
RARA 0.026 0.028 -10000 0 -0.48 1 1
NCOA1 0.027 0.027 -10000 0 -0.48 1 1
VDR/VDR/DNA 0.021 0.056 -10000 0 -0.48 4 4
RARs/RARs/DNA/9cRA 0.039 0.041 -10000 0 -0.26 4 4
RARG 0.027 0.013 -10000 0 -10000 0 0
RPS6KB1 0.025 0.1 0.59 9 -0.42 3 12
RARs/THRs/DNA/SMRT -0.001 0.087 -10000 0 -0.25 33 33
THRA 0.027 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.04 -10000 0 -0.35 4 4
RXRs/PPAR/9cRA/PGJ2/DNA -0.008 0.12 0.3 1 -0.26 47 48
NR1H4 0.002 0.054 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.021 0.13 -10000 0 -0.26 46 46
NR1H2 0.023 0.035 -10000 0 -0.48 1 1
NR1H3 0.024 0.027 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.001 0.11 -10000 0 -0.26 45 45
NR4A1 0.007 0.087 -10000 0 -0.48 9 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.019 0.078 -10000 0 -0.2 45 45
RXRG -0.059 0.17 -10000 0 -0.46 48 48
RXR alpha/CCPG 0.035 0.022 -10000 0 -10000 0 0
RXRA 0.024 0.023 -10000 0 -10000 0 0
RXRB 0.025 0.022 -10000 0 -10000 0 0
THRB -0.018 0.14 -10000 0 -0.48 31 31
PPARG -0.021 0.15 -10000 0 -0.45 36 36
PPARD 0.027 0.006 -10000 0 -10000 0 0
TNF -0.066 0.27 -10000 0 -1 24 24
mol:Oxysterols 0 0.014 -10000 0 -10000 0 0
cholesterol transport -0.022 0.14 -10000 0 -0.45 22 22
PPARA 0.026 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.022 0.048 -10000 0 -0.48 3 3
RXRs/NUR77/BCL2 -0.032 0.1 -10000 0 -0.26 53 53
SREBF1 -0.023 0.14 -10000 0 -0.59 8 8
RXRs/RXRs/DNA/9cRA -0.008 0.12 0.29 1 -0.26 47 48
ABCA1 -0.021 0.13 -10000 0 -0.53 8 8
RARs/THRs 0.043 0.1 -10000 0 -0.28 31 31
RXRs/FXR -0.014 0.12 -10000 0 -0.28 44 44
BCL2 0.017 0.058 -10000 0 -0.48 4 4
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.023 0.06 -10000 0 -0.36 7 7
PDGFRB 0.025 0.029 -10000 0 -0.5 1 1
SPHK1 -0.029 0.17 -10000 0 -0.79 15 15
mol:S1P -0.03 0.14 -10000 0 -0.7 14 14
S1P1/S1P/Gi -0.057 0.16 -10000 0 -0.42 44 44
GNAO1 0.001 0.093 -10000 0 -0.33 20 20
PDGFB-D/PDGFRB/PLCgamma1 -0.047 0.16 0.26 4 -0.4 37 41
PLCG1 -0.058 0.16 0.25 3 -0.4 45 48
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.028 -10000 0 -0.5 1 1
GNAI2 0.022 0.017 -10000 0 -10000 0 0
GNAI3 0.022 0.016 -10000 0 -10000 0 0
GNAI1 0.015 0.058 -10000 0 -0.49 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.016 0.043 -10000 0 -0.3 7 7
S1P1/S1P -0.034 0.12 0.23 1 -0.48 17 18
negative regulation of cAMP metabolic process -0.055 0.16 -10000 0 -0.41 44 44
MAPK3 -0.081 0.21 0.36 2 -0.58 46 48
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
KDR 0.012 0.07 -10000 0 -0.3 13 13
PLCB2 -0.026 0.12 0.25 4 -0.44 18 22
RAC1 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.027 0.1 -10000 0 -0.41 17 17
receptor internalization -0.034 0.11 -10000 0 -0.45 17 17
PTGS2 -0.13 0.34 -10000 0 -1 41 41
Rac1/GTP -0.026 0.1 -10000 0 -0.41 17 17
RHOA 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.022 0.031 -10000 0 -0.31 2 2
negative regulation of T cell proliferation -0.055 0.16 -10000 0 -0.41 44 44
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.022 0.14 -10000 0 -0.48 27 27
MAPK1 -0.078 0.2 -10000 0 -0.56 45 45
S1P1/S1P/PDGFB-D/PDGFRB -0.026 0.12 0.27 3 -0.46 16 19
ABCC1 0.027 0.01 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.005 0.098 -10000 0 -0.32 28 28
cell-cell adhesion 0.046 0.088 0.3 29 -10000 0 29
Ephrin B/EPHB2/RasGAP 0.023 0.12 -10000 0 -0.3 32 32
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
SHC1 0.023 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.027 0.045 -10000 0 -0.3 5 5
Ephrin B1/EPHB1 0.01 0.067 -10000 0 -0.3 11 11
HRAS/GDP -0.018 0.11 -10000 0 -0.34 25 25
Ephrin B/EPHB1/GRB7 0.014 0.12 -10000 0 -0.31 28 28
Endophilin/SYNJ1 -0.032 0.091 0.19 10 -0.29 29 39
KRAS 0.026 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.016 0.11 -10000 0 -0.31 27 27
endothelial cell migration 0.046 0.043 -10000 0 -0.26 5 5
GRB2 0.027 0.006 -10000 0 -10000 0 0
GRB7 0.021 0.055 -10000 0 -0.48 4 4
PAK1 -0.035 0.096 0.3 3 -0.38 10 13
HRAS 0.027 0.005 -10000 0 -10000 0 0
RRAS -0.035 0.092 0.27 2 -0.29 31 33
DNM1 0.013 0.082 -10000 0 -0.48 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.036 0.09 0.23 6 -0.3 27 33
lamellipodium assembly -0.046 0.088 -10000 0 -0.3 29 29
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.005 0.076 -10000 0 -0.32 8 8
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
EPHB2 0.007 0.095 -10000 0 -0.48 12 12
EPHB3 0.018 0.063 -10000 0 -0.33 9 9
EPHB1 -0.008 0.1 -10000 0 -0.48 11 11
EPHB4 0.024 0.039 -10000 0 -0.48 2 2
mol:GDP -0.03 0.1 0.24 1 -0.35 25 26
Ephrin B/EPHB2 0.014 0.11 -10000 0 -0.3 31 31
Ephrin B/EPHB3 0.02 0.095 -10000 0 -0.28 27 27
JNK cascade -0.032 0.089 0.29 8 -0.31 20 28
Ephrin B/EPHB1 0.006 0.11 -10000 0 -0.31 28 28
RAP1/GDP -0.011 0.11 0.27 3 -0.37 14 17
EFNB2 0.021 0.049 -10000 0 -0.48 3 3
EFNB3 -0.012 0.12 -10000 0 -0.48 21 21
EFNB1 0.023 0.027 -10000 0 -0.13 10 10
Ephrin B2/EPHB1-2 0.01 0.098 -10000 0 -0.31 23 23
RAP1B 0.026 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.012 0.13 -10000 0 -0.36 28 28
Rap1/GTP -0.021 0.1 -10000 0 -0.3 29 29
axon guidance 0.005 0.097 -10000 0 -0.31 28 28
MAPK3 -0.012 0.068 -10000 0 -0.38 4 4
MAPK1 -0.011 0.065 -10000 0 -0.38 4 4
Rac1/GDP -0.024 0.11 0.22 4 -0.34 23 27
actin cytoskeleton reorganization -0.047 0.079 -10000 0 -0.31 20 20
CDC42/GDP -0.022 0.11 0.24 7 -0.33 24 31
PI3K 0.051 0.045 -10000 0 -0.26 5 5
EFNA5 0 0.11 -10000 0 -0.48 18 18
Ephrin B2/EPHB4 0.029 0.042 -10000 0 -0.3 5 5
Ephrin B/EPHB2/Intersectin/N-WASP -0.011 0.095 -10000 0 -0.29 28 28
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.1 -10000 0 -0.38 14 14
PTK2 0.074 0.2 0.57 47 -10000 0 47
MAP4K4 -0.032 0.09 0.29 8 -0.31 20 28
SRC 0.027 0.006 -10000 0 -10000 0 0
KALRN 0.019 0.059 -10000 0 -0.48 4 4
Intersectin/N-WASP 0.039 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.026 0.11 0.25 9 -0.39 11 20
MAP2K1 -0.009 0.07 -10000 0 -0.39 4 4
WASL 0.027 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.024 0.1 -10000 0 -0.33 19 19
cell migration -0.004 0.11 0.31 6 -0.39 7 13
NRAS 0.027 0.006 -10000 0 -10000 0 0
SYNJ1 -0.032 0.092 0.19 10 -0.29 29 39
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.078 0.13 0.21 5 -0.3 70 75
HRAS/GTP -0.008 0.12 -10000 0 -0.3 35 35
Ephrin B1/EPHB1-2 0.011 0.095 -10000 0 -0.33 19 19
cell adhesion mediated by integrin 0.025 0.076 0.27 23 -0.22 6 29
RAC1 0.025 0.009 -10000 0 -10000 0 0
mol:GTP -0.007 0.12 -10000 0 -0.31 36 36
RAC1-CDC42/GTP -0.052 0.095 -10000 0 -0.33 27 27
RASA1 0.025 0.028 -10000 0 -0.48 1 1
RAC1-CDC42/GDP -0.015 0.11 0.22 1 -0.37 15 16
ruffle organization -0.022 0.12 0.41 6 -0.42 11 17
NCK1 0.028 0.004 -10000 0 -10000 0 0
receptor internalization -0.04 0.099 0.34 1 -0.3 35 36
Ephrin B/EPHB2/KALRN 0.02 0.12 -10000 0 -0.31 33 33
ROCK1 0.011 0.045 0.18 8 -0.27 5 13
RAS family/GDP -0.047 0.081 -10000 0 -0.31 21 21
Rac1/GTP -0.026 0.1 -10000 0 -0.32 28 28
Ephrin B/EPHB1/Src/Paxillin -0.014 0.095 -10000 0 -0.3 27 27
BCR signaling pathway

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
JUN -0.023 0.16 0.29 6 -0.49 24 30
IKBKB 0.004 0.099 0.27 3 -0.3 12 15
AKT1 -0.015 0.1 0.24 13 -0.25 25 38
IKBKG 0.008 0.09 0.29 2 -0.29 11 13
CALM1 -0.016 0.15 0.28 3 -0.53 19 22
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.045 0.22 0.28 8 -0.61 33 41
MAP3K7 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.16 0.24 1 -0.55 22 23
DOK1 0.025 0.039 -10000 0 -0.48 2 2
AP-1 -0.008 0.093 0.2 5 -0.28 18 23
LYN 0.022 0.039 -10000 0 -0.48 2 2
BLNK 0.016 0.076 -10000 0 -0.48 8 8
SHC1 0.023 0.013 -10000 0 -10000 0 0
BCR complex -0.013 0.15 -10000 0 -0.47 29 29
CD22 -0.045 0.19 -10000 0 -0.68 23 23
CAMK2G -0.016 0.14 0.29 2 -0.5 18 20
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
INPP5D 0.017 0.072 -10000 0 -0.49 7 7
SHC/GRB2/SOS1 -0.009 0.11 -10000 0 -0.44 15 15
GO:0007205 -0.022 0.17 0.24 1 -0.56 22 23
SYK 0.021 0.055 -10000 0 -0.48 4 4
ELK1 -0.022 0.16 0.25 1 -0.54 21 22
NFATC1 -0.046 0.18 0.29 6 -0.54 32 38
B-cell antigen/BCR complex -0.013 0.15 -10000 0 -0.47 29 29
PAG1/CSK 0.034 0.026 -10000 0 -0.35 1 1
NFKBIB 0.018 0.042 0.13 5 -0.12 8 13
HRAS -0.011 0.14 0.26 3 -0.52 17 20
NFKBIA 0.017 0.041 0.13 5 -0.12 7 12
NF-kappa-B/RelA/I kappa B beta 0.022 0.037 0.13 5 -10000 0 5
RasGAP/Csk 0.018 0.13 -10000 0 -0.35 29 29
mol:GDP -0.018 0.16 0.24 1 -0.54 21 22
PTEN 0.027 0.005 -10000 0 -10000 0 0
CD79B 0.004 0.099 -10000 0 -0.48 13 13
NF-kappa-B/RelA/I kappa B alpha 0.022 0.037 0.13 5 -10000 0 5
GRB2 0.027 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.049 0.2 0.29 1 -0.57 36 37
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:IP3 -0.021 0.17 0.24 1 -0.58 22 23
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.026 0.15 0.3 2 -0.51 21 23
CHUK 0.006 0.091 0.29 2 -0.27 14 16
IBTK 0.025 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.004 0.14 -10000 0 -0.46 20 20
PTPN6 -0.046 0.18 -10000 0 -0.69 20 20
RELA 0.028 0.004 -10000 0 -10000 0 0
BCL2A1 0.015 0.032 0.13 1 -0.11 2 3
VAV2 -0.065 0.23 -10000 0 -0.67 34 34
ubiquitin-dependent protein catabolic process 0.02 0.041 0.13 5 -0.12 8 13
BTK -0.03 0.24 -10000 0 -1 18 18
CD19 -0.066 0.21 -10000 0 -0.63 33 33
MAP4K1 0.014 0.077 -10000 0 -0.45 9 9
CD72 0.026 0.014 -10000 0 -10000 0 0
PAG1 0.023 0.03 -10000 0 -0.48 1 1
MAPK14 -0.03 0.18 0.31 10 -0.5 31 41
SH3BP5 0.027 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.027 0.19 -10000 0 -0.63 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.041 0.24 -10000 0 -0.62 35 35
RAF1 -0.011 0.13 0.25 3 -0.49 17 20
RasGAP/p62DOK/SHIP 0.018 0.14 -10000 0 -0.37 32 32
CD79A -0.026 0.15 -10000 0 -0.48 31 31
re-entry into mitotic cell cycle -0.008 0.092 0.21 4 -0.28 17 21
RASA1 0.025 0.028 -10000 0 -0.48 1 1
MAPK3 -0.009 0.11 0.24 3 -0.41 16 19
MAPK1 -0.007 0.1 0.24 3 -0.4 15 18
CD72/SHP1 -0.018 0.18 0.28 7 -0.66 19 26
NFKB1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 -0.035 0.18 0.26 9 -0.49 34 43
actin cytoskeleton organization -0.037 0.19 0.3 7 -0.58 28 35
NF-kappa-B/RelA 0.045 0.071 0.24 5 -0.22 1 6
Calcineurin 0.01 0.13 0.33 1 -0.48 16 17
PI3K -0.057 0.16 -10000 0 -0.5 33 33
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.026 0.19 -10000 0 -0.66 21 21
SOS1 0.028 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.061 0.29 -10000 0 -0.85 38 38
DAPP1 -0.086 0.33 -10000 0 -0.98 38 38
cytokine secretion -0.041 0.17 0.28 6 -0.49 32 38
mol:DAG -0.021 0.17 0.24 1 -0.58 22 23
PLCG2 0.021 0.055 -10000 0 -0.48 4 4
MAP2K1 -0.011 0.12 0.24 4 -0.46 16 20
B-cell antigen/BCR complex/FcgammaRIIB -0.002 0.14 -10000 0 -0.39 30 30
mol:PI-3-4-5-P3 -0.047 0.11 0.22 2 -0.35 30 32
ETS1 -0.012 0.12 0.27 4 -0.46 16 20
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.017 0.15 -10000 0 -0.4 30 30
B-cell antigen/BCR complex/LYN -0.03 0.17 -10000 0 -0.73 17 17
MALT1 0.024 0.015 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 -0.042 0.21 0.32 5 -0.64 28 33
B-cell antigen/BCR complex/LYN/SYK -0.018 0.19 0.3 1 -0.68 20 21
CARD11 -0.016 0.17 0.31 2 -0.54 23 25
FCGR2B 0.009 0.083 -10000 0 -0.48 9 9
PPP3CA 0.026 0.028 -10000 0 -0.48 1 1
BCL10 0.027 0.006 -10000 0 -10000 0 0
IKK complex 0.012 0.048 0.14 14 -0.12 2 16
PTPRC 0.011 0.085 -10000 0 -0.48 10 10
PDPK1 -0.023 0.095 0.21 16 -0.25 26 42
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.01 -10000 0 -10000 0 0
POU2F2 0.018 0.031 0.13 6 -0.11 1 7
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.027 -10000 0 -0.35 1 1
VLDLR 0.011 0.085 -10000 0 -0.48 10 10
CRKL 0.027 0.01 -10000 0 -10000 0 0
LRPAP1 0.026 0.028 -10000 0 -0.48 1 1
FYN 0.023 0.039 -10000 0 -0.48 2 2
ITGA3 0.007 0.1 -10000 0 -0.46 15 15
RELN/VLDLR/Fyn 0 0.11 -10000 0 -0.32 32 32
MAPK8IP1/MKK7/MAP3K11/JNK1 0.053 0.069 -10000 0 -0.28 10 10
AKT1 -0.021 0.083 -10000 0 -0.27 29 29
MAP2K7 0.026 0.007 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 0.02 0.025 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.01 0.091 -10000 0 -0.28 27 27
LRPAP1/LRP8 0.034 0.044 -10000 0 -0.35 4 4
RELN/LRP8/DAB1/Fyn 0.015 0.093 -10000 0 -0.26 28 28
DAB1/alpha3/beta1 Integrin 0.001 0.11 -10000 0 -0.29 33 33
long-term memory -0.028 0.12 -10000 0 -0.28 53 53
DAB1/LIS1 0.022 0.11 -10000 0 -0.28 30 30
DAB1/CRLK/C3G 0.009 0.1 -10000 0 -0.28 25 25
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DAB1/NCK2 0.028 0.11 -10000 0 -0.27 33 33
ARHGEF2 0.024 0.01 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.055 0.16 -10000 0 -0.48 36 36
CDK5R1 0.024 0.032 -10000 0 -0.48 1 1
RELN -0.021 0.13 -10000 0 -0.48 24 24
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.008 0.1 -10000 0 -0.3 28 28
GRIN2A/RELN/LRP8/DAB1/Fyn -0.025 0.13 -10000 0 -0.29 53 53
MAPK8 0.026 0.028 -10000 0 -0.48 1 1
RELN/VLDLR/DAB1 0.003 0.1 -10000 0 -0.3 30 30
ITGB1 0.027 0.01 -10000 0 -10000 0 0
MAP1B -0.033 0.11 -10000 0 -0.31 40 40
RELN/LRP8 0.012 0.1 -10000 0 -0.3 28 28
GRIN2B/RELN/LRP8/DAB1/Fyn 0.015 0.093 -10000 0 -0.26 28 28
PI3K 0.038 0.012 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.024 0.075 -10000 0 -0.34 14 14
RAP1A -0.03 0.091 0.32 2 -0.45 3 5
PAFAH1B1 0.026 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.012 0.086 -10000 0 -0.48 10 10
CRLK/C3G 0.039 0.012 -10000 0 -10000 0 0
GRIN2B 0 0 -10000 0 -10000 0 0
NCK2 0.026 0.027 -10000 0 -0.48 1 1
neuron differentiation -0.005 0.095 -10000 0 -0.38 12 12
neuron adhesion -0.036 0.1 0.31 4 -0.43 5 9
LRP8 0.021 0.05 -10000 0 -0.28 7 7
GSK3B -0.025 0.078 -10000 0 -0.26 29 29
RELN/VLDLR/DAB1/Fyn 0.008 0.1 -10000 0 -0.28 31 31
MAP3K11 0.026 0.028 -10000 0 -0.48 1 1
RELN/VLDLR/DAB1/P13K -0.01 0.087 -10000 0 -0.28 29 29
CDK5 0.027 0.006 -10000 0 -10000 0 0
MAPT -0.019 0.13 0.74 5 -0.44 16 21
neuron migration -0.025 0.1 0.33 1 -0.34 22 23
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.096 -10000 0 -0.39 12 12
RELN/VLDLR 0.013 0.11 -10000 0 -0.3 34 34
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.031 0.027 0.21 4 -10000 0 4
AES 0.028 0.022 0.21 2 -10000 0 2
FBXW11 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.039 -10000 0 -0.35 3 3
SMAD4 0.025 0.009 -10000 0 -10000 0 0
DKK2 0 0.12 -10000 0 -0.48 19 19
TLE1 0.027 0.025 0.18 1 -0.31 1 2
MACF1 0.022 0.055 -10000 0 -0.48 4 4
CTNNB1 0.028 0.1 0.29 11 -0.34 5 16
WIF1 -0.099 0.19 -10000 0 -0.48 66 66
beta catenin/RanBP3 0.019 0.12 0.46 19 -0.33 2 21
KREMEN2 -0.007 0.1 -10000 0 -0.21 52 52
DKK1 -0.11 0.2 -10000 0 -0.48 71 71
beta catenin/beta TrCP1 0.036 0.1 0.31 8 -0.35 3 11
FZD1 0.023 0.041 -10000 0 -0.48 2 2
AXIN2 -0.038 0.28 0.59 9 -1.3 14 23
AXIN1 0.028 0.005 -10000 0 -10000 0 0
RAN 0.026 0.013 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.025 0.093 -10000 0 -0.62 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.013 0.18 -10000 0 -0.63 20 20
Axin1/APC/GSK3 0.034 0.072 0.24 9 -0.38 2 11
Axin1/APC/GSK3/beta catenin/Macf1 0.02 0.089 0.29 5 -0.4 4 9
HNF1A -0.004 0.08 0.24 2 -0.47 3 5
CTBP1 0.03 0.026 0.21 4 -10000 0 4
MYC 0.067 0.3 0.59 54 -1.4 6 60
RANBP3 0.026 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.009 0.11 -10000 0 -0.32 29 29
NKD1 -0.01 0.12 -10000 0 -0.48 21 21
TCF4 0.024 0.042 0.2 2 -0.46 2 4
TCF3 0.029 0.025 0.24 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.048 0.063 -10000 0 -0.28 8 8
Ran/GTP 0.02 0.009 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.002 0.15 0.46 17 -0.5 9 26
LEF1 0.02 0.069 0.22 1 -0.47 6 7
DVL1 0.029 0.066 0.2 1 -0.39 4 5
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.009 0.19 -10000 0 -0.65 21 21
DKK1/LRP6/Kremen 2 -0.07 0.14 -10000 0 -0.31 82 82
LRP6 0.025 0.028 -10000 0 -0.48 1 1
CSNK1A1 0.03 0.025 0.22 3 -10000 0 3
NLK 0.026 0.011 -10000 0 -10000 0 0
CCND1 -0.024 0.3 0.61 15 -1.4 13 28
WNT1 0.009 0.081 -10000 0 -0.48 8 8
GSK3A 0.027 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.029 -10000 0 -0.49 1 1
PPP2R5D 0.039 0.08 0.29 21 -0.26 2 23
APC 0 0.071 0.19 28 -0.26 8 36
WNT1/LRP6/FZD1 0.042 0.088 0.22 50 -0.24 4 54
CREBBP 0.031 0.026 0.22 3 -10000 0 3
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.051 -10000 0 -0.5 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -0.013 1 1
cytokine production during immune response 0.065 0.19 0.62 26 -10000 0 26
IL27/IL27R/JAK1 -0.026 0.22 0.63 1 -1.1 10 11
TBX21 -0.068 0.17 0.75 1 -0.55 26 27
IL12B -0.007 0.12 -10000 0 -0.48 20 20
IL12A -0.007 0.057 -10000 0 -0.35 9 9
IL6ST 0.003 0.095 -10000 0 -0.5 12 12
IL27RA/JAK1 -0.025 0.21 -10000 0 -1.2 10 10
IL27 0.004 0.078 -10000 0 -0.49 7 7
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.014 0.11 -10000 0 -0.98 1 1
T-helper 2 cell differentiation 0.065 0.19 0.62 26 -10000 0 26
T cell proliferation during immune response 0.065 0.19 0.62 26 -10000 0 26
MAPKKK cascade -0.065 0.19 -10000 0 -0.62 26 26
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.006 -10000 0 -10000 0 0
IL12RB1 0.012 0.081 -10000 0 -0.49 9 9
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.074 0.18 0.7 1 -0.62 22 23
IL27/IL27R/JAK2/TYK2 -0.066 0.2 -10000 0 -0.63 26 26
positive regulation of T cell mediated cytotoxicity -0.065 0.19 -10000 0 -0.62 26 26
STAT1 (dimer) -0.043 0.24 0.99 1 -0.89 17 18
JAK2 0.02 0.018 -10000 0 -10000 0 0
JAK1 0.025 0.028 -10000 0 -0.48 1 1
STAT2 (dimer) -0.055 0.19 -10000 0 -0.62 23 23
T cell proliferation -0.076 0.19 -10000 0 -0.59 30 30
IL12/IL12R/TYK2/JAK2 -0.12 0.33 -10000 0 -0.91 47 47
IL17A 0.013 0.11 -10000 0 -0.98 1 1
mast cell activation 0.065 0.19 0.62 26 -10000 0 26
IFNG -0.017 0.046 -10000 0 -0.12 45 45
T cell differentiation -0.004 0.008 -10000 0 -0.022 46 46
STAT3 (dimer) -0.055 0.19 -10000 0 -0.6 26 26
STAT5A (dimer) -0.056 0.19 -10000 0 -0.6 26 26
STAT4 (dimer) -0.063 0.2 -10000 0 -0.59 30 30
STAT4 0.013 0.086 -10000 0 -0.45 11 11
T cell activation -0.003 0.019 0.12 8 -10000 0 8
IL27R/JAK2/TYK2 -0.018 0.2 -10000 0 -1.1 10 10
GATA3 0.01 0.087 0.82 3 -10000 0 3
IL18 -0.01 0.072 -10000 0 -0.35 15 15
positive regulation of mast cell cytokine production -0.054 0.19 -10000 0 -0.58 26 26
IL27/EBI3 0.005 0.09 -10000 0 -0.36 17 17
IL27RA -0.038 0.22 -10000 0 -1.3 10 10
IL6 -0.01 0.11 -10000 0 -0.48 15 15
STAT5A 0.026 0.028 -10000 0 -0.48 1 1
monocyte differentiation -0.001 0.002 -10000 0 -0.019 1 1
IL2 0.005 0.083 0.47 10 -10000 0 10
IL1B -0.019 0.087 -10000 0 -0.35 22 22
EBI3 0.004 0.091 -10000 0 -0.49 11 11
TNF -0.02 0.087 -10000 0 -0.35 22 22
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.009 0.1 -10000 0 -0.28 33 33
regulation of S phase of mitotic cell cycle -0.005 0.079 -10000 0 -0.25 30 30
GNAO1 0.007 0.092 -10000 0 -0.33 20 20
HRAS 0.027 0.005 -10000 0 -10000 0 0
SHBG/T-DHT 0.011 0.041 -10000 0 -0.29 6 6
PELP1 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.03 0.076 0.17 9 -0.25 28 37
T-DHT/AR -0.023 0.11 -10000 0 -0.35 33 33
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 11 11
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.056 -10000 0 -0.48 4 4
mol:GDP -0.038 0.12 -10000 0 -0.4 34 34
cell proliferation -0.033 0.11 0.25 1 -0.47 12 13
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
FOS -0.026 0.15 -10000 0 -0.82 11 11
mol:Ca2+ -0.008 0.025 -10000 0 -0.067 43 43
MAPK3 -0.032 0.096 0.26 2 -0.38 11 13
MAPK1 -0.015 0.088 -10000 0 -0.41 11 11
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 10 10
cAMP biosynthetic process -0.001 0.044 0.22 1 -0.28 6 7
GNG2 0.024 0.039 -10000 0 -0.48 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 10 10
HRAS/GTP 0.01 0.089 -10000 0 -0.25 31 31
actin cytoskeleton reorganization 0.035 0.018 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 10 10
PI3K 0.035 0.011 -10000 0 -10000 0 0
apoptosis 0.017 0.1 0.46 12 -10000 0 12
T-DHT/AR/PELP1 -0.005 0.098 -10000 0 -0.3 33 33
HRAS/GDP -0.022 0.12 -10000 0 -0.37 34 34
CREB1 -0.019 0.11 -10000 0 -0.5 12 12
RAC1-CDC42/GTP 0.044 0.023 -10000 0 -10000 0 0
AR -0.034 0.15 -10000 0 -0.49 33 33
GNB1 0.027 0.005 -10000 0 -10000 0 0
RAF1 -0.014 0.082 0.19 1 -0.25 28 29
RAC1-CDC42/GDP -0.006 0.12 -10000 0 -0.36 32 32
T-DHT/AR/PELP1/Src 0.009 0.096 -10000 0 -0.27 32 32
MAP2K2 -0.031 0.074 0.17 8 -0.25 27 35
T-DHT/AR/PELP1/Src/PI3K -0.005 0.079 -10000 0 -0.25 30 30
GNAZ -0.017 0.14 -10000 0 -0.48 26 26
SHBG 0.015 0.068 -10000 0 -0.48 6 6
Gi family/GNB1/GNG2/GDP -0.021 0.12 -10000 0 -0.43 19 19
mol:T-DHT 0 0 -10000 0 -0.003 6 6
RAC1 0.025 0.009 -10000 0 -10000 0 0
GNRH1 -0.002 0.05 -10000 0 -0.35 7 7
Gi family/GTP -0.03 0.095 -10000 0 -0.26 39 39
CDC42 0.027 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.026 0.24 -10000 0 -0.86 23 23
NCK1/PAK1/Dok-R -0.039 0.1 -10000 0 -0.42 21 21
NCK1/Dok-R -0.021 0.26 -10000 0 -1 19 19
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.006 0.05 0.24 15 -10000 0 15
RELA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.023 0.013 -10000 0 -10000 0 0
Rac/GDP 0.018 0.007 -10000 0 -10000 0 0
F2 -0.016 0.082 0.27 13 -0.48 2 15
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0 0.24 -10000 0 -0.95 19 19
FN1 0.009 0.089 -10000 0 -0.48 10 10
PLD2 -0.038 0.26 -10000 0 -1.1 19 19
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB14 -0.036 0.16 -10000 0 -0.48 38 38
ELK1 -0.033 0.23 -10000 0 -0.96 19 19
GRB7 0.021 0.055 -10000 0 -0.48 4 4
PAK1 0.027 0.006 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.009 0.26 -10000 0 -0.98 20 20
CDKN1A -0.023 0.2 -10000 0 -0.66 26 26
ITGA5 0.022 0.044 -10000 0 -0.22 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.021 0.26 -10000 0 -1 19 19
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:NO -0.016 0.19 0.34 1 -0.62 24 25
PLG -0.036 0.26 -10000 0 -1.1 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.029 0.22 -10000 0 -0.85 20 20
GRB2 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
ANGPT2 -0.064 0.26 -10000 0 -0.87 25 25
BMX -0.047 0.27 -10000 0 -1.1 19 19
ANGPT1 -0.045 0.26 -10000 0 -1.2 15 15
tube development -0.034 0.21 0.46 1 -0.7 28 29
ANGPT4 0.019 0.025 -10000 0 -10000 0 0
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.055 0.28 -10000 0 -1.1 19 19
alpha5/beta1 Integrin 0.035 0.036 -10000 0 -0.29 3 3
FGF2 0.012 0.08 -10000 0 -0.48 8 8
STAT5A (dimer) -0.032 0.25 -10000 0 -0.82 28 28
mol:L-citrulline -0.016 0.19 0.34 1 -0.62 24 25
AGTR1 -0.018 0.13 -10000 0 -0.46 26 26
MAPK14 -0.036 0.28 -10000 0 -1.1 19 19
Tie2/SHP2 -0.022 0.21 -10000 0 -0.98 11 11
TEK -0.018 0.22 -10000 0 -1.1 11 11
RPS6KB1 -0.021 0.23 -10000 0 -0.87 20 20
Angiotensin II/AT1 -0.011 0.095 -10000 0 -0.34 25 25
Tie2/Ang1/GRB2 -0.027 0.27 -10000 0 -1.1 19 19
MAPK3 -0.036 0.24 -10000 0 -0.98 19 19
MAPK1 -0.036 0.23 -10000 0 -0.97 19 19
Tie2/Ang1/GRB7 -0.03 0.28 -10000 0 -1.1 19 19
NFKB1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 -0.038 0.26 -10000 0 -1.1 19 19
PI3K -0.031 0.27 -10000 0 -1 20 20
FES -0.039 0.28 -10000 0 -1.1 19 19
Crk/Dok-R -0.021 0.26 -10000 0 -1 19 19
Tie2/Ang1/ABIN2 -0.027 0.27 -10000 0 -1.1 19 19
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.02 0.22 -10000 0 -0.77 23 23
STAT5A 0.026 0.028 -10000 0 -0.48 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.005 0.24 -10000 0 -0.85 20 20
Tie2/Ang2 -0.051 0.29 -10000 0 -0.98 27 27
Tie2/Ang1 -0.038 0.29 -10000 0 -1.2 19 19
FOXO1 -0.021 0.23 0.44 1 -0.77 26 27
ELF1 0.029 0.024 -10000 0 -10000 0 0
ELF2 -0.033 0.26 -10000 0 -1.1 19 19
mol:Choline -0.035 0.25 -10000 0 -1 19 19
cell migration -0.016 0.063 -10000 0 -0.23 21 21
FYN -0.041 0.24 0.46 1 -0.81 28 29
DOK2 0.015 0.067 -10000 0 -0.48 6 6
negative regulation of cell cycle -0.019 0.18 -10000 0 -0.59 27 27
ETS1 0.021 0.05 -10000 0 -0.26 10 10
PXN 0.003 0.2 0.39 3 -0.69 20 23
ITGB1 0.027 0.01 -10000 0 -10000 0 0
NOS3 -0.023 0.21 -10000 0 -0.73 23 23
RAC1 0.025 0.009 -10000 0 -10000 0 0
TNF -0.018 0.14 -10000 0 -0.42 33 33
MAPKKK cascade -0.035 0.25 -10000 0 -1 19 19
RASA1 0.025 0.028 -10000 0 -0.48 1 1
Tie2/Ang1/Shc -0.027 0.26 -10000 0 -1.1 19 19
NCK1 0.028 0.004 -10000 0 -10000 0 0
vasculogenesis -0.012 0.17 0.33 1 -0.56 24 25
mol:Phosphatidic acid -0.035 0.25 -10000 0 -1 19 19
mol:Angiotensin II 0 0.005 -10000 0 -10000 0 0
mol:NADP -0.016 0.19 0.34 1 -0.62 24 25
Rac1/GTP -0.02 0.22 -10000 0 -0.8 20 20
MMP2 -0.045 0.27 -10000 0 -1.1 19 19
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.013 0.13 -10000 0 -0.45 22 22
STMN1 -0.003 0.069 -10000 0 -0.36 12 12
Aurora B/RasGAP/Survivin 0.006 0.14 -10000 0 -0.4 33 33
Chromosomal passenger complex/Cul3 protein complex -0.038 0.13 -10000 0 -0.36 37 37
BIRC5 -0.022 0.15 -10000 0 -0.51 32 32
DES -0.14 0.34 -10000 0 -0.73 80 80
Aurora C/Aurora B/INCENP 0.027 0.08 -10000 0 -0.3 17 17
Aurora B/TACC1 0.017 0.071 -10000 0 -0.32 13 13
Aurora B/PP2A 0.021 0.075 -10000 0 -0.36 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.003 0.03 -10000 0 -0.16 12 12
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 -0.02 0.12 -10000 0 -0.48 21 21
Cul3 protein complex 0.026 0.073 -10000 0 -0.3 12 12
KIF2C -0.043 0.2 -10000 0 -0.63 30 30
PEBP1 0.025 0.012 -10000 0 -10000 0 0
KIF20A 0.011 0.091 -10000 0 -0.49 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.022 0.074 -10000 0 -0.36 11 11
SEPT1 0.019 0.067 -10000 0 -0.48 6 6
SMC2 0.027 0.005 -10000 0 -10000 0 0
SMC4 0.027 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.036 0.22 0.24 6 -0.6 41 47
PSMA3 0.027 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -10000 0 -10000 0 0
H3F3B 0.001 0.061 -10000 0 -0.32 12 12
AURKB 0.007 0.099 -10000 0 -0.41 16 16
AURKC 0.014 0.074 -10000 0 -0.32 13 13
CDCA8 0.017 0.066 -10000 0 -0.52 5 5
cytokinesis -0.051 0.23 -10000 0 -0.6 40 40
Aurora B/Septin1 -0.029 0.22 0.28 1 -0.64 31 32
AURKA 0.019 0.063 -10000 0 -0.49 5 5
INCENP 0.025 0.015 -10000 0 -10000 0 0
KLHL13 0 0.099 -10000 0 -0.48 12 12
BUB1 0.002 0.12 -10000 0 -0.49 18 18
hSgo1/Aurora B/Survivin -0.004 0.16 -10000 0 -0.47 34 34
EVI5 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.21 -10000 0 -0.62 29 29
SGOL1 0.003 0.11 -10000 0 -0.48 16 16
CENPA -0.049 0.23 -10000 0 -0.58 38 38
NCAPG 0.011 0.089 -10000 0 -0.48 11 11
Aurora B/HC8 Proteasome 0.022 0.075 -10000 0 -0.36 12 12
NCAPD2 0.026 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.022 0.075 -10000 0 -0.36 12 12
RHOA 0.027 0.005 -10000 0 -10000 0 0
NCAPH 0.002 0.11 -10000 0 -0.48 17 17
NPM1 -0.032 0.15 -10000 0 -0.44 35 35
RASA1 0.025 0.028 -10000 0 -0.48 1 1
KLHL9 0.023 0.011 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.075 -10000 0 -0.36 12 12
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin -0.024 0.23 -10000 0 -0.61 34 34
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
NSUN2 -0.026 0.14 -10000 0 -0.42 33 33
MYLK -0.003 0.077 -10000 0 -0.35 16 16
KIF23 0.006 0.1 -10000 0 -0.5 14 14
VIM -0.003 0.066 -10000 0 -0.36 11 11
RACGAP1 0.024 0.03 -10000 0 -0.5 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.034 0.16 -10000 0 -0.43 40 40
Chromosomal passenger complex -0.045 0.21 -10000 0 -0.56 36 36
Chromosomal passenger complex/EVI5 0.028 0.16 -10000 0 -0.41 32 32
TACC1 0.022 0.039 -10000 0 -0.48 2 2
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
CUL3 0.028 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 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
USP8 -0.006 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.089 -10000 0 -0.26 8 8
NFATC4 -0.025 0.071 0.24 9 -0.24 7 16
ERBB2IP 0.027 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.015 0.082 -10000 0 -0.27 24 24
JUN -0.003 0.09 0.21 3 -0.37 10 13
HRAS 0.027 0.005 -10000 0 -10000 0 0
DOCK7 -0.036 0.072 -10000 0 -0.26 21 21
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.088 -10000 0 -0.29 23 23
AKT1 0.003 0.008 -10000 0 -10000 0 0
BAD -0.007 0.016 -10000 0 -0.3 1 1
MAPK10 -0.017 0.081 0.18 14 -0.23 17 31
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.013 0.09 -10000 0 -0.29 24 24
RAF1 0.005 0.1 0.29 6 -0.29 5 11
ErbB2/ErbB3/neuregulin 2 0.002 0.085 -10000 0 -0.3 22 22
STAT3 0.014 0.13 -10000 0 -0.88 7 7
cell migration -0.006 0.081 0.22 16 -0.23 10 26
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.057 0.24 0.34 2 -0.6 49 51
FOS -0.027 0.16 0.29 3 -0.38 50 53
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.082 -10000 0 -0.27 24 24
MAPK3 -0.036 0.19 0.33 3 -0.48 40 43
MAPK1 -0.046 0.21 0.33 3 -0.52 44 47
JAK2 -0.034 0.072 -10000 0 -0.27 21 21
NF2 -0.023 0.14 -10000 0 -0.66 17 17
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.074 0.21 3 -0.26 22 25
NRG1 -0.017 0.12 -10000 0 -0.49 21 21
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
MAPK8 -0.017 0.087 0.21 1 -0.28 18 19
MAPK9 -0.007 0.063 0.18 14 -10000 0 14
ERBB2 -0.023 0.033 -10000 0 -0.36 3 3
ERBB3 0.011 0.09 -10000 0 -0.49 11 11
SHC1 0.023 0.013 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
apoptosis 0.003 0.025 0.25 1 -0.18 4 5
STAT3 (dimer) 0.014 0.12 -10000 0 -0.86 7 7
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.003 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.029 0.047 -10000 0 -0.2 17 17
ErbB2/ErbB2/HSP90 (dimer) -0.001 0.035 -10000 0 -0.31 3 3
CHRNA1 -0.051 0.23 0.3 3 -0.6 44 47
myelination -0.016 0.087 0.26 15 -0.29 2 17
PPP3CB -0.035 0.066 -10000 0 -0.25 21 21
KRAS 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.018 0.08 -10000 0 -0.23 17 17
NRG2 0 0.093 -10000 0 -0.48 10 10
mol:GDP -0.006 0.074 0.21 3 -0.26 22 25
SOS1 0.028 0.003 -10000 0 -10000 0 0
MAP2K2 -0.004 0.1 0.27 7 -0.3 5 12
SRC 0.027 0.006 -10000 0 -10000 0 0
mol:cAMP 0 0.002 -10000 0 -10000 0 0
PTPN11 -0.035 0.073 -10000 0 -0.27 21 21
MAP2K1 -0.04 0.19 0.34 1 -0.55 19 20
heart morphogenesis -0.015 0.082 -10000 0 -0.27 24 24
RAS family/GDP 0.023 0.09 0.24 1 -0.26 8 9
GRB2 0.027 0.006 -10000 0 -10000 0 0
PRKACA -0.026 0.16 -10000 0 -0.68 20 20
CHRNE 0 0.037 0.088 1 -0.17 12 13
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.008 -10000 0 -10000 0 0
nervous system development -0.015 0.082 -10000 0 -0.27 24 24
CDC42 0.027 0.005 -10000 0 -10000 0 0
Ephrin A reverse 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
MAPKKK cascade 0.008 0.078 -10000 0 -0.3 18 18
EFNA5 0 0.11 -10000 0 -0.48 18 18
FYN -0.013 0.069 0.18 4 -0.28 19 23
neuron projection morphogenesis 0.008 0.078 -10000 0 -0.3 18 18
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.008 0.078 -10000 0 -0.3 18 18
EPHA5 0.013 0.041 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.061 -10000 0 -0.32 10 10
EPHB2 0.007 0.095 -10000 0 -0.48 12 12
Syndecan-2/TACI -0.007 0.086 -10000 0 -0.29 27 27
LAMA1 -0.01 0.11 -10000 0 -0.48 15 15
Syndecan-2/alpha2 ITGB1 -0.003 0.11 -10000 0 -0.29 38 38
HRAS 0.027 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.005 0.028 -10000 0 -0.29 3 3
ITGA5 0.022 0.044 -10000 0 -0.22 8 8
BAX 0.002 0.02 -10000 0 -10000 0 0
EPB41 0.028 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.02 0.028 -10000 0 -0.26 3 3
LAMA3 -0.035 0.15 -10000 0 -0.48 35 35
EZR 0.024 0.028 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.007 0.097 -10000 0 -0.48 13 13
Syndecan-2/MMP2 0.015 0.06 -10000 0 -0.32 10 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.018 0.082 -10000 0 -0.35 15 15
dendrite morphogenesis 0.011 0.069 -10000 0 -0.34 12 12
Syndecan-2/GM-CSF -0.017 0.1 -10000 0 -0.31 37 37
determination of left/right symmetry 0.007 0.033 -10000 0 -0.34 3 3
Syndecan-2/PKC delta 0.022 0.031 -10000 0 -0.29 3 3
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.009 0.11 0.19 24 -0.28 36 60
MAPK1 -0.007 0.1 0.19 23 -0.28 34 57
Syndecan-2/RACK1 0.034 0.032 -10000 0 -0.25 3 3
NF1 0.025 0.039 -10000 0 -0.48 2 2
FGFR/FGF/Syndecan-2 0.007 0.033 -10000 0 -0.34 3 3
ITGA2 -0.001 0.11 -10000 0 -0.48 16 16
MAPK8 0.005 0.032 -10000 0 -0.29 4 4
Syndecan-2/alpha2/beta1 Integrin 0.01 0.094 -10000 0 -0.28 25 25
Syndecan-2/Kininogen 0.011 0.039 -10000 0 -0.29 3 3
ITGB1 0.027 0.01 -10000 0 -10000 0 0
SRC 0.031 0.059 0.18 40 -0.24 2 42
Syndecan-2/CASK/Protein 4.1 0.021 0.028 -10000 0 -0.26 3 3
extracellular matrix organization 0.021 0.048 -10000 0 -0.46 3 3
actin cytoskeleton reorganization 0.014 0.061 -10000 0 -0.32 10 10
Syndecan-2/Caveolin-2/Ras 0.025 0.06 -10000 0 -0.27 12 12
Syndecan-2/Laminin alpha3 -0.011 0.093 -10000 0 -0.29 32 32
Syndecan-2/RasGAP 0.042 0.038 -10000 0 -0.24 4 4
alpha5/beta1 Integrin 0.035 0.036 -10000 0 -0.29 3 3
PRKCD 0.027 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.011 0.07 -10000 0 -0.34 12 12
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.03 0.034 -10000 0 -0.23 3 3
RHOA 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.025 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.032 0.15 -10000 0 -0.48 31 31
RASA1 0.025 0.028 -10000 0 -0.48 1 1
alpha2/beta1 Integrin 0.018 0.082 -10000 0 -0.35 15 15
Syndecan-2/Synbindin 0.023 0.027 -10000 0 -0.29 2 2
TGFB1 0.023 0.047 -10000 0 -0.48 3 3
CASP3 0.028 0.059 0.19 34 -0.27 3 37
FN1 0.009 0.089 -10000 0 -0.48 10 10
Syndecan-2/IL8 -0.003 0.083 -10000 0 -0.29 24 24
SDC2 0.007 0.033 -10000 0 -0.34 3 3
KNG1 0.008 0.044 -10000 0 -0.13 31 31
Syndecan-2/Neurofibromin 0.022 0.035 -10000 0 -0.29 4 4
TRAPPC4 0.027 0.006 -10000 0 -10000 0 0
CSF2 -0.054 0.17 -10000 0 -0.48 47 47
Syndecan-2/TGFB1 0.021 0.048 -10000 0 -0.46 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.02 0.028 -10000 0 -0.26 3 3
Syndecan-2/Ezrin 0.033 0.034 -10000 0 -0.26 3 3
PRKACA 0.03 0.062 0.19 38 -0.27 3 41
angiogenesis -0.003 0.082 -10000 0 -0.29 24 24
MMP2 0.014 0.077 -10000 0 -0.48 8 8
IL8 -0.019 0.13 -10000 0 -0.3 50 50
calcineurin-NFAT signaling pathway -0.007 0.086 -10000 0 -0.29 27 27
Signaling events mediated by PTP1B

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
PDGFRB 0.026 0.028 -10000 0 -0.48 1 1
Jak2/Leptin Receptor -0.044 0.16 -10000 0 -0.47 24 24
PTP1B/AKT1 -0.003 0.094 0.2 2 -0.36 10 12
FYN 0.023 0.039 -10000 0 -0.48 2 2
p210 bcr-abl/PTP1B -0.014 0.099 0.23 3 -0.35 14 17
EGFR 0.001 0.092 -10000 0 -0.5 11 11
EGF/EGFR -0.04 0.14 -10000 0 -0.32 61 61
CSF1 0.021 0.05 -10000 0 -0.48 3 3
AKT1 0.027 0.007 -10000 0 -10000 0 0
INSR 0.022 0.048 -10000 0 -0.49 3 3
PTP1B/N-cadherin -0.023 0.12 0.21 2 -0.35 24 26
Insulin Receptor/Insulin 0.003 0.087 0.2 1 -0.32 10 11
HCK 0.014 0.077 -10000 0 -0.48 8 8
CRK 0.026 0.008 -10000 0 -10000 0 0
TYK2 -0.015 0.095 0.35 2 -0.36 11 13
EGF -0.059 0.19 -10000 0 -0.49 56 56
YES1 0.026 0.007 -10000 0 -10000 0 0
CAV1 -0.018 0.12 0.23 8 -0.36 17 25
TXN 0.025 0.013 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.002 0.11 0.26 1 -0.41 10 11
cell migration 0.014 0.099 0.35 14 -0.23 3 17
STAT3 0.028 0.004 -10000 0 -10000 0 0
PRLR -0.046 0.16 -10000 0 -0.49 38 38
ITGA2B -0.018 0.13 -10000 0 -0.49 21 21
CSF1R 0.011 0.086 -10000 0 -0.48 10 10
Prolactin Receptor/Prolactin -0.025 0.12 -10000 0 -0.35 39 39
FGR 0.02 0.061 -10000 0 -0.48 5 5
PTP1B/p130 Cas -0.006 0.1 0.22 3 -0.37 12 15
Crk/p130 Cas 0.005 0.1 0.24 2 -0.37 11 13
DOK1 -0.01 0.1 0.29 2 -0.4 11 13
JAK2 -0.052 0.16 0.23 1 -0.46 27 28
Jak2/Leptin Receptor/Leptin -0.014 0.13 0.24 2 -0.45 11 13
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
PTPN1 -0.014 0.099 0.23 3 -0.35 14 17
LYN 0.022 0.039 -10000 0 -0.48 2 2
CDH2 -0.03 0.13 -10000 0 -0.25 69 69
SRC 0.009 0.09 -10000 0 -0.46 9 9
ITGB3 -0.004 0.1 -10000 0 -0.49 12 12
CAT1/PTP1B -0.044 0.16 0.31 3 -0.48 26 29
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.013 0.084 -10000 0 -0.34 5 5
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.12 0.24 1 -0.41 10 11
negative regulation of transcription -0.051 0.16 0.23 1 -0.45 27 28
FCGR2A 0.02 0.048 -10000 0 -0.4 4 4
FER 0.026 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.018 0.12 -10000 0 -0.37 31 31
BLK -0.036 0.15 -10000 0 -0.48 34 34
Insulin Receptor/Insulin/Shc 0.028 0.03 -10000 0 -0.3 2 2
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.015 0.066 -10000 0 -0.48 5 5
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
p210 bcr-abl/Grb2 0.027 0.006 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.059 0.18 0.2 1 -0.47 39 40
PRL 0.009 0.031 -10000 0 -10000 0 0
SOCS3 0.016 0.12 -10000 0 -1.1 4 4
SPRY2 0.023 0.04 -10000 0 -0.49 2 2
Insulin Receptor/Insulin/IRS1 0.024 0.061 -10000 0 -0.29 12 12
CSF1/CSF1R 0 0.12 0.23 1 -0.43 15 16
Ras protein signal transduction 0.018 0.12 0.58 13 -10000 0 13
IRS1 0.015 0.081 -10000 0 -0.48 9 9
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.009 0.1 -10000 0 -0.49 12 12
STAT5B -0.021 0.11 0.23 3 -0.42 13 16
STAT5A -0.022 0.11 0.23 3 -0.39 16 19
GRB2 0.027 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.1 0.24 2 -0.38 11 13
CSN2 0 0.069 0.13 24 -0.15 38 62
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
LAT 0.007 0.09 -10000 0 -0.46 10 10
YBX1 0.033 0.006 -10000 0 -10000 0 0
LCK 0.017 0.072 -10000 0 -0.48 7 7
SHC1 0.023 0.013 -10000 0 -10000 0 0
NOX4 0.011 0.087 -10000 0 -0.49 10 10
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.026 0.028 -10000 0 -0.48 1 1
alphaV beta3 Integrin 0.017 0.078 -10000 0 -0.35 12 12
PTK2 -0.032 0.14 -10000 0 -0.43 25 25
positive regulation of JNK cascade -0.019 0.12 -10000 0 -0.31 28 28
CDC42/GDP -0.014 0.17 -10000 0 -0.42 29 29
Rac1/GDP -0.017 0.16 -10000 0 -0.42 25 25
RAP1B 0.026 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.027 0.01 -10000 0 -10000 0 0
CDC42/GTP -0.018 0.15 -10000 0 -0.38 28 28
nectin-3/I-afadin 0.005 0.1 -10000 0 -0.35 28 28
RAPGEF1 -0.036 0.16 0.3 1 -0.44 26 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.045 0.17 -10000 0 -0.5 28 28
PDGFB-D/PDGFRB 0.025 0.028 -10000 0 -0.48 1 1
TLN1 -0.013 0.05 -10000 0 -0.29 3 3
Rap1/GTP -0.024 0.12 -10000 0 -0.33 21 21
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.044 0.021 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.005 0.1 -10000 0 -0.35 28 28
PVR 0.027 0.006 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.006 -10000 0 -10000 0 0
mol:GDP -0.035 0.19 -10000 0 -0.51 30 30
MLLT4 0.025 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.044 0.09 -10000 0 -0.25 24 24
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.026 0.058 -10000 0 -0.35 7 7
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.34 27 27
PVRL1 0.014 0.074 -10000 0 -0.48 7 7
PVRL3 -0.017 0.14 -10000 0 -0.48 28 28
PVRL2 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
CDH1 0.02 0.061 -10000 0 -0.48 5 5
CLDN1 -0.01 0.13 -10000 0 -0.39 31 31
JAM-A/CLDN1 0.011 0.12 -10000 0 -0.32 34 34
SRC -0.05 0.19 -10000 0 -0.55 28 28
ITGB3 -0.003 0.1 -10000 0 -0.48 12 12
nectin-1(dimer)/I-afadin/I-afadin 0.026 0.058 -10000 0 -0.35 7 7
FARP2 -0.034 0.19 -10000 0 -0.51 28 28
RAC1 0.025 0.009 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.02 0.094 -10000 0 -0.3 26 26
nectin-1/I-afadin 0.026 0.058 -10000 0 -0.35 7 7
nectin-2/I-afadin 0.036 0.014 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.011 0.1 -10000 0 -0.3 32 32
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.023 0.029 -10000 0 -0.48 1 1
positive regulation of filopodium formation -0.019 0.12 -10000 0 -0.31 28 28
alphaV/beta3 Integrin/Talin -0.002 0.089 0.26 2 -0.34 7 9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.014 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.014 -10000 0 -10000 0 0
PIP5K1C -0.009 0.052 -10000 0 -0.34 2 2
VAV2 -0.039 0.21 -10000 0 -0.55 30 30
RAP1/GDP -0.013 0.15 -10000 0 -0.38 27 27
ITGAV 0.028 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.019 0.096 -10000 0 -0.3 28 28
nectin-3(dimer)/I-afadin/I-afadin 0.005 0.1 -10000 0 -0.35 28 28
Rac1/GTP -0.023 0.16 -10000 0 -0.42 27 27
PTPRM -0.008 0.065 -10000 0 -0.21 30 30
E-cadherin/beta catenin/alpha catenin 0.057 0.067 -10000 0 -0.29 8 8
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.25 0.48 2 -0.72 19 21
CRP -0.095 0.26 0.5 2 -0.76 15 17
cell cycle arrest -0.13 0.28 -10000 0 -0.77 29 29
TIMP1 -0.093 0.24 -10000 0 -0.74 18 18
IL6ST -0.006 0.095 -10000 0 -0.49 12 12
Rac1/GDP -0.029 0.12 -10000 0 -0.4 18 18
AP1 0.033 0.13 -10000 0 -0.5 10 10
GAB2 0.022 0.055 -10000 0 -0.48 4 4
TNFSF11 -0.16 0.34 0.47 1 -1 34 35
HSP90B1 -0.015 0.16 -10000 0 -0.81 9 9
GAB1 0.028 0.005 -10000 0 -10000 0 0
MAPK14 -0.02 0.11 -10000 0 -0.51 6 6
AKT1 0.021 0.093 0.27 2 -0.62 4 6
FOXO1 0.022 0.091 0.35 2 -0.59 4 6
MAP2K6 -0.037 0.11 0.22 1 -0.38 17 18
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.052 0.14 -10000 0 -0.45 18 18
MITF -0.033 0.11 0.23 1 -0.4 17 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.007 -10000 0 -10000 0 0
A2M -0.067 0.32 -10000 0 -1.2 26 26
CEBPB 0.029 0.013 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.012 0.095 -10000 0 -0.47 7 7
STAT3 -0.14 0.3 -10000 0 -0.82 29 29
STAT1 0.014 0.021 -10000 0 -10000 0 0
CEBPD -0.1 0.27 0.53 1 -0.81 17 18
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.012 -10000 0 -10000 0 0
JUN 0.024 0.04 -10000 0 -0.48 2 2
PIAS3/MITF -0.016 0.12 -10000 0 -0.45 9 9
MAPK11 -0.019 0.11 -10000 0 -0.52 6 6
STAT3 (dimer)/FOXO1 -0.092 0.23 0.47 1 -0.66 20 21
GRB2/SOS1/GAB family 0.029 0.12 -10000 0 -0.44 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.022 0.11 -10000 0 -0.4 20 20
GRB2 0.028 0.006 -10000 0 -10000 0 0
JAK2 0.025 0.009 -10000 0 -10000 0 0
LBP -0.1 0.25 0.42 2 -0.78 23 25
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
JAK1 0.018 0.034 -10000 0 -0.48 1 1
MYC -0.094 0.27 -10000 0 -0.82 18 18
FGG -0.32 0.49 -10000 0 -1 107 107
macrophage differentiation -0.13 0.28 -10000 0 -0.77 29 29
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.1 -10000 0 -0.32 22 22
JUNB -0.11 0.25 0.45 1 -0.73 21 22
FOS 0.004 0.094 -10000 0 -0.48 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.11 0.24 2 -0.38 19 21
STAT1/PIAS1 -0.022 0.13 0.31 1 -0.38 14 15
GRB2/SOS1/GAB family/SHP2/PI3K 0.02 0.093 -10000 0 -0.59 5 5
STAT3 (dimer) -0.14 0.3 -10000 0 -0.82 29 29
PRKCD -0.064 0.19 0.32 12 -0.54 16 28
IL6R 0.004 0.087 -10000 0 -0.5 10 10
SOCS3 -0.001 0.13 -10000 0 -0.89 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.084 -10000 0 -0.32 14 14
Rac1/GTP -0.039 0.13 -10000 0 -0.42 18 18
HCK 0.014 0.077 -10000 0 -0.48 8 8
MAPKKK cascade 0.02 0.12 -10000 0 -0.58 8 8
bone resorption -0.15 0.32 0.46 1 -0.95 34 35
IRF1 -0.11 0.24 -10000 0 -0.72 19 19
mol:GDP -0.034 0.11 0.23 1 -0.41 17 18
SOS1 0.028 0.005 -10000 0 -10000 0 0
VAV1 -0.035 0.11 0.23 1 -0.41 17 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.002 0.12 0.4 1 -0.51 11 12
PTPN11 -0.003 0.12 -10000 0 -0.77 8 8
IL6/IL6RA -0.016 0.1 -10000 0 -0.38 20 20
gp130 (dimer)/TYK2/TYK2/LMO4 0.028 0.074 -10000 0 -0.31 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.027 0.073 -10000 0 -0.31 13 13
IL6 -0.021 0.11 -10000 0 -0.49 15 15
PIAS3 0.027 0.005 -10000 0 -10000 0 0
PTPRE 0.022 0.073 -10000 0 -0.48 7 7
PIAS1 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.09 0.22 2 -0.32 21 23
LMO4 0.008 0.048 -10000 0 -0.51 2 2
STAT3 (dimer)/PIAS3 -0.12 0.28 -10000 0 -0.77 27 27
MCL1 0.053 0.11 0.44 2 -0.56 3 5
FAS signaling pathway (CD95)

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
SPTAN1 -0.006 0.046 0.2 7 -0.25 3 10
RFC1 0 0.048 0.21 13 -0.18 3 16
PRKDC 0.007 0.073 0.24 23 -0.42 1 24
RIPK1 0.028 0.005 -10000 0 -10000 0 0
CASP7 0.002 0.1 -10000 0 -0.71 6 6
FASLG/FAS/FADD/FAF1 0.004 0.077 0.2 14 -0.26 18 32
MAP2K4 -0.013 0.12 0.24 3 -0.41 17 20
mol:ceramide -0.006 0.096 -10000 0 -0.35 18 18
GSN -0.005 0.04 0.2 6 -10000 0 6
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.082 -10000 0 -0.32 14 14
FAS 0.006 0.098 -10000 0 -0.49 13 13
BID -0.014 0.031 0.27 4 -10000 0 4
MAP3K1 0.002 0.099 0.25 1 -0.45 8 9
MAP3K7 0.025 0.009 -10000 0 -10000 0 0
RB1 -0.005 0.042 0.2 6 -0.29 1 7
CFLAR 0.028 0.004 -10000 0 -10000 0 0
HGF/MET -0.033 0.15 -10000 0 -0.34 61 61
ARHGDIB -0.004 0.058 0.24 9 -0.35 3 12
FADD 0.025 0.013 -10000 0 -10000 0 0
actin filament polymerization 0.005 0.04 -10000 0 -0.2 6 6
NFKB1 0.002 0.087 -10000 0 -0.54 6 6
MAPK8 -0.022 0.15 0.25 1 -0.49 21 22
DFFA -0.005 0.041 0.2 7 -10000 0 7
DNA fragmentation during apoptosis -0.003 0.044 0.21 9 -10000 0 9
FAS/FADD/MET 0.001 0.12 -10000 0 -0.32 39 39
CFLAR/RIP1 0.041 0.009 -10000 0 -10000 0 0
FAIM3 0.018 0.057 -10000 0 -0.48 4 4
FAF1 0.025 0.013 -10000 0 -10000 0 0
PARP1 -0.005 0.041 0.2 7 -0.18 1 8
DFFB -0.003 0.045 0.21 9 -10000 0 9
CHUK -0.002 0.08 -10000 0 -0.5 6 6
FASLG -0.005 0.1 -10000 0 -0.49 12 12
FAS/FADD 0.024 0.069 -10000 0 -0.36 10 10
HGF 0 0.11 -10000 0 -0.48 16 16
LMNA 0 0.066 0.21 18 -0.36 2 20
CASP6 -0.003 0.042 0.21 8 -10000 0 8
CASP10 0.017 0.067 -10000 0 -0.49 6 6
CASP3 0.003 0.035 0.25 6 -10000 0 6
PTPN13 -0.02 0.14 -10000 0 -0.48 25 25
CASP8 -0.016 0.045 0.35 4 -0.36 1 5
IL6 -0.051 0.29 -10000 0 -1.2 19 19
MET -0.029 0.15 -10000 0 -0.48 34 34
ICAD/CAD -0.001 0.038 0.24 6 -10000 0 6
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.097 -10000 0 -0.36 18 18
activation of caspase activity by cytochrome c -0.014 0.031 0.26 4 -10000 0 4
PAK2 0 0.048 0.22 12 -10000 0 12
BCL2 0.017 0.058 -10000 0 -0.48 4 4
Regulation of Androgen receptor activity

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
HDAC1 0.013 0.002 -10000 0 -10000 0 0
SMARCC1 0.01 0.024 -10000 0 -10000 0 0
REL 0.018 0.072 -10000 0 -0.48 7 7
HDAC7 -0.036 0.11 0.3 1 -0.38 15 16
JUN 0.024 0.04 -10000 0 -0.48 2 2
EP300 0.027 0.005 -10000 0 -10000 0 0
KAT2B 0.027 0.005 -10000 0 -10000 0 0
KAT5 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.018 0.083 -10000 0 -0.36 18 18
FOXO1 0.024 0.03 -10000 0 -0.48 1 1
T-DHT/AR -0.015 0.13 -10000 0 -0.37 19 19
MAP2K6 -0.013 0.12 -10000 0 -0.46 20 20
BRM/BAF57 0.034 0.033 -10000 0 -0.35 2 2
MAP2K4 0.018 0.021 -10000 0 -10000 0 0
SMARCA2 0.022 0.039 -10000 0 -0.48 2 2
PDE9A -0.092 0.32 -10000 0 -1.1 31 31
NCOA2 0.013 0.077 -10000 0 -0.48 8 8
CEBPA 0.001 0.11 -10000 0 -0.48 16 16
EHMT2 0.027 0.006 -10000 0 -10000 0 0
cell proliferation -0.025 0.16 0.34 15 -0.43 23 38
NR0B1 -0.078 0.18 -10000 0 -0.48 50 50
EGR1 0.013 0.075 -10000 0 -0.48 7 7
RXRs/9cRA -0.006 0.11 -10000 0 -0.27 45 45
AR/RACK1/Src -0.017 0.097 0.3 4 -0.34 10 14
AR/GR -0.018 0.11 0.28 1 -0.33 22 23
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.003 0.027 -10000 0 -0.35 1 1
T-DHT/AR/TIF2/CARM1 -0.013 0.1 -10000 0 -0.33 17 17
SRC -0.029 0.065 0.2 4 -0.27 17 21
NR3C1 0.026 0.028 -10000 0 -0.48 1 1
KLK3 -0.075 0.12 0.22 2 -0.29 51 53
APPBP2 0.02 0.02 -10000 0 -10000 0 0
TRIM24 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.02 0.095 0.24 1 -0.32 16 17
TMPRSS2 -0.12 0.35 -10000 0 -1.1 40 40
RXRG -0.056 0.17 -10000 0 -0.34 78 78
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.005 -10000 0 -10000 0 0
RXRB 0.027 0.006 -10000 0 -10000 0 0
CARM1 0.026 0.007 -10000 0 -10000 0 0
NR2C2 0.027 0.005 -10000 0 -10000 0 0
KLK2 -0.021 0.088 -10000 0 -0.38 3 3
AR -0.033 0.1 -10000 0 -0.31 33 33
SENP1 0.028 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
MDM2 0.026 0.008 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.004 0.11 -10000 0 -0.48 16 16
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.099 0.2 -10000 0 -0.34 117 117
T-DHT/AR/RACK1/Src -0.018 0.099 0.31 4 -0.33 14 18
positive regulation of transcription 0.004 0.11 -10000 0 -0.48 16 16
DNAJA1 0.019 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.006 -10000 0 -10000 0 0
NCOA1 0.031 0.032 -10000 0 -0.52 1 1
SPDEF -0.033 0.16 -10000 0 -0.48 40 40
T-DHT/AR/TIF2 -0.009 0.094 0.24 5 -0.34 12 17
T-DHT/AR/Hsp90 -0.019 0.092 0.24 1 -0.31 16 17
GSK3B 0.027 0.007 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.065 -10000 0 -0.29 17 17
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.026 0.008 -10000 0 -10000 0 0
POU2F1 0.008 0.065 -10000 0 -0.24 10 10
T-DHT/AR/DAX-1 -0.067 0.13 0.28 2 -0.34 31 33
CREBBP 0.027 0.005 -10000 0 -10000 0 0
SMARCE1 0.027 0.005 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.012 0.11 -10000 0 -0.44 16 16
HDAC1 0.027 0.009 -10000 0 -10000 0 0
AES 0.026 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.007 -10000 0 -10000 0 0
DTX1 0.022 0.043 -10000 0 -0.48 2 2
LRP6/FZD1 0.032 0.039 -10000 0 -0.35 3 3
TLE1 0.025 0.028 -10000 0 -0.48 1 1
AP1 -0.012 0.088 -10000 0 -0.28 28 28
NCSTN 0.024 0.01 -10000 0 -10000 0 0
ADAM10 0.027 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.01 0.12 -10000 0 -0.7 7 7
NICD/RBPSUH 0.028 0.11 -10000 0 -0.44 16 16
WIF1 -0.099 0.2 -10000 0 -0.48 66 66
NOTCH1 0.005 0.096 -10000 0 -0.47 13 13
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 -0.007 0.1 -10000 0 -0.21 52 52
DKK1 -0.11 0.2 -10000 0 -0.48 71 71
beta catenin/beta TrCP1 0.033 0.075 -10000 0 -0.33 3 3
APH1B 0.026 0.028 -10000 0 -0.48 1 1
APH1A 0.023 0.011 -10000 0 -10000 0 0
AXIN1 0.006 0.073 -10000 0 -0.42 5 5
CtBP/CBP/TCF1/TLE1/AES 0.006 0.048 0.29 1 -0.24 3 4
PSEN1 0.027 0.006 -10000 0 -10000 0 0
FOS 0.004 0.094 -10000 0 -0.48 11 11
JUN 0.024 0.04 -10000 0 -0.48 2 2
MAP3K7 0.025 0.009 -10000 0 -10000 0 0
CTNNB1 0.022 0.077 0.26 1 -0.35 3 4
MAPK3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.009 0.11 -10000 0 -0.32 29 29
HNF1A -0.008 0.076 -10000 0 -0.49 3 3
CTBP1 0.027 0.007 -10000 0 -10000 0 0
MYC -0.003 0.18 -10000 0 -1.4 6 6
NKD1 -0.01 0.12 -10000 0 -0.48 21 21
FZD1 0.023 0.041 -10000 0 -0.48 2 2
NOTCH1 precursor/Deltex homolog 1 0.027 0.12 -10000 0 -0.45 16 16
apoptosis -0.011 0.087 -10000 0 -0.28 28 28
Delta 1/NOTCHprecursor 0.022 0.12 -10000 0 -0.44 16 16
DLL1 0.013 0.067 -10000 0 -0.48 5 5
PPARD 0.023 0.051 -10000 0 -0.83 1 1
Gamma Secretase 0.06 0.038 -10000 0 -10000 0 0
APC -0.003 0.095 -10000 0 -0.42 11 11
DVL1 -0.008 0.077 -10000 0 -0.37 11 11
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.07 0.14 -10000 0 -0.31 82 82
LRP6 0.025 0.028 -10000 0 -0.48 1 1
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.012 0.009 -10000 0 -10000 0 0
CCND1 -0.026 0.26 -10000 0 -1.3 14 14
WNT1 0.009 0.082 -10000 0 -0.48 8 8
Axin1/APC/beta catenin 0.029 0.11 0.29 6 -0.45 8 14
DKK2 0 0.12 -10000 0 -0.48 19 19
NOTCH1 precursor/DVL1 0.001 0.12 -10000 0 -0.51 11 11
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.029 -10000 0 -0.49 1 1
NOTCH/Deltex homolog 1 0.017 0.11 -10000 0 -0.45 16 16
PPP2R5D 0.023 0.076 0.26 20 -0.31 5 25
MAPK1 0.027 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.034 0.13 -10000 0 -0.29 62 62
RBPJ 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.002 0.066 -10000 0 -0.35 12 12
MAP4K4 -0.002 0.079 0.21 1 -0.33 7 8
BAG4 0.025 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.011 0.072 -10000 0 -0.19 36 36
NFKBIA 0.024 0.01 -10000 0 -10000 0 0
BIRC3 0.003 0.1 -10000 0 -0.48 14 14
BAX -0.013 0.079 -10000 0 -0.36 15 15
RIPK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.015 0.12 0.74 9 -10000 0 9
BAD -0.024 0.066 0.19 2 -0.19 31 33
SMPD1 0.006 0.069 0.23 7 -0.25 5 12
RB1 -0.025 0.067 0.16 1 -0.2 31 32
FADD/Caspase 8 0.007 0.087 0.25 2 -0.49 4 6
MAP2K4 -0.022 0.064 0.18 3 -0.23 5 8
NSMAF 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.025 0.071 0.2 6 -0.26 7 13
EGF -0.059 0.19 -10000 0 -0.48 56 56
mol:ceramide -0.023 0.069 0.15 5 -0.2 36 41
MADD 0.028 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.002 0.051 -10000 0 -0.35 7 7
ASAH1 0.022 0.029 -10000 0 -0.48 1 1
negative regulation of cell cycle -0.024 0.067 0.16 1 -0.2 31 32
cell proliferation -0.009 0.085 0.22 2 -0.33 5 7
BID -0.006 0.13 -10000 0 -0.62 11 11
MAP3K1 -0.021 0.068 0.18 4 -0.19 29 33
EIF2A -0.019 0.076 0.36 3 -0.23 4 7
TRADD 0.027 0.005 -10000 0 -10000 0 0
CRADD 0.027 0.01 -10000 0 -10000 0 0
MAPK3 -0.02 0.068 0.22 2 -0.25 6 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.023 0.07 0.22 2 -0.27 6 8
Cathepsin D/ceramide -0.01 0.072 -10000 0 -0.19 37 37
FADD 0.003 0.079 0.21 6 -0.33 7 13
KSR1 -0.023 0.075 0.21 6 -0.21 29 35
MAPK8 -0.017 0.071 -10000 0 -0.26 5 5
PRKRA -0.022 0.071 0.22 5 -0.19 30 35
PDGFA 0.011 0.082 -10000 0 -0.48 9 9
TRAF2 0.024 0.039 -10000 0 -0.48 2 2
IGF1 0.003 0.1 -10000 0 -0.48 13 13
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.069 0.14 8 -0.2 36 44
CTSD 0.024 0.039 -10000 0 -0.48 2 2
regulation of nitric oxide biosynthetic process 0.04 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.009 0.09 0.24 2 -0.35 5 7
PRKCD 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.044 -10000 0 -0.48 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.002 0.051 -10000 0 -0.35 7 7
RelA/NF kappa B1 0.04 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.077 -10000 0 -0.35 7 7
TNFR1A/BAG4/TNF-alpha 0.02 0.086 -10000 0 -0.3 21 21
mol:Sphingosine-1-phosphate -0.002 0.066 -10000 0 -0.35 12 12
MAP2K1 -0.025 0.07 0.21 3 -0.25 7 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0 0.06 0.21 7 -0.19 12 19
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.022 0.068 0.21 5 -0.24 4 9
TNF-alpha/TNFR1A/FAN 0.023 0.082 -10000 0 -0.3 18 18
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.073 -10000 0 -0.56 2 2
MAP2K2 -0.025 0.068 0.22 2 -0.25 7 9
SMPD3 -0.003 0.088 0.2 3 -0.32 14 17
TNF -0.011 0.13 -10000 0 -0.35 35 35
PKC zeta/PAR4 0.035 0.035 -10000 0 -0.35 2 2
mol:PHOSPHOCHOLINE 0.028 0.096 0.22 55 -0.18 5 60
NF kappa B1/RelA/I kappa B alpha 0.062 0.043 -10000 0 -0.26 1 1
AIFM1 -0.007 0.065 0.19 7 -0.19 11 18
BCL2 0.017 0.058 -10000 0 -0.48 4 4
IL1-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
UBC13/UEV1A 0.034 0.014 -10000 0 -10000 0 0
PRKCZ 0.022 0.044 -10000 0 -0.48 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.024 0.028 -10000 0 -0.48 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.078 -10000 0 -0.38 8 8
IRAK/TOLLIP 0.026 0.014 -10000 0 -10000 0 0
IKBKB 0.024 0.01 -10000 0 -10000 0 0
IKBKG 0.024 0.039 -10000 0 -0.48 2 2
IL1 alpha/IL1R2 -0.044 0.16 -10000 0 -0.38 55 55
IL1A -0.044 0.16 -10000 0 -0.48 37 37
IL1B -0.016 0.095 -10000 0 -0.36 23 23
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.046 -10000 0 -0.25 2 2
IL1R2 -0.015 0.13 -10000 0 -0.48 23 23
IL1R1 0.022 0.054 -10000 0 -0.48 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.065 -10000 0 -0.32 5 5
TOLLIP 0.027 0.005 -10000 0 -10000 0 0
TICAM2 0.023 0.047 -10000 0 -0.48 3 3
MAP3K3 0.026 0.028 -10000 0 -0.48 1 1
TAK1/TAB1/TAB2 0.017 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.016 0.076 0.25 1 -0.34 3 4
JUN -0.02 0.06 0.17 11 -0.23 10 21
MAP3K7 0.025 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.038 0.099 -10000 0 -0.28 25 25
IL1 alpha/IL1R1/IL1RAP/MYD88 0.013 0.12 -10000 0 -0.29 38 38
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.022 0.12 -10000 0 -0.28 38 38
IL1 beta fragment/IL1R1/IL1RAP 0.013 0.097 -10000 0 -0.32 25 25
NFKB1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.064 0.18 13 -0.24 15 28
IRAK1 -0.002 0.016 -10000 0 -10000 0 0
IL1RN/IL1R1 0.012 0.1 -10000 0 -0.39 20 20
IRAK4 0.027 0.005 -10000 0 -10000 0 0
PRKCI 0.026 0.011 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.038 0.012 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.085 -10000 0 -0.42 8 8
CHUK 0.028 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.013 0.097 -10000 0 -0.32 25 25
IL1 beta/IL1R2 -0.017 0.13 -10000 0 -0.35 39 39
IRAK/TRAF6/TAK1/TAB1/TAB2 0.031 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.025 0.089 -10000 0 -0.28 20 20
IRAK3 0.013 0.082 -10000 0 -0.48 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.1 -10000 0 -0.3 22 22
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.098 -10000 0 -0.27 36 36
IL1 alpha/IL1R1/IL1RAP -0.001 0.12 -10000 0 -0.32 38 38
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
MYD88 0.027 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.032 -10000 0 -10000 0 0
IL1RAP 0.025 0.028 -10000 0 -0.48 1 1
UBE2N 0.027 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.008 0.075 -10000 0 -0.32 4 4
CASP1 0.023 0.047 -10000 0 -0.48 3 3
IL1RN/IL1R2 -0.014 0.14 -10000 0 -0.4 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.098 -10000 0 -0.3 25 25
TMEM189-UBE2V1 0.02 0.014 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.089 -10000 0 -0.4 8 8
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL1RN -0.006 0.12 -10000 0 -0.48 19 19
TRAF6/TAK1/TAB1/TAB2 0.043 0.022 -10000 0 -10000 0 0
MAP2K6 -0.016 0.068 0.19 13 -0.24 16 29
TCGA08_p53

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
CDKN2A -0.022 0.075 -10000 0 -0.35 15 15
TP53 -0.012 0.064 0.27 1 -0.28 14 15
Senescence -0.012 0.064 0.27 1 -0.28 14 15
Apoptosis -0.012 0.064 0.27 1 -0.28 14 15
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.016 0.067 0.26 21 -10000 0 21
MDM4 0.024 0.028 -10000 0 -0.48 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.028 0.058 -10000 0 -0.35 7 7
alphaV beta3 Integrin 0.021 0.092 -10000 0 -0.33 17 17
PTK2 -0.011 0.14 0.35 8 -0.47 15 23
IGF1R 0.022 0.049 -10000 0 -0.48 3 3
PI4KB 0.023 0.011 -10000 0 -10000 0 0
MFGE8 0.023 0.047 -10000 0 -0.48 3 3
SRC 0.027 0.006 -10000 0 -10000 0 0
CDKN1B -0.017 0.11 -10000 0 -0.44 21 21
VEGFA 0.025 0.029 -10000 0 -0.31 2 2
ILK -0.012 0.1 -10000 0 -0.44 17 17
ROCK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.015 0.09 -10000 0 -0.41 15 15
PTK2B -0.021 0.079 0.19 16 -0.29 18 34
alphaV/beta3 Integrin/JAM-A 0.005 0.099 -10000 0 -0.29 26 26
CBL 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.023 0.075 -10000 0 -0.3 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.039 0.097 -10000 0 -0.31 22 22
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.003 0.073 -10000 0 -0.3 8 8
alphaV/beta3 Integrin/Syndecan-1 0.03 0.077 -10000 0 -0.3 14 14
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.004 0.14 -10000 0 -0.33 37 37
PI4 Kinase 0.034 0.017 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.018 0.14 -10000 0 -0.34 46 46
RPS6KB1 -0.051 0.11 0.33 2 -0.56 9 11
TLN1 0.025 0.028 -10000 0 -0.48 1 1
MAPK3 -0.028 0.14 -10000 0 -0.55 17 17
GPR124 0.021 0.039 -10000 0 -0.48 2 2
MAPK1 -0.028 0.14 -10000 0 -0.58 15 15
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.021 0.13 -10000 0 -0.31 56 56
cell adhesion 0.015 0.079 -10000 0 -0.29 18 18
ANGPTL3 0.015 0.035 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.052 -10000 0 -0.3 6 6
IGF-1R heterotetramer 0.022 0.049 -10000 0 -0.48 3 3
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
TGFBR2 0.026 0.028 -10000 0 -0.48 1 1
ITGB3 -0.003 0.1 -10000 0 -0.48 12 12
IGF1 0.003 0.1 -10000 0 -0.48 13 13
RAC1 0.025 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.079 -10000 0 -0.32 13 13
apoptosis 0.028 0.003 -10000 0 -10000 0 0
CD47 0.023 0.047 -10000 0 -0.48 3 3
alphaV/beta3 Integrin/CD47 0.028 0.079 -10000 0 -0.3 15 15
VCL 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.006 0.12 -10000 0 -0.35 28 28
CSF1 0.021 0.05 -10000 0 -0.48 3 3
PIK3C2A -0.012 0.1 -10000 0 -0.44 17 17
PI4 Kinase/Pyk2 -0.013 0.091 -10000 0 -0.37 10 10
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.034 0.087 -10000 0 -0.29 17 17
FAK1/Vinculin 0.005 0.12 0.33 8 -0.38 14 22
alphaV beta3/Integrin/ppsTEM5 0.024 0.08 -10000 0 -0.32 13 13
RHOA 0.027 0.005 -10000 0 -10000 0 0
VTN -0.007 0.11 -10000 0 -0.48 15 15
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
FGF2 0.012 0.08 -10000 0 -0.48 8 8
F11R 0 0.056 -10000 0 -0.35 8 8
alphaV/beta3 Integrin/Lactadherin 0.029 0.079 -10000 0 -0.3 15 15
alphaV/beta3 Integrin/TGFBR2 0.03 0.075 -10000 0 -0.3 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.052 -10000 0 -0.28 6 6
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.029 0.07 -10000 0 -0.29 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.089 -10000 0 -0.48 10 10
alphaV/beta3 Integrin/Pyk2 0.016 0.085 -10000 0 -0.29 18 18
SDC1 0.024 0.047 -10000 0 -0.48 3 3
VAV3 -0.016 0.063 0.18 13 -0.33 7 20
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.015 0.081 -10000 0 -0.48 9 9
FAK1/Paxillin 0.003 0.12 0.29 9 -0.37 15 24
cell migration 0 0.11 0.26 11 -0.34 14 25
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PI3K 0.025 0.1 -10000 0 -0.34 5 5
SPP1 -0.047 0.17 -10000 0 -0.48 41 41
KDR 0.015 0.07 -10000 0 -0.29 13 13
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.003 -10000 0 -10000 0 0
COL4A3 -0.049 0.17 -10000 0 -0.48 46 46
angiogenesis -0.012 0.15 0.29 1 -0.62 13 14
Rac1/GTP 0.017 0.062 -10000 0 -0.31 7 7
EDIL3 -0.012 0.12 -10000 0 -0.33 38 38
cell proliferation 0.029 0.074 -10000 0 -0.3 13 13
Caspase cascade in apoptosis

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
TOP1 -0.002 0.097 0.28 1 -0.4 10 11
ACTA1 -0.015 0.095 0.28 2 -0.36 14 16
NUMA1 0 0.09 0.28 1 -0.35 11 12
SPTAN1 -0.017 0.093 0.33 1 -0.37 14 15
LIMK1 -0.012 0.099 0.31 5 -0.37 13 18
BIRC3 0.002 0.1 -10000 0 -0.48 14 14
BIRC2 0.027 0.006 -10000 0 -10000 0 0
BAX 0.027 0.006 -10000 0 -10000 0 0
CASP10 -0.029 0.069 -10000 0 -0.34 14 14
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.003 -10000 0 -10000 0 0
PTK2 -0.001 0.087 0.25 1 -0.35 12 13
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.017 0.091 0.33 1 -0.36 14 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.01 -10000 0 -10000 0 0
GSN -0.017 0.092 0.33 1 -0.37 14 15
MADD 0.028 0.004 -10000 0 -10000 0 0
TFAP2A -0.061 0.23 -10000 0 -0.59 51 51
BID -0.006 0.044 -10000 0 -0.2 15 15
MAP3K1 -0.009 0.099 -10000 0 -0.43 15 15
TRADD 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.013 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.016 0.099 0.29 3 -0.37 14 17
CASP9 0.027 0.01 -10000 0 -0.13 1 1
DNA repair -0.008 0.045 0.19 2 -0.18 7 9
neuron apoptosis -0.001 0.12 -10000 0 -0.6 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.006 0.096 0.3 1 -0.34 16 17
APAF1 0.027 0.005 -10000 0 -10000 0 0
CASP6 0.003 0.12 -10000 0 -0.83 5 5
TRAF2 0.024 0.039 -10000 0 -0.48 2 2
ICAD/CAD -0.016 0.092 0.34 3 -0.37 12 15
CASP7 0.003 0.075 0.27 13 -0.24 2 15
KRT18 0.017 0.037 -10000 0 -0.48 1 1
apoptosis -0.009 0.094 0.31 2 -0.44 8 10
DFFA -0.015 0.093 0.26 2 -0.37 14 16
DFFB -0.015 0.093 0.31 1 -0.37 13 14
PARP1 0.008 0.046 0.18 7 -0.2 2 9
actin filament polymerization -0.01 0.11 0.33 12 -0.35 13 25
TNF -0.011 0.13 -10000 0 -0.35 35 35
CYCS 0.004 0.049 0.15 5 -0.27 3 8
SATB1 -0.003 0.12 -10000 0 -0.77 6 6
SLK -0.017 0.091 0.31 1 -0.37 14 15
p15 BID/BAX 0.012 0.054 0.19 1 -0.27 3 4
CASP2 0.002 0.074 0.21 8 -0.3 6 14
JNK cascade 0.009 0.099 0.43 15 -10000 0 15
CASP3 -0.015 0.097 0.34 1 -0.38 14 15
LMNB2 -0.006 0.14 0.24 3 -0.46 22 25
RIPK1 0.027 0.005 -10000 0 -10000 0 0
CASP4 0.024 0.039 -10000 0 -0.48 2 2
Mammalian IAPs/DIABLO 0.049 0.072 -10000 0 -0.27 14 14
negative regulation of DNA binding -0.06 0.23 -10000 0 -0.58 51 51
stress fiber formation -0.016 0.09 0.31 1 -0.36 14 15
GZMB -0.012 0.084 -10000 0 -0.4 13 13
CASP1 0.009 0.039 -10000 0 -0.31 5 5
LMNB1 0.004 0.13 0.25 3 -0.59 9 12
APP -0.002 0.13 -10000 0 -0.6 14 14
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.019 -10000 0 -0.35 1 1
VIM -0.006 0.095 0.33 2 -0.44 8 10
LMNA 0.01 0.085 0.24 2 -0.36 7 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.001 0.077 -10000 0 -0.32 8 8
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.015 0.095 0.33 2 -0.37 14 16
APAF-1/Caspase 9 0.006 0.1 -10000 0 -0.64 8 8
nuclear fragmentation during apoptosis 0 0.089 0.28 1 -0.35 11 12
CFL2 0.01 0.11 0.36 12 -0.34 12 24
GAS2 -0.037 0.11 0.32 2 -0.35 24 26
positive regulation of apoptosis 0.003 0.12 0.27 2 -0.48 12 14
PRF1 0.016 0.062 -10000 0 -0.48 4 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.006 -10000 0 -10000 0 0
VLDLR 0.011 0.085 -10000 0 -0.48 10 10
LRPAP1 0.026 0.028 -10000 0 -0.48 1 1
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.012 0.1 -10000 0 -0.3 28 28
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.009 0.089 0.18 16 -0.27 28 44
IQGAP1/CaM 0.039 0.011 -10000 0 -10000 0 0
DAB1 0.02 0.025 -10000 0 -10000 0 0
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
PLA2G7 0.01 0.087 -10000 0 -0.48 10 10
CALM1 0.027 0.006 -10000 0 -10000 0 0
DYNLT1 0.025 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.044 -10000 0 -0.35 4 4
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.024 0.032 -10000 0 -0.48 1 1
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 -0.057 0.17 -10000 0 -0.32 84 84
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.001 0.11 -10000 0 -0.32 30 30
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.028 0.12 0.3 6 -0.33 14 20
MAP1B -0.007 0.059 -10000 0 -0.3 13 13
RAC1 0.011 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.004 0.083 0.18 12 -0.25 28 40
RELN -0.021 0.13 -10000 0 -0.48 24 24
PAFAH/LIS1 0.016 0.053 -10000 0 -0.3 9 9
LIS1/CLIP170 0.026 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.024 0.096 -10000 0 -0.38 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.018 0.1 -10000 0 -0.34 17 17
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.043 0.11 0.21 1 -0.36 14 15
LIS1/IQGAP1 0.027 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.012 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.039 -10000 0 -0.48 2 2
PAFAH1B2 0.025 0.028 -10000 0 -0.48 1 1
MAP1B/LIS1/Dynein heavy chain 0.01 0.053 -10000 0 -0.31 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.023 0.12 0.32 4 -0.35 11 15
LRP8 0.021 0.05 -10000 0 -0.28 7 7
NDEL1/Katanin 60 -0.03 0.12 0.3 6 -0.34 14 20
P39/CDK5 -0.045 0.12 0.18 8 -0.26 63 71
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.011 -10000 0 -10000 0 0
CDK5 -0.029 0.078 0.18 14 -0.26 27 41
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.008 0.099 -10000 0 -0.28 30 30
RELN/VLDLR 0.013 0.11 -10000 0 -0.3 34 34
CDC42 0.012 0.005 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.011 0.059 0.2 27 -10000 0 27
BUB1B -0.01 0.078 -10000 0 -0.32 16 16
PLK1 0.003 0.037 0.091 5 -0.15 12 17
PLK1S1 0.004 0.036 -10000 0 -0.17 11 11
KIF2A 0.002 0.044 0.26 4 -0.21 4 8
regulation of mitotic centrosome separation 0.003 0.037 0.091 5 -0.14 12 17
GOLGA2 0.026 0.028 -10000 0 -0.48 1 1
Hec1/SPC24 0.006 0.11 -10000 0 -0.33 29 29
WEE1 0.005 0.062 -10000 0 -0.31 10 10
cytokinesis -0.006 0.1 0.28 1 -0.49 12 13
PP2A-alpha B56 0.021 0.17 -10000 0 -0.67 20 20
AURKA 0.002 0.048 -10000 0 -0.26 9 9
PICH/PLK1 0.006 0.058 -10000 0 -0.35 6 6
CENPE -0.011 0.07 0.25 1 -0.29 17 18
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.044 0.26 4 -0.21 4 8
PPP2CA 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.023 0.039 -10000 0 -0.48 2 2
TPX2 -0.008 0.079 -10000 0 -0.29 24 24
PAK1 0.027 0.007 -10000 0 -10000 0 0
SPC24 0.003 0.1 -10000 0 -0.48 15 15
FBXW11 0.026 0.007 -10000 0 -10000 0 0
CLSPN -0.01 0.084 -10000 0 -0.31 24 24
GORASP1 0.027 0.005 -10000 0 -10000 0 0
metaphase 0 0.005 0.016 6 -0.019 15 21
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.019 0.048 8 -0.071 12 20
G2 phase of mitotic cell cycle 0 0.003 0.016 4 -0.011 5 9
STAG2 0.028 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.006 0.098 -10000 0 -0.52 11 11
spindle elongation 0.003 0.037 0.091 5 -0.14 12 17
ODF2 0.027 0.007 -10000 0 -10000 0 0
BUB1 -0.01 0.18 -10000 0 -0.73 20 20
TPT1 -0.002 0.048 -10000 0 -0.18 21 21
CDC25C -0.028 0.13 -10000 0 -0.38 39 39
CDC25B 0.026 0.012 -10000 0 -10000 0 0
SGOL1 -0.011 0.06 -10000 0 -0.2 27 27
RHOA 0.027 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.052 -10000 0 -0.44 2 2
CDC14B 0.005 0.006 -10000 0 -10000 0 0
CDC20 0 0.11 -10000 0 -0.48 18 18
PLK1/PBIP1 -0.001 0.047 -10000 0 -0.19 14 14
mitosis -0.001 0.006 0.026 11 -10000 0 11
FBXO5 -0.002 0.039 0.14 3 -0.15 8 11
CDC2 0.001 0.003 -10000 0 -0.016 4 4
NDC80 0 0.11 -10000 0 -0.43 20 20
metaphase plate congression 0.005 0.043 -10000 0 -0.23 8 8
ERCC6L 0.007 0.061 -10000 0 -0.36 6 6
NLP/gamma Tubulin 0.004 0.023 0.08 3 -0.091 11 14
microtubule cytoskeleton organization -0.002 0.048 -10000 0 -0.18 21 21
G2/M transition DNA damage checkpoint 0 0.002 0.014 1 -10000 0 1
PPP1R12A 0.028 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.014 1 -10000 0 1
PLK1/PRC1-2 0.024 0.083 -10000 0 -0.37 12 12
GRASP65/GM130/RAB1/GTP/PLK1 0.042 0.044 -10000 0 -0.19 4 4
RAB1A 0.028 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.03 0.079 8 -0.13 7 15
mitotic prometaphase -0.001 0.004 0.017 8 -0.012 12 20
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.053 -10000 0 -0.31 3 3
microtubule-based process 0.011 0.072 -10000 0 -0.34 12 12
Golgi organization 0.003 0.037 0.091 5 -0.14 12 17
Cohesin/SA2 0.017 0.037 0.11 1 -0.15 10 11
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.011 0.09 -10000 0 -0.48 11 11
APC/C/CDC20 0.006 0.086 0.12 1 -0.35 18 19
PPP2R1A 0.027 0.006 -10000 0 -10000 0 0
chromosome segregation -0.001 0.047 -10000 0 -0.19 14 14
PRC1 0.025 0.039 -10000 0 -0.48 2 2
ECT2 0.007 0.058 0.22 14 -0.22 5 19
C13orf34 0.004 0.03 0.077 7 -0.11 12 19
NUDC 0.005 0.043 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.01 0.077 -10000 0 -0.31 16 16
spindle assembly 0.004 0.031 0.08 9 -0.12 11 20
spindle stabilization 0.004 0.036 -10000 0 -0.17 11 11
APC/C/HCDH1 0.021 0.026 -10000 0 -0.3 2 2
MKLP2/PLK1 0.011 0.073 -10000 0 -0.35 12 12
CCNB1 0.023 0.041 -10000 0 -0.5 2 2
PPP1CB 0.028 0.003 -10000 0 -10000 0 0
BTRC 0.028 0.004 -10000 0 -10000 0 0
ROCK2 0.008 0.056 -10000 0 -0.4 4 4
TUBG1 0.008 0.027 -10000 0 -0.25 2 2
G2/M transition of mitotic cell cycle 0.001 0.044 -10000 0 -0.43 2 2
MLF1IP -0.001 0.044 -10000 0 -0.36 5 5
INCENP 0.028 0.004 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.019 0.038 -10000 0 -0.28 5 5
epithelial cell differentiation 0.05 0.048 -10000 0 -0.3 5 5
CYFIP2 0.002 0.11 -10000 0 -0.48 17 17
ENAH -0.006 0.074 0.37 3 -0.32 3 6
EGFR 0.008 0.089 -10000 0 -0.48 11 11
EPHA2 0.011 0.086 -10000 0 -0.48 10 10
MYO6 -0.01 0.057 0.25 7 -0.29 6 13
CTNNB1 0.027 0.01 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.072 -10000 0 -0.3 14 14
AQP5 -0.098 0.19 -10000 0 -0.45 77 77
CTNND1 0.026 0.028 -10000 0 -0.48 1 1
mol:PI-4-5-P2 -0.01 0.055 0.44 2 -0.3 4 6
regulation of calcium-dependent cell-cell adhesion -0.02 0.058 0.2 6 -0.26 12 18
EGF -0.059 0.19 -10000 0 -0.48 56 56
NCKAP1 0.028 0.003 -10000 0 -10000 0 0
AQP3 -0.051 0.15 -10000 0 -0.45 39 39
cortical microtubule organization 0.05 0.048 -10000 0 -0.3 5 5
GO:0000145 -0.009 0.053 0.43 2 -0.29 4 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.055 0.049 -10000 0 -0.31 5 5
MLLT4 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.026 0.051 -10000 0 -0.38 3 3
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.069 -10000 0 -0.28 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.005 0.053 0.44 2 -0.44 1 3
PVRL2 0.027 0.006 -10000 0 -10000 0 0
ZYX -0.01 0.058 0.44 2 -0.29 6 8
ARF6/GTP 0.048 0.065 -10000 0 -0.26 10 10
CDH1 0.02 0.061 -10000 0 -0.48 5 5
EGFR/EGFR/EGF/EGF -0.015 0.12 -10000 0 -0.27 57 57
RhoA/GDP 0.052 0.046 -10000 0 -0.29 5 5
actin cytoskeleton organization -0.01 0.054 0.42 2 -0.29 5 7
IGF-1R heterotetramer 0.022 0.049 -10000 0 -0.48 3 3
GIT1 0.027 0.004 -10000 0 -10000 0 0
IGF1R 0.022 0.049 -10000 0 -0.48 3 3
IGF1 0.003 0.1 -10000 0 -0.48 13 13
DIAPH1 0.01 0.17 -10000 0 -0.57 20 20
Wnt receptor signaling pathway -0.05 0.048 0.3 5 -10000 0 5
RHOA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.028 0.054 -10000 0 -0.43 3 3
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
VCL -0.011 0.055 0.43 2 -0.29 5 7
EFNA1 0.018 0.055 -10000 0 -0.48 4 4
LPP -0.011 0.053 0.44 2 -0.45 1 3
Ephrin A1/EPHA2 0.025 0.075 -10000 0 -0.3 13 13
SEC6/SEC8 -0.015 0.027 -10000 0 -0.29 1 1
MGAT3 -0.02 0.058 0.2 6 -0.27 12 18
HGF/MET -0.002 0.11 -10000 0 -0.26 47 47
HGF 0 0.11 -10000 0 -0.48 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.019 0.039 -10000 0 -0.28 5 5
actin cable formation 0.026 0.096 0.26 25 -0.28 1 26
KIAA1543 -0.015 0.052 0.34 1 -0.26 9 10
KIFC3 -0.016 0.045 0.18 3 -0.28 7 10
NCK1 0.028 0.004 -10000 0 -10000 0 0
EXOC3 0.021 0.012 -10000 0 -10000 0 0
ACTN1 -0.01 0.056 0.24 8 -0.29 5 13
NCK1/GIT1 0.04 0.009 -10000 0 -10000 0 0
mol:GDP 0.05 0.048 -10000 0 -0.3 5 5
EXOC4 0.027 0.006 -10000 0 -10000 0 0
STX4 -0.011 0.047 0.2 6 -0.29 5 11
PIP5K1C -0.01 0.056 0.44 2 -0.3 4 6
LIMA1 0.027 0.013 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.007 0.097 0.36 7 -0.38 3 10
adherens junction assembly -0.017 0.12 0.37 6 -0.5 10 16
IGF-1R heterotetramer/IGF1 0.028 0.075 -10000 0 -0.26 18 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.014 -10000 0 -10000 0 0
MET -0.029 0.15 -10000 0 -0.48 34 34
PLEKHA7 -0.015 0.054 0.2 6 -0.27 9 15
mol:GTP 0.041 0.067 -10000 0 -0.27 12 12
establishment of epithelial cell apical/basal polarity 0.038 0.1 0.33 13 -10000 0 13
cortical actin cytoskeleton stabilization 0.019 0.038 -10000 0 -0.28 5 5
regulation of cell-cell adhesion -0.01 0.054 0.42 2 -0.29 5 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.019 0.039 -10000 0 -0.28 5 5
LPA4-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
ADCY4 -0.008 0.029 -10000 0 -0.56 1 1
ADCY5 -0.037 0.08 -10000 0 -0.31 26 26
ADCY6 -0.009 0.022 -10000 0 -0.3 2 2
ADCY7 -0.008 0.016 -10000 0 -0.3 1 1
ADCY1 -0.017 0.051 -10000 0 -0.3 11 11
ADCY2 -0.026 0.069 -10000 0 -0.3 20 20
ADCY3 -0.008 0.015 -10000 0 -0.3 1 1
ADCY8 -0.012 0.022 -10000 0 -0.3 1 1
PRKCE 0.006 0.019 -10000 0 -0.35 1 1
ADCY9 -0.012 0.038 -10000 0 -0.3 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.027 0.098 0.22 34 -0.28 6 40
Coregulation of Androgen receptor activity

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
NRIP1 0.025 0.028 -10000 0 -0.48 1 1
SVIL 0.023 0.047 -10000 0 -0.48 3 3
ZNF318 0.027 0.006 -10000 0 -10000 0 0
JMJD2C 0 0.008 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.019 0.12 -10000 0 -0.3 41 41
CARM1 0.026 0.007 -10000 0 -10000 0 0
PRDX1 0.027 0.009 -10000 0 -10000 0 0
PELP1 0.026 0.008 -10000 0 -10000 0 0
CTNNB1 0.027 0.01 -10000 0 -10000 0 0
AKT1 0.027 0.006 -10000 0 -10000 0 0
PTK2B 0.019 0.048 -10000 0 -0.48 3 3
MED1 0.027 0.005 -10000 0 -10000 0 0
MAK 0.006 0.09 -10000 0 -0.28 24 24
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.02 0.061 -10000 0 -0.48 5 5
GSN 0.026 0.013 -10000 0 -10000 0 0
NCOA2 0.013 0.077 -10000 0 -0.48 8 8
NCOA6 0.027 0.006 -10000 0 -10000 0 0
DNA-PK 0.048 0.027 -10000 0 -0.28 1 1
NCOA4 0.028 0.003 -10000 0 -10000 0 0
PIAS3 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.017 0.13 -10000 0 -0.76 10 10
XRCC5 0.028 0.003 -10000 0 -10000 0 0
UBE3A 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.032 0.13 -10000 0 -0.32 49 49
FHL2 -0.047 0.24 -10000 0 -0.98 20 20
RANBP9 0.027 0.005 -10000 0 -10000 0 0
JMJD1A -0.01 0.048 -10000 0 -0.14 31 31
CDK6 0.015 0.069 -10000 0 -0.31 12 12
TGFB1I1 0.024 0.04 -10000 0 -0.48 2 2
T-DHT/AR/CyclinD1 -0.029 0.12 -10000 0 -0.31 48 48
XRCC6 0.027 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.028 0.14 -10000 0 -0.34 45 45
CTDSP1 0.028 0.003 -10000 0 -10000 0 0
CTDSP2 0.026 0.007 -10000 0 -10000 0 0
BRCA1 0.026 0.028 -10000 0 -0.48 1 1
TCF4 0.022 0.039 -10000 0 -0.48 2 2
CDKN2A -0.021 0.11 -10000 0 -0.48 15 15
SRF 0.022 0.039 -10000 0 -10000 0 0
NKX3-1 -0.071 0.22 -10000 0 -0.7 30 30
KLK3 0 0.048 0.14 4 -0.2 6 10
TMF1 0.027 0.005 -10000 0 -10000 0 0
HNRNPA1 0.027 0.005 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 0.012 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.02 0.12 -10000 0 -0.32 38 38
AR -0.048 0.16 -10000 0 -0.47 38 38
UBA3 0.027 0.005 -10000 0 -10000 0 0
PATZ1 0.027 0.006 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.024 0.029 -10000 0 -0.48 1 1
PA2G4 0.027 0.005 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.11 -10000 0 -0.29 36 36
RPS6KA3 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.019 0.12 -10000 0 -0.3 40 40
LATS2 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.016 0.11 -10000 0 -0.29 36 36
Cyclin D3/CDK11 p58 0.019 0.02 -10000 0 -0.35 1 1
VAV3 0.012 0.06 -10000 0 -0.48 3 3
KLK2 -0.027 0.08 -10000 0 -0.45 3 3
CASP8 0.026 0.028 -10000 0 -0.48 1 1
T-DHT/AR/TIF2/CARM1 -0.01 0.12 -10000 0 -0.31 36 36
TMPRSS2 -0.098 0.3 -10000 0 -0.95 37 37
CCND1 0.008 0.094 -10000 0 -0.48 12 12
PIAS1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.027 -10000 0 -0.13 3 3
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.024 0.12 -10000 0 -0.3 43 43
CMTM2 0.014 0.075 -10000 0 -0.31 14 14
SNURF 0.007 0.097 -10000 0 -0.48 13 13
ZMIZ1 0.012 0.05 -10000 0 -0.35 2 2
CCND3 0.025 0.028 -10000 0 -0.48 1 1
TGIF1 0.026 0.008 -10000 0 -10000 0 0
FKBP4 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.029 0.083 -10000 0 -0.24 27 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.027 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.027 0.085 0.29 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.039 0.042 -10000 0 -0.3 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.058 -10000 0 -0.23 3 3
CaM/Ca2+ 0.03 0.081 -10000 0 -0.23 24 24
RAP1A 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.004 0.08 -10000 0 -0.23 25 25
AKT1 -0.013 0.079 0.31 4 -10000 0 4
MAP2K1 -0.016 0.074 0.24 5 -0.23 15 20
MAP3K11 -0.007 0.08 0.26 4 -0.23 25 29
IFNGR1 0.023 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.01 0.12 -10000 0 -0.43 13 13
Rap1/GTP -0.006 0.059 -10000 0 -10000 0 0
CRKL/C3G 0.039 0.012 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.036 0.091 -10000 0 -0.25 27 27
CEBPB 0.007 0.11 0.3 6 -0.43 8 14
STAT3 0.028 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.034 0.12 -10000 0 -0.83 3 3
STAT1 -0.006 0.08 0.29 3 -0.24 18 21
CALM1 0.027 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.032 0.14 -10000 0 -0.28 67 67
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.011 0.084 0.29 3 -0.23 18 21
CEBPB/PTGES2/Cbp/p300 0.016 0.073 -10000 0 -0.31 5 5
mol:Ca2+ 0.027 0.082 -10000 0 -0.24 27 27
MAPK3 0.008 0.085 -10000 0 -0.46 2 2
STAT1 (dimer) 0 0.081 -10000 0 -0.31 3 3
MAPK1 -0.01 0.14 -10000 0 -0.67 11 11
JAK2 0.022 0.02 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
JAK1 0.022 0.033 -10000 0 -0.49 1 1
CAMK2D 0.025 0.039 -10000 0 -0.48 2 2
DAPK1 0.007 0.1 0.26 7 -0.55 6 13
SMAD7 0.006 0.047 0.19 5 -0.28 1 6
CBL/CRKL/C3G 0.018 0.085 0.29 3 -10000 0 3
PI3K 0.029 0.077 -10000 0 -0.23 21 21
IFNG -0.032 0.14 -10000 0 -0.28 67 67
apoptosis 0.005 0.093 0.24 2 -0.43 9 11
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.004 -10000 0 -10000 0 0
CAMK2A 0.015 0.07 -10000 0 -0.28 14 14
CAMK2B -0.03 0.13 -10000 0 -0.48 22 22
FRAP1 -0.013 0.073 0.3 4 -10000 0 4
PRKCD -0.013 0.08 0.32 4 -10000 0 4
RAP1B 0.026 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.006 0.058 -10000 0 -0.23 3 3
PTPN2 0.027 0.006 -10000 0 -10000 0 0
EP300 0.028 0.005 -10000 0 -10000 0 0
IRF1 -0.005 0.068 0.25 2 -0.33 1 3
STAT1 (dimer)/PIASy 0.005 0.083 0.28 3 -0.24 1 4
SOCS1 0.018 0.11 -10000 0 -1.1 3 3
mol:GDP 0.015 0.08 0.27 3 -10000 0 3
CASP1 0.004 0.051 0.19 5 -0.24 3 8
PTGES2 0.027 0.005 -10000 0 -10000 0 0
IRF9 0.016 0.043 0.15 5 -0.3 1 6
mol:PI-3-4-5-P3 0.007 0.072 -10000 0 -0.22 21 21
RAP1/GDP 0.009 0.068 -10000 0 -10000 0 0
CBL -0.006 0.079 0.28 3 -0.23 24 27
MAP3K1 -0.004 0.077 0.26 4 -0.23 22 26
PIAS1 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.026 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.058 -10000 0 -0.23 3 3
PTPN11 -0.004 0.081 0.3 1 -0.24 27 28
CREBBP 0.028 0.005 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.012 0.13 -10000 0 -0.87 6 6
oxygen homeostasis 0 0.013 -10000 0 -10000 0 0
TCEB2 0.026 0.028 -10000 0 -0.48 1 1
TCEB1 0.025 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.026 0.12 0.28 2 -0.35 12 14
EPO -0.003 0.16 -10000 0 -0.6 6 6
FIH (dimer) 0.017 0.029 -10000 0 -10000 0 0
APEX1 0.018 0.029 -10000 0 -10000 0 0
SERPINE1 -0.021 0.19 -10000 0 -0.62 15 15
FLT1 -0.026 0.21 -10000 0 -0.79 19 19
ADORA2A 0.002 0.18 0.34 19 -0.59 8 27
germ cell development -0.034 0.2 0.32 1 -0.54 25 26
SLC11A2 -0.012 0.17 -10000 0 -0.61 9 9
BHLHE40 -0.014 0.18 -10000 0 -0.63 9 9
HIF1AN 0.017 0.029 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.014 0.13 0.3 1 -0.41 8 9
ETS1 0.03 0.025 -10000 0 -10000 0 0
CITED2 -0.027 0.19 -10000 0 -0.67 20 20
KDR -0.011 0.19 -10000 0 -0.86 14 14
PGK1 -0.015 0.17 -10000 0 -0.61 9 9
SIRT1 0.028 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.009 0.21 -10000 0 -0.71 9 9
EPAS1 -0.017 0.1 -10000 0 -0.37 15 15
SP1 0.031 0.012 -10000 0 -10000 0 0
ABCG2 -0.017 0.18 -10000 0 -0.63 11 11
EFNA1 -0.013 0.18 -10000 0 -0.61 11 11
FXN 0.001 0.18 0.34 17 -0.59 9 26
POU5F1 -0.036 0.21 -10000 0 -0.56 25 25
neuron apoptosis -0.009 0.2 0.68 9 -10000 0 9
EP300 0.027 0.005 -10000 0 -10000 0 0
EGLN3 -0.033 0.14 -10000 0 -0.5 29 29
EGLN2 0.017 0.038 -10000 0 -0.48 1 1
EGLN1 0.017 0.027 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.047 0.029 -10000 0 -0.3 1 1
VHL 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.015 0.028 -10000 0 -10000 0 0
SLC2A1 -0.005 0.21 0.34 20 -0.62 16 36
TWIST1 -0.029 0.22 0.34 15 -0.58 31 46
ELK1 0.031 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.021 0.14 0.32 1 -0.44 6 7
VEGFA -0.014 0.17 -10000 0 -0.59 10 10
CREBBP 0.027 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.022 -10000 0 -0.3 2 2
SNTA1 0.022 0.048 -10000 0 -0.48 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.022 -10000 0 -0.3 2 2
MAPK12 -0.014 0.059 -10000 0 -0.27 17 17
CCND1 -0.011 0.093 -10000 0 -0.44 14 14
p38 gamma/SNTA1 0.001 0.076 0.19 7 -0.26 21 28
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
PKN1 0.026 0.007 -10000 0 -10000 0 0
G2/M transition checkpoint -0.01 0.066 0.21 7 -0.26 17 24
MAP2K6 -0.012 0.067 -10000 0 -0.29 18 18
MAPT -0.011 0.084 0.23 6 -0.3 18 24
MAPK13 0.01 0.028 -10000 0 -0.35 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.026 -10000 0 -0.46 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.016 0.081 -10000 0 -0.34 6 6
NEF -0.009 0.045 -10000 0 -0.21 14 14
NFKBIA 0.021 0.021 -10000 0 -10000 0 0
BIRC3 0.017 0.1 -10000 0 -0.4 14 14
CYCS 0.002 0.075 0.18 1 -0.28 13 14
RIPK1 0.027 0.005 -10000 0 -10000 0 0
CD247 0.013 0.06 -10000 0 -0.24 13 13
MAP2K7 -0.021 0.2 -10000 0 -0.68 25 25
protein ubiquitination 0.013 0.088 0.34 4 -0.34 3 7
CRADD 0.027 0.01 -10000 0 -10000 0 0
DAXX 0.027 0.006 -10000 0 -10000 0 0
FAS 0.008 0.097 -10000 0 -0.48 13 13
BID 0.006 0.082 0.18 20 -0.28 14 34
NF-kappa-B/RelA/I kappa B alpha 0.043 0.053 -10000 0 -0.27 6 6
TRADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K5 0.025 0.008 -10000 0 -10000 0 0
CFLAR 0.028 0.003 -10000 0 -10000 0 0
FADD 0.027 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.053 -10000 0 -0.27 6 6
MAPK8 -0.019 0.2 0.39 2 -0.64 25 27
APAF1 0.027 0.005 -10000 0 -10000 0 0
TRAF1 0.027 0.01 -10000 0 -10000 0 0
TRAF2 0.024 0.039 -10000 0 -0.48 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.01 0.088 0.19 20 -0.3 15 35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.01 0.088 -10000 0 -0.38 7 7
CHUK 0.01 0.088 0.34 2 -0.38 3 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.059 0.062 -10000 0 -0.26 8 8
TCRz/NEF 0.005 0.069 -10000 0 -0.31 13 13
TNF -0.011 0.13 -10000 0 -0.35 35 35
FASLG -0.013 0.12 -10000 0 -0.56 13 13
NFKB1 0.021 0.034 -10000 0 -0.16 8 8
TNFR1A/BAG4/TNF-alpha 0.02 0.086 -10000 0 -0.3 21 21
CASP6 0.036 0.092 -10000 0 -0.55 3 3
CASP7 0.026 0.14 0.35 11 -0.48 11 22
RELA 0.021 0.034 -10000 0 -0.16 8 8
CASP2 0.027 0.006 -10000 0 -10000 0 0
CASP3 0.025 0.13 0.36 9 -0.46 12 21
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.016 -10000 0 -10000 0 0
CASP8 0.026 0.028 -10000 0 -0.48 1 1
CASP9 0.027 0.01 -10000 0 -0.13 1 1
MAP3K14 0.011 0.09 0.22 2 -0.37 6 8
APAF-1/Caspase 9 0.007 0.087 -10000 0 -0.34 7 7
BCL2 -0.019 0.18 0.37 2 -0.59 25 27
IGF1 pathway

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
NCK2 0.026 0.027 -10000 0 -0.48 1 1
PTK2 0.024 0.01 -10000 0 -10000 0 0
CRKL -0.004 0.069 0.16 1 -0.26 20 21
GRB2/SOS1/SHC 0.046 0.024 -10000 0 -10000 0 0
HRAS 0.027 0.005 -10000 0 -10000 0 0
IRS1/Crk 0.004 0.074 -10000 0 -0.26 22 22
IGF-1R heterotetramer/IGF1/PTP1B 0.029 0.074 -10000 0 -0.3 14 14
AKT1 -0.02 0.061 0.17 6 -0.28 11 17
BAD -0.022 0.058 0.17 1 -0.27 11 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.071 0.16 1 -0.26 22 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.077 0.21 1 -0.29 17 18
RAF1 -0.01 0.084 -10000 0 -0.42 9 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.042 0.079 -10000 0 -0.29 14 14
YWHAZ 0.025 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.012 0.082 -10000 0 -0.28 22 22
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.021 0.062 0.17 6 -0.27 12 18
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.001 0.08 0.27 2 -0.34 6 8
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.012 0.059 -10000 0 -0.28 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.054 0.063 -10000 0 -0.25 9 9
IGF-1R heterotetramer 0.017 0.056 -10000 0 -0.43 4 4
IGF-1R heterotetramer/IGF1/IRS/Nck 0.027 0.082 -10000 0 -0.26 21 21
Crk/p130 Cas/Paxillin 0.037 0.081 -10000 0 -0.26 18 18
IGF1R 0.017 0.056 -10000 0 -0.43 4 4
IGF1 0.001 0.11 -10000 0 -0.51 13 13
IRS2/Crk -0.001 0.078 0.16 1 -0.26 24 25
PI3K 0.04 0.079 -10000 0 -0.28 16 16
apoptosis 0.016 0.055 0.33 3 -10000 0 3
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
PRKCD -0.005 0.077 -10000 0 -0.35 13 13
RAF1/14-3-3 E 0.011 0.087 -10000 0 -0.38 7 7
BAD/14-3-3 -0.017 0.058 -10000 0 -0.35 3 3
PRKCZ -0.023 0.065 0.16 6 -0.28 14 20
Crk/p130 Cas/Paxillin/FAK1 0.014 0.06 -10000 0 -0.3 4 4
PTPN1 0.026 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.002 0.08 -10000 0 -0.37 13 13
BCAR1 0.021 0.055 -10000 0 -0.48 4 4
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.035 0.077 -10000 0 -0.29 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.011 0.076 -10000 0 -0.26 21 21
GRB10 0.014 0.077 -10000 0 -0.48 8 8
PTPN11 -0.005 0.072 0.16 1 -0.29 17 18
IRS1 -0.005 0.078 -10000 0 -0.28 22 22
IRS2 -0.01 0.079 0.16 1 -0.28 24 25
IGF-1R heterotetramer/IGF1 0.013 0.092 -10000 0 -0.39 16 16
GRB2 0.027 0.006 -10000 0 -10000 0 0
PDPK1 -0.021 0.065 0.17 6 -0.27 16 22
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKD1 -0.011 0.089 -10000 0 -0.42 11 11
SHC1 0.023 0.013 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.007 0.092 -10000 0 -0.33 20 20
CDC42/GTP -0.008 0.098 -10000 0 -0.31 14 14
PLCG1 -0.018 0.087 -10000 0 -0.33 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
G12/G13 0.036 0.015 -10000 0 -10000 0 0
cell migration -0.008 0.096 -10000 0 -0.3 14 14
S1PR5 0.015 0.061 -10000 0 -0.48 4 4
S1PR4 0.017 0.067 -10000 0 -0.48 6 6
MAPK3 -0.019 0.089 -10000 0 -0.28 20 20
MAPK1 -0.015 0.082 -10000 0 -0.28 16 16
S1P/S1P5/Gi -0.012 0.09 -10000 0 -0.27 21 21
GNAI1 0.02 0.056 -10000 0 -0.48 4 4
CDC42/GDP 0.02 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.042 -10000 0 -0.3 4 4
RHOA 0.027 0.068 0.19 38 -0.25 5 43
S1P/S1P4/Gi -0.014 0.096 -10000 0 -0.3 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.017 0.14 -10000 0 -0.48 26 26
S1P/S1P4/G12/G13 0.039 0.044 -10000 0 -0.27 5 5
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.056 -10000 0 -0.48 4 4
ANTXR2 0.025 0.039 -10000 0 -0.48 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.066 6 6
monocyte activation -0.034 0.16 -10000 0 -0.45 40 40
MAP2K2 -0.027 0.15 -10000 0 -0.57 26 26
MAP2K1 -0.004 0.01 0.13 1 -10000 0 1
MAP2K7 -0.004 0.007 -10000 0 -10000 0 0
MAP2K6 -0.019 0.056 0.13 1 -0.25 18 19
CYAA -0.01 0.032 -10000 0 -0.25 6 6
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.02 0.065 0.14 3 -0.25 23 26
Channel 0.03 0.04 -10000 0 -0.27 6 6
NLRP1 -0.008 0.032 -10000 0 -0.26 5 5
CALM1 0.027 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.06 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.066 6 -10000 0 6
MAPK3 -0.005 0.008 -10000 0 -10000 0 0
MAPK1 -0.004 0.007 -10000 0 -10000 0 0
PGR -0.015 0.048 -10000 0 -0.24 14 14
PA/Cellular Receptors 0.031 0.044 -10000 0 -0.3 6 6
apoptosis -0.002 0.008 -10000 0 -0.066 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.038 -10000 0 -0.26 6 6
macrophage activation -0.007 0.007 -10000 0 -10000 0 0
TNF -0.011 0.13 -10000 0 -0.35 35 35
VCAM1 -0.032 0.16 -10000 0 -0.47 37 37
platelet activation 0.002 0.06 -10000 0 -0.39 8 8
MAPKKK cascade 0.005 0.023 0.11 2 -0.11 1 3
IL18 -0.015 0.061 0.19 1 -0.27 16 17
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.066 6 6
LEF -0.002 0.008 -10000 0 -0.066 6 6
CASP1 -0.003 0.025 -10000 0 -0.16 7 7
mol:cAMP 0.002 0.061 -10000 0 -0.39 8 8
necrosis -0.002 0.008 -10000 0 -0.066 6 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.029 0.038 -10000 0 -0.25 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC2 0.026 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.04 0.057 -10000 0 -0.3 8 8
forebrain development -0.05 0.21 -10000 0 -0.7 22 22
GNAO1 0.006 0.092 -10000 0 -0.33 20 20
SMO/beta Arrestin2 0.021 0.059 -10000 0 -0.35 7 7
SMO 0.01 0.075 -10000 0 -0.44 8 8
ARRB2 0.024 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.092 -10000 0 -0.37 7 7
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
GSK3B 0.028 0.004 -10000 0 -10000 0 0
GNAI2 0.027 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.063 0.026 -10000 0 -10000 0 0
GNAI1 0.019 0.056 -10000 0 -0.49 4 4
XPO1 0.021 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) -0.041 0.2 -10000 0 -0.66 21 21
SAP30 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.01 0.075 -10000 0 -0.44 8 8
MIM/GLI2A 0.001 0.074 -10000 0 -0.44 5 5
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.008 -10000 0 -10000 0 0
GLI2 0.005 0.083 -10000 0 -0.36 9 9
GLI3 0.007 0.093 0.22 1 -0.38 8 9
CSNK1D 0.027 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.024 0.039 -10000 0 -0.48 2 2
Gi family/GTP -0.017 0.1 -10000 0 -0.29 29 29
SIN3B 0.027 0.007 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.011 0.093 -10000 0 -0.36 10 10
GLI2/Su(fu) 0.006 0.096 -10000 0 -0.41 10 10
FOXA2 -0.18 0.43 -10000 0 -1 66 66
neural tube patterning -0.05 0.21 -10000 0 -0.7 22 22
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.024 0.05 -10000 0 -0.33 1 1
GNB1 0.027 0.005 -10000 0 -10000 0 0
CSNK1G2 0.021 0.048 -10000 0 -0.48 3 3
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
MTSS1 0.001 0.074 -10000 0 -0.44 5 5
embryonic limb morphogenesis -0.05 0.21 -10000 0 -0.7 22 22
SUFU 0.013 0.037 -10000 0 -0.21 8 8
LGALS3 0.022 0.047 -10000 0 -0.48 3 3
catabolic process 0.02 0.13 -10000 0 -0.49 13 13
GLI3A/CBP 0.003 0.1 -10000 0 -0.38 21 21
KIF3A 0.027 0.006 -10000 0 -10000 0 0
GLI1 -0.052 0.22 -10000 0 -0.73 22 22
RAB23 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.025 0.039 -10000 0 -0.48 2 2
RBBP7 0.027 0.006 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.022 0.055 -10000 0 -0.28 4 4
GNAZ -0.018 0.14 -10000 0 -0.46 28 28
RBBP4 0.028 0.004 -10000 0 -10000 0 0
CSNK1G1 0.027 0.005 -10000 0 -10000 0 0
PIAS1 0.028 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.007 -10000 0 -10000 0 0
GLI2/SPOP 0.015 0.091 -10000 0 -0.4 9 9
STK36 0.019 0.033 -10000 0 -0.48 1 1
Gi family/GNB1/GNG2/GDP -0.011 0.092 -10000 0 -0.37 11 11
PTCH1 -0.049 0.21 -10000 0 -0.84 15 15
MIM/GLI1 -0.072 0.27 -10000 0 -0.59 61 61
CREBBP 0.003 0.1 -10000 0 -0.38 21 21
Su(fu)/SIN3/HDAC complex 0.015 0.065 -10000 0 -0.36 5 5
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.02 -10000 0 -0.3 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.006 0.12 -10000 0 -0.48 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.004 0.049 -10000 0 -0.2 15 15
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.028 -10000 0 -0.48 1 1
FYN 0.023 0.039 -10000 0 -0.48 2 2
MAP3K12 0.028 0.004 -10000 0 -10000 0 0
FGR 0.02 0.061 -10000 0 -0.48 5 5
p38 alpha/TAB1 -0.051 0.11 -10000 0 -0.33 35 35
PRKG1 -0.002 0.12 -10000 0 -0.48 20 20
DUSP8 0.017 0.072 -10000 0 -0.48 7 7
PGK/cGMP/p38 alpha -0.024 0.14 -10000 0 -0.38 33 33
apoptosis -0.049 0.11 -10000 0 -0.32 35 35
RAL/GTP 0.034 0.012 -10000 0 -10000 0 0
LYN 0.022 0.039 -10000 0 -0.48 2 2
DUSP1 0.014 0.073 -10000 0 -0.36 11 11
PAK1 0.027 0.006 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.056 0.035 -10000 0 -0.28 1 1
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
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 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.032 0.014 -10000 0 -10000 0 0
MAPK11 -0.027 0.15 0.29 4 -0.4 30 34
BLK -0.036 0.15 -10000 0 -0.48 34 34
HCK 0.014 0.077 -10000 0 -0.48 8 8
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
DUSP16 0.025 0.028 -10000 0 -0.48 1 1
DUSP10 0.024 0.028 -10000 0 -0.48 1 1
TRAF6/MEKK3 0.033 0.018 -10000 0 -0.27 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.018 0.14 0.25 5 -0.38 31 36
positive regulation of innate immune response -0.027 0.17 0.29 6 -0.45 30 36
LCK 0.017 0.072 -10000 0 -0.48 7 7
p38alpha-beta/MKP7 -0.015 0.17 0.3 6 -0.45 26 32
p38alpha-beta/MKP5 -0.012 0.16 0.3 6 -0.44 27 33
PGK/cGMP -0.001 0.086 -10000 0 -0.35 20 20
PAK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.02 0.17 0.31 5 -0.46 27 32
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.028 0.003 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
PAK3 -0.038 0.13 -10000 0 -0.48 23 23
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.076 -10000 0 -0.38 2 2
epithelial cell differentiation -0.002 0.097 -10000 0 -0.44 3 3
ITCH 0.033 0.016 -10000 0 -10000 0 0
WWP1 0.014 0.072 -10000 0 -10000 0 0
FYN 0.023 0.039 -10000 0 -0.48 2 2
EGFR 0.008 0.089 -10000 0 -0.48 11 11
PRL 0.016 0.028 -10000 0 -10000 0 0
neuron projection morphogenesis 0.016 0.094 0.28 9 -0.31 2 11
PTPRZ1 -0.098 0.19 -10000 0 -0.48 62 62
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.017 0.081 -10000 0 -0.33 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.011 0.082 -10000 0 -0.36 5 5
ADAM17 0.035 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.002 0.058 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.007 0.079 -10000 0 -0.3 1 1
NCOR1 0.025 0.028 -10000 0 -0.48 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.003 0.09 -10000 0 -0.4 6 6
GRIN2B -0.016 0.079 -10000 0 -0.38 6 6
ErbB4/ErbB2/betacellulin 0.007 0.094 -10000 0 -0.36 13 13
STAT1 0.028 0.003 -10000 0 -10000 0 0
HBEGF 0.021 0.055 -10000 0 -0.48 4 4
PRLR -0.046 0.16 -10000 0 -0.48 38 38
E4ICDs/ETO2 0.009 0.082 -10000 0 -0.34 4 4
axon guidance 0.028 0.086 0.28 3 -0.39 2 5
NEDD4 0.03 0.034 -10000 0 -0.48 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.025 0.12 -10000 0 -0.35 39 39
CBFA2T3 0.01 0.087 -10000 0 -0.48 10 10
ErbB4/ErbB2/HBEGF 0.019 0.065 -10000 0 -0.32 2 2
MAPK3 0.013 0.088 -10000 0 -0.31 3 3
STAT1 (dimer) 0.018 0.067 -10000 0 -10000 0 0
MAPK1 0.014 0.085 0.26 1 -0.31 2 3
JAK2 0.025 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.013 0.08 -10000 0 -0.34 4 4
NRG1 -0.015 0.089 -10000 0 -0.35 21 21
NRG3 0.008 0.082 -10000 0 -0.48 8 8
NRG2 0 0.093 -10000 0 -0.48 10 10
NRG4 -0.017 0.11 -10000 0 -0.48 14 14
heart development 0.028 0.086 0.28 3 -0.39 2 5
neural crest cell migration -0.013 0.079 -10000 0 -0.34 4 4
ERBB2 0.013 0.035 -10000 0 -0.35 3 3
WWOX/E4ICDs 0.019 0.065 -10000 0 -10000 0 0
SHC1 0.023 0.013 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.002 0.1 -10000 0 -0.35 9 9
apoptosis 0.013 0.099 0.43 9 -10000 0 9
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.004 0.085 -10000 0 -0.35 4 4
ErbB4/ErbB2/epiregulin -0.043 0.11 -10000 0 -0.32 9 9
ErbB4/ErbB4/betacellulin/betacellulin 0.003 0.1 -10000 0 -0.4 13 13
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.003 0.11 -10000 0 -0.35 8 8
MDM2 0.015 0.079 0.25 19 -10000 0 19
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.076 -10000 0 -0.31 6 6
STAT5A 0.024 0.083 -10000 0 -0.38 2 2
ErbB4/EGFR/neuregulin 1 beta -0.007 0.09 -10000 0 -0.4 6 6
DLG4 0.026 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.034 0.017 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.063 -10000 0 -0.38 1 1
STAT5A (dimer) 0.006 0.11 -10000 0 -0.47 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.04 0.085 -10000 0 -0.38 2 2
LRIG1 0.021 0.055 -10000 0 -0.48 4 4
EREG -0.11 0.18 -10000 0 -0.48 58 58
BTC -0.002 0.12 -10000 0 -0.48 19 19
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.025 0.083 0.29 2 -0.4 2 4
ERBB4 -0.002 0.058 -10000 0 -10000 0 0
STAT5B 0.028 0.004 -10000 0 -10000 0 0
YAP1 0.004 0.066 -10000 0 -0.46 6 6
GRB2 0.027 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0 0.082 -10000 0 -0.33 6 6
glial cell differentiation -0.015 0.063 0.37 1 -10000 0 1
WWOX 0.027 0.01 -10000 0 -10000 0 0
cell proliferation -0.015 0.12 0.36 3 -0.43 8 11
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.023 0.047 -9999 0 -0.48 3 3
SPHK1 0.006 0.095 -9999 0 -0.48 12 12
GNAI2 0.027 0.005 -9999 0 -10000 0 0
mol:S1P 0.001 0.066 -9999 0 -0.32 13 13
GNAO1 0.007 0.092 -9999 0 -0.33 20 20
mol:Sphinganine-1-P -0.003 0.073 -9999 0 -0.38 12 12
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.036 0.069 -9999 0 -0.36 4 4
GNAI3 0.027 0.006 -9999 0 -10000 0 0
G12/G13 0.036 0.015 -9999 0 -10000 0 0
S1PR3 0.025 0.029 -9999 0 -0.48 1 1
S1PR2 0.026 0.007 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.006 0.063 -9999 0 -0.28 14 14
S1PR5 0.015 0.061 -9999 0 -0.48 4 4
S1PR4 0.017 0.067 -9999 0 -0.48 6 6
GNAI1 0.02 0.056 -9999 0 -0.48 4 4
S1P/S1P5/G12 0.021 0.077 -9999 0 -0.33 9 9
S1P/S1P3/Gq -0.009 0.11 -9999 0 -0.31 33 33
S1P/S1P4/Gi -0.018 0.12 -9999 0 -0.42 15 15
GNAQ 0.025 0.028 -9999 0 -0.48 1 1
GNAZ -0.017 0.14 -9999 0 -0.48 26 26
GNA14 -0.01 0.13 -9999 0 -0.48 25 25
GNA15 0.019 0.061 -9999 0 -0.48 5 5
GNA12 0.025 0.009 -9999 0 -10000 0 0
GNA13 0.027 0.005 -9999 0 -10000 0 0
GNA11 0.023 0.039 -9999 0 -0.48 2 2
ABCC1 0.027 0.009 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.04 0.099 -10000 0 -0.35 17 17
MAP4K1 0.014 0.077 -10000 0 -0.45 9 9
MAP3K8 0.024 0.039 -10000 0 -0.48 2 2
PRKCB 0.016 0.073 -10000 0 -0.48 7 7
DBNL 0.026 0.008 -10000 0 -10000 0 0
CRKL 0.027 0.01 -10000 0 -10000 0 0
MAP3K1 0.006 0.083 -10000 0 -0.55 5 5
JUN 0.001 0.14 -10000 0 -0.61 15 15
MAP3K7 0.006 0.081 -10000 0 -0.47 6 6
GRAP2 0.014 0.081 -10000 0 -0.48 9 9
CRK 0.026 0.008 -10000 0 -10000 0 0
MAP2K4 0.006 0.096 0.21 1 -0.57 6 7
LAT 0.023 0.042 -10000 0 -0.48 2 2
LCP2 0.017 0.067 -10000 0 -0.48 6 6
MAPK8 0.003 0.14 -10000 0 -0.65 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.01 0.092 -10000 0 -0.42 10 10
LAT/GRAP2/SLP76/HPK1/HIP-55 0.048 0.092 -10000 0 -0.36 12 12
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.006 0.091 0.29 11 -10000 0 11
GNAI2 0.027 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.042 -10000 0 -0.3 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.007 0.092 -10000 0 -0.33 20 20
RhoA/GTP -0.006 0.093 -10000 0 -0.3 11 11
negative regulation of cAMP metabolic process -0.012 0.09 -10000 0 -0.27 21 21
GNAZ -0.017 0.14 -10000 0 -0.48 26 26
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNA12 0.025 0.009 -10000 0 -10000 0 0
S1PR5 0.015 0.061 -10000 0 -0.48 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.012 0.09 -10000 0 -0.27 21 21
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.056 -10000 0 -0.48 4 4
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.017 0.078 -10000 0 -0.35 12 12
AKT1 0.013 0.11 0.35 5 -0.48 8 13
PTK2B -0.008 0.11 0.34 1 -0.56 8 9
VEGFR2 homodimer/Frs2 0.016 0.088 -10000 0 -0.61 6 6
CAV1 0.017 0.055 -10000 0 -0.48 3 3
CALM1 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.028 0.089 -10000 0 -0.56 6 6
endothelial cell proliferation 0.006 0.12 0.36 8 -0.49 7 15
mol:Ca2+ 0.003 0.092 -10000 0 -0.4 13 13
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.037 0.095 -10000 0 -0.55 7 7
RP11-342D11.1 -0.007 0.092 -10000 0 -0.4 14 14
CDH5 0.027 0.01 -10000 0 -10000 0 0
VEGFA homodimer 0.053 0.037 -10000 0 -0.27 1 1
SHC1 0.023 0.013 -10000 0 -10000 0 0
SHC2 0.006 0.097 -10000 0 -0.48 13 13
HRAS/GDP 0.021 0.085 -10000 0 -0.46 7 7
SH2D2A 0.019 0.049 -10000 0 -0.48 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.002 0.14 -10000 0 -0.48 15 15
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.021 0.1 -10000 0 -0.48 10 10
VEGFR1 homodimer 0.022 0.047 -10000 0 -0.48 3 3
SHC/GRB2/SOS1 0.045 0.1 -10000 0 -0.5 7 7
GRB10 -0.004 0.12 -10000 0 -0.54 14 14
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
PAK1 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.053 0.097 -10000 0 -0.58 6 6
HRAS 0.027 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.006 0.073 -10000 0 -0.35 8 8
HIF1A 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.035 0.094 -10000 0 -0.54 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.055 -10000 0 -0.48 4 4
Nck/Pak 0.039 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.025 0.097 -10000 0 -0.57 7 7
mol:GDP 0.03 0.092 -10000 0 -0.49 7 7
mol:NADP -0.008 0.14 0.37 2 -0.43 20 22
eNOS/Hsp90 0.005 0.13 0.37 2 -0.4 20 22
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:IP3 0.003 0.093 -10000 0 -0.41 13 13
HIF1A/ARNT 0.033 0.017 -10000 0 -10000 0 0
SHB 0.026 0.007 -10000 0 -10000 0 0
VEGFA 0.023 0.034 -10000 0 -0.48 1 1
VEGFC 0.017 0.051 -10000 0 -0.48 2 2
FAK1/Vinculin 0.014 0.13 0.36 3 -0.59 9 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.12 -10000 0 -0.4 17 17
PTPN6 0.025 0.028 -10000 0 -0.48 1 1
EPAS1 0.021 0.062 -10000 0 -0.38 7 7
mol:L-citrulline -0.008 0.14 0.37 2 -0.43 20 22
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.04 0.087 -10000 0 -0.51 6 6
VEGFR2 homodimer/VEGFA homodimer 0.027 0.1 -10000 0 -0.44 14 14
VEGFR2/3 heterodimer 0.012 0.1 -10000 0 -0.57 9 9
VEGFB 0.028 0.004 -10000 0 -10000 0 0
MAPK11 -0.007 0.1 0.31 3 -0.55 7 10
VEGFR2 homodimer 0.002 0.1 -10000 0 -0.75 6 6
FLT1 0.022 0.048 -10000 0 -0.48 3 3
NEDD4 0.023 0.036 -10000 0 -0.48 1 1
MAPK3 -0.01 0.098 0.35 3 -0.5 7 10
MAPK1 -0.007 0.099 0.31 5 -0.49 7 12
VEGFA145/NRP2 0.027 0.068 -10000 0 -0.35 10 10
VEGFR1/2 heterodimer 0.012 0.099 -10000 0 -0.54 9 9
KDR 0.002 0.1 -10000 0 -0.75 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.023 0.12 -10000 0 -0.57 9 9
SRC 0.027 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.005 0.11 0.34 7 -0.51 7 14
PI3K 0.01 0.1 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.029 0.096 -10000 0 -0.57 7 7
FES -0.001 0.1 -10000 0 -0.42 13 13
GAB1 0.018 0.11 -10000 0 -0.54 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.094 -10000 0 -0.55 7 7
CTNNB1 0.027 0.01 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
ARNT 0.023 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.13 0.37 2 -0.41 20 22
VEGFR2 homodimer/VEGFA homodimer/Yes 0.026 0.097 -10000 0 -0.57 7 7
PI3K/GAB1 0.02 0.11 -10000 0 -0.47 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.051 0.092 -10000 0 -0.52 6 6
PRKACA 0.026 0.007 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.019 0.1 -10000 0 -0.48 11 11
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.002 0.097 -10000 0 -0.43 13 13
actin cytoskeleton reorganization 0.021 0.099 -10000 0 -0.48 10 10
PTK2 -0.005 0.12 0.36 3 -0.62 10 13
EDG1 -0.007 0.092 -10000 0 -0.4 14 14
mol:DAG 0.003 0.093 -10000 0 -0.41 13 13
CaM/Ca2+ 0.02 0.091 -10000 0 -0.51 6 6
MAP2K3 -0.005 0.091 -10000 0 -0.46 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.034 0.13 -10000 0 -0.55 14 14
PLCG1 0.003 0.094 -10000 0 -0.41 13 13
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.093 -10000 0 -0.52 7 7
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.096 -10000 0 -0.57 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.026 0.094 -10000 0 -0.55 7 7
cell migration 0.023 0.12 0.37 2 -0.55 8 10
mol:PI-3-4-5-P3 0.011 0.096 -10000 0 -0.46 8 8
FYN 0.023 0.039 -10000 0 -0.48 2 2
VEGFB/NRP1 0.008 0.091 -10000 0 -0.4 13 13
mol:NO -0.008 0.14 0.37 2 -0.43 20 22
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.006 0.08 -10000 0 -0.46 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.011 0.12 -10000 0 -0.55 14 14
VHL 0.027 0.005 -10000 0 -10000 0 0
ITGB3 -0.003 0.1 -10000 0 -0.48 12 12
NOS3 -0.011 0.15 0.38 2 -0.49 20 22
VEGFR2 homodimer/VEGFA homodimer/Sck 0.016 0.12 -10000 0 -0.44 17 17
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA -0.007 0.093 -10000 0 -0.49 7 7
PRKCB -0.008 0.099 -10000 0 -0.5 8 8
VCL 0.028 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.012 0.096 -10000 0 -0.4 14 14
VEGFR1/2 heterodimer/VEGFA homodimer 0.024 0.1 -10000 0 -0.48 10 10
VEGFA165/NRP2 0.027 0.068 -10000 0 -0.35 10 10
MAPKKK cascade 0.026 0.11 0.34 1 -0.48 12 13
NRP2 0.014 0.081 -10000 0 -0.48 9 9
VEGFC homodimer 0.017 0.05 -10000 0 -0.48 2 2
NCK1 0.028 0.004 -10000 0 -10000 0 0
ROCK1 0.027 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.012 0.13 0.29 2 -0.61 9 11
MAP3K13 0 0.094 -10000 0 -0.4 13 13
PDPK1 0.002 0.087 0.26 2 -0.42 8 10
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.003 0.063 0.29 2 -10000 0 2
DAPP1 -0.04 0.16 0.21 2 -0.43 35 37
Src family/SYK family/BLNK-LAT/BTK-ITK -0.052 0.21 -10000 0 -0.61 30 30
mol:DAG -0.012 0.086 0.2 6 -0.26 20 26
HRAS 0.028 0.007 -10000 0 -10000 0 0
RAP1A 0.028 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.013 0.091 0.2 2 -0.35 8 10
PLCG2 0.021 0.055 -10000 0 -0.48 4 4
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARF5 0.027 0.006 -10000 0 -10000 0 0
mol:GTP -0.008 0.046 0.26 3 -0.23 1 4
ARF1/GTP 0.001 0.042 0.28 2 -10000 0 2
RHOA 0.027 0.005 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.009 0.044 0.17 19 -0.22 1 20
ADAP1 -0.011 0.056 0.29 2 -0.29 5 7
ARAP3 -0.008 0.045 0.25 3 -0.23 1 4
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.024 0.039 -10000 0 -0.48 2 2
ARHGEF6 0.023 0.047 -10000 0 -0.48 3 3
ARHGEF7 0.027 0.007 -10000 0 -10000 0 0
ARF1 0.026 0.008 -10000 0 -10000 0 0
NRAS 0.027 0.008 -10000 0 -10000 0 0
FYN 0.023 0.039 -10000 0 -0.48 2 2
ARF6 0.027 0.006 -10000 0 -10000 0 0
FGR 0.02 0.061 -10000 0 -0.48 5 5
mol:Ca2+ -0.006 0.046 0.14 5 -0.15 4 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.073 -10000 0 -0.48 7 7
ZAP70 0.003 0.1 -10000 0 -0.48 15 15
mol:IP3 -0.011 0.062 0.17 6 -0.2 15 21
LYN 0.022 0.039 -10000 0 -0.48 2 2
ARF1/GDP 0.015 0.085 0.2 2 -0.32 8 10
RhoA/GDP 0.034 0.061 0.27 2 -0.3 2 4
PDK1/Src/Hsp90 0.052 0.017 -10000 0 -10000 0 0
BLNK 0.016 0.077 -10000 0 -0.48 8 8
actin cytoskeleton reorganization 0.015 0.09 0.29 7 -0.38 3 10
SRC 0.027 0.006 -10000 0 -10000 0 0
PLEKHA2 -0.013 0.04 -10000 0 -0.36 4 4
RAC1 0.025 0.009 -10000 0 -10000 0 0
PTEN 0.025 0.014 -10000 0 -10000 0 0
HSP90AA1 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.011 0.044 0.29 1 -10000 0 1
RhoA/GTP -0.009 0.048 0.26 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.036 0.16 -10000 0 -0.49 29 29
BLK -0.036 0.15 -10000 0 -0.48 34 34
PDPK1 0.028 0.004 -10000 0 -10000 0 0
CYTH1 -0.009 0.047 0.29 3 -10000 0 3
HCK 0.014 0.077 -10000 0 -0.48 8 8
CYTH3 -0.007 0.048 0.29 3 -10000 0 3
CYTH2 -0.009 0.047 0.29 3 -10000 0 3
KRAS 0.026 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.013 0.05 -10000 0 -0.31 5 5
SGK1 -0.002 0.098 -10000 0 -0.32 28 28
INPP5D 0.017 0.072 -10000 0 -0.48 7 7
mol:GDP 0.001 0.091 0.19 4 -0.34 10 14
SOS1 0.028 0.003 -10000 0 -10000 0 0
SYK 0.021 0.055 -10000 0 -0.48 4 4
ARF6/GDP 0.019 0.057 0.28 2 -0.3 2 4
mol:PI-3-4-5-P3 -0.01 0.04 0.28 1 -0.23 1 2
ARAP3/RAP1A/GTP -0.009 0.045 0.17 19 -0.23 1 20
VAV1 0.015 0.077 -10000 0 -0.48 8 8
mol:PI-3-4-P2 0.006 0.047 -10000 0 -0.35 6 6
RAS family/GTP/PI3K Class I 0.038 0.032 -10000 0 -0.23 1 1
PLEKHA1 -0.015 0.038 -10000 0 -0.3 6 6
Rac1/GDP 0.011 0.088 0.2 1 -0.35 8 9
LAT 0.023 0.042 -10000 0 -0.48 2 2
Rac1/GTP 0.011 0.086 -10000 0 -0.36 10 10
ITK -0.021 0.058 -10000 0 -0.25 13 13
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.022 0.12 0.22 4 -0.38 20 24
LCK 0.017 0.072 -10000 0 -0.48 7 7
BTK -0.019 0.066 0.28 2 -0.26 13 15
Regulation of Telomerase

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
Telomerase catalytic core complex -0.095 0.32 -9999 0 -1 32 32
RAD9A 0.027 0.005 -9999 0 -10000 0 0
AP1 0.014 0.077 -9999 0 -0.34 13 13
IFNAR2 0.022 0.018 -9999 0 -10000 0 0
AKT1 -0.003 0.06 -9999 0 -0.25 14 14
ER alpha/Oestrogen -0.008 0.078 -9999 0 -0.35 15 15
NFX1/SIN3/HDAC complex 0.014 0.046 -9999 0 -0.29 3 3
EGF -0.062 0.19 -9999 0 -0.49 56 56
SMG5 0.024 0.01 -9999 0 -10000 0 0
SMG6 0.026 0.008 -9999 0 -10000 0 0
SP3/HDAC2 0.031 0.027 -9999 0 -10000 0 0
TERT/c-Abl -0.08 0.3 -9999 0 -0.96 31 31
SAP18 0.026 0.007 -9999 0 -10000 0 0
MRN complex 0.047 0.022 -9999 0 -10000 0 0
WT1 -0.05