Skin Cutaneous Melanoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(metastatic tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 63 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
Ephrin A reverse signaling 46
E-cadherin signaling events 40
TCR signaling in naïve CD8+ T cells 36
Signaling events mediated by Stem cell factor receptor (c-Kit) 35
IL4-mediated signaling events 34
IL23-mediated signaling events 33
E-cadherin signaling in the nascent adherens junction 32
Angiopoietin receptor Tie2-mediated signaling 31
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 29
Signaling events regulated by Ret tyrosine kinase 28
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
Ephrin A reverse signaling 46 325 7 -0.044 0 1000 -1000 0 -1000
E-cadherin signaling events 40 203 5 -0.061 0.029 1000 -1000 0.02 -1000
TCR signaling in naïve CD8+ T cells 36 3348 93 -0.2 0.13 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 35 2793 78 -0.21 0.071 1000 -1000 -0.036 -1000
IL4-mediated signaling events 34 3125 91 -0.49 0.38 1000 -1000 -0.065 -1000
IL23-mediated signaling events 33 2021 60 -0.28 0.029 1000 -1000 -0.056 -1000
E-cadherin signaling in the nascent adherens junction 32 2460 76 -0.12 0.043 1000 -1000 -0.032 -1000
Angiopoietin receptor Tie2-mediated signaling 31 2751 88 -0.21 0.039 1000 -1000 -0.046 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 29 2019 68 -0.29 0.081 1000 -1000 -0.042 -1000
Signaling events regulated by Ret tyrosine kinase 28 2369 82 -0.055 0.033 1000 -1000 -0.03 -1000
Endothelins 28 2714 96 -0.12 0.051 1000 -1000 -0.029 -1000
IL12-mediated signaling events 27 2385 87 -0.27 0.06 1000 -1000 -0.038 -1000
BCR signaling pathway 26 2631 99 -0.14 0.035 1000 -1000 -0.032 -1000
E-cadherin signaling in keratinocytes 26 1153 43 -0.066 0.031 1000 -1000 -0.012 -1000
Nectin adhesion pathway 23 1503 63 -0.094 0.043 1000 -1000 -0.02 -1000
Stabilization and expansion of the E-cadherin adherens junction 23 1754 74 -0.061 0.061 1000 -1000 -0.04 -1000
LPA receptor mediated events 22 2268 102 -0.075 0.032 1000 -1000 -0.057 -1000
TCGA08_retinoblastoma 22 183 8 -0.007 0.049 1000 -1000 -0.004 -1000
EGFR-dependent Endothelin signaling events 22 465 21 -0.037 0.041 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 21 718 34 -0.05 0.029 1000 -1000 -0.019 -1000
Wnt signaling 21 147 7 -0.024 0.027 1000 -1000 -0.001 -1000
p75(NTR)-mediated signaling 20 2570 125 -0.054 0.072 1000 -1000 -0.038 -1000
BMP receptor signaling 20 1626 81 -0.048 0.05 1000 -1000 -0.018 -1000
Glypican 1 network 20 984 48 -0.036 0.042 1000 -1000 -0.02 -1000
Thromboxane A2 receptor signaling 19 2099 105 -0.088 0.034 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 19 904 47 -0.023 0.037 1000 -1000 -0.021 -1000
Signaling mediated by p38-alpha and p38-beta 19 878 44 -0.064 0.029 1000 -1000 -0.011 -1000
Integrins in angiogenesis 19 1630 84 -0.1 0.053 1000 -1000 -0.026 -1000
EPHB forward signaling 19 1678 85 -0.05 0.052 1000 -1000 -0.036 -1000
Glypican 2 network 19 78 4 0.011 0.014 1000 -1000 0.022 -1000
S1P4 pathway 19 499 25 -0.031 0.037 1000 -1000 -0.01 -1000
JNK signaling in the CD4+ TCR pathway 18 307 17 -0.087 0.041 1000 -1000 -0.02 -1000
Glucocorticoid receptor regulatory network 18 2129 114 -0.22 0.12 1000 -1000 -0.034 -1000
IL27-mediated signaling events 18 943 51 -0.16 0.098 1000 -1000 -0.029 -1000
Class IB PI3K non-lipid kinase events 18 54 3 -0.007 0.007 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 17 1304 74 -0.06 0.038 1000 -1000 -0.027 -1000
Noncanonical Wnt signaling pathway 17 445 26 -0.036 0.027 1000 -1000 -0.024 -1000
HIF-1-alpha transcription factor network 17 1320 76 -0.019 0.065 1000 -1000 -0.017 -1000
a4b1 and a4b7 Integrin signaling 17 89 5 0.002 0.019 1000 -1000 0.018 -1000
Signaling events mediated by PTP1B 17 1297 76 -0.059 0.043 1000 -1000 -0.021 -1000
TRAIL signaling pathway 17 831 48 -0.027 0.041 1000 -1000 -0.018 -1000
Osteopontin-mediated events 16 632 38 -0.046 0.032 1000 -1000 -0.016 -1000
Arf6 signaling events 16 1007 62 -0.028 0.056 1000 -1000 -0.018 -1000
Ceramide signaling pathway 16 1236 76 -0.041 0.049 1000 -1000 -0.018 -1000
Reelin signaling pathway 16 940 56 -0.025 0.057 1000 -1000 -0.012 -1000
Effects of Botulinum toxin 16 430 26 -0.017 0.042 1000 -1000 0 -1000
Calcium signaling in the CD4+ TCR pathway 16 520 31 -0.077 0.029 1000 -1000 -0.03 -1000
Syndecan-4-mediated signaling events 16 1130 67 -0.047 0.038 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 16 1393 86 -0.12 0.085 1000 -1000 -0.027 -1000
Fc-epsilon receptor I signaling in mast cells 15 1475 97 -0.045 0.05 1000 -1000 -0.034 -1000
Ephrin B reverse signaling 15 748 48 -0.05 0.039 1000 -1000 -0.031 -1000
IFN-gamma pathway 14 1013 68 -0.033 0.038 1000 -1000 -0.041 -1000
S1P5 pathway 14 242 17 -0.026 0.034 1000 -1000 -0.007 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 14 632 45 -0.041 0.058 1000 -1000 -0.027 -1000
Class I PI3K signaling events 14 1057 73 -0.097 0.051 1000 -1000 -0.023 -1000
Ras signaling in the CD4+ TCR pathway 14 240 17 -0.02 0.051 1000 -1000 -0.012 -1000
Signaling events mediated by the Hedgehog family 13 698 52 -0.027 0.045 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 13 1160 85 -0.027 0.041 1000 -1000 -0.041 -1000
RXR and RAR heterodimerization with other nuclear receptor 13 713 52 -0.051 0.06 1000 -1000 -0.023 -1000
IL2 signaling events mediated by PI3K 13 806 58 -0.09 0.042 1000 -1000 -0.019 -1000
amb2 Integrin signaling 12 1047 82 -0.034 0.047 1000 -1000 -0.021 -1000
Signaling mediated by p38-gamma and p38-delta 12 187 15 -0.018 0.027 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 12 1487 120 -0.07 0.07 1000 -1000 -0.041 -1000
ErbB2/ErbB3 signaling events 11 779 65 -0.035 0.041 1000 -1000 -0.06 -1000
Syndecan-2-mediated signaling events 11 780 69 -0.013 0.043 1000 -1000 -0.023 -1000
ceramide signaling pathway 11 573 49 -0.023 0.041 1000 -1000 -0.021 -1000
S1P1 pathway 11 417 36 -0.059 0.028 1000 -1000 -0.019 -1000
IGF1 pathway 11 647 57 -0.026 0.061 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 11 1120 97 -0.052 0.062 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 10 127 12 -0.039 0.006 1000 -1000 -0.018 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 558 54 -0.022 0.04 1000 -1000 -0.019 -1000
EPO signaling pathway 10 568 55 -0.001 0.049 1000 -1000 -0.019 -1000
PDGFR-alpha signaling pathway 10 445 44 -0.019 0.055 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 10 372 37 -0.032 0.048 1000 -1000 -0.016 -1000
TCGA08_p53 10 71 7 -0.01 0.024 1000 -1000 -0.001 -1000
IL2 signaling events mediated by STAT5 10 241 22 -0.037 0.029 1000 -1000 -0.021 -1000
Regulation of Androgen receptor activity 10 728 70 -0.1 0.037 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 9 389 39 -0.029 0.028 1000 -1000 -0.012 -1000
IL1-mediated signaling events 9 610 62 -0.025 0.075 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 9 336 36 -0.038 0.047 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 9 533 54 -0.057 0.058 1000 -1000 -0.035 -1000
Regulation of nuclear SMAD2/3 signaling 8 1168 136 -0.3 0.071 1000 -1000 -0.026 -1000
Sphingosine 1-phosphate (S1P) pathway 8 234 28 -0.026 0.044 1000 -1000 -0.017 -1000
Presenilin action in Notch and Wnt signaling 8 500 61 -0.01 0.072 1000 -1000 -0.035 -1000
FOXA2 and FOXA3 transcription factor networks 8 402 46 -0.15 0.038 1000 -1000 -0.053 -1000
Canonical Wnt signaling pathway 8 450 51 -0.024 0.063 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 8 425 52 -0.051 0.044 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 8 211 26 -0.021 0.06 1000 -1000 -0.013 -1000
S1P3 pathway 8 365 42 -0.025 0.045 1000 -1000 -0.019 -1000
Rapid glucocorticoid signaling 8 174 20 -0.008 0.028 1000 -1000 -0.001 -1000
Visual signal transduction: Rods 8 427 52 0 0.049 1000 -1000 -0.017 -1000
ErbB4 signaling events 7 491 69 -0.067 0.064 1000 -1000 -0.02 -1000
Hedgehog signaling events mediated by Gli proteins 7 482 65 -0.045 0.067 1000 -1000 -0.024 -1000
mTOR signaling pathway 7 379 53 -0.038 0.032 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 7 426 58 -0.038 0.055 1000 -1000 -0.033 -1000
Atypical NF-kappaB pathway 7 229 31 -0.014 0.036 1000 -1000 -0.016 -1000
Insulin Pathway 7 572 74 -0.084 0.071 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 7 242 33 -0.004 0.061 1000 -1000 -0.021 -1000
Aurora B signaling 7 496 67 -0.065 0.063 1000 -1000 -0.025 -1000
Coregulation of Androgen receptor activity 6 521 76 -0.071 0.049 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 6 279 40 -0.055 0.046 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 6 297 43 -0.11 0.11 1000 -1000 -0.032 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 557 83 -0.033 0.054 1000 -1000 -0.011 -1000
IL6-mediated signaling events 6 510 75 -0.035 0.085 1000 -1000 -0.033 -1000
Regulation of Telomerase 6 673 102 -0.088 0.057 1000 -1000 -0.019 -1000
FOXM1 transcription factor network 6 350 51 -0.02 0.082 1000 -1000 -0.06 -1000
PLK2 and PLK4 events 5 16 3 -0.018 -1000 1000 -1000 -0.016 -1000
Visual signal transduction: Cones 5 205 38 -0.016 0.052 1000 -1000 -0.017 -1000
Arf6 downstream pathway 5 233 43 -0.039 0.049 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 5 372 68 -0.038 0.052 1000 -1000 -0.017 -1000
FoxO family signaling 5 364 64 -0.18 0.042 1000 -1000 -0.029 -1000
Syndecan-3-mediated signaling events 5 201 35 0 0.072 1000 -1000 -0.011 -1000
Signaling events mediated by PRL 5 195 34 -0.023 0.046 1000 -1000 -0.022 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 140 34 -0.043 0.073 1000 -1000 -0.024 -1000
Canonical NF-kappaB pathway 4 176 39 -0.008 0.059 1000 -1000 -0.013 -1000
BARD1 signaling events 4 236 57 -0.054 0.061 1000 -1000 -0.039 -1000
PLK1 signaling events 4 389 85 -0.007 0.051 1000 -1000 -0.028 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 588 125 -0.012 0.068 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 4 201 44 -0.042 0.046 1000 -1000 -0.014 -1000
Insulin-mediated glucose transport 3 119 32 -0.02 0.051 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 3 323 104 -0.053 0.067 1000 -1000 -0.039 -1000
Arf6 trafficking events 3 272 71 -0.041 0.052 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class II 2 184 75 -0.03 0.071 1000 -1000 -0.019 -1000
Aurora A signaling 2 162 60 -0.024 0.06 1000 -1000 -0.017 -1000
Aurora C signaling 2 17 7 0 0.046 1000 -1000 -0.004 -1000
VEGFR1 specific signals 2 144 56 -0.032 0.054 1000 -1000 -0.027 -1000
Arf1 pathway 2 132 54 -0.002 0.048 1000 -1000 -0.011 -1000
Circadian rhythm pathway 1 42 22 -0.007 0.044 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 13 23 0.005 0.057 1000 -1000 -0.011 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 11 27 -0.011 0.067 1000 -1000 -0.021 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.073 1000 -1000 0 -1000
Total 1727 102685 7203 -7.8 -990 131000 -131000 -3 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.027 0.11 -10000 0 -0.2 62 62
EFNA5 0 0.095 -10000 0 -0.32 19 19
FYN -0.033 0.094 0.18 7 -0.18 58 65
neuron projection morphogenesis -0.027 0.11 -10000 0 -0.2 62 62
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.026 0.11 -10000 0 -0.2 62 62
EPHA5 -0.044 0.14 0.12 5 -0.32 50 55
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.01 0.11 -10000 0 -0.19 63 63
E-cadherin/beta catenin -0.027 0.12 -10000 0 -0.22 63 63
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
JUP 0.027 0.035 -10000 0 -0.32 2 2
CDH1 -0.061 0.16 0.12 12 -0.32 63 75
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.078 0.3 0.3 10 -0.57 53 63
FYN -0.15 0.39 0.26 8 -0.74 57 65
LAT/GRAP2/SLP76 -0.096 0.3 0.27 3 -0.6 52 55
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.078 0.24 0.22 5 -0.46 55 60
B2M 0.024 0.016 -10000 0 -10000 0 0
IKBKG -0.013 0.071 0.099 12 -0.14 40 52
MAP3K8 0.023 0.042 -10000 0 -0.32 3 3
mol:Ca2+ -0.017 0.02 0.086 2 -0.054 31 33
integrin-mediated signaling pathway 0.028 0.037 -10000 0 -0.18 6 6
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.13 0.36 0.29 3 -0.69 57 60
TRPV6 0.13 0.37 1.2 26 -10000 0 26
CD28 0.012 0.083 0.13 7 -0.32 13 20
SHC1 -0.14 0.38 0.3 10 -0.73 56 66
receptor internalization -0.17 0.44 0.2 8 -0.81 60 68
PRF1 -0.2 0.49 -10000 0 -1.1 49 49
KRAS 0.028 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.046 0.19 0.19 4 -0.38 48 52
LAT -0.15 0.39 0.21 5 -0.76 56 61
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.004 0.11 0.13 17 -0.32 24 41
CD3E -0.004 0.11 0.13 13 -0.33 23 36
CD3G -0.015 0.12 0.13 6 -0.32 31 37
RASGRP2 -0.003 0.046 0.074 1 -0.19 10 11
RASGRP1 -0.084 0.25 0.23 10 -0.52 51 61
HLA-A 0.017 0.038 -10000 0 -0.33 2 2
RASSF5 0.017 0.06 0.12 3 -0.32 7 10
RAP1A/GTP/RAPL 0.029 0.038 -10000 0 -0.18 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.083 0.15 19 -0.13 41 60
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.049 0.1 -10000 0 -0.22 52 52
PRKCA -0.043 0.14 0.17 5 -0.28 50 55
GRAP2 0.012 0.074 0.12 3 -0.32 11 14
mol:IP3 -0.089 0.2 -10000 0 -0.44 53 53
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.4 0.16 5 -0.9 44 49
ORAI1 -0.12 0.31 0.36 1 -1 26 27
CSK -0.15 0.39 0.24 6 -0.76 56 62
B7 family/CD28 -0.12 0.4 0.27 4 -0.85 47 51
CHUK 0.025 0.024 -10000 0 -0.32 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.19 0.47 0.2 8 -0.88 59 67
PTPN6 -0.15 0.4 0.21 8 -0.79 54 62
VAV1 -0.15 0.39 0.23 4 -0.75 57 61
Monovalent TCR/CD3 -0.074 0.24 0.14 7 -0.53 42 49
CBL 0.025 0.01 -10000 0 -10000 0 0
LCK -0.16 0.43 0.26 8 -0.85 54 62
PAG1 -0.15 0.39 0.26 6 -0.75 57 63
RAP1A 0.028 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.19 0.47 0.2 7 -0.9 57 64
CD80 0.011 0.079 -10000 0 -0.32 12 12
CD86 0.008 0.08 -10000 0 -0.32 13 13
PDK1/CARD11/BCL10/MALT1 -0.045 0.13 0.12 4 -0.27 49 53
HRAS 0.028 0.006 -10000 0 -10000 0 0
GO:0035030 -0.11 0.3 0.18 9 -0.61 52 61
CD8A -0.015 0.13 0.13 3 -0.32 34 37
CD8B -0.03 0.14 0.13 17 -0.32 43 60
PTPRC -0.001 0.1 0.12 12 -0.32 21 33
PDK1/PKC theta -0.1 0.29 0.26 5 -0.58 54 59
CSK/PAG1 -0.13 0.38 0.29 11 -0.73 55 66
SOS1 0.029 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.028 0.036 -10000 0 -0.24 2 2
GRAP2/SLP76 -0.12 0.36 0.24 3 -0.72 53 56
STIM1 -0.018 0.099 1.2 1 -10000 0 1
RAS family/GTP 0.001 0.11 0.18 16 -0.18 41 57
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.2 0.5 0.21 7 -0.92 60 67
mol:DAG -0.091 0.17 -10000 0 -0.39 53 53
RAP1A/GDP 0.006 0.039 0.084 11 -0.065 30 41
PLCG1 0.026 0.008 -10000 0 -10000 0 0
CD247 -0.002 0.11 -10000 0 -0.32 22 22
cytotoxic T cell degranulation -0.19 0.46 -10000 0 -1 49 49
RAP1A/GTP -0.001 0.017 -10000 0 -0.071 10 10
mol:PI-3-4-5-P3 -0.097 0.28 0.25 5 -0.55 56 61
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.11 0.28 -10000 0 -0.59 51 51
NRAS 0.028 0.006 -10000 0 -10000 0 0
ZAP70 -0.004 0.12 0.12 22 -0.32 28 50
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.11 0.28 0.21 1 -0.59 52 53
MALT1 0.025 0.032 -10000 0 -0.32 2 2
TRAF6 0.028 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.024 0.17 0.19 15 -0.35 46 61
CARD11 -0.006 0.11 0.12 14 -0.32 25 39
PRKCB -0.045 0.15 0.16 8 -0.31 49 57
PRKCE -0.041 0.14 0.18 6 -0.28 50 56
PRKCQ -0.13 0.34 0.28 4 -0.67 55 59
LCP2 0.018 0.055 -10000 0 -0.32 6 6
BCL10 0.028 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.061 0.2 0.22 5 -0.39 53 58
IKK complex -0.001 0.074 0.15 15 -0.12 41 56
RAS family/GDP -0.005 0.016 -10000 0 -0.041 20 20
MAP3K14 -0.036 0.14 0.14 8 -0.29 48 56
PDPK1 -0.073 0.22 0.22 6 -0.44 52 58
TCR/CD3/MHC I/CD8/Fyn -0.2 0.5 -10000 0 -0.95 58 58
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.064 0.18 0.29 3 -0.4 47 50
CRKL -0.061 0.18 0.27 4 -0.39 49 53
HRAS -0.054 0.16 -10000 0 -0.33 48 48
mol:PIP3 -0.032 0.18 0.29 4 -0.36 43 47
SPRED1 0.022 0.045 -10000 0 -0.32 4 4
SPRED2 0.029 0.003 -10000 0 -10000 0 0
GAB1 -0.067 0.19 -10000 0 -0.4 51 51
FOXO3 -0.044 0.18 -10000 0 -0.36 51 51
AKT1 -0.044 0.2 -10000 0 -0.38 52 52
BAD -0.04 0.19 0.32 1 -0.36 51 52
megakaryocyte differentiation -0.07 0.18 -10000 0 -0.4 50 50
GSK3B -0.041 0.19 0.3 2 -0.36 52 54
RAF1 -0.037 0.14 0.25 3 -0.28 44 47
SHC1 0.026 0.008 -10000 0 -10000 0 0
STAT3 -0.067 0.18 -10000 0 -0.4 51 51
STAT1 -0.19 0.42 -10000 0 -0.96 51 51
HRAS/SPRED1 -0.032 0.14 -10000 0 -0.28 46 46
cell proliferation -0.068 0.18 -10000 0 -0.4 50 50
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
TEC 0.016 0.063 -10000 0 -0.32 8 8
RPS6KB1 -0.053 0.19 -10000 0 -0.4 48 48
HRAS/SPRED2 -0.029 0.14 -10000 0 -0.28 46 46
LYN/TEC/p62DOK -0.041 0.19 -10000 0 -0.4 46 46
MAPK3 -0.023 0.11 0.21 5 -0.21 44 49
STAP1 -0.075 0.19 -10000 0 -0.42 50 50
GRAP2 0.012 0.074 0.12 3 -0.32 11 14
JAK2 -0.15 0.36 -10000 0 -0.8 52 52
STAT1 (dimer) -0.18 0.41 -10000 0 -0.94 51 51
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.041 0.2 -10000 0 -0.39 49 49
actin filament polymerization -0.069 0.17 -10000 0 -0.38 50 50
LYN 0.024 0.033 -10000 0 -0.32 2 2
STAP1/STAT5A (dimer) -0.12 0.26 0.3 1 -0.57 52 53
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
CBL/CRKL/GRB2 -0.039 0.18 0.29 2 -0.37 46 48
PI3K -0.035 0.2 -10000 0 -0.39 50 50
PTEN 0.026 0.009 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.2 0.5 -10000 0 -1.1 48 48
MAPK8 -0.069 0.18 -10000 0 -0.41 50 50
STAT3 (dimer) -0.066 0.18 -10000 0 -0.4 51 51
positive regulation of transcription -0.016 0.093 0.2 5 -0.17 43 48
mol:GDP -0.053 0.17 -10000 0 -0.36 47 47
PIK3C2B -0.067 0.18 -10000 0 -0.4 49 49
CBL/CRKL -0.049 0.18 0.3 3 -0.38 49 52
FER -0.07 0.18 -10000 0 -0.41 50 50
SH2B3 -0.068 0.18 -10000 0 -0.41 50 50
PDPK1 -0.031 0.17 0.26 5 -0.34 43 48
SNAI2 -0.071 0.18 -10000 0 -0.4 50 50
positive regulation of cell proliferation -0.14 0.31 -10000 0 -0.7 51 51
KITLG 0.007 0.063 0.13 1 -0.33 6 7
cell motility -0.14 0.31 -10000 0 -0.7 51 51
PTPN6 0.018 0.071 0.13 4 -0.3 10 14
EPOR -0.02 0.14 -10000 0 -0.55 1 1
STAT5A (dimer) -0.1 0.26 0.3 1 -0.57 51 52
SOCS1 0.024 0.047 0.12 4 -0.32 4 8
cell migration 0.071 0.18 0.42 49 -10000 0 49
SOS1 0.029 0.003 -10000 0 -10000 0 0
EPO 0.015 0.032 0.13 1 -10000 0 1
VAV1 0 0.097 0.12 2 -0.32 20 22
GRB10 -0.071 0.18 -10000 0 -0.4 51 51
PTPN11 0.03 0.01 -10000 0 -10000 0 0
SCF/KIT -0.065 0.19 -10000 0 -0.42 51 51
GO:0007205 0.003 0.01 -10000 0 -10000 0 0
MAP2K1 -0.029 0.12 0.22 6 -0.23 44 50
CBL 0.025 0.01 -10000 0 -10000 0 0
KIT -0.21 0.52 -10000 0 -1.2 49 49
MAP2K2 -0.03 0.12 0.23 4 -0.23 44 48
SHC/Grb2/SOS1 -0.034 0.19 -10000 0 -0.39 48 48
STAT5A -0.11 0.27 0.31 1 -0.59 51 52
GRB2 0.028 0.005 -10000 0 -10000 0 0
response to radiation -0.07 0.18 -10000 0 -0.39 50 50
SHC/GRAP2 0.026 0.055 -10000 0 -0.22 10 10
PTPRO -0.071 0.18 -10000 0 -0.4 50 50
SH2B2 -0.07 0.17 -10000 0 -0.39 50 50
DOK1 0.028 0.024 0.12 1 -0.32 1 2
MATK -0.073 0.19 -10000 0 -0.42 49 49
CREBBP 0.013 0.07 -10000 0 -0.12 48 48
BCL2 -0.055 0.27 -10000 0 -1.2 9 9
IL4-mediated signaling events

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
BCL2L1 -0.33 0.55 -10000 0 -1.2 50 50
STAT6 (cleaved dimer) -0.37 0.58 -10000 0 -1.2 62 62
IGHG1 -0.086 0.19 -10000 0 -0.37 19 19
IGHG3 -0.33 0.52 -10000 0 -1.1 61 61
AKT1 -0.21 0.4 -10000 0 -0.93 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.46 -10000 0 -1.1 36 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.45 -10000 0 -0.98 45 45
THY1 -0.34 0.55 -10000 0 -1.2 49 49
MYB 0.02 0.052 0.12 4 -0.32 5 9
HMGA1 0.027 0.013 0.12 2 -10000 0 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.46 -10000 0 -0.89 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.47 -10000 0 -1 43 43
SP1 0.03 0.025 -10000 0 -0.1 7 7
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
SOCS5 0.023 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.36 0.58 -10000 0 -1.2 60 60
SOCS1 -0.22 0.36 -10000 0 -0.74 58 58
SOCS3 -0.2 0.39 -10000 0 -0.87 42 42
FCER2 -0.36 0.6 -10000 0 -1.2 65 65
PARP14 0.025 0.028 -10000 0 -0.32 1 1
CCL17 -0.39 0.62 -10000 0 -1.3 57 57
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.36 -10000 0 -0.82 37 37
T cell proliferation -0.35 0.58 -10000 0 -1.2 58 58
IL4R/JAK1 -0.34 0.55 -10000 0 -1.2 50 50
EGR2 -0.36 0.58 -10000 0 -1.3 53 53
JAK2 -0.014 0.071 -10000 0 -0.34 5 5
JAK3 0.013 0.063 -10000 0 -0.29 8 8
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
JAK1 0.011 0.032 -10000 0 -10000 0 0
COL1A2 -0.12 0.32 -10000 0 -1.4 11 11
CCL26 -0.32 0.55 -10000 0 -1.2 51 51
IL4R -0.36 0.59 -10000 0 -1.3 48 48
PTPN6 0.011 0.073 0.13 3 -0.3 10 13
IL13RA2 -0.49 0.67 -10000 0 -1.3 86 86
IL13RA1 -0.007 0.062 -10000 0 -0.36 1 1
IRF4 -0.25 0.54 -10000 0 -1.3 44 44
ARG1 -0.096 0.24 -10000 0 -0.79 13 13
CBL -0.25 0.43 -10000 0 -0.84 62 62
GTF3A 0.029 0.027 -10000 0 -0.1 8 8
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
IL13RA1/JAK2 -0.008 0.085 -10000 0 -0.23 6 6
IRF4/BCL6 -0.23 0.5 -10000 0 -1.2 44 44
CD40LG -0.012 0.12 -10000 0 -0.22 46 46
MAPK14 -0.23 0.44 -10000 0 -0.85 58 58
mitosis -0.2 0.37 -10000 0 -0.85 42 42
STAT6 -0.4 0.7 -10000 0 -1.4 60 60
SPI1 0.021 0.055 -10000 0 -0.31 6 6
RPS6KB1 -0.19 0.36 -10000 0 -0.82 41 41
STAT6 (dimer) -0.4 0.7 -10000 0 -1.4 60 60
STAT6 (dimer)/PARP14 -0.38 0.62 -10000 0 -1.3 62 62
mast cell activation 0.007 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.48 -10000 0 -1.1 41 41
FRAP1 -0.21 0.4 -10000 0 -0.93 42 42
LTA -0.38 0.64 -10000 0 -1.4 56 56
FES 0.019 0.055 -10000 0 -0.32 6 6
T-helper 1 cell differentiation 0.38 0.64 1.3 60 -10000 0 60
CCL11 -0.35 0.56 -10000 0 -1.2 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.23 0.47 -10000 0 -1.1 39 39
IL2RG -0.015 0.11 0.13 7 -0.3 29 36
IL10 -0.34 0.59 -10000 0 -1.3 50 50
IRS1 0.011 0.076 -10000 0 -0.32 12 12
IRS2 0.026 0.023 -10000 0 -0.32 1 1
IL4 -0.083 0.25 -10000 0 -1.1 9 9
IL5 -0.34 0.55 -10000 0 -1.2 49 49
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.28 0.47 -10000 0 -0.97 56 56
COL1A1 -0.14 0.39 -10000 0 -1.3 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.35 0.57 -10000 0 -1.3 47 47
IL2R gamma/JAK3 0.002 0.11 0.19 2 -0.26 28 30
TFF3 -0.43 0.63 -10000 0 -1.3 68 68
ALOX15 -0.33 0.55 -10000 0 -1.2 49 49
MYBL1 0.022 0.039 -10000 0 -0.32 3 3
T-helper 2 cell differentiation -0.3 0.53 -10000 0 -1.1 59 59
SHC1 0.026 0.008 -10000 0 -10000 0 0
CEBPB 0.028 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.44 -10000 0 -0.95 46 46
mol:PI-3-4-5-P3 -0.21 0.4 -10000 0 -0.93 42 42
PI3K -0.23 0.45 -10000 0 -1 42 42
DOK2 0.015 0.063 -10000 0 -0.32 8 8
ETS1 0.019 0.035 0.15 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.33 -10000 0 -0.76 37 37
ITGB3 -0.42 0.63 -10000 0 -1.3 65 65
PIGR -0.36 0.6 -10000 0 -1.2 61 61
IGHE 0.026 0.068 0.17 22 -0.15 3 25
MAPKKK cascade -0.15 0.32 -10000 0 -0.74 37 37
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.34 0.55 -10000 0 -1.2 50 50
RETNLB -0.34 0.55 -10000 0 -1.2 50 50
SELP -0.42 0.66 -10000 0 -1.3 67 67
AICDA -0.32 0.52 -10000 0 -1.2 50 50
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 -0.2 0.52 -10000 0 -1.1 50 50
IL23A -0.2 0.53 -10000 0 -1.1 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.55 -10000 0 -1.1 54 54
positive regulation of T cell mediated cytotoxicity -0.24 0.62 -10000 0 -1.2 55 55
ITGA3 -0.23 0.55 -10000 0 -1.1 57 57
IL17F -0.13 0.34 -10000 0 -0.66 54 54
IL12B 0.018 0.06 0.19 7 -10000 0 7
STAT1 (dimer) -0.23 0.59 -10000 0 -1.1 56 56
CD4 -0.2 0.52 -10000 0 -1.1 47 47
IL23 -0.18 0.51 -10000 0 -1.1 42 42
IL23R 0.001 0.16 -10000 0 -1.1 3 3
IL1B -0.22 0.56 -10000 0 -1.2 50 50
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.22 0.57 0.58 1 -1.2 52 53
TYK2 0.012 0.044 -10000 0 -10000 0 0
STAT4 0.004 0.097 -10000 0 -0.32 19 19
STAT3 0.028 0.005 -10000 0 -10000 0 0
IL18RAP 0.005 0.089 0.12 14 -0.32 14 28
IL12RB1 -0.02 0.12 0.16 4 -0.35 26 30
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
IL12Rbeta1/TYK2 -0.002 0.1 0.15 3 -0.26 26 29
IL23R/JAK2 0.014 0.17 -10000 0 -1 3 3
positive regulation of chronic inflammatory response -0.24 0.62 -10000 0 -1.2 55 55
natural killer cell activation 0.001 0.008 -10000 0 -10000 0 0
JAK2 0.01 0.073 -10000 0 -0.34 5 5
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
NFKB1 0.028 0.006 -10000 0 -10000 0 0
RELA 0.028 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.48 -10000 0 -1 43 43
ALOX12B -0.2 0.51 -10000 0 -1 51 51
CXCL1 -0.24 0.57 -10000 0 -1.1 57 57
T cell proliferation -0.24 0.62 -10000 0 -1.2 55 55
NFKBIA 0.029 0.005 -10000 0 -10000 0 0
IL17A -0.083 0.28 -10000 0 -0.52 49 49
PI3K -0.21 0.56 -10000 0 -1.1 55 55
IFNG -0.019 0.059 -10000 0 -0.13 42 42
STAT3 (dimer) -0.2 0.54 -10000 0 -1 55 55
IL18R1 -0.002 0.093 -10000 0 -0.32 17 17
IL23/IL23R/JAK2/TYK2/SOCS3 -0.12 0.38 -10000 0 -0.74 48 48
IL18/IL18R 0.005 0.12 0.18 5 -0.21 41 46
macrophage activation -0.009 0.022 0.028 1 -0.043 40 41
TNF -0.21 0.56 -10000 0 -1.2 47 47
STAT3/STAT4 -0.22 0.57 -10000 0 -1.1 58 58
STAT4 (dimer) -0.24 0.6 -10000 0 -1.1 58 58
IL18 0.003 0.076 0.13 5 -0.32 11 16
IL19 -0.18 0.52 0.58 1 -1 49 50
STAT5A (dimer) -0.23 0.59 -10000 0 -1.1 55 55
STAT1 0.026 0.032 -10000 0 -0.32 2 2
SOCS3 0.025 0.033 0.12 1 -0.32 2 3
CXCL9 -0.28 0.63 -10000 0 -1.3 60 60
MPO -0.21 0.53 -10000 0 -1.1 52 52
positive regulation of humoral immune response -0.24 0.62 -10000 0 -1.2 55 55
IL23/IL23R/JAK2/TYK2 -0.28 0.72 -10000 0 -1.3 55 55
IL6 -0.18 0.53 -10000 0 -1.1 46 46
STAT5A 0.027 0.023 -10000 0 -0.32 1 1
IL2 0.003 0.033 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.008 -10000 0 -10000 0 0
CD3E -0.25 0.6 -10000 0 -1.3 51 51
keratinocyte proliferation -0.24 0.62 -10000 0 -1.2 55 55
NOS2 -0.22 0.54 -10000 0 -1.1 54 54
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.099 0.18 0.23 1 -0.36 73 74
KLHL20 -0.031 0.093 0.18 5 -0.21 21 26
CYFIP2 0.014 0.067 -10000 0 -0.32 9 9
Rac1/GDP -0.046 0.12 0.21 3 -0.23 53 56
ENAH -0.095 0.18 0.22 1 -0.37 65 66
AP1M1 0.029 0.003 -10000 0 -10000 0 0
RAP1B 0.028 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.019 0.082 -10000 0 -0.15 49 49
ABI1/Sra1/Nap1 -0.041 0.054 -10000 0 -0.14 27 27
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.007 0.12 -10000 0 -0.17 71 71
RAPGEF1 -0.081 0.17 0.22 3 -0.33 67 70
CTNND1 0.029 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.095 0.19 -10000 0 -0.37 75 75
CRK -0.087 0.18 0.22 1 -0.35 68 69
E-cadherin/gamma catenin/alpha catenin -0.011 0.11 -10000 0 -0.19 63 63
alphaE/beta7 Integrin 0.027 0.058 -10000 0 -0.21 12 12
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
NCKAP1 0.029 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.029 -10000 0 -0.16 2 2
DLG1 -0.098 0.18 -10000 0 -0.36 74 74
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.041 0.046 -10000 0 -0.12 50 50
MLLT4 0.022 0.033 -10000 0 -0.32 2 2
ARF6/GTP/NME1/Tiam1 0.041 0.05 -10000 0 -0.16 12 12
PI3K -0.05 0.059 -10000 0 -0.15 50 50
ARF6 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.029 0.12 -10000 0 -0.22 63 63
TIAM1 0.01 0.076 -10000 0 -0.32 12 12
E-cadherin(dimer)/Ca2+ 0.003 0.1 -10000 0 -0.16 63 63
AKT1 -0.024 0.049 0.12 4 -0.12 1 5
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
CDH1 -0.061 0.16 0.12 12 -0.32 63 75
RhoA/GDP -0.044 0.13 0.24 5 -0.22 58 63
actin cytoskeleton organization -0.021 0.072 0.16 6 -0.15 21 27
CDC42/GDP -0.045 0.13 0.24 5 -0.22 58 63
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.037 0.094 -10000 0 -0.19 63 63
ITGB7 0.011 0.076 -10000 0 -0.32 12 12
RAC1 0.025 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.004 0.11 -10000 0 -0.17 63 63
E-cadherin/Ca2+/beta catenin/alpha catenin -0.007 0.092 -10000 0 -0.16 63 63
mol:GDP -0.062 0.13 0.24 5 -0.25 58 63
CDC42/GTP/IQGAP1 0.036 0.01 -10000 0 -10000 0 0
JUP 0.027 0.035 -10000 0 -0.32 2 2
p120 catenin/RhoA/GDP -0.04 0.13 0.23 4 -0.23 56 60
RAC1/GTP/IQGAP1 0.033 0.015 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.043 0.004 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
CDC42 0.028 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.011 0.056 0.14 8 -0.11 21 29
NME1 0.028 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.1 0.19 -10000 0 -0.37 75 75
regulation of cell-cell adhesion -0.025 0.065 -10000 0 -0.14 49 49
WASF2 -0.014 0.04 0.093 3 -0.087 14 17
Rap1/GTP -0.018 0.094 0.25 3 -0.17 50 53
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0 0.12 -10000 0 -0.17 70 70
CCND1 -0.013 0.066 0.15 8 -0.13 21 29
VAV2 -0.12 0.25 0.36 1 -0.44 75 76
RAP1/GDP -0.025 0.11 0.26 3 -0.18 54 57
adherens junction assembly -0.099 0.18 -10000 0 -0.36 75 75
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.009 -10000 0 -10000 0 0
PIP5K1C 0.029 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.01 0.11 0.21 3 -0.17 70 73
E-cadherin/beta catenin -0.064 0.13 -10000 0 -0.28 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.096 0.18 0.22 1 -0.35 74 75
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
Rac1/GTP -0.076 0.12 -10000 0 -0.33 24 24
E-cadherin/beta catenin/alpha catenin -0.01 0.11 -10000 0 -0.18 63 63
ITGAE 0.027 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.098 0.2 -10000 0 -0.38 75 75
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.13 0.36 -10000 0 -0.79 49 49
NCK1/PAK1/Dok-R -0.09 0.16 -10000 0 -0.39 48 48
NCK1/Dok-R -0.15 0.41 -10000 0 -0.94 48 48
PIK3CA 0.025 0.032 -10000 0 -0.31 2 2
mol:beta2-estradiol 0.039 0.098 0.23 48 -10000 0 48
RELA 0.028 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.009 -10000 0 -10000 0 0
Rac/GDP 0.019 0.007 -10000 0 -10000 0 0
F2 0.029 0.11 0.25 43 -10000 0 43
TNIP2 0.028 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.39 -10000 0 -0.88 48 48
FN1 0.012 0.077 -10000 0 -0.32 12 12
PLD2 -0.17 0.4 -10000 0 -0.95 48 48
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GRB14 -0.003 0.12 0.12 25 -0.32 27 52
ELK1 -0.15 0.38 -10000 0 -0.87 48 48
GRB7 0.033 0.036 0.12 20 -0.32 1 21
PAK1 0.027 0.007 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.14 0.41 -10000 0 -0.92 48 48
CDKN1A -0.079 0.27 -10000 0 -0.56 46 46
ITGA5 0.028 0.035 0.12 5 -0.32 2 7
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.15 0.41 -10000 0 -0.94 48 48
CRK 0.027 0.007 -10000 0 -10000 0 0
mol:NO -0.076 0.28 -10000 0 -0.59 49 49
PLG -0.17 0.4 -10000 0 -0.95 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.34 -10000 0 -0.76 48 48
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.032 -10000 0 -0.32 2 2
ANGPT2 -0.081 0.26 -10000 0 -0.85 15 15
BMX -0.17 0.41 -10000 0 -0.96 48 48
ANGPT1 -0.21 0.47 -10000 0 -1.1 48 48
tube development -0.096 0.28 -10000 0 -0.59 52 52
ANGPT4 0.015 0.023 -10000 0 -10000 0 0
response to hypoxia -0.012 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.17 0.43 -10000 0 -1 48 48
alpha5/beta1 Integrin 0.038 0.03 0.18 1 -0.22 2 3
FGF2 -0.036 0.14 -10000 0 -0.31 44 44
STAT5A (dimer) -0.1 0.33 -10000 0 -0.68 50 50
mol:L-citrulline -0.076 0.28 -10000 0 -0.59 49 49
AGTR1 0.002 0.1 0.13 2 -0.32 21 23
MAPK14 -0.16 0.41 -10000 0 -0.94 48 48
Tie2/SHP2 -0.061 0.24 -10000 0 -0.94 12 12
TEK -0.067 0.26 -10000 0 -1 12 12
RPS6KB1 -0.12 0.34 0.42 1 -0.76 48 49
Angiotensin II/AT1 0.005 0.073 0.1 3 -0.22 21 24
Tie2/Ang1/GRB2 -0.16 0.42 -10000 0 -0.97 48 48
MAPK3 -0.16 0.38 -10000 0 -0.89 48 48
MAPK1 -0.15 0.38 -10000 0 -0.89 48 48
Tie2/Ang1/GRB7 -0.16 0.43 -10000 0 -0.98 48 48
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.17 0.4 -10000 0 -0.95 48 48
PI3K -0.14 0.4 -10000 0 -0.9 48 48
FES -0.16 0.41 -10000 0 -0.93 49 49
Crk/Dok-R -0.15 0.41 -10000 0 -0.94 48 48
Tie2/Ang1/ABIN2 -0.16 0.42 -10000 0 -0.98 48 48
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.11 0.32 -10000 0 -0.71 50 50
STAT5A 0.027 0.023 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.11 0.35 0.45 2 -0.75 48 50
Tie2/Ang2 -0.13 0.37 -10000 0 -0.79 49 49
Tie2/Ang1 -0.17 0.43 -10000 0 -1 48 48
FOXO1 -0.12 0.33 0.4 1 -0.71 52 53
ELF1 0.022 0.033 -10000 0 -0.12 1 1
ELF2 -0.16 0.4 -10000 0 -0.93 48 48
mol:Choline -0.16 0.39 -10000 0 -0.91 48 48
cell migration -0.046 0.094 -10000 0 -0.22 48 48
FYN -0.11 0.31 -10000 0 -0.66 51 51
DOK2 0.015 0.063 -10000 0 -0.32 8 8
negative regulation of cell cycle -0.069 0.25 0.37 1 -0.51 47 48
ETS1 -0.011 0.1 -10000 0 -0.24 38 38
PXN -0.087 0.3 0.4 3 -0.63 48 51
ITGB1 0.027 0.011 -10000 0 -10000 0 0
NOS3 -0.094 0.32 -10000 0 -0.67 49 49
RAC1 0.025 0.01 -10000 0 -10000 0 0
TNF -0.027 0.14 -10000 0 -0.28 47 47
MAPKKK cascade -0.16 0.39 -10000 0 -0.91 48 48
RASA1 0.024 0.032 -10000 0 -0.32 2 2
Tie2/Ang1/Shc -0.16 0.42 -10000 0 -0.96 48 48
NCK1 0.028 0.006 -10000 0 -10000 0 0
vasculogenesis -0.064 0.26 0.32 1 -0.53 50 51
mol:Phosphatidic acid -0.16 0.39 -10000 0 -0.91 48 48
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP -0.076 0.28 -10000 0 -0.59 49 49
Rac1/GTP -0.11 0.32 -10000 0 -0.72 48 48
MMP2 -0.17 0.41 -10000 0 -0.96 48 48
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.002 0.1 0.14 2 -0.26 24 26
NFATC2 -0.04 0.23 -10000 0 -0.5 34 34
NFATC3 -0.003 0.083 -10000 0 -0.21 19 19
CD40LG -0.15 0.36 -10000 0 -0.7 56 56
ITCH 0.002 0.073 -10000 0 -0.19 29 29
CBLB 0.003 0.074 -10000 0 -0.19 30 30
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.19 0.41 -10000 0 -0.86 54 54
JUNB 0.029 0.007 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.096 -10000 0 -0.22 32 32
T cell anergy -0.033 0.13 -10000 0 -0.34 32 32
TLE4 -0.029 0.16 0.26 1 -0.44 22 23
Jun/NFAT1-c-4/p21SNFT -0.081 0.33 -10000 0 -0.68 43 43
AP-1/NFAT1-c-4 -0.12 0.41 -10000 0 -0.78 52 52
IKZF1 -0.041 0.2 0.32 1 -0.48 29 30
T-helper 2 cell differentiation -0.13 0.31 -10000 0 -0.72 41 41
AP-1/NFAT1 -0.012 0.18 -10000 0 -0.35 30 30
CALM1 0.016 0.063 -10000 0 -0.14 31 31
EGR2 -0.11 0.35 -10000 0 -0.81 34 34
EGR3 -0.13 0.39 -10000 0 -0.98 32 32
NFAT1/FOXP3 -0.031 0.21 0.28 1 -0.39 45 46
EGR1 0.028 0.03 0.12 6 -0.32 1 7
JUN 0.01 0.035 -10000 0 -10000 0 0
EGR4 0.035 0.031 0.12 21 -10000 0 21
mol:Ca2+ -0.007 0.05 -10000 0 -0.13 32 32
GBP3 -0.05 0.2 -10000 0 -0.48 32 32
FOSL1 0.003 0.11 -10000 0 -0.32 22 22
NFAT1-c-4/MAF/IRF4 -0.085 0.31 -10000 0 -0.68 38 38
DGKA -0.037 0.17 -10000 0 -0.4 29 29
CREM 0.026 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.084 0.33 -10000 0 -0.71 39 39
CTLA4 -0.05 0.2 0.25 2 -0.44 39 41
NFAT1-c-4 (dimer)/EGR1 -0.079 0.33 -10000 0 -0.72 39 39
NFAT1-c-4 (dimer)/EGR4 -0.077 0.33 -10000 0 -0.72 39 39
FOS 0.015 0.04 -10000 0 -10000 0 0
IFNG -0.25 0.48 -10000 0 -0.98 63 63
T cell activation -0.052 0.2 -10000 0 -0.6 12 12
MAF 0.027 0.007 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.081 0.26 0.72 25 -10000 0 25
TNF -0.095 0.3 -10000 0 -0.7 37 37
FASLG -0.29 0.64 -10000 0 -1.4 53 53
TBX21 -0.02 0.13 0.15 16 -0.23 52 68
BATF3 0.022 0.041 -10000 0 -0.32 3 3
PRKCQ -0.02 0.13 0.14 6 -0.29 36 42
PTPN1 -0.034 0.16 -10000 0 -0.37 30 30
NFAT1-c-4/ICER1 -0.082 0.32 -10000 0 -0.7 38 38
GATA3 -0.005 0.11 0.14 1 -0.32 24 25
T-helper 1 cell differentiation -0.24 0.46 -10000 0 -0.95 63 63
IL2RA -0.16 0.39 -10000 0 -0.81 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.033 0.15 -10000 0 -0.41 23 23
E2F1 0.027 0.033 -10000 0 -0.31 2 2
PPARG 0.025 0.04 -10000 0 -0.32 3 3
SLC3A2 -0.032 0.15 -10000 0 -0.38 28 28
IRF4 -0.013 0.11 -10000 0 -0.32 26 26
PTGS2 -0.14 0.33 -10000 0 -0.68 53 53
CSF2 -0.14 0.34 -10000 0 -0.69 52 52
JunB/Fra1/NFAT1-c-4 -0.083 0.32 -10000 0 -0.68 39 39
IL4 -0.14 0.32 -10000 0 -0.76 41 41
IL5 -0.14 0.33 -10000 0 -0.69 52 52
IL2 -0.053 0.2 -10000 0 -0.62 11 11
IL3 -0.031 0.16 -10000 0 -0.77 8 8
RNF128 -0.017 0.16 -10000 0 -0.42 32 32
NFATC1 -0.082 0.26 -10000 0 -0.72 25 25
CDK4 0.061 0.19 0.54 19 -10000 0 19
PTPRK -0.031 0.16 -10000 0 -0.42 25 25
IL8 -0.14 0.34 -10000 0 -0.69 55 55
POU2F1 0.026 0.009 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.005 0.042 -10000 0 -0.3 2 2
Crk/p130 Cas/Paxillin -0.055 0.11 -10000 0 -0.24 45 45
JUN -0.034 0.11 0.19 2 -0.36 11 13
HRAS 0.028 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.009 0.12 0.2 10 -0.19 53 63
RAP1A 0.028 0.006 -10000 0 -10000 0 0
FRS2 0.028 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.013 0.12 0.2 11 -0.19 56 67
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.005 0.11 0.17 9 -0.18 52 61
RHOA 0.028 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.009 0.11 0.21 1 -0.17 56 57
GRB7 0.033 0.036 0.12 20 -0.32 1 21
RET51/GFRalpha1/GDNF 0.014 0.12 0.25 1 -0.19 55 56
MAPKKK cascade -0.018 0.11 0.16 2 -0.2 53 55
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
RET9/GFRalpha1/GDNF/IRS1 -0.003 0.12 0.17 9 -0.18 60 69
lamellipodium assembly -0.041 0.11 -10000 0 -0.22 43 43
RET51/GFRalpha1/GDNF/SHC 0.014 0.12 0.2 9 -0.19 48 57
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
RET9/GFRalpha1/GDNF/SHC 0.008 0.1 0.17 7 -0.18 45 52
RET9/GFRalpha1/GDNF/Shank3 0.005 0.11 0.17 9 -0.18 51 60
MAPK3 -0.036 0.091 0.18 13 -0.3 7 20
DOK1 0.028 0.024 0.12 1 -0.32 1 2
DOK6 0.021 0.084 0.12 26 -0.32 12 38
PXN 0.029 0.003 -10000 0 -10000 0 0
neurite development -0.03 0.087 0.18 11 -0.25 10 21
DOK5 0.023 0.087 0.12 35 -0.32 12 47
GFRA1 0.003 0.12 -10000 0 -0.32 25 25
MAPK8 -0.035 0.11 0.14 1 -0.22 46 47
HRAS/GTP -0.006 0.14 0.22 1 -0.22 55 56
tube development 0.006 0.1 0.21 2 -0.17 50 52
MAPK1 -0.035 0.091 0.18 13 -0.3 7 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.1 0.15 2 -0.2 52 54
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.027 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.019 0.13 0.27 4 -0.19 53 57
SHC1 0.026 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.01 0.12 0.2 10 -0.18 57 67
RET51/GFRalpha1/GDNF/Dok5 0.011 0.13 0.25 4 -0.18 59 63
PRKCA 0.019 0.06 0.12 2 -0.32 7 9
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
CREB1 -0.021 0.11 -10000 0 -0.28 24 24
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.021 0.1 0.15 3 -0.21 46 49
RET51/GFRalpha1/GDNF/Grb7 0.017 0.13 0.22 13 -0.19 54 67
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.023 0.054 0.12 9 -0.32 5 14
DOK4 0.024 0.032 -10000 0 -0.32 2 2
JNK cascade -0.033 0.11 0.19 3 -0.36 11 14
RET9/GFRalpha1/GDNF/FRS2 0.006 0.11 0.17 8 -0.18 51 59
SHANK3 0.025 0.024 -10000 0 -0.32 1 1
RASA1 0.024 0.032 -10000 0 -0.32 2 2
NCK1 0.028 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.099 0.15 3 -0.2 47 50
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.032 0.11 0.15 2 -0.21 61 63
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.12 0.15 1 -0.22 58 59
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.11 0.15 3 -0.22 45 48
PI3K -0.054 0.16 0.23 1 -0.32 46 47
SOS1 0.029 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.014 0.11 0.18 9 -0.17 50 59
GRB10 0.021 0.04 -10000 0 -0.32 3 3
activation of MAPKK activity -0.031 0.12 0.17 1 -0.27 40 41
RET51/GFRalpha1/GDNF/FRS2 0.013 0.12 0.2 10 -0.19 54 64
GAB1 0.026 0.032 -10000 0 -0.32 2 2
IRS1 0.011 0.076 -10000 0 -0.32 12 12
IRS2 0.026 0.023 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.022 0.11 0.15 3 -0.22 47 50
RET51/GFRalpha1/GDNF/PKC alpha 0.011 0.13 0.2 13 -0.19 56 69
GRB2 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GDNF -0.017 0.13 -10000 0 -0.32 34 34
RAC1 0.025 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.004 0.13 0.25 2 -0.19 63 65
Rac1/GTP -0.043 0.13 -10000 0 -0.26 43 43
RET9/GFRalpha1/GDNF -0.007 0.11 0.16 9 -0.2 52 61
GFRalpha1/GDNF -0.012 0.13 0.18 9 -0.24 52 61
Endothelins

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
AKT1 0.014 0.14 0.27 27 -0.26 26 53
PTK2B 0.026 0.025 0.12 2 -0.31 1 3
mol:Ca2+ -0.011 0.22 -10000 0 -0.58 19 19
EDN1 0.02 0.12 0.22 25 -0.23 24 49
EDN3 -0.001 0.13 0.12 47 -0.32 29 76
EDN2 0.026 0.017 0.12 6 -10000 0 6
HRAS/GDP -0.013 0.16 0.25 6 -0.33 30 36
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.014 0.12 0.18 20 -0.3 18 38
ADCY4 0.021 0.13 0.2 42 -0.26 17 59
ADCY5 0.017 0.13 0.21 39 -0.29 18 57
ADCY6 0.019 0.13 0.2 43 -0.25 20 63
ADCY7 0.017 0.12 0.2 40 -0.27 16 56
ADCY1 -0.004 0.12 0.2 28 -0.25 26 54
ADCY2 0.007 0.14 0.23 27 -0.25 34 61
ADCY3 0.017 0.13 0.2 40 -0.28 16 56
ADCY8 0.02 0.12 0.2 31 -0.27 14 45
ADCY9 0.02 0.13 0.2 42 -0.26 18 60
arachidonic acid secretion -0.01 0.15 0.28 4 -0.37 20 24
ETB receptor/Endothelin-1/Gq/GTP 0.021 0.086 0.15 1 -0.22 16 17
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
HRAS 0.028 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.051 0.14 0.35 21 -0.24 23 44
ETA receptor/Endothelin-1/Gs/GTP 0.043 0.14 0.33 23 -0.23 26 49
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
COL3A1 0.016 0.15 0.27 28 -0.31 22 50
EDNRB 0.014 0.07 -10000 0 -0.26 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.007 0.17 0.29 26 -0.38 23 49
CYSLTR1 0.01 0.16 0.27 28 -0.34 25 53
SLC9A1 0.014 0.087 0.19 24 -0.2 14 38
mol:GDP -0.023 0.16 0.24 7 -0.35 30 37
SLC9A3 -0.026 0.25 -10000 0 -0.7 19 19
RAF1 -0.021 0.15 0.24 2 -0.36 23 25
JUN -0.017 0.22 0.4 1 -0.61 18 19
JAK2 0.011 0.13 0.27 23 -0.28 23 46
mol:IP3 0.001 0.13 0.21 4 -0.39 15 19
ETA receptor/Endothelin-1 0.046 0.18 0.4 25 -0.3 27 52
PLCB1 0.001 0.096 0.12 4 -0.32 19 23
PLCB2 0.019 0.055 -10000 0 -0.32 6 6
ETA receptor/Endothelin-3 0.014 0.12 0.18 24 -0.2 40 64
FOS -0.004 0.13 0.36 1 -0.43 6 7
Gai/GDP -0.12 0.29 -10000 0 -0.66 49 49
CRK 0.027 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0.006 0.16 0.25 21 -0.37 23 44
BCAR1 0.025 0.032 -10000 0 -0.31 2 2
PRKCB1 -0.005 0.13 0.19 5 -0.33 22 27
GNAQ 0.028 0.009 -10000 0 -10000 0 0
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
GNAL 0.012 0.1 0.12 32 -0.32 19 51
Gs family/GDP -0.02 0.15 0.24 7 -0.34 27 34
ETA receptor/Endothelin-1/Gq/GTP 0.033 0.11 0.2 25 -0.27 13 38
MAPK14 -0.008 0.098 0.16 2 -0.34 12 14
TRPC6 -0.014 0.22 -10000 0 -0.64 17 17
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.005 0.1 0.18 1 -0.35 11 12
ETB receptor/Endothelin-2 0.028 0.055 -10000 0 -0.21 10 10
ETB receptor/Endothelin-3 0.006 0.11 -10000 0 -0.22 38 38
ETB receptor/Endothelin-1 0.025 0.11 0.2 7 -0.24 20 27
MAPK3 -0.01 0.14 0.36 1 -0.44 11 12
MAPK1 -0.011 0.14 0.36 1 -0.48 8 9
Rac1/GDP -0.012 0.15 0.23 5 -0.35 24 29
cAMP biosynthetic process -0.017 0.15 0.23 23 -0.31 28 51
MAPK8 -0.028 0.25 -10000 0 -0.66 25 25
SRC 0.026 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.024 0.11 -10000 0 -0.29 20 20
p130Cas/CRK/Src/PYK2 -0.017 0.17 0.28 2 -0.43 21 23
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.012 0.15 0.23 5 -0.35 24 29
COL1A2 0.007 0.17 0.27 25 -0.52 12 37
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.036 0.085 0.17 25 -0.18 15 40
mol:DAG 0.001 0.13 0.21 4 -0.39 15 19
MAP2K2 -0.018 0.14 0.33 3 -0.41 14 17
MAP2K1 -0.015 0.14 0.29 2 -0.44 12 14
EDNRA 0.023 0.11 0.21 29 -0.2 28 57
positive regulation of muscle contraction 0.025 0.13 0.24 39 -0.24 21 60
Gq family/GDP 0.014 0.15 0.28 1 -0.37 19 20
HRAS/GTP -0.022 0.15 0.21 5 -0.36 27 32
PRKCH -0.01 0.13 0.19 4 -0.33 23 27
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.012 0.14 0.28 5 -0.31 26 31
PRKCB -0.022 0.16 0.21 5 -0.35 30 35
PRKCE -0.01 0.13 0.21 3 -0.32 23 26
PRKCD -0.01 0.13 0.21 6 -0.31 24 30
PRKCG -0.011 0.13 0.21 2 -0.33 23 25
regulation of vascular smooth muscle contraction -0.01 0.14 0.4 1 -0.51 6 7
PRKCQ -0.019 0.15 0.19 4 -0.35 27 31
PLA2G4A -0.012 0.16 0.3 3 -0.4 20 23
GNA14 0.033 0.05 0.13 21 -0.31 3 24
GNA15 0.02 0.06 -10000 0 -0.32 7 7
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA11 0.03 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.05 0.14 0.35 21 -0.25 22 43
MMP1 -0.069 0.25 0.35 5 -0.7 29 34
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.06 0.18 0.22 3 -0.36 44 47
TBX21 -0.21 0.57 0.46 1 -1.3 46 47
B2M 0.024 0.02 -10000 0 -10000 0 0
TYK2 0.019 0.041 -10000 0 -10000 0 0
IL12RB1 -0.013 0.13 0.17 5 -0.35 26 31
GADD45B -0.15 0.47 -10000 0 -1.1 40 40
IL12RB2 -0.039 0.13 0.16 3 -0.31 42 45
GADD45G -0.19 0.53 0.46 1 -1.2 46 47
natural killer cell activation 0.004 0.024 -10000 0 -10000 0 0
RELB 0.028 0.004 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
IL18 0.01 0.079 0.14 4 -0.32 11 15
IL2RA 0.004 0.088 -10000 0 -0.32 16 16
IFNG -0.019 0.13 0.12 17 -0.32 35 52
STAT3 (dimer) -0.14 0.42 0.4 2 -0.89 48 50
HLA-DRB5 0.004 0.095 0.12 11 -0.32 18 29
FASLG -0.22 0.6 -10000 0 -1.3 49 49
NF kappa B2 p52/RelB -0.18 0.54 0.39 1 -1.2 46 47
CD4 0.017 0.063 -10000 0 -0.32 8 8
SOCS1 0.024 0.047 0.12 4 -0.32 4 8
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.005 0.11 0.13 17 -0.32 24 41
CD3E -0.005 0.11 0.13 13 -0.32 23 36
CD3G -0.016 0.12 0.13 3 -0.32 31 34
IL12Rbeta2/JAK2 -0.014 0.12 0.19 2 -0.22 46 48
CCL3 -0.19 0.53 0.46 1 -1.2 43 44
CCL4 -0.2 0.55 0.46 1 -1.3 42 43
HLA-A 0.019 0.037 -10000 0 -0.32 2 2
IL18/IL18R 0.032 0.13 0.23 9 -0.25 32 41
NOS2 -0.2 0.56 -10000 0 -1.2 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.06 0.18 0.21 3 -0.36 43 46
IL1R1 -0.2 0.54 -10000 0 -1.2 45 45
IL4 -0.012 0.037 -10000 0 -10000 0 0
JAK2 0.014 0.062 -10000 0 -0.33 5 5
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.46 -10000 0 -1 48 48
RAB7A -0.12 0.39 -10000 0 -0.85 42 42
lysosomal transport -0.1 0.36 0.42 1 -0.8 42 43
FOS -0.12 0.42 -10000 0 -1 35 35
STAT4 (dimer) -0.16 0.49 0.46 2 -1 49 51
STAT5A (dimer) -0.2 0.54 0.45 2 -1.2 47 49
GZMA -0.2 0.57 -10000 0 -1.3 43 43
GZMB -0.21 0.57 -10000 0 -1.3 43 43
HLX 0.024 0.024 -10000 0 -0.32 1 1
LCK -0.23 0.63 0.43 3 -1.4 46 49
TCR/CD3/MHC II/CD4 -0.098 0.31 0.15 1 -0.73 39 40
IL2/IL2R 0.017 0.13 0.2 6 -0.25 36 42
MAPK14 -0.17 0.51 0.44 2 -1.1 45 47
CCR5 -0.18 0.54 -10000 0 -1.3 40 40
IL1B 0.003 0.11 0.14 9 -0.34 17 26
STAT6 -0.011 0.13 0.26 2 -0.25 27 29
STAT4 0.004 0.097 -10000 0 -0.32 19 19
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.032 -10000 0 -0.32 2 2
NFKB1 0.028 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.008 -10000 0 -10000 0 0
IL12B 0.025 0.046 0.17 7 -10000 0 7
CD8A -0.017 0.13 -10000 0 -0.32 34 34
CD8B -0.031 0.14 0.13 17 -0.32 43 60
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.06 0.18 0.36 44 -0.22 3 47
IL2RB 0.007 0.09 -10000 0 -0.32 16 16
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.43 0.43 3 -0.89 49 52
IL2RG -0.011 0.12 0.12 7 -0.32 29 36
IL12 0.025 0.092 0.19 6 -0.24 15 21
STAT5A 0.027 0.023 -10000 0 -0.32 1 1
CD247 -0.004 0.11 -10000 0 -0.32 22 22
IL2 0.021 0.013 -10000 0 -10000 0 0
SPHK2 0.025 0.032 -10000 0 -0.32 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.099 0.15 2 -0.34 15 17
IL12/IL12R/TYK2/JAK2 -0.27 0.74 0.48 2 -1.6 46 48
MAP2K3 -0.18 0.52 0.45 1 -1.1 47 48
RIPK2 0.026 0.008 -10000 0 -10000 0 0
MAP2K6 -0.18 0.53 0.44 2 -1.1 48 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.088 0.12 4 -0.32 16 20
IL18RAP 0.011 0.091 0.13 15 -0.32 14 29
IL12Rbeta1/TYK2 0.008 0.11 0.17 4 -0.27 26 30
EOMES -0.089 0.34 -10000 0 -1.3 17 17
STAT1 (dimer) -0.16 0.44 0.43 3 -0.92 49 52
T cell proliferation -0.08 0.34 0.39 2 -0.69 47 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.096 0.14 1 -0.32 17 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.36 0.36 2 -0.75 49 51
ATF2 -0.15 0.45 0.43 1 -0.99 45 46
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.054 0.19 0.26 12 -0.43 36 48
IKBKB -0.018 0.11 0.26 4 -0.28 23 27
AKT1 -0.036 0.11 0.28 7 -0.22 32 39
IKBKG -0.011 0.11 0.25 4 -0.28 20 24
CALM1 -0.054 0.19 -10000 0 -0.49 28 28
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
MAP3K1 -0.095 0.27 0.3 7 -0.56 45 52
MAP3K7 0.023 0.033 -10000 0 -0.32 2 2
mol:Ca2+ -0.054 0.2 -10000 0 -0.5 30 30
DOK1 0.028 0.024 0.12 1 -0.32 1 2
AP-1 -0.027 0.11 0.18 2 -0.25 29 31
LYN 0.024 0.033 -10000 0 -0.31 2 2
BLNK -0.004 0.1 0.12 5 -0.31 22 27
SHC1 0.026 0.008 -10000 0 -10000 0 0
BCR complex -0.011 0.15 0.18 21 -0.28 50 71
CD22 -0.068 0.2 0.18 2 -0.4 48 50
CAMK2G -0.05 0.17 -10000 0 -0.46 27 27
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
SHC/GRB2/SOS1 -0.02 0.12 -10000 0 -0.25 43 43
GO:0007205 -0.056 0.2 -10000 0 -0.51 30 30
SYK 0.016 0.064 0.12 3 -0.31 8 11
ELK1 -0.061 0.19 -10000 0 -0.47 33 33
NFATC1 -0.082 0.2 0.28 7 -0.39 52 59
B-cell antigen/BCR complex -0.011 0.15 0.18 21 -0.28 50 71
PAG1/CSK 0.026 0.054 -10000 0 -0.22 10 10
NFKBIB 0.011 0.05 0.15 4 -0.13 9 13
HRAS -0.052 0.18 0.19 1 -0.42 33 34
NFKBIA 0.012 0.049 0.14 5 -0.12 9 14
NF-kappa-B/RelA/I kappa B beta 0.016 0.044 0.14 5 -0.093 5 10
RasGAP/Csk 0.027 0.13 -10000 0 -0.21 48 48
mol:GDP -0.058 0.2 -10000 0 -0.49 31 31
PTEN 0.026 0.009 -10000 0 -10000 0 0
CD79B 0.008 0.1 0.12 23 -0.31 20 43
NF-kappa-B/RelA/I kappa B alpha 0.016 0.043 0.14 5 -0.092 4 9
GRB2 0.028 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.092 0.24 0.29 1 -0.5 49 50
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
mol:IP3 -0.055 0.2 -10000 0 -0.53 29 29
CSK 0.028 0.005 -10000 0 -10000 0 0
FOS -0.059 0.18 -10000 0 -0.46 29 29
CHUK -0.03 0.14 0.25 4 -0.31 34 38
IBTK 0.017 0.055 -10000 0 -0.32 6 6
CARD11/BCL10/MALT1/TAK1 -0.027 0.19 0.26 3 -0.45 29 32
PTPN6 -0.072 0.2 0.18 6 -0.42 44 50
RELA 0.028 0.005 -10000 0 -10000 0 0
BCL2A1 0.01 0.033 0.11 4 -0.1 2 6
VAV2 -0.11 0.24 -10000 0 -0.51 49 49
ubiquitin-dependent protein catabolic process 0.014 0.049 0.15 4 -0.12 9 13
BTK -0.023 0.24 -10000 0 -1 12 12
CD19 -0.086 0.21 -10000 0 -0.43 50 50
MAP4K1 0.011 0.081 -10000 0 -0.32 13 13
CD72 0.016 0.069 0.12 8 -0.32 9 17
PAG1 0.011 0.07 -10000 0 -0.32 10 10
MAPK14 -0.062 0.23 0.33 13 -0.45 44 57
SH3BP5 0.028 0.024 -10000 0 -0.32 1 1
PIK3AP1 -0.052 0.22 -10000 0 -0.6 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.32 -10000 0 -0.59 53 53
RAF1 -0.051 0.16 -10000 0 -0.42 29 29
RasGAP/p62DOK/SHIP 0.018 0.15 0.23 2 -0.23 49 51
CD79A -0.03 0.15 -10000 0 -0.31 49 49
re-entry into mitotic cell cycle -0.027 0.11 0.18 2 -0.25 29 31
RASA1 0.024 0.032 -10000 0 -0.32 2 2
MAPK3 -0.043 0.14 0.22 3 -0.38 26 29
MAPK1 -0.039 0.14 0.23 3 -0.37 26 29
CD72/SHP1 -0.054 0.2 0.25 4 -0.45 37 41
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.078 0.22 0.28 7 -0.46 45 52
actin cytoskeleton organization -0.075 0.21 0.28 7 -0.43 45 52
NF-kappa-B/RelA 0.035 0.084 0.26 5 -0.19 8 13
Calcineurin -0.025 0.17 -10000 0 -0.42 28 28
PI3K -0.081 0.18 -10000 0 -0.35 54 54
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.049 0.22 -10000 0 -0.59 27 27
SOS1 0.029 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.36 -10000 0 -0.86 38 38
DAPP1 -0.14 0.4 -10000 0 -1 37 37
cytokine secretion -0.075 0.19 0.27 7 -0.36 52 59
mol:DAG -0.055 0.2 -10000 0 -0.53 29 29
PLCG2 0.021 0.051 -10000 0 -0.32 5 5
MAP2K1 -0.046 0.16 0.22 2 -0.4 28 30
B-cell antigen/BCR complex/FcgammaRIIB 0.007 0.14 0.18 22 -0.24 49 71
mol:PI-3-4-5-P3 -0.063 0.12 0.16 4 -0.28 37 41
ETS1 -0.049 0.15 -10000 0 -0.43 26 26
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.01 0.17 0.28 5 -0.26 51 56
B-cell antigen/BCR complex/LYN -0.058 0.21 -10000 0 -0.41 46 46
MALT1 0.025 0.032 -10000 0 -0.32 2 2
TRAF6 0.028 0.006 -10000 0 -10000 0 0
RAC1 -0.085 0.22 0.26 4 -0.46 46 50
B-cell antigen/BCR complex/LYN/SYK -0.037 0.21 0.25 3 -0.41 42 45
CARD11 -0.052 0.22 0.26 6 -0.53 30 36
FCGR2B 0.022 0.054 -10000 0 -0.32 5 5
PPP3CA 0.028 0.004 -10000 0 -10000 0 0
BCL10 0.028 0.005 -10000 0 -10000 0 0
IKK complex -0.002 0.053 0.18 4 -0.12 11 15
PTPRC 0 0.1 0.12 12 -0.32 21 33
PDPK1 -0.039 0.098 0.24 8 -0.2 33 41
PPP3CB 0.027 0.008 -10000 0 -10000 0 0
PPP3CC 0.027 0.007 -10000 0 -10000 0 0
POU2F2 0.012 0.037 0.16 3 -0.1 1 4
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.072 0.22 2 -0.22 10 12
adherens junction organization -0.055 0.12 0.18 1 -0.22 64 65
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.073 0.25 1 -0.22 7 8
FMN1 -0.058 0.12 0.14 1 -0.22 65 66
mol:IP3 -0.024 0.067 0.21 1 -0.21 7 8
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.047 0.12 -10000 0 -0.21 65 65
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
AKT1 -0.023 0.084 0.21 1 -0.25 6 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.066 0.16 -10000 0 -0.3 68 68
CTNND1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.044 0.1 0.14 1 -0.21 57 58
VASP -0.05 0.11 0.14 1 -0.21 65 66
ZYX -0.045 0.1 0.14 1 -0.21 57 58
JUB -0.047 0.11 0.15 1 -0.2 65 66
EGFR(dimer) -0.036 0.12 0.18 1 -0.21 61 62
E-cadherin/beta catenin-gamma catenin -0.006 0.11 -10000 0 -0.18 63 63
mol:PI-3-4-5-P3 -0.008 0.098 -10000 0 -0.25 7 7
PIK3CA 0.026 0.033 -10000 0 -0.32 2 2
PI3K -0.008 0.1 -10000 0 -0.25 7 7
FYN -0.03 0.079 0.21 2 -0.24 18 20
mol:Ca2+ -0.024 0.065 0.21 1 -0.21 7 8
JUP 0.029 0.035 0.13 1 -0.31 2 3
PIK3R1 0.025 0.033 -10000 0 -0.32 2 2
mol:DAG -0.024 0.067 0.21 1 -0.21 7 8
CDH1 -0.061 0.16 0.12 12 -0.32 63 75
RhoA/GDP -0.01 0.085 0.18 12 -0.22 6 18
establishment of polarity of embryonic epithelium -0.049 0.11 0.14 1 -0.2 65 66
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.061 0.12 16 -0.32 6 22
CASR -0.026 0.064 0.18 4 -0.23 4 8
RhoA/GTP -0.012 0.072 0.22 2 -0.22 5 7
AKT2 -0.025 0.085 0.21 1 -0.24 7 8
actin cable formation -0.058 0.12 0.18 4 -0.22 63 67
apoptosis 0.021 0.084 0.21 12 -0.2 5 17
CTNNA1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP -0.027 0.07 0.19 4 -0.23 6 10
PIP5K1A -0.045 0.1 0.14 1 -0.21 57 58
PLCG1 -0.025 0.068 0.21 1 -0.21 7 8
Rac1/GTP -0.03 0.12 -10000 0 -0.2 60 60
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.024 0.032 -10000 0 -0.32 2 2
alphaV beta3 Integrin 0.008 0.096 -10000 0 -0.23 31 31
PTK2 -0.054 0.14 -10000 0 -0.33 33 33
positive regulation of JNK cascade -0.045 0.14 -10000 0 -0.28 48 48
CDC42/GDP -0.055 0.19 -10000 0 -0.38 52 52
Rac1/GDP -0.056 0.18 -10000 0 -0.38 47 47
RAP1B 0.028 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.051 0.17 -10000 0 -0.34 48 48
nectin-3/I-afadin 0.004 0.087 -10000 0 -0.21 31 31
RAPGEF1 -0.064 0.18 0.27 1 -0.38 50 51
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.074 0.2 -10000 0 -0.42 51 51
PDGFB-D/PDGFRB 0.024 0.032 -10000 0 -0.31 2 2
TLN1 -0.014 0.036 0.1 1 -0.12 23 24
Rap1/GTP -0.047 0.13 -10000 0 -0.28 49 49
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.029 -10000 0 -0.16 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.004 0.087 -10000 0 -0.21 31 31
PVR 0.025 0.032 -10000 0 -0.32 2 2
Necl-5(dimer) 0.025 0.032 -10000 0 -0.31 2 2
mol:GDP -0.082 0.22 -10000 0 -0.46 52 52
MLLT4 0.022 0.033 -10000 0 -0.32 2 2
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
PI3K 0.035 0.093 -10000 0 -0.17 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.2 2 2
positive regulation of lamellipodium assembly -0.053 0.15 -10000 0 -0.31 49 49
PVRL1 0.026 0.012 0.12 1 -10000 0 1
PVRL3 -0.013 0.12 0.12 4 -0.32 29 33
PVRL2 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
CDH1 -0.061 0.16 0.12 12 -0.32 63 75
CLDN1 -0.01 0.14 0.12 50 -0.32 40 90
JAM-A/CLDN1 0.008 0.12 -10000 0 -0.18 57 57
SRC -0.082 0.21 -10000 0 -0.46 51 51
ITGB3 -0.012 0.12 -10000 0 -0.32 30 30
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.2 2 2
FARP2 -0.075 0.23 -10000 0 -0.47 44 44
RAC1 0.025 0.01 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.018 0.083 -10000 0 -0.18 33 33
nectin-1/I-afadin 0.032 0.029 -10000 0 -0.2 2 2
nectin-2/I-afadin 0.034 0.028 -10000 0 -0.22 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.015 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.018 0.08 -10000 0 -0.17 31 31
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.01 -10000 0 -10000 0 0
F11R 0.023 0.033 -10000 0 -0.32 2 2
positive regulation of filopodium formation -0.045 0.14 -10000 0 -0.28 48 48
alphaV/beta3 Integrin/Talin -0.009 0.088 0.24 2 -0.22 10 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.028 -10000 0 -0.22 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.028 -10000 0 -0.22 2 2
PIP5K1C -0.012 0.046 -10000 0 -0.13 29 29
VAV2 -0.094 0.25 -10000 0 -0.52 49 49
RAP1/GDP -0.047 0.18 -10000 0 -0.35 53 53
ITGAV 0.023 0.045 -10000 0 -0.32 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.02 0.081 -10000 0 -0.18 31 31
nectin-3(dimer)/I-afadin/I-afadin 0.004 0.087 -10000 0 -0.21 31 31
Rac1/GTP -0.062 0.18 -10000 0 -0.38 49 49
PTPRM -0.008 0.053 -10000 0 -0.14 29 29
E-cadherin/beta catenin/alpha catenin 0.001 0.1 -10000 0 -0.16 64 64
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.032 0.091 -10000 0 -0.18 64 64
epithelial cell differentiation -0.001 0.098 -10000 0 -0.16 63 63
CYFIP2 0.014 0.067 -10000 0 -0.32 9 9
ENAH -0.046 0.065 0.26 1 -0.23 3 4
EGFR 0.024 0.061 0.12 16 -0.32 6 22
EPHA2 0.02 0.056 0.12 3 -0.32 6 9
MYO6 -0.047 0.077 0.21 5 -0.29 1 6
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.042 0.049 -10000 0 -0.18 9 9
AQP5 -0.026 0.091 0.43 1 -0.43 4 5
CTNND1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.045 0.074 0.21 5 -10000 0 5
regulation of calcium-dependent cell-cell adhesion -0.043 0.079 0.22 5 -0.28 2 7
EGF -0.028 0.14 0.12 19 -0.32 43 62
NCKAP1 0.029 0.002 -10000 0 -10000 0 0
AQP3 -0.049 0.12 0.38 1 -0.34 20 21
cortical microtubule organization -0.001 0.098 -10000 0 -0.16 63 63
GO:0000145 -0.044 0.069 0.2 5 -0.14 61 66
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.003 0.1 -10000 0 -0.16 63 63
MLLT4 0.022 0.033 -10000 0 -0.32 2 2
ARF6/GDP -0.055 0.057 -10000 0 -0.15 59 59
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.056 0.047 -10000 0 -0.17 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.034 0.068 0.21 4 -10000 0 4
PVRL2 0.028 0.004 -10000 0 -10000 0 0
ZYX -0.042 0.072 0.22 4 -10000 0 4
ARF6/GTP 0.061 0.049 -10000 0 -0.16 6 6
CDH1 -0.061 0.16 0.12 12 -0.32 63 75
EGFR/EGFR/EGF/EGF -0.038 0.11 -10000 0 -0.17 91 91
RhoA/GDP 0.001 0.096 -10000 0 -0.15 63 63
actin cytoskeleton organization -0.052 0.076 0.19 5 -0.28 1 6
IGF-1R heterotetramer 0.025 0.032 -10000 0 -0.31 2 2
GIT1 0.028 0.005 -10000 0 -10000 0 0
IGF1R 0.025 0.032 -10000 0 -0.32 2 2
IGF1 0.008 0.086 0.12 4 -0.32 15 19
DIAPH1 -0.031 0.21 -10000 0 -0.56 23 23
Wnt receptor signaling pathway 0.001 0.098 0.16 63 -10000 0 63
RHOA 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.055 0.058 -10000 0 -0.15 59 59
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
VCL -0.05 0.076 0.2 5 -0.29 1 6
EFNA1 0.026 0.008 -10000 0 -10000 0 0
LPP -0.05 0.072 0.2 5 -10000 0 5
Ephrin A1/EPHA2 -0.009 0.089 -10000 0 -0.15 62 62
SEC6/SEC8 -0.048 0.059 -10000 0 -0.15 50 50
MGAT3 -0.044 0.08 0.22 5 -0.29 2 7
HGF/MET -0.022 0.11 -10000 0 -0.17 73 73
HGF 0.015 0.077 0.12 13 -0.32 11 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.032 0.092 -10000 0 -0.18 64 64
actin cable formation -0.017 0.11 0.27 13 -0.25 5 18
KIAA1543 -0.048 0.074 0.2 5 -0.15 62 67
KIFC3 -0.048 0.072 0.24 3 -0.15 62 65
NCK1 0.028 0.006 -10000 0 -10000 0 0
EXOC3 0.026 0.008 -10000 0 -10000 0 0
ACTN1 -0.048 0.076 0.21 5 -10000 0 5
NCK1/GIT1 0.04 0.011 -10000 0 -10000 0 0
mol:GDP -0.001 0.098 -10000 0 -0.16 63 63
EXOC4 0.026 0.009 -10000 0 -10000 0 0
STX4 -0.046 0.075 0.21 5 -10000 0 5
PIP5K1C -0.045 0.075 0.21 5 -10000 0 5
LIMA1 0.029 0.003 -10000 0 -10000 0 0
ABI1 0.026 0.009 -10000 0 -10000 0 0
ROCK1 -0.034 0.095 0.34 5 -10000 0 5
adherens junction assembly -0.046 0.089 0.32 2 -0.3 8 10
IGF-1R heterotetramer/IGF1 -0.017 0.1 -10000 0 -0.16 73 73
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.028 -10000 0 -0.22 2 2
MET 0.001 0.096 -10000 0 -0.32 19 19
PLEKHA7 -0.048 0.079 0.21 5 -0.2 6 11
mol:GTP 0.054 0.046 -10000 0 -0.16 6 6
establishment of epithelial cell apical/basal polarity -0.018 0.11 0.25 13 -10000 0 13
cortical actin cytoskeleton stabilization -0.032 0.091 -10000 0 -0.18 64 64
regulation of cell-cell adhesion -0.052 0.076 0.19 5 -0.28 1 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.032 0.092 -10000 0 -0.18 64 64
LPA receptor 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
GNB1/GNG2 0.025 0.094 -10000 0 -0.21 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.11 -10000 0 -0.22 26 26
AP1 0.008 0.094 -10000 0 -0.16 46 46
mol:PIP3 -0.026 0.08 -10000 0 -0.17 41 41
AKT1 -0.003 0.085 0.27 5 -0.29 5 10
PTK2B -0.027 0.098 -10000 0 -0.28 18 18
RHOA 0.009 0.059 0.23 2 -0.26 4 6
PIK3CB 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.083 0.2 8 -0.19 27 35
MAGI3 0.025 0.032 -10000 0 -0.31 2 2
RELA 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.023 0.094 0.18 1 -0.2 46 47
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.038 0.098 0.21 4 -0.3 14 18
NF kappa B1 p50/RelA -0.01 0.1 0.15 1 -0.21 35 36
endothelial cell migration -0.01 0.11 -10000 0 -0.33 20 20
ADCY4 -0.045 0.12 0.2 2 -0.29 36 38
ADCY5 -0.058 0.14 0.21 2 -0.33 40 42
ADCY6 -0.045 0.12 0.2 2 -0.3 35 37
ADCY7 -0.044 0.12 0.2 2 -0.3 33 35
ADCY1 -0.073 0.14 -10000 0 -0.31 45 45
ADCY2 -0.075 0.16 0.2 2 -0.32 54 56
ADCY3 -0.046 0.12 0.2 2 -0.3 35 37
ADCY8 -0.042 0.12 0.18 3 -0.29 34 37
ADCY9 -0.045 0.12 0.2 2 -0.29 35 37
GSK3B -0.027 0.097 0.22 3 -0.29 15 18
arachidonic acid secretion -0.056 0.13 0.15 1 -0.29 41 42
GNG2 0.015 0.066 -10000 0 -0.31 9 9
TRIP6 0.011 0.039 -10000 0 -0.23 5 5
GNAO1 -0.029 0.092 -10000 0 -0.19 52 52
HRAS 0.028 0.006 -10000 0 -10000 0 0
NFKBIA -0.031 0.1 -10000 0 -0.24 30 30
GAB1 0.026 0.032 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.039 0.27 -10000 0 -0.89 21 21
JUN 0.028 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.032 0.038 -10000 0 -0.12 10 10
TIAM1 -0.063 0.32 -10000 0 -1.1 21 21
PIK3R1 0.025 0.032 -10000 0 -0.31 2 2
mol:IP3 -0.016 0.079 0.2 7 -0.19 26 33
PLCB3 0.011 0.038 0.18 5 -0.17 4 9
FOS 0.032 0.018 -10000 0 -10000 0 0
positive regulation of mitosis -0.056 0.13 0.15 1 -0.29 41 42
LPA/LPA1-2-3 0.015 0.11 0.18 1 -0.18 48 49
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
stress fiber formation -0.017 0.095 -10000 0 -0.31 12 12
GNAZ -0.015 0.086 0.11 1 -0.21 33 34
EGFR/PI3K-beta/Gab1 -0.013 0.09 -10000 0 -0.18 42 42
positive regulation of dendritic cell cytokine production 0.014 0.11 0.17 1 -0.18 48 49
LPA/LPA2/MAGI-3 0.032 0.037 -10000 0 -0.12 10 10
ARHGEF1 0.016 0.088 0.2 24 -0.19 16 40
GNAI2 -0.005 0.073 -10000 0 -0.22 22 22
GNAI3 -0.003 0.069 -10000 0 -0.21 20 20
GNAI1 -0.007 0.075 -10000 0 -0.22 22 22
LPA/LPA3 0.002 0.085 0.1 1 -0.2 32 33
LPA/LPA2 0.016 0.035 -10000 0 -0.14 9 9
LPA/LPA1 0.004 0.091 0.14 2 -0.24 24 26
HB-EGF/EGFR 0.006 0.076 0.14 6 -0.19 27 33
HBEGF -0.022 0.063 -10000 0 -0.22 20 20
mol:DAG -0.016 0.079 0.2 7 -0.19 26 33
cAMP biosynthetic process -0.06 0.14 0.21 5 -0.27 50 55
NFKB1 0.028 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
LYN -0.026 0.12 0.25 3 -0.26 29 32
GNAQ -0.007 0.068 0.16 1 -0.19 27 28
LPAR2 0.025 0.039 0.12 1 -0.31 3 4
LPAR3 0.003 0.12 -10000 0 -0.32 27 27
LPAR1 0.004 0.1 0.13 11 -0.29 22 33
IL8 -0.031 0.15 0.28 2 -0.39 25 27
PTK2 -0.022 0.077 0.19 4 -0.17 40 44
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
CASP3 -0.023 0.094 0.18 1 -0.2 46 47
EGFR 0.024 0.061 0.12 16 -0.32 6 22
PLCG1 -0.016 0.083 0.17 3 -0.21 31 34
PLD2 -0.022 0.081 0.19 4 -0.18 39 43
G12/G13 0.03 0.079 -10000 0 -0.19 21 21
PI3K-beta -0.001 0.072 -10000 0 -0.3 6 6
cell migration -0.011 0.09 -10000 0 -0.26 21 21
SLC9A3R2 0.028 0.024 0.12 1 -0.32 1 2
PXN -0.018 0.097 -10000 0 -0.32 12 12
HRAS/GTP -0.056 0.13 0.16 1 -0.3 41 42
RAC1 0.025 0.01 -10000 0 -10000 0 0
MMP9 -0.002 0.11 0.12 20 -0.32 25 45
PRKCE 0.028 0.003 -10000 0 -10000 0 0
PRKCD -0.02 0.082 0.19 9 -0.25 8 17
Gi(beta/gamma) -0.043 0.12 0.16 1 -0.29 32 33
mol:LPA -0.003 0.025 -10000 0 -0.14 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.1 0.21 1 -0.29 11 12
MAPKKK cascade -0.056 0.13 0.15 1 -0.29 41 42
contractile ring contraction involved in cytokinesis 0.011 0.059 0.23 2 -0.25 4 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.006 0.074 0.17 2 -0.18 30 32
GNA15 -0.014 0.08 0.16 1 -0.2 35 36
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
MAPT -0.038 0.1 0.21 4 -0.31 14 18
GNA11 -0.009 0.072 0.16 1 -0.19 30 31
Rac1/GTP -0.042 0.29 -10000 0 -0.95 21 21
MMP2 -0.01 0.11 -10000 0 -0.33 20 20
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.019 0.051 0.13 14 -0.28 4 18
CDKN2C 0.019 0.019 -10000 0 -10000 0 0
CDKN2A 0.01 0.084 0.13 22 -0.29 14 36
CCND2 0.001 0.042 0.16 12 -0.096 2 14
RB1 -0.007 0.052 -10000 0 -0.18 15 15
CDK4 0.006 0.05 0.18 14 -10000 0 14
CDK6 0.002 0.054 0.19 13 -0.12 6 19
G1/S progression 0.049 0.09 0.18 67 -10000 0 67
EGFR-dependent Endothelin signaling events

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.006 -10000 0 -10000 0 0
EGFR 0.024 0.061 0.12 16 -0.32 6 22
EGF/EGFR 0.005 0.092 0.16 6 -0.16 51 57
EGF/EGFR dimer/SHC/GRB2/SOS1 0.029 0.097 0.2 1 -0.16 40 41
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.025 0.054 0.12 9 -0.32 5 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.028 0.14 0.12 19 -0.32 43 62
EGF/EGFR dimer/SHC 0.009 0.097 0.18 1 -0.18 42 43
mol:GDP 0.025 0.093 -10000 0 -0.16 40 40
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.017 0.061 -10000 0 -0.32 7 7
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.01 0.079 -10000 0 -0.15 40 40
SHC1 0.026 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.089 -10000 0 -0.16 40 40
FRAP1 -0.037 0.054 -10000 0 -0.15 40 40
EGF/EGFR dimer -0.008 0.11 0.18 1 -0.22 47 48
SOS1 0.029 0.003 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.029 0.062 0.18 1 -0.24 10 11
Syndecan-1-mediated signaling events

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.045 -10000 0 -0.32 4 4
CCL5 -0.002 0.11 -10000 0 -0.32 24 24
SDCBP 0.023 0.033 -10000 0 -0.32 2 2
FGFR/FGF2/Syndecan-1 -0.035 0.14 0.24 6 -0.4 19 25
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 -0.038 0.15 0.23 5 -0.37 25 30
Syndecan-1/Syntenin -0.033 0.14 0.21 3 -0.37 22 25
MAPK3 -0.036 0.14 0.21 6 -0.36 21 27
HGF/MET 0.01 0.091 -10000 0 -0.22 30 30
TGFB1/TGF beta receptor Type II 0.022 0.045 -10000 0 -0.31 4 4
BSG 0.029 0.003 -10000 0 -10000 0 0
keratinocyte migration -0.038 0.15 0.23 5 -0.36 25 30
Syndecan-1/RANTES -0.039 0.16 0.23 5 -0.37 30 35
Syndecan-1/CD147 -0.021 0.15 0.23 6 -0.37 21 27
Syndecan-1/Syntenin/PIP2 -0.033 0.14 0.2 3 -0.35 22 25
LAMA5 0.018 0.056 0.12 2 -0.32 6 8
positive regulation of cell-cell adhesion -0.032 0.13 0.19 3 -0.35 22 25
MMP7 0.01 0.1 0.12 27 -0.32 18 45
HGF 0.015 0.077 0.12 13 -0.32 11 24
Syndecan-1/CASK -0.05 0.13 -10000 0 -0.37 22 22
Syndecan-1/HGF/MET -0.04 0.16 0.25 6 -0.39 27 33
regulation of cell adhesion -0.041 0.13 0.19 7 -0.35 21 28
HPSE 0.02 0.055 -10000 0 -0.32 6 6
positive regulation of cell migration -0.035 0.14 0.24 6 -0.4 19 25
SDC1 -0.036 0.13 0.24 1 -0.26 43 44
Syndecan-1/Collagen -0.035 0.14 0.24 6 -0.4 19 25
PPIB 0.028 0.004 -10000 0 -10000 0 0
MET 0.001 0.096 -10000 0 -0.32 19 19
PRKACA 0.029 0.003 -10000 0 -10000 0 0
MMP9 -0.002 0.11 0.12 20 -0.32 25 45
MAPK1 -0.035 0.14 0.21 6 -0.36 21 27
homophilic cell adhesion -0.035 0.14 0.24 6 -0.39 19 25
MMP1 0.001 0.12 -10000 0 -0.32 29 29
Wnt 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
Noncanonical Wnts/FZD -0.024 0.12 0.15 1 -0.22 49 50
FZD6 0.007 0.079 -10000 0 -0.32 13 13
WNT6 0.027 0.056 -10000 0 -0.32 5 5
WNT4 -0.004 0.12 0.12 20 -0.32 27 47
FZD3 0.025 0.024 -10000 0 -0.32 1 1
WNT5A 0.02 0.08 -10000 0 -0.32 11 11
WNT11 0.011 0.081 0.12 7 -0.32 13 20
p75(NTR)-mediated signaling

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.031 0.048 -10000 0 -0.22 8 8
Necdin/E2F1 0.019 0.07 -10000 0 -0.22 18 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.043 0.1 0.2 4 -0.16 40 44
NGF (dimer)/p75(NTR)/BEX1 0.03 0.12 0.2 12 -0.2 40 52
NT-4/5 (dimer)/p75(NTR) 0.027 0.079 0.18 2 -0.22 19 21
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.022 0.071 0.2 9 -0.17 25 34
IKBKG 0.029 0.002 -10000 0 -10000 0 0
BDNF -0.009 0.13 0.12 34 -0.32 34 68
MGDIs/NGR/p75(NTR)/LINGO1 -0.006 0.12 -10000 0 -0.22 54 54
FURIN 0.028 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.008 0.12 0.18 8 -0.2 56 64
LINGO1 -0.01 0.11 0.12 2 -0.32 26 28
Sortilin/TRAF6/NRIF 0.024 0.042 -10000 0 -0.15 10 10
proBDNF (dimer) -0.009 0.13 0.12 34 -0.31 34 68
NTRK1 0.021 0.059 -10000 0 -0.32 6 6
RTN4R -0.003 0.1 0.12 6 -0.32 22 28
neuron apoptosis -0.033 0.12 0.33 4 -0.35 11 15
IRAK1 0.029 0.002 -10000 0 -10000 0 0
SHC1 -0.003 0.065 0.2 1 -0.19 22 23
ARHGDIA 0.026 0.023 -10000 0 -0.32 1 1
RhoA/GTP 0.021 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.037 -10000 0 -0.15 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.038 0.1 0.19 4 -0.18 37 41
MAGEH1 0.024 0.039 -10000 0 -0.32 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.026 0.12 0.19 4 -0.19 45 49
Mammalian IAPs/DIABLO 0.038 0.096 -10000 0 -0.2 28 28
proNGF (dimer) 0.016 0.072 0.12 8 -0.31 10 18
MAGED1 0.027 0.023 -10000 0 -0.32 1 1
APP 0.016 0.063 -10000 0 -0.32 8 8
NT-4/5 (dimer) 0.025 0.019 -10000 0 -10000 0 0
ZNF274 0.028 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.072 0.17 6 -0.16 28 34
NGF 0.016 0.073 0.12 8 -0.32 10 18
cell cycle arrest -0.024 0.091 0.33 8 -0.2 9 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.068 -10000 0 -0.19 23 23
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.074 0.18 2 -0.18 19 21
NCSTN 0.026 0.008 -10000 0 -10000 0 0
mol:GTP 0.032 0.093 0.18 5 -0.19 31 36
PSENEN 0.028 0.004 -10000 0 -10000 0 0
mol:ceramide -0.022 0.069 0.22 5 -0.18 27 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.004 0.076 0.14 1 -0.28 7 8
p75(NTR)/beta APP 0.02 0.092 -10000 0 -0.22 26 26
BEX1 0.023 0.096 0.12 43 -0.32 15 58
mol:GDP -0.024 0.062 -10000 0 -0.18 28 28
NGF (dimer) 0.034 0.082 0.19 1 -0.17 26 27
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.007 0.12 -10000 0 -0.2 54 54
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
RAC1/GTP 0.026 0.075 0.16 5 -0.16 27 32
MYD88 0.029 0.003 -10000 0 -10000 0 0
CHUK 0.025 0.024 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR)/PKA 0.032 0.093 0.18 5 -0.19 31 36
RHOB 0.028 0.005 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.036 0.027 -10000 0 -0.22 2 2
NT3 (dimer) 0.033 0.037 -10000 0 -0.31 1 1
TP53 -0.039 0.083 0.22 8 -0.28 4 12
PRDM4 -0.028 0.074 0.22 5 -0.18 34 39
BDNF (dimer) 0.012 0.12 0.18 14 -0.18 62 76
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
SORT1 0.016 0.063 -10000 0 -0.32 8 8
activation of caspase activity 0.037 0.098 -10000 0 -0.16 40 40
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.04 0.098 0.19 4 -0.18 35 39
RHOC 0.028 0.006 -10000 0 -10000 0 0
XIAP 0.026 0.032 -10000 0 -0.32 2 2
MAPK10 -0.034 0.13 0.34 6 -0.29 28 34
DIABLO 0.029 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.07 0.22 5 -0.18 27 32
APH1B 0.025 0.032 -10000 0 -0.32 2 2
APH1A 0.027 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.027 0.099 0.18 4 -0.19 35 39
PSEN1 0.028 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.031 -10000 0 -0.22 3 3
NT3 (dimer)/p75(NTR) 0.032 0.085 0.18 7 -0.22 20 27
MAPK8 -0.028 0.12 0.32 8 -0.27 24 32
MAPK9 -0.023 0.12 0.35 7 -0.27 23 30
APAF1 0.024 0.039 -10000 0 -0.32 3 3
NTF3 0.033 0.037 -10000 0 -0.32 1 1
NTF4 0.025 0.019 -10000 0 -10000 0 0
NDN 0 0.094 -10000 0 -0.32 19 19
RAC1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.085 -10000 0 -0.16 30 30
p75 CTF/Sortilin/TRAF6/NRIF 0.058 0.049 -10000 0 -0.17 8 8
RhoA-B-C/GTP 0.031 0.092 0.18 5 -0.19 31 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.032 0.12 0.2 8 -0.17 53 61
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.12 0.19 8 -0.18 55 63
PRKACB 0.024 0.039 -10000 0 -0.32 3 3
proBDNF (dimer)/p75 ECD 0.012 0.099 -10000 0 -0.22 34 34
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.008 0.11 -10000 0 -0.32 27 27
BIRC2 0.019 0.05 -10000 0 -0.32 5 5
neuron projection morphogenesis -0.036 0.084 0.12 9 -0.2 35 44
BAD -0.038 0.13 0.3 8 -0.29 26 34
RIPK2 0.026 0.008 -10000 0 -10000 0 0
NGFR 0.014 0.1 0.12 34 -0.32 19 53
CYCS -0.027 0.073 0.25 5 -0.17 30 35
ADAM17 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.049 0.083 0.19 5 -0.18 22 27
BCL2L11 -0.04 0.13 0.3 8 -0.29 27 35
BDNF (dimer)/p75(NTR) 0.001 0.13 0.18 9 -0.23 50 59
PI3K 0.045 0.092 0.19 5 -0.18 29 34
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.041 0.097 0.19 4 -0.18 34 38
NDNL2 0.028 0.005 -10000 0 -10000 0 0
YWHAE 0.027 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.039 -10000 0 -0.32 3 3
NGF (dimer)/p75(NTR) 0.02 0.097 0.18 5 -0.22 28 33
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.04 0.099 0.19 4 -0.18 36 40
TRAF6 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCZ 0.02 0.05 -10000 0 -0.32 5 5
PLG 0.016 0.01 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.033 0.1 0.15 2 -0.19 64 66
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
NGFRAP1 0.022 0.05 -10000 0 -0.32 5 5
CASP3 -0.036 0.13 0.29 8 -0.27 26 34
E2F1 0.024 0.033 -10000 0 -0.32 2 2
CASP9 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.019 0.1 -10000 0 -0.24 14 14
NGF (dimer)/TRKA 0.027 0.067 0.18 1 -0.22 14 15
MMP7 0.01 0.1 0.12 27 -0.32 18 45
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.099 0.2 4 -0.17 35 39
MMP3 0.014 0.099 -10000 0 -0.32 17 17
APAF-1/Caspase 9 -0.054 0.075 -10000 0 -0.2 38 38
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.003 0.15 0.2 19 -0.18 78 97
SMAD6-7/SMURF1 0.049 0.027 -10000 0 -0.18 1 1
NOG 0.036 0.032 0.12 26 -10000 0 26
SMAD9 -0.021 0.15 -10000 0 -0.5 18 18
SMAD4 0.028 0.004 -10000 0 -10000 0 0
SMAD5 -0.033 0.13 -10000 0 -0.35 20 20
BMP7/USAG1 0.018 0.12 0.18 20 -0.22 39 59
SMAD5/SKI -0.02 0.14 0.21 2 -0.35 20 22
SMAD1 0.015 0.067 -10000 0 -0.39 3 3
BMP2 0.019 0.083 -10000 0 -0.32 12 12
SMAD1/SMAD1/SMAD4 0.026 0.063 -10000 0 -0.32 4 4
BMPR1A 0.027 0.008 -10000 0 -10000 0 0
BMPR1B -0.035 0.15 0.12 31 -0.32 51 82
BMPR1A-1B/BAMBI -0.002 0.12 -10000 0 -0.19 60 60
AHSG 0.022 0.011 -10000 0 -10000 0 0
CER1 0.018 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.035 0.069 0.18 1 -0.18 17 18
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.026 0.12 0.18 1 -0.34 18 19
BMP2-4 (homodimer) 0.027 0.08 0.18 1 -0.23 18 19
RGMB 0.028 0.009 0.12 1 -10000 0 1
BMP6/BMPR2/BMPR1A-1B 0.025 0.1 0.19 1 -0.17 44 45
RGMA 0.021 0.072 0.12 15 -0.32 9 24
SMURF1 0.026 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.028 0.11 -10000 0 -0.3 18 18
BMP2-4/USAG1 0.033 0.11 0.19 10 -0.2 33 43
SMAD6/SMURF1/SMAD5 -0.023 0.13 0.27 1 -0.35 18 19
SOSTDC1 0.021 0.11 0.12 64 -0.32 20 84
BMP7/BMPR2/BMPR1A-1B 0.011 0.13 0.19 5 -0.18 63 68
SKI 0.027 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.032 0.028 0.12 17 -10000 0 17
HFE2 0.022 0.015 -10000 0 -10000 0 0
ZFYVE16 0.023 0.039 -10000 0 -0.32 3 3
MAP3K7 0.023 0.033 -10000 0 -0.32 2 2
BMP2-4/CHRD 0.038 0.086 0.21 2 -0.2 23 25
SMAD5/SMAD5/SMAD4 -0.02 0.14 0.23 3 -0.35 20 23
MAPK1 0.027 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.017 0.1 -10000 0 -0.26 19 19
BMP7 (homodimer) 0.015 0.12 0.12 59 -0.31 24 83
NUP214 0.027 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.036 0.023 -10000 0 -10000 0 0
SMAD1/SKI 0.023 0.073 -10000 0 -0.35 4 4
SMAD6 0.029 0.01 0.12 2 -10000 0 2
CTDSP2 0.028 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.038 0.073 0.18 1 -0.19 18 19
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.006 0.12 0.12 16 -0.32 27 43
BMPR2 (homodimer) 0.029 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.05 0.032 -10000 0 -0.18 3 3
BMPR1A-1B (homodimer) -0.008 0.11 -10000 0 -0.22 51 51
CHRDL1 -0.028 0.15 0.12 27 -0.32 46 73
ENDOFIN/SMAD1 0.022 0.074 -10000 0 -0.35 4 4
SMAD6-7/SMURF1/SMAD1 0.042 0.074 -10000 0 -0.34 4 4
SMAD6/SMURF1 0.026 0.009 -10000 0 -10000 0 0
BAMBI 0.008 0.076 -10000 0 -0.32 12 12
SMURF2 0.027 0.023 -10000 0 -0.32 1 1
BMP2-4/CHRDL1 0.006 0.13 0.18 6 -0.22 50 56
BMP2-4/GREM1 0.021 0.11 0.18 6 -0.2 38 44
SMAD7 0.027 0.023 -10000 0 -0.32 1 1
SMAD8A/SMAD8A/SMAD4 -0.007 0.15 -10000 0 -0.46 18 18
SMAD1/SMAD6 0.019 0.071 -10000 0 -0.35 4 4
TAK1/SMAD6 0.032 0.029 -10000 0 -0.22 2 2
BMP7 0.015 0.12 0.12 59 -0.32 24 83
BMP6 0.032 0.028 0.12 17 -10000 0 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.017 0.11 -10000 0 -0.31 17 17
PPM1A 0.028 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.024 0.075 -10000 0 -0.35 4 4
SMAD7/SMURF1 0.036 0.022 -10000 0 -0.22 1 1
CTDSPL 0.029 0.003 -10000 0 -10000 0 0
PPP1CA 0.028 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.032 -10000 0 -0.32 2 2
CTDSP1 0.029 0.003 -10000 0 -10000 0 0
PPP1R15A 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.048 0.15 -10000 0 -0.39 24 24
CHRD 0.021 0.062 0.12 8 -0.32 7 15
BMPR2 0.029 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.035 0.11 0.14 1 -0.33 18 19
BMP4 0.022 0.062 0.12 9 -0.32 7 16
FST 0.005 0.12 0.12 42 -0.32 27 69
BMP2-4/NOG 0.047 0.078 0.2 5 -0.19 17 22
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.016 0.12 0.2 4 -0.17 58 62
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.003 0.11 0.18 2 -0.19 59 61
fibroblast growth factor receptor signaling pathway -0.003 0.11 0.18 2 -0.19 59 61
LAMA1 -0.013 0.12 0.12 17 -0.32 32 49
PRNP 0.026 0.024 0.12 1 -0.32 1 2
GPC1/SLIT2 0.023 0.084 0.18 2 -0.22 23 25
SMAD2 -0.022 0.039 -10000 0 -0.17 12 12
GPC1/PrPc/Cu2+ 0.025 0.058 0.16 1 -0.18 15 16
GPC1/Laminin alpha1 -0.003 0.11 -10000 0 -0.24 40 40
TDGF1 0.025 0.017 0.12 6 -10000 0 6
CRIPTO/GPC1 0.026 0.067 -10000 0 -0.22 14 14
APP/GPC1 0.02 0.083 -10000 0 -0.24 20 20
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.013 0.052 -10000 0 -0.19 17 17
FLT1 0.026 0.023 -10000 0 -0.32 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.063 -10000 0 -0.18 15 15
SERPINC1 0.023 0.009 -10000 0 -10000 0 0
FYN -0.008 0.045 -10000 0 -0.19 12 12
FGR -0.014 0.056 -10000 0 -0.19 20 20
positive regulation of MAPKKK cascade -0.036 0.13 0.22 9 -0.31 31 40
SLIT2 0.021 0.072 -10000 0 -0.32 9 9
GPC1/NRG 0.022 0.091 0.18 3 -0.23 24 27
NRG1 0.021 0.082 -10000 0 -0.32 11 11
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.042 0.061 0.18 1 -0.18 12 13
LYN -0.01 0.05 -10000 0 -0.19 15 15
mol:Spermine -0.005 0.054 -10000 0 -0.21 14 14
cell growth -0.003 0.11 0.18 2 -0.19 59 61
BMP signaling pathway -0.013 0.086 0.31 14 -10000 0 14
SRC -0.01 0.048 -10000 0 -0.19 14 14
TGFBR1 0.025 0.024 -10000 0 -0.32 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.02 0.15 0.12 44 -0.32 44 88
GPC1 0.013 0.086 -10000 0 -0.32 14 14
TGFBR1 (dimer) 0.025 0.024 -10000 0 -0.31 1 1
VEGFA 0.029 0.019 0.12 7 -10000 0 7
BLK -0.023 0.08 -10000 0 -0.2 36 36
HCK -0.017 0.059 -10000 0 -0.19 23 23
FGF2 -0.036 0.14 -10000 0 -0.32 44 44
FGFR1 0.025 0.049 0.12 9 -0.32 4 13
VEGFR1 homodimer 0.026 0.023 -10000 0 -0.31 1 1
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
cell death 0.02 0.082 -10000 0 -0.24 20 20
ATIII/GPC1 0.025 0.064 -10000 0 -0.22 13 13
PLA2G2A/GPC1 -0.007 0.13 0.18 1 -0.22 55 56
LCK -0.029 0.078 -10000 0 -0.19 42 42
neuron differentiation 0.022 0.091 0.18 3 -0.22 24 27
PrPc/Cu2+ 0.02 0.017 -10000 0 -0.21 1 1
APP 0.016 0.063 -10000 0 -0.32 8 8
TGFBR2 (dimer) 0.029 0.003 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.022 0.047 -10000 0 -0.32 4 4
GNB1/GNG2 -0.041 0.076 -10000 0 -0.19 45 45
AKT1 -0.016 0.12 0.28 1 -0.23 36 37
EGF -0.028 0.14 0.12 19 -0.32 43 62
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.013 0.078 0.35 3 -0.24 8 11
mol:Ca2+ -0.033 0.15 0.26 1 -0.3 51 52
LYN -0.014 0.061 0.23 3 -0.21 4 7
RhoA/GTP -0.011 0.063 -10000 0 -0.13 40 40
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.046 0.16 0.25 1 -0.35 47 48
GNG2 0.015 0.066 -10000 0 -0.32 9 9
ARRB2 0.027 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.009 0.086 -10000 0 -0.33 11 11
G beta5/gamma2 -0.048 0.1 -10000 0 -0.25 44 44
PRKCH -0.042 0.17 -10000 0 -0.35 48 48
DNM1 0.024 0.042 -10000 0 -0.32 3 3
TXA2/TP beta/beta Arrestin3 0.008 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.016 0.068 -10000 0 -0.32 9 9
G12 family/GTP -0.041 0.14 -10000 0 -0.3 43 43
ADRBK1 0.028 0.005 -10000 0 -10000 0 0
ADRBK2 0.017 0.059 -10000 0 -0.32 7 7
RhoA/GTP/ROCK1 0.034 0.03 -10000 0 -0.18 4 4
mol:GDP 0.027 0.14 0.37 20 -0.28 1 21
mol:NADP 0.019 0.045 -10000 0 -0.32 4 4
RAB11A 0.028 0.005 -10000 0 -10000 0 0
PRKG1 0.015 0.073 0.12 8 -0.31 10 18
mol:IP3 -0.047 0.18 -10000 0 -0.38 51 51
cell morphogenesis 0.033 0.029 -10000 0 -0.18 4 4
PLCB2 -0.076 0.24 -10000 0 -0.51 51 51
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.014 0.083 0.31 3 -0.24 8 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.016 0.075 0.35 3 -0.23 9 12
RHOA 0.028 0.004 -10000 0 -10000 0 0
PTGIR 0.025 0.032 -10000 0 -0.32 2 2
PRKCB1 -0.047 0.18 -10000 0 -0.37 48 48
GNAQ 0.027 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.019 0.045 -10000 0 -0.32 4 4
TXA2/TXA2-R family -0.076 0.24 -10000 0 -0.52 47 47
LCK -0.023 0.087 0.27 2 -0.25 17 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.015 0.057 -10000 0 -0.18 10 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.002 0.095 -10000 0 -0.44 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.019 0.056 -10000 0 -0.18 8 8
MAPK14 -0.013 0.12 0.23 7 -0.24 41 48
TGM2/GTP -0.054 0.2 -10000 0 -0.42 46 46
MAPK11 -0.023 0.12 0.24 4 -0.24 42 46
ARHGEF1 -0.017 0.088 0.14 5 -0.18 42 47
GNAI2 0.028 0.004 -10000 0 -10000 0 0
JNK cascade -0.048 0.18 0.27 1 -0.38 47 48
RAB11/GDP 0.028 0.005 -10000 0 -10000 0 0
ICAM1 -0.033 0.14 -10000 0 -0.29 45 45
cAMP biosynthetic process -0.046 0.17 0.26 1 -0.35 51 52
Gq family/GTP/EBP50 -0.003 0.068 -10000 0 -0.19 25 25
actin cytoskeleton reorganization 0.033 0.029 -10000 0 -0.18 4 4
SRC -0.011 0.067 0.35 3 -0.19 4 7
GNB5 0.025 0.032 -10000 0 -0.31 2 2
GNB1 0.027 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.03 0.12 0.27 7 -0.27 28 35
VCAM1 -0.038 0.15 -10000 0 -0.32 46 46
TP beta/Gq family/GDP/G beta5/gamma2 -0.009 0.086 -10000 0 -0.33 11 11
platelet activation -0.023 0.16 0.37 2 -0.3 43 45
PGI2/IP 0.019 0.022 -10000 0 -0.22 2 2
PRKACA 0.009 0.044 -10000 0 -0.19 11 11
Gq family/GDP/G beta5/gamma2 -0.007 0.082 -10000 0 -0.31 11 11
TXA2/TP beta/beta Arrestin2 -0.006 0.082 -10000 0 -0.43 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.051 -10000 0 -0.17 19 19
mol:DAG -0.054 0.2 -10000 0 -0.42 48 48
EGFR 0.024 0.061 0.12 16 -0.32 6 22
TXA2/TP alpha -0.067 0.23 -10000 0 -0.48 51 51
Gq family/GTP 0.006 0.042 0.12 1 -0.2 8 9
YES1 -0.014 0.059 0.2 3 -0.2 3 6
GNAI2/GTP 0.004 0.06 -10000 0 -0.18 11 11
PGD2/DP 0.012 0.046 0.09 3 -0.22 9 12
SLC9A3R1 0.027 0.024 0.12 1 -0.32 1 2
FYN -0.007 0.069 0.35 3 -0.22 2 5
mol:NO 0.019 0.045 -10000 0 -0.32 4 4
GNA15 0.019 0.06 -10000 0 -0.32 7 7
PGK/cGMP 0.023 0.049 -10000 0 -0.2 9 9
RhoA/GDP 0.028 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.023 0.076 -10000 0 -0.25 6 6
NOS3 0.019 0.045 -10000 0 -0.32 4 4
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.042 0.17 -10000 0 -0.35 47 47
PRKCB -0.049 0.18 -10000 0 -0.37 47 47
PRKCE -0.041 0.17 0.26 1 -0.35 47 48
PRKCD -0.046 0.18 -10000 0 -0.37 47 47
PRKCG -0.048 0.18 0.29 1 -0.38 47 48
muscle contraction -0.07 0.23 -10000 0 -0.49 48 48
PRKCZ -0.044 0.16 0.28 1 -0.34 47 48
ARR3 0.02 0.011 0.12 2 -10000 0 2
TXA2/TP beta 0.016 0.065 -10000 0 -0.19 11 11
PRKCQ -0.054 0.18 0.26 1 -0.38 48 49
MAPKKK cascade -0.066 0.22 -10000 0 -0.46 49 49
SELE -0.04 0.16 -10000 0 -0.33 45 45
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.07 -10000 0 -0.24 2 2
ROCK1 0.022 0.045 -10000 0 -0.32 4 4
GNA14 0.032 0.05 -10000 0 -0.32 3 3
chemotaxis -0.088 0.27 -10000 0 -0.61 45 45
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.007 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.059 0.18 21 -0.18 2 23
RFC1 0.009 0.063 0.18 23 -0.18 3 26
PRKDC 0.02 0.084 0.21 31 -0.18 3 34
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CASP7 -0.021 0.17 -10000 0 -0.57 18 18
FASLG/FAS/FADD/FAF1 0.001 0.089 0.17 18 -0.23 20 38
MAP2K4 -0.02 0.15 -10000 0 -0.4 23 23
mol:ceramide -0.006 0.12 -10000 0 -0.29 28 28
GSN 0.007 0.061 0.18 21 -0.18 4 25
FASLG/FAS/FADD/FAF1/Caspase 8 -0.003 0.1 0.2 3 -0.28 20 23
FAS 0.02 0.046 -10000 0 -0.31 4 4
BID 0.005 0.084 0.26 22 -10000 0 22
MAP3K1 -0.017 0.14 0.22 2 -0.37 23 25
MAP3K7 0.022 0.033 -10000 0 -0.31 2 2
RB1 0.009 0.063 0.18 23 -0.18 3 26
CFLAR 0.029 0.003 -10000 0 -10000 0 0
HGF/MET 0.016 0.099 -10000 0 -0.2 36 36
ARHGDIB 0.009 0.078 0.2 24 -0.19 7 31
FADD 0.027 0.01 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.061 0.18 4 -0.18 21 25
NFKB1 0 0.11 -10000 0 -0.57 7 7
MAPK8 -0.023 0.16 -10000 0 -0.42 21 21
DFFA 0.009 0.063 0.18 23 -0.18 3 26
DNA fragmentation during apoptosis 0.009 0.063 0.18 22 -0.18 3 25
FAS/FADD/MET 0.024 0.075 -10000 0 -0.19 23 23
CFLAR/RIP1 0.037 0.015 -10000 0 -10000 0 0
FAIM3 -0.005 0.1 0.12 9 -0.32 23 32
FAF1 0.028 0.01 -10000 0 -10000 0 0
PARP1 0.009 0.063 0.18 23 -0.18 3 26
DFFB 0.009 0.063 0.18 22 -0.18 3 25
CHUK -0.008 0.094 -10000 0 -0.51 6 6
FASLG -0.01 0.12 0.13 4 -0.32 29 33
FAS/FADD 0.033 0.038 -10000 0 -0.22 4 4
HGF 0.015 0.077 0.12 13 -0.32 11 24
LMNA 0.004 0.054 0.16 21 -0.17 2 23
CASP6 0.007 0.058 0.18 20 -0.18 2 22
CASP10 0.021 0.051 -10000 0 -0.32 5 5
CASP3 0.017 0.07 0.22 22 -10000 0 22
PTPN13 0.012 0.073 -10000 0 -0.32 11 11
CASP8 0.009 0.097 0.3 23 -10000 0 23
IL6 -0.017 0.21 -10000 0 -0.88 10 10
MET 0.001 0.096 -10000 0 -0.32 19 19
ICAD/CAD 0.006 0.062 0.17 23 -0.17 3 26
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.12 -10000 0 -0.3 28 28
activation of caspase activity by cytochrome c 0.005 0.084 0.26 22 -10000 0 22
PAK2 0.008 0.062 0.18 22 -0.18 3 25
BCL2 0.018 0.059 -10000 0 -0.32 7 7
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.033 0.23 -10000 0 -0.7 21 21
MKNK1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 0.01 0.1 -10000 0 -0.31 21 21
ATF2/c-Jun -0.003 0.09 -10000 0 -0.26 20 20
MAPK11 0.006 0.11 -10000 0 -0.32 23 23
MITF -0.032 0.14 -10000 0 -0.32 35 35
MAPKAPK5 -0.006 0.12 -10000 0 -0.35 22 22
KRT8 -0.023 0.14 -10000 0 -0.32 38 38
MAPKAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.007 0.15 -10000 0 -0.44 22 22
CEBPB -0.008 0.12 -10000 0 -0.35 22 22
SLC9A1 -0.006 0.12 -10000 0 -0.35 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.004 0.12 0.23 1 -0.35 23 24
p38alpha-beta/MNK1 0.022 0.13 -10000 0 -0.36 22 22
JUN 0.002 0.093 -10000 0 -0.26 20 20
PPARGC1A -0.064 0.16 -10000 0 -0.31 57 57
USF1 -0.001 0.11 0.25 1 -0.35 19 20
RAB5/GDP/GDI1 0.005 0.091 -10000 0 -0.26 21 21
NOS2 -0.025 0.2 -10000 0 -0.58 22 22
DDIT3 -0.005 0.12 0.24 1 -0.35 22 23
RAB5A 0.029 0.003 -10000 0 -10000 0 0
HSPB1 0.003 0.12 0.29 14 -0.29 22 36
p38alpha-beta/HBP1 0.019 0.13 -10000 0 -0.38 19 19
CREB1 -0.006 0.13 -10000 0 -0.38 22 22
RAB5/GDP 0.021 0.002 -10000 0 -10000 0 0
EIF4E 0.006 0.12 0.23 2 -0.34 19 21
RPS6KA4 -0.004 0.11 -10000 0 -0.35 21 21
PLA2G4A -0.002 0.11 0.23 1 -0.33 19 20
GDI1 -0.004 0.11 -10000 0 -0.35 21 21
TP53 -0.021 0.14 0.2 3 -0.44 22 25
RPS6KA5 -0.009 0.12 -10000 0 -0.36 23 23
ESR1 -0.015 0.14 -10000 0 -0.39 23 23
HBP1 0.026 0.009 -10000 0 -10000 0 0
MEF2C -0.011 0.13 -10000 0 -0.36 24 24
MEF2A -0.008 0.13 -10000 0 -0.38 22 22
EIF4EBP1 -0.007 0.13 -10000 0 -0.39 22 22
KRT19 -0.007 0.12 -10000 0 -0.35 24 24
ELK4 0 0.1 0.25 1 -0.34 18 19
ATF6 -0.001 0.11 0.25 1 -0.35 19 20
ATF1 -0.006 0.13 -10000 0 -0.38 22 22
p38alpha-beta/MAPKAPK2 0.023 0.12 -10000 0 -0.34 20 20
p38alpha-beta/MAPKAPK3 0.025 0.13 -10000 0 -0.37 19 19
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.04 0.027 -10000 0 -0.22 1 1
alphaV beta3 Integrin -0.014 0.13 -10000 0 -0.23 60 60
PTK2 -0.019 0.16 0.32 11 -0.34 26 37
IGF1R 0.025 0.032 -10000 0 -0.32 2 2
PI4KB 0.026 0.008 -10000 0 -10000 0 0
MFGE8 0.027 0.024 0.12 1 -0.32 1 2
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.008 0.077 -10000 0 -0.36 6 6
VEGFA 0.029 0.019 0.12 7 -10000 0 7
ILK -0.007 0.073 -10000 0 -0.36 5 5
ROCK1 0.022 0.045 -10000 0 -0.32 4 4
AKT1 -0.014 0.065 -10000 0 -0.34 5 5
PTK2B -0.011 0.087 0.2 21 -0.17 23 44
alphaV/beta3 Integrin/JAM-A 0.001 0.13 0.21 2 -0.2 62 64
CBL 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.021 0.088 -10000 0 -0.2 31 31
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.042 0.082 0.19 1 -0.18 27 28
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.081 -10000 0 -0.32 5 5
alphaV/beta3 Integrin/Syndecan-1 0.017 0.098 -10000 0 -0.2 38 38
PI4KA 0.028 0.009 0.12 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1 -0.034 0.14 -10000 0 -0.2 85 85
PI4 Kinase 0.037 0.016 -10000 0 -10000 0 0
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/Osteopontin 0.002 0.12 0.18 2 -0.21 51 53
RPS6KB1 -0.076 0.11 0.24 2 -0.32 20 22
TLN1 0.026 0.009 -10000 0 -10000 0 0
MAPK3 -0.1 0.21 -10000 0 -0.44 58 58
GPR124 0.024 0.032 -10000 0 -0.32 2 2
MAPK1 -0.099 0.2 -10000 0 -0.44 57 57
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/Tumstatin 0.017 0.11 -10000 0 -0.21 42 42
cell adhesion 0.013 0.092 0.18 1 -0.21 31 32
ANGPTL3 0.022 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.032 -10000 0 -0.18 1 1
IGF-1R heterotetramer 0.025 0.032 -10000 0 -0.31 2 2
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
ITGB3 -0.012 0.12 -10000 0 -0.32 30 30
IGF1 0.008 0.086 0.12 4 -0.32 15 19
RAC1 0.025 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.021 0.09 -10000 0 -0.19 32 32
apoptosis 0.023 0.045 -10000 0 -0.31 4 4
CD47 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.024 0.089 -10000 0 -0.2 31 31
VCL 0.027 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.011 0.12 0.18 4 -0.22 45 49
CSF1 0.023 0.039 -10000 0 -0.32 3 3
PIK3C2A -0.018 0.11 -10000 0 -0.45 10 10
PI4 Kinase/Pyk2 -0.012 0.094 -10000 0 -0.2 33 33
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.088 0.19 2 -0.18 28 30
FAK1/Vinculin -0.002 0.14 0.32 11 -0.28 25 36
alphaV beta3/Integrin/ppsTEM5 0.021 0.09 -10000 0 -0.19 32 32
RHOA 0.028 0.004 -10000 0 -10000 0 0
VTN 0.032 0.06 -10000 0 -0.32 5 5
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
FGF2 -0.036 0.14 -10000 0 -0.32 44 44
F11R -0.047 0.082 -10000 0 -0.22 40 40
alphaV/beta3 Integrin/Lactadherin 0.024 0.089 -10000 0 -0.2 31 31
alphaV/beta3 Integrin/TGFBR2 0.026 0.088 -10000 0 -0.2 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.053 0.051 -10000 0 -0.16 9 9
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Talin 0.022 0.08 -10000 0 -0.17 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.012 0.077 -10000 0 -0.32 12 12
alphaV/beta3 Integrin/Pyk2 0.03 0.086 0.18 17 -0.17 28 45
SDC1 0.018 0.065 0.12 5 -0.32 8 13
VAV3 -0.017 0.045 0.18 1 -0.2 7 8
PTPN11 0.029 0.003 -10000 0 -10000 0 0
IRS1 0.011 0.076 -10000 0 -0.32 12 12
FAK1/Paxillin 0 0.15 0.31 12 -0.28 25 37
cell migration -0.004 0.13 0.3 12 -0.26 25 37
ITGAV 0.023 0.045 -10000 0 -0.32 4 4
PI3K 0.009 0.13 0.21 1 -0.2 58 59
SPP1 -0.006 0.11 0.12 11 -0.32 26 37
KDR 0.028 0.025 0.12 3 -0.32 1 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.045 -10000 0 -0.31 4 4
COL4A3 0.018 0.093 0.12 30 -0.32 15 45
angiogenesis -0.099 0.22 0.26 1 -0.45 56 57
Rac1/GTP 0.014 0.049 0.17 1 -0.27 2 3
EDIL3 0.004 0.11 -10000 0 -0.32 24 24
cell proliferation 0.025 0.088 -10000 0 -0.19 30 30
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.007 0.078 -10000 0 -0.18 32 32
cell-cell adhesion 0.038 0.064 0.16 39 -10000 0 39
Ephrin B/EPHB2/RasGAP 0.042 0.097 -10000 0 -0.16 38 38
ITSN1 0.028 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
SHC1 0.026 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.027 0.054 -10000 0 -0.18 14 14
Ephrin B1/EPHB1 0.035 0.05 -10000 0 -0.18 10 10
HRAS/GDP 0.004 0.096 0.19 1 -0.21 28 29
Ephrin B/EPHB1/GRB7 0.052 0.099 0.25 1 -0.16 35 36
Endophilin/SYNJ1 -0.029 0.059 0.18 3 -0.26 1 4
KRAS 0.028 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.044 0.095 0.21 4 -0.16 32 36
endothelial cell migration 0.042 0.055 -10000 0 -0.17 11 11
GRB2 0.028 0.005 -10000 0 -10000 0 0
GRB7 0.033 0.036 0.12 20 -0.32 1 21
PAK1 -0.033 0.063 0.18 2 -0.28 2 4
HRAS 0.028 0.006 -10000 0 -10000 0 0
RRAS -0.03 0.058 0.18 2 -0.27 1 3
DNM1 0.024 0.042 -10000 0 -0.32 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.025 0.062 0.18 5 -0.16 28 33
lamellipodium assembly -0.038 0.064 -10000 0 -0.16 39 39
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.072 -10000 0 -0.17 26 26
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
EPHB2 0.008 0.082 -10000 0 -0.32 14 14
EPHB3 0.01 0.083 -10000 0 -0.32 14 14
EPHB1 0.022 0.077 0.12 23 -0.32 10 33
EPHB4 0.013 0.066 -10000 0 -0.32 9 9
mol:GDP -0.021 0.089 0.23 5 -0.22 26 31
Ephrin B/EPHB2 0.033 0.089 0.18 2 -0.16 36 38
Ephrin B/EPHB3 0.031 0.089 0.18 2 -0.16 39 41
JNK cascade -0.023 0.063 0.27 4 -0.18 19 23
Ephrin B/EPHB1 0.038 0.09 0.19 4 -0.16 34 38
RAP1/GDP 0.009 0.11 0.23 15 -0.21 27 42
EFNB2 0.031 0.018 0.12 8 -10000 0 8
EFNB3 -0.002 0.11 0.12 19 -0.32 25 44
EFNB1 0.03 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.037 0.075 0.17 3 -0.18 21 24
RAP1B 0.028 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.11 0.2 1 -0.2 36 37
Rap1/GTP -0.004 0.074 -10000 0 -0.16 38 38
axon guidance 0.007 0.077 -10000 0 -0.18 32 32
MAPK3 0 0.073 0.2 8 -0.24 2 10
MAPK1 0.003 0.075 0.2 10 -0.18 7 17
Rac1/GDP -0.012 0.096 0.25 6 -0.22 25 31
actin cytoskeleton reorganization -0.039 0.065 -10000 0 -0.18 31 31
CDC42/GDP 0.001 0.11 0.23 16 -0.21 27 43
PI3K 0.047 0.057 -10000 0 -0.17 11 11
EFNA5 0 0.095 -10000 0 -0.32 19 19
Ephrin B2/EPHB4 0.028 0.046 -10000 0 -0.18 9 9
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.087 -10000 0 -0.19 39 39
CDC42 0.028 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.008 0.071 -10000 0 -0.16 38 38
PTK2 0.052 0.18 0.56 24 -10000 0 24
MAP4K4 -0.023 0.063 0.27 4 -0.18 19 23
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.026 0.043 0.12 7 -0.32 3 10
Intersectin/N-WASP 0.037 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.005 0.13 0.3 21 -0.27 8 29
MAP2K1 0.001 0.072 0.23 3 -0.18 12 15
WASL 0.026 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.052 0.08 -10000 0 -0.18 21 21
cell migration 0.003 0.1 0.22 14 -0.2 25 39
NRAS 0.028 0.006 -10000 0 -10000 0 0
SYNJ1 -0.029 0.06 0.18 3 -0.27 1 4
PXN 0.029 0.003 -10000 0 -10000 0 0
TF -0.05 0.085 0.17 3 -0.28 10 13
HRAS/GTP 0.017 0.089 0.18 2 -0.16 41 43
Ephrin B1/EPHB1-2 0.037 0.073 -10000 0 -0.18 21 21
cell adhesion mediated by integrin 0.028 0.051 0.16 24 -0.19 2 26
RAC1 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0.02 0.095 0.21 2 -0.16 46 48
RAC1-CDC42/GTP -0.043 0.067 -10000 0 -0.16 43 43
RASA1 0.024 0.032 -10000 0 -0.32 2 2
RAC1-CDC42/GDP -0.003 0.098 0.25 6 -0.21 24 30
ruffle organization -0.007 0.12 0.32 17 -0.25 7 24
NCK1 0.028 0.006 -10000 0 -10000 0 0
receptor internalization -0.032 0.056 0.17 3 -0.26 2 5
Ephrin B/EPHB2/KALRN 0.043 0.1 -10000 0 -0.16 38 38
ROCK1 0.002 0.05 0.18 2 -0.17 17 19
RAS family/GDP -0.044 0.064 -10000 0 -0.18 33 33
Rac1/GTP -0.037 0.069 -10000 0 -0.17 39 39
Ephrin B/EPHB1/Src/Paxillin 0 0.082 -10000 0 -0.19 33 33
Glypican 2 network

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
MDK 0.012 0.081 0.12 7 -0.32 13 20
GPC2 0.011 0.074 0.12 3 -0.32 11 14
GPC2/Midkine 0.014 0.085 -10000 0 -0.23 22 22
neuron projection morphogenesis 0.014 0.084 -10000 0 -0.23 22 22
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
CDC42/GTP -0.02 0.11 -10000 0 -0.22 42 42
PLCG1 -0.03 0.1 0.22 1 -0.21 48 49
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.015 -10000 0 -10000 0 0
cell migration -0.02 0.11 -10000 0 -0.21 42 42
S1PR5 0.027 0.043 0.12 8 -0.32 3 11
S1PR4 0.007 0.092 0.12 8 -0.32 17 25
MAPK3 -0.031 0.11 -10000 0 -0.2 52 52
MAPK1 -0.03 0.11 0.22 1 -0.2 52 53
S1P/S1P5/Gi -0.016 0.1 -10000 0 -0.2 45 45
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
CDC42/GDP 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.034 0.027 -10000 0 -0.18 2 2
RHOA 0.004 0.08 0.19 29 -0.16 13 42
S1P/S1P4/Gi -0.026 0.11 -10000 0 -0.21 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
S1P/S1P4/G12/G13 0.036 0.056 -10000 0 -0.16 14 14
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.005 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.036 0.1 0.19 3 -0.23 26 29
MAP4K1 0.011 0.081 -10000 0 -0.32 13 13
MAP3K8 0.023 0.042 -10000 0 -0.32 3 3
PRKCB -0.002 0.11 0.12 12 -0.32 24 36
DBNL 0.025 0.01 -10000 0 -10000 0 0
CRKL 0.028 0.009 0.12 1 -10000 0 1
MAP3K1 -0.015 0.11 -10000 0 -0.34 17 17
JUN -0.085 0.27 -10000 0 -0.64 41 41
MAP3K7 -0.009 0.11 -10000 0 -0.35 15 15
GRAP2 0.012 0.074 0.12 3 -0.32 11 14
CRK 0.027 0.007 -10000 0 -10000 0 0
MAP2K4 -0.011 0.12 0.22 6 -0.37 17 23
LAT 0.014 0.083 0.12 11 -0.32 13 24
LCP2 0.018 0.055 -10000 0 -0.32 6 6
MAPK8 -0.087 0.29 -10000 0 -0.67 41 41
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.005 0.12 -10000 0 -0.35 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.041 0.1 -10000 0 -0.22 25 25
Glucocorticoid receptor regulatory network

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
PCK2 0.045 0.084 -10000 0 -10000 0 0
SMARCC2 0.028 0.017 -10000 0 -0.12 3 3
SMARCC1 0.027 0.018 -10000 0 -0.12 3 3
TBX21 -0.075 0.21 0.49 1 -0.56 29 30
SUMO2 0.03 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.04 -10000 0 -0.23 5 5
FKBP4 0.028 0.005 -10000 0 -10000 0 0
FKBP5 0.007 0.079 0.12 1 -0.32 13 14
GR alpha/HSP90/FKBP51/HSP90 0.049 0.11 0.24 28 -0.23 4 32
PRL -0.009 0.084 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.091 0.22 0.46 42 -0.44 1 43
RELA 0.01 0.075 -10000 0 -0.17 25 25
FGG 0.082 0.19 0.4 38 -0.3 1 39
GR beta/TIF2 0.045 0.12 0.24 36 -0.28 4 40
IFNG -0.22 0.39 -10000 0 -0.87 53 53
apoptosis 0.041 0.14 0.52 13 -10000 0 13
CREB1 0.031 0.006 -10000 0 -10000 0 0
histone acetylation 0.003 0.12 0.34 12 -0.28 11 23
BGLAP -0.022 0.099 -10000 0 -0.36 2 2
GR/PKAc 0.067 0.11 0.25 24 -0.22 5 29
NF kappa B1 p50/RelA 0.02 0.13 -10000 0 -0.28 30 30
SMARCD1 0.028 0.013 -10000 0 -0.1 2 2
MDM2 0.049 0.083 0.18 50 -10000 0 50
GATA3 -0.004 0.11 -10000 0 -0.31 24 24
AKT1 0.025 0.005 -10000 0 -10000 0 0
CSF2 -0.021 0.098 -10000 0 -0.36 2 2
GSK3B 0.029 0.01 -10000 0 -10000 0 0
NR1I3 0.066 0.16 0.52 16 -10000 0 16
CSN2 0.066 0.16 0.34 38 -0.27 1 39
BRG1/BAF155/BAF170/BAF60A 0.071 0.044 -10000 0 -0.28 3 3
NFATC1 0.019 0.059 -10000 0 -0.32 7 7
POU2F1 0.03 0.012 -10000 0 -10000 0 0
CDKN1A -0.012 0.21 -10000 0 -1.4 5 5
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.009 -10000 0 -10000 0 0
SFN 0.028 0.089 0.12 44 -0.32 12 56
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.06 0.11 0.25 23 -0.19 7 30
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.055 0.15 0.46 15 -0.74 1 16
JUN -0.083 0.16 -10000 0 -0.35 36 36
IL4 -0.053 0.12 -10000 0 -0.38 12 12
CDK5R1 0.02 0.055 -10000 0 -0.32 6 6
PRKACA 0.029 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.035 0.11 0.2 24 -0.23 23 47
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.063 0.11 0.25 24 -0.21 4 28
cortisol/GR alpha (monomer) 0.12 0.25 0.51 50 -0.34 1 51
NCOA2 0.02 0.045 -10000 0 -0.32 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.016 0.084 0.18 1 -0.16 5 6
AP-1/NFAT1-c-4 -0.14 0.27 -10000 0 -0.47 73 73
AFP -0.079 0.13 -10000 0 -10000 0 0
SUV420H1 0.026 0.023 -10000 0 -0.32 1 1
IRF1 0.072 0.14 0.35 17 -0.58 2 19
TP53 0.025 0.082 -10000 0 -0.46 6 6
PPP5C 0.028 0.004 -10000 0 -10000 0 0
KRT17 -0.16 0.32 -10000 0 -0.74 41 41
KRT14 -0.21 0.45 -10000 0 -1.2 41 41
TBP 0.03 0.013 -10000 0 -10000 0 0
CREBBP 0.056 0.11 0.29 37 -0.27 1 38
HDAC1 0.026 0.023 -10000 0 -0.32 1 1
HDAC2 0.024 0.01 -10000 0 -10000 0 0
AP-1 -0.14 0.27 -10000 0 -0.48 73 73
MAPK14 0.026 0.012 -10000 0 -10000 0 0
MAPK10 0.023 0.08 0.12 24 -0.31 11 35
MAPK11 0.022 0.045 -10000 0 -0.31 4 4
KRT5 -0.22 0.41 -10000 0 -0.94 50 50
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.029 0.006 -10000 0 -10000 0 0
STAT1 0.029 0.04 -10000 0 -0.23 5 5
CGA -0.038 0.11 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.055 0.14 0.33 34 -0.26 1 35
MAPK3 0.03 0.01 -10000 0 -10000 0 0
MAPK1 0.029 0.01 -10000 0 -10000 0 0
ICAM1 -0.075 0.21 -10000 0 -0.64 17 17
NFKB1 0.008 0.082 -10000 0 -0.18 28 28
MAPK8 -0.064 0.14 -10000 0 -0.3 38 38
MAPK9 0.029 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.037 0.14 0.52 12 -10000 0 12
BAX -0.004 0.074 -10000 0 -0.38 3 3
POMC -0.12 0.35 -10000 0 -1.3 16 16
EP300 0.052 0.11 0.3 34 -0.27 1 35
cortisol/GR alpha (dimer)/p53 0.099 0.22 0.46 44 -10000 0 44
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.072 0.18 22 -10000 0 22
SGK1 0.047 0.19 0.5 1 -1 3 4
IL13 -0.14 0.25 -10000 0 -0.63 31 31
IL6 -0.05 0.18 -10000 0 -0.56 16 16
PRKACG 0.018 0.007 -10000 0 -10000 0 0
IL5 -0.13 0.22 -10000 0 -0.63 21 21
IL2 -0.13 0.23 -10000 0 -0.56 33 33
CDK5 0.026 0.011 -10000 0 -10000 0 0
PRKACB 0.024 0.039 -10000 0 -0.32 3 3
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
IL8 -0.08 0.22 -10000 0 -0.59 24 24
CDK5R1/CDK5 0.031 0.045 -10000 0 -0.22 6 6
NF kappa B1 p50/RelA/PKAc 0.044 0.12 -10000 0 -0.25 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.21 0.44 50 -10000 0 50
SMARCA4 0.028 0.017 -10000 0 -0.12 3 3
chromatin remodeling 0.073 0.14 0.32 33 -0.3 1 34
NF kappa B1 p50/RelA/Cbp 0.07 0.15 0.36 25 -0.27 10 35
JUN (dimer) -0.084 0.16 -10000 0 -0.35 37 37
YWHAH 0.027 0.007 -10000 0 -10000 0 0
VIPR1 -0.042 0.15 0.53 1 -0.41 17 18
NR3C1 0.07 0.16 0.33 45 -0.34 2 47
NR4A1 -0.003 0.14 -10000 0 -0.46 18 18
TIF2/SUV420H1 0.032 0.04 -10000 0 -0.22 5 5
MAPKKK cascade 0.041 0.14 0.52 13 -10000 0 13
cortisol/GR alpha (dimer)/Src-1 0.11 0.22 0.46 47 -10000 0 47
PBX1 0.036 0.028 -10000 0 -10000 0 0
POU1F1 0.023 0.009 -10000 0 -10000 0 0
SELE -0.098 0.27 -10000 0 -0.72 30 30
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.14 0.32 33 -0.3 1 34
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.21 0.44 50 -10000 0 50
mol:cortisol 0.065 0.14 0.28 51 -10000 0 51
MMP1 -0.16 0.39 -10000 0 -0.99 39 39
IL27-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
TGFB1 0.023 0.045 -10000 0 -0.32 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.098 0.24 0.6 32 -10000 0 32
IL27/IL27R/JAK1 -0.056 0.26 -10000 0 -0.89 16 16
TBX21 -0.097 0.19 -10000 0 -0.51 30 30
IL12B 0.021 0.027 0.13 7 -10000 0 7
IL12A -0.01 0.056 -10000 0 -0.22 15 15
IL6ST -0.002 0.079 -10000 0 -0.32 12 12
IL27RA/JAK1 -0.053 0.26 -10000 0 -1.1 13 13
IL27 0.005 0.069 -10000 0 -0.32 8 8
TYK2 0.017 0.027 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.033 0.097 0.42 5 -0.49 1 6
T-helper 2 cell differentiation 0.098 0.24 0.6 32 -10000 0 32
T cell proliferation during immune response 0.098 0.24 0.6 32 -10000 0 32
MAPKKK cascade -0.098 0.24 -10000 0 -0.6 32 32
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT2 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.032 -10000 0 -0.31 2 2
IL12RB1 -0.011 0.11 0.13 5 -0.32 26 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.11 0.2 -10000 0 -0.47 40 40
IL27/IL27R/JAK2/TYK2 -0.1 0.25 -10000 0 -0.61 32 32
positive regulation of T cell mediated cytotoxicity -0.098 0.24 -10000 0 -0.6 32 32
STAT1 (dimer) -0.076 0.28 0.51 1 -0.68 27 28
JAK2 0.008 0.054 -10000 0 -0.32 5 5
JAK1 0.028 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.084 0.24 -10000 0 -0.58 31 31
T cell proliferation -0.094 0.24 0.29 1 -0.6 29 30
IL12/IL12R/TYK2/JAK2 -0.079 0.24 -10000 0 -0.78 17 17
IL17A 0.033 0.097 0.42 5 -0.49 1 6
mast cell activation 0.098 0.24 0.6 32 -10000 0 32
IFNG -0.022 0.055 -10000 0 -0.12 46 46
T cell differentiation -0.006 0.009 -10000 0 -0.022 47 47
STAT3 (dimer) -0.087 0.24 -10000 0 -0.58 32 32
STAT5A (dimer) -0.088 0.24 -10000 0 -0.58 32 32
STAT4 (dimer) -0.094 0.26 -10000 0 -0.59 36 36
STAT4 0.004 0.097 -10000 0 -0.32 19 19
T cell activation -0.002 0.022 0.12 7 -0.043 1 8
IL27R/JAK2/TYK2 -0.052 0.25 -10000 0 -0.89 16 16
GATA3 -0.16 0.42 -10000 0 -1.2 33 33
IL18 -0.006 0.047 -10000 0 -0.22 11 11
positive regulation of mast cell cytokine production -0.085 0.24 -10000 0 -0.56 32 32
IL27/EBI3 0.002 0.096 0.19 1 -0.26 23 24
IL27RA -0.068 0.27 -10000 0 -1.2 13 13
IL6 0.027 0.053 -10000 0 -0.32 4 4
STAT5A 0.027 0.023 -10000 0 -0.32 1 1
monocyte differentiation -0.001 0.003 -10000 0 -0.011 3 3
IL2 0.021 0.12 0.5 13 -10000 0 13
IL1B -0.009 0.059 -10000 0 -0.22 17 17
EBI3 -0.007 0.096 -10000 0 -0.31 20 20
TNF -0.005 0.048 -10000 0 -0.22 11 11
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.007 0.085 0.31 15 -0.12 3 18
PI3K Class IB/PDE3B 0.007 0.085 0.12 3 -0.31 15 18
PDE3B 0.007 0.085 0.12 3 -0.32 15 18
Caspase cascade in apoptosis

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
TOP1 -0.023 0.14 -10000 0 -0.4 22 22
ACTA1 -0.045 0.16 0.18 2 -0.4 30 32
NUMA1 -0.029 0.16 -10000 0 -0.44 23 23
SPTAN1 -0.051 0.15 -10000 0 -0.4 30 30
LIMK1 -0.034 0.16 0.19 16 -0.41 27 43
BIRC3 -0.008 0.11 -10000 0 -0.32 27 27
BIRC2 0.019 0.05 -10000 0 -0.32 5 5
BAX 0.028 0.004 -10000 0 -10000 0 0
CASP10 -0.041 0.099 -10000 0 -0.29 28 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.032 -10000 0 -0.32 2 2
PTK2 -0.028 0.15 -10000 0 -0.42 23 23
DIABLO 0.029 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.05 0.15 -10000 0 -0.39 30 30
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.007 0.12 1 -10000 0 1
GSN -0.052 0.16 -10000 0 -0.41 30 30
MADD 0.028 0.005 -10000 0 -10000 0 0
TFAP2A -0.057 0.22 -10000 0 -0.55 35 35
BID -0.012 0.061 -10000 0 -0.19 21 21
MAP3K1 -0.027 0.12 -10000 0 -0.46 13 13
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.031 -10000 0 -0.22 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.052 0.16 0.23 3 -0.42 30 33
CASP9 0.028 0.006 -10000 0 -10000 0 0
DNA repair -0.002 0.064 0.2 6 -0.2 3 9
neuron apoptosis -0.026 0.18 -10000 0 -0.64 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.042 0.17 0.23 3 -0.49 23 26
APAF1 0.024 0.039 -10000 0 -0.31 3 3
CASP6 -0.011 0.16 -10000 0 -0.72 7 7
TRAF2 0.027 0.008 -10000 0 -10000 0 0
ICAD/CAD -0.049 0.16 0.3 4 -0.39 30 34
CASP7 0.008 0.12 0.29 13 -0.33 5 18
KRT18 -0.034 0.18 -10000 0 -0.56 23 23
apoptosis -0.039 0.13 -10000 0 -0.4 21 21
DFFA -0.049 0.16 0.19 3 -0.4 30 33
DFFB -0.05 0.16 0.23 3 -0.4 30 33
PARP1 0.002 0.064 0.2 3 -0.2 6 9
actin filament polymerization 0.037 0.15 0.39 27 -0.18 13 40
TNF 0.013 0.076 0.12 10 -0.32 11 21
CYCS -0.007 0.054 -10000 0 -0.16 19 19
SATB1 -0.026 0.17 -10000 0 -0.61 11 11
SLK -0.051 0.15 -10000 0 -0.39 31 31
p15 BID/BAX -0.006 0.079 -10000 0 -0.18 35 35
CASP2 0.001 0.1 0.21 16 -0.29 13 29
JNK cascade 0.026 0.12 0.45 13 -10000 0 13
CASP3 -0.051 0.16 0.16 1 -0.42 30 31
LMNB2 0.02 0.12 0.26 7 -0.38 11 18
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CASP4 0.025 0.024 -10000 0 -0.32 1 1
Mammalian IAPs/DIABLO 0.038 0.096 -10000 0 -0.2 28 28
negative regulation of DNA binding -0.051 0.22 -10000 0 -0.55 35 35
stress fiber formation -0.05 0.15 -10000 0 -0.38 31 31
GZMB -0.036 0.11 0.083 10 -0.31 27 37
CASP1 0.001 0.061 -10000 0 -0.27 10 10
LMNB1 0.008 0.16 0.26 7 -0.46 16 23
APP -0.027 0.18 -10000 0 -0.65 17 17
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.005 -10000 0 -10000 0 0
VIM -0.033 0.13 -10000 0 -0.38 22 22
LMNA 0.019 0.12 0.26 6 -0.38 11 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.01 0.096 -10000 0 -0.31 14 14
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.15 -10000 0 -0.39 30 30
APAF-1/Caspase 9 0.021 0.1 0.39 2 -0.63 4 6
nuclear fragmentation during apoptosis -0.028 0.15 -10000 0 -0.43 23 23
CFL2 -0.038 0.16 0.18 13 -0.4 27 40
GAS2 -0.06 0.16 0.31 1 -0.39 33 34
positive regulation of apoptosis 0.02 0.14 0.26 7 -0.4 13 20
PRF1 0.003 0.1 0.12 14 -0.32 20 34
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.001 0.093 0.12 4 -0.32 18 22
GNB1/GNG2 -0.005 0.14 0.2 1 -0.36 15 16
mol:DAG -0.025 0.11 0.2 1 -0.32 14 15
PLCG1 -0.026 0.11 0.2 1 -0.33 14 15
YES1 -0.032 0.11 0.14 1 -0.23 38 39
FZD3 0.025 0.024 -10000 0 -0.32 1 1
FZD6 0.007 0.079 -10000 0 -0.32 13 13
G protein -0.001 0.13 0.25 6 -0.33 14 20
MAP3K7 -0.036 0.091 0.16 2 -0.29 14 16
mol:Ca2+ -0.025 0.1 0.2 1 -0.31 14 15
mol:IP3 -0.025 0.11 0.2 1 -0.32 14 15
NLK -0.005 0.12 -10000 0 -0.78 5 5
GNB1 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.031 0.1 0.17 2 -0.3 15 17
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.024 0.12 0.15 1 -0.22 49 50
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
GNAS -0.023 0.1 0.21 4 -0.22 36 40
GO:0007205 -0.029 0.1 0.2 3 -0.32 14 17
WNT6 0.027 0.056 -10000 0 -0.32 5 5
WNT4 -0.004 0.12 0.12 20 -0.32 27 47
NFAT1/CK1 alpha -0.014 0.13 0.25 6 -0.3 18 24
GNG2 0.015 0.066 -10000 0 -0.32 9 9
WNT5A 0.02 0.08 -10000 0 -0.32 11 11
WNT11 0.011 0.081 0.12 7 -0.32 13 20
CDC42 -0.03 0.11 0.18 3 -0.38 10 13
HIF-1-alpha transcription factor network

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
PKM2 -0.003 0.26 0.38 1 -0.6 23 24
HDAC7 0.028 0.023 -10000 0 -0.31 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.04 0.26 -10000 0 -0.52 22 22
SMAD4 0.029 0.004 -10000 0 -10000 0 0
ID2 -0.003 0.26 0.38 1 -0.6 23 24
AP1 0.042 0.024 -10000 0 -0.096 1 1
ABCG2 -0.006 0.27 0.38 1 -0.62 23 24
HIF1A 0.016 0.067 -10000 0 -0.13 15 15
TFF3 -0.013 0.28 0.38 1 -0.62 26 27
GATA2 0.019 0.063 0.13 1 -0.32 7 8
AKT1 0.016 0.075 -10000 0 -0.16 12 12
response to hypoxia 0 0.059 -10000 0 -0.13 20 20
MCL1 -0.014 0.25 -10000 0 -0.6 22 22
NDRG1 0.002 0.25 0.38 1 -0.59 22 23
SERPINE1 -0.005 0.26 0.38 1 -0.62 23 24
FECH -0.001 0.26 0.38 1 -0.59 23 24
FURIN -0.006 0.25 0.38 1 -0.61 22 23
NCOA2 0.021 0.045 -10000 0 -0.32 4 4
EP300 0.018 0.086 -10000 0 -0.28 9 9
HMOX1 -0.002 0.26 0.38 1 -0.62 22 23
BHLHE40 -0.002 0.26 0.38 1 -0.6 23 24
BHLHE41 -0.009 0.26 0.38 1 -0.62 23 24
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.065 0.11 -10000 0 -0.21 5 5
ENG 0.023 0.084 0.24 7 -0.22 1 8
JUN 0.027 0.013 -10000 0 -10000 0 0
RORA -0.004 0.26 0.38 1 -0.61 23 24
ABCB1 -0.019 0.24 -10000 0 -0.94 12 12
TFRC 0 0.26 0.38 1 -0.61 22 23
CXCR4 -0.004 0.27 0.38 1 -0.6 25 26
TF -0.015 0.3 0.38 1 -0.64 28 29
CITED2 -0.001 0.26 0.38 1 -0.6 22 23
HIF1A/ARNT 0.054 0.34 0.55 5 -0.72 18 23
LDHA 0.021 0.12 -10000 0 -0.66 5 5
ETS1 -0.001 0.26 0.38 1 -0.6 22 23
PGK1 -0.001 0.26 0.38 1 -0.6 23 24
NOS2 -0.002 0.26 0.38 1 -0.61 24 25
ITGB2 -0.006 0.27 0.38 1 -0.62 24 25
ALDOA -0.002 0.26 0.38 1 -0.61 22 23
Cbp/p300/CITED2 0.006 0.28 0.4 1 -0.61 25 26
FOS 0.03 0.022 -10000 0 -10000 0 0
HK2 -0.003 0.26 0.38 1 -0.61 22 23
SP1 0.028 0.03 -10000 0 -0.11 10 10
GCK 0.014 0.24 -10000 0 -1.2 7 7
HK1 -0.002 0.26 0.38 1 -0.59 23 24
NPM1 -0.003 0.26 0.38 1 -0.6 23 24
EGLN1 -0.011 0.25 -10000 0 -0.59 22 22
CREB1 0.033 0.01 -10000 0 -0.12 1 1
PGM1 -0.005 0.26 0.38 1 -0.62 22 23
SMAD3 0.026 0.032 -10000 0 -0.31 2 2
EDN1 0.002 0.23 0.43 1 -0.98 9 10
IGFBP1 -0.006 0.25 0.45 1 -0.58 23 24
VEGFA 0.018 0.21 0.42 1 -0.46 21 22
HIF1A/JAB1 0.03 0.054 -10000 0 -0.14 1 1
CP -0.016 0.28 0.38 1 -0.59 29 30
CXCL12 -0.009 0.27 0.38 1 -0.62 24 25
COPS5 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.04 0.026 -10000 0 -0.22 2 2
BNIP3 -0.004 0.25 -10000 0 -0.6 22 22
EGLN3 -0.003 0.26 0.38 1 -0.63 22 23
CA9 -0.008 0.27 0.45 1 -0.58 28 29
TERT -0.01 0.26 0.38 1 -0.6 25 26
ENO1 -0.005 0.26 0.38 1 -0.61 22 23
PFKL 0 0.26 0.38 1 -0.61 22 23
NCOA1 0.028 0.006 -10000 0 -10000 0 0
ADM -0.007 0.27 0.38 1 -0.62 24 25
ARNT 0.016 0.064 -10000 0 -0.14 8 8
HNF4A 0.024 0.028 -10000 0 -0.11 6 6
ADFP -0.019 0.25 0.34 3 -0.56 26 29
SLC2A1 0.02 0.22 0.36 1 -0.47 23 24
LEP -0.001 0.25 0.38 1 -0.61 22 23
HIF1A/ARNT/Cbp/p300 0.036 0.27 -10000 0 -0.53 23 23
EPO 0.023 0.18 -10000 0 -0.52 8 8
CREBBP 0.019 0.088 -10000 0 -0.27 9 9
HIF1A/ARNT/Cbp/p300/HDAC7 0.049 0.27 -10000 0 -0.53 21 21
PFKFB3 -0.002 0.26 0.38 1 -0.6 22 23
NT5E -0.001 0.27 0.45 1 -0.64 22 23
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.011 -10000 0 -10000 0 0
ITGB7 0.011 0.076 -10000 0 -0.32 12 12
ITGA4 0.002 0.098 0.12 6 -0.32 20 26
alpha4/beta7 Integrin 0.009 0.092 -10000 0 -0.22 31 31
alpha4/beta1 Integrin 0.019 0.074 -10000 0 -0.21 20 20
Signaling events mediated by PTP1B

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.024 0.032 -10000 0 -0.32 2 2
Jak2/Leptin Receptor -0.051 0.19 -10000 0 -0.41 42 42
PTP1B/AKT1 -0.014 0.1 0.28 1 -0.25 23 24
FYN 0.025 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.026 0.1 0.24 2 -0.27 23 25
EGFR 0.014 0.065 0.13 11 -0.32 6 17
EGF/EGFR -0.033 0.13 0.22 1 -0.25 43 44
CSF1 0.023 0.039 -10000 0 -0.32 3 3
AKT1 0.028 0.006 -10000 0 -10000 0 0
INSR 0.027 0.023 -10000 0 -0.32 1 1
PTP1B/N-cadherin -0.031 0.12 0.23 2 -0.25 42 44
Insulin Receptor/Insulin 0 0.098 0.26 1 -0.26 14 15
HCK 0.012 0.07 -10000 0 -0.32 10 10
CRK 0.027 0.007 -10000 0 -10000 0 0
TYK2 -0.027 0.1 0.26 2 -0.27 22 24
EGF -0.03 0.14 0.13 18 -0.32 43 61
YES1 0.021 0.045 -10000 0 -0.32 4 4
CAV1 -0.019 0.12 0.27 6 -0.3 20 26
TXN 0.026 0.008 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.016 0.11 -10000 0 -0.25 26 26
cell migration 0.026 0.1 0.27 23 -0.24 2 25
STAT3 0.028 0.005 -10000 0 -10000 0 0
PRLR 0.011 0.11 0.12 34 -0.32 20 54
ITGA2B 0.02 0.074 -10000 0 -0.32 9 9
CSF1R 0.018 0.055 0.12 1 -0.32 6 7
Prolactin Receptor/Prolactin 0.023 0.081 0.18 2 -0.22 19 21
FGR 0.016 0.067 0.12 3 -0.32 9 12
PTP1B/p130 Cas -0.015 0.1 0.29 1 -0.26 23 24
Crk/p130 Cas -0.007 0.11 0.29 1 -0.26 19 20
DOK1 -0.025 0.11 0.28 1 -0.28 22 23
JAK2 -0.059 0.2 0.29 1 -0.43 40 41
Jak2/Leptin Receptor/Leptin -0.022 0.14 -10000 0 -0.33 25 25
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
PTPN1 -0.026 0.1 0.24 2 -0.27 23 25
LYN 0.024 0.033 -10000 0 -0.32 2 2
CDH2 -0.039 0.15 0.12 19 -0.32 51 70
SRC 0.018 0.049 -10000 0 -0.35 1 1
ITGB3 -0.013 0.12 0.13 2 -0.32 30 32
CAT1/PTP1B -0.036 0.18 0.28 9 -0.42 28 37
CAPN1 0.026 0.023 -10000 0 -0.32 1 1
CSK 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.012 0.1 0.24 1 -0.25 15 16
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.019 0.13 -10000 0 -0.32 21 21
negative regulation of transcription -0.058 0.19 0.29 1 -0.42 40 41
FCGR2A 0.022 0.04 0.12 1 -0.32 3 4
FER 0.021 0.046 -10000 0 -0.32 4 4
alphaIIb/beta3 Integrin 0.004 0.11 0.18 2 -0.23 38 40
BLK 0.002 0.12 0.12 35 -0.32 26 61
Insulin Receptor/Insulin/Shc 0.043 0.024 -10000 0 -0.19 1 1
RHOA 0.028 0.004 -10000 0 -10000 0 0
LEPR 0.022 0.051 0.12 2 -0.31 5 7
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
p210 bcr-abl/Grb2 0.028 0.005 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.046 0.21 0.25 5 -0.47 33 38
PRL 0.016 0.033 -10000 0 -10000 0 0
SOCS3 -0.003 0.21 -10000 0 -1.4 5 5
SPRY2 0.027 0.025 0.12 1 -0.32 1 2
Insulin Receptor/Insulin/IRS1 0.035 0.056 -10000 0 -0.19 13 13
CSF1/CSF1R -0.01 0.11 -10000 0 -0.27 23 23
Ras protein signal transduction 0.011 0.094 0.58 5 -10000 0 5
IRS1 0.011 0.076 -10000 0 -0.32 12 12
INS 0.008 0.016 -10000 0 -10000 0 0
LEP 0.027 0.048 0.12 24 -0.32 2 26
STAT5B -0.035 0.14 0.31 1 -0.32 30 31
STAT5A -0.035 0.14 0.31 1 -0.32 29 30
GRB2 0.028 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.013 0.11 0.29 1 -0.26 23 24
CSN2 0.014 0.063 -10000 0 -10000 0 0
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
LAT -0.015 0.15 -10000 0 -0.49 17 17
YBX1 0.035 0.007 -10000 0 -10000 0 0
LCK -0.014 0.12 0.12 13 -0.32 32 45
SHC1 0.026 0.008 -10000 0 -10000 0 0
NOX4 -0.006 0.11 0.12 5 -0.32 23 28
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.005 0.087 -10000 0 -0.32 16 16
positive regulation of NF-kappaB transcription factor activity 0.024 0.079 -10000 0 -0.21 21 21
MAP2K4 -0.01 0.098 -10000 0 -0.31 16 16
IKBKB 0.028 0.006 -10000 0 -10000 0 0
TNFRSF10B 0.008 0.079 -10000 0 -0.32 13 13
TNFRSF10A -0.001 0.1 0.12 12 -0.32 22 34
SMPD1 -0.007 0.054 -10000 0 -0.15 28 28
IKBKG 0.029 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.03 0.06 0.12 25 -0.32 5 30
TRAIL/TRAILR2 0.008 0.087 -10000 0 -0.22 28 28
TRAIL/TRAILR3 0.004 0.098 -10000 0 -0.23 32 32
TRAIL/TRAILR1 0.003 0.11 -10000 0 -0.25 32 32
TRAIL/TRAILR4 0.024 0.079 -10000 0 -0.22 21 21
TRAIL/TRAILR1/DAP3/GTP 0.022 0.081 -10000 0 -0.18 28 28
IKK complex 0.003 0.084 -10000 0 -0.29 10 10
RIPK1 0.025 0.01 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.006 -10000 0 -10000 0 0
MAPK3 -0.026 0.052 -10000 0 -0.22 16 16
MAP3K1 -0.015 0.1 -10000 0 -0.29 22 22
TRAILR4 (trimer) 0.03 0.06 0.12 25 -0.31 5 30
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.001 0.1 0.12 12 -0.31 22 34
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.012 0.096 -10000 0 -0.23 33 33
CFLAR 0.029 0.002 -10000 0 -10000 0 0
MAPK1 -0.025 0.051 -10000 0 -0.22 15 15
TRAIL/TRAILR1/FADD/TRADD/RIP 0.039 0.089 -10000 0 -0.18 27 27
mol:ceramide -0.007 0.054 -10000 0 -0.15 28 28
FADD 0.028 0.006 -10000 0 -10000 0 0
MAPK8 -0.009 0.092 0.2 1 -0.3 15 16
TRAF2 0.027 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.097 0.12 9 -0.31 19 28
CHUK 0.025 0.024 -10000 0 -0.32 1 1
TRAIL/TRAILR1/FADD 0.021 0.095 -10000 0 -0.21 31 31
DAP3 0.026 0.008 -10000 0 -10000 0 0
CASP10 -0.027 0.099 0.16 8 -0.28 21 29
JNK cascade 0.024 0.079 -10000 0 -0.21 21 21
TRAIL (trimer) 0.005 0.087 -10000 0 -0.31 16 16
TNFRSF10C 0.003 0.097 0.12 9 -0.32 19 28
TRAIL/TRAILR1/DAP3/GTP/FADD 0.033 0.08 -10000 0 -0.17 27 27
TRAIL/TRAILR2/FADD 0.025 0.079 -10000 0 -0.19 26 26
cell death -0.007 0.054 -10000 0 -0.15 28 28
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.006 0.08 -10000 0 -0.21 28 28
TRAILR2 (trimer) 0.008 0.079 -10000 0 -0.31 13 13
CASP8 0.01 0.077 -10000 0 -0.67 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.041 0.077 -10000 0 -0.16 23 23
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.012 0.098 0.19 2 -0.19 46 48
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.11 0.32 1 -0.32 10 11
alphaV/beta3 Integrin/Osteopontin/Src 0.013 0.092 -10000 0 -0.22 29 29
AP1 -0.005 0.13 -10000 0 -0.35 17 17
ILK -0.024 0.094 0.19 3 -0.31 10 13
bone resorption -0.028 0.1 0.18 3 -0.3 12 15
PTK2B 0.026 0.025 0.12 2 -0.32 1 3
PYK2/p130Cas 0.009 0.12 -10000 0 -0.18 51 51
ITGAV 0.023 0.046 -10000 0 -0.31 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.048 -10000 0 -0.22 8 8
alphaV/beta3 Integrin/Osteopontin 0.009 0.12 0.19 2 -0.21 51 53
MAP3K1 -0.026 0.097 0.19 2 -0.2 48 50
JUN 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.042 0.084 0.19 2 -0.3 11 13
MAPK1 -0.041 0.083 0.19 2 -0.31 10 12
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.046 0.091 0.18 2 -0.32 13 15
ITGB3 -0.011 0.12 -10000 0 -0.32 30 30
NFKBIA -0.037 0.092 0.18 2 -0.32 12 14
FOS 0.032 0.018 -10000 0 -10000 0 0
CD44 0.025 0.032 -10000 0 -0.32 2 2
CHUK 0.025 0.024 -10000 0 -0.32 1 1
PLAU -0.046 0.18 0.33 1 -0.95 6 7
NF kappa B1 p50/RelA 0.008 0.11 -10000 0 -0.31 10 10
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
RELA 0.028 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.011 0.098 -10000 0 -0.23 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.026 0.098 0.19 3 -0.2 49 52
VAV3 -0.043 0.085 0.18 2 -0.28 13 15
MAP3K14 -0.024 0.095 0.19 2 -0.19 48 50
ROCK2 0.019 0.055 -10000 0 -0.32 6 6
SPP1 -0.005 0.11 0.13 11 -0.31 26 37
RAC1 0.025 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.09 0.18 2 -0.28 12 14
MMP2 -0.046 0.12 0.31 2 -0.39 17 19
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.044 -10000 0 -0.18 9 9
ARNO/beta Arrestin1-2 0.032 0.086 -10000 0 -0.83 2 2
EGFR 0.023 0.061 0.12 16 -0.32 6 22
EPHA2 0.02 0.056 0.12 3 -0.32 6 9
USP6 0.027 0.007 -10000 0 -10000 0 0
IQSEC1 0.028 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.008 0.11 0.18 1 -0.22 47 48
ARRB2 0.009 0.004 -10000 0 -10000 0 0
mol:GTP -0.008 0.062 0.18 2 -0.16 21 23
ARRB1 0.026 0.023 -10000 0 -0.32 1 1
FBXO8 0.028 0.004 -10000 0 -10000 0 0
TSHR 0.018 0.078 0.12 16 -0.32 11 27
EGF -0.028 0.14 0.12 19 -0.32 43 62
somatostatin receptor activity 0 0 0.001 18 -0.001 22 40
ARAP2 0.002 0.092 -10000 0 -0.32 18 18
mol:GDP -0.007 0.1 0.18 13 -0.25 21 34
mol:PI-3-4-5-P3 0 0 0.001 12 -0.001 12 24
ITGA2B 0.022 0.073 -10000 0 -0.32 9 9
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.056 0.047 -10000 0 -0.17 6 6
ADAP1 0.013 0.067 -10000 0 -0.32 9 9
KIF13B 0.027 0.007 -10000 0 -10000 0 0
HGF/MET 0.01 0.091 -10000 0 -0.22 30 30
PXN 0.029 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.009 0.11 0.22 18 -0.25 22 40
EGFR/EGFR/EGF/EGF/ARFGEP100 0.009 0.1 0.18 1 -0.18 47 48
ADRB2 0.025 0.042 0.12 6 -0.32 3 9
receptor agonist activity 0 0 0 8 0 23 31
actin filament binding 0 0 0 18 0 22 40
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 -0.012 0.12 -10000 0 -0.32 30 30
GNAQ 0.027 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 19 -0.001 18 37
ARF6/GDP -0.026 0.16 0.19 1 -0.35 33 34
ARF6/GDP/GULP/ACAP1 0.004 0.13 0.21 7 -0.28 24 31
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.097 0.19 2 -0.17 38 40
ACAP1 0.002 0.1 0.12 15 -0.32 21 36
ACAP2 0.027 0.023 -10000 0 -0.32 1 1
LHCGR/beta Arrestin2 0.015 0.018 -10000 0 -10000 0 0
EFNA1 0.026 0.008 -10000 0 -10000 0 0
HGF 0.015 0.077 0.12 13 -0.32 11 24
CYTH3 -0.001 0.015 -10000 0 -0.21 1 1
CYTH2 0.011 0.097 -10000 0 -1 2 2
NCK1 0.028 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 15 0 18 33
endosomal lumen acidification 0 0 0 18 0 14 32
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.011 0.076 0.12 1 -0.32 12 13
GNAQ/ARNO 0.027 0.092 -10000 0 -0.95 2 2
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 10 0 6 16
MET 0.001 0.096 -10000 0 -0.32 19 19
GNA14 0.032 0.05 0.12 2 -0.32 3 5
GNA15 0.019 0.06 -10000 0 -0.32 7 7
GIT1 0.028 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 18 -0.001 19 37
GNA11 0.029 0.003 -10000 0 -10000 0 0
LHCGR 0.015 0.015 -10000 0 -10000 0 0
AGTR1 0.001 0.1 -10000 0 -0.32 21 21
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO 0.008 0.11 -10000 0 -0.87 2 2
alphaIIb/beta3 Integrin 0.005 0.1 0.18 2 -0.22 38 40
Ceramide 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
SPHK2 -0.022 0.053 -10000 0 -0.22 15 15
MAP4K4 -0.018 0.1 -10000 0 -0.35 14 14
BAG4 0.023 0.039 -10000 0 -0.32 3 3
PKC zeta/ceramide -0.012 0.082 0.12 1 -0.2 29 30
NFKBIA 0.029 0.003 -10000 0 -10000 0 0
BIRC3 -0.008 0.11 -10000 0 -0.32 27 27
BAX -0.001 0.046 -10000 0 -0.29 3 3
RIPK1 0.025 0.01 -10000 0 -10000 0 0
AKT1 -0.007 0.013 -10000 0 -10000 0 0
BAD -0.023 0.08 0.2 4 -0.2 30 34
SMPD1 0.015 0.084 0.18 23 -0.23 11 34
RB1 -0.026 0.079 0.2 3 -0.19 32 35
FADD/Caspase 8 -0.012 0.11 0.24 2 -0.36 14 16
MAP2K4 -0.03 0.074 0.18 2 -0.18 35 37
NSMAF 0.026 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.029 0.07 -10000 0 -0.19 29 29
EGF -0.028 0.14 0.12 19 -0.32 43 62
mol:ceramide -0.024 0.079 0.098 13 -0.2 30 43
MADD 0.028 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.019 0.048 -10000 0 -0.22 12 12
ASAH1 0.024 0.032 -10000 0 -0.32 2 2
negative regulation of cell cycle -0.026 0.078 0.2 3 -0.19 32 35
cell proliferation -0.011 0.081 -10000 0 -0.18 28 28
BID -0.012 0.15 -10000 0 -0.53 13 13
MAP3K1 -0.028 0.079 0.19 2 -0.19 35 37
EIF2A -0.027 0.071 0.17 4 -0.18 28 32
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.007 0.12 1 -10000 0 1
MAPK3 -0.024 0.068 -10000 0 -0.18 26 26
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.024 0.067 -10000 0 -0.18 27 27
Cathepsin D/ceramide -0.01 0.082 0.12 1 -0.2 30 31
FADD -0.016 0.098 0.2 1 -0.35 12 13
KSR1 -0.027 0.073 -10000 0 -0.2 29 29
MAPK8 -0.041 0.098 -10000 0 -0.23 33 33
PRKRA -0.026 0.073 -10000 0 -0.19 29 29
PDGFA 0.009 0.081 0.12 7 -0.32 13 20
TRAF2 0.027 0.008 -10000 0 -10000 0 0
IGF1 0.008 0.086 0.12 4 -0.32 15 19
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.024 0.079 0.098 13 -0.2 30 43
CTSD 0.029 0.011 0.12 2 -10000 0 2
regulation of nitric oxide biosynthetic process 0.041 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.011 0.086 -10000 0 -0.19 28 28
PRKCD 0.028 0.004 -10000 0 -10000 0 0
PRKCZ 0.02 0.05 -10000 0 -0.32 5 5
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.019 0.048 -10000 0 -0.22 12 12
RelA/NF kappa B1 0.041 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.005 0.1 -10000 0 -0.32 23 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.016 0.1 -10000 0 -0.4 11 11
TNFR1A/BAG4/TNF-alpha 0.037 0.062 -10000 0 -0.18 14 14
mol:Sphingosine-1-phosphate -0.022 0.053 -10000 0 -0.22 15 15
MAP2K1 -0.027 0.07 0.17 2 -0.19 27 29
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
CYCS 0.002 0.049 0.14 9 -0.17 6 15
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.036 0.031 -10000 0 -0.22 3 3
EIF2AK2 -0.028 0.07 0.18 1 -0.19 29 30
TNF-alpha/TNFR1A/FAN 0.04 0.057 -10000 0 -0.18 11 11
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.096 -10000 0 -0.43 7 7
MAP2K2 -0.029 0.068 0.17 1 -0.19 28 29
SMPD3 0.001 0.12 0.17 16 -0.37 14 30
TNF 0.013 0.076 0.12 10 -0.32 11 21
PKC zeta/PAR4 0.009 0.085 -10000 0 -0.22 28 28
mol:PHOSPHOCHOLINE 0.025 0.085 0.17 41 -0.13 19 60
NF kappa B1/RelA/I kappa B alpha 0.049 0.081 -10000 0 -0.16 27 27
AIFM1 -0.007 0.06 0.15 9 -0.18 8 17
BCL2 0.018 0.059 -10000 0 -0.32 7 7
Reelin 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
CDK5R1/CDK5 0.03 0.043 -10000 0 -0.22 6 6
VLDLR 0.016 0.055 0.12 1 -0.32 6 7
CRKL 0.028 0.009 0.12 1 -10000 0 1
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
ITGA3 0.009 0.083 0.12 4 -0.32 14 18
RELN/VLDLR/Fyn 0.023 0.087 -10000 0 -0.18 31 31
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.063 -10000 0 -0.16 13 13
AKT1 -0.013 0.078 0.13 8 -0.18 33 41
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
DAB1 0.034 0.032 0.12 25 -10000 0 25
RELN/LRP8/DAB1 0.039 0.079 0.17 8 -0.17 24 32
LRPAP1/LRP8 0.04 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.045 0.08 0.18 8 -0.15 24 32
DAB1/alpha3/beta1 Integrin 0.018 0.088 -10000 0 -0.16 35 35
long-term memory 0.051 0.091 0.25 5 -0.16 25 30
DAB1/LIS1 0.041 0.088 -10000 0 -0.15 29 29
DAB1/CRLK/C3G 0.027 0.078 -10000 0 -0.15 27 27
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
DAB1/NCK2 0.045 0.089 -10000 0 -0.16 29 29
ARHGEF2 0.026 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.029 0.058 0.12 20 -0.32 5 25
CDK5R1 0.019 0.055 -10000 0 -0.32 6 6
RELN 0.006 0.12 0.12 43 -0.32 25 68
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
RELN/LRP8/Fyn 0.035 0.081 -10000 0 -0.18 24 24
GRIN2A/RELN/LRP8/DAB1/Fyn 0.056 0.096 0.25 4 -0.16 27 31
MAPK8 0.022 0.039 -10000 0 -0.32 3 3
RELN/VLDLR/DAB1 0.027 0.084 0.17 8 -0.16 30 38
ITGB1 0.027 0.011 -10000 0 -10000 0 0
MAP1B -0.005 0.079 0.17 16 -0.17 30 46
RELN/LRP8 0.036 0.081 -10000 0 -0.18 23 23
GRIN2B/RELN/LRP8/DAB1/Fyn 0.057 0.089 0.23 2 -0.16 24 26
PI3K 0.036 0.039 -10000 0 -0.28 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.024 0.063 -10000 0 -0.21 14 14
RAP1A -0.006 0.091 0.25 9 -10000 0 9
PAFAH1B1 0.027 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.012 0.073 0.12 1 -0.32 11 12
CRLK/C3G 0.038 0.015 -10000 0 -10000 0 0
GRIN2B 0.03 0.026 0.12 15 -10000 0 15
NCK2 0.029 0.003 -10000 0 -10000 0 0
neuron differentiation -0.006 0.1 0.18 1 -0.31 13 14
neuron adhesion -0.015 0.095 0.28 4 -0.27 3 7
LRP8 0.028 0.004 -10000 0 -10000 0 0
GSK3B -0.014 0.073 0.13 3 -0.18 29 32
RELN/VLDLR/DAB1/Fyn 0.034 0.084 0.18 8 -0.15 30 38
MAP3K11 0.027 0.023 -10000 0 -0.32 1 1
RELN/VLDLR/DAB1/P13K -0.005 0.082 0.15 3 -0.2 32 35
CDK5 0.025 0.01 -10000 0 -10000 0 0
MAPT -0.025 0.11 0.71 2 -0.28 22 24
neuron migration -0.012 0.12 0.24 17 -0.26 23 40
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.1 0.18 1 -0.29 16 17
RELN/VLDLR 0.035 0.087 -10000 0 -0.16 29 29
Effects of Botulinum toxin

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
STX1A 0.006 0.017 -10000 0 -0.21 1 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.034 0.027 -10000 0 -0.22 1 1
STXBP1 0.026 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.008 0.07 0.1 25 -0.13 33 58
RAB3GAP2/RIMS1/UNC13B 0.042 0.035 -10000 0 -0.19 2 2
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 0.025 0.022 0.12 9 -10000 0 9
mol:ACh -0.001 0.049 0.094 25 -0.1 25 50
RAB3GAP2 0.024 0.024 -10000 0 -0.32 1 1
STX1A/SNAP25/VAMP2 0.02 0.065 0.18 3 -0.14 20 23
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.008 0.07 0.1 25 -0.13 33 58
UNC13B 0.024 0.024 -10000 0 -0.32 1 1
CHRNA1 -0.011 0.13 0.12 24 -0.32 33 57
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.023 0.063 0.11 41 -0.1 28 69
SNAP25 -0.017 0.074 -10000 0 -0.22 26 26
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.033 0.076 0.12 42 -0.32 8 50
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.022 0.018 -10000 0 -0.18 1 1
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.065 0.18 3 -0.14 20 23
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.048 -10000 0 -0.17 10 10
NFATC2 -0.015 0.061 -10000 0 -0.19 19 19
NFATC3 -0.004 0.034 -10000 0 -0.1 3 3
CD40LG -0.072 0.2 0.26 2 -0.42 44 46
PTGS2 -0.063 0.18 -10000 0 -0.37 44 44
JUNB 0.029 0.007 0.12 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.028 -10000 0 -10000 0 0
CaM/Ca2+ 0.005 0.028 -10000 0 -10000 0 0
CALM1 0.013 0.026 -10000 0 -10000 0 0
JUN 0.013 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.012 -10000 0 -10000 0 0
FOSL1 0.003 0.11 -10000 0 -0.32 22 22
CREM 0.026 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.01 0.14 0.21 2 -0.27 32 34
FOS 0.017 0.033 -10000 0 -10000 0 0
IFNG -0.077 0.2 -10000 0 -0.4 53 53
AP-1/NFAT1-c-4 -0.031 0.23 0.29 1 -0.43 39 40
FASLG -0.071 0.2 -10000 0 -0.43 43 43
NFAT1-c-4/ICER1 -0.017 0.092 -10000 0 -0.2 26 26
IL2RA -0.07 0.19 -10000 0 -0.4 43 43
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.061 0.18 0.21 1 -0.37 39 40
JunB/Fra1/NFAT1-c-4 -0.012 0.12 0.18 2 -0.19 40 42
IL4 -0.065 0.17 -10000 0 -0.37 39 39
IL2 0.001 0.12 -10000 0 -0.89 4 4
IL3 -0.01 0.15 -10000 0 -0.77 8 8
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
BATF3 0.022 0.041 -10000 0 -0.32 3 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.009 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.001 0.1 -10000 0 -0.38 15 15
Syndecan-4/Syndesmos -0.022 0.18 -10000 0 -0.46 27 27
positive regulation of JNK cascade -0.018 0.18 -10000 0 -0.44 28 28
Syndecan-4/ADAM12 -0.024 0.18 -10000 0 -0.47 27 27
CCL5 -0.002 0.11 -10000 0 -0.32 24 24
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 0.028 0.035 0.12 5 -0.32 2 7
SDCBP 0.023 0.033 -10000 0 -0.32 2 2
PLG 0.011 0.02 -10000 0 -10000 0 0
ADAM12 0.021 0.046 0.12 2 -0.32 4 6
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.03 0.19 -10000 0 -0.46 29 29
Syndecan-4/CXCL12/CXCR4 -0.02 0.2 -10000 0 -0.47 28 28
Syndecan-4/Laminin alpha3 -0.023 0.19 -10000 0 -0.47 26 26
MDK 0.012 0.081 0.12 7 -0.32 13 20
Syndecan-4/FZD7 -0.024 0.19 -10000 0 -0.46 29 29
Syndecan-4/Midkine -0.027 0.19 -10000 0 -0.47 29 29
FZD7 0.022 0.057 0.12 5 -0.32 6 11
Syndecan-4/FGFR1/FGF -0.037 0.2 -10000 0 -0.46 31 31
THBS1 0.015 0.072 0.12 6 -0.32 10 16
integrin-mediated signaling pathway -0.024 0.19 -10000 0 -0.45 30 30
positive regulation of MAPKKK cascade -0.018 0.18 -10000 0 -0.44 28 28
Syndecan-4/TACI -0.028 0.19 -10000 0 -0.48 27 27
CXCR4 0.021 0.056 0.12 3 -0.32 6 9
cell adhesion -0.004 0.068 0.2 3 -0.25 13 16
Syndecan-4/Dynamin -0.022 0.18 -10000 0 -0.46 27 27
Syndecan-4/TSP1 -0.025 0.19 -10000 0 -0.47 28 28
Syndecan-4/GIPC -0.022 0.18 -10000 0 -0.46 27 27
Syndecan-4/RANTES -0.029 0.19 -10000 0 -0.48 28 28
ITGB1 0.027 0.011 -10000 0 -10000 0 0
LAMA1 -0.013 0.12 0.12 17 -0.32 32 49
LAMA3 0.024 0.059 0.12 11 -0.32 6 17
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA 0.005 0.13 0.8 5 -0.3 6 11
Syndecan-4/alpha-Actinin -0.024 0.18 -10000 0 -0.46 27 27
TFPI 0.026 0.048 0.12 7 -0.32 4 11
F2 0.016 0.023 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.03 0.18 1 -0.22 2 3
positive regulation of cell adhesion -0.039 0.19 -10000 0 -0.46 29 29
ACTN1 0.024 0.039 -10000 0 -0.32 3 3
TNC -0.001 0.095 0.12 2 -0.32 19 21
Syndecan-4/CXCL12 -0.027 0.19 -10000 0 -0.47 27 27
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
CXCL12 0.011 0.074 -10000 0 -0.32 11 11
TNFRSF13B 0.002 0.11 -10000 0 -0.32 24 24
FGF2 -0.036 0.14 -10000 0 -0.32 44 44
FGFR1 0.025 0.049 0.12 9 -0.32 4 13
Syndecan-4/PI-4-5-P2 -0.047 0.17 -10000 0 -0.46 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.007 0.075 0.12 2 -0.3 12 14
cell migration -0.014 0.012 -10000 0 -10000 0 0
PRKCD 0.023 0.022 -10000 0 -10000 0 0
vasculogenesis -0.023 0.18 -10000 0 -0.45 28 28
SDC4 -0.04 0.18 -10000 0 -0.48 26 26
Syndecan-4/Tenascin C -0.026 0.2 -10000 0 -0.47 30 30
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.025 0.18 -10000 0 -0.47 25 25
MMP9 -0.002 0.11 0.12 20 -0.31 25 45
Rac1/GTP -0.004 0.07 0.2 3 -0.25 13 16
cytoskeleton organization -0.021 0.18 -10000 0 -0.44 27 27
GIPC1 0.029 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.022 0.19 -10000 0 -0.47 27 27
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.048 0.066 -10000 0 -0.17 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.081 0.2 -10000 0 -0.46 35 35
AKT1 -0.09 0.28 -10000 0 -0.72 37 37
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.089 0.29 -10000 0 -0.73 38 38
mol:Ca2+ -0.004 0.078 0.18 6 -0.33 8 14
IGF1R 0.025 0.032 -10000 0 -0.32 2 2
E2/ER alpha (dimer)/Striatin 0.026 0.044 -10000 0 -0.18 9 9
SHC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.085 0.27 0.69 37 -10000 0 37
RhoA/GTP 0.019 0.028 -10000 0 -0.15 5 5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.038 0.17 0.25 1 -0.4 29 30
regulation of stress fiber formation 0.011 0.059 -10000 0 -0.16 19 19
E2/ERA-ERB (dimer) 0.033 0.047 -10000 0 -0.21 6 6
KRAS 0.028 0.005 -10000 0 -10000 0 0
G13/GTP 0.027 0.032 -10000 0 -0.16 5 5
pseudopodium formation -0.011 0.059 0.16 19 -10000 0 19
E2/ER alpha (dimer)/PELP1 0.03 0.032 -10000 0 -0.18 4 4
GRB2 0.028 0.005 -10000 0 -10000 0 0
GNG2 0.015 0.066 -10000 0 -0.32 9 9
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
HRAS 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.06 0.2 0.25 2 -0.46 39 41
E2/ER beta (dimer) 0.026 0.031 -10000 0 -0.21 2 2
mol:GDP -0.005 0.077 -10000 0 -0.19 31 31
mol:NADP -0.06 0.2 0.25 2 -0.46 39 41
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
mol:IP3 -0.008 0.076 0.21 2 -0.34 8 10
IGF-1R heterotetramer 0.025 0.032 -10000 0 -0.31 2 2
PLCB1 0 0.075 0.22 2 -0.32 8 10
PLCB2 0.007 0.066 -10000 0 -0.33 7 7
IGF1 0.008 0.086 0.12 4 -0.32 15 19
mol:L-citrulline -0.06 0.2 0.25 2 -0.46 39 41
RHOA 0.028 0.004 -10000 0 -10000 0 0
Gai/GDP -0.12 0.28 -10000 0 -0.64 49 49
JNK cascade 0.026 0.031 -10000 0 -0.21 2 2
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
ESR2 0.036 0.045 0.12 26 -0.32 2 28
GNAQ 0.027 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.051 0.12 2 -0.32 5 7
Gq family/GDP/Gbeta gamma 0.008 0.098 -10000 0 -0.38 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.022 0.069 -10000 0 -0.48 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.035 0.16 0.25 1 -0.4 25 26
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
E2/ER alpha (dimer) 0.014 0.035 -10000 0 -0.21 5 5
STRN 0.023 0.045 -10000 0 -0.32 4 4
GNAL 0.012 0.1 0.12 32 -0.32 19 51
PELP1 0.027 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.032 -10000 0 -0.18 6 6
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
HBEGF -0.063 0.21 0.31 13 -0.46 34 47
cAMP biosynthetic process 0.016 0.062 0.11 9 -0.15 23 32
SRC -0.069 0.19 0.21 10 -0.45 33 43
PI3K 0.036 0.039 -10000 0 -0.28 3 3
GNB1 0.027 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.016 0.089 -10000 0 -0.26 10 10
SOS1 0.029 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.055 0.13 -10000 0 -0.32 32 32
Gs family/GTP 0.023 0.067 0.14 9 -0.16 23 32
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.051 0.016 -10000 0 -10000 0 0
vasodilation -0.056 0.19 0.25 2 -0.44 39 41
mol:DAG -0.008 0.076 0.21 2 -0.34 8 10
Gs family/GDP/Gbeta gamma -0.012 0.09 -10000 0 -0.22 22 22
MSN -0.012 0.061 0.16 19 -10000 0 19
Gq family/GTP 0.018 0.067 -10000 0 -0.37 5 5
mol:PI-3-4-5-P3 -0.085 0.28 -10000 0 -0.7 38 38
NRAS 0.028 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.056 0.19 0.44 39 -0.25 2 41
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.084 -10000 0 -0.18 29 29
NOS3 -0.064 0.21 0.25 2 -0.48 39 41
GNA11 0.029 0.003 -10000 0 -10000 0 0
MAPKKK cascade -0.049 0.21 0.29 2 -0.5 33 35
E2/ER alpha (dimer)/PELP1/Src -0.038 0.18 0.27 4 -0.41 30 34
ruffle organization -0.011 0.059 0.16 19 -10000 0 19
ROCK2 -0.006 0.064 0.18 19 -10000 0 19
GNA14 0.032 0.05 -10000 0 -0.32 3 3
GNA15 0.019 0.06 -10000 0 -0.32 7 7
GNA13 0.028 0.005 -10000 0 -10000 0 0
MMP9 -0.073 0.2 0.34 7 -0.44 36 43
MMP2 -0.064 0.18 0.27 3 -0.42 34 37
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.006 -10000 0 -10000 0 0
LAT2 -0.017 0.13 0.2 5 -0.4 16 21
AP1 -0.009 0.2 0.27 1 -0.51 24 25
mol:PIP3 -0.004 0.17 0.26 19 -0.46 18 37
IKBKB 0.003 0.11 0.2 23 -0.28 14 37
AKT1 -0.003 0.12 0.29 21 -0.27 5 26
IKBKG 0.001 0.11 0.2 20 -0.28 14 34
MS4A2 0.019 0.057 0.13 11 -0.31 5 16
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
MAP3K1 -0.016 0.15 0.24 8 -0.41 18 26
mol:Ca2+ 0.004 0.14 0.23 22 -0.34 18 40
LYN 0.024 0.034 -10000 0 -0.32 2 2
CBLB -0.016 0.11 0.19 1 -0.35 15 16
SHC1 0.026 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.031 -10000 0 -0.17 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
PLD2 -0.002 0.11 0.3 20 -0.19 16 36
PTPN13 -0.003 0.14 0.28 1 -0.55 10 11
PTPN11 0.026 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.004 0.1 0.24 16 -0.29 9 25
SYK 0.017 0.067 0.12 3 -0.33 8 11
GRB2 0.028 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.011 0.16 0.18 1 -0.45 19 20
LAT -0.02 0.12 0.19 1 -0.36 19 20
PAK2 -0.015 0.16 0.27 5 -0.49 16 21
NFATC2 -0.03 0.12 -10000 0 -0.46 17 17
HRAS -0.017 0.18 0.22 11 -0.49 19 30
GAB2 0.027 0.007 -10000 0 -10000 0 0
PLA2G1B 0.008 0.11 -10000 0 -0.91 3 3
Fc epsilon R1 0.03 0.096 0.18 6 -0.22 26 32
Antigen/IgE/Fc epsilon R1 0.03 0.088 0.17 6 -0.19 26 32
mol:GDP -0.029 0.18 -10000 0 -0.58 17 17
JUN 0.028 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
FOS 0.032 0.018 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.01 0.12 -10000 0 -0.36 16 16
CHUK 0.001 0.11 0.2 19 -0.28 14 33
KLRG1 -0.017 0.1 -10000 0 -0.26 23 23
VAV1 -0.024 0.13 0.19 1 -0.41 17 18
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.009 0.099 -10000 0 -0.38 11 11
negative regulation of mast cell degranulation 0.006 0.13 0.18 12 -0.42 13 25
BTK -0.029 0.2 -10000 0 -0.66 17 17
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.019 0.14 -10000 0 -0.35 23 23
GAB2/PI3K/SHP2 -0.034 0.058 -10000 0 -0.2 19 19
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.013 0.11 -10000 0 -0.27 25 25
RAF1 0.006 0.12 -10000 0 -1 3 3
Fc epsilon R1/FcgammaRIIB/SHIP 0.043 0.12 -10000 0 -0.23 31 31
FCER1G 0.018 0.069 0.13 10 -0.33 8 18
FCER1A 0.002 0.099 0.12 15 -0.32 18 33
Antigen/IgE/Fc epsilon R1/Fyn 0.035 0.087 0.18 6 -0.18 26 32
MAPK3 0.008 0.11 -10000 0 -0.92 3 3
MAPK1 0.007 0.11 -10000 0 -0.92 3 3
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.045 0.25 -10000 0 -0.66 28 28
DUSP1 0.029 0.014 0.12 4 -10000 0 4
NF-kappa-B/RelA 0.009 0.067 0.13 12 -0.18 13 25
actin cytoskeleton reorganization 0.005 0.15 -10000 0 -0.57 10 10
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.16 0.23 2 -0.48 15 17
FER -0.014 0.11 0.19 1 -0.35 14 15
RELA 0.028 0.005 -10000 0 -10000 0 0
ITK -0.04 0.12 -10000 0 -0.31 37 37
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG1 -0.008 0.19 0.28 6 -0.61 15 21
cytokine secretion -0.002 0.041 -10000 0 -0.14 10 10
SPHK1 -0.018 0.11 -10000 0 -0.36 16 16
PTK2 0.003 0.15 -10000 0 -0.6 10 10
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.004 0.16 0.2 6 -0.46 18 24
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.17 0.27 18 -0.48 16 34
MAP2K2 0.002 0.11 -10000 0 -0.94 3 3
MAP2K1 0.005 0.12 -10000 0 -0.94 3 3
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.1 0.2 3 -0.28 16 19
MAP2K4 -0.015 0.22 -10000 0 -0.87 14 14
Fc epsilon R1/FcgammaRIIB 0.041 0.1 0.19 6 -0.21 28 34
mol:Choline -0.002 0.11 0.3 20 -0.19 16 36
SHC/Grb2/SOS1 0.028 0.11 -10000 0 -0.32 14 14
FYN 0.025 0.01 -10000 0 -10000 0 0
DOK1 0.028 0.024 0.12 1 -0.32 1 2
PXN 0.002 0.14 -10000 0 -0.55 10 10
HCLS1 -0.022 0.13 -10000 0 -0.4 17 17
PRKCB -0.004 0.14 0.23 19 -0.38 16 35
FCGR2B 0.022 0.054 -10000 0 -0.32 5 5
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.13 0.18 13 -0.43 13 26
LCP2 0.018 0.055 -10000 0 -0.32 6 6
PLA2G4A -0.017 0.11 0.19 1 -0.36 14 15
RASA1 0.024 0.032 -10000 0 -0.32 2 2
mol:Phosphatidic acid -0.002 0.11 0.3 20 -0.19 16 36
IKK complex 0.004 0.09 0.18 21 -0.23 11 32
WIPF1 0.016 0.066 -10000 0 -0.32 9 9
Ephrin B 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
EFNB2 0.031 0.018 0.12 8 -10000 0 8
EPHB2 0.008 0.083 -10000 0 -0.32 14 14
EFNB1 -0.007 0.029 -10000 0 -0.22 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.088 -10000 0 -0.18 26 26
Ephrin B2/EPHB1-2 0.036 0.075 0.17 3 -0.18 21 24
neuron projection morphogenesis 0.015 0.076 -10000 0 -0.17 26 26
Ephrin B1/EPHB1-2/Tiam1 0.027 0.092 -10000 0 -0.18 32 32
DNM1 0.025 0.042 -10000 0 -0.31 3 3
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.034 0.13 -10000 0 -0.51 16 16
YES1 -0.038 0.2 -10000 0 -0.76 16 16
Ephrin B1/EPHB1-2/NCK2 0.039 0.079 -10000 0 -0.17 23 23
PI3K 0.004 0.15 -10000 0 -0.52 16 16
mol:GDP 0.025 0.09 -10000 0 -0.18 32 32
ITGA2B 0.022 0.073 -10000 0 -0.32 9 9
endothelial cell proliferation 0.027 0.046 -10000 0 -0.18 9 9
FYN -0.044 0.2 -10000 0 -0.75 16 16
MAP3K7 -0.034 0.14 0.22 1 -0.54 16 17
FGR -0.039 0.19 -10000 0 -0.74 16 16
TIAM1 0.01 0.076 -10000 0 -0.32 12 12
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
RGS3 0.026 0.025 -10000 0 -0.32 1 1
cell adhesion -0.029 0.16 -10000 0 -0.52 17 17
LYN -0.034 0.19 -10000 0 -0.75 15 15
Ephrin B1/EPHB1-2/Src Family Kinases -0.039 0.18 -10000 0 -0.7 16 16
Ephrin B1/EPHB1-2 -0.033 0.15 -10000 0 -0.59 15 15
SRC -0.033 0.19 -10000 0 -0.73 16 16
ITGB3 -0.012 0.12 -10000 0 -0.32 30 30
EPHB1 0.023 0.077 0.12 23 -0.31 10 33
EPHB4 0.013 0.066 -10000 0 -0.32 9 9
RAC1 0.025 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.046 -10000 0 -0.18 9 9
alphaIIb/beta3 Integrin 0.005 0.1 0.18 2 -0.22 38 40
BLK -0.046 0.2 -10000 0 -0.76 16 16
HCK -0.04 0.19 -10000 0 -0.73 16 16
regulation of stress fiber formation -0.037 0.077 0.17 23 -10000 0 23
MAPK8 -0.034 0.13 -10000 0 -0.5 15 15
Ephrin B1/EPHB1-2/RGS3 0.038 0.081 -10000 0 -0.18 22 22
endothelial cell migration -0.019 0.13 0.2 5 -0.46 14 19
NCK2 0.029 0.003 -10000 0 -10000 0 0
PTPN13 0.008 0.099 -10000 0 -0.44 11 11
regulation of focal adhesion formation -0.037 0.077 0.17 23 -10000 0 23
chemotaxis -0.036 0.079 0.18 22 -0.17 1 23
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
Rac1/GTP 0.023 0.082 -10000 0 -0.18 26 26
angiogenesis -0.032 0.15 -10000 0 -0.59 15 15
LCK -0.05 0.2 -10000 0 -0.74 16 16
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.088 -10000 0 -0.16 37 37
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.009 0.12 1 -10000 0 1
STAT1 (dimer)/Cbp/p300 0.021 0.083 0.24 2 -0.22 7 9
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.029 0.052 -10000 0 -0.2 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.016 0.07 -10000 0 -0.18 20 20
CaM/Ca2+ 0.024 0.086 -10000 0 -0.15 37 37
RAP1A 0.028 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.002 0.077 0.15 7 -0.16 36 43
AKT1 -0.025 0.076 0.18 5 -0.28 5 10
MAP2K1 -0.033 0.072 0.14 8 -0.28 7 15
MAP3K11 -0.027 0.066 0.16 8 -0.16 30 38
IFNGR1 0.018 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.017 0.13 -10000 0 -0.32 25 25
Rap1/GTP -0.031 0.046 -10000 0 -0.15 9 9
CRKL/C3G 0.038 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.031 0.095 -10000 0 -0.16 38 38
CEBPB -0.002 0.13 0.33 2 -0.42 12 14
STAT3 0.028 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.17 -10000 0 -0.98 5 5
STAT1 -0.029 0.07 0.16 8 -0.17 30 38
CALM1 0.028 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.022 0.13 0.13 17 -0.32 35 52
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
STAT1 (dimer)/PIAS1 -0.002 0.078 0.17 2 -0.16 30 32
CEBPB/PTGES2/Cbp/p300 0.012 0.089 -10000 0 -0.29 11 11
mol:Ca2+ 0.02 0.086 -10000 0 -0.16 37 37
MAPK3 -0.01 0.12 0.39 1 -0.58 4 5
STAT1 (dimer) -0.014 0.098 -10000 0 -0.25 17 17
MAPK1 -0.013 0.12 0.39 1 -0.61 5 6
JAK2 0.01 0.054 -10000 0 -0.32 5 5
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
JAK1 0.02 0.024 -10000 0 -10000 0 0
CAMK2D 0.027 0.023 -10000 0 -0.32 1 1
DAPK1 -0.003 0.12 0.29 2 -0.53 8 10
SMAD7 -0.005 0.046 0.12 5 -0.14 8 13
CBL/CRKL/C3G 0.012 0.074 0.28 1 -0.15 25 26
PI3K 0.017 0.092 -10000 0 -0.17 35 35
IFNG -0.022 0.13 0.13 17 -0.32 35 52
apoptosis -0.001 0.1 0.3 1 -0.43 8 9
CAMK2G 0.027 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.005 -10000 0 -10000 0 0
CAMK2A 0.021 0.077 0.12 22 -0.32 10 32
CAMK2B 0.022 0.07 -10000 0 -0.32 8 8
FRAP1 -0.026 0.07 0.16 5 -0.26 5 10
PRKCD -0.026 0.077 0.18 6 -0.28 5 11
RAP1B 0.028 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.016 0.07 -10000 0 -0.18 20 20
PTPN2 0.026 0.023 -10000 0 -0.32 1 1
EP300 0.026 0.009 -10000 0 -10000 0 0
IRF1 -0.013 0.077 0.25 2 -0.28 6 8
STAT1 (dimer)/PIASy 0 0.081 0.21 3 -0.17 24 27
SOCS1 0.002 0.18 -10000 0 -1.2 5 5
mol:GDP 0.01 0.071 0.26 1 -0.15 25 26
CASP1 -0.009 0.057 0.12 4 -0.19 13 17
PTGES2 0.027 0.008 -10000 0 -10000 0 0
IRF9 0.016 0.051 0.17 4 -0.15 3 7
mol:PI-3-4-5-P3 0.006 0.083 -10000 0 -0.16 35 35
RAP1/GDP 0.008 0.064 -10000 0 -0.18 4 4
CBL -0.024 0.062 0.16 7 -0.16 28 35
MAP3K1 -0.031 0.075 0.16 8 -0.18 31 39
PIAS1 0.028 0.005 -10000 0 -10000 0 0
PIAS4 0.029 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.016 0.07 -10000 0 -0.18 20 20
PTPN11 -0.021 0.073 0.16 13 -0.16 36 49
CREBBP 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.099 0.2 35 -10000 0 35
GNAI2 0.028 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.034 0.027 -10000 0 -0.18 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
RhoA/GTP -0.008 0.1 -10000 0 -0.2 35 35
negative regulation of cAMP metabolic process -0.016 0.099 -10000 0 -0.2 45 45
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNA12 0.025 0.01 -10000 0 -10000 0 0
S1PR5 0.027 0.043 0.12 8 -0.32 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.016 0.1 -10000 0 -0.2 45 45
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.023 0.039 -10000 0 -0.32 3 3
Caspase 8 (4 units) 0.007 0.098 -10000 0 -0.24 19 19
NEF -0.016 0.049 -10000 0 -0.15 21 21
NFKBIA 0.017 0.038 -10000 0 -0.12 1 1
BIRC3 -0.023 0.12 -10000 0 -0.37 26 26
CYCS -0.005 0.094 0.18 15 -0.26 20 35
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CD247 -0.015 0.13 0.14 6 -0.3 35 41
MAP2K7 0.003 0.13 0.29 3 -0.35 14 17
protein ubiquitination 0.009 0.1 0.23 8 -0.31 11 19
CRADD 0.029 0.007 0.12 1 -10000 0 1
DAXX 0.026 0.009 -10000 0 -10000 0 0
FAS 0.021 0.045 -10000 0 -0.32 4 4
BID -0.012 0.092 0.18 5 -0.25 25 30
NF-kappa-B/RelA/I kappa B alpha 0.034 0.089 -10000 0 -0.21 26 26
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.024 0.025 0.12 1 -0.32 1 2
CFLAR 0.029 0.002 -10000 0 -10000 0 0
FADD 0.028 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.034 0.09 -10000 0 -0.21 26 26
MAPK8 0.001 0.12 0.3 2 -0.35 10 12
APAF1 0.024 0.039 -10000 0 -0.32 3 3
TRAF1 0.035 0.029 -10000 0 -10000 0 0
TRAF2 0.027 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.1 0.19 6 -0.27 26 32
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.4 12 12
CHUK 0.008 0.11 0.23 8 -0.34 11 19
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.05 -10000 0 -0.16 5 5
TCRz/NEF -0.018 0.13 0.14 6 -0.3 35 41
TNF 0.013 0.076 0.12 10 -0.32 11 21
FASLG -0.041 0.16 -10000 0 -0.42 34 34
NFKB1 0.017 0.037 -10000 0 -0.088 25 25
TNFR1A/BAG4/TNF-alpha 0.037 0.062 -10000 0 -0.18 14 14
CASP6 0.016 0.12 -10000 0 -0.57 4 4
CASP7 -0.041 0.19 0.35 3 -0.42 40 43
RELA 0.017 0.037 -10000 0 -10000 0 0
CASP2 0.024 0.024 -10000 0 -0.32 1 1
CASP3 -0.032 0.18 0.35 3 -0.44 31 34
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.036 0.031 -10000 0 -0.22 3 3
CASP8 0.029 0.002 -10000 0 -10000 0 0
CASP9 0.028 0.006 -10000 0 -10000 0 0
MAP3K14 -0.002 0.11 0.22 2 -0.36 13 15
APAF-1/Caspase 9 -0.016 0.12 -10000 0 -0.3 29 29
BCL2 -0.002 0.12 0.26 4 -0.32 10 14
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.012 0.059 0.16 18 -10000 0 18
DAPP1 -0.056 0.22 0.22 7 -0.48 36 43
Src family/SYK family/BLNK-LAT/BTK-ITK -0.097 0.3 0.28 4 -0.64 43 47
mol:DAG -0.022 0.12 0.22 11 -0.25 33 44
HRAS 0.027 0.014 -10000 0 -10000 0 0
RAP1A 0.027 0.014 -10000 0 -10000 0 0
ARF5/GDP 0.005 0.1 0.19 1 -0.28 18 19
PLCG2 0.021 0.051 -10000 0 -0.32 5 5
PLCG1 0.026 0.008 -10000 0 -10000 0 0
ARF5 0.026 0.009 -10000 0 -10000 0 0
mol:GTP -0.014 0.062 0.2 13 -10000 0 13
ARF1/GTP -0.002 0.059 0.2 8 -0.16 1 9
RHOA 0.028 0.004 -10000 0 -10000 0 0
YES1 0.021 0.045 -10000 0 -0.32 4 4
RAP1A/GTP -0.019 0.048 0.17 9 -10000 0 9
ADAP1 -0.02 0.053 0.16 11 -0.16 6 17
ARAP3 -0.014 0.061 0.2 13 -10000 0 13
INPPL1 0.027 0.006 -10000 0 -10000 0 0
PREX1 0.02 0.045 -10000 0 -0.32 4 4
ARHGEF6 0.013 0.073 -10000 0 -0.32 11 11
ARHGEF7 0.028 0.006 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
NRAS 0.027 0.014 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
ARF6 0.028 0.004 -10000 0 -10000 0 0
FGR 0.016 0.067 0.12 3 -0.32 9 12
mol:Ca2+ -0.006 0.067 0.17 10 -0.14 18 28
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.01 0.076 -10000 0 -0.32 12 12
ZAP70 -0.004 0.12 0.12 22 -0.32 28 50
mol:IP3 -0.014 0.087 0.21 8 -0.19 23 31
LYN 0.024 0.033 -10000 0 -0.32 2 2
ARF1/GDP 0.008 0.1 0.19 1 -0.28 17 18
RhoA/GDP 0.022 0.08 0.24 7 -0.23 7 14
PDK1/Src/Hsp90 0.051 0.02 -10000 0 -10000 0 0
BLNK -0.004 0.1 0.12 5 -0.32 22 27
actin cytoskeleton reorganization 0.009 0.11 0.25 13 -0.3 10 23
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.019 0.037 -10000 0 -0.2 8 8
RAC1 0.025 0.01 -10000 0 -10000 0 0
PTEN 0.024 0.017 -10000 0 -10000 0 0
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
ARF6/GTP -0.018 0.06 0.19 13 -10000 0 13
RhoA/GTP -0.015 0.062 0.21 13 -10000 0 13
Src family/SYK family/BLNK-LAT -0.087 0.27 -10000 0 -0.56 43 43
BLK 0.002 0.12 0.12 35 -0.32 26 61
PDPK1 0.029 0.003 -10000 0 -10000 0 0
CYTH1 -0.016 0.059 0.19 13 -10000 0 13
HCK 0.012 0.07 -10000 0 -0.32 10 10
CYTH3 -0.017 0.047 0.16 10 -10000 0 10
CYTH2 -0.016 0.059 0.19 13 -10000 0 13
KRAS 0.028 0.014 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.075 0.21 4 -0.36 7 11
SGK1 -0.01 0.11 0.22 4 -0.34 20 24
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
mol:GDP -0.005 0.1 0.22 3 -0.28 21 24
SOS1 0.029 0.003 -10000 0 -10000 0 0
SYK 0.016 0.064 0.12 3 -0.32 8 11
ARF6/GDP -0.005 0.082 0.25 10 -0.23 7 17
mol:PI-3-4-5-P3 -0.014 0.06 0.19 14 -10000 0 14
ARAP3/RAP1A/GTP -0.019 0.048 0.17 9 -10000 0 9
VAV1 0 0.097 0.12 2 -0.32 20 22
mol:PI-3-4-P2 -0.019 0.041 -10000 0 -0.22 9 9
RAS family/GTP/PI3K Class I 0.043 0.063 0.2 21 -0.14 11 32
PLEKHA1 -0.018 0.03 -10000 0 -0.18 7 7
Rac1/GDP 0.003 0.1 0.19 1 -0.27 19 20
LAT 0.014 0.083 0.12 11 -0.32 13 24
Rac1/GTP -0.011 0.12 -10000 0 -0.34 19 19
ITK -0.03 0.069 0.18 11 -0.17 20 31
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.042 0.16 0.25 10 -0.35 35 45
LCK -0.014 0.12 0.12 13 -0.32 32 45
BTK -0.02 0.069 0.19 15 -0.17 9 24
Ras signaling in the CD4+ TCR pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.007 0.18 0.28 1 -0.49 20 21
MAP3K8 0.024 0.042 -10000 0 -0.32 3 3
FOS -0.011 0.18 0.25 1 -0.48 22 23
PRKCA 0.019 0.06 0.12 2 -0.31 7 9
PTPN7 0.01 0.085 0.12 11 -0.31 14 25
HRAS 0.028 0.006 -10000 0 -10000 0 0
PRKCB -0.001 0.11 0.12 12 -0.31 24 36
NRAS 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.051 0.017 -10000 0 -10000 0 0
MAPK3 -0.016 0.18 -10000 0 -0.53 21 21
MAP2K1 -0.014 0.14 -10000 0 -0.36 29 29
ELK1 0.03 0.003 -10000 0 -10000 0 0
BRAF -0.018 0.12 0.16 1 -0.35 24 25
mol:GTP 0 0 -10000 0 -10000 0 0
MAPK1 -0.015 0.17 -10000 0 -0.52 21 21
RAF1 -0.02 0.12 -10000 0 -0.34 27 27
KRAS 0.028 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.12 -10000 0 -0.45 12 12
IHH 0.033 0.053 0.14 6 -0.14 16 22
SHH Np/Cholesterol/GAS1 0.016 0.028 -10000 0 -0.17 4 4
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.016 0.027 0.17 4 -10000 0 4
SMO/beta Arrestin2 0.013 0.13 -10000 0 -0.34 13 13
SMO -0.01 0.12 -10000 0 -0.36 14 14
AKT1 0.001 0.1 -10000 0 -0.36 10 10
ARRB2 0.027 0.007 -10000 0 -10000 0 0
BOC 0.024 0.06 0.12 13 -0.32 6 19
ADRBK1 0.028 0.005 -10000 0 -10000 0 0
heart looping -0.01 0.12 -10000 0 -0.36 14 14
STIL 0.023 0.089 0.19 31 -0.23 13 44
DHH N/PTCH2 0.037 0.066 0.18 2 -0.22 12 14
DHH N/PTCH1 0.026 0.11 -10000 0 -0.29 20 20
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
DHH 0.027 0.071 -10000 0 -0.32 8 8
PTHLH 0 0.18 -10000 0 -0.62 15 15
determination of left/right symmetry -0.01 0.12 -10000 0 -0.36 14 14
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
skeletal system development 0 0.17 -10000 0 -0.62 15 15
IHH N/Hhip 0.045 0.043 0.19 3 -10000 0 3
DHH N/Hhip 0.042 0.058 0.18 3 -0.22 8 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.01 0.12 -10000 0 -0.36 14 14
pancreas development 0.032 0.026 -10000 0 -10000 0 0
HHAT 0.019 0.05 -10000 0 -0.32 5 5
PI3K 0.036 0.039 -10000 0 -0.28 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.024 0.033 0.12 1 -0.32 2 3
somite specification -0.01 0.12 -10000 0 -0.36 14 14
SHH Np/Cholesterol/PTCH1 0.01 0.069 -10000 0 -0.22 15 15
SHH Np/Cholesterol/PTCH2 0.017 0.036 0.16 2 -0.17 6 8
SHH Np/Cholesterol/Megalin 0.003 0.1 0.19 12 -0.17 49 61
SHH -0.013 0.027 -10000 0 -0.22 3 3
catabolic process 0.011 0.1 0.18 1 -0.36 16 17
SMO/Vitamin D3 0.01 0.099 0.22 11 -0.28 14 25
SHH Np/Cholesterol/Hhip 0.016 0.039 0.17 5 -0.17 3 8
LRP2 -0.027 0.17 -10000 0 -0.32 58 58
receptor-mediated endocytosis -0.025 0.12 0.21 3 -0.3 22 25
SHH Np/Cholesterol/BOC 0.018 0.04 0.2 1 -0.17 7 8
SHH Np/Cholesterol/CDO 0.014 0.035 -10000 0 -0.2 5 5
mesenchymal cell differentiation -0.015 0.038 0.17 3 -0.16 5 8
mol:Vitamin D3 0.038 0.099 0.21 32 -0.24 13 45
IHH N/PTCH2 0.039 0.053 0.2 1 -0.24 4 5
CDON 0.021 0.04 -10000 0 -0.32 3 3
IHH N/PTCH1 0.023 0.11 0.23 1 -0.36 16 17
Megalin/LRPAP1 -0.003 0.13 -10000 0 -0.22 58 58
PTCH2 0.025 0.048 0.12 6 -0.32 4 10
SHH Np/Cholesterol 0.01 0.021 -10000 0 -0.16 3 3
PTCH1 0.011 0.1 0.18 1 -0.36 16 17
HHIP 0.032 0.026 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.021 0.062 -10000 0 -0.22 13 13
CRKL 0.014 0.14 0.31 9 -0.5 6 15
mol:PIP3 0.003 0.011 -10000 0 -10000 0 0
AKT1 -0.005 0.022 -10000 0 -10000 0 0
PTK2B 0.026 0.025 0.12 2 -0.32 1 3
RAPGEF1 0.012 0.13 0.3 8 -0.47 6 14
RANBP10 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
HGF/MET/SHIP2 0.024 0.084 -10000 0 -0.18 29 29
MAP3K5 -0.004 0.14 0.31 6 -0.42 13 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.033 0.087 -10000 0 -0.17 30 30
AP1 0.036 0.051 0.16 8 -10000 0 8
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.019 0.14 -10000 0 -0.77 6 6
STAT3 (dimer) -0.006 0.092 0.21 2 -0.21 30 32
GAB1/CRKL/SHP2/PI3K 0.041 0.14 0.33 5 -0.48 6 11
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
CBL/CRK 0.016 0.12 0.31 3 -0.47 6 9
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.009 -10000 0 -10000 0 0
ELK1 0.025 0.14 0.37 27 -10000 0 27
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.061 -10000 0 -0.22 7 7
PAK1 0.002 0.045 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.025 0.084 -10000 0 -0.18 30 30
HRAS -0.026 0.16 -10000 0 -0.49 22 22
DOCK1 0.012 0.13 0.32 7 -0.47 6 13
GAB1 0 0.13 0.25 1 -0.53 6 7
CRK 0.005 0.13 0.28 5 -0.5 6 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.027 0.16 -10000 0 -0.42 31 31
JUN 0.028 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.015 0.068 0.11 1 -0.18 30 31
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
cell morphogenesis 0.012 0.14 0.35 12 -0.45 5 17
GRB2/SHC 0.019 0.081 0.18 11 -0.17 25 36
FOS 0.032 0.018 -10000 0 -10000 0 0
GLMN 0.001 0.023 -10000 0 -0.2 3 3
cell motility 0.025 0.14 0.37 27 -10000 0 27
HGF/MET/MUC20 0.012 0.077 -10000 0 -0.18 30 30
cell migration 0.019 0.08 0.17 11 -0.17 25 36
GRB2 0.028 0.005 -10000 0 -10000 0 0
CBL 0.025 0.01 -10000 0 -10000 0 0
MET/RANBP10 0.017 0.073 -10000 0 -0.22 19 19
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.081 -10000 0 -0.2 31 31
MET/MUC20 0.002 0.066 -10000 0 -0.21 19 19
RAP1B 0.014 0.13 0.32 8 -0.44 6 14
RAP1A 0.012 0.13 0.3 9 -0.44 6 15
HGF/MET/RANBP9 0.027 0.078 -10000 0 -0.18 24 24
RAF1 -0.012 0.16 0.28 2 -0.46 22 24
STAT3 -0.008 0.091 -10000 0 -0.21 30 30
cell proliferation 0.003 0.14 0.28 9 -0.31 25 34
RPS6KB1 -0.006 0.054 -10000 0 -0.33 4 4
MAPK3 0.016 0.14 0.49 12 -10000 0 12
MAPK1 0.02 0.15 0.54 11 -10000 0 11
RANBP9 0.025 0.01 -10000 0 -10000 0 0
MAPK8 -0.019 0.17 0.31 6 -0.41 23 29
SRC -0.012 0.079 0.22 3 -0.19 29 32
PI3K 0.016 0.09 0.18 12 -0.18 29 41
MET/Glomulin -0.003 0.065 -10000 0 -0.17 26 26
SOS1 0.029 0.003 -10000 0 -10000 0 0
MAP2K1 -0.01 0.15 0.27 2 -0.44 21 23
MET 0.001 0.096 -10000 0 -0.32 19 19
MAP4K1 -0.003 0.16 0.33 6 -0.44 14 20
PTK2 0.026 0.009 -10000 0 -10000 0 0
MAP2K2 -0.011 0.16 0.27 2 -0.44 22 24
BAD -0.005 0.03 -10000 0 -10000 0 0
MAP2K4 -0.004 0.13 0.3 6 -0.4 12 18
SHP2/GRB2/SOS1/GAB1 0.009 0.12 -10000 0 -0.3 23 23
INPPL1 0.027 0.006 -10000 0 -10000 0 0
PXN 0.029 0.003 -10000 0 -10000 0 0
SH3KBP1 0.027 0.023 -10000 0 -0.32 1 1
HGS -0.019 0.062 0.096 1 -0.17 30 31
PLCgamma1/PKC 0.02 0.006 -10000 0 -10000 0 0
HGF 0.015 0.077 0.12 13 -0.32 11 24
RASA1 0.024 0.032 -10000 0 -0.32 2 2
NCK1 0.028 0.006 -10000 0 -10000 0 0
PTPRJ 0.027 0.023 -10000 0 -0.32 1 1
NCK/PLCgamma1 0.022 0.084 0.18 12 -0.17 29 41
PDPK1 -0.001 0.024 -10000 0 -10000 0 0
HGF/MET/SHIP 0.016 0.1 -10000 0 -0.21 36 36
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.016 0.15 0.33 2 -1.1 4 6
VDR 0.021 0.05 -10000 0 -0.32 5 5
FAM120B 0.025 0.01 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.022 0.12 -10000 0 -0.33 17 17
RXRs/LXRs/DNA/Oxysterols -0.026 0.14 -10000 0 -0.5 13 13
MED1 0.028 0.006 -10000 0 -10000 0 0
mol:9cRA 0 0.015 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.003 0.08 -10000 0 -0.2 29 29
RXRs/NUR77 0.016 0.1 -10000 0 -0.18 40 40
RXRs/PPAR -0.017 0.088 -10000 0 -0.19 44 44
NCOR2 0.029 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.034 -10000 0 -0.21 5 5
RARs/VDR/DNA/Vit D3 0.046 0.067 -10000 0 -0.16 20 20
RARA 0.028 0.005 -10000 0 -10000 0 0
NCOA1 0.028 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.05 -10000 0 -0.31 5 5
RARs/RARs/DNA/9cRA 0.034 0.056 -10000 0 -0.16 16 16
RARG 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 0.005 0.086 0.56 3 -0.41 4 7
RARs/THRs/DNA/SMRT 0.003 0.082 -10000 0 -0.2 31 31
THRA 0.028 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.034 -10000 0 -0.21 5 5
RXRs/PPAR/9cRA/PGJ2/DNA 0.008 0.094 0.29 1 -0.16 47 48
NR1H4 0.026 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.023 0.12 -10000 0 -0.26 12 12
NR1H2 0.025 0.032 -10000 0 -0.34 1 1
NR1H3 0.025 0.036 -10000 0 -0.26 2 2
RXRs/VDR/DNA/Vit D3 0.011 0.093 -10000 0 -0.16 44 44
NR4A1 0.024 0.039 -10000 0 -0.32 3 3
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.021 0.084 -10000 0 -0.18 41 41
RXRG -0.04 0.14 0.13 2 -0.32 45 47
RXR alpha/CCPG 0.033 0.025 -10000 0 -0.085 1 1
RXRA 0.024 0.024 -10000 0 -0.12 1 1
RXRB 0.023 0.024 -10000 0 -10000 0 0
THRB 0.021 0.087 0.12 28 -0.32 13 41
PPARG 0.025 0.04 -10000 0 -0.32 3 3
PPARD 0.026 0.009 -10000 0 -10000 0 0
TNF -0.051 0.22 -10000 0 -0.9 13 13
mol:Oxysterols 0 0.014 -10000 0 -0.11 1 1
cholesterol transport -0.026 0.14 -10000 0 -0.5 13 13
PPARA 0.027 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.006 0.088 0.12 2 -0.32 16 18
RXRs/NUR77/BCL2 -0.024 0.095 -10000 0 -0.2 44 44
SREBF1 -0.028 0.14 -10000 0 -0.63 7 7
RXRs/RXRs/DNA/9cRA 0.008 0.094 0.28 1 -0.16 47 48
ABCA1 -0.033 0.18 -10000 0 -0.75 10 10
RARs/THRs 0.06 0.09 -10000 0 -0.18 24 24
RXRs/FXR 0.016 0.096 -10000 0 -0.17 40 40
BCL2 0.018 0.059 -10000 0 -0.32 7 7
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.027 0.18 -10000 0 -0.57 18 18
UGCG -0.034 0.19 -10000 0 -0.66 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT -0.025 0.2 0.28 1 -0.47 30 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.033 0.19 -10000 0 -0.65 18 18
mol:DAG -0.09 0.29 -10000 0 -0.89 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.015 0.19 0.28 1 -0.46 32 33
FRAP1 -0.03 0.22 0.3 1 -0.52 32 33
FOXO3 -0.03 0.2 0.28 2 -0.5 30 32
AKT1 -0.03 0.22 0.28 2 -0.55 30 32
GAB2 0.027 0.007 -10000 0 -10000 0 0
SMPD1 -0.001 0.14 -10000 0 -0.85 5 5
SGMS1 -0.065 0.25 -10000 0 -0.75 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.027 -10000 0 -0.23 3 3
CALM1 0.028 0.005 -10000 0 -10000 0 0
cell proliferation -0.047 0.22 0.26 1 -0.57 27 28
EIF3A 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.039 0.039 -10000 0 -0.28 3 3
RPS6KB1 0 0.14 -10000 0 -0.9 5 5
mol:sphingomyelin -0.09 0.29 -10000 0 -0.89 26 26
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.019 0.064 -10000 0 -0.31 8 8
PIK3R1 0.026 0.032 -10000 0 -0.31 2 2
JAK1 0.03 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MYC -0.002 0.19 0.36 3 -0.49 20 23
MYB -0.008 0.19 -10000 0 -0.96 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.034 0.21 -10000 0 -0.52 33 33
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.14 -10000 0 -0.81 5 5
mol:PI-3-4-5-P3 -0.033 0.21 -10000 0 -0.5 33 33
Rac1/GDP 0.016 0.03 -10000 0 -0.21 3 3
T cell proliferation -0.032 0.19 0.26 2 -0.48 31 33
SHC1 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.011 0.022 4 -0.064 6 10
PRKCZ -0.034 0.2 0.26 2 -0.51 30 32
NF kappa B1 p50/RelA -0.003 0.2 0.3 1 -0.45 32 33
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.035 0.2 -10000 0 -0.5 30 30
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
RELA 0.028 0.005 -10000 0 -10000 0 0
IL2RA 0.005 0.089 -10000 0 -0.32 16 16
IL2RB 0.008 0.09 -10000 0 -0.31 16 16
TERT 0.007 0.087 0.12 8 -0.32 15 23
E2F1 0.01 0.091 -10000 0 -0.44 8 8
SOS1 0.029 0.003 -10000 0 -10000 0 0
RPS6 0.025 0.01 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.032 5 -0.012 4 9
PTPN11 0.029 0.004 -10000 0 -10000 0 0
IL2RG -0.01 0.12 0.13 7 -0.31 29 36
actin cytoskeleton organization -0.032 0.19 0.26 2 -0.48 31 33
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.021 0.016 -10000 0 -10000 0 0
PIK3CA 0.027 0.032 -10000 0 -0.31 2 2
Rac1/GTP 0.042 0.039 -10000 0 -0.2 3 3
LCK -0.012 0.12 0.13 13 -0.31 32 45
BCL2 -0.028 0.21 -10000 0 -0.56 24 24
amb2 Integrin signaling

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.027 0.1 0.19 2 -0.29 19 21
alphaM/beta2 Integrin/GPIbA 0.032 0.1 0.18 1 -0.26 20 21
alphaM/beta2 Integrin/proMMP-9 0.018 0.12 0.19 2 -0.26 30 32
PLAUR 0.025 0.048 0.12 7 -0.32 4 11
HMGB1 0.024 0.022 -10000 0 -0.086 2 2
alphaM/beta2 Integrin/Talin 0.034 0.08 0.18 1 -0.26 12 13
AGER 0.023 0.023 0.13 1 -10000 0 1
RAP1A 0.028 0.006 -10000 0 -10000 0 0
SELPLG 0.017 0.063 0.12 1 -0.32 8 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.044 0.11 -10000 0 -0.28 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.11 0.12 20 -0.32 25 45
CYR61 0.028 0.037 -10000 0 -0.32 2 2
TLN1 0.026 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.11 -10000 0 -0.31 16 16
RHOA 0.028 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.022 0.12 0.12 9 -0.31 35 44
MYH2 -0.02 0.1 0.21 1 -0.35 9 10
MST1R 0.018 0.097 -10000 0 -0.32 16 16
leukocyte activation during inflammatory response 0.03 0.075 -10000 0 -0.25 12 12
APOB 0.026 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.015 0.076 -10000 0 -0.32 11 11
JAM3 0.012 0.07 -10000 0 -0.32 10 10
GP1BA 0.02 0.085 -10000 0 -0.32 12 12
alphaM/beta2 Integrin/CTGF 0.029 0.1 0.18 1 -0.29 16 17
alphaM/beta2 Integrin -0.021 0.11 -10000 0 -0.35 16 16
JAM3 homodimer 0.012 0.07 -10000 0 -0.31 10 10
ICAM2 0.028 0.008 -10000 0 -10000 0 0
ICAM1 0.018 0.059 -10000 0 -0.32 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.023 0.12 -10000 0 -0.34 18 18
cell adhesion 0.031 0.1 0.18 1 -0.25 20 21
NFKB1 0.016 0.14 0.36 5 -0.38 19 24
THY1 0.024 0.035 0.12 3 -0.32 2 5
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.026 0.017 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.046 0.089 0.2 1 -0.28 12 13
IL6 -0.008 0.14 0.35 5 -0.4 17 22
ITGB2 0.01 0.079 0.13 2 -0.31 12 14
elevation of cytosolic calcium ion concentration 0.045 0.098 0.21 4 -0.3 14 18
alphaM/beta2 Integrin/JAM2/JAM3 0.037 0.1 0.2 1 -0.25 21 22
JAM2 0.025 0.041 -10000 0 -0.32 3 3
alphaM/beta2 Integrin/ICAM1 0.044 0.12 -10000 0 -0.23 31 31
alphaM/beta2 Integrin/uPA/Plg 0.038 0.089 0.25 1 -0.28 13 14
RhoA/GTP -0.022 0.11 -10000 0 -0.35 11 11
positive regulation of phagocytosis -0.009 0.13 0.18 2 -0.39 17 19
Ron/MSP 0.032 0.078 -10000 0 -0.23 17 17
alphaM/beta2 Integrin/uPAR/uPA 0.047 0.099 0.21 4 -0.3 14 18
alphaM/beta2 Integrin/uPAR 0.035 0.093 0.18 1 -0.29 14 15
PLAU 0.025 0.043 0.12 7 -0.32 3 10
PLAT 0.024 0.041 0.12 3 -0.32 3 6
actin filament polymerization -0.02 0.099 0.21 1 -0.34 9 10
MST1 0.025 0.032 -10000 0 -0.32 2 2
alphaM/beta2 Integrin/lipoprotein(a) 0.034 0.077 -10000 0 -0.25 12 12
TNF -0.034 0.16 0.39 1 -0.52 18 19
RAP1B 0.028 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.034 0.093 0.25 1 -0.31 13 14
fibrinolysis 0.036 0.087 0.24 1 -0.28 13 14
HCK 0.012 0.07 -10000 0 -0.32 10 10
dendritic cell antigen processing and presentation -0.023 0.12 -10000 0 -0.34 18 18
VTN 0.032 0.06 -10000 0 -0.32 5 5
alphaM/beta2 Integrin/CYR61 0.036 0.088 0.18 1 -0.28 13 14
LPA 0.016 0.01 -10000 0 -10000 0 0
LRP1 0.028 0.005 -10000 0 -10000 0 0
cell migration 0.001 0.12 0.17 2 -0.26 33 35
FN1 0.012 0.077 -10000 0 -0.32 12 12
alphaM/beta2 Integrin/Thy1 0.031 0.087 0.18 1 -0.27 14 15
MPO 0.018 0.065 0.12 5 -0.32 8 13
KNG1 0.02 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.037 0.01 -10000 0 -10000 0 0
ROCK1 -0.025 0.11 0.24 2 -0.32 12 14
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.016 0.01 -10000 0 -10000 0 0
CTGF 0.019 0.063 -10000 0 -0.32 7 7
alphaM/beta2 Integrin/Hck 0.027 0.11 0.18 1 -0.4 12 13
ITGAM 0.015 0.064 -10000 0 -0.33 7 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.011 0.13 0.2 3 -0.24 40 43
HP 0.015 0.1 0.12 37 -0.32 17 54
leukocyte adhesion 0.02 0.11 -10000 0 -0.36 14 14
SELP -0.022 0.12 0.12 9 -0.32 35 44
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.014 0.021 -10000 0 -0.18 3 3
SNTA1 0.023 0.04 -10000 0 -0.32 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.026 -10000 0 -0.19 5 5
MAPK12 -0.01 0.079 0.2 12 -0.19 22 34
CCND1 0.002 0.058 -10000 0 -0.37 4 4
p38 gamma/SNTA1 0.006 0.077 0.2 10 -0.18 22 32
MAP2K3 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.027 0.023 -10000 0 -0.32 1 1
G2/M transition checkpoint -0.01 0.079 0.2 12 -0.19 22 34
MAP2K6 -0.004 0.062 0.24 3 -0.22 13 16
MAPT -0.018 0.11 0.15 19 -0.26 28 47
MAPK13 -0.012 0.025 -10000 0 -0.22 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.008 0.049 -10000 0 -0.3 5 5
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.009 0.12 1 -10000 0 1
RAS family/GTP/Tiam1 0.006 0.053 -10000 0 -0.18 11 11
NT3 (dimer)/TRKC 0.04 0.065 0.18 8 -0.22 10 18
NT3 (dimer)/TRKB 0.031 0.11 0.2 10 -0.2 33 43
SHC/Grb2/SOS1/GAB1/PI3K 0.02 0.047 -10000 0 -0.28 4 4
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
BDNF -0.009 0.13 0.12 34 -0.32 34 68
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
DYNLT1 0.025 0.01 -10000 0 -10000 0 0
NTRK1 0.021 0.059 -10000 0 -0.32 6 6
NTRK2 0.008 0.098 0.12 19 -0.32 18 37
NTRK3 0.023 0.074 -10000 0 -0.32 9 9
NT-4/5 (dimer)/TRKB 0.027 0.1 0.19 7 -0.2 32 39
neuron apoptosis 0.057 0.17 0.34 44 -10000 0 44
SHC 2-3/Grb2 -0.062 0.18 -10000 0 -0.37 43 43
SHC1 0.026 0.008 -10000 0 -10000 0 0
SHC2 -0.07 0.19 -10000 0 -0.48 32 32
SHC3 -0.058 0.18 -10000 0 -0.43 34 34
STAT3 (dimer) 0.032 0.032 -10000 0 -0.3 2 2
NT3 (dimer)/TRKA 0.04 0.087 0.19 10 -0.18 24 34
RIN/GDP 0.027 0.091 0.25 11 -0.21 6 17
GIPC1 0.029 0.003 -10000 0 -10000 0 0
KRAS 0.028 0.005 -10000 0 -10000 0 0
DNAJA3 -0.018 0.084 0.17 1 -0.21 30 31
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.014 0.062 0.29 2 -0.59 2 4
MAGED1 0.027 0.023 -10000 0 -0.32 1 1
PTPN11 0.029 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.025 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.02 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.029 0.089 0.18 1 -0.2 26 27
TRKA/NEDD4-2 0.033 0.049 -10000 0 -0.22 7 7
ELMO1 0.013 0.067 -10000 0 -0.32 9 9
RhoG/GTP/ELMO1/DOCK1 0.024 0.043 -10000 0 -0.17 9 9
NGF 0.016 0.073 0.12 8 -0.32 10 18
HRAS 0.028 0.006 -10000 0 -10000 0 0
DOCK1 0.026 0.008 -10000 0 -10000 0 0
GAB2 0.027 0.007 -10000 0 -10000 0 0
RIT2 0.018 0.004 -10000 0 -10000 0 0
RIT1 0.026 0.008 -10000 0 -10000 0 0
FRS2 0.028 0.005 -10000 0 -10000 0 0
DNM1 0.024 0.042 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.002 0.1 -10000 0 -0.23 31 31
mol:GDP 0.027 0.12 0.3 12 -0.3 7 19
NGF (dimer) 0.016 0.072 0.12 8 -0.31 10 18
RhoG/GDP 0.01 0.046 -10000 0 -0.21 9 9
RIT1/GDP 0.018 0.077 0.21 4 -0.21 6 10
TIAM1 0.01 0.076 -10000 0 -0.32 12 12
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
BDNF (dimer)/TRKB 0.011 0.11 0.18 6 -0.2 48 54
KIDINS220/CRKL/C3G 0.038 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.028 -10000 0 -0.22 2 2
FRS2 family/SHP2 0.05 0.021 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.034 -10000 0 -0.17 2 2
RIT1/GTP 0.02 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.033 0.037 -10000 0 -0.31 1 1
RAP1/GDP 0.017 0.066 0.14 6 -0.18 6 12
KIDINS220/CRKL 0.028 0.009 0.12 1 -10000 0 1
BDNF (dimer) -0.009 0.13 0.12 34 -0.31 34 68
ubiquitin-dependent protein catabolic process 0.04 0.064 0.18 1 -0.18 15 16
Schwann cell development -0.016 0.021 -10000 0 -10000 0 0
EHD4 0.028 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.028 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.046 -10000 0 -0.2 3 3
RAP1B 0.028 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.002 0.12 0.18 3 -0.18 54 57
ABL1 0.027 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.082 -10000 0 -0.28 6 6
STAT3 0.032 0.032 -10000 0 -0.3 2 2
axon guidance -0.013 0.1 -10000 0 -0.18 54 54
MAPK3 -0.015 0.084 0.19 17 -0.19 26 43
MAPK1 -0.016 0.076 0.18 15 -0.18 24 39
CDC42/GDP 0.032 0.094 0.25 13 -0.21 6 19
NTF3 0.033 0.037 -10000 0 -0.32 1 1
NTF4 0.025 0.019 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.04 0.064 0.18 1 -0.18 14 15
PI3K 0.036 0.039 -10000 0 -0.28 3 3
FRS3 0.026 0.009 -10000 0 -10000 0 0
FAIM 0.026 0.023 -10000 0 -0.32 1 1
GAB1 0.026 0.032 -10000 0 -0.32 2 2
RASGRF1 -0.028 0.095 0.15 2 -0.22 31 33
SOS1 0.029 0.003 -10000 0 -10000 0 0
MCF2L -0.003 0.074 0.21 4 -0.18 27 31
RGS19 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.028 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.087 0.3 4 -0.42 3 7
Rac1/GDP 0.023 0.085 0.24 9 -0.22 5 14
NGF (dimer)/TRKA/GRIT 0.026 0.057 0.16 1 -0.18 14 15
neuron projection morphogenesis -0.015 0.17 -10000 0 -0.89 6 6
NGF (dimer)/TRKA/NEDD4-2 0.04 0.065 0.18 1 -0.18 15 16
MAP2K1 0.004 0.07 0.19 26 -0.16 2 28
NGFR 0.014 0.1 0.12 34 -0.32 19 53
NGF (dimer)/TRKA/GIPC/GAIP 0.005 0.069 -10000 0 -0.21 19 19
RAS family/GTP/PI3K 0.018 0.032 -10000 0 -0.24 3 3
FRS2 family/SHP2/GRB2/SOS1 0.07 0.034 -10000 0 -10000 0 0
NRAS 0.028 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
PRKCI 0.024 0.039 -10000 0 -0.32 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCZ 0.02 0.05 -10000 0 -0.32 5 5
MAPKKK cascade -0.04 0.19 -10000 0 -0.56 24 24
RASA1 0.024 0.032 -10000 0 -0.32 2 2
TRKA/c-Abl 0.033 0.045 -10000 0 -0.21 6 6
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.025 0.11 0.19 6 -0.18 46 52
NGF (dimer)/TRKA/p62/Atypical PKCs 0.05 0.077 0.2 1 -0.16 20 21
MATK 0.006 0.095 0.12 10 -0.32 18 28
NEDD4L 0.027 0.023 -10000 0 -0.32 1 1
RAS family/GDP -0.013 0.039 -10000 0 -0.15 8 8
NGF (dimer)/TRKA -0.011 0.09 0.19 1 -0.22 31 32
Rac1/GTP -0.024 0.075 -10000 0 -0.2 25 25
FRS2 family/SHP2/CRK family 0.067 0.037 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.01 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.092 -10000 0 -0.2 14 14
NFATC4 -0.031 0.068 0.2 3 -0.23 6 9
ERBB2IP 0.024 0.039 -10000 0 -0.31 3 3
HSP90 (dimer) 0.026 0.023 -10000 0 -0.31 1 1
mammary gland morphogenesis 0.007 0.08 0.18 7 -0.19 22 29
JUN 0.021 0.071 0.25 3 -0.22 1 4
HRAS 0.028 0.007 -10000 0 -10000 0 0
DOCK7 -0.029 0.067 0.15 8 -0.19 15 23
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.081 0.23 3 -0.18 25 28
AKT1 -0.006 0.006 -10000 0 -10000 0 0
BAD -0.01 0.003 -10000 0 -10000 0 0
MAPK10 -0.01 0.062 0.16 6 -0.18 2 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.009 0.086 0.2 7 -0.2 22 29
RAF1 0.009 0.1 0.25 8 -0.26 9 17
ErbB2/ErbB3/neuregulin 2 0.005 0.082 0.22 2 -0.2 27 29
STAT3 0.006 0.14 -10000 0 -0.88 6 6
cell migration -0.006 0.07 0.23 7 -0.16 3 10
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.03 0.25 0.39 2 -0.61 33 35
FOS 0.001 0.16 0.36 2 -0.34 33 35
NRAS 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.08 0.18 7 -0.19 22 29
MAPK3 -0.019 0.2 0.42 1 -0.46 35 36
MAPK1 -0.022 0.21 0.42 1 -0.49 33 34
JAK2 -0.028 0.059 0.14 4 -0.19 15 19
NF2 0.01 0.013 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.065 -10000 0 -0.2 19 19
NRG1 0.019 0.082 0.13 1 -0.32 11 12
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.084 0.22 2 -0.24 17 19
MAPK9 -0.009 0.057 0.18 5 -0.17 1 6
ERBB2 -0.025 0.052 0.3 3 -0.23 7 10
ERBB3 0.013 0.07 -10000 0 -0.32 10 10
SHC1 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.006 0.14 -10000 0 -0.86 6 6
RNF41 -0.013 0.007 -10000 0 -10000 0 0
FRAP1 -0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.028 0.042 -10000 0 -0.15 18 18
ErbB2/ErbB2/HSP90 (dimer) -0.023 0.043 0.22 3 -0.19 8 11
CHRNA1 -0.035 0.24 0.34 2 -0.6 34 36
myelination -0.03 0.065 0.24 2 -0.24 4 6
PPP3CB -0.024 0.062 0.15 7 -0.18 15 22
KRAS 0.028 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.026 0.075 -10000 0 -0.18 16 16
NRG2 0.004 0.087 -10000 0 -0.32 16 16
mol:GDP -0.004 0.065 -10000 0 -0.2 19 19
SOS1 0.028 0.003 -10000 0 -10000 0 0
MAP2K2 -0.006 0.11 0.22 11 -0.23 26 37
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.029 0.068 0.15 10 -0.19 18 28
MAP2K1 -0.012 0.19 0.39 1 -0.56 12 13
heart morphogenesis 0.007 0.08 0.18 7 -0.19 22 29
RAS family/GDP 0.031 0.09 -10000 0 -0.19 15 15
GRB2 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.015 0.007 -10000 0 -10000 0 0
CHRNE 0.012 0.023 0.11 2 -0.13 1 3
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
activation of caspase activity 0.006 0.006 -10000 0 -10000 0 0
nervous system development 0.007 0.08 0.18 7 -0.19 22 29
CDC42 0.028 0.005 -10000 0 -10000 0 0
Syndecan-2-mediated 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
Syndecan-2/Fibronectin 0.012 0.058 -10000 0 -0.19 17 17
EPHB2 0.008 0.082 -10000 0 -0.32 14 14
Syndecan-2/TACI 0.007 0.076 0.13 2 -0.18 30 32
LAMA1 -0.013 0.12 0.12 17 -0.32 32 49
Syndecan-2/alpha2 ITGB1 0.04 0.074 0.18 5 -0.17 18 23
HRAS 0.028 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.002 0.034 -10000 0 -0.17 8 8
ITGA5 0.028 0.035 0.12 5 -0.32 2 7
BAX -0.009 0.038 -10000 0 -10000 0 0
EPB41 0.025 0.032 -10000 0 -0.32 2 2
positive regulation of cell-cell adhesion 0.017 0.037 -10000 0 -0.16 9 9
LAMA3 0.024 0.059 0.12 11 -0.32 6 17
EZR 0.024 0.024 -10000 0 -0.32 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.024 0.024 -10000 0 -0.32 1 1
Syndecan-2/MMP2 0.013 0.061 -10000 0 -0.2 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.029 0.056 0.18 1 -0.22 10 11
dendrite morphogenesis 0.011 0.061 -10000 0 -0.19 17 17
Syndecan-2/GM-CSF 0.02 0.039 0.13 1 -0.18 7 8
determination of left/right symmetry 0.004 0.041 -10000 0 -0.21 8 8
Syndecan-2/PKC delta 0.02 0.039 -10000 0 -0.18 8 8
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
MAPK3 0.014 0.058 0.19 17 -0.16 7 24
MAPK1 0.014 0.056 0.19 16 -0.16 6 22
Syndecan-2/RACK1 0.032 0.037 -10000 0 -0.15 7 7
NF1 0.024 0.039 -10000 0 -0.32 3 3
FGFR/FGF/Syndecan-2 0.004 0.041 -10000 0 -0.21 8 8
ITGA2 0.015 0.072 -10000 0 -0.32 10 10
MAPK8 -0.002 0.039 -10000 0 -0.17 11 11
Syndecan-2/alpha2/beta1 Integrin 0.016 0.097 0.2 5 -0.17 41 46
Syndecan-2/Kininogen 0.015 0.038 -10000 0 -0.18 8 8
ITGB1 0.027 0.011 -10000 0 -10000 0 0
SRC 0.019 0.051 0.18 17 -0.15 6 23
Syndecan-2/CASK/Protein 4.1 0.017 0.038 -10000 0 -0.16 10 10
extracellular matrix organization 0.018 0.051 -10000 0 -0.24 8 8
actin cytoskeleton reorganization 0.012 0.058 -10000 0 -0.19 17 17
Syndecan-2/Caveolin-2/Ras 0.029 0.044 -10000 0 -0.16 9 9
Syndecan-2/Laminin alpha3 0.02 0.054 0.13 1 -0.21 10 11
Syndecan-2/RasGAP 0.043 0.047 0.17 3 -0.15 9 12
alpha5/beta1 Integrin 0.038 0.03 0.18 1 -0.22 2 3
PRKCD 0.028 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.011 0.061 -10000 0 -0.19 17 17
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.042 0.17 5 -0.15 8 13
RHOA 0.028 0.004 -10000 0 -10000 0 0
SDCBP 0.023 0.033 -10000 0 -0.32 2 2
TNFRSF13B 0.002 0.11 -10000 0 -0.32 24 24
RASA1 0.024 0.032 -10000 0 -0.32 2 2
alpha2/beta1 Integrin 0.029 0.056 0.18 1 -0.22 10 11
Syndecan-2/Synbindin 0.018 0.039 -10000 0 -0.17 8 8
TGFB1 0.023 0.045 -10000 0 -0.32 4 4
CASP3 0.021 0.06 0.19 19 -0.16 8 27
FN1 0.012 0.077 -10000 0 -0.32 12 12
Syndecan-2/IL8 0.018 0.058 0.13 1 -0.19 15 16
SDC2 0.004 0.041 -10000 0 -0.21 8 8
KNG1 0.02 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.017 0.045 -10000 0 -0.18 11 11
TRAPPC4 0.025 0.009 -10000 0 -10000 0 0
CSF2 0.027 0.019 0.12 7 -10000 0 7
Syndecan-2/TGFB1 0.018 0.051 -10000 0 -0.24 8 8
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.037 -10000 0 -0.16 9 9
Syndecan-2/Ezrin 0.03 0.043 -10000 0 -0.16 9 9
PRKACA 0.018 0.063 0.19 18 -0.16 11 29
angiogenesis 0.018 0.058 0.13 1 -0.18 15 16
MMP2 0.015 0.076 -10000 0 -0.32 11 11
IL8 0.021 0.072 0.12 15 -0.32 9 24
calcineurin-NFAT signaling pathway 0.007 0.076 0.13 2 -0.18 30 32
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.014 0.14 0.24 2 -0.41 15 17
BAG4 0.023 0.039 -10000 0 -0.32 3 3
BAD 0.001 0.058 0.15 10 -0.14 12 22
NFKBIA 0.029 0.003 -10000 0 -10000 0 0
BIRC3 -0.008 0.11 -10000 0 -0.32 27 27
BAX 0.001 0.058 0.14 10 -0.15 12 22
EnzymeConsortium:3.1.4.12 0 0.037 0.074 8 -0.092 16 24
IKBKB -0.016 0.13 0.24 1 -0.39 15 16
MAP2K2 -0.002 0.059 0.19 4 -0.19 6 10
MAP2K1 0 0.062 0.2 6 -0.19 6 12
SMPD1 0.001 0.042 0.099 2 -0.13 9 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.005 0.14 0.32 6 -0.4 15 21
MAP2K4 -0.002 0.059 0.18 4 -0.18 8 12
protein ubiquitination -0.018 0.14 0.23 2 -0.38 17 19
EnzymeConsortium:2.7.1.37 -0.002 0.065 0.2 5 -0.19 8 13
response to UV 0 0.001 0.002 6 -0.002 7 13
RAF1 -0.001 0.057 0.14 8 -0.16 11 19
CRADD 0.029 0.007 0.12 1 -10000 0 1
mol:ceramide 0.002 0.056 0.13 8 -0.14 17 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.038 0.008 -10000 0 -10000 0 0
MADD 0.028 0.005 -10000 0 -10000 0 0
MAP3K1 -0.001 0.063 0.14 10 -0.15 18 28
TRADD 0.028 0.006 -10000 0 -10000 0 0
RELA/p50 0.028 0.005 -10000 0 -10000 0 0
MAPK3 0.002 0.062 0.21 4 -0.2 7 11
MAPK1 0.002 0.062 0.21 4 -0.2 6 10
p50/RELA/I-kappa-B-alpha 0.041 0.008 -10000 0 -10000 0 0
FADD -0.01 0.14 0.26 5 -0.43 12 17
KSR1 0 0.057 0.13 10 -0.15 14 24
MAPK8 -0.006 0.061 0.17 4 -0.24 6 10
TRAF2 0.027 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.003 2 -0.002 1 3
CHUK -0.018 0.13 0.23 2 -0.38 16 18
TNF R/SODD 0.036 0.031 -10000 0 -0.22 3 3
TNF 0.013 0.077 0.12 10 -0.32 11 21
CYCS 0.01 0.062 0.15 13 -0.15 11 24
IKBKG -0.017 0.13 0.24 3 -0.39 15 18
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.023 0.13 -10000 0 -0.38 19 19
RELA 0.028 0.005 -10000 0 -10000 0 0
RIPK1 0.025 0.01 -10000 0 -10000 0 0
AIFM1 0.003 0.058 0.16 6 -0.15 10 16
TNF/TNF R/SODD 0.037 0.062 -10000 0 -0.18 14 14
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.003 2 -0.002 1 3
CASP8 0.021 0.091 -10000 0 -0.67 3 3
NSMAF -0.013 0.14 0.22 8 -0.39 16 24
response to hydrogen peroxide 0 0.001 0.002 6 -0.002 7 13
BCL2 0.018 0.059 -10000 0 -0.32 7 7
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.037 0.031 -10000 0 -0.22 1 1
PDGFRB 0.024 0.033 -10000 0 -0.32 2 2
SPHK1 -0.014 0.13 -10000 0 -0.68 8 8
mol:S1P -0.014 0.12 -10000 0 -0.6 8 8
S1P1/S1P/Gi -0.041 0.16 0.24 2 -0.34 36 38
GNAO1 -0.028 0.13 0.13 5 -0.32 38 43
PDGFB-D/PDGFRB/PLCgamma1 -0.016 0.15 0.24 7 -0.35 25 32
PLCG1 -0.045 0.14 0.22 3 -0.37 25 28
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.033 -10000 0 -0.32 2 2
GNAI2 0.026 0.014 -10000 0 -10000 0 0
GNAI3 0.025 0.014 -10000 0 -10000 0 0
GNAI1 0.021 0.035 -10000 0 -0.32 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.017 -10000 0 -0.18 1 1
S1P1/S1P -0.006 0.095 0.19 1 -0.38 9 10
negative regulation of cAMP metabolic process -0.04 0.15 0.24 2 -0.33 36 38
MAPK3 -0.055 0.19 0.3 3 -0.51 24 27
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
KDR 0.026 0.028 0.12 3 -0.32 1 4
PLCB2 0.01 0.11 0.23 9 -0.38 8 17
RAC1 0.025 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.08 -10000 0 -0.33 9 9
receptor internalization -0.006 0.088 -10000 0 -0.35 9 9
PTGS2 -0.059 0.27 0.34 2 -0.93 16 18
Rac1/GTP -0.007 0.079 -10000 0 -0.32 9 9
RHOA 0.028 0.004 -10000 0 -10000 0 0
VEGFA 0.027 0.022 0.12 7 -10000 0 7
negative regulation of T cell proliferation -0.04 0.15 0.24 2 -0.33 36 38
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0 0.094 0.12 4 -0.32 18 22
MAPK1 -0.051 0.18 0.34 2 -0.48 25 27
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.1 0.2 4 -0.34 9 13
ABCC1 0.022 0.045 -10000 0 -0.32 4 4
IGF1 pathway

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
NCK2 0.029 0.003 -10000 0 -10000 0 0
PTK2 0.026 0.009 -10000 0 -10000 0 0
CRKL -0.002 0.054 0.14 3 -0.18 15 18
GRB2/SOS1/SHC 0.051 0.02 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.007 0.056 -10000 0 -0.18 15 15
IGF-1R heterotetramer/IGF1/PTP1B 0.035 0.062 -10000 0 -0.18 15 15
AKT1 -0.024 0.059 0.17 5 -0.18 16 21
BAD -0.026 0.056 0.16 5 -0.18 15 20
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.003 0.053 0.14 2 -0.18 15 17
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.014 0.061 0.15 2 -0.18 16 18
RAF1 -0.003 0.076 0.26 1 -0.47 3 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.043 0.07 0.18 2 -0.17 15 17
YWHAZ 0.026 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.017 0.065 0.16 2 -0.15 27 29
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
RPS6KB1 -0.024 0.055 0.17 4 -0.17 14 18
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.079 0.26 3 -0.38 3 6
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.015 0.052 -10000 0 -0.16 13 13
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.063 -10000 0 -0.14 14 14
IGF-1R heterotetramer 0.02 0.028 -10000 0 -0.052 25 25
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.068 0.17 2 -0.14 27 29
Crk/p130 Cas/Paxillin 0.036 0.068 -10000 0 -0.16 17 17
IGF1R 0.02 0.028 -10000 0 -0.052 25 25
IGF1 0.026 0.035 0.13 4 -0.064 14 18
IRS2/Crk 0.005 0.055 0.16 1 -0.17 16 17
PI3K 0.039 0.076 0.18 2 -0.18 18 20
apoptosis 0.02 0.055 0.23 3 -0.18 3 6
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
PRKCD -0.01 0.087 0.2 2 -0.29 18 20
RAF1/14-3-3 E 0.009 0.073 0.26 1 -0.4 3 4
BAD/14-3-3 -0.02 0.058 0.19 3 -0.25 3 6
PRKCZ -0.026 0.062 0.17 5 -0.17 21 26
Crk/p130 Cas/Paxillin/FAK1 0.013 0.058 0.14 1 -0.17 12 13
PTPN1 0.026 0.011 0.12 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.008 0.09 -10000 0 -0.3 18 18
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.063 -10000 0 -0.16 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.016 0.063 0.13 8 -0.14 27 35
GRB10 0.021 0.04 -10000 0 -0.32 3 3
PTPN11 -0.002 0.055 0.14 3 -0.18 16 19
IRS1 0.005 0.058 0.12 8 -0.19 16 24
IRS2 -0.004 0.056 0.14 3 -0.18 17 20
IGF-1R heterotetramer/IGF1 0.023 0.075 -10000 0 -0.24 17 17
GRB2 0.028 0.005 -10000 0 -10000 0 0
PDPK1 -0.022 0.062 0.18 5 -0.18 16 21
YWHAE 0.027 0.007 -10000 0 -10000 0 0
PRKD1 -0.009 0.083 -10000 0 -0.28 17 17
SHC1 0.026 0.008 -10000 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.007 0.12 0.21 13 -0.33 18 31
PDGFB-D/PDGFRB/SLAP 0.026 0.053 -10000 0 -0.21 10 10
PDGFB-D/PDGFRB/APS/CBL 0.038 0.046 -10000 0 -0.18 7 7
AKT1 0.007 0.087 0.3 8 -0.37 1 9
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0.13 0.23 14 -0.36 18 32
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
FGR -0.002 0.13 0.27 2 -0.47 12 14
mol:Ca2+ 0.005 0.14 0.23 13 -0.42 16 29
MYC 0.044 0.15 0.4 11 -0.36 8 19
SHC1 0.026 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.06 0.17 29 -0.19 4 33
LRP1/PDGFRB/PDGFB 0.049 0.031 -10000 0 -0.19 2 2
GRB10 0.021 0.04 -10000 0 -0.32 3 3
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0.004 0.14 0.23 13 -0.43 16 29
PTEN 0.026 0.009 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
GRB7 0.033 0.036 0.12 20 -0.32 1 21
PDGFB-D/PDGFRB/SHP2 0.038 0.027 -10000 0 -0.22 2 2
PDGFB-D/PDGFRB/GRB10 0.03 0.04 -10000 0 -0.22 5 5
cell cycle arrest 0.026 0.053 -10000 0 -0.21 10 10
HRAS 0.028 0.006 -10000 0 -10000 0 0
HIF1A 0.002 0.081 0.25 10 -0.34 1 11
GAB1 0 0.14 0.24 8 -0.41 16 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.003 0.13 0.23 15 -0.38 14 29
PDGFB-D/PDGFRB 0.044 0.038 -10000 0 -0.2 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.037 0.027 -10000 0 -0.22 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.098 -10000 0 -0.28 19 19
positive regulation of MAPKKK cascade 0.038 0.027 -10000 0 -0.22 2 2
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
mol:IP3 0.004 0.14 0.23 13 -0.43 16 29
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.027 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.034 -10000 0 -0.22 2 2
SHB 0.012 0.075 0.12 5 -0.32 11 16
BLK -0.05 0.2 0.24 2 -0.5 33 35
PTPN2 0.027 0.024 -10000 0 -0.32 1 1
PDGFB-D/PDGFRB/SNX15 0.038 0.027 -10000 0 -0.22 2 2
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
VAV2 0.002 0.15 0.26 10 -0.42 17 27
CBL 0.025 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.036 0.032 -10000 0 -0.22 3 3
LCK -0.052 0.21 -10000 0 -0.54 31 31
PDGFRB 0.025 0.034 -10000 0 -0.32 2 2
ACP1 0.028 0.005 -10000 0 -10000 0 0
HCK -0.012 0.14 0.22 1 -0.57 11 12
ABL1 -0.003 0.14 0.22 13 -0.34 20 33
PDGFB-D/PDGFRB/CBL -0.011 0.16 0.25 3 -0.48 18 21
PTPN1 0.027 0.011 0.13 1 -10000 0 1
SNX15 0.028 0.005 -10000 0 -10000 0 0
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.032 -10000 0 -0.32 2 2
cell proliferation 0.044 0.14 0.37 14 -0.33 8 22
SLA 0.014 0.063 -10000 0 -0.32 8 8
actin cytoskeleton reorganization 0.022 0.076 0.19 26 -0.17 12 38
SRC 0.012 0.057 0.22 1 -10000 0 1
PI3K -0.022 0.032 -10000 0 -0.22 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.052 0.037 -10000 0 -0.19 2 2
SH2B2 0.018 0.05 -10000 0 -0.32 5 5
PLCgamma1/SPHK1 0.013 0.14 0.23 14 -0.38 18 32
LYN 0.007 0.087 -10000 0 -0.54 3 3
LRP1 0.028 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.003 -10000 0 -10000 0 0
STAT5B 0.028 0.005 -10000 0 -10000 0 0
STAT5A 0.027 0.023 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.062 0.052 -10000 0 -0.16 5 5
SPHK1 0.024 0.059 0.12 10 -0.32 6 16
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.004 0.14 0.23 13 -0.43 16 29
PLCG1 0.004 0.14 0.24 11 -0.44 16 27
NHERF/PDGFRB 0.05 0.036 -10000 0 -0.18 4 4
YES1 -0.008 0.14 0.33 1 -0.55 11 12
cell migration 0.049 0.036 -10000 0 -0.18 4 4
SHC/Grb2/SOS1 0.059 0.05 -10000 0 -0.16 3 3
SLC9A3R2 0.028 0.024 0.12 1 -0.32 1 2
SLC9A3R1 0.027 0.024 0.12 1 -0.32 1 2
NHERF1-2/PDGFRB/PTEN 0.058 0.042 -10000 0 -0.17 4 4
FYN -0.033 0.17 0.23 1 -0.46 26 27
DOK1 0.01 0.069 0.18 31 -0.18 4 35
HRAS/GTP 0.021 0.004 -10000 0 -10000 0 0
PDGFB 0.028 0.012 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.32 13 -0.42 14 27
PRKCD 0.017 0.068 0.18 31 -0.18 3 34
FER 0.013 0.073 0.18 30 -0.2 6 36
MAPKKK cascade 0.02 0.093 0.2 43 -0.17 1 44
RASA1 0.015 0.072 0.18 31 -0.21 4 35
NCK1 0.028 0.006 -10000 0 -10000 0 0
NCK2 0.029 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.043 0.058 0.17 31 -0.16 4 35
PDGFB-D/PDGFRB/SHB 0.025 0.063 -10000 0 -0.22 13 13
chemotaxis -0.003 0.13 0.22 13 -0.34 20 33
STAT1-3-5/STAT1-3-5 0.051 0.049 -10000 0 -0.19 5 5
Bovine Papilomavirus E5/PDGFRB 0.018 0.024 -10000 0 -0.22 2 2
PTPRJ 0.027 0.023 -10000 0 -0.32 1 1
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.01 0.016 -10000 0 -0.18 2 2
ADCY5 -0.021 0.05 -10000 0 -0.18 20 20
ADCY6 -0.011 0.016 -10000 0 -0.18 2 2
ADCY7 -0.01 0.012 -10000 0 -0.18 1 1
ADCY1 -0.034 0.062 -10000 0 -0.18 35 35
ADCY2 -0.039 0.078 0.23 1 -0.18 51 52
ADCY3 -0.01 0.011 -10000 0 -0.18 1 1
ADCY8 -0.007 0.01 -10000 0 -10000 0 0
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.011 -10000 0 -0.18 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.072 0.2 9 -0.21 4 13
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.005 -10000 0 -10000 0 0
VLDLR 0.016 0.055 0.12 1 -0.32 6 7
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
NUDC 0.028 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.036 0.081 -10000 0 -0.18 23 23
CaM/Ca2+ 0.021 0.004 -10000 0 -10000 0 0
KATNA1 0.025 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0 0.082 0.19 24 -0.17 19 43
IQGAP1/CaM 0.04 0.011 -10000 0 -10000 0 0
DAB1 0.034 0.032 0.12 25 -10000 0 25
IQGAP1 0.028 0.006 -10000 0 -10000 0 0
PLA2G7 -0.001 0.098 -10000 0 -0.32 20 20
CALM1 0.028 0.005 -10000 0 -10000 0 0
DYNLT1 0.025 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.023 -10000 0 -0.32 1 1
CDK5R1 0.019 0.055 -10000 0 -0.32 6 6
LIS1/Poliovirus Protein 3A -0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.003 0.11 0.12 26 -0.32 24 50
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.027 0.091 0.18 8 -0.18 30 38
YWHAE 0.027 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.011 0.12 0.29 19 -0.26 7 26
MAP1B -0.002 0.039 -10000 0 -0.22 7 7
RAC1 0.01 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.021 0.062 0.18 5 -0.29 2 7
RELN 0.006 0.12 0.12 43 -0.32 25 68
PAFAH/LIS1 0.011 0.057 -10000 0 -0.18 17 17
LIS1/CLIP170 0.026 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.005 0.076 -10000 0 -0.25 5 5
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.099 0.17 3 -0.22 32 35
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.004 0.12 0.26 23 -0.29 5 28
LIS1/IQGAP1 0.025 0.011 -10000 0 -10000 0 0
RHOA 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B1 -0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.022 0.033 -10000 0 -0.32 2 2
MAP1B/LIS1/Dynein heavy chain 0.011 0.044 -10000 0 -0.14 7 7
NDEL1/Katanin 60/Dynein heavy chain 0.014 0.12 0.32 13 -0.27 6 19
LRP8 0.028 0.004 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.007 0.12 0.29 17 -0.26 7 24
P39/CDK5 -0.015 0.092 0.28 9 -0.29 1 10
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.01 -10000 0 -10000 0 0
CDK5 -0.022 0.052 0.18 5 -0.16 19 24
PPP2R5D 0.026 0.009 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.032 0.086 0.2 9 -0.16 28 37
RELN/VLDLR 0.035 0.087 -10000 0 -0.16 29 29
CDC42 0.011 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.092 0.36 1 -0.32 10 11
CRKL 0.006 0.062 0.15 22 -0.17 5 27
mol:DAG 0.013 0.059 -10000 0 -0.32 3 3
HRAS 0.007 0.085 0.28 7 -0.24 3 10
MAPK8 0.007 0.068 0.17 30 -0.2 4 34
RAP1A 0.007 0.065 0.16 24 -0.18 3 27
GAB1 0.005 0.071 0.16 24 -0.22 6 30
MAPK14 0.005 0.058 0.17 24 -0.19 1 25
EPO 0.022 0.028 0.13 7 -10000 0 7
PLCG1 0.013 0.06 -10000 0 -0.33 3 3
EPOR/TRPC2/IP3 Receptors 0.026 0.019 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.04 -10000 0 -0.2 2 2
GAB1/SHC/GRB2/SOS1 0.045 0.066 0.24 2 -0.22 4 6
EPO/EPOR (dimer) 0.034 0.03 -10000 0 -10000 0 0
IRS2 0.007 0.07 0.16 25 -0.25 2 27
STAT1 0.021 0.079 -10000 0 -0.29 9 9
STAT5B 0.017 0.065 -10000 0 -0.33 3 3
cell proliferation -0.001 0.061 0.17 21 -0.18 4 25
GAB1/SHIP/PIK3R1/SHP2/SHC 0.027 0.078 -10000 0 -0.25 12 12
TEC 0.002 0.071 0.16 22 -0.32 2 24
SOCS3 0.025 0.033 0.12 1 -0.32 2 3
STAT1 (dimer) 0.022 0.079 -10000 0 -0.29 9 9
JAK2 0.019 0.048 -10000 0 -0.32 4 4
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
EPO/EPOR (dimer)/JAK2 0.049 0.072 0.22 3 -0.16 14 17
EPO/EPOR 0.034 0.03 -10000 0 -10000 0 0
LYN 0.023 0.034 -10000 0 -0.31 2 2
TEC/VAV2 0.018 0.074 0.21 3 -0.2 7 10
elevation of cytosolic calcium ion concentration 0.026 0.019 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.046 0.042 -10000 0 -0.22 2 2
mol:IP3 0.013 0.059 -10000 0 -0.32 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.034 0.092 0.26 3 -0.24 13 16
SH2B3 0.023 0.044 -10000 0 -0.33 3 3
NFKB1 0.01 0.067 0.17 32 -0.2 2 34
EPO/EPOR (dimer)/JAK2/SOCS3 0.01 0.037 0.2 1 -0.2 5 6
PTPN6 0.02 0.062 0.16 24 -0.18 7 31
TEC/VAV2/GRB2 0.028 0.073 0.28 1 -0.19 4 5
EPOR 0.026 0.019 -10000 0 -10000 0 0
INPP5D 0.013 0.074 -10000 0 -0.32 11 11
mol:GDP 0.045 0.066 0.24 2 -0.22 4 6
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG2 0.021 0.051 -10000 0 -0.32 5 5
CRKL/CBL/C3G 0.032 0.06 0.19 1 -0.18 3 4
VAV2 0.007 0.071 0.16 22 -0.25 2 24
CBL 0.007 0.062 0.16 21 -0.24 2 23
SHC/Grb2/SOS1 0.026 0.05 -10000 0 -0.18 3 3
STAT5A 0.016 0.07 -10000 0 -0.4 3 3
GRB2 0.028 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.086 -10000 0 -0.33 8 8
LYN/PLCgamma2 0.031 0.052 -10000 0 -0.29 5 5
PTPN11 0.029 0.003 -10000 0 -10000 0 0
BTK 0 0.081 0.16 24 -0.24 11 35
BCL2 0.016 0.16 0.34 1 -0.71 8 9
PDGFR-alpha signaling 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
PDGFRA 0.01 0.087 0.14 2 -0.32 15 17
PDGF/PDGFRA/CRKL 0.028 0.061 -10000 0 -0.21 13 13
positive regulation of JUN kinase activity 0.053 0.054 -10000 0 -0.16 10 10
CRKL 0.028 0.009 0.12 1 -10000 0 1
PDGF/PDGFRA/Caveolin-3 0.022 0.064 -10000 0 -0.21 15 15
AP1 -0.008 0.055 -10000 0 -10000 0 0
mol:IP3 -0.018 0.054 0.25 1 -0.22 13 14
PLCG1 -0.018 0.054 0.25 1 -0.22 13 14
PDGF/PDGFRA/alphaV Integrin 0.024 0.074 -10000 0 -0.22 18 18
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.054 0.25 1 -0.22 13 14
CAV3 0.02 0.011 0.12 2 -10000 0 2
CAV1 0.024 0.024 -10000 0 -0.32 1 1
SHC/Grb2/SOS1 0.055 0.055 -10000 0 -0.16 10 10
PDGF/PDGFRA/Shf 0.023 0.073 -10000 0 -0.21 19 19
FOS -0.014 0.045 -10000 0 -10000 0 0
JUN -0.019 0.014 -10000 0 -10000 0 0
oligodendrocyte development 0.024 0.074 -10000 0 -0.22 18 18
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
mol:DAG -0.018 0.054 0.25 1 -0.22 13 14
PDGF/PDGFRA 0.01 0.087 0.14 2 -0.31 15 17
actin cytoskeleton reorganization 0.015 0.083 -10000 0 -0.22 24 24
SRF -0.01 0.008 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.04 0.067 -10000 0 -0.19 16 16
PDGF/PDGFRA/Crk/C3G 0.039 0.06 -10000 0 -0.17 15 15
JAK1 -0.019 0.053 -10000 0 -0.21 15 15
ELK1/SRF -0.013 0.055 0.15 13 -0.19 11 24
SHB 0.012 0.075 0.12 5 -0.32 11 16
SHF 0.023 0.046 0.12 3 -0.32 4 7
CSNK2A1 0.024 0.016 -10000 0 -10000 0 0
GO:0007205 -0.016 0.061 0.28 1 -0.25 13 14
SOS1 0.029 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.053 0.054 -10000 0 -0.16 10 10
PDGF/PDGFRA/SHB 0.015 0.083 -10000 0 -0.22 24 24
PDGF/PDGFRA/Caveolin-1 0.026 0.062 -10000 0 -0.21 13 13
ITGAV 0.023 0.045 -10000 0 -0.32 4 4
ELK1 -0.016 0.05 0.23 1 -0.21 12 13
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
PDGF/PDGFRA/Crk 0.026 0.063 -10000 0 -0.2 15 15
JAK-STAT cascade -0.019 0.052 -10000 0 -0.21 15 15
cell proliferation 0.023 0.073 -10000 0 -0.21 19 19
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.012 0.083 -10000 0 -0.24 26 26
CRKL 0.028 0.009 0.12 1 -10000 0 1
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DOCK1 0.026 0.008 -10000 0 -10000 0 0
ITGA4 0.002 0.098 0.12 6 -0.32 20 26
alpha4/beta7 Integrin/MAdCAM1 0.044 0.087 0.19 1 -0.17 30 31
EPO 0.025 0.021 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.092 -10000 0 -0.22 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.019 0.074 -10000 0 -0.21 20 20
EPO/EPOR (dimer) 0.038 0.019 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.075 -10000 0 -0.47 4 4
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
PI3K 0.036 0.039 -10000 0 -0.28 3 3
ARF6 0.028 0.004 -10000 0 -10000 0 0
JAK2 -0.001 0.081 -10000 0 -0.26 18 18
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
MADCAM1 0.032 0.023 0.12 13 -10000 0 13
cell adhesion 0.042 0.085 0.19 1 -0.17 30 31
CRKL/CBL 0.036 0.017 -10000 0 -10000 0 0
ITGB1 0.027 0.011 -10000 0 -10000 0 0
SRC -0.031 0.067 0.18 3 -0.19 28 31
ITGB7 0.011 0.076 -10000 0 -0.32 12 12
RAC1 0.025 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.021 0.095 -10000 0 -0.21 30 30
p130Cas/Crk/Dock1 0.015 0.08 0.19 3 -0.18 21 24
VCAM1 0.006 0.089 -10000 0 -0.32 16 16
RHOA 0.028 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.07 -10000 0 -0.16 20 20
BCAR1 -0.032 0.063 0.17 4 -0.19 23 27
EPOR 0.029 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.028 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.006 0.078 -10000 0 -0.49 4 4
TCGA08_p53

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
CDKN2A -0.005 0.054 -10000 0 -0.21 14 14
TP53 -0.006 0.045 0.23 1 -0.19 8 9
Senescence -0.01 0.055 0.23 1 -0.2 13 14
Apoptosis -0.01 0.055 0.23 1 -0.2 13 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.068 0.22 19 -10000 0 19
MDM4 0.024 0.024 -10000 0 -0.32 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.007 -10000 0 -10000 0 0
ELF1 0.006 0.091 -10000 0 -0.27 22 22
CCNA2 0.024 0.039 -10000 0 -0.32 3 3
PIK3CA 0.026 0.032 -10000 0 -0.31 2 2
JAK3 0.018 0.064 -10000 0 -0.32 8 8
PIK3R1 0.025 0.032 -10000 0 -0.31 2 2
JAK1 0.029 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.22 -10000 0 -0.52 34 34
SHC1 0.027 0.009 -10000 0 -10000 0 0
SP1 0.028 0.054 -10000 0 -0.33 5 5
IL2RA -0.025 0.16 -10000 0 -0.59 16 16
IL2RB 0.007 0.09 -10000 0 -0.32 16 16
SOS1 0.029 0.003 -10000 0 -10000 0 0
IL2RG -0.011 0.12 0.12 7 -0.31 29 36
G1/S transition of mitotic cell cycle -0.001 0.13 0.28 1 -0.4 16 17
PTPN11 0.029 0.003 -10000 0 -10000 0 0
CCND2 0.01 0.083 0.29 1 -0.59 4 5
LCK -0.013 0.12 0.12 13 -0.31 32 45
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.022 0.013 -10000 0 -10000 0 0
CDK6 0.014 0.063 -10000 0 -0.32 8 8
CCND3 -0.01 0.2 0.33 1 -0.53 21 22
Regulation of Androgen receptor activity

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
HDAC1 -0.007 0.017 -10000 0 -0.22 1 1
SMARCC1 0.011 0.008 -10000 0 -10000 0 0
REL 0.027 0.023 -10000 0 -0.32 1 1
HDAC7 -0.025 0.092 0.17 16 -0.29 5 21
JUN 0.029 0.004 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
KAT2B 0.02 0.055 -10000 0 -0.32 6 6
KAT5 0.028 0.005 -10000 0 -10000 0 0
MAPK14 -0.005 0.047 -10000 0 -0.22 9 9
FOXO1 0.027 0.023 -10000 0 -0.32 1 1
T-DHT/AR 0.008 0.11 0.24 1 -0.28 5 6
MAP2K6 0.007 0.068 -10000 0 -0.32 9 9
BRM/BAF57 0.037 0.016 -10000 0 -10000 0 0
MAP2K4 0.019 0.022 -10000 0 -10000 0 0
SMARCA2 0.025 0.01 -10000 0 -10000 0 0
PDE9A -0.1 0.32 -10000 0 -0.88 32 32
NCOA2 0.02 0.045 -10000 0 -0.31 4 4
CEBPA 0.012 0.078 -10000 0 -0.32 12 12
EHMT2 0.026 0.009 -10000 0 -10000 0 0
cell proliferation -0.008 0.16 0.33 13 -0.36 17 30
NR0B1 -0.018 0.14 0.12 30 -0.32 38 68
EGR1 0.028 0.028 0.12 6 -0.32 1 7
RXRs/9cRA 0.007 0.081 -10000 0 -0.16 40 40
AR/RACK1/Src 0.016 0.09 0.2 14 -0.23 3 17
AR/GR 0.005 0.085 -10000 0 -0.24 17 17
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.027 0.023 -10000 0 -0.32 1 1
RCHY1 0.029 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0 0.032 -10000 0 -0.22 3 3
T-DHT/AR/TIF2/CARM1 0.008 0.083 0.21 2 -0.2 11 13
SRC 0 0.076 0.18 29 -0.17 8 37
NR3C1 0.02 0.05 -10000 0 -0.32 5 5
KLK3 -0.033 0.089 -10000 0 -10000 0 0
APPBP2 0.02 0.022 -10000 0 -10000 0 0
TRIM24 0.026 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.001 0.079 0.18 17 -0.19 13 30
TMPRSS2 -0.055 0.24 -10000 0 -0.81 19 19
RXRG -0.04 0.14 0.12 2 -0.32 45 47
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.009 -10000 0 -10000 0 0
CARM1 0.028 0.006 -10000 0 -10000 0 0
NR2C2 0.025 0.032 -10000 0 -0.31 2 2
KLK2 0.005 0.1 0.24 2 -0.4 8 10
AR 0.005 0.064 0.14 18 -0.22 8 26
SENP1 0.029 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.023 -10000 0 -0.32 1 1
MDM2 0.027 0.006 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -10000 0 0
GATA2 0.02 0.061 -10000 0 -0.32 7 7
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.063 0.16 0.12 15 -0.31 65 80
T-DHT/AR/RACK1/Src 0.013 0.092 0.2 17 -0.25 2 19
positive regulation of transcription 0.02 0.061 -10000 0 -0.31 7 7
DNAJA1 0.018 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.011 -10000 0 -0.14 1 1
NCOA1 0.032 0.011 -10000 0 -10000 0 0
SPDEF 0.027 0.018 0.13 5 -10000 0 5
T-DHT/AR/TIF2 0.006 0.11 0.24 10 -0.31 15 25
T-DHT/AR/Hsp90 0.003 0.08 0.18 18 -0.19 11 29
GSK3B 0.027 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.02 0.046 0.21 3 -0.17 9 12
SIRT1 0.024 0.032 -10000 0 -0.32 2 2
ZMIZ2 0.025 0.01 -10000 0 -10000 0 0
POU2F1 0.016 0.053 -10000 0 -0.1 34 34
T-DHT/AR/DAX-1 -0.019 0.098 0.19 13 -0.22 19 32
CREBBP 0.029 0.003 -10000 0 -10000 0 0
SMARCE1 0.028 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.07 -10000 0 -0.32 10 10
ANTXR2 0.023 0.053 0.12 6 -0.32 5 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.011 -10000 0 -0.045 15 15
monocyte activation -0.029 0.15 -10000 0 -0.4 28 28
MAP2K2 0.013 0.039 -10000 0 -0.57 1 1
MAP2K1 -0.008 0.01 -10000 0 -10000 0 0
MAP2K7 -0.007 0.01 -10000 0 -0.045 14 14
MAP2K6 -0.013 0.029 -10000 0 -0.15 8 8
CYAA -0.016 0.035 -10000 0 -0.15 15 15
MAP2K4 -0.007 0.01 -10000 0 -10000 0 0
IL1B -0.021 0.059 -10000 0 -0.2 19 19
Channel 0.025 0.05 -10000 0 -0.16 15 15
NLRP1 -0.011 0.027 -10000 0 -0.17 6 6
CALM1 0.028 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.069 -10000 0 -0.39 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.011 0.045 15 -10000 0 15
MAPK3 -0.008 0.01 -10000 0 -10000 0 0
MAPK1 -0.007 0.009 -10000 0 -10000 0 0
PGR -0.012 0.028 -10000 0 -0.15 8 8
PA/Cellular Receptors 0.026 0.056 -10000 0 -0.18 15 15
apoptosis -0.004 0.011 -10000 0 -0.045 15 15
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.049 -10000 0 -0.16 15 15
macrophage activation -0.002 0.039 0.17 11 -10000 0 11
TNF 0.013 0.076 0.12 10 -0.32 11 21
VCAM1 -0.027 0.15 -10000 0 -0.42 26 26
platelet activation -0.003 0.069 -10000 0 -0.39 7 7
MAPKKK cascade 0.005 0.02 0.083 1 -0.066 9 10
IL18 -0.014 0.044 -10000 0 -0.18 12 12
negative regulation of macrophage activation -0.004 0.011 -10000 0 -0.045 15 15
LEF -0.004 0.011 -10000 0 -0.045 15 15
CASP1 -0.007 0.03 -10000 0 -0.09 18 18
mol:cAMP -0.003 0.07 -10000 0 -0.39 7 7
necrosis -0.004 0.011 -10000 0 -0.045 15 15
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.048 -10000 0 -0.15 15 15
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.035 0.013 -10000 0 -10000 0 0
PRKCZ 0.02 0.05 -10000 0 -0.32 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.028 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.008 0.061 -10000 0 -0.23 8 8
IRAK/TOLLIP 0.037 0.036 0.18 14 -10000 0 14
IKBKB 0.028 0.006 -10000 0 -10000 0 0
IKBKG 0.029 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.039 0.063 0.18 4 -0.22 11 15
IL1A 0.037 0.031 -10000 0 -10000 0 0
IL1B -0.025 0.067 -10000 0 -0.24 19 19
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.058 -10000 0 -0.16 7 7
IL1R2 0.016 0.076 -10000 0 -0.32 11 11
IL1R1 0.015 0.066 -10000 0 -0.32 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.082 0.23 1 -0.31 9 10
TOLLIP 0.028 0.006 -10000 0 -10000 0 0
TICAM2 0.021 0.045 -10000 0 -0.32 4 4
MAP3K3 0.028 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.019 -10000 0 -0.18 2 2
IKK complex/ELKS 0.025 0.077 -10000 0 -0.3 1 1
JUN -0.008 0.058 0.15 23 -10000 0 23
MAP3K7 0.023 0.033 -10000 0 -0.32 2 2
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.097 0.2 1 -0.18 34 35
IL1 alpha/IL1R1/IL1RAP/MYD88 0.065 0.063 -10000 0 -0.17 13 13
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.075 0.062 -10000 0 -0.16 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.088 0.18 1 -0.19 33 34
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.062 0.16 24 -10000 0 24
IRAK1 0.002 0.015 -10000 0 -10000 0 0
IL1RN/IL1R1 0.027 0.07 -10000 0 -0.23 15 15
IRAK4 0.028 0.004 -10000 0 -10000 0 0
PRKCI 0.024 0.039 -10000 0 -0.32 3 3
TRAF6 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.036 0.039 -10000 0 -0.28 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.073 -10000 0 -0.23 14 14
CHUK 0.025 0.024 -10000 0 -0.32 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.088 0.18 1 -0.19 33 34
IL1 beta/IL1R2 0.005 0.087 -10000 0 -0.2 33 33
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.024 -10000 0 -0.15 2 2
NF kappa B1 p50/RelA 0.021 0.087 -10000 0 -0.18 31 31
IRAK3 0.022 0.051 0.12 3 -0.32 5 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.097 -10000 0 -0.18 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.052 -10000 0 -0.18 13 13
IL1 alpha/IL1R1/IL1RAP 0.05 0.062 -10000 0 -0.19 13 13
RELA 0.028 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.007 -10000 0 -10000 0 0
MYD88 0.029 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.058 0.042 0.18 22 -10000 0 22
IL1RAP 0.024 0.047 0.12 4 -0.32 4 8
UBE2N 0.029 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.072 -10000 0 -0.2 14 14
CASP1 0.012 0.07 0.12 1 -0.32 10 11
IL1RN/IL1R2 0.028 0.076 0.18 1 -0.23 17 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.09 0.19 1 -0.18 33 34
TMEM189-UBE2V1 0.022 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.021 0.08 0.21 1 -0.3 9 10
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
IL1RN 0.022 0.062 -10000 0 -0.32 7 7
TRAF6/TAK1/TAB1/TAB2 0.041 0.029 -10000 0 -0.15 2 2
MAP2K6 0.003 0.067 0.17 26 -0.15 5 31
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.009 0.12 1 -10000 0 1
Rac1/GDP 0.028 0.013 -10000 0 -10000 0 0
DOCK1 0.026 0.008 -10000 0 -10000 0 0
ITGA4 0.002 0.098 0.12 6 -0.32 20 26
RAC1 0.025 0.01 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.092 -10000 0 -0.22 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.069 -10000 0 -0.18 20 20
alpha4/beta7 Integrin/Paxillin 0.019 0.076 -10000 0 -0.17 30 30
lamellipodium assembly -0.004 0.1 -10000 0 -0.39 12 12
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
PI3K 0.036 0.039 -10000 0 -0.28 3 3
ARF6 0.028 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.009 -10000 0 -10000 0 0
PXN -0.012 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
ARF6/GTP 0.038 0.061 -10000 0 -0.15 19 19
cell adhesion 0.037 0.063 -10000 0 -0.16 19 19
CRKL/CBL 0.036 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.061 -10000 0 -0.16 20 20
ITGB1 0.027 0.011 -10000 0 -10000 0 0
ITGB7 0.011 0.076 -10000 0 -0.32 12 12
ARF6/GDP 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.088 -10000 0 -0.18 30 30
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.18 2 2
VCAM1 0.006 0.089 -10000 0 -0.32 16 16
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.064 -10000 0 -0.16 19 19
alpha4/beta1 Integrin/Paxillin/GIT1 0.04 0.065 -10000 0 -0.16 19 19
BCAR1 0.024 0.032 -10000 0 -0.32 2 2
mol:GDP -0.038 0.063 0.16 20 -10000 0 20
CBL 0.025 0.01 -10000 0 -10000 0 0
PRKACA 0.029 0.003 -10000 0 -10000 0 0
GIT1 0.028 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.039 0.064 -10000 0 -0.16 19 19
Rac1/GTP -0.006 0.11 -10000 0 -0.44 12 12
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.014 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.066 -10000 0 -0.32 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.021 0.045 -10000 0 -0.32 4 4
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.028 0.005 -10000 0 -10000 0 0
FYN 0.025 0.01 -10000 0 -10000 0 0
MAP3K12 0.028 0.004 -10000 0 -10000 0 0
FGR 0.016 0.067 0.12 3 -0.32 9 12
p38 alpha/TAB1 -0.057 0.12 -10000 0 -0.31 32 32
PRKG1 0.015 0.073 0.12 8 -0.32 10 18
DUSP8 0.015 0.072 0.12 6 -0.32 10 16
PGK/cGMP/p38 alpha -0.014 0.15 0.19 5 -0.31 30 35
apoptosis -0.054 0.12 -10000 0 -0.3 32 32
RAL/GTP 0.034 0.013 -10000 0 -10000 0 0
LYN 0.024 0.033 -10000 0 -0.32 2 2
DUSP1 0.029 0.014 0.12 4 -10000 0 4
PAK1 0.027 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.058 0.031 -10000 0 -10000 0 0
TRAF6 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.01 -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 0.025 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.014 -10000 0 -10000 0 0
MAPK11 -0.019 0.17 0.28 7 -0.38 29 36
BLK 0.002 0.12 0.12 35 -0.32 26 61
HCK 0.012 0.07 -10000 0 -0.32 10 10
MAP2K3 0.027 0.007 -10000 0 -10000 0 0
DUSP16 0.028 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.05 -10000 0 -0.32 5 5
TRAF6/MEKK3 0.035 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.17 0.2 14 -0.35 29 43
positive regulation of innate immune response -0.019 0.19 0.28 10 -0.4 32 42
LCK -0.014 0.12 0.12 13 -0.32 32 45
p38alpha-beta/MKP7 -0.007 0.19 0.29 9 -0.39 31 40
p38alpha-beta/MKP5 -0.015 0.18 0.27 6 -0.39 32 38
PGK/cGMP 0.012 0.05 -10000 0 -0.21 10 10
PAK2 0.029 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.19 0.29 8 -0.39 31 39
CDC42 0.028 0.005 -10000 0 -10000 0 0
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.025 0.01 -10000 0 -10000 0 0
PAK3 0.036 0.03 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.027 0.017 -10000 0 -10000 0 0
HSPA8 0.025 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.033 0.075 0.21 6 -0.19 8 14
AKT1 0.013 0.043 -10000 0 -0.093 31 31
GSC -0.03 0.24 -10000 0 -1.2 8 8
NKX2-5 -0.009 0.14 -10000 0 -0.31 35 35
muscle cell differentiation -0.009 0.092 0.44 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.045 0.11 -10000 0 -0.21 8 8
SMAD4 0.014 0.049 -10000 0 -0.14 4 4
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.028 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.03 0.082 -10000 0 -0.18 26 26
SMAD3/SMAD4/VDR 0.071 0.067 0.22 1 -0.21 5 6
MYC 0.026 0.024 -10000 0 -10000 0 0
CDKN2B -0.3 0.54 -10000 0 -1.4 41 41
AP1 0.033 0.053 0.22 1 -0.19 2 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.003 0.079 -10000 0 -0.31 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.036 0.13 -10000 0 -0.34 34 34
SP3 0.026 0.033 -10000 0 -0.19 4 4
CREB1 0.029 0 -10000 0 -10000 0 0
FOXH1 0.02 0.037 0.13 1 -0.14 8 9
SMAD3/SMAD4/GR 0.034 0.073 -10000 0 -0.2 7 7
GATA3 -0.009 0.11 -10000 0 -0.31 27 27
SKI/SIN3/HDAC complex/NCoR1 0.014 0.051 -10000 0 -0.35 1 1
MEF2C/TIF2 -0.013 0.1 0.25 3 -0.27 15 18
endothelial cell migration 0.013 0.24 1.1 10 -10000 0 10
MAX 0.026 0.016 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.005 -10000 0 -10000 0 0
RUNX2 0.016 0.059 -10000 0 -0.32 7 7
RUNX3 -0.007 0.1 -10000 0 -0.32 24 24
RUNX1 0.022 0.045 -10000 0 -0.32 4 4
CTBP1 0.028 0.006 -10000 0 -10000 0 0
NR3C1 0.018 0.052 -10000 0 -0.32 5 5
VDR 0.021 0.05 -10000 0 -0.32 5 5
CDKN1A -0.018 0.18 -10000 0 -1.1 6 6
KAT2B 0.019 0.055 -10000 0 -0.31 6 6
SMAD2/SMAD2/SMAD4/FOXH1 0.033 0.082 -10000 0 -0.26 9 9
DCP1A 0.028 0.004 -10000 0 -10000 0 0
SKI 0.027 0.006 -10000 0 -10000 0 0
SERPINE1 -0.014 0.24 -10000 0 -1.1 10 10
SMAD3/SMAD4/ATF2 0.037 0.067 -10000 0 -0.18 5 5
SMAD3/SMAD4/ATF3 0.037 0.065 -10000 0 -0.21 4 4
SAP30 0.029 0.008 0.12 1 -10000 0 1
Cbp/p300/PIAS3 0.051 0.036 -10000 0 -10000 0 0
JUN 0.015 0.045 -10000 0 -0.19 2 2
SMAD3/SMAD4/IRF7 0.034 0.073 -10000 0 -0.2 8 8
TFE3 0.029 0.019 -10000 0 -0.078 1 1
COL1A2 0.001 0.13 -10000 0 -0.71 7 7
mesenchymal cell differentiation -0.03 0.075 0.21 10 -10000 0 10
DLX1 -0.001 0.12 0.12 26 -0.32 27 53
TCF3 0.028 0.004 -10000 0 -10000 0 0
FOS 0.033 0.025 0.15 2 -10000 0 2
SMAD3/SMAD4/Max 0.04 0.067 -10000 0 -0.19 3 3
Cbp/p300/SNIP1 0.051 0.025 -10000 0 -10000 0 0
ZBTB17 0.026 0.018 -10000 0 -10000 0 0
LAMC1 0.01 0.046 0.18 1 -0.19 1 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.037 0.062 -10000 0 -0.19 3 3
IRF7 0.021 0.05 -10000 0 -0.32 5 5
ESR1 0.017 0.055 0.13 3 -0.32 5 8
HNF4A 0.024 0.018 0.12 6 -10000 0 6
MEF2C -0.008 0.11 0.22 15 -0.28 14 29
SMAD2-3/SMAD4 0.031 0.085 -10000 0 -0.2 5 5
Cbp/p300/Src-1 0.052 0.029 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.019 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.025 0.024 -10000 0 -0.31 1 1
CREBBP 0.028 0.014 -10000 0 -10000 0 0
SKIL 0.018 0.059 -10000 0 -0.32 7 7
HDAC1 0.027 0.023 -10000 0 -0.32 1 1
HDAC2 0.025 0.01 -10000 0 -10000 0 0
SNIP1 0.028 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.045 0.068 -10000 0 -0.18 3 3
MSG1/HSC70 0.01 0.085 -10000 0 -0.21 28 28
SMAD2 0.012 0.046 -10000 0 -0.13 8 8
SMAD3 0.015 0.05 -10000 0 -0.17 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.052 -10000 0 -0.22 6 6
SMAD2/SMAD2/SMAD4 0.004 0.058 0.21 2 -0.23 8 10
NCOR1 0.027 0.007 -10000 0 -10000 0 0
NCOA2 0.02 0.045 -10000 0 -0.32 4 4
NCOA1 0.028 0.006 -10000 0 -10000 0 0
MYOD/E2A 0.039 0.017 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.051 0.11 -10000 0 -0.21 6 6
IFNB1 0.005 0.046 0.2 2 -0.2 2 4
SMAD3/SMAD4/MEF2C 0.008 0.12 0.24 1 -0.3 11 12
CITED1 -0.008 0.12 -10000 0 -0.32 28 28
SMAD2-3/SMAD4/ARC105 0.044 0.082 -10000 0 -0.16 1 1
RBL1 0.025 0.024 -10000 0 -0.32 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.05 0.19 -10000 0 -0.49 35 35
RUNX1-3/PEBPB2 0.024 0.08 -10000 0 -0.19 27 27
SMAD7 0.025 0.077 -10000 0 -0.49 2 2
MYC/MIZ-1 0.038 0.037 0.18 4 -10000 0 4
SMAD3/SMAD4 0.013 0.098 0.28 5 -0.38 7 12
IL10 -0.013 0.1 -10000 0 -0.32 17 17
PIASy/HDAC complex 0.022 0.02 -10000 0 -10000 0 0
PIAS3 0.026 0.012 -10000 0 -10000 0 0
CDK2 0.016 0.064 -10000 0 -0.32 8 8
IL5 -0.016 0.081 -10000 0 -0.26 10 10
CDK4 0.027 0.015 -10000 0 -10000 0 0
PIAS4 0.022 0.02 -10000 0 -10000 0 0
ATF3 0.026 0.027 0.12 4 -0.32 1 5
SMAD3/SMAD4/SP1 0.039 0.085 -10000 0 -0.22 5 5
FOXG1 0.011 0.077 0.12 24 -0.32 9 33
FOXO3 -0.004 0.042 -10000 0 -0.11 28 28
FOXO1 -0.004 0.045 -10000 0 -0.12 30 30
FOXO4 -0.003 0.044 -10000 0 -0.11 30 30
heart looping -0.008 0.11 0.22 15 -0.27 14 29
CEBPB 0.016 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.02 0.1 -10000 0 -0.2 29 29
MYOD1 0.026 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.036 0.06 -10000 0 -0.2 2 2
SMAD3/SMAD4/GATA3 0.018 0.11 -10000 0 -0.24 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.018 0.059 -10000 0 -0.31 7 7
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.033 0.1 -10000 0 -0.19 24 24
SMAD3/SMAD4/SP1-3 0.052 0.09 -10000 0 -0.19 7 7
MED15 0.027 0.007 -10000 0 -10000 0 0
SP1 0.018 0.038 -10000 0 -0.12 10 10
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.02 0.12 -10000 0 -0.2 39 39
ITGB5 0 0.065 -10000 0 -0.3 3 3
TGIF/SIN3/HDAC complex/CtBP 0.018 0.048 -10000 0 -0.24 1 1
SMAD3/SMAD4/AR 0.034 0.085 -10000 0 -0.21 13 13
AR 0.019 0.079 -10000 0 -0.32 11 11
negative regulation of cell growth 0.017 0.058 -10000 0 -0.27 3 3
SMAD3/SMAD4/MYOD 0.039 0.064 -10000 0 -0.18 3 3
E2F5 0.017 0.055 -10000 0 -0.32 6 6
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.052 0.078 -10000 0 -0.2 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.035 0.14 -10000 0 -0.36 34 34
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.052 0.063 -10000 0 -0.19 2 2
SMAD3/SMAD4/RUNX2 0.031 0.075 -10000 0 -0.21 10 10
TGIF2 0.025 0.024 -10000 0 -0.32 1 1
TGIF1 0.026 0.023 -10000 0 -0.32 1 1
ATF2 0.026 0.032 -10000 0 -0.32 2 2
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.032 -10000 0 -0.32 2 2
SPHK1 0.023 0.059 0.12 10 -0.32 6 16
GNAI2 0.028 0.004 -10000 0 -10000 0 0
mol:S1P 0.004 0.055 -10000 0 -0.24 10 10
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
mol:Sphinganine-1-P -0.016 0.04 -10000 0 -0.22 8 8
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.059 -10000 0 -0.19 9 9
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.015 -10000 0 -10000 0 0
S1PR3 0.027 0.037 0.12 7 -0.32 2 9
S1PR2 0.029 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.002 0.049 -10000 0 -0.2 10 10
S1PR5 0.027 0.043 0.12 8 -0.32 3 11
S1PR4 0.007 0.092 0.12 8 -0.32 17 25
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
S1P/S1P5/G12 0.033 0.061 -10000 0 -0.19 11 11
S1P/S1P3/Gq -0.007 0.12 -10000 0 -0.35 23 23
S1P/S1P4/Gi -0.021 0.12 0.19 2 -0.34 15 17
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
GNA14 0.032 0.05 -10000 0 -0.32 3 3
GNA15 0.019 0.06 -10000 0 -0.32 7 7
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.029 0.003 -10000 0 -10000 0 0
ABCC1 0.023 0.045 -10000 0 -0.32 4 4
Presenilin action in Notch and Wnt signaling

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.12 -10000 0 -0.4 17 17
HDAC1 0.024 0.024 -10000 0 -0.32 1 1
AES 0.027 0.023 -10000 0 -0.32 1 1
FBXW11 0.027 0.007 -10000 0 -10000 0 0
DTX1 0.024 0.069 0.12 17 -0.32 8 25
LRP6/FZD1 0.034 0.037 -10000 0 -0.22 4 4
TLE1 0.022 0.039 -10000 0 -0.32 3 3
AP1 -0.004 0.069 -10000 0 -0.19 26 26
NCSTN 0.026 0.008 -10000 0 -10000 0 0
ADAM10 0.028 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.034 0.059 -10000 0 -0.6 1 1
NICD/RBPSUH 0.013 0.12 -10000 0 -0.4 17 17
WIF1 0.031 0.038 0.12 22 -0.32 1 23
NOTCH1 -0.004 0.11 -10000 0 -0.42 16 16
PSENEN 0.028 0.004 -10000 0 -10000 0 0
KREMEN2 0.01 0.087 0.12 9 -0.32 15 24
DKK1 0.005 0.12 -10000 0 -0.32 26 26
beta catenin/beta TrCP1 0.057 0.067 0.34 3 -10000 0 3
APH1B 0.026 0.032 -10000 0 -0.32 2 2
APH1A 0.027 0.008 -10000 0 -10000 0 0
AXIN1 0.004 0.061 0.29 2 -10000 0 2
CtBP/CBP/TCF1/TLE1/AES 0.007 0.049 0.16 2 -0.19 9 11
PSEN1 0.028 0.004 -10000 0 -10000 0 0
FOS 0.032 0.018 -10000 0 -10000 0 0
JUN 0.028 0.004 -10000 0 -10000 0 0
MAP3K7 0.022 0.033 -10000 0 -0.32 2 2
CTNNB1 0.044 0.072 0.33 4 -10000 0 4
MAPK3 0.028 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.084 -10000 0 -0.19 28 28
HNF1A 0.026 0.023 -10000 0 -0.32 1 1
CTBP1 0.027 0.007 -10000 0 -10000 0 0
MYC 0.025 0.018 -10000 0 -10000 0 0
NKD1 -0.01 0.11 0.12 7 -0.32 27 34
FZD1 0.024 0.035 0.12 3 -0.32 2 5
NOTCH1 precursor/Deltex homolog 1 0.016 0.13 -10000 0 -0.41 18 18
apoptosis -0.004 0.069 -10000 0 -0.19 26 26
Delta 1/NOTCHprecursor 0.012 0.12 -10000 0 -0.4 17 17
DLL1 0.023 0.043 0.12 6 -0.32 3 9
PPARD 0.021 0.051 -10000 0 -0.7 1 1
Gamma Secretase 0.072 0.037 -10000 0 -0.15 2 2
APC -0.01 0.11 0.29 2 -0.47 7 9
DVL1 0.019 0.036 -10000 0 -0.31 2 2
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.025 0.1 0.18 1 -0.19 37 38
LRP6 0.025 0.032 -10000 0 -0.32 2 2
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
NLK 0.008 0.024 -10000 0 -0.25 2 2
CCND1 0.006 0.18 -10000 0 -1.3 4 4
WNT1 0.031 0.02 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.034 0.12 0.39 5 -0.39 5 10
DKK2 0.014 0.079 0.12 8 -0.32 12 20
NOTCH1 precursor/DVL1 -0.004 0.14 -10000 0 -0.44 19 19
GSK3B 0.028 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.024 -10000 0 -0.32 1 1
NOTCH/Deltex homolog 1 0.012 0.13 -10000 0 -0.41 18 18
PPP2R5D 0.034 0.055 0.21 19 -10000 0 19
MAPK1 0.027 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.063 0.049 0.19 2 -0.17 5 7
RBPJ 0.028 0.005 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.027 0.2 -10000 0 -0.66 8 8
PCK1 0.012 0.13 0.38 1 -0.65 1 2
HNF4A -0.025 0.22 0.59 2 -0.69 8 10
KCNJ11 -0.043 0.29 -10000 0 -0.81 17 17
AKT1 0.004 0.15 -10000 0 -0.36 7 7
response to starvation -0.002 0.013 -10000 0 -10000 0 0
DLK1 -0.015 0.23 -10000 0 -0.63 14 14
NKX2-1 0.015 0.14 -10000 0 -10000 0 0
ACADM -0.028 0.22 -10000 0 -0.64 13 13
TAT -0.007 0.15 -10000 0 -0.57 4 4
CEBPB 0.016 0.031 -10000 0 -10000 0 0
CEBPA 0.002 0.082 -10000 0 -0.31 12 12
TTR -0.15 0.46 0.51 1 -1.1 40 41
PKLR -0.091 0.35 0.48 2 -0.74 44 46
APOA1 -0.033 0.25 0.57 1 -0.81 8 9
CPT1C -0.05 0.27 -10000 0 -0.73 21 21
ALAS1 0.009 0.14 -10000 0 -0.51 2 2
TFRC 0.011 0.17 -10000 0 -1 1 1
FOXF1 0.025 0.063 -10000 0 -0.32 6 6
NF1 0.028 0.039 -10000 0 -0.31 3 3
HNF1A (dimer) 0.03 0.024 -10000 0 -0.31 1 1
CPT1A -0.028 0.24 -10000 0 -0.7 13 13
HMGCS1 -0.024 0.22 -10000 0 -0.65 12 12
NR3C1 0.025 0.051 -10000 0 -0.31 5 5
CPT1B -0.028 0.22 -10000 0 -0.64 13 13
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.03 0.007 -10000 0 -10000 0 0
GCK -0.021 0.26 0.44 3 -0.75 14 17
CREB1 0.034 0.008 -10000 0 -10000 0 0
IGFBP1 0.005 0.14 -10000 0 -0.49 1 1
PDX1 0.007 0.14 -10000 0 -0.69 1 1
UCP2 -0.025 0.24 0.41 1 -0.79 10 11
ALDOB -0.021 0.23 -10000 0 -0.6 16 16
AFP -0.002 0.063 -10000 0 -10000 0 0
BDH1 -0.051 0.26 0.46 1 -0.76 19 20
HADH -0.021 0.24 -10000 0 -0.62 17 17
F2 -0.025 0.25 0.54 1 -0.84 7 8
HNF1A 0.03 0.024 -10000 0 -0.32 1 1
G6PC 0.01 0.074 -10000 0 -10000 0 0
SLC2A2 0.002 0.16 -10000 0 -0.54 2 2
INS -0.024 0.009 -10000 0 -10000 0 0
FOXA1 0.007 0.089 -10000 0 -0.32 13 13
FOXA3 0.038 0.069 -10000 0 -0.31 4 4
FOXA2 -0.005 0.28 -10000 0 -0.68 18 18
ABCC8 -0.019 0.23 -10000 0 -0.64 13 13
ALB 0 0.063 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.028 -10000 0 -0.32 1 1
AES 0.028 0.013 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.037 -10000 0 -0.22 4 4
SMAD4 0.028 0.004 -10000 0 -10000 0 0
DKK2 0.014 0.079 0.12 8 -0.32 12 20
TLE1 0.022 0.035 -10000 0 -0.32 2 2
MACF1 0.028 0.005 -10000 0 -10000 0 0
CTNNB1 0.023 0.089 0.31 4 -0.33 3 7
WIF1 0.027 0.041 0.12 22 -0.31 1 23
beta catenin/RanBP3 0.019 0.098 0.36 10 -0.33 2 12
KREMEN2 0.01 0.087 0.12 9 -0.32 15 24
DKK1 0.005 0.12 0.12 31 -0.32 26 57
beta catenin/beta TrCP1 0.036 0.084 0.38 2 -0.34 2 4
FZD1 0.025 0.035 0.12 3 -0.32 2 5
AXIN2 -0.024 0.24 0.56 5 -1.3 7 12
AXIN1 0.029 0.003 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.015 0.1 -10000 0 -0.55 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.009 0.1 -10000 0 -0.38 8 8
Axin1/APC/GSK3 0.032 0.067 0.32 4 -0.2 1 5
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.094 0.27 2 -0.37 5 7
HNF1A 0.026 0.027 -10000 0 -0.32 1 1
CTBP1 0.027 0.015 -10000 0 -10000 0 0
MYC 0.061 0.19 0.58 25 -10000 0 25
RANBP3 0.029 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.084 -10000 0 -0.19 28 28
NKD1 -0.01 0.11 0.12 7 -0.31 27 34
TCF4 0.027 0.046 -10000 0 -0.32 3 3
TCF3 0.028 0.014 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.063 0.043 -10000 0 -0.17 4 4
Ran/GTP 0.021 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.009 0.11 0.4 7 -0.32 3 10
LEF1 0.007 0.083 -10000 0 -0.32 14 14
DVL1 0.008 0.059 -10000 0 -0.23 9 9
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.008 0.12 -10000 0 -0.43 10 10
DKK1/LRP6/Kremen 2 0.025 0.1 0.18 1 -0.19 37 38
LRP6 0.025 0.032 -10000 0 -0.32 2 2
CSNK1A1 0.027 0.018 0.12 1 -10000 0 1
NLK 0.027 0.01 -10000 0 -10000 0 0
CCND1 0.007 0.2 0.59 10 -1.3 3 13
WNT1 0.03 0.021 -10000 0 -10000 0 0
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.028 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.024 -10000 0 -0.32 1 1
PPP2R5D 0.04 0.064 0.21 21 -0.2 1 22
APC 0.006 0.079 0.2 27 -0.3 1 28
WNT1/LRP6/FZD1 0.01 0.046 0.17 1 -0.18 8 9
CREBBP 0.028 0.015 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.065 -10000 0 -0.16 20 20
regulation of S phase of mitotic cell cycle 0.011 0.052 -10000 0 -0.2 12 12
GNAO1 -0.026 0.13 0.12 7 -0.32 38 45
HRAS 0.028 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.017 0.02 0.081 3 -0.18 2 5
PELP1 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.006 0.003 -10000 0 -10000 0 0
MAP2K1 0.001 0.066 0.18 22 -10000 0 22
T-DHT/AR 0.015 0.054 -10000 0 -0.21 11 11
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.32 2 2
mol:GDP -0.01 0.067 -10000 0 -0.28 12 12
cell proliferation 0.016 0.07 0.26 6 -10000 0 6
PIK3CA 0.025 0.032 -10000 0 -0.32 2 2
FOS 0.023 0.049 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.021 0.036 1 -0.047 41 42
MAPK3 0.009 0.065 0.31 2 -10000 0 2
MAPK1 0.016 0.052 0.21 2 -0.3 3 5
PIK3R1 0.025 0.032 -10000 0 -0.32 2 2
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.001 0.021 0.08 1 -0.14 2 3
GNG2 0.015 0.066 -10000 0 -0.32 9 9
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.043 0.046 -10000 0 -0.15 9 9
actin cytoskeleton reorganization 0.033 0.033 -10000 0 -0.19 3 3
SRC 0.026 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.033 -10000 0 -0.23 3 3
apoptosis -0.025 0.052 -10000 0 -0.27 2 2
T-DHT/AR/PELP1 0.031 0.048 -10000 0 -0.18 10 10
HRAS/GDP 0.007 0.069 -10000 0 -0.27 12 12
CREB1 0.026 0.053 0.27 2 -10000 0 2
RAC1-CDC42/GTP 0.041 0.037 -10000 0 -0.2 3 3
AR 0.019 0.078 -10000 0 -0.31 11 11
GNB1 0.027 0.006 -10000 0 -10000 0 0
RAF1 0.005 0.069 0.19 22 -10000 0 22
RAC1-CDC42/GDP 0.024 0.07 -10000 0 -0.26 10 10
T-DHT/AR/PELP1/Src 0.044 0.049 -10000 0 -0.16 9 9
MAP2K2 0.001 0.066 0.18 22 -10000 0 22
T-DHT/AR/PELP1/Src/PI3K 0.011 0.052 -10000 0 -0.2 12 12
GNAZ 0.003 0.093 0.12 4 -0.32 18 22
SHBG 0.025 0.034 0.12 3 -0.32 2 5
Gi family/GNB1/GNG2/GDP -0.051 0.14 -10000 0 -0.32 38 38
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
GNRH1 -0.001 0.038 -10000 0 -0.21 7 7
Gi family/GTP -0.024 0.079 -10000 0 -0.2 23 23
CDC42 0.028 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.009 0.087 -10000 0 -0.32 15 15
HRAS 0.028 0.006 -10000 0 -10000 0 0
EGFR 0.024 0.061 0.12 16 -0.32 6 22
AKT 0.037 0.095 0.27 12 -0.24 6 18
FOXO3 0.025 0.01 -10000 0 -10000 0 0
AKT1 0.028 0.005 -10000 0 -10000 0 0
FOXO1 0.026 </