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

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

Summary

There were 131 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
TCGA08_p53 23
Syndecan-2-mediated signaling events 17
EPO signaling pathway 14
TRAIL signaling pathway 14
Glypican 2 network 13
E-cadherin signaling events 13
ErbB4 signaling events 12
Signaling events mediated by PRL 12
BARD1 signaling events 11
FOXA2 and FOXA3 transcription factor networks 11
Results

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_p53 23 161 7 -0.016 0.009 1000 -1000 -0.016 -1000
Syndecan-2-mediated signaling events 17 1180 69 -0.021 0.024 1000 -1000 -0.019 -1000
EPO signaling pathway 14 808 55 -0.026 0.031 1000 -1000 -0.028 -1000
TRAIL signaling pathway 14 690 48 -0.019 0.035 1000 -1000 -0.023 -1000
Glypican 2 network 13 55 4 -0.016 0.021 1000 -1000 -0.016 -1000
E-cadherin signaling events 13 65 5 -0.017 0.028 1000 -1000 -0.016 -1000
ErbB4 signaling events 12 878 69 -0.028 0.033 1000 -1000 -0.017 -1000
Signaling events mediated by PRL 12 413 34 -0.022 0.023 1000 -1000 -0.022 -1000
BARD1 signaling events 11 653 57 -0.036 0.04 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 11 539 46 -0.021 0.028 1000 -1000 -0.021 -1000
Glypican 1 network 11 558 48 -0.023 0.03 1000 -1000 -0.021 -1000
Atypical NF-kappaB pathway 11 371 31 -0.021 0.021 1000 -1000 -0.021 -1000
IL23-mediated signaling events 11 709 60 -0.03 0.032 1000 -1000 -0.016 -1000
E-cadherin signaling in keratinocytes 11 498 43 -0.016 0.029 1000 -1000 -0.016 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 566 54 -0.037 0.035 1000 -1000 -0.026 -1000
Arf6 signaling events 10 630 62 -0.017 0.039 1000 -1000 -0.016 -1000
BMP receptor signaling 10 859 81 -0.026 0.038 1000 -1000 -0.025 -1000
PDGFR-alpha signaling pathway 10 442 44 -0.02 0.038 1000 -1000 -0.019 -1000
Nectin adhesion pathway 10 663 63 -0.017 0.04 1000 -1000 -0.016 -1000
Class I PI3K signaling events 10 756 73 -0.022 0.02 1000 -1000 -0.021 -1000
Syndecan-1-mediated signaling events 9 329 34 -0.017 0.025 1000 -1000 -0.02 -1000
Visual signal transduction: Cones 9 378 38 -0.019 0.039 1000 -1000 -0.018 -1000
Ephrin A reverse signaling 9 67 7 -0.019 0.02 1000 -1000 -0.018 -1000
Noncanonical Wnt signaling pathway 9 258 26 -0.017 0.023 1000 -1000 -0.023 -1000
amb2 Integrin signaling 9 790 82 -0.027 0.044 1000 -1000 -0.026 -1000
Ceramide signaling pathway 9 702 76 -0.021 0.043 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 9 784 82 -0.03 0.037 1000 -1000 -0.03 -1000
EPHB forward signaling 9 799 85 -0.039 0.066 1000 -1000 -0.036 -1000
Effects of Botulinum toxin 9 237 26 -0.02 0.029 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 9 293 31 -0.027 0.012 1000 -1000 -0.027 -1000
Wnt signaling 9 67 7 -0.017 0.005 1000 -1000 -0.016 -1000
Syndecan-4-mediated signaling events 9 622 67 -0.029 0.028 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 9 893 97 -0.03 0.055 1000 -1000 -0.033 -1000
ErbB2/ErbB3 signaling events 8 571 65 -0.028 0.034 1000 -1000 -0.028 -1000
IL12-mediated signaling events 8 751 87 -0.017 0.04 1000 -1000 -0.016 -1000
PLK2 and PLK4 events 8 24 3 -0.019 -1000 1000 -1000 -0.019 -1000
HIF-1-alpha transcription factor network 8 638 76 -0.022 0.039 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 8 643 76 -0.018 0.029 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 8 282 32 -0.026 0.021 1000 -1000 -0.018 -1000
IFN-gamma pathway 8 566 68 -0.034 0.036 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 8 565 68 -0.021 0.034 1000 -1000 -0.023 -1000
ceramide signaling pathway 8 403 49 -0.02 0.027 1000 -1000 -0.016 -1000
Endothelins 8 781 96 -0.028 0.028 1000 -1000 -0.021 -1000
FoxO family signaling 8 534 64 -0.022 0.027 1000 -1000 -0.016 -1000
Canonical Wnt signaling pathway 8 441 51 -0.036 0.13 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 8 441 54 -0.017 0.038 1000 -1000 -0.016 -1000
Nongenotropic Androgen signaling 8 437 52 -0.017 0.029 1000 -1000 -0.019 -1000
TCGA08_rtk_signaling 8 227 26 -0.017 0.036 1000 -1000 -0.017 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 8 586 68 -0.017 0.035 1000 -1000 -0.019 -1000
Stabilization and expansion of the E-cadherin adherens junction 8 649 74 -0.038 0.039 1000 -1000 -0.035 -1000
Insulin Pathway 8 630 74 -0.032 0.046 1000 -1000 -0.032 -1000
Plasma membrane estrogen receptor signaling 8 732 86 -0.028 0.034 1000 -1000 -0.027 -1000
Angiopoietin receptor Tie2-mediated signaling 8 719 88 -0.017 0.028 1000 -1000 -0.021 -1000
Regulation of nuclear SMAD2/3 signaling 7 1018 136 -0.074 0.04 1000 -1000 -0.03 -1000
Coregulation of Androgen receptor activity 7 563 76 -0.017 0.029 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 7 121 17 -0.017 0.042 1000 -1000 -0.016 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 7 675 85 -0.035 0.038 1000 -1000 -0.023 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 659 83 -0.024 0.032 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class I 7 762 104 -0.021 0.04 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 7 112 15 -0.022 0 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 7 262 36 -0.031 0.031 1000 -1000 -0.028 -1000
Integrins in angiogenesis 7 604 84 -0.036 0.039 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 7 337 45 -0.03 0.041 1000 -1000 -0.023 -1000
Signaling events mediated by VEGFR1 and VEGFR2 7 890 125 -0.033 0.029 1000 -1000 -0.03 -1000
IL27-mediated signaling events 7 402 51 -0.04 0.031 1000 -1000 -0.016 -1000
IL6-mediated signaling events 7 562 75 -0.021 0.035 1000 -1000 -0.023 -1000
E-cadherin signaling in the nascent adherens junction 7 575 76 -0.03 0.039 1000 -1000 -0.033 -1000
Regulation of Telomerase 7 724 102 -0.022 0.037 1000 -1000 -0.021 -1000
BCR signaling pathway 7 693 99 -0.035 0.038 1000 -1000 -0.036 -1000
EGFR-dependent Endothelin signaling events 7 166 21 -0.029 0.04 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 7 916 120 -0.032 0.041 1000 -1000 -0.03 -1000
Visual signal transduction: Rods 7 368 52 -0.04 0.04 1000 -1000 -0.032 -1000
Arf1 pathway 7 386 54 -0.018 0.028 1000 -1000 -0.016 -1000
Ras signaling in the CD4+ TCR pathway 7 135 17 -0.017 0.026 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 6 490 74 -0.034 0.034 1000 -1000 -0.02 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 6 157 23 -0.017 0.029 1000 -1000 -0.016 -1000
Canonical NF-kappaB pathway 6 252 39 -0.024 0.031 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class II 6 491 75 -0.021 0.044 1000 -1000 -0.019 -1000
Signaling events mediated by the Hedgehog family 6 347 52 -0.019 0.025 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 6 396 65 -0.017 0.038 1000 -1000 -0.017 -1000
p75(NTR)-mediated signaling 6 860 125 -0.041 0.043 1000 -1000 -0.033 -1000
IL4-mediated signaling events 6 632 91 -0.024 0.022 1000 -1000 -0.016 -1000
Glucocorticoid receptor regulatory network 6 772 114 -0.029 0.046 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 247 37 -0.03 0.039 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class III 6 244 40 -0.03 0.031 1000 -1000 -0.029 -1000
Reelin signaling pathway 6 388 56 -0.034 0.043 1000 -1000 -0.031 -1000
IL1-mediated signaling events 6 397 62 -0.039 0.041 1000 -1000 -0.035 -1000
HIF-2-alpha transcription factor network 6 269 43 -0.018 0.028 1000 -1000 -0.018 -1000
FAS signaling pathway (CD95) 6 297 47 -0.023 0.03 1000 -1000 -0.021 -1000
IL2 signaling events mediated by PI3K 6 399 58 -0.02 0.028 1000 -1000 -0.018 -1000
TCR signaling in naïve CD8+ T cells 6 618 93 -0.039 0.038 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 6 150 22 -0.019 0.007 1000 -1000 -0.018 -1000
Arf6 trafficking events 6 446 71 -0.024 0.021 1000 -1000 -0.018 -1000
IGF1 pathway 6 392 57 -0.029 0.044 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 213 33 -0.017 0.04 1000 -1000 -0.016 -1000
Rapid glucocorticoid signaling 6 120 20 -0.016 0.02 1000 -1000 -0.016 -1000
FOXM1 transcription factor network 6 335 51 -0.03 0.027 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 6 302 44 -0.024 0.036 1000 -1000 -0.016 -1000
Alternative NF-kappaB pathway 6 82 13 -0.017 0.042 1000 -1000 -0.016 -1000
Sphingosine 1-phosphate (S1P) pathway 5 147 28 -0.018 0.023 1000 -1000 -0.019 -1000
Osteopontin-mediated events 5 192 38 -0.04 0.031 1000 -1000 -0.022 -1000
Thromboxane A2 receptor signaling 5 593 105 -0.026 0.021 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 5 330 61 -0.017 0.042 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 5 491 97 -0.063 0.041 1000 -1000 -0.035 -1000
mTOR signaling pathway 5 317 53 -0.041 0.021 1000 -1000 -0.024 -1000
RXR and RAR heterodimerization with other nuclear receptor 5 285 52 -0.017 0.042 1000 -1000 -0.016 -1000
Retinoic acid receptors-mediated signaling 5 317 58 -0.031 0.032 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 5 196 35 -0.021 0.042 1000 -1000 -0.023 -1000
LPA receptor mediated events 5 526 102 -0.027 0.019 1000 -1000 -0.036 -1000
Sumoylation by RanBP2 regulates transcriptional repression 5 143 27 -0.024 0.034 1000 -1000 -0.021 -1000
VEGFR1 specific signals 5 329 56 -0.031 0.031 1000 -1000 -0.025 -1000
Class IB PI3K non-lipid kinase events 5 15 3 -0.016 -1000 1000 -1000 -0.016 -1000
Regulation of Androgen receptor activity 5 366 70 -0.03 0.029 1000 -1000 -0.025 -1000
Aurora B signaling 5 388 67 -0.024 0.042 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 4 57 12 -0.016 0.006 1000 -1000 -0.015 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 139 34 -0.024 0.047 1000 -1000 -0.024 -1000
Circadian rhythm pathway 4 105 22 -0.017 0.032 1000 -1000 -0.016 -1000
Cellular roles of Anthrax toxin 4 165 39 -0.017 0.022 1000 -1000 -0.016 -1000
Aurora A signaling 4 245 60 -0.019 0.031 1000 -1000 -0.018 -1000
Arf6 downstream pathway 4 178 43 -0.024 0.027 1000 -1000 -0.024 -1000
Aurora C signaling 4 33 7 -0.017 0.028 1000 -1000 -0.016 -1000
PLK1 signaling events 4 402 85 -0.017 0.029 1000 -1000 -0.016 -1000
Ephrin B reverse signaling 4 239 48 -0.027 0.027 1000 -1000 -0.025 -1000
S1P1 pathway 4 156 36 -0.016 0.012 1000 -1000 -0.016 -1000
S1P3 pathway 4 177 42 -0.017 0.023 1000 -1000 -0.016 -1000
S1P4 pathway 4 115 25 -0.017 0.023 1000 -1000 -0.016 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 4 356 78 -0.033 0.026 1000 -1000 -0.016 -1000
a4b1 and a4b7 Integrin signaling 3 17 5 -0.017 0.024 1000 -1000 -0.016 -1000
S1P5 pathway 3 55 17 -0.017 0.012 1000 -1000 -0.016 -1000
Signaling mediated by p38-alpha and p38-beta 3 133 44 -0.025 0.029 1000 -1000 -0.02 -1000
TCGA08_retinoblastoma 1 15 8 -0.012 0.016 1000 -1000 -0.016 -1000
Total 955 55781 7203 -3.3 -2000 131000 -131000 -2.8 -131000
TCGA08_p53

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
CDKN2A -0.009 0.004 0 23 -9999 0 23
TP53 0.006 0.004 -10000 0 0 42 42
Senescence 0.006 0.004 -10000 0 0 42 42
Apoptosis 0.006 0.004 -10000 0 0 42 42
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 0.009 0.071 0.3 8 -9999 0 8
MDM4 -0.016 0.003 0 4 -9999 0 4
Syndecan-2-mediated 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
Syndecan-2/Fibronectin -0.013 0.006 0 26 -9999 0 26
EPHB2 -0.016 0.005 0 11 -9999 0 11
Syndecan-2/TACI -0.013 0.007 0 30 -9999 0 30
LAMA1 -0.016 0.003 0 6 -9999 0 6
Syndecan-2/alpha2 ITGB1 0.024 0.014 -10000 0 0 35 35
HRAS -0.016 0.004 0 9 -9999 0 9
Syndecan-2/CASK -0.007 0.003 0 24 -9999 0 24
ITGA5 -0.016 0.003 0 6 -9999 0 6
BAX -0.017 0.009 0 29 -9999 0 29
EPB41 -0.016 0.004 0 8 -9999 0 8
positive regulation of cell-cell adhesion -0.011 0.006 0 26 -9999 0 26
LAMA3 -0.016 0.004 0 8 -9999 0 8
EZR 0 0 -10000 0 -9999 0 0
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
CAV2 -0.015 0.005 0 12 -9999 0 12
Syndecan-2/MMP2 -0.013 0.006 0 27 -9999 0 27
RP11-540L11.1 0 0 -10000 0 -9999 0 0
alpha2 ITGB1 0.023 0.007 -10000 0 0 11 11
dendrite morphogenesis -0.012 0.007 0 31 -9999 0 31
Syndecan-2/GM-CSF -0.013 0.007 0 28 -9999 0 28
determination of left/right symmetry -0.008 0.004 0 24 -9999 0 24
Syndecan-2/PKC delta -0.013 0.006 0 26 -9999 0 26
GNB2L1 -0.016 0.003 0 5 -9999 0 5
MAPK3 0.008 0.068 0.18 19 -9999 0 19
MAPK1 0.008 0.068 0.18 19 -9999 0 19
Syndecan-2/RACK1 0.017 0.009 -10000 0 0 30 30
NF1 -0.017 0.002 0 3 -9999 0 3
FGFR/FGF/Syndecan-2 -0.008 0.004 0 24 -9999 0 24
ITGA2 -0.016 0.004 0 8 -9999 0 8
MAPK8 -0.013 0.006 0 25 -9999 0 25
Syndecan-2/alpha2/beta1 Integrin 0.024 0.014 -10000 0 0 34 34
Syndecan-2/Kininogen -0.013 0.007 0 30 -9999 0 30
ITGB1 -0.017 0.002 0 3 -9999 0 3
SRC -0.003 0.055 0.16 13 -9999 0 13
Syndecan-2/CASK/Protein 4.1 -0.011 0.006 0 28 -9999 0 28
extracellular matrix organization -0.013 0.007 0 29 -9999 0 29
actin cytoskeleton reorganization -0.013 0.006 0 26 -9999 0 26
Syndecan-2/Caveolin-2/Ras 0.017 0.01 -10000 0 0 34 34
Syndecan-2/Laminin alpha3 -0.012 0.007 0 31 -9999 0 31
Syndecan-2/RasGAP 0.023 0.012 -10000 0 0 30 30
alpha5/beta1 Integrin 0.023 0.006 -10000 0 0 9 9
PRKCD -0.016 0.003 0 6 -9999 0 6
Syndecan-2 dimer -0.012 0.007 0 31 -9999 0 31
GO:0007205 0 0 -10000 0 -9999 0 0
DNA mediated transformation 0 0 -10000 0 -9999 0 0
Syndecan-2/RasGAP/Src -0.021 0.02 0.16 1 -9999 0 1
RHOA -0.016 0.003 0 5 -9999 0 5
SDCBP -0.015 0.005 0 15 -9999 0 15
TNFRSF13B -0.015 0.005 0 12 -9999 0 12
RASA1 -0.016 0.004 0 9 -9999 0 9
alpha2/beta1 Integrin 0.023 0.007 -10000 0 0 11 11
Syndecan-2/Synbindin -0.013 0.006 0 26 -9999 0 26
TGFB1 -0.016 0.004 0 9 -9999 0 9
CASP3 0.002 0.059 0.18 14 -9999 0 14
FN1 -0.016 0.003 0 4 -9999 0 4
Syndecan-2/IL8 -0.013 0.006 0 25 -9999 0 25
SDC2 -0.008 0.004 0 24 -9999 0 24
KNG1 -0.016 0.004 0 8 -9999 0 8
Syndecan-2/Neurofibromin -0.013 0.006 0 27 -9999 0 27
TRAPPC4 -0.016 0.003 0 6 -9999 0 6
CSF2 -0.016 0.004 0 8 -9999 0 8
Syndecan-2/TGFB1 -0.013 0.007 0 29 -9999 0 29
Syndecan-2/Syntenin/PI-4-5-P2 -0.011 0.006 0 26 -9999 0 26
Syndecan-2/Ezrin -0.012 0.005 0 25 -9999 0 25
PRKACA 0.009 0.069 0.18 20 -9999 0 20
angiogenesis -0.013 0.006 0 25 -9999 0 25
MMP2 -0.016 0.003 0 4 -9999 0 4
IL8 -0.017 0.002 0 3 -9999 0 3
calcineurin-NFAT signaling pathway -0.013 0.007 0 30 -9999 0 30
EPO signaling pathway

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
BCL2L1 0.014 0.052 0.14 11 -0.12 2 13
CRKL 0.004 0.059 0.13 24 -10000 0 24
mol:DAG -0.004 0.029 0.099 9 -0.085 1 10
HRAS -0.004 0.073 0.22 6 -10000 0 6
MAPK8 0.002 0.063 0.16 18 -10000 0 18
RAP1A 0.002 0.057 0.13 22 -10000 0 22
GAB1 0.002 0.057 0.13 22 -10000 0 22
MAPK14 -0.001 0.059 0.15 16 -10000 0 16
EPO -0.01 0.018 0.029 20 -10000 0 20
PLCG1 -0.004 0.03 0.1 9 -0.086 1 10
EPOR/TRPC2/IP3 Receptors -0.008 0.02 0.031 27 -10000 0 27
RAPGEF1 -0.016 0.003 0 5 -10000 0 5
EPO/EPOR (dimer)/SOCS3 0.031 0.014 0.066 3 0 19 22
GAB1/SHC/GRB2/SOS1 -0.01 0.057 0.12 20 -10000 0 20
EPO/EPOR (dimer) 0.022 0.016 0.061 3 -0.02 8 11
IRS2 0.001 0.056 0.13 21 -10000 0 21
STAT1 -0.004 0.031 0.1 10 -0.086 1 11
STAT5B -0.004 0.031 0.1 10 -0.086 1 11
cell proliferation 0.005 0.082 0.18 22 -10000 0 22
GAB1/SHIP/PIK3R1/SHP2/SHC -0.02 0.047 0.093 18 -10000 0 18
TEC 0.001 0.056 0.13 21 -10000 0 21
SOCS3 -0.016 0.003 0 6 -10000 0 6
STAT1 (dimer) -0.004 0.031 0.099 10 -0.085 1 11
JAK2 -0.01 0.017 0.031 16 -10000 0 16
PIK3R1 -0.016 0.004 0 9 -10000 0 9
EPO/EPOR (dimer)/JAK2 0.023 0.022 0.17 2 -10000 0 2
EPO/EPOR 0.022 0.016 0.061 3 -0.02 8 11
LYN -0.015 0.005 0 14 -10000 0 14
TEC/VAV2 -0.005 0.054 0.12 21 -10000 0 21
elevation of cytosolic calcium ion concentration -0.008 0.02 0.031 27 -10000 0 27
SHC1 -0.016 0.004 0 9 -10000 0 9
EPO/EPOR (dimer)/LYN 0.029 0.016 0.065 1 0 27 28
mol:IP3 -0.004 0.029 0.099 9 -0.085 1 10
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.004 0.062 0.14 20 -10000 0 20
SH2B3 -0.002 0.003 0.017 3 -10000 0 3
NFKB1 0.001 0.063 0.16 18 -10000 0 18
EPO/EPOR (dimer)/JAK2/SOCS3 0.004 0.019 0.077 2 -0.18 1 3
PTPN6 0.007 0.059 0.14 22 -10000 0 22
TEC/VAV2/GRB2 -0.008 0.056 0.12 20 -10000 0 20
EPOR -0.008 0.021 0.031 27 -10000 0 27
INPP5D -0.017 0.002 0 2 -10000 0 2
mol:GDP -0.011 0.058 0.12 20 -10000 0 20
SOS1 -0.017 0 -10000 0 -10000 0 0
PLCG2 -0.016 0.003 0 5 -10000 0 5
CRKL/CBL/C3G -0.008 0.055 0.12 20 -10000 0 20
VAV2 0.004 0.059 0.13 24 -10000 0 24
CBL 0.001 0.056 0.13 21 -10000 0 21
SHC/Grb2/SOS1 -0.026 0.016 -10000 0 -10000 0 0
STAT5A -0.004 0.031 0.1 10 -0.086 1 11
GRB2 -0.016 0.003 0 6 -10000 0 6
STAT5 (dimer) -0.01 0.033 0.099 10 -10000 0 10
LYN/PLCgamma2 0.021 0.008 -10000 0 0 18 18
PTPN11 -0.017 0.002 0 3 -10000 0 3
BTK 0.004 0.059 0.13 24 -10000 0 24
BCL2 0.013 0.059 0.14 13 -0.15 4 17
TRAIL signaling pathway

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
TNFSF10 -0.016 0.004 0 10 -10000 0 10
positive regulation of NF-kappaB transcription factor activity 0.02 0.01 -10000 0 0 27 27
MAP2K4 -0.006 0.034 -10000 0 -0.16 4 4
IKBKB -0.015 0.006 0 18 -10000 0 18
TNFRSF10B -0.015 0.006 0 19 -10000 0 19
TNFRSF10A -0.015 0.006 0 19 -10000 0 19
SMPD1 -0.005 0.002 0 30 -10000 0 30
IKBKG -0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.006 0 19 -10000 0 19
TRAIL/TRAILR2 0.02 0.01 -10000 0 0 27 27
TRAIL/TRAILR3 0.02 0.01 -10000 0 0 27 27
TRAIL/TRAILR1 0.02 0.01 -10000 0 0 27 27
TRAIL/TRAILR4 0.02 0.01 -10000 0 0 27 27
TRAIL/TRAILR1/DAP3/GTP 0.025 0.013 -10000 0 0 31 31
IKK complex -0.017 0.036 -10000 0 -0.18 6 6
RIPK1 -0.016 0.004 0 7 -10000 0 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0.003 -10000 0 0 8 8
MAPK3 -0.019 0.006 0 12 -10000 0 12
MAP3K1 0.003 0.033 0.086 4 -0.22 2 6
TRAILR4 (trimer) -0.015 0.006 0 19 -10000 0 19
TRADD -0.017 0.002 0 3 -10000 0 3
TRAILR1 (trimer) -0.015 0.006 0 19 -10000 0 19
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.004 0.015 -10000 0 -0.17 1 1
CFLAR -0.017 0.002 0 2 -10000 0 2
MAPK1 -0.018 0.006 0 13 -10000 0 13
TRAIL/TRAILR1/FADD/TRADD/RIP 0.035 0.023 -10000 0 -10000 0 0
mol:ceramide -0.005 0.002 0 30 -10000 0 30
FADD -0.016 0.004 0 9 -10000 0 9
MAPK8 -0.011 0.053 -10000 0 -0.27 3 3
TRAF2 -0.016 0.004 0 7 -10000 0 7
TRAILR3 (trimer) -0.015 0.006 0 19 -10000 0 19
CHUK -0.017 0.002 0 3 -10000 0 3
TRAIL/TRAILR1/FADD 0.025 0.015 -10000 0 0 35 35
DAP3 -0.016 0.004 0 8 -10000 0 8
CASP10 0.003 0.05 0.14 15 -10000 0 15
JNK cascade 0.02 0.01 -10000 0 0 27 27
TRAIL (trimer) -0.016 0.004 0 10 -10000 0 10
TNFRSF10C -0.015 0.006 0 19 -10000 0 19
TRAIL/TRAILR1/DAP3/GTP/FADD 0.029 0.018 -10000 0 0 37 37
TRAIL/TRAILR2/FADD 0.025 0.015 -10000 0 0 35 35
cell death -0.005 0.002 0 30 -10000 0 30
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.004 0.015 -10000 0 -0.17 1 1
TRAILR2 (trimer) -0.015 0.006 0 19 -10000 0 19
CASP8 -0.003 0.077 -10000 0 -0.6 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.035 0.023 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.016 0.003 0 5 -9999 0 5
GPC2 -0.015 0.005 0 14 -9999 0 14
GPC2/Midkine 0.021 0.008 -9999 0 0 18 18
neuron projection morphogenesis 0.021 0.008 -9999 0 0 18 18
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.028 0.013 -9999 0 0 25 25
E-cadherin/beta catenin 0.022 0.007 -9999 0 0 13 13
CTNNB1 -0.016 0.005 0 11 -9999 0 11
JUP -0.015 0.005 0 13 -9999 0 13
CDH1 -0.017 0.002 0 3 -9999 0 3
ErbB4 signaling events

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.022 0.039 0.1 17 -0.085 5 22
epithelial cell differentiation -0.007 0.041 0.11 12 -10000 0 12
ITCH -0.011 0.016 0.028 18 -10000 0 18
WWP1 0.01 0.054 0.19 11 -10000 0 11
FYN -0.016 0.003 0 5 -10000 0 5
EGFR -0.016 0.004 0 10 -10000 0 10
PRL -0.016 0.004 0 7 -10000 0 7
neuron projection morphogenesis -0.003 0.075 0.18 16 -10000 0 16
PTPRZ1 -0.016 0.004 0 8 -10000 0 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.026 0.029 0.11 5 -0.078 3 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.008 0.018 0.048 9 -0.062 4 13
ADAM17 -0.013 0.016 0.026 18 -10000 0 18
ErbB4/ErbB4 -0.002 0.001 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.024 0.039 0.1 19 -0.085 4 23
NCOR1 -0.015 0.005 0 12 -10000 0 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.01 0.025 0.063 12 -0.072 3 15
GRIN2B -0.004 0.054 0.16 10 -10000 0 10
ErbB4/ErbB2/betacellulin -0.005 0.032 0.065 19 -0.069 5 24
STAT1 -0.017 0.002 0 3 -10000 0 3
HBEGF -0.016 0.003 0 6 -10000 0 6
PRLR -0.015 0.005 0 15 -10000 0 15
E4ICDs/ETO2 0.022 0.039 0.1 18 -0.085 5 23
axon guidance 0.005 0.044 0.16 8 -10000 0 8
NEDD4 -0.013 0.014 0.024 15 -10000 0 15
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.009 -10000 0 0 21 21
CBFA2T3 -0.016 0.003 0 6 -10000 0 6
ErbB4/ErbB2/HBEGF -0.005 0.031 0.065 19 -0.069 5 24
MAPK3 -0.003 0.065 0.16 14 -10000 0 14
STAT1 (dimer) 0.023 0.04 0.1 19 -0.085 5 24
MAPK1 -0.002 0.066 0.17 15 -10000 0 15
JAK2 -0.014 0.007 0 25 -10000 0 25
ErbB4/ErbB2/neuregulin 1 beta -0.012 0.016 0.04 6 -0.064 4 10
NRG1 -0.017 0.009 0.012 5 -10000 0 5
NRG3 -0.016 0.003 0 6 -10000 0 6
NRG2 -0.016 0.003 0 6 -10000 0 6
NRG4 -0.017 0.002 0 3 -10000 0 3
heart development 0.005 0.044 0.16 8 -10000 0 8
neural crest cell migration -0.012 0.016 0.04 6 -0.064 4 10
ERBB2 -0.016 0.01 0.015 6 -10000 0 6
WWOX/E4ICDs 0.017 0.039 0.1 16 -0.085 5 21
SHC1 -0.016 0.004 0 9 -10000 0 9
ErbB4/EGFR/neuregulin 4 0.03 0.037 0.1 18 -0.084 4 22
apoptosis -0.018 0.035 0.072 4 -0.1 15 19
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.022 0.039 0.1 17 -0.085 5 22
ErbB4/ErbB2/epiregulin -0.005 0.032 0.065 19 -0.069 5 24
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.04 0.1 19 -0.085 5 24
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.033 0.035 0.14 4 -0.071 3 7
MDM2 0.002 0.044 0.23 5 -10000 0 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.014 0.011 0.03 2 -0.048 5 7
STAT5A 0.003 0.046 0.17 7 -10000 0 7
ErbB4/EGFR/neuregulin 1 beta -0.009 0.026 0.063 12 -0.07 4 16
DLG4 -0.016 0.004 0 8 -10000 0 8
GRB2/SHC 0.022 0.008 -10000 0 0 14 14
E4ICDs/TAB2/NCoR1 0.028 0.035 0.11 16 -0.084 3 19
STAT5A (dimer) -0.002 0.053 0.14 12 -10000 0 12
MAP3K7IP2 -0.016 0.004 0 8 -10000 0 8
STAT5B (dimer) 0.022 0.05 0.16 11 -10000 0 11
LRIG1 -0.016 0.003 0 6 -10000 0 6
EREG -0.017 0.002 0 2 -10000 0 2
BTC -0.017 0.002 0 2 -10000 0 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0 0.027 0.11 4 -10000 0 4
ERBB4 -0.002 0.001 -10000 0 -10000 0 0
STAT5B -0.016 0.004 0 7 -10000 0 7
YAP1 -0.006 0.051 -10000 0 -0.51 1 1
GRB2 -0.016 0.003 0 6 -10000 0 6
ErbB4/ErbB2/neuregulin 4 -0.005 0.032 0.067 19 -0.069 5 24
glial cell differentiation -0.028 0.034 0.083 3 -0.1 16 19
WWOX -0.012 0.008 0 42 -10000 0 42
cell proliferation 0.023 0.078 0.18 24 -0.22 1 25
Signaling events mediated by PRL

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
CCNE1 -0.014 0.006 0 20 -10000 0 20
mol:Halofuginone 0 0 -10000 0 -10000 0 0
ITGA1 -0.016 0.004 0 8 -10000 0 8
CDKN1A -0.005 0.048 -10000 0 -0.32 3 3
PRL-3/alpha Tubulin 0.01 0.004 -10000 0 0 21 21
mol:Ca2+ -0.016 0.008 0 26 -10000 0 26
AGT -0.016 0.004 0 7 -10000 0 7
CCNA2 -0.022 0.01 0 23 -10000 0 23
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.01 0.002 0 6 -10000 0 6
CDK2/Cyclin E1 0.015 0.064 -10000 0 -0.26 6 6
MAPK3 -0.017 0.008 0 22 -10000 0 22
PRL-2 /Rab GGTase beta 0.023 0.006 -10000 0 0 9 9
MAPK1 -0.017 0.008 0 25 -10000 0 25
PTP4A1 -0.018 0.008 0 22 -10000 0 22
PTP4A3 -0.014 0.006 0 21 -10000 0 21
PTP4A2 -0.016 0.003 0 6 -10000 0 6
ITGB1 -0.017 0.008 0 23 -10000 0 23
SRC -0.015 0.005 0 13 -10000 0 13
RAC1 -0.001 0.028 -10000 0 -0.32 1 1
Rab GGTase beta/Rab GGTase alpha 0.023 0.006 -10000 0 0 9 9
PRL-1/ATF-5 -0.005 0.056 0.16 13 -10000 0 13
RABGGTA -0.016 0.003 0 5 -10000 0 5
BCAR1 -0.016 0.008 0 25 -10000 0 25
RHOC -0.003 0.039 -10000 0 -0.32 2 2
RHOA -0.003 0.039 -10000 0 -0.32 2 2
cell motility 0.015 0.055 0.15 4 -0.35 1 5
PRL-1/alpha Tubulin -0.016 0.007 0 22 -10000 0 22
PRL-3/alpha1 Integrin 0.02 0.01 -10000 0 0 26 26
ROCK1 0.009 0.034 -10000 0 -10000 0 0
RABGGTB -0.016 0.003 0 5 -10000 0 5
CDK2 -0.016 0.004 0 7 -10000 0 7
mitosis -0.018 0.008 0 22 -10000 0 22
ATF5 -0.016 0.004 0 8 -10000 0 8
BARD1 signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.02 0.01 -10000 0 0 25 25
ATM -0.016 0.003 0 4 -10000 0 4
UBE2D3 -0.017 0.002 0 2 -10000 0 2
PRKDC -0.015 0.005 0 15 -10000 0 15
ATR -0.017 0.002 0 3 -10000 0 3
UBE2L3 -0.016 0.003 0 4 -10000 0 4
FANCD2 0.005 0.001 -10000 0 -10000 0 0
protein ubiquitination 0.034 0.019 -10000 0 0 32 32
XRCC5 -0.016 0.003 0 4 -10000 0 4
XRCC6 -0.016 0.003 0 4 -10000 0 4
M/R/N Complex 0.027 0.013 -10000 0 0 26 26
MRE11A -0.017 0.002 0 3 -10000 0 3
DNA-PK 0.029 0.012 -10000 0 0 20 20
FA complex/FANCD2/Ubiquitin -0.013 0.074 -10000 0 -0.29 7 7
FANCF -0.016 0.004 0 7 -10000 0 7
BRCA1 -0.016 0.003 0 4 -10000 0 4
CCNE1 -0.014 0.006 0 20 -10000 0 20
CDK2/Cyclin E1 0.02 0.009 -10000 0 0 24 24
FANCG -0.016 0.004 0 9 -10000 0 9
BRCA1/BACH1/BARD1 0.023 0.006 -10000 0 0 8 8
FANCE -0.016 0.003 0 6 -10000 0 6
FANCC -0.016 0.003 0 5 -10000 0 5
NBN -0.014 0.006 0 23 -10000 0 23
FANCA -0.016 0.003 0 6 -10000 0 6
DNA repair -0.003 0.067 0.15 14 -0.22 3 17
BRCA1/BARD1/ubiquitin 0.023 0.006 -10000 0 0 8 8
BARD1/DNA-PK 0.037 0.015 -10000 0 0 20 20
FANCL -0.017 0.001 0 1 -10000 0 1
mRNA polyadenylation -0.02 0.01 0 25 -10000 0 25
BRCA1/BARD1/CTIP/M/R/N Complex 0 0.032 0.072 18 -0.12 2 20
BRCA1/BACH1/BARD1/TopBP1 0.031 0.01 -10000 0 0 12 12
BRCA1/BARD1/P53 0.038 0.014 -10000 0 0 17 17
BARD1/CSTF1/BRCA1 0.027 0.013 -10000 0 0 26 26
BRCA1/BACH1 -0.016 0.003 0 4 -10000 0 4
BARD1 -0.016 0.003 0 4 -10000 0 4
PCNA -0.015 0.006 0 18 -10000 0 18
BRCA1/BARD1/UbcH5C 0.032 0.008 -10000 0 0 9 9
BRCA1/BARD1/UbcH7 0.031 0.009 -10000 0 0 11 11
BRCA1/BARD1/RAD51/PCNA 0.035 0.017 -10000 0 0 26 26
BARD1/DNA-PK/P53 0.04 0.02 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.023 0.006 -10000 0 0 8 8
BRCA1/BARD1/CTIP -0.025 0.01 0 18 -10000 0 18
FA complex -0.008 0.033 0.079 3 -0.2 3 6
BARD1/EWS 0.023 0.005 -10000 0 0 7 7
RBBP8 -0.019 0.006 0 12 -10000 0 12
TP53 -0.016 0.004 0 10 -10000 0 10
TOPBP1 -0.016 0.003 0 4 -10000 0 4
G1/S transition of mitotic cell cycle -0.036 0.014 0 17 -10000 0 17
BRCA1/BARD1 0.038 0.021 -10000 0 0 32 32
CSTF1 -0.014 0.006 0 24 -10000 0 24
BARD1/EWS-Fli1 0.012 0.002 -10000 0 0 4 4
CDK2 -0.016 0.004 0 7 -10000 0 7
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.016 0.003 0 4 -10000 0 4
RAD50 -0.016 0.004 0 8 -10000 0 8
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.023 0.006 -10000 0 0 8 8
EWSR1 -0.016 0.003 0 5 -10000 0 5
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.018 0.008 0 21 -10000 0 21
PCK1 -0.004 0.002 -10000 0 -10000 0 0
HNF4A -0.017 0.008 0 25 -10000 0 25
KCNJ11 -0.021 0.008 0 18 -10000 0 18
AKT1 -0.016 0.003 0 5 -10000 0 5
response to starvation 0 0 -10000 0 -10000 0 0
DLK1 -0.021 0.008 0 17 -10000 0 17
NKX2-1 -0.004 0.002 -10000 0 -10000 0 0
ACADM -0.018 0.007 0 18 -10000 0 18
TAT -0.004 0.002 -10000 0 -10000 0 0
CEBPB -0.014 0.007 0 27 -10000 0 27
CEBPA -0.015 0.005 0 12 -10000 0 12
TTR 0.028 0.11 0.25 17 -0.33 4 21
PKLR -0.017 0.008 0 24 -10000 0 24
APOA1 -0.007 0.004 -10000 0 -10000 0 0
CPT1C -0.018 0.008 0 23 -10000 0 23
ALAS1 -0.004 0.002 -10000 0 -10000 0 0
TFRC -0.003 0.001 -10000 0 -10000 0 0
FOXF1 -0.016 0.003 0 6 -10000 0 6
NF1 -0.017 0.002 0 3 -10000 0 3
HNF1A (dimer) 0 0 -10000 0 -10000 0 0
CPT1A -0.017 0.008 0 25 -10000 0 25
HMGCS1 -0.016 0.009 0 30 -10000 0 30
NR3C1 -0.016 0.003 0 6 -10000 0 6
CPT1B -0.018 0.008 0 23 -10000 0 23
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.017 0.002 0 3 -10000 0 3
GCK -0.018 0.007 0 19 -10000 0 19
CREB1 -0.017 0.002 0 3 -10000 0 3
IGFBP1 -0.004 0.002 -10000 0 -10000 0 0
PDX1 -0.005 0.002 0 18 -10000 0 18
UCP2 -0.018 0.008 0 21 -10000 0 21
ALDOB -0.021 0.008 0 19 -10000 0 19
AFP -0.003 0.001 0 15 -10000 0 15
BDH1 -0.018 0.008 0 22 -10000 0 22
HADH -0.014 0.005 0 16 -10000 0 16
F2 -0.008 0.004 -10000 0 -10000 0 0
HNF1A 0 0 -10000 0 -10000 0 0
G6PC -0.004 0.003 -10000 0 -10000 0 0
SLC2A2 -0.005 0.002 0 25 -10000 0 25
INS -0.016 0.004 0 10 -10000 0 10
FOXA1 -0.016 0.003 0 5 -10000 0 5
FOXA3 -0.016 0.004 0 9 -10000 0 9
FOXA2 -0.018 0.007 0 16 -10000 0 16
ABCC8 -0.021 0.008 0 19 -10000 0 19
ALB -0.003 0.001 0 15 -10000 0 15
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.027 0.014 -10000 0 0 28 28
fibroblast growth factor receptor signaling pathway 0.027 0.014 -10000 0 0 28 28
LAMA1 -0.016 0.003 0 6 -10000 0 6
PRNP -0.015 0.005 0 16 -10000 0 16
GPC1/SLIT2 0.023 0.005 -10000 0 0 7 7
SMAD2 -0.023 0.011 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.019 0.008 -10000 0 0 19 19
GPC1/Laminin alpha1 0.023 0.006 -10000 0 0 10 10
TDGF1 -0.016 0.003 0 6 -10000 0 6
CRIPTO/GPC1 0.023 0.006 -10000 0 0 10 10
APP/GPC1 0.023 0.007 -10000 0 0 12 12
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.021 0.008 0 16 -10000 0 16
FLT1 -0.016 0.003 0 4 -10000 0 4
GPC1/TGFB/TGFBR1/TGFBR2 0.03 0.01 -10000 0 0 14 14
SERPINC1 -0.016 0.003 0 5 -10000 0 5
FYN -0.022 0.007 0 12 -10000 0 12
FGR -0.021 0.008 0 16 -10000 0 16
positive regulation of MAPKKK cascade 0.006 0.065 0.18 11 -0.17 1 12
SLIT2 -0.016 0.003 0 4 -10000 0 4
GPC1/NRG 0.021 0.009 -10000 0 0 19 19
NRG1 -0.015 0.005 0 16 -10000 0 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.021 0.005 -10000 0 0 8 8
LYN -0.02 0.009 0 21 -10000 0 21
mol:Spermine -0.01 0.002 0 4 -10000 0 4
cell growth 0.027 0.014 -10000 0 0 28 28
BMP signaling pathway 0.016 0.003 -10000 0 0 4 4
SRC -0.02 0.009 0 21 -10000 0 21
TGFBR1 -0.016 0.003 0 5 -10000 0 5
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.016 0.004 0 10 -10000 0 10
GPC1 -0.016 0.003 0 4 -10000 0 4
TGFBR1 (dimer) -0.016 0.003 0 5 -10000 0 5
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.018 0.01 0 33 -10000 0 33
HCK -0.021 0.009 0 20 -10000 0 20
FGF2 -0.017 0.002 0 3 -10000 0 3
FGFR1 -0.014 0.006 0 23 -10000 0 23
VEGFR1 homodimer -0.016 0.003 0 4 -10000 0 4
TGFBR2 -0.016 0.003 0 6 -10000 0 6
cell death 0.022 0.007 -10000 0 0 12 12
ATIII/GPC1 0.023 0.006 -10000 0 0 9 9
PLA2G2A/GPC1 0.022 0.008 -10000 0 0 14 14
LCK -0.022 0.008 0 15 -10000 0 15
neuron differentiation 0.021 0.009 -10000 0 0 19 19
PrPc/Cu2+ 0.011 0.004 -10000 0 0 16 16
APP -0.016 0.004 0 8 -10000 0 8
TGFBR2 (dimer) -0.016 0.003 0 6 -10000 0 6
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.022 0.007 -10000 0 0 13 13
FBXW11 -0.016 0.004 0 7 -10000 0 7
NF kappa B1 p50/c-Rel -0.021 0.008 0 18 -10000 0 18
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.043 0.092 10 -0.24 2 12
NFKBIA -0.003 0.001 0 22 -10000 0 22
MAPK14 -0.016 0.003 0 6 -10000 0 6
NF kappa B1 p105/p50 -0.02 0.009 0 22 -10000 0 22
ARRB2 -0.003 0.001 0 13 -10000 0 13
REL -0.017 0.001 0 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.02 0.009 0 25 -10000 0 25
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.021 0.008 0 19 -10000 0 19
PIK3CA -0.016 0.004 0 10 -10000 0 10
NF kappa B1 p50 dimer -0.018 0.007 -10000 0 -10000 0 0
PIK3R1 -0.016 0.004 0 9 -10000 0 9
NFKB1 -0.018 0.007 0 18 -10000 0 18
RELA -0.017 0.002 0 3 -10000 0 3
positive regulation of anti-apoptosis 0.004 0.033 0.082 17 -0.18 1 18
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.019 0.046 0.085 9 -0.18 5 14
SRC -0.015 0.005 0 13 -10000 0 13
PI3K 0.021 0.008 -10000 0 0 18 18
NF kappa B1 p50/RelA 0.004 0.033 0.082 17 -0.18 1 18
IKBKB -0.015 0.006 0 18 -10000 0 18
beta TrCP1/SCF ubiquitin ligase complex -0.016 0.004 0 7 -10000 0 7
SYK -0.016 0.003 0 5 -10000 0 5
I kappa B alpha/PIK3R1 -0.007 0.048 0.098 11 -0.24 3 14
cell death -0.018 0.044 0.082 9 -0.18 5 14
NF kappa B1 p105/c-Rel -0.021 0.008 0 18 -10000 0 18
LCK -0.016 0.003 0 6 -10000 0 6
BCL3 -0.016 0.004 0 10 -10000 0 10
IL23-mediated signaling events

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
CCL2 -0.027 0.087 0.18 1 -0.24 16 17
IL23A -0.009 0.054 0.15 8 -0.17 5 13
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.079 -10000 0 -0.19 16 16
positive regulation of T cell mediated cytotoxicity -0.024 0.09 0.13 1 -0.26 16 17
ITGA3 -0.017 0.073 0.15 5 -0.19 15 20
IL17F -0.023 0.078 0.14 10 -0.2 15 25
IL12B -0.01 0.013 -10000 0 -10000 0 0
STAT1 (dimer) -0.017 0.093 0.13 1 -0.25 17 18
CD4 -0.022 0.086 0.22 2 -0.25 14 16
IL23 -0.007 0.041 0.13 7 -0.18 2 9
IL23R -0.001 0.078 -10000 0 -0.62 2 2
IL1B -0.014 0.062 0.14 7 -0.16 14 21
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.022 0.092 0.23 4 -0.23 17 21
TYK2 -0.011 0.015 0.032 2 -10000 0 2
STAT4 -0.017 0.002 0 3 -10000 0 3
STAT3 -0.016 0.003 0 5 -10000 0 5
IL18RAP -0.012 0.012 0.017 19 -10000 0 19
IL12RB1 -0.011 0.016 0.032 2 -10000 0 2
PIK3CA -0.016 0.004 0 10 -10000 0 10
IL12Rbeta1/TYK2 0.025 0.009 0.053 2 -0.021 1 3
IL23R/JAK2 0.008 0.062 -10000 0 -0.47 2 2
positive regulation of chronic inflammatory response -0.024 0.09 0.13 1 -0.26 16 17
natural killer cell activation 0.001 0.001 0.005 1 -0.006 1 2
JAK2 -0.011 0.012 -10000 0 -10000 0 0
PIK3R1 -0.016 0.004 0 9 -10000 0 9
NFKB1 -0.01 0.014 -10000 0 -10000 0 0
RELA -0.01 0.014 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.007 0.041 0.13 7 -0.18 2 9
ALOX12B -0.029 0.084 -10000 0 -0.24 17 17
CXCL1 -0.028 0.088 0.18 1 -0.24 17 18
T cell proliferation -0.024 0.09 0.13 1 -0.26 16 17
NFKBIA -0.009 0.014 -10000 0 -10000 0 0
IL17A -0.02 0.046 0.073 2 -0.14 15 17
PI3K -0.008 0.089 0.13 1 -0.24 16 17
IFNG -0.001 0.023 0.082 2 -0.088 6 8
STAT3 (dimer) -0.002 0.089 -10000 0 -0.24 15 15
IL18R1 -0.012 0.012 0.017 19 -10000 0 19
IL23/IL23R/JAK2/TYK2/SOCS3 -0.022 0.094 0.18 2 -0.24 16 18
IL18/IL18R 0.032 0.009 -10000 0 0 10 10
macrophage activation -0.002 0.002 -10000 0 -0.01 4 4
TNF -0.013 0.064 0.16 6 -0.16 14 20
STAT3/STAT4 -0.009 0.094 0.13 1 -0.25 16 17
STAT4 (dimer) -0.017 0.093 0.13 1 -0.25 17 18
IL18 -0.012 0.011 0.017 16 -10000 0 16
IL19 -0.022 0.092 0.23 4 -0.23 17 21
STAT5A (dimer) -0.015 0.092 0.13 1 -0.25 16 17
STAT1 -0.017 0.002 0 3 -10000 0 3
SOCS3 -0.016 0.003 0 6 -10000 0 6
CXCL9 -0.03 0.086 0.12 1 -0.24 17 18
MPO -0.026 0.091 0.18 3 -0.24 17 20
positive regulation of humoral immune response -0.024 0.09 0.13 1 -0.26 16 17
IL23/IL23R/JAK2/TYK2 -0.024 0.09 0.13 1 -0.26 16 17
IL6 -0.015 0.073 0.16 6 -0.19 14 20
STAT5A -0.016 0.003 0 6 -10000 0 6
IL2 0.01 0.014 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.001 0.005 1 -0.006 1 2
CD3E -0.028 0.086 0.17 1 -0.24 17 18
keratinocyte proliferation -0.024 0.09 0.13 1 -0.26 16 17
NOS2 -0.024 0.086 0.12 1 -0.24 17 18
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 0.002 0.038 0.13 7 -10000 0 7
adherens junction organization 0.006 0.042 0.14 5 -0.14 3 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.05 0.14 10 -10000 0 10
FMN1 0.005 0.035 0.12 2 -0.13 2 4
mol:IP3 -0.008 0.026 0.057 15 -0.083 3 18
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.036 -10000 0 -0.14 3 3
CTNNB1 -0.01 0.014 0.02 20 -10000 0 20
AKT1 0 0.044 0.1 12 -10000 0 12
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.006 0.074 0.13 1 -0.3 5 6
CTNND1 -0.006 0.018 0.022 37 -10000 0 37
mol:PI-4-5-P2 0.004 0.035 0.12 2 -0.15 2 4
VASP 0.003 0.035 0.12 2 -0.15 2 4
ZYX 0.004 0.034 0.12 2 -0.13 2 4
JUB 0.004 0.038 0.12 2 -0.14 3 5
EGFR(dimer) 0.019 0.045 0.13 4 -0.13 5 9
E-cadherin/beta catenin-gamma catenin 0.027 0.014 -10000 0 -0.001 26 26
mol:PI-3-4-5-P3 0.029 0.045 0.15 10 -0.082 4 14
PIK3CA -0.008 0.017 0.026 11 -10000 0 11
PI3K 0.029 0.046 0.15 10 -0.084 4 14
FYN -0.005 0.045 0.13 6 -0.2 2 8
mol:Ca2+ -0.007 0.026 0.056 15 -0.082 3 18
JUP -0.01 0.015 0.021 23 -10000 0 23
PIK3R1 -0.006 0.018 0.026 15 -10000 0 15
mol:DAG -0.008 0.026 0.057 15 -0.083 3 18
CDH1 -0.011 0.014 0.02 20 -10000 0 20
RhoA/GDP -0.001 0.053 0.14 12 -10000 0 12
establishment of polarity of embryonic epithelium 0.003 0.035 0.12 2 -0.15 2 4
SRC -0.015 0.005 0 13 -10000 0 13
RAC1 -0.016 0.004 0 9 -10000 0 9
RHOA -0.016 0.003 0 5 -10000 0 5
EGFR -0.016 0.004 0 10 -10000 0 10
CASR -0.006 0.039 0.14 5 -10000 0 5
RhoA/GTP -0.01 0.028 0.06 15 -10000 0 15
AKT2 -0.001 0.042 0.11 10 -10000 0 10
actin cable formation 0.001 0.034 0.11 4 -0.13 1 5
apoptosis -0.006 0.042 -10000 0 -0.11 11 11
CTNNA1 -0.006 0.017 0.022 34 -10000 0 34
mol:GDP -0.007 0.037 0.12 6 -10000 0 6
PIP5K1A 0.004 0.035 0.12 2 -0.15 2 4
PLCG1 -0.008 0.027 0.057 15 -0.084 3 18
Rac1/GTP 0.024 0.043 0.12 4 -0.12 5 9
homophilic cell adhesion 0 0.003 0.009 10 -10000 0 10
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 -0.016 0.003 0 5 -10000 0 5
VLDLR -0.015 0.005 0 16 -10000 0 16
LRPAP1 -0.016 0.003 0 4 -10000 0 4
NUDC -0.016 0.004 0 9 -10000 0 9
RELN/LRP8 0.03 0.01 -10000 0 0 14 14
CaM/Ca2+ 0.012 0.002 -10000 0 0 4 4
KATNA1 -0.016 0.004 0 8 -10000 0 8
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.015 0.045 0.16 8 -10000 0 8
IQGAP1/CaM 0.023 0.007 -10000 0 0 12 12
DAB1 -0.017 0.002 0 3 -10000 0 3
IQGAP1 -0.016 0.004 0 9 -10000 0 9
PLA2G7 -0.016 0.003 0 4 -10000 0 4
CALM1 -0.016 0.003 0 4 -10000 0 4
DYNLT1 -0.016 0.004 0 7 -10000 0 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.024 0.005 -10000 0 0 6 6
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 -0.017 0.002 0 3 -10000 0 3
LIS1/Poliovirus Protein 3A -0.013 0.006 0 23 -10000 0 23
CDK5R2 -0.016 0.003 0 4 -10000 0 4
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.028 0.012 -10000 0 0 22 22
YWHAE -0.016 0.004 0 7 -10000 0 7
NDEL1/14-3-3 E -0.021 0.052 0.19 7 -10000 0 7
MAP1B -0.001 0.001 -10000 0 -10000 0 0
RAC1 -0.004 0.002 0 33 -10000 0 33
p35/CDK5 -0.025 0.038 0.16 5 -10000 0 5
RELN -0.016 0.004 0 9 -10000 0 9
PAFAH/LIS1 -0.02 0.009 0 25 -10000 0 25
LIS1/CLIP170 -0.013 0.006 0 23 -10000 0 23
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.037 0.031 0.095 4 -10000 0 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.014 0.052 0.11 5 -0.18 10 15
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.021 0.032 0.15 4 -10000 0 4
LIS1/IQGAP1 -0.019 0.01 0 30 -10000 0 30
RHOA -0.004 0.002 0 31 -10000 0 31
PAFAH1B1 -0.017 0.008 0 23 -10000 0 23
PAFAH1B3 -0.016 0.004 0 8 -10000 0 8
PAFAH1B2 -0.016 0.004 0 7 -10000 0 7
MAP1B/LIS1/Dynein heavy chain -0.017 0.022 0.077 2 -0.087 8 10
NDEL1/Katanin 60/Dynein heavy chain -0.024 0.058 0.19 8 -10000 0 8
LRP8 -0.017 0.002 0 3 -10000 0 3
NDEL1/Katanin 60 -0.022 0.052 0.19 7 -10000 0 7
P39/CDK5 -0.026 0.038 0.16 5 -10000 0 5
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.02 0.009 0 25 -10000 0 25
CDK5 -0.022 0.037 0.16 5 -10000 0 5
PPP2R5D -0.016 0.004 0 7 -10000 0 7
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.011 0.005 0 23 -10000 0 23
CSNK2A1 -0.015 0.005 0 16 -10000 0 16
RELN/VLDLR/DAB1/LIS1 -0.024 0.014 -10000 0 -10000 0 0
RELN/VLDLR 0.035 0.017 -10000 0 0 25 25
CDC42 -0.004 0.002 0 36 -10000 0 36
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.01 0.004 -10000 0 0 18 18
ARNO/beta Arrestin1-2 0.014 0.015 -10000 0 -0.043 6 6
EGFR -0.015 0.006 0.003 12 -10000 0 12
EPHA2 -0.016 0.004 0 7 -10000 0 7
USP6 -0.016 0.004 0 9 -10000 0 9
IQSEC1 -0.015 0.007 0.011 8 -10000 0 8
EGFR/EGFR/EGF/EGF 0.022 0.008 -10000 0 0 14 14
ARRB2 -0.002 0.003 -10000 0 -10000 0 0
mol:GTP 0 0.022 0.1 4 -0.046 8 12
ARRB1 -0.017 0.002 0 3 -10000 0 3
FBXO8 -0.016 0.005 0 11 -10000 0 11
TSHR -0.015 0.007 0.011 8 -10000 0 8
EGF -0.015 0.006 0.008 8 -10000 0 8
somatostatin receptor activity 0 0 0 7 0 8 15
ARAP2 0 0 0 7 0 4 11
mol:GDP 0.001 0.056 0.1 4 -0.21 7 11
mol:PI-3-4-5-P3 0 0 0 5 0 8 13
ITGA2B -0.017 0.002 0 3 -10000 0 3
ARF6 -0.015 0.007 0.007 10 -10000 0 10
Ephrin A1/EPHA2/NCK1/GIT1 0.037 0.015 -10000 0 0 20 20
ADAP1 0 0 0 5 0 4 9
KIF13B -0.015 0.006 0 18 -10000 0 18
HGF/MET 0.022 0.007 -10000 0 0 13 13
PXN -0.016 0.003 0 4 -10000 0 4
ARF6/GTP 0.003 0.065 0.13 6 -0.2 8 14
EGFR/EGFR/EGF/EGF/ARFGEP100 0.03 0.011 -10000 0 0 17 17
ADRB2 -0.015 0.007 0.006 13 -10000 0 13
receptor agonist activity 0 0 0 7 0 5 12
actin filament binding 0 0 0 7 0 8 15
SRC -0.015 0.007 0.003 16 -10000 0 16
ITGB3 -0.016 0.003 0 4 -10000 0 4
GNAQ -0.012 0.011 0.017 16 -10000 0 16
EFA6/PI-4-5-P2 0 0 0.001 11 -0.001 7 18
ARF6/GDP -0.009 0.065 0.12 2 -0.26 6 8
ARF6/GDP/GULP/ACAP1 0.016 0.054 0.11 3 -0.18 7 10
alphaIIb/beta3 Integrin/paxillin/GIT1 0.039 0.012 -10000 0 -10000 0 0
ACAP1 0 0 0 2 0 1 3
ACAP2 0 0 0 6 0 6 12
LHCGR/beta Arrestin2 0.01 0.015 -10000 0 -0.051 8 8
EFNA1 -0.016 0.004 0 9 -10000 0 9
HGF -0.016 0.003 0 5 -10000 0 5
CYTH3 0 0 0 7 -0.001 5 12
CYTH2 0 0.001 0.002 1 -0.003 8 9
NCK1 -0.017 0.002 0 2 -10000 0 2
fibronectin binding 0 0 0 6 0 8 14
endosomal lumen acidification 0 0 0 10 0 5 15
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.017 0.002 0 3 -10000 0 3
GNAQ/ARNO 0.011 0.004 -10000 0 -0.005 8 8
mol:Phosphatidic acid 0 0 0 6 0 6 12
PIP3-E -0.016 0.004 0 7 -10000 0 7
MET -0.015 0.005 0 12 -10000 0 12
GNA14 -0.013 0.01 0.012 17 -10000 0 17
GNA15 -0.016 0.006 0.006 8 -10000 0 8
GIT1 -0.016 0.003 0 4 -10000 0 4
mol:PI-4-5-P2 0 0 0 10 -0.001 7 17
GNA11 -0.015 0.007 0.008 10 -10000 0 10
LHCGR -0.014 0.01 0.017 13 -10000 0 13
AGTR1 -0.015 0.007 0.008 10 -10000 0 10
desensitization of G-protein coupled receptor protein signaling pathway 0.01 0.015 -10000 0 -0.051 8 8
IPCEF1/ARNO 0.026 0.011 -10000 0 -0.001 20 20
alphaIIb/beta3 Integrin 0.024 0.005 -10000 0 0 6 6
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.037 0.021 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.026 0.014 -10000 0 0 32 32
NOG -0.016 0.003 0 4 -10000 0 4
SMAD9 0.001 0.078 -10000 0 -0.5 3 3
SMAD4 -0.015 0.005 0 15 -10000 0 15
SMAD5 -0.004 0.029 -10000 0 -0.25 1 1
BMP7/USAG1 0.019 0.01 -10000 0 0 29 29
SMAD5/SKI -0.021 0.079 -10000 0 -0.26 9 9
SMAD1 -0.005 0.049 -10000 0 -0.26 3 3
BMP2 -0.015 0.005 0 16 -10000 0 16
SMAD1/SMAD1/SMAD4 -0.026 0.044 -10000 0 -0.24 3 3
BMPR1A -0.016 0.004 0 7 -10000 0 7
BMPR1B -0.017 0.002 0 3 -10000 0 3
BMPR1A-1B/BAMBI 0.031 0.01 -10000 0 0 13 13
AHSG -0.016 0.004 0 8 -10000 0 8
CER1 -0.015 0.006 0 17 -10000 0 17
BMP2-4/CER1 0.027 0.014 -10000 0 0 28 28
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.01 0.061 -10000 0 -0.23 7 7
BMP2-4 (homodimer) 0.021 0.009 -10000 0 0 19 19
RGMB -0.016 0.005 0 11 -10000 0 11
BMP6/BMPR2/BMPR1A-1B 0.038 0.013 -10000 0 0 14 14
RGMA -0.016 0.004 0 10 -10000 0 10
SMURF1 -0.015 0.005 0 16 -10000 0 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0 0.041 0.066 10 -0.14 7 17
BMP2-4/USAG1 0.029 0.012 -10000 0 0 21 21
SMAD6/SMURF1/SMAD5 -0.019 0.072 -10000 0 -0.24 9 9
SOSTDC1 -0.016 0.003 0 6 -10000 0 6
BMP7/BMPR2/BMPR1A-1B 0.034 0.018 -10000 0 0 29 29
SKI -0.016 0.004 0 10 -10000 0 10
BMP6 (homodimer) -0.016 0.004 0 8 -10000 0 8
HFE2 -0.016 0.004 0 10 -10000 0 10
ZFYVE16 -0.016 0.004 0 8 -10000 0 8
MAP3K7 -0.016 0.004 0 7 -10000 0 7
BMP2-4/CHRD 0.028 0.013 -10000 0 0 25 25
SMAD5/SMAD5/SMAD4 -0.019 0.078 -10000 0 -0.26 9 9
MAPK1 -0.016 0.003 0 4 -10000 0 4
TAK1/TAB family 0.024 0.051 0.13 4 -0.12 9 13
BMP7 (homodimer) -0.014 0.006 0 24 -10000 0 24
NUP214 -0.016 0.003 0 4 -10000 0 4
BMP6/FETUA 0.022 0.008 -10000 0 0 14 14
SMAD1/SKI -0.012 0.065 -10000 0 -0.32 4 4
SMAD6 -0.016 0.003 0 5 -10000 0 5
CTDSP2 -0.016 0.003 0 6 -10000 0 6
BMP2-4/FETUA 0.028 0.013 -10000 0 0 24 24
MAP3K7IP1 -0.016 0.003 0 4 -10000 0 4
GREM1 -0.016 0.003 0 4 -10000 0 4
BMPR2 (homodimer) -0.017 0.002 0 3 -10000 0 3
GADD34/PP1CA 0.029 0.012 -10000 0 0 20 20
BMPR1A-1B (homodimer) 0.023 0.006 -10000 0 0 9 9
CHRDL1 -0.017 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.014 0.064 -10000 0 -0.28 5 5
SMAD6-7/SMURF1/SMAD1 0.013 0.053 -10000 0 -0.21 5 5
SMAD6/SMURF1 -0.015 0.005 0 16 -10000 0 16
BAMBI -0.016 0.003 0 5 -10000 0 5
SMURF2 -0.016 0.003 0 6 -10000 0 6
BMP2-4/CHRDL1 0.029 0.012 -10000 0 0 19 19
BMP2-4/GREM1 0.029 0.012 -10000 0 0 20 20
SMAD7 -0.015 0.005 0 16 -10000 0 16
SMAD8A/SMAD8A/SMAD4 0.006 0.086 -10000 0 -0.4 5 5
SMAD1/SMAD6 -0.013 0.057 -10000 0 -0.26 5 5
TAK1/SMAD6 0.021 0.009 -10000 0 0 21 21
BMP7 -0.014 0.006 0 24 -10000 0 24
BMP6 -0.016 0.004 0 8 -10000 0 8
MAP3K7IP2 -0.016 0.004 0 8 -10000 0 8
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.006 0.033 -10000 0 -0.21 2 2
PPM1A -0.016 0.003 0 4 -10000 0 4
SMAD1/SMURF2 -0.013 0.06 -10000 0 -0.26 5 5
SMAD7/SMURF1 0.019 0.01 -10000 0 0 30 30
CTDSPL -0.016 0.004 0 7 -10000 0 7
PPP1CA -0.016 0.003 0 6 -10000 0 6
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 -0.017 0.002 0 3 -10000 0 3
PPP1R15A -0.016 0.004 0 9 -10000 0 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.002 0.05 -10000 0 -0.15 8 8
CHRD -0.016 0.004 0 9 -10000 0 9
BMPR2 -0.017 0.002 0 3 -10000 0 3
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.011 0.037 -10000 0 -0.12 9 9
BMP4 -0.016 0.003 0 5 -10000 0 5
FST -0.016 0.004 0 9 -10000 0 9
BMP2-4/NOG 0.028 0.012 -10000 0 0 22 22
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.035 0.022 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.017 0.03 19 -10000 0 19
PDGF/PDGFRA/CRKL 0.023 0.007 -10000 0 0 10 10
positive regulation of JUN kinase activity 0.036 0.015 -10000 0 0 18 18
CRKL -0.016 0.003 0 5 -10000 0 5
PDGF/PDGFRA/Caveolin-3 0.024 0.007 -10000 0 0 8 8
AP1 -0.017 0.038 0.13 8 -10000 0 8
mol:IP3 -0.018 0.012 0.025 6 -10000 0 6
PLCG1 -0.018 0.012 0.025 6 -10000 0 6
PDGF/PDGFRA/alphaV Integrin 0.024 0.007 -10000 0 0 9 9
RAPGEF1 -0.016 0.003 0 5 -10000 0 5
CRK -0.016 0.004 0 7 -10000 0 7
mol:Ca2+ -0.018 0.012 0.025 6 -10000 0 6
CAV3 -0.016 0.003 0 4 -10000 0 4
CAV1 -0.015 0.005 0 12 -10000 0 12
SHC/Grb2/SOS1 0.038 0.015 -10000 0 0 18 18
PDGF/PDGFRA/Shf 0.023 0.008 -10000 0 0 11 11
FOS -0.02 0.033 0.14 5 -10000 0 5
JUN -0.018 0.012 0.021 8 -10000 0 8
oligodendrocyte development 0.024 0.007 -10000 0 0 9 9
GRB2 -0.016 0.003 0 6 -10000 0 6
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:DAG -0.018 0.012 0.025 6 -10000 0 6
PDGF/PDGFRA -0.012 0.017 0.03 19 -10000 0 19
actin cytoskeleton reorganization 0.023 0.008 -10000 0 0 11 11
SRF -0.018 0.008 0 20 -10000 0 20
SHC1 -0.016 0.004 0 9 -10000 0 9
PI3K 0.029 0.013 -10000 0 0 22 22
PDGF/PDGFRA/Crk/C3G 0.031 0.011 -10000 0 0 14 14
JAK1 -0.018 0.009 0.006 15 -10000 0 15
ELK1/SRF -0.019 0.037 0.13 7 -10000 0 7
SHB -0.016 0.003 0 6 -10000 0 6
SHF -0.016 0.003 0 6 -10000 0 6
CSNK2A1 0.013 0.014 -10000 0 -0.026 10 10
GO:0007205 -0.014 0.009 0.019 6 -10000 0 6
SOS1 -0.017 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.015 -10000 0 0 18 18
PDGF/PDGFRA/SHB 0.023 0.008 -10000 0 0 11 11
PDGF/PDGFRA/Caveolin-1 0.022 0.009 -10000 0 0 16 16
ITGAV -0.016 0.003 0 4 -10000 0 4
ELK1 -0.018 0.012 0.024 6 -10000 0 6
PIK3CA -0.016 0.004 0 10 -10000 0 10
PDGF/PDGFRA/Crk 0.023 0.008 -10000 0 0 11 11
JAK-STAT cascade -0.018 0.009 0.006 15 -10000 0 15
cell proliferation 0.023 0.008 -10000 0 0 11 11
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.016 0.004 0 8 -10000 0 8
alphaV beta3 Integrin 0.023 0.006 -10000 0 0 8 8
PTK2 -0.001 0.056 0.1 5 -0.2 9 14
positive regulation of JNK cascade -0.001 0.071 -10000 0 -0.24 10 10
CDC42/GDP 0.011 0.096 -10000 0 -0.32 9 9
Rac1/GDP 0.009 0.095 0.19 1 -0.34 8 9
RAP1B -0.015 0.005 0 13 -10000 0 13
RAP1A -0.016 0.003 0 5 -10000 0 5
CTNNB1 -0.016 0.005 0 11 -10000 0 11
CDC42/GTP 0.007 0.089 -10000 0 -0.29 10 10
nectin-3/I-afadin 0.023 0.007 -10000 0 0 12 12
RAPGEF1 -0.005 0.086 0.21 2 -0.32 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.009 0.085 -10000 0 -0.36 7 7
PDGFB-D/PDGFRB -0.016 0.004 0 8 -10000 0 8
TLN1 -0.014 0.007 0 26 -10000 0 26
Rap1/GTP -0.002 0.056 -10000 0 -0.22 7 7
IQGAP1 -0.016 0.004 0 9 -10000 0 9
Rap1/GTP/I-afadin 0.027 0.012 -10000 0 0 23 23
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.023 0.007 -10000 0 0 12 12
PVR -0.016 0.004 0 9 -10000 0 9
Necl-5(dimer) -0.016 0.004 0 9 -10000 0 9
mol:GDP 0.001 0.11 0.2 1 -0.4 8 9
MLLT4 -0.016 0.005 0 11 -10000 0 11
PIK3CA -0.016 0.004 0 10 -10000 0 10
PI3K 0.04 0.019 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.022 0.008 -10000 0 0 15 15
positive regulation of lamellipodium assembly 0.004 0.074 -10000 0 -0.26 9 9
PVRL1 -0.016 0.004 0 7 -10000 0 7
PVRL3 -0.017 0.002 0 2 -10000 0 2
PVRL2 -0.016 0.004 0 10 -10000 0 10
PIK3R1 -0.016 0.004 0 9 -10000 0 9
CDH1 -0.017 0.002 0 3 -10000 0 3
CLDN1 -0.016 0.004 0 10 -10000 0 10
JAM-A/CLDN1 0.036 0.016 -10000 0 0 23 23
SRC -0.007 0.092 -10000 0 -0.4 7 7
ITGB3 -0.016 0.003 0 4 -10000 0 4
nectin-1(dimer)/I-afadin/I-afadin 0.022 0.008 -10000 0 0 15 15
FARP2 0.002 0.12 -10000 0 -0.4 10 10
RAC1 -0.016 0.004 0 9 -10000 0 9
CTNNA1 -0.016 0.004 0 9 -10000 0 9
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.029 0.011 -10000 0 0 18 18
nectin-1/I-afadin 0.022 0.008 -10000 0 0 15 15
nectin-2/I-afadin 0.021 0.008 -10000 0 0 18 18
RAC1/GTP/IQGAP1/filamentous actin 0.02 0.007 -10000 0 0 17 17
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.03 0.011 -10000 0 0 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.02 0.007 -10000 0 0 17 17
F11R -0.016 0.004 0 8 -10000 0 8
positive regulation of filopodium formation -0.001 0.071 -10000 0 -0.24 10 10
alphaV/beta3 Integrin/Talin -0.013 0.054 0.14 12 -0.14 3 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.021 0.008 -10000 0 0 18 18
nectin-2(dimer)/I-afadin/I-afadin 0.021 0.008 -10000 0 0 18 18
PIP5K1C -0.011 0.004 0 19 -10000 0 19
VAV2 0.005 0.12 -10000 0 -0.4 9 9
RAP1/GDP 0.012 0.082 0.18 1 -0.28 8 9
ITGAV -0.016 0.003 0 4 -10000 0 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.029 0.012 -10000 0 0 19 19
nectin-3(dimer)/I-afadin/I-afadin 0.023 0.007 -10000 0 0 12 12
Rac1/GTP 0.007 0.09 -10000 0 -0.31 9 9
PTPRM -0.005 0.002 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.037 0.022 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 -0.016 0.005 0 11 -10000 0 11
Class I PI3K 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
ARF5/GTP -0.009 0.054 0.14 14 -10000 0 14
DAPP1 0.011 0.074 0.16 12 -0.26 4 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.002 0.12 0.19 5 -0.46 7 12
mol:DAG 0.009 0.065 0.15 15 -0.15 2 17
HRAS -0.011 0.017 0.027 21 -10000 0 21
RAP1A -0.011 0.018 0.027 23 -10000 0 23
ARF5/GDP 0.016 0.045 0.13 1 -0.16 4 5
PLCG2 -0.016 0.003 0 5 -10000 0 5
PLCG1 -0.015 0.005 0 15 -10000 0 15
ARF5 -0.016 0.003 0 5 -10000 0 5
mol:GTP -0.004 0.056 0.15 15 -10000 0 15
ARF1/GTP -0.001 0.048 0.14 13 -10000 0 13
RHOA -0.016 0.003 0 5 -10000 0 5
YES1 -0.016 0.003 0 6 -10000 0 6
RAP1A/GTP -0.005 0.056 0.15 14 -10000 0 14
ADAP1 -0.006 0.05 0.14 14 -10000 0 14
ARAP3 -0.004 0.055 0.15 15 -10000 0 15
INPPL1 -0.016 0.003 0 5 -10000 0 5
PREX1 -0.015 0.006 0 19 -10000 0 19
ARHGEF6 -0.017 0 -10000 0 -10000 0 0
ARHGEF7 -0.016 0.003 0 5 -10000 0 5
ARF1 -0.016 0.003 0 6 -10000 0 6
NRAS -0.011 0.017 0.026 22 -10000 0 22
FYN -0.016 0.003 0 5 -10000 0 5
ARF6 -0.016 0.003 0 6 -10000 0 6
FGR -0.016 0.004 0 8 -10000 0 8
mol:Ca2+ 0.007 0.049 0.14 10 -0.092 1 11
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.016 0.003 0 5 -10000 0 5
ZAP70 -0.017 0.002 0 3 -10000 0 3
mol:IP3 0.006 0.06 0.17 10 -0.12 2 12
LYN -0.015 0.005 0 14 -10000 0 14
ARF1/GDP 0.014 0.045 0.13 1 -0.16 4 5
RhoA/GDP -0.001 0.057 0.15 14 -10000 0 14
PDK1/Src/Hsp90 0.02 0.007 -10000 0 0 16 16
BLNK -0.017 0.002 0 3 -10000 0 3
actin cytoskeleton reorganization 0.008 0.06 0.14 18 -0.16 2 20
SRC -0.015 0.005 0 13 -10000 0 13
PLEKHA2 -0.021 0.009 0 20 -10000 0 20
RAC1 -0.016 0.004 0 9 -10000 0 9
PTEN 0.01 0.017 -10000 0 -0.028 17 17
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.054 0.14 14 -10000 0 14
RhoA/GTP -0.009 0.055 0.14 14 -10000 0 14
Src family/SYK family/BLNK-LAT -0.012 0.043 -10000 0 -0.27 3 3
BLK -0.014 0.007 0 26 -10000 0 26
PDPK1 -0.016 0.003 0 4 -10000 0 4
CYTH1 -0.006 0.05 0.14 14 -10000 0 14
HCK -0.016 0.005 0 11 -10000 0 11
CYTH3 -0.006 0.05 0.14 14 -10000 0 14
CYTH2 -0.006 0.05 0.14 14 -10000 0 14
KRAS -0.013 0.014 0.026 10 -10000 0 10
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.001 0.037 0.094 14 -0.13 3 17
SGK1 0 0.035 0.089 13 -0.14 3 16
INPP5D -0.017 0.002 0 2 -10000 0 2
mol:GDP 0.007 0.045 0.13 1 -0.16 4 5
SOS1 -0.017 0 -10000 0 -10000 0 0
SYK -0.016 0.003 0 5 -10000 0 5
ARF6/GDP -0.002 0.054 0.14 14 -10000 0 14
mol:PI-3-4-5-P3 -0.009 0.045 0.13 13 -10000 0 13
ARAP3/RAP1A/GTP -0.005 0.056 0.16 14 -10000 0 14
VAV1 -0.016 0.003 0 6 -10000 0 6
mol:PI-3-4-P2 -0.019 0.005 0 7 -10000 0 7
RAS family/GTP/PI3K Class I -0.015 0.032 0.17 3 -10000 0 3
PLEKHA1 -0.022 0.007 0 13 -10000 0 13
Rac1/GDP 0.015 0.045 0.13 1 -0.16 4 5
LAT -0.017 0.002 0 3 -10000 0 3
Rac1/GTP 0.002 0.039 -10000 0 -0.19 4 4
ITK -0.009 0.054 0.14 15 -10000 0 15
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.004 0.07 0.17 12 -0.17 4 16
LCK -0.016 0.003 0 6 -10000 0 6
BTK -0.01 0.054 0.14 15 -10000 0 15
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.016 0.004 0 9 -10000 0 9
CCL5 -0.017 0.002 0 3 -10000 0 3
SDCBP -0.015 0.005 0 15 -10000 0 15
FGFR/FGF2/Syndecan-1 0.004 0.034 0.099 12 -10000 0 12
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 -0.008 0.034 0.12 3 -0.17 2 5
Syndecan-1/Syntenin 0 0.047 0.12 12 -0.17 2 14
MAPK3 -0.009 0.042 0.092 15 -0.14 2 17
HGF/MET 0.022 0.007 -10000 0 0 13 13
TGFB1/TGF beta receptor Type II -0.016 0.004 0 9 -10000 0 9
BSG -0.016 0.003 0 6 -10000 0 6
keratinocyte migration -0.008 0.034 0.12 3 -0.17 2 5
Syndecan-1/RANTES 0.001 0.055 0.12 16 -0.17 3 19
Syndecan-1/CD147 0.025 0.042 0.17 2 -0.13 3 5
Syndecan-1/Syntenin/PIP2 -0.001 0.045 0.11 12 -0.16 2 14
LAMA5 -0.014 0.006 0 23 -10000 0 23
positive regulation of cell-cell adhesion -0.001 0.044 0.11 12 -0.16 2 14
MMP7 -0.016 0.003 0 6 -10000 0 6
HGF -0.016 0.003 0 5 -10000 0 5
Syndecan-1/CASK -0.01 0.027 -10000 0 -0.12 7 7
Syndecan-1/HGF/MET 0.021 0.046 0.2 3 -0.14 3 6
regulation of cell adhesion -0.011 0.05 0.18 4 -0.14 1 5
HPSE -0.017 0.002 0 3 -10000 0 3
positive regulation of cell migration 0.004 0.034 0.099 12 -10000 0 12
SDC1 0.003 0.032 0.099 12 -0.087 3 15
Syndecan-1/Collagen 0.004 0.034 0.099 12 -10000 0 12
PPIB -0.016 0.003 0 4 -10000 0 4
MET -0.015 0.005 0 12 -10000 0 12
PRKACA -0.016 0.003 0 5 -10000 0 5
MMP9 -0.015 0.006 0 19 -10000 0 19
MAPK1 -0.009 0.041 0.092 14 -0.14 1 15
homophilic cell adhesion 0.006 0.044 0.11 14 -0.18 1 15
MMP1 -0.016 0.003 0 5 -10000 0 5
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.027 0.009 -9999 0 0 14 14
RGS9BP -0.015 0.005 0 12 -10000 0 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.016 0.003 0 6 -10000 0 6
mol:Na + 0.018 0.009 -9999 0 0 27 27
mol:ADP -0.019 0.005 0 9 -10000 0 9
GNAT2 -0.016 0.003 0 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.029 0.012 -9999 0 0 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.021 0.006 -9999 0 0 9 9
GRK7 -0.017 0.002 0 3 -10000 0 3
CNGB3 -0.014 0.006 0 24 -10000 0 24
Cone Metarhodopsin II/X-Arrestin 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.016 0.009 0 32 -10000 0 32
Cone PDE6 0.039 0.02 -9999 0 -10000 0 0
Cone Metarhodopsin II 0.02 0.005 -9999 0 0 9 9
Na + (4 Units) 0.024 0.013 -9999 0 0 32 32
GNAT2/GDP 0.033 0.015 -9999 0 0 23 23
GNB5 -0.016 0.003 0 5 -10000 0 5
mol:GMP (4 units) -0.019 0.006 0 12 -10000 0 12
Cone Transducin 0.029 0.01 -9999 0 0 14 14
SLC24A2 -0.015 0.005 0 13 -10000 0 13
GNB3/GNGT2 0.023 0.007 -9999 0 0 12 12
GNB3 -0.016 0.004 0 8 -10000 0 8
GNAT2/GTP 0.012 0.002 -9999 0 0 4 4
CNGA3 -0.017 0.002 0 3 -10000 0 3
ARR3 -0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.009 -9999 0 0 27 27
mol:Pi 0.028 0.012 -9999 0 0 21 21
Cone CNG Channel 0.031 0.017 -9999 0 -0.005 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.015 0.005 0 13 -10000 0 13
RGS9 -0.016 0.003 0 5 -10000 0 5
PDE6C -0.016 0.003 0 4 -10000 0 4
GNGT2 -0.016 0.003 0 4 -10000 0 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.016 0.004 0 7 -10000 0 7
Ephrin A reverse 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
MAPKKK cascade 0.02 0.007 -9999 0 0 13 13
EFNA5 -0.016 0.005 0 11 -9999 0 11
FYN -0.019 0.006 0 14 -9999 0 14
neuron projection morphogenesis 0.02 0.007 -9999 0 0 13 13
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.02 0.007 -9999 0 0 13 13
EPHA5 -0.017 0.002 0 3 -9999 0 3
Noncanonical Wnt signaling pathway

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.014 0.007 0 25 -10000 0 25
GNB1/GNG2 0.023 0.038 -10000 0 -0.11 5 5
mol:DAG -0.003 0.045 0.1 18 -10000 0 18
PLCG1 -0.004 0.044 0.1 17 -10000 0 17
YES1 -0.013 0.019 -10000 0 -0.09 7 7
FZD3 -0.015 0.006 0 18 -10000 0 18
FZD6 -0.014 0.007 0 27 -10000 0 27
G protein 0 0.053 0.16 9 -10000 0 9
MAP3K7 -0.006 0.056 0.17 9 -10000 0 9
mol:Ca2+ -0.003 0.044 0.1 18 -10000 0 18
mol:IP3 -0.003 0.045 0.1 18 -10000 0 18
NLK 0.011 0.065 -10000 0 -0.73 1 1
GNB1 -0.016 0.004 0 9 -10000 0 9
CAMK2A -0.002 0.058 0.18 9 -10000 0 9
MAP3K7IP1 -0.016 0.003 0 4 -10000 0 4
Noncanonical Wnts/FZD 0.005 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.004 0 8 -10000 0 8
GNAS -0.01 0.013 -10000 0 -0.09 3 3
GO:0007205 -0.001 0.042 0.096 18 -10000 0 18
WNT6 -0.016 0.003 0 4 -10000 0 4
WNT4 -0.016 0.005 0 11 -10000 0 11
NFAT1/CK1 alpha -0.011 0.04 0.18 3 -10000 0 3
GNG2 -0.016 0.003 0 6 -10000 0 6
WNT5A -0.016 0.003 0 4 -10000 0 4
WNT11 -0.017 0.002 0 3 -10000 0 3
CDC42 -0.015 0.016 -10000 0 -0.091 4 4
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.031 0.01 -10000 0 0 12 12
alphaM/beta2 Integrin/GPIbA 0.03 0.011 -10000 0 0 17 17
alphaM/beta2 Integrin/proMMP-9 0.027 0.013 -10000 0 0 27 27
PLAUR -0.016 0.004 0 7 -10000 0 7
HMGB1 -0.016 0.004 0 7 -10000 0 7
alphaM/beta2 Integrin/Talin 0.03 0.011 -10000 0 0 17 17
AGER -0.016 0.004 0 8 -10000 0 8
RAP1A -0.016 0.003 0 5 -10000 0 5
SELPLG -0.017 0.002 0 2 -10000 0 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.036 0.016 -10000 0 0 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.015 0.006 0 19 -10000 0 19
CYR61 -0.016 0.003 0 4 -10000 0 4
TLN1 -0.016 0.004 0 10 -10000 0 10
Rap1/GTP 0.008 0.048 0.11 1 -0.18 5 6
RHOA -0.016 0.003 0 5 -10000 0 5
P-selectin oligomer -0.016 0.003 0 6 -10000 0 6
MYH2 -0.012 0.03 -10000 0 -0.15 4 4
MST1R -0.016 0.003 0 5 -10000 0 5
leukocyte activation during inflammatory response 0.031 0.013 -10000 0 0 20 20
APOB -0.017 0 -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 -0.016 0.003 0 4 -10000 0 4
JAM3 -0.016 0.003 0 6 -10000 0 6
GP1BA -0.016 0.004 0 9 -10000 0 9
alphaM/beta2 Integrin/CTGF 0.03 0.011 -10000 0 0 15 15
alphaM/beta2 Integrin -0.007 0.036 -10000 0 -0.2 3 3
JAM3 homodimer -0.016 0.003 0 6 -10000 0 6
ICAM2 -0.016 0.003 0 6 -10000 0 6
ICAM1 -0.016 0.003 0 5 -10000 0 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.006 0.035 -10000 0 -0.2 3 3
cell adhesion 0.029 0.011 -10000 0 0 17 17
NFKB1 -0.015 0.052 0.16 11 -10000 0 11
THY1 -0.016 0.003 0 6 -10000 0 6
RhoA/GDP 0.012 0.002 -10000 0 0 5 5
Lipoprotein(a) 0.02 0.007 -10000 0 0 15 15
alphaM/beta2 Integrin/LRP/tPA 0.034 0.017 -10000 0 0 28 28
IL6 -0.014 0.055 0.15 13 -10000 0 13
ITGB2 -0.016 0.004 0 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.035 0.015 -10000 0 0 20 20
alphaM/beta2 Integrin/JAM2/JAM3 0.037 0.015 -10000 0 0 18 18
JAM2 -0.016 0.004 0 9 -10000 0 9
alphaM/beta2 Integrin/ICAM1 0.044 0.016 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.037 0.015 -10000 0 0 18 18
RhoA/GTP -0.007 0.04 -10000 0 -0.17 6 6
positive regulation of phagocytosis -0.019 0.04 0.1 3 -0.17 4 7
Ron/MSP 0.024 0.005 -10000 0 0 6 6
alphaM/beta2 Integrin/uPAR/uPA 0.037 0.015 -10000 0 0 20 20
alphaM/beta2 Integrin/uPAR 0.03 0.011 -10000 0 0 15 15
PLAU -0.016 0.003 0 5 -10000 0 5
PLAT -0.015 0.006 0 18 -10000 0 18
actin filament polymerization -0.005 0.037 0.14 1 -0.16 3 4
MST1 -0.016 0.003 0 5 -10000 0 5
alphaM/beta2 Integrin/lipoprotein(a) 0.034 0.014 -10000 0 0 20 20
TNF -0.019 0.05 0.15 10 -10000 0 10
RAP1B -0.015 0.005 0 13 -10000 0 13
alphaM/beta2 Integrin/uPA 0.03 0.011 -10000 0 0 16 16
fibrinolysis 0.036 0.014 -10000 0 0 18 18
HCK -0.016 0.005 0 11 -10000 0 11
dendritic cell antigen processing and presentation -0.006 0.035 -10000 0 -0.2 3 3
VTN -0.016 0.003 0 4 -10000 0 4
alphaM/beta2 Integrin/CYR61 0.031 0.01 -10000 0 0 13 13
LPA -0.015 0.005 0 15 -10000 0 15
LRP1 -0.016 0.003 0 4 -10000 0 4
cell migration -0.022 0.011 0 28 -10000 0 28
FN1 -0.016 0.003 0 4 -10000 0 4
alphaM/beta2 Integrin/Thy1 0.03 0.01 -10000 0 0 14 14
MPO -0.016 0.003 0 5 -10000 0 5
KNG1 -0.016 0.004 0 8 -10000 0 8
RAP1/GDP 0.02 0.007 -10000 0 0 16 16
ROCK1 -0.013 0.036 -10000 0 -0.17 5 5
ELA2 -0.016 0.003 0 5 -10000 0 5
PLG -0.016 0.003 0 6 -10000 0 6
CTGF -0.016 0.003 0 6 -10000 0 6
alphaM/beta2 Integrin/Hck 0.029 0.012 -10000 0 0 21 21
ITGAM -0.016 0.003 0 4 -10000 0 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.038 0.013 -10000 0 0 15 15
HP -0.016 0.003 0 5 -10000 0 5
leukocyte adhesion -0.027 0.012 -10000 0 -10000 0 0
SELP -0.016 0.003 0 6 -10000 0 6
Ceramide signaling pathway

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
SPHK2 -0.018 0.006 0 14 -10000 0 14
MAP4K4 -0.014 0.024 -10000 0 -0.1 8 8
BAG4 -0.015 0.005 0 15 -10000 0 15
PKC zeta/ceramide 0.003 0.05 -10000 0 -0.18 9 9
NFKBIA -0.017 0.002 0 3 -10000 0 3
BIRC3 -0.016 0.003 0 4 -10000 0 4
BAX -0.004 0.057 -10000 0 -0.35 3 3
RIPK1 -0.016 0.004 0 7 -10000 0 7
AKT1 -0.014 0.01 -10000 0 -10000 0 0
BAD -0.012 0.046 -10000 0 -0.18 9 9
SMPD1 0.001 0.068 0.11 17 -0.22 6 23
RB1 -0.001 0.065 0.18 8 -0.18 9 17
FADD/Caspase 8 -0.008 0.071 0.17 4 -0.29 4 8
MAP2K4 -0.013 0.044 0.18 1 -0.18 8 9
NSMAF -0.015 0.005 0 15 -10000 0 15
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.057 0.18 5 -0.18 9 14
EGF -0.016 0.003 0 4 -10000 0 4
mol:ceramide -0.006 0.049 -10000 0 -0.19 9 9
MADD -0.017 0.002 0 3 -10000 0 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.008 0 25 -10000 0 25
ASAH1 -0.014 0.006 0 20 -10000 0 20
negative regulation of cell cycle 0 0.065 0.18 8 -0.18 9 17
cell proliferation -0.021 0.054 0.16 5 -0.17 9 14
BID -0.015 0.15 -10000 0 -0.71 5 5
MAP3K1 -0.01 0.049 0.2 1 -0.18 9 10
EIF2A -0.016 0.054 0.16 5 -0.18 9 14
TRADD -0.017 0.002 0 3 -10000 0 3
CRADD -0.017 0.002 0 2 -10000 0 2
MAPK3 -0.014 0.057 0.16 5 -0.17 9 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.056 0.16 5 -0.17 10 15
Cathepsin D/ceramide 0.004 0.05 -10000 0 -0.18 9 9
FADD -0.013 0.024 -10000 0 -0.11 7 7
KSR1 -0.009 0.052 0.2 2 -0.18 9 11
MAPK8 -0.012 0.054 0.13 1 -0.16 12 13
PRKRA -0.01 0.049 0.2 1 -0.18 9 10
PDGFA -0.016 0.004 0 7 -10000 0 7
TRAF2 -0.016 0.004 0 7 -10000 0 7
IGF1 -0.016 0.003 0 4 -10000 0 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.049 -10000 0 -0.19 9 9
CTSD -0.016 0.004 0 8 -10000 0 8
regulation of nitric oxide biosynthetic process 0.024 0.004 -10000 0 0 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.02 0.059 0.17 5 -0.18 9 14
PRKCD -0.016 0.003 0 6 -10000 0 6
PRKCZ -0.016 0.004 0 9 -10000 0 9
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.008 0 25 -10000 0 25
RelA/NF kappa B1 0.024 0.004 -10000 0 0 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.016 0.003 0 6 -10000 0 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.009 0.026 -10000 0 -0.1 8 8
TNFR1A/BAG4/TNF-alpha 0.027 0.013 -10000 0 0 27 27
mol:Sphingosine-1-phosphate -0.018 0.006 0 14 -10000 0 14
MAP2K1 -0.014 0.056 0.16 6 -0.18 9 15
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA -0.017 0.002 0 3 -10000 0 3
CYCS 0.001 0.047 0.099 5 -0.14 9 14
TNFRSF1A -0.016 0.004 0 9 -10000 0 9
NFKB1 -0.017 0.002 0 2 -10000 0 2
TNFR1A/BAG4 0.021 0.009 -10000 0 0 22 22
EIF2AK2 -0.016 0.047 0.18 1 -0.18 9 10
TNF-alpha/TNFR1A/FAN 0.028 0.013 -10000 0 0 25 25
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.034 -10000 0 -0.3 1 1
MAP2K2 -0.015 0.054 0.16 5 -0.18 9 14
SMPD3 0.008 0.029 0.1 6 -10000 0 6
TNF -0.016 0.004 0 10 -10000 0 10
PKC zeta/PAR4 0.022 0.008 -10000 0 0 14 14
mol:PHOSPHOCHOLINE 0.003 0.038 0.11 3 -0.12 9 12
NF kappa B1/RelA/I kappa B alpha 0.043 0.017 -10000 0 -10000 0 0
AIFM1 -0.001 0.046 0.094 8 -0.13 11 19
BCL2 -0.016 0.005 0 11 -10000 0 11
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.002 0.038 -10000 0 -0.31 2 2
Crk/p130 Cas/Paxillin -0.025 0.023 -10000 0 -0.12 3 3
JUN -0.019 0.02 -10000 0 -0.1 6 6
HRAS -0.016 0.004 0 9 -10000 0 9
RET51/GFRalpha1/GDNF/GRB10 0.036 0.015 -10000 0 0 21 21
RAP1A -0.016 0.003 0 5 -10000 0 5
FRS2 -0.015 0.005 0 12 -10000 0 12
RAP1A/GDP 0.012 0.002 -10000 0 0 5 5
RET51/GFRalpha1/GDNF/DOK1 0.037 0.015 -10000 0 0 20 20
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 -0.017 0.002 0 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.004 0 7 -10000 0 7
RET9/GFRalpha1/GDNF/Enigma 0.028 0.011 -10000 0 0 19 19
RHOA -0.016 0.003 0 5 -10000 0 5
RAP1A/GTP 0.033 0.015 -10000 0 -10000 0 0
GRB7 -0.014 0.006 0 20 -10000 0 20
RET51/GFRalpha1/GDNF 0.036 0.015 -10000 0 0 21 21
MAPKKK cascade -0.03 0.015 -10000 0 -10000 0 0
BCAR1 -0.016 0.003 0 5 -10000 0 5
RET9/GFRalpha1/GDNF/IRS1 0.027 0.012 -10000 0 0 21 21
lamellipodium assembly -0.014 0.025 0.054 2 -0.13 3 5
RET51/GFRalpha1/GDNF/SHC 0.035 0.016 -10000 0 0 24 24
PIK3CA -0.016 0.004 0 10 -10000 0 10
RET9/GFRalpha1/GDNF/SHC 0.027 0.012 -10000 0 0 23 23
RET9/GFRalpha1/GDNF/Shank3 0.026 0.012 -10000 0 0 25 25
MAPK3 -0.014 0.058 0.16 14 -10000 0 14
DOK1 -0.017 0.001 0 1 -10000 0 1
DOK6 -0.015 0.005 0 12 -10000 0 12
PXN -0.016 0.003 0 4 -10000 0 4
neurite development -0.018 0.043 0.14 9 -10000 0 9
DOK5 -0.014 0.007 0 27 -10000 0 27
GFRA1 -0.016 0.003 0 4 -10000 0 4
MAPK8 -0.015 0.02 -10000 0 -0.1 6 6
HRAS/GTP 0.032 0.02 -10000 0 -0.047 4 4
tube development -0.016 0.032 0.15 4 -10000 0 4
MAPK1 -0.015 0.056 0.15 13 -10000 0 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.003 -10000 0 0 9 9
SRC -0.015 0.005 0 13 -10000 0 13
PDLIM7 -0.016 0.003 0 4 -10000 0 4
RET51/GFRalpha1/GDNF/Dok6 0.037 0.022 -10000 0 -10000 0 0
SHC1 -0.016 0.004 0 9 -10000 0 9
RET51/GFRalpha1/GDNF/Dok4 0.036 0.015 -10000 0 0 21 21
RET51/GFRalpha1/GDNF/Dok5 0.032 0.019 -10000 0 0 36 36
PRKCA -0.016 0.003 0 5 -10000 0 5
HRAS/GDP 0.012 0.003 -10000 0 0 9 9
CREB1 0.004 0.005 -10000 0 -10000 0 0
PIK3R1 -0.016 0.004 0 9 -10000 0 9
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.005 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 0.032 0.019 -10000 0 0 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.017 0.002 0 2 -10000 0 2
DOK4 -0.017 0.002 0 2 -10000 0 2
JNK cascade -0.019 0.02 -10000 0 -0.1 6 6
RET9/GFRalpha1/GDNF/FRS2 0.026 0.013 -10000 0 0 26 26
SHANK3 -0.016 0.004 0 9 -10000 0 9
RASA1 -0.016 0.004 0 9 -10000 0 9
NCK1 -0.017 0.002 0 2 -10000 0 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.005 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.005 0.015 -10000 0 -0.17 1 1
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.006 0.003 -10000 0 -10000 0 0
PI3K -0.004 0.036 0.12 2 -0.14 1 3
SOS1 -0.017 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.031 0.016 -10000 0 0 29 29
GRB10 -0.017 0.002 0 2 -10000 0 2
activation of MAPKK activity -0.009 0.02 -10000 0 -0.12 4 4
RET51/GFRalpha1/GDNF/FRS2 0.034 0.017 -10000 0 0 27 27
GAB1 -0.016 0.003 0 4 -10000 0 4
IRS1 -0.016 0.003 0 5 -10000 0 5
IRS2 -0.016 0.004 0 7 -10000 0 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.005 0.015 -10000 0 -0.17 1 1
RET51/GFRalpha1/GDNF/PKC alpha 0.036 0.016 -10000 0 0 23 23
GRB2 -0.016 0.003 0 6 -10000 0 6
PRKACA -0.016 0.003 0 5 -10000 0 5
GDNF -0.015 0.005 0 16 -10000 0 16
RAC1 -0.016 0.004 0 9 -10000 0 9
RET51/GFRalpha1/GDNF/IRS1 0.036 0.016 -10000 0 0 22 22
Rac1/GTP -0.011 0.038 0.086 5 -0.14 3 8
RET9/GFRalpha1/GDNF 0.02 0.008 -10000 0 0 18 18
GFRalpha1/GDNF 0.021 0.008 -10000 0 0 18 18
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.02 0.008 -10000 0 0 18 18
cell-cell adhesion 0.032 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.04 0.019 -10000 0 -10000 0 0
ITSN1 -0.016 0.004 0 7 -10000 0 7
PIK3CA -0.016 0.004 0 10 -10000 0 10
SHC1 -0.016 0.004 0 9 -10000 0 9
Ephrin B1/EPHB3 0.021 0.006 -10000 0 0 11 11
Ephrin B1/EPHB1 0.022 0.003 -10000 0 0 2 2
HRAS/GDP -0.036 0.039 0.047 2 -0.15 12 14
Ephrin B/EPHB1/GRB7 0.038 0.021 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.013 0.054 0.18 9 -10000 0 9
KRAS -0.015 0.005 0 16 -10000 0 16
Ephrin B/EPHB1/Src 0.04 0.019 -10000 0 -10000 0 0
endothelial cell migration 0.028 0.015 -10000 0 0 31 31
GRB2 -0.016 0.003 0 6 -10000 0 6
GRB7 -0.014 0.006 0 20 -10000 0 20
PAK1 -0.017 0.058 0.17 11 -10000 0 11
HRAS -0.016 0.004 0 9 -10000 0 9
RRAS -0.016 0.049 0.18 7 -10000 0 7
DNM1 -0.016 0.003 0 6 -10000 0 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.021 0.039 0.16 6 -10000 0 6
lamellipodium assembly -0.032 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0 0.031 0.079 12 -0.11 4 16
PIK3R1 -0.016 0.004 0 9 -10000 0 9
EPHB2 -0.016 0.005 0 11 -10000 0 11
EPHB3 -0.016 0.005 0 11 -10000 0 11
EPHB1 -0.017 0.002 0 2 -10000 0 2
EPHB4 -0.015 0.005 0 12 -10000 0 12
mol:GDP -0.016 0.045 0.12 7 -0.16 6 13
Ephrin B/EPHB2 0.033 0.015 -10000 0 0 22 22
Ephrin B/EPHB3 0.033 0.015 -10000 0 0 23 23
JNK cascade -0.022 0.045 0.19 5 -10000 0 5
Ephrin B/EPHB1 0.035 0.012 -10000 0 0 14 14
RAP1/GDP -0.016 0.072 0.18 10 -0.16 10 20
EFNB2 -0.016 0.003 0 6 -10000 0 6
EFNB3 -0.016 0.004 0 9 -10000 0 9
EFNB1 -0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.028 0.011 -10000 0 0 18 18
RAP1B -0.015 0.005 0 13 -10000 0 13
RAP1A -0.016 0.003 0 5 -10000 0 5
CDC42/GTP -0.032 0.018 0.031 4 -10000 0 4
Rap1/GTP -0.038 0.02 -10000 0 -10000 0 0
axon guidance 0.019 0.008 -10000 0 0 18 18
MAPK3 -0.01 0.027 0.06 11 -0.12 3 14
MAPK1 -0.01 0.027 0.06 10 -0.12 3 13
Rac1/GDP -0.015 0.076 0.18 11 -0.16 12 23
actin cytoskeleton reorganization -0.038 0.029 -10000 0 -0.11 10 10
CDC42/GDP -0.018 0.074 0.18 10 -0.15 13 23
PI3K 0.03 0.017 -10000 0 0 31 31
EFNA5 -0.016 0.005 0 11 -10000 0 11
Ephrin B2/EPHB4 0.02 0.007 -10000 0 0 15 15
Ephrin B/EPHB2/Intersectin/N-WASP 0.003 0.021 -10000 0 -0.17 2 2
CDC42 -0.016 0.005 0 11 -10000 0 11
RAS family/GTP -0.036 0.021 -10000 0 -10000 0 0
PTK2 0.066 0.2 0.54 20 -10000 0 20
MAP4K4 -0.022 0.045 0.2 5 -10000 0 5
SRC -0.015 0.005 0 13 -10000 0 13
KALRN -0.017 0.002 0 3 -10000 0 3
Intersectin/N-WASP 0.022 0.007 -10000 0 0 13 13
neuron projection morphogenesis -0.019 0.059 0.2 4 -10000 0 4
MAP2K1 -0.005 0.028 0.069 11 -0.12 3 14
WASL -0.016 0.004 0 8 -10000 0 8
Ephrin B1/EPHB1-2/NCK1 0.039 0.012 -10000 0 0 12 12
cell migration 0.001 0.054 0.18 5 -0.15 3 8
NRAS -0.016 0.003 0 5 -10000 0 5
SYNJ1 -0.013 0.054 0.18 9 -10000 0 9
PXN -0.016 0.003 0 4 -10000 0 4
TF -0.02 0.044 0.15 8 -10000 0 8
HRAS/GTP -0.033 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.029 0.009 -10000 0 0 12 12
cell adhesion mediated by integrin 0.008 0.04 -10000 0 -0.18 4 4
RAC1 -0.016 0.004 0 9 -10000 0 9
mol:GTP -0.03 0.013 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.037 0.021 -10000 0 -10000 0 0
RASA1 -0.016 0.004 0 9 -10000 0 9
RAC1-CDC42/GDP -0.019 0.073 0.18 10 -0.15 12 22
ruffle organization -0.008 0.083 0.31 4 -10000 0 4
NCK1 -0.017 0.002 0 2 -10000 0 2
receptor internalization -0.019 0.051 0.17 8 -10000 0 8
Ephrin B/EPHB2/KALRN 0.041 0.019 -10000 0 -10000 0 0
ROCK1 -0.019 0.007 0 17 -10000 0 17
RAS family/GDP -0.039 0.03 -10000 0 -0.12 10 10
Rac1/GTP -0.034 0.019 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.006 0.003 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.01 0.002 0 4 -10000 0 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.022 0.008 -10000 0 0 17 17
STXBP1 -0.016 0.003 0 6 -10000 0 6
ACh/CHRNA1 0.012 0.02 0.049 15 -0.052 7 22
RAB3GAP2/RIMS1/UNC13B 0.029 0.012 -10000 0 0 20 20
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 -0.016 0.005 0 11 -10000 0 11
mol:ACh 0.001 0.027 0.064 15 -0.065 8 23
RAB3GAP2 -0.016 0.004 0 7 -10000 0 7
STX1A/SNAP25/VAMP2 -0.02 0.03 0.069 10 -0.09 6 16
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.012 0.02 0.049 15 -0.052 7 22
UNC13B -0.016 0.004 0 9 -10000 0 9
CHRNA1 -0.017 0.002 0 3 -10000 0 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.013 0.019 0.049 15 -0.055 5 20
SNAP25 -0.001 0 0 18 -10000 0 18
VAMP2 0 0 -10000 0 0 8 8
SYT1 -0.016 0.003 0 6 -10000 0 6
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.015 0.004 0 9 -10000 0 9
STX1A/SNAP25 fragment 1/VAMP2 -0.02 0.03 0.069 10 -0.09 6 16
Calcium signaling in the CD4+ TCR pathway

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.014 0.005 0 18 -10000 0 18
NFATC2 -0.013 0.007 0 28 -10000 0 28
NFATC3 -0.015 0.003 0 6 -10000 0 6
CD40LG -0.002 0.076 0.16 23 -10000 0 23
PTGS2 -0.004 0.074 0.16 21 -10000 0 21
JUNB -0.016 0.003 0 5 -10000 0 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.002 -10000 0 0 4 4
CaM/Ca2+ 0.012 0.002 -10000 0 0 4 4
CALM1 -0.016 0.003 0 4 -10000 0 4
JUN -0.016 0.003 0 4 -10000 0 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.004 -10000 0 0 17 17
FOSL1 -0.017 0.002 0 3 -10000 0 3
CREM -0.017 0.002 0 3 -10000 0 3
Jun/NFAT1-c-4/p21SNFT -0.022 0.013 -10000 0 -10000 0 0
FOS -0.016 0.003 0 4 -10000 0 4
IFNG -0.005 0.068 0.15 19 -10000 0 19
AP-1/NFAT1-c-4 -0.027 0.015 -10000 0 -10000 0 0
FASLG -0.004 0.074 0.16 21 -10000 0 21
NFAT1-c-4/ICER1 -0.023 0.014 -10000 0 -10000 0 0
IL2RA -0.003 0.074 0.16 21 -10000 0 21
FKBP12/FK506 0.011 0.004 -10000 0 0 17 17
CSF2 -0.006 0.069 0.16 19 -10000 0 19
JunB/Fra1/NFAT1-c-4 -0.026 0.015 -10000 0 -10000 0 0
IL4 -0.006 0.069 0.16 19 -10000 0 19
IL2 -0.01 0.13 -10000 0 -0.76 4 4
IL3 -0.01 0.11 -10000 0 -0.52 6 6
FKBP1A -0.015 0.006 0 17 -10000 0 17
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 -0.016 0.003 0 6 -10000 0 6
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.005 0.003 -9999 0 -9999 0 0
FZD6 -0.014 0.007 0 27 -9999 0 27
WNT6 -0.016 0.003 0 4 -9999 0 4
WNT4 -0.016 0.005 0 11 -9999 0 11
FZD3 -0.015 0.006 0 18 -9999 0 18
WNT5A -0.016 0.003 0 4 -9999 0 4
WNT11 -0.017 0.002 0 3 -9999 0 3
Syndecan-4-mediated signaling events

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
PTK2 0.012 0.04 0.13 1 -0.23 2 3
Syndecan-4/Syndesmos 0.019 0.065 0.16 13 -0.27 3 16
positive regulation of JNK cascade 0.027 0.065 0.22 2 -0.26 3 5
Syndecan-4/ADAM12 0.022 0.069 0.16 15 -0.28 3 18
CCL5 -0.017 0.002 0 3 -10000 0 3
Rac1/GDP 0.012 0.003 -10000 0 0 9 9
DNM2 -0.016 0.003 0 6 -10000 0 6
ITGA5 -0.016 0.003 0 6 -10000 0 6
SDCBP -0.015 0.005 0 15 -10000 0 15
PLG 0.009 0.021 -10000 0 -0.041 18 18
ADAM12 -0.016 0.003 0 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 -0.017 0.002 0 3 -10000 0 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.015 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.021 0.067 0.16 14 -0.26 3 17
Syndecan-4/CXCL12/CXCR4 0.028 0.067 0.23 2 -0.27 3 5
Syndecan-4/Laminin alpha3 0.023 0.067 0.16 15 -0.26 3 18
MDK -0.016 0.003 0 5 -10000 0 5
Syndecan-4/FZD7 0.021 0.069 0.16 15 -0.28 3 18
Syndecan-4/Midkine 0.022 0.067 0.16 15 -0.26 3 18
FZD7 -0.017 0.002 0 2 -10000 0 2
Syndecan-4/FGFR1/FGF 0.025 0.055 0.19 1 -0.23 2 3
THBS1 -0.016 0.003 0 4 -10000 0 4
integrin-mediated signaling pathway 0.02 0.064 0.15 14 -0.26 3 17
positive regulation of MAPKKK cascade 0.027 0.065 0.22 2 -0.26 3 5
Syndecan-4/TACI 0.023 0.067 0.16 15 -0.27 3 18
CXCR4 -0.017 0.002 0 3 -10000 0 3
cell adhesion -0.006 0.028 0.17 3 -10000 0 3
Syndecan-4/Dynamin 0.023 0.068 0.16 15 -0.27 3 18
Syndecan-4/TSP1 0.022 0.067 0.16 14 -0.27 3 17
Syndecan-4/GIPC 0.023 0.068 0.16 15 -0.27 3 18
Syndecan-4/RANTES 0.021 0.07 0.16 15 -0.28 3 18
ITGB1 -0.017 0.002 0 3 -10000 0 3
LAMA1 -0.016 0.003 0 6 -10000 0 6
LAMA3 -0.016 0.004 0 8 -10000 0 8
RAC1 -0.016 0.004 0 9 -10000 0 9
PRKCA 0.005 0.11 0.72 3 -10000 0 3
Syndecan-4/alpha-Actinin 0.02 0.064 0.16 13 -0.27 3 16
TFPI -0.017 0.002 0 3 -10000 0 3
F2 0.021 0.015 0.055 18 -0.032 2 20
alpha5/beta1 Integrin 0.023 0.006 -10000 0 0 9 9
positive regulation of cell adhesion 0.005 0.058 0.15 14 -0.3 1 15
ACTN1 -0.016 0.003 0 5 -10000 0 5
TNC -0.016 0.003 0 5 -10000 0 5
Syndecan-4/CXCL12 0.022 0.069 0.16 15 -0.28 3 18
FGF6 -0.016 0.004 0 9 -10000 0 9
RHOA -0.016 0.003 0 5 -10000 0 5
CXCL12 -0.017 0.002 0 3 -10000 0 3
TNFRSF13B -0.015 0.005 0 12 -10000 0 12
FGF2 -0.017 0.002 0 3 -10000 0 3
FGFR1 -0.014 0.006 0 23 -10000 0 23
Syndecan-4/PI-4-5-P2 -0.007 0.043 -10000 0 -0.28 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.022 -10000 0 -0.044 18 18
cell migration -0.016 0.009 -10000 0 -10000 0 0
PRKCD 0.005 0.028 -10000 0 -0.05 22 22
vasculogenesis 0.021 0.066 0.16 14 -0.26 3 17
SDC4 -0.002 0.029 -10000 0 -0.3 1 1
Syndecan-4/Tenascin C 0.02 0.065 0.16 14 -0.27 3 17
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.019 0.059 0.17 11 -0.26 2 13
MMP9 0.013 0.01 -10000 0 -0.03 3 3
Rac1/GTP -0.006 0.029 0.18 3 -10000 0 3
cytoskeleton organization 0.019 0.063 0.15 13 -0.26 3 16
GIPC1 -0.016 0.003 0 4 -10000 0 4
Syndecan-4/TFPI 0.02 0.066 0.16 14 -0.27 3 17
PDGFR-beta signaling pathway

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.031 0.075 0.19 13 -0.21 5 18
PDGFB-D/PDGFRB/SLAP 0.02 0.012 -10000 0 -0.023 3 3
PDGFB-D/PDGFRB/APS/CBL 0.021 0.008 -10000 0 -0.002 13 13
AKT1 0.015 0.099 0.25 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.026 0.081 0.19 13 -0.25 5 18
PIK3CA -0.016 0.004 0 10 -10000 0 10
FGR 0 0.1 0.2 5 -0.48 4 9
mol:Ca2+ 0.02 0.091 0.19 16 -0.27 6 22
MYC 0.055 0.12 0.22 34 -0.26 2 36
SHC1 -0.016 0.004 0 9 -10000 0 9
HRAS/GDP -0.011 0.048 0.15 11 -10000 0 11
LRP1/PDGFRB/PDGFB 0.031 0.01 -10000 0 0 13 13
GRB10 -0.017 0.002 0 2 -10000 0 2
PTPN11 -0.017 0.002 0 3 -10000 0 3
GO:0007205 0.02 0.092 0.18 16 -0.28 6 22
PTEN -0.016 0.004 0 10 -10000 0 10
GRB2 -0.016 0.003 0 6 -10000 0 6
GRB7 -0.014 0.006 0 20 -10000 0 20
PDGFB-D/PDGFRB/SHP2 0.023 0.009 -10000 0 -0.023 3 3
PDGFB-D/PDGFRB/GRB10 0.023 0.01 -10000 0 -0.023 3 3
cell cycle arrest 0.02 0.012 -10000 0 -0.023 3 3
HRAS -0.016 0.004 0 9 -10000 0 9
HIF1A 0.004 0.085 0.21 9 -10000 0 9
GAB1 0.02 0.085 0.18 14 -0.27 5 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.02 0.084 0.19 17 -0.24 4 21
PDGFB-D/PDGFRB 0.024 0.016 -10000 0 -0.034 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.023 0.01 -10000 0 -0.023 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.046 0.17 2 -0.18 3 5
positive regulation of MAPKKK cascade 0.023 0.009 -10000 0 -0.023 3 3
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:IP3 0.02 0.093 0.19 16 -0.28 6 22
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.006 0.017 -10000 0 -0.027 3 3
PDGFB-D/PDGFRB/GRB7 0.019 0.012 -10000 0 -0.023 3 3
SHB -0.016 0.003 0 6 -10000 0 6
BLK -0.007 0.1 0.2 4 -0.41 6 10
PTPN2 -0.008 0.016 0.023 14 -10000 0 14
PDGFB-D/PDGFRB/SNX15 0.023 0.01 -10000 0 -0.023 3 3
BCAR1 -0.016 0.003 0 5 -10000 0 5
VAV2 0.022 0.092 0.2 14 -0.27 5 19
CBL -0.016 0.003 0 6 -10000 0 6
PDGFB-D/PDGFRB/DEP1 0.023 0.009 -10000 0 -0.023 2 2
LCK 0.002 0.1 0.2 5 -0.48 4 9
PDGFRB -0.005 0.017 0.027 4 -10000 0 4
ACP1 -0.017 0.001 0 1 -10000 0 1
HCK 0.013 0.053 0.19 5 -10000 0 5
ABL1 0.02 0.091 0.18 18 -0.22 8 26
PDGFB-D/PDGFRB/CBL 0.016 0.095 0.18 11 -0.32 6 17
PTPN1 -0.012 0.011 0.023 2 -10000 0 2
SNX15 -0.017 0.002 0 2 -10000 0 2
STAT3 -0.016 0.003 0 5 -10000 0 5
STAT1 -0.017 0.002 0 3 -10000 0 3
cell proliferation 0.055 0.11 0.22 34 -0.24 2 36
SLA -0.014 0.006 0 20 -10000 0 20
actin cytoskeleton reorganization -0.001 0.075 0.15 26 -10000 0 26
SRC 0.011 0.05 0.17 9 -0.16 1 10
PI3K -0.03 0.021 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.026 0.015 -10000 0 -0.001 32 32
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.026 0.083 0.19 13 -0.26 5 18
LYN 0.011 0.063 0.2 4 -0.39 1 5
LRP1 -0.016 0.003 0 4 -10000 0 4
SOS1 -0.017 0 -10000 0 -10000 0 0
STAT5B -0.016 0.004 0 7 -10000 0 7
STAT5A -0.016 0.003 0 6 -10000 0 6
NCK1-2/p130 Cas 0.036 0.023 -10000 0 -0.017 1 1
SPHK1 -0.005 0.017 0.027 1 -10000 0 1
EDG1 -0.005 0.018 0.027 1 -10000 0 1
mol:DAG 0.02 0.093 0.19 16 -0.28 6 22
PLCG1 0.02 0.094 0.19 16 -0.28 6 22
NHERF/PDGFRB 0.031 0.011 -10000 0 -0.002 14 14
YES1 0.006 0.08 0.2 5 -0.48 2 7
cell migration 0.03 0.011 -10000 0 -0.002 14 14
SHC/Grb2/SOS1 0.035 0.024 -10000 0 -0.02 3 3
SLC9A3R2 -0.016 0.003 0 4 -10000 0 4
SLC9A3R1 -0.016 0.003 0 6 -10000 0 6
NHERF1-2/PDGFRB/PTEN 0.037 0.015 -10000 0 -10000 0 0
FYN -0.002 0.099 0.19 5 -0.42 5 10
DOK1 -0.019 0.019 0.15 1 -10000 0 1
HRAS/GTP 0.012 0.003 -10000 0 0 9 9
PDGFB -0.016 0.003 0 4 -10000 0 4
RAC1 0.024 0.098 0.21 16 -0.28 4 20
PRKCD -0.017 0.029 0.16 3 -10000 0 3
FER -0.018 0.025 0.16 2 -10000 0 2
MAPKKK cascade 0.004 0.082 0.17 25 -10000 0 25
RASA1 -0.017 0.029 0.16 3 -10000 0 3
NCK1 -0.017 0.002 0 2 -10000 0 2
NCK2 -0.017 0.001 0 1 -10000 0 1
p62DOK/Csk 0 0.066 0.15 22 -10000 0 22
PDGFB-D/PDGFRB/SHB 0.023 0.009 -10000 0 -0.023 2 2
chemotaxis 0.02 0.09 0.18 18 -0.23 7 25
STAT1-3-5/STAT1-3-5 -0.027 0.023 0.046 4 -10000 0 4
Bovine Papilomavirus E5/PDGFRB 0.011 0.007 0.032 1 -0.015 5 6
PTPRJ -0.017 0.002 0 3 -10000 0 3
ErbB2/ErbB3 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
USP8 -0.013 0.009 0.006 20 -10000 0 20
RAS family/GTP 0.03 0.04 0.14 8 -0.09 4 12
NFATC4 -0.009 0.062 0.2 6 -10000 0 6
ERBB2IP 0.008 0.015 -10000 0 -0.026 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.027 0.017 -10000 0 -10000 0 0
JUN 0.012 0.038 0.11 10 -0.077 3 13
HRAS -0.016 0.004 0 9 -10000 0 9
DOCK7 -0.02 0.043 0.11 11 -10000 0 11
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.022 0.017 0.039 2 -10000 0 2
AKT1 -0.008 0.007 0.012 13 -10000 0 13
BAD -0.014 0.005 0.002 9 -10000 0 9
MAPK10 -0.007 0.054 0.18 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.028 0.018 -10000 0 -10000 0 0
RAF1 0.01 0.073 0.16 21 -10000 0 21
ErbB2/ErbB3/neuregulin 2 -0.02 0.016 0.026 6 -10000 0 6
STAT3 0.009 0.064 -10000 0 -0.72 1 1
cell migration 0.007 0.071 0.2 12 -10000 0 12
mol:PI-3-4-5-P3 0 0.002 0.008 1 -10000 0 1
cell proliferation 0.023 0.084 0.22 8 -0.35 2 10
FOS 0.02 0.066 0.18 10 -0.2 2 12
NRAS -0.016 0.003 0 5 -10000 0 5
mol:Ca2+ -0.027 0.017 -10000 0 -10000 0 0
MAPK3 0.023 0.083 0.24 8 -0.28 2 10
MAPK1 0.023 0.091 0.24 8 -0.37 2 10
JAK2 -0.019 0.038 0.11 8 -10000 0 8
NF2 -0.012 0.086 -10000 0 -0.59 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.041 0.11 16 -0.067 1 17
NRG1 -0.009 0.015 0.02 24 -10000 0 24
GRB2/SOS1 0.024 0.005 -10000 0 0 6 6
MAPK8 -0.012 0.04 0.1 9 -0.15 4 13
MAPK9 -0.01 0.05 0.18 4 -10000 0 4
ERBB2 -0.017 0.009 0.001 26 -10000 0 26
ERBB3 -0.009 0.015 0.022 8 -10000 0 8
SHC1 -0.016 0.004 0 9 -10000 0 9
RAC1 -0.016 0.004 0 9 -10000 0 9
apoptosis 0.009 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.01 0.063 -10000 0 -0.71 1 1
RNF41 -0.017 0.011 0.006 20 -10000 0 20
FRAP1 -0.014 0.006 0.001 16 -10000 0 16
RAC1-CDC42/GTP -0.028 0.02 0.011 1 -10000 0 1
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.007 0.001 26 -10000 0 26
CHRNA1 0.024 0.077 0.2 10 -0.28 2 12
myelination 0.009 0.098 0.25 15 -10000 0 15
PPP3CB -0.019 0.041 0.11 11 -10000 0 11
KRAS -0.015 0.005 0 16 -10000 0 16
RAC1-CDC42/GDP 0 0.047 0.14 7 -10000 0 7
NRG2 -0.016 0.003 0 6 -10000 0 6
mol:GDP 0.006 0.041 0.11 16 -0.067 1 17
SOS1 -0.017 0 -10000 0 -10000 0 0
MAP2K2 0.009 0.077 0.16 23 -10000 0 23
SRC -0.015 0.005 0 13 -10000 0 13
mol:cAMP 0 0.001 0.008 2 -10000 0 2
PTPN11 -0.021 0.043 0.11 11 -10000 0 11
MAP2K1 0.025 0.084 0.25 3 -0.56 1 4
heart morphogenesis -0.027 0.017 -10000 0 -10000 0 0
RAS family/GDP 0.034 0.044 0.15 8 -0.093 4 12
GRB2 -0.016 0.003 0 6 -10000 0 6
PRKACA -0.007 0.092 -10000 0 -0.62 3 3
CHRNE 0.003 0.01 0.031 8 -10000 0 8
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.007 -10000 0 -0.012 13 13
nervous system development -0.027 0.017 -10000 0 -10000 0 0
CDC42 -0.016 0.005 0 11 -10000 0 11
IL12-mediated signaling 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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.038 0.075 15 -0.098 11 26
TBX21 -0.003 0.05 0.16 4 -0.2 3 7
B2M -0.016 0.004 0 8 -10000 0 8
TYK2 -0.009 0.015 0.023 5 -10000 0 5
IL12RB1 -0.009 0.015 0.023 5 -10000 0 5
GADD45B -0.002 0.071 0.15 2 -0.3 5 7
IL12RB2 -0.01 0.015 0.018 28 -10000 0 28
GADD45G -0.002 0.069 0.14 2 -0.29 5 7
natural killer cell activation 0 0.001 0.007 3 -10000 0 3
RELB -0.016 0.004 0 9 -10000 0 9
RELA -0.017 0.002 0 3 -10000 0 3
IL18 -0.01 0.014 0.023 2 -10000 0 2
IL2RA -0.016 0.003 0 6 -10000 0 6
IFNG -0.015 0.005 0 13 -10000 0 13
STAT3 (dimer) -0.006 0.075 -10000 0 -0.28 7 7
HLA-DRB5 -0.008 0.008 0 68 -10000 0 68
FASLG -0.003 0.051 0.16 4 -0.2 3 7
NF kappa B2 p52/RelB 0.012 0.049 0.11 2 -0.17 4 6
CD4 -0.016 0.004 0 8 -10000 0 8
SOCS1 -0.016 0.003 0 4 -10000 0 4
EntrezGene:6955 0 0 -10000 0 -10000 0 0
CD3D -0.016 0.003 0 6 -10000 0 6
CD3E -0.016 0.003 0 6 -10000 0 6
CD3G -0.016 0.003 0 6 -10000 0 6
IL12Rbeta2/JAK2 0.02 0.01 -10000 0 0 26 26
CCL3 -0.005 0.048 0.15 3 -0.2 3 6
CCL4 -0.005 0.048 0.18 2 -0.2 3 5
HLA-A -0.016 0.005 0 11 -10000 0 11
IL18/IL18R 0.031 0.011 -10000 0 -0.003 11 11
NOS2 -0.003 0.041 0.1 1 -0.16 5 6
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.042 0.075 15 -0.1 11 26
IL1R1 -0.004 0.051 0.26 2 -0.22 2 4
IL4 -0.013 0.01 0.019 11 -10000 0 11
JAK2 -0.009 0.013 0.025 3 -10000 0 3
EntrezGene:6957 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.039 -10000 0 -0.12 11 11
RAB7A -0.004 0.073 0.12 3 -0.24 8 11
lysosomal transport -0.004 0.071 0.12 3 -0.23 8 11
FOS -0.012 0.13 -10000 0 -0.65 4 4
STAT4 (dimer) -0.003 0.075 0.14 7 -0.21 9 16
STAT5A (dimer) 0.014 0.045 0.11 2 -0.16 4 6
GZMA -0.006 0.045 0.14 2 -0.17 4 6
GZMB -0.007 0.04 0.11 1 -0.18 3 4
HLX 0 0 -10000 0 -10000 0 0
LCK -0.005 0.031 -10000 0 -0.16 1 1
TCR/CD3/MHC II/CD4 -0.008 0.055 0.066 28 -0.092 34 62
IL2/IL2R 0.04 0.011 -10000 0 0 10 10
MAPK14 -0.005 0.081 0.12 3 -0.27 8 11
CCR5 0 0.046 0.12 3 -0.16 6 9
IL1B -0.009 0.015 0.025 2 -10000 0 2
STAT6 0.004 0.043 -10000 0 -0.47 1 1
STAT4 -0.017 0.002 0 3 -10000 0 3
STAT3 -0.016 0.003 0 5 -10000 0 5
STAT1 -0.017 0.002 0 3 -10000 0 3
NFKB1 -0.017 0.002 0 2 -10000 0 2
NFKB2 -0.016 0.003 0 6 -10000 0 6
IL12B -0.011 0.014 0.018 22 -10000 0 22
CD8A -0.017 0 -10000 0 -10000 0 0
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.038 0.097 11 -0.075 15 26
IL2RB -0.017 0.002 0 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.073 0.14 8 -0.2 9 17
IL2RG -0.017 0 -10000 0 -10000 0 0
IL12 0.022 0.009 -10000 0 -0.002 15 15
STAT5A -0.016 0.003 0 6 -10000 0 6
CD247 0 0 -10000 0 -10000 0 0
IL2 -0.016 0.003 0 4 -10000 0 4
SPHK2 -0.016 0.004 0 8 -10000 0 8
FRAP1 -0.016 0.004 0 10 -10000 0 10
IL12A -0.01 0.014 0.023 5 -10000 0 5
IL12/IL12R/TYK2/JAK2 -0.001 0.02 -10000 0 -0.16 2 2
MAP2K3 -0.007 0.082 0.13 1 -0.27 8 9
RIPK2 -0.014 0.006 0 22 -10000 0 22
MAP2K6 -0.002 0.074 0.14 3 -0.25 7 10
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.016 0.004 0 8 -10000 0 8
IL18RAP -0.01 0.014 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.024 0.006 -10000 0 0 7 7
EOMES 0.007 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0 0.06 -10000 0 -0.28 4 4
T cell proliferation 0.005 0.061 0.15 9 -0.17 6 15
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.01 0.014 -10000 0 -10000 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.015 0.064 -10000 0 -0.18 9 9
ATF2 -0.009 0.079 0.15 3 -0.28 7 10
PLK2 and PLK4 events

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
PLK2 -0.016 0.004 0 9 -9999 0 9
PLK4 -0.016 0.003 0 4 -9999 0 4
regulation of centriole replication -0.019 0.006 0 11 -9999 0 11
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.012 0.044 0.16 8 -10000 0 8
HDAC7 0 0 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.025 0.034 -10000 0 -0.13 5 5
SMAD4 -0.015 0.005 0 15 -10000 0 15
ID2 -0.01 0.049 0.16 10 -10000 0 10
AP1 0.023 0.006 -10000 0 0 8 8
ABCG2 -0.011 0.047 0.16 9 -10000 0 9
HIF1A -0.016 0.003 0 4 -10000 0 4
TFF3 -0.009 0.049 0.16 10 -10000 0 10
GATA2 -0.017 0.002 0 2 -10000 0 2
AKT1 -0.016 0.003 0 5 -10000 0 5
response to hypoxia 0 0 -10000 0 -10000 0 0
MCL1 -0.022 0.009 -10000 0 -10000 0 0
NDRG1 -0.01 0.044 0.16 8 -10000 0 8
SERPINE1 -0.01 0.047 0.16 9 -10000 0 9
FECH -0.012 0.042 0.16 7 -10000 0 7
FURIN -0.012 0.044 0.16 8 -10000 0 8
NCOA2 -0.015 0.006 0 18 -10000 0 18
EP300 -0.003 0.001 -10000 0 -10000 0 0
HMOX1 -0.012 0.047 0.16 9 -10000 0 9
BHLHE40 -0.017 0.007 0 18 -10000 0 18
BHLHE41 -0.017 0.007 0 18 -10000 0 18
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.039 0.02 -10000 0 -10000 0 0
ENG -0.014 0.056 0.15 13 -10000 0 13
JUN -0.016 0.003 0 4 -10000 0 4
RORA -0.011 0.047 0.16 9 -10000 0 9
ABCB1 0.008 0.004 -10000 0 -10000 0 0
TFRC -0.009 0.049 0.16 10 -10000 0 10
CXCR4 -0.01 0.049 0.16 10 -10000 0 10
TF -0.011 0.047 0.16 9 -10000 0 9
CITED2 -0.011 0.047 0.16 9 -10000 0 9
HIF1A/ARNT 0.028 0.011 -10000 0 0 18 18
LDHA 0 0.072 -10000 0 -0.41 4 4
ETS1 -0.012 0.044 0.16 8 -10000 0 8
PGK1 -0.01 0.049 0.16 10 -10000 0 10
NOS2 -0.017 0.007 0 18 -10000 0 18
ITGB2 -0.011 0.047 0.16 9 -10000 0 9
ALDOA -0.012 0.047 0.16 9 -10000 0 9
Cbp/p300/CITED2 -0.017 0.042 0.15 7 -0.12 3 10
FOS -0.016 0.003 0 4 -10000 0 4
HK2 -0.012 0.047 0.16 9 -10000 0 9
SP1 -0.017 0.002 0 3 -10000 0 3
GCK -0.003 0.025 -10000 0 -0.15 3 3
HK1 -0.011 0.047 0.16 9 -10000 0 9
NPM1 -0.012 0.044 0.16 8 -10000 0 8
EGLN1 -0.013 0.042 0.16 7 -10000 0 7
CREB1 -0.017 0.002 0 3 -10000 0 3
PGM1 -0.011 0.047 0.16 9 -10000 0 9
SMAD3 -0.016 0.003 0 4 -10000 0 4
EDN1 -0.011 0.044 -10000 0 -0.15 9 9
IGFBP1 -0.01 0.049 0.16 10 -10000 0 10
VEGFA -0.017 0.023 0.073 2 -0.12 5 7
HIF1A/JAB1 0.021 0.008 -10000 0 0 18 18
CP -0.01 0.049 0.16 10 -10000 0 10
CXCL12 -0.01 0.049 0.16 10 -10000 0 10
COPS5 -0.015 0.005 0 15 -10000 0 15
SMAD3/SMAD4 0.022 0.008 -10000 0 0 17 17
BNIP3 -0.011 0.047 0.16 9 -10000 0 9
EGLN3 -0.01 0.049 0.16 10 -10000 0 10
CA9 -0.013 0.042 0.16 7 -10000 0 7
TERT -0.01 0.047 0.16 9 -10000 0 9
ENO1 -0.01 0.047 0.16 9 -10000 0 9
PFKL -0.012 0.044 0.16 8 -10000 0 8
NCOA1 -0.017 0 -10000 0 -10000 0 0
ADM -0.012 0.047 0.16 9 -10000 0 9
ARNT -0.016 0.005 0 11 -10000 0 11
HNF4A -0.014 0.006 0 20 -10000 0 20
ADFP -0.011 0.044 0.16 8 -10000 0 8
SLC2A1 -0.014 0.044 0.14 7 -0.12 5 12
LEP -0.01 0.049 0.16 10 -10000 0 10
HIF1A/ARNT/Cbp/p300 0.017 0.031 0.091 2 -0.13 5 7
EPO 0.003 0.039 0.12 6 -0.19 3 9
CREBBP -0.003 0.001 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 0.016 0.03 0.086 2 -0.13 5 7
PFKFB3 -0.011 0.047 0.16 9 -10000 0 9
NT5E -0.012 0.044 0.16 8 -10000 0 8
Signaling events mediated by PTP1B

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
PDGFRB -0.016 0.004 0 8 -10000 0 8
Jak2/Leptin Receptor -0.008 0.1 -10000 0 -0.28 15 15
PTP1B/AKT1 0.011 0.057 0.13 6 -0.17 7 13
FYN -0.016 0.003 0 5 -10000 0 5
p210 bcr-abl/PTP1B 0.003 0.06 0.13 7 -0.18 7 14
EGFR -0.007 0.016 -10000 0 -10000 0 0
EGF/EGFR 0.016 0.053 0.13 4 -0.16 7 11
CSF1 -0.016 0.003 0 5 -10000 0 5
AKT1 -0.009 0.015 -10000 0 -10000 0 0
INSR -0.008 0.015 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.01 0.056 0.12 6 -0.16 8 14
Insulin Receptor/Insulin 0.022 0.053 0.13 4 -0.15 8 12
HCK -0.016 0.005 0 11 -10000 0 11
CRK -0.016 0.004 0 7 -10000 0 7
TYK2 -0.001 0.063 0.16 7 -0.18 6 13
EGF -0.005 0.017 -10000 0 -10000 0 0
YES1 -0.016 0.003 0 6 -10000 0 6
CAV1 0.01 0.068 0.14 15 -0.18 7 22
TXN -0.007 0.016 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.015 0.059 0.13 4 -0.17 8 12
cell migration -0.003 0.06 0.18 7 -0.13 7 14
STAT3 -0.008 0.015 -10000 0 -10000 0 0
PRLR -0.008 0.014 0.017 30 -10000 0 30
ITGA2B -0.011 0.013 -10000 0 -10000 0 0
CSF1R -0.016 0.004 0 7 -10000 0 7
Prolactin Receptor/Prolactin 0.021 0.009 -10000 0 0 21 21
FGR -0.016 0.004 0 8 -10000 0 8
PTP1B/p130 Cas 0.012 0.056 0.12 7 -0.17 7 14
Crk/p130 Cas 0.02 0.057 0.13 6 -0.15 8 14
DOK1 -0.004 0.062 0.13 5 -0.22 6 11
JAK2 -0.018 0.11 -10000 0 -0.3 14 14
Jak2/Leptin Receptor/Leptin 0.015 0.062 0.13 1 -0.17 9 10
PIK3R1 -0.016 0.004 0 9 -10000 0 9
PTPN1 0.003 0.06 0.13 7 -0.18 7 14
LYN -0.015 0.005 0 14 -10000 0 14
CDH2 -0.016 0.004 0 8 -10000 0 8
SRC 0.014 0.041 0.16 1 -0.33 1 2
ITGB3 -0.011 0.013 -10000 0 -10000 0 0
CAT1/PTP1B 0.012 0.1 0.16 16 -0.33 6 22
CAPN1 -0.012 0.012 -10000 0 -10000 0 0
CSK -0.017 0.002 0 3 -10000 0 3
PI3K 0.025 0.045 0.12 2 -0.14 4 6
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) 0.014 0.057 0.12 1 -0.16 9 10
negative regulation of transcription -0.018 0.1 -10000 0 -0.3 14 14
FCGR2A -0.016 0.004 0 7 -10000 0 7
FER -0.007 0.015 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.006 -10000 0 -0.003 7 7
BLK -0.014 0.007 0 26 -10000 0 26
Insulin Receptor/Insulin/Shc 0.029 0.014 -10000 0 -0.026 2 2
RHOA -0.012 0.013 -10000 0 -10000 0 0
LEPR -0.013 0.011 0.016 15 -10000 0 15
BCAR1 -0.016 0.003 0 5 -10000 0 5
p210 bcr-abl/Grb2 -0.016 0.003 0 6 -10000 0 6
mol:NADPH 0 0.002 0.007 1 -10000 0 1
TRPV6 0.004 0.11 0.2 7 -0.35 7 14
PRL -0.007 0.015 0.017 35 -10000 0 35
SOCS3 0 0.12 -10000 0 -1 2 2
SPRY2 -0.01 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.029 0.013 -10000 0 -0.026 2 2
CSF1/CSF1R 0.019 0.057 0.13 6 -0.15 9 15
Ras protein signal transduction 0.002 0.09 0.51 4 -10000 0 4
IRS1 -0.016 0.003 0 5 -10000 0 5
INS -0.008 0.015 -10000 0 -10000 0 0
LEP -0.008 0.015 -10000 0 -10000 0 0
STAT5B -0.002 0.069 0.12 3 -0.19 12 15
STAT5A -0.002 0.069 0.12 3 -0.19 12 15
GRB2 -0.016 0.003 0 6 -10000 0 6
PDGFB-D/PDGFRB 0.012 0.056 0.12 7 -0.18 6 13
CSN2 0.004 0.037 0.11 2 -0.26 1 3
PIK3CA -0.016 0.004 0 10 -10000 0 10
LAT 0.008 0.062 -10000 0 -0.37 3 3
YBX1 -0.006 0.018 0.026 4 -10000 0 4
LCK -0.016 0.003 0 6 -10000 0 6
SHC1 -0.016 0.004 0 9 -10000 0 9
NOX4 -0.01 0.015 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.01 0.11 -10000 0 -0.27 15 15
CaM/Ca2+ 0.012 0.002 -10000 0 0 4 4
AKT1 -0.016 0.003 0 5 -10000 0 5
AKT2 -0.016 0.004 0 9 -10000 0 9
STXBP4 -0.016 0.003 0 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.022 0.11 -10000 0 -0.28 16 16
YWHAZ -0.013 0.007 0 29 -10000 0 29
CALM1 -0.016 0.003 0 4 -10000 0 4
YWHAQ -0.017 0.001 0 1 -10000 0 1
TBC1D4 -0.019 0.006 0 11 -10000 0 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.017 0.002 0 3 -10000 0 3
YWHAB -0.015 0.006 0 19 -10000 0 19
SNARE/Synip 0.021 0.006 -10000 0 0 12 12
YWHAG -0.016 0.003 0 6 -10000 0 6
ASIP -0.015 0.005 0 13 -10000 0 13
PRKCI -0.015 0.005 0 12 -10000 0 12
AS160/CaM/Ca2+ 0.012 0.002 -10000 0 0 4 4
RHOQ -0.017 0.001 0 1 -10000 0 1
GYS1 -0.01 0.004 0 17 -10000 0 17
PRKCZ -0.016 0.004 0 9 -10000 0 9
TRIP10 -0.016 0.003 0 6 -10000 0 6
TC10/GTP/CIP4/Exocyst 0.021 0.005 -10000 0 0 7 7
AS160/14-3-3 0.003 0.043 0.078 21 -0.15 5 26
VAMP2 -0.016 0.004 0 8 -10000 0 8
SLC2A4 -0.026 0.12 -10000 0 -0.32 15 15
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.005 0.002 -10000 0 -10000 0 0
SFN -0.016 0.004 0 9 -10000 0 9
LNPEP -0.016 0.004 0 10 -10000 0 10
YWHAE -0.016 0.004 0 7 -10000 0 7
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.029 0.019 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL -0.016 0.003 0 5 -10000 0 5
STAT1 (dimer)/Cbp/p300 -0.009 0.067 0.15 20 -10000 0 20
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.028 0.016 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.026 0.02 -10000 0 -0.077 3 3
CaM/Ca2+ 0.029 0.021 -10000 0 -10000 0 0
RAP1A -0.016 0.003 0 5 -10000 0 5
STAT1 (dimer)/SHP2 -0.011 0.048 0.12 15 -10000 0 15
AKT1 0.005 0.083 0.19 15 -10000 0 15
MAP2K1 -0.007 0.062 0.14 18 -10000 0 18
MAP3K11 -0.007 0.058 0.14 17 -10000 0 17
IFNGR1 -0.012 0.018 0.031 19 -10000 0 19
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.001 0.041 -10000 0 -0.18 6 6
Rap1/GTP -0.034 0.021 0.018 1 -10000 0 1
CRKL/C3G 0.023 0.006 -10000 0 0 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.036 0.025 0.12 1 -10000 0 1
CEBPB 0.013 0.075 0.22 8 -0.2 2 10
STAT3 -0.016 0.003 0 5 -10000 0 5
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.023 0.094 -10000 0 -0.58 3 3
STAT1 -0.007 0.058 0.14 17 -10000 0 17
CALM1 -0.016 0.003 0 4 -10000 0 4
IFN-gamma (dimer) -0.013 0.016 0.031 13 -10000 0 13
PIK3CA -0.016 0.004 0 10 -10000 0 10
STAT1 (dimer)/PIAS1 -0.008 0.062 0.14 19 -10000 0 19
CEBPB/PTGES2/Cbp/p300 -0.012 0.037 -10000 0 -0.14 2 2
mol:Ca2+ 0.027 0.018 -10000 0 -10000 0 0
MAPK3 -0.004 0.098 0.25 3 -0.62 2 5
STAT1 (dimer) -0.032 0.025 -10000 0 -0.11 1 1
MAPK1 0.001 0.086 0.25 3 -0.67 1 4
JAK2 -0.013 0.014 0.03 10 -10000 0 10
PIK3R1 -0.016 0.004 0 9 -10000 0 9
JAK1 -0.011 0.02 0.032 22 -10000 0 22
CAMK2D -0.016 0.003 0 4 -10000 0 4
DAPK1 0.011 0.062 0.18 8 -0.16 1 9
SMAD7 -0.007 0.031 0.096 6 -10000 0 6
CBL/CRKL/C3G -0.008 0.067 0.15 20 -10000 0 20
PI3K 0.024 0.022 -10000 0 -0.027 7 7
IFNG -0.013 0.016 0.031 13 -10000 0 13
apoptosis 0.004 0.087 0.22 2 -0.39 4 6
CAMK2G -0.016 0.003 0 5 -10000 0 5
STAT3 (dimer) -0.016 0.003 0 5 -10000 0 5
CAMK2A -0.016 0.004 0 8 -10000 0 8
CAMK2B -0.017 0.002 0 3 -10000 0 3
FRAP1 -0.005 0.073 0.17 14 -10000 0 14
PRKCD 0.002 0.078 0.18 14 -10000 0 14
RAP1B -0.015 0.005 0 13 -10000 0 13
negative regulation of cell growth -0.026 0.02 -10000 0 -0.077 3 3
PTPN2 -0.016 0.004 0 7 -10000 0 7
EP300 -0.016 0.003 0 4 -10000 0 4
IRF1 -0.011 0.057 0.16 6 -10000 0 6
STAT1 (dimer)/PIASy -0.005 0.065 0.14 22 -10000 0 22
SOCS1 -0.008 0.15 -10000 0 -0.99 3 3
mol:GDP -0.011 0.06 0.13 19 -10000 0 19
CASP1 -0.006 0.033 0.091 7 -10000 0 7
PTGES2 -0.016 0.003 0 6 -10000 0 6
IRF9 0 0.028 0.084 7 -0.073 1 8
mol:PI-3-4-5-P3 -0.025 0.015 -10000 0 -10000 0 0
RAP1/GDP -0.03 0.034 0.084 8 -10000 0 8
CBL -0.007 0.058 0.14 17 -10000 0 17
MAP3K1 -0.007 0.055 0.14 15 -10000 0 15
PIAS1 -0.016 0.003 0 4 -10000 0 4
PIAS4 -0.016 0.003 0 5 -10000 0 5
antigen processing and presentation of peptide antigen via MHC class II -0.026 0.02 -10000 0 -0.077 3 3
PTPN11 0.006 0.072 0.16 23 -10000 0 23
CREBBP -0.016 0.003 0 5 -10000 0 5
RAPGEF1 -0.016 0.003 0 5 -10000 0 5
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.018 0.007 0 16 -10000 0 16
BAD/BCL-XL/YWHAZ -0.021 0.012 0 36 -10000 0 36
CDKN1B -0.004 0.055 0.18 2 -0.27 4 6
CDKN1A -0.006 0.051 -10000 0 -0.27 4 4
FRAP1 -0.016 0.004 0 10 -10000 0 10
PRKDC -0.015 0.005 0 15 -10000 0 15
FOXO3 -0.001 0.05 -10000 0 -0.27 4 4
AKT1 -0.009 0.047 -10000 0 -0.28 4 4
BAD -0.017 0.002 0 2 -10000 0 2
AKT3 -0.003 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.001 0.05 -10000 0 -0.27 4 4
AKT1/ASK1 0.012 0.063 0.17 1 -0.22 7 8
BAD/YWHAZ 0.026 0.014 -10000 0 0 31 31
RICTOR -0.015 0.005 0 15 -10000 0 15
RAF1 -0.016 0.003 0 4 -10000 0 4
JNK cascade -0.011 0.061 0.21 7 -0.17 1 8
TSC1 -0.006 0.051 -10000 0 -0.27 4 4
YWHAZ -0.013 0.007 0 29 -10000 0 29
AKT1/RAF1 0.012 0.067 0.14 4 -0.23 7 11
EP300 -0.016 0.003 0 4 -10000 0 4
mol:GDP -0.006 0.049 -10000 0 -0.28 4 4
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.004 0.044 -10000 0 -0.26 3 3
YWHAQ -0.017 0.001 0 1 -10000 0 1
TBC1D4 -0.009 0.003 0 16 -10000 0 16
MAP3K5 -0.016 0.004 0 8 -10000 0 8
MAPKAP1 -0.016 0.003 0 5 -10000 0 5
negative regulation of cell cycle -0.014 0.065 0.18 6 -0.14 9 15
YWHAH -0.017 0.002 0 3 -10000 0 3
AKT1S1 -0.003 0.057 0.18 3 -0.27 4 7
CASP9 -0.007 0.05 -10000 0 -0.27 4 4
YWHAB -0.015 0.006 0 19 -10000 0 19
p27Kip1/KPNA1 0.003 0.076 0.16 10 -0.23 7 17
GBL -0.016 0.003 0 4 -10000 0 4
PDK1/Src/Hsp90 0.02 0.007 -10000 0 0 16 16
YWHAE -0.016 0.004 0 7 -10000 0 7
SRC -0.015 0.005 0 13 -10000 0 13
AKT2/p21CIP1 -0.007 0.052 0.23 1 -0.23 5 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL -0.009 0.098 -10000 0 -0.38 8 8
CHUK -0.006 0.051 -10000 0 -0.27 4 4
BAD/BCL-XL -0.011 0.055 0.11 2 -0.24 5 7
mTORC2 0.034 0.017 -10000 0 -10000 0 0
AKT2 -0.003 0.001 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.014 0.079 0.17 6 -0.22 8 14
PDPK1 -0.016 0.003 0 4 -10000 0 4
MDM2 0.001 0.054 0.18 5 -0.26 3 8
MAPKKK cascade -0.012 0.066 0.23 7 -0.14 4 11
MDM2/Cbp/p300 0.006 0.085 0.18 14 -0.22 7 21
TSC1/TSC2 -0.009 0.042 -10000 0 -0.26 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.081 0.18 14 -0.21 7 21
glucose import -0.006 0.039 0.19 5 -10000 0 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 -0.007 0.08 0.17 2 -0.22 12 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.014 0.006 0 23 -10000 0 23
GSK3A -0.002 0.048 0.18 2 -0.26 3 5
FOXO1 -0.001 0.05 -10000 0 -0.27 4 4
GSK3B -0.005 0.053 0.18 1 -0.27 4 5
SFN -0.016 0.004 0 9 -10000 0 9
G1/S transition of mitotic cell cycle -0.006 0.056 0.16 4 -0.23 5 9
p27Kip1/14-3-3 family 0.012 0.028 0.18 1 -10000 0 1
PRKACA -0.016 0.003 0 5 -10000 0 5
KPNA1 -0.017 0.002 0 3 -10000 0 3
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG -0.016 0.003 0 6 -10000 0 6
RHEB -0.016 0.004 0 7 -10000 0 7
CREBBP -0.016 0.003 0 5 -10000 0 5
ceramide signaling pathway

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
MAP4K4 -0.017 0.1 0.18 1 -0.3 9 10
BAG4 -0.015 0.005 0 15 -10000 0 15
BAD -0.009 0.036 0.13 1 -0.18 3 4
NFKBIA -0.017 0.002 0 3 -10000 0 3
BIRC3 -0.014 0.01 0.017 12 -10000 0 12
BAX -0.002 0.045 0.16 5 -0.24 2 7
EnzymeConsortium:3.1.4.12 -0.002 0.023 0.051 4 -0.072 7 11
IKBKB -0.005 0.11 0.18 11 -0.32 7 18
MAP2K2 -0.011 0.049 0.15 6 -0.26 2 8
MAP2K1 -0.011 0.051 0.15 7 -0.25 2 9
SMPD1 -0.006 0.033 0.077 1 -0.12 7 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.008 0.12 0.18 8 -0.31 9 17
MAP2K4 -0.009 0.04 0.15 2 -0.19 3 5
protein ubiquitination -0.014 0.11 0.17 3 -0.35 7 10
EnzymeConsortium:2.7.1.37 -0.013 0.054 0.15 6 -0.29 2 8
response to UV 0 0.001 0.002 6 -0.002 2 8
RAF1 -0.008 0.051 0.16 6 -0.26 2 8
CRADD -0.01 0.014 -10000 0 -10000 0 0
mol:ceramide -0.003 0.038 0.1 2 -0.12 7 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.022 0.005 -10000 0 0 6 6
MADD -0.01 0.013 -10000 0 -10000 0 0
MAP3K1 -0.007 0.041 0.16 2 -0.19 3 5
TRADD -0.01 0.014 -10000 0 -10000 0 0
RELA/p50 -0.017 0.002 0 3 -10000 0 3
MAPK3 -0.01 0.055 0.15 6 -0.26 3 9
MAPK1 -0.01 0.051 0.15 6 -0.22 3 9
p50/RELA/I-kappa-B-alpha 0.024 0.005 -10000 0 0 6 6
FADD -0.013 0.11 0.22 3 -0.32 8 11
KSR1 -0.006 0.045 0.17 3 -0.2 3 6
MAPK8 -0.014 0.038 0.14 2 -0.23 2 4
TRAF2 -0.013 0.01 0.017 11 -10000 0 11
response to radiation 0 0 0.001 1 -0.001 2 3
CHUK -0.018 0.098 0.18 2 -0.3 8 10
TNF R/SODD 0.021 0.009 -10000 0 0 22 22
TNF -0.011 0.012 -10000 0 -10000 0 0
CYCS -0.001 0.041 0.093 12 -0.14 3 15
IKBKG -0.02 0.1 0.18 2 -0.29 9 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.012 0.11 -10000 0 -0.32 9 9
RELA -0.017 0.002 0 3 -10000 0 3
RIPK1 -0.014 0.009 0.017 8 -10000 0 8
AIFM1 -0.002 0.038 0.092 9 -0.14 3 12
TNF/TNF R/SODD 0.027 0.013 -10000 0 0 27 27
TNFRSF1A -0.013 0.01 0.017 10 -10000 0 10
response to heat 0 0 0.001 1 -0.001 2 3
CASP8 -0.003 0.11 -10000 0 -0.58 4 4
NSMAF -0.008 0.09 0.17 2 -0.32 5 7
response to hydrogen peroxide 0 0.001 0.002 6 -0.002 2 8
BCL2 -0.016 0.005 0 11 -10000 0 11
Endothelins

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
AKT1 -0.022 0.007 0 14 -10000 0 14
PTK2B -0.012 0.011 0.017 13 -10000 0 13
mol:Ca2+ -0.018 0.1 0.16 1 -0.37 8 9
EDN1 -0.011 0.013 -10000 0 -10000 0 0
EDN3 -0.014 0.006 0 22 -10000 0 22
EDN2 -0.016 0.003 0 4 -10000 0 4
HRAS/GDP -0.025 0.094 0.14 1 -0.39 6 7
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.006 0.066 0.069 8 -0.22 7 15
ADCY4 -0.016 0.033 0.16 4 -10000 0 4
ADCY5 -0.015 0.036 0.16 5 -10000 0 5
ADCY6 -0.015 0.037 0.16 5 -10000 0 5
ADCY7 -0.017 0.033 0.16 4 -10000 0 4
ADCY1 -0.014 0.037 0.16 5 -10000 0 5
ADCY2 -0.017 0.029 0.16 3 -10000 0 3
ADCY3 -0.015 0.037 0.16 5 -10000 0 5
ADCY8 -0.012 0.036 0.16 5 -10000 0 5
ADCY9 -0.016 0.033 0.16 4 -10000 0 4
arachidonic acid secretion -0.021 0.084 0.14 1 -0.35 6 7
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.027 0.078 1 -0.12 6 7
GNAO1 -0.016 0.003 0 4 -10000 0 4
HRAS -0.016 0.004 0 9 -10000 0 9
ETA receptor/Endothelin-1/G12/GTP 0.028 0.01 -10000 0 0 15 15
ETA receptor/Endothelin-1/Gs/GTP 0.027 0.009 -10000 0 0 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
COL3A1 -0.022 0.006 0 10 -10000 0 10
EDNRB -0.013 0.01 0.017 13 -10000 0 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.021 0.008 0 17 -10000 0 17
CYSLTR1 -0.022 0.006 0 9 -10000 0 9
SLC9A1 -0.005 0.002 -10000 0 -10000 0 0
mol:GDP -0.026 0.1 0.14 1 -0.42 6 7
SLC9A3 -0.014 0.14 -10000 0 -0.53 8 8
RAF1 -0.025 0.1 0.15 4 -0.35 8 12
JUN -0.018 0.11 0.17 1 -0.42 7 8
JAK2 -0.019 0.01 0 31 -10000 0 31
mol:IP3 -0.01 0.057 -10000 0 -0.2 6 6
ETA receptor/Endothelin-1 0.023 0.006 -10000 0 0 9 9
PLCB1 -0.012 0.011 0.017 13 -10000 0 13
PLCB2 -0.01 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.02 0.009 -10000 0 0 24 24
FOS -0.023 0.083 0.14 4 -0.27 9 13
Gai/GDP -0.021 0.18 -10000 0 -0.75 7 7
CRK -0.012 0.012 0.017 18 -10000 0 18
mol:Ca ++ -0.011 0.022 0.13 1 -0.11 3 4
BCAR1 -0.014 0.009 0.017 8 -10000 0 8
PRKCB1 -0.016 0.084 0.17 1 -0.35 6 7
GNAQ -0.009 0.014 -10000 0 -10000 0 0
GNAZ -0.017 0.002 0 3 -10000 0 3
GNAL -0.016 0.004 0 7 -10000 0 7
Gs family/GDP -0.027 0.092 0.13 1 -0.38 6 7
ETA receptor/Endothelin-1/Gq/GTP -0.004 0.021 0.077 1 -0.12 3 4
MAPK14 -0.014 0.06 0.057 9 -0.22 7 16
TRPC6 -0.019 0.11 0.16 1 -0.39 8 9
GNAI2 -0.016 0.003 0 5 -10000 0 5
GNAI3 -0.016 0.003 0 4 -10000 0 4
GNAI1 -0.016 0.003 0 5 -10000 0 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.006 0.059 0.07 6 -0.19 7 13
ETB receptor/Endothelin-2 0.023 0.006 -10000 0 0 10 10
ETB receptor/Endothelin-3 0.02 0.01 -10000 0 0 26 26
ETB receptor/Endothelin-1 0.022 0.008 -10000 0 0 14 14
MAPK3 -0.027 0.09 0.14 4 -0.3 9 13
MAPK1 -0.026 0.092 0.14 4 -0.35 7 11
Rac1/GDP -0.028 0.095 0.14 1 -0.4 6 7
cAMP biosynthetic process 0 0.041 0.16 4 -0.14 2 6
MAPK8 -0.019 0.13 -10000 0 -0.42 9 9
SRC -0.014 0.008 0.017 6 -10000 0 6
ETB receptor/Endothelin-1/Gi/GTP -0.007 0.022 -10000 0 -0.097 7 7
p130Cas/CRK/Src/PYK2 -0.022 0.11 0.16 5 -0.36 8 13
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.028 0.095 0.14 1 -0.4 6 7
COL1A2 -0.012 0.006 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.023 0.005 -10000 0 0 7 7
mol:DAG -0.01 0.057 -10000 0 -0.2 6 6
MAP2K2 -0.027 0.091 0.14 3 -0.34 7 10
MAP2K1 -0.026 0.089 0.16 4 -0.33 7 11
EDNRA -0.011 0.013 0.017 5 -10000 0 5
positive regulation of muscle contraction -0.013 0.045 0.18 7 -10000 0 7
Gq family/GDP -0.025 0.081 0.13 2 -0.36 5 7
HRAS/GTP -0.025 0.1 0.13 2 -0.36 8 10
PRKCH -0.007 0.04 -10000 0 -0.2 3 3
RAC1 -0.016 0.004 0 9 -10000 0 9
PRKCA -0.013 0.086 0.17 3 -0.39 5 8
PRKCB -0.014 0.081 0.083 1 -0.31 7 8
PRKCE -0.018 0.083 -10000 0 -0.32 7 7
PRKCD -0.006 0.039 -10000 0 -0.18 4 4
PRKCG -0.015 0.087 0.18 3 -0.35 6 9
regulation of vascular smooth muscle contraction -0.028 0.088 0.15 4 -0.29 9 13
PRKCQ -0.015 0.083 0.18 1 -0.34 6 7
PLA2G4A -0.022 0.09 0.14 1 -0.38 6 7
GNA14 -0.009 0.014 -10000 0 -10000 0 0
GNA15 -0.011 0.013 -10000 0 -10000 0 0
GNA12 -0.016 0.004 0 7 -10000 0 7
GNA11 -0.011 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.011 -10000 0 0 17 17
MMP1 -0.019 0.006 0 13 -10000 0 13
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.004 0.05 0.15 9 -0.13 3 12
PLK1 -0.01 0.04 0.14 2 -0.15 2 4
CDKN1B -0.001 0.069 0.14 5 -0.24 7 12
FOXO3 -0.004 0.034 0.083 10 -0.085 13 23
KAT2B 0 0.001 0.003 3 -0.002 5 8
FOXO1/SIRT1 -0.009 0.035 0.1 7 -0.12 5 12
CAT -0.006 0.044 0.18 3 -0.15 2 5
CTNNB1 -0.016 0.005 0 11 -10000 0 11
AKT1 -0.013 0.01 0.018 12 -10000 0 12
FOXO1 -0.004 0.036 0.11 7 -0.12 5 12
MAPK10 -0.012 0.036 0.17 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.017 0.041 0.14 4 -0.14 5 9
response to oxidative stress 0 0.001 0.002 5 -0.002 7 12
FOXO3A/SIRT1 0.005 0.037 0.094 1 -0.086 13 14
XPO1 -0.017 0.001 0 1 -10000 0 1
EP300 -0.012 0.012 0.017 18 -10000 0 18
BCL2L11 0.012 0.007 -10000 0 -10000 0 0
FOXO1/SKP2 -0.008 0.03 0.097 6 -0.12 3 9
mol:GDP 0 0.001 0.002 5 -0.002 7 12
RAN -0.017 0.002 0 2 -10000 0 2
GADD45A -0.009 0.087 -10000 0 -0.42 5 5
YWHAQ -0.017 0.001 0 1 -10000 0 1
FOXO1/14-3-3 family 0.002 0.082 0.12 4 -0.32 6 10
MST1 -0.014 0.009 0.017 9 -10000 0 9
CSNK1D -0.016 0.004 0 7 -10000 0 7
CSNK1E -0.016 0.003 0 4 -10000 0 4
FOXO4/14-3-3 family -0.007 0.086 0.13 1 -0.28 10 11
YWHAB -0.015 0.006 0 19 -10000 0 19
MAPK8 -0.014 0.032 0.17 4 -10000 0 4
MAPK9 -0.013 0.032 0.17 4 -10000 0 4
YWHAG -0.016 0.003 0 6 -10000 0 6
YWHAE -0.016 0.004 0 7 -10000 0 7
YWHAZ -0.013 0.007 0 29 -10000 0 29
SIRT1 -0.013 0.011 0.018 13 -10000 0 13
SOD2 -0.018 0.068 0.1 1 -0.21 10 11
RBL2 -0.022 0.13 -10000 0 -0.65 5 5
RAL/GDP 0.022 0.004 -10000 0 0 5 5
CHUK -0.015 0.008 0.017 8 -10000 0 8
Ran/GTP 0.012 0.001 -10000 0 0 2 2
CSNK1G2 -0.016 0.003 0 5 -10000 0 5
RAL/GTP 0.021 0.004 -10000 0 0 5 5
CSNK1G1 -0.016 0.003 0 4 -10000 0 4
FASLG 0.012 0.007 -10000 0 -10000 0 0
SKP2 -0.015 0.005 0 15 -10000 0 15
USP7 -0.016 0.003 0 4 -10000 0 4
IKBKB -0.013 0.01 0.018 8 -10000 0 8
CCNB1 -0.008 0.039 0.13 3 -0.13 2 5
FOXO1-3a-4/beta catenin -0.012 0.045 0.098 4 -0.17 6 10
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.03 0.096 6 -0.11 3 9
CSNK1A1 -0.016 0.004 0 8 -10000 0 8
SGK1 0 0.001 0.003 3 -0.002 5 8
CSNK1G3 -0.016 0.004 0 9 -10000 0 9
Ran/GTP/Exportin 1 0.022 0.003 -10000 0 0 3 3
ZFAND5 -0.014 0.036 0.13 4 -0.12 5 9
SFN -0.016 0.004 0 9 -10000 0 9
CDK2 -0.013 0.01 0.018 12 -10000 0 12
FOXO3A/14-3-3 -0.004 0.071 0.11 1 -0.22 10 11
CREBBP -0.014 0.01 0.018 11 -10000 0 11
FBXO32 0.027 0.084 0.18 27 -0.14 1 28
BCL6 0 0.034 -10000 0 -10000 0 0
RALB -0.017 0.002 0 2 -10000 0 2
RALA -0.017 0.002 0 3 -10000 0 3
YWHAH -0.017 0.002 0 3 -10000 0 3
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.016 0.003 0 6 -10000 0 6
AES -0.016 0.003 0 5 -10000 0 5
FBXW11 -0.016 0.004 0 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.02 0.009 -10000 0 0 23 23
SMAD4 -0.015 0.005 0 15 -10000 0 15
DKK2 -0.015 0.009 0.017 9 -10000 0 9
TLE1 -0.016 0.003 0 4 -10000 0 4
MACF1 -0.01 0.014 -10000 0 -10000 0 0
CTNNB1 0.002 0.081 0.15 8 -0.27 6 14
WIF1 -0.014 0.009 0.017 8 -10000 0 8
beta catenin/RanBP3 -0.008 0.064 0.11 4 -0.21 7 11
KREMEN2 -0.012 0.011 0.017 17 -10000 0 17
DKK1 -0.013 0.011 0.017 17 -10000 0 17
beta catenin/beta TrCP1 0.003 0.076 0.16 8 -0.24 6 14
FZD1 -0.01 0.013 -10000 0 -10000 0 0
AXIN2 0.013 0.11 0.6 4 -10000 0 4
AXIN1 -0.007 0.015 -10000 0 -10000 0 0
RAN -0.017 0.002 0 2 -10000 0 2
Axin1/APC/GSK3/beta catenin -0.013 0.11 -10000 0 -0.52 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.036 0.15 -10000 0 -0.36 17 17
Axin1/APC/GSK3 0.002 0.056 0.13 8 -0.15 7 15
Axin1/APC/GSK3/beta catenin/Macf1 -0.006 0.085 0.15 13 -0.27 8 21
HNF1A 0 0 -10000 0 -10000 0 0
CTBP1 -0.016 0.003 0 5 -10000 0 5
MYC 0.13 0.25 0.58 32 -10000 0 32
RANBP3 -0.016 0.003 0 5 -10000 0 5
DKK2/LRP6/Kremen 2 0.031 0.01 -10000 0 0 13 13
NKD1 -0.015 0.007 0.017 6 -10000 0 6
TCF4 -0.015 0.005 0 13 -10000 0 13
TCF3 -0.016 0.003 0 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.035 0.017 -10000 0 0 26 26
Ran/GTP 0.012 0.001 -10000 0 0 2 2
CtBP/CBP/TCF/TLE1/AES -0.025 0.085 -10000 0 -0.18 21 21
LEF1 -0.016 0.003 0 4 -10000 0 4
DVL1 -0.003 0.028 -10000 0 -0.18 3 3
CSNK2A1 -0.009 0.013 0.018 6 -10000 0 6
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.014 0.12 0.16 1 -0.48 7 8
DKK1/LRP6/Kremen 2 0.03 0.01 -10000 0 0 14 14
LRP6 -0.009 0.014 -10000 0 -10000 0 0
CSNK1A1 -0.01 0.014 0.021 1 -10000 0 1
NLK -0.017 0.002 0 3 -10000 0 3
CCND1 0.025 0.13 0.57 7 -10000 0 7
WNT1 -0.007 0.016 -10000 0 -10000 0 0
GSK3A -0.01 0.014 -10000 0 -10000 0 0
GSK3B -0.009 0.015 0.02 2 -10000 0 2
FRAT1 -0.014 0.01 0.017 12 -10000 0 12
PPP2R5D 0.01 0.036 -10000 0 -0.22 2 2
APC -0.002 0.07 0.17 19 -10000 0 19
WNT1/LRP6/FZD1 -0.005 0.028 0.082 5 -0.099 7 12
CREBBP -0.016 0.003 0 5 -10000 0 5
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.02 0.007 -10000 0 0 13 13
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 -0.016 0.004 0 7 -10000 0 7
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.016 0.003 0 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.016 0.005 0 11 -10000 0 11
RAC1-CDC42/GTP/PAK family -0.002 0.001 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 -0.016 0.003 0 6 -10000 0 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 -0.016 0.003 0 6 -10000 0 6
FYN -0.016 0.003 0 5 -10000 0 5
MAP3K12 -0.017 0.002 0 3 -10000 0 3
FGR -0.016 0.004 0 8 -10000 0 8
p38 alpha/TAB1 -0.001 0.11 0.14 7 -0.32 10 17
PRKG1 -0.016 0.003 0 4 -10000 0 4
DUSP8 -0.016 0.004 0 8 -10000 0 8
PGK/cGMP/p38 alpha -0.006 0.1 0.12 5 -0.31 10 15
apoptosis -0.001 0.1 0.13 7 -0.31 10 17
RAL/GTP 0.022 0.004 -10000 0 0 5 5
LYN -0.015 0.005 0 14 -10000 0 14
DUSP1 -0.016 0.004 0 7 -10000 0 7
PAK1 -0.017 0.002 0 3 -10000 0 3
SRC -0.015 0.005 0 13 -10000 0 13
RAC1/OSM/MEKK3/MKK3 0.038 0.014 -10000 0 0 17 17
TRAF6 -0.016 0.003 0 6 -10000 0 6
RAC1 -0.016 0.004 0 9 -10000 0 9
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 -0.017 0.002 0 3 -10000 0 3
RAC1-CDC42/GTP 0.019 0.008 -10000 0 0 20 20
MAPK11 -0.002 0.1 0.15 11 -0.3 9 20
BLK -0.014 0.007 0 26 -10000 0 26
HCK -0.016 0.005 0 11 -10000 0 11
MAP2K3 -0.016 0.003 0 5 -10000 0 5
DUSP16 -0.016 0.004 0 10 -10000 0 10
DUSP10 -0.016 0.004 0 8 -10000 0 8
TRAF6/MEKK3 0.02 0.006 -10000 0 0 11 11
MAP3K7IP1 -0.016 0.003 0 4 -10000 0 4
MAPK14 -0.008 0.12 0.13 11 -0.35 10 21
positive regulation of innate immune response -0.005 0.12 0.16 10 -0.41 8 18
LCK -0.016 0.003 0 6 -10000 0 6
p38alpha-beta/MKP7 0.002 0.12 0.17 10 -0.39 8 18
p38alpha-beta/MKP5 0.002 0.11 0.17 9 -0.36 8 17
PGK/cGMP 0.012 0.002 -10000 0 0 4 4
PAK2 -0.016 0.004 0 8 -10000 0 8
p38alpha-beta/MKP1 0.004 0.12 0.17 9 -0.4 8 17
CDC42 -0.016 0.005 0 11 -10000 0 11
RALB -0.017 0.002 0 2 -10000 0 2
RALA -0.017 0.002 0 3 -10000 0 3
PAK3 -0.017 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.009 0.004 0 22 -10000 0 22
GNB1/GNG2 0.029 0.01 -10000 0 0 14 14
regulation of S phase of mitotic cell cycle 0.005 0.003 -10000 0 -10000 0 0
GNAO1 -0.016 0.003 0 4 -10000 0 4
HRAS -0.016 0.004 0 9 -10000 0 9
SHBG/T-DHT 0.01 0.003 -10000 0 0 10 10
PELP1 -0.016 0.004 0 8 -10000 0 8
AKT1 -0.01 0.002 0 5 -10000 0 5
MAP2K1 -0.013 0.053 0.15 13 -10000 0 13
T-DHT/AR 0.012 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 -0.016 0.003 0 5 -10000 0 5
GNAI3 -0.016 0.003 0 4 -10000 0 4
GNAI1 -0.016 0.003 0 5 -10000 0 5
mol:GDP -0.012 0.006 -10000 0 -10000 0 0
cell proliferation -0.011 0.061 0.14 14 -0.21 2 16
PIK3CA -0.016 0.004 0 10 -10000 0 10
FOS -0.006 0.048 0.14 3 -0.2 3 6
mol:Ca2+ -0.001 0 -10000 0 -10000 0 0
MAPK3 -0.011 0.056 0.14 14 -10000 0 14
MAPK1 -0.003 0.064 0.14 1 -0.46 2 3
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.021 0.23 1 -10000 0 1
GNG2 -0.016 0.003 0 6 -10000 0 6
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.026 0.012 -10000 0 0 25 25
actin cytoskeleton reorganization 0.02 0.011 -10000 0 0 33 33
SRC -0.015 0.005 0 13 -10000 0 13
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.02 0.008 -10000 0 0 18 18
apoptosis 0.004 0.053 0.23 3 -0.15 3 6
T-DHT/AR/PELP1 0.021 0.005 -10000 0 0 8 8
HRAS/GDP -0.016 0.009 -10000 0 -10000 0 0
CREB1 -0.005 0.055 0.15 3 -0.25 3 6
RAC1-CDC42/GTP 0.025 0.014 -10000 0 0 33 33
AR -0.017 0 -10000 0 -10000 0 0
GNB1 -0.016 0.004 0 9 -10000 0 9
RAF1 -0.007 0.057 0.16 14 -10000 0 14
RAC1-CDC42/GDP -0.009 0.035 0.092 13 -10000 0 13
T-DHT/AR/PELP1/Src 0.027 0.011 -10000 0 0 20 20
MAP2K2 -0.012 0.054 0.15 14 -10000 0 14
T-DHT/AR/PELP1/Src/PI3K 0.005 0.003 -10000 0 -10000 0 0
GNAZ -0.017 0.002 0 3 -10000 0 3
SHBG -0.016 0.004 0 10 -10000 0 10
Gi family/GNB1/GNG2/GDP -0.008 0.083 -10000 0 -0.27 8 8
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 -0.016 0.004 0 9 -10000 0 9
GNRH1 -0.009 0.004 0 20 -10000 0 20
Gi family/GTP -0.007 0.002 -10000 0 -10000 0 0
CDC42 -0.016 0.005 0 11 -10000 0 11
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.016 0.003 0 5 -10000 0 5
HRAS -0.016 0.004 0 9 -10000 0 9
EGFR -0.016 0.004 0 10 -10000 0 10
AKT 0.011 0.063 0.12 19 -10000 0 19
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 -0.016 0.003 0 5 -10000 0 5
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.016 0.003 0 6 -10000 0 6
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.015 0.005 0 12 -10000 0 12
PIK3CA -0.016 0.004 0 10 -10000 0 10
PIK3CB -0.017 0.002 0 3 -10000 0 3
NRAS -0.016 0.003 0 5 -10000 0 5
PIK3CG -0.016 0.004 0 10 -10000 0 10
PIK3R3 -0.017 0.002 0 3 -10000 0 3
PIK3R2 -0.017 0.002 0 3 -10000 0 3
NF1 -0.017 0.002 0 3 -10000 0 3
RAS -0.002 0.001 -10000 0 -10000 0 0
ERBB2 -0.015 0.006 0 19 -10000 0 19
proliferation/survival/translation -0.011 0.038 0.13 3 -0.16 3 6
PI3K 0.019 0.041 0.096 27 -10000 0 27
PIK3R1 -0.016 0.004 0 9 -10000 0 9
KRAS -0.015 0.005 0 16 -10000 0 16
FOXO 0.036 0.039 0.1 28 -10000 0 28
AKT2 -0.016 0.004 0 9 -10000 0 9
PTEN -0.016 0.004 0 10 -10000 0 10
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.017 0 -10000 0 -10000 0 0
NFATC2 -0.013 0.018 0.049 8 -10000 0 8
NFATC3 -0.016 0.014 0.042 7 -10000 0 7
CD40LG 0.004 0.07 0.15 23 -10000 0 23
ITCH -0.014 0.005 0 16 -10000 0 16
CBLB -0.015 0.003 0 6 -10000 0 6
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.008 0.01 0.065 1 -10000 0 1
JUNB -0.016 0.003 0 5 -10000 0 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.002 -10000 0 0 4 4
T cell anergy -0.006 0.004 -10000 0 -10000 0 0
TLE4 -0.015 0.013 0.025 7 -10000 0 7
Jun/NFAT1-c-4/p21SNFT 0.027 0.013 -10000 0 0 26 26
AP-1/NFAT1-c-4 0.035 0.018 -10000 0 -10000 0 0
IKZF1 -0.007 0.011 0.031 8 -10000 0 8
T-helper 2 cell differentiation 0.001 0.051 0.12 1 -0.2 6 7
AP-1/NFAT1 0.029 0.015 -10000 0 -10000 0 0
CALM1 -0.016 0.003 0 4 -10000 0 4
EGR2 -0.002 0.001 -10000 0 -10000 0 0
EGR3 -0.002 0.001 -10000 0 -10000 0 0
NFAT1/FOXP3 0.023 0.013 0.086 1 -10000 0 1
EGR1 -0.016 0.003 0 6 -10000 0 6
JUN -0.016 0.003 0 4 -10000 0 4
EGR4 -0.017 0.001 0 1 -10000 0 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
GBP3 -0.014 0.013 0.025 7 -10000 0 7
FOSL1 -0.017 0.002 0 3 -10000 0 3
NFAT1-c-4/MAF/IRF4 0.034 0.019 -10000 0 -10000 0 0
DGKA -0.015 0.013 0.025 7 -10000 0 7
CREM -0.017 0.002 0 3 -10000 0 3
NFAT1-c-4/PPARG 0.028 0.015 -10000 0 0 29 29
CTLA4 -0.017 0.015 0.024 8 -10000 0 8
NFAT1-c-4 (dimer)/EGR1 0.028 0.015 -10000 0 0 29 29
NFAT1-c-4 (dimer)/EGR4 0.029 0.014 -10000 0 0 27 27
FOS -0.016 0.003 0 4 -10000 0 4
IFNG 0.002 0.004 -10000 0 -10000 0 0
T cell activation 0.018 0.067 0.16 22 -10000 0 22
MAF -0.016 0.003 0 4 -10000 0 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.003 0.002 -10000 0 0 33 33
TNF -0.014 0.011 0.016 6 -10000 0 6
FASLG 0.01 0.039 0.1 15 -0.098 2 17
TBX21 -0.016 0.003 0 5 -10000 0 5
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.016 0.003 0 5 -10000 0 5
PTPN1 -0.015 0.015 0.031 8 -10000 0 8
NFAT1-c-4/ICER1 0.028 0.015 -10000 0 0 28 28
GATA3 -0.016 0.003 0 6 -10000 0 6
T-helper 1 cell differentiation 0.002 0.004 -10000 0 -10000 0 0
IL2RA 0.01 0.006 -10000 0 -10000 0 0
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.014 0.015 0.033 6 -10000 0 6
E2F1 -0.015 0.005 0 13 -10000 0 13
PPARG -0.017 0.002 0 3 -10000 0 3
SLC3A2 -0.015 0.015 0.031 8 -10000 0 8
IRF4 -0.016 0.004 0 7 -10000 0 7
PTGS2 0.002 0.068 0.15 21 -10000 0 21
CSF2 -0.001 0.062 0.14 19 -10000 0 19
JunB/Fra1/NFAT1-c-4 0.034 0.019 -10000 0 -10000 0 0
IL4 0.001 0.052 0.12 1 -0.2 6 7
IL5 -0.001 0.062 0.14 19 -10000 0 19
IL2 0.018 0.067 0.16 22 -10000 0 22
IL3 0.002 0.059 -10000 0 -0.39 3 3
RNF128 -0.016 0.003 0 4 -10000 0 4
NFATC1 -0.003 0.002 0 33 -10000 0 33
CDK4 0.002 0.001 -10000 0 -10000 0 0
PTPRK -0.015 0.015 0.031 8 -10000 0 8
IL8 0.003 0.069 0.15 22 -10000 0 22
POU2F1 -0.016 0.003 0 6 -10000 0 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.004 0.002 -10000 0 -10000 0 0
epithelial cell differentiation 0.03 0.013 -10000 0 0 21 21
CYFIP2 -0.016 0.004 0 8 -10000 0 8
ENAH -0.021 0.059 0.19 4 -10000 0 4
EGFR -0.016 0.004 0 10 -10000 0 10
EPHA2 -0.016 0.004 0 7 -10000 0 7
MYO6 -0.013 0.051 0.16 11 -10000 0 11
CTNNB1 -0.016 0.005 0 11 -10000 0 11
ABI1/Sra1/Nap1 0.03 0.011 -10000 0 0 15 15
AQP5 -0.009 0.043 0.14 10 -10000 0 10
CTNND1 -0.017 0.001 0 1 -10000 0 1
mol:PI-4-5-P2 -0.013 0.051 0.16 11 -10000 0 11
regulation of calcium-dependent cell-cell adhesion -0.013 0.051 0.16 11 -10000 0 11
EGF -0.016 0.003 0 4 -10000 0 4
NCKAP1 -0.017 0.002 0 3 -10000 0 3
AQP3 -0.012 0.047 0.14 9 -0.29 1 10
cortical microtubule organization 0.03 0.013 -10000 0 0 21 21
GO:0000145 -0.012 0.048 0.15 11 -10000 0 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.014 -10000 0 0 21 21
MLLT4 -0.016 0.005 0 11 -10000 0 11
ARF6/GDP -0.037 0.02 -10000 0 -10000 0 0
ARF6 -0.016 0.003 0 6 -10000 0 6
Ephrin A1/EPHA2/NCK1/GIT1 0.037 0.015 -10000 0 0 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.043 0.15 8 -0.17 1 9
PVRL2 -0.016 0.004 0 10 -10000 0 10
ZYX -0.013 0.049 0.16 10 -10000 0 10
ARF6/GTP 0.039 0.018 -10000 0 -10000 0 0
CDH1 -0.017 0.002 0 3 -10000 0 3
EGFR/EGFR/EGF/EGF -0.028 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.014 -10000 0 -10000 0 0
actin cytoskeleton organization -0.015 0.048 0.14 11 -10000 0 11
IGF-1R heterotetramer -0.016 0.003 0 5 -10000 0 5
GIT1 -0.016 0.003 0 4 -10000 0 4
IGF1R -0.016 0.003 0 5 -10000 0 5
IGF1 -0.016 0.003 0 4 -10000 0 4
DIAPH1 -0.016 0.14 -10000 0 -0.47 12 12
Wnt receptor signaling pathway -0.03 0.013 0 21 -10000 0 21
RHOA -0.016 0.003 0 5 -10000 0 5
RhoA/GTP -0.038 0.02 -10000 0 -10000 0 0
CTNNA1 -0.016 0.004 0 9 -10000 0 9
VCL -0.015 0.048 0.14 11 -10000 0 11
EFNA1 -0.016 0.004 0 9 -10000 0 9
LPP -0.017 0.048 0.15 10 -10000 0 10
Ephrin A1/EPHA2 -0.028 0.014 -10000 0 -10000 0 0
SEC6/SEC8 -0.034 0.019 -10000 0 -10000 0 0
MGAT3 -0.013 0.051 0.16 11 -10000 0 11
HGF/MET -0.028 0.014 -10000 0 -10000 0 0
HGF -0.016 0.003 0 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.004 0.002 -10000 0 0 21 21
actin cable formation -0.003 0.076 0.19 9 -0.19 4 13
KIAA1543 -0.018 0.05 0.15 11 -10000 0 11
KIFC3 -0.013 0.051 0.16 11 -10000 0 11
NCK1 -0.017 0.002 0 2 -10000 0 2
EXOC3 -0.016 0.004 0 9 -10000 0 9
ACTN1 -0.013 0.051 0.16 11 -10000 0 11
NCK1/GIT1 0.024 0.005 -10000 0 0 6 6
mol:GDP 0.03 0.013 -10000 0 0 21 21
EXOC4 -0.016 0.004 0 7 -10000 0 7
STX4 -0.021 0.009 0 21 -10000 0 21
PIP5K1C -0.013 0.051 0.16 11 -10000 0 11
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 -0.016 0.003 0 6 -10000 0 6
ROCK1 -0.017 0.068 0.21 4 -10000 0 4
adherens junction assembly -0.028 0.097 0.14 3 -0.34 7 10
IGF-1R heterotetramer/IGF1 -0.03 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.021 0.008 -10000 0 0 18 18
MET -0.015 0.005 0 12 -10000 0 12
PLEKHA7 -0.013 0.051 0.16 11 -10000 0 11
mol:GTP 0.035 0.015 -10000 0 0 20 20
establishment of epithelial cell apical/basal polarity -0.022 0.051 0.13 11 -10000 0 11
cortical actin cytoskeleton stabilization 0.004 0.002 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.015 0.048 0.14 11 -10000 0 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.004 0.002 -10000 0 0 21 21
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.015 0.028 0.048 20 -10000 0 20
TC10/GTP -0.027 0.009 0 10 -10000 0 10
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.02 0.079 18 -10000 0 18
HRAS -0.016 0.004 0 9 -10000 0 9
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.017 0.002 0 2 -10000 0 2
FOXO3 -0.007 0.005 0.003 8 -10000 0 8
AKT1 -0.015 0.057 0.16 4 -10000 0 4
INSR -0.006 0.025 0.041 28 -10000 0 28
Insulin Receptor/Insulin 0.038 0.045 0.17 13 -10000 0 13
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 -0.017 0.002 0 2 -10000 0 2
SORBS1 -0.017 0.002 0 3 -10000 0 3
CRK -0.016 0.004 0 7 -10000 0 7
PTPN1 -0.013 0.024 0.14 3 -10000 0 3
CAV1 -0.011 0.035 0.16 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.036 0.012 -10000 0 0 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.042 0.021 0.079 18 0 17 35
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.03 0.018 0.069 5 -0.009 2 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.007 0.075 0.16 5 -0.32 5 10
RPS6KB1 -0.02 0.052 0.16 3 -10000 0 3
PARD6A -0.017 0.002 0 3 -10000 0 3
CBL -0.016 0.003 0 6 -10000 0 6
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.012 0.005 -10000 0 -10000 0 0
PIK3R1 -0.016 0.004 0 9 -10000 0 9
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.029 0.042 0.11 7 -10000 0 7
HRAS/GTP -0.032 0.02 0.022 5 -10000 0 5
Insulin Receptor -0.006 0.025 0.041 28 -10000 0 28
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.044 0.025 0.099 5 -0.01 3 8
PRKCI 0.005 0.049 -10000 0 -0.27 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.027 0.033 18 -10000 0 18
SHC1 -0.016 0.004 0 9 -10000 0 9
negative regulation of MAPKKK cascade 0.028 0.013 -10000 0 -10000 0 0
PI3K 0.037 0.021 0.084 5 -0.009 2 7
NCK2 -0.017 0.001 0 1 -10000 0 1
RHOQ -0.017 0.001 0 1 -10000 0 1
mol:H2O2 -0.002 0.005 0.018 7 -10000 0 7
HRAS/GDP 0.012 0.003 -10000 0 0 9 9
AKT2 -0.015 0.057 0.14 12 -10000 0 12
PRKCZ 0.002 0.056 -10000 0 -0.28 5 5
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.013 0.036 0.16 3 -10000 0 3
F2RL2 -0.016 0.004 0 9 -10000 0 9
TRIP10 -0.016 0.003 0 6 -10000 0 6
Insulin Receptor/Insulin/Shc 0.033 0.019 0.071 17 0 19 36
TC10/GTP/CIP4/Exocyst 0.021 0.005 -10000 0 0 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.046 0.025 0.099 7 -0.01 3 10
RAPGEF1 -0.016 0.003 0 5 -10000 0 5
RASA1 -0.016 0.004 0 9 -10000 0 9
NCK1 -0.017 0.002 0 2 -10000 0 2
CBL/APS/CAP/Crk-II 0.03 0.009 -10000 0 0 11 11
TC10/GDP 0.012 0.001 -10000 0 0 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.041 0.022 0.082 17 -10000 0 17
INPP5D -0.012 0.033 0.16 3 -10000 0 3
SOS1 -0.017 0 -10000 0 -10000 0 0
SGK1 -0.004 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 -0.017 0.002 0 3 -10000 0 3
IRS1 -0.016 0.003 0 5 -10000 0 5
p62DOK/RasGAP 0.028 0.014 -10000 0 -10000 0 0
INS -0.008 0.023 0.04 23 -10000 0 23
mol:PI-3-4-P2 -0.012 0.033 0.16 3 -10000 0 3
GRB2 -0.016 0.003 0 6 -10000 0 6
EIF4EBP1 -0.021 0.049 0.12 11 -10000 0 11
PTPRA -0.01 0.019 0.034 19 -10000 0 19
PIK3CA -0.016 0.004 0 10 -10000 0 10
TC10/GTP/CIP4 0.021 0.005 -10000 0 0 7 7
PDPK1 -0.016 0.003 0 4 -10000 0 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.007 0.03 0.047 5 -0.13 6 11
Insulin Receptor/Insulin/IRS1 0.033 0.018 0.068 18 0 16 34
Insulin Receptor/Insulin/IRS3 0.029 0.02 0.069 20 -0.02 2 22
Par3/Par6 0.035 0.012 -10000 0 0 15 15
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.014 -10000 0 0 19 19
ER alpha/Gai/GDP/Gbeta gamma -0.015 0.12 -10000 0 -0.32 11 11
AKT1 -0.014 0.14 -10000 0 -0.74 5 5
PIK3CA -0.016 0.004 0 10 -10000 0 10
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.01 0.15 -10000 0 -0.74 5 5
mol:Ca2+ -0.011 0.011 -10000 0 -10000 0 0
IGF1R -0.016 0.003 0 5 -10000 0 5
E2/ER alpha (dimer)/Striatin 0.021 0.005 -10000 0 0 8 8
SHC1 -0.016 0.004 0 9 -10000 0 9
apoptosis 0.014 0.14 0.7 5 -10000 0 5
RhoA/GTP -0.027 0.014 0 26 -10000 0 26
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.007 0.097 0.15 7 -0.31 8 15
regulation of stress fiber formation 0.009 0.068 -10000 0 -0.14 21 21
E2/ERA-ERB (dimer) 0.021 0.006 -10000 0 0 11 11
KRAS -0.015 0.005 0 16 -10000 0 16
G13/GTP 0.02 0.006 -10000 0 0 10 10
pseudopodium formation -0.009 0.068 0.14 21 -10000 0 21
E2/ER alpha (dimer)/PELP1 0.02 0.007 -10000 0 0 13 13
GRB2 -0.016 0.003 0 6 -10000 0 6
GNG2 -0.016 0.003 0 6 -10000 0 6
GNAO1 -0.016 0.003 0 4 -10000 0 4
HRAS -0.016 0.004 0 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.025 0.13 -10000 0 -0.47 9 9
E2/ER beta (dimer) 0.012 0.002 -10000 0 0 4 4
mol:GDP -0.016 0.019 -10000 0 -0.13 3 3
mol:NADP -0.025 0.13 -10000 0 -0.47 9 9
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:IP3 -0.012 0.011 0.063 2 -10000 0 2
IGF-1R heterotetramer -0.016 0.003 0 5 -10000 0 5
PLCB1 -0.007 0.01 -10000 0 -10000 0 0
PLCB2 -0.008 0.01 -10000 0 -10000 0 0
IGF1 -0.016 0.003 0 4 -10000 0 4
mol:L-citrulline -0.025 0.13 -10000 0 -0.47 9 9
RHOA -0.016 0.003 0 5 -10000 0 5
Gai/GDP -0.01 0.13 -10000 0 -0.57 7 7
JNK cascade 0.012 0.002 -10000 0 0 4 4
BCAR1 -0.016 0.003 0 5 -10000 0 5
ESR2 -0.016 0.003 0 4 -10000 0 4
GNAQ -0.016 0.003 0 4 -10000 0 4
ESR1 -0.016 0.004 0 8 -10000 0 8
Gq family/GDP/Gbeta gamma -0.021 0.14 -10000 0 -0.49 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.008 0.078 -10000 0 -0.55 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.008 0.093 0.15 7 -0.3 8 15
GNAZ -0.017 0.002 0 3 -10000 0 3
E2/ER alpha (dimer) 0.012 0.003 -10000 0 0 8 8
STRN -0.017 0 -10000 0 -10000 0 0
GNAL -0.016 0.004 0 7 -10000 0 7
PELP1 -0.016 0.004 0 8 -10000 0 8
MAPK11 -0.015 0.005 0 12 -10000 0 12
GNAI2 -0.016 0.003 0 5 -10000 0 5
GNAI3 -0.016 0.003 0 4 -10000 0 4
GNAI1 -0.016 0.003 0 5 -10000 0 5
HBEGF 0.002 0.13 0.25 13 -0.37 8 21
cAMP biosynthetic process 0.017 0.006 -10000 0 0 15 15
SRC -0.008 0.11 0.18 8 -0.33 9 17
PI3K 0.021 0.008 -10000 0 0 18 18
GNB1 -0.016 0.004 0 9 -10000 0 9
G13/GDP/Gbeta gamma 0.021 0.025 -10000 0 -0.11 3 3
SOS1 -0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.028 0.065 -10000 0 -0.22 10 10
Gs family/GTP 0.022 0.008 -10000 0 0 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.012 -10000 0 0 24 24
vasodilation -0.024 0.13 -10000 0 -0.45 9 9
mol:DAG -0.012 0.011 0.063 2 -10000 0 2
Gs family/GDP/Gbeta gamma -0.026 0.019 -10000 0 -0.14 2 2
MSN -0.01 0.071 0.15 21 -10000 0 21
Gq family/GTP 0.008 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.14 -10000 0 -0.72 5 5
NRAS -0.016 0.003 0 5 -10000 0 5
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.024 0.13 0.45 9 -10000 0 9
GRB2/SOS1 0.024 0.005 -10000 0 0 6 6
RhoA/GDP -0.019 0.026 0.12 2 -0.14 3 5
NOS3 -0.027 0.14 -10000 0 -0.5 9 9
GNA11 -0.016 0.003 0 5 -10000 0 5
MAPKKK cascade -0.006 0.11 -10000 0 -0.48 6 6
E2/ER alpha (dimer)/PELP1/Src 0.007 0.11 0.18 9 -0.3 9 18
ruffle organization -0.009 0.068 0.14 21 -10000 0 21
ROCK2 -0.004 0.075 0.16 21 -10000 0 21
GNA14 -0.016 0.003 0 5 -10000 0 5
GNA15 -0.016 0.003 0 5 -10000 0 5
GNA13 -0.016 0.003 0 5 -10000 0 5
MMP9 0.006 0.12 0.28 12 -0.34 7 19
MMP2 -0.009 0.11 0.18 11 -0.38 7 18
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.003 0.036 0.12 1 -0.13 2 3
NCK1/PAK1/Dok-R -0.014 0.018 -10000 0 -0.098 2 2
NCK1/Dok-R 0.015 0.035 0.1 3 -0.084 10 13
PIK3CA -0.013 0.011 0.017 13 -10000 0 13
mol:beta2-estradiol 0 0.004 -10000 0 -0.013 10 10
RELA -0.017 0.002 0 3 -10000 0 3
SHC1 -0.007 0.015 0.019 6 -10000 0 6
Rac/GDP 0.012 0.003 -10000 0 0 9 9
F2 0.004 0.019 -10000 0 -0.039 5 5
TNIP2 -0.016 0.003 0 6 -10000 0 6
NF kappa B/RelA 0.027 0.04 0.12 2 -0.086 9 11
FN1 -0.016 0.003 0 4 -10000 0 4
PLD2 -0.001 0.023 0.049 21 -0.082 1 22
PTPN11 -0.017 0.002 0 3 -10000 0 3
GRB14 -0.017 0.002 0 2 -10000 0 2
ELK1 -0.004 0.036 0.1 3 -10000 0 3
GRB7 -0.014 0.006 0 20 -10000 0 20
PAK1 -0.017 0.002 0 3 -10000 0 3
Tie2/Ang1/alpha5/beta1 Integrin 0.028 0.039 0.12 2 -0.093 7 9
CDKN1A 0.004 0.05 0.15 5 -0.14 3 8
ITGA5 -0.016 0.003 0 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.035 0.1 3 -0.085 9 12
CRK -0.016 0.004 0 7 -10000 0 7
mol:NO 0.006 0.043 0.16 5 -10000 0 5
PLG -0.002 0.024 0.049 21 -0.079 2 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0 0.033 0.097 4 -10000 0 4
GRB2 -0.016 0.003 0 6 -10000 0 6
PIK3R1 -0.008 0.014 -10000 0 -10000 0 0
ANGPT2 0.002 0.067 0.14 4 -0.19 11 15
BMX -0.002 0.024 0.049 21 -0.079 2 23
ANGPT1 -0.001 0.012 0.068 3 -10000 0 3
tube development -0.001 0.042 0.14 3 -0.12 3 6
ANGPT4 -0.01 0.012 0.017 5 -10000 0 5
response to hypoxia 0 0.006 0.015 12 -0.013 3 15
Tie2/Ang1/GRB14 -0.002 0.036 0.094 2 -0.12 1 3
alpha5/beta1 Integrin 0.023 0.006 -10000 0 0 9 9
FGF2 -0.012 0.012 0.017 18 -10000 0 18
STAT5A (dimer) 0.011 0.048 0.15 3 -0.12 5 8
mol:L-citrulline 0.006 0.043 0.16 5 -10000 0 5
AGTR1 -0.014 0.01 0.017 11 -10000 0 11
MAPK14 -0.002 0.08 -10000 0 -0.39 5 5
Tie2/SHP2 0.001 0.065 -10000 0 -0.24 8 8
TEK -0.002 0.064 -10000 0 -0.27 7 7
RPS6KB1 0.006 0.049 0.17 5 -0.14 2 7
Angiotensin II/AT1 0.011 0.006 -10000 0 -0.007 12 12
Tie2/Ang1/GRB2 -0.002 0.036 0.094 2 -0.12 1 3
MAPK3 -0.006 0.022 0.092 1 -10000 0 1
MAPK1 -0.006 0.022 0.092 1 -10000 0 1
Tie2/Ang1/GRB7 -0.003 0.032 0.12 1 -0.12 1 2
NFKB1 -0.017 0.002 0 2 -10000 0 2
MAPK8 -0.002 0.024 0.05 20 -0.079 2 22
PI3K 0.004 0.035 0.11 2 -0.16 1 3
FES 0.009 0.039 -10000 0 -0.23 2 2
Crk/Dok-R 0.016 0.034 0.1 1 -0.085 9 10
Tie2/Ang1/ABIN2 -0.001 0.035 0.12 1 -10000 0 1
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.007 0.043 0.15 4 -0.13 2 6
STAT5A -0.016 0.003 0 6 -10000 0 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.022 0.078 0.22 16 -0.14 2 18
Tie2/Ang2 0.004 0.037 0.12 3 -0.12 4 7
Tie2/Ang1 0.004 0.026 0.06 21 -0.077 2 23
FOXO1 0.007 0.044 0.16 4 -0.12 2 6
ELF1 -0.008 0.019 0.042 9 -10000 0 9
ELF2 0.001 0.026 0.056 21 -0.078 2 23
mol:Choline -0.001 0.023 0.049 21 -0.081 1 22
cell migration -0.012 0.014 -10000 0 -0.061 2 2
FYN -0.003 0.038 0.11 3 -0.12 3 6
DOK2 -0.015 0.006 0 19 -10000 0 19
negative regulation of cell cycle 0.005 0.048 0.14 5 -0.15 2 7
ETS1 -0.006 0.018 0.035 5 -10000 0 5
PXN 0.02 0.077 0.19 19 -0.15 1 20
ITGB1 -0.017 0.002 0 3 -10000 0 3
NOS3 0.005 0.042 0.17 4 -10000 0 4
RAC1 -0.016 0.004 0 9 -10000 0 9
TNF -0.006 0.018 0.035 5 -10000 0 5
MAPKKK cascade -0.001 0.023 0.049 21 -0.081 1 22
RASA1 -0.016 0.004 0 9 -10000 0 9
Tie2/Ang1/Shc -0.002 0.033 0.09 3 -10000 0 3
NCK1 -0.017 0.002 0 2 -10000 0 2
vasculogenesis 0.006 0.042 0.15 5 -10000 0 5
mol:Phosphatidic acid -0.001 0.023 0.049 21 -0.081 1 22
mol:Angiotensin II 0 0 -10000 0 -10000 0 0
mol:NADP 0.006 0.043 0.16 5 -10000 0 5
Rac1/GTP 0.012 0.038 0.11 2 -0.15 1 3
MMP2 -0.002 0.024 0.049 21 -0.079 2 23
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 -0.016 0.003 0 4 -10000 0 4
HSPA8 -0.016 0.003 0 6 -10000 0 6
SMAD3/SMAD4/ER alpha 0.028 0.015 0.083 1 -0.026 3 4
AKT1 -0.016 0.003 0 5 -10000 0 5
GSC 0.001 0.062 -10000 0 -0.38 3 3
NKX2-5 -0.016 0.004 0 7 -10000 0 7
muscle cell differentiation -0.005 0.06 0.18 12 -10000 0 12
SMAD2-3/SMAD4/SP1 0.035 0.018 0.09 1 -0.029 2 3
SMAD4 -0.016 0.013 0.039 5 -10000 0 5
CBFB -0.017 0.002 0 3 -10000 0 3
SAP18 -0.017 0.002 0 2 -10000 0 2
Cbp/p300/MSG1 0.032 0.008 -10000 0 0 9 9
SMAD3/SMAD4/VDR 0.04 0.026 -10000 0 -0.038 2 2
MYC -0.013 0.007 0 33 -10000 0 33
CDKN2B -0.074 0.14 -10000 0 -0.38 20 20
AP1 -0.019 0.006 0 11 -10000 0 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.033 0.085 -10000 0 -0.26 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.02 0.062 -10000 0 -0.18 16 16
SP3 -0.017 0.002 0 3 -10000 0 3
CREB1 -0.017 0.002 0 3 -10000 0 3
FOXH1 -0.014 0.006 0 24 -10000 0 24
SMAD3/SMAD4/GR 0.028 0.015 0.083 1 -0.026 2 3
GATA3 -0.016 0.003 0 6 -10000 0 6
SKI/SIN3/HDAC complex/NCoR1 -0.016 0.07 -10000 0 -0.17 15 15
MEF2C/TIF2 -0.014 0.049 0.16 9 -10000 0 9
endothelial cell migration -0.01 0.051 0.54 1 -10000 0 1
MAX -0.016 0.003 0 5 -10000 0 5
RBBP7 -0.017 0 -10000 0 -10000 0 0
RBBP4 -0.016 0.003 0 6 -10000 0 6
RUNX2 -0.016 0.003 0 4 -10000 0 4
RUNX3 -0.016 0.004 0 10 -10000 0 10
RUNX1 -0.016 0.004 0 10 -10000 0 10
CTBP1 -0.016 0.003 0 5 -10000 0 5
NR3C1 -0.016 0.003 0 6 -10000 0 6
VDR -0.017 0.002 0 3 -10000 0 3
CDKN1A -0.019 0.09 0.13 3 -0.46 5 8
KAT2B 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.025 0.015 -10000 0 0 35 35
DCP1A -0.016 0.003 0 6 -10000 0 6
SKI -0.016 0.004 0 10 -10000 0 10
SERPINE1 0.01 0.051 -10000 0 -0.54 1 1
SMAD3/SMAD4/ATF2 0.029 0.015 0.083 2 -0.026 2 4
SMAD3/SMAD4/ATF3 0.029 0.016 0.083 2 -0.026 2 4
SAP30 -0.016 0.005 0 11 -10000 0 11
Cbp/p300/PIAS3 0.03 0.011 -10000 0 0 16 16
JUN -0.017 0.022 0.13 3 -10000 0 3
SMAD3/SMAD4/IRF7 0.028 0.014 0.083 1 -0.026 1 2
TFE3 -0.017 0 -10000 0 -10000 0 0
COL1A2 0.008 0.005 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.028 0.016 0.026 3 -0.082 2 5
DLX1 -0.017 0.002 0 3 -10000 0 3
TCF3 -0.016 0.003 0 5 -10000 0 5
FOS -0.018 0.011 0.041 4 -10000 0 4
SMAD3/SMAD4/Max 0.029 0.015 0.083 2 -0.026 1 3
Cbp/p300/SNIP1 0.031 0.009 -10000 0 0 10 10
ZBTB17 -0.016 0.004 0 7 -10000 0 7
LAMC1 -0.023 0.013 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.027 0.017 0.083 2 -0.026 3 5
IRF7 -0.016 0.004 0 9 -10000 0 9
ESR1 -0.016 0.004 0 8 -10000 0 8
HNF4A -0.014 0.006 0 20 -10000 0 20
MEF2C -0.006 0.059 0.16 15 -10000 0 15
SMAD2-3/SMAD4 0.029 0.016 0.083 2 -0.026 3 5
Cbp/p300/Src-1 0.032 0.008 -10000 0 0 9 9
IGHV3OR16-13 -0.009 0.042 -10000 0 -0.35 2 2
TGIF2/HDAC complex -0.015 0.005 0 14 -10000 0 14
CREBBP -0.016 0.003 0 5 -10000 0 5
SKIL -0.015 0.005 0 12 -10000 0 12
HDAC1 -0.016 0.003 0 6 -10000 0 6
HDAC2 -0.016 0.003 0 5 -10000 0 5
SNIP1 -0.016 0.003 0 4 -10000 0 4
GCN5L2 -0.016 0.004 0 9 -10000 0 9
SMAD3/SMAD4/TFE3 0.029 0.015 0.083 2 -0.026 3 5
MSG1/HSC70 0.024 0.005 -10000 0 0 6 6
SMAD2 -0.015 0.005 0 15 -10000 0 15
SMAD3 -0.019 0.01 0.043 3 -10000 0 3
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.012 0.03 0.036 1 -0.12 8 9
SMAD2/SMAD2/SMAD4 -0.011 0.047 0.14 1 -0.14 12 13
NCOR1 -0.015 0.005 0 12 -10000 0 12
NCOA2 -0.015 0.006 0 18 -10000 0 18
NCOA1 -0.017 0 -10000 0 -10000 0 0
MYOD/E2A 0.023 0.006 -10000 0 0 8 8
SMAD2-3/SMAD4/SP1/MIZ-1 0.04 0.023 0.094 1 -0.033 2 3
IFNB1 -0.023 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.007 0.062 0.16 15 -10000 0 15
CITED1 -0.017 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.027 0.015 0.079 2 -0.022 3 5
RBL1 -0.015 0.005 0 13 -10000 0 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.015 0.055 0.095 1 -0.2 10 11
RUNX1-3/PEBPB2 0.029 0.012 -10000 0 0 19 19
SMAD7 -0.012 0.025 0.096 2 -0.12 5 7
MYC/MIZ-1 0.018 0.011 -10000 0 0 37 37
SMAD3/SMAD4 0.002 0.034 -10000 0 -0.12 6 6
IL10 -0.023 0.013 -10000 0 -10000 0 0
PIASy/HDAC complex -0.016 0.003 0 5 -10000 0 5
PIAS3 -0.016 0.004 0 10 -10000 0 10
CDK2 -0.016 0.004 0 7 -10000 0 7
IL5 -0.023 0.013 -10000 0 -10000 0 0
CDK4 -0.016 0.003 0 5 -10000 0 5
PIAS4 -0.016 0.003 0 5 -10000 0 5
ATF3 -0.016 0.003 0 6 -10000 0 6
SMAD3/SMAD4/SP1 0.028 0.015 0.083 1 -0.026 2 3
FOXG1 0 0 -10000 0 -10000 0 0
FOXO3 -0.01 0.002 0 5 -10000 0 5
FOXO1 -0.01 0.002 0 5 -10000 0 5
FOXO4 -0.01 0.002 0 5 -10000 0 5
heart looping -0.006 0.059 0.16 15 -10000 0 15
CEBPB -0.014 0.007 0 27 -10000 0 27
SMAD3/SMAD4/DLX1 0.029 0.015 0.083 2 -0.026 2 4
MYOD1 -0.016 0.003 0 5 -10000 0 5
SMAD3/SMAD4/HNF4 0.024 0.016 -10000 0 -0.026 3 3
SMAD3/SMAD4/GATA3 0.028 0.016 0.083 2 -0.026 3 5
SnoN/SIN3/HDAC complex/NCoR1 -0.015 0.005 0 12 -10000 0 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.039 0.024 0.094 1 -0.018 9 10
SMAD3/SMAD4/SP1-3 0.035 0.018 0.09 1 -0.029 2 3
MED15 0 0 -10000 0 -10000 0 0
SP1 -0.017 0.002 0 3 -10000 0 3
SIN3B -0.017 0.002 0 3 -10000 0 3
SIN3A -0.016 0.003 0 4 -10000 0 4
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.02 -10000 0 0 37 37
ITGB5 -0.024 0.031 0.14 4 -10000 0 4
TGIF/SIN3/HDAC complex/CtBP -0.008 0.05 -10000 0 -0.13 11 11
SMAD3/SMAD4/AR 0.029 0.015 0.083 2 -0.026 3 5
AR -0.017 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.011 0.054 -10000 0 -0.21 9 9
SMAD3/SMAD4/MYOD 0.028 0.015 0.083 1 -0.026 2 3
E2F5 -0.014 0.006 0 22 -10000 0 22
E2F4 -0.017 0.002 0 3 -10000 0 3
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.036 0.023 -10000 0 -0.012 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.002 0.014 -10000 0 -0.11 2 2
TFDP1 -0.016 0.003 0 5 -10000 0 5
SMAD3/SMAD4/AP1 0.028 0.02 0.16 2 -10000 0 2
SMAD3/SMAD4/RUNX2 0.029 0.016 0.083 2 -0.026 3 5
TGIF2 -0.015 0.005 0 14 -10000 0 14
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.017 0.002 0 3 -10000 0 3
Coregulation of Androgen receptor activity

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
NRIP1 -0.016 0.003 0 4 -10000 0 4
SVIL -0.016 0.003 0 6 -10000 0 6
ZNF318 -0.016 0.004 0 7 -10000 0 7
JMJD2C -0.015 0.005 0 16 -10000 0 16
T-DHT/AR/Ubc9 0.022 0.004 -10000 0 0 5 5
CARM1 -0.016 0.003 0 6 -10000 0 6
PRDX1 -0.017 0.002 0 3 -10000 0 3
PELP1 -0.016 0.004 0 8 -10000 0 8
CTNNB1 -0.016 0.005 0 11 -10000 0 11
AKT1 -0.016 0.003 0 5 -10000 0 5
PTK2B -0.015 0.006 0 18 -10000 0 18
MED1 0 0 -10000 0 -10000 0 0
MAK -0.016 0.004 0 9 -10000 0 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 -0.016 0.003 0 6 -10000 0 6
GSN -0.016 0.003 0 4 -10000 0 4
NCOA2 -0.015 0.006 0 18 -10000 0 18
NCOA6 -0.015 0.005 0 12 -10000 0 12
DNA-PK 0.029 0.012 -10000 0 0 20 20
NCOA4 -0.016 0.003 0 4 -10000 0 4
PIAS3 -0.016 0.004 0 10 -10000 0 10
cell proliferation -0.006 0.08 -10000 0 -0.38 6 6
XRCC5 -0.016 0.003 0 4 -10000 0 4
UBE3A -0.017 0.002 0 3 -10000 0 3
T-DHT/AR/SNURF 0.022 0.003 -10000 0 0 3 3
FHL2 0.009 0.002 -10000 0 0 8 8
RANBP9 -0.016 0.004 0 8 -10000 0 8
JMJD1A -0.017 0 -10000 0 -10000 0 0
CDK6 -0.014 0.006 0 20 -10000 0 20
TGFB1I1 -0.016 0.003 0 4 -10000 0 4
T-DHT/AR/CyclinD1 0.021 0.006 -10000 0 0 9 9
XRCC6 -0.016 0.003 0 4 -10000 0 4
T-DHT/AR 0.011 0 -10000 0 -10000 0 0
CTDSP1 -0.017 0.002 0 3 -10000 0 3
CTDSP2 -0.016 0.003 0 6 -10000 0 6
BRCA1 -0.016 0.003 0 4 -10000 0 4
TCF4 -0.015 0.005 0 13 -10000 0 13
CDKN2A -0.014 0.006 0 23 -10000 0 23
SRF -0.016 0.004 0 7 -10000 0 7
NKX3-1 0.008 0.003 -10000 0 0 19 19
KLK3 0.006 0.037 0.11 5 -0.11 5 10
TMF1 -0.016 0.003 0 4 -10000 0 4
HNRNPA1 0 0 -10000 0 -10000 0 0
AOF2 -0.016 0.005 0 11 -10000 0 11
APPL1 -0.01 0.002 0 5 -10000 0 5
T-DHT/AR/Caspase 8 0.022 0.003 -10000 0 0 2 2
AR -0.017 0 -10000 0 -10000 0 0
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0 0 -10000 0 -10000 0 0
PAWR -0.016 0.003 0 6 -10000 0 6
PRKDC -0.015 0.005 0 15 -10000 0 15
PA2G4 -0.016 0.003 0 6 -10000 0 6
UBE2I -0.016 0.003 0 5 -10000 0 5
T-DHT/AR/Cyclin D3/CDK11 p58 0.027 0.011 -10000 0 0 20 20
RPS6KA3 -0.017 0 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.022 0.004 -10000 0 0 4 4
LATS2 -0.017 0.002 0 2 -10000 0 2
T-DHT/AR/PRX1 0.021 0.003 -10000 0 0 3 3
Cyclin D3/CDK11 p58 0.021 0.009 -10000 0 0 20 20
VAV3 -0.016 0.003 0 4 -10000 0 4
KLK2 0.008 0.004 -10000 0 0 24 24
CASP8 -0.017 0.002 0 2 -10000 0 2
T-DHT/AR/TIF2/CARM1 0.027 0.012 -10000 0 0 22 22
TMPRSS2 0.009 0.002 -10000 0 0 7 7
CCND1 -0.016 0.004 0 9 -10000 0 9
PIAS1 -0.016 0.003 0 4 -10000 0 4
mol:T-DHT 0 0 -10000 0 -10000 0 0
CDC2L1 -0.015 0.005 0 12 -10000 0 12
PIAS4 -0.016 0.003 0 5 -10000 0 5
T-DHT/AR/CDK6 0.019 0.008 -10000 0 0 20 20
CMTM2 -0.017 0.002 0 3 -10000 0 3
SNURF -0.017 0.002 0 3 -10000 0 3
ZMIZ1 0 0 -10000 0 -10000 0 0
CCND3 -0.016 0.004 0 8 -10000 0 8
TGIF1 0 0 -10000 0 -10000 0 0
FKBP4 -0.016 0.005 0 11 -10000 0 11
JNK 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
LAT/GRAP2/SLP76/HPK1 0.037 0.015 -10000 0 0 19 19
MAP4K1 -0.016 0.004 0 10 -10000 0 10
MAP3K8 -0.016 0.003 0 6 -10000 0 6
PRKCB 0 0 -10000 0 -10000 0 0
DBNL -0.016 0.003 0 4 -10000 0 4
CRKL -0.016 0.003 0 5 -10000 0 5
MAP3K1 -0.011 0.03 0.069 7 -0.098 9 16
JUN -0.008 0.068 0.19 1 -0.54 2 3
MAP3K7 -0.009 0.029 0.069 8 -0.1 6 14
GRAP2 -0.017 0.002 0 3 -10000 0 3
CRK -0.016 0.004 0 7 -10000 0 7
MAP2K4 -0.009 0.036 0.14 1 -0.15 3 4
LAT -0.017 0.002 0 3 -10000 0 3
LCP2 -0.016 0.004 0 8 -10000 0 8
MAPK8 -0.002 0.069 -10000 0 -0.56 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.033 0.079 8 -0.098 9 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.042 0.018 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.022 0.008 -10000 0 0 16 16
CRKL 0.006 0.071 0.2 3 -0.36 3 6
mol:PIP3 -0.02 0.15 -10000 0 -0.8 5 5
AKT1 -0.031 0.13 -10000 0 -0.71 5 5
PTK2B -0.015 0.006 0 18 -10000 0 18
RAPGEF1 0.006 0.081 0.2 6 -0.31 4 10
RANBP10 -0.017 0.002 0 3 -10000 0 3
PIK3CA -0.016 0.004 0 10 -10000 0 10
HGF/MET/SHIP2 0.03 0.011 -10000 0 0 17 17
MAP3K5 0.005 0.086 0.18 6 -0.3 6 12
HGF/MET/CIN85/CBL/ENDOPHILINS 0.038 0.014 -10000 0 0 16 16
AP1 -0.014 0.037 0.1 11 -10000 0 11
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.016 0.004 0 9 -10000 0 9
apoptosis -0.004 0.14 -10000 0 -0.72 5 5
STAT3 (dimer) -0.003 0.043 -10000 0 -0.17 5 5
GAB1/CRKL/SHP2/PI3K 0.027 0.073 0.23 2 -0.33 3 5
INPP5D -0.017 0.002 0 2 -10000 0 2
CBL/CRK 0.014 0.069 0.17 2 -0.3 4 6
PTPN11 -0.017 0.002 0 3 -10000 0 3
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.015 0.005 0 15 -10000 0 15
PTEN -0.016 0.004 0 10 -10000 0 10
ELK1 0.014 0.099 0.3 14 -10000 0 14
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.035 -10000 0 -0.18 4 4
PAK1 -0.032 0.13 -10000 0 -0.68 5 5
HGF/MET/RANBP10 0.03 0.011 -10000 0 0 15 15
HRAS -0.01 0.083 -10000 0 -0.38 6 6
DOCK1 0.004 0.08 0.21 5 -0.32 4 9
GAB1 0.008 0.052 0.16 2 -0.32 2 4
CRK 0.005 0.068 0.17 2 -0.36 3 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.066 -10000 0 -0.32 5 5
JUN -0.016 0.003 0 4 -10000 0 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.001 0.015 -10000 0 -0.052 11 11
PIK3R1 -0.016 0.004 0 9 -10000 0 9
cell morphogenesis 0.011 0.083 0.24 8 -0.27 2 10
GRB2/SHC 0.015 0.028 0.085 3 -0.064 12 15
FOS -0.016 0.003 0 4 -10000 0 4
GLMN 0.001 0 -10000 0 -10000 0 0
cell motility 0.014 0.098 0.3 14 -10000 0 14
HGF/MET/MUC20 0.02 0.007 -10000 0 0 13 13
cell migration 0.014 0.027 0.083 3 -0.063 12 15
GRB2 -0.016 0.003 0 6 -10000 0 6
CBL -0.016 0.003 0 6 -10000 0 6
MET/RANBP10 0.022 0.008 -10000 0 0 14 14
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.003 0.021 -10000 0 -0.17 2 2
MET/MUC20 0.011 0.003 -10000 0 0 12 12
RAP1B 0.017 0.09 0.23 7 -0.34 3 10
RAP1A 0.005 0.071 0.2 4 -0.38 2 6
HGF/MET/RANBP9 0.03 0.011 -10000 0 0 17 17
RAF1 -0.007 0.087 0.18 3 -0.36 6 9
STAT3 -0.009 0.036 -10000 0 -0.17 5 5
cell proliferation 0.007 0.058 0.17 12 -0.2 1 13
RPS6KB1 0.001 0.029 -10000 0 -0.27 1 1
MAPK3 0.013 0.12 0.42 8 -10000 0 8
MAPK1 0.01 0.11 0.35 10 -10000 0 10
RANBP9 -0.016 0.004 0 8 -10000 0 8
MAPK8 0.003 0.085 0.19 2 -0.29 7 9
SRC -0.012 0.019 -10000 0 -0.11 4 4
PI3K 0.015 0.028 0.085 3 -0.068 10 13
MET/Glomulin 0.005 0.027 0.077 1 -0.074 12 13
SOS1 -0.017 0 -10000 0 -10000 0 0
MAP2K1 -0.012 0.085 0.16 4 -0.33 7 11
MET -0.015 0.005 0 12 -10000 0 12
MAP4K1 0.007 0.09 0.19 4 -0.32 6 10
PTK2 -0.014 0.006 0 22 -10000 0 22
MAP2K2 -0.011 0.081 0.16 3 -0.34 6 9
BAD -0.035 0.13 -10000 0 -0.68 5 5
MAP2K4 0 0.079 0.19 2 -0.27 6 8
SHP2/GRB2/SOS1/GAB1 0.019 0.059 -10000 0 -0.28 4 4
INPPL1 -0.016 0.003 0 5 -10000 0 5
PXN -0.016 0.003 0 4 -10000 0 4
SH3KBP1 -0.017 0 -10000 0 -10000 0 0
HGS -0.01 0.011 -10000 0 -0.053 8 8
PLCgamma1/PKC 0.011 0.004 -10000 0 0 15 15
HGF -0.016 0.003 0 5 -10000 0 5
RASA1 -0.016 0.004 0 9 -10000 0 9
NCK1 -0.017 0.002 0 2 -10000 0 2
PTPRJ -0.017 0.002 0 3 -10000 0 3
NCK/PLCgamma1 0.02 0.022 0.084 4 -0.094 3 7
PDPK1 -0.026 0.14 -10000 0 -0.75 5 5
HGF/MET/SHIP 0.03 0.01 -10000 0 0 14 14
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 -0.016 0.005 0 11 -10000 0 11
NFATC1 -0.02 0.097 0.16 2 -0.26 13 15
NFATC2 -0.007 0.048 0.11 3 -0.15 8 11
NFATC3 0.006 0.002 -10000 0 0 13 13
YWHAE -0.016 0.004 0 7 -10000 0 7
Calcineurin A alpha-beta B1/CABIN1 -0.009 0.054 0.14 1 -0.26 4 5
Exportin 1/Ran/NUP214 0.032 0.007 -10000 0 0 7 7
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.013 0.046 0.12 1 -0.13 9 10
BCL2/BAX 0.021 0.008 -10000 0 0 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.002 -10000 0 0 4 4
CaM/Ca2+ 0.012 0.002 -10000 0 0 4 4
BAX -0.016 0.004 0 7 -10000 0 7
MAPK14 -0.016 0.003 0 6 -10000 0 6
BAD -0.017 0.002 0 2 -10000 0 2
CABIN1/MEF2D 0.002 0.047 0.14 1 -0.21 4 5
Calcineurin A alpha-beta B1/BCL2 -0.016 0.005 0 11 -10000 0 11
FKBP8 -0.017 0.002 0 3 -10000 0 3
activation-induced cell death of T cells -0.002 0.047 0.2 4 -0.13 1 5
KPNB1 -0.016 0.003 0 5 -10000 0 5
KPNA2 -0.016 0.003 0 5 -10000 0 5
XPO1 -0.017 0.001 0 1 -10000 0 1
SFN -0.016 0.004 0 9 -10000 0 9
MAP3K8 -0.016 0.003 0 6 -10000 0 6
NFAT4/CK1 alpha -0.022 0.01 -10000 0 -0.055 3 3
MEF2D/NFAT1/Cbp/p300 0.015 0.049 -10000 0 -0.14 7 7
CABIN1 -0.009 0.054 0.14 1 -0.26 4 5
CALM1 -0.016 0.003 0 4 -10000 0 4
RAN -0.017 0.002 0 2 -10000 0 2
MAP3K1 -0.016 0.005 0 11 -10000 0 11
CAMK4 -0.016 0.005 0 11 -10000 0 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 -0.017 0.002 0 2 -10000 0 2
YWHAH -0.017 0.002 0 3 -10000 0 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.005 -10000 0 0 7 7
YWHAB -0.015 0.006 0 19 -10000 0 19
MAPK8 -0.017 0.002 0 2 -10000 0 2
MAPK9 -0.016 0.003 0 6 -10000 0 6
YWHAG -0.016 0.003 0 6 -10000 0 6
FKBP1A -0.015 0.006 0 17 -10000 0 17
NFAT1-c-4/YWHAQ -0.024 0.091 0.14 3 -0.29 9 12
PRKCH -0.016 0.003 0 4 -10000 0 4
CABIN1/Cbp/p300 0.023 0.006 -10000 0 0 9 9
CASP3 -0.015 0.006 0 17 -10000 0 17
PIM1 -0.016 0.004 0 8 -10000 0 8
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.004 -10000 0 0 17 17
apoptosis 0.008 0.008 -10000 0 -0.052 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.018 -10000 0 -0.083 6 6
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE -0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.034 -10000 0 -0.14 6 6
BAD/BCL-XL 0.023 0.007 -10000 0 0 12 12
PRKCD -0.016 0.003 0 6 -10000 0 6
NUP214 -0.016 0.003 0 4 -10000 0 4
PRKCZ -0.016 0.004 0 9 -10000 0 9
PRKCA -0.016 0.003 0 5 -10000 0 5
PRKCG -0.016 0.004 0 7 -10000 0 7
PRKCQ -0.016 0.003 0 5 -10000 0 5
FKBP38/BCL2 0.022 0.008 -10000 0 0 14 14
EP300 -0.016 0.003 0 4 -10000 0 4
PRKCB1 -0.016 0.003 0 4 -10000 0 4
CSNK2A1 -0.015 0.005 0 16 -10000 0 16
NFATc/JNK1 -0.012 0.095 0.16 2 -0.25 13 15
CaM/Ca2+/FKBP38 0.022 0.005 -10000 0 0 6 6
FKBP12/FK506 0.011 0.004 -10000 0 0 17 17
CSNK1A1 -0.015 0.005 0 12 -10000 0 12
CaM/Ca2+/CAMK IV 0.02 0.007 -10000 0 0 14 14
NFATc/ERK1 -0.01 0.096 0.16 2 -0.25 13 15
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.013 0.051 0.12 1 -0.14 9 10
NR4A1 -0.023 0.035 0.075 2 -0.14 6 8
GSK3B -0.017 0.002 0 2 -10000 0 2
positive T cell selection 0.006 0.002 -10000 0 0 13 13
NFAT1/CK1 alpha -0.006 0.032 0.055 15 -0.11 5 20
RCH1/ KPNB1 0.023 0.005 -10000 0 0 7 7
YWHAQ -0.017 0.001 0 1 -10000 0 1
PRKACA -0.016 0.003 0 5 -10000 0 5
AKAP5 -0.016 0.003 0 4 -10000 0 4
MEF2D -0.016 0.004 0 8 -10000 0 8
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.013 0.007 0 29 -10000 0 29
NFATc/p38 alpha -0.009 0.093 0.16 2 -0.25 13 15
CREBBP -0.016 0.003 0 5 -10000 0 5
BCL2 -0.016 0.005 0 11 -10000 0 11
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.025 0.05 -10000 0 -0.14 10 10
Ran/GTP/Exportin 1/HDAC1 -0.021 0.006 0 10 -10000 0 10
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.065 0.15 1 -0.19 11 12
SUMO1 -0.017 0.002 0 2 -10000 0 2
ZFPM1 -0.016 0.003 0 6 -10000 0 6
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.001 -10000 0 -10000 0 0
FKBP3 -0.016 0.003 0 4 -10000 0 4
Histones 0.027 0.039 -10000 0 -0.13 6 6
YY1/LSF 0.007 0.036 0.086 4 -0.11 9 13
SMG5 0 0 -10000 0 -10000 0 0
RAN -0.017 0.002 0 2 -10000 0 2
I kappa B alpha/HDAC3 -0.009 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.011 0.035 0.087 5 -0.14 5 10
SAP18 -0.017 0.002 0 2 -10000 0 2
RELA 0.007 0.036 0.17 5 -0.078 2 7
HDAC1/Smad7 0.026 0.014 -10000 0 0 32 32
RANGAP1 -0.017 0.002 0 3 -10000 0 3
HDAC3/TR2 0.011 0.035 0.087 5 -0.14 5 10
NuRD/MBD3 Complex -0.004 0.035 -10000 0 -0.13 7 7
NF kappa B1 p50/RelA 0.003 0.074 0.2 3 -0.24 8 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.017 0.002 0 2 -10000 0 2
GATA1 -0.017 0 -10000 0 -10000 0 0
Mad/Max 0.024 0.005 -10000 0 0 6 6
NuRD/MBD3 Complex/GATA1/Fog1 -0.013 0.04 -10000 0 -0.2 5 5
RBBP7 -0.017 0 -10000 0 -10000 0 0
NPC 0.01 0.001 -10000 0 0 2 2
RBBP4 -0.016 0.003 0 6 -10000 0 6
MAX -0.016 0.003 0 5 -10000 0 5
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 -0.016 0.004 0 7 -10000 0 7
NFKBIA -0.005 0.002 0 20 -10000 0 20
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.012 0.037 -10000 0 -0.11 11 11
SIN3 complex 0.038 0.014 -10000 0 0 17 17
SMURF1 -0.015 0.005 0 16 -10000 0 16
CHD3 -0.016 0.004 0 8 -10000 0 8
SAP30 -0.016 0.005 0 11 -10000 0 11
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 -0.015 0.005 0 12 -10000 0 12
YY1/HDAC3 -0.009 0.034 0.075 4 -0.12 7 11
YY1/HDAC2 0.009 0.032 0.086 4 -0.11 7 11
YY1/HDAC1 0.008 0.033 0.086 4 -0.12 7 11
NuRD/MBD2 Complex (MeCP1) -0.005 0.032 -10000 0 -0.11 9 9
PPARG -0.001 0.027 0.12 4 -0.097 4 8
HDAC8/hEST1B 0.022 0.004 -10000 0 0 5 5
UBE2I -0.016 0.003 0 5 -10000 0 5
beta TrCP1/SCF ubiquitin ligase complex -0.016 0.004 0 7 -10000 0 7
TNFRSF1A -0.016 0.004 0 9 -10000 0 9
HDAC3/SMRT (N-CoR2) 0.012 0.033 0.087 5 -0.15 4 9
MBD3L2 -0.016 0.003 0 6 -10000 0 6
ubiquitin-dependent protein catabolic process 0.026 0.014 -10000 0 0 32 32
CREBBP -0.016 0.003 0 5 -10000 0 5
NuRD/MBD3/MBD3L2 Complex -0.018 0.074 -10000 0 -0.29 7 7
HDAC1 -0.016 0.003 0 6 -10000 0 6
HDAC3 -0.005 0.002 0 21 -10000 0 21
HDAC2 -0.016 0.003 0 5 -10000 0 5
YY1 -0.002 0.001 -10000 0 -10000 0 0
HDAC8 -0.017 0 -10000 0 -10000 0 0
SMAD7 -0.015 0.005 0 16 -10000 0 16
NCOR2 -0.017 0.002 0 3 -10000 0 3
MXD1 -0.017 0.001 0 1 -10000 0 1
STAT3 0.005 0.002 -10000 0 0 13 13
NFKB1 -0.017 0.002 0 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.017 0.002 0 2 -10000 0 2
YY1/LSF/HDAC1 0.016 0.035 -10000 0 -0.1 9 9
YY1/SAP30/HDAC1 0.016 0.033 -10000 0 -0.1 8 8
EP300 -0.016 0.003 0 4 -10000 0 4
STAT3 (dimer non-phopshorylated) 0.005 0.002 -10000 0 0 13 13
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.002 0 20 -10000 0 20
histone deacetylation -0.005 0.032 -10000 0 -0.11 9 9
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.027 -10000 0 -0.14 4 4
nuclear export -0.021 0.004 0 5 -10000 0 5
PRKACA -0.016 0.003 0 5 -10000 0 5
GATAD2B -0.016 0.004 0 10 -10000 0 10
GATAD2A -0.016 0.003 0 4 -10000 0 4
GATA2/HDAC3 0.009 0.038 0.087 5 -0.14 6 11
GATA1/HDAC1 0.024 0.005 -10000 0 0 6 6
GATA1/HDAC3 0.009 0.038 0.087 5 -0.14 6 11
CHD4 -0.016 0.004 0 9 -10000 0 9
TNF-alpha/TNFR1A 0.022 0.008 -10000 0 0 16 16
SIN3/HDAC complex/Mad/Max -0.014 0.068 -10000 0 -0.36 4 4
NuRD Complex -0.02 0.07 -10000 0 -0.26 8 8
positive regulation of chromatin silencing 0.025 0.039 -10000 0 -0.13 6 6
SIN3B -0.017 0.002 0 3 -10000 0 3
MTA2 -0.017 0.002 0 3 -10000 0 3
SIN3A -0.016 0.003 0 4 -10000 0 4
XPO1 -0.017 0.001 0 1 -10000 0 1
SUMO1/HDAC1 0.019 0.024 0.085 4 -0.087 5 9
HDAC complex 0.04 0.011 -10000 0 0 9 9
GATA1/Fog1 0.024 0.005 -10000 0 0 6 6
FKBP25/HDAC1/HDAC2 0.032 0.008 -10000 0 0 9 9
TNF -0.016 0.004 0 10 -10000 0 10
negative regulation of cell growth -0.014 0.067 -10000 0 -0.36 4 4
NuRD/MBD2/PRMT5 Complex -0.005 0.032 -10000 0 -0.11 9 9
Ran/GTP/Exportin 1 0.017 0.026 -10000 0 -0.079 8 8
NF kappa B/RelA/I kappa B alpha -0.012 0.047 -10000 0 -0.21 6 6
SIN3/HDAC complex/NCoR1 -0.019 0.077 -10000 0 -0.18 18 18
TFCP2 -0.017 0.001 0 1 -10000 0 1
NR2C1 -0.017 0.002 0 2 -10000 0 2
MBD3 -0.016 0.003 0 5 -10000 0 5
MBD2 -0.015 0.005 0 14 -10000 0 14
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.022 0.007 0 13 -10000 0 13
SNTA1 -0.015 0.005 0 12 -10000 0 12
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.021 0.008 0 16 -10000 0 16
MAPK12 -0.014 0.006 0 19 -10000 0 19
CCND1 -0.004 0.043 0.11 3 -0.33 2 5
p38 gamma/SNTA1 -0.012 0.036 0.17 3 -0.12 1 4
MAP2K3 -0.016 0.003 0 5 -10000 0 5
PKN1 -0.016 0.003 0 4 -10000 0 4
G2/M transition checkpoint -0.01 0.031 0.19 3 -10000 0 3
MAP2K6 -0.01 0.003 0 10 -10000 0 10
MAPT -0.006 0.029 0.12 4 -10000 0 4
MAPK13 -0.019 0.006 0 11 -10000 0 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.003 0.001 0 6 -10000 0 6
Paxillin-dependent events mediated by a4b1

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
CRKL -0.016 0.003 0 5 -10000 0 5
Rac1/GDP 0.018 0.009 -10000 0 -0.016 5 5
DOCK1 -0.016 0.003 0 5 -10000 0 5
ITGA4 -0.017 0.002 0 3 -10000 0 3
RAC1 -0.016 0.004 0 9 -10000 0 9
alpha4/beta7 Integrin 0.024 0.004 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.004 0 7 -10000 0 7
alpha4/beta1 Integrin 0.031 0.009 -10000 0 0 10 10
alpha4/beta7 Integrin/Paxillin -0.027 0.007 0 8 -10000 0 8
lamellipodium assembly -0.024 0.068 0.12 2 -0.25 9 11
PIK3CA -0.016 0.004 0 10 -10000 0 10
PI3K 0.021 0.008 -10000 0 0 18 18
ARF6 -0.016 0.003 0 6 -10000 0 6
TLN1 -0.016 0.004 0 10 -10000 0 10
PXN -0.019 0.005 0 7 -10000 0 7
PIK3R1 -0.016 0.004 0 9 -10000 0 9
ARF6/GTP -0.031 0.011 -10000 0 -10000 0 0
cell adhesion -0.028 0.011 0 17 -10000 0 17
CRKL/CBL 0.023 0.006 -10000 0 0 9 9
alpha4/beta1 Integrin/Paxillin -0.026 0.008 0 11 -10000 0 11
ITGB1 -0.017 0.002 0 3 -10000 0 3
ITGB7 -0.017 0.001 0 1 -10000 0 1
ARF6/GDP 0.018 0.009 -10000 0 -0.017 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.029 0.01 -10000 0 -10000 0 0
p130Cas/Crk/Dock1 0.03 0.011 -10000 0 0 16 16
VCAM1 -0.016 0.003 0 6 -10000 0 6
alpha4/beta1 Integrin/Paxillin/Talin -0.028 0.011 0 17 -10000 0 17
alpha4/beta1 Integrin/Paxillin/GIT1 -0.029 0.01 -10000 0 -10000 0 0
BCAR1 -0.016 0.003 0 5 -10000 0 5
mol:GDP 0.029 0.01 -10000 0 -10000 0 0
CBL -0.016 0.003 0 6 -10000 0 6
PRKACA -0.016 0.003 0 5 -10000 0 5
GIT1 -0.016 0.003 0 4 -10000 0 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.028 0.011 0 17 -10000 0 17
Rac1/GTP -0.026 0.075 0.12 2 -0.27 9 11
Integrins in angiogenesis

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.012 0.002 -10000 0 0 5 5
alphaV beta3 Integrin 0.031 0.009 -10000 0 0 10 10
PTK2 0.016 0.077 0.2 15 -0.15 2 17
IGF1R -0.016 0.003 0 5 -10000 0 5
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 -0.016 0.004 0 7 -10000 0 7
SRC -0.015 0.005 0 13 -10000 0 13
CDKN1B 0.006 0.004 -10000 0 -0.013 4 4
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.006 0.003 -10000 0 -0.013 3 3
ROCK1 -0.016 0.004 0 7 -10000 0 7
AKT1 -0.01 0.004 -10000 0 -10000 0 0
PTK2B -0.014 0.039 0.16 6 -10000 0 6
alphaV/beta3 Integrin/JAM-A -0.028 0.011 -10000 0 -10000 0 0
CBL -0.016 0.003 0 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.031 0.009 -10000 0 0 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.038 0.013 -10000 0 0 14 14
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.008 0.025 -10000 0 -0.11 7 7
alphaV/beta3 Integrin/Syndecan-1 0.032 0.008 -10000 0 0 8 8
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.036 0.014 -10000 0 -10000 0 0
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA -0.016 0.004 0 10 -10000 0 10
alphaV/beta3 Integrin/Osteopontin 0.031 0.009 -10000 0 0 10 10
RPS6KB1 -0.028 0.057 0.31 2 -10000 0 2
TLN1 -0.016 0.004 0 10 -10000 0 10
MAPK3 -0.016 0.041 -10000 0 -0.23 4 4
GPR124 -0.015 0.005 0 16 -10000 0 16
MAPK1 -0.016 0.042 -10000 0 -0.24 4 4
PXN -0.016 0.003 0 4 -10000 0 4
PIK3R1 -0.016 0.004 0 9 -10000 0 9
alphaV/beta3 Integrin/Tumstatin 0.031 0.01 -10000 0 0 12 12
cell adhesion 0.022 0.011 -10000 0 -0.031 2 2
ANGPTL3 -0.017 0.002 0 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.007 -10000 0 0 16 16
IGF-1R heterotetramer -0.016 0.003 0 5 -10000 0 5
Rac1/GDP 0.012 0.003 -10000 0 0 9 9
TGFBR2 -0.016 0.003 0 6 -10000 0 6
ITGB3 -0.016 0.003 0 4 -10000 0 4
IGF1 -0.016 0.003 0 4 -10000 0 4
RAC1 -0.016 0.004 0 9 -10000 0 9
regulation of cell-matrix adhesion 0.028 0.013 -10000 0 0 23 23
apoptosis -0.016 0.003 0 4 -10000 0 4
CD47 -0.017 0.002 0 2 -10000 0 2
alphaV/beta3 Integrin/CD47 0.031 0.009 -10000 0 0 10 10
VCL -0.016 0.003 0 6 -10000 0 6
alphaV/beta3 Integrin/Del1 0.03 0.011 -10000 0 0 15 15
CSF1 -0.016 0.003 0 5 -10000 0 5
PIK3C2A 0.006 0.003 -10000 0 -0.013 3 3
PI4 Kinase/Pyk2 -0.027 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.009 -10000 0 0 13 13
FAK1/Vinculin 0.016 0.075 0.18 17 -0.14 2 19
alphaV beta3/Integrin/ppsTEM5 0.028 0.013 -10000 0 0 23 23
RHOA -0.016 0.003 0 5 -10000 0 5
VTN -0.016 0.003 0 4 -10000 0 4
BCAR1 -0.016 0.003 0 5 -10000 0 5
FGF2 -0.017 0.002 0 3 -10000 0 3
F11R -0.019 0.005 0 9 -10000 0 9
alphaV/beta3 Integrin/Lactadherin 0.03 0.01 -10000 0 0 14 14
alphaV/beta3 Integrin/TGFBR2 0.03 0.01 -10000 0 0 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.039 0.013 -10000 0 0 13 13
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.028 0.011 -10000 0 0 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.016 0.003 0 4 -10000 0 4
alphaV/beta3 Integrin/Pyk2 -0.021 0.01 0 27 -10000 0 27
SDC1 -0.017 0 -10000 0 -10000 0 0
VAV3 -0.027 0.024 0.16 2 -10000 0 2
PTPN11 -0.017 0.002 0 3 -10000 0 3
IRS1 -0.016 0.003 0 5 -10000 0 5
FAK1/Paxillin 0.016 0.075 0.18 16 -0.14 2 18
cell migration 0.011 0.071 0.17 16 -0.13 2 18
ITGAV -0.016 0.003 0 4 -10000 0 4
PI3K -0.033 0.016 -10000 0 -10000 0 0
SPP1 -0.017 0.002 0 2 -10000 0 2
KDR -0.016 0.003 0 5 -10000 0 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.016 0.003 0 4 -10000 0 4
COL4A3 -0.016 0.003 0 4 -10000 0 4
angiogenesis -0.004 0.065 0.16 10 -0.26 4 14
Rac1/GTP -0.028 0.025 0.15 2 -10000 0 2
EDIL3 -0.016 0.004 0 9 -10000 0 9
cell proliferation 0.03 0.01 -10000 0 0 14 14
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.015 0.005 0 15 -10000 0 15
Caspase 8 (4 units) 0.018 0.04 -10000 0 -0.1 11 11
NEF 0 0 -10000 0 -10000 0 0
NFKBIA -0.017 0.002 0 3 -10000 0 3
BIRC3 -0.025 0.018 0.16 1 -10000 0 1
CYCS -0.011 0.023 0.056 8 -0.12 2 10
RIPK1 -0.016 0.004 0 7 -10000 0 7
CD247 0 0 -10000 0 -10000 0 0
MAP2K7 -0.018 0.14 -10000 0 -0.49 9 9
protein ubiquitination -0.011 0.084 0.17 7 -0.23 9 16
CRADD -0.017 0.002 0 2 -10000 0 2
DAXX -0.016 0.004 0 7 -10000 0 7
FAS -0.016 0.003 0 4 -10000 0 4
BID -0.007 0.023 0.065 8 -0.12 2 10
NF-kappa-B/RelA/I kappa B alpha 0.032 0.007 -10000 0 0 7 7
TRADD -0.017 0.002 0 3 -10000 0 3
MAP3K5 -0.016 0.004 0 8 -10000 0 8
CFLAR -0.017 0.002 0 2 -10000 0 2
FADD -0.016 0.004 0 9 -10000 0 9
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.032 0.007 -10000 0 0 7 7
MAPK8 -0.022 0.13 -10000 0 -0.46 9 9
APAF1 -0.017 0.002 0 2 -10000 0 2
TRAF1 -0.016 0.003 0 4 -10000 0 4
TRAF2 -0.016 0.004 0 7 -10000 0 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.001 0.02 0.073 8 -0.084 1 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.019 0.09 -10000 0 -0.32 7 7
CHUK -0.013 0.091 0.18 7 -0.25 9 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.041 0.019 -10000 0 -10000 0 0
TCRz/NEF 0 0 -10000 0 -10000 0 0
TNF -0.016 0.004 0 10 -10000 0 10
FASLG -0.008 0.002 0 5 -10000 0 5
NFKB1 -0.017 0.002 0 2 -10000 0 2
TNFR1A/BAG4/TNF-alpha 0.027 0.013 -10000 0 0 27 27
CASP6 0.002 0.1 -10000 0 -0.47 5 5
CASP7 -0.019 0.054 0.19 1 -0.21 6 7
RELA -0.017 0.002 0 3 -10000 0 3
CASP2 -0.016 0.004 0 9 -10000 0 9
CASP3 -0.03 0.069 0.19 1 -0.2 14 15
TNFRSF1A -0.016 0.004 0 9 -10000 0 9
TNFR1A/BAG4 0.021 0.009 -10000 0 0 22 22
CASP8 -0.017 0.002 0 2 -10000 0 2
CASP9 -0.016 0.004 0 7 -10000 0 7
MAP3K14 -0.018 0.089 0.16 2 -0.27 9 11
APAF-1/Caspase 9 -0.03 0.04 0.099 6 -0.15 2 8
BCL2 -0.025 0.12 0.25 1 -0.42 9 10
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.023 0.006 -10000 0 0 8 8
AKT1 0 0.053 0.17 6 -0.15 1 7
PTK2B -0.018 0.038 0.15 6 -10000 0 6
VEGFR2 homodimer/Frs2 -0.021 0.008 0 16 -10000 0 16
CAV1 -0.015 0.005 0 12 -10000 0 12
CALM1 -0.016 0.003 0 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.019 0.007 0 16 -10000 0 16
endothelial cell proliferation 0.005 0.078 0.2 11 -0.2 2 13
mol:Ca2+ -0.019 0.024 0.16 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.022 0.009 0 21 -10000 0 21
RP11-342D11.1 -0.018 0.005 0 10 -10000 0 10
CDH5 -0.017 0.002 0 3 -10000 0 3
VEGFA homodimer 0.029 0.01 -10000 0 0 15 15
SHC1 -0.016 0.004 0 9 -10000 0 9
SHC2 -0.016 0.003 0 6 -10000 0 6
HRAS/GDP -0.033 0.014 -10000 0 -10000 0 0
SH2D2A -0.016 0.004 0 7 -10000 0 7
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.016 0.084 0.15 6 -0.29 8 14
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.019 0.006 0 11 -10000 0 11
VEGFR1 homodimer -0.016 0.003 0 4 -10000 0 4
SHC/GRB2/SOS1 -0.031 0.012 -10000 0 -10000 0 0
GRB10 -0.021 0.024 0.16 2 -10000 0 2
PTPN11 -0.017 0.002 0 3 -10000 0 3
GRB2 -0.016 0.003 0 6 -10000 0 6
PAK1 -0.017 0.002 0 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.025 0.012 -10000 0 -10000 0 0
HRAS -0.016 0.004 0 9 -10000 0 9
VEGF/Rho/ROCK1/Integrin Complex -0.012 0.037 -10000 0 -0.18 5 5
HIF1A -0.016 0.003 0 4 -10000 0 4
FRS2 -0.015 0.005 0 12 -10000 0 12
oxygen and reactive oxygen species metabolic process -0.022 0.009 0 21 -10000 0 21
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.016 0.003 0 5 -10000 0 5
Nck/Pak 0.024 0.005 -10000 0 0 5 5
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.02 0.005 0 9 -10000 0 9
mol:GDP -0.03 0.012 -10000 0 -10000 0 0
mol:NADP -0.01 0.084 -10000 0 -0.28 8 8
eNOS/Hsp90 -0.01 0.08 -10000 0 -0.27 8 8
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:IP3 -0.019 0.024 0.16 2 -10000 0 2
HIF1A/ARNT 0.022 0.008 -10000 0 0 14 14
SHB -0.016 0.003 0 6 -10000 0 6
VEGFA 0 0 -10000 0 -10000 0 0
VEGFC -0.016 0.005 0 11 -10000 0 11
FAK1/Vinculin 0.003 0.057 0.14 14 -0.13 2 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA -0.016 0.003 0 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.008 0 13 -10000 0 13
PTPN6 -0.016 0.004 0 9 -10000 0 9
EPAS1 -0.017 0 -10000 0 -10000 0 0
mol:L-citrulline -0.01 0.084 -10000 0 -0.28 8 8
ITGAV -0.016 0.003 0 4 -10000 0 4
PIK3CA -0.016 0.004 0 10 -10000 0 10
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.022 0.009 0 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer -0.02 0.006 0 10 -10000 0 10
VEGFR2/3 heterodimer -0.022 0.006 0 10 -10000 0 10
VEGFB -0.017 0.001 0 1 -10000 0 1
MAPK11 -0.016 0.024 0.17 1 -10000 0 1
VEGFR2 homodimer -0.02 0.004 0 5 -10000 0 5
FLT1 -0.016 0.003 0 4 -10000 0 4
NEDD4 -0.016 0.003 0 5 -10000 0 5
MAPK3 -0.009 0.045 0.14 10 -10000 0 10
MAPK1 -0.007 0.049 0.15 11 -10000 0 11
VEGFA145/NRP2 0.012 0.002 -10000 0 0 4 4
VEGFR1/2 heterodimer -0.023 0.006 0 9 -10000 0 9
KDR -0.02 0.004 0 5 -10000 0 5
VEGFA165/NRP1/VEGFR2 homodimer -0.022 0.007 0 13 -10000 0 13
SRC -0.015 0.005 0 13 -10000 0 13
platelet activating factor biosynthetic process -0.004 0.054 0.14 15 -10000 0 15
PI3K -0.023 0.024 0.13 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.02 0.005 0 7 -10000 0 7
FES -0.021 0.024 0.17 2 -10000 0 2
GAB1 -0.018 0.02 0.13 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.019 0.007 0 16 -10000 0 16
CTNNB1 -0.016 0.005 0 11 -10000 0 11
SOS1 -0.017 0 -10000 0 -10000 0 0
ARNT -0.016 0.005 0 11 -10000 0 11
eNOS/Caveolin-1 -0.014 0.074 0.15 2 -0.28 6 8
VEGFR2 homodimer/VEGFA homodimer/Yes -0.02 0.006 0 10 -10000 0 10
PI3K/GAB1 -0.012 0.04 0.12 2 -0.17 4 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.027 0.011 -10000 0 -10000 0 0
PRKACA -0.016 0.003 0 5 -10000 0 5
VEGFR2/3 heterodimer/VEGFC homodimer -0.025 0.009 0 14 -10000 0 14
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 -0.02 0.024 0.17 2 -10000 0 2
actin cytoskeleton reorganization -0.019 0.006 0 11 -10000 0 11
PTK2 -0.004 0.035 0.15 5 -10000 0 5
EDG1 -0.021 0.024 0.16 2 -10000 0 2
mol:DAG -0.019 0.024 0.16 2 -10000 0 2
CaM/Ca2+ -0.022 0.024 0.16 2 -10000 0 2
MAP2K3 -0.025 0.019 0.16 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.021 0.025 0.18 2 -10000 0 2
PLCG1 -0.019 0.024 0.17 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.022 0.009 0 21 -10000 0 21
IQGAP1 -0.016 0.004 0 9 -10000 0 9
YES1 -0.016 0.003 0 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.02 0.005 0 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.019 0.006 0 14 -10000 0 14
cell migration 0.01 0.071 0.17 12 -0.16 4 16
mol:PI-3-4-5-P3 -0.022 0.023 0.12 2 -10000 0 2
FYN -0.016 0.003 0 5 -10000 0 5
VEGFB/NRP1 -0.02 0.022 0.16 2 -10000 0 2
mol:NO -0.01 0.084 -10000 0 -0.28 8 8
PXN -0.016 0.003 0 4 -10000 0 4
HRAS/GTP -0.033 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.024 0.007 0 12 -10000 0 12
VHL -0.017 0.002 0 3 -10000 0 3
ITGB3 -0.016 0.003 0 4 -10000 0 4
NOS3 -0.012 0.091 -10000 0 -0.31 8 8
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.006 0 11 -10000 0 11
RAC1 -0.016 0.004 0 9 -10000 0 9
PRKCA -0.022 0.025 0.16 2 -10000 0 2
PRKCB -0.018 0.023 0.16 2 -10000 0 2
VCL -0.016 0.003 0 6 -10000 0 6
VEGFA165/NRP1 -0.018 0.005 0 10 -10000 0 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.02 0.005 0 9 -10000 0 9
VEGFA165/NRP2 0.012 0.002 -10000 0 0 4 4
MAPKKK cascade -0.025 0.05 0.14 11 -10000 0 11
NRP2 -0.016 0.003 0 4 -10000 0 4
VEGFC homodimer -0.016 0.005 0 11 -10000 0 11
NCK1 -0.017 0.002 0 2 -10000 0 2
ROCK1 -0.016 0.004 0 7 -10000 0 7
FAK1/Paxillin 0.004 0.056 0.14 13 -0.13 2 15
MAP3K13 -0.02 0.024 0.17 2 -10000 0 2
PDPK1 -0.018 0.037 0.09 12 -10000 0 12
IL27-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
TGFB1 -0.016 0.004 0 9 -10000 0 9
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.017 0.068 0.2 15 -10000 0 15
IL27/IL27R/JAK1 0.031 0.021 0.18 1 -10000 0 1
TBX21 -0.022 0.036 0.16 2 -10000 0 2
IL12B -0.016 0.004 0 8 -10000 0 8
IL12A -0.01 0.002 0 7 -10000 0 7
IL6ST -0.012 0.013 0.027 1 -10000 0 1
IL27RA/JAK1 0.006 0.022 0.2 1 -10000 0 1
IL27 -0.012 0.013 0.027 1 -10000 0 1
TYK2 -0.012 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.007 0.048 0.18 9 -0.1 3 12
T-helper 2 cell differentiation 0.017 0.068 0.2 15 -10000 0 15
T cell proliferation during immune response 0.017 0.068 0.2 15 -10000 0 15
MAPKKK cascade -0.017 0.068 -10000 0 -0.2 15 15
STAT3 -0.016 0.003 0 5 -10000 0 5
STAT2 -0.017 0.002 0 3 -10000 0 3
STAT1 -0.017 0.002 0 3 -10000 0 3
IL12RB1 -0.017 0.002 0 3 -10000 0 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.022 0.037 0.14 3 -10000 0 3
IL27/IL27R/JAK2/TYK2 -0.017 0.068 -10000 0 -0.2 15 15
positive regulation of T cell mediated cytotoxicity -0.017 0.068 -10000 0 -0.2 15 15
STAT1 (dimer) 0.024 0.033 -10000 0 -0.083 9 9
JAK2 -0.013 0.01 0.021 7 -10000 0 7
JAK1 -0.017 0.002 0 3 -10000 0 3
STAT2 (dimer) -0.009 0.075 0.19 1 -0.21 14 15
T cell proliferation -0.023 0.061 -10000 0 -0.19 14 14
IL12/IL12R/TYK2/JAK2 -0.04 0.2 -10000 0 -0.74 10 10
IL17A 0.009 0.047 0.18 9 -0.1 1 10
mast cell activation 0.017 0.068 0.2 15 -10000 0 15
IFNG -0.003 0.022 0.045 1 -0.061 12 13
T cell differentiation -0.001 0.002 -10000 0 -0.007 10 10
STAT3 (dimer) -0.011 0.077 0.19 1 -0.2 16 17
STAT5A (dimer) -0.011 0.077 0.19 1 -0.2 16 17
STAT4 (dimer) -0.012 0.077 0.19 1 -0.2 16 17
STAT4 -0.017 0.002 0 3 -10000 0 3
T cell activation -0.001 0.002 -10000 0 -0.007 10 10
IL27R/JAK2/TYK2 0.02 0.012 -10000 0 -10000 0 0
GATA3 -0.006 0.052 0.58 1 -10000 0 1
IL18 -0.01 0.002 0 7 -10000 0 7
positive regulation of mast cell cytokine production -0.01 0.076 0.19 1 -0.2 16 17
IL27/EBI3 0.024 0.008 0.041 10 0 8 18
IL27RA -0.001 0.022 0.25 1 -10000 0 1
IL6 -0.016 0.003 0 6 -10000 0 6
STAT5A -0.016 0.003 0 6 -10000 0 6
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.008 -10000 0 -10000 0 0
IL1B -0.01 0.002 0 4 -10000 0 4
EBI3 -0.01 0.016 0.029 13 -10000 0 13
TNF -0.01 0.003 0 10 -10000 0 10
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.007 0.07 0.18 13 -0.14 5 18
CRP 0.002 0.072 0.23 8 -0.14 5 13
cell cycle arrest 0 0.051 0.15 5 -0.14 4 9
TIMP1 0.01 0.047 -10000 0 -10000 0 0
IL6ST -0.016 0.004 0 10 -10000 0 10
Rac1/GDP -0.012 0.032 -10000 0 -0.16 1 1
AP1 0.028 0.055 -10000 0 -0.26 3 3
GAB2 -0.016 0.003 0 4 -10000 0 4
TNFSF11 0.001 0.063 0.18 8 -0.14 5 13
HSP90B1 0.006 0.013 -10000 0 -10000 0 0
GAB1 -0.016 0.003 0 4 -10000 0 4
MAPK14 -0.017 0.015 -10000 0 -0.091 4 4
AKT1 0.001 0.044 -10000 0 -0.28 3 3
FOXO1 -0.002 0.046 -10000 0 -0.25 4 4
MAP2K6 -0.013 0.014 -10000 0 -0.09 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.012 0.037 0.16 2 -0.16 1 3
MITF -0.013 0.016 -10000 0 -0.09 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 -0.016 0.003 0 6 -10000 0 6
A2M -0.021 0.19 -10000 0 -1.1 4 4
CEBPB -0.014 0.007 0 27 -10000 0 27
GRB2/SOS1/GAB family/SHP2 0.011 0.046 -10000 0 -0.25 3 3
STAT3 0.001 0.047 0.15 4 -0.16 2 6
STAT1 0.003 0.083 -10000 0 -0.67 2 2
CEBPD 0.008 0.069 0.18 13 -0.14 4 17
PIK3CA -0.016 0.004 0 10 -10000 0 10
PI3K 0.021 0.008 -10000 0 0 18 18
JUN -0.016 0.003 0 4 -10000 0 4
PIAS3/MITF -0.012 0.037 0.16 1 -0.16 1 2
MAPK11 -0.016 0.015 -10000 0 -0.091 4 4
STAT3 (dimer)/FOXO1 -0.011 0.043 0.13 3 -0.17 5 8
GRB2/SOS1/GAB family 0.035 0.037 -10000 0 -0.13 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.006 0.003 -10000 0 -10000 0 0
GRB2 -0.016 0.003 0 6 -10000 0 6
JAK2 -0.014 0.007 0 25 -10000 0 25
LBP 0.025 0.072 0.17 18 -0.14 2 20
PIK3R1 -0.016 0.004 0 9 -10000 0 9
JAK1 -0.017 0.002 0 3 -10000 0 3
MYC 0.033 0.091 0.18 31 -0.14 1 32
FGG -0.003 0.049 0.14 5 -0.15 2 7
macrophage differentiation 0 0.051 0.15 5 -0.14 4 9
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.035 0.023 -10000 0 -10000 0 0
JUNB -0.003 0.049 0.15 5 -0.13 4 9
FOS -0.016 0.003 0 4 -10000 0 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.006 0.003 -10000 0 -10000 0 0
STAT1/PIAS1 0.012 0.036 0.1 4 -0.13 5 9
GRB2/SOS1/GAB family/SHP2/PI3K 0.008 0.047 -10000 0 -0.29 3 3
STAT3 (dimer) 0.001 0.05 0.15 5 -0.15 3 8
PRKCD -0.007 0.05 0.16 8 -10000 0 8
IL6R -0.016 0.004 0 9 -10000 0 9
SOCS3 -0.004 0.044 0.2 3 -0.13 1 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.03 0.01 -10000 0 0 14 14
Rac1/GTP -0.012 0.03 -10000 0 -0.16 1 1
HCK -0.016 0.005 0 11 -10000 0 11
MAPKKK cascade 0.013 0.06 -10000 0 -0.35 3 3
bone resorption 0.002 0.062 0.18 8 -0.14 4 12
IRF1 -0.002 0.049 0.15 5 -0.13 3 8
mol:GDP -0.012 0.013 -10000 0 -0.089 3 3
SOS1 -0.017 0 -10000 0 -10000 0 0
VAV1 -0.012 0.013 -10000 0 -0.09 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.005 0.042 0.23 1 -0.26 2 3
PTPN11 0.002 0.089 -10000 0 -0.72 2 2
IL6/IL6RA 0.022 0.008 -10000 0 0 15 15
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.011 -10000 0 0 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 0.026 0.014 -10000 0 0 32 32
IL6 -0.016 0.003 0 6 -10000 0 6
PIAS3 -0.016 0.004 0 10 -10000 0 10
PTPRE -0.016 0.003 0 5 -10000 0 5
PIAS1 -0.016 0.003 0 4 -10000 0 4
RAC1 -0.016 0.004 0 9 -10000 0 9
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.005 0.015 -10000 0 -0.17 1 1
LMO4 -0.016 0.003 0 5 -10000 0 5
STAT3 (dimer)/PIAS3 -0.011 0.046 0.13 2 -0.15 6 8
MCL1 0.006 0.062 0.18 9 -0.24 3 12
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.029 -10000 0 -0.27 1 1
KLHL20 0.002 0.04 0.12 1 -0.2 1 2
CYFIP2 -0.016 0.004 0 8 -10000 0 8
Rac1/GDP 0.006 0.062 0.16 12 -0.15 1 13
ENAH -0.005 0.028 -10000 0 -0.27 1 1
AP1M1 -0.016 0.003 0 4 -10000 0 4
RAP1B -0.015 0.005 0 13 -10000 0 13
RAP1A -0.016 0.003 0 5 -10000 0 5
CTNNB1 -0.016 0.005 0 11 -10000 0 11
CDC42/GTP -0.025 0.023 0.053 3 -0.091 1 4
ABI1/Sra1/Nap1 -0.014 0.016 -10000 0 -0.11 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.037 0.015 -10000 0 0 20 20
RAPGEF1 0.002 0.06 0.16 12 -0.21 2 14
CTNND1 -0.017 0.001 0 1 -10000 0 1
regulation of calcium-dependent cell-cell adhesion 0.004 0.036 -10000 0 -0.29 2 2
CRK -0.009 0.032 -10000 0 -0.22 2 2
E-cadherin/gamma catenin/alpha catenin 0.028 0.012 -10000 0 0 22 22
alphaE/beta7 Integrin 0.023 0.006 -10000 0 0 8 8
IQGAP1 -0.016 0.004 0 9 -10000 0 9
NCKAP1 -0.017 0.002 0 3 -10000 0 3
Rap1/GTP/I-afadin 0.027 0.012 -10000 0 0 23 23
DLG1 -0.008 0.038 -10000 0 -0.28 2 2
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.018 -10000 0 -0.076 1 1
MLLT4 -0.016 0.005 0 11 -10000 0 11
ARF6/GTP/NME1/Tiam1 0.029 0.01 -10000 0 0 14 14
PI3K -0.03 0.022 -10000 0 -0.094 1 1
ARF6 -0.016 0.003 0 6 -10000 0 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.022 0.008 -10000 0 0 16 16
TIAM1 -0.016 0.003 0 5 -10000 0 5
E-cadherin(dimer)/Ca2+ 0.033 0.014 -10000 0 0 21 21
AKT1 -0.012 0.033 0.06 11 -10000 0 11
PIK3R1 -0.016 0.004 0 9 -10000 0 9
CDH1 -0.017 0.002 0 3 -10000 0 3
RhoA/GDP 0.007 0.065 0.17 12 -10000 0 12
actin cytoskeleton organization 0.003 0.034 0.12 2 -0.15 1 3
CDC42/GDP 0.008 0.065 0.17 13 -0.15 1 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.002 -10000 0 -10000 0 0
ITGB7 -0.017 0.001 0 1 -10000 0 1
RAC1 -0.016 0.004 0 9 -10000 0 9
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.036 0.015 -10000 0 0 21 21
E-cadherin/Ca2+/beta catenin/alpha catenin 0.025 0.011 -10000 0 0 21 21
mol:GDP 0.008 0.068 0.17 13 -0.16 1 14
CDC42/GTP/IQGAP1 0.02 0.007 -10000 0 0 17 17
JUP -0.015 0.005 0 13 -10000 0 13
p120 catenin/RhoA/GDP 0.004 0.063 0.16 13 -10000 0 13
RAC1/GTP/IQGAP1 0.02 0.007 -10000 0 0 17 17
PIP5K1C/AP1M1 0.023 0.005 -10000 0 0 7 7
RHOA -0.016 0.003 0 5 -10000 0 5
CDC42 -0.016 0.005 0 11 -10000 0 11
CTNNA1 -0.016 0.004 0 9 -10000 0 9
positive regulation of S phase of mitotic cell cycle 0.004 0.032 0.15 3 -0.096 1 4
NME1 -0.016 0.003 0 5 -10000 0 5
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.008 0.039 -10000 0 -0.28 2 2
regulation of cell-cell adhesion -0.023 0.019 0.038 2 -0.082 1 3
WASF2 -0.004 0.018 0.046 2 -0.08 1 3
Rap1/GTP -0.015 0.046 0.12 12 -10000 0 12
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.02 -10000 0 -10000 0 0
CCND1 0.002 0.027 0.1 2 -0.12 1 3
VAV2 0.016 0.078 0.26 2 -0.41 2 4
RAP1/GDP -0.004 0.054 0.15 10 -10000 0 10
adherens junction assembly -0.008 0.038 -10000 0 -0.28 2 2
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 -0.016 0.003 0 6 -10000 0 6
PIP5K1C -0.016 0.003 0 5 -10000 0 5
regulation of heterotypic cell-cell adhesion -0.015 0.052 0.15 11 -10000 0 11
E-cadherin/beta catenin -0.008 0.009 0.011 1 -0.045 6 7
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.005 0.028 -10000 0 -0.27 1 1
PIK3CA -0.016 0.004 0 10 -10000 0 10
Rac1/GTP -0.017 0.032 -10000 0 -0.31 1 1
E-cadherin/beta catenin/alpha catenin 0.029 0.012 -10000 0 0 21 21
ITGAE -0.016 0.004 0 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.004 0.037 -10000 0 -0.29 2 2
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.074 0.12 4 -0.28 6 10
RAD9A -0.016 0.003 0 6 -10000 0 6
AP1 0.023 0.006 -10000 0 0 8 8
IFNAR2 -0.016 0.003 0 4 -10000 0 4
AKT1 0.006 0.002 -10000 0 -10000 0 0
ER alpha/Oestrogen 0.012 0.003 -10000 0 0 8 8
NFX1/SIN3/HDAC complex -0.003 0.043 0.066 3 -0.19 5 8
EGF -0.016 0.003 0 4 -10000 0 4
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.023 0.005 -10000 0 0 7 7
TERT/c-Abl 0.005 0.073 0.12 3 -0.25 7 10
SAP18 -0.017 0.002 0 2 -10000 0 2
MRN complex 0.027 0.013 -10000 0 0 26 26
WT1 -0.016 0.003 0 6 -10000 0 6
WRN -0.015 0.005 0 16 -10000 0 16
SP1 -0.017 0.002 0 3 -10000 0 3
SP3 -0.017 0.002 0 3 -10000 0 3
TERF2IP -0.016 0.003 0 5 -10000 0 5
Telomerase/Nucleolin 0.01 0.07 -10000 0 -0.22 7 7
Mad/Max 0.024 0.005 -10000 0 0 6 6
TERT -0.002 0.075 0.13 4 -0.29 6 10
CCND1 0.001 0.079 0.18 7 -0.26 6 13
MAX -0.016 0.003 0 5 -10000 0 5
RBBP7 -0.017 0 -10000 0 -10000 0 0
RBBP4 -0.016 0.003 0 6 -10000 0 6
TERF2 -0.021 0.011 0.061 2 -10000 0 2
PTGES3 -0.016 0.003 0 4 -10000 0 4
SIN3A -0.016 0.003 0 4 -10000 0 4
Telomerase/911 0.013 0.039 0.11 1 -0.22 2 3
CDKN1B -0.02 0.009 0 24 -10000 0 24
RAD1 -0.015 0.005 0 15 -10000 0 15
XRCC5 -0.016 0.003 0 4 -10000 0 4
XRCC6 -0.016 0.003 0 4 -10000 0 4
SAP30 -0.016 0.005 0 11 -10000 0 11
TRF2/PARP2 -0.022 0.012 0.044 3 -10000 0 3
UBE3A -0.017 0.002 0 3 -10000 0 3
JUN -0.016 0.003 0 4 -10000 0 4
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.002 -10000 0 0 3 3
FOS -0.016 0.003 0 4 -10000 0 4
IFN-gamma/IRF1 0.021 0.009 -10000 0 0 19 19
PARP2 -0.016 0.003 0 5 -10000 0 5
BLM -0.016 0.004 0 9 -10000 0 9
Telomerase 0.003 0.018 -10000 0 -0.077 4 4
IRF1 -0.016 0.004 0 8 -10000 0 8
ESR1 -0.016 0.004 0 8 -10000 0 8
KU/TER 0.023 0.005 -10000 0 0 7 7
ATM/TRF2 0.023 0.005 -10000 0 0 6 6
ubiquitin-dependent protein catabolic process -0.017 0.052 0.071 2 -0.29 4 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.017 0.053 0.071 2 -0.29 4 6
HDAC1 -0.016 0.003 0 6 -10000 0 6
HDAC2 -0.016 0.003 0 5 -10000 0 5
ATM 0.008 0.007 0.063 2 -10000 0 2
SMAD3 -0.019 0.006 0 12 -10000 0 12
ABL1 -0.016 0.003 0 5 -10000 0 5
MXD1 -0.017 0.001 0 1 -10000 0 1
MRE11A -0.017 0.002 0 3 -10000 0 3
HUS1 -0.016 0.003 0 4 -10000 0 4
RPS6KB1 -0.016 0.003 0 5 -10000 0 5
TERT/NF kappa B1/14-3-3 0.013 0.08 0.14 1 -0.23 9 10
NR2F2 -0.016 0.003 0 6 -10000 0 6
MAPK3 -0.02 0.003 0 4 -10000 0 4
MAPK1 -0.019 0.005 0 8 -10000 0 8
TGFB1/TGF beta receptor Type II -0.016 0.004 0 9 -10000 0 9
NFKB1 -0.017 0.002 0 2 -10000 0 2
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.008 0.007 0.063 2 -10000 0 2
NBN -0.014 0.006 0 23 -10000 0 23
EGFR -0.016 0.004 0 10 -10000 0 10
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.022 0.008 -10000 0 0 14 14
MYC -0.013 0.007 0 33 -10000 0 33
IL2 -0.016 0.003 0 4 -10000 0 4
KU 0.023 0.005 -10000 0 0 7 7
RAD50 -0.016 0.004 0 8 -10000 0 8
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 -0.016 0.004 0 9 -10000 0 9
TRF2/BLM -0.022 0.01 0.036 2 -10000 0 2
FRAP1 -0.016 0.004 0 10 -10000 0 10
KU/TERT 0.013 0.073 0.13 3 -0.24 6 9
SP1/HDAC2 0.024 0.005 -10000 0 0 6 6
PINX1 -0.014 0.006 0 23 -10000 0 23
Telomerase/EST1A 0.002 0.065 -10000 0 -0.22 7 7
Smad3/Myc -0.017 0.011 0 40 -10000 0 40
911 complex 0.028 0.013 -10000 0 0 23 23
IFNG -0.015 0.005 0 13 -10000 0 13
Telomerase/PinX1 0.004 0.066 -10000 0 -0.24 6 6
Telomerase/AKT1/mTOR/p70S6K -0.003 0.057 0.098 1 -0.27 5 6
SIN3B -0.017 0.002 0 3 -10000 0 3
YWHAE -0.016 0.004 0 7 -10000 0 7
Telomerase/EST1B 0.002 0.065 -10000 0 -0.22 7 7
response to DNA damage stimulus 0.001 0.014 0.045 1 -0.08 3 4
MRN complex/TRF2/Rap1 0.037 0.02 -10000 0 -0.01 3 3
TRF2/WRN -0.02 0.013 0.062 2 -10000 0 2
Telomerase/hnRNP C1/C2 0.002 0.065 -10000 0 -0.22 7 7
E2F1 -0.015 0.005 0 13 -10000 0 13
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL -0.017 0.002 0 2 -10000 0 2
DKC1 -0.017 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BCR 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
JUN -0.024 0.091 0.3 1 -0.22 17 18
IKBKB -0.006 0.083 0.24 2 -0.24 10 12
AKT1 0.002 0.071 0.22 8 -0.16 1 9
IKBKG 0.002 0.054 0.14 1 -0.24 4 5
CALM1 0.009 0.038 -10000 0 -10000 0 0
PIK3CA -0.016 0.004 0 10 -10000 0 10
MAP3K1 -0.014 0.092 0.24 1 -0.3 8 9
MAP3K7 -0.014 0.008 0.017 7 -10000 0 7
mol:Ca2+ 0.014 0.042 0.14 2 -0.15 1 3
DOK1 -0.017 0.001 0 1 -10000 0 1
AP-1 -0.015 0.06 0.17 1 -0.17 11 12
LYN -0.013 0.009 0.017 9 -10000 0 9
BLNK -0.015 0.007 0.011 9 -10000 0 9
SHC1 -0.016 0.004 0 9 -10000 0 9
BCR complex 0.022 0.008 -10000 0 0 14 14
CD22 -0.008 0.034 -10000 0 -0.29 1 1
CAMK2G 0.007 0.047 0.2 3 -10000 0 3
CSNK2A1 -0.015 0.005 0 16 -10000 0 16
INPP5D -0.015 0.007 0.017 6 -10000 0 6
SHC/GRB2/SOS1 -0.035 0.019 -10000 0 -10000 0 0
GO:0007205 0.014 0.042 0.14 2 -0.15 1 3
SYK -0.015 0.008 0.009 11 -10000 0 11
ELK1 0.008 0.04 -10000 0 -10000 0 0
NFATC1 -0.005 0.065 0.2 3 -0.25 4 7
B-cell antigen/BCR complex 0.022 0.008 -10000 0 0 14 14
PAG1/CSK 0.02 0.01 -10000 0 0 25 25
NFKBIB 0.008 0.032 0.11 1 -0.097 7 8
HRAS 0.007 0.054 0.15 6 -0.18 2 8
NFKBIA 0.008 0.031 0.11 1 -0.094 7 8
NF-kappa-B/RelA/I kappa B beta 0.01 0.027 0.088 2 -0.07 7 9
RasGAP/Csk 0.036 0.022 -10000 0 -10000 0 0
mol:GDP 0.015 0.041 0.14 2 -0.16 1 3
PTEN -0.015 0.005 0.002 11 -10000 0 11
CD79B -0.014 0.01 0.017 11 -10000 0 11
NF-kappa-B/RelA/I kappa B alpha 0.01 0.027 0.088 2 -0.072 6 8
GRB2 -0.016 0.003 0 6 -10000 0 6
PI3K/BCAP/CD19 -0.008 0.071 0.26 1 -0.26 5 6
PIK3R1 -0.016 0.004 0 9 -10000 0 9
mol:IP3 0.015 0.039 0.14 2 -10000 0 2
CSK -0.017 0.002 0 3 -10000 0 3
FOS 0.003 0.041 0.17 1 -10000 0 1
CHUK -0.004 0.062 -10000 0 -0.25 6 6
IBTK -0.016 0.004 0 7 -10000 0 7
CARD11/BCL10/MALT1/TAK1 0.027 0.043 0.16 5 -0.15 1 6
PTPN6 -0.012 0.035 -10000 0 -0.29 1 1
RELA -0.016 0.004 0.004 4 -10000 0 4
BCL2A1 0.006 0.017 0.072 1 -0.059 4 5
VAV2 -0.008 0.044 -10000 0 -0.23 3 3
ubiquitin-dependent protein catabolic process 0.008 0.031 0.11 1 -0.1 6 7
BTK 0.021 0.008 -10000 0 -10000 0 0
CD19 -0.009 0.037 -10000 0 -0.22 2 2
MAP4K1 -0.016 0.004 0 10 -10000 0 10
CD72 -0.016 0.004 0 9 -10000 0 9
PAG1 -0.014 0.006 0 23 -10000 0 23
MAPK14 -0.014 0.086 0.39 1 -0.27 8 9
SH3BP5 -0.017 0.002 0 2 -10000 0 2
PIK3AP1 0.012 0.04 0.14 2 -0.15 3 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.005 0.068 -10000 0 -0.24 7 7
RAF1 0.005 0.057 0.16 7 -0.18 2 9
RasGAP/p62DOK/SHIP 0.035 0.023 -10000 0 -10000 0 0
CD79A -0.015 0.007 0.006 14 -10000 0 14
re-entry into mitotic cell cycle -0.015 0.059 0.16 1 -0.17 11 12
RASA1 -0.016 0.004 0 9 -10000 0 9
MAPK3 -0.003 0.052 0.16 4 -0.16 1 5
MAPK1 -0.002 0.055 0.16 6 -0.17 2 8
CD72/SHP1 -0.004 0.054 0.19 5 -0.28 1 6
NFKB1 -0.016 0.004 0.006 3 -10000 0 3
MAPK8 -0.016 0.082 0.23 1 -0.27 8 9
actin cytoskeleton organization -0.001 0.058 0.17 6 -0.27 2 8
NF-kappa-B/RelA 0.02 0.054 0.21 1 -0.19 4 5
Calcineurin 0.021 0.035 -10000 0 -10000 0 0
PI3K -0.027 0.033 -10000 0 -0.19 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.016 0.032 -10000 0 -0.15 2 2
SOS1 -0.017 0 -10000 0 -10000 0 0
Bam32/HPK1 0.003 0.11 -10000 0 -0.57 4 4
DAPP1 -0.01 0.12 -10000 0 -0.62 4 4
cytokine secretion -0.005 0.062 0.2 3 -0.24 4 7
mol:DAG 0.015 0.039 0.14 2 -10000 0 2
PLCG2 -0.015 0.006 0.007 9 -10000 0 9
MAP2K1 0.001 0.054 0.17 4 -0.18 2 6
B-cell antigen/BCR complex/FcgammaRIIB 0.026 0.015 -10000 0 0 33 33
mol:PI-3-4-5-P3 -0.008 0.054 0.16 5 -0.19 1 6
ETS1 0.006 0.058 0.26 4 -10000 0 4
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.038 0.021 -10000 0 -10000 0 0
B-cell antigen/BCR complex/LYN 0.002 0.033 -10000 0 -0.22 2 2
MALT1 -0.014 0.009 0.017 7 -10000 0 7
TRAF6 -0.014 0.009 0.017 10 -10000 0 10
RAC1 -0.002 0.059 0.17 6 -0.28 2 8
B-cell antigen/BCR complex/LYN/SYK -0.009 0.053 0.18 4 -0.27 1 5
CARD11 0.015 0.051 0.17 6 -0.15 1 7
FCGR2B -0.014 0.006 0 20 -10000 0 20
PPP3CA -0.017 0.002 0 2 -10000 0 2
BCL10 -0.015 0.008 0.017 7 -10000 0 7
IKK complex 0.003 0.039 0.18 2 -0.11 4 6
PTPRC -0.016 0.003 0 4 -10000 0 4
PDPK1 -0.007 0.05 0.18 5 -0.14 1 6
PPP3CB -0.016 0.003 0 5 -10000 0 5
PPP3CC -0.015 0.006 0 18 -10000 0 18
POU2F2 0.006 0.021 0.14 1 -0.056 6 7
EGFR-dependent Endothelin 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
HRAS -0.016 0.004 0 9 -10000 0 9
EGFR -0.016 0.004 0 10 -10000 0 10
EGF/EGFR 0.028 0.011 -10000 0 0 19 19
EGF/EGFR dimer/SHC/GRB2/SOS1 0.04 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.016 0.003 0 4 -10000 0 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.016 0.003 0 4 -10000 0 4
EGF/EGFR dimer/SHC 0.029 0.012 -10000 0 0 20 20
mol:GDP 0.037 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.016 0.004 0 8 -10000 0 8
GRB2/SOS1 0.024 0.005 -10000 0 0 6 6
HRAS/GTP -0.029 0.014 0 23 -10000 0 23
SHC1 -0.016 0.004 0 9 -10000 0 9
HRAS/GDP 0.034 0.019 -10000 0 -0.011 6 6
FRAP1 -0.006 0.07 0.16 19 -10000 0 19
EGF/EGFR dimer 0.022 0.008 -10000 0 0 14 14
SOS1 -0.017 0 -10000 0 -10000 0 0
GRB2 -0.016 0.003 0 6 -10000 0 6
ETA receptor/Endothelin-1 0.023 0.006 -10000 0 0 9 9
Neurotrophic factor-mediated Trk receptor signaling

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL -0.016 0.003 0 5 -10000 0 5
RAS family/GTP/Tiam1 -0.011 0.019 -10000 0 -0.09 7 7
NT3 (dimer)/TRKC 0.022 0.007 -10000 0 0 13 13
NT3 (dimer)/TRKB 0.03 0.01 -10000 0 0 14 14
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.021 -10000 0 -0.17 2 2
RAPGEF1 -0.016 0.003 0 5 -10000 0 5
BDNF -0.016 0.004 0 9 -10000 0 9
PIK3CA -0.016 0.004 0 10 -10000 0 10
DYNLT1 -0.016 0.004 0 7 -10000 0 7
NTRK1 -0.016 0.003 0 6 -10000 0 6
NTRK2 -0.016 0.003 0 4 -10000 0 4
NTRK3 -0.016 0.003 0 6 -10000 0 6
NT-4/5 (dimer)/TRKB 0.021 0.005 -10000 0 0 8 8
neuron apoptosis -0.012 0.045 0.17 5 -0.12 1 6
SHC 2-3/Grb2 0.013 0.048 -10000 0 -0.2 4 4
SHC1 -0.016 0.004 0 9 -10000 0 9
SHC2 0 0.062 -10000 0 -0.33 4 4
SHC3 0.005 0.046 -10000 0 -0.26 3 3
STAT3 (dimer) -0.016 0.003 0 5 -10000 0 5
NT3 (dimer)/TRKA 0.03 0.011 -10000 0 0 16 16
RIN/GDP 0.012 0.057 0.15 9 -0.15 5 14
GIPC1 -0.016 0.003 0 4 -10000 0 4
KRAS -0.015 0.005 0 16 -10000 0 16
DNAJA3 -0.011 0.007 -10000 0 -10000 0 0
RIN/GTP 0.011 0.004 -10000 0 0 15 15
CCND1 -0.018 0.006 0 13 -10000 0 13
MAGED1 -0.017 0 -10000 0 -10000 0 0
PTPN11 -0.017 0.002 0 3 -10000 0 3
RICS -0.016 0.003 0 5 -10000 0 5
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.03 0.01 -10000 0 0 14 14
GRB2 -0.016 0.003 0 6 -10000 0 6
NGF (dimer)/TRKA/MATK 0.021 0.006 -10000 0 0 10 10
TRKA/NEDD4-2 0.022 0.008 -10000 0 0 16 16
ELMO1 -0.017 0.002 0 3 -10000 0 3
RhoG/GTP/ELMO1/DOCK1 0.021 0.005 -10000 0 0 7 7
NGF 0 0 -10000 0 -10000 0 0
HRAS -0.016 0.004 0 9 -10000 0 9
DOCK1 -0.016 0.003 0 5 -10000 0 5
GAB2 -0.016 0.003 0 4 -10000 0 4
RIT2 -0.015 0.005 0 15 -10000 0 15
RIT1 -0.016 0.004 0 10 -10000 0 10
FRS2 -0.015 0.005 0 12 -10000 0 12
DNM1 -0.016 0.003 0 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.004 0 7 -10000 0 7
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.016 0.019 -10000 0 -10000 0 0
mol:GDP 0.016 0.078 0.2 8 -0.22 5 13
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.012 0.002 -10000 0 0 3 3
RIT1/GDP 0.009 0.054 0.13 8 -0.16 5 13
TIAM1 -0.016 0.003 0 5 -10000 0 5
PIK3R1 -0.016 0.004 0 9 -10000 0 9
BDNF (dimer)/TRKB 0.031 0.01 -10000 0 0 12 12
KIDINS220/CRKL/C3G 0.023 0.006 -10000 0 0 10 10
SHC/RasGAP 0.022 0.008 -10000 0 0 15 15
FRS2 family/SHP2 0.029 0.012 -10000 0 0 20 20
SHC/GRB2/SOS1/GAB1 0.038 0.014 -10000 0 0 16 16
RIT1/GTP 0.011 0.003 -10000 0 0 10 10
NT3 (dimer) -0.016 0.004 0 8 -10000 0 8
RAP1/GDP 0 0.036 0.095 3 -0.12 4 7
KIDINS220/CRKL -0.016 0.003 0 5 -10000 0 5
BDNF (dimer) -0.016 0.004 0 9 -10000 0 9
ubiquitin-dependent protein catabolic process 0.02 0.007 -10000 0 0 16 16
Schwann cell development -0.01 0.008 -10000 0 -10000 0 0
EHD4 -0.016 0.003 0 4 -10000 0 4
FRS2 family/GRB2/SOS1 0.036 0.016 -10000 0 0 23 23
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.002 0.039 0.079 13 -0.13 6 19
RAP1B -0.015 0.005 0 13 -10000 0 13
RAP1A -0.016 0.003 0 5 -10000 0 5
CDC42/GTP -0.032 0.016 -10000 0 -10000 0 0
ABL1 -0.016 0.003 0 5 -10000 0 5
SH2B family/GRB2/SOS1 0.024 0.005 -10000 0 0 6 6
Rap1/GTP -0.001 0.058 -10000 0 -0.26 5 5
STAT3 -0.016 0.003 0 5 -10000 0 5
axon guidance -0.031 0.016 -10000 0 -10000 0 0
MAPK3 -0.02 0.006 0 10 -10000 0 10
MAPK1 -0.019 0.006 0 12 -10000 0 12
CDC42/GDP 0.012 0.06 0.15 10 -0.16 5 15
NTF3 -0.016 0.004 0 8 -10000 0 8
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.021 0.006 -10000 0 0 9 9
PI3K 0.021 0.008 -10000 0 0 18 18
FRS3 -0.016 0.004 0 8 -10000 0 8
FAIM -0.017 0.002 0 3 -10000 0 3
GAB1 -0.016 0.003 0 4 -10000 0 4
RASGRF1 -0.011 0.008 -10000 0 -10000 0 0
SOS1 -0.017 0 -10000 0 -10000 0 0
MCF2L -0.021 0.009 0 20 -10000 0 20
RGS19 -0.014 0.006 0 21 -10000 0 21
CDC42 -0.016 0.005 0 11 -10000 0 11
RAS family/GTP 0.018 0.057 0.17 3 -0.21 4 7
Rac1/GDP 0.013 0.061 0.15 10 -0.15 5 15
NGF (dimer)/TRKA/GRIT 0.021 0.006 -10000 0 0 10 10
neuron projection morphogenesis 0.006 0.075 -10000 0 -0.79 1 1
NGF (dimer)/TRKA/NEDD4-2 0.02 0.007 -10000 0 0 16 16
MAP2K1 -0.014 0.058 0.18 11 -10000 0 11
NGFR -0.016 0.003 0 4 -10000 0 4
NGF (dimer)/TRKA/GIPC/GAIP 0.005 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.005 0.003 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.041 0.019 -10000 0 -10000 0 0
NRAS -0.016 0.003 0 5 -10000 0 5
GRB2/SOS1 0.024 0.005 -10000 0 0 6 6
PRKCI -0.015 0.005 0 12 -10000 0 12
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 -0.016 0.004 0 9 -10000 0 9
PRKCZ -0.016 0.004 0 9 -10000 0 9
MAPKKK cascade 0.011 0.015 -10000 0 -10000 0 0
RASA1 -0.016 0.004 0 9 -10000 0 9
TRKA/c-Abl 0.023 0.007 -10000 0 0 11 11
SQSTM1 -0.016 0.003 0 6 -10000 0 6
BDNF (dimer)/TRKB/GIPC 0.038 0.014 -10000 0 -10000 0 0
NGF (dimer)/TRKA/p62/Atypical PKCs 0.031 0.016 -10000 0 0 28 28
MATK -0.016 0.003 0 5 -10000 0 5
NEDD4L -0.015 0.005 0 12 -10000 0 12
RAS family/GDP -0.014 0.02 -10000 0 -0.096 6 6
NGF (dimer)/TRKA 0.003 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.022 0.018 -10000 0 -0.094 2 2
FRS2 family/SHP2/CRK family 0.04 0.02 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + -0.016 0.003 0 4 -9999 0 4
GNAT1/GTP 0.012 0.002 -10000 0 0 5 5
Metarhodopsin II/Arrestin 0.022 0.004 -10000 0 0 5 5
PDE6G/GNAT1/GTP 0.021 0.006 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -9999 0 0
absorption of light 0 0 -10000 0 -9999 0 0
GNAT1 -0.016 0.003 0 5 -9999 0 5
GRK1 -0.016 0.003 0 6 -9999 0 6
CNG Channel -0.031 0.011 -10000 0 -9999 0 0
mol:Na + -0.037 0.012 -10000 0 -9999 0 0
mol:ADP -0.016 0.003 0 6 -9999 0 6
RGS9-1/Gbeta5/R9AP 0.029 0.012 -10000 0 0 21 21
mol:GDP 0 0 -10000 0 -9999 0 0
cGMP/CNG Channel -0.037 0.012 -10000 0 -9999 0 0
CNGB1 -0.017 0.002 0 3 -9999 0 3
RDH5 -0.016 0.003 0 6 -9999 0 6
SAG -0.017 0.002 0 3 -9999 0 3
mol:Ca2+ -0.029 0.064 0.28 5 -9999 0 5
Na + (4 Units) -0.04 0.014 -10000 0 -9999 0 0
RGS9 -0.016 0.003 0 5 -9999 0 5
GNB1/GNGT1 0.02 0.01 -10000 0 0 27 27
GNAT1/GDP 0.032 0.015 -10000 0 0 24 24
GUCY2D -0.016 0.004 0 8 -9999 0 8
GNGT1 -0.015 0.006 0 19 -9999 0 19
GUCY2F -0.017 0 -10000 0 -9999 0 0
GNB5 -0.016 0.003 0 5 -9999 0 5
mol:GMP (4 units) -0.022 0.009 0 19 -9999 0 19
mol:11-cis-retinal -0.016 0.003 0 6 -9999 0 6
mol:cGMP -0.029 0.01 -10000 0 -9999 0 0
GNB1 -0.016 0.004 0 9 -9999 0 9
Rhodopsin 0.023 0.005 -10000 0 0 7 7
SLC24A1 -0.016 0.003 0 4 -9999 0 4
CNGA1 -0.017 0.002 0 3 -9999 0 3
Metarhodopsin II 0.02 0.005 -10000 0 0 9 9
mol:Ca ++ 0 0 -10000 0 -9999 0 0
GC1/GCAP Family 0.038 0.013 -10000 0 0 15 15
RGS9BP -0.015 0.005 0 12 -9999 0 12
Metarhodopsin II/Transducin 0.004 0.002 -10000 0 -9999 0 0
GCAP Family/Ca ++ 0.03 0.008 -10000 0 0 9 9
PDE6A/B 0.023 0.006 -10000 0 0 9 9
mol:Pi 0.028 0.012 -10000 0 0 21 21
mol:all-trans-retinal 0 0 -10000 0 -9999 0 0
Transducin 0.025 0.013 -10000 0 0 30 30
PDE6B -0.016 0.003 0 4 -9999 0 4
PDE6A -0.016 0.003 0 6 -9999 0 6
PDE6G -0.016 0.004 0 7 -9999 0 7
RHO -0.017 0.002 0 3 -9999 0 3
PDE6 0.038 0.022 -10000 0 -9999 0 0
GUCA1A -0.016 0.004 0 8 -9999 0 8
GC2/GCAP Family 0.04 0.011 -10000 0 0 9 9
GUCA1C -0.017 0.002 0 2 -9999 0 2
GUCA1B -0.016 0.004 0 7 -9999 0 7
Arf1 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
coatomer protein complex 0.011 0.045 0.13 16 -10000 0 16
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.008 0.023 0.12 2 -0.11 1 3
AP2 0.022 0.008 -10000 0 0 17 17
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0.011 -10000 0 -0.026 5 5
CLTB -0.016 0.003 0 4 -10000 0 4
coatomer protein complex/ARF1/GTP/ER cargo protein -0.004 0.006 0.019 6 -10000 0 6
CD4 -0.016 0.004 0 8 -10000 0 8
CLTA -0.016 0.004 0 10 -10000 0 10
mol:GTP -0.002 0.003 0.006 9 -10000 0 9
ARFGAP1 -0.009 0.004 0 22 -10000 0 22
mol:PI-4-5-P2 -0.002 0.011 0.072 3 -10000 0 3
ARF1/GTP -0.01 0.008 0.024 5 -10000 0 5
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.006 0.004 -10000 0 -10000 0 0
mol:Choline -0.002 0.011 0.073 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.012 0.015 0.026 17 -10000 0 17
DDEF1 -0.001 0.009 0.074 2 -10000 0 2
ARF1/GDP -0.004 0.014 0.026 1 -0.088 3 4
AP2M1 -0.016 0.004 0 9 -10000 0 9
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.01 0.019 10 -10000 0 10
Rac/GTP -0.006 0.012 0.02 21 -10000 0 21
ARF1/GTP/GGA3/ARF-GAP1 -0.012 0.015 0.029 10 -10000 0 10
ARFIP2 -0.018 0.005 -10000 0 -10000 0 0
COPA -0.016 0.003 0 6 -10000 0 6
RAC1 -0.016 0.004 0 9 -10000 0 9
ARF1/GTP/coatomer protein complex 0.001 0.02 0.075 3 -0.12 2 5
ARF1/GTP/ARHGAP10 0.01 0.005 0.031 3 0 14 17
GGA3 -0.016 0.004 0 7 -10000 0 7
ARF1/GTP/Membrin 0.011 0.01 -10000 0 -10000 0 0
AP2A1 -0.016 0.004 0 9 -10000 0 9
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.005 0.021 -10000 0 -0.18 2 2
ARF1/GDP/Membrin 0.015 0.013 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.015 0.016 -10000 0 -0.021 17 17
CYTH2 -0.002 0.003 0.006 9 -10000 0 9
ARF1/GTP/GGA3 0.021 0.007 0.043 1 0 13 14
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.012 0.003 -10000 0 0 9 9
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.002 0.02 0.076 2 -0.078 2 4
PLD2 -0.004 0.002 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0.004 0 22 -10000 0 22
PIP5K1A -0.003 0.001 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.013 0.047 4 -0.047 5 9
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.011 0.073 3 -10000 0 3
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.004 0 22 -10000 0 22
GOSR2 0.005 0.006 -10000 0 -10000 0 0
USO1 -0.001 0 -10000 0 -10000 0 0
GBF1 0.005 0.005 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.019 0.011 -10000 0 -0.007 16 16
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.028 0.012 -10000 0 0 22 22
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.019 0.045 -10000 0 -0.23 2 2
MAP3K8 -0.016 0.003 0 6 -10000 0 6
FOS 0.01 0.044 -10000 0 -0.24 2 2
PRKCA -0.016 0.003 0 5 -10000 0 5
PTPN7 -0.016 0.003 0 5 -10000 0 5
HRAS -0.016 0.004 0 9 -10000 0 9
PRKCB 0 0 -10000 0 -10000 0 0
NRAS -0.016 0.003 0 5 -10000 0 5
RAS family/GTP 0.026 0.012 -10000 0 0 24 24
MAPK3 0.009 0.052 -10000 0 -0.31 3 3
MAP2K1 0.004 0.029 0.082 3 -0.21 1 4
ELK1 -0.017 0 -10000 0 -10000 0 0
BRAF -0.001 0.001 0 27 -10000 0 27
mol:GTP 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.051 -10000 0 -0.31 3 3
RAF1 -0.001 0.001 0 24 -10000 0 24
KRAS -0.015 0.005 0 16 -10000 0 16
Caspase cascade in apoptosis

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
TOP1 -0.021 0.076 -10000 0 -0.32 6 6
ACTA1 -0.025 0.051 -10000 0 -0.15 15 15
NUMA1 -0.026 0.11 -10000 0 -0.43 6 6
SPTAN1 -0.027 0.052 0.18 1 -0.16 11 12
LIMK1 -0.026 0.052 0.18 1 -0.19 7 8
BIRC3 -0.016 0.004 0.003 5 -10000 0 5
BIRC2 -0.016 0.006 0.017 3 -10000 0 3
BAX -0.016 0.004 0 7 -10000 0 7
CASP10 -0.023 0.006 0 9 -10000 0 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.027 0.1 -10000 0 -0.42 6 6
DIABLO -0.016 0.003 0 4 -10000 0 4
apoptotic nuclear changes -0.026 0.052 0.18 1 -0.16 11 12
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.017 0.002 0 2 -10000 0 2
GSN -0.029 0.05 -10000 0 -0.18 8 8
MADD -0.017 0.002 0 3 -10000 0 3
TFAP2A -0.032 0.21 -10000 0 -0.8 8 8
BID -0.007 0.002 0 11 -10000 0 11
MAP3K1 -0.034 0.12 -10000 0 -0.43 10 10
TRADD -0.017 0.002 0 3 -10000 0 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.006 -10000 0 0 8 8
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.025 0.056 0.17 3 -0.16 11 14
CASP9 -0.016 0.006 0.018 2 -10000 0 2
DNA repair 0.003 0.028 0.13 3 -10000 0 3
neuron apoptosis -0.029 0.14 -10000 0 -0.59 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.03 0.097 0.18 2 -0.35 7 9
APAF1 -0.016 0.005 0.01 5 -10000 0 5
CASP6 -0.03 0.17 -10000 0 -0.96 4 4
TRAF2 -0.016 0.004 0 7 -10000 0 7
ICAD/CAD -0.026 0.07 0.26 4 -0.19 6 10
CASP7 0 0.044 0.11 1 -0.21 5 6
KRT18 0 0.056 -10000 0 -0.56 1 1
apoptosis -0.031 0.082 -10000 0 -0.35 6 6
DFFA -0.025 0.059 0.18 4 -0.16 11 15
DFFB -0.027 0.054 0.18 2 -0.18 8 10
PARP1 -0.003 0.028 -10000 0 -0.13 3 3
actin filament polymerization 0.028 0.051 0.18 6 -0.16 2 8
TNF -0.016 0.004 0 10 -10000 0 10
CYCS -0.002 0.015 -10000 0 -10000 0 0
SATB1 -0.034 0.16 -10000 0 -0.9 4 4
SLK -0.028 0.048 -10000 0 -0.17 8 8
p15 BID/BAX -0.015 0.016 0.086 1 -0.15 1 2
CASP2 -0.012 0.052 -10000 0 -0.18 7 7
JNK cascade 0.034 0.12 0.43 10 -10000 0 10
CASP3 -0.026 0.052 -10000 0 -0.16 16 16
LMNB2 -0.017 0.14 0.16 6 -0.54 7 13
RIPK1 -0.016 0.004 0 7 -10000 0 7
CASP4 -0.016 0.004 0.003 5 -10000 0 5
Mammalian IAPs/DIABLO 0.03 0.008 -10000 0 0 8 8
negative regulation of DNA binding -0.031 0.2 -10000 0 -0.78 8 8
stress fiber formation -0.027 0.049 -10000 0 -0.18 7 7
GZMB -0.019 0.005 0 8 -10000 0 8
CASP1 -0.003 0.002 -10000 0 -10000 0 0
LMNB1 -0.025 0.14 0.16 6 -0.43 11 17
APP -0.029 0.15 -10000 0 -0.59 8 8
TNFRSF1A -0.016 0.004 0 9 -10000 0 9
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.01 0.001 0 2 -10000 0 2
VIM -0.029 0.085 -10000 0 -0.37 6 6
LMNA -0.011 0.11 0.15 5 -0.48 5 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.001 0.04 -10000 0 -0.15 7 7
LRDD -0.016 0.004 0 8 -10000 0 8
SREBF1 -0.03 0.046 -10000 0 -0.18 7 7
APAF-1/Caspase 9 -0.002 0.11 -10000 0 -0.64 4 4
nuclear fragmentation during apoptosis -0.025 0.1 -10000 0 -0.42 6 6
CFL2 -0.028 0.051 0.16 2 -0.18 6 8
GAS2 -0.028 0.05 0.18 1 -0.17 8 9
positive regulation of apoptosis -0.018 0.14 0.16 6 -0.45 9 15
PRF1 -0.015 0.006 0.017 4 -10000 0 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.015 0.005 0 15 -10000 0 15
SMAD2 0.007 0.038 0.13 6 -0.14 1 7
SMAD3 -0.005 0.025 0.099 4 -0.087 6 10
SMAD3/SMAD4 -0.007 0.088 -10000 0 -0.38 7 7
SMAD4/Ubc9/PIASy 0.029 0.012 -10000 0 0 20 20
SMAD2/SMAD2/SMAD4 0.024 0.038 -10000 0 -0.13 4 4
PPM1A -0.016 0.003 0 4 -10000 0 4
CALM1 -0.016 0.003 0 4 -10000 0 4
SMAD2/SMAD4 -0.008 0.031 -10000 0 -0.14 3 3
MAP3K1 -0.016 0.005 0 11 -10000 0 11
TRAP-1/SMAD4 0.022 0.008 -10000 0 0 16 16
MAPK3 -0.017 0.002 0 2 -10000 0 2
MAPK1 -0.016 0.003 0 4 -10000 0 4
NUP214 -0.016 0.003 0 4 -10000 0 4
CTDSP1 -0.017 0.002 0 3 -10000 0 3
CTDSP2 -0.016 0.003 0 6 -10000 0 6
CTDSPL -0.016 0.004 0 7 -10000 0 7
KPNB1 -0.016 0.003 0 5 -10000 0 5
TGFBRAP1 -0.017 0.002 0 2 -10000 0 2
UBE2I -0.016 0.003 0 5 -10000 0 5
NUP153 -0.016 0.004 0 8 -10000 0 8
KPNA2 -0.016 0.003 0 5 -10000 0 5
PIAS4 -0.016 0.003 0 5 -10000 0 5
Canonical NF-kappaB pathway

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 -0.016 0.004 0 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.057 0.14 5 -0.2 5 10
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.01 0.005 -10000 0 0 22 22
NFKBIA -0.024 0.021 0.19 1 -10000 0 1
BIRC2 -0.016 0.003 0 5 -10000 0 5
IKBKB -0.015 0.006 0 18 -10000 0 18
RIPK2 -0.014 0.006 0 22 -10000 0 22
IKBKG -0.001 0.02 -10000 0 -0.22 1 1
IKK complex/A20 0.02 0.051 -10000 0 -0.22 4 4
NEMO/A20/RIP2 -0.014 0.006 0 22 -10000 0 22
XPO1 -0.017 0.001 0 1 -10000 0 1
NEMO/ATM 0.014 0.054 -10000 0 -0.28 3 3
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN -0.017 0.002 0 2 -10000 0 2
Exportin 1/RanGTP 0.022 0.003 -10000 0 0 3 3
IKK complex/ELKS 0.01 0.048 -10000 0 -0.23 4 4
BCL10/MALT1/TRAF6 0.03 0.011 -10000 0 0 15 15
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 -0.017 0.002 0 2 -10000 0 2
RELA -0.017 0.002 0 3 -10000 0 3
MALT1 -0.016 0.005 0 11 -10000 0 11
cIAP1/UbcH5C 0.024 0.005 -10000 0 0 6 6
ATM -0.016 0.003 0 4 -10000 0 4
TNF/TNFR1A 0.022 0.008 -10000 0 0 16 16
TRAF6 -0.016 0.003 0 6 -10000 0 6
PRKCA -0.016 0.003 0 5 -10000 0 5
CHUK -0.017 0.002 0 3 -10000 0 3
UBE2D3 -0.017 0.002 0 2 -10000 0 2
TNF -0.016 0.004 0 10 -10000 0 10
NF kappa B1 p50/RelA 0.031 0.009 -10000 0 0 11 11
BCL10 -0.016 0.003 0 5 -10000 0 5
proteasomal ubiquitin-dependent protein catabolic process -0.023 0.021 0.19 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex -0.016 0.004 0 7 -10000 0 7
TNFRSF1A -0.016 0.004 0 9 -10000 0 9
IKK complex 0.015 0.053 -10000 0 -0.24 4 4
CYLD -0.017 0.002 0 3 -10000 0 3
IKK complex/PKC alpha 0.021 0.054 -10000 0 -0.24 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.037 0.015 -10000 0 0 20 20
HDAC3 -0.016 0.004 0 7 -10000 0 7
Ran/GTP/Exportin 1/HDAC4 -0.021 0.006 0 9 -10000 0 9
GATA1/HDAC4 0.024 0.004 -10000 0 0 4 4
GATA1/HDAC5 0.024 0.004 -10000 0 0 3 3
GATA2/HDAC5 0.024 0.005 -10000 0 0 5 5
HDAC5/BCL6/BCoR 0.031 0.009 -10000 0 0 10 10
HDAC9 -0.016 0.003 0 6 -10000 0 6
Glucocorticoid receptor/Hsp90/HDAC6 0.022 0.005 -10000 0 0 6 6
HDAC4/ANKRA2 0.023 0.006 -10000 0 0 10 10
HDAC5/YWHAB 0.021 0.009 -10000 0 0 22 22
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.001 -10000 0 -10000 0 0
GATA2 -0.017 0.002 0 2 -10000 0 2
HDAC4/RFXANK 0.023 0.005 -10000 0 0 7 7
BCOR -0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.016 0.004 0 9 -10000 0 9
HDAC5 -0.017 0.002 0 3 -10000 0 3
GNB1/GNG2 0.022 0.008 -10000 0 0 14 14
Histones -0.011 0.025 -10000 0 -0.096 10 10
ADRBK1 -0.016 0.003 0 6 -10000 0 6
HDAC4 -0.016 0.003 0 4 -10000 0 4
XPO1 -0.017 0.001 0 1 -10000 0 1
HDAC5/ANKRA2 0.023 0.006 -10000 0 0 10 10
HDAC4/Ubc9 0.023 0.006 -10000 0 0 9 9
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.023 0.006 -10000 0 0 10 10
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 -0.017 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.024 0.005 -10000 0 0 6 6
CAMK4 -0.016 0.005 0 11 -10000 0 11
Tubulin/HDAC6 0.021 0.005 -10000 0 0 7 7
SUMO1 -0.017 0.002 0 2 -10000 0 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB -0.015 0.006 0 19 -10000 0 19
GATA1 -0.017 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE -0.016 0.004 0 7 -10000 0 7
NR3C1 -0.016 0.003 0 6 -10000 0 6
SUMO1/HDAC4 0.018 0.027 0.085 4 -0.086 7 11
SRF -0.016 0.004 0 7 -10000 0 7
HDAC4/YWHAB 0.021 0.009 -10000 0 0 21 21
Tubulin 0.012 0.003 -10000 0 0 7 7
HDAC4/14-3-3 E 0.023 0.006 -10000 0 0 10 10
GNB1 -0.016 0.004 0 9 -10000 0 9
RANGAP1 -0.017 0.002 0 3 -10000 0 3
BCL6/BCoR 0.023 0.005 -10000 0 0 7 7
HDAC4/HDAC3/SMRT (N-CoR2) 0.031 0.009 -10000 0 0 11 11
HDAC4/SRF 0.029 0.011 -10000 0 0 18 18
HDAC4/ER alpha 0.023 0.007 -10000 0 0 11 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.011 0.025 -10000 0 -0.096 10 10
cell motility 0.021 0.005 -10000 0 0 7 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I -0.016 0.003 0 5 -10000 0 5
HDAC7/HDAC3 0.012 0.003 -10000 0 0 7 7
BCL6 -0.016 0.004 0 7 -10000 0 7
HDAC4/CaMK II delta B -0.016 0.003 0 4 -10000 0 4
Hsp90/HDAC6 0.012 0 -10000 0 -10000 0 0
ESR1 -0.016 0.004 0 8 -10000 0 8
HDAC6/HDAC11 0.024 0.003 -10000 0 0 2 2
Ran/GTP/Exportin 1 0.017 0.026 -10000 0 -0.079 8 8
NPC 0.01 0.001 -10000 0 0 2 2
MEF2C -0.016 0.004 0 9 -10000 0 9
RAN -0.017 0.002 0 2 -10000 0 2
HDAC4/MEF2C 0.044 0.015 -10000 0 -10000 0 0
GNG2 -0.016 0.003 0 6 -10000 0 6
NCOR2 -0.017 0.002 0 3 -10000 0 3
TUBB2A -0.016 0.004 0 7 -10000 0 7
HDAC11 -0.017 0.002 0 2 -10000 0 2
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 -0.017 0.002 0 2 -10000 0 2
ANKRA2 -0.016 0.004 0 8 -10000 0 8
RFXANK -0.017 0.002 0 3 -10000 0 3
nuclear import -0.013 0.007 0 29 -10000 0 29
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.009 0.002 0 10 -10000 0 10
IHH 0.02 0.004 -10000 0 0 4 4
SHH Np/Cholesterol/GAS1 -0.019 0.007 0 16 -10000 0 16
LRPAP1 -0.016 0.003 0 4 -10000 0 4
dorsoventral neural tube patterning 0.019 0.007 -10000 0 0 16 16
SMO/beta Arrestin2 0.015 0.03 -10000 0 -0.13 3 3
SMO 0.001 0.017 -10000 0 -0.19 1 1
AKT1 -0.007 0.075 -10000 0 -0.27 9 9
ARRB2 -0.016 0.004 0 8 -10000 0 8
BOC -0.017 0.002 0 2 -10000 0 2
ADRBK1 -0.016 0.003 0 6 -10000 0 6
heart looping 0.001 0.017 -10000 0 -0.19 1 1
STIL -0.008 0.043 0.15 9 -10000 0 9
DHH N/PTCH2 0.024 0.004 -10000 0 0 4 4
DHH N/PTCH1 0.011 0.009 -10000 0 -0.065 2 2
PIK3CA -0.016 0.004 0 10 -10000 0 10
DHH -0.017 0 -10000 0 -10000 0 0
PTHLH -0.006 0.015 -10000 0 -0.18 1 1
determination of left/right symmetry 0.001 0.017 -10000 0 -0.19 1 1
PIK3R1 -0.016 0.004 0 9 -10000 0 9
skeletal system development -0.006 0.015 -10000 0 -0.18 1 1
IHH N/Hhip 0.025 0.006 -10000 0 0 7 7
DHH N/Hhip 0.024 0.004 -10000 0 0 4 4
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.001 0.017 -10000 0 -0.19 1 1
pancreas development -0.016 0.003 0 4 -10000 0 4
HHAT -0.016 0.004 0 7 -10000 0 7
PI3K 0.021 0.008 -10000 0 0 18 18
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.016 0.003 0 4 -10000 0 4
somite specification 0.001 0.017 -10000 0 -0.19 1 1
SHH Np/Cholesterol/PTCH1 -0.013 0.008 -10000 0 -0.062 2 2
SHH Np/Cholesterol/PTCH2 -0.019 0.007 0 16 -10000 0 16
SHH Np/Cholesterol/Megalin -0.019 0.007 0 16 -10000 0 16
SHH -0.018 0.006 0 15 -10000 0 15
catabolic process -0.003 0.008 -10000 0 -0.068 2 2
SMO/Vitamin D3 -0.007 0.037 0.16 6 -0.14 1 7
SHH Np/Cholesterol/Hhip -0.018 0.007 0 18 -10000 0 18
LRP2 -0.017 0.002 0 2 -10000 0 2
receptor-mediated endocytosis -0.011 0.031 0.13 5 -0.14 1 6
SHH Np/Cholesterol/BOC -0.019 0.007 0 16 -10000 0 16
SHH Np/Cholesterol/CDO -0.018 0.007 0 19 -10000 0 19
mesenchymal cell differentiation 0.018 0.007 -10000 0 0 18 18
mol:Vitamin D3 0 0.046 0.16 10 -10000 0 10
IHH N/PTCH2 0.025 0.006 -10000 0 0 8 8
CDON -0.016 0.003 0 6 -10000 0 6
IHH N/PTCH1 0.013 0.002 -10000 0 0 4 4
Megalin/LRPAP1 0.024 0.005 -10000 0 0 5 5
PTCH2 -0.016 0.003 0 4 -10000 0 4
SHH Np/Cholesterol -0.012 0.008 0.03 4 -10000 0 4
PTCH1 -0.003 0.008 -10000 0 -0.068 2 2
HHIP -0.016 0.003 0 4 -10000 0 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.016 0.003 0 6 -10000 0 6
HDAC2 -0.016 0.003 0 5 -10000 0 5
GNB1/GNG2 0.029 0.012 -10000 0 0 19 19
forebrain development 0.001 0.052 -10000 0 -0.29 3 3
GNAO1 -0.016 0.003 0 4 -10000 0 4
SMO/beta Arrestin2 0.022 0.008 -10000 0 0 14 14
SMO -0.016 0.004 0 7 -10000 0 7
ARRB2 -0.016 0.004 0 8 -10000 0 8
GLI3/SPOP -0.001 0.073 -10000 0 -0.23 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B -0.017 0.002 0 2 -10000 0 2
GNAI2 -0.016 0.003 0 5 -10000 0 5
SIN3/HDAC complex 0.038 0.014 -10000 0 0 17 17
GNAI1 -0.016 0.003 0 5 -10000 0 5
XPO1 -0.017 0.001 0 1 -10000 0 1
GLI1/Su(fu) 0.008 0.031 -10000 0 -10000 0 0
SAP30 -0.016 0.005 0 11 -10000 0 11
mol:GDP -0.016 0.004 0 7 -10000 0 7
MIM/GLI2A -0.013 0.007 0 28 -10000 0 28
IFT88 -0.017 0.002 0 2 -10000 0 2
GNAI3 -0.016 0.003 0 4 -10000 0 4
GLI2 -0.006 0.055 0.23 1 -0.21 7 8
GLI3 -0.009 0.073 -10000 0 -0.23 8 8
CSNK1D -0.016 0.004 0 7 -10000 0 7
CSNK1E -0.016 0.003 0 4 -10000 0 4
SAP18 -0.017 0.002 0 2 -10000 0 2
embryonic digit morphogenesis -0.017 0.002 0 2 -10000 0 2
GNG2 -0.016 0.003 0 6 -10000 0 6
Gi family/GTP -0.005 0.016 0.078 1 -0.17 1 2
SIN3B -0.017 0.002 0 3 -10000 0 3
SIN3A -0.016 0.003 0 4 -10000 0 4
GLI3/Su(fu) -0.002 0.053 -10000 0 -0.24 4 4
GLI2/Su(fu) -0.011 0.055 0.2 1 -0.22 7 8
FOXA2 0.012 0.045 -10000 0 -0.49 1 1
neural tube patterning 0.001 0.052 -10000 0 -0.29 3 3
SPOP -0.016 0.003 0 4 -10000 0 4
Su(fu)/PIAS1 0.015 0.021 0.087 4 -0.13 1 5
GNB1 -0.016 0.004 0 9 -10000 0 9
CSNK1G2 -0.016 0.003 0 5 -10000 0 5
CSNK1G3 -0.016 0.004 0 9 -10000 0 9
MTSS1 -0.013 0.007 0 28 -10000 0 28
embryonic limb morphogenesis 0.001 0.052 -10000 0 -0.29 3 3
SUFU -0.006 0.002 -10000 0 -10000 0 0
LGALS3 -0.016 0.003 0 4 -10000 0 4
catabolic process -0.007 0.1 0.21 1 -0.31 10 11
GLI3A/CBP -0.016 0.003 0 5 -10000 0 5
KIF3A -0.016 0.004 0 8 -10000 0 8
GLI1 0.001 0.053 -10000 0 -0.3 3 3
RAB23 -0.016 0.004 0 9 -10000 0 9
CSNK1A1 -0.016 0.004 0 8 -10000 0 8
IFT172 -0.017 0 -10000 0 -10000 0 0
RBBP7 -0.017 0 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.014 0.024 0.087 4 -0.14 2 6
GNAZ -0.017 0.002 0 3 -10000 0 3
RBBP4 -0.016 0.003 0 6 -10000 0 6
CSNK1G1 -0.016 0.003 0 4 -10000 0 4
PIAS1 -0.016 0.003 0 4 -10000 0 4
PRKACA -0.016 0.003 0 5 -10000 0 5
GLI2/SPOP -0.002 0.067 0.21 1 -0.23 9 10
STK36 -0.016 0.003 0 4 -10000 0 4
Gi family/GNB1/GNG2/GDP -0.009 0.025 -10000 0 -0.1 8 8
PTCH1 0.001 0.048 -10000 0 -0.27 3 3
MIM/GLI1 0.009 0.038 -10000 0 -0.19 2 2
CREBBP -0.016 0.003 0 5 -10000 0 5
Su(fu)/SIN3/HDAC complex -0.007 0.063 -10000 0 -0.25 7 7
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.023 0.005 -10000 0 0 7 7
Necdin/E2F1 0.022 0.008 -10000 0 0 15 15
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.035 0.012 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 0.022 0.004 -10000 0 0 4 4
NT-4/5 (dimer)/p75(NTR) 0.012 0.002 -10000 0 0 4 4
IKBKB -0.015 0.006 0 18 -10000 0 18
AKT1 -0.007 0.054 0.16 12 -10000 0 12
IKBKG -0.017 0 -10000 0 -10000 0 0
BDNF -0.016 0.004 0 9 -10000 0 9
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.005 -10000 0 0 8 8
FURIN -0.016 0.004 0 8 -10000 0 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.031 0.01 -10000 0 0 13 13
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.038 0.017 -10000 0 -10000 0 0
proBDNF (dimer) -0.016 0.004 0 9 -10000 0 9
NTRK1 -0.016 0.003 0 6 -10000 0 6
RTN4R -0.016 0.003 0 4 -10000 0 4
neuron apoptosis -0.01 0.07 0.24 3 -0.24 5 8
IRAK1 -0.017 0 -10000 0 -10000 0 0
SHC1 -0.015 0.005 0 13 -10000 0 13
ARHGDIA -0.016 0.003 0 6 -10000 0 6
RhoA/GTP 0.012 0.002 -10000 0 0 5 5
Gamma Secretase 0.042 0.018 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.03 0.008 -10000 0 0 8 8
MAGEH1 -0.017 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.03 0.008 -10000 0 0 8 8
Mammalian IAPs/DIABLO 0.03 0.008 -10000 0 0 8 8
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.017 0 -10000 0 -10000 0 0
APP -0.016 0.004 0 8 -10000 0 8
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 -0.016 0.003 0 6 -10000 0 6
RhoA/GDP/RHOGDI -0.018 0.006 0 13 -10000 0 13
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.037 0.19 4 -10000 0 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.005 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.021 0.006 -10000 0 0 10 10
NCSTN -0.016 0.004 0 7 -10000 0 7
mol:GTP 0.021 0.005 -10000 0 0 8 8
PSENEN -0.016 0.003 0 5 -10000 0 5
mol:ceramide -0.019 0.006 0 11 -10000 0 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.006 0.021 -10000 0 -0.098 6 6
p75(NTR)/beta APP 0.023 0.007 -10000 0 0 11 11
BEX1 -0.017 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.001 0 4 -10000 0 4
NGF (dimer) 0.028 0.01 -10000 0 0 16 16
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.03 0.009 -10000 0 0 11 11
PIK3R1 -0.016 0.004 0 9 -10000 0 9
RAC1/GTP 0.018 0.006 -10000 0 0 12 12
MYD88 -0.016 0.003 0 5 -10000 0 5
CHUK -0.017 0.002 0 3 -10000 0 3
NGF (dimer)/p75(NTR)/PKA 0.021 0.005 -10000 0 0 8 8
RHOB -0.017 0.001 0 1 -10000 0 1
RHOA -0.016 0.003 0 5 -10000 0 5
MAGE-G1/E2F1 0.022 0.008 -10000 0 0 16 16
NT3 (dimer) -0.016 0.004 0 8 -10000 0 8
TP53 -0.017 0.061 0.19 9 -10000 0 9
PRDM4 -0.02 0.005 0 8 -10000 0 8
BDNF (dimer) 0.038 0.013 -10000 0 0 15 15
PIK3CA -0.016 0.004 0 10 -10000 0 10
SORT1 -0.016 0.003 0 4 -10000 0 4
activation of caspase activity 0.032 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.03 0.009 -10000 0 0 11 11
RHOC -0.016 0.003 0 6 -10000 0 6
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.009 0.063 0.18 11 -10000 0 11
DIABLO -0.016 0.003 0 4 -10000 0 4
SMPD2 -0.02 0.006 0 11 -10000 0 11
APH1B -0.016 0.003 0 6 -10000 0 6
APH1A -0.016 0.004 0 10 -10000 0 10
proNGF (dimer)/p75(NTR)/Sortilin 0.021 0.005 -10000 0 0 8 8
PSEN1 -0.016 0.003 0 4 -10000 0 4
APAF-1/Pro-Caspase 9 0.023 0.006 -10000 0 0 8 8
NT3 (dimer)/p75(NTR) 0.023 0.007 -10000 0 0 12 12
MAPK8 -0.009 0.063 0.18 11 -10000 0 11
MAPK9 -0.01 0.06 0.17 10 -10000 0 10
APAF1 -0.017 0.002 0 2 -10000 0 2
NTF3 -0.016 0.004 0 8 -10000 0 8
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.017 0.002 0 2 -10000 0 2
RAC1/GDP 0.012 0.003 -10000 0 0 9 9
RhoA-B-C/GDP 0.032 0.012 -10000 0 -10000 0 0
p75 CTF/Sortilin/TRAF6/NRIF 0.038 0.013 -10000 0 0 14 14
RhoA-B-C/GTP 0.021 0.005 -10000 0 0 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.043 0.016 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.013 -10000 0 0 13 13
PRKACB -0.016 0.003 0 4 -10000 0 4
proBDNF (dimer)/p75 ECD 0.023 0.006 -10000 0 0 10 10
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.003 0 4 -10000 0 4
BIRC2 -0.016 0.003 0 5 -10000 0 5
neuron projection morphogenesis -0.017 0.005 -10000 0 -10000 0 0
BAD -0.017 0.066 0.27 4 -0.16 2 6
RIPK2 -0.014 0.006 0 22 -10000 0 22
NGFR -0.016 0.003 0 4 -10000 0 4
CYCS -0.02 0.028 0.16 3 -10000 0 3
ADAM17 -0.017 0.002 0 2 -10000 0 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.025 0.013 -10000 0 0 29 29
BCL2L11 -0.015 0.068 0.29 4 -0.16 2 6
BDNF (dimer)/p75(NTR) 0.022 0.007 -10000 0 0 13 13
PI3K 0.027 0.012 -10000 0 0 22 22
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.03 0.008 -10000 0 0 9 9
NDNL2 -0.017 0.002 0 3 -10000 0 3
YWHAE -0.016 0.004 0 7 -10000 0 7
PRKCI -0.015 0.005 0 12 -10000 0 12
NGF (dimer)/p75(NTR) 0.012 0.002 -10000 0 0 4 4
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.03 0.008 -10000 0 0 8 8
TRAF6 -0.016 0.003 0 6 -10000 0 6
RAC1 -0.016 0.004 0 9 -10000 0 9
PRKCZ -0.016 0.004 0 9 -10000 0 9
PLG -0.016 0.003 0 6 -10000 0 6
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.018 0.006 0 13 -10000 0 13
SQSTM1 -0.016 0.003 0 6 -10000 0 6
NGFRAP1 -0.017 0 -10000 0 -10000 0 0
CASP3 -0.022 0.07 0.3 3 -0.18 5 8
E2F1 -0.015 0.005 0 13 -10000 0 13
CASP9 -0.016 0.004 0 7 -10000 0 7
IKK complex 0.025 0.033 0.12 1 -0.11 3 4
NGF (dimer)/TRKA 0.012 0.003 -10000 0 0 6 6
MMP7 -0.016 0.003 0 6 -10000 0 6
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.035 0.012 -10000 0 0 15 15
MMP3 -0.016 0.003 0 5 -10000 0 5
APAF-1/Caspase 9 -0.041 0.016 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 0.001 0.059 0.18 11 -0.11 3 14
STAT6 (cleaved dimer) -0.002 0.03 -10000 0 -0.096 4 4
IGHG1 0.001 0.057 -10000 0 -0.26 5 5
IGHG3 -0.01 0.036 0.16 3 -0.11 3 6
AKT1 -0.01 0.071 -10000 0 -0.27 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.003 0.054 -10000 0 -0.3 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.003 0.045 0.14 1 -0.2 4 5
THY1 -0.012 0.034 0.16 2 -0.12 3 5
MYB -0.016 0.004 0 7 -10000 0 7
HMGA1 -0.016 0.003 0 6 -10000 0 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.002 0.028 0.083 1 -0.12 4 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.005 0.041 -10000 0 -0.16 6 6
SP1 -0.017 0.002 0 3 -10000 0 3
INPP5D -0.017 0.002 0 2 -10000 0 2
SOCS5 -0.014 0.013 0.027 6 -10000 0 6
STAT6 (dimer)/ETS1 0.004 0.034 -10000 0 -0.16 2 2
SOCS1 -0.024 0.032 0.11 1 -0.15 2 3
SOCS3 -0.008 0.04 0.17 4 -0.13 2 6
FCER2 -0.012 0.041 0.11 2 -0.16 5 7
PARP14 -0.017 0.002 0 2 -10000 0 2
CCL17 -0.015 0.031 0.12 1 -0.12 3 4
GRB2 -0.016 0.003 0 6 -10000 0 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.004 0.047 -10000 0 -0.16 8 8
T cell proliferation -0.005 0.033 0.1 3 -0.1 1 4
IL4R/JAK1 -0.013 0.027 0.13 1 -0.096 2 3
EGR2 -0.011 0.034 0.14 3 -0.11 2 5
JAK2 -0.013 0.012 0.029 4 -10000 0 4
JAK3 0.012 0.013 -10000 0 -0.034 2 2
PIK3R1 -0.016 0.004 0 9 -10000 0 9
JAK1 -0.01 0.017 0.029 11 -10000 0 11
COL1A2 0.004 0.043 -10000 0 -0.29 2 2
CCL26 -0.008 0.04 0.17 4 -0.11 1 5
IL4R -0.009 0.024 0.13 1 -10000 0 1
PTPN6 -0.012 0.011 0.019 13 -10000 0 13
IL13RA2 -0.015 0.031 0.12 1 -0.12 3 4
IL13RA1 -0.008 0.022 0.043 18 -10000 0 18
IRF4 -0.005 0.077 -10000 0 -0.36 6 6
ARG1 0.004 0.065 0.11 4 -0.2 8 12
CBL -0.006 0.029 0.19 1 -0.12 2 3
GTF3A -0.016 0.003 0 4 -10000 0 4
PIK3CA -0.016 0.004 0 10 -10000 0 10
IL13RA1/JAK2 0.02 0.015 0.067 4 -0.027 3 7
IRF4/BCL6 0.005 0.07 -10000 0 -0.31 6 6
CD40LG -0.017 0 -10000 0 -10000 0 0
MAPK14 -0.009 0.028 -10000 0 -0.12 3 3
mitosis -0.01 0.069 -10000 0 -0.26 7 7
STAT6 -0.008 0.032 0.15 1 -0.1 11 12
SPI1 -0.017 0.002 0 3 -10000 0 3
RPS6KB1 -0.011 0.075 0.19 4 -0.26 7 11
STAT6 (dimer) -0.009 0.033 0.15 1 -0.1 11 12
STAT6 (dimer)/PARP14 0 0.037 0.13 1 -0.1 12 13
mast cell activation 0.001 0.002 -10000 0 -0.015 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.01 0.06 -10000 0 -0.23 6 6
FRAP1 -0.011 0.071 -10000 0 -0.27 7 7
LTA -0.006 0.052 0.18 7 -0.11 4 11
FES -0.016 0.004 0 8 -10000 0 8
T-helper 1 cell differentiation 0.009 0.033 0.1 11 -0.15 1 12
CCL11 -0.011 0.033 0.15 2 -0.1 3 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.002 0.045 -10000 0 -0.2 4 4
IL2RG 0.012 0.014 -10000 0 -0.032 3 3
IL10 -0.007 0.046 0.16 6 -0.11 4 10
IRS1 -0.016 0.003 0 5 -10000 0 5
IRS2 -0.016 0.004 0 7 -10000 0 7
IL4 -0.018 0.11 -10000 0 -0.49 7 7
IL5 -0.011 0.034 0.17 2 -0.11 2 4
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.01 0.049 0.097 1 -0.17 11 12
COL1A1 0.007 0.017 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.017 0.032 0.12 2 -0.11 3 5
IL2R gamma/JAK3 0.022 0.014 -10000 0 -0.033 6 6
TFF3 -0.014 0.035 0.16 2 -0.11 4 6
ALOX15 -0.012 0.033 0.16 2 -0.12 3 5
MYBL1 -0.015 0.005 0 15 -10000 0 15
T-helper 2 cell differentiation -0.013 0.065 0.12 1 -0.26 7 8
SHC1 -0.016 0.004 0 9 -10000 0 9
CEBPB -0.014 0.007 0 27 -10000 0 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.001 0.04 -10000 0 -0.16 3 3
mol:PI-3-4-5-P3 -0.011 0.071 -10000 0 -0.27 7 7
PI3K -0.011 0.074 -10000 0 -0.28 7 7
DOK2 -0.015 0.006 0 19 -10000 0 19
ETS1 0.012 0.012 -10000 0 -0.033 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.004 0.039 -10000 0 -0.14 5 5
ITGB3 -0.009 0.044 0.18 4 -0.12 3 7
PIGR -0.007 0.046 0.16 6 -0.11 4 10
IGHE 0.012 0.054 0.11 25 -0.089 8 33
MAPKKK cascade -0.004 0.038 -10000 0 -0.14 5 5
BCL6 -0.016 0.004 0 7 -10000 0 7
OPRM1 -0.012 0.036 0.18 2 -0.1 9 11
RETNLB -0.014 0.036 0.16 2 -0.12 3 5
SELP -0.006 0.052 0.18 7 -0.11 4 11
AICDA -0.009 0.036 0.15 3 -0.1 2 5
Glucocorticoid receptor regulatory network

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
PCK2 0.008 0.002 -10000 0 0 13 13
SMARCC2 -0.016 0.003 0 5 -10000 0 5
SMARCC1 -0.016 0.003 0 5 -10000 0 5
TBX21 -0.016 0.005 0 10 -10000 0 10
SUMO2 -0.016 0.004 0 7 -10000 0 7
STAT1 (dimer) -0.017 0.002 0 3 -10000 0 3
FKBP4 -0.016 0.005 0 11 -10000 0 11
FKBP5 -0.016 0.003 0 6 -10000 0 6
GR alpha/HSP90/FKBP51/HSP90 0.021 0.006 -10000 0 0 12 12
PRL 0.001 0 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.019 0.008 -10000 0 0 19 19
RELA -0.017 0.002 0 3 -10000 0 3
FGG -0.015 0.004 0 9 -10000 0 9
GR beta/TIF2 0.021 0.009 -10000 0 0 19 19
IFNG -0.003 0.001 -10000 0 -10000 0 0
apoptosis -0.018 0.057 0.12 1 -0.2 8 9
CREB1 -0.017 0.002 0 3 -10000 0 3
histone acetylation -0.004 0.001 0 12 -10000 0 12
BGLAP -0.004 0.002 0 16 -10000 0 16
GR/PKAc 0.039 0.013 -10000 0 0 13 13
NF kappa B1 p50/RelA 0.024 0.004 -10000 0 0 4 4
SMARCD1 -0.017 0.001 0 1 -10000 0 1
MDM2 -0.002 0.001 -10000 0 -10000 0 0
GATA3 -0.016 0.003 0 6 -10000 0 6
AKT1 -0.016 0.003 0 5 -10000 0 5
CSF2 -0.008 0.022 0.24 1 -10000 0 1
GSK3B -0.017 0.002 0 2 -10000 0 2
NR1I3 -0.013 0.047 0.14 3 -0.2 4 7
CSN2 -0.013 0.003 0 7 -10000 0 7
BRG1/BAF155/BAF170/BAF60A 0.038 0.014 -10000 0 0 16 16
NFATC1 -0.015 0.005 0 14 -10000 0 14
POU2F1 -0.016 0.003 0 6 -10000 0 6
CDKN1A -0.012 0.054 0.16 2 -0.17 12 14
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
SFN -0.016 0.004 0 9 -10000 0 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.028 0.01 -10000 0 0 16 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.016 0.05 0.13 2 -0.23 4 6
JUN -0.019 0.005 0 10 -10000 0 10
IL4 -0.004 0.002 0 21 -10000 0 21
CDK5R1 -0.017 0.002 0 3 -10000 0 3
PRKACA -0.016 0.003 0 5 -10000 0 5
cortisol/GR alpha (monomer)/AP-1 -0.029 0.009 0 9 -10000 0 9
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.028 0.011 -10000 0 0 17 17
cortisol/GR alpha (monomer) 0.012 0.003 -10000 0 0 6 6
NCOA2 -0.015 0.006 0 18 -10000 0 18
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.016 0.003 0 4 -10000 0 4
AP-1/NFAT1-c-4 -0.02 0.021 0.18 1 -10000 0 1
AFP -0.011 0.032 0.19 3 -10000 0 3
SUV420H1 -0.016 0.003 0 5 -10000 0 5
IRF1 0.006 0.002 -10000 0 0 10 10
TP53 -0.016 0.004 0 10 -10000 0 10
PPP5C -0.016 0.004 0 8 -10000 0 8
KRT17 -0.003 0.001 -10000 0 -10000 0 0
KRT14 -0.002 0.001 -10000 0 -10000 0 0
TBP -0.016 0.004 0 9 -10000 0 9
CREBBP -0.016 0.003 0 5 -10000 0 5
HDAC1 -0.016 0.003 0 6 -10000 0 6
HDAC2 -0.016 0.003 0 5 -10000 0 5
AP-1 -0.02 0.021 0.18 1 -10000 0 1
MAPK14 -0.016 0.003 0 6 -10000 0 6
MAPK10 -0.017 0.002 0 2 -10000 0 2
MAPK11 -0.016 0.004 0 9 -10000 0 9
KRT5 -0.003 0.001 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 -0.017 0 -10000 0 -10000 0 0
STAT1 -0.017 0.002 0 3 -10000 0 3
CGA -0.004 0.001 0 12 -10000 0 12
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.002 0.001 -10000 0 -10000 0 0
MAPK3 -0.017 0.002 0 2 -10000 0 2
MAPK1 -0.016 0.003 0 4 -10000 0 4
ICAM1 -0.005 0.001 0 13 -10000 0 13
NFKB1 -0.017 0.002 0 2 -10000 0 2
MAPK8 -0.016 0.004 0 7 -10000 0 7
MAPK9 -0.016 0.003 0 6 -10000 0 6
cortisol/GR alpha (dimer) -0.019 0.057 -10000 0 -0.21 8 8
BAX -0.002 0.052 0.17 5 -0.17 8 13
POMC -0.003 0.013 -10000 0 -10000 0 0
EP300 -0.016 0.003 0 4 -10000 0 4
cortisol/GR alpha (dimer)/p53 0.02 0.007 -10000 0 0 14 14
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.003 0 14 -10000 0 14
SGK1 -0.004 0.04 0.1 2 -0.17 6 8
IL13 -0.004 0.002 -10000 0 -10000 0 0
IL6 -0.004 0.002 0 15 -10000 0 15
PRKACG -0.017 0.002 0 3 -10000 0 3
IL5 -0.006 0.029 0.075 1 -0.14 6 7
IL2 -0.007 0.031 -10000 0 -0.26 2 2
CDK5 -0.016 0.004 0 7 -10000 0 7
PRKACB -0.016 0.003 0 4 -10000 0 4
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.005 0.001 0 11 -10000 0 11
CDK5R1/CDK5 0.023 0.006 -10000 0 0 10 10
NF kappa B1 p50/RelA/PKAc 0.046 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.019 0.007 -10000 0 0 15 15
SMARCA4 -0.016 0.004 0 9 -10000 0 9
chromatin remodeling 0.005 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp 0.039 0.012 -10000 0 0 12 12
JUN (dimer) -0.019 0.005 0 10 -10000 0 10
YWHAH -0.017 0.002 0 3 -10000 0 3
VIPR1 -0.016 0.004 0 9 -10000 0 9
NR3C1 -0.016 0.003 0 6 -10000 0 6
NR4A1 -0.017 0.001 0 1 -10000 0 1
TIF2/SUV420H1 0.021 0.009 -10000 0 0 21 21
MAPKKK cascade -0.018 0.057 0.12 1 -0.2 8 9
cortisol/GR alpha (dimer)/Src-1 0.022 0.005 -10000 0 0 6 6
PBX1 -0.016 0.003 0 6 -10000 0 6
POU1F1 -0.017 0.002 0 2 -10000 0 2
SELE -0.004 0.002 0 15 -10000 0 15
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.005 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.019 0.007 -10000 0 0 15 15
mol:cortisol 0 0 -10000 0 -10000 0 0
MMP1 0.001 0.053 -10000 0 -0.43 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.013 0.008 -10000 0 -0.054 2 2
CRKL -0.016 0.003 0 5 -10000 0 5
Rac1/GDP 0.012 0.003 -10000 0 0 9 9
DOCK1 -0.016 0.003 0 5 -10000 0 5
ITGA4 -0.017 0.002 0 3 -10000 0 3
alpha4/beta7 Integrin/MAdCAM1 0.039 0.012 -10000 0 0 11 11
EPO -0.015 0.005 0 13 -10000 0 13
alpha4/beta7 Integrin 0.024 0.004 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.004 0 7 -10000 0 7
alpha4/beta1 Integrin 0.024 0.005 -10000 0 0 6 6
EPO/EPOR (dimer) 0.022 0.008 -10000 0 0 16 16
lamellipodium assembly -0.01 0.086 0.12 8 -0.44 4 12
PIK3CA -0.016 0.004 0 10 -10000 0 10
PI3K 0.021 0.008 -10000 0 0 18 18
ARF6 -0.016 0.003 0 6 -10000 0 6
JAK2 -0.008 0.005 -10000 0 -10000 0 0
PXN -0.016 0.003 0 4 -10000 0 4
PIK3R1 -0.016 0.004 0 9 -10000 0 9
MADCAM1 -0.016 0.003 0 6 -10000 0 6
cell adhesion 0.038 0.011 -10000 0 0 11 11
CRKL/CBL 0.023 0.006 -10000 0 0 9 9
ITGB1 -0.017 0.002 0 3 -10000 0 3
SRC -0.02 0.029 0.16 3 -10000 0 3
ITGB7 -0.017 0.001 0 1 -10000 0 1
RAC1 -0.016 0.004 0 9 -10000 0 9
alpha4/b