Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNASeq expression data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 48 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
Class IB PI3K non-lipid kinase events 230
Signaling events mediated by Stem cell factor receptor (c-Kit) 218
Reelin signaling pathway 188
EGFR-dependent Endothelin signaling events 184
Signaling mediated by p38-alpha and p38-beta 177
p75(NTR)-mediated signaling 136
HIF-1-alpha transcription factor network 132
FOXA2 and FOXA3 transcription factor networks 129
Glucocorticoid receptor regulatory network 126
Lissencephaly gene (LIS1) in neuronal migration and development 122
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Class IB PI3K non-lipid kinase events 230 690 3 -0.23 -1000 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 218 17044 78 -0.62 0.19 1000 -1000 -0.078 -1000
Reelin signaling pathway 188 10581 56 -0.52 0 1000 -1000 -0.1 -1000
EGFR-dependent Endothelin signaling events 184 3871 21 -0.35 0 1000 -1000 -0.067 -1000
Signaling mediated by p38-alpha and p38-beta 177 7805 44 -0.4 0 1000 -1000 -0.049 -1000
p75(NTR)-mediated signaling 136 17060 125 -0.44 0 1000 -1000 -0.098 -1000
HIF-1-alpha transcription factor network 132 10059 76 -0.8 0.018 1000 -1000 -0.1 -1000
FOXA2 and FOXA3 transcription factor networks 129 5972 46 -1.2 0.026 1000 -1000 -0.036 -1000
Glucocorticoid receptor regulatory network 126 14422 114 -1 0.37 1000 -1000 -0.068 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 122 6626 54 -0.52 0.022 1000 -1000 -0.09 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 119 8150 68 -0.53 0.16 1000 -1000 -0.1 -1000
Wnt signaling 110 773 7 -0.2 -0.006 1000 -1000 -0.054 -1000
Arf6 signaling events 103 6427 62 -0.35 0.017 1000 -1000 -0.056 -1000
Ephrin B reverse signaling 101 4872 48 -0.36 0.21 1000 -1000 -0.07 -1000
EPHB forward signaling 100 8576 85 -0.36 0.2 1000 -1000 -0.092 -1000
IL4-mediated signaling events 98 8964 91 -1 0.51 1000 -1000 -0.13 -1000
Angiopoietin receptor Tie2-mediated signaling 97 8580 88 -0.35 0.031 1000 -1000 -0.1 -1000
Endothelins 95 9204 96 -0.4 0.037 1000 -1000 -0.077 -1000
ErbB2/ErbB3 signaling events 94 6136 65 -0.45 0.018 1000 -1000 -0.066 -1000
IGF1 pathway 93 5301 57 -0.19 0.081 1000 -1000 -0.089 -1000
FOXM1 transcription factor network 90 4622 51 -0.46 0.012 1000 -1000 -0.13 -1000
ErbB4 signaling events 81 5634 69 -0.45 0.061 1000 -1000 -0.085 -1000
Calcium signaling in the CD4+ TCR pathway 79 2451 31 -0.38 0.011 1000 -1000 -0.093 -1000
Neurotrophic factor-mediated Trk receptor signaling 79 9496 120 -0.66 0.26 1000 -1000 -0.075 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 78 6713 85 -0.27 0.012 1000 -1000 -0.064 -1000
BMP receptor signaling 78 6375 81 -0.58 0.024 1000 -1000 -0.08 -1000
Nongenotropic Androgen signaling 77 4013 52 -0.25 0.11 1000 -1000 -0.063 -1000
Noncanonical Wnt signaling pathway 76 2000 26 -0.2 0 1000 -1000 -0.08 -1000
Signaling events regulated by Ret tyrosine kinase 75 6215 82 -0.17 0 1000 -1000 -0.081 -1000
Glypican 1 network 73 3549 48 -0.34 0.026 1000 -1000 -0.054 -1000
IL23-mediated signaling events 72 4353 60 -0.49 0.018 1000 -1000 -0.13 -1000
Plasma membrane estrogen receptor signaling 68 5926 86 -0.2 0.081 1000 -1000 -0.075 -1000
Aurora B signaling 68 4608 67 -0.33 0.013 1000 -1000 -0.07 -1000
Signaling events mediated by PTP1B 64 4928 76 -0.68 0.068 1000 -1000 -0.072 -1000
IL6-mediated signaling events 62 4689 75 -0.31 0.054 1000 -1000 -0.08 -1000
Visual signal transduction: Rods 62 3270 52 -0.53 0 1000 -1000 -0.089 -1000
Ephrin A reverse signaling 59 419 7 -0.083 0 1000 -1000 -0.039 -1000
RXR and RAR heterodimerization with other nuclear receptor 59 3079 52 -0.2 0.03 1000 -1000 -0.06 -1000
amb2 Integrin signaling 57 4692 82 -0.54 0 1000 -1000 -0.078 -1000
Fc-epsilon receptor I signaling in mast cells 56 5511 97 -0.27 0.028 1000 -1000 -0.083 -1000
Integrins in angiogenesis 56 4728 84 -0.34 0 1000 -1000 -0.095 -1000
Syndecan-1-mediated signaling events 54 1866 34 -0.22 0 1000 -1000 -0.075 -1000
S1P1 pathway 54 1951 36 -0.33 0.007 1000 -1000 -0.067 -1000
Syndecan-3-mediated signaling events 53 1876 35 -0.37 0 1000 -1000 -0.067 -1000
LPA receptor mediated events 51 5219 102 -0.29 0.029 1000 -1000 -0.081 -1000
Signaling events mediated by the Hedgehog family 50 2635 52 -0.22 0.031 1000 -1000 -0.07 -1000
PDGFR-alpha signaling pathway 48 2123 44 -0.4 0.02 1000 -1000 -0.064 -1000
Ras signaling in the CD4+ TCR pathway 47 803 17 -0.13 0 1000 -1000 -0.059 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 42 1408 33 -0.6 0 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class III 40 1606 40 -0.61 0.03 1000 -1000 -0.045 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 2962 74 -0.29 0.071 1000 -1000 -0.087 -1000
E-cadherin signaling in keratinocytes 40 1748 43 -0.29 0.044 1000 -1000 -0.073 -1000
Rapid glucocorticoid signaling 39 784 20 -0.19 0.027 1000 -1000 -0.044 -1000
Signaling events mediated by PRL 39 1341 34 -0.2 0.021 1000 -1000 -0.063 -1000
Nephrin/Neph1 signaling in the kidney podocyte 38 1301 34 -0.075 0 1000 -1000 -0.066 -1000
LPA4-mediated signaling events 37 445 12 -0.17 0.019 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 37 1752 47 -0.5 0.01 1000 -1000 -0.055 -1000
Presenilin action in Notch and Wnt signaling 36 2256 61 -0.44 0.013 1000 -1000 -0.076 -1000
TCGA08_rtk_signaling 32 849 26 -0.29 0.027 1000 -1000 -0.03 -1000
Nectin adhesion pathway 31 1995 63 -0.067 0.015 1000 -1000 -0.07 -1000
Effects of Botulinum toxin 30 783 26 -0.1 0 1000 -1000 -0.058 -1000
TCR signaling in naïve CD8+ T cells 29 2772 93 -0.18 0.085 1000 -1000 -0.076 -1000
Regulation of Androgen receptor activity 28 1966 70 -0.29 0.026 1000 -1000 -0.071 -1000
Canonical Wnt signaling pathway 27 1377 51 -0.44 0.15 1000 -1000 -0.065 -1000
IL27-mediated signaling events 27 1418 51 -0.32 0.014 1000 -1000 -0.07 -1000
Insulin Pathway 27 2047 74 -0.19 0.032 1000 -1000 -0.089 -1000
Coregulation of Androgen receptor activity 26 2036 76 -0.18 0.034 1000 -1000 -0.053 -1000
BCR signaling pathway 26 2580 99 -0.15 0.043 1000 -1000 -0.078 -1000
Regulation of nuclear SMAD2/3 signaling 25 3466 136 -0.34 0.05 1000 -1000 -0.088 -1000
PLK1 signaling events 24 2121 85 -0.22 0.037 1000 -1000 -0.057 -1000
Regulation of p38-alpha and p38-beta 24 1326 54 -0.38 0.028 1000 -1000 -0.066 -1000
IL12-mediated signaling events 23 2076 87 -0.38 0.055 1000 -1000 -0.12 -1000
Arf6 trafficking events 23 1636 71 -0.47 0.032 1000 -1000 -0.065 -1000
TCGA08_retinoblastoma 22 181 8 -0.045 0.008 1000 -1000 -0.021 -1000
Thromboxane A2 receptor signaling 20 2184 105 -0.29 0.071 1000 -1000 -0.069 -1000
Aurora A signaling 20 1207 60 -0.2 0.006 1000 -1000 -0.064 -1000
Regulation of Telomerase 20 2132 102 -0.35 0.021 1000 -1000 -0.1 -1000
Syndecan-2-mediated signaling events 19 1379 69 -0.2 0.038 1000 -1000 -0.06 -1000
S1P5 pathway 19 324 17 -0.043 0.024 1000 -1000 -0.046 -1000
Syndecan-4-mediated signaling events 19 1328 67 -0.34 0.004 1000 -1000 -0.089 -1000
S1P4 pathway 18 453 25 -0.043 0 1000 -1000 -0.053 -1000
Visual signal transduction: Cones 15 606 38 -0.18 0.007 1000 -1000 -0.055 -1000
Hedgehog signaling events mediated by Gli proteins 15 1028 65 -0.063 0.041 1000 -1000 -0.082 -1000
E-cadherin signaling events 15 76 5 -0.024 0 1000 -1000 -0.038 -1000
PLK2 and PLK4 events 14 42 3 -0.014 0.012 1000 -1000 -0.026 -1000
Osteopontin-mediated events 14 539 38 -0.27 0.029 1000 -1000 -0.099 -1000
Class I PI3K signaling events mediated by Akt 14 998 68 -0.28 0.053 1000 -1000 -0.058 -1000
Ceramide signaling pathway 14 1102 76 -0.18 0.048 1000 -1000 -0.065 -1000
Caspase cascade in apoptosis 13 980 74 -0.054 0.046 1000 -1000 -0.053 -1000
TRAIL signaling pathway 13 669 48 -0.08 0.048 1000 -1000 -0.071 -1000
Cellular roles of Anthrax toxin 12 471 39 -0.15 0.02 1000 -1000 -0.03 -1000
BARD1 signaling events 11 662 57 -0.11 0.022 1000 -1000 -0.064 -1000
Signaling mediated by p38-gamma and p38-delta 11 171 15 -0.016 0.021 1000 -1000 -0.051 -1000
Retinoic acid receptors-mediated signaling 10 615 58 -0.11 0.039 1000 -1000 -0.071 -1000
E-cadherin signaling in the nascent adherens junction 10 788 76 -0.024 0.048 1000 -1000 -0.075 -1000
S1P3 pathway 9 384 42 -0.043 0.02 1000 -1000 -0.056 -1000
JNK signaling in the CD4+ TCR pathway 8 150 17 -0.019 0.044 1000 -1000 -0.069 -1000
Glypican 2 network 8 33 4 -0.033 -0.027 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 7 210 28 -0.043 0.019 1000 -1000 -0.059 -1000
IL1-mediated signaling events 7 495 62 -0.039 0.032 1000 -1000 -0.091 -1000
Signaling events mediated by HDAC Class II 6 462 75 -0.15 0.001 1000 -1000 -0.074 -1000
mTOR signaling pathway 6 331 53 -0.016 0.028 1000 -1000 -0.06 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 535 83 -0.074 0.048 1000 -1000 -0.076 -1000
p38 MAPK signaling pathway 6 297 44 -0.075 0.032 1000 -1000 -0.066 -1000
IL2 signaling events mediated by PI3K 5 296 58 -0.034 0.065 1000 -1000 -0.077 -1000
VEGFR1 specific signals 5 304 56 -0.17 0.062 1000 -1000 -0.081 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 4 107 23 -0.034 0.041 1000 -1000 -0.061 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 199 45 -0.026 0.074 1000 -1000 -0.087 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 562 125 -0.17 0.086 1000 -1000 -0.093 -1000
Signaling events mediated by HDAC Class I 3 316 104 -0.096 0.045 1000 -1000 -0.069 -1000
FoxO family signaling 3 217 64 -0.048 0.092 1000 -1000 -0.074 -1000
IL2 signaling events mediated by STAT5 3 73 22 -0.12 0.067 1000 -1000 -0.056 -1000
Class I PI3K signaling events 3 286 73 -0.036 0.061 1000 -1000 -0.072 -1000
PDGFR-beta signaling pathway 3 345 97 -0.027 0.055 1000 -1000 -0.086 -1000
Arf6 downstream pathway 2 86 43 -0.014 0.022 1000 -1000 -0.042 -1000
Aurora C signaling 2 16 7 -0.16 0 1000 -1000 -0.041 -1000
EPO signaling pathway 2 127 55 -0.037 0.058 1000 -1000 -0.08 -1000
Paxillin-independent events mediated by a4b1 and a4b7 2 83 37 -0.048 0.035 1000 -1000 -0.074 -1000
ceramide signaling pathway 2 140 49 -0.024 0.053 1000 -1000 -0.047 -1000
HIF-2-alpha transcription factor network 2 127 43 -0.056 0.17 1000 -1000 -0.074 -1000
Canonical NF-kappaB pathway 1 76 39 -0.022 0.076 1000 -1000 -0.077 -1000
Circadian rhythm pathway 1 26 22 -0.018 0.046 1000 -1000 -0.065 -1000
a4b1 and a4b7 Integrin signaling 1 8 5 -0.007 -0.002 1000 -1000 -0.041 -1000
Insulin-mediated glucose transport 1 49 32 -0.14 0.021 1000 -1000 -0.06 -1000
IFN-gamma pathway 1 126 68 -0.075 0.075 1000 -1000 -0.087 -1000
Atypical NF-kappaB pathway 1 53 31 -0.019 0.024 1000 -1000 -0.063 -1000
TCGA08_p53 0 0 7 -0.02 0.014 1000 -1000 -0.026 -1000
Paxillin-dependent events mediated by a4b1 0 27 36 -0.008 0.022 1000 -1000 -0.074 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 7 27 -0.001 0.028 1000 -1000 -0.055 -1000
Arf1 pathway 0 0 54 0 0.025 1000 -1000 -0.046 -1000
Alternative NF-kappaB pathway 0 0 13 -0.002 0 1000 -1000 -0.061 -1000
Total 5724 343396 7203 -32 -990 131000 -131000 -9.1 -131000
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.23 0.37 0.83 230 -10000 0 230
PI3K Class IB/PDE3B -0.23 0.37 -10000 0 -0.84 230 230
PDE3B -0.23 0.37 -10000 0 -0.84 230 230
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.15 0.22 -10000 0 -0.39 379 379
CRKL -0.16 0.23 -10000 0 -0.41 378 378
HRAS -0.16 0.17 -10000 0 -0.57 21 21
mol:PIP3 -0.17 0.21 -10000 0 -0.4 378 378
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.2 0.22 -10000 0 -0.44 379 379
FOXO3 -0.14 0.21 -10000 0 -0.38 378 378
AKT1 -0.16 0.22 -10000 0 -0.41 378 378
BAD -0.14 0.21 -10000 0 -0.37 378 378
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 379 379
GSK3B -0.14 0.21 -10000 0 -0.37 378 378
RAF1 -0.089 0.17 -10000 0 -0.46 18 18
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 379 379
STAT1 -0.45 0.56 -10000 0 -1.1 385 385
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.46 18 18
cell proliferation -0.18 0.24 -10000 0 -0.43 379 379
PIK3CA 0 0.01 -10000 0 -0.28 1 1
TEC -0.002 0.041 -10000 0 -0.84 2 2
RPS6KB1 -0.18 0.24 -10000 0 -0.44 379 379
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.46 19 19
LYN/TEC/p62DOK -0.18 0.2 -10000 0 -0.4 379 379
MAPK3 -0.052 0.13 -10000 0 -0.32 16 16
STAP1 -0.2 0.24 -10000 0 -0.46 381 381
GRAP2 -0.014 0.1 -10000 0 -0.84 13 13
JAK2 -0.4 0.44 -10000 0 -0.87 385 385
STAT1 (dimer) -0.44 0.55 -10000 0 -1 385 385
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.18 0.2 -10000 0 -0.41 379 379
actin filament polymerization -0.18 0.24 -10000 0 -0.44 379 379
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.29 0.32 -10000 0 -0.63 380 380
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.37 377 377
PI3K -0.19 0.2 -10000 0 -0.41 378 378
PTEN -0.002 0.041 -10000 0 -0.84 2 2
SCF/KIT/EPO/EPOR -0.59 0.68 -10000 0 -1.3 378 378
MAPK8 -0.18 0.24 -10000 0 -0.44 379 379
STAT3 (dimer) -0.18 0.24 -10000 0 -0.43 379 379
positive regulation of transcription -0.04 0.11 -10000 0 -0.26 15 15
mol:GDP -0.16 0.18 -10000 0 -0.6 23 23
PIK3C2B -0.18 0.24 -10000 0 -0.44 379 379
CBL/CRKL -0.18 0.19 -10000 0 -0.38 378 378
FER -0.18 0.24 -10000 0 -0.44 382 382
SH2B3 -0.18 0.24 -10000 0 -0.44 379 379
PDPK1 -0.15 0.2 -10000 0 -0.36 378 378
SNAI2 -0.18 0.24 -10000 0 -0.45 380 380
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.76 385 385
KITLG 0.001 0.068 -10000 0 -0.68 6 6
cell motility -0.32 0.41 -10000 0 -0.76 385 385
PTPN6 0.014 0.021 -10000 0 -0.27 2 2
EPOR -0.095 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 386 386
SOCS1 -0.004 0.039 -10000 0 -0.34 9 9
cell migration 0.19 0.25 0.45 385 -10000 0 385
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.045 0.11 -10000 0 -0.3 84 84
VAV1 -0.002 0.032 -10000 0 -0.84 1 1
GRB10 -0.2 0.22 -10000 0 -0.44 379 379
PTPN11 0.012 0.013 -10000 0 -10000 0 0
SCF/KIT -0.21 0.24 -10000 0 -0.47 379 379
GO:0007205 0.008 0.013 -10000 0 -10000 0 0
MAP2K1 -0.061 0.14 -10000 0 -0.36 16 16
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.74 -10000 0 -1.4 377 377
MAP2K2 -0.061 0.14 -10000 0 -0.36 16 16
SHC/Grb2/SOS1 -0.18 0.2 -10000 0 -0.4 378 378
STAT5A -0.27 0.35 -10000 0 -0.64 386 386
GRB2 0 0.01 -10000 0 -10000 0 0
response to radiation -0.18 0.24 -10000 0 -0.44 380 380
SHC/GRAP2 -0.011 0.08 -10000 0 -0.64 13 13
PTPRO -0.18 0.24 -10000 0 -0.44 379 379
SH2B2 -0.18 0.24 -10000 0 -0.44 379 379
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.19 0.25 -10000 0 -0.46 385 385
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.12 0.29 -10000 0 -1.6 24 24
Reelin 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
CDK5R1/CDK5 -0.006 0.032 -9999 0 -10000 0 0
VLDLR -0.021 0.13 -9999 0 -0.84 21 21
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
ITGA3 -0.004 0.058 -9999 0 -0.72 5 5
RELN/VLDLR/Fyn -0.36 0.29 -9999 0 -0.57 529 529
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.002 0.029 -9999 0 -0.48 3 3
AKT1 -0.21 0.17 -9999 0 -0.33 529 529
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.066 -9999 0 -0.28 51 51
RELN/LRP8/DAB1 -0.35 0.26 -9999 0 -0.54 525 525
LRPAP1/LRP8 -0.022 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.32 0.24 -9999 0 -0.51 525 525
DAB1/alpha3/beta1 Integrin -0.3 0.23 -9999 0 -0.6 121 121
long-term memory -0.4 0.31 -9999 0 -0.57 571 571
DAB1/LIS1 -0.31 0.24 -9999 0 -0.49 529 529
DAB1/CRLK/C3G -0.3 0.23 -9999 0 -0.6 120 120
PIK3CA 0 0.01 -9999 0 -0.28 1 1
DAB1/NCK2 -0.31 0.24 -9999 0 -0.49 529 529
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.093 0.26 -9999 0 -0.84 90 90
CDK5R1 -0.009 0.048 -9999 0 -0.28 26 26
RELN -0.52 0.4 -9999 0 -0.84 524 524
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.37 0.28 -9999 0 -0.58 524 524
GRIN2A/RELN/LRP8/DAB1/Fyn -0.37 0.3 -9999 0 -0.57 538 538
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.34 0.27 -9999 0 -0.54 529 529
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.33 0.26 -9999 0 -0.52 532 532
RELN/LRP8 -0.36 0.28 -9999 0 -0.58 524 524
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.27 -9999 0 -0.54 558 558
PI3K 0 0.006 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.045 -9999 0 -0.64 4 4
RAP1A -0.28 0.22 -9999 0 -0.55 119 119
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.053 -9999 0 -0.84 3 3
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.071 0.23 -9999 0 -0.82 73 73
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.14 0.11 -9999 0 -0.56 3 3
neuron adhesion -0.26 0.2 -9999 0 -0.52 120 120
LRP8 -0.034 0.091 -9999 0 -0.28 104 104
GSK3B -0.18 0.17 -9999 0 -0.44 48 48
RELN/VLDLR/DAB1/Fyn -0.32 0.25 -9999 0 -0.51 529 529
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.23 0.18 -9999 0 -0.36 529 529
CDK5 -0.001 0.019 -9999 0 -0.28 4 4
MAPT -0.042 0.25 -9999 0 -0.78 83 83
neuron migration -0.25 0.24 -9999 0 -0.43 525 525
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.56 3 3
RELN/VLDLR -0.34 0.27 -9999 0 -0.54 529 529
EGFR-dependent Endothelin signaling events

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
HRAS 0 0.01 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.84 291 291
EGF/EGFR -0.29 0.33 -9999 0 -0.58 418 418
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.29 -9999 0 -0.53 409 409
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.84 167 167
EGF/EGFR dimer/SHC -0.3 0.33 -9999 0 -0.62 409 409
mol:GDP -0.26 0.28 -9999 0 -0.53 409 409
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.066 0.22 -9999 0 -0.84 66 66
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.26 -9999 0 -0.48 409 409
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.24 0.26 -9999 0 -0.49 409 409
FRAP1 -0.25 0.27 -9999 0 -0.51 409 409
EGF/EGFR dimer -0.35 0.37 -9999 0 -0.71 409 409
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.051 0.17 -9999 0 -0.64 66 66
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.64 -9999 0 -1.3 282 282
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.082 0.15 -9999 0 -0.3 282 282
ATF2/c-Jun -0.056 0.17 -9999 0 -0.97 12 12
MAPK11 -0.084 0.16 -9999 0 -0.48 13 13
MITF -0.093 0.2 -9999 0 -0.36 287 287
MAPKAPK5 -0.089 0.19 -9999 0 -0.35 284 284
KRT8 -0.095 0.19 -9999 0 -0.36 285 285
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.01 -9999 0 -0.28 1 1
p38alpha-beta/CK2 -0.13 0.23 -9999 0 -0.45 284 284
CEBPB -0.089 0.19 -9999 0 -0.35 284 284
SLC9A1 -0.089 0.19 -9999 0 -0.35 284 284
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 284 284
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.52 14 14
JUN -0.054 0.16 -9999 0 -0.95 12 12
PPARGC1A -0.22 0.38 -9999 0 -0.58 357 357
USF1 -0.089 0.19 -9999 0 -0.35 284 284
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.37 13 13
NOS2 -0.092 0.21 -9999 0 -1.1 7 7
DDIT3 -0.089 0.19 -9999 0 -0.35 284 284
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.069 0.16 -9999 0 -0.42 27 27
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.35 284 284
CREB1 -0.092 0.2 -9999 0 -0.37 284 284
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.47 13 13
RPS6KA4 -0.089 0.19 -9999 0 -0.35 284 284
PLA2G4A -0.13 0.27 -9999 0 -0.74 99 99
GDI1 -0.089 0.19 -9999 0 -0.35 284 284
TP53 -0.12 0.24 -9999 0 -0.44 284 284
RPS6KA5 -0.093 0.19 -9999 0 -0.36 290 290
ESR1 -0.17 0.25 -9999 0 -0.42 383 383
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.19 -9999 0 -0.36 284 284
MEF2A -0.089 0.19 -9999 0 -0.35 284 284
EIF4EBP1 -0.092 0.2 -9999 0 -0.37 284 284
KRT19 -0.1 0.21 -9999 0 -0.37 288 288
ELK4 -0.089 0.19 -9999 0 -0.35 284 284
ATF6 -0.089 0.19 -9999 0 -0.35 284 284
ATF1 -0.092 0.2 -9999 0 -0.37 284 284
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.52 15 15
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.54 13 13
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.022 -9999 0 -0.64 1 1
Necdin/E2F1 -0.081 0.14 -9999 0 -0.72 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.17 0.24 -9999 0 -0.49 286 286
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.34 -9999 0 -0.66 346 346
NT-4/5 (dimer)/p75(NTR) -0.44 0.44 -9999 0 -0.81 459 459
IKBKB -0.001 0.013 -9999 0 -0.28 2 2
AKT1 -0.16 0.23 -9999 0 -0.48 284 284
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.073 0.23 -9999 0 -0.7 87 87
MGDIs/NGR/p75(NTR)/LINGO1 -0.22 0.27 -9999 0 -0.59 277 277
FURIN -0.001 0.013 -9999 0 -0.28 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.23 0.31 -9999 0 -0.61 312 312
LINGO1 -0.062 0.12 -9999 0 -0.28 187 187
Sortilin/TRAF6/NRIF -0.001 0.029 -9999 0 -0.84 1 1
proBDNF (dimer) -0.073 0.23 -9999 0 -0.7 87 87
NTRK1 -0.009 0.053 -9999 0 -0.3 24 24
RTN4R -0.007 0.042 -9999 0 -10000 0 0
neuron apoptosis -0.16 0.28 -9999 0 -0.52 295 295
IRAK1 -0.001 0.013 -9999 0 -10000 0 0
SHC1 -0.18 0.29 -9999 0 -0.57 284 284
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.017 -9999 0 -0.48 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.18 0.25 -9999 0 -0.52 284 284
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.28 -9999 0 -0.55 295 295
Mammalian IAPs/DIABLO -0.006 0.048 -9999 0 -0.51 7 7
proNGF (dimer) -0.017 0.11 -9999 0 -0.84 15 15
MAGED1 -0.001 0.013 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.32 0.41 -9999 0 -0.84 324 324
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.17 0.24 -9999 0 -0.49 284 284
NGF -0.017 0.11 -9999 0 -0.84 15 15
cell cycle arrest -0.14 0.25 -9999 0 -0.48 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.12 0.17 -9999 0 -0.35 284 284
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.39 0.4 -9999 0 -0.72 459 459
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.2 0.28 -9999 0 -0.58 284 284
PSENEN 0 0.01 -9999 0 -0.28 1 1
mol:ceramide -0.18 0.25 -9999 0 -0.52 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.093 0.13 -9999 0 -0.58 9 9
p75(NTR)/beta APP -0.21 0.3 -9999 0 -0.64 277 277
BEX1 -0.16 0.28 -9999 0 -0.84 112 112
mol:GDP -0.18 0.29 -9999 0 -0.58 284 284
NGF (dimer) -0.086 0.19 -9999 0 -0.53 129 129
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.2 0.24 -9999 0 -0.54 277 277
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.17 0.24 -9999 0 -0.5 284 284
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.2 0.28 -9999 0 -0.59 284 284
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.059 0.082 -9999 0 -10000 0 0
NT3 (dimer) -0.14 0.31 -9999 0 -0.79 147 147
TP53 -0.18 0.25 -9999 0 -0.49 312 312
PRDM4 -0.18 0.25 -9999 0 -0.52 284 284
BDNF (dimer) -0.17 0.24 -9999 0 -0.61 174 174
PIK3CA 0 0.01 -9999 0 -0.28 1 1
SORT1 -0.001 0.029 -9999 0 -0.84 1 1
activation of caspase activity -0.17 0.23 -9999 0 -0.48 286 286
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.25 -9999 0 -0.52 284 284
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.18 0.28 -9999 0 -0.52 288 288
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.18 0.25 -9999 0 -0.52 284 284
APH1B -0.001 0.029 -9999 0 -0.84 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -9999 0 -0.57 284 284
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.31 0.38 -9999 0 -0.74 353 353
MAPK8 -0.13 0.25 -9999 0 -0.46 277 277
MAPK9 -0.13 0.25 -9999 0 -0.46 277 277
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.14 0.31 -9999 0 -0.79 147 147
NTF4 -0.32 0.41 -9999 0 -0.84 324 324
NDN -0.029 0.15 -9999 0 -0.84 29 29
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.16 0.22 -9999 0 -0.46 284 284
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.018 -9999 0 -0.51 1 1
RhoA-B-C/GTP -0.2 0.28 -9999 0 -0.58 284 284
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.2 0.27 -9999 0 -0.53 312 312
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.21 0.28 -9999 0 -0.56 312 312
PRKACB -0.017 0.078 -9999 0 -0.31 46 46
proBDNF (dimer)/p75 ECD -0.055 0.17 -9999 0 -0.64 66 66
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.082 -9999 0 -0.51 17 17
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.27 -9999 0 -0.5 284 284
BAD -0.14 0.26 -9999 0 -0.47 288 288
RIPK2 -0.001 0.019 -9999 0 -0.28 4 4
NGFR -0.28 0.39 -9999 0 -0.84 277 277
CYCS -0.17 0.24 -9999 0 -0.49 284 284
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.18 0.25 -9999 0 -0.52 284 284
BCL2L11 -0.14 0.26 -9999 0 -0.47 288 288
BDNF (dimer)/p75(NTR) -0.26 0.35 -9999 0 -0.7 312 312
PI3K -0.18 0.25 -9999 0 -0.52 284 284
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.18 0.25 -9999 0 -0.52 284 284
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.01 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.22 0.32 -9999 0 -0.66 284 284
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.18 0.25 -9999 0 -0.52 284 284
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.029 -9999 0 -0.84 1 1
PLG -0.001 0.019 -9999 0 -0.28 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.22 0.29 -9999 0 -0.56 319 319
SQSTM1 -0.001 0.013 -9999 0 -10000 0 0
NGFRAP1 -0.002 0.041 -9999 0 -0.84 2 2
CASP3 -0.12 0.24 -9999 0 -0.43 288 288
E2F1 -0.094 0.13 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.073 0.12 -9999 0 -0.6 17 17
NGF (dimer)/TRKA -0.019 0.093 -9999 0 -0.65 16 16
MMP7 -0.12 0.29 -9999 0 -0.84 116 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.49 284 284
MMP3 -0.12 0.16 -9999 0 -0.3 328 328
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.69 13 13
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.42 0.45 -9999 0 -1.1 161 161
HDAC7 0 0 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.31 -9999 0 -0.83 145 145
SMAD4 0 0 -9999 0 -10000 0 0
ID2 -0.42 0.45 -9999 0 -1.1 178 178
AP1 -0.22 0.31 -9999 0 -0.66 272 272
ABCG2 -0.45 0.48 -9999 0 -1.1 190 190
HIF1A -0.054 0.06 -9999 0 -10000 0 0
TFF3 -0.5 0.52 -9999 0 -1.2 222 222
GATA2 -0.017 0.13 -9999 0 -0.79 21 21
AKT1 -0.057 0.079 -9999 0 -10000 0 0
response to hypoxia -0.079 0.085 -9999 0 -0.26 15 15
MCL1 -0.42 0.45 -9999 0 -1.1 163 163
NDRG1 -0.43 0.45 -9999 0 -1.1 182 182
SERPINE1 -0.43 0.45 -9999 0 -1.1 172 172
FECH -0.42 0.45 -9999 0 -1.1 163 163
FURIN -0.42 0.45 -9999 0 -1.1 179 179
NCOA2 -0.004 0.077 -9999 0 -0.84 7 7
EP300 -0.058 0.12 -9999 0 -0.36 52 52
HMOX1 -0.43 0.45 -9999 0 -1.1 180 180
BHLHE40 -0.42 0.45 -9999 0 -1.1 168 168
BHLHE41 -0.43 0.47 -9999 0 -1.1 170 170
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.051 -9999 0 -10000 0 0
ENG -0.04 0.046 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
RORA -0.42 0.45 -9999 0 -1.1 169 169
ABCB1 -0.34 0.55 -9999 0 -1.5 160 160
TFRC -0.43 0.45 -9999 0 -1.1 187 187
CXCR4 -0.43 0.45 -9999 0 -1.1 176 176
TF -0.69 0.57 -9999 0 -1.2 407 407
CITED2 -0.42 0.45 -9999 0 -1.1 184 184
HIF1A/ARNT -0.51 0.51 -9999 0 -1.2 221 221
LDHA -0.051 0.047 -9999 0 -10000 0 0
ETS1 -0.42 0.45 -9999 0 -1.1 179 179
PGK1 -0.42 0.45 -9999 0 -1.1 169 169
NOS2 -0.43 0.46 -9999 0 -1.1 174 174
ITGB2 -0.42 0.45 -9999 0 -1.1 171 171
ALDOA -0.42 0.45 -9999 0 -1.1 173 173
Cbp/p300/CITED2 -0.44 0.44 -9999 0 -1.1 185 185
FOS -0.27 0.39 -9999 0 -0.84 271 271
HK2 -0.42 0.45 -9999 0 -1.1 164 164
SP1 0.011 0.024 -9999 0 -10000 0 0
GCK -0.15 0.4 -9999 0 -1.6 53 53
HK1 -0.42 0.45 -9999 0 -1.1 179 179
NPM1 -0.42 0.45 -9999 0 -1.1 173 173
EGLN1 -0.42 0.45 -9999 0 -1.1 185 185
CREB1 0.018 0 -9999 0 -10000 0 0
PGM1 -0.42 0.45 -9999 0 -1.1 172 172
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.21 0.41 -9999 0 -1.2 103 103
IGFBP1 -0.53 0.53 -9999 0 -1.2 261 261
VEGFA -0.26 0.31 -9999 0 -0.8 74 74
HIF1A/JAB1 -0.029 0.026 -9999 0 -10000 0 0
CP -0.54 0.54 -9999 0 -1.2 268 268
CXCL12 -0.45 0.49 -9999 0 -1.2 187 187
COPS5 0.001 0.01 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.42 0.45 -9999 0 -1.1 173 173
EGLN3 -0.43 0.46 -9999 0 -1.1 183 183
CA9 -0.47 0.48 -9999 0 -1.1 204 204
TERT -0.44 0.46 -9999 0 -1.1 180 180
ENO1 -0.42 0.45 -9999 0 -1.1 176 176
PFKL -0.42 0.45 -9999 0 -1.1 176 176
NCOA1 -0.001 0.029 -9999 0 -0.84 1 1
ADM -0.46 0.49 -9999 0 -1.1 201 201
ARNT -0.058 0.052 -9999 0 -10000 0 0
HNF4A -0.002 0.041 -9999 0 -0.37 1 1
ADFP -0.43 0.45 -9999 0 -1 221 221
SLC2A1 -0.26 0.31 -9999 0 -0.8 81 81
LEP -0.8 0.52 -9999 0 -1.2 452 452
HIF1A/ARNT/Cbp/p300 -0.35 0.32 -9999 0 -0.84 167 167
EPO -0.23 0.24 -9999 0 -0.7 10 10
CREBBP -0.058 0.12 -9999 0 -0.36 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.31 -9999 0 -0.85 132 132
PFKFB3 -0.43 0.46 -9999 0 -1.1 182 182
NT5E -0.43 0.46 -9999 0 -1.1 173 173
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.84 70 70
PCK1 -1.1 0.72 -9999 0 -1.6 520 520
HNF4A -0.25 0.28 -9999 0 -0.88 61 61
KCNJ11 -0.27 0.31 -9999 0 -0.84 115 115
AKT1 -0.14 0.14 -9999 0 -0.39 47 47
response to starvation -0.001 0.006 -9999 0 -10000 0 0
DLK1 -0.49 0.57 -9999 0 -1.3 274 274
NKX2-1 -0.055 0.15 -9999 0 -10000 0 0
ACADM -0.24 0.28 -9999 0 -0.83 84 84
TAT -1.2 0.68 -9999 0 -1.6 611 611
CEBPB 0.002 0.005 -9999 0 -10000 0 0
CEBPA -0.004 0.077 -9999 0 -0.84 7 7
TTR -0.46 0.28 -9999 0 -0.73 309 309
PKLR -0.24 0.28 -9999 0 -0.8 94 94
APOA1 -0.29 0.3 -9999 0 -0.87 94 94
CPT1C -0.24 0.28 -9999 0 -0.82 81 81
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.69 349 349
FOXF1 -0.004 0.056 -9999 0 -0.47 9 9
NF1 0.016 0.029 -9999 0 -0.83 1 1
HNF1A (dimer) 0.003 0.025 -9999 0 -10000 0 0
CPT1A -0.24 0.28 -9999 0 -0.8 89 89
HMGCS1 -0.24 0.28 -9999 0 -0.79 94 94
NR3C1 -0.11 0.12 -9999 0 -0.42 37 37
CPT1B -0.24 0.28 -9999 0 -0.83 83 83
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.006 -9999 0 -10000 0 0
GCK -0.29 0.37 -9999 0 -1 122 122
CREB1 -0.057 0.066 -9999 0 -10000 0 0
IGFBP1 -0.46 0.61 -9999 0 -1.5 197 197
PDX1 -0.13 0.14 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.81 84 84
ALDOB -0.26 0.31 -9999 0 -0.88 88 88
AFP -0.71 0.62 -9999 0 -1.1 473 473
BDH1 -0.24 0.28 -9999 0 -0.82 82 82
HADH -0.26 0.3 -9999 0 -0.84 99 99
F2 -0.29 0.3 -9999 0 -0.94 65 65
HNF1A 0.003 0.025 -9999 0 -10000 0 0
G6PC -0.2 0.11 -9999 0 -0.64 7 7
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.026 0.068 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.55 252 252
FOXA3 -0.43 0.22 -9999 0 -0.52 644 644
FOXA2 -0.32 0.34 -9999 0 -0.87 148 148
ABCC8 -0.34 0.44 -9999 0 -1.2 129 129
ALB -0.98 0.65 -9999 0 -1.4 553 553
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.025 0.079 -10000 0 -10000 0 0
SMARCC2 0.003 0.01 -10000 0 -10000 0 0
SMARCC1 0.003 0.01 -10000 0 -10000 0 0
TBX21 -0.14 0.26 -10000 0 -0.54 157 157
SUMO2 0 0.01 -10000 0 -0.28 1 1
STAT1 (dimer) 0.012 0.042 -10000 0 -0.27 18 18
FKBP4 -0.002 0.025 -10000 0 -10000 0 0
FKBP5 -0.012 0.097 -10000 0 -0.84 11 11
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.34 55 -0.44 12 67
PRL -0.096 0.12 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.31 0.26 0.54 400 -0.56 5 405
RELA -0.043 0.083 -10000 0 -10000 0 0
FGG 0.25 0.22 0.47 316 -0.51 1 317
GR beta/TIF2 0.14 0.14 0.34 104 -0.58 9 113
IFNG -0.45 0.35 -10000 0 -0.78 383 383
apoptosis -0.29 0.3 0.59 3 -0.67 229 232
CREB1 -0.008 0.028 -10000 0 -10000 0 0
histone acetylation 0.021 0.14 0.41 25 -0.39 23 48
BGLAP -0.11 0.15 -10000 0 -0.55 6 6
GR/PKAc 0.12 0.12 0.32 56 -0.47 3 59
NF kappa B1 p50/RelA -0.074 0.15 -10000 0 -0.43 21 21
SMARCD1 0.003 0.01 -10000 0 -10000 0 0
MDM2 0.13 0.1 0.25 220 -10000 0 220
GATA3 -0.029 0.16 -10000 0 -0.62 49 49
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.043 0.11 0.4 1 -0.57 5 6
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.22 0.27 0.56 3 -0.61 157 160
CSN2 0.21 0.17 0.41 214 -10000 0 214
BRG1/BAF155/BAF170/BAF60A -0.002 0.032 -10000 0 -0.46 4 4
NFATC1 0.001 0.03 -10000 0 -0.84 1 1
POU2F1 0.007 0.013 -10000 0 -10000 0 0
CDKN1A 0.047 0.061 -10000 0 -1.5 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.008 0.008 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.84 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.14 0.34 46 -0.42 19 65
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.39 0.44 0.54 3 -0.91 319 322
JUN -0.33 0.29 -10000 0 -0.59 382 382
IL4 -0.14 0.15 -10000 0 -0.54 12 12
CDK5R1 -0.009 0.049 -10000 0 -0.28 26 26
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.46 0.42 -10000 0 -0.77 483 483
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.34 46 -0.42 8 54
cortisol/GR alpha (monomer) 0.37 0.31 0.63 431 -0.46 1 432
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.32 0.41 -10000 0 -0.9 271 271
AP-1/NFAT1-c-4 -0.7 0.53 -10000 0 -1 547 547
AFP -0.63 0.71 -10000 0 -1.6 294 294
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.2 0.16 0.51 50 -10000 0 50
TP53 0.031 0.018 -10000 0 -0.5 1 1
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.89 0.82 -10000 0 -1.7 404 404
KRT14 -0.9 0.78 -10000 0 -1.6 473 473
TBP 0.019 0.001 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.29 294 -10000 0 294
HDAC1 0 0.003 -10000 0 -10000 0 0
HDAC2 0 0.003 -10000 0 -10000 0 0
AP-1 -0.71 0.54 -10000 0 -1 548 548
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.14 0.31 -10000 0 -0.84 137 137
MAPK11 -0.002 0.042 -10000 0 -0.85 2 2
KRT5 -1 0.83 -10000 0 -1.7 472 472
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.005 0.03 -10000 0 -0.83 1 1
STAT1 0.012 0.042 -10000 0 -0.27 18 18
CGA -0.17 0.18 -10000 0 -0.5 77 77
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.21 0.18 0.37 432 -10000 0 432
MAPK3 0 0.004 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.19 0.25 -10000 0 -0.58 174 174
NFKB1 -0.043 0.083 -10000 0 -10000 0 0
MAPK8 -0.24 0.21 -10000 0 -0.44 361 361
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.31 0.32 0.59 3 -0.71 234 237
BAX 0.049 0.03 -10000 0 -10000 0 0
POMC -0.2 0.31 -10000 0 -0.96 68 68
EP300 0.15 0.14 0.29 266 -10000 0 266
cortisol/GR alpha (dimer)/p53 0.33 0.25 0.55 406 -10000 0 406
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.079 0.24 51 -10000 0 51
SGK1 0.24 0.2 -10000 0 -1.2 4 4
IL13 -0.34 0.28 -10000 0 -0.76 125 125
IL6 -0.53 0.64 -10000 0 -1.3 333 333
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.29 0.22 -10000 0 -0.68 82 82
IL2 -0.44 0.35 -10000 0 -0.76 385 385
CDK5 -0.001 0.02 -10000 0 -0.28 4 4
PRKACB -0.017 0.078 -10000 0 -0.31 46 46
HSP90AA1 0 0.01 -10000 0 -10000 0 0
IL8 -0.22 0.31 -10000 0 -0.64 200 200
CDK5R1/CDK5 -0.006 0.035 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.062 0.098 -10000 0 -0.57 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.52 384 -10000 0 384
SMARCA4 0.002 0.014 -10000 0 -0.27 1 1
chromatin remodeling 0.21 0.15 0.39 242 -10000 0 242
NF kappa B1 p50/RelA/Cbp 0.057 0.17 0.35 35 -10000 0 35
JUN (dimer) -0.33 0.29 -10000 0 -0.59 383 383
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.26 -10000 0 -0.78 76 76
NR3C1 0.21 0.2 0.43 275 -0.63 2 277
NR4A1 -0.069 0.25 -10000 0 -0.79 90 90
TIF2/SUV420H1 -0.005 0.059 -10000 0 -0.64 7 7
MAPKKK cascade -0.29 0.3 0.59 3 -0.67 229 232
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.54 402 -10000 0 402
PBX1 0.005 0.044 -10000 0 -0.55 4 4
POU1F1 0.003 0.012 -10000 0 -10000 0 0
SELE -0.23 0.36 -10000 0 -0.78 165 165
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.16 0.39 239 -10000 0 239
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.52 384 -10000 0 384
mol:cortisol 0.21 0.2 0.36 443 -10000 0 443
MMP1 -0.21 0.1 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.021 0.13 -9999 0 -0.84 21 21
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.36 0.28 -9999 0 -0.58 524 524
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.01 -9999 0 -0.28 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.33 0.25 -9999 0 -0.52 524 524
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.066 -9999 0 -0.28 51 51
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.089 -9999 0 -0.4 32 32
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.022 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.009 0.048 -9999 0 -0.28 26 26
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.04 0.097 -9999 0 -0.28 122 122
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.37 0.29 -9999 0 -0.58 529 529
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.26 0.2 -9999 0 -0.47 152 152
MAP1B -0.006 0.046 -9999 0 -0.39 12 12
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.29 0.22 -9999 0 -0.46 524 524
RELN -0.52 0.4 -9999 0 -0.84 524 524
PAFAH/LIS1 -0.009 0.055 -9999 0 -0.56 7 7
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.2 0.16 -9999 0 -0.44 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.22 0.17 -9999 0 -0.34 529 529
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.28 0.22 -9999 0 -0.44 524 524
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.023 0.077 -9999 0 -0.28 71 71
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.004 0.029 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.25 0.19 -9999 0 -0.48 87 87
LRP8 -0.034 0.091 -9999 0 -0.28 104 104
NDEL1/Katanin 60 -0.26 0.2 -9999 0 -0.47 153 153
P39/CDK5 -0.3 0.24 -9999 0 -0.48 524 524
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.29 0.25 -9999 0 -0.49 524 524
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.32 0.25 -9999 0 -0.5 529 529
RELN/VLDLR -0.34 0.27 -9999 0 -0.54 529 529
CDC42 0 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.074 0.15 -10000 0 -0.31 224 224
NFATC2 -0.031 0.24 -10000 0 -0.78 65 65
NFATC3 -0.064 0.12 -10000 0 -10000 0 0
CD40LG -0.38 0.58 -10000 0 -1.1 266 266
ITCH 0.013 0.099 -10000 0 -10000 0 0
CBLB 0.013 0.099 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.34 -10000 0 -1 75 75
JUNB 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.1 -10000 0 -0.34 86 86
T cell anergy -0.023 0.16 -10000 0 -0.48 86 86
TLE4 -0.01 0.24 -10000 0 -0.82 51 51
Jun/NFAT1-c-4/p21SNFT -0.29 0.42 -10000 0 -0.9 243 243
AP-1/NFAT1-c-4 -0.53 0.66 -10000 0 -1.3 296 296
IKZF1 0.001 0.18 -10000 0 -0.63 51 51
T-helper 2 cell differentiation -0.096 0.28 -10000 0 -0.88 62 62
AP-1/NFAT1 -0.24 0.34 -10000 0 -0.68 290 290
CALM1 -0.019 0.055 -10000 0 -10000 0 0
EGR2 -0.26 0.62 -10000 0 -1.1 240 240
EGR3 -0.38 0.73 -10000 0 -1.5 226 226
NFAT1/FOXP3 -0.089 0.2 -10000 0 -0.56 85 85
EGR1 -0.28 0.4 -10000 0 -0.84 286 286
JUN -0.012 0.087 -10000 0 -0.84 9 9
EGR4 -0.016 0.064 -10000 0 -0.3 2 2
mol:Ca2+ -0.022 0.063 -10000 0 -10000 0 0
GBP3 -0.006 0.21 -10000 0 -0.69 60 60
FOSL1 -0.007 0.055 -10000 0 -0.34 18 18
NFAT1-c-4/MAF/IRF4 -0.31 0.46 -10000 0 -0.92 251 251
DGKA 0.002 0.18 -10000 0 -0.63 52 52
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.39 0.52 -10000 0 -1 276 276
CTLA4 -0.067 0.22 -10000 0 -0.58 75 75
NFAT1-c-4 (dimer)/EGR1 -0.44 0.57 -10000 0 -1.2 276 276
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.89 258 258
FOS -0.28 0.4 -10000 0 -0.85 271 271
IFNG -0.14 0.25 -10000 0 -0.86 67 67
T cell activation -0.17 0.35 -10000 0 -0.8 151 151
MAF -0.001 0.029 -10000 0 -0.84 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.35 0.66 237 -10000 0 237
TNF -0.32 0.52 -10000 0 -1.1 250 250
FASLG -0.34 0.66 -10000 0 -1.2 267 267
TBX21 -0.026 0.17 -10000 0 -0.73 43 43
BATF3 -0.001 0.029 -10000 0 -0.84 1 1
PRKCQ -0.027 0.16 -10000 0 -0.76 37 37
PTPN1 0 0.18 -10000 0 -0.63 52 52
NFAT1-c-4/ICER1 -0.29 0.43 -10000 0 -0.88 263 263
GATA3 -0.038 0.16 -10000 0 -0.56 59 59
T-helper 1 cell differentiation -0.14 0.24 -10000 0 -0.84 67 67
IL2RA -0.22 0.32 -10000 0 -0.94 80 80
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.002 0.18 -10000 0 -0.63 52 52
E2F1 -0.081 0.14 -10000 0 -10000 0 0
PPARG -0.2 0.36 -10000 0 -0.84 197 197
SLC3A2 0.002 0.18 -10000 0 -0.63 52 52
IRF4 -0.074 0.23 -10000 0 -0.84 71 71
PTGS2 -0.48 0.66 -10000 0 -1.2 347 347
CSF2 -0.37 0.56 -10000 0 -1.1 269 269
JunB/Fra1/NFAT1-c-4 -0.27 0.41 -10000 0 -0.85 252 252
IL4 -0.1 0.3 -10000 0 -0.96 58 58
IL5 -0.37 0.56 -10000 0 -1.1 264 264
IL2 -0.17 0.36 -10000 0 -0.82 146 146
IL3 -0.064 0.066 -10000 0 -10000 0 0
RNF128 -0.062 0.28 -10000 0 -0.89 86 86
NFATC1 -0.16 0.35 -10000 0 -0.66 234 234
CDK4 0.077 0.22 0.55 51 -10000 0 51
PTPRK -0.002 0.2 -10000 0 -0.7 48 48
IL8 -0.38 0.57 -10000 0 -1.1 268 268
POU2F1 0.001 0.01 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.18 0.26 -9999 0 -0.46 322 322
FZD6 -0.006 0.071 -9999 0 -0.84 6 6
WNT6 -0.18 0.34 -9999 0 -0.78 198 198
WNT4 -0.024 0.13 -9999 0 -0.58 35 35
FZD3 -0.008 0.081 -9999 0 -0.84 8 8
WNT5A -0.014 0.099 -9999 0 -0.84 11 11
WNT11 -0.2 0.35 -9999 0 -0.84 193 193
Arf6 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
CENTA1/KIF3B -0.004 0.05 -9999 0 -0.69 4 4
ARNO/beta Arrestin1-2 -0.14 0.21 -9999 0 -0.46 215 215
EGFR -0.29 0.4 -9999 0 -0.84 291 291
EPHA2 -0.006 0.071 -9999 0 -0.84 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.35 0.37 -9999 0 -0.71 409 409
ARRB2 -0.062 0.16 -9999 0 -0.46 115 115
mol:GTP 0.017 0.019 -9999 0 -0.16 5 5
ARRB1 -0.002 0.042 -9999 0 -0.65 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.038 0.17 -9999 0 -0.84 37 37
EGF -0.17 0.33 -9999 0 -0.84 167 167
somatostatin receptor activity 0 0 -9999 0 -0.001 286 286
ARAP2 -0.005 0.064 -9999 0 -0.84 5 5
mol:GDP -0.14 0.18 -9999 0 -0.37 252 252
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 227 227
ITGA2B -0.017 0.078 -9999 0 -0.31 45 45
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.044 -9999 0 -0.51 6 6
ADAP1 -0.004 0.052 -9999 0 -0.61 5 5
KIF13B -0.002 0.041 -9999 0 -0.84 2 2
HGF/MET -0.15 0.29 -9999 0 -0.69 178 178
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.16 -9999 0 -0.32 274 274
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.3 0.33 -9999 0 -0.62 409 409
ADRB2 -0.21 0.36 -9999 0 -0.84 214 214
receptor agonist activity 0 0 -9999 0 0 284 284
actin filament binding 0 0 -9999 0 -0.001 278 278
SRC 0 0.01 -9999 0 -0.28 1 1
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 255 255
ARF6/GDP -0.016 0.088 -9999 0 -0.44 15 15
ARF6/GDP/GULP/ACAP1 -0.15 0.21 -9999 0 -0.51 157 157
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.017 0.076 -9999 0 -0.52 17 17
ACAP1 -0.016 0.096 -9999 0 -0.84 9 9
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.095 0.24 -9999 0 -0.69 115 115
EFNA1 0 0.01 -9999 0 -10000 0 0
HGF -0.05 0.2 -9999 0 -0.84 50 50
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 224 224
endosomal lumen acidification 0 0 -9999 0 -0.001 210 210
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.052 0.2 -9999 0 -0.84 52 52
GNAQ/ARNO -0.001 0.024 -9999 0 -0.48 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 274 274
MET -0.14 0.32 -9999 0 -0.83 144 144
GNA14 -0.013 0.082 -9999 0 -0.84 6 6
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GIT1 -0.001 0.019 -9999 0 -0.28 4 4
mol:PI-4-5-P2 0 0 -9999 0 -0.001 257 257
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.12 0.29 -9999 0 -0.84 115 115
AGTR1 -0.2 0.35 -9999 0 -0.71 241 241
desensitization of G-protein coupled receptor protein signaling pathway -0.094 0.24 -9999 0 -0.69 115 115
IPCEF1/ARNO -0.24 0.26 -9999 0 -0.5 409 409
alphaIIb/beta3 Integrin -0.023 0.099 -9999 0 -0.65 17 17
Ephrin B reverse signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.037 -10000 0 -10000 0 0
EFNB1 0.017 0.052 -10000 0 -0.65 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.19 0.22 -10000 0 -0.44 364 364
Ephrin B2/EPHB1-2 -0.22 0.25 -10000 0 -0.51 363 363
neuron projection morphogenesis -0.18 0.21 -10000 0 -0.42 364 364
Ephrin B1/EPHB1-2/Tiam1 -0.21 0.24 -10000 0 -0.48 364 364
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.77 23 23
YES1 -0.023 0.16 -10000 0 -1 22 22
Ephrin B1/EPHB1-2/NCK2 -0.21 0.24 -10000 0 -0.48 364 364
PI3K -0.021 0.13 -10000 0 -0.79 22 22
mol:GDP -0.21 0.24 -10000 0 -0.47 364 364
ITGA2B -0.017 0.078 -10000 0 -0.31 45 45
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.023 0.16 -10000 0 -1 22 22
MAP3K7 -0.021 0.13 -10000 0 -0.83 22 22
FGR -0.025 0.16 -10000 0 -1 22 22
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.033 0.14 -10000 0 -0.63 38 38
LYN -0.023 0.16 -10000 0 -1 22 22
Ephrin B1/EPHB1-2/Src Family Kinases -0.025 0.15 -10000 0 -0.95 22 22
Ephrin B1/EPHB1-2 -0.028 0.14 -10000 0 -0.9 22 22
SRC -0.025 0.16 -10000 0 -1 22 22
ITGB3 -0.015 0.11 -10000 0 -0.84 14 14
EPHB1 -0.36 0.41 -10000 0 -0.84 364 364
EPHB4 0 0.01 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.023 0.099 -10000 0 -0.65 17 17
BLK -0.025 0.16 -10000 0 -1 22 22
HCK -0.025 0.16 -10000 0 -1 22 22
regulation of stress fiber formation 0.21 0.24 0.47 364 -10000 0 364
MAPK8 0.005 0.12 -10000 0 -0.72 23 23
Ephrin B1/EPHB1-2/RGS3 -0.21 0.24 -10000 0 -0.48 364 364
endothelial cell migration -0.015 0.12 -10000 0 -0.73 22 22
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.015 0.15 -10000 0 -0.95 22 22
regulation of focal adhesion formation 0.21 0.24 0.47 364 -10000 0 364
chemotaxis 0.21 0.24 0.47 364 -10000 0 364
PIK3CA 0 0.01 -10000 0 -0.28 1 1
Rac1/GTP -0.19 0.22 -10000 0 -0.44 364 364
angiogenesis -0.028 0.14 -10000 0 -0.89 22 22
LCK -0.027 0.16 -10000 0 -1 22 22
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.059 0.17 -10000 0 -0.57 83 83
cell-cell adhesion 0.2 0.23 0.72 59 -10000 0 59
Ephrin B/EPHB2/RasGAP -0.042 0.13 -10000 0 -0.48 71 71
ITSN1 -0.002 0.041 -10000 0 -0.84 2 2
PIK3CA 0 0.01 -10000 0 -0.28 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.24 0.28 -10000 0 -0.57 363 363
HRAS/GDP -0.2 0.24 -10000 0 -0.69 75 75
Ephrin B/EPHB1/GRB7 -0.25 0.3 -10000 0 -0.55 380 380
Endophilin/SYNJ1 -0.039 0.12 -10000 0 -0.45 71 71
KRAS 0 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.25 0.29 -10000 0 -0.55 379 379
endothelial cell migration 0 0.005 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
GRB7 -0.021 0.077 -10000 0 -0.29 62 62
PAK1 -0.045 0.15 -10000 0 -0.48 79 79
HRAS 0 0.01 -10000 0 -10000 0 0
RRAS -0.04 0.13 -10000 0 -0.45 71 71
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.23 0.28 -10000 0 -0.52 379 379
lamellipodium assembly -0.2 0.23 -10000 0 -0.72 59 59
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.17 0.2 -10000 0 -0.38 363 363
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.005 0.037 -10000 0 -10000 0 0
EPHB3 -0.003 0.028 -10000 0 -10000 0 0
EPHB1 -0.36 0.42 -10000 0 -0.84 364 364
EPHB4 0 0.01 -10000 0 -10000 0 0
mol:GDP -0.18 0.22 -10000 0 -0.69 72 72
Ephrin B/EPHB2 -0.043 0.14 -10000 0 -0.48 71 71
Ephrin B/EPHB3 -0.042 0.14 -10000 0 -0.48 71 71
JNK cascade -0.2 0.23 -10000 0 -0.47 363 363
Ephrin B/EPHB1 -0.25 0.3 -10000 0 -0.55 379 379
RAP1/GDP -0.15 0.19 -10000 0 -0.58 71 71
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.071 0.23 -10000 0 -0.84 71 71
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.23 0.26 -10000 0 -0.52 363 363
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.25 -10000 0 -0.8 59 59
Rap1/GTP -0.2 0.23 -10000 0 -0.75 58 58
axon guidance -0.058 0.17 -10000 0 -0.56 83 83
MAPK3 -0.12 0.2 -10000 0 -0.54 55 55
MAPK1 -0.12 0.2 -10000 0 -0.54 55 55
Rac1/GDP -0.16 0.2 -10000 0 -0.61 71 71
actin cytoskeleton reorganization -0.15 0.18 -10000 0 -0.56 56 56
CDC42/GDP -0.16 0.2 -10000 0 -0.61 71 71
PI3K 0 0.005 -10000 0 -10000 0 0
EFNA5 -0.083 0.25 -10000 0 -0.84 83 83
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.031 0.1 -10000 0 -0.36 71 71
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.19 0.23 -10000 0 -0.71 59 59
PTK2 0.047 0.053 -10000 0 -10000 0 0
MAP4K4 -0.21 0.23 -10000 0 -0.47 363 363
SRC 0 0.01 -10000 0 -0.28 1 1
KALRN -0.014 0.11 -10000 0 -0.84 14 14
Intersectin/N-WASP -0.002 0.031 -10000 0 -0.64 2 2
neuron projection morphogenesis -0.15 0.18 -10000 0 -0.56 64 64
MAP2K1 -0.16 0.18 -10000 0 -0.57 56 56
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.22 0.25 -10000 0 -0.51 363 363
cell migration -0.14 0.23 -10000 0 -0.57 78 78
NRAS -0.001 0.013 -10000 0 -10000 0 0
SYNJ1 -0.04 0.13 -10000 0 -0.45 71 71
PXN 0 0 -10000 0 -10000 0 0
TF -0.28 0.28 -10000 0 -0.48 505 505
HRAS/GTP -0.21 0.25 -10000 0 -0.47 379 379
Ephrin B1/EPHB1-2 -0.23 0.26 -10000 0 -0.52 363 363
cell adhesion mediated by integrin 0.006 0.14 0.45 71 -10000 0 71
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.23 0.27 -10000 0 -0.5 379 379
RAC1-CDC42/GTP -0.2 0.23 -10000 0 -0.73 59 59
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.15 0.19 -10000 0 -0.63 56 56
ruffle organization -0.2 0.24 -10000 0 -0.74 59 59
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.001 0.14 -10000 0 -0.45 72 72
Ephrin B/EPHB2/KALRN -0.05 0.16 -10000 0 -0.51 79 79
ROCK1 -0.001 0.012 -10000 0 -10000 0 0
RAS family/GDP -0.13 0.16 -10000 0 -0.55 56 56
Rac1/GTP -0.21 0.25 -10000 0 -0.79 59 59
Ephrin B/EPHB1/Src/Paxillin -0.18 0.21 -10000 0 -0.39 379 379
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.45 -10000 0 -1.1 194 194
STAT6 (cleaved dimer) -0.5 0.44 -10000 0 -0.99 296 296
IGHG1 -0.16 0.16 -10000 0 -0.36 69 69
IGHG3 -0.45 0.44 -10000 0 -0.98 252 252
AKT1 -0.21 0.24 -10000 0 -0.65 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.19 -10000 0 -0.64 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.68 59 59
THY1 -0.46 0.45 -10000 0 -1.1 194 194
MYB -0.015 0.11 -10000 0 -0.77 16 16
HMGA1 -0.009 0.049 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.66 186 186
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.23 -10000 0 -0.64 43 43
SP1 0.017 0.005 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.025 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.43 -10000 0 -1 244 244
SOCS1 -0.3 0.3 -10000 0 -0.73 160 160
SOCS3 -0.23 0.26 -10000 0 -0.8 53 53
FCER2 -0.62 0.66 -10000 0 -1.4 282 282
PARP14 0 0.019 -10000 0 -0.28 3 3
CCL17 -0.47 0.45 -10000 0 -1.1 193 193
GRB2 0 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.76 9 9
T cell proliferation -0.46 0.47 -10000 0 -1.2 181 181
IL4R/JAK1 -0.46 0.45 -10000 0 -1.2 167 167
EGR2 -0.59 0.61 -10000 0 -1.3 285 285
JAK2 -0.007 0.025 -10000 0 -10000 0 0
JAK3 0.008 0.035 -10000 0 -0.28 5 5
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.005 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.15 -10000 0 -1.7 1 1
CCL26 -0.46 0.45 -10000 0 -1.2 166 166
IL4R -0.49 0.48 -10000 0 -1.2 173 173
PTPN6 0.022 0.018 -10000 0 -0.26 2 2
IL13RA2 -0.46 0.45 -10000 0 -1.1 181 181
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.6 86 86
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.27 -10000 0 -0.64 159 159
GTF3A 0.013 0.016 -10000 0 -0.27 1 1
PIK3CA 0 0.01 -10000 0 -0.28 1 1
IL13RA1/JAK2 -0.013 0.036 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.42 -10000 0 -1.4 87 87
CD40LG -0.035 0.19 -10000 0 -0.79 46 46
MAPK14 -0.26 0.27 -10000 0 -0.64 159 159
mitosis -0.2 0.23 -10000 0 -0.61 63 63
STAT6 -0.52 0.52 -10000 0 -1.2 244 244
SPI1 0.007 0.021 -10000 0 -0.27 4 4
RPS6KB1 -0.19 0.22 -10000 0 -0.64 39 39
STAT6 (dimer) -0.52 0.52 -10000 0 -1.2 244 244
STAT6 (dimer)/PARP14 -0.52 0.5 -10000 0 -1.1 269 269
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.23 -10000 0 -0.66 48 48
FRAP1 -0.21 0.24 -10000 0 -0.65 63 63
LTA -0.47 0.45 -10000 0 -1.1 179 179
FES -0.003 0.05 -10000 0 -0.84 3 3
T-helper 1 cell differentiation 0.51 0.51 1.1 245 -10000 0 245
CCL11 -0.48 0.43 -10000 0 -1.1 189 189
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.23 -10000 0 -0.67 49 49
IL2RG -0.004 0.085 -10000 0 -0.38 27 27
IL10 -0.46 0.46 -10000 0 -1.1 172 172
IRS1 -0.031 0.16 -10000 0 -0.84 31 31
IRS2 -0.038 0.17 -10000 0 -0.84 38 38
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.45 -10000 0 -1.1 180 180
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.35 -10000 0 -0.84 198 198
COL1A1 -0.18 0.16 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.46 -10000 0 -1.2 151 151
IL2R gamma/JAK3 -0.013 0.069 -10000 0 -0.44 17 17
TFF3 -0.56 0.58 -10000 0 -1.4 223 223
ALOX15 -0.55 0.57 -10000 0 -1.4 211 211
MYBL1 -0.046 0.1 -10000 0 -0.28 139 139
T-helper 2 cell differentiation -0.4 0.37 -10000 0 -0.88 218 218
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.23 -10000 0 -0.67 53 53
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.65 63 63
PI3K -0.22 0.25 -10000 0 -0.7 59 59
DOK2 -0.002 0.041 -10000 0 -0.84 2 2
ETS1 0.02 0.042 -10000 0 -0.8 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.18 -10000 0 -0.97 5 5
ITGB3 -0.47 0.47 -10000 0 -1.2 170 170
PIGR -1 0.75 -10000 0 -1.5 550 550
IGHE 0.047 0.039 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.94 5 5
BCL6 0.003 0.042 -10000 0 -0.82 2 2
OPRM1 -0.47 0.45 -10000 0 -1.1 173 173
RETNLB -0.47 0.45 -10000 0 -1.1 174 174
SELP -0.65 0.68 -10000 0 -1.6 251 251
AICDA -0.45 0.44 -10000 0 -1.1 164 164
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.087 0.39 -10000 0 -0.91 149 149
NCK1/PAK1/Dok-R -0.076 0.16 -10000 0 -0.42 149 149
NCK1/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
PIK3CA 0.002 0.011 -10000 0 -0.28 1 1
mol:beta2-estradiol 0.03 0.094 0.25 131 -10000 0 131
RELA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.031 0.1 0.38 2 -10000 0 2
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.19 0.41 -10000 0 -1.1 149 149
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.15 0.49 -10000 0 -1.2 149 149
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.23 -10000 0 -0.47 183 183
ELK1 -0.12 0.44 -10000 0 -1 149 149
GRB7 -0.021 0.077 -10000 0 -0.29 62 62
PAK1 -0.006 0.04 -10000 0 -0.28 18 18
Tie2/Ang1/alpha5/beta1 Integrin -0.15 0.46 -10000 0 -1.1 149 149
CDKN1A -0.041 0.26 -10000 0 -0.61 103 103
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.041 0.29 -10000 0 -0.66 149 149
PLG -0.16 0.49 -10000 0 -1.2 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.34 -10000 0 -0.88 149 149
GRB2 0 0.01 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ANGPT2 -0.095 0.27 -10000 0 -0.78 74 74
BMX -0.35 0.56 -10000 0 -1.4 152 152
ANGPT1 -0.2 0.54 -10000 0 -1.4 136 136
tube development -0.055 0.29 -10000 0 -0.64 149 149
ANGPT4 -0.28 0.39 -10000 0 -0.84 277 277
response to hypoxia -0.007 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.51 -10000 0 -1.3 149 149
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.34 0.41 -10000 0 -0.84 336 336
STAT5A (dimer) -0.069 0.33 -10000 0 -0.78 120 120
mol:L-citrulline -0.041 0.29 -10000 0 -0.66 149 149
AGTR1 -0.2 0.35 -10000 0 -0.71 241 241
MAPK14 -0.14 0.47 -10000 0 -1.1 149 149
Tie2/SHP2 -0.075 0.24 -10000 0 -1.3 27 27
TEK -0.086 0.28 -10000 0 -1.5 27 27
RPS6KB1 -0.082 0.37 -10000 0 -0.87 149 149
Angiotensin II/AT1 -0.16 0.27 -10000 0 -0.65 188 188
Tie2/Ang1/GRB2 -0.22 0.48 -10000 0 -1.2 149 149
MAPK3 -0.13 0.45 -10000 0 -1.1 149 149
MAPK1 -0.13 0.45 -10000 0 -1.1 149 149
Tie2/Ang1/GRB7 -0.21 0.49 -10000 0 -1.2 149 149
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.15 0.49 -10000 0 -1.2 149 149
PI3K -0.12 0.44 -10000 0 -1.1 149 149
FES -0.14 0.46 -10000 0 -1.1 149 149
Crk/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
Tie2/Ang1/ABIN2 -0.22 0.48 -10000 0 -1.2 149 149
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.069 0.34 -10000 0 -0.8 149 149
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.082 0.37 -10000 0 -0.87 149 149
Tie2/Ang2 -0.099 0.38 -10000 0 -0.92 124 124
Tie2/Ang1 -0.18 0.54 -10000 0 -1.3 149 149
FOXO1 -0.066 0.35 -10000 0 -0.81 150 150
ELF1 0.015 0.019 -10000 0 -10000 0 0
ELF2 -0.15 0.48 -10000 0 -1.2 149 149
mol:Choline -0.14 0.46 -10000 0 -1.1 149 149
cell migration -0.03 0.099 -10000 0 -0.24 149 149
FYN -0.07 0.32 -10000 0 -0.76 124 124
DOK2 -0.002 0.041 -10000 0 -0.84 2 2
negative regulation of cell cycle -0.033 0.24 -10000 0 -0.54 120 120
ETS1 -0.02 0.1 -10000 0 -1 2 2
PXN -0.051 0.31 -10000 0 -0.71 149 149
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.057 0.33 -10000 0 -0.75 149 149
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.033 0.14 -10000 0 -0.84 12 12
MAPKKK cascade -0.14 0.46 -10000 0 -1.1 149 149
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.2 0.49 -10000 0 -1.2 149 149
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.031 0.26 -10000 0 -0.59 149 149
mol:Phosphatidic acid -0.14 0.46 -10000 0 -1.1 149 149
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.041 0.29 -10000 0 -0.66 149 149
Rac1/GTP -0.15 0.31 -10000 0 -0.81 149 149
MMP2 -0.15 0.5 -10000 0 -1.2 150 150
Endothelins

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
AKT1 -0.02 0.19 -9999 0 -0.6 67 67
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.029 0.16 -9999 0 -0.94 14 14
EDN1 -0.041 0.25 -9999 0 -0.85 67 67
EDN3 -0.4 0.42 -9999 0 -0.84 398 398
EDN2 -0.075 0.14 -9999 0 -0.29 215 215
HRAS/GDP -0.027 0.19 -9999 0 -0.52 64 64
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.001 0.13 -9999 0 -0.48 24 24
ADCY4 -0.15 0.29 -9999 0 -0.58 232 232
ADCY5 -0.29 0.36 -9999 0 -0.63 393 393
ADCY6 -0.13 0.27 -9999 0 -0.55 219 219
ADCY7 -0.13 0.27 -9999 0 -0.55 219 219
ADCY1 -0.15 0.29 -9999 0 -0.58 228 228
ADCY2 -0.17 0.33 -9999 0 -0.63 243 243
ADCY3 -0.13 0.27 -9999 0 -0.55 219 219
ADCY8 -0.14 0.27 -9999 0 -0.56 219 219
ADCY9 -0.13 0.27 -9999 0 -0.55 219 219
arachidonic acid secretion -0.11 0.29 -9999 0 -0.59 153 153
ETB receptor/Endothelin-1/Gq/GTP -0.029 0.17 -9999 0 -0.4 100 100
GNAO1 -0.033 0.14 -9999 0 -0.48 57 57
HRAS 0 0.01 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.037 0.2 -9999 0 -0.56 67 67
ETA receptor/Endothelin-1/Gs/GTP -0.093 0.32 -9999 0 -0.59 219 219
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.029 0.2 -9999 0 -0.6 67 67
EDNRB -0.06 0.23 -9999 0 -0.84 68 68
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.028 0.22 -9999 0 -0.65 74 74
CYSLTR1 -0.026 0.21 -9999 0 -0.64 74 74
SLC9A1 0.002 0.099 -9999 0 -0.31 67 67
mol:GDP -0.035 0.21 -9999 0 -0.55 71 71
SLC9A3 -0.04 0.25 -9999 0 -0.61 126 126
RAF1 -0.086 0.24 -9999 0 -0.54 116 116
JUN 0.029 0.17 -9999 0 -0.98 15 15
JAK2 -0.02 0.19 -9999 0 -0.6 67 67
mol:IP3 -0.025 0.16 -9999 0 -0.55 37 37
ETA receptor/Endothelin-1 0.035 0.24 -9999 0 -0.69 67 67
PLCB1 -0.049 0.2 -9999 0 -0.84 49 49
PLCB2 -0.001 0.03 -9999 0 -0.56 2 2
ETA receptor/Endothelin-3 -0.29 0.34 -9999 0 -0.65 398 398
FOS -0.28 0.51 -9999 0 -1 275 275
Gai/GDP -0.04 0.15 -9999 0 -0.68 29 29
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.045 0.23 -9999 0 -0.65 81 81
BCAR1 0 0.002 -9999 0 -10000 0 0
PRKCB1 -0.028 0.16 -9999 0 -0.51 41 41
GNAQ 0.007 0.042 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
GNAL -0.19 0.35 -9999 0 -0.84 190 190
Gs family/GDP -0.17 0.26 -9999 0 -0.6 186 186
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.12 -9999 0 -0.49 15 15
MAPK14 -0.025 0.16 -9999 0 -0.59 33 33
TRPC6 0.027 0.17 -9999 0 -1 14 14
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.17 -9999 0 -0.45 76 76
ETB receptor/Endothelin-2 -0.099 0.2 -9999 0 -0.69 73 73
ETB receptor/Endothelin-3 -0.35 0.35 -9999 0 -0.68 435 435
ETB receptor/Endothelin-1 -0.077 0.27 -9999 0 -0.69 126 126
MAPK3 -0.21 0.42 -9999 0 -0.79 277 277
MAPK1 -0.21 0.42 -9999 0 -0.79 277 277
Rac1/GDP -0.03 0.19 -9999 0 -0.57 48 48
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.62 220 220
MAPK8 0.026 0.14 -9999 0 -0.6 22 22
SRC 0 0.01 -9999 0 -0.28 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.045 0.18 -9999 0 -0.48 77 77
p130Cas/CRK/Src/PYK2 -0.011 0.2 -9999 0 -0.59 46 46
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.03 0.19 -9999 0 -0.57 48 48
COL1A2 -0.049 0.24 -9999 0 -0.67 74 74
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.64 6 6
mol:DAG -0.025 0.16 -9999 0 -0.55 37 37
MAP2K2 -0.14 0.31 -9999 0 -0.56 279 279
MAP2K1 -0.14 0.31 -9999 0 -0.56 279 279
EDNRA 0.028 0.057 -9999 0 -10000 0 0
positive regulation of muscle contraction -0.011 0.17 -9999 0 -0.52 67 67
Gq family/GDP -0.072 0.15 -9999 0 -0.61 34 34
HRAS/GTP -0.05 0.2 -9999 0 -0.5 79 79
PRKCH -0.02 0.16 -9999 0 -0.59 29 29
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.032 0.19 -9999 0 -0.64 45 45
PRKCB -0.03 0.18 -9999 0 -0.57 45 45
PRKCE -0.02 0.16 -9999 0 -0.58 30 30
PRKCD -0.02 0.16 -9999 0 -0.59 28 28
PRKCG -0.029 0.16 -9999 0 -0.57 33 33
regulation of vascular smooth muscle contraction -0.32 0.58 -9999 0 -1.1 275 275
PRKCQ -0.041 0.2 -9999 0 -0.63 58 58
PLA2G4A -0.12 0.32 -9999 0 -0.65 153 153
GNA14 -0.004 0.084 -9999 0 -0.84 6 6
GNA15 0.006 0.036 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.006 -9999 0 -10000 0 0
Rac1/GTP 0.037 0.2 -9999 0 -0.56 67 67
MMP1 -0.12 0.12 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.36 17 17
NFATC4 -0.09 0.16 -9999 0 -0.37 20 20
ERBB2IP 0.006 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.01 -9999 0 -10000 0 0
mammary gland morphogenesis -0.15 0.2 -9999 0 -0.41 299 299
JUN -0.019 0.079 -9999 0 -0.37 4 4
HRAS 0 0.01 -9999 0 -10000 0 0
DOCK7 -0.14 0.18 -9999 0 -0.39 299 299
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.24 -9999 0 -0.5 299 299
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.004 -9999 0 -10000 0 0
MAPK10 -0.12 0.14 -9999 0 -0.37 137 137
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.21 -9999 0 -0.45 299 299
RAF1 -0.083 0.16 -9999 0 -0.37 13 13
ErbB2/ErbB3/neuregulin 2 -0.29 0.27 -9999 0 -0.54 448 448
STAT3 0 0.004 -9999 0 -10000 0 0
cell migration -0.064 0.13 -9999 0 -0.32 67 67
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.23 -9999 0 -0.52 139 139
FOS -0.17 0.27 -9999 0 -0.54 272 272
NRAS -0.001 0.014 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.2 -9999 0 -0.41 299 299
MAPK3 -0.11 0.19 -9999 0 -0.43 138 138
MAPK1 -0.11 0.19 -9999 0 -0.43 138 138
JAK2 -0.14 0.18 -9999 0 -0.4 143 143
NF2 -0.007 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.37 299 299
NRG1 -0.3 0.4 -9999 0 -0.84 298 298
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.34 299 299
MAPK9 -0.07 0.092 -9999 0 -10000 0 0
ERBB2 -0.017 0.055 -9999 0 -10000 0 0
ERBB3 -0.001 0.029 -9999 0 -0.84 1 1
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.017 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.004 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.005 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.13 -9999 0 -0.33 19 19
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.042 -9999 0 -10000 0 0
CHRNA1 -0.097 0.16 -9999 0 -0.41 53 53
myelination -0.084 0.17 -9999 0 -0.36 20 20
PPP3CB -0.13 0.17 -9999 0 -0.36 299 299
KRAS 0 0.01 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.35 17 17
NRG2 -0.45 0.42 -9999 0 -0.84 447 447
mol:GDP -0.13 0.18 -9999 0 -0.37 299 299
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.075 0.15 -9999 0 -0.38 13 13
SRC 0 0.01 -9999 0 -0.28 1 1
mol:cAMP -0.002 0.003 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.39 299 299
MAP2K1 -0.14 0.21 -9999 0 -0.49 138 138
heart morphogenesis -0.15 0.2 -9999 0 -0.41 299 299
RAS family/GDP -0.11 0.14 -9999 0 -0.37 1 1
GRB2 0 0.01 -9999 0 -10000 0 0
PRKACA -0.011 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.022 -9999 0 -0.18 4 4
HSP90AA1 0 0.01 -9999 0 -10000 0 0
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.2 -9999 0 -0.41 299 299
CDC42 0 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.12 0.24 -10000 0 -0.51 204 204
GRB2/SOS1/SHC 0 0.005 -10000 0 -10000 0 0
HRAS 0 0.01 -10000 0 -10000 0 0
IRS1/Crk -0.13 0.24 -10000 0 -0.52 204 204
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.57 194 194
AKT1 -0.068 0.21 -10000 0 -0.43 194 194
BAD -0.055 0.2 -10000 0 -0.68 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.24 -10000 0 -0.51 204 204
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.24 -10000 0 -0.52 204 204
RAF1 -0.048 0.19 -10000 0 -0.63 29 29
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.23 -10000 0 -0.49 204 204
YWHAZ -0.001 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.26 -10000 0 -0.56 204 204
PIK3CA 0 0.01 -10000 0 -0.28 1 1
RPS6KB1 -0.068 0.21 -10000 0 -0.75 29 29
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.16 -10000 0 -0.52 29 29
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.2 -10000 0 -0.44 194 194
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.2 -10000 0 -0.45 194 194
IGF-1R heterotetramer -0.042 0.13 -10000 0 -0.86 18 18
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.24 -10000 0 -0.52 204 204
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.47 194 194
IGF1R -0.042 0.13 -10000 0 -0.86 18 18
IGF1 -0.19 0.36 -10000 0 -0.86 186 186
IRS2/Crk -0.14 0.26 -10000 0 -0.54 216 216
PI3K -0.12 0.22 -10000 0 -0.48 204 204
apoptosis 0.081 0.15 0.56 30 -10000 0 30
HRAS/GDP 0 0.006 -10000 0 -10000 0 0
PRKCD -0.099 0.26 -10000 0 -0.55 194 194
RAF1/14-3-3 E -0.076 0.14 -10000 0 -0.54 27 27
BAD/14-3-3 -0.086 0.16 -10000 0 -0.62 28 28
PRKCZ -0.069 0.21 -10000 0 -0.74 30 30
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.64 27 27
PTPN1 -0.004 0.031 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.14 0.26 -10000 0 -0.59 194 194
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.22 -10000 0 -0.49 194 194
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.23 -10000 0 -0.51 204 204
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.24 -10000 0 -0.51 204 204
IRS1 -0.14 0.25 -10000 0 -0.56 204 204
IRS2 -0.15 0.28 -10000 0 -0.57 216 216
IGF-1R heterotetramer/IGF1 -0.16 0.3 -10000 0 -0.7 194 194
GRB2 0 0.01 -10000 0 -10000 0 0
PDPK1 -0.11 0.21 -10000 0 -0.46 194 194
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.12 0.28 -10000 0 -0.59 204 204
SHC1 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.23 0.41 -9999 0 -0.97 92 92
PLK1 -0.081 0.094 -9999 0 -10000 0 0
BIRC5 -0.089 0.09 -9999 0 -10000 0 0
HSPA1B -0.23 0.41 -9999 0 -0.91 120 120
MAP2K1 0.007 0.028 -9999 0 -10000 0 0
BRCA2 -0.23 0.42 -9999 0 -0.93 118 118
FOXM1 -0.28 0.48 -9999 0 -1 172 172
XRCC1 -0.23 0.41 -9999 0 -0.91 119 119
FOXM1B/p19 -0.27 0.4 -9999 0 -0.89 178 178
Cyclin D1/CDK4 -0.22 0.39 -9999 0 -0.9 96 96
CDC2 -0.25 0.43 -9999 0 -0.88 173 173
TGFA -0.22 0.4 -9999 0 -0.92 109 109
SKP2 -0.23 0.41 -9999 0 -0.96 95 95
CCNE1 -0.051 0.12 -9999 0 -0.29 162 162
CKS1B -0.23 0.41 -9999 0 -0.94 107 107
RB1 -0.11 0.12 -9999 0 -1.2 1 1
FOXM1C/SP1 -0.3 0.4 -9999 0 -0.92 178 178
AURKB -0.07 0.096 -9999 0 -10000 0 0
CENPF -0.26 0.43 -9999 0 -0.92 149 149
CDK4 0.007 0.018 -9999 0 -0.28 2 2
MYC -0.21 0.4 -9999 0 -0.88 114 114
CHEK2 0.006 0.031 -9999 0 -0.3 2 2
ONECUT1 -0.23 0.41 -9999 0 -0.91 119 119
CDKN2A -0.032 0.1 -9999 0 -0.27 118 118
LAMA4 -0.23 0.42 -9999 0 -0.94 110 110
FOXM1B/HNF6 -0.26 0.46 -9999 0 -1.1 119 119
FOS -0.46 0.68 -9999 0 -1.4 278 278
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.23 0.41 -9999 0 -0.97 95 95
response to radiation -0.008 0.028 -9999 0 -10000 0 0
CENPB -0.23 0.41 -9999 0 -0.97 93 93
CENPA -0.26 0.43 -9999 0 -0.94 136 136
NEK2 -0.28 0.42 -9999 0 -0.93 145 145
HIST1H2BA -0.24 0.41 -9999 0 -0.93 116 116
CCNA2 -0.12 0.15 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.27 0.46 -9999 0 -1 139 139
CCNB2 -0.26 0.43 -9999 0 -0.94 136 136
CCNB1 -0.25 0.44 -9999 0 -0.93 150 150
ETV5 -0.23 0.41 -9999 0 -0.93 115 115
ESR1 -0.32 0.56 -9999 0 -1.3 166 166
CCND1 -0.22 0.4 -9999 0 -0.93 96 96
GSK3A 0.012 0.02 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.083 0.13 -9999 0 -10000 0 0
CDK2 0.005 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.31 0.36 -9999 0 -0.89 170 170
GAS1 -0.26 0.47 -9999 0 -1.1 124 124
MMP2 -0.23 0.42 -9999 0 -0.98 101 101
RB1/FOXM1C -0.23 0.42 -9999 0 -0.95 109 109
CREBBP 0 0 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.025 0.063 -10000 0 -0.53 2 2
epithelial cell differentiation -0.018 0.054 -10000 0 -0.45 1 1
ITCH 0.008 0.021 -10000 0 -10000 0 0
WWP1 0.009 0.067 -10000 0 -10000 0 0
FYN -0.001 0.029 -10000 0 -0.84 1 1
EGFR -0.29 0.4 -10000 0 -0.84 291 291
PRL -0.004 0.031 -10000 0 -0.28 11 11
neuron projection morphogenesis -0.11 0.22 -10000 0 -0.49 50 50
PTPRZ1 -0.45 0.42 -10000 0 -0.84 449 449
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.17 0.21 -10000 0 -0.45 298 298
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.25 -10000 0 -0.53 298 298
ADAM17 0.008 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.029 0.071 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.06 0.15 -10000 0 -0.57 52 52
NCOR1 -0.001 0.029 -10000 0 -0.84 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.19 0.23 -10000 0 -0.5 298 298
GRIN2B -0.21 0.25 -10000 0 -0.5 347 347
ErbB4/ErbB2/betacellulin -0.049 0.12 -10000 0 -0.5 45 45
STAT1 -0.006 0.04 -10000 0 -0.28 18 18
HBEGF -0.002 0.041 -10000 0 -0.84 2 2
PRLR -0.002 0.025 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.035 0.096 -10000 0 -0.58 16 16
axon guidance 0.048 0.13 -10000 0 -0.39 1 1
NEDD4 0.008 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.004 0.026 -10000 0 -10000 0 0
CBFA2T3 -0.017 0.12 -10000 0 -0.84 16 16
ErbB4/ErbB2/HBEGF -0.025 0.052 -10000 0 -0.47 2 2
MAPK3 -0.16 0.2 -10000 0 -0.51 50 50
STAT1 (dimer) -0.027 0.064 -10000 0 -10000 0 0
MAPK1 -0.16 0.2 -10000 0 -0.51 50 50
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.23 -10000 0 -0.5 298 298
NRG1 -0.22 0.32 -10000 0 -0.65 298 298
NRG3 -0.059 0.2 -10000 0 -0.84 52 52
NRG2 -0.45 0.42 -10000 0 -0.84 447 447
NRG4 -0.004 0.034 -10000 0 -10000 0 0
heart development 0.048 0.13 -10000 0 -0.39 1 1
neural crest cell migration -0.19 0.23 -10000 0 -0.5 298 298
ERBB2 0.008 0.058 -10000 0 -10000 0 0
WWOX/E4ICDs -0.024 0.058 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.23 -10000 0 -0.49 291 291
apoptosis 0.061 0.16 0.57 52 -10000 0 52
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.3 0.26 -10000 0 -0.54 447 447
ErbB4/ErbB2/epiregulin -0.087 0.16 -10000 0 -0.49 98 98
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.13 -10000 0 -0.54 45 45
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.018 0.051 -10000 0 -10000 0 0
MDM2 0.01 0.073 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.19 0.24 -10000 0 -0.5 298 298
STAT5A 0.048 0.12 -10000 0 -0.48 5 5
ErbB4/EGFR/neuregulin 1 beta -0.35 0.38 -10000 0 -0.7 411 411
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.023 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.019 0.058 -10000 0 -0.49 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.025 0.061 -10000 0 -0.48 3 3
LRIG1 -0.001 0.029 -10000 0 -0.84 1 1
EREG -0.12 0.27 -10000 0 -0.62 162 162
BTC -0.046 0.19 -10000 0 -0.84 45 45
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.048 0.13 -10000 0 -0.4 1 1
ERBB4 -0.029 0.071 -10000 0 -10000 0 0
STAT5B -0.003 0.05 -10000 0 -0.84 3 3
YAP1 -0.009 0.038 -10000 0 -0.7 2 2
GRB2 0 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.025 0.051 -10000 0 -10000 0 0
glial cell differentiation 0.022 0.055 0.49 1 -10000 0 1
WWOX 0 0.01 -10000 0 -10000 0 0
cell proliferation -0.12 0.24 -10000 0 -0.54 74 74
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.032 -9999 0 -0.55 1 1
NFATC2 -0.022 0.14 -9999 0 -0.58 47 47
NFATC3 0.011 0.025 -9999 0 -10000 0 0
CD40LG -0.27 0.33 -9999 0 -0.74 233 233
PTGS2 -0.38 0.43 -9999 0 -0.88 327 327
JUNB 0 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.002 -9999 0 -10000 0 0
JUN -0.009 0.087 -9999 0 -0.85 9 9
mol:Ca2+ -0.006 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
FOSL1 -0.007 0.055 -9999 0 -0.34 18 18
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.061 0.14 -9999 0 -0.52 46 46
FOS -0.28 0.4 -9999 0 -0.85 271 271
IFNG -0.27 0.31 -9999 0 -0.7 240 240
AP-1/NFAT1-c-4 -0.32 0.39 -9999 0 -0.84 247 247
FASLG -0.26 0.31 -9999 0 -0.7 228 228
NFAT1-c-4/ICER1 -0.043 0.12 -9999 0 -0.49 48 48
IL2RA -0.26 0.31 -9999 0 -0.71 231 231
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.23 0.33 -9999 0 -0.69 229 229
JunB/Fra1/NFAT1-c-4 -0.04 0.12 -9999 0 -0.48 49 49
IL4 -0.22 0.34 -9999 0 -0.7 226 226
IL2 -0.012 0.025 -9999 0 -10000 0 0
IL3 -0.024 0.027 -9999 0 -10000 0 0
FKBP1A 0 0.01 -9999 0 -10000 0 0
BATF3 -0.001 0.029 -9999 0 -0.84 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.13 -10000 0 -0.34 67 67
NT3 (dimer)/TRKC -0.32 0.39 -10000 0 -0.74 361 361
NT3 (dimer)/TRKB -0.55 0.48 -10000 0 -0.85 536 536
SHC/Grb2/SOS1/GAB1/PI3K 0 0.001 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.073 0.23 -10000 0 -0.7 87 87
PIK3CA 0 0.01 -10000 0 -0.28 1 1
DYNLT1 0 0.01 -10000 0 -10000 0 0
NTRK1 -0.009 0.053 -10000 0 -0.3 24 24
NTRK2 -0.44 0.42 -10000 0 -0.84 439 439
NTRK3 -0.29 0.4 -10000 0 -0.83 297 297
NT-4/5 (dimer)/TRKB -0.66 0.53 -10000 0 -0.95 583 583
neuron apoptosis 0.26 0.25 0.6 246 -10000 0 246
SHC 2-3/Grb2 -0.28 0.29 -10000 0 -0.68 246 246
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.26 0.3 -10000 0 -0.7 233 233
SHC3 -0.26 0.28 -10000 0 -0.66 241 241
STAT3 (dimer) -0.005 0.029 -10000 0 -0.39 3 3
NT3 (dimer)/TRKA -0.28 0.34 -10000 0 -0.65 353 353
RIN/GDP -0.073 0.13 -10000 0 -0.28 55 55
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -10000 0 0
DNAJA3 -0.15 0.21 -10000 0 -0.44 284 284
RIN/GTP 0 0.009 -10000 0 -10000 0 0
CCND1 0.017 0.075 -10000 0 -1 3 3
MAGED1 -0.001 0.013 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.32 0.41 -10000 0 -0.84 324 324
SHC/GRB2/SOS1 0 0.005 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.028 0.12 -10000 0 -0.58 32 32
TRKA/NEDD4-2 -0.006 0.042 -10000 0 -0.64 2 2
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.017 0.11 -10000 0 -0.84 15 15
HRAS 0 0.01 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.003 0.027 -10000 0 -10000 0 0
RIT2 -0.001 0.013 -10000 0 -0.28 2 2
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.03 -10000 0 -10000 0 0
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.15 0.2 -10000 0 -0.43 284 284
mol:GDP -0.11 0.19 -10000 0 -0.38 197 197
NGF (dimer) -0.017 0.11 -10000 0 -0.84 15 15
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.069 0.13 -10000 0 -0.29 49 49
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.34 0.32 -10000 0 -0.61 462 462
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.002 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.14 0.31 -10000 0 -0.79 147 147
RAP1/GDP -0.077 0.089 -10000 0 -0.25 35 35
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.073 0.23 -10000 0 -0.7 87 87
ubiquitin-dependent protein catabolic process -0.016 0.081 -10000 0 -0.56 17 17
Schwann cell development -0.061 0.045 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0.001 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.46 0.41 -10000 0 -0.71 545 545
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.11 0.1 -10000 0 -10000 0 0
STAT3 -0.005 0.029 -10000 0 -0.38 3 3
axon guidance -0.43 0.37 -10000 0 -0.66 545 545
MAPK3 -0.025 0.1 -10000 0 -0.53 32 32
MAPK1 -0.025 0.1 -10000 0 -0.53 32 32
CDC42/GDP -0.069 0.13 -10000 0 -0.29 49 49
NTF3 -0.14 0.31 -10000 0 -0.79 147 147
NTF4 -0.32 0.41 -10000 0 -0.84 324 324
NGF (dimer)/TRKA/FAIM -0.015 0.08 -10000 0 -0.56 16 16
PI3K 0 0.006 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.17 0.22 -10000 0 -0.46 285 285
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.27 0.36 -10000 0 -0.65 362 362
RGS19 -0.001 0.013 -10000 0 -0.28 2 2
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.007 0.084 -10000 0 -10000 0 0
Rac1/GDP -0.069 0.13 -10000 0 -0.29 49 49
NGF (dimer)/TRKA/GRIT -0.016 0.081 -10000 0 -0.57 16 16
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.59 16 16
NGF (dimer)/TRKA/NEDD4-2 -0.016 0.082 -10000 0 -0.56 17 17
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.28 0.39 -10000 0 -0.84 277 277
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.055 -10000 0 -0.36 20 20
RAS family/GTP/PI3K 0 0.002 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.01 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
MAPKKK cascade -0.068 0.12 -10000 0 -0.81 16 16
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.036 -10000 0 -0.64 1 1
SQSTM1 -0.001 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.31 0.3 -10000 0 -0.56 462 462
NGF (dimer)/TRKA/p62/Atypical PKCs -0.013 0.069 -10000 0 -0.48 17 17
MATK -0.02 0.12 -10000 0 -0.63 27 27
NEDD4L -0.001 0.029 -10000 0 -0.84 1 1
RAS family/GDP -0.07 0.083 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.16 0.22 -10000 0 -0.47 284 284
Rac1/GTP -0.13 0.14 -10000 0 -0.35 214 214
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.24 -10000 0 -0.64 143 143
CRKL -0.041 0.16 -10000 0 -0.36 143 143
mol:PIP3 -0.017 0.041 0.82 2 -10000 0 2
AKT1 0.004 0.025 0.5 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.031 0.15 -10000 0 -0.56 15 15
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -0.28 1 1
HGF/MET/SHIP2 -0.13 0.25 -10000 0 -0.6 178 178
MAP3K5 -0.021 0.15 -10000 0 -0.55 17 17
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.23 -10000 0 -0.55 178 178
AP1 -0.22 0.29 -10000 0 -0.62 272 272
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.25 0.37 -10000 0 -0.78 272 272
STAT3 (dimer) -0.073 0.15 -10000 0 -0.34 178 178
GAB1/CRKL/SHP2/PI3K -0.062 0.12 -10000 0 -0.53 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.067 0.13 -10000 0 -0.33 143 143
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
ELK1 -0.045 0.11 -10000 0 -0.28 143 143
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.047 0.095 -10000 0 -0.43 15 15
PAK1 0.009 0.03 0.46 2 -10000 0 2
HGF/MET/RANBP10 -0.13 0.25 -10000 0 -0.6 178 178
HRAS -0.15 0.3 -10000 0 -0.72 178 178
DOCK1 -0.031 0.15 -10000 0 -0.56 15 15
GAB1 -0.051 0.17 -10000 0 -0.36 178 178
CRK -0.041 0.16 -10000 0 -0.36 143 143
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.16 0.31 -10000 0 -0.73 178 178
JUN -0.009 0.086 -10000 0 -0.84 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.079 0.16 -10000 0 -0.37 178 178
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.015 0.17 -10000 0 -0.6 15 15
GRB2/SHC -0.068 0.14 -10000 0 -0.34 143 143
FOS -0.27 0.39 -10000 0 -0.84 271 271
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.045 0.11 -10000 0 -0.28 143 143
HGF/MET/MUC20 -0.13 0.26 -10000 0 -0.61 178 178
cell migration -0.067 0.13 -10000 0 -0.34 143 143
GRB2 0 0.01 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.24 -10000 0 -0.64 143 143
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.078 0.16 -10000 0 -0.37 178 178
MET/MUC20 -0.11 0.25 -10000 0 -0.65 143 143
RAP1B -0.021 0.14 -10000 0 -0.52 15 15
RAP1A -0.021 0.14 -10000 0 -0.52 15 15
HGF/MET/RANBP9 -0.13 0.25 -10000 0 -0.6 178 178
RAF1 -0.11 0.3 -10000 0 -0.73 143 143
STAT3 -0.074 0.15 -10000 0 -0.35 178 178
cell proliferation -0.062 0.23 -10000 0 -0.5 178 178
RPS6KB1 -0.027 0.054 -10000 0 -0.19 15 15
MAPK3 -0.045 0.095 -10000 0 -0.26 143 143
MAPK1 -0.045 0.095 -10000 0 -0.26 143 143
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.13 -10000 0 -0.43 16 16
SRC -0.072 0.14 -10000 0 -0.64 15 15
PI3K -0.068 0.14 -10000 0 -0.34 143 143
MET/Glomulin -0.1 0.22 -10000 0 -0.59 143 143
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.087 0.27 -10000 0 -0.66 143 143
MET -0.14 0.32 -10000 0 -0.83 144 144
MAP4K1 -0.03 0.16 -10000 0 -0.34 144 144
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.087 0.27 -10000 0 -0.66 143 143
BAD 0.012 0.023 0.46 2 -10000 0 2
MAP2K4 -0.012 0.14 -10000 0 -0.48 18 18
SHP2/GRB2/SOS1/GAB1 -0.099 0.2 -10000 0 -0.53 143 143
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.072 0.14 -10000 0 -0.36 143 143
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.05 0.2 -10000 0 -0.84 50 50
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.068 0.14 -10000 0 -0.34 143 143
PDPK1 -0.006 0.03 0.59 2 -10000 0 2
HGF/MET/SHIP -0.13 0.25 -10000 0 -0.6 178 178
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.2 -9999 0 -0.63 95 95
SMAD6-7/SMURF1 -0.001 0.019 -9999 0 -0.56 1 1
NOG -0.025 0.13 -9999 0 -0.61 34 34
SMAD9 -0.096 0.25 -9999 0 -0.85 70 70
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.079 0.18 -9999 0 -0.49 109 109
BMP7/USAG1 -0.36 0.36 -9999 0 -0.7 434 434
SMAD5/SKI -0.089 0.16 -9999 0 -0.52 76 76
SMAD1 0.024 0.031 -9999 0 -10000 0 0
BMP2 -0.15 0.32 -9999 0 -0.83 153 153
SMAD1/SMAD1/SMAD4 -0.002 0.013 -9999 0 -10000 0 0
BMPR1A -0.001 0.029 -9999 0 -0.84 1 1
BMPR1B -0.14 0.17 -9999 0 -0.3 377 377
BMPR1A-1B/BAMBI -0.092 0.15 -9999 0 -0.63 45 45
AHSG -0.002 0.025 -9999 0 -0.28 7 7
CER1 -0.001 0.013 -9999 0 -10000 0 0
BMP2-4/CER1 -0.14 0.26 -9999 0 -0.61 188 188
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.2 -9999 0 -0.52 116 116
BMP2-4 (homodimer) -0.15 0.29 -9999 0 -0.69 188 188
RGMB -0.001 0.029 -9999 0 -0.84 1 1
BMP6/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.57 89 89
RGMA -0.11 0.28 -9999 0 -0.84 112 112
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.55 107 107
BMP2-4/USAG1 -0.4 0.39 -9999 0 -0.69 483 483
SMAD6/SMURF1/SMAD5 -0.089 0.16 -9999 0 -0.52 76 76
SOSTDC1 -0.41 0.42 -9999 0 -0.84 410 410
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.6 77 77
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.072 0.23 -9999 0 -0.83 73 73
HFE2 -0.002 0.025 -9999 0 -0.28 7 7
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD -0.15 0.28 -9999 0 -0.64 190 190
SMAD5/SMAD5/SMAD4 -0.089 0.16 -9999 0 -0.51 77 77
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.087 0.17 -9999 0 -0.54 79 79
BMP7 (homodimer) -0.074 0.22 -9999 0 -0.84 62 62
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.058 0.18 -9999 0 -0.65 72 72
SMAD1/SKI -0.005 0.014 -9999 0 -10000 0 0
SMAD6 -0.001 0.029 -9999 0 -0.84 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.14 0.26 -9999 0 -0.61 188 188
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.042 0.12 -9999 0 -0.84 10 10
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.089 0.12 -9999 0 -0.65 19 19
CHRDL1 -0.58 0.39 -9999 0 -0.84 582 582
ENDOFIN/SMAD1 -0.005 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.004 0.016 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.036 0.15 -9999 0 -0.84 26 26
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.51 0.39 -9999 0 -0.72 597 597
BMP2-4/GREM1 -0.16 0.27 -9999 0 -0.62 191 191
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.091 0.23 -9999 0 -0.8 70 70
SMAD1/SMAD6 -0.005 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.074 0.22 -9999 0 -0.84 62 62
BMP6 -0.072 0.24 -9999 0 -0.83 73 73
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.19 -9999 0 -0.61 79 79
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.002 0.021 -9999 0 -0.28 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.58 130 130
CHRD -0.03 0.13 -9999 0 -0.84 16 16
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.24 -9999 0 -0.55 154 154
BMP4 -0.051 0.2 -9999 0 -0.83 52 52
FST -0.033 0.16 -9999 0 -0.79 35 35
BMP2-4/NOG -0.15 0.28 -9999 0 -0.62 199 199
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.092 0.16 -9999 0 -0.56 77 77
Nongenotropic Androgen signaling

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 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.061 0.17 -10000 0 -0.52 97 97
regulation of S phase of mitotic cell cycle -0.038 0.11 -10000 0 -0.34 92 92
GNAO1 -0.033 0.14 -10000 0 -0.48 57 57
HRAS 0 0.01 -10000 0 -10000 0 0
SHBG/T-DHT 0 0.005 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 -0.041 0.16 -10000 0 -0.46 92 92
T-DHT/AR -0.072 0.21 -10000 0 -0.66 92 92
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 271 271
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
mol:GDP -0.069 0.2 -10000 0 -0.63 92 92
cell proliferation -0.11 0.24 -10000 0 -0.57 82 82
PIK3CA 0 0.01 -10000 0 -0.28 1 1
FOS -0.25 0.43 -10000 0 -0.87 271 271
mol:Ca2+ -0.016 0.028 -10000 0 -0.078 111 111
MAPK3 -0.076 0.2 -10000 0 -0.51 92 92
MAPK1 -0.049 0.12 -10000 0 -0.31 48 48
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 271 271
cAMP biosynthetic process 0.012 0.025 -10000 0 -10000 0 0
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 271 271
HRAS/GTP -0.061 0.15 -10000 0 -0.49 92 92
actin cytoskeleton reorganization 0 0.003 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -0.28 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 271 271
PI3K 0 0.005 -10000 0 -10000 0 0
apoptosis 0.11 0.23 0.43 271 -10000 0 271
T-DHT/AR/PELP1 -0.063 0.18 -10000 0 -0.57 92 92
HRAS/GDP -0.066 0.19 -10000 0 -0.6 92 92
CREB1 -0.12 0.25 -10000 0 -0.46 271 271
RAC1-CDC42/GTP 0 0.003 -10000 0 -10000 0 0
AR -0.093 0.26 -10000 0 -0.84 92 92
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.04 0.16 -10000 0 -0.48 92 92
RAC1-CDC42/GDP -0.062 0.18 -10000 0 -0.57 92 92
T-DHT/AR/PELP1/Src -0.058 0.16 -10000 0 -0.53 92 92
MAP2K2 -0.041 0.16 -10000 0 -0.46 92 92
T-DHT/AR/PELP1/Src/PI3K -0.038 0.11 -10000 0 -0.35 92 92
GNAZ -0.006 0.071 -10000 0 -0.84 6 6
SHBG 0 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.036 0.1 -10000 0 -0.46 29 29
mol:T-DHT -0.001 0.001 0.002 48 -0.003 222 270
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.005 0.061 -10000 0 -0.66 7 7
Gi family/GTP -0.047 0.1 -10000 0 -0.31 70 70
CDC42 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.047 0.19 -9999 0 -0.84 47 47
GNB1/GNG2 -0.16 0.24 -9999 0 -0.72 86 86
mol:DAG -0.14 0.21 -9999 0 -0.64 86 86
PLCG1 -0.14 0.22 -9999 0 -0.67 86 86
YES1 -0.16 0.24 -9999 0 -0.69 95 95
FZD3 -0.008 0.081 -9999 0 -0.84 8 8
FZD6 -0.006 0.071 -9999 0 -0.84 6 6
G protein -0.15 0.22 -9999 0 -0.67 87 87
MAP3K7 -0.079 0.19 -9999 0 -0.51 86 86
mol:Ca2+ -0.14 0.2 -9999 0 -0.61 86 86
mol:IP3 -0.14 0.21 -9999 0 -0.64 86 86
NLK -0.006 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.094 0.21 -9999 0 -0.56 87 87
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.18 0.26 -9999 0 -0.46 322 322
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.16 0.24 -9999 0 -0.7 94 94
GO:0007205 -0.11 0.23 -9999 0 -0.62 86 86
WNT6 -0.18 0.34 -9999 0 -0.78 198 198
WNT4 -0.024 0.13 -9999 0 -0.58 35 35
NFAT1/CK1 alpha -0.16 0.24 -9999 0 -0.62 126 126
GNG2 -0.006 0.071 -9999 0 -0.84 6 6
WNT5A -0.014 0.099 -9999 0 -0.84 11 11
WNT11 -0.2 0.35 -9999 0 -0.84 193 193
CDC42 -0.12 0.25 -9999 0 -0.69 83 83
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.077 0.16 -9999 0 -0.48 65 65
JUN -0.046 0.14 -9999 0 -0.45 32 32
HRAS 0 0.01 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.56 147 147
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.56 147 147
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.53 138 138
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.5 144 144
GRB7 -0.021 0.077 -9999 0 -0.29 62 62
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.56 147 147
MAPKKK cascade -0.094 0.17 -9999 0 -0.45 144 144
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.6 147 147
lamellipodium assembly -0.076 0.15 -9999 0 -0.38 144 144
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.56 147 147
PIK3CA 0 0.01 -9999 0 -0.28 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.53 138 138
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.53 138 138
MAPK3 -0.12 0.17 -9999 0 -0.47 144 144
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.01 0.084 -9999 0 -0.84 8 8
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.56 38 38
DOK5 -0.018 0.12 -9999 0 -0.84 16 16
GFRA1 -0.16 0.31 -9999 0 -0.84 138 138
MAPK8 -0.069 0.13 -9999 0 -0.36 98 98
HRAS/GTP -0.098 0.2 -9999 0 -0.52 144 144
tube development -0.093 0.18 -9999 0 -0.49 138 138
MAPK1 -0.12 0.17 -9999 0 -0.47 144 144
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.062 0.13 -9999 0 -0.35 138 138
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.54 149 149
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.56 147 147
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.58 160 160
PRKCA -0.022 0.13 -9999 0 -0.84 21 21
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
CREB1 -0.067 0.15 -9999 0 -0.39 138 138
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.061 0.13 -9999 0 -0.35 138 138
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.58 149 149
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.16 -9999 0 -0.3 335 335
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.045 0.14 -9999 0 -0.44 32 32
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.53 138 138
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.061 0.13 -9999 0 -0.35 138 138
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.078 0.14 -9999 0 -0.37 144 144
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.078 0.14 -9999 0 -0.37 144 144
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.079 0.15 -9999 0 -0.38 144 144
PI3K -0.12 0.24 -9999 0 -0.61 149 149
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.093 0.18 -9999 0 -0.49 138 138
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.074 0.13 -9999 0 -0.36 92 92
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.56 147 147
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
IRS2 -0.038 0.17 -9999 0 -0.84 38 38
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.079 0.15 -9999 0 -0.38 144 144
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.57 168 168
GRB2 0 0.01 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.016 0.065 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.63 155 155
Rac1/GTP -0.092 0.18 -9999 0 -0.46 144 144
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.57 142 142
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.65 142 142
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.23 0.28 -9999 0 -0.56 340 340
fibroblast growth factor receptor signaling pathway -0.23 0.28 -9999 0 -0.56 340 340
LAMA1 -0.094 0.26 -9999 0 -0.84 94 94
PRNP -0.011 0.095 -9999 0 -0.84 11 11
GPC1/SLIT2 -0.049 0.17 -9999 0 -0.64 63 63
SMAD2 -0.014 0.081 -9999 0 -0.51 22 22
GPC1/PrPc/Cu2+ -0.008 0.065 -9999 0 -0.57 11 11
GPC1/Laminin alpha1 -0.073 0.2 -9999 0 -0.64 94 94
TDGF1 -0.018 0.12 -9999 0 -0.81 19 19
CRIPTO/GPC1 -0.014 0.094 -9999 0 -0.64 18 18
APP/GPC1 0 0.008 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.009 0.087 -9999 0 -0.56 19 19
FLT1 -0.001 0.029 -9999 0 -0.84 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.015 0.089 -9999 0 -0.56 22 22
SERPINC1 -0.013 0.06 -9999 0 -0.28 41 41
FYN 0.009 0.087 -9999 0 -0.56 19 19
FGR 0.009 0.085 -9999 0 -0.56 18 18
positive regulation of MAPKKK cascade 0.026 0.095 -9999 0 -0.55 18 18
SLIT2 -0.063 0.22 -9999 0 -0.84 63 63
GPC1/NRG -0.23 0.31 -9999 0 -0.64 298 298
NRG1 -0.3 0.4 -9999 0 -0.84 298 298
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.024 -9999 0 -0.56 1 1
LYN 0.009 0.085 -9999 0 -0.56 18 18
mol:Spermine 0.011 0.01 -9999 0 -10000 0 0
cell growth -0.23 0.28 -9999 0 -0.56 340 340
BMP signaling pathway 0.001 0.013 -9999 0 -10000 0 0
SRC 0.009 0.085 -9999 0 -0.56 18 18
TGFBR1 0 0.01 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.29 0.4 -9999 0 -0.8 308 308
GPC1 -0.001 0.013 -9999 0 -10000 0 0
TGFBR1 (dimer) 0 0.01 -9999 0 -10000 0 0
VEGFA -0.003 0.028 -9999 0 -10000 0 0
BLK -0.012 0.1 -9999 0 -0.59 20 20
HCK 0.007 0.087 -9999 0 -0.56 18 18
FGF2 -0.34 0.41 -9999 0 -0.84 336 336
FGFR1 -0.008 0.077 -9999 0 -0.71 9 9
VEGFR1 homodimer -0.001 0.029 -9999 0 -0.84 1 1
TGFBR2 -0.022 0.13 -9999 0 -0.84 22 22
cell death 0 0.008 -9999 0 -10000 0 0
ATIII/GPC1 -0.009 0.038 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.23 0.3 -9999 0 -0.64 289 289
LCK -0.003 0.11 -9999 0 -0.56 29 29
neuron differentiation -0.23 0.31 -9999 0 -0.64 298 298
PrPc/Cu2+ -0.009 0.074 -9999 0 -0.65 11 11
APP 0 0 -9999 0 -10000 0 0
TGFBR2 (dimer) -0.022 0.13 -9999 0 -0.84 22 22
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.4 -9999 0 -1.1 59 59
IL23A -0.18 0.4 -9999 0 -1 68 68
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.32 -9999 0 -0.88 111 111
positive regulation of T cell mediated cytotoxicity -0.2 0.43 -9999 0 -0.87 177 177
ITGA3 -0.17 0.39 -9999 0 -0.98 78 78
IL17F -0.11 0.29 -9999 0 -0.68 57 57
IL12B -0.041 0.11 -9999 0 -0.29 75 75
STAT1 (dimer) -0.23 0.38 -9999 0 -0.83 177 177
CD4 -0.17 0.38 -9999 0 -0.9 91 91
IL23 -0.19 0.38 -9999 0 -1 65 65
IL23R -0.014 0.088 -9999 0 -10000 0 0
IL1B -0.19 0.41 -9999 0 -1 83 83
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.38 -9999 0 -0.96 76 76
TYK2 0.011 0.016 -9999 0 -10000 0 0
STAT4 -0.033 0.16 -9999 0 -0.82 34 34
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.034 0.16 -9999 0 -0.78 37 37
IL12RB1 0.001 0.06 -9999 0 -0.87 1 1
PIK3CA 0 0.01 -9999 0 -0.28 1 1
IL12Rbeta1/TYK2 -0.002 0.045 -9999 0 -0.69 1 1
IL23R/JAK2 -0.013 0.11 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.2 0.43 -9999 0 -0.87 177 177
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.021 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.37 -9999 0 -0.97 66 66
ALOX12B -0.18 0.38 -9999 0 -0.96 75 75
CXCL1 -0.38 0.66 -9999 0 -1.4 235 235
T cell proliferation -0.2 0.43 -9999 0 -0.87 177 177
NFKBIA 0 0 -9999 0 -10000 0 0
IL17A -0.073 0.24 -9999 0 -0.54 45 45
PI3K -0.25 0.33 -9999 0 -0.84 143 143
IFNG -0.005 0.026 -9999 0 -0.094 11 11
STAT3 (dimer) -0.24 0.31 -9999 0 -0.86 108 108
IL18R1 -0.011 0.095 -9999 0 -0.84 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.088 0.24 -9999 0 -0.59 27 27
IL18/IL18R -0.033 0.13 -9999 0 -0.58 42 42
macrophage activation -0.014 0.017 -9999 0 -0.042 86 86
TNF -0.19 0.41 -9999 0 -1.1 77 77
STAT3/STAT4 -0.27 0.35 -9999 0 -0.88 153 153
STAT4 (dimer) -0.24 0.4 -9999 0 -0.89 173 173
IL18 -0.007 0.044 -9999 0 -10000 0 0
IL19 -0.18 0.38 -9999 0 -0.89 106 106
STAT5A (dimer) -0.23 0.38 -9999 0 -0.84 174 174
STAT1 -0.006 0.04 -9999 0 -0.28 18 18
SOCS3 -0.005 0.064 -9999 0 -0.84 5 5
CXCL9 -0.19 0.39 -9999 0 -0.9 109 109
MPO -0.22 0.48 -9999 0 -1.2 110 110
positive regulation of humoral immune response -0.2 0.43 -9999 0 -0.87 177 177
IL23/IL23R/JAK2/TYK2 -0.21 0.45 -9999 0 -0.91 174 174
IL6 -0.49 0.72 -9999 0 -1.4 328 328
STAT5A -0.007 0.076 -9999 0 -0.84 7 7
IL2 0.003 0.03 -9999 0 -0.29 7 7
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.19 0.42 -9999 0 -1 90 90
keratinocyte proliferation -0.2 0.43 -9999 0 -0.87 177 177
NOS2 -0.17 0.39 -9999 0 -0.98 74 74
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.099 0.19 -10000 0 -0.5 146 146
ER alpha/Gai/GDP/Gbeta gamma -0.086 0.19 -10000 0 -0.48 125 125
AKT1 -0.11 0.3 -10000 0 -0.85 117 117
PIK3CA 0 0.01 -10000 0 -0.28 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.3 -10000 0 -0.86 117 117
mol:Ca2+ -0.023 0.14 -10000 0 -0.49 56 56
IGF1R -0.02 0.12 -10000 0 -0.84 16 16
E2/ER alpha (dimer)/Striatin -0.098 0.2 -10000 0 -0.57 117 117
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.081 0.29 0.81 117 -10000 0 117
RhoA/GTP -0.069 0.14 -10000 0 -0.42 117 117
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.087 0.21 -10000 0 -0.56 122 122
regulation of stress fiber formation 0.014 0.13 0.41 2 -10000 0 2
E2/ERA-ERB (dimer) -0.12 0.21 -10000 0 -0.58 141 141
KRAS 0 0.01 -10000 0 -10000 0 0
G13/GTP -0.09 0.18 -10000 0 -0.52 117 117
pseudopodium formation -0.014 0.13 -10000 0 -0.41 2 2
E2/ER alpha (dimer)/PELP1 -0.098 0.2 -10000 0 -0.57 117 117
GRB2 0 0.01 -10000 0 -10000 0 0
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
GNAO1 -0.033 0.14 -10000 0 -0.48 57 57
HRAS 0 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.056 0.22 -10000 0 -0.55 124 124
E2/ER beta (dimer) -0.019 0.11 -10000 0 -0.65 25 25
mol:GDP -0.086 0.21 -10000 0 -0.55 141 141
mol:NADP -0.056 0.22 -10000 0 -0.55 124 124
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.025 0.15 -10000 0 -0.51 56 56
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.84 16 16
PLCB1 -0.059 0.14 -10000 0 -0.53 55 55
PLCB2 -0.033 0.088 -10000 0 -0.67 9 9
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
mol:L-citrulline -0.056 0.22 -10000 0 -0.55 124 124
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.039 0.15 -10000 0 -0.84 21 21
JNK cascade -0.019 0.11 -10000 0 -0.65 25 25
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.025 0.14 -10000 0 -0.84 25 25
GNAQ -0.002 0.041 -10000 0 -0.84 2 2
ESR1 -0.15 0.29 -10000 0 -0.56 230 230
Gq family/GDP/Gbeta gamma -0.004 0.061 -10000 0 -0.78 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.022 0.13 -10000 0 -0.33 117 117
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.21 -10000 0 -0.56 122 122
GNAZ -0.006 0.071 -10000 0 -0.84 6 6
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.65 117 117
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.19 0.35 -10000 0 -0.84 190 190
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 -0.018 0.1 -10000 0 -0.58 26 26
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
HBEGF -0.063 0.19 -10000 0 -0.45 128 128
cAMP biosynthetic process -0.2 0.27 -10000 0 -0.54 291 291
SRC -0.047 0.19 -10000 0 -0.45 125 125
PI3K 0 0.006 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.077 0.19 -10000 0 -0.5 129 129
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.53 181 181
Gs family/GTP -0.2 0.28 -10000 0 -0.56 291 291
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.008 -10000 0 -10000 0 0
vasodilation -0.052 0.21 -10000 0 -0.52 124 124
mol:DAG -0.025 0.15 -10000 0 -0.51 56 56
Gs family/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.52 176 176
MSN -0.017 0.14 -10000 0 -0.45 2 2
Gq family/GTP -0.036 0.092 -10000 0 -0.71 8 8
mol:PI-3-4-5-P3 -0.087 0.3 -10000 0 -0.82 117 117
NRAS -0.001 0.013 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.21 0.52 124 -10000 0 124
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.079 0.2 -10000 0 -0.52 141 141
NOS3 -0.06 0.23 -10000 0 -0.58 124 124
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.054 0.25 -10000 0 -0.66 117 117
E2/ER alpha (dimer)/PELP1/Src -0.092 0.22 -10000 0 -0.59 122 122
ruffle organization -0.014 0.13 -10000 0 -0.41 2 2
ROCK2 -0.064 0.13 -10000 0 -0.39 119 119
GNA14 -0.013 0.082 -10000 0 -0.84 6 6
GNA15 -0.002 0.035 -10000 0 -0.39 5 5
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.087 0.19 -10000 0 -0.48 130 130
MMP2 -0.04 0.19 -10000 0 -0.43 128 128
Aurora B signaling

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
Condensin I complex -0.054 0.053 -9999 0 -10000 0 0
STMN1 -0.1 0.12 -9999 0 -0.35 65 65
Aurora B/RasGAP/Survivin -0.17 0.12 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.15 0.15 -9999 0 -0.33 330 330
BIRC5 -0.2 0.12 -9999 0 -0.28 619 619
DES -0.31 0.34 -9999 0 -0.65 414 414
Aurora C/Aurora B/INCENP -0.065 0.072 -9999 0 -0.65 1 1
Aurora B/TACC1 -0.089 0.11 -9999 0 -0.63 20 20
Aurora B/PP2A -0.094 0.09 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.006 0.014 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.16 -9999 0 -0.35 450 450
Cul3 protein complex -0.22 0.27 -9999 0 -0.56 330 330
KIF2C -0.035 0.025 -9999 0 -10000 0 0
PEBP1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.11 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.094 0.09 -9999 0 -10000 0 0
SEPT1 -0.004 0.034 -9999 0 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.006 0.039 -9999 0 -0.28 17 17
NSUN2/NPM1/Nucleolin 0.013 0.013 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.031 0.039 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -10000 0 0
AURKC -0.006 0.046 -9999 0 -0.31 15 15
CDCA8 -0.1 0.14 -9999 0 -0.28 309 309
cytokinesis -0.1 0.065 -9999 0 -10000 0 0
Aurora B/Septin1 -0.086 0.075 -9999 0 -10000 0 0
AURKA -0.14 0.14 -9999 0 -0.28 432 432
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.33 0.41 -9999 0 -0.84 330 330
BUB1 -0.2 0.12 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.25 0.16 -9999 0 -0.38 454 454
EVI5 0.007 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.093 0.091 -9999 0 -10000 0 0
SGOL1 -0.19 0.13 -9999 0 -10000 0 0
CENPA -0.048 0.051 -9999 0 -10000 0 0
NCAPG -0.15 0.14 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome -0.094 0.09 -9999 0 -10000 0 0
NCAPD2 -0.003 0.027 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.094 0.09 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.12 0.14 -9999 0 -0.28 362 362
NPM1 -0.011 0.018 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.001 0.029 -9999 0 -0.84 1 1
mitotic prometaphase -0.006 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.094 0.09 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.11 0.1 -9999 0 -0.33 36 36
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.011 0.018 -9999 0 -10000 0 0
MYLK -0.072 0.14 -9999 0 -0.48 80 80
KIF23 -0.094 0.13 -9999 0 -0.28 278 278
VIM -0.09 0.1 -9999 0 -0.72 2 2
RACGAP1 -0.013 0.062 -9999 0 -0.28 43 43
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.011 0.018 -9999 0 -10000 0 0
Chromosomal passenger complex -0.075 0.061 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.15 0.17 -9999 0 -10000 0 0
TACC1 -0.02 0.13 -9999 0 -0.84 20 20
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.041 -10000 0 -0.84 2 2
Jak2/Leptin Receptor -0.15 0.24 -10000 0 -0.55 202 202
PTP1B/AKT1 -0.067 0.099 -10000 0 -0.32 84 84
FYN -0.001 0.029 -10000 0 -0.84 1 1
p210 bcr-abl/PTP1B -0.068 0.12 -10000 0 -0.34 104 104
EGFR -0.3 0.4 -10000 0 -0.85 292 292
EGF/EGFR -0.3 0.32 -10000 0 -0.6 409 409
CSF1 -0.003 0.05 -10000 0 -0.84 3 3
AKT1 0 0 -10000 0 -10000 0 0
INSR 0 0.01 -10000 0 -0.28 1 1
PTP1B/N-cadherin -0.094 0.12 -10000 0 -0.36 88 88
Insulin Receptor/Insulin -0.047 0.072 -10000 0 -0.4 7 7
HCK -0.004 0.033 -10000 0 -0.28 12 12
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.057 0.12 -10000 0 -0.35 84 84
EGF -0.17 0.34 -10000 0 -0.85 167 167
YES1 -0.001 0.029 -10000 0 -0.84 1 1
CAV1 -0.17 0.24 -10000 0 -0.51 216 216
TXN 0 0.01 -10000 0 -0.27 1 1
PTP1B/IRS1/GRB2 -0.083 0.14 -10000 0 -0.4 107 107
cell migration 0.068 0.12 0.34 104 -10000 0 104
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.001 0.026 -10000 0 -10000 0 0
ITGA2B -0.017 0.078 -10000 0 -0.32 45 45
CSF1R 0 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin -0.003 0.027 -10000 0 -10000 0 0
FGR 0 0.01 -10000 0 -0.28 1 1
PTP1B/p130 Cas -0.072 0.11 -10000 0 -0.35 84 84
Crk/p130 Cas -0.066 0.1 -10000 0 -0.33 83 83
DOK1 -0.043 0.11 -10000 0 -0.3 84 84
JAK2 -0.038 0.07 -10000 0 -0.33 2 2
Jak2/Leptin Receptor/Leptin -0.39 0.18 -10000 0 -0.5 482 482
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 -0.069 0.12 -10000 0 -0.35 104 104
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.058 0.12 -10000 0 -0.84 2 2
SRC -0.013 0.046 -10000 0 -10000 0 0
ITGB3 -0.015 0.11 -10000 0 -0.84 14 14
CAT1/PTP1B -0.086 0.17 -10000 0 -0.37 155 155
CAPN1 0 0.002 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.037 0.064 -10000 0 -0.42 2 2
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.34 0.16 -10000 0 -0.45 412 412
negative regulation of transcription -0.038 0.069 -10000 0 -0.33 2 2
FCGR2A 0 0.01 -10000 0 -10000 0 0
FER -0.006 0.071 -10000 0 -0.85 6 6
alphaIIb/beta3 Integrin -0.023 0.1 -10000 0 -0.66 17 17
BLK -0.036 0.1 -10000 0 -0.29 102 102
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0 0.002 -10000 0 -10000 0 0
LEPR -0.19 0.36 -10000 0 -0.84 201 201
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.01 -10000 0 -10000 0 0
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.036 0.13 -10000 0 -0.35 44 44
PRL -0.004 0.032 -10000 0 -0.28 8 8
SOCS3 0.016 0.12 -10000 0 -1.5 5 5
SPRY2 -0.096 0.27 -10000 0 -0.85 95 95
Insulin Receptor/Insulin/IRS1 -0.021 0.11 -10000 0 -0.58 31 31
CSF1/CSF1R -0.068 0.1 -10000 0 -0.35 74 74
Ras protein signal transduction 0.036 0.035 -10000 0 -10000 0 0
IRS1 -0.031 0.16 -10000 0 -0.84 31 31
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.68 0.32 -10000 0 -0.84 686 686
STAT5B -0.056 0.1 -10000 0 -0.31 84 84
STAT5A -0.057 0.1 -10000 0 -0.31 86 86
GRB2 0 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.073 0.11 -10000 0 -0.36 85 85
CSN2 0.02 0.029 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -0.28 1 1
LAT -0.014 0.054 -10000 0 -0.59 2 2
YBX1 -0.002 0.015 -10000 0 -10000 0 0
LCK -0.019 0.1 -10000 0 -0.84 11 11
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.003 0.04 -10000 0 -0.57 2 2
IL6-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
BCL2L1 -0.055 0.21 -9999 0 -0.64 39 39
CRP -0.059 0.21 -9999 0 -0.64 39 39
cell cycle arrest -0.073 0.24 -9999 0 -0.72 44 44
TIMP1 -0.055 0.2 -9999 0 -0.57 40 40
IL6ST -0.043 0.21 -9999 0 -0.84 55 55
Rac1/GDP -0.14 0.19 -9999 0 -0.65 54 54
AP1 -0.14 0.25 -9999 0 -0.5 237 237
GAB2 -0.002 0.027 -9999 0 -10000 0 0
TNFSF11 -0.065 0.22 -9999 0 -0.67 30 30
HSP90B1 0.017 0.047 -9999 0 -10000 0 0
GAB1 0 0.002 -9999 0 -10000 0 0
MAPK14 -0.12 0.24 -9999 0 -0.73 55 55
AKT1 0.041 0.026 -9999 0 -10000 0 0
FOXO1 0.051 0.044 -9999 0 -0.44 6 6
MAP2K6 -0.14 0.24 -9999 0 -0.64 81 81
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.075 0.22 -9999 0 -0.63 52 52
MITF -0.13 0.24 -9999 0 -0.47 153 153
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.016 0.11 -9999 0 -1.5 4 4
CEBPB 0.015 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.052 0.069 -9999 0 -0.28 2 2
STAT3 -0.08 0.26 -9999 0 -0.8 43 43
STAT1 -0.012 0.023 -9999 0 -10000 0 0
CEBPD -0.057 0.22 -9999 0 -0.67 39 39
PIK3CA 0.01 0.011 -9999 0 -0.28 1 1
PI3K 0 0.006 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
PIAS3/MITF -0.14 0.2 -9999 0 -0.66 57 57
MAPK11 -0.12 0.24 -9999 0 -0.75 55 55
STAT3 (dimer)/FOXO1 -0.022 0.21 -9999 0 -0.59 34 34
GRB2/SOS1/GAB family -0.13 0.18 -9999 0 -0.73 36 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.24 -9999 0 -0.38 364 364
GRB2 0 0.01 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
LBP -0.23 0.45 -9999 0 -0.97 205 205
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0.002 -9999 0 -10000 0 0
MYC -0.07 0.26 -9999 0 -0.87 44 44
FGG -0.064 0.22 -9999 0 -0.65 39 39
macrophage differentiation -0.073 0.24 -9999 0 -0.72 44 44
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.28 -9999 0 -0.52 366 366
JUNB -0.054 0.21 -9999 0 -0.62 37 37
FOS -0.27 0.39 -9999 0 -0.84 271 271
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.25 -9999 0 -0.45 206 206
STAT1/PIAS1 -0.14 0.2 -9999 0 -0.49 117 117
GRB2/SOS1/GAB family/SHP2/PI3K 0.001 0.009 -9999 0 -10000 0 0
STAT3 (dimer) -0.076 0.25 -9999 0 -0.77 43 43
PRKCD -0.05 0.22 -9999 0 -0.6 49 49
IL6R -0.022 0.13 -9999 0 -0.84 22 22
SOCS3 -0.11 0.23 -9999 0 -0.79 46 46
gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.14 -9999 0 -0.56 58 58
Rac1/GTP -0.14 0.19 -9999 0 -0.66 54 54
HCK -0.004 0.033 -9999 0 -0.28 12 12
MAPKKK cascade 0 0.068 -9999 0 -10000 0 0
bone resorption -0.062 0.21 -9999 0 -0.62 35 35
IRF1 -0.056 0.21 -9999 0 -0.67 28 28
mol:GDP -0.12 0.23 -9999 0 -0.49 122 122
SOS1 0 0.002 -9999 0 -10000 0 0
VAV1 -0.12 0.24 -9999 0 -0.5 121 121
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.22 -9999 0 -0.8 51 51
PTPN11 -0.013 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.26 0.33 -9999 0 -0.66 332 332
gp130 (dimer)/TYK2/TYK2/LMO4 -0.032 0.14 -9999 0 -0.56 58 58
gp130 (dimer)/JAK2/JAK2/LMO4 -0.032 0.14 -9999 0 -0.56 58 58
IL6 -0.31 0.41 -9999 0 -0.83 324 324
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.002 0.03 -9999 0 -0.84 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.23 -9999 0 -0.39 365 365
LMO4 0.008 0.057 -9999 0 -0.46 9 9
STAT3 (dimer)/PIAS3 -0.14 0.2 -9999 0 -0.78 43 43
MCL1 0.054 0.014 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.022 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.038 -9999 0 -0.29 2 2
PDE6G/GNAT1/GTP -0.007 0.032 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.033 -9999 0 -0.28 12 12
GRK1 -0.003 0.027 -9999 0 -10000 0 0
CNG Channel -0.16 0.22 -9999 0 -0.47 263 263
mol:Na + -0.15 0.2 -9999 0 -0.46 152 152
mol:ADP -0.003 0.027 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.071 0.18 -9999 0 -0.57 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.15 0.21 -9999 0 -0.47 152 152
CNGB1 -0.014 0.06 -9999 0 -10000 0 0
RDH5 -0.53 0.4 -9999 0 -0.84 532 532
SAG -0.014 0.061 -9999 0 -0.28 43 43
mol:Ca2+ -0.14 0.2 -9999 0 -0.57 17 17
Na + (4 Units) -0.14 0.19 -9999 0 -0.56 17 17
RGS9 -0.095 0.26 -9999 0 -0.84 92 92
GNB1/GNGT1 -0.028 0.064 -9999 0 -10000 0 0
GNAT1/GDP -0.063 0.16 -9999 0 -0.5 92 92
GUCY2D -0.004 0.042 -9999 0 -0.84 1 1
GNGT1 -0.045 0.1 -9999 0 -0.28 137 137
GUCY2F -0.001 0.013 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.017 0.073 -9999 0 -0.48 17 17
mol:11-cis-retinal -0.53 0.4 -9999 0 -0.84 532 532
mol:cGMP -0.011 0.049 -9999 0 -0.49 6 6
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.41 0.31 -9999 0 -0.65 532 532
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.26 0.38 -9999 0 -0.84 255 255
Metarhodopsin II -0.003 0.021 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.011 0.052 -9999 0 -0.52 6 6
RGS9BP -0.017 0.066 -9999 0 -10000 0 0
Metarhodopsin II/Transducin -0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.009 0.049 -9999 0 -0.52 5 5
PDE6A/B -0.017 0.094 -9999 0 -0.65 17 17
mol:Pi -0.071 0.18 -9999 0 -0.57 92 92
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.022 0.047 -9999 0 -10000 0 0
PDE6B -0.017 0.12 -9999 0 -0.81 18 18
PDE6A -0.006 0.039 -9999 0 -10000 0 0
PDE6G -0.01 0.05 -9999 0 -0.28 29 29
RHO -0.005 0.035 -9999 0 -10000 0 0
PDE6 -0.07 0.16 -9999 0 -0.48 105 105
GUCA1A -0.013 0.06 -9999 0 -0.28 41 41
GC2/GCAP Family -0.01 0.049 -9999 0 -0.52 5 5
GUCA1C 0 0.01 -9999 0 -0.28 1 1
GUCA1B -0.005 0.064 -9999 0 -0.84 5 5
Ephrin A reverse signaling

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
MAPKKK cascade -0.057 0.17 -9999 0 -0.57 83 83
EFNA5 -0.083 0.25 -9999 0 -0.84 83 83
FYN -0.052 0.16 -9999 0 -0.52 83 83
neuron projection morphogenesis -0.057 0.17 -9999 0 -0.57 83 83
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.057 0.17 -9999 0 -0.57 83 83
EPHA5 -0.001 0.019 -9999 0 -0.28 4 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.03 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.037 0.16 -9999 0 -0.32 204 204
RXRs/LXRs/DNA/Oxysterols -0.015 0.14 -9999 0 -0.47 13 13
MED1 -0.008 0.045 -9999 0 -0.28 23 23
mol:9cRA 0.005 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.087 -9999 0 -0.38 42 42
RXRs/NUR77 -0.17 0.26 -9999 0 -0.55 258 258
RXRs/PPAR -0.16 0.21 -9999 0 -0.39 346 346
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.006 0.048 -9999 0 -0.48 8 8
RARA -0.004 0.033 -9999 0 -0.28 12 12
NCOA1 -0.001 0.029 -9999 0 -0.84 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.006 0.049 -9999 0 -0.49 8 8
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.018 0.081 -9999 0 -0.36 42 42
THRA -0.001 0.029 -9999 0 -0.84 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.22 -9999 0 -0.5 204 204
NR1H4 -0.002 0.025 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.11 0.2 -9999 0 -0.46 204 204
NR1H2 0.016 0.005 -9999 0 -10000 0 0
NR1H3 0.016 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.2 -9999 0 -0.48 204 204
NR4A1 -0.079 0.24 -9999 0 -0.84 79 79
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.049 0.13 -9999 0 -0.28 204 204
RXRG -0.19 0.36 -9999 0 -0.83 206 206
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.005 -9999 0 -10000 0 0
RXRB 0.015 0.006 -9999 0 -10000 0 0
THRB -0.036 0.17 -9999 0 -0.84 36 36
PPARG -0.2 0.36 -9999 0 -0.84 197 197
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.016 0.19 -9999 0 -1.3 10 10
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.015 0.14 -9999 0 -0.47 13 13
PPARA -0.003 0.05 -9999 0 -0.84 3 3
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.008 0.081 -9999 0 -0.84 8 8
RXRs/NUR77/BCL2 -0.13 0.2 -9999 0 -0.4 270 270
SREBF1 -0.005 0.14 -9999 0 -0.68 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.22 -9999 0 -0.5 204 204
ABCA1 -0.008 0.15 -9999 0 -0.94 6 6
RARs/THRs -0.027 0.12 -9999 0 -0.51 42 42
RXRs/FXR -0.12 0.22 -9999 0 -0.51 204 204
BCL2 -0.024 0.14 -9999 0 -0.84 24 24
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.6 8 8
alphaM/beta2 Integrin/GPIbA -0.025 0.06 -9999 0 -0.57 7 7
alphaM/beta2 Integrin/proMMP-9 -0.076 0.077 -9999 0 -0.44 3 3
PLAUR -0.02 0.072 -9999 0 -10000 0 0
HMGB1 -0.014 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.026 -9999 0 -10000 0 0
AGER -0.017 0.048 -9999 0 -0.71 3 3
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.077 0.1 -9999 0 -0.73 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.84 1 1
CYR61 -0.047 0.19 -9999 0 -0.84 47 47
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.06 0.12 -9999 0 -0.54 20 20
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.21 0.36 -9999 0 -0.84 208 208
MYH2 -0.074 0.17 -9999 0 -0.41 114 114
MST1R -0.011 0.089 -9999 0 -0.84 9 9
leukocyte activation during inflammatory response -0.33 0.24 -9999 0 -0.5 542 542
APOB -0.54 0.4 -9999 0 -0.84 542 542
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.081 -9999 0 -0.84 8 8
JAM3 -0.003 0.05 -9999 0 -0.84 3 3
GP1BA -0.012 0.08 -9999 0 -0.84 6 6
alphaM/beta2 Integrin/CTGF -0.024 0.068 -9999 0 -0.63 9 9
alphaM/beta2 Integrin -0.075 0.14 -9999 0 -0.37 81 81
JAM3 homodimer -0.003 0.05 -9999 0 -0.84 3 3
ICAM2 -0.005 0.064 -9999 0 -0.84 5 5
ICAM1 -0.004 0.031 -9999 0 -0.28 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 -9999 0 -0.36 87 87
cell adhesion -0.025 0.06 -9999 0 -0.57 7 7
NFKB1 -0.14 0.18 -9999 0 -0.65 12 12
THY1 -0.002 0.023 -9999 0 -0.28 6 6
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.37 0.28 -9999 0 -0.57 542 542
alphaM/beta2 Integrin/LRP/tPA -0.033 0.11 -9999 0 -0.58 31 31
IL6 -0.33 0.5 -9999 0 -0.96 323 323
ITGB2 -0.017 0.033 -9999 0 -0.34 1 1
elevation of cytosolic calcium ion concentration -0.024 0.046 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.04 0.12 -9999 0 -0.55 45 45
JAM2 -0.043 0.18 -9999 0 -0.84 43 43
alphaM/beta2 Integrin/ICAM1 -0.022 0.082 -9999 0 -0.53 19 19
alphaM/beta2 Integrin/uPA/Plg -0.02 0.031 -9999 0 -10000 0 0
RhoA/GTP -0.093 0.17 -9999 0 -0.4 172 172
positive regulation of phagocytosis -0.052 0.095 -9999 0 -0.48 17 17
Ron/MSP -0.017 0.1 -9999 0 -0.67 19 19
alphaM/beta2 Integrin/uPAR/uPA -0.024 0.046 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR -0.028 0.043 -9999 0 -10000 0 0
PLAU -0.009 0.048 -9999 0 -0.28 26 26
PLAT -0.026 0.14 -9999 0 -0.84 25 25
actin filament polymerization -0.07 0.16 -9999 0 -0.39 114 114
MST1 -0.011 0.096 -9999 0 -0.79 12 12
alphaM/beta2 Integrin/lipoprotein(a) -0.34 0.24 -9999 0 -0.51 542 542
TNF -0.096 0.22 -9999 0 -0.95 14 14
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.022 0.035 -9999 0 -10000 0 0
fibrinolysis -0.019 0.031 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -0.28 12 12
dendritic cell antigen processing and presentation -0.066 0.14 -9999 0 -0.36 87 87
VTN -0.023 0.09 -9999 0 -0.31 61 61
alphaM/beta2 Integrin/CYR61 -0.05 0.14 -9999 0 -0.61 47 47
LPA -0.001 0.019 -9999 0 -10000 0 0
LRP1 -0.009 0.086 -9999 0 -0.84 9 9
cell migration -0.067 0.082 -9999 0 -0.55 9 9
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.019 0.028 -9999 0 -10000 0 0
MPO -0.06 0.22 -9999 0 -0.84 60 60
KNG1 -0.004 0.033 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.069 0.17 -9999 0 -0.45 68 68
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.019 -9999 0 -0.28 4 4
CTGF -0.01 0.087 -9999 0 -0.74 11 11
alphaM/beta2 Integrin/Hck -0.02 0.032 -9999 0 -10000 0 0
ITGAM -0.015 0.027 -9999 0 -0.32 3 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.23 -9999 0 -0.54 208 208
HP -0.17 0.33 -9999 0 -0.75 188 188
leukocyte adhesion -0.076 0.13 -9999 0 -0.6 28 28
SELP -0.21 0.36 -9999 0 -0.84 208 208
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.001 0.029 -9999 0 -0.84 1 1
LAT2 -0.064 0.14 -9999 0 -0.44 66 66
AP1 -0.17 0.23 -9999 0 -0.46 283 283
mol:PIP3 -0.031 0.21 -9999 0 -0.43 170 170
IKBKB 0 0.12 -9999 0 -0.33 35 35
AKT1 -0.084 0.18 -9999 0 -0.68 30 30
IKBKG 0 0.12 -9999 0 -0.33 35 35
MS4A2 -0.066 0.22 -9999 0 -0.8 69 69
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
MAP3K1 0.006 0.13 -9999 0 -0.45 28 28
mol:Ca2+ -0.015 0.16 -9999 0 -0.32 170 170
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.063 0.14 -9999 0 -0.44 66 66
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.072 0.18 -9999 0 -0.52 117 117
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.1 0.22 -9999 0 -0.51 170 170
PTPN13 -0.032 0.17 -9999 0 -0.57 45 45
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.005 0.15 -9999 0 -0.42 28 28
SYK 0.01 0.011 -9999 0 -0.28 1 1
GRB2 0 0.01 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.09 0.19 -9999 0 -0.44 170 170
LAT -0.065 0.14 -9999 0 -0.44 67 67
PAK2 -0.003 0.14 -9999 0 -0.5 28 28
NFATC2 -0.079 0.21 -9999 0 -0.7 66 66
HRAS -0.013 0.15 -9999 0 -0.42 67 67
GAB2 -0.003 0.027 -9999 0 -10000 0 0
PLA2G1B 0.028 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.13 0.27 -9999 0 -0.63 170 170
Antigen/IgE/Fc epsilon R1 -0.12 0.25 -9999 0 -0.59 170 170
mol:GDP -0.02 0.15 -9999 0 -0.43 67 67
JUN -0.009 0.086 -9999 0 -0.84 9 9
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 271 271
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.068 0.15 -9999 0 -0.33 170 170
CHUK 0 0.12 -9999 0 -0.33 35 35
KLRG1 -0.063 0.14 -9999 0 -0.41 69 69
VAV1 -0.064 0.14 -9999 0 -0.44 67 67
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.063 0.14 -9999 0 -0.44 66 66
negative regulation of mast cell degranulation -0.057 0.12 -9999 0 -0.52 28 28
BTK -0.061 0.14 -9999 0 -0.43 67 67
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.089 0.2 -9999 0 -0.44 171 171
GAB2/PI3K/SHP2 -0.093 0.2 -9999 0 -0.75 31 31
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.072 0.16 -9999 0 -0.37 137 137
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.23 -9999 0 -0.54 171 171
FCER1G 0.003 0.013 -9999 0 -0.28 1 1
FCER1A -0.12 0.31 -9999 0 -0.85 131 131
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.23 -9999 0 -0.55 170 170
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.013 0.05 -9999 0 -0.61 1 1
DUSP1 -0.12 0.29 -9999 0 -0.84 117 117
NF-kappa-B/RelA -0.028 0.055 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.029 0.15 -9999 0 -0.43 66 66
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.054 0.12 -9999 0 -0.52 29 29
FER -0.066 0.14 -9999 0 -0.45 70 70
RELA 0 0 -9999 0 -10000 0 0
ITK -0.033 0.11 -9999 0 -0.62 25 25
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.018 0.16 -9999 0 -0.44 67 67
cytokine secretion -0.02 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.44 69 69
PTK2 -0.031 0.16 -9999 0 -0.45 66 66
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.094 0.2 -9999 0 -0.46 170 170
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.026 0.2 -9999 0 -0.42 170 170
MAP2K2 0.023 0.019 -9999 0 -10000 0 0
MAP2K1 0.023 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.059 0.13 -9999 0 -0.53 28 28
MAP2K4 0.015 0.038 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.12 0.25 -9999 0 -0.58 171 171
mol:Choline -0.1 0.21 -9999 0 -0.5 170 170
SHC/Grb2/SOS1 -0.057 0.13 -9999 0 -0.55 27 27
FYN -0.001 0.029 -9999 0 -0.84 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.02 0.15 -9999 0 -0.54 27 27
HCLS1 -0.063 0.14 -9999 0 -0.44 66 66
PRKCB -0.017 0.16 -9999 0 -0.38 79 79
FCGR2B -0.003 0.051 -9999 0 -0.84 3 3
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.058 0.13 -9999 0 -0.53 28 28
LCP2 0 0.01 -9999 0 -10000 0 0
PLA2G4A -0.11 0.21 -9999 0 -0.53 142 142
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.1 0.21 -9999 0 -0.5 170 170
IKK complex 0.018 0.095 -9999 0 -0.23 33 33
WIPF1 0 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.003 0.036 -9999 0 -0.64 2 2
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.57 342 342
PTK2 -0.086 0.18 -9999 0 -0.67 17 17
IGF1R -0.02 0.12 -9999 0 -0.84 16 16
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.094 -9999 0 -0.63 16 16
SRC 0 0.01 -9999 0 -0.28 1 1
CDKN1B -0.088 0.12 -9999 0 -0.94 7 7
VEGFA -0.003 0.028 -9999 0 -10000 0 0
ILK -0.084 0.11 -9999 0 -0.84 4 4
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.074 0.099 -9999 0 -0.78 4 4
PTK2B -0.01 0.069 -9999 0 -0.5 15 15
alphaV/beta3 Integrin/JAM-A -0.21 0.25 -9999 0 -0.5 344 344
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.011 0.073 -9999 0 -0.56 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.58 204 204
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.043 -9999 0 -0.43 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.08 -9999 0 -0.56 15 15
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.34 0.36 -9999 0 -0.78 272 272
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
alphaV/beta3 Integrin/Osteopontin -0.048 0.092 -9999 0 -0.58 14 14
RPS6KB1 -0.31 0.33 -9999 0 -0.71 272 272
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.79 342 342
GPR124 -0.008 0.081 -9999 0 -0.84 8 8
MAPK1 -0.33 0.39 -9999 0 -0.79 342 342
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.12 0.23 -9999 0 -0.56 177 177
cell adhesion -0.016 0.086 -9999 0 -0.5 24 24
ANGPTL3 -0.002 0.021 -9999 0 -0.28 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.031 -9999 0 -0.56 2 2
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.84 16 16
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.022 0.13 -9999 0 -0.84 22 22
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
IGF1 -0.18 0.35 -9999 0 -0.84 186 186
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.015 0.098 -9999 0 -0.63 19 19
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.029 -9999 0 -0.84 1 1
alphaV/beta3 Integrin/CD47 -0.011 0.074 -9999 0 -0.56 15 15
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.027 0.14 -9999 0 -0.7 29 29
CSF1 -0.003 0.05 -9999 0 -0.84 3 3
PIK3C2A -0.084 0.11 -9999 0 -0.84 4 4
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.59 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.011 0.075 -9999 0 -0.54 15 15
FAK1/Vinculin -0.063 0.15 -9999 0 -0.51 16 16
alphaV beta3/Integrin/ppsTEM5 -0.015 0.099 -9999 0 -0.64 19 19
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.023 0.09 -9999 0 -0.31 61 61
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.34 0.41 -9999 0 -0.84 336 336
F11R -0.24 0.33 -9999 0 -0.64 336 336
alphaV/beta3 Integrin/Lactadherin -0.017 0.097 -9999 0 -0.58 23 23
alphaV/beta3 Integrin/TGFBR2 -0.024 0.13 -9999 0 -0.64 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.03 -9999 0 -0.51 3 3
HSP90AA1 0 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.009 0.067 -9999 0 -0.52 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.01 0.07 -9999 0 -0.51 15 15
SDC1 -0.02 0.075 -9999 0 -0.29 58 58
VAV3 -0.005 0.042 -9999 0 -0.47 6 6
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
FAK1/Paxillin -0.063 0.15 -9999 0 -0.51 16 16
cell migration -0.049 0.14 -9999 0 -0.45 16 16
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.18 0.22 -9999 0 -0.45 344 344
SPP1 -0.079 0.12 -9999 0 -10000 0 0
KDR -0.002 0.041 -9999 0 -0.84 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.17 0.33 -9999 0 -0.82 169 169
angiogenesis -0.3 0.39 -9999 0 -0.76 344 344
Rac1/GTP -0.005 0.038 -9999 0 -0.43 6 6
EDIL3 -0.028 0.14 -9999 0 -0.84 23 23
cell proliferation -0.024 0.12 -9999 0 -0.64 31 31
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.011 0.063 -9999 0 -0.84 2 2
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.072 0.11 -9999 0 -0.35 82 82
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.066 0.1 -9999 0 -0.56 4 4
Syndecan-1/Syntenin -0.066 0.1 -9999 0 -0.63 3 3
MAPK3 -0.049 0.09 -9999 0 -0.52 4 4
HGF/MET -0.15 0.29 -9999 0 -0.69 178 178
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.065 0.098 -9999 0 -0.55 4 4
Syndecan-1/RANTES -0.071 0.11 -9999 0 -0.66 6 6
Syndecan-1/CD147 -0.057 0.096 -9999 0 -0.56 4 4
Syndecan-1/Syntenin/PIP2 -0.063 0.096 -9999 0 -0.61 3 3
LAMA5 0 0.01 -9999 0 -0.28 1 1
positive regulation of cell-cell adhesion -0.062 0.094 -9999 0 -0.59 3 3
MMP7 -0.12 0.29 -9999 0 -0.84 116 116
HGF -0.05 0.2 -9999 0 -0.84 50 50
Syndecan-1/CASK -0.068 0.1 -9999 0 -0.33 82 82
Syndecan-1/HGF/MET -0.17 0.26 -9999 0 -0.61 180 180
regulation of cell adhesion -0.036 0.093 -9999 0 -0.54 3 3
HPSE -0.008 0.056 -9999 0 -0.84 2 2
positive regulation of cell migration -0.072 0.11 -9999 0 -0.35 82 82
SDC1 -0.072 0.11 -9999 0 -0.35 82 82
Syndecan-1/Collagen -0.072 0.11 -9999 0 -0.35 82 82
PPIB 0 0.01 -9999 0 -0.28 1 1
MET -0.14 0.32 -9999 0 -0.83 144 144
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.84 1 1
MAPK1 -0.049 0.09 -9999 0 -0.52 4 4
homophilic cell adhesion -0.071 0.11 -9999 0 -0.34 82 82
MMP1 -0.22 0.11 -9999 0 -0.28 661 661
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.003 0.037 -9999 0 -0.66 2 2
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
SPHK1 -0.026 0.061 -9999 0 -1.1 2 2
mol:S1P -0.031 0.062 -9999 0 -0.99 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.39 291 291
GNAO1 -0.033 0.14 -9999 0 -0.58 41 41
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.61 51 51
PLCG1 -0.089 0.22 -9999 0 -0.64 51 51
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
GNAI2 0 0.001 -9999 0 -10000 0 0
GNAI3 0 0.001 -9999 0 -10000 0 0
GNAI1 -0.043 0.19 -9999 0 -0.85 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.007 0.035 -9999 0 -0.58 2 2
S1P1/S1P -0.044 0.073 -9999 0 -0.69 4 4
negative regulation of cAMP metabolic process -0.096 0.22 -9999 0 -0.38 292 292
MAPK3 -0.16 0.31 -9999 0 -0.57 281 281
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.002 0.041 -9999 0 -0.84 2 2
PLCB2 -0.007 0.085 -9999 0 -0.57 5 5
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.06 -9999 0 -0.55 4 4
receptor internalization -0.042 0.068 -9999 0 -0.62 4 4
PTGS2 -0.33 0.56 -9999 0 -1.1 281 281
Rac1/GTP -0.037 0.06 -9999 0 -0.55 4 4
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.029 -9999 0 -0.29 1 1
negative regulation of T cell proliferation -0.096 0.22 -9999 0 -0.38 292 292
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
MAPK1 -0.16 0.31 -9999 0 -0.57 281 281
S1P1/S1P/PDGFB-D/PDGFRB -0.052 0.086 -9999 0 -0.72 5 5
ABCC1 0 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.003 0.027 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.2 0.22 -9999 0 -0.44 373 373
Syndecan-3/Neurocan -0.007 0.025 -9999 0 -10000 0 0
POMC -0.022 0.12 -9999 0 -0.52 35 35
EGFR -0.29 0.4 -9999 0 -0.84 291 291
Syndecan-3/EGFR -0.17 0.23 -9999 0 -0.48 291 291
AGRP -0.002 0.025 -9999 0 -0.28 7 7
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.01 -9999 0 -0.28 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.029 -9999 0 -0.84 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.017 0.067 -9999 0 -10000 0 0
long-term memory -0.001 0.018 -9999 0 -0.44 1 1
Syndecan-3/IL8 -0.017 0.071 -9999 0 -0.48 17 17
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.004 0.033 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
PTN -0.37 0.42 -9999 0 -0.84 374 374
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.19 0.21 -9999 0 -0.43 373 373
Syndecan-3/AgRP -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.014 -9999 0 -10000 0 0
Fyn/Cortactin -0.002 0.028 -9999 0 -0.64 1 1
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.016 0.07 -9999 0 -0.47 17 17
IL8 -0.035 0.13 -9999 0 -0.41 73 73
Syndecan-3/Fyn/Cortactin -0.001 0.018 -9999 0 -0.46 1 1
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.018 0.092 -9999 0 -0.62 17 17
Gamma Secretase -0.001 0.017 -9999 0 -0.48 1 1
LPA receptor mediated events

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
GNB1/GNG2 -0.013 0.081 -9999 0 -0.55 16 16
NF kappa B1 p50/RelA/I kappa B alpha -0.045 0.12 -9999 0 -0.42 11 11
AP1 -0.21 0.28 -9999 0 -0.52 338 338
mol:PIP3 -0.19 0.25 -9999 0 -0.48 336 336
AKT1 -0.008 0.053 -9999 0 -0.57 2 2
PTK2B 0.015 0.057 -9999 0 -0.3 13 13
RHOA 0.029 0.025 -9999 0 -0.24 1 1
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.14 -9999 0 -0.37 101 101
MAGI3 -0.001 0.029 -9999 0 -0.84 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.43 116 116
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.018 0.15 -9999 0 -0.44 86 86
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.52 14 14
endothelial cell migration 0.011 0.11 -9999 0 -0.7 19 19
ADCY4 0.001 0.14 -9999 0 -0.62 25 25
ADCY5 -0.068 0.18 -9999 0 -0.6 53 53
ADCY6 0.01 0.12 -9999 0 -0.6 18 18
ADCY7 0.01 0.12 -9999 0 -0.6 18 18
ADCY1 0.003 0.13 -9999 0 -0.61 22 22
ADCY2 -0.01 0.15 -9999 0 -0.62 30 30
ADCY3 0.01 0.12 -9999 0 -0.6 18 18
ADCY8 0.007 0.12 -9999 0 -0.61 18 18
ADCY9 0.01 0.12 -9999 0 -0.6 18 18
GSK3B 0.023 0.054 -9999 0 -0.4 4 4
arachidonic acid secretion 0.014 0.12 -9999 0 -0.57 18 18
GNG2 -0.006 0.071 -9999 0 -0.84 6 6
TRIP6 -0.001 0.019 -9999 0 -0.53 1 1
GNAO1 -0.005 0.12 -9999 0 -0.53 39 39
HRAS 0 0.01 -9999 0 -10000 0 0
NFKBIA -0.005 0.16 -9999 0 -0.42 101 101
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.033 -9999 0 -0.95 1 1
JUN -0.009 0.086 -9999 0 -0.84 9 9
LPA/LPA2/NHERF2 -0.001 0.011 -9999 0 -10000 0 0
TIAM1 -0.001 0.04 -9999 0 -1.1 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.01 0.14 -9999 0 -0.38 101 101
PLCB3 -0.001 0.009 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 271 271
positive regulation of mitosis 0.014 0.12 -9999 0 -0.57 18 18
LPA/LPA1-2-3 -0.075 0.18 -9999 0 -0.52 109 109
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.003 0.1 -9999 0 -0.41 12 12
GNAZ 0.012 0.088 -9999 0 -0.48 25 25
EGFR/PI3K-beta/Gab1 -0.2 0.27 -9999 0 -0.5 336 336
positive regulation of dendritic cell cytokine production -0.074 0.18 -9999 0 -0.52 109 109
LPA/LPA2/MAGI-3 -0.002 0.022 -9999 0 -0.56 1 1
ARHGEF1 -0.008 0.058 -9999 0 -0.46 11 11
GNAI2 0.017 0.073 -9999 0 -0.45 19 19
GNAI3 0.017 0.073 -9999 0 -0.45 19 19
GNAI1 -0.013 0.16 -9999 0 -0.59 55 55
LPA/LPA3 -0.086 0.21 -9999 0 -0.65 101 101
LPA/LPA2 -0.001 0.014 -9999 0 -10000 0 0
LPA/LPA1 -0.012 0.081 -9999 0 -0.53 19 19
HB-EGF/EGFR -0.25 0.27 -9999 0 -0.61 291 291
HBEGF -0.062 0.1 -9999 0 -0.65 3 3
mol:DAG -0.01 0.14 -9999 0 -0.38 101 101
cAMP biosynthetic process -0.008 0.14 -9999 0 -0.55 38 38
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.005 0.16 -9999 0 -0.42 101 101
GNAQ -0.057 0.14 -9999 0 -0.43 103 103
LPAR2 0 0.01 -9999 0 -0.28 1 1
LPAR3 -0.11 0.27 -9999 0 -0.7 134 134
LPAR1 -0.013 0.096 -9999 0 -0.83 11 11
IL8 -0.19 0.23 -9999 0 -0.45 312 312
PTK2 -0.069 0.17 -9999 0 -0.49 109 109
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.063 0.16 -9999 0 -0.44 116 116
EGFR -0.29 0.4 -9999 0 -0.84 291 291
PLCG1 -0.058 0.15 -9999 0 -0.45 102 102
PLD2 -0.069 0.17 -9999 0 -0.49 109 109
G12/G13 -0.009 0.063 -9999 0 -0.5 11 11
PI3K-beta -0.01 0.061 -9999 0 -0.42 16 16
cell migration -0.022 0.055 -9999 0 -0.25 6 6
SLC9A3R2 0 0 -9999 0 -10000 0 0
PXN 0.002 0.1 -9999 0 -0.42 12 12
HRAS/GTP -0.03 0.1 -9999 0 -0.59 18 18
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.84 1 1
PRKCE -0.001 0.029 -9999 0 -0.84 1 1
PRKCD -0.001 0.13 -9999 0 -0.36 101 101
Gi(beta/gamma) -0.031 0.11 -9999 0 -0.6 20 20
mol:LPA -0.002 0.021 -9999 0 -0.22 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.42 109 109
MAPKKK cascade 0.014 0.12 -9999 0 -0.57 18 18
contractile ring contraction involved in cytokinesis 0.029 0.024 -9999 0 -0.24 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.061 0.15 -9999 0 -0.45 105 105
GNA15 -0.057 0.14 -9999 0 -0.43 102 102
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.019 0.15 -9999 0 -0.45 86 86
GNA11 -0.056 0.14 -9999 0 -0.43 101 101
Rac1/GTP -0.001 0.035 -9999 0 -1 1 1
MMP2 0.011 0.11 -9999 0 -0.7 19 19
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.046 0.29 -10000 0 -0.84 91 91
IHH -0.011 0.075 -10000 0 -0.39 4 4
SHH Np/Cholesterol/GAS1 -0.031 0.12 -10000 0 -0.53 46 46
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.031 0.12 0.53 46 -10000 0 46
SMO/beta Arrestin2 -0.07 0.23 -10000 0 -0.87 57 57
SMO -0.046 0.25 -10000 0 -0.87 64 64
AKT1 0 0.093 -10000 0 -0.31 55 55
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.06 0.22 -10000 0 -0.84 60 60
ADRBK1 0 0.01 -10000 0 -10000 0 0
heart looping -0.028 0.25 -10000 0 -0.83 66 66
STIL -0.035 0.21 -10000 0 -0.72 59 59
DHH N/PTCH2 -0.073 0.21 -10000 0 -0.68 91 91
DHH N/PTCH1 -0.084 0.24 -10000 0 -0.77 82 82
PIK3CA 0 0.01 -10000 0 -0.28 1 1
DHH -0.023 0.14 -10000 0 -0.81 24 24
PTHLH -0.07 0.37 -10000 0 -1.1 91 91
determination of left/right symmetry -0.028 0.25 -10000 0 -0.83 66 66
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.068 0.36 -10000 0 -1.1 91 91
IHH N/Hhip -0.009 0.047 -10000 0 -0.49 2 2
DHH N/Hhip -0.02 0.11 -10000 0 -0.66 24 24
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.028 0.25 -10000 0 -0.83 66 66
pancreas development -0.004 0.04 -10000 0 -0.33 10 10
HHAT -0.001 0.029 -10000 0 -0.84 1 1
PI3K 0 0.006 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.045 0.19 -10000 0 -0.84 45 45
somite specification -0.028 0.25 -10000 0 -0.83 66 66
SHH Np/Cholesterol/PTCH1 -0.066 0.2 -10000 0 -0.74 63 63
SHH Np/Cholesterol/PTCH2 -0.049 0.15 -10000 0 -0.53 74 74
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.52 219 219
SHH 0.01 0.036 -10000 0 -0.65 1 1
catabolic process -0.041 0.25 -10000 0 -0.85 66 66
SMO/Vitamin D3 -0.069 0.22 -10000 0 -0.83 58 58
SHH Np/Cholesterol/Hhip -0.005 0.036 -10000 0 -0.53 2 2
LRP2 -0.22 0.37 -10000 0 -0.84 218 218
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.84 71 71
SHH Np/Cholesterol/BOC -0.04 0.14 -10000 0 -0.53 61 61
SHH Np/Cholesterol/CDO -0.009 0.061 -10000 0 -0.52 11 11
mesenchymal cell differentiation 0.005 0.036 0.52 2 -10000 0 2
mol:Vitamin D3 -0.025 0.22 -10000 0 -0.74 64 64
IHH N/PTCH2 -0.067 0.2 -10000 0 -0.72 73 73
CDON -0.01 0.091 -10000 0 -0.84 10 10
IHH N/PTCH1 -0.039 0.26 -10000 0 -0.86 66 66
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.64 218 218
PTCH2 -0.073 0.24 -10000 0 -0.84 73 73
SHH Np/Cholesterol -0.003 0.026 -10000 0 -0.53 1 1
PTCH1 -0.041 0.26 -10000 0 -0.86 66 66
HHIP -0.004 0.04 -10000 0 -0.33 10 10
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.056 0.2 -9999 0 -0.85 49 49
PDGF/PDGFRA/CRKL -0.037 0.15 -9999 0 -0.65 48 48
positive regulation of JUN kinase activity -0.029 0.12 -9999 0 -0.5 48 48
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.041 0.15 -9999 0 -0.65 48 48
AP1 -0.4 0.56 -9999 0 -1.2 271 271
mol:IP3 -0.034 0.16 -9999 0 -0.67 48 48
PLCG1 -0.034 0.16 -9999 0 -0.68 48 48
PDGF/PDGFRA/alphaV Integrin -0.037 0.15 -9999 0 -0.65 48 48
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.16 -9999 0 -0.67 48 48
CAV3 -0.001 0.016 -9999 0 -10000 0 0
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
SHC/Grb2/SOS1 -0.029 0.12 -9999 0 -0.5 48 48
PDGF/PDGFRA/Shf -0.038 0.15 -9999 0 -0.66 48 48
FOS -0.36 0.57 -9999 0 -1.2 271 271
JUN -0.028 0.077 -9999 0 -0.72 9 9
oligodendrocyte development -0.037 0.15 -9999 0 -0.65 48 48
GRB2 0 0.01 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG -0.034 0.16 -9999 0 -0.67 48 48
PDGF/PDGFRA -0.056 0.2 -9999 0 -0.85 49 49
actin cytoskeleton reorganization -0.038 0.15 -9999 0 -0.65 49 49
SRF 0.016 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.032 0.13 -9999 0 -0.56 48 48
PDGF/PDGFRA/Crk/C3G -0.032 0.13 -9999 0 -0.56 48 48
JAK1 -0.022 0.16 -9999 0 -0.65 48 48
ELK1/SRF -0.025 0.12 -9999 0 -0.51 48 48
SHB -0.001 0.03 -9999 0 -0.84 1 1
SHF -0.001 0.03 -9999 0 -0.56 2 2
CSNK2A1 0.02 0.027 -9999 0 -10000 0 0
GO:0007205 -0.035 0.16 -9999 0 -0.69 48 48
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.029 0.12 -9999 0 -0.5 48 48
PDGF/PDGFRA/SHB -0.038 0.15 -9999 0 -0.65 49 49
PDGF/PDGFRA/Caveolin-1 -0.17 0.33 -9999 0 -0.75 190 190
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.15 -9999 0 -0.62 48 48
PIK3CA 0 0.01 -9999 0 -0.28 1 1
PDGF/PDGFRA/Crk -0.037 0.15 -9999 0 -0.65 48 48
JAK-STAT cascade -0.022 0.15 -9999 0 -0.64 48 48
cell proliferation -0.038 0.15 -9999 0 -0.66 48 48
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.13 0.19 -9999 0 -0.39 273 273
MAP3K8 -0.005 0.066 -9999 0 -0.75 6 6
FOS -0.041 0.14 -9999 0 -0.46 27 27
PRKCA -0.022 0.13 -9999 0 -0.78 24 24
PTPN7 -0.008 0.068 -9999 0 -0.29 46 46
HRAS 0 0.01 -9999 0 -10000 0 0
PRKCB -0.019 0.11 -9999 0 -0.56 28 28
NRAS -0.001 0.014 -9999 0 -0.28 2 2
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.01 0.073 -9999 0 -10000 0 0
MAP2K1 -0.015 0.14 -9999 0 -0.6 37 37
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.033 0.12 -9999 0 -0.61 33 33
mol:GTP -0.002 0.003 -9999 0 -0.006 271 271
MAPK1 -0.01 0.073 -9999 0 -0.26 23 23
RAF1 -0.033 0.12 -9999 0 -0.61 33 33
KRAS 0 0.01 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.6 0.38 -9999 0 -0.84 601 601
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.001 0.019 -9999 0 -10000 0 0
TCEB1 -0.001 0.016 -9999 0 -0.28 3 3
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.007 -9999 0 -10000 0 0
COPS5 0 0.01 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.008 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.043 0.1 -9999 0 -0.28 132 132
ARNT/IPAS -0.46 0.29 -9999 0 -0.64 601 601
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0.01 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.005 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.035 -9999 0 -0.51 1 1
HIF1A/RACK1/Elongin B/Elongin C 0 0.008 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -10000 0 0
HIF1A/JAB1 -0.001 0.006 -9999 0 -10000 0 0
EGLN3 -0.023 0.076 -9999 0 -0.28 69 69
EGLN2 -0.001 0.016 -9999 0 -10000 0 0
EGLN1 -0.001 0.029 -9999 0 -0.84 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.004 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.016 0.036 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.029 -10000 0 -0.84 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.03 0.069 0.64 1 -10000 0 1
CDKN1A -0.001 0.034 -10000 0 -0.98 1 1
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
FOXO3 -0.001 0.017 -10000 0 -0.34 2 2
FOXO1 -0.006 0.071 -10000 0 -0.84 6 6
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.61 0.37 -10000 0 -0.84 601 601
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.19 0.35 -10000 0 -0.84 186 186
FHL2 -0.006 0.066 -10000 0 -0.84 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.005 -10000 0 -10000 0 0
HIST2H4A -0.03 0.069 -10000 0 -0.65 1 1
SIRT1/FOXO3a 0 0.014 -10000 0 -0.26 2 2
SIRT1 0 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.02 -10000 0 -0.56 1 1
SIRT1/Histone H1b -0.002 0.009 -10000 0 -10000 0 0
apoptosis 0 0.005 -10000 0 -10000 0 0
SIRT1/PGC1A -0.13 0.24 -10000 0 -0.57 186 186
p53/SIRT1 0.001 0.016 0.43 1 -10000 0 1
SIRT1/FOXO4 0 0.006 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.059 -10000 0 -0.52 11 11
HIST1H1E -0.004 0.012 -10000 0 -10000 0 0
SIRT1/p300 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.015 -10000 0 -10000 0 0
TP53 0 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.005 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.47 0.28 -10000 0 -0.65 601 601
ACSS2 0 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.001 0.015 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.058 -10000 0 -0.34 25 25
epithelial cell differentiation -0.014 0.08 -10000 0 -0.48 24 24
CYFIP2 -0.01 0.061 -10000 0 -0.32 25 25
ENAH 0.056 0.064 -10000 0 -10000 0 0
EGFR -0.29 0.4 -10000 0 -0.84 291 291
EPHA2 -0.006 0.071 -10000 0 -0.84 6 6
MYO6 -0.014 0.077 -10000 0 -0.45 25 25
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.035 -10000 0 -0.56 2 2
AQP5 -0.26 0.31 -10000 0 -0.62 346 346
CTNND1 0 0.01 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.074 -10000 0 -0.44 24 24
regulation of calcium-dependent cell-cell adhesion -0.037 0.13 -10000 0 -0.46 68 68
EGF -0.17 0.33 -10000 0 -0.84 167 167
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.041 0.15 -10000 0 -0.61 44 44
cortical microtubule organization -0.014 0.08 -10000 0 -0.48 24 24
GO:0000145 0.024 0.077 -10000 0 -0.42 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.081 -10000 0 -0.48 24 24
MLLT4 -0.003 0.05 -10000 0 -0.84 3 3
ARF6/GDP -0.014 0.069 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.044 -10000 0 -0.51 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.079 -10000 0 -0.42 24 24
PVRL2 -0.001 0.016 -10000 0 -10000 0 0
ZYX -0.013 0.075 -10000 0 -0.45 24 24
ARF6/GTP -0.004 0.04 -10000 0 -0.47 6 6
CDH1 -0.024 0.14 -10000 0 -0.84 24 24
EGFR/EGFR/EGF/EGF -0.25 0.28 -10000 0 -0.5 422 422
RhoA/GDP -0.013 0.075 -10000 0 -0.45 24 24
actin cytoskeleton organization 0.031 0.08 -10000 0 -0.42 25 25
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.84 16 16
GIT1 -0.001 0.019 -10000 0 -0.28 4 4
IGF1R -0.02 0.12 -10000 0 -0.84 16 16
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
DIAPH1 -0.001 0.035 -10000 0 -0.68 2 2
Wnt receptor signaling pathway 0.014 0.08 0.48 24 -10000 0 24
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.07 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL -0.013 0.074 -10000 0 -0.44 25 25
EFNA1 0 0.01 -10000 0 -10000 0 0
LPP 0.031 0.082 -10000 0 -0.42 26 26
Ephrin A1/EPHA2 -0.016 0.081 -10000 0 -0.43 30 30
SEC6/SEC8 -0.013 0.07 -10000 0 -10000 0 0
MGAT3 -0.038 0.13 -10000 0 -0.47 68 68
HGF/MET -0.11 0.22 -10000 0 -0.49 195 195
HGF -0.05 0.2 -10000 0 -0.84 50 50
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.058 -10000 0 -0.34 25 25
actin cable formation 0.071 0.06 -10000 0 -10000 0 0
KIAA1543 0.031 0.089 -10000 0 -0.46 24 24
KIFC3 -0.014 0.079 -10000 0 -0.45 26 26
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.014 0.077 -10000 0 -0.45 25 25
NCK1/GIT1 -0.001 0.012 -10000 0 -10000 0 0
mol:GDP -0.014 0.08 -10000 0 -0.48 24 24
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.013 0.075 -10000 0 -0.45 24 24
PIP5K1C -0.013 0.075 -10000 0 -0.45 24 24
LIMA1 -0.001 0.029 -10000 0 -0.84 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.012 0.06 -10000 0 -10000 0 0
adherens junction assembly 0.047 0.085 -10000 0 -0.63 3 3
IGF-1R heterotetramer/IGF1 -0.12 0.21 -10000 0 -0.46 215 215
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -10000 0 -0.64 3 3
MET -0.14 0.32 -10000 0 -0.83 144 144
PLEKHA7 -0.014 0.08 -10000 0 -0.47 24 24
mol:GTP -0.004 0.043 -10000 0 -0.5 6 6
establishment of epithelial cell apical/basal polarity -0.012 0.066 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.01 0.058 -10000 0 -0.34 25 25
regulation of cell-cell adhesion 0.031 0.08 -10000 0 -0.42 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.058 -10000 0 -0.34 25 25
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation -0.005 0.027 -9999 0 -10000 0 0
adherens junction organization 0.033 0.064 -9999 0 -0.31 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.14 0.19 -9999 0 -0.57 11 11
FMN1 0.027 0.083 -9999 0 -0.48 11 11
mol:IP3 -0.005 0.029 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.056 -9999 0 -0.33 25 25
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 -0.006 0.033 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.088 -9999 0 -0.52 24 24
CTNND1 0 0.009 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.058 -9999 0 -0.3 25 25
VASP 0.033 0.059 -9999 0 -0.3 25 25
ZYX 0.033 0.059 -9999 0 -0.3 25 25
JUB 0.031 0.068 -9999 0 -0.32 29 29
EGFR(dimer) -0.16 0.22 -9999 0 -0.46 292 292
E-cadherin/beta catenin-gamma catenin -0.016 0.092 -9999 0 -0.54 25 25
mol:PI-3-4-5-P3 -0.006 0.036 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.27 1 1
PI3K -0.006 0.037 -9999 0 -10000 0 0
FYN 0.044 0.036 -9999 0 -0.4 1 1
mol:Ca2+ -0.005 0.028 -9999 0 -10000 0 0
JUP -0.001 0.032 -9999 0 -0.46 3 3
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG -0.005 0.029 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
RhoA/GDP -0.14 0.19 -9999 0 -0.4 291 291
establishment of polarity of embryonic epithelium 0.033 0.058 -9999 0 -0.3 25 25
SRC 0 0.01 -9999 0 -0.28 1 1
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.84 291 291
CASR -0.005 0.027 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.025 -9999 0 -10000 0 0
AKT2 -0.006 0.033 -9999 0 -10000 0 0
actin cable formation 0.034 0.081 -9999 0 -0.46 11 11
apoptosis 0.006 0.032 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
mol:GDP -0.15 0.2 -9999 0 -0.43 291 291
PIP5K1A 0.033 0.059 -9999 0 -10000 0 0
PLCG1 -0.005 0.029 -9999 0 -10000 0 0
Rac1/GTP -0.15 0.2 -9999 0 -0.42 292 292
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.5 191 191
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0.02 -10000 0 -10000 0 0
GNB1/GNG2 -0.004 0.048 -10000 0 -0.57 6 6
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.22 -10000 0 -0.53 190 190
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.027 0.049 0.12 190 -10000 0 190
GNAL -0.19 0.35 -10000 0 -0.84 190 190
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
CRH -0.003 0.028 -10000 0 -0.28 9 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
MAPK11 -0.001 0.023 -10000 0 -0.46 2 2
Signaling events mediated by PRL

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
CCNE1 -0.053 0.11 -9999 0 -0.28 162 162
mol:Halofuginone 0 0.002 -9999 0 -10000 0 0
ITGA1 -0.002 0.041 -9999 0 -0.84 2 2
CDKN1A -0.064 0.093 -9999 0 -0.88 1 1
PRL-3/alpha Tubulin -0.001 0.012 -9999 0 -10000 0 0
mol:Ca2+ -0.036 0.1 -9999 0 -0.66 13 13
AGT -0.051 0.14 -9999 0 -0.33 128 128
CCNA2 -0.19 0.26 -9999 0 -0.59 162 162
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.2 0.32 -9999 0 -0.64 286 286
CDK2/Cyclin E1 -0.071 0.091 -9999 0 -0.79 1 1
MAPK3 0.021 0.013 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.008 -9999 0 -10000 0 0
MAPK1 0.021 0.013 -9999 0 -10000 0 0
PTP4A1 -0.14 0.25 -9999 0 -0.5 286 286
PTP4A3 -0.001 0.019 -9999 0 -10000 0 0
PTP4A2 -0.001 0.013 -9999 0 -0.28 2 2
ITGB1 0.021 0.013 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
RAC1 -0.063 0.088 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.16 0.22 -9999 0 -0.62 3 3
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0.006 -9999 0 -10000 0 0
RHOC -0.063 0.088 -9999 0 -10000 0 0
RHOA -0.063 0.088 -9999 0 -10000 0 0
cell motility -0.044 0.11 -9999 0 -0.25 2 2
PRL-1/alpha Tubulin -0.16 0.22 -9999 0 -0.64 2 2
PRL-3/alpha1 Integrin -0.002 0.034 -9999 0 -0.64 2 2
ROCK1 -0.044 0.11 -9999 0 -0.25 2 2
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.14 0.25 -9999 0 -0.49 286 286
ATF5 -0.001 0.019 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.075 0.18 0.68 61 -10000 0 61
KIRREL -0.061 0.22 -10000 0 -0.84 61 61
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.075 0.18 -10000 0 -0.68 61 61
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.054 0.14 -10000 0 -0.52 61 61
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.03 0.098 -10000 0 -0.38 61 61
FYN -0.05 0.13 -10000 0 -0.5 61 61
mol:Ca2+ -0.053 0.14 -10000 0 -0.52 61 61
mol:DAG -0.054 0.14 -10000 0 -0.52 61 61
NPHS2 -0.008 0.03 -10000 0 -0.29 1 1
mol:IP3 -0.054 0.14 -10000 0 -0.52 61 61
regulation of endocytosis -0.022 0.13 -10000 0 -0.46 61 61
Nephrin/NEPH1/podocin/Cholesterol -0.056 0.14 -10000 0 -0.53 61 61
establishment of cell polarity -0.075 0.18 -10000 0 -0.68 61 61
Nephrin/NEPH1/podocin/NCK1-2 -0.021 0.13 -10000 0 -0.48 61 61
Nephrin/NEPH1/beta Arrestin2 -0.022 0.13 -10000 0 -0.47 61 61
NPHS1 -0.049 0.1 -10000 0 -0.35 11 11
Nephrin/NEPH1/podocin -0.044 0.13 -10000 0 -0.5 61 61
TJP1 -0.001 0.029 -10000 0 -0.84 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.054 0.14 -10000 0 -0.52 61 61
CD2AP 0 0.01 -10000 0 -0.28 1 1
Nephrin/NEPH1/podocin/GRB2 -0.054 0.14 -10000 0 -0.52 61 61
GRB2 0 0.01 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.055 0.14 -10000 0 -0.52 67 67
cytoskeleton organization -0.039 0.12 -10000 0 -0.48 61 61
Nephrin/NEPH1 -0.054 0.14 -10000 0 -0.51 61 61
Nephrin/NEPH1/ZO-1 -0.059 0.15 -10000 0 -0.57 61 61
LPA4-mediated signaling events

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
ADCY4 -0.002 0.11 -9999 0 -0.57 31 31
ADCY5 -0.17 0.28 -9999 0 -0.57 267 267
ADCY6 0.019 0.02 -9999 0 -0.57 1 1
ADCY7 0.019 0.02 -9999 0 -0.57 1 1
ADCY1 -0.007 0.097 -9999 0 -0.57 19 19
ADCY2 -0.034 0.16 -9999 0 -0.57 67 67
ADCY3 0.019 0.021 -9999 0 -0.57 1 1
ADCY8 0.009 0.033 -9999 0 -0.57 1 1
PRKCE 0.01 0.023 -9999 0 -0.66 1 1
ADCY9 0.019 0.02 -9999 0 -0.57 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.033 0.11 -9999 0 -0.33 55 55
FAS signaling pathway (CD95)

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
SPTAN1 0.009 0.049 0.29 24 -10000 0 24
RFC1 0.009 0.049 0.29 24 -10000 0 24
PRKDC 0.008 0.05 0.29 24 -10000 0 24
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.024 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.016 0.059 0.26 9 -0.4 7 16
MAP2K4 -0.063 0.16 -10000 0 -0.54 11 11
mol:ceramide -0.058 0.093 -10000 0 -0.6 10 10
GSN 0 0.082 0.29 23 -0.53 13 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.063 0.23 9 -0.52 6 15
FAS -0.002 0.041 -10000 0 -0.85 2 2
BID 0 0.004 -10000 0 -10000 0 0
MAP3K1 -0.024 0.093 -10000 0 -0.3 6 6
MAP3K7 0 0.01 -10000 0 -10000 0 0
RB1 0.008 0.052 0.29 24 -0.55 1 25
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.28 -10000 0 -0.63 187 187
ARHGDIB 0.008 0.049 0.29 24 -10000 0 24
FADD -0.006 0.04 -10000 0 -0.3 11 11
actin filament polymerization 0 0.082 0.53 13 -0.29 23 36
NFKB1 -0.08 0.1 -10000 0 -0.33 1 1
MAPK8 -0.12 0.24 -10000 0 -0.43 323 323
DFFA 0.009 0.049 0.29 24 -10000 0 24
DNA fragmentation during apoptosis 0.009 0.049 0.29 24 -10000 0 24
FAS/FADD/MET -0.1 0.22 -10000 0 -0.59 143 143
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.001 0.047 -10000 0 -10000 0 0
FAF1 0 0 -10000 0 -10000 0 0
PARP1 0.009 0.049 0.29 24 -10000 0 24
DFFB 0.009 0.049 0.29 24 -10000 0 24
CHUK -0.069 0.089 -10000 0 -10000 0 0
FASLG -0.018 0.09 -10000 0 -0.36 40 40
FAS/FADD -0.005 0.044 -10000 0 -0.73 2 2
HGF -0.05 0.2 -10000 0 -0.84 50 50
LMNA 0.008 0.044 0.26 24 -10000 0 24
CASP6 0.009 0.049 0.29 24 -10000 0 24
CASP10 -0.003 0.051 -10000 0 -0.85 3 3
CASP3 0.01 0.059 0.36 24 -10000 0 24
PTPN13 -0.022 0.13 -10000 0 -0.84 22 22
CASP8 0.002 0.013 -10000 0 -10000 0 0
IL6 -0.5 0.69 -10000 0 -1.4 323 323
MET -0.14 0.32 -10000 0 -0.83 144 144
ICAD/CAD 0.008 0.045 0.27 24 -10000 0 24
FASLG/FAS/FADD/FAF1/Caspase 10 -0.058 0.094 -10000 0 -0.61 10 10
activation of caspase activity by cytochrome c 0 0.004 -10000 0 -10000 0 0
PAK2 0.009 0.048 0.29 24 -10000 0 24
BCL2 -0.02 0.14 -10000 0 -0.84 24 24
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.002 0.032 -10000 0 -0.47 4 4
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.003 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.077 0.24 -10000 0 -0.84 77 77
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
TLE1 -0.006 0.071 -10000 0 -0.84 6 6
AP1 -0.13 0.19 -10000 0 -0.39 274 274
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.046 -10000 0 -0.34 1 1
NICD/RBPSUH 0 0.003 -10000 0 -10000 0 0
WIF1 -0.44 0.42 -10000 0 -0.82 451 451
NOTCH1 0 0.003 -10000 0 -10000 0 0
PSENEN 0 0.01 -10000 0 -0.28 1 1
KREMEN2 -0.13 0.14 -10000 0 -10000 0 0
DKK1 -0.08 0.2 -10000 0 -0.43 157 157
beta catenin/beta TrCP1 -0.011 0.024 0.23 2 -10000 0 2
APH1B -0.001 0.029 -10000 0 -0.84 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.009 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.35 6 6
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.27 0.39 -10000 0 -0.84 271 271
JUN -0.009 0.086 -10000 0 -0.84 9 9
MAP3K7 0 0.011 -10000 0 -10000 0 0
CTNNB1 -0.004 0.037 0.24 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.073 0.11 -10000 0 -0.66 17 17
HNF1A -0.001 0.024 -10000 0 -0.28 3 3
CTBP1 0.001 0.003 -10000 0 -10000 0 0
MYC -0.036 0.23 -10000 0 -1.5 20 20
NKD1 -0.011 0.08 -10000 0 -0.84 6 6
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.043 0.14 -10000 0 -0.47 77 77
apoptosis -0.13 0.19 -10000 0 -0.39 274 274
Delta 1/NOTCHprecursor -0.002 0.032 -10000 0 -0.47 4 4
DLL1 -0.004 0.058 -10000 0 -0.84 4 4
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.017 -10000 0 -0.48 1 1
APC 0.003 0.009 -10000 0 -10000 0 0
DVL1 -0.04 0.038 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.6 45 45
LRP6 -0.001 0.013 -10000 0 -10000 0 0
CSNK1A1 0 0 -10000 0 -10000 0 0
NLK 0.002 0.011 -10000 0 -10000 0 0
CCND1 -0.011 0.094 -10000 0 -1.5 3 3
WNT1 0 0.01 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.009 0.037 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.84 17 17
NOTCH1 precursor/DVL1 -0.019 0.019 -10000 0 -10000 0 0
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 0 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.043 0.14 -10000 0 -0.47 77 77
PPP2R5D -0.016 0.042 0.36 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.27 0.25 -10000 0 -0.51 440 440
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.004 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.048 0.2 -10000 0 -0.84 48 48
HRAS 0 0.01 -10000 0 -10000 0 0
EGFR -0.29 0.4 -10000 0 -0.84 291 291
AKT 0.016 0.073 -10000 0 -0.58 11 11
FOXO3 -0.002 0.041 -10000 0 -0.84 2 2
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.006 0.071 -10000 0 -0.84 6 6
AKT3 -0.011 0.095 -10000 0 -0.84 11 11
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.32 -10000 0 -0.83 144 144
PIK3CA 0 0.01 -10000 0 -0.28 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
PIK3CG -0.008 0.078 -10000 0 -0.63 11 11
PIK3R3 0 0.01 -10000 0 -10000 0 0
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.029 -10000 0 -0.84 1 1
RAS -0.091 0.16 0.26 1 -0.37 157 158
ERBB2 -0.025 0.079 -10000 0 -10000 0 0
proliferation/survival/translation -0.006 0.054 0.28 4 -10000 0 4
PI3K -0.08 0.16 -10000 0 -0.36 159 159
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -10000 0 0
FOXO 0.027 0.024 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
Nectin adhesion pathway

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
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
alphaV beta3 Integrin -0.012 0.083 -9999 0 -0.64 14 14
PTK2 -0.048 0.16 -9999 0 -0.56 68 68
positive regulation of JNK cascade -0.028 0.093 -9999 0 -0.34 68 68
CDC42/GDP 0.013 0.14 -9999 0 -0.46 68 68
Rac1/GDP 0.015 0.14 -9999 0 -0.45 68 68
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.034 0.12 -9999 0 -0.42 68 68
nectin-3/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
RAPGEF1 0.007 0.16 -9999 0 -0.52 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.005 0.18 -9999 0 -0.61 68 68
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
TLN1 -0.024 0.089 -9999 0 -0.61 8 8
Rap1/GTP -0.03 0.099 -9999 0 -0.36 68 68
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.031 -9999 0 -0.52 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP 0.005 0.17 -9999 0 -0.58 68 68
MLLT4 -0.003 0.05 -9999 0 -0.84 3 3
PIK3CA 0 0.01 -9999 0 -0.28 1 1
PI3K -0.041 0.14 -9999 0 -0.49 70 70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
positive regulation of lamellipodium assembly -0.029 0.097 -9999 0 -0.36 68 68
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.067 0.23 -9999 0 -0.84 67 67
PVRL2 -0.001 0.016 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
CLDN1 -0.04 0.16 -9999 0 -0.6 56 56
JAM-A/CLDN1 -0.065 0.18 -9999 0 -0.56 93 93
SRC -0.057 0.19 -9999 0 -0.69 68 68
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
FARP2 0 0.17 -9999 0 -0.57 68 68
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.046 0.16 -9999 0 -0.57 68 68
nectin-1/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
nectin-2/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.046 0.16 -9999 0 -0.57 68 68
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.028 0.093 -9999 0 -0.34 68 68
alphaV/beta3 Integrin/Talin -0.028 0.11 -9999 0 -0.63 18 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
PIP5K1C -0.026 0.096 -9999 0 -0.66 8 8
VAV2 -0.001 0.17 -9999 0 -0.58 68 68
RAP1/GDP -0.035 0.12 -9999 0 -0.42 68 68
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.047 0.16 -9999 0 -0.57 68 68
nectin-3(dimer)/I-afadin/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
Rac1/GTP -0.036 0.12 -9999 0 -0.44 68 68
PTPRM -0.029 0.11 -9999 0 -0.34 71 71
E-cadherin/beta catenin/alpha catenin -0.015 0.08 -9999 0 -0.45 27 27
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.003 0.038 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.048 0.14 -9999 0 -0.64 37 37
STXBP1 -0.004 0.058 -9999 0 -0.84 4 4
ACh/CHRNA1 -0.065 0.079 -9999 0 -0.23 22 22
RAB3GAP2/RIMS1/UNC13B -0.039 0.12 -9999 0 -0.56 37 37
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.068 0.19 -9999 0 -0.44 131 131
mol:ACh 0 0.033 -9999 0 -0.15 30 30
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.099 -9999 0 -0.42 41 41
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.064 0.079 -9999 0 -0.22 22 22
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.13 -9999 0 -0.28 316 316
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.059 0.13 -9999 0 -0.55 37 37
SNAP25 -0.017 0.072 -9999 0 -0.39 30 30
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.086 0.18 -9999 0 -0.84 31 31
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.048 -9999 0 -0.57 4 4
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.099 -9999 0 -0.42 41 41
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.035 0.13 -10000 0 -0.62 30 30
FYN 0.017 0.18 -10000 0 -0.78 32 32
LAT/GRAP2/SLP76 -0.027 0.15 -10000 0 -0.66 35 35
IKBKB -0.001 0.013 -10000 0 -0.28 2 2
AKT1 0.031 0.12 -10000 0 -0.48 34 34
B2M 0.008 0.006 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.19 1 1
MAP3K8 -0.005 0.065 -10000 0 -0.74 6 6
mol:Ca2+ -0.028 0.051 -10000 0 -0.12 175 175
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.56 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.023 0.18 -10000 0 -0.73 35 35
TRPV6 -0.18 0.34 -10000 0 -0.81 187 187
CD28 -0.006 0.063 -10000 0 -0.84 4 4
SHC1 0.011 0.19 -10000 0 -0.8 33 33
receptor internalization -0.001 0.21 -10000 0 -0.85 37 37
PRF1 -0.002 0.23 -10000 0 -1.1 29 29
KRAS 0 0.01 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
COT/AKT1 0.033 0.1 -10000 0 -0.39 35 35
LAT 0.01 0.19 -10000 0 -0.78 37 37
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.85 21 21
CD3E -0.018 0.14 -10000 0 -0.55 45 45
CD3G -0.038 0.16 -10000 0 -0.53 61 61
RASGRP2 -0.006 0.04 -10000 0 -0.19 37 37
RASGRP1 0.038 0.12 -10000 0 -0.48 34 34
HLA-A 0.01 0.015 -10000 0 -10000 0 0
RASSF5 -0.002 0.042 -10000 0 -0.84 2 2
RAP1A/GTP/RAPL -0.002 0.028 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.042 -10000 0 -0.12 32 32
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.048 -10000 0 -0.23 23 23
PRKCA -0.011 0.087 -10000 0 -0.32 43 43
GRAP2 -0.014 0.1 -10000 0 -0.84 13 13
mol:IP3 0.024 0.15 0.28 149 -0.45 34 183
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.22 -10000 0 -0.96 31 31
ORAI1 0.085 0.16 0.39 175 -10000 0 175
CSK 0.009 0.19 -10000 0 -0.82 33 33
B7 family/CD28 -0.019 0.18 -10000 0 -0.74 38 38
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.22 -10000 0 -0.84 43 43
PTPN6 0.007 0.19 -10000 0 -0.81 34 34
VAV1 0.011 0.19 -10000 0 -0.79 35 35
Monovalent TCR/CD3 -0.029 0.21 -10000 0 -0.73 49 49
CBL 0 0 -10000 0 -10000 0 0
LCK 0.009 0.2 -10000 0 -0.86 32 32
PAG1 0.008 0.19 -10000 0 -0.83 33 33
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.22 -10000 0 -0.97 33 33
CD80 -0.08 0.12 -10000 0 -10000 0 0
CD86 -0.001 0.019 -10000 0 -0.28 4 4
PDK1/CARD11/BCL10/MALT1 -0.017 0.058 -10000 0 -0.28 27 27
HRAS 0 0.01 -10000 0 -10000 0 0
GO:0035030 -0.045 0.13 -10000 0 -0.59 39 39
CD8A -0.004 0.079 -10000 0 -0.85 5 5
CD8B -0.026 0.16 -10000 0 -0.6 51 51
PTPRC -0.007 0.06 -10000 0 -0.39 15 15
PDK1/PKC theta 0.036 0.16 -10000 0 -0.6 37 37
CSK/PAG1 0.013 0.18 -10000 0 -0.81 32 32
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0.008 -10000 0 -10000 0 0
GRAP2/SLP76 -0.034 0.17 -10000 0 -0.78 35 35
STIM1 0.045 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.053 -10000 0 -0.18 22 22
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.23 -10000 0 -0.95 37 37
mol:DAG -0.005 0.1 -10000 0 -0.41 35 35
RAP1A/GDP 0.015 0.018 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.022 0.13 -10000 0 -0.62 30 30
cytotoxic T cell degranulation 0.001 0.21 -10000 0 -1 29 29
RAP1A/GTP -0.003 0.014 -10000 0 -0.066 37 37
mol:PI-3-4-5-P3 0.028 0.14 -10000 0 -0.58 35 35
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.017 0.18 0.29 144 -0.61 35 179
NRAS -0.001 0.013 -10000 0 -10000 0 0
ZAP70 -0.027 0.13 -10000 0 -0.78 20 20
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.024 0.14 -10000 0 -0.63 35 35
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.035 0.15 -10000 0 -0.62 43 43
CARD11 -0.007 0.055 -10000 0 -0.34 18 18
PRKCB -0.01 0.086 -10000 0 -0.33 39 39
PRKCE -0.005 0.07 -10000 0 -0.29 30 30
PRKCQ 0.026 0.18 -10000 0 -0.7 38 38
LCP2 0 0.01 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.033 0.1 -10000 0 -0.4 34 34
IKK complex 0.042 0.044 -10000 0 -0.12 18 18
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.037 0.08 -10000 0 -0.3 30 30
PDPK1 0.035 0.12 -10000 0 -0.46 32 32
TCR/CD3/MHC I/CD8/Fyn -0.007 0.24 -10000 0 -0.97 40 40
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.006 -9999 0 -10000 0 0
SMARCC1 0.004 0.022 -9999 0 -0.59 1 1
REL 0.003 0.031 -9999 0 -0.84 1 1
HDAC7 0.011 0.12 -9999 0 -0.49 18 18
JUN -0.009 0.086 -9999 0 -0.84 9 9
EP300 0 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0.001 0.004 -9999 0 -10000 0 0
MAPK14 0.005 0.099 -9999 0 -0.65 18 18
FOXO1 -0.006 0.071 -9999 0 -0.84 6 6
T-DHT/AR -0.003 0.13 -9999 0 -0.52 19 19
MAP2K6 -0.018 0.12 -9999 0 -0.81 19 19
BRM/BAF57 -0.001 0.009 -9999 0 -10000 0 0
MAP2K4 0 0.029 -9999 0 -0.84 1 1
SMARCA2 0 0 -9999 0 -10000 0 0
PDE9A -0.093 0.3 -9999 0 -1.2 52 52
NCOA2 -0.007 0.076 -9999 0 -0.84 7 7
CEBPA -0.006 0.076 -9999 0 -0.84 7 7
EHMT2 0 0 -9999 0 -10000 0 0
cell proliferation 0.02 0.14 -9999 0 -0.5 15 15
NR0B1 -0.01 0.052 -9999 0 -10000 0 0
EGR1 -0.29 0.4 -9999 0 -0.84 286 286
RXRs/9cRA -0.13 0.22 -9999 0 -0.52 204 204
AR/RACK1/Src -0.002 0.1 -9999 0 -0.5 18 18
AR/GR -0.044 0.11 -9999 0 -0.42 32 32
GNB2L1 0.001 0.003 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.019 0.027 -9999 0 -0.65 1 1
T-DHT/AR/TIF2/CARM1 -0.029 0.096 -9999 0 -0.5 25 25
SRC 0.024 0.088 -9999 0 -0.51 18 18
NR3C1 -0.007 0.076 -9999 0 -0.84 7 7
KLK3 -0.21 0.42 -9999 0 -1.2 119 119
APPBP2 -0.001 0.013 -9999 0 -10000 0 0
TRIM24 0 0.01 -9999 0 -0.28 1 1
T-DHT/AR/TIP60 -0.024 0.088 -9999 0 -0.52 18 18
TMPRSS2 -0.17 0.43 -9999 0 -1.3 110 110
RXRG -0.2 0.36 -9999 0 -0.83 206 206
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0 0 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.035 0.25 -9999 0 -0.81 73 73
AR -0.02 0.13 -9999 0 -0.33 110 110
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -10000 0 0
MDM2 0.004 0.024 -9999 0 -0.28 4 4
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.023 0.13 -9999 0 -0.84 19 19
MYST2 0 0.01 -9999 0 -0.28 1 1
HOXB13 -0.13 0.14 -9999 0 -0.28 383 383
T-DHT/AR/RACK1/Src -0.024 0.086 -9999 0 -0.51 18 18
positive regulation of transcription -0.023 0.13 -9999 0 -0.84 19 19
DNAJA1 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.013 -9999 0 -10000 0 0
NCOA1 0.011 0.031 -9999 0 -0.87 1 1
SPDEF -0.047 0.2 -9999 0 -0.72 60 60
T-DHT/AR/TIF2 0.026 0.067 -9999 0 -0.38 3 3
T-DHT/AR/Hsp90 -0.03 0.084 -9999 0 -0.52 18 18
GSK3B 0.001 0.004 -9999 0 -10000 0 0
NR2C1 0.002 0.005 -9999 0 -10000 0 0
mol:T-DHT 0.017 0.092 -9999 0 -0.55 18 18
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.005 0.013 -9999 0 -10000 0 0
POU2F1 0.02 0.027 -9999 0 -0.41 1 1
T-DHT/AR/DAX-1 -0.031 0.089 -9999 0 -0.53 18 18
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.013 -9999 0 -0.28 2 2
Canonical Wnt signaling pathway

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
HDAC1 0.004 0.017 -10000 0 -10000 0 0
AES 0.003 0.014 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.84 17 17
TLE1 -0.003 0.072 -10000 0 -0.84 6 6
MACF1 0 0 -10000 0 -10000 0 0
CTNNB1 0.11 0.088 -10000 0 -10000 0 0
WIF1 -0.44 0.42 -10000 0 -0.82 451 451
beta catenin/RanBP3 0.013 0.075 0.38 30 -10000 0 30
KREMEN2 -0.13 0.14 -10000 0 -10000 0 0
DKK1 -0.08 0.2 -10000 0 -0.43 157 157
beta catenin/beta TrCP1 0.1 0.087 -10000 0 -10000 0 0
FZD1 0 0 -10000 0 -10000 0 0
AXIN2 -0.007 0.18 -10000 0 -1.6 11 11
AXIN1 0 0.002 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.017 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.095 0.073 -10000 0 -0.53 3 3
Axin1/APC/GSK3 0.001 0.015 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.078 0.034 -10000 0 -10000 0 0
HNF1A 0.002 0.027 -10000 0 -0.28 2 2
CTBP1 0.004 0.015 -10000 0 -10000 0 0
MYC -0.022 0.24 -10000 0 -1.6 20 20
RANBP3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.073 0.11 -10000 0 -0.66 17 17
NKD1 -0.011 0.08 -10000 0 -0.84 6 6
TCF4 -0.001 0.067 -10000 0 -0.84 5 5
TCF3 0.004 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.094 0.44 34 -0.44 1 35
LEF1 -0.037 0.1 -10000 0 -0.28 118 118
DVL1 0.073 0.066 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.082 -10000 0 -0.58 2 2
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.6 45 45
LRP6 -0.001 0.013 -10000 0 -10000 0 0
CSNK1A1 0.004 0.017 -10000 0 -10000 0 0
NLK 0 0.009 -10000 0 -0.28 1 1
CCND1 0.002 0.11 -10000 0 -1.6 3 3
WNT1 0 0.009 -10000 0 -10000 0 0
GSK3A 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.045 0.048 0.35 7 -10000 0 7
APC 0 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.15 0.14 0.28 440 -10000 0 440
CREBBP 0.004 0.015 -10000 0 -10000 0 0
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 0.002 0.007 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.014 0.1 0.47 11 -10000 0 11
IL27/IL27R/JAK1 -0.045 0.16 -10000 0 -0.64 27 27
TBX21 -0.023 0.2 -10000 0 -0.62 55 55
IL12B -0.052 0.11 -10000 0 -0.28 157 157
IL12A -0.031 0.16 -10000 0 -0.66 48 48
IL6ST -0.051 0.21 -10000 0 -0.84 55 55
IL27RA/JAK1 -0.006 0.068 -10000 0 -1.4 2 2
IL27 -0.023 0.084 -10000 0 -10000 0 0
TYK2 0.008 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.14 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.014 0.1 0.47 11 -10000 0 11
T cell proliferation during immune response 0.014 0.1 0.47 11 -10000 0 11
MAPKKK cascade -0.014 0.1 -10000 0 -0.47 11 11
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.041 -10000 0 -0.28 18 18
IL12RB1 -0.009 0.055 -10000 0 -0.84 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.038 0.22 -10000 0 -0.64 64 64
IL27/IL27R/JAK2/TYK2 -0.017 0.1 -10000 0 -0.48 11 11
positive regulation of T cell mediated cytotoxicity -0.014 0.1 -10000 0 -0.47 11 11
STAT1 (dimer) -0.063 0.2 0.47 19 -0.73 31 50
JAK2 0.004 0.006 -10000 0 -10000 0 0
JAK1 0 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.088 -10000 0 -0.56 4 4
T cell proliferation -0.19 0.25 -10000 0 -0.49 326 326
IL12/IL12R/TYK2/JAK2 0.013 0.071 -10000 0 -10000 0 0
IL17A -0.14 0.18 -10000 0 -10000 0 0
mast cell activation 0.014 0.1 0.47 11 -10000 0 11
IFNG 0.003 0.021 -10000 0 -0.083 2 2
T cell differentiation -0.003 0.005 -10000 0 -0.019 15 15
STAT3 (dimer) -0.028 0.088 -10000 0 -0.56 4 4
STAT5A (dimer) -0.032 0.1 -10000 0 -0.56 11 11
STAT4 (dimer) -0.047 0.13 -10000 0 -0.54 37 37
STAT4 -0.033 0.16 -10000 0 -0.82 34 34
T cell activation -0.008 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.036 0.14 -10000 0 -0.61 21 21
GATA3 -0.045 0.28 -10000 0 -1.5 30 30
IL18 0.006 0.031 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.027 0.087 -10000 0 -0.55 4 4
IL27/EBI3 -0.022 0.074 -10000 0 -0.57 7 7
IL27RA 0.001 0.074 -10000 0 -1.5 2 2
IL6 -0.32 0.41 -10000 0 -0.84 323 323
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.002 0.027 0.48 2 -10000 0 2
IL1B 0.003 0.07 -10000 0 -0.54 12 12
EBI3 -0.003 0.07 -10000 0 -0.54 11 11
TNF -0.001 0.077 -10000 0 -0.66 10 10
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.12 0.22 -9999 0 -0.5 202 202
TC10/GTP -0.1 0.18 -9999 0 -0.44 190 190
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.1 -9999 0 -0.53 31 31
HRAS 0 0.01 -9999 0 -10000 0 0
APS homodimer -0.01 0.05 -9999 0 -10000 0 0
GRB14 -0.1 0.23 -9999 0 -0.47 183 183
FOXO3 -0.013 0.065 -9999 0 -0.73 6 6
AKT1 -0.054 0.13 -9999 0 -0.41 69 69
INSR 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.028 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.19 0.35 -9999 0 -0.84 190 190
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.032 0.032 -9999 0 -10000 0 0
CAV1 -0.12 0.24 -9999 0 -0.54 187 187
CBL/APS/CAP/Crk-II/C3G -0.11 0.2 -9999 0 -0.48 190 190
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.1 -9999 0 -0.53 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.087 -9999 0 -0.46 31 31
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.005 0.13 -9999 0 -0.48 6 6
PARD6A -0.001 0.016 -9999 0 -0.28 3 3
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.001 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.11 -9999 0 -0.5 6 6
HRAS/GTP -0.015 0.075 -9999 0 -0.49 1 1
Insulin Receptor 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.018 0.093 -9999 0 -0.49 31 31
PRKCI -0.012 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.059 0.14 -9999 0 -0.44 94 94
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.001 -9999 0 -10000 0 0
PI3K -0.017 0.089 -9999 0 -0.47 31 31
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
AKT2 -0.054 0.13 -9999 0 -0.54 6 6
PRKCZ -0.013 0.039 -9999 0 -0.63 1 1
SH2B2 -0.01 0.05 -9999 0 -10000 0 0
SHC/SHIP -0.017 0.087 -9999 0 -0.46 31 31
F2RL2 -0.06 0.14 -9999 0 -0.33 153 153
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.005 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.22 -9999 0 -0.52 190 190
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.004 -9999 0 -10000 0 0
INPP5D -0.018 0.094 -9999 0 -0.5 31 31
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.008 0.071 -9999 0 -1 4 4
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
p62DOK/RasGAP 0 0.001 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.018 0.093 -9999 0 -0.49 31 31
GRB2 0 0.01 -9999 0 -10000 0 0
EIF4EBP1 -0.01 0.14 -9999 0 -0.48 10 10
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.064 -9999 0 -0.34 31 31
Insulin Receptor/Insulin/IRS1 -0.02 0.1 -9999 0 -0.54 31 31
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.025 0.072 -9999 0 -0.49 14 14
Coregulation of Androgen receptor activity

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
NRIP1 -0.008 0.034 -9999 0 -0.84 1 1
SVIL -0.009 0.052 -9999 0 -0.84 3 3
ZNF318 0.022 0.058 -9999 0 -10000 0 0
JMJD2C -0.004 0.043 -9999 0 -0.14 70 70
T-DHT/AR/Ubc9 -0.075 0.18 -9999 0 -0.58 92 92
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0.002 0.007 -9999 0 -10000 0 0
PELP1 0.005 0.012 -9999 0 -10000 0 0
CTNNB1 -0.005 0.012 -9999 0 -10000 0 0
AKT1 0.007 0.018 -9999 0 -10000 0 0
PTK2B -0.004 0.01 -9999 0 -10000 0 0
MED1 0 0.049 -9999 0 -0.28 19 19
MAK 0.011 0.1 -9999 0 -0.8 8 8
response to oxidative stress 0.001 0.004 -9999 0 -10000 0 0
HIP1 -0.006 0.017 -9999 0 -10000 0 0
GSN -0.02 0.1 -9999 0 -0.84 13 13
NCOA2 -0.007 0.076 -9999 0 -0.84 7 7
NCOA6 -0.005 0.019 -9999 0 -10000 0 0
DNA-PK 0.021 0.059 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 -0.005 0.012 -9999 0 -10000 0 0
cell proliferation -0.006 0.11 -9999 0 -0.86 8 8
XRCC5 0.006 0.015 -9999 0 -10000 0 0
UBE3A -0.006 0.031 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.09 0.22 -9999 0 -0.63 105 105
FHL2 -0.018 0.12 -9999 0 -1.2 5 5
RANBP9 -0.005 0.017 -9999 0 -10000 0 0
JMJD1A -0.012 0.057 -9999 0 -0.15 121 121
CDK6 -0.005 0.072 -9999 0 -0.7 8 8
TGFB1I1 -0.009 0.052 -9999 0 -0.84 3 3
T-DHT/AR/CyclinD1 -0.087 0.19 -9999 0 -0.6 94 94
XRCC6 0.006 0.015 -9999 0 -10000 0 0
T-DHT/AR -0.063 0.21 -9999 0 -0.56 107 107
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0.015 0.039 -9999 0 -10000 0 0
BRCA1 -0.007 0.023 -9999 0 -0.36 1 1
TCF4 0.006 0.071 -9999 0 -0.82 5 5
CDKN2A -0.035 0.1 -9999 0 -0.28 114 114
SRF 0.023 0.02 -9999 0 -10000 0 0
NKX3-1 -0.083 0.2 -9999 0 -1.3 18 18
KLK3 -0.18 0.52 -9999 0 -1.6 102 102
TMF1 0 0 -9999 0 -10000 0 0
HNRNPA1 0.008 0.022 -9999 0 -10000 0 0
AOF2 -0.008 0.024 -9999 0 -0.072 102 102
APPL1 0.034 0.033 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.067 0.19 -9999 0 -0.58 92 92
AR -0.09 0.27 -9999 0 -0.84 93 93
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.008 0.022 -9999 0 -10000 0 0
PAWR 0 0 -9999 0 -10000 0 0
PRKDC 0.004 0.025 -9999 0 -0.28 2 2
PA2G4 0.011 0.028 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.063 0.17 -9999 0 -0.54 92 92
RPS6KA3 -0.009 0.045 -9999 0 -0.84 2 2
T-DHT/AR/ARA70 -0.079 0.18 -9999 0 -0.58 92 92
LATS2 0.009 0.023 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.058 0.18 -9999 0 -0.53 92 92
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.013 0.064 -9999 0 -0.64 5 5
KLK2 -0.13 0.34 -9999 0 -1.2 70 70
CASP8 0.004 0.011 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.075 0.17 -9999 0 -0.54 97 97
TMPRSS2 -0.18 0.4 -9999 0 -1.2 108 108
CCND1 -0.016 0.073 -9999 0 -0.58 6 6
PIAS1 -0.006 0.031 -9999 0 -10000 0 0
mol:T-DHT -0.01 0.035 -9999 0 -0.08 156 156
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.012 0.05 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.076 0.19 -9999 0 -0.58 98 98
CMTM2 0.003 0.013 -9999 0 -0.27 1 1
SNURF -0.023 0.14 -9999 0 -0.84 23 23
ZMIZ1 0.002 0.032 -9999 0 -0.34 1 1
CCND3 0.001 0.005 -9999 0 -10000 0 0
TGIF1 0.008 0.022 -9999 0 -10000 0 0
FKBP4 -0.007 0.03 -9999 0 -10000 0 0
BCR signaling pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.12 -10000 0 -0.46 30 30
IKBKB 0.016 0.055 -10000 0 -0.25 3 3
AKT1 0.007 0.082 0.25 2 -0.26 27 29
IKBKG 0.018 0.057 -10000 0 -0.27 3 3
CALM1 -0.013 0.098 -10000 0 -0.46 26 26
PIK3CA 0 0.01 -10000 0 -0.28 1 1
MAP3K1 -0.009 0.16 -10000 0 -0.68 27 27
MAP3K7 0 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.1 -10000 0 -0.5 26 26
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.049 0.12 -10000 0 -0.28 55 55
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.082 0.22 -10000 0 -0.7 87 87
CD22 -0.062 0.19 -10000 0 -0.57 80 80
CAMK2G -0.004 0.092 -10000 0 -0.42 26 26
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.05 0.15 -10000 0 -0.48 78 78
GO:0007205 -0.022 0.1 -10000 0 -0.5 26 26
SYK 0 0.01 -10000 0 -0.28 1 1
ELK1 -0.013 0.1 -10000 0 -0.47 26 26
NFATC1 -0.016 0.14 -10000 0 -0.56 29 29
B-cell antigen/BCR complex -0.082 0.22 -10000 0 -0.7 87 87
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.01 0.11 -10000 0 -0.49 26 26
NFKBIA 0.015 0.02 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.061 0.17 -10000 0 -0.56 80 80
mol:GDP -0.022 0.097 -10000 0 -0.47 26 26
PTEN -0.002 0.041 -10000 0 -0.84 2 2
CD79B -0.029 0.15 -10000 0 -0.84 26 26
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.023 0.16 -10000 0 -0.48 78 78
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.031 0.1 -10000 0 -0.51 26 26
CSK 0 0 -10000 0 -10000 0 0
FOS -0.15 0.24 -10000 0 -0.47 289 289
CHUK 0.018 0.057 -10000 0 -0.27 3 3
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.025 0.083 -10000 0 -0.48 16 16
PTPN6 -0.058 0.17 -10000 0 -0.77 32 32
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.13 1 1
VAV2 -0.07 0.18 -10000 0 -0.55 78 78
ubiquitin-dependent protein catabolic process 0.019 0.02 -10000 0 -10000 0 0
BTK -0.004 0.006 -10000 0 -10000 0 0
CD19 -0.08 0.18 -10000 0 -0.57 78 78
MAP4K1 -0.01 0.062 -10000 0 -0.84 2 2
CD72 -0.006 0.047 -10000 0 -0.84 1 1
PAG1 -0.002 0.021 -10000 0 -0.28 5 5
MAPK14 0.002 0.13 -10000 0 -0.55 27 27
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.013 0.11 -10000 0 -0.55 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.044 0.14 -10000 0 -0.5 67 67
RAF1 -0.002 0.1 -10000 0 -0.45 26 26
RasGAP/p62DOK/SHIP -0.058 0.17 -10000 0 -0.53 80 80
CD79A -0.084 0.23 -10000 0 -0.58 121 121
re-entry into mitotic cell cycle -0.048 0.12 -10000 0 -0.28 54 54
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.087 -10000 0 -0.44 14 14
MAPK1 0.015 0.087 -10000 0 -0.44 14 14
CD72/SHP1 -0.055 0.16 -10000 0 -0.71 33 33
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.13 -10000 0 -0.55 27 27
actin cytoskeleton organization -0.025 0.16 -10000 0 -0.67 28 28
NF-kappa-B/RelA 0.043 0.032 -10000 0 -10000 0 0
Calcineurin -0.022 0.076 -10000 0 -0.46 14 14
PI3K -0.055 0.13 -10000 0 -0.54 31 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.034 0.12 -10000 0 -0.59 26 26
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.055 0.18 -10000 0 -0.85 30 30
DAPP1 -0.054 0.21 -10000 0 -1 29 29
cytokine secretion -0.014 0.12 -10000 0 -0.51 29 29
mol:DAG -0.031 0.1 -10000 0 -0.51 26 26
PLCG2 -0.001 0.03 -10000 0 -0.56 2 2
MAP2K1 0.007 0.096 -10000 0 -0.5 14 14
B-cell antigen/BCR complex/FcgammaRIIB -0.073 0.2 -10000 0 -0.65 80 80
mol:PI-3-4-5-P3 -0.04 0.093 0.35 2 -0.37 31 33
ETS1 0.004 0.089 -10000 0 -0.48 15 15
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.06 0.17 -10000 0 -0.56 78 78
B-cell antigen/BCR complex/LYN -0.061 0.2 -10000 0 -0.6 78 78
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 -0.028 0.17 -10000 0 -0.73 28 28
B-cell antigen/BCR complex/LYN/SYK -0.059 0.19 -10000 0 -0.58 78 78
CARD11 -0.017 0.11 -10000 0 -0.49 27 27
FCGR2B -0.003 0.051 -10000 0 -0.84 3 3
PPP3CA 0 0.01 -10000 0 -0.28 1 1
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.007 0.06 -10000 0 -0.39 15 15
PDPK1 -0.026 0.063 0.23 2 -0.28 15 17
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.013 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.21 0.26 1 -0.6 117 118
AKT1 0.013 0.005 -10000 0 -10000 0 0
GSC -0.053 0.33 -10000 0 -1.5 39 39
NKX2-5 -0.037 0.094 -10000 0 -0.37 1 1
muscle cell differentiation 0.006 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.002 0.029 -10000 0 -10000 0 0
SMAD4 0.012 0.033 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.23 0.27 -10000 0 -0.56 342 342
SMAD3/SMAD4/VDR 0.006 0.03 -10000 0 -0.49 1 1
MYC -0.02 0.13 -10000 0 -0.84 20 20
CDKN2B 0.031 0.11 -10000 0 -1.5 4 4
AP1 -0.14 0.23 -10000 0 -0.45 272 272
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.012 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.038 -10000 0 -0.33 2 2
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.04 0.093 -10000 0 -0.39 4 4
SMAD3/SMAD4/GR -0.007 0.062 -10000 0 -0.63 7 7
GATA3 -0.04 0.16 -10000 0 -0.83 30 30
SKI/SIN3/HDAC complex/NCoR1 0.002 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.03 0.075 -10000 0 -0.65 5 5
endothelial cell migration -0.01 0.035 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.003 0.027 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 -0.004 0.033 -10000 0 -0.28 12 12
RUNX3 -0.004 0.052 -10000 0 -0.84 3 3
RUNX1 -0.001 0.029 -10000 0 -0.84 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.006 0.077 -10000 0 -0.84 7 7
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.049 0.065 -10000 0 -1.4 1 1
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.012 0.069 -10000 0 -0.42 4 4
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.001 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.09 0.22 -10000 0 -0.6 125 125
SAP30 -0.001 0.016 -10000 0 -0.28 3 3
Cbp/p300/PIAS3 0.006 0.024 -10000 0 -10000 0 0
JUN -0.099 0.25 -10000 0 -0.44 272 272
SMAD3/SMAD4/IRF7 -0.011 0.057 -10000 0 -0.35 1 1
TFE3 0.011 0.01 -10000 0 -10000 0 0
COL1A2 0.029 0.092 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.004 0.029 -10000 0 -10000 0 0
DLX1 -0.05 0.13 -10000 0 -0.31 136 136
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.26 0.4 -10000 0 -0.83 271 271
SMAD3/SMAD4/Max -0.002 0.024 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0 0.005 -10000 0 -10000 0 0
LAMC1 0.041 0.048 -10000 0 -0.82 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.023 -10000 0 -10000 0 0
IRF7 -0.019 0.071 -10000 0 -0.35 18 18
ESR1 -0.15 0.29 -10000 0 -0.56 229 229
HNF4A -0.004 0.034 -10000 0 -10000 0 0
MEF2C 0.001 0.085 -10000 0 -0.94 1 1
SMAD2-3/SMAD4 -0.003 0.03 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.003 0.025 -10000 0 -0.56 1 1
IGHV3OR16-13 0 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.004 0.031 -10000 0 -0.28 11 11
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 0 0 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.002 0.026 -10000 0 -10000 0 0
MSG1/HSC70 -0.26 0.32 -10000 0 -0.64 342 342
SMAD2 0.014 0.022 -10000 0 -10000 0 0
SMAD3 0.012 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.021 -10000 0 -10000 0 0
NCOR1 -0.001 0.029 -10000 0 -0.84 1 1
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
NCOA1 -0.001 0.029 -10000 0 -0.84 1 1
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.006 0.031 -10000 0 -10000 0 0
IFNB1 0.016 0.082 -10000 0 -0.4 10 10
SMAD3/SMAD4/MEF2C -0.021 0.068 -10000 0 -0.91 1 1
CITED1 -0.34 0.41 -10000 0 -0.84 342 342
SMAD2-3/SMAD4/ARC105 0 0.026 -10000 0 -10000 0 0
RBL1 -0.001 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.007 0.05 -10000 0 -0.5 4 4
RUNX1-3/PEBPB2 -0.003 0.046 -10000 0 -0.73 3 3
SMAD7 -0.087 0.14 -10000 0 -0.54 10 10
MYC/MIZ-1 -0.015 0.1 -10000 0 -0.65 20 20
SMAD3/SMAD4 0.02 0.061 0.27 37 -10000 0 37
IL10 0.014 0.12 -10000 0 -0.54 32 32
PIASy/HDAC complex 0.001 0.003 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.011 0.12 -10000 0 -0.54 30 30
CDK4 0.001 0.016 -10000 0 -0.28 2 2
PIAS4 0.001 0.003 -10000 0 -10000 0 0
ATF3 -0.12 0.3 -10000 0 -0.84 125 125
SMAD3/SMAD4/SP1 0.001 0.025 -10000 0 -10000 0 0
FOXG1 -0.02 0.07 -10000 0 -10000 0 0
FOXO3 0.025 0.033 -10000 0 -0.64 2 2
FOXO1 0.021 0.057 -10000 0 -0.64 6 6
FOXO4 0.026 0.007 -10000 0 -10000 0 0
heart looping 0.002 0.085 -10000 0 -0.92 1 1
CEBPB 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.026 0.081 -10000 0 -0.6 8 8
MYOD1 -0.003 0.028 -10000 0 -0.28 9 9
SMAD3/SMAD4/HNF4 -0.006 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.024 0.12 -10000 0 -0.6 30 30
SnoN/SIN3/HDAC complex/NCoR1 -0.004 0.031 -10000 0 -0.28 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.002 0.048 -10000 0 -0.68 3 3
SMAD3/SMAD4/SP1-3 0.004 0.024 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.012 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.007 0.082 -10000 0 -0.46 3 3
ITGB5 0.05 0.042 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.067 0.19 -10000 0 -0.6 92 92
AR -0.092 0.26 -10000 0 -0.84 92 92
negative regulation of cell growth -0.027 0.075 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.006 0.03 -10000 0 -10000 0 0
E2F5 -0.006 0.041 -10000 0 -0.28 19 19
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.002 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.04 -10000 0 -0.34 4 4
TFDP1 -0.001 0.019 -10000 0 -0.28 4 4
SMAD3/SMAD4/AP1 -0.14 0.23 -10000 0 -0.45 272 272
SMAD3/SMAD4/RUNX2 -0.004 0.029 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion 0.028 0.025 -9999 0 -10000 0 0
BUB1B -0.038 0.045 -9999 0 -10000 0 0
PLK1 -0.007 0.021 -9999 0 -10000 0 0
PLK1S1 0.001 0.012 -9999 0 -10000 0 0
KIF2A 0.003 0.019 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.007 0.021 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.16 0.11 -9999 0 -0.26 414 414
WEE1 -0.002 0.021 -9999 0 -10000 0 0
cytokinesis -0.043 0.042 -9999 0 -0.27 2 2
PP2A-alpha B56 0.037 0.022 -9999 0 -10000 0 0
AURKA 0.003 0.011 -9999 0 -10000 0 0
PICH/PLK1 -0.077 0.092 -9999 0 -0.32 10 10
CENPE -0.055 0.083 -9999 0 -0.2 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.019 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.002 0.013 -9999 0 -10000 0 0
PAK1 -0.006 0.039 -9999 0 -0.27 18 18
SPC24 -0.17 0.14 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.002 0.014 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.004 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
STAG2 0 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.007 0.021 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.032 0.019 -9999 0 -10000 0 0
TPT1 0.001 0.012 -9999 0 -10000 0 0
CDC25C -0.001 0.012 -9999 0 -10000 0 0
CDC25B -0.003 0.038 -9999 0 -10000 0 0
SGOL1 -0.028 0.025 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.022 0.04 -9999 0 -10000 0 0
CDC14B -0.01 0.12 -9999 0 -0.66 25 25
CDC20 -0.15 0.14 -9999 0 -0.28 468 468
PLK1/PBIP1 -0.03 0.053 -9999 0 -10000 0 0
mitosis -0.007 0.007 -9999 0 -0.022 2 2
FBXO5 0.001 0.021 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.13 -9999 0 -0.28 552 552
metaphase plate congression -0.002 0.014 -9999 0 -10000 0 0
ERCC6L -0.067 0.084 -9999 0 -10000 0 0
NLP/gamma Tubulin 0 0.012 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.001 0.012 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.093 -9999 0 -0.27 210 210
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.002 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.002 0.022 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.049 -9999 0 -10000 0 0
microtubule-based process -0.12 0.058 -9999 0 -10000 0 0
Golgi organization -0.007 0.021 -9999 0 -10000 0 0
Cohesin/SA2 -0.008 0.009 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.11 -9999 0 -10000 0 0
APC/C/CDC20 -0.084 0.074 -9999 0 -0.16 190 190
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.03 0.053 -9999 0 -0.17 2 2
PRC1 -0.078 0.12 -9999 0 -10000 0 0
ECT2 -0.004 0.039 -9999 0 -10000 0 0
C13orf34 0 0.02 -9999 0 -10000 0 0
NUDC -0.002 0.014 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.038 0.045 -9999 0 -10000 0 0
spindle assembly -0.003 0.018 -9999 0 -10000 0 0
spindle stabilization 0.001 0.012 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.097 -9999 0 -0.57 25 25
MKLP2/PLK1 -0.12 0.059 -9999 0 -10000 0 0
CCNB1 -0.065 0.12 -9999 0 -0.27 199 199
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 0.006 0.031 -9999 0 -0.55 2 2
TUBG1 0.001 0.012 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.022 0.039 -9999 0 -10000 0 0
MLF1IP -0.032 0.076 -9999 0 -10000 0 0
INCENP 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.018 0.12 -9999 0 -0.81 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.029 -9999 0 -0.84 1 1
RAC1-CDC42/GTP/PAK family -0.13 0.14 -9999 0 -0.28 376 376
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.029 -9999 0 -0.84 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR 0 0.01 -9999 0 -0.28 1 1
p38 alpha/TAB1 -0.007 0.035 -9999 0 -0.38 2 2
PRKG1 -0.032 0.16 -9999 0 -0.84 32 32
DUSP8 -0.003 0.051 -9999 0 -0.7 4 4
PGK/cGMP/p38 alpha -0.022 0.088 -9999 0 -0.43 34 34
apoptosis -0.007 0.034 -9999 0 -0.37 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.29 -9999 0 -0.84 117 117
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
SRC 0 0.01 -9999 0 -0.28 1 1
RAC1/OSM/MEKK3/MKK3 0 0.004 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.017 0.07 -9999 0 -0.36 14 14
BLK -0.036 0.1 -9999 0 -0.29 102 102
HCK -0.004 0.033 -9999 0 -0.28 12 12
MAP2K3 0 0.01 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.013 -9999 0 -10000 0 0
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.028 0.049 -9999 0 -0.41 2 2
positive regulation of innate immune response 0.023 0.075 -9999 0 -0.38 14 14
LCK -0.019 0.1 -9999 0 -0.84 11 11
p38alpha-beta/MKP7 -0.012 0.056 -9999 0 -0.36 14 14
p38alpha-beta/MKP5 -0.012 0.056 -9999 0 -0.36 13 13
PGK/cGMP -0.025 0.12 -9999 0 -0.65 32 32
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.066 0.15 -9999 0 -0.4 127 127
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.38 0.42 -9999 0 -0.84 376 376
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.001 0.13 -10000 0 -0.42 40 40
TBX21 -0.01 0.35 -10000 0 -1.3 44 44
B2M 0.002 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.007 0.062 -10000 0 -0.88 1 1
GADD45B 0.038 0.21 -10000 0 -0.88 18 18
IL12RB2 -0.057 0.2 -10000 0 -0.5 104 104
GADD45G 0.034 0.21 -10000 0 -0.82 23 23
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.002 0.021 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.046 -10000 0 -10000 0 0
IL2RA -0.028 0.11 -10000 0 -0.84 10 10
IFNG -0.04 0.098 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.21 -10000 0 -0.69 30 30
HLA-DRB5 -0.022 0.093 -10000 0 -0.34 55 55
FASLG 0.015 0.26 -10000 0 -1 25 25
NF kappa B2 p52/RelB -0.074 0.18 -10000 0 -0.81 32 32
CD4 0 0 -10000 0 -10000 0 0
SOCS1 -0.004 0.039 -10000 0 -0.34 9 9
EntrezGene:6955 -0.007 0.014 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.8 23 23
CD3E -0.022 0.14 -10000 0 -0.55 45 45
CD3G -0.031 0.16 -10000 0 -0.54 61 61
IL12Rbeta2/JAK2 -0.026 0.16 -10000 0 -0.66 39 39
CCL3 0.019 0.25 -10000 0 -1 25 25
CCL4 0.022 0.24 -10000 0 -0.97 22 22
HLA-A 0.001 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.023 0.15 -10000 0 -0.59 42 42
NOS2 0.025 0.24 -10000 0 -1 22 22
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.13 -10000 0 -0.42 38 38
IL1R1 0.014 0.27 -10000 0 -1.1 27 27
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.017 0.015 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.26 -10000 0 -1.1 36 36
RAB7A 0.054 0.19 -10000 0 -0.76 14 14
lysosomal transport 0.055 0.18 -10000 0 -0.71 15 15
FOS -0.38 0.68 -10000 0 -1.3 280 280
STAT4 (dimer) 0.028 0.26 -10000 0 -0.9 36 36
STAT5A (dimer) -0.077 0.2 -10000 0 -0.78 38 38
GZMA 0.011 0.27 -10000 0 -1.2 24 24
GZMB -0.001 0.3 -10000 0 -1.2 30 30
HLX 0 0.01 -10000 0 -10000 0 0
LCK 0.014 0.27 -10000 0 -0.93 37 37
TCR/CD3/MHC II/CD4 -0.068 0.2 -10000 0 -0.59 62 62
IL2/IL2R -0.028 0.098 -10000 0 -0.47 31 31
MAPK14 0.044 0.22 -10000 0 -0.83 23 23
CCR5 0.032 0.22 -10000 0 -0.93 18 18
IL1B 0.007 0.092 -10000 0 -0.7 12 12
STAT6 0.028 0.085 -10000 0 -0.26 2 2
STAT4 -0.033 0.16 -10000 0 -0.82 34 34
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.04 -10000 0 -0.28 18 18
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B -0.038 0.11 -10000 0 -0.28 83 83
CD8A -0.01 0.078 -10000 0 -0.84 5 5
CD8B -0.034 0.16 -10000 0 -0.6 51 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.001 0.13 0.41 40 -10000 0 40
IL2RB -0.011 0.054 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.24 -10000 0 -0.8 36 36
IL2RG -0.016 0.083 -10000 0 -0.84 5 5
IL12 -0.049 0.17 -10000 0 -0.64 50 50
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
CD247 -0.014 0.13 -10000 0 -0.62 30 30
IL2 -0.003 0.027 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.036 0.2 -10000 0 -0.85 48 48
IL12/IL12R/TYK2/JAK2 0.017 0.27 -10000 0 -0.82 45 45
MAP2K3 0.04 0.22 -10000 0 -0.82 25 25
RIPK2 -0.001 0.019 -10000 0 -0.28 4 4
MAP2K6 0.036 0.22 -10000 0 -0.8 28 28
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.032 -10000 0 -0.47 3 3
IL18RAP -0.02 0.17 -10000 0 -0.78 37 37
IL12Rbeta1/TYK2 0.016 0.049 -10000 0 -0.7 1 1
EOMES -0.023 0.18 -10000 0 -1.5 12 12
STAT1 (dimer) 0.037 0.21 -10000 0 -0.72 24 24
T cell proliferation 0.038 0.2 -10000 0 -0.66 33 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.097 -10000 0 -0.84 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.059 0.17 -10000 0 -0.76 31 31
ATF2 0.052 0.2 -10000 0 -0.77 22 22
Arf6 trafficking events

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
SLC2A4 -0.47 0.42 -10000 0 -0.84 475 475
CLTC 0.027 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.025 0.017 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.026 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.016 -10000 0 -10000 0 0
CPE -0.012 0.08 -10000 0 -0.57 17 17
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.016 -10000 0 -10000 0 0
CTNND1 -0.005 0.022 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.012 -10000 0 -10000 0 0
TSHR -0.025 0.12 -10000 0 -0.57 37 37
INS 0.011 0.004 -10000 0 -10000 0 0
BIN1 -0.009 0.087 -10000 0 -0.78 10 10
mol:Choline -0.001 0.016 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.035 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.026 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -0.28 1 1
ASAP2/amphiphysin II -0.006 0.056 -10000 0 -0.52 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.017 0.052 -10000 0 -0.28 24 24
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.004 0.034 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.033 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.014 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.02 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 -0.005 0.022 -10000 0 -10000 0 0
NME1 -0.007 0.031 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.016 -10000 0 -10000 0 0
IL2RA 0.018 0.042 -10000 0 -0.38 5 5
VAMP3 0 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.24 0.21 -10000 0 -0.43 475 475
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.002 0.027 -10000 0 -0.35 5 5
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.023 -10000 0 -0.36 1 1
ARF6/GDP -0.007 0.031 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.016 -10000 0 -10000 0 0
endocytosis 0.006 0.056 0.51 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.091 0.22 -10000 0 -0.46 214 214
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.029 -10000 0 -0.84 1 1
Dynamin 2/GDP -0.006 0.026 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.17 0.24 -10000 0 -0.46 351 351
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.029 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.002 0.057 -10000 0 -0.7 5 5
CDKN2C 0.006 0.032 -10000 0 -0.82 1 1
CDKN2A -0.045 0.11 -10000 0 -0.29 132 132
CCND2 0.005 0.028 0.25 5 -0.17 6 11
RB1 -0.006 0.028 0.14 4 -0.26 5 9
CDK4 0.008 0.026 0.26 5 -10000 0 5
CDK6 0.005 0.032 0.28 5 -0.22 6 11
G1/S progression -0.008 0.031 0.26 5 -0.17 2 7
Thromboxane A2 receptor signaling

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
TGM2 -0.005 0.036 -10000 0 -0.28 15 15
GNB1/GNG2 -0.013 0.044 -10000 0 -0.2 22 22
AKT1 0.054 0.068 -10000 0 -0.2 43 43
EGF -0.17 0.33 -10000 0 -0.84 167 167
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.008 0.044 -10000 0 -0.34 2 2
mol:Ca2+ 0.052 0.092 -10000 0 -0.3 43 43
LYN -0.008 0.044 -10000 0 -0.34 2 2
RhoA/GTP -0.007 0.028 -10000 0 -0.14 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.058 0.1 -10000 0 -0.34 43 43
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.031 0.047 -10000 0 -0.6 3 3
G beta5/gamma2 -0.016 0.058 -10000 0 -0.28 20 20
PRKCH 0.054 0.1 -10000 0 -0.35 43 43
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
TXA2/TP beta/beta Arrestin3 -0.004 0.026 -10000 0 -0.31 5 5
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.027 0.14 -10000 0 -0.84 25 25
G12 family/GTP -0.018 0.068 -10000 0 -0.3 43 43
ADRBK1 0 0.01 -10000 0 -10000 0 0
ADRBK2 -0.002 0.041 -10000 0 -0.84 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.072 0.38 11 -10000 0 11
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -10000 0 0
PRKG1 -0.032 0.16 -10000 0 -0.84 32 32
mol:IP3 0.053 0.11 -10000 0 -0.38 43 43
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.052 0.14 -10000 0 -0.51 43 43
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0 0.06 -10000 0 -0.4 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.007 0.045 -10000 0 -0.34 2 2
RHOA 0 0 -10000 0 -10000 0 0
PTGIR 0 0.01 -10000 0 -10000 0 0
PRKCB1 0.051 0.11 -10000 0 -0.37 43 43
GNAQ -0.002 0.041 -10000 0 -0.84 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.054 0.15 -10000 0 -0.54 43 43
LCK -0.011 0.07 -10000 0 -0.47 12 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.054 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.025 0.028 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.009 0.053 -10000 0 -10000 0 0
MAPK14 0.055 0.074 -10000 0 -0.22 43 43
TGM2/GTP 0.054 0.12 -10000 0 -0.42 43 43
MAPK11 0.055 0.076 -10000 0 -0.23 43 43
ARHGEF1 0.041 0.058 -10000 0 -0.19 16 16
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.055 0.12 -10000 0 -0.39 43 43
RAB11/GDP -0.001 0.013 -10000 0 -10000 0 0
ICAM1 0.05 0.087 -10000 0 -0.28 43 43
cAMP biosynthetic process 0.049 0.11 -10000 0 -0.35 43 43
Gq family/GTP/EBP50 -0.005 0.027 -10000 0 -0.36 1 1
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.008 0.044 -10000 0 -0.34 2 2
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.1 -10000 0 -0.32 28 28
VCAM1 0.049 0.094 -10000 0 -0.31 43 43
TP beta/Gq family/GDP/G beta5/gamma2 0.031 0.047 -10000 0 -0.6 3 3
platelet activation 0.071 0.098 -10000 0 -0.3 43 43
PGI2/IP 0 0.006 -10000 0 -10000 0 0
PRKACA -0.012 0.066 -10000 0 -0.39 25 25
Gq family/GDP/G beta5/gamma2 0.029 0.049 -10000 0 -0.6 3 3
TXA2/TP beta/beta Arrestin2 -0.005 0.052 -10000 0 -0.67 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.061 -10000 0 -0.36 25 25
mol:DAG 0.053 0.12 -10000 0 -0.42 43 43
EGFR -0.29 0.4 -10000 0 -0.84 291 291
TXA2/TP alpha 0.056 0.14 -10000 0 -0.48 43 43
Gq family/GTP -0.003 0.031 -10000 0 -0.29 9 9
YES1 -0.009 0.046 -10000 0 -0.36 3 3
GNAI2/GTP -0.009 0.051 -10000 0 -0.39 2 2
PGD2/DP -0.021 0.11 -10000 0 -0.65 25 25
SLC9A3R1 -0.027 0.082 -10000 0 -10000 0 0
FYN -0.009 0.046 -10000 0 -0.36 3 3
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.002 0.035 -10000 0 -0.39 5 5
PGK/cGMP -0.022 0.11 -10000 0 -0.57 32 32
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.068 -10000 0 -0.52 6 6
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.047 0.12 -10000 0 -0.37 57 57
PRKCB 0.049 0.11 -10000 0 -0.36 53 53
PRKCE 0.055 0.1 -10000 0 -0.34 44 44
PRKCD 0.054 0.11 -10000 0 -0.37 43 43
PRKCG 0.05 0.11 -10000 0 -0.38 43 43
muscle contraction 0.057 0.14 -10000 0 -0.49 43 43
PRKCZ 0.058 0.1 -10000 0 -0.34 44 44
ARR3 -0.002 0.023 -10000 0 -10000 0 0
TXA2/TP beta -0.01 0.057 -10000 0 -0.44 2 2
PRKCQ 0.042 0.13 -10000 0 -0.37 66 66
MAPKKK cascade 0.052 0.13 -10000 0 -0.46 44 44
SELE 0.043 0.12 -10000 0 -0.42 43 43
TP beta/GNAI2/GDP/G beta/gamma -0.012 0.067 -10000 0 -0.52 6 6
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.013 0.082 -10000 0 -0.84 6 6
chemotaxis 0.054 0.17 -10000 0 -0.62 43 43
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A -0.026 0.028 -9999 0 -10000 0 0
BIRC5 -0.2 0.12 -9999 0 -0.28 619 619
NFKBIA -0.025 0.031 -9999 0 -10000 0 0
CPEB1 -0.16 0.33 -9999 0 -0.84 163 163
AKT1 -0.025 0.031 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.026 -9999 0 -10000 0 0
NDEL1/TACC3 -0.038 0.056 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.001 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.036 -9999 0 -10000 0 0
MDM2 -0.001 0.019 -9999 0 -0.28 4 4
JUB -0.004 0.058 -9999 0 -0.84 4 4
TPX2 -0.11 0.092 -9999 0 -10000 0 0
TP53 -0.011 0.015 -9999 0 -10000 0 0
DLG7 -0.032 0.033 -9999 0 -10000 0 0
AURKAIP1 0 0.01 -9999 0 -0.28 1 1
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.041 0.06 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.025 0.025 -9999 0 -10000 0 0
AURKA -0.039 0.042 -9999 0 -10000 0 0
AURKB -0.002 0.008 -9999 0 -10000 0 0
CDC25B -0.018 0.023 -9999 0 -10000 0 0
G2/M transition checkpoint -0.027 0.042 -9999 0 -0.53 4 4
mRNA polyadenylation -0.13 0.21 -9999 0 -0.56 163 163
Aurora A/CPEB -0.13 0.22 -9999 0 -0.56 163 163
Aurora A/TACC1/TRAP/chTOG -0.025 0.077 -9999 0 -0.51 20 20
BRCA1 -0.001 0.013 -9999 0 -10000 0 0
centrosome duplication -0.029 0.036 -9999 0 -10000 0 0
regulation of centrosome cycle -0.038 0.056 -9999 0 -10000 0 0
spindle assembly -0.025 0.076 -9999 0 -0.5 20 20
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.064 -9999 0 -10000 0 0
CENPA 0.003 0.011 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.028 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.026 -9999 0 -10000 0 0
negative regulation of DNA binding -0.011 0.015 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.012 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.026 0.043 -9999 0 -0.53 4 4
mitotic prometaphase -0.014 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.042 -9999 0 -10000 0 0
TACC1 -0.02 0.13 -9999 0 -0.84 20 20
TACC3 -0.041 0.099 -9999 0 -10000 0 0
Aurora A/Antizyme1 -0.02 0.02 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.028 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.001 0.003 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -0.28 4 4
GIT1/beta-PIX/PAK1 -0.003 0.021 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.092 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.08 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
CKAP5 0 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.05 0.11 -9999 0 -0.64 3 3
RAD9A 0 0.01 -9999 0 -10000 0 0
AP1 -0.21 0.31 -9999 0 -0.66 272 272
IFNAR2 0.008 0.006 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.3 117 117
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.65 117 117
NFX1/SIN3/HDAC complex 0 0.001 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.84 167 167
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.063 0.084 -9999 0 -0.6 3 3
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.14 -9999 0 -10000 0 0
WRN 0 0 -9999 0 -10000 0 0
SP1 0.01 0.006 -9999 0 -10000 0 0
SP3 0 0 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.048 0.074 -9999 0 -0.57 2 2
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.051 0.12 -9999 0 -0.66 3 3
CCND1 -0.043 0.13 -9999 0 -1.3 3 3
MAX 0 0 -9999 0 -10000 0 0
RBBP7 -0.003 0.027 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 -0.001 0.005 -9999 0 -10000 0 0
CDKN1B 0.006 0.078 -9999 0 -0.91 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.016 -9999 0 -0.28 3 3
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0 0 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 271 271
IFN-gamma/IRF1 -0.025 0.061 -9999 0 -0.37 3 3
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.032 0.089 -9999 0 -10000 0 0
Telomerase -0.002 0.025 -9999 0 -10000 0 0
IRF1 -0.001 0.018 -9999 0 -10000 0 0
ESR1 -0.15 0.29 -9999 0 -0.56 230 230
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.009 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.002 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.013 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.061 0.097 -9999 0 -0.67 3 3
NR2F2 -0.001 0.05 -9999 0 -0.84 3 3
MAPK3 0.014 0.02 -9999 0 -10000 0 0
MAPK1 0.014 0.02 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.001 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.84 291 291
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.35 0.37 -9999 0 -0.71 409 409
MYC -0.02 0.13 -9999 0 -0.84 20 20
IL2 0.003 0.028 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -10000 0 0
TGFB1 0 0.001 -9999 0 -10000 0 0
TRF2/BLM -0.018 0.05 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.059 0.082 -9999 0 -0.64 2 2
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.048 0.074 -9999 0 -0.57 2 2
Smad3/Myc -0.013 0.085 -9999 0 -0.56 20 20
911 complex 0 0.005 -9999 0 -10000 0 0
IFNG -0.039 0.095 -9999 0 -10000 0 0
Telomerase/PinX1 -0.048 0.074 -9999 0 -0.57 2 2
Telomerase/AKT1/mTOR/p70S6K 0.004 0.054 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.048 0.074 -9999 0 -0.57 2 2
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.048 0.074 -9999 0 -0.57 2 2
E2F1 -0.088 0.14 -9999 0 -0.29 11 11
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.052 0.11 -9999 0 -0.28 157 157
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -0.28 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.063 0.075 -9999 0 -0.56 3 3
EPHB2 -0.005 0.037 -9999 0 -10000 0 0
Syndecan-2/TACI -0.017 0.081 -9999 0 -0.56 16 16
LAMA1 -0.094 0.26 -9999 0 -0.84 94 94
Syndecan-2/alpha2 ITGB1 -0.13 0.22 -9999 0 -0.49 213 213
HRAS 0 0.01 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.035 -9999 0 -0.56 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.038 0.033 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.032 -9999 0 -0.51 3 3
LAMA3 -0.2 0.36 -9999 0 -0.84 201 201
EZR -0.001 0.013 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.11 0.28 -9999 0 -0.84 106 106
Syndecan-2/MMP2 -0.008 0.077 -9999 0 -0.75 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.012 0.088 -9999 0 -0.64 16 16
dendrite morphogenesis -0.005 0.038 -9999 0 -0.55 3 3
Syndecan-2/GM-CSF -0.005 0.039 -9999 0 -0.56 3 3
determination of left/right symmetry 0.016 0.042 -9999 0 -0.64 3 3
Syndecan-2/PKC delta -0.003 0.035 -9999 0 -0.56 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.038 -9999 0 -0.51 3 3
MAPK1 0.022 0.038 -9999 0 -0.51 3 3
Syndecan-2/RACK1 -0.002 0.03 -9999 0 -0.48 3 3
NF1 -0.001 0.029 -9999 0 -0.84 1 1
FGFR/FGF/Syndecan-2 0.016 0.042 -9999 0 -0.64 3 3
ITGA2 -0.016 0.11 -9999 0 -0.84 16 16
MAPK8 0.031 0.037 -9999 0 -0.55 3 3
Syndecan-2/alpha2/beta1 Integrin -0.065 0.19 -9999 0 -0.55 98 98
Syndecan-2/Kininogen -0.005 0.038 -9999 0 -0.56 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.028 -9999 0 -0.45 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.032 -9999 0 -0.52 3 3
extracellular matrix organization -0.003 0.034 -9999 0 -0.55 3 3
actin cytoskeleton reorganization -0.063 0.074 -9999 0 -0.55 3 3
Syndecan-2/Caveolin-2/Ras -0.067 0.18 -9999 0 -0.52 106 106
Syndecan-2/Laminin alpha3 -0.14 0.24 -9999 0 -0.56 204 204
Syndecan-2/RasGAP -0.002 0.028 -9999 0 -0.46 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0.01 -9999 0 -10000 0 0
Syndecan-2 dimer -0.005 0.039 -9999 0 -0.56 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.027 -9999 0 -0.44 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.023 0.12 -9999 0 -0.44 45 45
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.012 0.088 -9999 0 -0.64 16 16
Syndecan-2/Synbindin -0.003 0.034 -9999 0 -0.56 3 3
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.029 0.034 -9999 0 -0.5 3 3
FN1 -0.12 0.14 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.023 0.091 -9999 0 -0.56 20 20
SDC2 0.016 0.042 -9999 0 -0.64 3 3
KNG1 -0.004 0.033 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.003 0.039 -9999 0 -0.56 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.005 0.038 -9999 0 -0.28 16 16
Syndecan-2/TGFB1 -0.003 0.034 -9999 0 -0.56 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.032 -9999 0 -0.52 3 3
Syndecan-2/Ezrin -0.003 0.032 -9999 0 -0.51 3 3
PRKACA 0.029 0.038 -9999 0 -0.5 4 4
angiogenesis -0.023 0.09 -9999 0 -0.56 20 20
MMP2 -0.008 0.081 -9999 0 -0.84 8 8
IL8 -0.035 0.13 -9999 0 -0.41 73 73
calcineurin-NFAT signaling pathway -0.016 0.08 -9999 0 -0.56 16 16
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.079 0.33 30 -10000 0 30
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.038 -10000 0 -0.57 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.033 0.14 -10000 0 -0.48 57 57
RhoA/GTP -0.024 0.081 -10000 0 -0.34 30 30
negative regulation of cAMP metabolic process -0.027 0.09 -10000 0 -0.32 69 69
GNAZ -0.006 0.071 -10000 0 -0.84 6 6
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.061 -10000 0 -0.38 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.091 -10000 0 -0.32 69 69
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
Syndecan-4-mediated signaling events

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
PTK2 0 0.03 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.019 0.033 -9999 0 -0.66 1 1
positive regulation of JNK cascade -0.048 0.11 -9999 0 -0.6 1 1
Syndecan-4/ADAM12 -0.029 0.055 -9999 0 -0.66 1 1
CCL5 -0.011 0.063 -9999 0 -0.84 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.021 -9999 0 -0.28 4 4
ADAM12 -0.023 0.084 -9999 0 -0.84 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.013 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.07 0.14 -9999 0 -0.65 4 4
Syndecan-4/CXCL12/CXCR4 -0.049 0.12 -9999 0 -0.64 1 1
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.52 107 107
MDK -0.01 0.05 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.027 0.069 -9999 0 -0.54 3 3
Syndecan-4/Midkine -0.021 0.039 -9999 0 -0.66 1 1
FZD7 -0.016 0.11 -9999 0 -0.84 16 16
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.7 11 11
THBS1 -0.001 0.029 -9999 0 -0.84 1 1
integrin-mediated signaling pathway -0.028 0.072 -9999 0 -0.74 2 2
positive regulation of MAPKKK cascade -0.048 0.11 -9999 0 -0.6 1 1
Syndecan-4/TACI -0.029 0.068 -9999 0 -0.54 5 5
CXCR4 -0.009 0.048 -9999 0 -10000 0 0
cell adhesion -0.027 0.057 -9999 0 -0.36 21 21
Syndecan-4/Dynamin -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/TSP1 -0.019 0.036 -9999 0 -0.66 1 1
Syndecan-4/GIPC -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/RANTES -0.024 0.045 -9999 0 -0.6 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.094 0.26 -9999 0 -0.84 94 94
LAMA3 -0.2 0.36 -9999 0 -0.84 201 201
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.002 0.13 -9999 0 -0.8 21 21
Syndecan-4/alpha-Actinin -0.019 0.037 -9999 0 -0.66 1 1
TFPI -0.034 0.16 -9999 0 -0.84 34 34
F2 0.001 0.028 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.24 -9999 0 -0.6 82 82
ACTN1 -0.001 0.029 -9999 0 -0.84 1 1
TNC -0.019 0.12 -9999 0 -0.69 23 23
Syndecan-4/CXCL12 -0.052 0.12 -9999 0 -0.52 8 8
FGF6 -0.002 0.041 -9999 0 -0.84 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.22 -9999 0 -0.84 62 62
TNFRSF13B -0.023 0.12 -9999 0 -0.44 45 45
FGF2 -0.34 0.41 -9999 0 -0.84 336 336
FGFR1 -0.008 0.077 -9999 0 -0.71 9 9
Syndecan-4/PI-4-5-P2 -0.013 0.044 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.15 -9999 0 -0.29 183 183
cell migration -0.025 0.019 -9999 0 -10000 0 0
PRKCD 0.004 0.014 -9999 0 -10000 0 0
vasculogenesis -0.019 0.035 -9999 0 -0.63 1 1
SDC4 -0.014 0.047 -9999 0 -0.71 1 1
Syndecan-4/Tenascin C -0.029 0.076 -9999 0 -0.78 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.044 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.019 0.033 -9999 0 -0.66 1 1
MMP9 -0.11 0.14 -9999 0 -0.82 1 1
Rac1/GTP -0.027 0.059 -9999 0 -0.37 21 21
cytoskeleton organization -0.018 0.032 -9999 0 -0.63 1 1
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.037 0.094 -9999 0 -0.53 8 8
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.033 0.14 -9999 0 -0.48 57 57
CDC42/GTP -0.025 0.08 -9999 0 -0.32 32 32
PLCG1 -0.026 0.082 -9999 0 -0.33 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.078 -9999 0 -0.31 32 32
S1PR5 -0.008 0.061 -9999 0 -0.38 17 17
S1PR4 -0.011 0.08 -9999 0 -0.43 22 22
MAPK3 -0.026 0.082 -9999 0 -0.33 27 27
MAPK1 -0.026 0.082 -9999 0 -0.33 32 32
S1P/S1P5/Gi -0.028 0.091 -9999 0 -0.32 69 69
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.038 -9999 0 -0.57 3 3
RHOA -0.005 0.043 -9999 0 -0.48 6 6
S1P/S1P4/Gi -0.029 0.09 -9999 0 -0.31 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
S1P/S1P4/G12/G13 -0.006 0.046 -9999 0 -0.52 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.061 -9999 0 -0.49 13 13
RGS9BP -0.017 0.066 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.027 -9999 0 -10000 0 0
mol:Na + -0.021 0.051 -9999 0 -10000 0 0
mol:ADP 0.007 0.026 -9999 0 -10000 0 0
GNAT2 -0.001 0.016 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.071 0.18 -9999 0 -0.57 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.013 -9999 0 -10000 0 0
GRK7 -0.002 0.025 -9999 0 -10000 0 0
CNGB3 -0.011 0.053 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin -0.001 0.016 -9999 0 -10000 0 0
mol:Ca2+ -0.098 0.076 -9999 0 -10000 0 0
Cone PDE6 -0.061 0.16 -9999 0 -0.49 92 92
Cone Metarhodopsin II -0.002 0.017 -9999 0 -10000 0 0
Na + (4 Units) -0.099 0.075 -9999 0 -10000 0 0
GNAT2/GDP -0.061 0.15 -9999 0 -0.49 92 92
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.005 0.013 -9999 0 -10000 0 0
Cone Transducin -0.009 0.064 -9999 0 -0.52 13 13
SLC24A2 -0.18 0.13 -9999 0 -10000 0 0
GNB3/GNGT2 -0.01 0.08 -9999 0 -0.64 13 13
GNB3 -0.013 0.1 -9999 0 -0.76 14 14
GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
CNGA3 -0.029 0.085 -9999 0 -0.28 88 88
ARR3 -0.002 0.023 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.051 -9999 0 -10000 0 0
mol:Pi -0.071 0.18 -9999 0 -0.57 92 92
Cone CNG Channel -0.016 0.038 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.13 -9999 0 -10000 0 0
RGS9 -0.095 0.26 -9999 0 -0.84 92 92
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.001 0.029 -9999 0 -0.84 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.019 -9999 0 -0.28 4 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.003 -9999 0 -10000 0 0
HDAC2 0.001 0.003 -9999 0 -10000 0 0
GNB1/GNG2 -0.009 0.073 -9999 0 -0.6 12 12
forebrain development -0.026 0.2 -9999 0 -0.53 101 101
GNAO1 -0.033 0.14 -9999 0 -0.67 30 30
SMO/beta Arrestin2 -0.006 0.059 -9999 0 -0.65 7 7
SMO -0.005 0.077 -9999 0 -0.77 8 8
ARRB2 0 0.001 -9999 0 -10000 0 0
GLI3/SPOP -0.003 0.038 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.053 0.16 -9999 0 -0.51 67 67
SAP30 0 0.017 -9999 0 -0.28 3 3
mol:GDP -0.005 0.077 -9999 0 -0.77 8 8
MIM/GLI2A 0.001 0.03 -9999 0 -0.28 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GLI2 0.041 0.032 -9999 0 -10000 0 0
GLI3 0.038 0.043 -9999 0 -0.31 9 9
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.003 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.006 0.071 -9999 0 -0.84 6 6
Gi family/GTP -0.031 0.095 -9999 0 -0.33 73 73
SIN3B 0.001 0.003 -9999 0 -10000 0 0
SIN3A 0.001 0.003 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.025 -9999 0 -10000 0 0
GLI2/Su(fu) -0.004 0.035 -9999 0 -0.41 4 4
FOXA2 -0.012 0.033 -9999 0 -10000 0 0
neural tube patterning -0.026 0.2 -9999 0 -0.53 101 101
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.023 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.001 0.03 -9999 0 -0.28 9 9
embryonic limb morphogenesis -0.026 0.2 -9999 0 -0.53 101 101
SUFU -0.002 0.027 -9999 0 -0.29 7 7
LGALS3 -0.009 0.086 -9999 0 -0.84 9 9
catabolic process -0.004 0.029 -9999 0 -10000 0 0
GLI3A/CBP -0.027 0.099 -9999 0 -0.39 59 59
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.027 0.21 -9999 0 -0.54 101 101
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.029 -9999 0 -0.84 1 1
RBBP7 -0.002 0.027 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.008 0.063 -9999 0 -0.57 9 9
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
RBBP4 0.001 0.003 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.003 0.024 -9999 0 -10000 0 0
STK36 0.011 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.027 0.096 -9999 0 -0.46 16 16
PTCH1 -0.063 0.34 -9999 0 -1.1 69 69
MIM/GLI1 -0.053 0.19 -9999 0 -0.5 101 101
CREBBP -0.027 0.099 -9999 0 -0.39 59 59
Su(fu)/SIN3/HDAC complex 0.006 0.019 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.017 0.095 -9999 0 -0.56 25 25
E-cadherin/beta catenin -0.018 0.11 -9999 0 -0.64 24 24
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.032 -9999 0 -0.46 3 3
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0 -9999 0 -10000 0 0
PLK4 -0.014 0.06 -9999 0 -0.28 42 42
regulation of centriole replication 0.012 0.043 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.029 0.067 -9999 0 -0.47 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.054 -9999 0 -0.49 2 2
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.073 -9999 0 -10000 0 0
AP1 -0.16 0.22 -9999 0 -0.79 24 24
ILK -0.01 0.088 -9999 0 -0.5 14 14
bone resorption -0.021 0.063 -9999 0 -0.7 2 2
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.014 0.076 -9999 0 -0.46 9 9
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.002 0.033 -9999 0 -0.64 2 2
alphaV/beta3 Integrin/Osteopontin -0.042 0.086 -9999 0 -0.56 14 14
MAP3K1 -0.035 0.075 -9999 0 -0.51 14 14
JUN -0.009 0.086 -9999 0 -0.84 9 9
MAPK3 0.015 0.089 -9999 0 -0.46 14 14
MAPK1 0.015 0.089 -9999 0 -0.46 14 14
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.013 0.088 -9999 0 -0.47 14 14
ITGB3 -0.015 0.11 -9999 0 -0.83 14 14
NFKBIA 0.029 0.085 -9999 0 -0.45 14 14
FOS -0.27 0.39 -9999 0 -0.84 271 271
CD44 -0.001 0.016 -9999 0 -0.28 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.025 0.087 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.016 0.051 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.011 0.082 -9999 0 -0.63 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.035 0.075 -9999 0 -0.51 14 14
VAV3 0.006 0.094 -9999 0 -0.48 17 17
MAP3K14 0.002 0.093 -9999 0 -0.5 14 14
ROCK2 -0.002 0.041 -9999 0 -0.84 2 2
SPP1 -0.076 0.12 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.028 0.067 -9999 0 -0.48 6 6
MMP2 -0.13 0.18 -9999 0 -0.7 24 24
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.035 0.03 -10000 0 -0.46 3 3
CDKN1A 0.036 0.018 -10000 0 -0.46 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.019 -10000 0 -10000 0 0
FOXO3 0.035 0.024 -10000 0 -0.46 2 2
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
AKT3 -0.006 0.052 -10000 0 -0.46 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.022 -10000 0 -0.44 2 2
BAD/YWHAZ 0 0.008 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.021 0.43 2 -10000 0 2
TSC1 0.037 0.002 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -10000 0 0
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.002 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.024 0.02 -10000 0 -0.55 1 1
MAP3K5 -0.002 0.041 -10000 0 -0.84 2 2
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.039 0.024 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.002 -10000 0 -10000 0 0
CASP9 0.037 0.002 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.026 -10000 0 -0.43 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -0.28 1 1
AKT2/p21CIP1 -0.001 0.015 -10000 0 -0.44 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.002 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.031 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.009 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.043 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.27 0.27 -10000 0 -0.5 475 475
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.28 0.27 -10000 0 -0.51 475 475
GSK3A 0.037 0.002 -10000 0 -10000 0 0
FOXO1 0.033 0.042 -10000 0 -0.46 6 6
GSK3B 0.037 0.002 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.84 13 13
G1/S transition of mitotic cell cycle 0.043 0.002 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.041 0.035 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.01 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.023 -10000 0 -0.64 1 1
MAP4K4 -0.005 0.034 -10000 0 -10000 0 0
BAG4 -0.003 0.03 -10000 0 -0.28 10 10
PKC zeta/ceramide -0.025 0.05 -10000 0 -0.61 1 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.51 17 17
BAX -0.009 0.023 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.01 -10000 0 -10000 0 0
BAD -0.023 0.047 0.21 1 -10000 0 1
SMPD1 0.025 0.032 -10000 0 -0.25 10 10
RB1 -0.024 0.05 0.21 1 -0.51 1 2
FADD/Caspase 8 -0.005 0.035 -10000 0 -10000 0 0
MAP2K4 -0.015 0.047 0.2 1 -0.49 1 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.015 0.048 0.2 1 -0.31 3 4
EGF -0.17 0.33 -10000 0 -0.84 167 167
mol:ceramide -0.034 0.05 0.22 1 -10000 0 1
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.026 -10000 0 -0.64 1 1
ASAH1 -0.001 0.016 -10000 0 -10000 0 0
negative regulation of cell cycle -0.023 0.05 0.21 1 -0.5 1 2
cell proliferation -0.1 0.17 -10000 0 -0.41 186 186
BID 0.023 0.033 -10000 0 -10000 0 0
MAP3K1 -0.023 0.047 0.21 1 -10000 0 1
EIF2A -0.006 0.043 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.046 0.2 1 -0.44 1 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.046 0.2 1 -0.44 1 2
Cathepsin D/ceramide -0.029 0.05 -10000 0 -10000 0 0
FADD -0.006 0.038 -10000 0 -0.37 2 2
KSR1 -0.024 0.051 0.21 1 -0.34 3 4
MAPK8 -0.011 0.046 0.2 1 -0.32 2 3
PRKRA -0.023 0.047 0.21 1 -10000 0 1
PDGFA -0.001 0.029 -10000 0 -0.84 1 1
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.034 0.05 0.22 1 -10000 0 1
CTSD -0.01 0.052 -10000 0 -0.28 31 31
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.18 -10000 0 -0.44 186 186
PRKCD 0 0.01 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.026 -10000 0 -0.64 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.005 0.037 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.065 -10000 0 -0.56 10 10
mol:Sphingosine-1-phosphate 0.021 0.023 -10000 0 -0.64 1 1
MAP2K1 -0.007 0.046 -10000 0 -0.45 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.009 0.044 0.19 18 -10000 0 18
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.019 -10000 0 -10000 0 0
EIF2AK2 -0.014 0.045 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.009 0.063 -10000 0 -0.56 10 10
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -10000 0 0
MAP2K2 -0.007 0.046 -10000 0 -0.45 1 1
SMPD3 0.026 0.039 -10000 0 -0.27 12 12
TNF -0.016 0.098 -10000 0 -0.84 10 10
PKC zeta/PAR4 -0.001 0.022 -10000 0 -0.64 1 1
mol:PHOSPHOCHOLINE 0.048 0.12 0.28 168 -10000 0 168
NF kappa B1/RelA/I kappa B alpha -0.001 0.016 -10000 0 -0.47 1 1
AIFM1 -0.009 0.044 0.19 18 -10000 0 18
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.005 0.096 -10000 0 -0.46 29 29
ACTA1 -0.018 0.14 -10000 0 -0.64 30 30
NUMA1 0.005 0.096 -10000 0 -0.46 29 29
SPTAN1 -0.005 0.13 -10000 0 -0.65 26 26
LIMK1 -0.005 0.13 -10000 0 -0.65 26 26
BIRC3 -0.01 0.082 -10000 0 -0.51 17 17
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.016 0.15 -10000 0 -0.69 30 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.096 -10000 0 -0.46 29 29
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.13 -10000 0 -0.63 26 26
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.012 0.15 -10000 0 -0.66 35 35
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.08 -10000 0 -0.67 11 11
BID 0.005 0.064 -10000 0 -0.3 29 29
MAP3K1 0.004 0.04 -10000 0 -0.24 6 6
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.005 0.13 -10000 0 -0.63 28 28
CASP9 0 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 6 -0.22 3 9
neuron apoptosis 0.021 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.12 -10000 0 -0.62 26 26
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.022 0.056 -10000 0 -0.36 3 3
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0.003 0.13 -10000 0 -0.62 26 26
CASP7 -0.007 0.037 0.36 7 -10000 0 7
KRT18 0.015 0.017 -10000 0 -10000 0 0
apoptosis 0.008 0.11 -10000 0 -0.55 26 26
DFFA -0.005 0.13 -10000 0 -0.65 26 26
DFFB -0.005 0.13 -10000 0 -0.62 29 29
PARP1 0.002 0.031 0.22 3 -0.18 6 9
actin filament polymerization -0.003 0.12 0.6 26 -10000 0 26
TNF -0.016 0.098 -10000 0 -0.84 10 10
CYCS 0.007 0.051 -10000 0 -0.22 27 27
SATB1 0.019 0.095 -10000 0 -0.51 18 18
SLK -0.005 0.13 -10000 0 -0.65 26 26
p15 BID/BAX -0.013 0.05 -10000 0 -0.35 6 6
CASP2 0.043 0.039 -10000 0 -10000 0 0
JNK cascade -0.004 0.039 0.24 6 -10000 0 6
CASP3 -0.014 0.14 -10000 0 -0.65 30 30
LMNB2 0.04 0.035 -10000 0 -0.28 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.029 -10000 0 -0.84 1 1
Mammalian IAPs/DIABLO -0.006 0.048 -10000 0 -0.51 7 7
negative regulation of DNA binding 0.014 0.079 -10000 0 -0.66 11 11
stress fiber formation -0.004 0.13 -10000 0 -0.63 26 26
GZMB -0.029 0.16 -10000 0 -0.66 38 38
CASP1 -0.002 0.027 -10000 0 -0.46 3 3
LMNB1 0.046 0.036 -10000 0 -0.28 1 1
APP 0.021 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.003 0.11 -10000 0 -0.53 27 27
LMNA 0.04 0.035 -10000 0 -0.28 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.035 -10000 0 -10000 0 0
LRDD 0 0.01 -10000 0 -0.28 1 1
SREBF1 -0.007 0.13 -10000 0 -0.66 26 26
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.094 -10000 0 -0.45 29 29
CFL2 0.003 0.13 -10000 0 -0.62 26 26
GAS2 -0.054 0.2 -10000 0 -0.54 103 103
positive regulation of apoptosis 0.046 0.035 -10000 0 -0.28 1 1
PRF1 -0.02 0.12 -10000 0 -0.84 17 17
TRAIL signaling pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.077 -10000 0 -0.84 7 7
positive regulation of NF-kappaB transcription factor activity -0.067 0.2 -10000 0 -0.64 87 87
MAP2K4 -0.004 0.033 -10000 0 -0.46 1 1
IKBKB -0.001 0.013 -10000 0 -0.28 2 2
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.004 0.058 -10000 0 -0.84 4 4
SMPD1 -0.003 0.027 -10000 0 -0.3 7 7
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.08 0.25 -10000 0 -0.83 81 81
TRAIL/TRAILR2 -0.006 0.059 -10000 0 -0.64 7 7
TRAIL/TRAILR3 -0.009 0.076 -10000 0 -0.7 9 9
TRAIL/TRAILR1 -0.009 0.074 -10000 0 -0.64 11 11
TRAIL/TRAILR4 -0.067 0.2 -10000 0 -0.64 87 87
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -10000 0 -0.52 11 11
IKK complex -0.003 0.02 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -10000 0 0
MAPK3 0.016 0.061 -10000 0 -0.64 7 7
MAP3K1 -0.004 0.032 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.08 0.24 -10000 0 -0.83 81 81
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.004 0.058 -10000 0 -0.84 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.37 1 1
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.061 -10000 0 -0.64 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.057 -10000 0 -0.49 11 11
mol:ceramide -0.003 0.027 -10000 0 -0.3 7 7
FADD -0.005 0.038 -10000 0 -10000 0 0
MAPK8 0.048 0.037 -10000 0 -0.43 1 1
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.006 0.056 -10000 0 -0.84 3 3
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.067 -10000 0 -0.57 11 11
DAP3 0 0.01 -10000 0 -10000 0 0
CASP10 0.021 0.11 0.31 76 -0.53 10 86
JNK cascade -0.067 0.2 -10000 0 -0.64 87 87
TRAIL (trimer) -0.007 0.077 -10000 0 -0.84 7 7
TNFRSF10C -0.006 0.057 -10000 0 -0.84 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD -0.009 0.058 -10000 0 -0.49 11 11
TRAIL/TRAILR2/FADD -0.007 0.054 -10000 0 -0.56 7 7
cell death -0.003 0.027 -10000 0 -0.3 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.031 -10000 0 -0.34 7 7
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.015 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.006 0.045 -10000 0 -0.48 7 7
Cellular roles of Anthrax toxin

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0 0.01 -10000 0 -0.28 1 1
ANTXR2 -0.009 0.086 -10000 0 -0.84 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 9 9
monocyte activation 0.006 0.065 -10000 0 -0.46 16 16
MAP2K2 0 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.012 0.074 -10000 0 -0.51 18 18
CYAA -0.005 0.051 -10000 0 -0.5 9 9
MAP2K4 -0.002 0.02 -10000 0 -0.5 1 1
IL1B 0.009 0.061 -10000 0 -0.35 20 20
Channel -0.006 0.054 -10000 0 -0.52 9 9
NLRP1 -0.008 0.06 -10000 0 -0.52 11 11
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 9 -10000 0 9
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.15 0.22 -10000 0 -0.5 230 230
PA/Cellular Receptors -0.006 0.059 -10000 0 -0.57 9 9
apoptosis -0.001 0.011 -10000 0 -0.1 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.005 0.051 -10000 0 -0.49 9 9
macrophage activation 0.02 0.01 -10000 0 -10000 0 0
TNF -0.016 0.098 -10000 0 -0.84 10 10
VCAM1 -0.009 0.064 -10000 0 -0.46 16 16
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.023 0.11 18 -10000 0 18
IL18 0.011 0.036 -10000 0 -0.22 11 11
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 9 9
LEF -0.001 0.011 -10000 0 -0.1 9 9
CASP1 -0.004 0.03 -10000 0 -0.25 11 11
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0.051 -10000 0 -0.5 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
BARD1 signaling events

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0 0.008 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
PRKDC -0.001 0.019 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
UBE2L3 0 0 -9999 0 -10000 0 0
FANCD2 -0.001 0.007 -9999 0 -10000 0 0
protein ubiquitination -0.018 0.038 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
M/R/N Complex 0 0 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
DNA-PK -0.001 0.009 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.002 0.01 -9999 0 -10000 0 0
FANCF 0 0.01 -9999 0 -0.28 1 1
BRCA1 -0.001 0.013 -9999 0 -10000 0 0
CCNE1 -0.053 0.11 -9999 0 -0.28 162 162
CDK2/Cyclin E1 -0.034 0.069 -9999 0 -10000 0 0
FANCG 0 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.001 0.01 -9999 0 -10000 0 0
FANCE 0 0 -9999 0 -10000 0 0
FANCC 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
FANCA -0.052 0.11 -9999 0 -0.28 157 157
DNA repair 0.014 0.074 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.001 0.01 -9999 0 -10000 0 0
BARD1/DNA-PK -0.001 0.008 -9999 0 -10000 0 0
FANCL 0 0 -9999 0 -10000 0 0
mRNA polyadenylation 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0.001 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0 0.007 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.001 0.009 -9999 0 -10000 0 0
BRCA1/BACH1 -0.001 0.013 -9999 0 -10000 0 0
BARD1 0 0.01 -9999 0 -0.28 1 1
PCNA -0.001 0.016 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.045 0.055 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 -0.001 0.007 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.001 0.01 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP -0.001 0.008 -9999 0 -10000 0 0
FA complex -0.004 0.009 -9999 0 -10000 0 0
BARD1/EWS 0 0.006 -9999 0 -10000 0 0
RBBP8 0.022 0.007 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
TOPBP1 0 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0 0.006 -9999 0 -10000 0 0
BRCA1/BARD1 -0.018 0.038 -9999 0 -10000 0 0
CSTF1 0 0.01 -9999 0 -0.28 1 1
BARD1/EWS-Fli1 0 0.006 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.11 0.14 -9999 0 -0.28 340 340
RAD50 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.01 -9999 0 -10000 0 0
EWSR1 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.03 0.01 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.045 -9999 0 -10000 0 0
MAPK12 0.017 0.086 -9999 0 -0.51 21 21
CCND1 0.015 0.043 -9999 0 -0.41 4 4
p38 gamma/SNTA1 -0.012 0.076 -9999 0 -0.5 18 18
MAP2K3 0 0.01 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.017 0.086 -9999 0 -0.5 21 21
MAP2K6 0.01 0.087 -9999 0 -0.53 21 21
MAPT -0.016 0.13 -9999 0 -0.41 83 83
MAPK13 0.021 0.012 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.002 0.027 -9999 0 -0.46 3 3
Retinoic acid receptors-mediated signaling

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.039 0.034 -10000 0 -0.33 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.021 0.043 0.24 3 -0.36 6 9
RAR alpha/9cRA/Cyclin H -0.01 0.06 -10000 0 -0.39 21 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.035 0.046 -10000 0 -0.36 8 8
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.007 0.039 -10000 0 -0.29 1 1
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.12 -10000 0 -0.6 22 22
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
NCOA3 0 0.01 -10000 0 -10000 0 0
NCOA1 -0.001 0.029 -10000 0 -0.84 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.64 21 21
RARA 0.016 0.054 -10000 0 -0.31 21 21
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.033 0.047 -10000 0 -0.28 15 15
PRKCA -0.009 0.13 -10000 0 -0.84 21 21
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.005 0.13 -10000 0 -0.61 24 24
RXRG -0.11 0.22 -10000 0 -0.46 221 221
RXRA 0.024 0.06 -10000 0 -0.34 21 21
RXRB 0.01 0.076 -10000 0 -0.45 21 21
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.021 0.094 -10000 0 -0.84 6 6
CRBP1/9-cic-RA -0.015 0.069 -10000 0 -0.65 6 6
RARB 0.004 0.083 -10000 0 -0.84 8 8
PRKCG -0.002 0.056 -10000 0 -10000 0 0
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.027 0.12 -10000 0 -0.64 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.014 0.1 -10000 0 -0.51 22 22
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.048 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.005 0.13 -10000 0 -0.61 24 24
positive regulation of DNA binding -0.009 0.057 -10000 0 -0.36 21 21
NRIP1 -0.003 0.12 -10000 0 -0.6 22 22
RXRs/RARs -0.011 0.13 -10000 0 -0.59 25 25
RXRs/RXRs/DNA/9cRA -0.045 0.12 -10000 0 -0.66 21 21
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.029 -10000 0 -10000 0 0
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.018 0.1 -9999 0 -0.6 24 24
KLHL20 -0.008 0.033 -9999 0 -0.25 2 2
CYFIP2 -0.01 0.061 -9999 0 -0.32 25 25
Rac1/GDP 0.048 0.07 -9999 0 -0.35 24 24
ENAH -0.017 0.098 -9999 0 -0.59 24 24
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.009 0.049 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.023 -9999 0 -0.17 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.089 -9999 0 -0.51 26 26
RAPGEF1 0.038 0.091 -9999 0 -0.49 24 24
CTNND1 0 0.01 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.1 -9999 0 -0.61 24 24
CRK 0.029 0.099 -9999 0 -0.55 24 24
E-cadherin/gamma catenin/alpha catenin -0.017 0.095 -9999 0 -0.56 25 25
alphaE/beta7 Integrin -0.005 0.039 -9999 0 -0.64 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.031 -9999 0 -0.52 3 3
DLG1 -0.017 0.098 -9999 0 -0.59 24 24
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.035 -9999 0 -10000 0 0
MLLT4 -0.003 0.05 -9999 0 -0.84 3 3
ARF6/GTP/NME1/Tiam1 -0.006 0.027 -9999 0 -10000 0 0
PI3K -0.008 0.046 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.11 -9999 0 -0.64 25 25
TIAM1 -0.001 0.019 -9999 0 -0.28 4 4
E-cadherin(dimer)/Ca2+ -0.014 0.081 -9999 0 -0.48 24 24
AKT1 -0.005 0.026 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
RhoA/GDP 0.048 0.07 -9999 0 -0.35 24 24
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 2 2
CDC42/GDP 0.048 0.07 -9999 0 -0.35 24 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.06 -9999 0 -0.35 25 25
ITGB7 -0.007 0.055 -9999 0 -0.84 2 2
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.015 0.085 -9999 0 -0.51 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.082 -9999 0 -0.49 24 24
mol:GDP 0.045 0.081 -9999 0 -0.42 24 24
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.032 -9999 0 -0.46 3 3
p120 catenin/RhoA/GDP -0.011 0.06 -9999 0 -0.36 24 24
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.029 -9999 0 -0.25 4 4
NME1 -0.014 0.06 -9999 0 -0.28 42 42
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.018 0.1 -9999 0 -0.58 25 25
regulation of cell-cell adhesion -0.008 0.043 -9999 0 -10000 0 0
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.01 0.057 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.085 -9999 0 -0.48 27 27
CCND1 -0.009 0.035 -9999 0 -0.32 4 4
VAV2 0.033 0.096 -9999 0 -0.52 24 24
RAP1/GDP -0.01 0.058 -9999 0 -0.35 1 1
adherens junction assembly -0.017 0.096 -9999 0 -0.56 25 25
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.08 -9999 0 -0.45 27 27
E-cadherin/beta catenin -0.015 0.085 -9999 0 -0.51 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.017 0.098 -9999 0 -0.59 24 24
PIK3CA 0 0.01 -9999 0 -0.28 1 1
Rac1/GTP -0.011 0.054 -9999 0 -0.37 4 4
E-cadherin/beta catenin/alpha catenin -0.016 0.093 -9999 0 -0.56 24 24
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.1 -9999 0 -0.63 24 24
S1P3 pathway

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.096 -9999 0 -0.34 68 68
GNAO1 -0.033 0.14 -9999 0 -0.81 22 22
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.01 0.046 -9999 0 -0.68 2 2
AKT3 0.018 0.17 -9999 0 -1.4 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
GNAI2 0.001 0.003 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.002 0.029 -9999 0 -0.32 1 1
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.1 -9999 0 -0.39 31 31
MAPK3 0.018 0.1 -9999 0 -0.53 9 9
MAPK1 0.018 0.1 -9999 0 -0.53 9 9
JAK2 0.02 0.1 -9999 0 -0.46 14 14
CXCR4 0.014 0.1 -9999 0 -0.48 14 14
FLT1 0.012 0.03 -9999 0 -0.85 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.1 -9999 0 -0.53 9 9
S1P/S1P3/Gi 0.01 0.11 -9999 0 -0.4 31 31
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.084 -9999 0 -0.51 9 9
VEGFA 0.01 0.03 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.027 0.089 -9999 0 -0.32 68 68
VEGFR1 homodimer/VEGFA homodimer 0.02 0.031 -9999 0 -0.67 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.005 0.037 -9999 0 -0.35 9 9
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.082 -9999 0 -0.84 6 6
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.024 0.084 -9999 0 -0.51 9 9
JNK signaling in the CD4+ TCR pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.015 0.085 -9999 0 -0.55 18 18
MAP4K1 -0.01 0.062 -9999 0 -0.84 2 2
MAP3K8 -0.005 0.065 -9999 0 -0.74 6 6
PRKCB -0.019 0.11 -9999 0 -0.56 28 28
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.006 0.047 -9999 0 -0.58 2 2
JUN 0.02 0.1 -9999 0 -0.58 23 23
MAP3K7 -0.006 0.047 -9999 0 -0.58 2 2
GRAP2 -0.014 0.1 -9999 0 -0.84 13 13
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.044 0.058 -9999 0 -0.52 4 4
LAT -0.004 0.048 -9999 0 -0.4 9 9
LCP2 0 0.01 -9999 0 -10000 0 0
MAPK8 0.018 0.094 -9999 0 -0.68 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.05 -9999 0 -0.38 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.014 0.08 -9999 0 -0.54 16 16
Glypican 2 network

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.01 0.05 -9999 0 -10000 0 0
GPC2 -0.033 0.098 -9999 0 -0.84 3 3
GPC2/Midkine -0.027 0.077 -9999 0 -0.41 15 15
neuron projection morphogenesis -0.027 0.077 -9999 0 -0.41 15 15
Sphingosine 1-phosphate (S1P) pathway

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.004 0.048 -9999 0 -0.4 9 9
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.018 -9999 0 -0.37 2 2
GNAO1 -0.033 0.14 -9999 0 -0.48 57 57
mol:Sphinganine-1-P 0.019 0.037 -9999 0 -0.64 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.028 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.016 -9999 0 -0.32 2 2
S1PR5 -0.008 0.061 -9999 0 -0.38 17 17
S1PR4 -0.011 0.08 -9999 0 -0.43 22 22
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
S1P/S1P5/G12 -0.004 0.036 -9999 0 -0.5 3 3
S1P/S1P3/Gq -0.003 0.032 -9999 0 -0.33 1 1
S1P/S1P4/Gi -0.027 0.086 -9999 0 -0.34 33 33
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
GNA14 -0.013 0.082 -9999 0 -0.84 6 6
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.034 -10000 0 -0.57 1 1
IRAK/TOLLIP -0.001 0.008 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -0.28 2 2
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.032 0.13 -10000 0 -0.63 35 35
IL1A -0.005 0.038 -10000 0 -10000 0 0
IL1B 0.013 0.081 -10000 0 -0.7 10 10
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.016 -10000 0 -10000 0 0
IL1R2 -0.039 0.17 -10000 0 -0.84 33 33
IL1R1 -0.01 0.091 -10000 0 -0.84 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.057 0.24 23 -0.33 9 32
TOLLIP 0 0.01 -10000 0 -0.28 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.005 -10000 0 -10000 0 0
JUN 0.032 0.081 -10000 0 -0.41 26 26
MAP3K7 0 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.012 0.08 -10000 0 -0.5 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.008 0.057 -10000 0 -0.51 10 10
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.053 -10000 0 -0.48 10 10
IL1 beta fragment/IL1R1/IL1RAP -0.013 0.089 -10000 0 -0.56 19 19
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.03 0.067 -10000 0 -0.42 18 18
IRAK1 0.012 0.017 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.015 0.082 -10000 0 -0.64 12 12
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.01 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.05 -10000 0 -0.37 10 10
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.013 0.089 -10000 0 -0.56 19 19
IL1 beta/IL1R2 -0.032 0.13 -10000 0 -0.58 42 42
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.07 -10000 0 -1.1 1 1
IRAK3 -0.025 0.14 -10000 0 -0.84 25 25
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.012 0.08 -10000 0 -0.5 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.037 -10000 0 -0.34 10 10
IL1 alpha/IL1R1/IL1RAP -0.009 0.063 -10000 0 -0.56 10 10
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 -0.001 0.013 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0.006 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.009 0.063 -10000 0 -0.98 1 1
CASP1 -0.002 0.041 -10000 0 -0.84 2 2
IL1RN/IL1R2 -0.037 0.13 -10000 0 -0.63 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.012 0.084 -10000 0 -0.52 19 19
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.042 -10000 0 -0.38 10 10
PIK3CA 0 0.01 -10000 0 -0.28 1 1
IL1RN -0.012 0.065 -10000 0 -0.31 32 32
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.01 0.065 -10000 0 -0.45 18 18
Signaling events mediated by HDAC Class II

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.004 0.043 -10000 0 -0.51 6 6
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.015 -10000 0 -0.43 1 1
GATA1/HDAC4 -0.003 0.029 -10000 0 -0.64 1 1
GATA1/HDAC5 -0.002 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 -0.017 0.098 -10000 0 -0.64 19 19
HDAC5/BCL6/BCoR -0.002 0.033 -10000 0 -0.56 3 3
HDAC9 -0.01 0.077 -10000 0 -0.46 18 18
Glucocorticoid receptor/Hsp90/HDAC6 -0.005 0.051 -10000 0 -0.56 7 7
HDAC4/ANKRA2 -0.001 0.022 -10000 0 -0.64 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.023 0.13 -10000 0 -0.84 19 19
HDAC4/RFXANK -0.001 0.023 -10000 0 -0.64 1 1
BCOR -0.001 0.029 -10000 0 -0.84 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.054 -10000 0 -0.64 6 6
Histones -0.002 0.024 -10000 0 -10000 0 0
ADRBK1 0 0.01 -10000 0 -10000 0 0
HDAC4 -0.001 0.029 -10000 0 -0.84 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.022 -10000 0 -0.64 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0 0.006 -10000 0 -10000 0 0
CAMK4 -0.011 0.053 -10000 0 -10000 0 0
Tubulin/HDAC6 0 0.006 -10000 0 -10000 0 0
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.003 0.03 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.007 0.076 -10000 0 -0.84 7 7
SUMO1/HDAC4 -0.001 0.016 -10000 0 -0.47 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.022 -10000 0 -0.64 1 1
Tubulin 0 0.008 -10000 0 -10000 0 0
HDAC4/14-3-3 E -0.001 0.022 -10000 0 -0.64 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.002 0.038 -10000 0 -0.64 3 3
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.019 -10000 0 -0.56 1 1
HDAC4/SRF -0.006 0.032 -10000 0 -0.56 1 1
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.64 118 118
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.002 0.024 -10000 0 -10000 0 0
cell motility 0 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.002 0.041 -10000 0 -0.84 2 2
HDAC4/CaMK II delta B -0.001 0.029 -10000 0 -0.84 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.29 -10000 0 -0.56 230 230
HDAC6/HDAC11 -0.001 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.029 -10000 0 -0.84 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.023 -10000 0 -0.48 2 2
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.013 -10000 0 -10000 0 0
HDAC11 -0.001 0.016 -10000 0 -10000 0 0
HSP90AA1 0 0.01 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK 0 0.01 -10000 0 -0.28 1 1
nuclear import 0.001 0.016 0.45 1 -10000 0 1
mTOR signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.012 0.067 0.34 1 -0.35 30 31
FRAP1 0.012 0.015 -10000 0 -10000 0 0
AKT1 -0.011 0.057 0.24 1 -0.29 30 31
INSR 0 0.01 -10000 0 -0.28 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.009 0.042 -10000 0 -0.41 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.012 -10000 0 -10000 0 0
TSC2 0 0 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.036 -10000 0 -0.36 1 1
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.016 0.081 -10000 0 -0.43 31 31
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.015 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.034 -10000 0 -0.28 1 1
MAP3K5 0.009 0.023 -10000 0 -0.45 2 2
PIK3R1 0 0 -10000 0 -10000 0 0
apoptosis 0.009 0.023 -10000 0 -0.45 2 2
mol:LY294002 0 0 -10000 0 -0.002 31 31
EIF4B 0.028 0.031 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.022 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.003 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.014 0.072 -10000 0 -0.38 31 31
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.023 0.18 1 -10000 0 1
FKBP1A 0 0.01 -10000 0 -10000 0 0
RHEB/GTP -0.007 0.035 -10000 0 -0.35 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 31 31
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.011 0.06 0.26 1 -0.32 30 31
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.002 0.031 -10000 0 -0.63 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.009 0.045 -10000 0 -0.44 1 1
tumor necrosis factor receptor activity 0 0 0.002 31 -10000 0 31
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.009 0.088 -10000 0 -0.46 31 31
INS 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
PDK2 -0.013 0.069 0.26 1 -0.34 33 34
EIF4EBP1 0.013 0.014 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -0.28 1 1
PPP2R5D 0.019 0.014 -10000 0 -10000 0 0
peptide biosynthetic process 0 0.004 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -10000 0 2
EEF2 0 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.048 0.025 -10000 0 -0.36 1 1
NFATC2 0.022 0.052 -10000 0 -0.26 4 4
NFATC3 -0.001 0.018 -10000 0 -0.53 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.096 -10000 0 -0.4 27 27
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.018 0.075 -10000 0 -0.53 10 10
BCL2/BAX -0.018 0.11 -10000 0 -0.64 24 24
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.019 0.082 -10000 0 -0.59 10 10
Calcineurin A alpha-beta B1/BCL2 -0.024 0.14 -10000 0 -0.84 24 24
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.019 0.081 0.58 10 -10000 0 10
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.034 0.09 -10000 0 -0.28 102 102
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.84 13 13
MAP3K8 -0.005 0.065 -10000 0 -0.74 6 6
NFAT4/CK1 alpha 0 0.012 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.036 0.097 -10000 0 -0.48 3 3
CABIN1 0.012 0.097 -10000 0 -0.4 27 27
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.011 0.053 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.04 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.01 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.018 -10000 0 -0.42 1 1
PRKCH -0.001 0.029 -10000 0 -0.84 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.006 0.033 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.027 -10000 0 -10000 0 0
PRKCB -0.019 0.11 -10000 0 -0.56 28 28
PRKCE -0.001 0.029 -10000 0 -0.84 1 1
JNK2/NFAT4 -0.001 0.017 -10000 0 -0.48 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0.01 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
PRKCA -0.022 0.13 -10000 0 -0.84 21 21
PRKCG -0.011 0.054 -10000 0 -10000 0 0
PRKCQ -0.036 0.16 -10000 0 -0.84 32 32
FKBP38/BCL2 -0.018 0.11 -10000 0 -0.64 24 24
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.047 0.031 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.027 -10000 0 -10000 0 0
NFATc/ERK1 -0.001 0.016 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.018 0.074 -10000 0 -0.53 10 10
NR4A1 -0.074 0.22 -10000 0 -0.74 79 79
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.001 0.018 -10000 0 -0.53 1 1
NFAT1/CK1 alpha -0.011 0.031 -10000 0 -0.3 1 1
RCH1/ KPNB1 -0.021 0.057 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.016 0.064 -10000 0 -0.28 48 48
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -10000 0 0
NFATc/p38 alpha 0.047 0.03 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
p38 MAPK signaling pathway

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.001 0.024 -10000 0 -0.5 2 2
TRAF2/ASK1 -0.001 0.028 -10000 0 -0.57 2 2
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.029 0.036 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.053 -10000 0 -0.37 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.015 0.062 -10000 0 -0.28 45 45
TXN 0 0.003 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
MAP3K6 0 0 -10000 0 -10000 0 0
MAP3K7 0 0.01 -10000 0 -10000 0 0
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.002 0.031 -10000 0 -0.64 2 2
TAK1/TAB family 0 0.011 0.22 2 -10000 0 2
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.015 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.075 0.23 -10000 0 -0.64 98 98
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.049 0.15 -10000 0 -0.57 64 64
MAPK11 -0.002 0.041 -10000 0 -0.84 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.045 0.14 -10000 0 -0.52 66 66
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.003 0.038 -10000 0 -0.46 6 6
TAOK2 0 0 -10000 0 -10000 0 0
TAOK3 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.002 0.041 -10000 0 -0.84 2 2
MAP3K10 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.001 0.027 -10000 0 -0.56 2 2
GADD45/MTK1/MTK1 -0.005 0.023 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.049 0.05 -10000 0 -0.49 2 2
UGCG 0 0.027 -10000 0 -0.64 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.058 0.082 -10000 0 -0.38 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.024 0.03 -10000 0 -0.63 1 1
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.022 0.08 -10000 0 -0.37 19 19
FRAP1 0.058 0.12 -10000 0 -0.4 37 37
FOXO3 0.065 0.099 -10000 0 -0.55 5 5
AKT1 0.06 0.1 -10000 0 -0.41 24 24
GAB2 -0.003 0.027 -10000 0 -10000 0 0
SMPD1 -0.001 0.013 -10000 0 -10000 0 0
SGMS1 -0.001 0.013 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.008 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.039 0.056 -10000 0 -0.25 22 22
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0.006 -10000 0 -10000 0 0
RPS6KB1 0.022 0.03 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 20 20
JAK3 0.008 0.034 -10000 0 -10000 0 0
PIK3R1 0.013 0.004 -10000 0 -10000 0 0
JAK1 0.013 0.004 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.048 0.18 -10000 0 -1 22 22
MYB 0.014 0.18 -10000 0 -1.3 14 14
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.08 -10000 0 -0.6 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.057 0.079 -10000 0 -0.58 4 4
Rac1/GDP 0 0.004 -10000 0 -10000 0 0
T cell proliferation 0.062 0.076 -10000 0 -0.5 5 5
SHC1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.009 -10000 0 -0.067 14 14
PRKCZ 0.062 0.078 -10000 0 -0.52 5 5
NF kappa B1 p50/RelA -0.021 0.078 -10000 0 -0.52 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.007 0.043 -10000 0 -0.54 2 2
HSP90AA1 0 0.01 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.028 0.11 -10000 0 -0.84 10 10
IL2RB 0.001 0.056 -10000 0 -0.28 1 1
TERT -0.034 0.09 -10000 0 -10000 0 0
E2F1 0.026 0.061 -10000 0 -0.43 14 14
SOS1 0 0 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.03 14 -10000 0 14
PTPN11 0 0 -10000 0 -10000 0 0
IL2RG -0.003 0.085 -10000 0 -0.84 5 5
actin cytoskeleton organization 0.062 0.076 -10000 0 -0.5 5 5
GRB2 0 0.009 -10000 0 -10000 0 0
IL2 0.005 0.028 -10000 0 -10000 0 0
PIK3CA 0.012 0.01 -10000 0 -0.27 1 1
Rac1/GTP 0.03 0.009 -10000 0 -10000 0 0
LCK -0.006 0.11 -10000 0 -0.84 11 11
BCL2 0.046 0.18 -10000 0 -0.9 26 26
VEGFR1 specific signals

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.001 0.032 -9999 0 -0.94 1 1
VEGFR1 homodimer/NRP1 -0.001 0.033 -9999 0 -0.95 1 1
mol:DAG 0.038 0.036 -9999 0 -0.68 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.033 -9999 0 -0.88 1 1
CaM/Ca2+ -0.002 0.032 -9999 0 -0.64 2 2
HIF1A 0 0.013 -9999 0 -0.39 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.03 -9999 0 -0.74 1 1
PLCG1 0.038 0.036 -9999 0 -0.68 2 2
NOS3 0.062 0.032 -9999 0 -0.73 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.062 0.031 -9999 0 -0.7 1 1
FLT1 0.028 0.037 -9999 0 -1 1 1
PGF -0.001 0.029 -9999 0 -0.84 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.047 -9999 0 -1.3 1 1
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
eNOS/Hsp90 -0.001 0.027 -9999 0 -0.67 1 1
endothelial cell proliferation 0.037 0.094 -9999 0 -0.89 3 3
mol:Ca2+ 0.038 0.036 -9999 0 -0.67 2 2
MAPK3 0.039 0.088 -9999 0 -0.48 21 21
MAPK1 0.039 0.088 -9999 0 -0.48 21 21
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.001 0.029 -9999 0 -0.84 1 1
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
VEGFA homodimer -0.003 0.028 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.002 0.035 -9999 0 -0.94 1 1
platelet activating factor biosynthetic process 0.046 0.085 -9999 0 -1.1 1 1
PI3K -0.002 0.033 -9999 0 -0.65 2 2
PRKCA 0.032 0.093 -9999 0 -0.51 22 22
PRKCB 0.034 0.081 -9999 0 -0.52 15 15
VEGFR1 homodimer/PLGF homodimer -0.002 0.038 -9999 0 -0.75 2 2
VEGFA -0.003 0.028 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.036 -9999 0 -0.68 2 2
RASA1 0.038 0.031 -9999 0 -0.87 1 1
NRP2 -0.001 0.03 -9999 0 -0.56 2 2
VEGFR1 homodimer 0.028 0.037 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.084 0.17 -9999 0 -0.93 2 2
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.032 -9999 0 -0.64 2 2
mol:L-citrulline 0.062 0.031 -9999 0 -0.7 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.031 -9999 0 -0.83 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.032 -9999 0 -0.88 1 1
CD2AP 0 0.01 -9999 0 -0.28 1 1
PI3K/GAB1 -0.001 0.031 -9999 0 -0.61 2 2
PDPK1 -0.002 0.03 -9999 0 -0.76 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.032 -9999 0 -0.88 1 1
mol:NADP 0.062 0.031 -9999 0 -0.7 1 1
HSP90AA1 0 0.01 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.03 -9999 0 -0.82 1 1
VEGFR1 homodimer/NRP2 -0.002 0.049 -9999 0 -1.4 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0 0 -9999 0 -10000 0 0
SMAD2 0.014 0 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.01 0.027 -9999 0 -10000 0 0
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
MAP3K1 0 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.002 0.031 -9999 0 -0.64 2 2
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.002 0.041 -9999 0 -0.84 2 2
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.01 -9999 0 -0.28 1 1
KPNA2 -0.034 0.09 -9999 0 -0.28 102 102
PIAS4 0 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 -0.003 0.03 -9999 0 -0.28 10 10
Caspase 8 (4 units) -0.007 0.045 -9999 0 -1 1 1
NEF -0.005 0.023 -9999 0 -0.22 4 4
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 -0.01 0.08 -9999 0 -0.84 7 7
CYCS 0.042 0.055 -9999 0 -0.98 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.026 0.13 -9999 0 -0.64 30 30
MAP2K7 0.043 0.046 -9999 0 -0.82 1 1
protein ubiquitination 0.066 0.033 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.002 0.041 -9999 0 -0.84 2 2
BID -0.008 0.05 -9999 0 -1.1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.034 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.002 0.041 -9999 0 -0.84 2 2
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.005 0.038 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -10000 0 0
MAPK8 0.049 0.043 -9999 0 -0.75 1 1
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.016 -9999 0 -0.28 3 3
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.054 -9999 0 -0.43 7 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.03 -9999 0 -0.39 1 1
CHUK 0.068 0.034 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.004 0.045 -9999 0 -0.67 3 3
TCRz/NEF -0.024 0.11 -9999 0 -0.55 29 29
TNF -0.016 0.098 -9999 0 -0.84 10 10
FASLG -0.003 0.13 -9999 0 -0.61 29 29
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.065 -9999 0 -0.56 10 10
CASP6 -0.003 0.03 -9999 0 -0.72 1 1
CASP7 0.074 0.075 -9999 0 -0.64 7 7
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.074 0.075 -9999 0 -0.64 7 7
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.019 -9999 0 -10000 0 0
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.037 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.008 0.054 -9999 0 -0.54 7 7
BCL2 0.042 0.089 -9999 0 -0.43 25 25
Signaling events mediated by VEGFR1 and VEGFR2

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.012 0.083 -9999 0 -0.64 14 14
AKT1 0.085 0.044 -9999 0 -0.69 2 2
PTK2B -0.01 0.072 -9999 0 -0.98 2 2
VEGFR2 homodimer/Frs2 -0.004 0.047 -9999 0 -0.93 2 2
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.004 0.044 -9999 0 -0.87 2 2
endothelial cell proliferation 0.086 0.071 -9999 0 -0.65 3 3
mol:Ca2+ -0.003 0.039 -9999 0 -0.78 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.001 0.041 -9999 0 -0.82 2 2
RP11-342D11.1 0.046 0.043 -9999 0 -0.78 2 2
CDH5 -0.004 0.058 -9999 0 -0.84 4 4
VEGFA homodimer -0.001 0.011 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.024 0.14 -9999 0 -0.84 24 24
HRAS/GDP -0.001 0.033 -9999 0 -0.66 2 2
SH2D2A -0.029 0.088 -9999 0 -0.28 86 86
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0 0.034 -9999 0 -0.64 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.013 0.056 -9999 0 -0.78 3 3
VEGFR1 homodimer -0.001 0.029 -9999 0 -0.84 1 1
SHC/GRB2/SOS1 -0.001 0.038 -9999 0 -0.75 2 2
GRB10 -0.003 0.039 -9999 0 -0.78 2 2
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.003 0.064 -9999 0 -1.2 2 2
HRAS 0 0.01 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.005 0.04 -9999 0 -0.52 2 2
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.001 0.04 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.041 -9999 0 -0.84 2 2
Nck/Pak -0.004 0.025 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.004 0.055 -9999 0 -1.1 2 2
mol:GDP -0.001 0.036 -9999 0 -0.72 2 2
mol:NADP 0.076 0.031 -9999 0 -0.52 2 2
eNOS/Hsp90 0.077 0.029 -9999 0 -0.49 2 2
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.003 0.039 -9999 0 -0.79 2 2
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.03 -9999 0 -0.84 1 1
VEGFA -0.003 0.028 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.006 0.055 -9999 0 -0.9 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.008 0.078 -9999 0 -0.54 15 15
PTPN6 -0.001 0.013 -9999 0 -0.28 2 2
EPAS1 -0.001 0.019 -9999 0 -0.38 2 2
mol:L-citrulline 0.076 0.031 -9999 0 -0.52 2 2
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0 0.043 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer -0.001 0.043 -9999 0 -0.86 2 2
VEGFR2/3 heterodimer -0.003 0.061 -9999 0 -0.96 3 3
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.059 0.044 -9999 0 -0.8 2 2
VEGFR2 homodimer 0.032 0.052 -9999 0 -1 2 2
FLT1 -0.001 0.029 -9999 0 -0.84 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.054 0.064 -9999 0 -0.8 3 3
MAPK1 0.054 0.064 -9999 0 -0.8 3 3
VEGFA145/NRP2 -0.003 0.029 -9999 0 -0.64 1 1
VEGFR1/2 heterodimer -0.003 0.058 -9999 0 -1.2 2 2
KDR 0.032 0.052 -9999 0 -1 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.001 0.051 -9999 0 -1 2 2
SRC 0 0.01 -9999 0 -0.28 1 1
platelet activating factor biosynthetic process 0.057 0.064 -9999 0 -0.81 3 3
PI3K -0.003 0.049 -9999 0 -0.91 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.003 0.043 -9999 0 -0.87 2 2
FES -0.004 0.048 -9999 0 -0.6 5 5
GAB1 -0.002 0.047 -9999 0 -0.95 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.043 -9999 0 -0.87 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.17 -9999 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.004 0.047 -9999 0 -0.74 3 3
PI3K/GAB1 -0.002 0.038 -9999 0 -0.71 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.002 0.043 -9999 0 -0.79 2 2
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.057 -9999 0 -0.9 3 3
HSP90AA1 0 0.01 -9999 0 -10000 0 0
CDC42 -0.003 0.04 -9999 0 -0.81 2 2
actin cytoskeleton reorganization -0.013 0.056 -9999 0 -0.77 3 3
PTK2 0.061 0.07 -9999 0 -1 2 2
EDG1 0.046 0.043 -9999 0 -0.78 2 2
mol:DAG -0.003 0.039 -9999 0 -0.79 2 2
CaM/Ca2+ -0.002 0.036 -9999 0 -0.72 2 2
MAP2K3 0.062 0.042 -9999 0 -0.76 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.041 -9999 0 -0.82 2 2
PLCG1 -0.003 0.04 -9999 0 -0.81 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.001 0.044 -9999 0 -0.7 3 3
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.029 -9999 0 -0.84 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.003 0.043 -9999 0 -0.87 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.003 0.044 -9999 0 -0.87 2 2
cell migration 0.085 0.059 -9999 0 -0.79 2 2
mol:PI-3-4-5-P3 -0.002 0.044 -9999 0 -0.8 2 2
FYN -0.001 0.029 -9999 0 -0.84 1 1
VEGFB/NRP1 -0.002 0.037 -9999 0 -0.74 2 2
mol:NO 0.076 0.031 -9999 0 -0.52 2 2
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.033 -9999 0 -0.66 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.001 0.041 -9999 0 -0.82 2 2
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
NOS3 0.078 0.035 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck -0.017 0.093 -9999 0 -0.52 26 26
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.049 0.092 -9999 0 -0.95 2 2
PRKCB 0.051 0.087 -9999 0 -0.54 14 14
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.001 0.04 -9999 0 -0.79 2 2
VEGFR1/2 heterodimer/VEGFA homodimer -0.004 0.055 -9999 0 -1.1 2 2
VEGFA165/NRP2 -0.003 0.029 -9999 0 -0.64 1 1
MAPKKK cascade 0 0.035 -9999 0 -0.66 2 2
NRP2 -0.001 0.03 -9999 0 -0.56 2 2
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.006 0.055 -9999 0 -0.9 2 2
MAP3K13 -0.003 0.04 -9999 0 -0.81 2 2
PDPK1 0.078 0.043 -9999 0 -0.68 2 2
Signaling events mediated by HDAC Class I

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.005 0.057 -9999 0 -0.52 10 10
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.046 -9999 0 -0.43 10 10
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.001 0.013 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.023 -9999 0 -10000 0 0
YY1/LSF 0 0 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.041 -9999 0 -0.38 10 10
I kappa B alpha/HDAC1 -0.004 0.028 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.036 -9999 0 -0.33 10 10
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.032 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.023 0.13 -9999 0 -0.84 19 19
GATA1 -0.003 0.03 -9999 0 -10000 0 0
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.003 -9999 0 -10000 0 0
RBBP7 -0.003 0.027 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.032 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.001 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.016 -9999 0 -0.28 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.029 -9999 0 -0.84 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0 -9999 0 -10000 0 0
YY1/HDAC1 0 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0.001 -9999 0 -10000 0 0
PPARG -0.096 0.17 -9999 0 -0.39 204 204
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.028 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.032 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 0 -9999 0 -10000 0 0
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.01 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0.006 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.032 -9999 0 -10000 0 0
histone deacetylation 0.045 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.025 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.017 0.081 -9999 0 -0.51 19 19
GATA1/HDAC1 -0.002 0.019 -9999 0 -10000 0 0
GATA1/HDAC3 -0.005 0.031 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.074 -9999 0 -0.64 10 10
SIN3/HDAC complex/Mad/Max 0 0.002 -9999 0 -10000 0 0
NuRD Complex 0 0.002 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.023 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.011 -9999 0 -10000 0 0
GATA1/Fog1 -0.002 0.021 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.098 -9999 0 -0.84 10 10
negative regulation of cell growth 0.045 0.004 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.001 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.049 -9999 0 -0.45 10 10
SIN3/HDAC complex/NCoR1 0 0.007 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0 -9999 0 -10000 0 0
MBD2 0 0 -9999 0 -10000 0 0
FoxO family signaling

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.03 0.033 -9999 0 -10000 0 0
PLK1 0.013 0.11 -9999 0 -0.6 1 1
CDKN1B 0.082 0.066 -9999 0 -0.55 3 3
FOXO3 0.044 0.096 -9999 0 -0.56 3 3
KAT2B 0.008 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 0.008 0.035 -9999 0 -0.34 6 6
CAT 0.047 0.11 -9999 0 -1.1 3 3
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.014 0.011 -9999 0 -10000 0 0
FOXO1 0.033 0.035 -9999 0 -0.37 6 6
MAPK10 -0.048 0.19 -9999 0 -0.48 137 137
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.062 0.088 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.012 0.059 -9999 0 -0.53 3 3
XPO1 0 0 -9999 0 -10000 0 0
EP300 0.002 0.005 -9999 0 -10000 0 0
BCL2L11 0.029 0.017 -9999 0 -10000 0 0
FOXO1/SKP2 -0.002 0.028 -9999 0 -0.34 6 6
mol:GDP 0.005 0.011 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
GADD45A 0.068 0.058 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.067 0.029 -9999 0 -10000 0 0
MST1 -0.004 0.098 -9999 0 -0.8 12 12
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.001 0.044 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.037 0.006 -9999 0 -10000 0 0
MAPK9 0.036 0.005 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.016 -9999 0 -10000 0 0
SIRT1 0.002 0.007 -9999 0 -10000 0 0
SOD2 0.092 0.068 -9999 0 -10000 0 0
RBL2 0.062 0.071 -9999 0 -10000 0 0
RAL/GDP 0.01 0.015 -9999 0 -10000 0 0
CHUK 0.008 0.012 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.029 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.013 0.14 -9999 0 -1.5 6 6
SKP2 0 0 -9999 0 -10000 0 0
USP7 0 0 -9999 0 -10000 0 0
IKBKB 0.007 0.017 -9999 0 -10000 0 0
CCNB1 0.036 0.1 -9999 0 -0.6 1 1
FOXO1-3a-4/beta catenin -0.006 0.032 -9999 0 -0.41 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.028 -9999 0 -0.33 6 6
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.06 -9999 0 -0.84 4 4
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.067 0.078 -9999 0 -10000 0 0
SFN -0.016 0.11 -9999 0 -0.84 13 13
CDK2 0.002 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.051 -9999 0 -10000 0 0
CREBBP 0.002 0.005 -9999 0 -10000 0 0
FBXO32 0.046 0.12 -9999 0 -1.4 3 3
BCL6 0.06 0.095 -9999 0 -1.2 2 2
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 -0.003 0.027 -9999 0 -10000 0 0
ELF1 -0.011 0.047 -9999 0 -0.39 10 10
CCNA2 -0.12 0.14 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
JAK3 -0.004 0.033 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.069 -9999 0 -0.61 4 4
SHC1 0 0 -9999 0 -10000 0 0
SP1 -0.003 0.033 -9999 0 -0.39 6 6
IL2RA 0.004 0.13 -9999 0 -1 10 10
IL2RB -0.011 0.054 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IL2RG -0.015 0.083 -9999 0 -0.84 5 5
G1/S transition of mitotic cell cycle 0.012 0.1 -9999 0 -0.84 10 10
PTPN11 0 0 -9999 0 -10000 0 0
CCND2 0.021 0.091 -9999 0 -1 6 6
LCK -0.019 0.1 -9999 0 -0.84 11 11
GRB2 0 0.01 -9999 0 -10000 0 0
IL2 -0.002 0.027 -9999 0 -10000 0 0
CDK6 -0.007 0.072 -9999 0 -0.7 8 8
CCND3 0.067 0.059 -9999 0 -0.63 2 2
Class I PI3K signaling events

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0.021 0.3 2 -10000 0 2
DAPP1 0.036 0.051 -10000 0 -0.54 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.047 0.079 -10000 0 -0.54 8 8
mol:DAG 0.054 0.049 0.21 1 -0.27 5 6
HRAS 0 0.009 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.001 0.016 -10000 0 -10000 0 0
PLCG2 -0.001 0.03 -10000 0 -0.56 2 2
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.01 -10000 0 -10000 0 0
mol:GTP 0 0.02 0.27 2 -0.42 1 3
ARF1/GTP 0 0.02 0.28 2 -0.4 1 3
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.029 -10000 0 -0.84 1 1
RAP1A/GTP 0 0.02 0.25 2 -0.42 1 3
ADAP1 -0.002 0.033 0.26 2 -0.43 4 6
ARAP3 0 0.02 0.27 2 -0.42 1 3
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.052 -10000 0 -10000 0 0
ARHGEF6 -0.005 0.064 -10000 0 -0.84 5 5
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
FYN -0.001 0.029 -10000 0 -0.84 1 1
ARF6 0 0 -10000 0 -10000 0 0
FGR 0 0.01 -10000 0 -0.28 1 1
mol:Ca2+ 0.04 0.028 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
ZAP70 -0.027 0.13 -10000 0 -0.84 18 18
mol:IP3 0.049 0.037 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.015 -10000 0 -10000 0 0
RhoA/GDP 0 0.019 0.28 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.064 0.024 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -0.28 1 1
PLEKHA2 0.03 0.006 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.04 -10000 0 -0.82 2 2
HSP90AA1 0 0.01 -10000 0 -10000 0 0
ARF6/GTP 0 0.02 0.3 2 -10000 0 2
RhoA/GTP 0 0.019 0.26 2 -0.4 1 3
Src family/SYK family/BLNK-LAT -0.01 0.057 -10000 0 -0.55 4 4
BLK -0.036 0.1 -10000 0 -0.29 102 102
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0 0.019 0.26 2 -0.39 1 3
HCK -0.004 0.033 -10000 0 -0.28 12 12
CYTH3 0 0.019 -10000 0 -0.39 1 1
CYTH2 0 0.019 0.26 2 -0.39 1 3
KRAS 0 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.049 -10000 0 -0.56 6 6
SGK1 -0.003 0.05 -10000 0 -0.69 4 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.036 0.021 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.01 -10000 0 -0.28 1 1
ARF6/GDP 0 0.02 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 0 0.024 0.37 2 -0.42 1 3
ARAP3/RAP1A/GTP 0 0.02 0.26 2 -0.42 1 3
VAV1 -0.002 0.032 -10000 0 -0.84 1 1
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.016 -10000 0 -0.42 1 1
PLEKHA1 0.029 0.021 -10000 0 -0.56 1 1
Rac1/GDP -0.001 0.015 -10000 0 -10000 0 0
LAT -0.004 0.048 -10000 0 -0.4 9 9
Rac1/GTP -0.002 0.028 -10000 0 -0.34 5 5
ITK -0.017 0.08 0.26 1 -0.46 24 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.061 0.063 0.24 1 -0.38 5 6
LCK -0.019 0.1 -10000 0 -0.84 11 11
BTK 0 0.02 0.26 2 -0.39 1 3
PDGFR-beta signaling pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.041 -9999 0 -0.55 4 4
PDGFB-D/PDGFRB/SLAP -0.003 0.036 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/APS/CBL -0.006 0.036 -9999 0 -0.55 2 2
AKT1 -0.007 0.031 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.004 0.042 -9999 0 -0.57 4 4
PIK3CA 0 0.01 -9999 0 -0.28 1 1
FGR -0.003 0.029 -9999 0 -0.53 2 2
mol:Ca2+ 0.033 0.04 -9999 0 -0.68 2 2
MYC 0.038 0.14 -9999 0 -0.83 22 22
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.024 -9999 0 -0.45 2 2
LRP1/PDGFRB/PDGFB -0.007 0.072 -9999 0 -0.67 9 9
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.041 -9999 0 -0.69 2 2
PTEN -0.002 0.041 -9999 0 -0.84 2 2
GRB2 0 0.01 -9999 0 -10000 0 0
GRB7 -0.021 0.077 -9999 0 -0.29 62 62
PDGFB-D/PDGFRB/SHP2 -0.002 0.031 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB10 -0.002 0.031 -9999 0 -0.64 2 2
cell cycle arrest -0.003 0.035 -9999 0 -0.64 2 2
HRAS 0 0.01 -9999 0 -10000 0 0
HIF1A 0.055 0.043 -9999 0 -10000 0 0
GAB1 0.036 0.048 -9999 0 -0.66 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.047 -9999 0 -0.61 2 2
PDGFB-D/PDGFRB -0.003 0.032 -9999 0 -0.56 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.031 -9999 0 -0.64 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.046 -9999 0 -0.57 4 4
positive regulation of MAPKKK cascade -0.002 0.031 -9999 0 -0.64 2 2
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.033 0.041 -9999 0 -0.7 2 2
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.015 0.059 -9999 0 -0.64 3 3
SHB -0.001 0.03 -9999 0 -0.84 1 1
BLK -0.002 0.052 -9999 0 -0.63 5 5
PTPN2 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.031 -9999 0 -0.64 2 2
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.057 -9999 0 -0.56 3 3
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.031 -9999 0 -0.64 2 2
LCK -0.01 0.076 -9999 0 -0.61 13 13
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.003 0.029 -9999 0 -0.53 2 2
ABL1 0.034 0.042 -9999 0 -0.62 2 2
PDGFB-D/PDGFRB/CBL 0.035 0.051 -9999 0 -0.76 2 2
PTPN1 -0.003 0.031 -9999 0 -0.29 1 1
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.006 0.04 -9999 0 -0.28 18 18
cell proliferation 0.039 0.13 -9999 0 -0.72 22 22
SLA -0.003 0.027 -9999 0 -0.28 8 8
actin cytoskeleton reorganization -0.002 0.027 -9999 0 -0.43 3 3
SRC -0.002 0.028 -9999 0 -0.53 2 2
PI3K -0.009 0.035 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.012 0.048 -9999 0 -0.56 3 3
SH2B2 -0.01 0.05 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.004 0.043 -9999 0 -0.6 4 4
LYN -0.002 0.029 -9999 0 -0.53 2 2
LRP1 -0.009 0.086 -9999 0 -0.84 9 9
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.003 0.05 -9999 0 -0.84 3 3
STAT5A -0.007 0.076 -9999 0 -0.84 7 7
NCK1-2/p130 Cas -0.002 0.024 -9999 0 -0.45 2 2
SPHK1 -0.004 0.048 -9999 0 -0.4 9 9
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.041 -9999 0 -0.7 2 2
PLCG1 0.034 0.042 -9999 0 -0.72 2 2
NHERF/PDGFRB -0.014 0.047 -9999 0 -0.55 2 2
YES1 -0.003 0.035 -9999 0 -0.56 3 3
cell migration -0.014 0.047 -9999 0 -0.55 2 2
SHC/Grb2/SOS1 -0.002 0.024 -9999 0 -0.45 2 2
SLC9A3R2 0 0 -9999 0 -10000 0 0
SLC9A3R1 -0.027 0.082 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.013 0.047 -9999 0 -0.51 4 4
FYN -0.003 0.05 -9999 0 -0.92 2 2
DOK1 -0.001 0.028 -9999 0 -0.51 2 2
HRAS/GTP 0 0.006 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.081 -9999 0 -0.43 22 22
PRKCD 0.002 0.031 -9999 0 -0.51 2 2
FER -0.001 0.053 -9999 0 -0.52 8 8
MAPKKK cascade -0.002 0.023 -9999 0 -0.44 2 2
RASA1 0.002 0.03 -9999 0 -0.51 2 2
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.025 -9999 0 -0.47 2 2
PDGFB-D/PDGFRB/SHB -0.003 0.039 -9999 0 -0.64 3 3
chemotaxis 0.034 0.041 -9999 0 -0.6 2 2
STAT1-3-5/STAT1-3-5 -0.009 0.057 -9999 0 -0.47 11 11
Bovine Papilomavirus E5/PDGFRB -0.002 0.032 -9999 0 -0.65 2 2
PTPRJ 0 0 -9999 0 -10000 0 0
Arf6 downstream pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.029 0.041 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.025 0.33 5 -10000 0 5
myoblast fusion 0.007 0.024 -10000 0 -10000 0 0
mol:GTP -0.004 0.014 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.028 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.006 0.013 -10000 0 -10000 0 0
mol:Choline 0.022 0.045 -10000 0 -0.55 5 5
lamellipodium assembly -0.003 0.03 -10000 0 -10000 0 0
MAPK3 0.02 0.023 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.008 0.028 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.024 -10000 0 -10000 0 0
ARF1/GDP -0.005 0.02 -10000 0 -10000 0 0
ARF6 0.007 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -10000 0 0
TIAM1 -0.001 0.019 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.023 -10000 0 -10000 0 0
actin filament bundle formation 0.005 0.02 -10000 0 -10000 0 0
KALRN -0.01 0.067 -10000 0 -0.51 14 14
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.005 0.02 -10000 0 -10000 0 0
NME1 -0.014 0.06 -10000 0 -0.27 42 42
Rac1/GDP -0.005 0.02 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.004 0.014 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.03 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.004 0.014 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GDP -0.004 0.027 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.013 0.05 -10000 0 -0.62 5 5
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.03 -10000 0 -10000 0 0
ruffle organization -0.003 0.025 -10000 0 -0.33 5 5
regulation of epithelial cell migration -0.004 0.014 -10000 0 -10000 0 0
PLD2 0.016 0.012 -10000 0 -10000 0 0
PIP5K1A -0.003 0.025 -10000 0 -0.33 5 5
mol:Phosphatidic acid 0.022 0.045 -10000 0 -0.55 5 5
Rac1/GTP -0.003 0.03 -10000 0 -10000 0 0
Aurora C signaling

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.072 0.064 -9999 0 -0.64 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.018 0.016 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -10000 0 0
AURKC -0.006 0.046 -9999 0 -0.31 15 15
EPO signaling pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.06 0.071 -9999 0 -10000 0 0
CRKL 0.029 0.045 -9999 0 -10000 0 0
mol:DAG 0 0.024 -9999 0 -10000 0 0
HRAS -0.005 0.015 -9999 0 -10000 0 0
MAPK8 0.014 0.05 -9999 0 -10000 0 0
RAP1A 0.029 0.045 -9999 0 -10000 0 0
GAB1 0.029 0.045 -9999 0 -10000 0 0
MAPK14 0.014 0.05 -9999 0 -10000 0 0
EPO -0.037 0.11 -9999 0 -0.29 9 9
PLCG1 0 0.024 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.067 -9999 0 -0.68 5 5
GAB1/SHC/GRB2/SOS1 -0.006 0.017 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.029 0.063 -9999 0 -10000 0 0
IRS2 0.006 0.12 -9999 0 -0.5 38 38
STAT1 0.05 0.051 -9999 0 -10000 0 0
STAT5B -0.003 0.043 -9999 0 -0.46 3 3
cell proliferation 0.024 0.046 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.014 -9999 0 -10000 0 0
TEC 0.027 0.052 -9999 0 -0.49 2 2
SOCS3 -0.005 0.064 -9999 0 -0.84 5 5
STAT1 (dimer) 0.05 0.051 -9999 0 -10000 0 0
JAK2 0.001 0.002 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.055 0.038 -9999 0 -10000 0 0
EPO/EPOR -0.029 0.063 -9999 0 -10000 0 0
LYN 0.002 0.005 -9999 0 -10000 0 0
TEC/VAV2 -0.011 0.032 -9999 0 -0.47 2 2
elevation of cytosolic calcium ion concentration 0.012 0.004 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.047 -9999 0 -10000 0 0
mol:IP3 0 0.024 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.027 0.095 -9999 0 -0.5 19 19
SH2B3 0.001 0.002 -9999 0 -10000 0 0
NFKB1 0.014 0.05 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.029 -9999 0 -0.32 5 5
PTPN6 0.021 0.047 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.009 0.03 -9999 0 -0.45 2 2
EPOR 0.012 0.004 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.006 0.018 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.001 0.03 -9999 0 -0.56 2 2
CRKL/CBL/C3G -0.008 0.02 -9999 0 -10000 0 0
VAV2 0.028 0.046 -9999 0 -10000 0 0
CBL 0.029 0.045 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.006 0.026 -9999 0 -10000 0 0
STAT5A -0.005 0.057 -9999 0 -0.5 7 7
GRB2 0 0.01 -9999 0 -10000 0 0
STAT5 (dimer) 0.058 0.085 -9999 0 -0.63 3 3
LYN/PLCgamma2 -0.001 0.023 -9999 0 -0.64 1 1
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.046 -9999 0 -10000 0 0
BCL2 0.041 0.18 -9999 0 -1 24 24
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.026 -9999 0 -0.43 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.042 -9999 0 -0.45 4 4
EPO -0.048 0.1 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.019 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.066 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
PI3K 0 0.006 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.008 0.018 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.01 0.051 -9999 0 -0.28 30 30
cell adhesion -0.009 0.042 -9999 0 -0.44 4 4
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.006 0.045 -9999 0 -0.51 6 6
ITGB7 -0.007 0.055 -9999 0 -0.84 2 2
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.007 0.05 -9999 0 -0.56 6 6
p130Cas/Crk/Dock1 -0.004 0.036 -9999 0 -0.42 6 6
VCAM1 -0.008 0.074 -9999 0 -0.84 6 6
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.035 0.047 -9999 0 -0.47 6 6
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -0.28 4 4
Rac1/GTP 0.001 0.006 -9999 0 -10000 0 0
ceramide signaling pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.045 0.045 -10000 0 -10000 0 0
BAG4 -0.003 0.03 -10000 0 -0.28 10 10
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.51 17 17
BAX 0.032 0.017 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.09 1 1
IKBKB 0.051 0.043 -10000 0 -10000 0 0
MAP2K2 0.044 0.026 -10000 0 -0.49 1 1
MAP2K1 0.044 0.026 -10000 0 -0.49 1 1
SMPD1 0.02 0.012 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.049 -10000 0 -0.42 2 2
MAP2K4 0.038 0.023 -10000 0 -0.42 1 1
protein ubiquitination 0.053 0.044 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.049 0.028 -10000 0 -0.52 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.026 -10000 0 -0.53 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.018 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.017 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.046 0.025 -10000 0 -0.48 1 1
MAPK1 0.046 0.025 -10000 0 -0.48 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.043 0.05 -10000 0 -0.44 2 2
KSR1 0.032 0.027 -10000 0 -0.56 1 1
MAPK8 0.044 0.022 -10000 0 -0.38 1 1
TRAF2 0 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.051 0.043 -10000 0 -10000 0 0
TNF R/SODD -0.002 0.019 -10000 0 -10000 0 0
TNF -0.016 0.098 -10000 0 -0.84 10 10
CYCS 0.037 0.024 0.15 22 -10000 0 22
IKBKG 0.051 0.043 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.038 0.047 -10000 0 -0.34 7 7
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.024 0.15 22 -10000 0 22
TNF/TNF R/SODD -0.011 0.064 -10000 0 -0.56 10 10
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.045 0.045 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
HIF-2-alpha transcription factor network

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.001 0.014 -10000 0 -10000 0 0
oxygen homeostasis 0.013 0.012 -10000 0 -10000 0 0
TCEB2 -0.001 0.019 -10000 0 -10000 0 0
TCEB1 -0.001 0.016 -10000 0 -0.28 3 3
VHL/Elongin B/Elongin C/HIF2A -0.003 0.023 -10000 0 -10000 0 0
EPO 0.16 0.14 -10000 0 -10000 0 0
FIH (dimer) 0.023 0.011 -10000 0 -10000 0 0
APEX1 0.02 0.011 -10000 0 -10000 0 0
SERPINE1 0.17 0.14 -10000 0 -0.59 1 1
FLT1 -0.001 0.073 -10000 0 -1.4 2 2
ADORA2A 0.15 0.14 -10000 0 -10000 0 0
germ cell development 0.17 0.13 -10000 0 -0.66 1 1
SLC11A2 0.17 0.13 -10000 0 -0.59 1 1
BHLHE40 0.17 0.14 -10000 0 -0.98 2 2
HIF1AN 0.023 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.02 0.065 -10000 0 -10000 0 0
ETS1 0.023 0.044 -10000 0 -0.87 2 2
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.002 0.086 -10000 0 -1.7 2 2
PGK1 0.17 0.13 -10000 0 -0.59 1 1
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.17 0.15 -10000 0 -0.69 1 1
EPAS1 0.1 0.072 -10000 0 -0.41 1 1
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.14 0.23 -10000 0 -0.71 50 50
EFNA1 0.17 0.13 -10000 0 -0.59 1 1
FXN 0.16 0.13 -10000 0 -0.57 1 1
POU5F1 0.17 0.14 -10000 0 -0.69 1 1
neuron apoptosis -0.056 0.13 0.67 1 -10000 0 1
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.079 -10000 0 -0.28 27 27
EGLN2 0.022 0.02 -10000 0 -0.29 1 1
EGLN1 0.022 0.032 -10000 0 -0.85 1 1
VHL/Elongin B/Elongin C -0.001 0.012 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.021 0.011 -10000 0 -10000 0 0
SLC2A1 0.16 0.14 -10000 0 -0.57 1 1
TWIST1 0.15 0.19 -10000 0 -0.7 25 25
ELK1 0.018 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.012 0.056 -10000 0 -10000 0 0
VEGFA 0.17 0.14 -10000 0 -0.59 1 1
CREBBP 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.076 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.006 0.032 -9999 0 -0.35 1 1
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -0.28 2 2
RIPK2 -0.001 0.019 -9999 0 -0.28 4 4
IKBKG 0 0.001 -9999 0 -10000 0 0
IKK complex/A20 -0.003 0.046 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.019 -9999 0 -0.28 4 4
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.002 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.004 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.008 0.046 -9999 0 -0.28 24 24
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.011 0.074 -9999 0 -0.64 10 10
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.022 0.13 -9999 0 -0.84 21 21
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.098 -9999 0 -0.84 10 10
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0.001 0.006 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.01 0.063 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.001 0.019 -9999 0 -10000 0 0
CLOCK 0 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 -0.001 0.007 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.01 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.042 0.01 -9999 0 -10000 0 0
ARNTL 0 0.001 -9999 0 -10000 0 0
TIMELESS 0.041 0.014 -9999 0 -10000 0 0
NPAS2 -0.005 0.06 -9999 0 -0.83 4 4
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.013 0.003 -9999 0 -10000 0 0
CHEK1 -0.008 0.047 -9999 0 -10000 0 0
mol:HEME 0.013 0.003 -9999 0 -10000 0 0
PER1 -0.018 0.12 -9999 0 -0.84 18 18
BMAL/CLOCK/NPAS2 -0.003 0.038 -9999 0 -0.55 4 4
BMAL1/CLOCK 0.046 0.026 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.001 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.001 0.019 -9999 0 -10000 0 0
mol:NADPH 0.013 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.011 0.071 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.016 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.055 -9999 0 -0.84 2 2
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
alpha4/beta1 Integrin -0.002 0.019 -9999 0 -10000 0 0
Insulin-mediated glucose transport

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.53 5 5
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -0.28 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.13 0.15 -9999 0 -0.36 10 10
YWHAZ -0.001 0.016 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.021 0.023 -9999 0 -0.65 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.001 0.016 -9999 0 -0.28 3 3
PRKCI 0 0.01 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.029 -9999 0 -0.84 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.032 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.14 0.16 -9999 0 -0.4 10 10
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
SFN -0.016 0.11 -9999 0 -0.84 13 13
LNPEP -0.004 0.058 -9999 0 -0.84 4 4
YWHAE 0 0 -9999 0 -10000 0 0
IFN-gamma pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.013 0.033 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.006 0.024 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.001 0.003 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.008 0.031 -9999 0 -10000 0 0
CaM/Ca2+ 0.012 0.029 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.03 -9999 0 -10000 0 0
AKT1 -0.005 0.013 -9999 0 -10000 0 0
MAP2K1 0.041 0.037 -9999 0 -10000 0 0
MAP3K11 -0.008 0.021 -9999 0 -10000 0 0
IFNGR1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.1 -9999 0 -0.42 20 20
Rap1/GTP -0.003 0.008 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.013 0.032 -9999 0 -10000 0 0
CEBPB 0.075 0.033 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.011 0.058 -9999 0 -1.3 1 1
STAT1 -0.01 0.031 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.039 0.095 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
STAT1 (dimer)/PIAS1 -0.008 0.027 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.031 -9999 0 -10000 0 0
MAPK3 0.055 0.032 -9999 0 -10000 0 0
STAT1 (dimer) -0.002 0.046 -9999 0 -10000 0 0
MAPK1 0.055 0.032 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0 -9999 0 -10000 0 0
CAMK2D -0.003 0.05 -9999 0 -0.84 3 3
DAPK1 0.069 0.03 -9999 0 -10000 0 0
SMAD7 0.051 0.035 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.006 0.014 -9999 0 -10000 0 0
PI3K 0.01 0.026 -9999 0 -10000 0 0
IFNG -0.039 0.095 -9999 0 -10000 0 0
apoptosis 0.054 0.025 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.008 0.046 -9999 0 -10000 0 0
CAMK2B -0.075 0.23 -9999 0 -0.64 98 98
FRAP1 0.043 0.033 -9999 0 -10000 0 0
PRKCD -0.005 0.014 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.008 0.031 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.065 0.044 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.008 0.029 -9999 0 -10000 0 0
SOCS1 0.001 0.055 -9999 0 -1.5 1 1
mol:GDP -0.006 0.014 -9999 0 -10000 0 0
CASP1 0.05 0.039 -9999 0 -0.36 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.057 0.018 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.007 0.02 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.008 -9999 0 -10000 0 0
CBL -0.009 0.021 -9999 0 -10000 0 0
MAP3K1 0.031 0.037 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.008 0.031 -9999 0 -10000 0 0
PTPN11 -0.01 0.025 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0.006 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.02 -9999 0 -0.56 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.026 -9999 0 -10000 0 0
NFKBIA 0.024 0.036 -9999 0 -0.28 11 11
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0 0 -9999 0 -10000 0 0
REL -0.001 0.029 -9999 0 -0.84 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0 0.008 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.022 0.01 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.031 -9999 0 -0.28 11 11
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.025 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
PI3K 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.032 -9999 0 -0.28 11 11
IKBKB -0.001 0.013 -9999 0 -0.28 2 2
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.01 -9999 0 -0.28 1 1
I kappa B alpha/PIK3R1 -0.004 0.029 -9999 0 -10000 0 0
cell death -0.003 0.024 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.02 -9999 0 -0.56 1 1
LCK -0.019 0.1 -9999 0 -0.84 11 11
BCL3 0 0.01 -9999 0 -0.28 1 1
TCGA08_p53

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.02 0.072 -9999 0 -9999 0 0
TP53 -0.007 0.018 -9999 0 -9999 0 0
Senescence -0.007 0.018 -9999 0 -9999 0 0
Apoptosis -0.007 0.018 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.014 0.037 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Paxillin-dependent events mediated by a4b1

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.034 -9999 0 -0.51 2 2
lamellipodium assembly 0.001 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -0.28 1 1
PI3K 0 0.006 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.012 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.055 -9999 0 -0.84 2 2
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.005 0.042 -9999 0 -0.48 6 6
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.008 0.074 -9999 0 -0.84 6 6
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.002 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -0.28 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.007 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -9999 0 -0.4 1 1
MDM2/SUMO1 0 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.029 -9999 0 -0.84 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.016 -9999 0 -0.47 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.019 -9999 0 -0.28 4 4
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.004 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -9999 0 0
AP2 0 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -9999 0 0
CLTB 0 0.01 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -9999 0 0
CD4 0 0 -9999 0 -9999 0 0
CLTA 0 0 -9999 0 -9999 0 0
mol:GTP 0.002 0 -9999 0 -9999 0 0
ARFGAP1 0.011 0.01 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.004 -9999 0 -9999 0 0
mol:Choline 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0 0 -9999 0 -9999 0 0
DDEF1 0 0 -9999 0 -9999 0 0
ARF1/GDP 0 0.005 -9999 0 -9999 0 0
AP2M1 0 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0 0 -9999 0 -9999 0 0
Rac/GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.005 -9999 0 -9999 0 0
ARFIP2 0 0 -9999 0 -9999 0 0
COPA 0 0 -9999 0 -9999 0 0
RAC1 0 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.025 0.001 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -9999 0 0
GGA3 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -9999 0 0
AP2A1 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.002 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -9999 0 0
CYTH2 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0 0 -9999 0 -9999 0 0
mol:Brefeldin A 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.011 0.01 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0 0 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.01 -9999 0 -9999 0 0
GOSR2 0 0 -9999 0 -9999 0 0
USO1 0 0 -9999 0 -9999 0 0
GBF1 0 0 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -9999 0 0
FBXW11 0 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -9999 0 0
CHUK 0 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB -0.001 0.007 -9999 0 -9999 0 0
NFKB1 0 0 -9999 0 -9999 0 0
MAP3K14 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB -0.001 0.013 -9999 0 -9999 0 0
RELB -0.002 0.021 -9999 0 -9999 0 0
NFKB2 0 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB -0.001 0.011 -9999 0 -9999 0 0
regulation of B cell activation -0.001 0.011 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 840 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.053 0.053 0.044 0.053
47_PPARGC1A -0.28 0 0 0
105_BMP4 -0.84 0 -0.84 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 0
131_RELN/VLDLR 0 -1 -0.51 -0.51
30_TGFB1/TGF beta receptor Type II 0.015 0 0 0
84_STAT5B -0.012 -0.076 -0.16 0.019
84_STAT5A -0.012 -0.076 -0.16 0.019
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/2843240/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle