Prostate Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number 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 40 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
Glucocorticoid receptor regulatory network 28
Signaling mediated by p38-alpha and p38-beta 28
Angiopoietin receptor Tie2-mediated signaling 26
Ephrin A reverse signaling 24
IL23-mediated signaling events 24
Glypican 2 network 23
Endothelins 21
Syndecan-1-mediated signaling events 18
p75(NTR)-mediated signaling 17
Reelin signaling pathway 17
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
Glucocorticoid receptor regulatory network 28 3192 114 -0.54 0.34 1000 -1000 -0.06 -1000
Signaling mediated by p38-alpha and p38-beta 28 1255 44 -0.16 0.027 1000 -1000 -0.035 -1000
Angiopoietin receptor Tie2-mediated signaling 26 2325 88 -0.25 0.051 1000 -1000 -0.064 -1000
Ephrin A reverse signaling 24 171 7 -0.044 0 1000 -1000 -0.01 -1000
IL23-mediated signaling events 24 1475 60 -0.46 0.026 1000 -1000 -0.11 -1000
Glypican 2 network 23 93 4 -0.019 0.001 1000 -1000 0.008 -1000
Endothelins 21 2019 96 -0.16 0.056 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 18 643 34 -0.14 0.027 1000 -1000 -0.04 -1000
p75(NTR)-mediated signaling 17 2147 125 -0.17 0.072 1000 -1000 -0.06 -1000
Reelin signaling pathway 17 954 56 -0.15 0.069 1000 -1000 -0.04 -1000
Aurora B signaling 17 1157 67 -0.13 0.047 1000 -1000 -0.027 -1000
Thromboxane A2 receptor signaling 15 1661 105 -0.12 0.033 1000 -1000 -0.039 -1000
EPO signaling pathway 15 860 55 -0.052 0.027 1000 -1000 -0.036 -1000
EPHB forward signaling 15 1286 85 -0.086 0.099 1000 -1000 -0.057 -1000
Wnt signaling 15 110 7 -0.11 0.022 1000 -1000 -0.018 -1000
Visual signal transduction: Cones 14 532 38 -0.11 0.025 1000 -1000 -0.012 -1000
Noncanonical Wnt signaling pathway 14 368 26 -0.11 0.027 1000 -1000 -0.041 -1000
S1P5 pathway 14 245 17 -0.08 0.069 1000 -1000 -0.015 -1000
Glypican 1 network 13 633 48 -0.1 0.051 1000 -1000 -0.031 -1000
Effects of Botulinum toxin 13 357 26 -0.075 0.04 1000 -1000 -0.007 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 13 1076 78 -0.12 0.086 1000 -1000 -0.046 -1000
IL4-mediated signaling events 12 1093 91 -0.39 0.28 1000 -1000 -0.14 -1000
amb2 Integrin signaling 12 1000 82 -0.16 0.034 1000 -1000 -0.034 -1000
S1P1 pathway 12 449 36 -0.19 0.026 1000 -1000 -0.046 -1000
Neurotrophic factor-mediated Trk receptor signaling 12 1514 120 -0.14 0.08 1000 -1000 -0.039 -1000
RXR and RAR heterodimerization with other nuclear receptor 11 596 52 -0.1 0.066 1000 -1000 -0.041 -1000
Ephrin B reverse signaling 11 540 48 -0.086 0.033 1000 -1000 -0.026 -1000
TCGA08_p53 11 82 7 -0.029 0.026 1000 -1000 -0.004 -1000
Integrins in angiogenesis 11 982 84 -0.087 0.055 1000 -1000 -0.043 -1000
IL6-mediated signaling events 11 882 75 -0.19 0.038 1000 -1000 -0.054 -1000
Ras signaling in the CD4+ TCR pathway 11 194 17 -0.06 0.039 1000 -1000 -0.021 -1000
Signaling events mediated by the Hedgehog family 10 533 52 -0.059 0.04 1000 -1000 -0.032 -1000
HIF-1-alpha transcription factor network 10 812 76 -0.15 0.048 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 10 730 68 -0.18 0.048 1000 -1000 -0.093 -1000
FOXM1 transcription factor network 10 518 51 -0.23 0.026 1000 -1000 -0.13 -1000
S1P4 pathway 10 250 25 -0.08 0.042 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 9 431 46 -0.36 0.031 1000 -1000 -0.11 -1000
BMP receptor signaling 9 736 81 -0.12 0.051 1000 -1000 -0.04 -1000
Calcium signaling in the CD4+ TCR pathway 9 295 31 -0.11 0.026 1000 -1000 -0.049 -1000
LPA receptor mediated events 9 948 102 -0.14 0.043 1000 -1000 -0.068 -1000
ErbB2/ErbB3 signaling events 8 536 65 -0.13 0.038 1000 -1000 -0.047 -1000
IL12-mediated signaling events 8 700 87 -0.15 0.027 1000 -1000 -0.074 -1000
Osteopontin-mediated events 8 338 38 -0.063 0.035 1000 -1000 -0.047 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 8 449 54 -0.15 0.039 1000 -1000 -0.046 -1000
JNK signaling in the CD4+ TCR pathway 8 151 17 -0.071 0.045 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 8 42 5 0.006 0.023 1000 -1000 0.007 -1000
Arf6 signaling events 8 515 62 -0.037 0.034 1000 -1000 -0.038 -1000
Aurora C signaling 8 58 7 -0.052 0.024 1000 -1000 -0.012 -1000
PLK1 signaling events 8 704 85 -0.091 0.041 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 8 764 93 -0.069 0.091 1000 -1000 -0.049 -1000
EGFR-dependent Endothelin signaling events 8 170 21 -0.03 0.038 1000 -1000 -0.038 -1000
Visual signal transduction: Rods 8 454 52 -0.11 0.049 1000 -1000 -0.036 -1000
Nephrin/Neph1 signaling in the kidney podocyte 7 247 34 -0.053 0.039 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 7 433 61 -0.18 0.072 1000 -1000 -0.045 -1000
Fc-epsilon receptor I signaling in mast cells 7 752 97 -0.048 0.042 1000 -1000 -0.05 -1000
IL1-mediated signaling events 7 495 62 -0.084 0.062 1000 -1000 -0.035 -1000
Canonical Wnt signaling pathway 7 378 51 -0.18 0.09 1000 -1000 -0.04 -1000
Regulation of p38-alpha and p38-beta 7 417 54 -0.16 0.059 1000 -1000 -0.042 -1000
Nongenotropic Androgen signaling 7 395 52 -0.088 0.047 1000 -1000 -0.032 -1000
ErbB4 signaling events 6 464 69 -0.13 0.063 1000 -1000 -0.031 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 6 564 85 -0.081 0.036 1000 -1000 -0.043 -1000
Signaling events mediated by PTP1B 6 518 76 -0.18 0.046 1000 -1000 -0.034 -1000
Ceramide signaling pathway 6 496 76 -0.031 0.074 1000 -1000 -0.03 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 247 37 -0.053 0.049 1000 -1000 -0.026 -1000
Signaling events regulated by Ret tyrosine kinase 6 508 82 -0.03 0.038 1000 -1000 -0.051 -1000
Stabilization and expansion of the E-cadherin adherens junction 6 477 74 -0.21 0.055 1000 -1000 -0.061 -1000
BCR signaling pathway 6 619 99 -0.12 0.039 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 6 413 67 -0.14 0.031 1000 -1000 -0.041 -1000
IGF1 pathway 6 382 57 -0.013 0.052 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 6 529 86 -0.13 0.045 1000 -1000 -0.045 -1000
S1P3 pathway 6 259 42 -0.049 0.041 1000 -1000 -0.041 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 201 33 -0.1 0.06 1000 -1000 -0.033 -1000
Class IB PI3K non-lipid kinase events 6 18 3 -0.017 0.017 1000 -1000 -0.01 -1000
Regulation of nuclear SMAD2/3 signaling 5 700 136 -0.22 0.086 1000 -1000 -0.037 -1000
Sphingosine 1-phosphate (S1P) pathway 5 141 28 -0.064 0.052 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 5 381 69 -0.03 0.046 1000 -1000 -0.029 -1000
PDGFR-alpha signaling pathway 5 259 44 -0.13 0.056 1000 -1000 -0.037 -1000
ceramide signaling pathway 5 252 49 -0.002 0.039 1000 -1000 -0.036 -1000
FAS signaling pathway (CD95) 5 275 47 -0.28 0.043 1000 -1000 -0.034 -1000
IL27-mediated signaling events 5 303 51 -0.37 0.12 1000 -1000 -0.055 -1000
TCGA08_retinoblastoma 5 45 8 -0.036 0.032 1000 -1000 -0.001 -1000
Hedgehog signaling events mediated by Gli proteins 4 301 65 -0.33 0.067 1000 -1000 -0.034 -1000
Aurora A signaling 4 255 60 -0.09 0.045 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 4 151 35 -0.072 0.072 1000 -1000 -0.027 -1000
Insulin Pathway 4 322 74 -0.16 0.068 1000 -1000 -0.038 -1000
VEGFR1 specific signals 4 228 56 -0.074 0.032 1000 -1000 -0.046 -1000
Signaling events mediated by PRL 4 168 34 -0.042 0.039 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 3 39 12 -0.028 0.017 1000 -1000 -0.023 -1000
Caspase cascade in apoptosis 3 294 74 -0.039 0.062 1000 -1000 -0.041 -1000
BARD1 signaling events 3 172 57 -0.037 0.057 1000 -1000 -0.034 -1000
Cellular roles of Anthrax toxin 3 135 39 -0.037 0.034 1000 -1000 -0.018 -1000
mTOR signaling pathway 3 176 53 -0.19 0.067 1000 -1000 -0.033 -1000
IFN-gamma pathway 3 262 68 -0.07 0.061 1000 -1000 -0.048 -1000
Nectin adhesion pathway 3 247 63 -0.033 0.066 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class III 3 139 40 -0.098 0.049 1000 -1000 -0.02 -1000
HIF-2-alpha transcription factor network 3 170 43 -0.082 0.042 1000 -1000 -0.068 -1000
Retinoic acid receptors-mediated signaling 3 208 58 -0.066 0.051 1000 -1000 -0.031 -1000
IL2 signaling events mediated by PI3K 3 176 58 -0.045 0.05 1000 -1000 -0.038 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 415 125 -0.048 0.039 1000 -1000 -0.045 -1000
TCGA08_rtk_signaling 3 91 26 -0.02 0.058 1000 -1000 -0.011 -1000
IL2 signaling events mediated by STAT5 3 72 22 -0.023 0.028 1000 -1000 -0.038 -1000
Class I PI3K signaling events 3 223 73 -0.071 0.058 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 2 219 76 -0.042 0.043 1000 -1000 -0.03 -1000
Canonical NF-kappaB pathway 2 87 39 -0.002 0.058 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 2 6 3 0.007 0.024 1000 -1000 -0.013 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 2 203 83 -0.051 0.049 1000 -1000 -0.036 -1000
FoxO family signaling 2 164 64 -0.071 0.065 1000 -1000 -0.056 -1000
Paxillin-dependent events mediated by a4b1 2 106 36 -0.04 0.043 1000 -1000 -0.026 -1000
Regulation of Telomerase 2 284 102 -0.13 0.053 1000 -1000 -0.044 -1000
Rapid glucocorticoid signaling 2 58 20 -0.014 0.036 1000 -1000 -0.005 -1000
PDGFR-beta signaling pathway 2 269 97 -0.14 0.062 1000 -1000 -0.048 -1000
Regulation of Androgen receptor activity 2 194 70 -0.094 0.071 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class II 1 94 75 -0.029 0.065 1000 -1000 -0.025 -1000
Insulin-mediated glucose transport 1 52 32 -0.017 0.048 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 1 108 68 -0.039 0.052 1000 -1000 -0.035 -1000
TRAIL signaling pathway 1 56 48 0 0.042 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 1 29 15 -0.012 0.027 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 1 71 45 -0.002 0.061 1000 -1000 -0.043 -1000
p38 MAPK signaling pathway 1 73 44 -0.01 0.045 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 12 23 0.018 0.053 1000 -1000 -0.021 -1000
Circadian rhythm pathway 0 10 22 -0.008 0.06 1000 -1000 -0.047 -1000
Arf6 downstream pathway 0 26 43 -0.052 0.053 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 0 102 104 -0.05 0.064 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 0 27 31 0 0.033 1000 -1000 -0.017 -1000
E-cadherin signaling in the nascent adherens junction 0 61 76 -0.004 0.059 1000 -1000 -0.049 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 2 27 0 0.06 1000 -1000 -0.031 -1000
Arf6 trafficking events 0 65 71 -0.046 0.051 1000 -1000 -0.027 -1000
E-cadherin signaling in keratinocytes 0 27 43 -0.027 0.046 1000 -1000 -0.032 -1000
E-cadherin signaling events 0 0 5 0.024 0.047 1000 -1000 0.01 -1000
Arf1 pathway 0 34 54 -0.001 0.042 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0 4 13 0 0.068 1000 -1000 0 -1000
Total 949 57880 7203 -13 6.8 131000 -131000 -5 -131000
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.12 0.1 0.31 7 -10000 0 7
SMARCC2 0.002 0.052 -10000 0 -0.16 2 2
SMARCC1 0.002 0.05 -10000 0 -10000 0 0
TBX21 -0.15 0.19 -10000 0 -0.44 36 36
SUMO2 0.032 0.022 -10000 0 -10000 0 0
STAT1 (dimer) 0.022 0.049 -10000 0 -0.25 5 5
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 0.027 0.003 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.16 0.12 0.31 47 -10000 0 47
PRL -0.11 0.14 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/TIF2 0.2 0.26 0.56 48 -10000 0 48
RELA -0.05 0.11 -10000 0 -0.25 20 20
FGG 0.24 0.24 0.49 63 -0.57 2 65
GR beta/TIF2 0.1 0.14 0.31 37 -0.27 2 39
IFNG -0.32 0.33 -10000 0 -0.72 59 59
apoptosis 0.15 0.24 0.5 45 -0.49 1 46
CREB1 -0.031 0.11 -10000 0 -0.3 22 22
histone acetylation -0.11 0.17 0.26 5 -0.35 44 49
BGLAP -0.13 0.17 -10000 0 -0.44 24 24
GR/PKAc 0.14 0.11 0.32 30 -10000 0 30
NF kappa B1 p50/RelA -0.088 0.19 -10000 0 -0.38 40 40
SMARCD1 0.002 0.051 -10000 0 -10000 0 0
MDM2 0.12 0.11 0.25 65 -10000 0 65
GATA3 -0.12 0.22 -10000 0 -0.46 51 51
AKT1 0.022 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.45 7 7
GSK3B 0.031 0.022 -10000 0 -10000 0 0
NR1I3 0.16 0.22 0.49 41 -0.43 1 42
CSN2 0.19 0.19 0.4 67 -10000 0 67
BRG1/BAF155/BAF170/BAF60A -0.008 0.16 -10000 0 -0.34 28 28
NFATC1 0.024 0.01 -10000 0 -10000 0 0
POU2F1 0.023 0.026 -10000 0 -0.3 1 1
CDKN1A -0.016 0.072 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.008 0.016 -10000 0 -10000 0 0
SFN -0.017 0.14 -10000 0 -0.46 16 16
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.13 0.14 0.31 39 -0.21 1 40
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.11 0.29 0.48 35 -0.69 12 47
JUN -0.19 0.2 -10000 0 -0.46 49 49
IL4 -0.14 0.17 -10000 0 -0.51 12 12
CDK5R1 0.009 0.071 -10000 0 -0.23 14 14
PRKACA 0.026 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.19 0.2 19 -0.39 40 59
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.16 0.11 0.32 44 -10000 0 44
cortisol/GR alpha (monomer) 0.34 0.33 0.69 69 -10000 0 69
NCOA2 0.003 0.094 -10000 0 -0.46 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.17 -10000 0 -0.49 24 24
AP-1/NFAT1-c-4 -0.33 0.33 -10000 0 -0.72 61 61
AFP -0.12 0.14 -10000 0 -0.51 5 5
SUV420H1 0.026 0.005 -10000 0 -10000 0 0
IRF1 0.19 0.18 0.44 39 -10000 0 39
TP53 0.034 0.016 -10000 0 -10000 0 0
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.47 0.53 -10000 0 -1.1 61 61
KRT14 -0.48 0.6 -10000 0 -1.2 64 64
TBP 0.03 0.022 -10000 0 -0.23 1 1
CREBBP 0.051 0.14 0.25 41 -0.25 16 57
HDAC1 0.026 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.009 -10000 0 -10000 0 0
AP-1 -0.33 0.33 -10000 0 -0.72 62 62
MAPK14 0.032 0.018 -10000 0 -10000 0 0
MAPK10 0.027 0.054 -10000 0 -0.44 2 2
MAPK11 0.031 0.03 -10000 0 -0.24 1 1
KRT5 -0.54 0.57 -10000 0 -1.1 75 75
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.028 0.007 -10000 0 -10000 0 0
STAT1 0.022 0.049 -10000 0 -0.25 5 5
CGA -0.27 0.36 -10000 0 -0.83 42 42
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.18 0.38 42 -0.29 1 43
MAPK3 0.032 0.02 -10000 0 -10000 0 0
MAPK1 0.031 0.019 -10000 0 -10000 0 0
ICAM1 -0.24 0.28 -10000 0 -0.6 51 51
NFKB1 -0.052 0.11 -10000 0 -0.24 29 29
MAPK8 -0.17 0.19 -10000 0 -0.4 59 59
MAPK9 0.032 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.14 0.24 0.5 44 -0.52 1 45
BAX -0.016 0.07 -10000 0 -10000 0 0
POMC -0.42 0.6 -10000 0 -1.5 39 39
EP300 0.051 0.14 0.26 35 -0.25 16 51
cortisol/GR alpha (dimer)/p53 0.26 0.27 0.6 55 -10000 0 55
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.097 0.21 51 -10000 0 51
SGK1 -0.12 0.52 -10000 0 -1.1 35 35
IL13 -0.4 0.42 -10000 0 -0.95 56 56
IL6 -0.36 0.45 -10000 0 -0.93 57 57
PRKACG 0.019 0.005 -10000 0 -10000 0 0
IL5 -0.34 0.35 -10000 0 -0.81 52 52
IL2 -0.33 0.33 -10000 0 -0.72 59 59
CDK5 0.028 0.012 -10000 0 -10000 0 0
PRKACB 0.025 0.007 -10000 0 -10000 0 0
HSP90AA1 0.027 0.003 -10000 0 -10000 0 0
IL8 -0.28 0.36 -10000 0 -0.76 47 47
CDK5R1/CDK5 0.029 0.055 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.033 0.16 -10000 0 -0.35 21 21
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.27 0.25 0.54 71 -10000 0 71
SMARCA4 0.004 0.049 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.24 0.4 44 -0.37 12 56
NF kappa B1 p50/RelA/Cbp -0.049 0.22 0.34 11 -0.4 28 39
JUN (dimer) -0.19 0.2 -10000 0 -0.46 49 49
YWHAH 0.026 0.005 -10000 0 -10000 0 0
VIPR1 -0.14 0.18 0.32 1 -0.4 41 42
NR3C1 0.22 0.22 0.45 65 -10000 0 65
NR4A1 -0.085 0.22 -10000 0 -0.46 41 41
TIF2/SUV420H1 0.017 0.072 -10000 0 -0.33 7 7
MAPKKK cascade 0.15 0.24 0.5 45 -0.49 1 46
cortisol/GR alpha (dimer)/Src-1 0.3 0.27 0.57 71 -10000 0 71
PBX1 0.025 0.009 -10000 0 -10000 0 0
POU1F1 0.02 0.009 -10000 0 -10000 0 0
SELE -0.35 0.44 -10000 0 -0.9 57 57
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.24 0.4 43 -0.38 12 55
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.27 0.25 0.54 71 -10000 0 71
mol:cortisol 0.2 0.21 0.4 76 -0.18 1 77
MMP1 -0.29 0.47 -10000 0 -1.2 38 38
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.16 0.38 -10000 0 -0.98 29 29
MKNK1 0.027 0.003 -10000 0 -10000 0 0
MAPK14 -0.044 0.14 -10000 0 -0.32 35 35
ATF2/c-Jun -0.039 0.11 -10000 0 -0.38 6 6
MAPK11 -0.049 0.15 -10000 0 -0.32 37 37
MITF -0.055 0.16 -10000 0 -0.37 34 34
MAPKAPK5 -0.051 0.16 -10000 0 -0.36 33 33
KRT8 -0.051 0.16 -10000 0 -0.37 33 33
MAPKAPK3 0.026 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.067 0.22 -10000 0 -0.48 35 35
CEBPB -0.053 0.16 -10000 0 -0.36 34 34
SLC9A1 -0.054 0.16 -10000 0 -0.36 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.053 0.16 -10000 0 -0.36 34 34
p38alpha-beta/MNK1 -0.041 0.18 -10000 0 -0.39 35 35
JUN -0.038 0.11 -10000 0 -0.37 6 6
PPARGC1A -0.15 0.25 -10000 0 -0.44 63 63
USF1 -0.056 0.16 -10000 0 -0.37 34 34
RAB5/GDP/GDI1 -0.034 0.12 -10000 0 -0.27 34 34
NOS2 -0.1 0.28 -10000 0 -0.93 14 14
DDIT3 -0.055 0.16 -10000 0 -0.36 35 35
RAB5A 0.026 0.005 -10000 0 -10000 0 0
HSPB1 -0.049 0.16 0.28 9 -0.3 41 50
p38alpha-beta/HBP1 -0.04 0.17 -10000 0 -0.38 33 33
CREB1 -0.056 0.17 -10000 0 -0.38 35 35
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.057 0.15 -10000 0 -0.35 35 35
RPS6KA4 -0.054 0.16 -10000 0 -0.36 35 35
PLA2G4A -0.061 0.16 -10000 0 -0.36 35 35
GDI1 -0.054 0.16 -10000 0 -0.36 35 35
TP53 -0.085 0.2 -10000 0 -0.47 35 35
RPS6KA5 -0.057 0.17 -10000 0 -0.38 35 35
ESR1 -0.06 0.17 -10000 0 -0.37 37 37
HBP1 0.024 0.009 -10000 0 -10000 0 0
MEF2C -0.067 0.19 -10000 0 -0.41 36 36
MEF2A -0.055 0.16 -10000 0 -0.36 35 35
EIF4EBP1 -0.074 0.2 -10000 0 -0.44 35 35
KRT19 -0.096 0.23 -10000 0 -0.45 44 44
ELK4 -0.057 0.16 -10000 0 -0.36 36 36
ATF6 -0.055 0.16 -10000 0 -0.37 34 34
ATF1 -0.056 0.17 -10000 0 -0.39 35 35
p38alpha-beta/MAPKAPK2 -0.04 0.18 -10000 0 -0.38 35 35
p38alpha-beta/MAPKAPK3 -0.04 0.18 -10000 0 -0.39 34 34
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.16 0.36 -10000 0 -0.81 41 41
NCK1/PAK1/Dok-R -0.096 0.16 -10000 0 -0.4 37 37
NCK1/Dok-R -0.18 0.4 -10000 0 -0.9 41 41
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
mol:beta2-estradiol 0.051 0.11 0.24 41 -10000 0 41
RELA 0.026 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 0.045 0.13 0.27 39 -0.24 7 46
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.16 0.4 -10000 0 -0.88 41 41
FN1 0.025 0.02 -10000 0 -0.23 1 1
PLD2 -0.2 0.42 -10000 0 -0.96 41 41
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GRB14 -0.016 0.099 -10000 0 -0.24 27 27
ELK1 -0.18 0.39 -10000 0 -0.87 41 41
GRB7 0.027 0.002 -10000 0 -10000 0 0
PAK1 0.018 0.063 -10000 0 -0.46 3 3
Tie2/Ang1/alpha5/beta1 Integrin -0.17 0.42 -10000 0 -0.92 41 41
CDKN1A -0.11 0.26 -10000 0 -0.56 39 39
ITGA5 0.017 0.066 -10000 0 -0.4 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.18 0.41 -10000 0 -0.91 41 41
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.28 -10000 0 -0.59 41 41
PLG -0.21 0.42 -10000 0 -0.96 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.34 -10000 0 -0.76 41 41
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
ANGPT2 -0.14 0.26 -10000 0 -0.67 24 24
BMX -0.22 0.44 -10000 0 -1 40 40
ANGPT1 -0.25 0.49 -10000 0 -1.1 41 41
tube development -0.13 0.28 -10000 0 -0.62 41 41
ANGPT4 0.019 0.043 -10000 0 -0.35 2 2
response to hypoxia -0.014 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.21 0.45 -10000 0 -1 41 41
alpha5/beta1 Integrin 0.031 0.05 -10000 0 -0.28 4 4
FGF2 0.015 0.072 -10000 0 -0.45 4 4
STAT5A (dimer) -0.14 0.33 -10000 0 -0.72 39 39
mol:L-citrulline -0.11 0.28 -10000 0 -0.59 41 41
AGTR1 -0.037 0.11 -10000 0 -0.24 41 41
MAPK14 -0.19 0.42 -10000 0 -0.95 41 41
Tie2/SHP2 -0.11 0.28 -10000 0 -0.89 17 17
TEK -0.1 0.31 -10000 0 -0.97 17 17
RPS6KB1 -0.16 0.36 -10000 0 -0.79 41 41
Angiotensin II/AT1 -0.022 0.076 -10000 0 -0.16 41 41
Tie2/Ang1/GRB2 -0.2 0.44 -10000 0 -0.98 41 41
MAPK3 -0.19 0.39 -10000 0 -0.89 41 41
MAPK1 -0.19 0.39 -10000 0 -0.89 41 41
Tie2/Ang1/GRB7 -0.2 0.44 -10000 0 -0.98 41 41
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.2 0.42 -10000 0 -0.95 41 41
PI3K -0.19 0.41 -10000 0 -0.92 41 41
FES -0.2 0.43 -10000 0 -0.94 42 42
Crk/Dok-R -0.18 0.41 -10000 0 -0.91 41 41
Tie2/Ang1/ABIN2 -0.2 0.44 -10000 0 -0.98 41 41
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.14 0.33 -10000 0 -0.73 41 41
STAT5A 0.026 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.36 0.45 1 -0.75 41 42
Tie2/Ang2 -0.18 0.37 -10000 0 -0.84 39 39
Tie2/Ang1 -0.21 0.46 -10000 0 -1 41 41
FOXO1 -0.14 0.33 -10000 0 -0.73 41 41
ELF1 0.016 0.026 -10000 0 -10000 0 0
ELF2 -0.19 0.42 -10000 0 -0.93 41 41
mol:Choline -0.19 0.41 -10000 0 -0.92 41 41
cell migration -0.051 0.097 -10000 0 -0.22 40 40
FYN -0.15 0.32 -10000 0 -0.71 40 40
DOK2 0.014 0.03 -10000 0 -0.23 2 2
negative regulation of cell cycle -0.1 0.24 -10000 0 -0.51 39 39
ETS1 -0.034 0.12 -10000 0 -0.25 41 41
PXN -0.1 0.31 0.41 3 -0.63 41 44
ITGB1 0.026 0.005 -10000 0 -10000 0 0
NOS3 -0.13 0.31 -10000 0 -0.68 40 40
RAC1 0.024 0.008 -10000 0 -10000 0 0
TNF -0.061 0.15 -10000 0 -0.29 52 52
MAPKKK cascade -0.19 0.41 -10000 0 -0.92 41 41
RASA1 0.026 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.19 0.44 -10000 0 -0.97 41 41
NCK1 0.024 0.008 -10000 0 -10000 0 0
vasculogenesis -0.093 0.25 -10000 0 -0.53 41 41
mol:Phosphatidic acid -0.19 0.41 -10000 0 -0.92 41 41
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.28 -10000 0 -0.59 41 41
Rac1/GTP -0.14 0.33 -10000 0 -0.72 41 41
MMP2 -0.2 0.43 -10000 0 -0.96 41 41
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.031 0.14 -9999 0 -0.3 33 33
EFNA5 -0.011 0.13 -9999 0 -0.46 13 13
FYN -0.041 0.12 -9999 0 -0.28 32 32
neuron projection morphogenesis -0.031 0.14 -9999 0 -0.3 33 33
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.031 0.14 -9999 0 -0.31 33 33
EPHA5 -0.044 0.17 -9999 0 -0.43 27 27
IL23-mediated signaling events

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.35 0.52 -9999 0 -1.2 38 38
IL23A -0.36 0.52 -9999 0 -1.2 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.51 -9999 0 -1.1 40 40
positive regulation of T cell mediated cytotoxicity -0.38 0.56 -9999 0 -1.2 42 42
ITGA3 -0.33 0.49 -9999 0 -1.2 35 35
IL17F -0.22 0.32 -9999 0 -0.72 36 36
IL12B -0.028 0.077 -9999 0 -0.25 13 13
STAT1 (dimer) -0.36 0.54 -9999 0 -1.2 41 41
CD4 -0.32 0.47 -9999 0 -1.1 37 37
IL23 -0.34 0.51 -9999 0 -1.2 36 36
IL23R -0.06 0.17 -9999 0 -0.86 6 6
IL1B -0.38 0.56 -9999 0 -1.3 37 37
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.32 0.47 -9999 0 -1.1 37 37
TYK2 -0.004 0.037 -9999 0 -10000 0 0
STAT4 0.005 0.09 -9999 0 -0.34 10 10
STAT3 0.026 0.005 -9999 0 -10000 0 0
IL18RAP -0.007 0.12 -9999 0 -0.41 14 14
IL12RB1 -0.013 0.06 -9999 0 -0.26 6 6
PIK3CA 0.023 0.021 -9999 0 -0.23 1 1
IL12Rbeta1/TYK2 -0.007 0.059 -9999 0 -0.2 4 4
IL23R/JAK2 -0.062 0.17 -9999 0 -0.82 5 5
positive regulation of chronic inflammatory response -0.38 0.56 -9999 0 -1.2 42 42
natural killer cell activation 0.005 0.008 -9999 0 -10000 0 0
JAK2 -0.007 0.044 -9999 0 -10000 0 0
PIK3R1 0.025 0.007 -9999 0 -10000 0 0
NFKB1 0.025 0.004 -9999 0 -10000 0 0
RELA 0.025 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.32 0.48 -9999 0 -1.1 36 36
ALOX12B -0.34 0.5 -9999 0 -1.1 40 40
CXCL1 -0.46 0.61 -9999 0 -1.3 57 57
T cell proliferation -0.38 0.56 -9999 0 -1.2 42 42
NFKBIA 0.025 0.005 -9999 0 -10000 0 0
IL17A -0.17 0.25 -9999 0 -0.57 29 29
PI3K -0.34 0.51 -9999 0 -1.2 38 38
IFNG -0.01 0.029 -9999 0 -0.1 4 4
STAT3 (dimer) -0.32 0.48 -9999 0 -1.1 37 37
IL18R1 0.018 0.065 -9999 0 -0.4 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 -0.21 0.32 -9999 0 -0.72 36 36
IL18/IL18R 0.014 0.12 -9999 0 -0.31 18 18
macrophage activation -0.017 0.02 -9999 0 -0.044 34 34
TNF -0.36 0.53 -9999 0 -1.3 36 36
STAT3/STAT4 -0.35 0.52 -9999 0 -1.1 42 42
STAT4 (dimer) -0.36 0.55 -9999 0 -1.2 42 42
IL18 0.008 0.089 -9999 0 -0.42 7 7
IL19 -0.33 0.48 -9999 0 -1.1 38 38
STAT5A (dimer) -0.36 0.54 -9999 0 -1.2 42 42
STAT1 0.019 0.043 -9999 0 -0.23 5 5
SOCS3 -0.047 0.17 -9999 0 -0.43 28 28
CXCL9 -0.34 0.47 -9999 0 -1.1 39 39
MPO -0.39 0.54 -9999 0 -1.1 50 50
positive regulation of humoral immune response -0.38 0.56 -9999 0 -1.2 42 42
IL23/IL23R/JAK2/TYK2 -0.4 0.61 -9999 0 -1.3 41 41
IL6 -0.44 0.6 -9999 0 -1.3 54 54
STAT5A 0.026 0.005 -9999 0 -10000 0 0
IL2 0.02 0.017 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.008 -9999 0 -10000 0 0
CD3E -0.32 0.48 -9999 0 -1.1 36 36
keratinocyte proliferation -0.38 0.56 -9999 0 -1.2 42 42
NOS2 -0.36 0.52 -9999 0 -1.2 40 40
Glypican 2 network

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
MDK 0.024 0.028 -9999 0 -0.23 2 2
GPC2 -0.019 0.095 -9999 0 -0.23 29 29
GPC2/Midkine 0.001 0.074 -9999 0 -0.16 31 31
neuron projection morphogenesis 0.001 0.074 -9999 0 -0.16 31 31
Endothelins

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
AKT1 0.016 0.16 0.25 26 -0.32 18 44
PTK2B 0.018 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.4 -10000 0 -0.93 34 34
EDN1 0.022 0.14 0.21 28 -0.35 14 42
EDN3 -0.14 0.23 -10000 0 -0.46 61 61
EDN2 -0.013 0.13 -10000 0 -0.39 17 17
HRAS/GDP -0.033 0.19 0.3 2 -0.52 14 16
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.13 0.22 1 -0.39 12 13
ADCY4 -0.008 0.16 0.3 3 -0.43 14 17
ADCY5 -0.025 0.2 0.34 2 -0.5 19 21
ADCY6 -0.006 0.16 0.3 3 -0.46 12 15
ADCY7 -0.006 0.16 0.3 3 -0.48 11 14
ADCY1 -0.018 0.16 0.3 3 -0.41 14 17
ADCY2 -0.009 0.16 0.3 3 -0.45 12 15
ADCY3 -0.007 0.16 0.3 3 -0.46 12 15
ADCY8 -0.015 0.15 0.22 1 -0.46 11 12
ADCY9 -0.005 0.16 0.3 3 -0.46 12 15
arachidonic acid secretion -0.083 0.26 0.33 4 -0.52 33 37
ETB receptor/Endothelin-1/Gq/GTP -0.023 0.13 -10000 0 -0.34 21 21
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
HRAS 0.026 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.054 0.17 0.35 26 -0.32 15 41
ETA receptor/Endothelin-1/Gs/GTP 0.028 0.2 0.33 24 -0.41 16 40
mol:GTP -0.003 0.008 -10000 0 -10000 0 0
COL3A1 0.017 0.16 0.25 26 -0.36 12 38
EDNRB 0 0.11 -10000 0 -0.46 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.003 0.18 0.25 24 -0.47 15 39
CYSLTR1 0.009 0.18 0.25 26 -0.46 14 40
SLC9A1 0.02 0.099 0.18 27 -0.21 14 41
mol:GDP -0.044 0.2 0.27 4 -0.54 16 20
SLC9A3 -0.13 0.38 -10000 0 -0.84 31 31
RAF1 -0.054 0.2 0.3 5 -0.45 25 30
JUN -0.049 0.24 -10000 0 -0.73 9 9
JAK2 0.017 0.16 0.25 26 -0.34 15 41
mol:IP3 -0.018 0.13 0.2 1 -0.39 13 14
ETA receptor/Endothelin-1 0.056 0.22 0.4 29 -0.36 21 50
PLCB1 0.022 0.037 -10000 0 -0.46 1 1
PLCB2 0.021 0.023 -10000 0 -0.23 1 1
ETA receptor/Endothelin-3 -0.086 0.21 -10000 0 -0.35 61 61
FOS -0.11 0.34 0.36 3 -0.9 25 28
Gai/GDP -0.15 0.35 -10000 0 -0.74 41 41
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.016 0.18 0.31 4 -0.51 13 17
BCAR1 0.023 0.01 -10000 0 -10000 0 0
PRKCB1 -0.02 0.14 0.25 2 -0.38 13 15
GNAQ 0.017 0.021 -10000 0 -10000 0 0
GNAZ -0.012 0.13 -10000 0 -0.46 14 14
GNAL -0.014 0.13 -10000 0 -0.46 14 14
Gs family/GDP -0.052 0.2 0.29 2 -0.52 20 22
ETA receptor/Endothelin-1/Gq/GTP -0.006 0.15 0.2 18 -0.38 16 34
MAPK14 -0.023 0.12 -10000 0 -0.33 15 15
TRPC6 -0.15 0.44 -10000 0 -1 34 34
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.02 0.12 -10000 0 -0.32 18 18
ETB receptor/Endothelin-2 -0.01 0.12 -10000 0 -0.3 23 23
ETB receptor/Endothelin-3 -0.1 0.19 -10000 0 -0.35 61 61
ETB receptor/Endothelin-1 0.012 0.14 -10000 0 -0.34 17 17
MAPK3 -0.099 0.3 0.37 3 -0.74 27 30
MAPK1 -0.1 0.31 0.36 3 -0.75 27 30
Rac1/GDP -0.028 0.19 0.28 3 -0.51 14 17
cAMP biosynthetic process 0 0.18 0.28 7 -0.49 14 21
MAPK8 -0.065 0.29 0.32 1 -0.6 30 31
SRC 0.026 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.054 0.17 -10000 0 -0.45 22 22
p130Cas/CRK/Src/PYK2 -0.1 0.27 0.33 2 -0.56 36 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.028 0.19 0.3 2 -0.53 13 15
COL1A2 0.01 0.16 0.26 19 -0.43 12 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.008 0.14 -10000 0 -0.34 19 19
mol:DAG -0.018 0.13 0.2 1 -0.39 13 14
MAP2K2 -0.079 0.25 0.31 4 -0.56 30 34
MAP2K1 -0.072 0.24 0.35 4 -0.53 30 34
EDNRA 0.027 0.14 0.22 21 -0.5 8 29
positive regulation of muscle contraction 0.024 0.14 0.22 33 -0.3 15 48
Gq family/GDP -0.038 0.2 0.36 1 -0.55 14 15
HRAS/GTP -0.043 0.18 0.27 2 -0.46 17 19
PRKCH -0.021 0.14 0.3 1 -0.4 11 12
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.024 0.15 0.27 2 -0.44 12 14
PRKCB -0.052 0.18 0.22 2 -0.44 24 26
PRKCE -0.018 0.14 0.26 2 -0.4 11 13
PRKCD -0.018 0.14 0.26 2 -0.41 10 12
PRKCG -0.026 0.14 0.3 1 -0.4 13 14
regulation of vascular smooth muscle contraction -0.14 0.39 0.4 2 -1 25 27
PRKCQ -0.03 0.15 0.27 2 -0.43 15 17
PLA2G4A -0.095 0.29 0.36 3 -0.58 32 35
GNA14 0.017 0.021 -10000 0 -10000 0 0
GNA15 -0.006 0.11 -10000 0 -0.46 9 9
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA11 0.016 0.041 -10000 0 -0.46 1 1
Rac1/GTP 0.054 0.17 0.35 26 -0.32 15 41
MMP1 -0.16 0.33 0.45 3 -0.81 34 37
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.003 -10000 0 -10000 0 0
CCL5 0.017 0.061 -10000 0 -0.32 5 5
SDCBP 0.022 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -10000 0 -0.43 23 23
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.097 0.16 0.2 1 -0.42 22 23
Syndecan-1/Syntenin -0.088 0.16 0.2 1 -0.42 21 22
MAPK3 -0.091 0.15 0.18 1 -0.46 15 16
HGF/MET -0.002 0.11 -10000 0 -0.26 22 22
TGFB1/TGF beta receptor Type II 0.027 0.003 -10000 0 -10000 0 0
BSG 0.025 0.02 -10000 0 -0.23 1 1
keratinocyte migration -0.096 0.15 0.2 1 -0.41 22 23
Syndecan-1/RANTES -0.1 0.16 0.2 1 -0.42 23 24
Syndecan-1/CD147 -0.092 0.16 -10000 0 -0.41 23 23
Syndecan-1/Syntenin/PIP2 -0.085 0.15 -10000 0 -0.4 21 21
LAMA5 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.084 0.15 -10000 0 -0.39 21 21
MMP7 -0.053 0.16 -10000 0 -0.32 39 39
HGF 0.004 0.078 -10000 0 -0.27 12 12
Syndecan-1/CASK -0.1 0.15 -10000 0 -0.35 32 32
Syndecan-1/HGF/MET -0.11 0.18 -10000 0 -0.43 28 28
regulation of cell adhesion -0.091 0.14 -10000 0 -0.48 13 13
HPSE 0 0.1 -10000 0 -0.4 11 11
positive regulation of cell migration -0.1 0.16 -10000 0 -0.43 23 23
SDC1 -0.1 0.16 -10000 0 -0.38 32 32
Syndecan-1/Collagen -0.1 0.16 -10000 0 -0.43 23 23
PPIB 0.025 0.02 -10000 0 -0.23 1 1
MET -0.006 0.12 -10000 0 -0.46 11 11
PRKACA 0.026 0.004 -10000 0 -10000 0 0
MMP9 -0.14 0.13 -10000 0 -0.24 108 108
MAPK1 -0.092 0.15 0.18 1 -0.48 14 15
homophilic cell adhesion -0.1 0.16 0.21 1 -0.42 23 24
MMP1 -0.086 0.19 -10000 0 -0.39 47 47
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.038 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.03 0.043 -10000 0 -0.18 6 6
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.021 0.12 -10000 0 -0.24 27 27
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.2 -10000 0 -0.32 79 79
NT-4/5 (dimer)/p75(NTR) -0.1 0.2 -10000 0 -0.38 60 60
IKBKB 0.02 0.012 -10000 0 -10000 0 0
AKT1 -0.012 0.11 0.18 14 -0.24 25 39
IKBKG 0.027 0 -10000 0 -10000 0 0
BDNF -0.086 0.2 -10000 0 -0.46 41 41
MGDIs/NGR/p75(NTR)/LINGO1 -0.001 0.1 -10000 0 -0.29 13 13
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.049 0.16 -10000 0 -0.3 50 50
LINGO1 -0.015 0.095 -10000 0 -0.23 28 28
Sortilin/TRAF6/NRIF 0.032 0.014 -10000 0 -10000 0 0
proBDNF (dimer) -0.086 0.2 -10000 0 -0.46 41 41
NTRK1 -0.002 0.1 -10000 0 -0.4 11 11
RTN4R 0.026 0.005 -10000 0 -10000 0 0
neuron apoptosis -0.073 0.16 0.63 1 -0.39 20 21
IRAK1 0.027 0 -10000 0 -10000 0 0
SHC1 -0.028 0.11 -10000 0 -0.29 25 25
ARHGDIA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.026 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.013 0.12 -10000 0 -0.26 26 26
MAGEH1 0.022 0.034 -10000 0 -0.23 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.011 0.12 -10000 0 -0.26 28 28
Mammalian IAPs/DIABLO 0.062 0.027 -10000 0 -10000 0 0
proNGF (dimer) -0.016 0.14 -10000 0 -0.46 15 15
MAGED1 0.025 0.02 -10000 0 -0.23 1 1
APP 0.023 0.037 -10000 0 -0.46 1 1
NT-4/5 (dimer) -0.14 0.23 -10000 0 -0.46 59 59
ZNF274 0.027 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.007 0.1 -10000 0 -0.24 27 27
NGF -0.016 0.14 -10000 0 -0.46 15 15
cell cycle arrest 0.004 0.12 0.3 7 -0.22 25 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.01 0.09 -10000 0 -0.23 23 23
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.076 0.18 -10000 0 -0.32 59 59
NCSTN 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.003 0.12 -10000 0 -0.28 27 27
PSENEN 0.027 0.002 -10000 0 -10000 0 0
mol:ceramide -0.027 0.1 0.18 2 -0.25 27 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.006 0.074 -10000 0 -0.37 1 1
p75(NTR)/beta APP 0.009 0.1 -10000 0 -0.35 13 13
BEX1 -0.17 0.24 -10000 0 -0.45 72 72
mol:GDP -0.039 0.11 -10000 0 -0.28 27 27
NGF (dimer) -0.029 0.13 -10000 0 -0.27 29 29
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.1 -10000 0 -0.27 13 13
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
RAC1/GTP -0.004 0.1 -10000 0 -0.24 27 27
MYD88 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.003 0.12 -10000 0 -0.28 27 27
RHOB 0.01 0.088 -10000 0 -0.46 6 6
RHOA 0.026 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.034 -10000 0 -0.16 5 5
NT3 (dimer) -0.019 0.14 -10000 0 -0.46 16 16
TP53 -0.071 0.11 -10000 0 -0.25 40 40
PRDM4 -0.026 0.1 0.18 2 -0.26 27 29
BDNF (dimer) -0.1 0.18 -10000 0 -0.32 61 61
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
SORT1 0.026 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.016 0.11 -10000 0 -0.24 27 27
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.013 0.12 -10000 0 -0.26 27 27
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
MAPK10 -0.062 0.16 0.6 2 -0.37 22 24
DIABLO 0.026 0.006 -10000 0 -10000 0 0
SMPD2 -0.027 0.1 0.18 2 -0.26 27 29
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.001 0.12 -10000 0 -0.28 27 27
PSEN1 0.027 0.003 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.023 0.14 -10000 0 -0.35 27 27
MAPK8 -0.061 0.16 0.6 2 -0.36 22 24
MAPK9 -0.059 0.16 0.6 2 -0.36 22 24
APAF1 0.026 0.006 -10000 0 -10000 0 0
NTF3 -0.019 0.14 -10000 0 -0.46 16 16
NTF4 -0.14 0.23 -10000 0 -0.46 59 59
NDN 0.024 0.037 -10000 0 -0.46 1 1
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.01 0.13 -10000 0 -0.26 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.065 0.018 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.003 0.12 -10000 0 -0.28 27 27
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.021 0.15 -10000 0 -0.26 49 49
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.032 0.16 -10000 0 -0.27 50 50
PRKACB 0.025 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.043 0.15 -10000 0 -0.33 39 39
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.028 -10000 0 -0.23 2 2
BIRC2 0.026 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.007 0.12 0.3 3 -0.27 13 16
BAD -0.057 0.17 0.55 3 -0.36 22 25
RIPK2 0.022 0.011 -10000 0 -10000 0 0
NGFR -0.01 0.13 -10000 0 -0.46 13 13
CYCS -0.025 0.097 0.18 2 -0.25 26 28
ADAM17 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.008 0.11 -10000 0 -0.26 23 23
BCL2L11 -0.058 0.16 0.5 3 -0.36 22 25
BDNF (dimer)/p75(NTR) -0.073 0.18 -10000 0 -0.35 50 50
PI3K 0.007 0.12 -10000 0 -0.26 26 26
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.013 0.12 -10000 0 -0.26 27 27
NDNL2 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.009 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.021 0.14 -10000 0 -0.34 27 27
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.014 0.12 -10000 0 -0.26 26 26
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.003 -10000 0 -10000 0 0
PLG 0.011 0.05 -10000 0 -0.23 7 7
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.081 0.16 -10000 0 -0.3 56 56
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.027 0.002 -10000 0 -10000 0 0
CASP3 -0.051 0.16 0.51 3 -0.34 22 25
E2F1 0.019 0.043 -10000 0 -0.23 5 5
CASP9 0.027 0.003 -10000 0 -10000 0 0
IKK complex 0.003 0.12 -10000 0 -0.3 14 14
NGF (dimer)/TRKA -0.016 0.12 -10000 0 -0.3 26 26
MMP7 -0.053 0.16 -10000 0 -0.32 39 39
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.12 -10000 0 -0.25 27 27
MMP3 -0.038 0.15 -10000 0 -0.36 28 28
APAF-1/Caspase 9 -0.018 0.083 -10000 0 -0.33 2 2
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.022 0.051 -10000 0 -10000 0 0
VLDLR 0.024 0.02 -10000 0 -0.23 1 1
CRKL 0.026 0.005 -10000 0 -10000 0 0
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.024 0.009 -10000 0 -10000 0 0
ITGA3 0.021 0.051 -10000 0 -0.46 2 2
RELN/VLDLR/Fyn 0.017 0.066 -10000 0 -0.28 1 1
MAPK8IP1/MKK7/MAP3K11/JNK1 0.069 0.028 -10000 0 -10000 0 0
AKT1 -0.07 0.12 -10000 0 -0.23 55 55
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
DAB1 -0.15 0.23 -10000 0 -0.45 66 66
RELN/LRP8/DAB1 -0.078 0.14 -10000 0 -0.26 58 58
LRPAP1/LRP8 0.035 0.025 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.066 0.14 -10000 0 -0.25 57 57
DAB1/alpha3/beta1 Integrin -0.061 0.13 -10000 0 -0.32 8 8
long-term memory -0.095 0.17 -10000 0 -0.28 67 67
DAB1/LIS1 -0.055 0.14 -10000 0 -0.25 44 44
DAB1/CRLK/C3G -0.057 0.13 -10000 0 -0.24 48 48
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
DAB1/NCK2 -0.055 0.14 -10000 0 -0.24 49 49
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.049 0.17 -10000 0 -0.44 28 28
CDK5R1 0.006 0.07 -10000 0 -0.23 14 14
RELN -0.015 0.096 -10000 0 -0.24 26 26
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.019 0.067 -10000 0 -0.28 1 1
GRIN2A/RELN/LRP8/DAB1/Fyn -0.098 0.18 -10000 0 -0.29 68 68
MAPK8 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.076 0.14 -10000 0 -0.26 56 56
ITGB1 0.026 0.005 -10000 0 -10000 0 0
MAP1B -0.088 0.14 0.17 1 -0.27 56 57
RELN/LRP8 0.022 0.066 -10000 0 -0.28 1 1
GRIN2B/RELN/LRP8/DAB1/Fyn -0.062 0.14 -10000 0 -0.25 55 55
PI3K 0.033 0.021 -10000 0 -0.16 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.04 -10000 0 -0.33 2 2
RAP1A -0.07 0.13 0.38 4 -0.3 6 10
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.038 0.01 -10000 0 -10000 0 0
GRIN2B 0.016 0.02 -10000 0 -0.23 1 1
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation -0.052 0.11 -10000 0 -0.27 10 10
neuron adhesion -0.069 0.13 0.37 4 -0.3 7 11
LRP8 0.022 0.034 -10000 0 -0.23 3 3
GSK3B -0.068 0.11 -10000 0 -0.28 13 13
RELN/VLDLR/DAB1/Fyn -0.064 0.14 -10000 0 -0.25 55 55
MAP3K11 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.072 0.12 -10000 0 -0.24 56 56
CDK5 0.024 0.008 -10000 0 -10000 0 0
MAPT 0.008 0.072 0.89 1 -10000 0 1
neuron migration -0.074 0.14 0.29 5 -0.31 12 17
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.052 0.11 -10000 0 -0.27 10 10
RELN/VLDLR 0.032 0.067 -10000 0 -0.25 1 1
Aurora B signaling

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
Condensin I complex -0.029 0.084 -10000 0 -0.28 9 9
STMN1 -0.037 0.08 -10000 0 -0.2 8 8
Aurora B/RasGAP/Survivin -0.036 0.13 -10000 0 -0.24 42 42
Chromosomal passenger complex/Cul3 protein complex -0.015 0.07 -10000 0 -0.24 10 10
BIRC5 -0.054 0.12 -10000 0 -0.24 53 53
DES -0.13 0.3 -10000 0 -0.66 42 42
Aurora C/Aurora B/INCENP 0.001 0.077 -10000 0 -0.18 5 5
Aurora B/TACC1 -0.01 0.065 -10000 0 -0.12 33 33
Aurora B/PP2A -0.019 0.09 -10000 0 -0.16 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0 0.022 -10000 0 -0.12 4 4
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 -0.031 0.08 0.18 2 -0.2 6 8
Cul3 protein complex 0.047 0.045 -10000 0 -0.28 3 3
KIF2C -0.01 0.043 -10000 0 -0.2 2 2
PEBP1 0.024 0.007 -10000 0 -10000 0 0
KIF20A -0.091 0.13 -10000 0 -0.23 79 79
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.018 0.088 -10000 0 -0.16 45 45
SEPT1 0.023 0.028 -10000 0 -0.23 2 2
SMC2 0.026 0.006 -10000 0 -10000 0 0
SMC4 0.023 0.021 -10000 0 -0.23 1 1
NSUN2/NPM1/Nucleolin -0.032 0.16 -10000 0 -0.52 16 16
PSMA3 0.027 0.002 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.01 0.046 -10000 0 -0.23 4 4
AURKB -0.051 0.12 -10000 0 -0.24 51 51
AURKC 0.024 0.037 -10000 0 -0.46 1 1
CDCA8 -0.007 0.088 -10000 0 -0.24 22 22
cytokinesis -0.038 0.12 -10000 0 -0.49 7 7
Aurora B/Septin1 -0.021 0.13 -10000 0 -0.45 8 8
AURKA 0.013 0.058 -10000 0 -0.24 9 9
INCENP 0.023 0.011 -10000 0 -10000 0 0
KLHL13 0.016 0.072 -10000 0 -0.46 4 4
BUB1 -0.042 0.12 -10000 0 -0.23 46 46
hSgo1/Aurora B/Survivin -0.062 0.15 -10000 0 -0.29 47 47
EVI5 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.11 -10000 0 -0.33 8 8
SGOL1 -0.045 0.12 -10000 0 -0.23 48 48
CENPA -0.027 0.084 0.17 1 -0.26 12 13
NCAPG -0.079 0.13 -10000 0 -0.23 71 71
Aurora B/HC8 Proteasome -0.019 0.09 -10000 0 -0.16 50 50
NCAPD2 0.025 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.017 0.087 -10000 0 -0.16 47 47
RHOA 0.026 0.005 -10000 0 -10000 0 0
NCAPH -0.061 0.12 -10000 0 -0.23 59 59
NPM1 -0.025 0.12 0.24 1 -0.35 16 17
RASA1 0.026 0.006 -10000 0 -10000 0 0
KLHL9 0.026 0.005 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.019 0.089 -10000 0 -0.16 50 50
PPP1CC 0.025 0.007 -10000 0 -10000 0 0
Centraspindlin -0.023 0.12 -10000 0 -0.34 11 11
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
NSUN2 -0.023 0.099 -10000 0 -0.31 16 16
MYLK -0.062 0.14 -10000 0 -0.34 31 31
KIF23 0.007 0.069 -10000 0 -0.24 13 13
VIM -0.036 0.077 -10000 0 -0.16 36 36
RACGAP1 0.019 0.045 -10000 0 -0.24 5 5
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.022 0.097 -10000 0 -0.31 16 16
Chromosomal passenger complex -0.035 0.09 0.17 1 -0.28 11 12
Chromosomal passenger complex/EVI5 -0.016 0.14 -10000 0 -0.24 42 42
TACC1 0.019 0.012 -10000 0 -10000 0 0
PPP2R5D 0.027 0.002 -10000 0 -10000 0 0
CUL3 0.027 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.013 0.054 -10000 0 -0.23 8 8
GNB1/GNG2 -0.052 0.074 -10000 0 -0.18 37 37
AKT1 -0.021 0.1 0.24 5 -0.22 8 13
EGF -0.023 0.11 -10000 0 -0.25 31 31
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.005 0.084 0.3 4 -0.29 2 6
mol:Ca2+ -0.05 0.14 0.31 3 -0.29 36 39
LYN -0.008 0.066 0.26 2 -0.29 2 4
RhoA/GTP -0.023 0.059 -10000 0 -0.13 30 30
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.057 0.16 0.3 3 -0.33 34 37
GNG2 0.027 0.002 -10000 0 -10000 0 0
ARRB2 0.024 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.42 13 13
G beta5/gamma2 -0.06 0.1 -10000 0 -0.24 37 37
PRKCH -0.062 0.16 0.29 3 -0.34 35 38
DNM1 0.026 0.006 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.009 0.018 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.004 0.12 -10000 0 -0.46 11 11
G12 family/GTP -0.061 0.13 -10000 0 -0.3 31 31
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
ADRBK2 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0.03 0.1 0.31 8 -0.22 2 10
mol:NADP 0.024 0.008 -10000 0 -10000 0 0
RAB11A 0.026 0.005 -10000 0 -10000 0 0
PRKG1 -0.059 0.18 -10000 0 -0.46 31 31
mol:IP3 -0.065 0.17 0.33 3 -0.36 36 39
cell morphogenesis 0.032 0.011 -10000 0 -10000 0 0
PLCB2 -0.093 0.22 0.37 2 -0.49 35 37
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.033 0.085 0.27 1 -0.24 9 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.011 0.078 0.28 2 -0.37 2 4
RHOA 0.026 0.005 -10000 0 -10000 0 0
PTGIR -0.001 0.087 -10000 0 -0.26 17 17
PRKCB1 -0.065 0.17 0.3 3 -0.36 36 39
GNAQ 0.026 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.024 0.008 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.098 0.23 0.35 3 -0.51 36 39
LCK -0.008 0.082 0.32 3 -0.29 2 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0 0.077 -10000 0 -0.22 15 15
TXA2-R family/G12 family/GDP/G beta/gamma 0.016 0.051 -10000 0 -0.4 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.002 0.078 -10000 0 -0.22 14 14
MAPK14 -0.035 0.11 0.23 4 -0.22 33 37
TGM2/GTP -0.077 0.19 0.36 2 -0.41 35 37
MAPK11 -0.035 0.11 0.26 4 -0.22 33 37
ARHGEF1 -0.034 0.079 0.18 1 -0.18 30 31
GNAI2 0.026 0.005 -10000 0 -10000 0 0
JNK cascade -0.069 0.18 0.32 3 -0.38 36 39
RAB11/GDP 0.026 0.005 -10000 0 -10000 0 0
ICAM1 -0.048 0.13 0.27 3 -0.28 36 39
cAMP biosynthetic process -0.065 0.16 0.32 3 -0.34 36 39
Gq family/GTP/EBP50 0.012 0.071 0.24 5 -0.23 10 15
actin cytoskeleton reorganization 0.032 0.011 -10000 0 -10000 0 0
SRC -0.008 0.074 0.28 3 -0.29 2 5
GNB5 0.024 0.037 -10000 0 -0.46 1 1
GNB1 0.027 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.083 0.26 4 -0.24 4 8
VCAM1 -0.051 0.14 0.28 3 -0.29 36 39
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.42 13 13
platelet activation -0.046 0.15 0.32 4 -0.29 36 40
PGI2/IP 0.001 0.06 -10000 0 -0.17 17 17
PRKACA -0.007 0.07 -10000 0 -0.24 13 13
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.36 12 12
TXA2/TP beta/beta Arrestin2 0.003 0.039 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.021 0.078 -10000 0 -0.24 18 18
mol:DAG -0.073 0.18 0.33 3 -0.4 36 39
EGFR 0.008 0.088 -10000 0 -0.46 6 6
TXA2/TP alpha -0.09 0.21 0.37 3 -0.46 35 38
Gq family/GTP 0.001 0.067 0.33 2 -0.19 14 16
YES1 -0.009 0.073 0.26 2 -0.29 2 4
GNAI2/GTP -0.004 0.074 -10000 0 -0.22 9 9
PGD2/DP -0.002 0.084 -10000 0 -0.32 11 11
SLC9A3R1 0.026 0.005 -10000 0 -10000 0 0
FYN -0.009 0.076 0.33 2 -0.29 2 4
mol:NO 0.024 0.008 -10000 0 -10000 0 0
GNA15 0.002 0.11 -10000 0 -0.46 9 9
PGK/cGMP -0.023 0.12 -10000 0 -0.28 31 31
RhoA/GDP 0.026 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.013 0.09 -10000 0 -0.32 3 3
NOS3 0.024 0.008 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.06 0.16 0.32 3 -0.34 36 39
PRKCB -0.08 0.18 0.28 3 -0.38 37 40
PRKCE -0.058 0.16 0.28 3 -0.34 34 37
PRKCD -0.066 0.17 0.31 4 -0.37 36 40
PRKCG -0.069 0.17 0.32 3 -0.38 36 39
muscle contraction -0.09 0.22 0.36 3 -0.47 36 39
PRKCZ -0.06 0.16 0.3 3 -0.34 36 39
ARR3 0.018 0.019 -10000 0 -0.23 1 1
TXA2/TP beta 0.002 0.082 -10000 0 -0.22 16 16
PRKCQ -0.066 0.16 0.35 3 -0.35 37 40
MAPKKK cascade -0.084 0.2 0.34 3 -0.44 36 39
SELE -0.072 0.17 0.28 3 -0.39 36 39
TP beta/GNAI2/GDP/G beta/gamma 0.018 0.089 0.25 1 -0.25 6 7
ROCK1 0.025 0.007 -10000 0 -10000 0 0
GNA14 0.026 0.006 -10000 0 -10000 0 0
chemotaxis -0.12 0.26 0.37 2 -0.6 36 38
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.037 -10000 0 -0.46 1 1
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.009 0.14 0.36 4 -0.45 2 6
CRKL -0.002 0.1 0.29 3 -0.22 19 22
mol:DAG -0.018 0.11 -10000 0 -0.28 22 22
HRAS 0.01 0.11 0.31 9 -10000 0 9
MAPK8 -0.001 0.11 0.19 13 -0.24 22 35
RAP1A -0.001 0.1 0.29 4 -0.22 18 22
GAB1 -0.001 0.11 0.26 5 -0.22 22 27
MAPK14 0.001 0.11 0.2 15 -0.24 22 37
EPO -0.051 0.17 -10000 0 -0.42 30 30
PLCG1 -0.019 0.11 -10000 0 -0.29 22 22
EPOR/TRPC2/IP3 Receptors 0.019 0.032 -10000 0 -0.23 1 1
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.047 0.15 -10000 0 -0.28 45 45
GAB1/SHC/GRB2/SOS1 0.02 0.1 0.27 2 -0.25 1 3
EPO/EPOR (dimer) -0.021 0.13 -10000 0 -0.3 30 30
IRS2 -0.005 0.1 0.29 3 -0.22 19 22
STAT1 -0.015 0.12 0.22 1 -0.29 20 21
STAT5B -0.018 0.11 -10000 0 -0.29 21 21
cell proliferation -0.004 0.12 0.22 26 -0.22 22 48
GAB1/SHIP/PIK3R1/SHP2/SHC 0 0.098 -10000 0 -0.36 2 2
TEC 0 0.11 0.26 5 -0.22 22 27
SOCS3 -0.047 0.17 -10000 0 -0.43 28 28
STAT1 (dimer) -0.014 0.11 0.22 1 -0.29 20 21
JAK2 0.02 0.025 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.021 0.11 -10000 0 -0.22 25 25
EPO/EPOR -0.021 0.13 -10000 0 -0.3 30 30
LYN 0.022 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.005 0.1 0.28 2 -0.25 2 4
elevation of cytosolic calcium ion concentration 0.019 0.032 -10000 0 -0.23 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.002 0.11 -10000 0 -0.27 22 22
mol:IP3 -0.018 0.11 -10000 0 -0.28 22 22
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.006 0.11 0.29 2 -0.31 4 6
SH2B3 0.02 0.024 -10000 0 -10000 0 0
NFKB1 0 0.11 0.18 22 -0.24 22 44
EPO/EPOR (dimer)/JAK2/SOCS3 -0.052 0.11 -10000 0 -0.23 43 43
PTPN6 -0.002 0.11 0.3 2 -0.22 24 26
TEC/VAV2/GRB2 0.014 0.1 0.28 2 -0.24 2 4
EPOR 0.019 0.032 -10000 0 -0.23 1 1
INPP5D 0.013 0.081 -10000 0 -0.46 5 5
mol:GDP 0.019 0.1 0.27 2 -0.25 1 3
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG2 0.018 0.042 -10000 0 -0.34 2 2
CRKL/CBL/C3G 0.01 0.1 0.28 2 -0.24 2 4
VAV2 -0.005 0.1 0.29 3 -0.22 22 25
CBL -0.003 0.1 0.29 4 -0.22 22 26
SHC/Grb2/SOS1 -0.002 0.089 -10000 0 -0.24 2 2
STAT5A -0.018 0.11 -10000 0 -0.29 22 22
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.002 0.12 -10000 0 -0.37 4 4
LYN/PLCgamma2 0.027 0.035 -10000 0 -0.24 2 2
PTPN11 0.026 0.006 -10000 0 -10000 0 0
BTK -0.001 0.11 0.29 4 -0.22 22 26
BCL2 -0.017 0.2 0.36 3 -0.78 7 10
EPHB forward 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
Ephrin A5/EPHB2 0.009 0.083 -10000 0 -0.26 15 15
cell-cell adhesion 0.066 0.098 0.33 9 -10000 0 9
Ephrin B/EPHB2/RasGAP 0.027 0.1 -10000 0 -0.26 16 16
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.038 0.13 -10000 0 -0.28 39 39
HRAS/GDP -0.046 0.12 -10000 0 -0.29 21 21
Ephrin B/EPHB1/GRB7 -0.036 0.15 -10000 0 -0.27 48 48
Endophilin/SYNJ1 -0.013 0.082 0.18 3 -0.25 15 18
KRAS 0.025 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.037 0.15 -10000 0 -0.27 48 48
endothelial cell migration 0.037 0.039 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.027 0.002 -10000 0 -10000 0 0
PAK1 -0.021 0.098 0.19 12 -0.36 4 16
HRAS 0.027 0.004 -10000 0 -10000 0 0
RRAS -0.017 0.099 0.18 4 -0.27 17 21
DNM1 0.026 0.006 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.051 0.14 0.19 12 -0.26 44 56
lamellipodium assembly -0.066 0.098 -10000 0 -0.33 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.056 0.13 -10000 0 -0.27 38 38
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
EPHB2 0.024 0.028 -10000 0 -0.23 2 2
EPHB3 0.025 0.008 -10000 0 -10000 0 0
EPHB1 -0.086 0.2 -10000 0 -0.46 40 40
EPHB4 0.024 0.008 -10000 0 -10000 0 0
mol:GDP -0.051 0.11 0.29 1 -0.3 20 21
Ephrin B/EPHB2 0.017 0.098 -10000 0 -0.26 16 16
Ephrin B/EPHB3 0.016 0.09 -10000 0 -0.24 15 15
JNK cascade -0.025 0.14 0.36 10 -0.24 39 49
Ephrin B/EPHB1 -0.043 0.14 -10000 0 -0.26 48 48
RAP1/GDP -0.025 0.13 0.26 7 -0.31 9 16
EFNB2 0.014 0.054 -10000 0 -0.23 8 8
EFNB3 -0.02 0.14 -10000 0 -0.46 16 16
EFNB1 0.024 0.036 -10000 0 -0.46 1 1
Ephrin B2/EPHB1-2 -0.031 0.13 -10000 0 -0.26 40 40
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.04 0.13 -10000 0 -0.29 23 23
Rap1/GTP -0.051 0.12 -10000 0 -0.33 10 10
axon guidance 0.009 0.083 -10000 0 -0.26 15 15
MAPK3 -0.054 0.12 0.19 1 -0.33 15 16
MAPK1 -0.055 0.12 0.19 1 -0.34 14 15
Rac1/GDP -0.044 0.11 0.29 1 -0.28 19 20
actin cytoskeleton reorganization -0.046 0.089 -10000 0 -0.26 9 9
CDC42/GDP -0.036 0.13 0.26 6 -0.31 12 18
PI3K 0.041 0.042 -10000 0 -10000 0 0
EFNA5 -0.011 0.13 -10000 0 -0.46 13 13
Ephrin B2/EPHB4 0.025 0.034 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.088 -10000 0 -0.25 16 16
CDC42 0.027 0 -10000 0 -10000 0 0
RAS family/GTP -0.051 0.11 -10000 0 -0.33 9 9
PTK2 0.099 0.21 0.58 28 -10000 0 28
MAP4K4 -0.025 0.14 0.36 10 -0.24 39 49
SRC 0.026 0.006 -10000 0 -10000 0 0
KALRN 0.024 0.021 -10000 0 -0.23 1 1
Intersectin/N-WASP 0.035 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.031 0.13 0.36 7 -0.36 5 12
MAP2K1 -0.058 0.12 -10000 0 -0.33 16 16
WASL 0.024 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.012 0.13 -10000 0 -0.26 39 39
cell migration -0.065 0.15 0.29 4 -0.38 17 21
NRAS 0.026 0.005 -10000 0 -10000 0 0
SYNJ1 -0.013 0.083 0.18 3 -0.25 15 18
PXN 0.026 0.006 -10000 0 -10000 0 0
TF -0.073 0.12 0.17 1 -0.3 32 33
HRAS/GTP -0.039 0.13 -10000 0 -0.25 40 40
Ephrin B1/EPHB1-2 -0.024 0.13 -10000 0 -0.25 39 39
cell adhesion mediated by integrin 0.021 0.081 0.25 15 -0.19 2 17
RAC1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP -0.041 0.14 -10000 0 -0.25 47 47
RAC1-CDC42/GTP -0.053 0.11 -10000 0 -0.35 9 9
RASA1 0.026 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.12 0.29 1 -0.31 10 11
ruffle organization -0.034 0.16 0.39 10 -0.34 9 19
NCK1 0.024 0.008 -10000 0 -10000 0 0
receptor internalization -0.029 0.073 0.17 2 -0.33 3 5
Ephrin B/EPHB2/KALRN 0.026 0.099 -10000 0 -0.25 15 15
ROCK1 0.027 0.046 0.18 14 -10000 0 14
RAS family/GDP -0.047 0.084 -10000 0 -0.3 5 5
Rac1/GTP -0.051 0.11 -10000 0 -0.35 9 9
Ephrin B/EPHB1/Src/Paxillin -0.064 0.14 -10000 0 -0.27 48 48
Wnt 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
Noncanonical Wnts/FZD -0.056 0.16 -9999 0 -0.31 39 39
FZD6 0.022 0.011 -9999 0 -10000 0 0
WNT6 -0.11 0.22 -9999 0 -0.45 49 49
WNT4 0.019 0.063 -9999 0 -0.46 3 3
FZD3 0.019 0.013 -9999 0 -10000 0 0
WNT5A 0.004 0.098 -9999 0 -0.41 9 9
WNT11 0.006 0.085 -9999 0 -0.32 10 10
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.021 0.12 -10000 0 -0.24 36 36
RGS9BP 0.024 0.036 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.006 -10000 0 -10000 0 0
mol:Na + 0.016 0.034 -10000 0 -0.13 4 4
mol:ADP -0.009 0.011 -10000 0 -10000 0 0
GNAT2 0.021 0.034 -10000 0 -0.23 3 3
RGS9-1/Gbeta5/R9AP -0.045 0.15 -10000 0 -0.28 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.031 -10000 0 -0.16 4 4
GRK7 0.021 0.008 -10000 0 -10000 0 0
CNGB3 0.014 0.028 -10000 0 -0.23 2 2
Cone Metarhodopsin II/X-Arrestin 0.014 0.013 -10000 0 -0.15 1 1
mol:Ca2+ 0.002 0.092 0.18 30 -0.22 1 31
Cone PDE6 -0.026 0.14 -10000 0 -0.24 49 49
Cone Metarhodopsin II 0.024 0.01 -10000 0 -10000 0 0
Na + (4 Units) 0.004 0.063 -10000 0 -0.22 1 1
GNAT2/GDP -0.03 0.14 -10000 0 -0.24 50 50
GNB5 0.024 0.037 -10000 0 -0.46 1 1
mol:GMP (4 units) -0.01 0.032 0.18 3 -0.2 1 4
Cone Transducin -0.021 0.12 -10000 0 -0.26 36 36
SLC24A2 -0.025 0.1 -10000 0 -0.23 33 33
GNB3/GNGT2 -0.041 0.15 -10000 0 -0.33 37 37
GNB3 -0.076 0.2 -10000 0 -0.45 37 37
GNAT2/GTP 0.016 0.023 -10000 0 -0.15 3 3
CNGA3 0.012 0.05 -10000 0 -0.23 7 7
ARR3 0.018 0.019 -10000 0 -0.23 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.016 0.034 -10000 0 -0.13 4 4
mol:Pi -0.045 0.15 -10000 0 -0.28 50 50
Cone CNG Channel 0.025 0.046 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.025 0.1 -10000 0 -0.23 33 33
RGS9 -0.11 0.22 -10000 0 -0.45 50 50
PDE6C 0.018 0.006 -10000 0 -10000 0 0
GNGT2 0.021 0.051 -10000 0 -0.46 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.016 0.028 -10000 0 -0.23 2 2
Noncanonical Wnt signaling pathway

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
NFATC2 -0.01 0.13 -10000 0 -0.46 13 13
GNB1/GNG2 -0.04 0.16 -10000 0 -0.37 19 19
mol:DAG -0.048 0.14 0.19 2 -0.34 19 21
PLCG1 -0.049 0.15 -10000 0 -0.36 19 19
YES1 -0.059 0.15 -10000 0 -0.38 20 20
FZD3 0.019 0.013 -10000 0 -10000 0 0
FZD6 0.022 0.011 -10000 0 -10000 0 0
G protein -0.038 0.16 -10000 0 -0.36 19 19
MAP3K7 -0.078 0.15 -10000 0 -0.41 19 19
mol:Ca2+ -0.046 0.14 0.19 2 -0.33 19 21
mol:IP3 -0.048 0.14 0.19 2 -0.34 19 21
NLK -0.004 0.099 -10000 0 -0.74 3 3
GNB1 0.027 0.003 -10000 0 -10000 0 0
CAMK2A -0.088 0.16 -10000 0 -0.43 21 21
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.056 0.16 -10000 0 -0.31 39 39
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.062 0.15 -10000 0 -0.37 21 21
GO:0007205 -0.051 0.14 0.18 2 -0.52 6 8
WNT6 -0.11 0.22 -10000 0 -0.45 49 49
WNT4 0.019 0.063 -10000 0 -0.46 3 3
NFAT1/CK1 alpha -0.054 0.16 -10000 0 -0.48 12 12
GNG2 0.027 0.002 -10000 0 -10000 0 0
WNT5A 0.004 0.098 -10000 0 -0.41 9 9
WNT11 0.006 0.085 -10000 0 -0.32 10 10
CDC42 -0.063 0.14 -10000 0 -0.36 21 21
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.069 0.17 0.46 19 -10000 0 19
GNAI2 0.026 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.12 -10000 0 -0.28 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
RhoA/GTP -0.07 0.18 -10000 0 -0.47 19 19
negative regulation of cAMP metabolic process -0.079 0.18 -10000 0 -0.33 49 49
GNAZ -0.012 0.13 -10000 0 -0.46 14 14
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
S1PR5 -0.064 0.19 -10000 0 -0.46 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.08 0.19 -10000 0 -0.33 49 49
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.032 0.048 -10000 0 -0.27 3 3
fibroblast growth factor receptor signaling pathway 0.032 0.047 -10000 0 -0.27 3 3
LAMA1 0.011 0.068 -10000 0 -0.31 7 7
PRNP 0.026 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 0.024 0.072 -10000 0 -0.33 7 7
SMAD2 0.021 0.033 0.18 7 -10000 0 7
GPC1/PrPc/Cu2+ 0.035 0.008 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.027 0.05 -10000 0 -0.29 3 3
TDGF1 -0.064 0.18 -10000 0 -0.44 34 34
CRIPTO/GPC1 -0.029 0.14 -10000 0 -0.33 31 31
APP/GPC1 0.036 0.029 -10000 0 -0.33 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.036 0.11 -10000 0 -0.28 30 30
FLT1 0.026 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.015 -10000 0 -10000 0 0
SERPINC1 0.021 0.028 -10000 0 -0.23 2 2
FYN -0.039 0.11 -10000 0 -0.27 31 31
FGR -0.039 0.11 -10000 0 -0.28 31 31
positive regulation of MAPKKK cascade -0.067 0.14 -10000 0 -0.37 26 26
SLIT2 0.007 0.095 -10000 0 -0.46 7 7
GPC1/NRG -0.01 0.11 -10000 0 -0.33 19 19
NRG1 -0.033 0.15 -10000 0 -0.46 19 19
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.022 0.093 -10000 0 -0.28 14 14
LYN -0.028 0.1 -10000 0 -0.28 24 24
mol:Spermine 0.007 0.001 -10000 0 -10000 0 0
cell growth 0.032 0.047 -10000 0 -0.27 3 3
BMP signaling pathway -0.027 0.002 -10000 0 -10000 0 0
SRC -0.037 0.11 -10000 0 -0.28 30 30
TGFBR1 0.026 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.1 0.15 -10000 0 -0.26 79 79
GPC1 0.027 0.002 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.026 0.005 -10000 0 -10000 0 0
VEGFA -0.018 0.14 -10000 0 -0.41 18 18
BLK -0.072 0.13 -10000 0 -0.29 41 41
HCK -0.038 0.11 -10000 0 -0.28 30 30
FGF2 0.015 0.072 -10000 0 -0.46 4 4
FGFR1 0.019 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer 0.026 0.006 -10000 0 -10000 0 0
TGFBR2 0.026 0.005 -10000 0 -10000 0 0
cell death 0.036 0.029 -10000 0 -0.33 1 1
ATIII/GPC1 0.034 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.055 0.11 -10000 0 -0.17 78 78
LCK -0.04 0.11 -10000 0 -0.28 30 30
neuron differentiation -0.01 0.11 -10000 0 -0.33 19 19
PrPc/Cu2+ 0.019 0.004 -10000 0 -10000 0 0
APP 0.023 0.037 -10000 0 -0.46 1 1
TGFBR2 (dimer) 0.026 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.007 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.028 0.047 -10000 0 -0.33 2 2
STXBP1 0.023 0.037 -10000 0 -0.46 1 1
ACh/CHRNA1 -0.046 0.086 -10000 0 -0.15 63 63
RAB3GAP2/RIMS1/UNC13B 0.04 0.046 -10000 0 -0.28 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.012 0.071 -10000 0 -0.34 6 6
mol:ACh -0.013 0.055 0.098 11 -0.13 23 34
RAB3GAP2 0.026 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.006 0.086 -10000 0 -0.28 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.046 0.086 -10000 0 -0.15 63 63
UNC13B 0.026 0.005 -10000 0 -10000 0 0
CHRNA1 -0.075 0.13 -10000 0 -0.24 67 67
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.052 0.14 -10000 0 -0.3 38 38
SNAP25 -0.038 0.1 -10000 0 -0.27 28 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.068 0.19 -10000 0 -0.43 36 36
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.02 0.024 -10000 0 -0.28 1 1
STX1A/SNAP25 fragment 1/VAMP2 0.006 0.086 -10000 0 -0.28 8 8
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.037 0.15 0.3 2 -0.42 18 20
CRKL -0.039 0.14 -10000 0 -0.41 19 19
HRAS -0.02 0.15 -10000 0 -0.39 18 18
mol:PIP3 -0.006 0.14 0.25 1 -0.37 17 18
SPRED1 0.024 0.037 -10000 0 -0.46 1 1
SPRED2 0.027 0.004 -10000 0 -10000 0 0
GAB1 -0.037 0.15 -10000 0 -0.43 19 19
FOXO3 -0.004 0.14 0.27 1 -0.37 15 16
AKT1 -0.004 0.15 0.26 1 -0.4 15 16
BAD -0.001 0.14 0.3 3 -0.37 15 18
megakaryocyte differentiation -0.044 0.15 -10000 0 -0.44 20 20
GSK3B 0.004 0.14 0.33 4 -0.37 15 19
RAF1 -0.016 0.12 -10000 0 -0.32 17 17
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.039 0.15 -10000 0 -0.43 19 19
STAT1 -0.1 0.32 -10000 0 -0.9 23 23
HRAS/SPRED1 -0.002 0.13 -10000 0 -0.33 17 17
cell proliferation -0.037 0.14 -10000 0 -0.42 19 19
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
TEC 0.027 0 -10000 0 -10000 0 0
RPS6KB1 -0.018 0.16 -10000 0 -0.41 19 19
HRAS/SPRED2 -0.003 0.13 -10000 0 -0.32 17 17
LYN/TEC/p62DOK 0 0.15 -10000 0 -0.43 15 15
MAPK3 0 0.1 0.3 5 -0.27 8 13
STAP1 -0.077 0.18 -10000 0 -0.48 23 23
GRAP2 0.012 0.077 -10000 0 -0.38 6 6
JAK2 -0.087 0.27 -10000 0 -0.8 20 20
STAT1 (dimer) -0.099 0.32 -10000 0 -0.88 23 23
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.015 0.18 -10000 0 -0.46 20 20
actin filament polymerization -0.039 0.14 -10000 0 -0.4 18 18
LYN 0.023 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.096 0.24 -10000 0 -0.66 22 22
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.01 0.14 -10000 0 -0.39 17 17
PI3K -0.001 0.15 -10000 0 -0.4 17 17
PTEN 0.021 0.011 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.38 -10000 0 -1.1 19 19
MAPK8 -0.038 0.15 -10000 0 -0.42 19 19
STAT3 (dimer) -0.038 0.14 -10000 0 -0.42 19 19
positive regulation of transcription 0.003 0.091 0.28 5 -0.22 7 12
mol:GDP -0.02 0.16 -10000 0 -0.42 18 18
PIK3C2B -0.038 0.14 -10000 0 -0.43 18 18
CBL/CRKL -0.02 0.14 -10000 0 -0.4 17 17
FER -0.045 0.16 -10000 0 -0.44 21 21
SH2B3 -0.036 0.14 -10000 0 -0.42 19 19
PDPK1 -0.004 0.14 0.27 2 -0.35 16 18
SNAI2 -0.074 0.18 -10000 0 -0.45 27 27
positive regulation of cell proliferation -0.066 0.25 -10000 0 -0.71 21 21
KITLG 0.007 0.068 -10000 0 -0.47 3 3
cell motility -0.066 0.25 -10000 0 -0.71 21 21
PTPN6 0.025 0.013 -10000 0 -10000 0 0
EPOR -0.003 0.13 -10000 0 -1.1 1 1
STAT5A (dimer) -0.055 0.22 -10000 0 -0.6 21 21
SOCS1 0.012 0.077 -10000 0 -0.38 6 6
cell migration 0.086 0.15 0.45 22 -10000 0 22
SOS1 0.026 0.004 -10000 0 -10000 0 0
EPO -0.057 0.17 -10000 0 -0.42 30 30
VAV1 0.006 0.096 -10000 0 -0.43 8 8
GRB10 -0.039 0.14 -10000 0 -0.42 18 18
PTPN11 0.026 0.008 -10000 0 -10000 0 0
SCF/KIT -0.038 0.16 -10000 0 -0.45 19 19
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.007 0.1 0.26 3 -0.28 10 13
CBL 0.026 0.006 -10000 0 -10000 0 0
KIT -0.098 0.39 -10000 0 -1.2 18 18
MAP2K2 -0.009 0.1 0.22 3 -0.26 14 17
SHC/Grb2/SOS1 0 0.15 -10000 0 -0.41 17 17
STAT5A -0.061 0.22 -10000 0 -0.62 21 21
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.073 0.18 -10000 0 -0.44 27 27
SHC/GRAP2 0.028 0.052 -10000 0 -0.26 5 5
PTPRO -0.045 0.16 -10000 0 -0.45 20 20
SH2B2 -0.04 0.14 -10000 0 -0.41 18 18
DOK1 0.026 0.004 -10000 0 -10000 0 0
MATK -0.087 0.16 -10000 0 -0.46 22 22
CREBBP 0.023 0.047 -10000 0 -0.17 1 1
BCL2 -0.086 0.34 -10000 0 -1.4 10 10
IL4-mediated 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
BCL2L1 -0.26 0.38 -10000 0 -1.1 17 17
STAT6 (cleaved dimer) -0.28 0.42 -10000 0 -1.1 27 27
IGHG1 -0.088 0.14 -10000 0 -0.57 1 1
IGHG3 -0.25 0.37 -10000 0 -1 25 25
AKT1 -0.15 0.25 -10000 0 -0.7 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.2 -10000 0 -0.63 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.23 -10000 0 -0.78 8 8
THY1 -0.26 0.39 -10000 0 -1.1 18 18
MYB 0.01 0.063 -10000 0 -0.23 11 11
HMGA1 0.027 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.19 0.29 -10000 0 -0.79 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.25 -10000 0 -0.79 12 12
SP1 0.03 0.008 -10000 0 -10000 0 0
INPP5D 0.013 0.081 -10000 0 -0.46 5 5
SOCS5 0.038 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.28 0.42 -10000 0 -1.1 24 24
SOCS1 -0.2 0.28 -10000 0 -0.74 23 23
SOCS3 -0.27 0.45 -10000 0 -1.2 28 28
FCER2 -0.34 0.5 -10000 0 -1.2 35 35
PARP14 0.019 0.022 -10000 0 -10000 0 0
CCL17 -0.27 0.4 -10000 0 -1.2 18 18
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.2 -10000 0 -0.66 10 10
T cell proliferation -0.26 0.41 -10000 0 -1.1 22 22
IL4R/JAK1 -0.26 0.4 -10000 0 -1.1 21 21
EGR2 -0.29 0.42 -10000 0 -1.2 19 19
JAK2 -0.009 0.04 -10000 0 -10000 0 0
JAK3 0.013 0.044 -10000 0 -0.24 4 4
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.005 0.025 -10000 0 -10000 0 0
COL1A2 -0.067 0.14 -10000 0 -0.81 1 1
CCL26 -0.25 0.39 -10000 0 -1.1 17 17
IL4R -0.28 0.41 -10000 0 -1.2 20 20
PTPN6 0.031 0.014 -10000 0 -10000 0 0
IL13RA2 -0.35 0.53 -10000 0 -1.4 32 32
IL13RA1 -0.008 0.041 -10000 0 -10000 0 0
IRF4 -0.1 0.27 -10000 0 -1.2 8 8
ARG1 -0.062 0.12 -10000 0 -10000 0 0
CBL -0.18 0.27 -10000 0 -0.76 21 21
GTF3A 0.026 0.017 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
IL13RA1/JAK2 -0.008 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.078 0.26 -10000 0 -1.1 8 8
CD40LG -0.004 0.09 -10000 0 -0.3 13 13
MAPK14 -0.21 0.32 -10000 0 -0.85 26 26
mitosis -0.14 0.24 -10000 0 -0.67 16 16
STAT6 -0.29 0.44 -10000 0 -1.2 25 25
SPI1 0.025 0.024 -10000 0 -0.23 1 1
RPS6KB1 -0.14 0.23 -10000 0 -0.66 14 14
STAT6 (dimer) -0.29 0.44 -10000 0 -1.2 24 24
STAT6 (dimer)/PARP14 -0.28 0.43 -10000 0 -1.1 27 27
mast cell activation 0.007 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.24 -10000 0 -0.72 15 15
FRAP1 -0.15 0.25 -10000 0 -0.7 16 16
LTA -0.27 0.41 -10000 0 -1.2 19 19
FES 0.015 0.072 -10000 0 -0.46 4 4
T-helper 1 cell differentiation 0.28 0.43 1.2 25 -10000 0 25
CCL11 -0.27 0.39 -10000 0 -1.1 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.13 0.23 -10000 0 -0.74 10 10
IL2RG 0.009 0.055 -10000 0 -0.24 7 7
IL10 -0.28 0.44 -10000 0 -1.3 20 20
IRS1 0.024 0.037 -10000 0 -0.46 1 1
IRS2 0.021 0.034 -10000 0 -0.23 3 3
IL4 -0.081 0.19 -10000 0 -1.1 4 4
IL5 -0.26 0.39 -10000 0 -1.2 16 16
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.21 0.31 -10000 0 -0.86 18 18
COL1A1 -0.084 0.15 -10000 0 -0.73 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.4 -10000 0 -1.2 16 16
IL2R gamma/JAK3 0.017 0.063 -10000 0 -0.3 4 4
TFF3 -0.28 0.39 -10000 0 -1.2 18 18
ALOX15 -0.31 0.42 -10000 0 -1.2 21 21
MYBL1 0.019 0.038 -10000 0 -0.46 1 1
T-helper 2 cell differentiation -0.25 0.35 -10000 0 -0.96 23 23
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.025 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.24 -10000 0 -0.79 10 10
mol:PI-3-4-5-P3 -0.15 0.25 -10000 0 -0.7 16 16
PI3K -0.15 0.26 -10000 0 -0.75 16 16
DOK2 0.014 0.03 -10000 0 -0.23 2 2
ETS1 0.031 0.023 -10000 0 -0.21 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.18 -10000 0 -0.59 9 9
ITGB3 -0.32 0.5 -10000 0 -1.4 24 24
PIGR -0.39 0.57 -10000 0 -1.4 37 37
IGHE 0.018 0.055 0.19 6 -10000 0 6
MAPKKK cascade -0.1 0.18 -10000 0 -0.58 9 9
BCL6 0.027 0.011 -10000 0 -10000 0 0
OPRM1 -0.27 0.39 -10000 0 -1.1 20 20
RETNLB -0.26 0.39 -10000 0 -1.2 16 16
SELP -0.26 0.4 -10000 0 -1.1 18 18
AICDA -0.25 0.38 -10000 0 -1.1 18 18
amb2 Integrin signaling

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.009 0.072 -10000 0 -0.27 4 4
alphaM/beta2 Integrin/GPIbA 0.001 0.084 -10000 0 -0.28 8 8
alphaM/beta2 Integrin/proMMP-9 -0.088 0.09 -10000 0 -0.22 22 22
PLAUR 0.024 0.028 -10000 0 -0.23 2 2
HMGB1 0.001 0.035 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.014 0.062 -10000 0 -0.28 1 1
AGER -0.017 0.093 -10000 0 -0.42 7 7
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.021 0.034 -10000 0 -0.23 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.14 -10000 0 -0.34 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.14 0.13 -10000 0 -0.24 108 108
CYR61 0.009 0.085 -10000 0 -0.39 7 7
TLN1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.036 0.11 -10000 0 -0.32 12 12
RHOA 0.026 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.022 0.037 -10000 0 -0.46 1 1
MYH2 -0.095 0.14 0.16 1 -0.38 24 25
MST1R 0.009 0.085 -10000 0 -0.39 7 7
leukocyte activation during inflammatory response -0.073 0.16 -10000 0 -0.29 53 53
APOB -0.081 0.2 -10000 0 -0.46 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.052 -10000 0 -0.46 2 2
JAM3 0.015 0.072 -10000 0 -0.46 4 4
GP1BA 0.009 0.08 -10000 0 -0.37 7 7
alphaM/beta2 Integrin/CTGF 0 0.091 -10000 0 -0.3 9 9
alphaM/beta2 Integrin -0.053 0.11 -10000 0 -0.3 19 19
JAM3 homodimer 0.015 0.072 -10000 0 -0.46 4 4
ICAM2 0.021 0.051 -10000 0 -0.46 2 2
ICAM1 0.01 0.063 -10000 0 -0.23 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.051 0.11 -10000 0 -0.32 17 17
cell adhesion 0.001 0.084 -10000 0 -0.28 8 8
NFKB1 -0.1 0.2 -10000 0 -0.4 47 47
THY1 0.02 0.042 -10000 0 -0.25 4 4
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.077 0.17 -10000 0 -0.32 55 55
alphaM/beta2 Integrin/LRP/tPA 0.007 0.076 -10000 0 -0.25 4 4
IL6 -0.16 0.3 -10000 0 -0.66 42 42
ITGB2 -0.006 0.054 -10000 0 -0.26 4 4
elevation of cytosolic calcium ion concentration 0.009 0.09 -10000 0 -0.26 10 10
alphaM/beta2 Integrin/JAM2/JAM3 0.02 0.082 -10000 0 -0.28 6 6
JAM2 0.023 0.037 -10000 0 -0.46 1 1
alphaM/beta2 Integrin/ICAM1 0.01 0.097 -10000 0 -0.26 9 9
alphaM/beta2 Integrin/uPA/Plg 0.002 0.093 -10000 0 -0.26 11 11
RhoA/GTP -0.068 0.14 -10000 0 -0.36 23 23
positive regulation of phagocytosis -0.035 0.098 -10000 0 -0.29 10 10
Ron/MSP 0.021 0.073 -10000 0 -0.25 11 11
alphaM/beta2 Integrin/uPAR/uPA 0.01 0.092 -10000 0 -0.27 10 10
alphaM/beta2 Integrin/uPAR 0.012 0.067 -10000 0 -0.22 3 3
PLAU 0.003 0.1 -10000 0 -0.46 8 8
PLAT -0.001 0.081 -10000 0 -0.29 12 12
actin filament polymerization -0.092 0.14 -10000 0 -0.38 22 22
MST1 0.019 0.049 -10000 0 -0.29 4 4
alphaM/beta2 Integrin/lipoprotein(a) -0.071 0.16 -10000 0 -0.3 53 53
TNF -0.11 0.22 -10000 0 -0.63 17 17
RAP1B 0.026 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.001 0.091 -10000 0 -0.29 10 10
fibrinolysis 0.001 0.092 -10000 0 -0.26 11 11
HCK 0.022 0.041 -10000 0 -0.34 2 2
dendritic cell antigen processing and presentation -0.051 0.11 -10000 0 -0.32 17 17
VTN -0.065 0.17 -10000 0 -0.36 41 41
alphaM/beta2 Integrin/CYR61 0.004 0.084 -10000 0 -0.31 6 6
LPA -0.047 0.17 -10000 0 -0.45 27 27
LRP1 0.025 0.02 -10000 0 -0.23 1 1
cell migration -0.08 0.089 0.19 1 -0.27 9 10
FN1 0.025 0.02 -10000 0 -0.23 1 1
alphaM/beta2 Integrin/Thy1 0.009 0.069 -10000 0 -0.22 3 3
MPO -0.02 0.14 -10000 0 -0.44 17 17
KNG1 -0.003 0.071 -10000 0 -0.23 15 15
RAP1/GDP 0.034 0.01 -10000 0 -10000 0 0
ROCK1 -0.063 0.13 0.17 1 -0.39 16 17
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.011 0.05 -10000 0 -0.23 7 7
CTGF 0.006 0.096 -10000 0 -0.43 8 8
alphaM/beta2 Integrin/Hck 0.011 0.073 -10000 0 -0.31 3 3
ITGAM -0.001 0.043 -10000 0 -0.26 1 1
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.022 0.074 -10000 0 -0.3 3 3
HP -0.025 0.12 -10000 0 -0.3 26 26
leukocyte adhesion -0.03 0.12 -10000 0 -0.32 11 11
SELP 0.022 0.037 -10000 0 -0.46 1 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.004 0.11 -10000 0 -0.29 20 20
PDGFRB 0.023 0.028 -10000 0 -0.23 2 2
SPHK1 -0.017 0.11 -10000 0 -0.7 4 4
mol:S1P -0.017 0.1 -10000 0 -0.6 4 4
S1P1/S1P/Gi -0.11 0.21 -10000 0 -0.45 39 39
GNAO1 -0.055 0.17 -10000 0 -0.46 27 27
PDGFB-D/PDGFRB/PLCgamma1 -0.083 0.19 0.34 1 -0.41 34 35
PLCG1 -0.11 0.19 -10000 0 -0.43 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.028 -10000 0 -0.23 2 2
GNAI2 0.02 0.018 -10000 0 -10000 0 0
GNAI3 0.019 0.018 -10000 0 -10000 0 0
GNAI1 0.015 0.032 -10000 0 -0.24 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.027 0.082 -10000 0 -0.28 16 16
S1P1/S1P -0.035 0.11 -10000 0 -0.46 6 6
negative regulation of cAMP metabolic process -0.11 0.2 -10000 0 -0.44 39 39
MAPK3 -0.14 0.25 -10000 0 -0.57 37 37
calcium-dependent phospholipase C activity -0.002 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
KDR 0.018 0.052 -10000 0 -0.46 2 2
PLCB2 -0.028 0.1 -10000 0 -0.39 6 6
RAC1 0.024 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.093 -10000 0 -0.37 6 6
receptor internalization -0.033 0.1 -10000 0 -0.38 8 8
PTGS2 -0.19 0.38 -10000 0 -0.93 34 34
Rac1/GTP -0.027 0.091 -10000 0 -0.37 6 6
RHOA 0.026 0.005 -10000 0 -10000 0 0
VEGFA -0.021 0.14 -10000 0 -0.41 18 18
negative regulation of T cell proliferation -0.11 0.2 -10000 0 -0.44 39 39
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.019 0.13 -10000 0 -0.46 14 14
MAPK1 -0.14 0.26 -10000 0 -0.59 38 38
S1P1/S1P/PDGFB-D/PDGFRB -0.029 0.12 0.42 1 -0.4 8 9
ABCC1 0.025 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.021 0.1 -10000 0 -0.29 13 13
NT3 (dimer)/TRKC -0.047 0.17 -10000 0 -0.38 35 35
NT3 (dimer)/TRKB -0.02 0.15 -10000 0 -0.32 32 32
SHC/Grb2/SOS1/GAB1/PI3K 0.024 0.017 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
BDNF -0.086 0.2 -10000 0 -0.46 41 41
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
NTRK1 -0.002 0.1 -10000 0 -0.4 11 11
NTRK2 0.001 0.11 -10000 0 -0.46 9 9
NTRK3 -0.051 0.18 -10000 0 -0.46 28 28
NT-4/5 (dimer)/TRKB -0.088 0.2 -10000 0 -0.34 61 61
neuron apoptosis 0.08 0.18 0.4 34 -10000 0 34
SHC 2-3/Grb2 -0.087 0.2 -10000 0 -0.44 34 34
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 -0.066 0.16 -10000 0 -0.44 20 20
SHC3 -0.11 0.22 -10000 0 -0.49 36 36
STAT3 (dimer) 0.03 0.012 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.022 0.15 -10000 0 -0.31 31 31
RIN/GDP -0.003 0.09 0.21 4 -0.24 6 10
GIPC1 0.027 0.004 -10000 0 -10000 0 0
KRAS 0.025 0.008 -10000 0 -10000 0 0
DNAJA3 -0.045 0.12 -10000 0 -0.28 30 30
RIN/GTP 0.002 0.048 -10000 0 -0.16 13 13
CCND1 0.017 0.015 -10000 0 -10000 0 0
MAGED1 0.025 0.02 -10000 0 -0.23 1 1
PTPN11 0.026 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.14 0.23 -10000 0 -0.46 59 59
SHC/GRB2/SOS1 0.049 0.018 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.074 0.14 -10000 0 -0.34 24 24
TRKA/NEDD4-2 0.008 0.084 -10000 0 -0.32 8 8
ELMO1 0.024 0.009 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.013 -10000 0 -10000 0 0
NGF -0.016 0.14 -10000 0 -0.46 15 15
HRAS 0.027 0.004 -10000 0 -10000 0 0
DOCK1 0.026 0.006 -10000 0 -10000 0 0
GAB2 0.026 0.005 -10000 0 -10000 0 0
RIT2 0.001 0.071 -10000 0 -0.25 13 13
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
DNM1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.03 0.12 -10000 0 -0.27 30 30
mol:GDP -0.013 0.13 0.29 4 -0.34 9 13
NGF (dimer) -0.016 0.14 -10000 0 -0.46 15 15
RhoG/GDP 0.018 0.007 -10000 0 -10000 0 0
RIT1/GDP -0.005 0.089 0.21 3 -0.24 6 9
TIAM1 0.025 0.02 -10000 0 -0.23 1 1
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.037 0.16 -10000 0 -0.3 43 43
KIDINS220/CRKL/C3G 0.038 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.051 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.14 -10000 0 -0.46 16 16
RAP1/GDP -0.007 0.073 -10000 0 -0.21 6 6
KIDINS220/CRKL 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.086 0.2 -10000 0 -0.46 41 41
ubiquitin-dependent protein catabolic process -0.006 0.11 -10000 0 -0.27 23 23
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.026 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.024 -10000 0 -10000 0 0
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.076 0.18 -10000 0 -0.3 58 58
ABL1 0.026 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.091 -10000 0 -0.37 4 4
STAT3 0.03 0.012 -10000 0 -10000 0 0
axon guidance -0.081 0.17 -10000 0 -0.29 58 58
MAPK3 -0.075 0.12 0.18 2 -0.31 24 26
MAPK1 -0.078 0.12 0.18 2 -0.31 24 26
CDC42/GDP 0 0.095 0.22 6 -0.24 7 13
NTF3 -0.019 0.14 -10000 0 -0.46 16 16
NTF4 -0.14 0.23 -10000 0 -0.46 59 59
NGF (dimer)/TRKA/FAIM -0.002 0.11 -10000 0 -0.27 22 22
PI3K 0.033 0.021 -10000 0 -0.16 1 1
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.024 0.009 -10000 0 -10000 0 0
GAB1 0.027 0.003 -10000 0 -10000 0 0
RASGRF1 -0.08 0.15 -10000 0 -0.31 49 49
SOS1 0.026 0.004 -10000 0 -10000 0 0
MCF2L -0.051 0.14 -10000 0 -0.32 34 34
RGS19 0.024 0.02 -10000 0 -0.23 1 1
CDC42 0.027 0 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.12 0.27 2 -0.46 6 8
Rac1/GDP -0.004 0.086 0.21 3 -0.24 5 8
NGF (dimer)/TRKA/GRIT -0.012 0.1 -10000 0 -0.26 26 26
neuron projection morphogenesis -0.046 0.2 -10000 0 -0.67 11 11
NGF (dimer)/TRKA/NEDD4-2 -0.006 0.11 -10000 0 -0.27 23 23
MAP2K1 0.024 0.042 0.18 12 -10000 0 12
NGFR -0.01 0.13 -10000 0 -0.46 13 13
NGF (dimer)/TRKA/GIPC/GAIP -0.006 0.081 -10000 0 -0.22 20 20
RAS family/GTP/PI3K 0.019 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.027 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
PRKCI 0.024 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.003 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.25 -10000 0 -0.57 40 40
RASA1 0.026 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.019 0.071 -10000 0 -0.27 9 9
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.024 0.15 -10000 0 -0.27 44 44
NGF (dimer)/TRKA/p62/Atypical PKCs 0.02 0.1 -10000 0 -0.24 20 20
MATK -0.1 0.13 -10000 0 -0.24 87 87
NEDD4L 0.012 0.054 -10000 0 -0.23 8 8
RAS family/GDP -0.028 0.05 -10000 0 -0.19 4 4
NGF (dimer)/TRKA -0.042 0.13 -10000 0 -0.29 31 31
Rac1/GTP -0.065 0.11 -10000 0 -0.27 27 27
FRS2 family/SHP2/CRK family 0.069 0.028 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.025 -10000 0 -10000 0 0
VDR 0.025 0.02 -10000 0 -0.23 1 1
FAM120B 0.026 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.031 0.12 -10000 0 -0.35 7 7
RXRs/LXRs/DNA/Oxysterols -0.025 0.13 -10000 0 -0.47 6 6
MED1 0.027 0.002 -10000 0 -10000 0 0
mol:9cRA 0.001 0.01 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.036 -10000 0 -0.22 3 3
RXRs/NUR77 -0.026 0.15 -10000 0 -0.27 42 42
RXRs/PPAR -0.045 0.12 -10000 0 -0.24 44 44
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.013 -10000 0 -0.15 1 1
RARs/VDR/DNA/Vit D3 0.053 0.044 -10000 0 -0.24 3 3
RARA 0.027 0.002 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.02 -10000 0 -0.23 1 1
RARs/RARs/DNA/9cRA 0.039 0.041 -10000 0 -0.24 3 3
RARG 0.018 0.063 -10000 0 -0.46 3 3
RPS6KB1 0.022 0.045 0.53 1 -10000 0 1
RARs/THRs/DNA/SMRT 0.023 0.036 -10000 0 -0.22 3 3
THRA 0.027 0.002 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.013 -10000 0 -0.15 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.022 0.13 -10000 0 -0.25 38 38
NR1H4 -0.1 0.21 -10000 0 -0.43 49 49
RXRs/LXRs/DNA 0.002 0.14 -10000 0 -0.24 36 36
NR1H2 0.027 0.016 -10000 0 -10000 0 0
NR1H3 0.026 0.017 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.013 0.13 -10000 0 -0.24 38 38
NR4A1 0.001 0.1 -10000 0 -0.38 11 11
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.092 0.14 -10000 0 -0.24 71 71
RXRG -0.093 0.21 -10000 0 -0.45 44 44
RXR alpha/CCPG 0.036 0.018 -10000 0 -10000 0 0
RXRA 0.025 0.017 -10000 0 -10000 0 0
RXRB 0.027 0.016 -10000 0 -10000 0 0
THRB 0.023 0.028 -10000 0 -0.23 2 2
PPARG -0.011 0.13 -10000 0 -0.44 14 14
PPARD 0.027 0.004 -10000 0 -10000 0 0
TNF -0.052 0.22 -10000 0 -1 7 7
mol:Oxysterols 0.001 0.009 -10000 0 -10000 0 0
cholesterol transport -0.025 0.13 -10000 0 -0.47 6 6
PPARA 0.026 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.026 0.005 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.052 0.13 -10000 0 -0.26 43 43
SREBF1 -0.028 0.12 -10000 0 -0.53 3 3
RXRs/RXRs/DNA/9cRA -0.022 0.13 -10000 0 -0.25 38 38
ABCA1 -0.024 0.12 -10000 0 -0.53 3 3
RARs/THRs 0.066 0.051 -10000 0 -0.24 3 3
RXRs/FXR -0.092 0.18 -10000 0 -0.29 69 69
BCL2 0.018 0.052 -10000 0 -0.46 2 2
Ephrin B reverse 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
EFNB2 0.014 0.054 -10000 0 -0.23 8 8
EPHB2 0.024 0.027 -10000 0 -0.23 2 2
EFNB1 0.01 0.026 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.008 0.12 -10000 0 -0.23 34 34
Ephrin B2/EPHB1-2 -0.031 0.13 -10000 0 -0.26 40 40
neuron projection morphogenesis -0.018 0.1 -10000 0 -0.22 34 34
Ephrin B1/EPHB1-2/Tiam1 -0.017 0.12 -10000 0 -0.24 38 38
DNM1 0.026 0.006 -10000 0 -10000 0 0
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 0 0.037 -10000 0 -0.47 1 1
YES1 0.008 0.056 -10000 0 -0.68 1 1
Ephrin B1/EPHB1-2/NCK2 -0.016 0.12 -10000 0 -0.24 38 38
PI3K 0.033 0.046 -10000 0 -0.48 1 1
mol:GDP -0.018 0.12 -10000 0 -0.24 38 38
ITGA2B 0.002 0.1 -10000 0 -0.46 8 8
endothelial cell proliferation 0.024 0.034 -10000 0 -10000 0 0
FYN 0.009 0.055 -10000 0 -0.68 1 1
MAP3K7 0 0.038 -10000 0 -0.5 1 1
FGR 0.009 0.068 -10000 0 -0.61 2 2
TIAM1 0.025 0.02 -10000 0 -0.23 1 1
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
RGS3 0.026 0.006 -10000 0 -10000 0 0
cell adhesion -0.008 0.094 -10000 0 -0.51 2 2
LYN 0.01 0.053 -10000 0 -0.68 1 1
Ephrin B1/EPHB1-2/Src Family Kinases 0.003 0.051 -10000 0 -0.66 1 1
Ephrin B1/EPHB1-2 0.001 0.041 -10000 0 -0.54 1 1
SRC 0.008 0.069 -10000 0 -0.61 2 2
ITGB3 -0.018 0.14 -10000 0 -0.46 16 16
EPHB1 -0.086 0.2 -10000 0 -0.46 40 40
EPHB4 0.024 0.008 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.024 0.034 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.014 0.13 -10000 0 -0.34 23 23
BLK -0.015 0.082 -10000 0 -0.75 1 1
HCK 0.005 0.069 -10000 0 -0.61 2 2
regulation of stress fiber formation 0.017 0.12 0.24 38 -10000 0 38
MAPK8 0.004 0.042 0.21 2 -0.45 1 3
Ephrin B1/EPHB1-2/RGS3 -0.016 0.12 -10000 0 -0.24 38 38
endothelial cell migration 0.008 0.066 0.22 8 -0.41 1 9
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.009 -10000 0 -10000 0 0
regulation of focal adhesion formation 0.017 0.12 0.24 38 -10000 0 38
chemotaxis 0.017 0.12 0.24 38 -10000 0 38
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
Rac1/GTP -0.012 0.11 -10000 0 -0.22 34 34
angiogenesis 0.001 0.041 -10000 0 -0.54 1 1
LCK 0.009 0.068 -10000 0 -0.61 2 2
TCGA08_p53

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
CDKN2A -0.029 0.074 0.22 2 -0.15 42 44
TP53 -0.016 0.062 -10000 0 -0.24 11 11
Senescence -0.016 0.062 -10000 0 -0.24 11 11
Apoptosis -0.016 0.062 -10000 0 -0.24 11 11
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.067 0.36 5 -10000 0 5
MDM4 0.026 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.001 0.11 -10000 0 -0.29 20 20
alphaV beta3 Integrin 0.014 0.12 -10000 0 -0.34 16 16
PTK2 -0.067 0.18 0.33 4 -0.48 17 21
IGF1R 0.024 0.028 -10000 0 -0.23 2 2
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.026 0.004 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
CDKN1B -0.073 0.19 -10000 0 -0.44 32 32
VEGFA -0.018 0.14 -10000 0 -0.41 18 18
ILK -0.06 0.17 -10000 0 -0.45 26 26
ROCK1 0.025 0.007 -10000 0 -10000 0 0
AKT1 -0.061 0.16 -10000 0 -0.43 25 25
PTK2B -0.032 0.098 0.18 1 -0.28 13 14
alphaV/beta3 Integrin/JAM-A -0.025 0.15 -10000 0 -0.29 34 34
CBL 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.052 0.13 -10000 0 -0.35 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.036 0.086 -10000 0 -0.25 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.046 0.12 -10000 0 -0.31 19 19
alphaV/beta3 Integrin/Syndecan-1 0.01 0.12 -10000 0 -0.32 19 19
PI4KA 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0 0.13 -10000 0 -0.28 23 23
PI4 Kinase 0.036 0.012 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
alphaV/beta3 Integrin/Osteopontin -0.012 0.11 -10000 0 -0.29 17 17
RPS6KB1 -0.033 0.13 0.56 2 -0.47 5 7
TLN1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.055 0.18 -10000 0 -0.54 15 15
GPR124 0.008 0.072 -10000 0 -0.46 4 4
MAPK1 -0.056 0.18 -10000 0 -0.53 16 16
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.005 0.12 -10000 0 -0.3 23 23
cell adhesion -0.033 0.11 -10000 0 -0.35 14 14
ANGPTL3 -0.087 0.13 -10000 0 -0.23 76 76
VEGFR2 homodimer/VEGFA homodimer/Src 0.017 0.098 -10000 0 -0.28 16 16
IGF-1R heterotetramer 0.023 0.028 -10000 0 -0.23 2 2
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.026 0.005 -10000 0 -10000 0 0
ITGB3 -0.018 0.14 -10000 0 -0.46 16 16
IGF1 -0.014 0.12 -10000 0 -0.38 17 17
RAC1 0.024 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.007 0.11 -10000 0 -0.32 14 14
apoptosis 0.026 0.005 -10000 0 -10000 0 0
CD47 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.021 0.094 -10000 0 -0.28 15 15
VCL 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.003 0.14 -10000 0 -0.34 24 24
CSF1 0.026 0.006 -10000 0 -10000 0 0
PIK3C2A -0.06 0.17 -10000 0 -0.45 26 26
PI4 Kinase/Pyk2 -0.051 0.14 -10000 0 -0.48 8 8
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.006 0.13 -10000 0 -0.27 28 28
FAK1/Vinculin -0.038 0.15 0.3 5 -0.38 16 21
alphaV beta3/Integrin/ppsTEM5 0.007 0.11 -10000 0 -0.32 14 14
RHOA 0.026 0.005 -10000 0 -10000 0 0
VTN -0.065 0.17 -10000 0 -0.36 41 41
BCAR1 0.023 0.01 -10000 0 -10000 0 0
FGF2 0.015 0.072 -10000 0 -0.46 4 4
F11R 0.009 0.036 -10000 0 -0.33 2 2
alphaV/beta3 Integrin/Lactadherin 0.022 0.094 -10000 0 -0.28 15 15
alphaV/beta3 Integrin/TGFBR2 0.02 0.096 -10000 0 -0.28 16 16
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.029 -10000 0 -10000 0 0
HSP90AA1 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.021 0.086 -10000 0 -0.25 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.025 0.02 -10000 0 -0.23 1 1
alphaV/beta3 Integrin/Pyk2 -0.014 0.11 -10000 0 -0.25 27 27
SDC1 0.01 0.088 -10000 0 -0.46 6 6
VAV3 -0.018 0.089 0.27 2 -0.24 22 24
PTPN11 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.46 1 1
FAK1/Paxillin -0.041 0.15 0.3 4 -0.39 16 20
cell migration -0.039 0.14 0.3 4 -0.34 16 20
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PI3K -0.017 0.14 -10000 0 -0.51 5 5
SPP1 -0.024 0.1 -10000 0 -0.24 33 33
KDR 0.021 0.051 -10000 0 -0.46 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.005 -10000 0 -10000 0 0
COL4A3 0.002 0.11 -10000 0 -0.46 9 9
angiogenesis -0.063 0.19 0.34 2 -0.53 17 19
Rac1/GTP -0.005 0.082 -10000 0 -0.22 21 21
EDIL3 -0.012 0.13 -10000 0 -0.46 14 14
cell proliferation 0.019 0.096 -10000 0 -0.28 16 16
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.064 0.21 0.53 2 -0.77 4 6
CRP -0.068 0.21 0.56 2 -0.77 4 6
cell cycle arrest -0.079 0.23 0.48 1 -0.66 12 13
TIMP1 -0.049 0.2 0.46 1 -0.74 5 6
IL6ST -0.018 0.12 -10000 0 -0.46 12 12
Rac1/GDP -0.076 0.19 -10000 0 -0.44 25 25
AP1 0.015 0.14 0.4 1 -0.67 2 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.12 0.31 0.44 1 -0.97 16 17
HSP90B1 0.01 0.097 -10000 0 -0.7 1 1
GAB1 0.027 0.003 -10000 0 -10000 0 0
MAPK14 -0.13 0.27 -10000 0 -0.7 28 28
AKT1 0.03 0.043 -10000 0 -10000 0 0
FOXO1 0.024 0.041 -10000 0 -10000 0 0
MAP2K6 -0.11 0.22 -10000 0 -0.5 34 34
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.085 0.19 -10000 0 -0.53 16 16
MITF -0.082 0.18 -10000 0 -0.39 33 33
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.004 -10000 0 -10000 0 0
A2M -0.068 0.32 -10000 0 -1.1 14 14
CEBPB 0.03 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.001 0.09 -10000 0 -0.79 1 1
STAT3 -0.086 0.24 0.48 1 -0.7 12 13
STAT1 0.014 0.02 -10000 0 -10000 0 0
CEBPD -0.051 0.24 0.56 2 -0.88 5 7
PIK3CA 0.024 0.021 -10000 0 -0.23 1 1
PI3K 0.034 0.021 -10000 0 -0.16 1 1
JUN 0.026 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.067 0.18 0.21 2 -0.4 29 31
MAPK11 -0.13 0.27 -10000 0 -0.7 28 28
STAT3 (dimer)/FOXO1 -0.046 0.17 -10000 0 -0.62 4 4
GRB2/SOS1/GAB family -0.028 0.16 -10000 0 -0.36 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.066 0.17 -10000 0 -0.34 36 36
GRB2 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.026 0.006 -10000 0 -10000 0 0
LBP -0.046 0.18 0.52 2 -0.58 5 7
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
JAK1 0.018 0.021 -10000 0 -10000 0 0
MYC -0.044 0.23 0.56 2 -0.8 4 6
FGG -0.081 0.22 0.44 1 -0.85 6 7
macrophage differentiation -0.079 0.23 0.48 1 -0.66 12 13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.03 0.15 -10000 0 -0.3 35 35
JUNB -0.093 0.26 0.43 1 -0.97 10 11
FOS -0.038 0.16 -10000 0 -0.45 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.081 0.19 -10000 0 -0.41 33 33
STAT1/PIAS1 -0.057 0.16 -10000 0 -0.41 17 17
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.045 -10000 0 -0.3 1 1
STAT3 (dimer) -0.082 0.24 0.48 1 -0.73 10 11
PRKCD -0.079 0.2 0.3 2 -0.61 13 15
IL6R 0.019 0.02 -10000 0 -10000 0 0
SOCS3 -0.19 0.42 -10000 0 -1.2 25 25
gp130 (dimer)/JAK1/JAK1/LMO4 0.007 0.093 -10000 0 -0.28 13 13
Rac1/GTP -0.08 0.19 -10000 0 -0.48 22 22
HCK 0.022 0.041 -10000 0 -0.34 2 2
MAPKKK cascade 0.015 0.094 -10000 0 -0.59 2 2
bone resorption -0.1 0.29 0.44 1 -0.89 16 17
IRF1 -0.07 0.2 0.45 1 -0.77 4 5
mol:GDP -0.092 0.19 -10000 0 -0.4 36 36
SOS1 0.027 0.004 -10000 0 -10000 0 0
VAV1 -0.092 0.19 -10000 0 -0.41 36 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.25 -10000 0 -0.62 29 29
PTPN11 0.009 0.068 -10000 0 -0.85 1 1
IL6/IL6RA -0.05 0.15 -10000 0 -0.34 32 32
gp130 (dimer)/TYK2/TYK2/LMO4 0.013 0.088 -10000 0 -0.28 12 12
gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.088 -10000 0 -0.28 12 12
IL6 -0.093 0.2 -10000 0 -0.4 47 47
PIAS3 0.026 0.006 -10000 0 -10000 0 0
PTPRE 0.026 0.024 -10000 0 -0.22 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.15 -10000 0 -0.31 39 39
LMO4 0.015 0.026 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.082 0.23 -10000 0 -0.67 12 12
MCL1 0.038 0.058 0.37 1 -10000 0 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.031 0.17 0.46 1 -0.39 20 21
MAP3K8 0.004 0.096 -10000 0 -0.43 8 8
FOS -0.026 0.14 0.36 2 -0.39 12 14
PRKCA 0.013 0.064 -10000 0 -0.46 3 3
PTPN7 0.011 0.051 -10000 0 -0.24 6 6
HRAS 0.026 0.004 -10000 0 -10000 0 0
PRKCB -0.056 0.18 -10000 0 -0.46 28 28
NRAS 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.039 0.026 -10000 0 -10000 0 0
MAPK3 -0.008 0.097 -10000 0 -0.37 6 6
MAP2K1 -0.06 0.2 -10000 0 -0.46 27 27
ELK1 0.02 0.02 -10000 0 -10000 0 0
BRAF -0.049 0.17 -10000 0 -0.44 25 25
mol:GTP -0.001 0.002 -10000 0 -0.005 23 23
MAPK1 -0.009 0.094 -10000 0 -0.37 5 5
RAF1 -0.053 0.17 -10000 0 -0.42 28 28
KRAS 0.025 0.008 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.01 0.11 -10000 0 -0.53 6 6
IHH 0.004 0.097 0.2 1 -0.26 17 18
SHH Np/Cholesterol/GAS1 -0.04 0.12 -10000 0 -0.26 32 32
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.04 0.11 0.26 32 -10000 0 32
SMO/beta Arrestin2 0.021 0.086 -10000 0 -0.35 4 4
SMO 0.004 0.08 -10000 0 -0.37 4 4
AKT1 0.012 0.075 -10000 0 -0.35 3 3
ARRB2 0.024 0.008 -10000 0 -10000 0 0
BOC 0.023 0.037 -10000 0 -0.46 1 1
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
heart looping 0.004 0.08 -10000 0 -0.36 4 4
STIL -0.026 0.12 0.26 2 -0.37 7 9
DHH N/PTCH2 0.034 0.042 -10000 0 -0.33 2 2
DHH N/PTCH1 0.019 0.076 -10000 0 -0.26 10 10
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
DHH 0.02 0.055 -10000 0 -0.38 3 3
PTHLH -0.003 0.17 -10000 0 -0.85 6 6
determination of left/right symmetry 0.004 0.08 -10000 0 -0.36 4 4
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
skeletal system development -0.002 0.17 -10000 0 -0.84 6 6
IHH N/Hhip 0.005 0.1 -10000 0 -0.35 11 11
DHH N/Hhip 0.016 0.087 -10000 0 -0.33 10 10
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.004 0.08 -10000 0 -0.36 4 4
pancreas development 0.003 0.1 -10000 0 -0.43 9 9
HHAT 0.02 0.052 -10000 0 -0.46 2 2
PI3K 0.033 0.021 -10000 0 -0.16 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.007 0.12 -10000 0 -0.46 12 12
somite specification 0.004 0.08 -10000 0 -0.36 4 4
SHH Np/Cholesterol/PTCH1 -0.026 0.11 -10000 0 -0.32 8 8
SHH Np/Cholesterol/PTCH2 -0.025 0.098 -10000 0 -0.25 24 24
SHH Np/Cholesterol/Megalin -0.059 0.13 -10000 0 -0.28 41 41
SHH -0.047 0.12 0.24 1 -0.33 24 25
catabolic process 0.011 0.072 -10000 0 -0.29 8 8
SMO/Vitamin D3 -0.013 0.12 0.31 3 -0.35 8 11
SHH Np/Cholesterol/Hhip -0.034 0.12 -10000 0 -0.3 25 25
LRP2 -0.036 0.16 -10000 0 -0.44 23 23
receptor-mediated endocytosis -0.047 0.13 -10000 0 -0.45 8 8
SHH Np/Cholesterol/BOC -0.025 0.098 -10000 0 -0.26 23 23
SHH Np/Cholesterol/CDO -0.028 0.098 -10000 0 -0.25 24 24
mesenchymal cell differentiation 0.034 0.12 0.3 25 -10000 0 25
mol:Vitamin D3 -0.013 0.12 0.26 3 -0.32 8 11
IHH N/PTCH2 0.024 0.062 -10000 0 -0.27 3 3
CDON 0.019 0.049 -10000 0 -0.29 4 4
IHH N/PTCH1 0.029 0.075 -10000 0 -0.29 8 8
Megalin/LRPAP1 -0.009 0.12 -10000 0 -0.31 23 23
PTCH2 0.027 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.032 0.094 -10000 0 -0.25 24 24
PTCH1 0.011 0.072 -10000 0 -0.29 8 8
HHIP 0.003 0.1 -10000 0 -0.43 9 9
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.065 0.3 -10000 0 -0.8 13 13
HDAC7 0.023 0.017 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.042 0.32 -10000 0 -0.82 15 15
SMAD4 0.025 0.009 -10000 0 -10000 0 0
ID2 -0.067 0.3 -10000 0 -0.82 12 12
AP1 -0.012 0.13 -10000 0 -0.32 24 24
ABCG2 -0.076 0.31 -10000 0 -0.81 15 15
HIF1A -0.004 0.07 -10000 0 -0.22 1 1
TFF3 -0.089 0.32 -10000 0 -0.82 15 15
GATA2 0.023 0.014 -10000 0 -10000 0 0
AKT1 -0.006 0.085 -10000 0 -0.25 4 4
response to hypoxia -0.022 0.07 -10000 0 -0.22 8 8
MCL1 -0.063 0.29 -10000 0 -0.79 13 13
NDRG1 -0.06 0.28 -10000 0 -0.81 10 10
SERPINE1 -0.087 0.3 -10000 0 -0.78 17 17
FECH -0.067 0.3 -10000 0 -0.8 13 13
FURIN -0.066 0.29 -10000 0 -0.8 13 13
NCOA2 -0.005 0.095 -10000 0 -0.46 7 7
EP300 -0.01 0.12 -10000 0 -0.34 12 12
HMOX1 -0.066 0.3 -10000 0 -0.81 13 13
BHLHE40 -0.067 0.3 -10000 0 -0.81 13 13
BHLHE41 -0.067 0.29 -10000 0 -0.8 13 13
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.048 0.095 -10000 0 -10000 0 0
ENG 0.023 0.082 0.27 2 -10000 0 2
JUN 0.025 0.01 -10000 0 -10000 0 0
RORA -0.064 0.3 -10000 0 -0.8 13 13
ABCB1 -0.011 0.12 -10000 0 -0.87 2 2
TFRC -0.067 0.3 -10000 0 -0.82 13 13
CXCR4 -0.067 0.3 -10000 0 -0.8 13 13
TF -0.12 0.34 -10000 0 -0.85 19 19
CITED2 -0.068 0.3 -10000 0 -0.8 13 13
HIF1A/ARNT -0.027 0.37 -10000 0 -0.91 12 12
LDHA 0.013 0.072 -10000 0 -0.5 1 1
ETS1 -0.068 0.29 -10000 0 -0.8 13 13
PGK1 -0.062 0.3 -10000 0 -0.81 12 12
NOS2 -0.087 0.32 -10000 0 -0.85 14 14
ITGB2 -0.067 0.3 -10000 0 -0.8 13 13
ALDOA -0.063 0.3 -10000 0 -0.8 13 13
Cbp/p300/CITED2 -0.083 0.35 -10000 0 -0.9 17 17
FOS -0.039 0.16 -10000 0 -0.45 24 24
HK2 -0.066 0.3 -10000 0 -0.8 13 13
SP1 0.031 0.011 -10000 0 -10000 0 0
GCK -0.056 0.34 -10000 0 -1.4 10 10
HK1 -0.064 0.29 -10000 0 -0.78 13 13
NPM1 -0.064 0.29 -10000 0 -0.81 12 12
EGLN1 -0.065 0.29 -10000 0 -0.79 13 13
CREB1 0.031 0.006 -10000 0 -10000 0 0
PGM1 -0.067 0.3 -10000 0 -0.8 13 13
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.067 0.31 -10000 0 -0.92 16 16
IGFBP1 -0.076 0.28 -10000 0 -0.78 13 13
VEGFA -0.077 0.28 0.39 1 -0.75 13 14
HIF1A/JAB1 0.013 0.054 -10000 0 -10000 0 0
CP -0.097 0.33 -10000 0 -0.85 17 17
CXCL12 -0.07 0.3 -10000 0 -0.8 14 14
COPS5 0.015 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.014 -10000 0 -10000 0 0
BNIP3 -0.067 0.29 -10000 0 -0.79 13 13
EGLN3 -0.068 0.3 -10000 0 -0.83 14 14
CA9 -0.079 0.3 -10000 0 -0.8 12 12
TERT -0.081 0.31 -10000 0 -0.83 14 14
ENO1 -0.064 0.3 -10000 0 -0.8 13 13
PFKL -0.065 0.3 -10000 0 -0.8 13 13
NCOA1 0.023 0.014 -10000 0 -10000 0 0
ADM -0.07 0.3 -10000 0 -0.8 14 14
ARNT 0.003 0.063 -10000 0 -10000 0 0
HNF4A 0.005 0.059 -10000 0 -0.23 8 8
ADFP -0.078 0.29 -10000 0 -0.77 15 15
SLC2A1 -0.055 0.26 0.39 1 -0.7 14 15
LEP -0.073 0.29 -10000 0 -0.81 12 12
HIF1A/ARNT/Cbp/p300 -0.044 0.32 -10000 0 -0.82 15 15
EPO -0.15 0.39 -10000 0 -0.91 31 31
CREBBP -0.008 0.11 -10000 0 -0.33 11 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.045 0.32 -10000 0 -0.82 14 14
PFKFB3 -0.07 0.3 -10000 0 -0.81 13 13
NT5E -0.075 0.3 -10000 0 -0.85 12 12
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.005 0.07 -10000 0 -0.3 7 7
NFATC2 -0.034 0.17 -10000 0 -0.5 9 9
NFATC3 0.003 0.068 -10000 0 -0.27 2 2
CD40LG -0.14 0.25 -10000 0 -0.76 13 13
ITCH -0.01 0.091 -10000 0 -10000 0 0
CBLB -0.007 0.087 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.21 -10000 0 -0.76 7 7
JUNB -0.001 0.11 -10000 0 -0.38 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.11 -10000 0 -0.27 26 26
T cell anergy -0.041 0.15 -10000 0 -0.38 25 25
TLE4 -0.016 0.11 -10000 0 -0.4 4 4
Jun/NFAT1-c-4/p21SNFT -0.05 0.21 -10000 0 -0.73 6 6
AP-1/NFAT1-c-4 -0.11 0.29 -10000 0 -0.88 10 10
IKZF1 -0.025 0.12 -10000 0 -0.44 5 5
T-helper 2 cell differentiation -0.17 0.26 -10000 0 -0.67 19 19
AP-1/NFAT1 -0.05 0.17 -10000 0 -0.41 17 17
CALM1 0.005 0.071 -10000 0 -10000 0 0
EGR2 -0.065 0.2 -10000 0 -1.1 2 2
EGR3 -0.096 0.28 -10000 0 -1.1 9 9
NFAT1/FOXP3 -0.015 0.14 -10000 0 -0.41 9 9
EGR1 -0.033 0.14 -10000 0 -0.32 29 29
JUN 0.01 0.031 -10000 0 -10000 0 0
EGR4 -0.059 0.13 -10000 0 -0.24 54 54
mol:Ca2+ -0.018 0.06 -10000 0 -0.16 26 26
GBP3 -0.083 0.24 -10000 0 -0.65 25 25
FOSL1 -0.1 0.2 -10000 0 -0.41 51 51
NFAT1-c-4/MAF/IRF4 -0.048 0.21 -10000 0 -0.7 7 7
DGKA -0.022 0.12 -10000 0 -0.45 4 4
CREM 0.026 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.06 0.22 -10000 0 -0.77 7 7
CTLA4 -0.031 0.12 -10000 0 -0.38 8 8
NFAT1-c-4 (dimer)/EGR1 -0.068 0.23 -10000 0 -0.83 7 7
NFAT1-c-4 (dimer)/EGR4 -0.071 0.22 -10000 0 -0.73 6 6
FOS -0.055 0.17 -10000 0 -0.46 24 24
IFNG -0.042 0.14 -10000 0 -0.55 4 4
T cell activation -0.049 0.15 -10000 0 -0.66 3 3
MAF 0.022 0.011 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.048 0.15 0.63 5 -10000 0 5
TNF -0.12 0.24 -10000 0 -0.76 12 12
FASLG -0.11 0.3 -10000 0 -1.2 9 9
TBX21 0.015 0.067 -10000 0 -0.32 6 6
BATF3 0.02 0.039 -10000 0 -0.23 4 4
PRKCQ -0.005 0.11 -10000 0 -0.39 13 13
PTPN1 -0.021 0.12 -10000 0 -0.42 4 4
NFAT1-c-4/ICER1 -0.045 0.2 -10000 0 -0.72 6 6
GATA3 -0.12 0.22 -10000 0 -0.46 51 51
T-helper 1 cell differentiation -0.043 0.14 -10000 0 -0.54 4 4
IL2RA -0.096 0.21 -10000 0 -0.73 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.021 0.12 -10000 0 -0.42 4 4
E2F1 0.022 0.043 -10000 0 -0.23 5 5
PPARG -0.011 0.13 -10000 0 -0.44 14 14
SLC3A2 -0.02 0.12 -10000 0 -0.4 5 5
IRF4 -0.005 0.1 -10000 0 -0.32 16 16
PTGS2 -0.16 0.28 -10000 0 -0.78 17 17
CSF2 -0.13 0.24 -10000 0 -0.78 10 10
JunB/Fra1/NFAT1-c-4 -0.11 0.24 -10000 0 -0.89 7 7
IL4 -0.18 0.26 -10000 0 -0.7 19 19
IL5 -0.13 0.24 -10000 0 -0.79 9 9
IL2 -0.05 0.16 -10000 0 -0.67 3 3
IL3 -0.029 0.14 -10000 0 -0.7 6 6
RNF128 -0.061 0.21 -10000 0 -0.53 28 28
NFATC1 -0.049 0.15 -10000 0 -0.63 5 5
CDK4 0.048 0.12 0.48 2 -10000 0 2
PTPRK -0.022 0.12 -10000 0 -0.44 3 3
IL8 -0.15 0.28 -10000 0 -0.78 17 17
POU2F1 0.023 0.025 -10000 0 -0.3 1 1
FOXM1 transcription factor network

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
NFATC3 -0.14 0.35 -9999 0 -1.1 9 9
PLK1 -0.027 0.12 -9999 0 -0.78 2 2
BIRC5 -0.039 0.18 -9999 0 -1.1 4 4
HSPA1B -0.14 0.36 -9999 0 -1.1 9 9
MAP2K1 0.006 0.042 -9999 0 -10000 0 0
BRCA2 -0.16 0.39 -9999 0 -1.2 12 12
FOXM1 -0.17 0.43 -9999 0 -1.2 14 14
XRCC1 -0.14 0.35 -9999 0 -1.1 9 9
FOXM1B/p19 -0.15 0.38 -9999 0 -1.1 14 14
Cyclin D1/CDK4 -0.13 0.33 -9999 0 -0.92 12 12
CDC2 -0.15 0.37 -9999 0 -1 14 14
TGFA -0.14 0.34 -9999 0 -0.96 12 12
SKP2 -0.14 0.36 -9999 0 -1.1 9 9
CCNE1 0.022 0.016 -9999 0 -10000 0 0
CKS1B -0.13 0.35 -9999 0 -1.1 10 10
RB1 -0.11 0.29 -9999 0 -0.76 19 19
FOXM1C/SP1 -0.16 0.4 -9999 0 -1.1 14 14
AURKB -0.1 0.29 -9999 0 -0.98 16 16
CENPF -0.16 0.36 -9999 0 -1.1 10 10
CDK4 0.015 0.024 -9999 0 -10000 0 0
MYC -0.13 0.32 -9999 0 -0.88 13 13
CHEK2 0.007 0.041 -9999 0 -10000 0 0
ONECUT1 -0.14 0.35 -9999 0 -0.98 12 12
CDKN2A -0.035 0.11 -9999 0 -0.23 42 42
LAMA4 -0.14 0.36 -9999 0 -1.1 9 9
FOXM1B/HNF6 -0.16 0.4 -9999 0 -1.2 12 12
FOS -0.23 0.48 -9999 0 -1.2 27 27
SP1 0.026 0.007 -9999 0 -10000 0 0
CDC25B -0.14 0.35 -9999 0 -1.1 10 10
response to radiation -0.004 0.023 -9999 0 -10000 0 0
CENPB -0.14 0.35 -9999 0 -1.1 9 9
CENPA -0.16 0.37 -9999 0 -1.1 10 10
NEK2 -0.16 0.36 -9999 0 -1.1 10 10
HIST1H2BA -0.15 0.35 -9999 0 -1 11 11
CCNA2 -0.025 0.1 -9999 0 -0.24 32 32
EP300 0.026 0.004 -9999 0 -10000 0 0
CCNB1/CDK1 -0.16 0.4 -9999 0 -1.2 12 12
CCNB2 -0.15 0.36 -9999 0 -1.1 9 9
CCNB1 -0.15 0.37 -9999 0 -1.1 12 12
ETV5 -0.16 0.41 -9999 0 -1.2 15 15
ESR1 -0.15 0.37 -9999 0 -1.1 13 13
CCND1 -0.13 0.34 -9999 0 -0.94 12 12
GSK3A 0.009 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.006 0.084 -9999 0 -0.21 1 1
CDK2 0.021 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.14 0.38 -9999 0 -1.1 13 13
GAS1 -0.18 0.44 -9999 0 -1.2 19 19
MMP2 -0.15 0.37 -9999 0 -1.1 13 13
RB1/FOXM1C -0.16 0.36 -9999 0 -1 13 13
CREBBP 0.026 0.004 -9999 0 -10000 0 0
S1P4 pathway

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:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
CDC42/GTP -0.024 0.12 -10000 0 -0.38 10 10
PLCG1 -0.036 0.12 -10000 0 -0.39 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
G12/G13 0.035 0.014 -10000 0 -10000 0 0
cell migration -0.024 0.12 -10000 0 -0.37 10 10
S1PR5 -0.064 0.19 -10000 0 -0.46 33 33
S1PR4 0.021 0.039 -10000 0 -0.23 4 4
MAPK3 -0.034 0.11 -10000 0 -0.39 10 10
MAPK1 -0.033 0.11 -10000 0 -0.4 9 9
S1P/S1P5/Gi -0.08 0.19 -10000 0 -0.33 49 49
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
CDC42/GDP 0.02 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.12 -10000 0 -0.28 33 33
RHOA 0.026 0.054 0.19 14 -10000 0 14
S1P/S1P4/Gi -0.029 0.12 -10000 0 -0.29 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.012 0.13 -10000 0 -0.46 14 14
S1P/S1P4/G12/G13 0.042 0.028 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.027 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.19 0.26 -9999 0 -0.75 13 13
PCK1 -0.12 0.21 -9999 0 -0.72 10 10
HNF4A -0.27 0.36 -9999 0 -0.86 37 37
KCNJ11 -0.17 0.26 -9999 0 -0.77 9 9
AKT1 -0.031 0.12 -9999 0 -10000 0 0
response to starvation -0.017 0.036 -9999 0 -10000 0 0
DLK1 -0.24 0.34 -9999 0 -0.91 26 26
NKX2-1 -0.11 0.16 -9999 0 -10000 0 0
ACADM -0.19 0.26 -9999 0 -0.75 13 13
TAT -0.13 0.2 -9999 0 -0.63 12 12
CEBPB 0.021 0.018 -9999 0 -10000 0 0
CEBPA 0.019 0.021 -9999 0 -10000 0 0
TTR -0.13 0.26 -9999 0 -1.2 7 7
PKLR -0.19 0.26 -9999 0 -0.78 11 11
APOA1 -0.36 0.52 -9999 0 -1.2 38 38
CPT1C -0.2 0.28 -9999 0 -0.81 15 15
ALAS1 -0.078 0.14 -9999 0 -0.53 1 1
TFRC -0.15 0.25 -9999 0 -0.76 15 15
FOXF1 0.021 0.065 -9999 0 -0.44 3 3
NF1 0.031 0.003 -9999 0 -10000 0 0
HNF1A (dimer) -0.012 0.09 -9999 0 -0.24 23 23
CPT1A -0.19 0.26 -9999 0 -0.76 12 12
HMGCS1 -0.19 0.26 -9999 0 -0.74 13 13
NR3C1 0.028 0.014 -9999 0 -10000 0 0
CPT1B -0.19 0.26 -9999 0 -0.76 13 13
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.022 0.024 -9999 0 -10000 0 0
GCK -0.2 0.3 -9999 0 -0.81 20 20
CREB1 0.02 0.028 -9999 0 -0.18 1 1
IGFBP1 -0.087 0.14 -9999 0 -0.54 1 1
PDX1 -0.1 0.2 -9999 0 -1.4 2 2
UCP2 -0.19 0.27 -9999 0 -0.81 9 9
ALDOB -0.17 0.26 -9999 0 -0.77 9 9
AFP -0.019 0.084 -9999 0 -0.4 2 2
BDH1 -0.18 0.26 -9999 0 -0.76 11 11
HADH -0.18 0.25 -9999 0 -0.76 9 9
F2 -0.25 0.33 -9999 0 -0.91 15 15
HNF1A -0.012 0.09 -9999 0 -0.24 23 23
G6PC -0.017 0.079 -9999 0 -10000 0 0
SLC2A2 -0.11 0.16 -9999 0 -0.57 1 1
INS -0.021 0.02 -9999 0 -0.24 1 1
FOXA1 0.014 0.058 -9999 0 -0.26 2 2
FOXA3 -0.04 0.14 -9999 0 -0.4 19 19
FOXA2 -0.2 0.3 -9999 0 -0.83 11 11
ABCC8 -0.22 0.33 -9999 0 -0.91 21 21
ALB -0.034 0.11 -9999 0 -0.57 3 3
BMP receptor signaling

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0 0.13 -10000 0 -0.25 34 34
SMAD6-7/SMURF1 0.04 0.041 -10000 0 -0.28 2 2
NOG -0.038 0.16 -10000 0 -0.46 23 23
SMAD9 -0.044 0.16 -10000 0 -0.39 28 28
SMAD4 0.024 0.009 -10000 0 -10000 0 0
SMAD5 0.001 0.058 0.23 1 -10000 0 1
BMP7/USAG1 -0.11 0.22 -10000 0 -0.41 56 56
SMAD5/SKI 0.007 0.07 0.23 1 -10000 0 1
SMAD1 0.025 0.035 -10000 0 -10000 0 0
BMP2 0.007 0.095 -10000 0 -0.46 7 7
SMAD1/SMAD1/SMAD4 0.032 0.036 -10000 0 -10000 0 0
BMPR1A 0.024 0.009 -10000 0 -10000 0 0
BMPR1B 0.022 0.034 -10000 0 -0.23 3 3
BMPR1A-1B/BAMBI 0.035 0.05 -10000 0 -0.28 1 1
AHSG 0.013 0.038 -10000 0 -0.23 4 4
CER1 0.012 0.042 -10000 0 -0.23 5 5
BMP2-4/CER1 0.021 0.09 -10000 0 -0.32 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0 0.078 -10000 0 -0.31 4 4
BMP2-4 (homodimer) 0.016 0.093 -10000 0 -0.35 10 10
RGMB 0.025 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.043 0.056 -10000 0 -10000 0 0
RGMA 0.013 0.081 -10000 0 -0.46 5 5
SMURF1 0.024 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.005 0.072 -10000 0 -0.34 3 3
BMP2-4/USAG1 -0.062 0.17 -10000 0 -0.31 52 52
SMAD6/SMURF1/SMAD5 0.008 0.063 0.23 1 -10000 0 1
SOSTDC1 -0.12 0.22 -10000 0 -0.46 51 51
BMP7/BMPR2/BMPR1A-1B 0.005 0.12 -10000 0 -0.25 28 28
SKI 0.027 0.003 -10000 0 -10000 0 0
BMP6 (homodimer) 0.001 0.078 -10000 0 -0.24 17 17
HFE2 -0.002 0.073 -10000 0 -0.23 16 16
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.022 0.011 -10000 0 -10000 0 0
BMP2-4/CHRD 0.012 0.09 -10000 0 -0.31 7 7
SMAD5/SMAD5/SMAD4 0.011 0.064 0.23 1 -10000 0 1
MAPK1 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB family 0.008 0.065 -10000 0 -0.3 1 1
BMP7 (homodimer) -0.052 0.18 -10000 0 -0.46 28 28
NUP214 0.026 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.013 0.058 -10000 0 -0.16 16 16
SMAD1/SKI 0.041 0.046 0.31 1 -10000 0 1
SMAD6 0.021 0.051 -10000 0 -0.46 2 2
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.023 0.081 -10000 0 -0.31 8 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.032 0.14 -10000 0 -0.31 31 31
BMPR2 (homodimer) 0.027 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.051 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.032 0.027 -10000 0 -0.16 2 2
CHRDL1 -0.056 0.18 -10000 0 -0.46 30 30
ENDOFIN/SMAD1 0.041 0.047 0.31 1 -10000 0 1
SMAD6-7/SMURF1/SMAD1 0.048 0.051 0.3 1 -10000 0 1
SMAD6/SMURF1 0.024 0.009 -10000 0 -10000 0 0
BAMBI 0.013 0.062 -10000 0 -0.26 8 8
SMURF2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.022 0.15 -10000 0 -0.31 36 36
BMP2-4/GREM1 -0.006 0.12 -10000 0 -0.32 19 19
SMAD7 0.024 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.036 0.16 -10000 0 -0.36 30 30
SMAD1/SMAD6 0.035 0.043 0.31 1 -10000 0 1
TAK1/SMAD6 0.029 0.018 -10000 0 -10000 0 0
BMP7 -0.052 0.18 -10000 0 -0.46 28 28
BMP6 0.001 0.078 -10000 0 -0.24 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.076 -10000 0 -0.33 4 4
PPM1A 0.027 0.003 -10000 0 -10000 0 0
SMAD1/SMURF2 0.04 0.046 0.31 1 -10000 0 1
SMAD7/SMURF1 0.032 0.016 -10000 0 -10000 0 0
CTDSPL 0.026 0.005 -10000 0 -10000 0 0
PPP1CA 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
CTDSP1 0.027 0.003 -10000 0 -10000 0 0
PPP1R15A 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.023 0.12 -10000 0 -0.41 10 10
CHRD -0.004 0.08 -10000 0 -0.23 19 19
BMPR2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.005 0.076 -10000 0 -0.35 4 4
BMP4 0.016 0.072 -10000 0 -0.46 4 4
FST -0.004 0.11 -10000 0 -0.44 11 11
BMP2-4/NOG -0.011 0.14 -10000 0 -0.31 30 30
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.015 0.11 -10000 0 -0.24 23 23
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.001 0.026 -9999 0 -10000 0 0
NFATC2 -0.023 0.08 -9999 0 -0.29 13 13
NFATC3 -0.001 0.026 -9999 0 -10000 0 0
CD40LG -0.087 0.18 -9999 0 -0.48 16 16
PTGS2 -0.11 0.21 -9999 0 -0.51 27 27
JUNB -0.001 0.11 -9999 0 -0.38 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.022 -9999 0 -10000 0 0
CaM/Ca2+ 0.009 0.021 -9999 0 -10000 0 0
CALM1 0.018 0.019 -9999 0 -10000 0 0
JUN 0.02 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.004 0.008 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.013 -9999 0 -0.12 1 1
FOSL1 -0.1 0.2 -9999 0 -0.41 51 51
CREM 0.026 0.005 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.022 0.11 -9999 0 -0.34 7 7
FOS -0.045 0.16 -9999 0 -0.46 24 24
IFNG -0.085 0.17 -9999 0 -0.45 16 16
AP-1/NFAT1-c-4 -0.078 0.2 -9999 0 -0.51 14 14
FASLG -0.083 0.16 -9999 0 -0.46 14 14
NFAT1-c-4/ICER1 -0.02 0.087 -9999 0 -0.3 6 6
IL2RA -0.095 0.18 -9999 0 -0.45 18 18
FKBP12/FK506 0.018 0.014 -9999 0 -0.15 1 1
CSF2 -0.083 0.16 -9999 0 -0.46 13 13
JunB/Fra1/NFAT1-c-4 -0.083 0.15 -9999 0 -0.33 32 32
IL4 -0.083 0.16 -9999 0 -0.47 11 11
IL2 -0.013 0.16 -9999 0 -0.86 6 6
IL3 -0.016 0.15 -9999 0 -0.74 7 7
FKBP1A 0.025 0.02 -9999 0 -0.23 1 1
BATF3 0.02 0.039 -9999 0 -0.23 4 4
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.023 0.025 -9999 0 -0.3 1 1
LPA receptor mediated events

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
GNB1/GNG2 0.043 0.06 -10000 0 -0.28 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.098 0.3 2 -0.32 5 7
AP1 -0.023 0.13 -10000 0 -0.29 28 28
mol:PIP3 -0.015 0.079 -10000 0 -0.26 11 11
AKT1 0.043 0.082 0.28 10 -0.33 1 11
PTK2B -0.044 0.11 0.17 1 -0.27 18 19
RHOA 0.014 0.033 -10000 0 -10000 0 0
PIK3CB 0.024 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.093 0.26 6 -0.26 9 15
MAGI3 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.012 0.093 -10000 0 -0.27 16 16
HRAS/GDP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.035 0.095 0.21 2 -0.27 10 12
NF kappa B1 p50/RelA -0.005 0.092 -10000 0 -0.33 7 7
endothelial cell migration 0.007 0.076 -10000 0 -0.45 4 4
ADCY4 -0.021 0.13 -10000 0 -0.48 9 9
ADCY5 -0.039 0.17 -10000 0 -0.54 14 14
ADCY6 -0.021 0.13 -10000 0 -0.44 10 10
ADCY7 -0.022 0.13 -10000 0 -0.45 10 10
ADCY1 -0.026 0.12 -10000 0 -0.44 9 9
ADCY2 -0.021 0.13 -10000 0 -0.48 9 9
ADCY3 -0.021 0.13 -10000 0 -0.48 9 9
ADCY8 -0.025 0.12 -10000 0 -0.46 9 9
ADCY9 -0.02 0.12 -10000 0 -0.46 9 9
GSK3B -0.037 0.1 0.22 2 -0.28 11 13
arachidonic acid secretion -0.031 0.13 -10000 0 -0.42 12 12
GNG2 0.027 0.002 -10000 0 -10000 0 0
TRIP6 0.011 0.055 -10000 0 -0.35 4 4
GNAO1 -0.033 0.12 -10000 0 -0.31 27 27
HRAS 0.027 0.004 -10000 0 -10000 0 0
NFKBIA -0.002 0.11 0.33 4 -0.31 10 14
GAB1 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.02 0.14 -10000 0 -0.8 5 5
JUN 0.026 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.018 -10000 0 -10000 0 0
TIAM1 0.004 0.16 -10000 0 -0.93 5 5
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
mol:IP3 -0.009 0.093 0.26 6 -0.25 12 18
PLCB3 0.02 0.031 0.18 5 -10000 0 5
FOS -0.038 0.16 -10000 0 -0.45 24 24
positive regulation of mitosis -0.031 0.13 -10000 0 -0.42 12 12
LPA/LPA1-2-3 0.015 0.1 -10000 0 -0.27 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.023 0.01 -10000 0 -10000 0 0
stress fiber formation -0.016 0.1 0.26 2 -0.3 8 10
GNAZ -0.013 0.11 -10000 0 -0.35 15 15
EGFR/PI3K-beta/Gab1 -0.006 0.086 -10000 0 -0.31 6 6
positive regulation of dendritic cell cytokine production 0.014 0.1 -10000 0 -0.27 15 15
LPA/LPA2/MAGI-3 0.036 0.014 -10000 0 -10000 0 0
ARHGEF1 0.034 0.075 0.18 23 -0.27 4 27
GNAI2 0.011 0.053 -10000 0 -0.32 4 4
GNAI3 0.009 0.057 -10000 0 -0.31 5 5
GNAI1 0.008 0.058 -10000 0 -0.31 5 5
LPA/LPA3 -0.012 0.095 -10000 0 -0.26 20 20
LPA/LPA2 0.021 0.011 -10000 0 -0.11 1 1
LPA/LPA1 0.013 0.067 -10000 0 -0.36 5 5
HB-EGF/EGFR -0.076 0.094 0.18 1 -0.28 11 12
HBEGF -0.092 0.093 0.24 2 -0.27 5 7
mol:DAG -0.009 0.093 0.26 6 -0.25 12 18
cAMP biosynthetic process -0.029 0.15 0.23 4 -0.42 15 19
NFKB1 0.027 0.003 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.027 0.003 -10000 0 -10000 0 0
LYN 0.008 0.12 0.34 9 -0.3 10 19
GNAQ -0.006 0.07 -10000 0 -0.25 12 12
LPAR2 0.027 0.003 -10000 0 -10000 0 0
LPAR3 -0.019 0.13 -10000 0 -0.38 19 19
LPAR1 0.015 0.079 -10000 0 -0.42 5 5
IL8 -0.074 0.16 0.34 1 -0.44 21 22
PTK2 -0.007 0.084 0.19 3 -0.26 13 16
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.012 0.093 -10000 0 -0.27 16 16
EGFR 0.007 0.088 -10000 0 -0.46 6 6
PLCG1 -0.016 0.086 0.16 1 -0.28 14 15
PLD2 -0.006 0.092 0.18 7 -0.26 15 22
G12/G13 0.039 0.057 -10000 0 -0.28 4 4
PI3K-beta 0.014 0.042 -10000 0 -0.37 1 1
cell migration 0.004 0.057 -10000 0 -0.23 5 5
SLC9A3R2 0.025 0.02 -10000 0 -0.23 1 1
PXN -0.017 0.1 0.26 2 -0.31 8 10
HRAS/GTP -0.034 0.13 -10000 0 -0.43 12 12
RAC1 0.024 0.008 -10000 0 -10000 0 0
MMP9 -0.14 0.13 -10000 0 -0.24 108 108
PRKCE 0.027 0.004 -10000 0 -10000 0 0
PRKCD -0.006 0.095 0.24 9 -0.31 4 13
Gi(beta/gamma) -0.019 0.12 -10000 0 -0.44 9 9
mol:LPA 0.001 0.014 -10000 0 -0.16 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.005 0.096 -10000 0 -0.37 5 5
MAPKKK cascade -0.031 0.13 -10000 0 -0.42 12 12
contractile ring contraction involved in cytokinesis 0.018 0.048 0.47 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.006 0.07 -10000 0 -0.25 12 12
GNA15 -0.022 0.099 -10000 0 -0.28 21 21
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.036 0.097 0.21 2 -0.27 10 12
GNA11 -0.01 0.077 -10000 0 -0.26 14 14
Rac1/GTP 0.021 0.15 -10000 0 -0.85 5 5
MMP2 0.007 0.076 -10000 0 -0.45 4 4
ErbB2/ErbB3 signaling events

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
USP8 -0.006 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.095 -10000 0 -0.24 8 8
NFATC4 -0.038 0.079 0.24 4 -0.24 6 10
ERBB2IP 0.026 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.003 -10000 0 -10000 0 0
mammary gland morphogenesis -0.024 0.09 -10000 0 -0.25 18 18
JUN -0.013 0.074 0.2 2 -0.34 2 4
HRAS 0.026 0.004 -10000 0 -10000 0 0
DOCK7 -0.048 0.076 -10000 0 -0.25 17 17
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.004 0.095 -10000 0 -0.26 17 17
AKT1 0.003 0.007 -10000 0 -10000 0 0
BAD -0.005 0.004 -10000 0 -10000 0 0
MAPK10 -0.021 0.062 0.19 4 -0.21 1 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.025 0.096 -10000 0 -0.27 18 18
RAF1 -0.029 0.088 0.24 2 -0.26 4 6
ErbB2/ErbB3/neuregulin 2 -0.063 0.14 -10000 0 -0.27 51 51
STAT3 -0.014 0.2 -10000 0 -0.93 8 8
cell migration -0.008 0.076 0.22 9 -0.2 1 10
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.061 0.16 -10000 0 -0.48 7 7
FOS -0.07 0.18 -10000 0 -0.48 25 25
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.09 -10000 0 -0.25 18 18
MAPK3 -0.045 0.13 0.4 1 -0.39 4 5
MAPK1 -0.047 0.14 0.36 1 -0.7 2 3
JAK2 -0.047 0.076 -10000 0 -0.25 17 17
NF2 0.004 0.055 -10000 0 -0.71 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.016 0.082 -10000 0 -0.24 19 19
NRG1 -0.033 0.15 -10000 0 -0.46 19 19
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
MAPK8 -0.046 0.1 -10000 0 -0.26 18 18
MAPK9 -0.021 0.06 0.19 4 -0.21 1 5
ERBB2 -0.021 0.026 -10000 0 -0.34 1 1
ERBB3 0.025 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
apoptosis 0.008 0.018 -10000 0 -0.15 1 1
STAT3 (dimer) -0.012 0.2 -10000 0 -0.9 8 8
RNF41 -0.009 0.006 -10000 0 -10000 0 0
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.03 0.063 -10000 0 -0.19 17 17
ErbB2/ErbB2/HSP90 (dimer) 0.002 0.03 -10000 0 -0.29 1 1
CHRNA1 -0.048 0.13 0.32 1 -0.4 5 6
myelination -0.027 0.091 0.25 6 -0.28 2 8
PPP3CB -0.046 0.071 -10000 0 -0.23 18 18
KRAS 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.01 0.093 -10000 0 -0.22 18 18
NRG2 -0.13 0.22 -10000 0 -0.46 56 56
mol:GDP -0.016 0.082 -10000 0 -0.24 19 19
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K2 -0.035 0.087 0.24 2 -0.28 4 6
SRC 0.026 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.048 0.076 -10000 0 -0.25 18 18
MAP2K1 -0.06 0.14 -10000 0 -0.47 4 4
heart morphogenesis -0.024 0.09 -10000 0 -0.25 18 18
RAS family/GDP -0.003 0.099 -10000 0 -0.24 7 7
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.007 0.058 -10000 0 -0.75 1 1
CHRNE 0.001 0.025 -10000 0 -0.18 2 2
HSP90AA1 0.027 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.007 -10000 0 -10000 0 0
nervous system development -0.024 0.09 -10000 0 -0.25 18 18
CDC42 0.027 0 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.008 0.11 0.2 1 -0.32 10 11
TBX21 -0.052 0.26 -10000 0 -0.75 11 11
B2M 0.025 0.016 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.011 0.057 -10000 0 -0.25 6 6
GADD45B -0.038 0.23 -10000 0 -0.71 11 11
IL12RB2 -0.002 0.099 -10000 0 -0.38 10 10
GADD45G -0.047 0.24 -10000 0 -0.72 12 12
natural killer cell activation 0.002 0.015 -10000 0 -10000 0 0
RELB 0.025 0.02 -10000 0 -0.23 1 1
RELA 0.026 0.005 -10000 0 -10000 0 0
IL18 0.005 0.092 -10000 0 -0.43 7 7
IL2RA -0.026 0.1 -10000 0 -0.23 35 35
IFNG 0.008 0.062 -10000 0 -0.23 11 11
STAT3 (dimer) -0.041 0.21 -10000 0 -0.55 15 15
HLA-DRB5 0.008 0.063 -10000 0 -0.26 8 8
FASLG -0.044 0.24 -10000 0 -0.73 9 9
NF kappa B2 p52/RelB -0.035 0.23 -10000 0 -0.61 14 14
CD4 0.015 0.038 -10000 0 -0.24 3 3
SOCS1 0.012 0.077 -10000 0 -0.38 6 6
EntrezGene:6955 -0.004 0.014 -10000 0 -10000 0 0
CD3D 0.01 0.058 -10000 0 -0.29 5 5
CD3E 0.014 0.041 -10000 0 -0.25 3 3
CD3G -0.016 0.12 -10000 0 -0.37 16 16
IL12Rbeta2/JAK2 0.016 0.082 -10000 0 -0.3 8 8
CCL3 -0.071 0.3 -10000 0 -0.92 13 13
CCL4 -0.049 0.24 -10000 0 -0.77 8 8
HLA-A 0.021 0.04 -10000 0 -0.46 1 1
IL18/IL18R 0.016 0.13 -10000 0 -0.32 18 18
NOS2 -0.088 0.34 -10000 0 -1.1 15 15
IL12/IL12R/TYK2/JAK2/SPHK2 0 0.093 0.2 1 -0.26 7 8
IL1R1 -0.046 0.22 -10000 0 -0.66 9 9
IL4 -0.006 0.03 -10000 0 -10000 0 0
JAK2 0.019 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.033 0.17 -10000 0 -0.59 11 11
RAB7A -0.016 0.21 0.48 1 -0.62 9 10
lysosomal transport -0.013 0.2 0.47 1 -0.59 9 10
FOS -0.15 0.45 -10000 0 -1.2 24 24
STAT4 (dimer) -0.024 0.22 0.5 1 -0.59 12 13
STAT5A (dimer) -0.044 0.23 -10000 0 -0.6 15 15
GZMA -0.049 0.23 -10000 0 -0.7 10 10
GZMB -0.064 0.27 -10000 0 -0.84 11 11
HLX 0.02 0.039 -10000 0 -0.23 4 4
LCK -0.052 0.24 -10000 0 -0.64 15 15
TCR/CD3/MHC II/CD4 -0.028 0.12 -10000 0 -0.31 17 17
IL2/IL2R 0.014 0.093 -10000 0 -0.28 7 7
MAPK14 -0.037 0.24 -10000 0 -0.72 11 11
CCR5 -0.035 0.22 0.43 1 -0.65 10 11
IL1B -0.039 0.15 -10000 0 -0.38 27 27
STAT6 -0.001 0.11 0.2 1 -0.92 1 2
STAT4 0.005 0.09 -10000 0 -0.34 10 10
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.019 0.043 -10000 0 -0.23 5 5
NFKB1 0.027 0.003 -10000 0 -10000 0 0
NFKB2 0.026 0.006 -10000 0 -10000 0 0
IL12B 0.001 0.074 -10000 0 -0.24 13 13
CD8A 0.015 0.061 -10000 0 -0.35 4 4
CD8B 0.005 0.088 -10000 0 -0.38 8 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.008 0.11 0.32 10 -0.2 1 11
IL2RB 0.017 0.061 -10000 0 -0.32 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.21 0.49 1 -0.55 12 13
IL2RG 0.017 0.051 -10000 0 -0.23 7 7
IL12 -0.01 0.11 -10000 0 -0.3 18 18
STAT5A 0.026 0.005 -10000 0 -10000 0 0
CD247 0.014 0.041 -10000 0 -0.25 3 3
IL2 0.022 0.006 -10000 0 -10000 0 0
SPHK2 0.026 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.023 0.14 -10000 0 -0.45 15 15
IL12/IL12R/TYK2/JAK2 -0.049 0.25 -10000 0 -0.65 16 16
MAP2K3 -0.042 0.24 -10000 0 -0.74 11 11
RIPK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K6 -0.041 0.24 -10000 0 -0.69 12 12
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.027 -10000 0 -0.24 1 1
IL18RAP -0.01 0.12 -10000 0 -0.41 14 14
IL12Rbeta1/TYK2 0.027 0.054 -10000 0 -0.18 5 5
EOMES -0.033 0.23 -10000 0 -1.1 7 7
STAT1 (dimer) -0.027 0.21 -10000 0 -0.56 13 13
T cell proliferation -0.024 0.19 0.44 1 -0.48 10 11
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.015 0.068 -10000 0 -0.41 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.035 0.21 -10000 0 -0.58 11 11
ATF2 -0.034 0.22 -10000 0 -0.67 11 11
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.013 0.097 -10000 0 -0.31 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.12 0.33 2 -0.42 5 7
alphaV/beta3 Integrin/Osteopontin/Src 0.003 0.079 -10000 0 -0.32 1 1
AP1 -0.024 0.14 -10000 0 -0.43 8 8
ILK -0.021 0.1 0.37 1 -0.31 6 7
bone resorption -0.014 0.09 0.33 1 -0.33 5 6
PTK2B 0.018 0.013 -10000 0 -10000 0 0
PYK2/p130Cas 0 0.095 -10000 0 -0.28 5 5
ITGAV 0.027 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.035 0.04 -10000 0 -0.33 2 2
alphaV/beta3 Integrin/Osteopontin -0.007 0.12 -10000 0 -0.3 17 17
MAP3K1 -0.023 0.097 0.19 3 -0.27 17 20
JUN 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.029 0.1 0.24 4 -0.35 7 11
MAPK1 -0.032 0.1 0.25 3 -0.35 7 10
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.023 0.087 0.2 4 -0.26 14 18
ITGB3 -0.018 0.14 -10000 0 -0.46 16 16
NFKBIA -0.031 0.11 0.25 3 -0.42 6 9
FOS -0.038 0.16 -10000 0 -0.45 24 24
CD44 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.025 0.007 -10000 0 -10000 0 0
PLAU -0.063 0.25 -10000 0 -1.1 8 8
NF kappa B1 p50/RelA 0.001 0.12 0.31 1 -0.38 8 9
BCAR1 0.023 0.01 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.006 0.11 -10000 0 -0.34 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.021 0.099 0.23 4 -0.27 15 19
VAV3 -0.054 0.13 0.24 4 -0.3 26 30
MAP3K14 -0.026 0.1 0.25 3 -0.28 17 20
ROCK2 0.021 0.051 -10000 0 -0.46 2 2
SPP1 -0.023 0.1 -10000 0 -0.23 33 33
RAC1 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.041 0.12 0.23 3 -0.28 23 26
MMP2 -0.039 0.12 -10000 0 -0.4 8 8
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.003 -10000 0 -10000 0 0
VLDLR 0.024 0.02 -10000 0 -0.23 1 1
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.027 0 -10000 0 -10000 0 0
RELN/LRP8 0.022 0.066 -10000 0 -0.28 1 1
CaM/Ca2+ 0.02 0.003 -10000 0 -10000 0 0
KATNA1 0.026 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.014 0.067 0.18 13 -0.25 1 14
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 -0.15 0.23 -10000 0 -0.45 66 66
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
PLA2G7 -0.067 0.13 -10000 0 -0.24 62 62
CALM1 0.027 0.004 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.025 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.006 -10000 0 -10000 0 0
CDK5R1 0.006 0.07 -10000 0 -0.23 14 14
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 -0.026 0.1 -10000 0 -0.23 35 35
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.085 0.15 -10000 0 -0.29 56 56
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.016 0.096 0.3 10 -10000 0 10
MAP1B 0 0.041 -10000 0 -0.27 4 4
RAC1 0.012 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.001 0.06 0.2 3 -0.23 1 4
RELN -0.015 0.096 -10000 0 -0.24 26 26
PAFAH/LIS1 -0.028 0.076 -10000 0 -0.28 1 1
LIS1/CLIP170 0.026 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.001 0.059 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.068 0.13 -10000 0 -0.24 56 56
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.003 0.094 0.32 9 -0.26 1 10
LIS1/IQGAP1 0.027 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.012 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.023 0.028 -10000 0 -0.23 2 2
PAFAH1B2 0.026 0.006 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.041 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.019 0.1 0.3 10 -10000 0 10
LRP8 0.022 0.034 -10000 0 -0.23 3 3
NDEL1/Katanin 60 0.012 0.098 0.3 10 -10000 0 10
P39/CDK5 -0.005 0.085 0.29 5 -0.32 1 6
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.027 0.01 -10000 0 -10000 0 0
CDK5 -0.017 0.044 0.18 2 -0.24 1 3
PPP2R5D 0.027 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.066 0.14 -10000 0 -0.25 54 54
RELN/VLDLR 0.032 0.067 -10000 0 -0.25 1 1
CDC42 0.013 0.005 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.038 0.089 -10000 0 -0.27 12 12
MAP4K1 0.011 0.075 -10000 0 -0.32 8 8
MAP3K8 0.005 0.096 -10000 0 -0.43 8 8
PRKCB -0.051 0.18 -10000 0 -0.46 28 28
DBNL 0.024 0.008 -10000 0 -10000 0 0
CRKL 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.012 0.055 -10000 0 -0.3 1 1
JUN -0.071 0.22 -10000 0 -0.54 30 30
MAP3K7 0.012 0.052 -10000 0 -0.27 2 2
GRAP2 0.012 0.077 -10000 0 -0.38 6 6
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 0.002 0.069 0.23 1 -0.33 3 4
LAT 0.018 0.058 -10000 0 -0.34 4 4
LCP2 0.022 0.034 -10000 0 -0.23 3 3
MAPK8 -0.071 0.23 -10000 0 -0.57 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.07 -10000 0 -0.26 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.045 0.083 -10000 0 -0.26 9 9
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.026 0.005 -9999 0 -10000 0 0
ITGB7 0.007 0.092 -9999 0 -0.4 8 8
ITGA4 0.006 0.085 -9999 0 -0.32 10 10
alpha4/beta7 Integrin 0.01 0.099 -9999 0 -0.31 14 14
alpha4/beta1 Integrin 0.023 0.065 -9999 0 -0.22 10 10
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.017 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.03 0.09 -10000 0 -0.78 2 2
EGFR 0.008 0.088 -10000 0 -0.46 6 6
EPHA2 -0.02 0.14 -10000 0 -0.43 18 18
USP6 0.025 0.008 -10000 0 -10000 0 0
IQSEC1 0.026 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.008 0.099 -10000 0 -0.2 31 31
ARRB2 0.01 0.004 -10000 0 -10000 0 0
mol:GTP 0.012 0.038 0.13 6 -0.14 1 7
ARRB1 0.026 0.005 -10000 0 -10000 0 0
FBXO8 0.026 0.004 -10000 0 -10000 0 0
TSHR -0.006 0.11 -10000 0 -0.35 15 15
EGF -0.023 0.11 -10000 0 -0.25 31 31
somatostatin receptor activity 0 0 0.001 16 -0.001 2 18
ARAP2 0.026 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.085 0.2 15 -0.22 4 19
mol:PI-3-4-5-P3 0 0 0.001 14 -0.001 1 15
ITGA2B 0.002 0.1 -10000 0 -0.46 8 8
ARF6 0.027 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.034 0.083 -10000 0 -0.25 11 11
ADAP1 0.024 0.008 -10000 0 -10000 0 0
KIF13B 0.019 0.012 -10000 0 -10000 0 0
HGF/MET -0.002 0.11 -10000 0 -0.26 22 22
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.022 0.1 0.27 15 -0.28 2 17
EGFR/EGFR/EGF/EGF/ARFGEP100 0.008 0.091 -10000 0 -0.29 8 8
ADRB2 0.024 0.028 -10000 0 -0.23 2 2
receptor agonist activity 0 0 0 9 0 2 11
actin filament binding 0 0 0.001 16 -0.001 2 18
SRC 0.026 0.006 -10000 0 -10000 0 0
ITGB3 -0.018 0.14 -10000 0 -0.46 16 16
GNAQ 0.026 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 21 -0.001 1 22
ARF6/GDP 0.006 0.1 0.25 5 -0.38 2 7
ARF6/GDP/GULP/ACAP1 0.032 0.088 0.23 5 -0.29 1 6
alphaIIb/beta3 Integrin/paxillin/GIT1 0.013 0.11 -10000 0 -0.26 23 23
ACAP1 0.014 0.055 -10000 0 -0.29 5 5
ACAP2 0.025 0.008 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.021 -10000 0 -10000 0 0
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF 0.004 0.078 -10000 0 -0.27 12 12
CYTH3 0.007 0.021 0.23 1 -0.15 1 2
CYTH2 0.008 0.11 -10000 0 -0.98 2 2
NCK1 0.024 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 18 -0.001 1 19
endosomal lumen acidification 0 0 0.001 14 0 2 16
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.023 0.028 -10000 0 -0.23 2 2
GNAQ/ARNO 0.024 0.1 -10000 0 -0.91 2 2
mol:Phosphatidic acid 0 0 0 5 -10000 0 5
PIP3-E 0 0 0 11 -10000 0 11
MET -0.006 0.12 -10000 0 -0.46 11 11
GNA14 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.002 0.11 -10000 0 -0.46 9 9
GIT1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 17 -0.001 1 18
GNA11 0.024 0.037 -10000 0 -0.46 1 1
LHCGR 0.02 0.006 -10000 0 -10000 0 0
AGTR1 -0.037 0.11 -10000 0 -0.24 41 41
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.021 -10000 0 -10000 0 0
IPCEF1/ARNO 0.004 0.11 -10000 0 -0.83 2 2
alphaIIb/beta3 Integrin -0.014 0.13 -10000 0 -0.34 23 23
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.026 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0 0.077 -9999 0 -0.17 5 5
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.001 0.037 -9999 0 -0.42 1 1
AURKB -0.052 0.12 -9999 0 -0.24 51 51
AURKC 0.024 0.037 -9999 0 -0.46 1 1
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.001 0.035 0.11 1 -0.14 6 7
BUB1B -0.013 0.043 0.15 3 -10000 0 3
PLK1 0.006 0.031 0.11 5 -0.1 3 8
PLK1S1 0.006 0.034 0.19 1 -0.16 4 5
KIF2A 0.004 0.026 0.14 2 -10000 0 2
regulation of mitotic centrosome separation 0.006 0.031 0.11 5 -0.1 3 8
GOLGA2 0.026 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.003 0.068 -10000 0 -0.18 3 3
WEE1 0.009 0.05 0.22 1 -0.36 2 3
cytokinesis -0.011 0.059 0.2 3 -0.24 3 6
PP2A-alpha B56 0.034 0.12 -10000 0 -0.52 8 8
AURKA 0.011 0.023 0.15 2 -10000 0 2
PICH/PLK1 -0.004 0.054 -10000 0 -0.2 6 6
CENPE -0.015 0.051 0.18 1 -0.15 6 7
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.004 0.027 0.14 2 -10000 0 2
PPP2CA 0.026 0.005 -10000 0 -10000 0 0
FZR1 0.026 0.004 -10000 0 -10000 0 0
TPX2 0.006 0.03 0.16 3 -10000 0 3
PAK1 0.018 0.064 -10000 0 -0.46 3 3
SPC24 -0.036 0.11 -10000 0 -0.24 42 42
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN 0.004 0.035 0.13 1 -0.26 2 3
GORASP1 0.026 0.005 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.015 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.017 0.062 5 -0.053 4 9
G2 phase of mitotic cell cycle -0.001 0.001 -10000 0 -10000 0 0
STAG2 0.027 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.019 0.031 -10000 0 -0.37 1 1
spindle elongation 0.006 0.031 0.11 5 -0.1 3 8
ODF2 0.026 0.006 -10000 0 -10000 0 0
BUB1 0.004 0.13 -10000 0 -0.58 8 8
TPT1 -0.037 0.085 0.13 1 -0.18 43 44
CDC25C 0.003 0.042 0.14 1 -0.25 3 4
CDC25B 0.024 0.011 -10000 0 -10000 0 0
SGOL1 -0.001 0.035 0.14 6 -0.11 1 7
RHOA 0.026 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.028 0.043 -10000 0 -0.19 2 2
CDC14B 0.004 0.026 -10000 0 -0.33 1 1
CDC20 -0.05 0.12 -10000 0 -0.23 52 52
PLK1/PBIP1 -0.004 0.038 0.15 1 -0.12 9 10
mitosis -0.002 0.003 -10000 0 -10000 0 0
FBXO5 0.002 0.027 0.19 1 -10000 0 1
CDC2 0 0.003 -10000 0 -0.01 4 4
NDC80 0.022 0.037 -10000 0 -0.46 1 1
metaphase plate congression 0.011 0.018 0.14 1 -10000 0 1
ERCC6L -0.002 0.058 -10000 0 -0.19 8 8
NLP/gamma Tubulin 0.002 0.025 0.14 1 -0.081 7 8
microtubule cytoskeleton organization -0.037 0.085 0.13 1 -0.18 43 44
G2/M transition DNA damage checkpoint 0 0.002 0.01 1 -10000 0 1
PPP1R12A 0.026 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.01 1 -10000 0 1
PLK1/PRC1-2 -0.023 0.09 0.14 2 -0.19 16 18
GRASP65/GM130/RAB1/GTP/PLK1 0.041 0.029 -10000 0 -10000 0 0
RAB1A 0.027 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.027 0.11 5 -0.076 3 8
mitotic prometaphase -0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.057 -10000 0 -0.49 1 1
microtubule-based process -0.028 0.075 0.16 2 -0.12 47 49
Golgi organization 0.006 0.031 0.11 5 -0.1 3 8
Cohesin/SA2 0.014 0.03 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.038 0.008 -10000 0 -10000 0 0
KIF20A -0.091 0.13 -10000 0 -0.23 79 79
APC/C/CDC20 -0.009 0.07 0.16 2 -0.12 41 43
PPP2R1A 0.027 0.003 -10000 0 -10000 0 0
chromosome segregation -0.004 0.037 0.15 1 -0.12 9 10
PRC1 0.007 0.068 -10000 0 -0.23 13 13
ECT2 0.018 0.072 0.2 18 -0.14 4 22
C13orf34 0.006 0.027 0.097 5 -0.09 3 8
NUDC 0.011 0.018 0.14 1 -10000 0 1
regulation of attachment of spindle microtubules to kinetochore -0.013 0.043 0.14 3 -10000 0 3
spindle assembly 0.004 0.026 0.1 3 -0.09 3 6
spindle stabilization 0.006 0.034 0.19 1 -0.16 4 5
APC/C/HCDH1 0.022 0.022 -10000 0 -0.25 1 1
MKLP2/PLK1 -0.029 0.075 0.16 2 -0.12 47 49
CCNB1 0.016 0.05 -10000 0 -0.24 6 6
PPP1CB 0.027 0.003 -10000 0 -10000 0 0
BTRC 0.025 0.007 -10000 0 -10000 0 0
ROCK2 0.015 0.049 0.16 1 -0.39 2 3
TUBG1 0.001 0.044 0.13 1 -0.19 7 8
G2/M transition of mitotic cell cycle -0.001 0.034 -10000 0 -0.19 2 2
MLF1IP -0.008 0.05 0.23 1 -0.16 15 16
INCENP 0.026 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.027 0.12 0.33 4 -0.51 3 7
FYN 0.015 0.14 0.33 6 -0.49 6 12
LAT/GRAP2/SLP76 0.013 0.13 0.29 4 -0.4 8 12
IKBKB 0.02 0.012 -10000 0 -10000 0 0
AKT1 0.011 0.12 0.28 8 -0.33 8 16
B2M 0.028 0.005 -10000 0 -10000 0 0
IKBKG 0.007 0.044 0.11 10 -0.13 2 12
MAP3K8 0.005 0.096 -10000 0 -0.43 8 8
mol:Ca2+ -0.01 0.013 0.089 1 -0.061 2 3
integrin-mediated signaling pathway 0.027 0.046 -10000 0 -0.27 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.004 0.15 0.3 6 -0.44 9 15
TRPV6 0.091 0.34 1.1 16 -0.45 2 18
CD28 -0.003 0.094 -10000 0 -0.27 18 18
SHC1 0.009 0.13 0.33 3 -0.52 5 8
receptor internalization -0.006 0.14 0.2 1 -0.43 11 12
PRF1 0 0.16 -10000 0 -0.7 5 5
KRAS 0.025 0.008 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 0.012 0.11 0.26 6 -0.3 10 16
LAT 0.005 0.14 0.28 6 -0.46 7 13
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.018 0.054 -10000 0 -0.28 5 5
CD3E 0.022 0.035 -10000 0 -0.24 3 3
CD3G -0.009 0.12 -10000 0 -0.36 16 16
RASGRP2 -0.002 0.04 -10000 0 -0.16 9 9
RASGRP1 0.008 0.12 0.29 8 -0.32 10 18
HLA-A 0.025 0.038 -10000 0 -0.47 1 1
RASSF5 0.015 0.072 -10000 0 -0.46 4 4
RAP1A/GTP/RAPL 0.027 0.046 -10000 0 -0.27 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.071 0.22 11 -0.14 1 12
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.051 -10000 0 -0.19 8 8
PRKCA -0.005 0.078 0.16 6 -0.23 9 15
GRAP2 0.012 0.077 -10000 0 -0.38 6 6
mol:IP3 -0.013 0.098 0.21 2 -0.31 11 13
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.001 0.094 -10000 0 -0.41 5 5
ORAI1 -0.069 0.28 -10000 0 -0.95 15 15
CSK 0.009 0.13 0.23 4 -0.54 5 9
B7 family/CD28 0.025 0.14 0.26 2 -0.41 9 11
CHUK 0.025 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.14 0.25 1 -0.49 8 9
PTPN6 0.004 0.13 0.28 3 -0.45 7 10
VAV1 -0.002 0.14 0.28 3 -0.42 11 14
Monovalent TCR/CD3 0.002 0.065 -10000 0 -0.22 13 13
CBL 0.026 0.006 -10000 0 -10000 0 0
LCK 0.017 0.14 0.32 6 -0.51 5 11
PAG1 0.02 0.14 0.28 4 -0.52 5 9
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.14 0.26 1 -0.44 9 10
CD80 0.005 0.07 -10000 0 -0.24 13 13
CD86 0.021 0.034 -10000 0 -0.24 3 3
PDK1/CARD11/BCL10/MALT1 -0.003 0.066 -10000 0 -0.22 9 9
HRAS 0.027 0.004 -10000 0 -10000 0 0
GO:0035030 -0.005 0.11 0.25 3 -0.36 9 12
CD8A 0.019 0.059 -10000 0 -0.35 4 4
CD8B 0.01 0.088 -10000 0 -0.38 8 8
PTPRC 0.009 0.082 -10000 0 -0.35 8 8
PDK1/PKC theta 0.005 0.15 0.36 8 -0.41 9 17
CSK/PAG1 0.025 0.14 0.27 8 -0.5 5 13
SOS1 0.026 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.039 0.03 -10000 0 -0.35 1 1
GRAP2/SLP76 0.016 0.14 0.23 1 -0.43 9 10
STIM1 -0.008 0.12 0.97 2 -10000 0 2
RAS family/GTP 0.02 0.084 0.29 6 -0.17 6 12
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.006 0.14 0.21 1 -0.45 11 12
mol:DAG -0.023 0.082 -10000 0 -0.28 11 11
RAP1A/GDP 0.013 0.029 0.1 8 -0.063 1 9
PLCG1 0.026 0.006 -10000 0 -10000 0 0
CD247 0.021 0.035 -10000 0 -0.24 3 3
cytotoxic T cell degranulation 0.001 0.16 -10000 0 -0.67 5 5
RAP1A/GTP 0 0.015 -10000 0 -0.06 9 9
mol:PI-3-4-5-P3 0.008 0.13 0.27 8 -0.37 9 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.12 0.23 2 -0.38 11 13
NRAS 0.026 0.005 -10000 0 -10000 0 0
ZAP70 0.013 0.069 -10000 0 -0.29 8 8
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.008 0.12 0.21 1 -0.38 12 13
MALT1 0.023 0.021 -10000 0 -0.23 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.087 -10000 0 -0.33 9 9
CARD11 0.013 0.068 -10000 0 -0.37 5 5
PRKCB -0.028 0.1 0.15 3 -0.26 20 23
PRKCE -0.001 0.072 0.16 6 -0.22 7 13
PRKCQ -0.001 0.15 0.35 6 -0.44 10 16
LCP2 0.022 0.034 -10000 0 -0.23 3 3
BCL10 0.026 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression 0.013 0.11 0.27 8 -0.3 7 15
IKK complex 0.009 0.079 0.24 11 -0.11 9 20
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.005 0.087 0.22 6 -0.24 9 15
PDPK1 0.012 0.12 0.3 8 -0.33 7 15
TCR/CD3/MHC I/CD8/Fyn -0.002 0.14 -10000 0 -0.52 8 8
EGFR-dependent Endothelin signaling events

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
HRAS 0.027 0.004 -9999 0 -10000 0 0
EGFR 0.008 0.088 -9999 0 -0.46 6 6
EGF/EGFR -0.013 0.11 -9999 0 -0.28 20 20
EGF/EGFR dimer/SHC/GRB2/SOS1 0.028 0.088 -9999 0 -0.25 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.005 0.1 -9999 0 -0.46 8 8
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.023 0.11 -9999 0 -0.25 31 31
EGF/EGFR dimer/SHC 0.008 0.088 -9999 0 -0.29 7 7
mol:GDP 0.023 0.084 -9999 0 -0.25 7 7
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.004 0.11 -9999 0 -0.39 13 13
GRB2/SOS1 0.038 0.009 -9999 0 -10000 0 0
HRAS/GTP 0.011 0.073 -9999 0 -0.23 7 7
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP 0.023 0.081 -9999 0 -0.24 7 7
FRAP1 -0.03 0.054 -9999 0 -0.24 7 7
EGF/EGFR dimer -0.008 0.099 -9999 0 -0.2 31 31
SOS1 0.026 0.004 -9999 0 -10000 0 0
GRB2 0.026 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0 0.12 -9999 0 -0.32 19 19
Visual signal transduction: Rods

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
mol:K + 0.026 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.013 -10000 0 -0.15 1 1
Metarhodopsin II/Arrestin 0.023 0.015 -10000 0 -0.13 1 1
PDE6G/GNAT1/GTP 0.015 0.052 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.018 0.02 -10000 0 -0.23 1 1
GRK1 0.019 0.006 -10000 0 -10000 0 0
CNG Channel -0.012 0.11 -10000 0 -0.25 19 19
mol:Na + 0.016 0.063 -10000 0 -0.23 4 4
mol:ADP 0.019 0.006 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.045 0.15 -10000 0 -0.28 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.023 0.068 -10000 0 -0.23 4 4
CNGB1 0.008 0.059 -10000 0 -0.24 9 9
RDH5 -0.02 0.14 -10000 0 -0.44 17 17
SAG 0.019 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.064 0.32 1 -10000 0 1
Na + (4 Units) 0.011 0.059 -10000 0 -10000 0 0
RGS9 -0.11 0.22 -10000 0 -0.45 50 50
GNB1/GNGT1 0.03 0.011 -10000 0 -10000 0 0
GNAT1/GDP -0.028 0.14 -10000 0 -0.25 47 47
GUCY2D 0.007 0.077 -10000 0 -0.31 9 9
GNGT1 0.016 0.006 -10000 0 -10000 0 0
GUCY2F 0.018 0.003 -10000 0 -10000 0 0
GNB5 0.024 0.037 -10000 0 -0.46 1 1
mol:GMP (4 units) -0.022 0.098 -10000 0 -0.26 21 21
mol:11-cis-retinal -0.02 0.14 -10000 0 -0.44 17 17
mol:cGMP 0.023 0.059 -10000 0 -0.25 4 4
GNB1 0.027 0.003 -10000 0 -10000 0 0
Rhodopsin 0 0.1 -10000 0 -0.31 16 16
SLC24A1 0.026 0.005 -10000 0 -10000 0 0
CNGA1 0.023 0.041 -10000 0 -0.34 2 2
Metarhodopsin II 0.022 0.014 -10000 0 -0.12 1 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.034 0.064 -10000 0 -0.26 4 4
RGS9BP 0.024 0.036 -10000 0 -0.46 1 1
Metarhodopsin II/Transducin 0.01 0.007 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.03 -10000 0 -0.26 1 1
PDE6A/B -0.009 0.13 -10000 0 -0.33 22 22
mol:Pi -0.045 0.15 -10000 0 -0.28 50 50
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.036 0.018 -10000 0 -10000 0 0
PDE6B -0.026 0.15 -10000 0 -0.46 19 19
PDE6A 0.013 0.077 -10000 0 -0.38 6 6
PDE6G 0.004 0.08 -10000 0 -0.27 13 13
RHO 0.017 0.02 -10000 0 -0.23 1 1
PDE6 -0.06 0.18 -10000 0 -0.28 56 56
GUCA1A 0.022 0.02 -10000 0 -0.23 1 1
GC2/GCAP Family 0.049 0.033 -10000 0 -0.26 1 1
GUCA1C 0.017 0.004 -10000 0 -10000 0 0
GUCA1B 0.023 0.041 -10000 0 -0.34 2 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.009 0.094 0.34 10 -10000 0 10
KIRREL -0.003 0.11 -10000 0 -0.46 10 10
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.009 0.094 -10000 0 -0.34 10 10
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARRB2 0.024 0.008 -10000 0 -10000 0 0
WASL 0.024 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.037 0.084 -10000 0 -0.25 10 10
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.004 0.061 -10000 0 -0.24 9 9
FYN -0.009 0.077 0.3 4 -0.24 10 14
mol:Ca2+ 0.033 0.083 -10000 0 -0.25 10 10
mol:DAG 0.034 0.084 -10000 0 -0.25 10 10
NPHS2 0.013 0.03 -10000 0 -0.23 1 1
mol:IP3 0.034 0.084 -10000 0 -0.25 10 10
regulation of endocytosis 0.02 0.069 -10000 0 -0.22 10 10
Nephrin/NEPH1/podocin/Cholesterol 0.023 0.078 -10000 0 -0.25 10 10
establishment of cell polarity 0.009 0.094 -10000 0 -0.34 10 10
Nephrin/NEPH1/podocin/NCK1-2 0.039 0.082 -10000 0 -0.23 10 10
Nephrin/NEPH1/beta Arrestin2 0.022 0.07 -10000 0 -0.23 10 10
NPHS1 0.011 0.051 -10000 0 -0.23 6 6
Nephrin/NEPH1/podocin 0.021 0.071 -10000 0 -0.24 10 10
TJP1 0.025 0.02 -10000 0 -0.23 1 1
NCK1 0.024 0.008 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.035 0.084 -10000 0 -0.25 10 10
CD2AP 0.027 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.036 0.084 -10000 0 -0.25 10 10
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.053 0.12 0.22 2 -0.29 34 36
cytoskeleton organization -0.005 0.066 0.2 1 -0.27 9 10
Nephrin/NEPH1 0.011 0.067 -10000 0 -0.23 10 10
Nephrin/NEPH1/ZO-1 0.024 0.082 -10000 0 -0.27 10 10
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.031 0.081 -10000 0 -0.47 4 4
HDAC1 0.026 0.003 -10000 0 -10000 0 0
AES 0.026 0.004 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.017 0.047 -10000 0 -0.23 6 6
LRP6/FZD1 0.031 0.017 -10000 0 -10000 0 0
TLE1 0.026 0.006 -10000 0 -10000 0 0
AP1 -0.027 0.12 -10000 0 -0.31 22 22
NCSTN 0.025 0.008 -10000 0 -10000 0 0
ADAM10 0.021 0.051 -10000 0 -0.46 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.034 0.035 -10000 0 -10000 0 0
NICD/RBPSUH 0.034 0.08 -10000 0 -0.46 4 4
WIF1 -0.18 0.24 -10000 0 -0.44 78 78
NOTCH1 0.015 0.078 -10000 0 -0.48 4 4
PSENEN 0.027 0.002 -10000 0 -10000 0 0
KREMEN2 -0.011 0.12 -10000 0 -0.39 16 16
DKK1 -0.076 0.19 -10000 0 -0.43 39 39
beta catenin/beta TrCP1 0.023 0.061 0.25 4 -10000 0 4
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 0.008 0.057 0.25 2 -0.3 3 5
CtBP/CBP/TCF1/TLE1/AES 0.015 0.028 -10000 0 -10000 0 0
PSEN1 0.027 0.003 -10000 0 -10000 0 0
FOS -0.038 0.16 -10000 0 -0.45 24 24
JUN 0.026 0.004 -10000 0 -10000 0 0
MAP3K7 0.021 0.011 -10000 0 -10000 0 0
CTNNB1 0.015 0.061 0.26 4 -10000 0 4
MAPK3 0.026 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.012 0.095 -10000 0 -0.3 11 11
HNF1A -0.009 0.087 -10000 0 -0.23 23 23
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.005 0.055 -10000 0 -10000 0 0
NKD1 0.01 0.077 -10000 0 -0.38 6 6
FZD1 0.024 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.029 0.079 -10000 0 -0.49 3 3
apoptosis -0.027 0.12 -10000 0 -0.31 22 22
Delta 1/NOTCHprecursor 0.034 0.082 -10000 0 -0.46 4 4
DLL1 0.024 0.037 -10000 0 -0.46 1 1
PPARD 0.019 0.089 -10000 0 -0.79 2 2
Gamma Secretase 0.072 0.026 -10000 0 -10000 0 0
APC -0.006 0.083 0.25 1 -0.33 8 9
DVL1 -0.006 0.039 -10000 0 -0.26 2 2
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.047 0.15 -10000 0 -0.29 44 44
LRP6 0.023 0.01 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.011 0.006 -10000 0 -10000 0 0
CCND1 0.027 0.018 -10000 0 -10000 0 0
WNT1 0.023 0.02 -10000 0 -0.23 1 1
Axin1/APC/beta catenin 0.02 0.086 0.32 4 -0.35 2 6
DKK2 0.014 0.062 -10000 0 -0.26 8 8
NOTCH1 precursor/DVL1 0.01 0.084 -10000 0 -0.55 2 2
GSK3B 0.026 0.006 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.028 0.078 -10000 0 -0.5 3 3
PPP2R5D 0.014 0.063 0.25 4 -0.4 2 6
MAPK1 0.026 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.072 0.15 -10000 0 -0.25 68 68
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.028 0.005 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.019 0.039 -10000 0 -0.23 4 4
LAT2 -0.009 0.084 0.18 1 -0.33 7 8
AP1 0.01 0.13 0.29 1 -0.4 8 9
mol:PIP3 0.01 0.15 0.34 11 -0.41 6 17
IKBKB 0.012 0.12 0.27 15 -0.25 9 24
AKT1 0.012 0.12 0.34 13 -0.37 2 15
IKBKG -0.003 0.11 0.24 12 -0.25 11 23
MS4A2 0.01 0.087 -10000 0 -0.45 6 6
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
MAP3K1 0.018 0.11 0.26 12 -0.35 5 17
mol:Ca2+ 0.013 0.13 0.29 13 -0.31 6 19
LYN 0.023 0.011 -10000 0 -10000 0 0
CBLB -0.007 0.077 -10000 0 -0.31 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.042 0.045 -10000 0 -0.24 4 4
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.013 0.081 -10000 0 -0.46 5 5
PLD2 -0.016 0.098 0.29 6 -0.24 17 23
PTPN13 0.003 0.12 -10000 0 -0.52 4 4
PTPN11 0.024 0.017 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.021 0.12 0.34 11 -0.33 3 14
SYK 0.026 0.022 -10000 0 -0.24 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.017 0.11 -10000 0 -0.36 10 10
LAT -0.013 0.084 -10000 0 -0.3 8 8
PAK2 0.018 0.12 0.27 12 -0.38 5 17
NFATC2 -0.034 0.14 -10000 0 -0.52 12 12
HRAS 0.006 0.11 0.26 4 -0.39 6 10
GAB2 0.026 0.005 -10000 0 -10000 0 0
PLA2G1B 0.019 0.076 -10000 0 -0.88 1 1
Fc epsilon R1 0.009 0.11 -10000 0 -0.3 19 19
Antigen/IgE/Fc epsilon R1 0.01 0.1 -10000 0 -0.27 19 19
mol:GDP -0.001 0.11 0.23 1 -0.4 6 7
JUN 0.026 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
FOS -0.038 0.16 -10000 0 -0.45 24 24
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.004 0.085 -10000 0 -0.33 7 7
CHUK 0.001 0.11 0.25 13 -0.25 10 23
KLRG1 -0.003 0.076 0.16 2 -0.31 5 7
VAV1 -0.016 0.099 -10000 0 -0.34 10 10
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.081 -10000 0 -0.31 7 7
negative regulation of mast cell degranulation 0 0.097 -10000 0 -0.38 6 6
BTK 0.004 0.093 0.23 1 -0.35 6 7
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.13 -10000 0 -0.34 19 19
GAB2/PI3K/SHP2 -0.011 0.07 -10000 0 -0.3 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.008 0.086 -10000 0 -0.28 11 11
RAF1 0.019 0.075 -10000 0 -0.91 1 1
Fc epsilon R1/FcgammaRIIB/SHIP 0.019 0.14 -10000 0 -0.31 22 22
FCER1G 0.024 0.022 -10000 0 -0.25 1 1
FCER1A -0.02 0.14 -10000 0 -0.46 16 16
Antigen/IgE/Fc epsilon R1/Fyn 0.018 0.099 -10000 0 -0.25 18 18
MAPK3 0.017 0.074 -10000 0 -0.83 1 1
MAPK1 0.017 0.081 -10000 0 -0.96 1 1
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.001 0.14 -10000 0 -0.52 7 7
DUSP1 0.015 0.072 -10000 0 -0.46 4 4
NF-kappa-B/RelA 0 0.056 0.12 1 -0.16 6 7
actin cytoskeleton reorganization 0.002 0.12 -10000 0 -0.54 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.009 0.1 -10000 0 -0.4 5 5
FER -0.011 0.085 -10000 0 -0.29 10 10
RELA 0.026 0.005 -10000 0 -10000 0 0
ITK 0.001 0.046 -10000 0 -0.53 1 1
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG1 0.008 0.12 0.3 5 -0.39 7 12
cytokine secretion -0.004 0.037 -10000 0 -10000 0 0
SPHK1 -0.009 0.082 -10000 0 -0.3 8 8
PTK2 0.001 0.13 -10000 0 -0.57 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.008 0.11 -10000 0 -0.41 7 7
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.003 0.14 0.35 7 -0.38 8 15
MAP2K2 0.013 0.07 -10000 0 -0.85 1 1
MAP2K1 0.017 0.075 -10000 0 -0.85 1 1
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.004 0.074 -10000 0 -0.28 4 4
MAP2K4 -0.048 0.26 -10000 0 -0.82 18 18
Fc epsilon R1/FcgammaRIIB 0.017 0.12 -10000 0 -0.3 20 20
mol:Choline -0.016 0.097 0.28 6 -0.24 17 23
SHC/Grb2/SOS1 0.034 0.096 0.24 1 -0.33 5 6
FYN 0.024 0.009 -10000 0 -10000 0 0
DOK1 0.026 0.004 -10000 0 -10000 0 0
PXN 0.007 0.13 0.34 3 -0.52 4 7
HCLS1 -0.008 0.078 -10000 0 -0.3 7 7
PRKCB -0.009 0.14 0.29 11 -0.33 12 23
FCGR2B 0.012 0.071 -10000 0 -0.34 6 6
IGHE 0.001 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.001 0.099 -10000 0 -0.39 6 6
LCP2 0.022 0.034 -10000 0 -0.23 3 3
PLA2G4A -0.011 0.09 -10000 0 -0.35 7 7
RASA1 0.026 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.016 0.097 0.28 6 -0.24 17 23
IKK complex 0.013 0.11 0.25 17 -0.2 6 23
WIPF1 0.024 0.02 -10000 0 -0.23 1 1
IL1-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
UBC13/UEV1A 0.033 0.011 -10000 0 -10000 0 0
PRKCZ 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.074 -10000 0 -0.3 5 5
IRAK/TOLLIP 0.028 0.01 -10000 0 -10000 0 0
IKBKB 0.02 0.012 -10000 0 -10000 0 0
IKBKG 0.027 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.072 0.17 -10000 0 -0.34 51 51
IL1A -0.012 0.12 -10000 0 -0.44 13 13
IL1B -0.038 0.12 -10000 0 -0.28 30 30
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.034 -10000 0 -10000 0 0
IL1R2 -0.084 0.2 -10000 0 -0.46 40 40
IL1R1 0.027 0.002 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.057 -10000 0 -0.24 2 2
TOLLIP 0.027 0.004 -10000 0 -10000 0 0
TICAM2 0.009 0.088 -10000 0 -0.46 6 6
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.013 0.086 0.26 4 -0.33 2 6
JUN 0.005 0.062 0.19 15 -10000 0 15
MAP3K7 0.022 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.012 0.11 -10000 0 -0.25 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.082 -10000 0 -0.25 12 12
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.044 0.082 -10000 0 -0.24 12 12
IL1 beta fragment/IL1R1/IL1RAP -0.008 0.11 -10000 0 -0.27 20 20
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.008 0.065 0.2 15 -10000 0 15
IRAK1 0.002 0.014 -10000 0 -10000 0 0
IL1RN/IL1R1 0.015 0.087 -10000 0 -0.3 12 12
IRAK4 0.027 0.004 -10000 0 -10000 0 0
PRKCI 0.024 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.033 0.021 -10000 0 -0.16 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.078 -10000 0 -0.3 5 5
CHUK 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.008 0.11 -10000 0 -0.27 20 20
IL1 beta/IL1R2 -0.082 0.17 -10000 0 -0.33 51 51
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.002 0.096 -10000 0 -0.41 2 2
IRAK3 0.023 0.037 -10000 0 -0.46 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.003 0.12 -10000 0 -0.24 25 25
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.067 -10000 0 -0.23 12 12
IL1 alpha/IL1R1/IL1RAP 0.022 0.084 -10000 0 -0.28 12 12
RELA 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.026 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.055 0.036 -10000 0 -10000 0 0
IL1RAP 0.024 0.008 -10000 0 -10000 0 0
UBE2N 0.026 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 -0.013 0.091 -10000 0 -0.39 2 2
CASP1 0.009 0.088 -10000 0 -0.46 6 6
IL1RN/IL1R2 -0.067 0.18 -10000 0 -0.34 49 49
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.004 0.11 -10000 0 -0.26 20 20
TMEM189-UBE2V1 0.022 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.068 -10000 0 -0.28 2 2
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
IL1RN -0.005 0.12 -10000 0 -0.42 12 12
TRAF6/TAK1/TAB1/TAB2 0.038 0.023 -10000 0 -10000 0 0
MAP2K6 0.017 0.066 0.2 16 -10000 0 16
Canonical Wnt signaling pathway

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.005 -10000 0 -10000 0 0
AES 0.025 0.006 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.017 -10000 0 -10000 0 0
SMAD4 0.024 0.009 -10000 0 -10000 0 0
DKK2 0.013 0.062 -10000 0 -0.26 8 8
TLE1 0.025 0.007 -10000 0 -10000 0 0
MACF1 0.028 0.001 -10000 0 -10000 0 0
CTNNB1 0.069 0.091 0.31 9 -10000 0 9
WIF1 -0.18 0.24 -10000 0 -0.44 78 78
beta catenin/RanBP3 0.023 0.058 0.29 1 -10000 0 1
KREMEN2 -0.011 0.12 -10000 0 -0.39 16 16
DKK1 -0.076 0.19 -10000 0 -0.43 39 39
beta catenin/beta TrCP1 0.076 0.087 0.31 8 -10000 0 8
FZD1 0.025 0.008 -10000 0 -10000 0 0
AXIN2 0.01 0.086 0.55 4 -10000 0 4
AXIN1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.037 0.062 -10000 0 -0.48 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.099 0.25 2 -0.49 2 4
Axin1/APC/GSK3 0.051 0.056 0.26 5 -10000 0 5
Axin1/APC/GSK3/beta catenin/Macf1 0.047 0.072 0.26 5 -0.31 1 6
HNF1A -0.01 0.087 -10000 0 -0.23 23 23
CTBP1 0.025 0.006 -10000 0 -10000 0 0
MYC 0.09 0.22 0.56 25 -10000 0 25
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.012 0.095 -10000 0 -0.3 11 11
NKD1 0.01 0.077 -10000 0 -0.38 6 6
TCF4 0.022 0.009 -10000 0 -10000 0 0
TCF3 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.051 0.034 -10000 0 -10000 0 0
Ran/GTP 0.019 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.051 -10000 0 -10000 0 0
LEF1 0.009 0.067 -10000 0 -0.26 10 10
DVL1 0.045 0.044 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.061 0.07 0.27 1 -10000 0 1
DKK1/LRP6/Kremen 2 -0.047 0.15 -10000 0 -0.29 44 44
LRP6 0.024 0.01 -10000 0 -10000 0 0
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 0.011 0.094 0.55 5 -10000 0 5
WNT1 0.024 0.02 -10000 0 -0.23 1 1
GSK3A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.006 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
PPP2R5D 0.038 0.069 0.29 5 -0.34 2 7
APC 0.026 0.052 0.18 17 -10000 0 17
WNT1/LRP6/FZD1 0.064 0.087 0.2 48 -10000 0 48
CREBBP 0.025 0.005 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.057 -10000 0 -0.23 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.024 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.059 0.11 -10000 0 -0.2 57 57
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
FYN 0.024 0.009 -10000 0 -10000 0 0
MAP3K12 0.018 0.063 -10000 0 -0.46 3 3
FGR 0.026 0.02 -10000 0 -0.23 1 1
p38 alpha/TAB1 -0.049 0.086 -10000 0 -0.28 15 15
PRKG1 -0.059 0.18 -10000 0 -0.46 31 31
DUSP8 0.025 0.02 -10000 0 -0.23 1 1
PGK/cGMP/p38 alpha -0.048 0.15 -10000 0 -0.34 26 26
apoptosis -0.047 0.083 -10000 0 -0.27 15 15
RAL/GTP 0.031 0.013 -10000 0 -10000 0 0
LYN 0.023 0.01 -10000 0 -10000 0 0
DUSP1 0.015 0.072 -10000 0 -0.46 4 4
PAK1 0.018 0.063 -10000 0 -0.46 3 3
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.059 0.026 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.011 -10000 0 -10000 0 0
MAPK11 -0.032 0.13 0.19 8 -0.35 13 21
BLK -0.038 0.14 -10000 0 -0.36 26 26
HCK 0.022 0.041 -10000 0 -0.34 2 2
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
DUSP16 0.023 0.01 -10000 0 -10000 0 0
DUSP10 0.026 0.006 -10000 0 -10000 0 0
TRAF6/MEKK3 0.034 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.022 0.12 0.16 4 -0.31 14 18
positive regulation of innate immune response -0.034 0.15 0.21 9 -0.38 15 24
LCK 0.021 0.039 -10000 0 -0.23 4 4
p38alpha-beta/MKP7 -0.023 0.14 0.22 7 -0.37 14 21
p38alpha-beta/MKP5 -0.027 0.14 0.21 3 -0.37 14 17
PGK/cGMP -0.041 0.13 -10000 0 -0.32 31 31
PAK2 0.025 0.008 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.029 0.15 0.22 7 -0.39 15 22
CDC42 0.027 0 -10000 0 -10000 0 0
RALB 0.025 0.007 -10000 0 -10000 0 0
RALA 0.024 0.008 -10000 0 -10000 0 0
PAK3 -0.16 0.23 -10000 0 -0.46 66 66
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.033 -10000 0 -0.25 2 2
regulation of S phase of mitotic cell cycle 0.016 0.03 -10000 0 -0.22 2 2
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
HRAS 0.026 0.004 -10000 0 -10000 0 0
SHBG/T-DHT 0.014 0.023 -10000 0 -0.27 1 1
PELP1 0.024 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.018 0.049 0.17 2 -10000 0 2
T-DHT/AR 0.015 0.037 -10000 0 -0.32 2 2
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 24 24
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
mol:GDP 0 0.042 -10000 0 -0.39 2 2
cell proliferation -0.036 0.14 0.4 2 -0.37 22 24
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
FOS -0.088 0.28 0.31 2 -0.77 24 26
mol:Ca2+ -0.01 0.027 -10000 0 -0.066 29 29
MAPK3 -0.023 0.1 0.4 2 -0.27 18 20
MAPK1 -0.016 0.1 0.26 2 -0.5 3 5
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 24 24
cAMP biosynthetic process 0.004 0.03 -10000 0 -0.26 1 1
GNG2 0.027 0.002 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 24 24
HRAS/GTP 0.03 0.048 -10000 0 -0.22 2 2
actin cytoskeleton reorganization 0.033 0.02 -10000 0 -10000 0 0
SRC 0.025 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 24 24
PI3K 0.03 0.018 -10000 0 -0.13 1 1
apoptosis 0.032 0.15 0.38 24 -0.34 2 26
T-DHT/AR/PELP1 0.028 0.035 -10000 0 -0.28 2 2
HRAS/GDP 0.013 0.045 -10000 0 -0.37 2 2
CREB1 -0.035 0.16 0.34 2 -0.4 24 26
RAC1-CDC42/GTP 0.041 0.024 -10000 0 -10000 0 0
AR 0.021 0.051 -10000 0 -0.46 2 2
GNB1 0.027 0.003 -10000 0 -10000 0 0
RAF1 0.002 0.046 0.18 2 -0.22 2 4
RAC1-CDC42/GDP 0.035 0.049 -10000 0 -0.36 2 2
T-DHT/AR/PELP1/Src 0.038 0.038 -10000 0 -0.25 2 2
MAP2K2 -0.019 0.052 0.17 2 -0.23 1 3
T-DHT/AR/PELP1/Src/PI3K 0.016 0.03 -10000 0 -0.22 2 2
GNAZ -0.013 0.13 -10000 0 -0.46 14 14
SHBG 0.021 0.037 -10000 0 -0.46 1 1
Gi family/GNB1/GNG2/GDP -0.044 0.15 -10000 0 -0.36 24 24
mol:T-DHT 0 0.001 -10000 0 -0.003 22 22
RAC1 0.024 0.008 -10000 0 -10000 0 0
GNRH1 0.002 0.021 -10000 0 -0.15 3 3
Gi family/GTP -0.031 0.1 -10000 0 -0.3 15 15
CDC42 0.027 0 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.037 0.058 -10000 0 -10000 0 0
epithelial cell differentiation 0.029 0.076 -10000 0 -0.34 1 1
ITCH 0.029 0.012 -10000 0 -10000 0 0
WWP1 0.037 0.075 -10000 0 -10000 0 0
FYN 0.024 0.009 -10000 0 -10000 0 0
EGFR 0.008 0.088 -10000 0 -0.46 6 6
PRL 0.017 0.019 -10000 0 -0.23 1 1
neuron projection morphogenesis -0.001 0.095 0.25 7 -0.31 2 9
PTPRZ1 -0.13 0.22 -10000 0 -0.46 55 55
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.009 0.094 -10000 0 -0.33 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.014 0.09 -10000 0 -0.34 3 3
ADAM17 0.03 0.012 -10000 0 -10000 0 0
ErbB4/ErbB4 0.008 0.046 -10000 0 -0.26 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.11 -10000 0 -0.4 2 2
NCOR1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.007 0.088 -10000 0 -0.32 3 3
GRIN2B -0.013 0.076 -10000 0 -0.3 3 3
ErbB4/ErbB2/betacellulin 0.033 0.066 -10000 0 -0.35 2 2
STAT1 0.019 0.043 -10000 0 -0.23 5 5
HBEGF 0.023 0.028 -10000 0 -0.23 2 2
PRLR -0.01 0.1 -10000 0 -0.28 21 21
E4ICDs/ETO2 0.028 0.055 -10000 0 -10000 0 0
axon guidance 0.039 0.08 0.36 1 -0.32 1 2
NEDD4 0.029 0.011 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.004 0.079 -10000 0 -0.2 20 20
CBFA2T3 0.02 0.038 -10000 0 -0.46 1 1
ErbB4/ErbB2/HBEGF 0.036 0.054 -10000 0 -0.38 1 1
MAPK3 0.002 0.097 0.28 5 -0.32 2 7
STAT1 (dimer) 0.038 0.059 -10000 0 -10000 0 0
MAPK1 0.002 0.095 0.28 4 -0.32 2 6
JAK2 0.026 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.015 0.093 -10000 0 -0.39 3 3
NRG1 -0.027 0.11 -10000 0 -0.33 19 19
NRG3 -0.056 0.17 -10000 0 -0.42 31 31
NRG2 -0.13 0.22 -10000 0 -0.46 56 56
NRG4 -0.11 0.22 -10000 0 -0.45 51 51
heart development 0.039 0.08 0.36 1 -0.32 1 2
neural crest cell migration -0.015 0.092 -10000 0 -0.39 3 3
ERBB2 0.012 0.036 -10000 0 -0.32 2 2
WWOX/E4ICDs 0.03 0.052 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.036 0.14 -10000 0 -0.4 7 7
apoptosis 0.038 0.14 0.35 22 -10000 0 22
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.05 0.14 -10000 0 -0.37 10 10
ErbB4/ErbB2/epiregulin -0.001 0.1 -10000 0 -0.34 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0.033 0.073 -10000 0 -0.38 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.044 0.091 -10000 0 -0.32 3 3
MDM2 0.023 0.057 0.31 2 -10000 0 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.007 0.087 -10000 0 -0.24 18 18
STAT5A 0.043 0.08 0.32 2 -0.31 1 3
ErbB4/EGFR/neuregulin 1 beta -0.015 0.1 -10000 0 -0.33 7 7
DLG4 0.018 0.052 -10000 0 -0.46 2 2
GRB2/SHC 0.037 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.033 0.052 -10000 0 -10000 0 0
STAT5A (dimer) 0.05 0.094 -10000 0 -0.36 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.063 0.086 0.3 5 -0.31 1 6
LRIG1 0.024 0.02 -10000 0 -0.23 1 1
EREG -0.051 0.17 -10000 0 -0.38 33 33
BTC 0.016 0.072 -10000 0 -0.46 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.028 0.072 0.36 1 -0.32 1 2
ERBB4 0.011 0.035 -10000 0 -10000 0 0
STAT5B 0.026 0.006 -10000 0 -10000 0 0
YAP1 0.015 0.083 -10000 0 -0.39 5 5
GRB2 0.026 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.034 0.13 -10000 0 -0.34 7 7
glial cell differentiation -0.033 0.051 -10000 0 -10000 0 0
WWOX 0.022 0.01 -10000 0 -10000 0 0
cell proliferation -0.022 0.11 0.26 1 -0.37 5 6
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.089 -10000 0 -0.33 11 11
CRKL 0.013 0.089 0.28 2 -0.34 3 5
mol:PIP3 -0.013 0.11 -10000 0 -0.8 3 3
AKT1 -0.012 0.099 0.3 1 -0.7 3 4
PTK2B 0.018 0.013 -10000 0 -10000 0 0
RAPGEF1 0.022 0.099 0.3 5 -0.44 1 6
RANBP10 0.024 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
HGF/MET/SHIP2 0.015 0.095 -10000 0 -0.3 11 11
MAP3K5 0.018 0.1 0.33 3 -0.41 4 7
HGF/MET/CIN85/CBL/ENDOPHILINS 0.025 0.095 -10000 0 -0.27 12 12
AP1 -0.012 0.12 -10000 0 -0.28 23 23
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.081 0.27 -10000 0 -0.7 28 28
STAT3 (dimer) -0.014 0.092 -10000 0 -0.38 6 6
GAB1/CRKL/SHP2/PI3K 0.036 0.088 0.28 2 -0.42 1 3
INPP5D 0.013 0.081 -10000 0 -0.46 5 5
CBL/CRK 0.024 0.087 0.27 1 -0.32 3 4
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.021 0.011 -10000 0 -10000 0 0
ELK1 0.012 0.12 0.31 19 -10000 0 19
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.003 0.048 -10000 0 -0.24 2 2
PAK1 -0.012 0.099 0.31 2 -0.61 3 5
HGF/MET/RANBP10 0.012 0.096 -10000 0 -0.3 12 12
HRAS -0.014 0.15 -10000 0 -0.58 10 10
DOCK1 0.017 0.091 0.29 4 -0.44 1 5
GAB1 0.004 0.077 -10000 0 -0.35 3 3
CRK 0.01 0.087 0.28 2 -0.34 3 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.011 0.14 -10000 0 -0.52 12 12
JUN 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.008 0.066 -10000 0 -0.25 11 11
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
cell morphogenesis 0.012 0.12 0.36 8 -0.4 4 12
GRB2/SHC 0.018 0.067 -10000 0 -0.22 10 10
FOS -0.038 0.16 -10000 0 -0.45 24 24
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.012 0.12 0.31 19 -10000 0 19
HGF/MET/MUC20 0.001 0.091 -10000 0 -0.22 22 22
cell migration 0.017 0.066 -10000 0 -0.21 10 10
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.026 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.011 0.088 -10000 0 -0.32 11 11
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.081 -10000 0 -0.29 11 11
MET/MUC20 -0.004 0.083 -10000 0 -0.32 11 11
RAP1B 0.027 0.11 0.29 9 -0.41 1 10
RAP1A 0.022 0.099 0.31 6 -0.41 1 7
HGF/MET/RANBP9 0.014 0.097 -10000 0 -0.3 12 12
RAF1 -0.002 0.15 0.34 1 -0.55 10 11
STAT3 -0.014 0.093 -10000 0 -0.39 6 6
cell proliferation -0.008 0.11 0.26 2 -0.37 10 12
RPS6KB1 0.001 0.046 -10000 0 -0.26 3 3
MAPK3 0.006 0.13 0.53 5 -10000 0 5
MAPK1 0.005 0.13 0.58 4 -10000 0 4
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.031 0.097 0.32 4 -0.39 3 7
SRC -0.008 0.074 -10000 0 -0.28 10 10
PI3K 0.015 0.071 -10000 0 -0.23 10 10
MET/Glomulin -0.002 0.078 -10000 0 -0.29 11 11
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K1 0.006 0.15 0.32 3 -0.51 10 13
MET -0.006 0.12 -10000 0 -0.46 11 11
MAP4K1 0.02 0.11 0.34 3 -0.44 4 7
PTK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K2 0.005 0.15 0.39 3 -0.52 10 13
BAD -0.01 0.099 0.31 2 -0.67 3 5
MAP2K4 0.016 0.097 0.32 3 -0.38 4 7
SHP2/GRB2/SOS1/GAB1 0.019 0.092 -10000 0 -0.34 8 8
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.026 0.006 -10000 0 -10000 0 0
SH3KBP1 0.027 0.003 -10000 0 -10000 0 0
HGS -0.011 0.061 -10000 0 -0.24 11 11
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF 0.004 0.078 -10000 0 -0.27 12 12
RASA1 0.026 0.006 -10000 0 -10000 0 0
NCK1 0.024 0.008 -10000 0 -10000 0 0
PTPRJ 0.026 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.019 0.068 -10000 0 -0.23 10 10
PDPK1 -0.011 0.1 0.34 1 -0.74 3 4
HGF/MET/SHIP 0.007 0.12 -10000 0 -0.4 12 12
Signaling events mediated by PTP1B

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
PDGFRB 0.024 0.028 -10000 0 -0.23 2 2
Jak2/Leptin Receptor 0.028 0.1 0.24 2 -0.3 5 7
PTP1B/AKT1 0.005 0.072 0.23 1 -0.23 3 4
FYN 0.024 0.009 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.006 0.071 0.24 1 -0.24 4 5
EGFR 0.007 0.089 -10000 0 -0.46 6 6
EGF/EGFR -0.004 0.093 -10000 0 -0.31 8 8
CSF1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.027 0.003 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.049 0.12 -10000 0 -0.26 35 35
Insulin Receptor/Insulin 0.026 0.071 -10000 0 -10000 0 0
HCK 0.022 0.041 -10000 0 -0.34 2 2
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 -0.008 0.067 0.22 1 -0.24 3 4
EGF -0.023 0.11 -10000 0 -0.25 31 31
YES1 0.025 0.008 -10000 0 -10000 0 0
CAV1 -0.005 0.094 0.23 6 -0.28 7 13
TXN 0.026 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.011 0.075 -10000 0 -0.24 3 3
cell migration 0.006 0.071 0.24 4 -0.24 1 5
STAT3 0.026 0.005 -10000 0 -10000 0 0
PRLR -0.008 0.1 -10000 0 -0.27 21 21
ITGA2B 0.001 0.1 -10000 0 -0.46 8 8
CSF1R 0.025 0.02 -10000 0 -0.23 1 1
Prolactin Receptor/Prolactin 0.01 0.082 -10000 0 -0.33 4 4
FGR 0.026 0.02 -10000 0 -0.23 1 1
PTP1B/p130 Cas 0.004 0.062 -10000 0 -0.22 3 3
Crk/p130 Cas 0.012 0.068 -10000 0 -0.22 1 1
DOK1 0.001 0.067 0.17 1 -0.25 2 3
JAK2 0.009 0.089 0.22 1 -0.32 5 6
Jak2/Leptin Receptor/Leptin -0.041 0.14 -10000 0 -0.34 22 22
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
PTPN1 -0.007 0.071 0.24 1 -0.24 4 5
LYN 0.023 0.01 -10000 0 -10000 0 0
CDH2 -0.089 0.2 -10000 0 -0.44 42 42
SRC 0.017 0.054 -10000 0 -0.36 2 2
ITGB3 -0.018 0.14 -10000 0 -0.46 16 16
CAT1/PTP1B -0.012 0.11 0.25 6 -0.3 8 14
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.031 0.068 -10000 0 -10000 0 0
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.044 0.14 -10000 0 -0.38 21 21
negative regulation of transcription 0.011 0.089 0.21 1 -0.31 5 6
FCGR2A 0.023 0.021 -10000 0 -0.23 1 1
FER 0.015 0.073 -10000 0 -0.46 4 4
alphaIIb/beta3 Integrin -0.014 0.13 -10000 0 -0.34 23 23
BLK -0.038 0.14 -10000 0 -0.36 26 26
Insulin Receptor/Insulin/Shc 0.045 0.019 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.027 0.008 -10000 0 -10000 0 0
BCAR1 0.023 0.01 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.038 0.13 -10000 0 -0.33 14 14
PRL 0.016 0.023 -10000 0 -0.23 1 1
SOCS3 -0.18 0.45 -10000 0 -1.2 29 29
SPRY2 0.022 0.037 -10000 0 -0.45 1 1
Insulin Receptor/Insulin/IRS1 0.046 0.03 -10000 0 -0.29 1 1
CSF1/CSF1R 0.014 0.074 -10000 0 -0.23 3 3
Ras protein signal transduction 0.003 0.047 0.39 2 -10000 0 2
IRS1 0.024 0.037 -10000 0 -0.46 1 1
INS 0.012 0.023 -10000 0 -0.23 1 1
LEP 0.009 0.04 -10000 0 -0.23 4 4
STAT5B 0.002 0.076 0.24 1 -0.26 1 2
STAT5A 0.003 0.076 0.24 1 -0.24 2 3
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.074 0.22 1 -0.24 3 4
CSN2 -0.002 0.049 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
LAT 0 0.1 -10000 0 -0.41 9 9
YBX1 0.033 0.003 -10000 0 -10000 0 0
LCK 0.021 0.039 -10000 0 -0.23 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.095 0.13 -10000 0 -0.23 83 83
Ceramide signaling pathway

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
SPHK2 0.012 0.005 -10000 0 -10000 0 0
MAP4K4 0.006 0.051 -10000 0 -0.25 1 1
BAG4 0.02 0.012 -10000 0 -10000 0 0
PKC zeta/ceramide -0.007 0.077 -10000 0 -0.21 17 17
NFKBIA 0.027 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.028 -10000 0 -0.23 2 2
BAX -0.001 0.048 -10000 0 -0.31 3 3
RIPK1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0 0.059 0.76 1 -10000 0 1
BAD -0.02 0.064 0.15 1 -0.2 16 17
SMPD1 0.017 0.056 0.17 7 -0.16 6 13
RB1 -0.022 0.07 -10000 0 -0.21 16 16
FADD/Caspase 8 0.012 0.051 -10000 0 -10000 0 0
MAP2K4 -0.023 0.066 -10000 0 -0.22 12 12
NSMAF 0.022 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.026 0.079 0.18 4 -0.21 22 26
EGF -0.023 0.11 -10000 0 -0.25 31 31
mol:ceramide -0.022 0.076 -10000 0 -0.22 17 17
MADD 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.007 -10000 0 -10000 0 0
ASAH1 0.018 0.013 -10000 0 -10000 0 0
negative regulation of cell cycle -0.022 0.069 -10000 0 -0.21 16 16
cell proliferation -0.022 0.091 0.18 2 -0.23 17 19
BID 0.004 0.11 -10000 0 -0.59 5 5
MAP3K1 -0.023 0.071 -10000 0 -0.21 16 16
EIF2A -0.006 0.078 0.18 11 -0.22 11 22
TRADD 0.024 0.008 -10000 0 -10000 0 0
CRADD 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.023 0.076 0.17 4 -0.23 11 15
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.023 0.077 0.16 4 -0.23 12 16
Cathepsin D/ceramide -0.006 0.069 -10000 0 -0.2 16 16
FADD 0.006 0.049 -10000 0 -0.25 1 1
KSR1 -0.031 0.087 0.19 2 -0.22 24 26
MAPK8 -0.008 0.068 -10000 0 -0.59 1 1
PRKRA -0.022 0.07 -10000 0 -0.21 16 16
PDGFA 0.024 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.006 -10000 0 -10000 0 0
IGF1 -0.014 0.12 -10000 0 -0.38 17 17
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.075 -10000 0 -0.22 17 17
CTSD 0.026 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.023 0.098 0.19 2 -0.24 17 19
PRKCD 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.003 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.007 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.013 0.046 -10000 0 -0.26 1 1
TNFR1A/BAG4/TNF-alpha 0.022 0.068 -10000 0 -0.26 7 7
mol:Sphingosine-1-phosphate 0.012 0.005 -10000 0 -10000 0 0
MAP2K1 -0.024 0.077 0.17 6 -0.24 11 17
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
CYCS 0.011 0.048 0.17 3 -0.18 2 5
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.019 -10000 0 -10000 0 0
EIF2AK2 -0.021 0.072 0.19 2 -0.21 15 17
TNF-alpha/TNFR1A/FAN 0.026 0.067 -10000 0 -0.28 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.033 -10000 0 -10000 0 0
MAP2K2 -0.028 0.075 0.17 4 -0.21 19 23
SMPD3 0.001 0.073 0.19 1 -0.25 8 9
TNF -0.002 0.1 -10000 0 -0.35 13 13
PKC zeta/PAR4 0.039 0.008 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.003 0.052 0.19 2 -0.15 11 13
NF kappa B1/RelA/I kappa B alpha 0.074 0.023 -10000 0 -10000 0 0
AIFM1 0.003 0.057 0.15 3 -0.2 2 5
BCL2 0.018 0.052 -10000 0 -0.46 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0 0.079 -10000 0 -0.34 8 8
CRKL 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DOCK1 0.026 0.006 -10000 0 -10000 0 0
ITGA4 0.006 0.085 -10000 0 -0.32 10 10
alpha4/beta7 Integrin/MAdCAM1 0.005 0.11 -10000 0 -0.3 12 12
EPO -0.053 0.17 -10000 0 -0.42 30 30
alpha4/beta7 Integrin 0.01 0.099 -10000 0 -0.31 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.023 0.065 -10000 0 -0.22 10 10
EPO/EPOR (dimer) -0.024 0.13 -10000 0 -0.29 31 31
lamellipodium assembly 0.018 0.058 -10000 0 -0.61 1 1
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
PI3K 0.033 0.021 -10000 0 -0.16 1 1
ARF6 0.027 0.003 -10000 0 -10000 0 0
JAK2 -0.023 0.097 -10000 0 -0.24 29 29
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
MADCAM1 -0.027 0.11 -10000 0 -0.24 35 35
cell adhesion 0.004 0.11 -10000 0 -0.3 12 12
CRKL/CBL 0.037 0.011 -10000 0 -10000 0 0
ITGB1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.002 0.064 0.18 4 -0.24 8 12
ITGB7 0.007 0.092 -10000 0 -0.4 8 8
RAC1 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.029 0.074 -10000 0 -0.27 8 8
p130Cas/Crk/Dock1 0.015 0.058 -10000 0 -0.22 6 6
VCAM1 0.016 0.061 -10000 0 -0.32 5 5
RHOA 0.026 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.059 -10000 0 -0.25 4 4
BCAR1 -0.018 0.052 0.18 2 -0.24 6 8
EPOR 0.025 0.02 -10000 0 -0.23 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.006 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.06 -10000 0 -0.63 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.007 0.045 -10000 0 -0.34 2 2
Crk/p130 Cas/Paxillin -0.019 0.071 -10000 0 -0.26 8 8
JUN -0.012 0.07 -10000 0 -0.28 6 6
HRAS 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.011 0.096 -10000 0 -0.28 9 9
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.006 0.1 -10000 0 -0.27 11 11
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.022 0.092 -10000 0 -0.29 12 12
RHOA 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.003 0.094 -10000 0 -0.24 12 12
GRB7 0.027 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.006 0.1 -10000 0 -0.27 11 11
MAPKKK cascade 0 0.08 -10000 0 -0.26 7 7
BCAR1 0.023 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.027 0.075 -10000 0 -0.25 11 11
lamellipodium assembly -0.006 0.068 -10000 0 -0.24 9 9
RET51/GFRalpha1/GDNF/SHC 0.006 0.099 -10000 0 -0.28 9 9
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
RET9/GFRalpha1/GDNF/SHC 0.029 0.067 -10000 0 -0.25 8 8
RET9/GFRalpha1/GDNF/Shank3 0.028 0.072 -10000 0 -0.25 10 10
MAPK3 -0.03 0.095 0.32 6 -0.31 2 8
DOK1 0.026 0.004 -10000 0 -10000 0 0
DOK6 0.012 0.054 -10000 0 -0.23 8 8
PXN 0.026 0.006 -10000 0 -10000 0 0
neurite development -0.023 0.079 0.32 2 -0.29 3 5
DOK5 -0.004 0.11 -10000 0 -0.4 12 12
GFRA1 0.013 0.075 -10000 0 -0.41 5 5
MAPK8 -0.008 0.07 -10000 0 -0.3 6 6
HRAS/GTP 0.013 0.092 -10000 0 -0.27 10 10
tube development 0.026 0.07 0.21 1 -0.24 10 11
MAPK1 -0.03 0.092 0.32 5 -0.31 2 7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.007 0.06 -10000 0 -0.22 11 11
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
PDLIM7 0.009 0.09 -10000 0 -0.42 7 7
RET51/GFRalpha1/GDNF/Dok6 0.003 0.1 -10000 0 -0.25 12 12
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.002 0.1 -10000 0 -0.27 12 12
RET51/GFRalpha1/GDNF/Dok5 -0.013 0.12 -10000 0 -0.29 19 19
PRKCA 0.018 0.063 -10000 0 -0.46 3 3
HRAS/GDP 0.02 0.003 -10000 0 -10000 0 0
CREB1 0.004 0.065 -10000 0 -0.23 10 10
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.056 -10000 0 -0.22 9 9
RET51/GFRalpha1/GDNF/Grb7 0.007 0.1 -10000 0 -0.27 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.027 0.11 -10000 0 -0.24 35 35
DOK4 0.021 0.037 -10000 0 -0.46 1 1
JNK cascade -0.012 0.069 -10000 0 -0.28 6 6
RET9/GFRalpha1/GDNF/FRS2 0.028 0.072 -10000 0 -0.25 10 10
SHANK3 0.026 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.006 -10000 0 -10000 0 0
NCK1 0.024 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.009 0.054 -10000 0 -0.22 8 8
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.004 0.072 -10000 0 -0.23 14 14
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.002 0.076 -10000 0 -0.27 11 11
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.001 0.065 -10000 0 -0.23 11 11
PI3K -0.007 0.1 0.24 1 -0.34 10 11
SOS1 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.038 0.073 -10000 0 -0.24 10 10
GRB10 0.024 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.01 0.084 -10000 0 -0.29 11 11
RET51/GFRalpha1/GDNF/FRS2 0.006 0.1 -10000 0 -0.27 11 11
GAB1 0.027 0.003 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.46 1 1
IRS2 0.021 0.034 -10000 0 -0.23 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.003 0.072 -10000 0 -0.24 12 12
RET51/GFRalpha1/GDNF/PKC alpha 0.004 0.11 -10000 0 -0.3 12 12
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GDNF 0.007 0.095 -10000 0 -0.46 7 7
RAC1 0.024 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.005 0.11 -10000 0 -0.28 12 12
Rac1/GTP -0.001 0.083 -10000 0 -0.29 8 8
RET9/GFRalpha1/GDNF 0.014 0.074 -10000 0 -0.26 11 11
GFRalpha1/GDNF 0.014 0.087 -10000 0 -0.31 11 11
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.022 0.01 -10000 0 -10000 0 0
epithelial cell differentiation 0.05 0.021 -10000 0 -10000 0 0
CYFIP2 0.027 0.004 -10000 0 -10000 0 0
ENAH 0 0.087 0.4 4 -10000 0 4
EGFR 0.008 0.088 -10000 0 -0.46 6 6
EPHA2 -0.02 0.14 -10000 0 -0.43 18 18
MYO6 0.001 0.071 0.23 9 -10000 0 9
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.051 0.014 -10000 0 -10000 0 0
AQP5 -0.21 0.22 -10000 0 -0.43 87 87
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.054 0.21 12 -10000 0 12
regulation of calcium-dependent cell-cell adhesion 0.016 0.062 0.2 10 -0.23 5 15
EGF -0.023 0.11 -10000 0 -0.25 31 31
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
AQP3 0.007 0.087 0.36 1 -0.45 5 6
cortical microtubule organization 0.05 0.021 -10000 0 -10000 0 0
GO:0000145 0.007 0.056 0.2 12 -10000 0 12
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.055 0.023 -10000 0 -10000 0 0
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.026 0.049 -10000 0 -10000 0 0
ARF6 0.027 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.034 0.083 -10000 0 -0.25 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.01 0.028 0.19 1 -10000 0 1
PVRL2 0.027 0.004 -10000 0 -10000 0 0
ZYX 0.018 0.033 0.18 7 -10000 0 7
ARF6/GTP 0.04 0.081 -10000 0 -0.24 11 11
CDH1 0.024 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.011 0.073 -10000 0 -0.23 7 7
RhoA/GDP 0.051 0.022 -10000 0 -10000 0 0
actin cytoskeleton organization -0.012 0.057 0.2 7 -10000 0 7
IGF-1R heterotetramer 0.023 0.028 -10000 0 -0.23 2 2
GIT1 0.027 0.004 -10000 0 -10000 0 0
IGF1R 0.024 0.028 -10000 0 -0.23 2 2
IGF1 -0.014 0.12 -10000 0 -0.38 17 17
DIAPH1 0.029 0.1 -10000 0 -0.56 1 1
Wnt receptor signaling pathway -0.05 0.021 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.049 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
VCL -0.012 0.058 0.2 7 -10000 0 7
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.002 0.055 0.23 8 -0.22 1 9
Ephrin A1/EPHA2 0.021 0.076 -10000 0 -0.22 14 14
SEC6/SEC8 0.012 0.007 -10000 0 -10000 0 0
MGAT3 0.016 0.063 0.2 10 -0.23 5 15
HGF/MET 0.015 0.08 -10000 0 -0.24 12 12
HGF 0.004 0.078 -10000 0 -0.27 12 12
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.022 0.01 -10000 0 -10000 0 0
actin cable formation 0.038 0.1 0.3 16 -0.26 1 17
KIAA1543 0.005 0.05 0.19 11 -10000 0 11
KIFC3 0.014 0.041 0.18 6 -0.23 2 8
NCK1 0.024 0.008 -10000 0 -10000 0 0
EXOC3 0.027 0.003 -10000 0 -10000 0 0
ACTN1 0.025 0.053 0.22 11 -10000 0 11
NCK1/GIT1 0.036 0.013 -10000 0 -10000 0 0
mol:GDP 0.05 0.021 -10000 0 -10000 0 0
EXOC4 0.024 0.008 -10000 0 -10000 0 0
STX4 0.025 0.053 0.22 11 -10000 0 11
PIP5K1C 0.026 0.054 0.21 12 -10000 0 12
LIMA1 0.026 0.004 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.007 0.1 0.4 6 -10000 0 6
adherens junction assembly 0.001 0.1 0.3 4 -0.48 4 8
IGF-1R heterotetramer/IGF1 0.022 0.07 -10000 0 -0.22 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
MET -0.006 0.12 -10000 0 -0.46 11 11
PLEKHA7 0.024 0.047 0.2 11 -10000 0 11
mol:GTP 0.032 0.082 -10000 0 -0.25 11 11
establishment of epithelial cell apical/basal polarity 0.019 0.095 0.38 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.022 0.01 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.012 0.057 0.2 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.022 0.01 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.025 0.11 0.26 3 -0.35 8 11
IKBKB -0.016 0.11 0.25 3 -0.26 13 16
AKT1 0.021 0.1 0.28 14 -0.22 2 16
IKBKG 0.032 0.062 0.27 4 -10000 0 4
CALM1 0.002 0.079 0.22 3 -0.39 2 5
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
MAP3K1 -0.059 0.18 0.42 2 -0.44 18 20
MAP3K7 0.022 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.082 0.23 3 -0.33 4 7
DOK1 0.026 0.004 -10000 0 -10000 0 0
AP-1 -0.016 0.069 0.19 1 -0.23 5 6
LYN 0.023 0.01 -10000 0 -10000 0 0
BLNK 0.026 0.006 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex 0.001 0.1 -10000 0 -0.24 24 24
CD22 -0.023 0.12 -10000 0 -0.4 11 11
CAMK2G 0.005 0.073 -10000 0 -0.47 1 1
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.013 0.081 -10000 0 -0.46 5 5
SHC/GRB2/SOS1 0.008 0.062 -10000 0 -0.23 7 7
GO:0007205 0.003 0.084 0.23 3 -0.34 4 7
SYK 0.024 0.02 -10000 0 -0.23 1 1
ELK1 0.002 0.083 0.23 4 -0.35 3 7
NFATC1 -0.003 0.11 0.32 4 -0.35 3 7
B-cell antigen/BCR complex 0.001 0.1 -10000 0 -0.24 24 24
PAG1/CSK 0.032 0.017 -10000 0 -10000 0 0
NFKBIB 0.013 0.043 0.14 4 -0.12 2 6
HRAS 0.013 0.075 0.22 5 -0.34 1 6
NFKBIA 0.013 0.043 0.14 4 -0.12 2 6
NF-kappa-B/RelA/I kappa B beta 0.018 0.038 0.14 4 -10000 0 4
RasGAP/Csk 0.027 0.1 -10000 0 -0.24 16 16
mol:GDP 0.005 0.084 0.24 3 -0.32 4 7
PTEN 0.021 0.011 -10000 0 -10000 0 0
CD79B 0.016 0.061 -10000 0 -0.32 5 5
NF-kappa-B/RelA/I kappa B alpha 0.018 0.038 0.14 4 -10000 0 4
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.13 -10000 0 -0.46 6 6
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
mol:IP3 0.006 0.081 0.24 3 -0.34 4 7
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.027 0.11 0.21 3 -0.37 7 10
CHUK 0.019 0.086 0.27 4 -0.28 6 10
IBTK 0.024 0.009 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.024 0.077 0.23 2 -0.43 1 3
PTPN6 -0.029 0.11 -10000 0 -0.46 7 7
RELA 0.026 0.005 -10000 0 -10000 0 0
BCL2A1 0.013 0.03 0.11 3 -10000 0 3
VAV2 -0.026 0.098 -10000 0 -0.56 2 2
ubiquitin-dependent protein catabolic process 0.016 0.042 0.14 4 -0.12 2 6
BTK 0.01 0.14 -10000 0 -0.94 3 3
CD19 -0.038 0.11 -10000 0 -0.35 10 10
MAP4K1 0.011 0.075 -10000 0 -0.32 8 8
CD72 0.021 0.046 -10000 0 -0.31 3 3
PAG1 0.022 0.011 -10000 0 -10000 0 0
MAPK14 -0.049 0.15 0.4 2 -0.4 15 17
SH3BP5 0.026 0.005 -10000 0 -10000 0 0
PIK3AP1 0.009 0.079 -10000 0 -0.46 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.013 0.09 0.23 1 -0.36 6 7
RAF1 0.016 0.077 0.31 3 -0.32 1 4
RasGAP/p62DOK/SHIP 0.021 0.11 -10000 0 -0.26 18 18
CD79A -0.016 0.12 -10000 0 -0.3 23 23
re-entry into mitotic cell cycle -0.015 0.069 0.19 1 -0.22 5 6
RASA1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.018 0.075 0.28 4 -0.26 1 5
MAPK1 0.017 0.082 0.34 4 -0.28 1 5
CD72/SHP1 -0.011 0.12 0.25 1 -0.43 8 9
NFKB1 0.027 0.003 -10000 0 -10000 0 0
MAPK8 -0.048 0.15 0.36 3 -0.39 15 18
actin cytoskeleton organization -0.015 0.096 0.22 1 -0.39 3 4
NF-kappa-B/RelA 0.038 0.073 0.26 4 -0.19 1 5
Calcineurin 0.015 0.072 -10000 0 -0.38 2 2
PI3K -0.028 0.091 -10000 0 -0.35 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.085 -10000 0 -0.38 5 5
SOS1 0.026 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.094 0.29 -10000 0 -0.75 27 27
DAPP1 -0.12 0.32 -10000 0 -0.84 27 27
cytokine secretion -0.002 0.1 0.29 5 -0.33 3 8
mol:DAG 0.006 0.081 0.24 3 -0.34 4 7
PLCG2 0.018 0.042 -10000 0 -0.34 2 2
MAP2K1 0.017 0.075 0.36 2 -0.3 1 3
B-cell antigen/BCR complex/FcgammaRIIB 0.007 0.1 -10000 0 -0.28 16 16
mol:PI-3-4-5-P3 -0.023 0.065 0.18 1 -0.25 3 4
ETS1 0.01 0.073 0.24 2 -0.29 1 3
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.039 0.081 -10000 0 -0.25 8 8
B-cell antigen/BCR complex/LYN -0.012 0.1 -10000 0 -0.39 8 8
MALT1 0.023 0.021 -10000 0 -0.23 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 -0.017 0.094 0.22 1 -0.45 2 3
B-cell antigen/BCR complex/LYN/SYK 0.003 0.12 -10000 0 -0.36 11 11
CARD11 0.011 0.089 0.24 4 -0.38 2 6
FCGR2B 0.012 0.071 -10000 0 -0.34 6 6
PPP3CA 0.018 0.047 -10000 0 -0.23 6 6
BCL10 0.026 0.006 -10000 0 -10000 0 0
IKK complex 0.011 0.047 0.17 7 -10000 0 7
PTPRC 0.009 0.081 -10000 0 -0.34 8 8
PDPK1 -0.004 0.085 0.31 7 -0.18 2 9
PPP3CB 0.025 0.007 -10000 0 -10000 0 0
PPP3CC 0.017 0.013 -10000 0 -10000 0 0
POU2F2 0.014 0.027 0.11 2 -10000 0 2
Syndecan-4-mediated signaling events

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
PTK2 0.027 0.046 0.27 1 -10000 0 1
Syndecan-4/Syndesmos -0.013 0.14 0.37 3 -0.68 5 8
positive regulation of JNK cascade -0.001 0.12 0.34 2 -0.58 5 7
Syndecan-4/ADAM12 -0.019 0.13 0.36 2 -0.67 5 7
CCL5 0.017 0.061 -10000 0 -0.32 5 5
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.004 -10000 0 -10000 0 0
ITGA5 0.017 0.066 -10000 0 -0.4 4 4
SDCBP 0.022 0.01 -10000 0 -10000 0 0
PLG 0.009 0.054 -10000 0 -0.23 7 7
ADAM12 0.009 0.065 -10000 0 -0.24 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.055 0.028 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.019 0.14 0.36 2 -0.69 5 7
Syndecan-4/CXCL12/CXCR4 0.001 0.13 0.36 2 -0.63 5 7
Syndecan-4/Laminin alpha3 -0.03 0.14 0.36 2 -0.68 5 7
MDK 0.024 0.028 -10000 0 -0.23 2 2
Syndecan-4/FZD7 -0.016 0.14 0.38 2 -0.68 5 7
Syndecan-4/Midkine -0.013 0.14 0.37 3 -0.67 5 8
FZD7 0.024 0.037 -10000 0 -0.46 1 1
Syndecan-4/FGFR1/FGF -0.006 0.13 0.33 1 -0.63 5 6
THBS1 0.013 0.059 -10000 0 -0.24 9 9
integrin-mediated signaling pathway -0.011 0.13 0.37 3 -0.62 5 8
positive regulation of MAPKKK cascade -0.001 0.12 0.34 2 -0.58 5 7
Syndecan-4/TACI -0.026 0.14 0.36 2 -0.68 5 7
CXCR4 0.021 0.042 -10000 0 -0.34 2 2
cell adhesion 0.015 0.038 0.2 2 -0.32 1 3
Syndecan-4/Dynamin -0.013 0.14 0.37 3 -0.67 5 8
Syndecan-4/TSP1 -0.017 0.14 0.37 3 -0.65 5 8
Syndecan-4/GIPC -0.014 0.14 0.37 3 -0.68 5 8
Syndecan-4/RANTES -0.017 0.15 0.37 3 -0.71 5 8
ITGB1 0.026 0.005 -10000 0 -10000 0 0
LAMA1 0.011 0.068 -10000 0 -0.31 7 7
LAMA3 -0.009 0.12 -10000 0 -0.43 13 13
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA 0.007 0.11 0.74 3 -0.4 3 6
Syndecan-4/alpha-Actinin -0.013 0.14 0.37 3 -0.68 5 8
TFPI 0.017 0.047 -10000 0 -0.23 6 6
F2 -0.001 0.059 -10000 0 -0.23 9 9
alpha5/beta1 Integrin 0.031 0.05 -10000 0 -0.28 4 4
positive regulation of cell adhesion -0.034 0.14 0.35 2 -0.67 5 7
ACTN1 0.026 0.004 -10000 0 -10000 0 0
TNC 0.02 0.052 -10000 0 -0.46 2 2
Syndecan-4/CXCL12 -0.017 0.13 0.36 2 -0.65 5 7
FGF6 0.015 0.027 -10000 0 -0.23 2 2
RHOA 0.026 0.005 -10000 0 -10000 0 0
CXCL12 0.02 0.052 -10000 0 -0.46 2 2
TNFRSF13B -0.003 0.1 -10000 0 -0.34 13 13
FGF2 0.015 0.072 -10000 0 -0.46 4 4
FGFR1 0.019 0.012 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.028 0.12 -10000 0 -0.68 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.024 0.027 -10000 0 -0.23 1 1
cell migration -0.027 0.014 -10000 0 -10000 0 0
PRKCD 0.026 0.019 -10000 0 -10000 0 0
vasculogenesis -0.016 0.13 0.37 3 -0.62 5 8
SDC4 -0.026 0.14 0.42 1 -0.72 5 6
Syndecan-4/Tenascin C -0.012 0.14 0.37 3 -0.65 5 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.045 0.022 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.017 0.13 0.35 1 -0.67 5 6
MMP9 -0.14 0.13 -10000 0 -0.23 108 108
Rac1/GTP 0.015 0.039 0.2 2 -0.33 1 3
cytoskeleton organization -0.012 0.13 0.37 3 -0.64 5 8
GIPC1 0.027 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.018 0.14 0.38 2 -0.67 5 7
IGF1 pathway

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTK2 0.022 0.011 -10000 0 -10000 0 0
CRKL -0.003 0.063 -10000 0 -0.23 11 11
GRB2/SOS1/SHC 0.049 0.018 -10000 0 -10000 0 0
HRAS 0.027 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.005 0.065 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.021 0.08 -10000 0 -0.26 11 11
AKT1 -0.001 0.082 0.2 15 -0.21 9 24
BAD -0.002 0.078 0.18 15 -10000 0 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.061 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.067 -10000 0 -0.24 10 10
RAF1 0.013 0.077 0.28 2 -0.42 1 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.073 -10000 0 -0.23 10 10
YWHAZ 0.022 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.011 0.072 -10000 0 -0.24 12 12
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
RPS6KB1 0 0.081 0.2 15 -0.21 9 24
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.022 0.089 0.3 7 -0.35 1 8
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.012 0.058 -10000 0 -0.21 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.052 0.071 -10000 0 -0.21 9 9
IGF-1R heterotetramer 0.018 0.039 -10000 0 -0.24 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.029 0.071 -10000 0 -0.23 11 11
Crk/p130 Cas/Paxillin 0.03 0.069 -10000 0 -0.21 10 10
IGF1R 0.018 0.039 -10000 0 -0.24 2 2
IGF1 -0.013 0.13 -10000 0 -0.38 17 17
IRS2/Crk 0.005 0.066 0.16 1 -0.24 10 11
PI3K 0.034 0.072 -10000 0 -0.22 10 10
apoptosis -0.013 0.066 -10000 0 -0.23 3 3
HRAS/GDP 0.02 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.082 -10000 0 -0.31 11 11
RAF1/14-3-3 E 0.031 0.076 0.27 2 -0.37 1 3
BAD/14-3-3 0.014 0.069 0.24 3 -10000 0 3
PRKCZ -0.001 0.082 0.2 15 -10000 0 15
Crk/p130 Cas/Paxillin/FAK1 0.018 0.059 -10000 0 -10000 0 0
PTPN1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.083 -10000 0 -0.33 10 10
BCAR1 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.068 -10000 0 -0.22 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
IRS1/NCK2 0.016 0.071 -10000 0 -0.24 10 10
GRB10 0.024 0.008 -10000 0 -10000 0 0
PTPN11 -0.004 0.062 -10000 0 -0.24 10 10
IRS1 0.001 0.073 0.14 2 -0.24 12 14
IRS2 -0.003 0.066 -10000 0 -0.25 10 10
IGF-1R heterotetramer/IGF1 0.005 0.096 -10000 0 -0.27 17 17
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 0.011 0.078 0.19 13 -0.22 9 22
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.003 0.082 -10000 0 -0.31 11 11
SHC1 0.025 0.007 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.045 0.057 -10000 0 -0.24 3 3
ER alpha/Gai/GDP/Gbeta gamma -0.046 0.14 -10000 0 -0.4 13 13
AKT1 -0.011 0.15 -10000 0 -0.62 9 9
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.15 -10000 0 -0.61 10 10
mol:Ca2+ -0.001 0.059 -10000 0 -0.32 2 2
IGF1R 0.024 0.028 -10000 0 -0.23 2 2
E2/ER alpha (dimer)/Striatin 0.03 0.041 -10000 0 -0.28 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.01 0.14 0.6 9 -10000 0 9
RhoA/GTP 0.018 0.033 -10000 0 -0.22 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.019 0.12 -10000 0 -0.35 10 10
regulation of stress fiber formation 0.001 0.064 -10000 0 -0.27 4 4
E2/ERA-ERB (dimer) 0.02 0.056 -10000 0 -0.16 14 14
KRAS 0.025 0.008 -10000 0 -10000 0 0
G13/GTP 0.028 0.037 -10000 0 -0.25 3 3
pseudopodium formation -0.001 0.064 0.27 4 -10000 0 4
E2/ER alpha (dimer)/PELP1 0.027 0.042 -10000 0 -0.28 3 3
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.027 0.002 -10000 0 -10000 0 0
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
HRAS 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.021 0.11 -10000 0 -0.33 10 10
E2/ER beta (dimer) 0.009 0.042 -10000 0 -0.15 11 11
mol:GDP 0.005 0.059 -10000 0 -0.36 3 3
mol:NADP -0.021 0.11 -10000 0 -0.33 10 10
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
mol:IP3 -0.002 0.059 -10000 0 -0.33 2 2
IGF-1R heterotetramer 0.023 0.028 -10000 0 -0.23 2 2
PLCB1 0.002 0.061 -10000 0 -0.33 2 2
PLCB2 0.003 0.06 -10000 0 -0.33 2 2
IGF1 -0.014 0.12 -10000 0 -0.38 17 17
mol:L-citrulline -0.021 0.11 -10000 0 -0.33 10 10
RHOA 0.026 0.005 -10000 0 -10000 0 0
Gai/GDP -0.13 0.29 -10000 0 -0.63 43 43
JNK cascade 0.009 0.042 -10000 0 -0.15 11 11
BCAR1 0.023 0.01 -10000 0 -10000 0 0
ESR2 0.01 0.063 -10000 0 -0.23 11 11
GNAQ 0.026 0.005 -10000 0 -10000 0 0
ESR1 0.018 0.063 -10000 0 -0.46 3 3
Gq family/GDP/Gbeta gamma -0.003 0.14 -10000 0 -0.44 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.011 0.1 -10000 0 -0.57 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.016 0.12 -10000 0 -0.36 10 10
GNAZ -0.012 0.13 -10000 0 -0.46 14 14
E2/ER alpha (dimer) 0.014 0.045 -10000 0 -0.32 3 3
STRN 0.027 0.004 -10000 0 -10000 0 0
GNAL -0.014 0.13 -10000 0 -0.46 14 14
PELP1 0.024 0.008 -10000 0 -10000 0 0
MAPK11 0.004 0.036 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
HBEGF -0.068 0.15 0.37 2 -0.42 13 15
cAMP biosynthetic process -0.006 0.078 -10000 0 -0.22 17 17
SRC -0.046 0.13 -10000 0 -0.39 12 12
PI3K 0.033 0.021 -10000 0 -0.16 1 1
GNB1 0.027 0.003 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.034 0.064 -10000 0 -0.32 3 3
SOS1 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.11 -10000 0 -0.34 13 13
Gs family/GTP 0 0.082 -10000 0 -0.22 17 17
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.018 -10000 0 -10000 0 0
vasodilation -0.02 0.11 -10000 0 -0.32 10 10
mol:DAG -0.002 0.059 -10000 0 -0.33 2 2
Gs family/GDP/Gbeta gamma -0.004 0.079 -10000 0 -0.31 4 4
MSN -0.001 0.066 0.28 4 -10000 0 4
Gq family/GTP 0.01 0.064 -10000 0 -0.35 2 2
mol:PI-3-4-5-P3 -0.008 0.15 -10000 0 -0.59 10 10
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.02 0.11 0.32 10 -10000 0 10
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.062 -10000 0 -0.35 3 3
NOS3 -0.022 0.12 -10000 0 -0.34 10 10
GNA11 0.024 0.037 -10000 0 -0.46 1 1
MAPKKK cascade -0.009 0.12 0.28 1 -0.4 10 11
E2/ER alpha (dimer)/PELP1/Src -0.023 0.13 -10000 0 -0.37 10 10
ruffle organization -0.001 0.064 0.27 4 -10000 0 4
ROCK2 0.001 0.07 0.29 4 -10000 0 4
GNA14 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.002 0.11 -10000 0 -0.46 9 9
GNA13 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.093 0.15 0.43 2 -0.38 24 26
MMP2 -0.034 0.14 0.29 2 -0.41 11 13
S1P3 pathway

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
PDGFRB 0.024 0.028 -9999 0 -0.23 2 2
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.11 -9999 0 -0.27 27 27
GNAO1 -0.049 0.17 -9999 0 -0.46 27 27
S1P/S1P3/G12/G13 0.041 0.038 -9999 0 -0.25 2 2
AKT1 0.01 0.056 -9999 0 -0.32 1 1
AKT3 -0.02 0.12 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.028 -9999 0 -0.23 2 2
GNAI2 0.027 0.005 -9999 0 -10000 0 0
GNAI3 0.027 0.006 -9999 0 -10000 0 0
GNAI1 0.022 0.028 -9999 0 -0.23 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.02 0.055 -9999 0 -0.38 3 3
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.027 0.14 -9999 0 -0.45 11 11
MAPK3 -0.03 0.13 -9999 0 -0.44 11 11
MAPK1 -0.029 0.13 -9999 0 -0.45 10 10
JAK2 -0.029 0.14 -9999 0 -0.43 13 13
CXCR4 -0.029 0.13 -9999 0 -0.44 11 11
FLT1 0.027 0.006 -9999 0 -10000 0 0
RhoA/GDP 0.019 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.018 0.006 -9999 0 -10000 0 0
SRC -0.031 0.13 -9999 0 -0.44 11 11
S1P/S1P3/Gi -0.027 0.14 -9999 0 -0.46 11 11
RAC1 0.024 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.02 0.13 -9999 0 -0.42 11 11
VEGFA -0.016 0.14 -9999 0 -0.41 18 18
S1P/S1P2/Gi -0.024 0.12 -9999 0 -0.29 25 25
VEGFR1 homodimer/VEGFA homodimer 0.009 0.1 -9999 0 -0.32 14 14
RHOA 0.026 0.005 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.007 0.072 -9999 0 -0.24 12 12
GNAQ 0.026 0.005 -9999 0 -10000 0 0
GNAZ -0.012 0.13 -9999 0 -0.46 14 14
G12/G13 0.035 0.014 -9999 0 -10000 0 0
GNA14 0.026 0.006 -9999 0 -10000 0 0
GNA15 0.002 0.11 -9999 0 -0.46 9 9
GNA12 0.024 0.008 -9999 0 -10000 0 0
GNA13 0.026 0.005 -9999 0 -10000 0 0
GNA11 0.024 0.037 -9999 0 -0.46 1 1
Rac1/GTP -0.018 0.13 -9999 0 -0.44 10 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.1 0.21 -9999 0 -0.45 48 48
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.026 0.004 -9999 0 -10000 0 0
TCEB1 0.022 0.011 -9999 0 -10000 0 0
HIF1A/p53 0.014 0.061 -9999 0 -0.24 8 8
HIF1A -0.001 0.059 -9999 0 -0.26 8 8
COPS5 0.022 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.06 0.035 -9999 0 -10000 0 0
FIH (dimer) 0.025 0.007 -9999 0 -10000 0 0
CDKN2A -0.036 0.11 -9999 0 -0.23 42 42
ARNT/IPAS -0.054 0.16 -9999 0 -0.32 44 44
HIF1AN 0.025 0.007 -9999 0 -10000 0 0
GNB2L1 0.027 0.004 -9999 0 -10000 0 0
HIF1A/ARNT 0.015 0.062 -9999 0 -0.25 8 8
CUL2 0.026 0.005 -9999 0 -10000 0 0
OS9 0.026 0.005 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.044 0.022 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.018 0.064 -9999 0 -0.25 8 8
PHD1-3/OS9 0.058 0.041 -9999 0 -0.25 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.063 -9999 0 -0.24 5 5
VHL 0.025 0.007 -9999 0 -10000 0 0
HSP90AA1 0.027 0.003 -9999 0 -10000 0 0
HIF1A/JAB1 0.011 0.06 -9999 0 -0.24 8 8
EGLN3 0.019 0.063 -9999 0 -0.46 3 3
EGLN2 0.027 0.003 -9999 0 -10000 0 0
EGLN1 0.025 0.007 -9999 0 -10000 0 0
TP53 0.023 0.009 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.011 0.11 -9999 0 -0.47 9 9
ARNT 0.026 0.006 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.026 0.004 -9999 0 -10000 0 0
HIF1A/p19ARF -0.008 0.081 -9999 0 -0.28 8 8
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.017 0.047 0.23 6 -10000 0 6
PI3K Class IB/PDE3B 0.017 0.047 -10000 0 -0.23 6 6
PDE3B 0.017 0.047 -10000 0 -0.23 6 6
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.013 -10000 0 -10000 0 0
HSPA8 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.037 0.064 -10000 0 -0.28 3 3
AKT1 0.029 0.003 -10000 0 -10000 0 0
GSC 0 0.066 -10000 0 -10000 0 0
NKX2-5 0.004 0.062 -10000 0 -0.23 11 11
muscle cell differentiation -0.011 0.1 0.36 8 -10000 0 8
SMAD2-3/SMAD4/SP1 0.076 0.05 -10000 0 -10000 0 0
SMAD4 0.021 0.038 -10000 0 -10000 0 0
CBFB 0.024 0.008 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.029 0.14 -10000 0 -0.28 39 39
SMAD3/SMAD4/VDR 0.07 0.052 -10000 0 -10000 0 0
MYC -0.003 0.074 -10000 0 -0.24 16 16
CDKN2B -0.003 0.077 -10000 0 -0.44 1 1
AP1 0.012 0.095 -10000 0 -0.29 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.024 0.065 -10000 0 -0.3 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.005 0.057 -10000 0 -0.27 2 2
SP3 0.027 0.007 -10000 0 -10000 0 0
CREB1 0.027 0.004 -10000 0 -10000 0 0
FOXH1 0.008 0.049 -10000 0 -0.25 5 5
SMAD3/SMAD4/GR 0.05 0.051 -10000 0 -10000 0 0
GATA3 -0.12 0.22 -10000 0 -0.45 52 52
SKI/SIN3/HDAC complex/NCoR1 0.026 0.036 -10000 0 -10000 0 0
MEF2C/TIF2 0.001 0.099 0.36 1 -0.4 6 7
endothelial cell migration 0.031 0.22 1 7 -10000 0 7
MAX 0.028 0.01 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.027 0.002 -10000 0 -10000 0 0
RUNX2 0.026 0.004 -10000 0 -10000 0 0
RUNX3 0.022 0.034 -10000 0 -0.23 3 3
RUNX1 0.026 0.006 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.028 0.009 -10000 0 -10000 0 0
VDR 0.025 0.02 -10000 0 -0.23 1 1
CDKN1A 0.026 0.045 -10000 0 -10000 0 0
KAT2B 0.025 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.031 0.059 -10000 0 -0.24 1 1
DCP1A 0.026 0.005 -10000 0 -10000 0 0
SKI 0.027 0.003 -10000 0 -10000 0 0
SERPINE1 -0.032 0.22 -10000 0 -1 7 7
SMAD3/SMAD4/ATF2 0.046 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.005 0.13 -10000 0 -0.31 22 22
SAP30 0.027 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.048 0.026 -10000 0 -10000 0 0
JUN -0.002 0.087 -10000 0 -0.3 3 3
SMAD3/SMAD4/IRF7 0.048 0.049 -10000 0 -10000 0 0
TFE3 0.027 0.017 -10000 0 -10000 0 0
COL1A2 0.022 0.022 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.045 0.049 -10000 0 -10000 0 0
DLX1 -0.22 0.069 -10000 0 -0.24 162 162
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS -0.035 0.17 -10000 0 -0.45 24 24
SMAD3/SMAD4/Max 0.051 0.052 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.05 0.019 -10000 0 -10000 0 0
ZBTB17 0.025 0.002 -10000 0 -10000 0 0
LAMC1 0.019 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.046 0.048 -10000 0 -10000 0 0
IRF7 0.025 0.02 -10000 0 -0.23 1 1
ESR1 0.016 0.063 -10000 0 -0.46 3 3
HNF4A 0.009 0.053 -10000 0 -0.23 8 8
MEF2C 0.018 0.1 0.44 2 -0.44 3 5
SMAD2-3/SMAD4 0.05 0.051 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.05 0.02 -10000 0 -10000 0 0
IGHV3OR16-13 0.013 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.011 -10000 0 -10000 0 0
SKIL 0.02 0.042 -10000 0 -0.34 2 2
HDAC1 0.027 0.002 -10000 0 -10000 0 0
HDAC2 0.024 0.009 -10000 0 -10000 0 0
SNIP1 0.027 0.002 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.051 0.051 -10000 0 -10000 0 0
MSG1/HSC70 -0.054 0.16 -10000 0 -0.31 46 46
SMAD2 0.022 0.02 -10000 0 -10000 0 0
SMAD3 0.024 0.036 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.022 0.045 -10000 0 -0.33 1 1
SMAD2/SMAD2/SMAD4 0.001 0.056 0.17 2 -0.19 3 5
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 0.003 0.094 -10000 0 -0.46 7 7
NCOA1 0.027 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.018 0.069 -10000 0 -0.27 9 9
SMAD2-3/SMAD4/SP1/MIZ-1 0.086 0.053 -10000 0 -10000 0 0
IFNB1 0.012 0.034 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.044 0.1 0.37 1 -0.43 3 4
CITED1 -0.095 0.21 -10000 0 -0.44 46 46
SMAD2-3/SMAD4/ARC105 0.064 0.049 -10000 0 -10000 0 0
RBL1 0.02 0.052 -10000 0 -0.46 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.015 0.047 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.044 0.029 -10000 0 -10000 0 0
SMAD7 0.025 0.091 -10000 0 -0.39 1 1
MYC/MIZ-1 0.012 0.056 -10000 0 -0.16 16 16
SMAD3/SMAD4 0 0.084 -10000 0 -0.38 6 6
IL10 -0.069 0.15 -10000 0 -0.37 16 16
PIASy/HDAC complex 0.027 0.006 -10000 0 -10000 0 0
PIAS3 0.025 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.011 -10000 0 -10000 0 0
IL5 -0.062 0.13 -10000 0 -0.32 7 7
CDK4 0.025 0.011 -10000 0 -10000 0 0
PIAS4 0.027 0.006 -10000 0 -10000 0 0
ATF3 -0.054 0.17 -10000 0 -0.37 35 35
SMAD3/SMAD4/SP1 0.059 0.047 -10000 0 -10000 0 0
FOXG1 -0.014 0.049 -10000 0 -0.23 7 7
FOXO3 0.014 0.006 -10000 0 -10000 0 0
FOXO1 0.013 0.007 -10000 0 -10000 0 0
FOXO4 0.016 0.002 -10000 0 -10000 0 0
heart looping 0.018 0.1 0.44 2 -0.44 3 5
CEBPB 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.11 0.067 -10000 0 -0.26 5 5
MYOD1 -0.002 0.092 -10000 0 -0.38 9 9
SMAD3/SMAD4/HNF4 0.033 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.05 0.16 -10000 0 -0.29 52 52
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.042 -10000 0 -0.34 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.064 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.072 0.051 -10000 0 -10000 0 0
MED15 0.026 0.005 -10000 0 -10000 0 0
SP1 0.031 0.01 -10000 0 -10000 0 0
SIN3B 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.035 0.075 -10000 0 -0.27 4 4
ITGB5 0.027 0.045 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.026 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.043 0.06 -10000 0 -0.29 2 2
AR 0.021 0.051 -10000 0 -0.46 2 2
negative regulation of cell growth 0 0.078 -10000 0 -0.27 2 2
SMAD3/SMAD4/MYOD 0.026 0.079 -10000 0 -0.28 6 6
E2F5 0.02 0.022 -10000 0 -0.23 1 1
E2F4 0.024 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.053 0.059 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.021 0.021 -10000 0 -10000 0 0
TFDP1 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.03 0.1 -10000 0 -0.29 4 4
SMAD3/SMAD4/RUNX2 0.046 0.049 -10000 0 -10000 0 0
TGIF2 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.025 0.008 -10000 0 -10000 0 0
ATF2 0.026 0.005 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.026 0.004 -10000 0 -10000 0 0
SPHK1 0.025 0.02 -10000 0 -0.23 1 1
GNAI2 0.026 0.005 -10000 0 -10000 0 0
mol:S1P 0.015 0.006 -10000 0 -10000 0 0
GNAO1 -0.05 0.17 -10000 0 -0.46 27 27
mol:Sphinganine-1-P 0.012 0.013 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.052 0.03 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
G12/G13 0.035 0.014 -10000 0 -10000 0 0
S1PR3 0.019 0.055 -10000 0 -0.38 3 3
S1PR2 0.027 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.007 0.018 -10000 0 -10000 0 0
S1PR5 -0.064 0.19 -10000 0 -0.46 33 33
S1PR4 0.021 0.039 -10000 0 -0.23 4 4
GNAI1 0.021 0.028 -10000 0 -0.23 2 2
S1P/S1P5/G12 -0.013 0.11 -10000 0 -0.24 32 32
S1P/S1P3/Gq 0.015 0.077 0.21 1 -0.62 1 2
S1P/S1P4/Gi -0.027 0.12 -10000 0 -0.37 13 13
GNAQ 0.026 0.005 -10000 0 -10000 0 0
GNAZ -0.012 0.13 -10000 0 -0.46 14 14
GNA14 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.002 0.11 -10000 0 -0.46 9 9
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.037 -10000 0 -0.46 1 1
ABCC1 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.021 0.027 -10000 0 -0.27 1 1
EPHB2 0.024 0.028 -10000 0 -0.23 2 2
Syndecan-2/TACI 0.011 0.056 0.16 2 -0.27 5 7
LAMA1 0.011 0.068 -10000 0 -0.31 7 7
Syndecan-2/alpha2 ITGB1 0.017 0.092 -10000 0 -0.27 14 14
HRAS 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.006 0.021 -10000 0 -0.27 1 1
ITGA5 0.017 0.066 -10000 0 -0.4 4 4
BAX 0.004 0.019 -10000 0 -10000 0 0
EPB41 0.027 0 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.019 0.023 -10000 0 -0.24 1 1
LAMA3 -0.009 0.12 -10000 0 -0.43 13 13
EZR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.005 0.094 -10000 0 -0.46 7 7
Syndecan-2/MMP2 0.017 0.04 -10000 0 -0.27 3 3
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.072 -10000 0 -0.33 7 7
dendrite morphogenesis 0.022 0.029 0.16 1 -0.27 1 2
Syndecan-2/GM-CSF 0.016 0.029 -10000 0 -0.28 1 1
determination of left/right symmetry 0.008 0.025 -10000 0 -0.32 1 1
Syndecan-2/PKC delta 0.022 0.025 -10000 0 -0.27 1 1
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.036 0.069 0.19 27 -0.25 1 28
MAPK1 0.037 0.07 0.19 28 -0.25 1 29
Syndecan-2/RACK1 0.032 0.026 -10000 0 -0.23 1 1
NF1 0.027 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.008 0.025 -10000 0 -0.32 1 1
ITGA2 0.006 0.095 -10000 0 -0.46 7 7
MAPK8 0.007 0.021 -10000 0 -0.27 1 1
Syndecan-2/alpha2/beta1 Integrin 0.026 0.069 -10000 0 -0.23 9 9
Syndecan-2/Kininogen 0.005 0.046 0.16 1 -0.28 1 2
ITGB1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.045 0.072 0.19 30 -0.22 1 31
Syndecan-2/CASK/Protein 4.1 0.02 0.023 -10000 0 -0.24 1 1
extracellular matrix organization 0.022 0.025 -10000 0 -0.27 1 1
actin cytoskeleton reorganization 0.021 0.027 -10000 0 -0.27 1 1
Syndecan-2/Caveolin-2/Ras 0.022 0.063 -10000 0 -0.28 6 6
Syndecan-2/Laminin alpha3 0.005 0.071 0.16 1 -0.26 11 12
Syndecan-2/RasGAP 0.04 0.031 -10000 0 -0.22 1 1
alpha5/beta1 Integrin 0.031 0.05 -10000 0 -0.28 4 4
PRKCD 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.029 0.16 1 -0.27 1 2
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.028 0.18 1 -0.22 1 2
RHOA 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.022 0.01 -10000 0 -10000 0 0
TNFRSF13B -0.003 0.1 -10000 0 -0.34 13 13
RASA1 0.026 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.072 -10000 0 -0.33 7 7
Syndecan-2/Synbindin 0.021 0.025 -10000 0 -0.27 1 1
TGFB1 0.027 0.003 -10000 0 -10000 0 0
CASP3 0.044 0.07 0.19 30 -0.24 1 31
FN1 0.025 0.02 -10000 0 -0.23 1 1
Syndecan-2/IL8 -0.001 0.079 0.16 3 -0.27 10 13
SDC2 0.008 0.025 -10000 0 -0.32 1 1
KNG1 -0.003 0.071 -10000 0 -0.23 15 15
Syndecan-2/Neurofibromin 0.022 0.025 -10000 0 -0.27 1 1
TRAPPC4 0.026 0.006 -10000 0 -10000 0 0
CSF2 0.017 0.027 -10000 0 -0.23 2 2
Syndecan-2/TGFB1 0.022 0.025 -10000 0 -0.27 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.019 0.023 -10000 0 -0.24 1 1
Syndecan-2/Ezrin 0.034 0.028 -10000 0 -0.25 1 1
PRKACA 0.046 0.072 0.19 32 -0.24 1 33
angiogenesis -0.001 0.078 0.16 3 -0.27 10 13
MMP2 0.019 0.052 -10000 0 -0.46 2 2
IL8 -0.03 0.14 -10000 0 -0.34 27 27
calcineurin-NFAT signaling pathway 0.011 0.056 0.16 2 -0.27 5 7
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.009 0.069 -10000 0 -0.47 3 3
PDGF/PDGFRA/CRKL 0.024 0.053 -10000 0 -0.33 3 3
positive regulation of JUN kinase activity 0.054 0.04 -10000 0 -0.24 2 2
CRKL 0.026 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.084 0.17 -10000 0 -0.33 55 55
AP1 -0.13 0.3 -10000 0 -0.87 24 24
mol:IP3 -0.003 0.054 -10000 0 -0.35 3 3
PLCG1 -0.003 0.054 -10000 0 -0.35 3 3
PDGF/PDGFRA/alphaV Integrin 0.024 0.055 -10000 0 -0.35 3 3
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.053 -10000 0 -0.35 3 3
CAV3 -0.12 0.22 -10000 0 -0.44 54 54
CAV1 -0.014 0.13 -10000 0 -0.46 14 14
SHC/Grb2/SOS1 0.056 0.041 -10000 0 -0.24 2 2
PDGF/PDGFRA/Shf 0.024 0.053 -10000 0 -0.33 3 3
FOS -0.12 0.3 0.31 2 -0.86 24 26
JUN -0.027 0.023 -10000 0 -10000 0 0
oligodendrocyte development 0.024 0.055 -10000 0 -0.35 3 3
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
mol:DAG -0.003 0.054 -10000 0 -0.35 3 3
PDGF/PDGFRA 0.009 0.069 -10000 0 -0.47 3 3
actin cytoskeleton reorganization 0.025 0.052 -10000 0 -0.33 3 3
SRF 0.016 0.009 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.038 0.048 -10000 0 -0.28 3 3
PDGF/PDGFRA/Crk/C3G 0.041 0.046 -10000 0 -0.28 3 3
JAK1 0.005 0.039 -10000 0 -0.34 2 2
ELK1/SRF -0.001 0.046 0.15 3 -0.28 3 6
SHB 0.026 0.005 -10000 0 -10000 0 0
SHF 0.027 0.003 -10000 0 -10000 0 0
CSNK2A1 0.032 0.017 -10000 0 -10000 0 0
GO:0007205 -0.009 0.054 -10000 0 -0.38 3 3
SOS1 0.026 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.054 0.04 -10000 0 -0.24 2 2
PDGF/PDGFRA/SHB 0.025 0.052 -10000 0 -0.33 3 3
PDGF/PDGFRA/Caveolin-1 -0.005 0.12 -10000 0 -0.37 15 15
ITGAV 0.026 0.005 -10000 0 -10000 0 0
ELK1 -0.02 0.053 -10000 0 -0.34 3 3
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
PDGF/PDGFRA/Crk 0.023 0.053 -10000 0 -0.33 3 3
JAK-STAT cascade 0.005 0.039 -10000 0 -0.33 2 2
cell proliferation 0.024 0.053 -10000 0 -0.33 3 3
ceramide signaling pathway

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
MAP4K4 0.005 0.068 -10000 0 -0.32 3 3
BAG4 0.02 0.012 -10000 0 -10000 0 0
BAD 0.012 0.044 0.18 5 -10000 0 5
NFKBIA 0.027 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.028 -10000 0 -0.23 2 2
BAX 0.01 0.043 0.2 4 -10000 0 4
EnzymeConsortium:3.1.4.12 0.004 0.022 0.061 5 -0.081 2 7
IKBKB 0.018 0.074 0.22 6 -0.32 2 8
MAP2K2 0.004 0.065 0.2 6 -0.19 8 14
MAP2K1 0.007 0.068 0.21 7 -0.19 8 15
SMPD1 0.007 0.025 0.16 1 -10000 0 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.016 0.074 0.26 2 -0.33 2 4
MAP2K4 0.008 0.033 0.17 2 -10000 0 2
protein ubiquitination 0.013 0.074 0.21 1 -0.33 2 3
EnzymeConsortium:2.7.1.37 0.006 0.07 0.21 7 -0.19 7 14
response to UV 0 0.001 0.002 8 -0.002 1 9
RAF1 0.005 0.067 0.19 8 -0.2 8 16
CRADD 0.026 0.006 -10000 0 -10000 0 0
mol:ceramide 0.011 0.035 0.12 5 -0.12 1 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.007 -10000 0 -10000 0 0
MADD 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.009 0.033 0.14 3 -10000 0 3
TRADD 0.024 0.008 -10000 0 -10000 0 0
RELA/p50 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0.008 0.067 0.2 7 -0.18 7 14
MAPK1 0.008 0.066 0.19 8 -0.19 3 11
p50/RELA/I-kappa-B-alpha 0.039 0.008 -10000 0 -10000 0 0
FADD 0.007 0.071 0.26 1 -0.32 3 4
KSR1 0.003 0.06 0.16 5 -0.2 8 13
MAPK8 0.012 0.046 0.21 5 -10000 0 5
TRAF2 0.026 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 5 -10000 0 5
CHUK 0.012 0.07 0.26 2 -0.33 2 4
TNF R/SODD 0.028 0.019 -10000 0 -10000 0 0
TNF -0.002 0.1 -10000 0 -0.35 13 13
CYCS 0.025 0.057 0.16 15 -10000 0 15
IKBKG 0.007 0.069 -10000 0 -0.33 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.008 0.072 -10000 0 -0.33 3 3
RELA 0.026 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.005 -10000 0 -10000 0 0
AIFM1 0.02 0.053 0.16 10 -10000 0 10
TNF/TNF R/SODD 0.022 0.068 -10000 0 -0.26 7 7
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 5 -10000 0 5
CASP8 0.029 0.022 -10000 0 -10000 0 0
NSMAF 0.019 0.081 0.22 12 -0.32 2 14
response to hydrogen peroxide 0 0.001 0.002 8 -0.002 1 9
BCL2 0.018 0.052 -10000 0 -0.46 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.04 0.21 6 -10000 0 6
RFC1 -0.004 0.016 0.19 1 -10000 0 1
PRKDC 0.015 0.064 0.22 16 -10000 0 16
RIPK1 0.029 0.007 -10000 0 -10000 0 0
CASP7 -0.012 0.089 -10000 0 -0.54 4 4
FASLG/FAS/FADD/FAF1 -0.012 0.056 -10000 0 -0.25 5 5
MAP2K4 -0.07 0.16 0.24 1 -0.38 22 23
mol:ceramide -0.024 0.097 -10000 0 -0.28 10 10
GSN 0.002 0.04 0.21 6 -10000 0 6
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.073 -10000 0 -0.29 5 5
FAS 0.008 0.055 -10000 0 -0.47 2 2
BID -0.018 0.006 -10000 0 -10000 0 0
MAP3K1 -0.018 0.1 0.25 3 -0.34 4 7
MAP3K7 0.02 0.011 -10000 0 -10000 0 0
RB1 -0.003 0.015 0.19 1 -10000 0 1
CFLAR 0.029 0.006 -10000 0 -10000 0 0
HGF/MET 0.015 0.094 -10000 0 -0.3 11 11
ARHGDIB -0.005 0.03 0.21 2 -10000 0 2
FADD 0.014 0.022 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.04 -10000 0 -0.21 6 6
NFKB1 -0.029 0.097 -10000 0 -0.55 1 1
MAPK8 -0.11 0.21 -10000 0 -0.47 41 41
DFFA -0.004 0.016 0.19 1 -10000 0 1
DNA fragmentation during apoptosis -0.003 0.023 0.2 2 -10000 0 2
FAS/FADD/MET 0.01 0.089 -10000 0 -0.32 10 10
CFLAR/RIP1 0.043 0.012 -10000 0 -10000 0 0
FAIM3 0.021 0.039 -10000 0 -0.23 4 4
FAF1 0.013 0.024 -10000 0 -10000 0 0
PARP1 -0.003 0.023 0.2 2 -10000 0 2
DFFB -0.003 0.023 0.2 2 -10000 0 2
CHUK -0.028 0.088 -10000 0 -0.51 1 1
FASLG 0.002 0.062 -10000 0 -0.27 7 7
FAS/FADD 0.016 0.05 -10000 0 -0.35 2 2
HGF 0.004 0.078 -10000 0 -0.27 12 12
LMNA 0 0.034 0.18 5 -10000 0 5
CASP6 -0.004 0.016 0.19 1 -10000 0 1
CASP10 0.014 0.023 -10000 0 -10000 0 0
CASP3 -0.002 0.02 0.23 1 -10000 0 1
PTPN13 0.026 0.004 -10000 0 -10000 0 0
CASP8 -0.018 0.014 -10000 0 -10000 0 0
IL6 -0.28 0.52 -10000 0 -1.2 43 43
MET -0.006 0.12 -10000 0 -0.46 11 11
ICAD/CAD -0.004 0.021 0.18 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.098 -10000 0 -0.28 10 10
activation of caspase activity by cytochrome c -0.018 0.006 -10000 0 -10000 0 0
PAK2 0.007 0.05 0.21 10 -10000 0 10
BCL2 0.019 0.052 -10000 0 -0.46 2 2
IL27-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
TGFB1 0.024 0.021 -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 -0.019 0.08 -10000 0 -0.47 1 1
IL27/IL27R/JAK1 0.076 0.14 0.81 1 -10000 0 1
TBX21 0.043 0.15 0.47 4 -0.51 2 6
IL12B 0.006 0.068 -10000 0 -0.23 13 13
IL12A -0.022 0.09 -10000 0 -0.31 15 15
IL6ST -0.006 0.12 -10000 0 -0.46 12 12
IL27RA/JAK1 0.034 0.047 -10000 0 -10000 0 0
IL27 0.019 0.041 -10000 0 -0.23 4 4
TYK2 0.028 0.009 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.044 0.13 0.45 1 -10000 0 1
T-helper 2 cell differentiation -0.019 0.08 -10000 0 -0.47 1 1
T cell proliferation during immune response -0.019 0.08 -10000 0 -0.47 1 1
MAPKKK cascade 0.019 0.08 0.47 1 -10000 0 1
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT2 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.022 0.045 -10000 0 -0.23 5 5
IL12RB1 0.018 0.047 -10000 0 -0.23 6 6
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.039 0.16 0.47 4 -0.43 7 11
IL27/IL27R/JAK2/TYK2 0.019 0.08 0.47 1 -10000 0 1
positive regulation of T cell mediated cytotoxicity 0.019 0.08 0.47 1 -10000 0 1
STAT1 (dimer) 0.12 0.23 0.52 34 -0.49 2 36
JAK2 0.026 0.008 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.087 0.42 1 -10000 0 1
T cell proliferation -0.03 0.12 0.43 1 -0.39 4 5
IL12/IL12R/TYK2/JAK2 0.015 0.11 -10000 0 -0.64 2 2
IL17A -0.044 0.13 0.45 1 -10000 0 1
mast cell activation -0.019 0.08 -10000 0 -0.47 1 1
IFNG 0.008 0.025 0.16 1 -0.086 1 2
T cell differentiation 0 0.005 0.011 2 -0.015 4 6
STAT3 (dimer) 0.025 0.086 0.42 1 -10000 0 1
STAT5A (dimer) 0.026 0.086 0.42 1 -10000 0 1
STAT4 (dimer) 0.018 0.1 0.42 1 -0.38 2 3
STAT4 0.005 0.09 -10000 0 -0.34 10 10
T cell activation -0.006 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.034 0.081 -10000 0 -10000 0 0
GATA3 -0.37 0.56 0.5 1 -1.2 52 53
IL18 -0.005 0.061 -10000 0 -0.3 7 7
positive regulation of mast cell cytokine production 0.025 0.085 0.41 1 -10000 0 1
IL27/EBI3 0.034 0.043 0.2 1 -0.17 3 4
IL27RA 0.013 0.037 -10000 0 -10000 0 0
IL6 -0.092 0.19 -10000 0 -0.4 47 47
STAT5A 0.026 0.005 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.015 0.015 -10000 0 -10000 0 0
IL1B -0.034 0.1 -10000 0 -0.26 27 27
EBI3 0.026 0.031 -10000 0 -0.24 2 2
TNF -0.012 0.07 -10000 0 -0.25 13 13
TCGA08_retinoblastoma

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
CDKN2B 0.025 0.019 -10000 0 -10000 0 0
CDKN2C 0.032 0.028 -10000 0 -0.26 1 1
CDKN2A -0.036 0.11 -10000 0 -0.24 42 42
CCND2 0.001 0.025 -10000 0 -10000 0 0
RB1 -0.003 0.032 0.29 1 -10000 0 1
CDK4 0.004 0.024 -10000 0 -10000 0 0
CDK6 0.003 0.023 -10000 0 -10000 0 0
G1/S progression 0.003 0.033 -10000 0 -0.29 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC2 0.025 0.009 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.018 -10000 0 -10000 0 0
forebrain development -0.073 0.17 -10000 0 -0.43 14 14
GNAO1 -0.052 0.17 -10000 0 -0.46 27 27
SMO/beta Arrestin2 0.018 0.027 -10000 0 -10000 0 0
SMO 0.013 0.019 -10000 0 -10000 0 0
ARRB2 0.022 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.046 0.061 0.25 3 -10000 0 3
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
GSK3B 0.026 0.006 -10000 0 -10000 0 0
GNAI2 0.024 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.067 0.021 -10000 0 -10000 0 0
GNAI1 0.02 0.029 -10000 0 -0.24 2 2
XPO1 0.01 0.025 -10000 0 -10000 0 0
GLI1/Su(fu) -0.074 0.16 -10000 0 -0.5 11 11
SAP30 0.027 0.004 -10000 0 -10000 0 0
mol:GDP 0.013 0.019 -10000 0 -10000 0 0
MIM/GLI2A -0.014 0.06 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.024 0.007 -10000 0 -10000 0 0
GLI2 0.021 0.044 0.18 2 -0.24 1 3
GLI3 0.033 0.062 0.26 3 -0.25 1 4
CSNK1D 0.027 0.003 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.027 0.002 -10000 0 -10000 0 0
Gi family/GTP -0.042 0.12 -10000 0 -0.31 23 23
SIN3B 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.032 0.051 0.26 1 -10000 0 1
GLI2/Su(fu) 0.023 0.044 -10000 0 -0.31 1 1
FOXA2 -0.33 0.48 -10000 0 -0.96 65 65
neural tube patterning -0.073 0.17 -10000 0 -0.43 14 14
SPOP 0.026 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.041 -10000 0 -10000 0 0
GNB1 0.027 0.003 -10000 0 -10000 0 0
CSNK1G2 0.026 0.004 -10000 0 -10000 0 0
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 -0.014 0.06 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.073 0.17 -10000 0 -0.43 14 14
SUFU 0.014 0.014 -10000 0 -10000 0 0
LGALS3 -0.015 0.14 -10000 0 -0.46 15 15
catabolic process 0.055 0.072 0.31 2 -10000 0 2
GLI3A/CBP 0.025 0.018 -10000 0 -10000 0 0
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 -0.075 0.17 -10000 0 -0.45 13 13
RAB23 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.027 0.004 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.007 0.08 -10000 0 -0.24 12 12
GNAZ -0.015 0.13 -10000 0 -0.46 14 14
RBBP4 0.028 0.002 -10000 0 -10000 0 0
CSNK1G1 0.026 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.034 0.047 -10000 0 -10000 0 0
STK36 0.01 0.024 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.029 0.11 -10000 0 -0.37 10 10
PTCH1 -0.06 0.16 -10000 0 -0.6 4 4
MIM/GLI1 -0.12 0.25 -10000 0 -0.48 49 49
CREBBP 0.025 0.018 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.034 0.034 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.025 0.046 -10000 0 -0.27 2 2
BIRC5 -0.053 0.12 -10000 0 -0.24 53 53
NFKBIA 0.006 0.032 0.19 2 -0.19 1 3
CPEB1 -0.09 0.21 -10000 0 -0.46 42 42
AKT1 0.005 0.03 0.19 1 -0.19 1 2
NDEL1 0.024 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.021 0.027 -10000 0 -10000 0 0
NDEL1/TACC3 0.034 0.046 -10000 0 -10000 0 0
GADD45A 0.021 0.051 -10000 0 -0.46 2 2
GSK3B 0.024 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.023 0.05 -10000 0 -0.25 4 4
MDM2 0.026 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.045 0.092 0.24 3 -10000 0 3
TP53 0.001 0.067 -10000 0 -0.21 15 15
DLG7 0.006 0.026 -10000 0 -0.19 1 1
AURKAIP1 0.027 0.003 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.036 0.049 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.021 0.027 -10000 0 -10000 0 0
AURKA 0.013 0.033 -10000 0 -0.23 1 1
AURKB 0.002 0.041 -10000 0 -0.16 9 9
CDC25B 0.014 0.024 -10000 0 -10000 0 0
G2/M transition checkpoint 0.006 0.021 -10000 0 -0.17 1 1
mRNA polyadenylation -0.039 0.12 -10000 0 -0.25 40 40
Aurora A/CPEB -0.039 0.12 -10000 0 -0.25 40 40
Aurora A/TACC1/TRAP/chTOG 0.042 0.04 -10000 0 -10000 0 0
BRCA1 0.026 0.005 -10000 0 -10000 0 0
centrosome duplication 0.023 0.05 -10000 0 -0.25 4 4
regulation of centrosome cycle 0.032 0.045 -10000 0 -10000 0 0
spindle assembly 0.041 0.039 -10000 0 -10000 0 0
TDRD7 0.026 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.017 0.078 -10000 0 -0.25 1 1
CENPA 0.011 0.037 -10000 0 -0.25 2 2
Aurora A/PP2A 0.028 0.033 -10000 0 -0.19 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.026 0.2 1 -10000 0 1
negative regulation of DNA binding 0 0.068 -10000 0 -0.24 6 6
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.011 -10000 0 -10000 0 0
RASA1 0.026 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.021 -10000 0 -0.17 1 1
mitotic prometaphase 0 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.033 -10000 0 -0.23 1 1
TACC1 0.019 0.012 -10000 0 -10000 0 0
TACC3 0.012 0.059 -10000 0 -0.24 9 9
Aurora A/Antizyme1 0.044 0.029 -10000 0 -10000 0 0
Aurora A/RasGAP 0.028 0.031 -10000 0 -0.19 1 1
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.045 0.045 -10000 0 -0.28 3 3
Importin alpha/Importin beta/TPX2 -0.045 0.092 0.24 3 -10000 0 3
PPP2R5D 0.027 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 -0.026 0.068 -10000 0 -0.28 1 1
PAK1 0.018 0.063 -10000 0 -0.46 3 3
CKAP5 0.027 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated 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
CTTN 0.026 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.016 0.091 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.019 0.035 -9999 0 -10000 0 0
POMC -0.072 0.19 -9999 0 -0.45 36 36
EGFR 0.008 0.088 -9999 0 -0.46 6 6
Syndecan-3/EGFR 0.021 0.043 -9999 0 -10000 0 0
AGRP 0.019 0.008 -9999 0 -10000 0 0
NCSTN 0.025 0.008 -9999 0 -10000 0 0
PSENEN 0.027 0.002 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN 0.001 0.074 -9999 0 -0.23 16 16
long-term memory 0.041 0.023 -9999 0 -10000 0 0
Syndecan-3/IL8 0.003 0.07 -9999 0 -10000 0 0
PSEN1 0.027 0.003 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.01 -9999 0 -10000 0 0
FYN 0.024 0.009 -9999 0 -10000 0 0
limb bud formation 0.014 0.004 -9999 0 -10000 0 0
MC4R 0.017 0.02 -9999 0 -0.23 1 1
SRC 0.026 0.006 -9999 0 -10000 0 0
PTN -0.052 0.17 -9999 0 -0.45 28 28
FGFR/FGF/Syndecan-3 0.014 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.009 0.093 -9999 0 -0.29 1 1
Syndecan-3/AgRP 0.025 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.035 0.024 -9999 0 -10000 0 0
Fyn/Cortactin 0.034 0.014 -9999 0 -10000 0 0
SDC3 0.014 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.069 -9999 0 -10000 0 0
IL8 -0.03 0.14 -9999 0 -0.34 27 27
Syndecan-3/Fyn/Cortactin 0.043 0.023 -9999 0 -10000 0 0
Syndecan-3/CASK 0.012 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.041 0.14 -9999 0 -0.32 36 36
Gamma Secretase 0.072 0.026 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.028 0.065 -10000 0 -0.23 8 8
TC10/GTP 0.026 0.056 -10000 0 -0.22 6 6
Insulin Receptor/Insulin/IRS1/Shp2 0.06 0.031 -10000 0 -0.26 1 1
HRAS 0.027 0.004 -10000 0 -10000 0 0
APS homodimer 0.018 0.046 -10000 0 -0.31 3 3
GRB14 -0.016 0.099 -10000 0 -0.24 27 27
FOXO3 -0.16 0.28 -10000 0 -0.55 57 57
AKT1 -0.003 0.067 0.22 2 -10000 0 2
INSR 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.054 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.008 -10000 0 -10000 0 0
SORBS1 0.004 0.1 -10000 0 -0.46 8 8
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 0.006 0.014 -10000 0 -10000 0 0
CAV1 -0.009 0.071 0.21 1 -0.24 14 15
CBL/APS/CAP/Crk-II/C3G 0.045 0.069 -10000 0 -0.24 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.061 0.032 -10000 0 -0.26 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.027 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.023 0.043 -10000 0 -10000 0 0
RPS6KB1 -0.004 0.063 0.19 4 -10000 0 4
PARD6A 0.024 0.008 -10000 0 -10000 0 0
CBL 0.026 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.063 -10000 0 -0.56 2 2
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.03 0.058 -10000 0 -10000 0 0
HRAS/GTP 0.011 0.04 -10000 0 -0.21 5 5
Insulin Receptor 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.068 0.035 -10000 0 -0.25 1 1
PRKCI 0.027 0.03 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.01 0.047 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.037 0.052 -10000 0 -0.4 2 2
PI3K 0.053 0.032 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.003 -10000 0 -10000 0 0
AKT2 -0.004 0.066 0.22 2 -10000 0 2
PRKCZ 0.03 0.025 -10000 0 -10000 0 0
SH2B2 0.018 0.046 -10000 0 -0.31 3 3
SHC/SHIP 0.019 0.046 -10000 0 -0.23 5 5
F2RL2 -0.12 0.13 -10000 0 -0.24 100 100
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.044 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.068 0.027 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.026 0.006 -10000 0 -10000 0 0
NCK1 0.024 0.008 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.037 0.07 -10000 0 -0.25 7 7
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.054 0.028 -10000 0 -10000 0 0
INPP5D 0.006 0.046 0.19 1 -0.24 5 6
SOS1 0.026 0.004 -10000 0 -10000 0 0
SGK1 -0.16 0.33 -10000 0 -0.8 37 37
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.46 1 1
p62DOK/RasGAP 0.037 0.053 -10000 0 -0.4 2 2
INS 0.019 0.02 -10000 0 -0.23 1 1
mol:PI-3-4-P2 0.006 0.046 0.19 1 -0.24 5 6
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.013 0.051 0.17 1 -10000 0 1
PTPRA 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
TC10/GTP/CIP4 0.036 0.006 -10000 0 -10000 0 0
PDPK1 0.026 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.024 0.021 -10000 0 -0.22 1 1
Insulin Receptor/Insulin/IRS1 0.045 0.028 -10000 0 -0.26 1 1
Insulin Receptor/Insulin/IRS3 0.035 0.017 -10000 0 -10000 0 0
Par3/Par6 -0.035 0.084 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.013 0.003 -10000 0 -10000 0 0
mol:DAG -0.027 0.1 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.004 0.077 -10000 0 -0.25 12 12
CaM/Ca2+ -0.013 0.1 -10000 0 -10000 0 0
HIF1A 0.032 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.021 0.11 0.27 1 -0.31 1 2
PLCG1 -0.027 0.1 -10000 0 -10000 0 0
NOS3 -0.014 0.1 0.25 1 -10000 0 1
CBL 0.026 0.006 -10000 0 -10000 0 0
mol:NO -0.011 0.099 0.25 1 -10000 0 1
FLT1 0.018 0.004 -10000 0 -10000 0 0
PGF -0.058 0.18 -10000 0 -0.45 31 31
VEGFR1 homodimer/NRP2/VEGFR121 0.012 0.092 -10000 0 -10000 0 0
CALM1 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.021 -10000 0 -0.23 1 1
eNOS/Hsp90 0.006 0.11 0.35 2 -10000 0 2
endothelial cell proliferation -0.064 0.16 0.33 1 -0.49 14 15
mol:Ca2+ -0.027 0.1 -10000 0 -10000 0 0
MAPK3 -0.042 0.092 -10000 0 -0.43 2 2
MAPK1 -0.042 0.092 -10000 0 -0.43 2 2
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
PLGF homodimer -0.057 0.18 -10000 0 -0.45 31 31
PRKACA 0.026 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.014 0.13 -10000 0 -0.46 14 14
VEGFA homodimer -0.018 0.14 -10000 0 -0.41 18 18
VEGFR1 homodimer/VEGFA homodimer 0.004 0.085 -10000 0 -0.27 12 12
platelet activating factor biosynthetic process -0.042 0.089 -10000 0 -0.42 2 2
PI3K 0.004 0.11 -10000 0 -0.31 1 1
PRKCA -0.044 0.098 -10000 0 -0.45 2 2
PRKCB -0.074 0.14 -10000 0 -0.45 12 12
VEGFR1 homodimer/PLGF homodimer -0.021 0.12 -10000 0 -0.27 29 29
VEGFA -0.018 0.14 -10000 0 -0.41 18 18
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 -0.027 0.1 -10000 0 -10000 0 0
RASA1 0.015 0.014 -10000 0 -10000 0 0
NRP2 0.016 0.072 -10000 0 -0.46 4 4
VEGFR1 homodimer 0.018 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.12 0.34 1 -0.4 6 7
PTPN11 0.026 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.11 -10000 0 -0.31 1 1
mol:L-citrulline -0.011 0.099 0.25 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.03 0.084 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.016 0.08 -10000 0 -10000 0 0
CD2AP 0.027 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.014 0.11 -10000 0 -0.3 1 1
PDPK1 -0.014 0.099 -10000 0 -0.29 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.018 0.082 -10000 0 -10000 0 0
mol:NADP -0.011 0.099 0.25 1 -10000 0 1
HSP90AA1 0.027 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.029 0.082 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.025 0.047 -10000 0 -0.27 4 4
Signaling events mediated by PRL

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
CCNE1 0.027 0.003 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.015 0.072 -10000 0 -0.46 4 4
CDKN1A 0.008 0.037 -10000 0 -0.3 1 1
PRL-3/alpha Tubulin 0.004 0.067 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.092 0.26 2 -0.27 10 12
AGT -0.038 0.13 -10000 0 -0.28 36 36
CCNA2 -0.042 0.068 -10000 0 -0.32 1 1
TUBA1B 0.027 0.004 -10000 0 -10000 0 0
EGR1 -0.023 0.09 -10000 0 -0.32 11 11
CDK2/Cyclin E1 0.039 0.044 -10000 0 -10000 0 0
MAPK3 0 0.082 0.24 10 -10000 0 10
PRL-2 /Rab GGTase beta 0.038 0.009 -10000 0 -10000 0 0
MAPK1 0.002 0.084 0.24 11 -10000 0 11
PTP4A1 -0.022 0.064 -10000 0 -10000 0 0
PTP4A3 -0.015 0.089 -10000 0 -0.23 25 25
PTP4A2 0.027 0.002 -10000 0 -10000 0 0
ITGB1 0.003 0.086 0.24 12 -10000 0 12
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.007 0.053 -10000 0 -0.35 2 2
Rab GGTase beta/Rab GGTase alpha 0.038 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.003 0.075 -10000 0 -10000 0 0
RABGGTA 0.027 0 -10000 0 -10000 0 0
BCAR1 -0.003 0.029 -10000 0 -10000 0 0
RHOC 0.001 0.073 -10000 0 -0.33 6 6
RHOA 0.008 0.052 -10000 0 -0.39 1 1
cell motility 0.017 0.073 0.28 3 -0.37 1 4
PRL-1/alpha Tubulin -0.002 0.076 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.004 0.083 -10000 0 -0.18 27 27
ROCK1 0.016 0.069 0.28 3 -0.38 1 4
RABGGTB 0.026 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.005