PARADIGM pathway analysis of mRNA expression and copy number data
Lung Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1GX4B0C
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 45 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
HIF-1-alpha transcription factor network 26
TCGA08_retinoblastoma 26
IL23-mediated signaling events 22
IL4-mediated signaling events 21
Signaling mediated by p38-alpha and p38-beta 21
Fc-epsilon receptor I signaling in mast cells 19
Glucocorticoid receptor regulatory network 19
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 19
Osteopontin-mediated events 18
Wnt signaling 18
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 154 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 154 ).

Pathway.Name Significance.Ratio 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
HIF-1-alpha transcription factor network 0.1688 26 1988 76 -0.28 0.033 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 0.1688 26 211 8 -0.061 0.082 1000 -1000 -0.002 -1000
IL23-mediated signaling events 0.1429 22 1367 60 -0.51 0.032 1000 -1000 -0.047 -1000
IL4-mediated signaling events 0.1364 21 1931 91 -0.56 0.52 1000 -1000 -0.069 -1000
Signaling mediated by p38-alpha and p38-beta 0.1364 21 924 44 -0.17 0.032 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 0.1234 19 1915 97 -0.12 0.042 1000 -1000 -0.043 -1000
Glucocorticoid receptor regulatory network 0.1234 19 2180 114 -0.46 0.29 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1234 19 1325 68 -0.39 0.19 1000 -1000 -0.069 -1000
Osteopontin-mediated events 0.1169 18 688 38 -0.19 0.033 1000 -1000 -0.026 -1000
Wnt signaling 0.1169 18 131 7 -0.13 0.027 1000 -1000 -0.014 -1000
Noncanonical Wnt signaling pathway 0.1104 17 456 26 -0.13 0.032 1000 -1000 -0.032 -1000
Syndecan-1-mediated signaling events 0.1039 16 563 34 -0.14 0.035 1000 -1000 -0.032 -1000
Signaling events mediated by the Hedgehog family 0.1039 16 844 52 -0.25 0.047 1000 -1000 -0.035 -1000
Ephrin B reverse signaling 0.1039 16 787 48 -0.11 0.041 1000 -1000 -0.017 -1000
Endothelins 0.1039 16 1572 96 -0.24 0.033 1000 -1000 -0.035 -1000
EPHB forward signaling 0.1039 16 1416 85 -0.11 0.067 1000 -1000 -0.052 -1000
Thromboxane A2 receptor signaling 0.0974 15 1673 105 -0.16 0.055 1000 -1000 -0.041 -1000
BCR signaling pathway 0.0974 15 1529 99 -0.21 0.046 1000 -1000 -0.051 -1000
FOXM1 transcription factor network 0.0974 15 785 51 -0.25 0.04 1000 -1000 -0.055 -1000
IGF1 pathway 0.0909 14 823 57 -0.072 0.059 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0909 14 1144 78 -0.18 0.074 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0844 13 875 63 -0.1 0.051 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 0.0844 13 1298 93 -0.11 0.046 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 0.0844 13 280 21 -0.075 0.046 1000 -1000 -0.038 -1000
IL12-mediated signaling events 0.0779 12 1110 87 -0.2 0.036 1000 -1000 -0.056 -1000
IL1-mediated signaling events 0.0779 12 792 62 -0.15 0.048 1000 -1000 -0.027 -1000
Calcium signaling in the CD4+ TCR pathway 0.0779 12 388 31 -0.2 0.037 1000 -1000 -0.042 -1000
Glypican 1 network 0.0714 11 566 48 -0.051 0.032 1000 -1000 -0.02 -1000
FAS signaling pathway (CD95) 0.0714 11 530 47 -0.15 0.08 1000 -1000 -0.028 -1000
LPA receptor mediated events 0.0714 11 1204 102 -0.2 0.033 1000 -1000 -0.056 -1000
BMP receptor signaling 0.0649 10 879 81 -0.16 0.054 1000 -1000 -0.041 -1000
IFN-gamma pathway 0.0649 10 716 68 -0.1 0.042 1000 -1000 -0.039 -1000
S1P1 pathway 0.0649 10 387 36 -0.19 0.032 1000 -1000 -0.029 -1000
TCGA08_p53 0.0649 10 74 7 -0.039 0.032 1000 -1000 -0.002 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0649 10 749 74 -0.099 0.05 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 0.0584 9 669 74 -0.056 0.045 1000 -1000 -0.038 -1000
Syndecan-2-mediated signaling events 0.0584 9 662 69 -0.12 0.035 1000 -1000 -0.026 -1000
Arf6 signaling events 0.0584 9 595 62 -0.072 0.067 1000 -1000 -0.012 -1000
amb2 Integrin signaling 0.0584 9 786 82 -0.11 0.037 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 0.0584 9 400 43 -0.066 0.049 1000 -1000 -0.035 -1000
IL27-mediated signaling events 0.0584 9 495 51 -0.19 0.12 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.0584 9 664 67 -0.069 0.032 1000 -1000 -0.036 -1000
E-cadherin signaling in keratinocytes 0.0584 9 421 43 -0.033 0.042 1000 -1000 -0.026 -1000
TRAIL signaling pathway 0.0519 8 388 48 -0.039 0.032 1000 -1000 -0.028 -1000
E-cadherin signaling events 0.0519 8 40 5 -0.004 0.028 1000 -1000 0.012 -1000
PLK2 and PLK4 events 0.0455 7 22 3 -0.014 0.03 1000 -1000 0 -1000
Signaling events mediated by PTP1B 0.0455 7 572 76 -0.088 0.066 1000 -1000 -0.032 -1000
Arf6 downstream pathway 0.0455 7 341 43 -0.052 0.045 1000 -1000 -0.022 -1000
PDGFR-alpha signaling pathway 0.0455 7 317 44 -0.12 0.049 1000 -1000 -0.035 -1000
Integrins in angiogenesis 0.0455 7 595 84 -0.1 0.061 1000 -1000 -0.039 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0455 7 330 45 -0.074 0.036 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0455 7 366 51 -0.12 0.064 1000 -1000 -0.041 -1000
IL6-mediated signaling events 0.0455 7 555 75 -0.077 0.049 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0390 6 831 136 -0.4 0.097 1000 -1000 -0.032 -1000
Hedgehog signaling events mediated by Gli proteins 0.0390 6 413 65 -0.16 0.076 1000 -1000 -0.035 -1000
Presenilin action in Notch and Wnt signaling 0.0390 6 393 61 -0.12 0.065 1000 -1000 -0.037 -1000
Reelin signaling pathway 0.0390 6 384 56 -0.073 0.077 1000 -1000 -0.03 -1000
Glypican 2 network 0.0390 6 25 4 0 0.002 1000 -1000 0 -1000
Nongenotropic Androgen signaling 0.0390 6 319 52 -0.08 0.052 1000 -1000 -0.029 -1000
Plasma membrane estrogen receptor signaling 0.0390 6 594 86 -0.067 0.046 1000 -1000 -0.048 -1000
VEGFR1 specific signals 0.0390 6 387 56 -0.04 0.035 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0325 5 401 76 -0.2 0.054 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0325 5 161 28 -0.036 0.043 1000 -1000 -0.012 -1000
Visual signal transduction: Cones 0.0325 5 214 38 -0.024 0.043 1000 -1000 -0.003 -1000
p75(NTR)-mediated signaling 0.0325 5 626 125 -0.13 0.066 1000 -1000 -0.041 -1000
FOXA2 and FOXA3 transcription factor networks 0.0325 5 242 46 -0.064 0.076 1000 -1000 -0.061 -1000
mTOR signaling pathway 0.0325 5 303 53 -0.019 0.083 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0325 5 295 58 -0.054 0.059 1000 -1000 -0.03 -1000
Syndecan-3-mediated signaling events 0.0325 5 198 35 -0.13 0.065 1000 -1000 -0.024 -1000
IL2 signaling events mediated by PI3K 0.0325 5 293 58 -0.087 0.036 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0325 5 668 125 -0.029 0.051 1000 -1000 -0.044 -1000
E-cadherin signaling in the nascent adherens junction 0.0325 5 417 76 -0.062 0.053 1000 -1000 -0.054 -1000
IL2 signaling events mediated by STAT5 0.0325 5 115 22 -0.071 0.032 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0325 5 616 120 -0.14 0.087 1000 -1000 -0.044 -1000
Visual signal transduction: Rods 0.0325 5 281 52 -0.073 0.05 1000 -1000 -0.028 -1000
Regulation of Androgen receptor activity 0.0325 5 351 70 -0.21 0.052 1000 -1000 -0.043 -1000
Ras signaling in the CD4+ TCR pathway 0.0325 5 98 17 -0.014 0.032 1000 -1000 -0.009 -1000
ErbB2/ErbB3 signaling events 0.0260 4 266 65 -0.031 0.046 1000 -1000 -0.058 -1000
ErbB4 signaling events 0.0260 4 325 69 -0.086 0.045 1000 -1000 -0.027 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0260 4 231 54 -0.059 0.046 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 0.0260 4 80 17 -0.022 0.044 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.0260 4 187 39 -0.057 0.031 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0260 4 383 85 -0.097 0.078 1000 -1000 -0.031 -1000
Ceramide signaling pathway 0.0260 4 372 76 -0.049 0.058 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class III 0.0260 4 176 40 -0.06 0.061 1000 -1000 -0.026 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0260 4 214 52 -0.026 0.079 1000 -1000 -0.031 -1000
FoxO family signaling 0.0260 4 273 64 -0.12 0.059 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 0.0260 4 69 15 -0.032 0.031 1000 -1000 -0.029 -1000
TCGA08_rtk_signaling 0.0260 4 117 26 -0.067 0.078 1000 -1000 -0.014 -1000
Class I PI3K signaling events 0.0260 4 343 73 -0.027 0.056 1000 -1000 -0.029 -1000
Insulin Pathway 0.0260 4 298 74 -0.048 0.084 1000 -1000 -0.031 -1000
S1P3 pathway 0.0260 4 185 42 -0.043 0.043 1000 -1000 -0.046 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0260 4 362 88 -0.048 0.038 1000 -1000 -0.059 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0260 4 138 33 -0.066 0.073 1000 -1000 -0.037 -1000
a4b1 and a4b7 Integrin signaling 0.0195 3 18 5 0.012 0.032 1000 -1000 0.012 -1000
EPO signaling pathway 0.0195 3 189 55 -0.008 0.065 1000 -1000 -0.032 -1000
PLK1 signaling events 0.0195 3 305 85 -0.016 0.089 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0195 3 123 37 -0.033 0.059 1000 -1000 -0.032 -1000
S1P5 pathway 0.0195 3 66 17 -0.007 0.032 1000 -1000 -0.01 -1000
ceramide signaling pathway 0.0195 3 169 49 -0.028 0.042 1000 -1000 -0.03 -1000
Paxillin-dependent events mediated by a4b1 0.0195 3 126 36 -0.043 0.059 1000 -1000 -0.04 -1000
Atypical NF-kappaB pathway 0.0195 3 110 31 -0.006 0.033 1000 -1000 -0.014 -1000
Regulation of Telomerase 0.0195 3 366 102 -0.095 0.078 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0195 3 365 97 -0.045 0.08 1000 -1000 -0.039 -1000
S1P4 pathway 0.0195 3 93 25 -0.012 0.043 1000 -1000 -0.02 -1000
Aurora B signaling 0.0195 3 265 67 -0.1 0.052 1000 -1000 -0.043 -1000
LPA4-mediated signaling events 0.0130 2 30 12 -0.012 0.046 1000 -1000 -0.021 -1000
Aurora A signaling 0.0130 2 145 60 -0.004 0.061 1000 -1000 -0.012 -1000
Insulin-mediated glucose transport 0.0130 2 76 32 -0.028 0.058 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 0.0130 2 195 68 -0.041 0.056 1000 -1000 -0.031 -1000
Signaling events regulated by Ret tyrosine kinase 0.0130 2 188 82 -0.031 0.056 1000 -1000 -0.05 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0130 2 179 83 -0.028 0.059 1000 -1000 -0.022 -1000
Regulation of p38-alpha and p38-beta 0.0130 2 147 54 -0.035 0.074 1000 -1000 -0.043 -1000
Arf6 trafficking events 0.0130 2 195 71 -0.034 0.053 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 0.0130 2 100 44 -0.016 0.059 1000 -1000 -0.02 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0065 1 36 23 0.008 0.058 1000 -1000 -0.024 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0065 1 42 34 -0.04 0.063 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0065 1 73 39 -0.019 0.068 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0065 1 75 75 -0.039 0.06 1000 -1000 -0.017 -1000
BARD1 signaling events 0.0065 1 68 57 -0.047 0.073 1000 -1000 -0.043 -1000
Circadian rhythm pathway 0.0065 1 36 22 -0.01 0.047 1000 -1000 -0.03 -1000
Ephrin A reverse signaling 0.0065 1 11 7 0 0.031 1000 -1000 -0.007 -1000
Signaling events mediated by HDAC Class I 0.0065 1 177 104 -0.06 0.075 1000 -1000 -0.028 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0065 1 27 27 0 0.063 1000 -1000 -0.029 -1000
Rapid glucocorticoid signaling 0.0065 1 20 20 0 0.042 1000 -1000 -0.001 -1000
Signaling events mediated by PRL 0.0065 1 62 34 -0.032 0.046 1000 -1000 -0.038 -1000
Class IB PI3K non-lipid kinase events 0.0065 1 3 3 -0.027 0.027 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0065 1 21 13 0 0.074 1000 -1000 0 -1000
Aurora C signaling 0.0000 0 4 7 0 0.053 1000 -1000 -0.014 -1000
Effects of Botulinum toxin 0.0000 0 20 26 -0.008 0.054 1000 -1000 -0.003 -1000
Arf1 pathway 0.0000 0 26 54 -0.002 0.043 1000 -1000 -0.019 -1000
Total NA 944 59113 7203 -12 7.7 131000 -131000 -4 -131000
HIF-1-alpha transcription factor 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
PKM2 -0.24 0.5 -9999 0 -0.93 41 41
HDAC7 -0.001 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.17 0.46 -9999 0 -0.9 30 30
SMAD4 0.021 0.075 -9999 0 -0.51 3 3
ID2 -0.24 0.52 -9999 0 -1 35 35
AP1 -0.034 0.16 -9999 0 -0.43 18 18
ABCG2 -0.24 0.5 -9999 0 -0.98 37 37
HIF1A -0.029 0.12 -9999 0 -0.38 7 7
TFF3 -0.27 0.53 -9999 0 -0.98 43 43
GATA2 0.016 0.05 -9999 0 -0.51 1 1
AKT1 -0.029 0.12 -9999 0 -0.66 2 2
response to hypoxia -0.037 0.085 -9999 0 -0.18 19 19
MCL1 -0.23 0.5 -9999 0 -0.98 36 36
NDRG1 -0.26 0.53 -9999 0 -0.98 42 42
SERPINE1 -0.25 0.53 -9999 0 -0.99 40 40
FECH -0.24 0.51 -9999 0 -1 37 37
FURIN -0.23 0.51 -9999 0 -0.94 41 41
NCOA2 0.025 0.062 -9999 0 -0.51 2 2
EP300 -0.039 0.16 -9999 0 -0.44 12 12
HMOX1 -0.24 0.51 -9999 0 -1 36 36
BHLHE40 -0.24 0.5 -9999 0 -0.93 41 41
BHLHE41 -0.24 0.5 -9999 0 -0.93 41 41
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.004 0.18 -9999 0 -0.42 13 13
ENG -0.02 0.15 -9999 0 -0.4 12 12
JUN -0.005 0.12 -9999 0 -0.51 7 7
RORA -0.27 0.53 -9999 0 -0.95 46 46
ABCB1 -0.047 0.16 -9999 0 -1.1 2 2
TFRC -0.27 0.48 -9999 0 -1 35 35
CXCR4 -0.26 0.54 -9999 0 -1 42 42
TF -0.24 0.49 -9999 0 -0.95 38 38
CITED2 -0.23 0.51 -9999 0 -0.99 36 36
HIF1A/ARNT -0.26 0.67 -9999 0 -1.2 35 35
LDHA -0.071 0.3 -9999 0 -1.1 10 10
ETS1 -0.23 0.51 -9999 0 -0.98 38 38
PGK1 -0.23 0.51 -9999 0 -0.99 37 37
NOS2 -0.24 0.5 -9999 0 -0.93 41 41
ITGB2 -0.24 0.53 -9999 0 -0.98 41 41
ALDOA -0.23 0.51 -9999 0 -1 35 35
Cbp/p300/CITED2 -0.24 0.53 -9999 0 -1.1 33 33
FOS -0.037 0.16 -9999 0 -0.51 14 14
HK2 -0.23 0.52 -9999 0 -1 35 35
SP1 0.031 0.063 -9999 0 -0.51 2 2
GCK -0.041 0.21 -9999 0 -0.94 3 3
HK1 -0.23 0.51 -9999 0 -1 35 35
NPM1 -0.23 0.51 -9999 0 -0.98 37 37
EGLN1 -0.23 0.51 -9999 0 -0.99 36 36
CREB1 0.027 0.066 -9999 0 -0.51 2 2
PGM1 -0.23 0.5 -9999 0 -0.99 36 36
SMAD3 0.008 0.11 -9999 0 -0.51 7 7
EDN1 -0.18 0.46 -9999 0 -1.2 23 23
IGFBP1 -0.23 0.51 -9999 0 -0.99 36 36
VEGFA -0.16 0.39 -9999 0 -0.78 29 29
HIF1A/JAB1 -0.003 0.1 -9999 0 -0.46 3 3
CP -0.28 0.5 -9999 0 -0.98 40 40
CXCL12 -0.25 0.54 -9999 0 -1 39 39
COPS5 0.032 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0.02 0.1 -9999 0 -0.37 10 10
BNIP3 -0.25 0.52 -9999 0 -0.98 39 39
EGLN3 -0.27 0.54 -9999 0 -1 41 41
CA9 -0.27 0.53 -9999 0 -1 40 40
TERT -0.22 0.5 -9999 0 -0.94 38 38
ENO1 -0.23 0.51 -9999 0 -1 36 36
PFKL -0.23 0.51 -9999 0 -1 36 36
NCOA1 0.032 0.005 -9999 0 -10000 0 0
ADM -0.27 0.53 -9999 0 -1 40 40
ARNT -0.016 0.092 -9999 0 -0.37 1 1
HNF4A 0.033 0.017 -9999 0 -10000 0 0
ADFP -0.24 0.5 -9999 0 -0.93 41 41
SLC2A1 -0.19 0.41 -9999 0 -0.79 35 35
LEP -0.24 0.5 -9999 0 -1 36 36
HIF1A/ARNT/Cbp/p300 -0.18 0.48 -9999 0 -0.91 32 32
EPO -0.087 0.31 -9999 0 -0.74 12 12
CREBBP -0.02 0.12 -9999 0 -0.37 5 5
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.48 -9999 0 -0.93 31 31
PFKFB3 -0.23 0.51 -9999 0 -1 36 36
NT5E -0.24 0.51 -9999 0 -1 37 37
TCGA08_retinoblastoma

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
CDKN2B 0.007 0.05 -10000 0 -0.47 1 1
CDKN2C 0.025 0.028 -10000 0 -10000 0 0
CDKN2A -0.042 0.16 -10000 0 -0.49 16 16
CCND2 0.041 0.099 0.23 30 -10000 0 30
RB1 -0.061 0.12 0.36 2 -0.25 39 41
CDK4 0.06 0.12 0.26 35 -10000 0 35
CDK6 0.049 0.13 0.26 32 -0.4 2 34
G1/S progression 0.082 0.14 0.25 51 -0.32 3 54
IL23-mediated signaling events

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
CCL2 -0.38 0.51 -10000 0 -1.2 32 32
IL23A -0.47 0.57 -10000 0 -1.2 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.36 0.5 -10000 0 -1.1 36 36
positive regulation of T cell mediated cytotoxicity -0.41 0.57 -10000 0 -1.3 36 36
ITGA3 -0.41 0.52 -10000 0 -1.2 37 37
IL17F -0.2 0.32 -10000 0 -0.71 30 30
IL12B -0.016 0.088 -10000 0 -0.54 3 3
STAT1 (dimer) -0.4 0.54 -10000 0 -1.2 35 35
CD4 -0.34 0.47 -10000 0 -1.1 30 30
IL23 -0.45 0.55 -10000 0 -1.2 48 48
IL23R -0.049 0.18 -10000 0 -1 4 4
IL1B -0.48 0.6 -10000 0 -1.4 40 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.36 0.46 -10000 0 -1.1 31 31
TYK2 -0.007 0.04 -10000 0 -10000 0 0
STAT4 0.012 0.097 -10000 0 -0.51 5 5
STAT3 0.032 0.005 -10000 0 -10000 0 0
IL18RAP -0.053 0.18 -10000 0 -0.52 20 20
IL12RB1 -0.005 0.039 -10000 0 -10000 0 0
PIK3CA 0.01 0.062 -10000 0 -0.51 2 2
IL12Rbeta1/TYK2 -0.003 0.051 -10000 0 -10000 0 0
IL23R/JAK2 -0.049 0.18 -10000 0 -0.94 4 4
positive regulation of chronic inflammatory response -0.41 0.57 -10000 0 -1.3 36 36
natural killer cell activation 0.005 0.009 0.083 1 -10000 0 1
JAK2 -0.007 0.064 -10000 0 -0.55 1 1
PIK3R1 0.005 0.098 -10000 0 -0.51 5 5
NFKB1 0.029 0.007 -10000 0 -10000 0 0
RELA 0.031 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.42 0.51 -10000 0 -1.1 48 48
ALOX12B -0.36 0.47 -10000 0 -1.1 33 33
CXCL1 -0.51 0.6 -10000 0 -1.3 50 50
T cell proliferation -0.41 0.57 -10000 0 -1.3 36 36
NFKBIA 0.024 0.045 -10000 0 -0.52 1 1
IL17A -0.16 0.26 -10000 0 -0.56 22 22
PI3K -0.34 0.49 -10000 0 -1.2 32 32
IFNG -0.041 0.06 0.15 1 -0.13 38 39
STAT3 (dimer) -0.32 0.47 -10000 0 -1.1 31 31
IL18R1 -0.004 0.12 -10000 0 -0.51 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.21 0.3 -10000 0 -0.7 24 24
IL18/IL18R -0.065 0.2 -10000 0 -0.4 33 33
macrophage activation -0.021 0.022 -10000 0 -0.048 41 41
TNF -0.41 0.51 -10000 0 -1.2 34 34
STAT3/STAT4 -0.37 0.52 -10000 0 -1.2 34 34
STAT4 (dimer) -0.4 0.55 -10000 0 -1.2 35 35
IL18 -0.024 0.15 -10000 0 -0.51 13 13
IL19 -0.37 0.47 -10000 0 -1.1 33 33
STAT5A (dimer) -0.39 0.54 -10000 0 -1.2 36 36
STAT1 0.009 0.1 -10000 0 -0.51 6 6
SOCS3 0.019 0.077 -10000 0 -0.51 3 3
CXCL9 -0.48 0.6 -10000 0 -1.3 52 52
MPO -0.36 0.47 -10000 0 -1.2 27 27
positive regulation of humoral immune response -0.41 0.57 -10000 0 -1.3 36 36
IL23/IL23R/JAK2/TYK2 -0.44 0.64 -10000 0 -1.4 36 36
IL6 -0.42 0.54 -10000 0 -1.2 37 37
STAT5A 0.031 0.01 -10000 0 -10000 0 0
IL2 0.019 0.027 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.009 0.083 1 -10000 0 1
CD3E -0.36 0.47 -10000 0 -1.1 31 31
keratinocyte proliferation -0.41 0.57 -10000 0 -1.3 36 36
NOS2 -0.36 0.47 -10000 0 -1 37 37
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.43 0.61 -10000 0 -1.3 40 40
STAT6 (cleaved dimer) -0.46 0.62 -10000 0 -1.3 46 46
IGHG1 -0.13 0.22 -10000 0 -0.66 5 5
IGHG3 -0.43 0.58 -10000 0 -1.2 45 45
AKT1 -0.2 0.31 -10000 0 -0.85 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.27 -10000 0 -0.84 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.35 -10000 0 -0.95 15 15
THY1 -0.45 0.62 -10000 0 -1.3 41 41
MYB -0.027 0.15 -10000 0 -0.51 12 12
HMGA1 0.029 0.044 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.23 0.36 -10000 0 -0.74 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.34 -10000 0 -0.98 12 12
SP1 0.014 0.073 -10000 0 -0.51 2 2
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.029 0.032 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.62 -10000 0 -1.3 44 44
SOCS1 -0.27 0.37 -10000 0 -0.77 42 42
SOCS3 -0.2 0.32 -10000 0 -0.98 9 9
FCER2 -0.38 0.5 -10000 0 -1.1 42 42
PARP14 0.025 0.021 -10000 0 -10000 0 0
CCL17 -0.5 0.66 -10000 0 -1.4 44 44
GRB2 0.032 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.26 -10000 0 -0.75 10 10
T cell proliferation -0.46 0.63 -10000 0 -1.4 43 43
IL4R/JAK1 -0.46 0.62 -10000 0 -1.3 44 44
EGR2 -0.52 0.67 -10000 0 -1.4 49 49
JAK2 -0.018 0.068 -10000 0 -0.55 1 1
JAK3 0.036 0.013 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
JAK1 0.012 0.05 -10000 0 -0.5 1 1
COL1A2 -0.22 0.48 -10000 0 -1.6 15 15
CCL26 -0.54 0.67 -10000 0 -1.4 54 54
IL4R -0.48 0.67 -10000 0 -1.4 43 43
PTPN6 0.031 0.049 -10000 0 -0.5 1 1
IL13RA2 -0.56 0.72 -10000 0 -1.5 49 49
IL13RA1 -0.019 0.082 -10000 0 -0.55 2 2
IRF4 -0.058 0.21 -10000 0 -1.1 4 4
ARG1 -0.15 0.32 -10000 0 -1.2 10 10
CBL -0.22 0.33 -10000 0 -0.7 30 30
GTF3A 0.012 0.051 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
IL13RA1/JAK2 -0.02 0.095 -10000 0 -0.42 3 3
IRF4/BCL6 -0.051 0.18 -10000 0 -1.1 3 3
CD40LG 0.031 0.049 -10000 0 -0.51 1 1
MAPK14 -0.22 0.35 -10000 0 -0.79 22 22
mitosis -0.19 0.29 -10000 0 -0.78 16 16
STAT6 -0.56 0.84 -10000 0 -1.6 45 45
SPI1 0.004 0.095 -10000 0 -0.45 5 5
RPS6KB1 -0.18 0.28 -10000 0 -0.75 16 16
STAT6 (dimer) -0.56 0.84 -10000 0 -1.7 45 45
STAT6 (dimer)/PARP14 -0.48 0.68 -10000 0 -1.4 43 43
mast cell activation 0.008 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.35 -10000 0 -0.85 21 21
FRAP1 -0.2 0.31 -10000 0 -0.84 16 16
LTA -0.44 0.61 -10000 0 -1.3 41 41
FES 0.019 0.076 -10000 0 -0.51 3 3
T-helper 1 cell differentiation 0.52 0.73 1.5 45 -10000 0 45
CCL11 -0.56 0.7 -10000 0 -1.4 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.18 0.32 -10000 0 -0.96 11 11
IL2RG 0.024 0.066 -10000 0 -0.5 2 2
IL10 -0.44 0.61 -10000 0 -1.3 41 41
IRS1 0.004 0.11 -10000 0 -0.51 7 7
IRS2 -0.005 0.13 -10000 0 -0.51 10 10
IL4 -0.098 0.24 -10000 0 -1.1 6 6
IL5 -0.44 0.61 -10000 0 -1.3 41 41
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.52 -10000 0 -1 43 43
COL1A1 -0.33 0.61 -10000 0 -1.6 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.65 -10000 0 -1.4 42 42
IL2R gamma/JAK3 0.04 0.054 -10000 0 -0.37 2 2
TFF3 -0.53 0.67 -10000 0 -1.4 52 52
ALOX15 -0.46 0.61 -10000 0 -1.3 45 45
MYBL1 0.03 0.011 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.48 0.55 -10000 0 -1.2 50 50
SHC1 0.031 0.007 -10000 0 -10000 0 0
CEBPB 0.017 0.059 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.34 -10000 0 -0.94 15 15
mol:PI-3-4-5-P3 -0.2 0.31 -10000 0 -0.84 16 16
PI3K -0.22 0.34 -10000 0 -0.93 16 16
DOK2 -0.029 0.16 -10000 0 -0.51 16 16
ETS1 0.025 0.066 -10000 0 -0.48 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.68 9 9
ITGB3 -0.45 0.61 -10000 0 -1.3 41 41
PIGR -0.54 0.7 -10000 0 -1.4 51 51
IGHE 0.03 0.067 0.21 3 -0.26 1 4
MAPKKK cascade -0.12 0.23 -10000 0 -0.67 9 9
BCL6 -0.003 0.1 -10000 0 -0.51 6 6
OPRM1 -0.45 0.61 -10000 0 -1.3 41 41
RETNLB -0.42 0.62 -10000 0 -1.4 37 37
SELP -0.52 0.71 -10000 0 -1.5 47 47
AICDA -0.44 0.6 -10000 0 -1.3 42 42
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.17 0.4 -9999 0 -1.1 24 24
MKNK1 0.032 0.005 -9999 0 -10000 0 0
MAPK14 -0.041 0.14 -9999 0 -0.34 24 24
ATF2/c-Jun -0.057 0.19 -9999 0 -0.63 11 11
MAPK11 -0.04 0.13 -9999 0 -0.34 23 23
MITF -0.056 0.17 -9999 0 -0.44 23 23
MAPKAPK5 -0.049 0.15 -9999 0 -0.38 24 24
KRT8 -0.058 0.16 -9999 0 -0.39 27 27
MAPKAPK3 0.029 0.013 -9999 0 -10000 0 0
MAPKAPK2 0.032 0.004 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.064 0.2 -9999 0 -0.5 24 24
CEBPB -0.049 0.16 -9999 0 -0.41 23 23
SLC9A1 -0.05 0.15 -9999 0 -0.39 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.051 0.16 -9999 0 -0.39 25 25
p38alpha-beta/MNK1 -0.037 0.18 -9999 0 -0.41 24 24
JUN -0.055 0.19 -9999 0 -0.62 11 11
PPARGC1A -0.069 0.18 -9999 0 -0.41 29 29
USF1 -0.061 0.18 -9999 0 -0.43 25 25
RAB5/GDP/GDI1 -0.034 0.13 -9999 0 -0.31 23 23
NOS2 -0.055 0.15 -9999 0 -0.39 24 24
DDIT3 -0.057 0.16 -9999 0 -0.38 28 28
RAB5A 0.027 0.044 -9999 0 -0.51 1 1
HSPB1 -0.056 0.14 -9999 0 -0.34 27 27
p38alpha-beta/HBP1 -0.041 0.18 -9999 0 -0.4 25 25
CREB1 -0.062 0.18 -9999 0 -0.43 26 26
RAB5/GDP 0.019 0.034 -9999 0 -0.37 1 1
EIF4E -0.051 0.14 -9999 0 -0.38 23 23
RPS6KA4 -0.052 0.16 -9999 0 -0.39 25 25
PLA2G4A -0.097 0.2 -9999 0 -0.43 34 34
GDI1 -0.051 0.16 -9999 0 -0.4 24 24
TP53 -0.082 0.19 -9999 0 -0.51 24 24
RPS6KA5 -0.061 0.18 -9999 0 -0.42 26 26
ESR1 -0.068 0.17 -9999 0 -0.41 28 28
HBP1 0.021 0.075 -9999 0 -0.51 3 3
MEF2C -0.069 0.19 -9999 0 -0.44 27 27
MEF2A -0.049 0.15 -9999 0 -0.38 24 24
EIF4EBP1 -0.061 0.17 -9999 0 -0.43 25 25
KRT19 -0.1 0.21 -9999 0 -0.41 43 43
ELK4 -0.06 0.18 -9999 0 -0.41 27 27
ATF6 -0.046 0.15 -9999 0 -0.38 23 23
ATF1 -0.057 0.17 -9999 0 -0.42 25 25
p38alpha-beta/MAPKAPK2 -0.034 0.17 -9999 0 -0.4 24 24
p38alpha-beta/MAPKAPK3 -0.038 0.17 -9999 0 -0.42 23 23
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.087 -10000 0 -0.51 4 4
LAT2 -0.075 0.18 -10000 0 -0.41 28 28
AP1 -0.076 0.26 -10000 0 -0.57 25 25
mol:PIP3 -0.092 0.24 0.26 5 -0.47 34 39
IKBKB -0.031 0.14 0.19 14 -0.26 28 42
AKT1 -0.015 0.21 0.46 7 -0.46 12 19
IKBKG -0.041 0.13 0.2 6 -0.27 26 32
MS4A2 -0.057 0.19 -10000 0 -0.51 23 23
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
MAP3K1 0.003 0.22 0.25 35 -0.44 20 55
mol:Ca2+ -0.063 0.18 0.23 6 -0.35 33 39
LYN 0.024 0.047 -10000 0 -0.52 1 1
CBLB -0.068 0.17 -10000 0 -0.4 26 26
SHC1 0.031 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.042 0.055 -10000 0 -0.29 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.085 0.18 0.34 4 -0.34 41 45
PTPN13 -0.077 0.22 -10000 0 -0.54 21 21
PTPN11 0.018 0.052 -10000 0 -0.52 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.001 0.18 0.32 10 -0.34 16 26
SYK 0.008 0.11 -10000 0 -0.53 6 6
GRB2 0.032 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.23 -10000 0 -0.48 35 35
LAT -0.073 0.18 -10000 0 -0.41 27 27
PAK2 0.004 0.24 0.26 39 -0.48 21 60
NFATC2 -0.022 0.057 -10000 0 -10000 0 0
HRAS -0.074 0.23 0.24 4 -0.52 26 30
GAB2 0.03 0.014 -10000 0 -10000 0 0
PLA2G1B -0.027 0.23 -10000 0 -0.88 10 10
Fc epsilon R1 -0.083 0.21 -10000 0 -0.41 42 42
Antigen/IgE/Fc epsilon R1 -0.073 0.2 -10000 0 -0.37 42 42
mol:GDP -0.082 0.25 0.28 1 -0.56 26 27
JUN 0.002 0.11 -10000 0 -0.51 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.004 0.099 -10000 0 -0.51 5 5
FOS -0.03 0.16 -10000 0 -0.51 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.07 0.19 -10000 0 -0.4 30 30
CHUK -0.046 0.13 0.2 6 -0.28 26 32
KLRG1 -0.073 0.17 -10000 0 -0.36 32 32
VAV1 -0.079 0.19 -10000 0 -0.42 29 29
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.072 0.18 -10000 0 -0.41 27 27
negative regulation of mast cell degranulation -0.069 0.16 -10000 0 -0.34 31 31
BTK -0.098 0.28 -10000 0 -0.63 26 26
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.24 -10000 0 -0.41 48 48
GAB2/PI3K/SHP2 -0.079 0.14 -10000 0 -0.38 23 23
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.093 0.21 -10000 0 -0.38 42 42
RAF1 -0.024 0.25 -10000 0 -0.95 10 10
Fc epsilon R1/FcgammaRIIB/SHIP -0.089 0.23 -10000 0 -0.39 48 48
FCER1G 0.023 0.064 -10000 0 -0.51 2 2
FCER1A -0.099 0.22 -10000 0 -0.52 32 32
Antigen/IgE/Fc epsilon R1/Fyn -0.062 0.2 -10000 0 -0.35 43 43
MAPK3 -0.021 0.23 -10000 0 -0.87 10 10
MAPK1 -0.026 0.24 -10000 0 -0.91 10 10
NFKB1 0.031 0.007 -10000 0 -10000 0 0
MAPK8 -0.019 0.22 -10000 0 -0.77 8 8
DUSP1 0.017 0.066 -10000 0 -0.51 2 2
NF-kappa-B/RelA -0.013 0.088 0.17 1 -0.18 20 21
actin cytoskeleton reorganization -0.056 0.21 -10000 0 -0.55 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.077 0.19 -10000 0 -0.48 23 23
FER -0.076 0.18 -10000 0 -0.4 28 28
RELA 0.033 0 -10000 0 -10000 0 0
ITK -0.027 0.095 -10000 0 -0.34 9 9
SOS1 0.032 0.005 -10000 0 -10000 0 0
PLCG1 -0.081 0.25 0.29 1 -0.54 28 29
cytokine secretion -0.018 0.057 -10000 0 -10000 0 0
SPHK1 -0.089 0.2 -10000 0 -0.42 33 33
PTK2 -0.06 0.22 -10000 0 -0.58 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.24 -10000 0 -0.48 38 38
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.094 0.24 0.26 6 -0.48 34 40
MAP2K2 -0.026 0.23 -10000 0 -0.89 10 10
MAP2K1 -0.027 0.23 -10000 0 -0.89 10 10
MAP2K7 0.029 0.018 -10000 0 -10000 0 0
KLRG1/SHP2 -0.055 0.17 0.2 2 -0.41 21 23
MAP2K4 -0.029 0.25 -10000 0 -0.85 13 13
Fc epsilon R1/FcgammaRIIB -0.094 0.24 -10000 0 -0.42 48 48
mol:Choline -0.084 0.18 0.34 4 -0.34 41 45
SHC/Grb2/SOS1 -0.033 0.19 -10000 0 -0.4 23 23
FYN 0.024 0.062 -10000 0 -0.51 2 2
DOK1 0.032 0.006 -10000 0 -10000 0 0
PXN -0.055 0.2 -10000 0 -0.55 15 15
HCLS1 -0.084 0.2 -10000 0 -0.42 31 31
PRKCB -0.065 0.17 0.23 6 -0.35 33 39
FCGR2B -0.025 0.16 -10000 0 -0.51 16 16
IGHE -0.002 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.071 0.16 -10000 0 -0.35 31 31
LCP2 -0.016 0.15 -10000 0 -0.51 13 13
PLA2G4A -0.11 0.2 -10000 0 -0.38 41 41
RASA1 0.026 0.044 -10000 0 -0.51 1 1
mol:Phosphatidic acid -0.084 0.18 0.34 4 -0.34 41 45
IKK complex -0.018 0.11 0.18 9 -0.22 20 29
WIPF1 0.009 0.1 -10000 0 -0.51 6 6
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.1 0.11 0.37 10 -10000 0 10
SMARCC2 0.032 0.003 -10000 0 -10000 0 0
SMARCC1 0.023 0.062 -10000 0 -0.51 2 2
TBX21 -0.19 0.31 0.38 1 -0.68 36 37
SUMO2 0.031 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.002 0.13 -10000 0 -0.47 10 10
FKBP4 0.027 0.044 -10000 0 -0.51 1 1
FKBP5 0.022 0.064 -10000 0 -0.51 2 2
GR alpha/HSP90/FKBP51/HSP90 0.14 0.12 0.31 34 -10000 0 34
PRL -0.079 0.14 -10000 0 -0.51 1 1
cortisol/GR alpha (dimer)/TIF2 0.23 0.26 0.58 44 -10000 0 44
RELA -0.069 0.1 -10000 0 -0.25 15 15
FGG 0.18 0.24 0.51 36 -0.56 3 39
GR beta/TIF2 0.13 0.14 0.34 32 -10000 0 32
IFNG -0.46 0.52 -10000 0 -1.1 58 58
apoptosis 0.047 0.21 0.5 12 -0.52 5 17
CREB1 0.032 0.063 -10000 0 -0.5 2 2
histone acetylation -0.062 0.17 0.3 3 -0.4 20 23
BGLAP -0.11 0.16 -10000 0 -0.54 8 8
GR/PKAc 0.15 0.11 0.34 24 -10000 0 24
NF kappa B1 p50/RelA -0.13 0.18 -10000 0 -0.36 44 44
SMARCD1 0.032 0.003 -10000 0 -10000 0 0
MDM2 0.11 0.11 0.24 49 -10000 0 49
GATA3 0.036 0.029 -10000 0 -10000 0 0
AKT1 0.018 0.062 -10000 0 -0.52 2 2
CSF2 -0.18 0.38 -10000 0 -1.3 13 13
GSK3B 0.027 0.02 -10000 0 -10000 0 0
NR1I3 0.064 0.21 0.55 8 -0.72 2 10
CSN2 0.17 0.18 0.4 43 -10000 0 43
BRG1/BAF155/BAF170/BAF60A 0.067 0.057 -10000 0 -0.29 3 3
NFATC1 0.011 0.12 -10000 0 -0.5 8 8
POU2F1 0.035 0.015 -10000 0 -10000 0 0
CDKN1A -0.027 0.21 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.011 -10000 0 -10000 0 0
SFN -0.028 0.17 -10000 0 -0.51 17 17
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.14 0.32 20 -0.32 3 23
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.002 0.3 0.49 10 -0.8 15 25
JUN -0.19 0.25 0.37 1 -0.5 48 49
IL4 -0.13 0.21 -10000 0 -0.64 16 16
CDK5R1 0.031 0.017 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.23 0.22 12 -0.48 36 48
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.14 0.11 0.32 23 -10000 0 23
cortisol/GR alpha (monomer) 0.29 0.33 0.68 53 -10000 0 53
NCOA2 0.024 0.062 -10000 0 -0.51 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.095 0.17 -10000 0 -0.49 18 18
AP-1/NFAT1-c-4 -0.33 0.39 -10000 0 -0.76 56 56
AFP -0.15 0.22 -10000 0 -0.88 4 4
SUV420H1 0.032 0.005 -10000 0 -10000 0 0
IRF1 0.12 0.23 0.44 23 -0.85 4 27
TP53 0.019 0.12 -10000 0 -0.5 7 7
PPP5C 0.028 0.044 -10000 0 -0.51 1 1
KRT17 -0.44 0.56 -10000 0 -1.3 41 41
KRT14 -0.38 0.55 -10000 0 -1.3 36 36
TBP 0.039 0.012 -10000 0 -10000 0 0
CREBBP 0.096 0.11 0.3 32 -10000 0 32
HDAC1 0.027 0.011 -10000 0 -10000 0 0
HDAC2 0.04 0.026 -10000 0 -10000 0 0
AP-1 -0.34 0.39 -10000 0 -0.77 56 56
MAPK14 0.032 0.015 -10000 0 -10000 0 0
MAPK10 0 0.091 -10000 0 -0.5 4 4
MAPK11 0.03 0.019 -10000 0 -10000 0 0
KRT5 -0.42 0.55 -10000 0 -1.1 51 51
interleukin-1 receptor activity 0.008 0.025 -10000 0 -10000 0 0
NCOA1 0.034 0.008 -10000 0 -10000 0 0
STAT1 0.002 0.13 -10000 0 -0.47 10 10
CGA -0.11 0.17 -10000 0 -0.56 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.14 0.23 0.48 36 -10000 0 36
MAPK3 0.031 0.018 -10000 0 -10000 0 0
MAPK1 0.027 0.046 -10000 0 -0.51 1 1
ICAM1 -0.26 0.36 -10000 0 -0.81 32 32
NFKB1 -0.068 0.1 -10000 0 -0.26 12 12
MAPK8 -0.15 0.22 0.43 1 -0.43 45 46
MAPK9 0.031 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.045 0.21 0.51 12 -0.54 5 17
BAX -0.007 0.09 -10000 0 -10000 0 0
POMC -0.25 0.48 -10000 0 -1.5 17 17
EP300 0.066 0.15 0.29 25 -0.45 7 32
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.58 43 -10000 0 43
proteasomal ubiquitin-dependent protein catabolic process 0.072 0.1 0.25 28 -10000 0 28
SGK1 0.1 0.15 0.35 31 -0.28 3 34
IL13 -0.22 0.27 -10000 0 -0.73 22 22
IL6 -0.3 0.41 -10000 0 -0.92 36 36
PRKACG 0.032 0.006 -10000 0 -10000 0 0
IL5 -0.19 0.23 -10000 0 -0.68 15 15
IL2 -0.29 0.36 -10000 0 -0.77 42 42
CDK5 0.033 0.007 -10000 0 -10000 0 0
PRKACB 0.027 0.045 -10000 0 -0.51 1 1
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
IL8 -0.42 0.5 -10000 0 -1 54 54
CDK5R1/CDK5 0.047 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.062 0.16 -10000 0 -0.39 12 12
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.25 0.56 48 -10000 0 48
SMARCA4 0.028 0.045 -10000 0 -0.51 1 1
chromatin remodeling 0.16 0.17 0.36 47 -10000 0 47
NF kappa B1 p50/RelA/Cbp -0.046 0.2 0.37 5 -0.41 17 22
JUN (dimer) -0.19 0.25 0.37 1 -0.5 48 49
YWHAH 0.024 0.062 -10000 0 -0.51 2 2
VIPR1 -0.12 0.2 -10000 0 -0.58 17 17
NR3C1 0.19 0.22 0.46 48 -10000 0 48
NR4A1 -0.01 0.14 -10000 0 -0.43 14 14
TIF2/SUV420H1 0.041 0.038 -10000 0 -0.37 1 1
MAPKKK cascade 0.047 0.21 0.5 12 -0.52 5 17
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.58 50 -10000 0 50
PBX1 0.013 0.11 -10000 0 -0.5 6 6
POU1F1 0.033 0.017 -10000 0 -10000 0 0
SELE -0.39 0.48 -10000 0 -1.1 45 45
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.17 0.36 47 -10000 0 47
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.25 0.56 48 -10000 0 48
mol:cortisol 0.17 0.21 0.4 56 -10000 0 56
MMP1 -0.38 0.56 -10000 0 -1.3 39 39
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.028 0.052 -10000 0 -0.37 2 2
NFATC2 -0.099 0.27 -10000 0 -0.67 20 20
NFATC3 -0.037 0.1 -10000 0 -0.28 9 9
CD40LG -0.33 0.42 -10000 0 -0.91 44 44
ITCH -0.025 0.1 -10000 0 -10000 0 0
CBLB -0.019 0.095 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.41 -10000 0 -1 25 25
JUNB 0.009 0.098 -10000 0 -0.51 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.13 -10000 0 -0.28 30 30
T cell anergy -0.063 0.17 -10000 0 -0.39 27 27
TLE4 -0.084 0.24 -10000 0 -0.64 17 17
Jun/NFAT1-c-4/p21SNFT -0.26 0.44 -10000 0 -0.99 34 34
AP-1/NFAT1-c-4 -0.38 0.56 -10000 0 -1.1 43 43
IKZF1 -0.083 0.24 -10000 0 -0.71 15 15
T-helper 2 cell differentiation -0.098 0.24 -10000 0 -0.71 14 14
AP-1/NFAT1 -0.12 0.23 -10000 0 -0.54 27 27
CALM1 -0.009 0.083 -10000 0 -10000 0 0
EGR2 -0.27 0.55 -10000 0 -1.4 25 25
EGR3 -0.23 0.46 -10000 0 -1.1 24 24
NFAT1/FOXP3 -0.056 0.22 -10000 0 -0.52 19 19
EGR1 -0.022 0.15 -10000 0 -0.51 13 13
JUN -0.023 0.12 -10000 0 -0.53 7 7
EGR4 0.001 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.071 -10000 0 -0.16 32 32
GBP3 -0.14 0.32 -10000 0 -0.75 30 30
FOSL1 0.026 0.027 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.22 0.45 -10000 0 -0.99 33 33
DGKA -0.098 0.27 -10000 0 -0.64 23 23
CREM 0.031 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.25 0.45 -10000 0 -1 33 33
CTLA4 -0.064 0.19 -10000 0 -0.62 11 11
NFAT1-c-4 (dimer)/EGR1 -0.24 0.46 -10000 0 -1 32 32
NFAT1-c-4 (dimer)/EGR4 -0.22 0.44 -10000 0 -0.98 32 32
FOS -0.055 0.16 -10000 0 -0.52 14 14
IFNG -0.38 0.6 -10000 0 -1.3 40 40
T cell activation -0.15 0.26 -10000 0 -0.76 13 13
MAF -0.029 0.16 -10000 0 -0.51 16 16
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.19 0.38 0.9 25 -10000 0 25
TNF -0.22 0.39 -10000 0 -0.9 32 32
FASLG -0.37 0.65 -10000 0 -1.4 39 39
TBX21 -0.078 0.2 -10000 0 -0.43 31 31
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.002 0.11 -10000 0 -0.52 6 6
PTPN1 -0.066 0.2 -10000 0 -0.62 11 11
NFAT1-c-4/ICER1 -0.22 0.44 -10000 0 -0.98 32 32
GATA3 0.028 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.37 0.57 -10000 0 -1.3 40 40
IL2RA -0.23 0.4 -10000 0 -0.97 27 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.061 0.2 -10000 0 -0.62 11 11
E2F1 0.036 0.01 -10000 0 -10000 0 0
PPARG -0.026 0.16 -10000 0 -0.51 15 15
SLC3A2 -0.075 0.22 -10000 0 -0.57 16 16
IRF4 0.022 0.064 -10000 0 -0.51 2 2
PTGS2 -0.37 0.44 -10000 0 -0.94 48 48
CSF2 -0.35 0.44 -10000 0 -0.95 44 44
JunB/Fra1/NFAT1-c-4 -0.21 0.44 -10000 0 -0.95 33 33
IL4 -0.1 0.26 -10000 0 -0.74 14 14
IL5 -0.33 0.42 -10000 0 -0.91 43 43
IL2 -0.15 0.26 -10000 0 -0.79 12 12
IL3 -0.053 0.18 -10000 0 -0.81 6 6
RNF128 -0.11 0.25 -10000 0 -0.59 32 32
NFATC1 -0.19 0.39 -10000 0 -0.91 25 25
CDK4 0.12 0.21 0.62 10 -10000 0 10
PTPRK -0.085 0.24 -10000 0 -0.72 14 14
IL8 -0.39 0.44 -10000 0 -0.95 48 48
POU2F1 0.037 0.01 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.064 0.16 -9999 0 -0.33 34 34
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.18 -9999 0 -0.49 13 13
alphaV/beta3 Integrin/Osteopontin/Src -0.075 0.18 -9999 0 -0.4 34 34
AP1 -0.12 0.23 -9999 0 -0.54 26 26
ILK -0.07 0.15 -9999 0 -0.33 34 34
bone resorption -0.07 0.15 -9999 0 -0.4 14 14
PTK2B 0.028 0.015 -9999 0 -10000 0 0
PYK2/p130Cas -0.046 0.17 -9999 0 -0.31 36 36
ITGAV 0.007 0.1 -9999 0 -0.53 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.033 0.075 -9999 0 -0.37 5 5
alphaV/beta3 Integrin/Osteopontin -0.056 0.17 -9999 0 -0.35 34 34
MAP3K1 -0.079 0.16 -9999 0 -0.33 37 37
JUN 0.002 0.11 -9999 0 -0.51 7 7
MAPK3 -0.088 0.16 -9999 0 -0.38 25 25
MAPK1 -0.08 0.16 -9999 0 -0.36 30 30
Rac1/GDP 0.024 0.003 -9999 0 -10000 0 0
NFKB1 0.031 0.007 -9999 0 -10000 0 0
MAPK8 -0.081 0.15 -9999 0 -0.32 37 37
ITGB3 0.019 0.052 -9999 0 -0.52 1 1
NFKBIA -0.087 0.17 -9999 0 -0.46 18 18
FOS -0.031 0.16 -9999 0 -0.51 14 14
CD44 0.014 0.096 -9999 0 -0.51 5 5
CHUK 0.028 0.044 -9999 0 -0.51 1 1
PLAU -0.19 0.41 -9999 0 -1.1 23 23
NF kappa B1 p50/RelA -0.052 0.2 -9999 0 -0.47 18 18
BCAR1 0.031 0.007 -9999 0 -10000 0 0
RELA 0.033 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.018 0.092 -9999 0 -0.39 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.081 0.16 -9999 0 -0.34 38 38
VAV3 -0.14 0.18 -9999 0 -0.33 62 62
MAP3K14 -0.078 0.16 -9999 0 -0.34 34 34
ROCK2 0.032 0.005 -9999 0 -10000 0 0
SPP1 -0.1 0.22 -9999 0 -0.52 33 33
RAC1 0.032 0.005 -9999 0 -10000 0 0
Rac1/GTP -0.12 0.17 -9999 0 -0.36 35 35
MMP2 -0.14 0.22 -9999 0 -0.54 29 29
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.19 -9999 0 -0.35 56 56
FZD6 0.012 0.096 -9999 0 -0.51 5 5
WNT6 0.027 0.023 -9999 0 -10000 0 0
WNT4 -0.074 0.21 -9999 0 -0.51 28 28
FZD3 -0.006 0.13 -9999 0 -0.51 9 9
WNT5A -0.088 0.21 -9999 0 -0.51 29 29
WNT11 0.003 0.092 -9999 0 -0.51 4 4
Noncanonical Wnt signaling pathway

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
NFATC2 0.032 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.1 0.19 -9999 0 -0.4 29 29
mol:DAG -0.11 0.16 -9999 0 -0.38 25 25
PLCG1 -0.11 0.17 -9999 0 -0.4 25 25
YES1 -0.12 0.18 -9999 0 -0.4 34 34
FZD3 -0.006 0.13 -9999 0 -0.51 9 9
FZD6 0.012 0.096 -9999 0 -0.51 5 5
G protein -0.1 0.18 -9999 0 -0.44 20 20
MAP3K7 -0.096 0.14 -9999 0 -0.37 18 18
mol:Ca2+ -0.1 0.16 -9999 0 -0.37 25 25
mol:IP3 -0.11 0.16 -9999 0 -0.38 25 25
NLK 0.002 0.097 -9999 0 -0.84 2 2
GNB1 0.032 0.005 -9999 0 -10000 0 0
CAMK2A -0.1 0.15 -9999 0 -0.4 18 18
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.19 -9999 0 -0.35 56 56
CSNK1A1 0.028 0.044 -9999 0 -0.51 1 1
GNAS -0.12 0.18 -9999 0 -0.38 37 37
GO:0007205 -0.11 0.16 -9999 0 -0.42 19 19
WNT6 0.027 0.023 -9999 0 -10000 0 0
WNT4 -0.074 0.21 -9999 0 -0.51 28 28
NFAT1/CK1 alpha -0.086 0.19 -9999 0 -0.45 20 20
GNG2 0.032 0.005 -9999 0 -10000 0 0
WNT5A -0.088 0.21 -9999 0 -0.51 29 29
WNT11 0.003 0.092 -9999 0 -0.51 4 4
CDC42 -0.11 0.18 -9999 0 -0.41 27 27
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.004 -9999 0 -10000 0 0
CCL5 -0.023 0.16 -9999 0 -0.51 15 15
SDCBP 0.027 0.044 -9999 0 -0.51 1 1
FGFR/FGF2/Syndecan-1 -0.13 0.25 -9999 0 -0.6 26 26
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.26 -9999 0 -0.59 27 27
Syndecan-1/Syntenin -0.11 0.25 -9999 0 -0.62 23 23
MAPK3 -0.11 0.22 -9999 0 -0.55 25 25
HGF/MET 0.035 0.061 -9999 0 -0.37 3 3
TGFB1/TGF beta receptor Type II 0.032 0.004 -9999 0 -10000 0 0
BSG 0.032 0.005 -9999 0 -10000 0 0
keratinocyte migration -0.12 0.25 -9999 0 -0.58 27 27
Syndecan-1/RANTES -0.14 0.28 -9999 0 -0.62 30 30
Syndecan-1/CD147 -0.1 0.25 -9999 0 -0.58 25 25
Syndecan-1/Syntenin/PIP2 -0.11 0.24 -9999 0 -0.6 23 23
LAMA5 0.01 0.1 -9999 0 -0.51 6 6
positive regulation of cell-cell adhesion -0.11 0.23 -9999 0 -0.58 23 23
MMP7 -0.046 0.19 -9999 0 -0.51 22 22
HGF 0.028 0.02 -9999 0 -10000 0 0
Syndecan-1/CASK -0.13 0.24 -9999 0 -0.57 26 26
Syndecan-1/HGF/MET -0.1 0.25 -9999 0 -0.58 25 25
regulation of cell adhesion -0.11 0.21 -9999 0 -0.54 23 23
HPSE 0.003 0.11 -9999 0 -0.51 7 7
positive regulation of cell migration -0.13 0.25 -9999 0 -0.6 26 26
SDC1 -0.13 0.25 -9999 0 -0.43 48 48
Syndecan-1/Collagen -0.13 0.25 -9999 0 -0.6 26 26
PPIB 0.028 0.044 -9999 0 -0.51 1 1
MET 0.02 0.076 -9999 0 -0.51 3 3
PRKACA 0.031 0.006 -9999 0 -10000 0 0
MMP9 -0.015 0.15 -9999 0 -0.51 13 13
MAPK1 -0.11 0.22 -9999 0 -0.55 24 24
homophilic cell adhesion -0.13 0.24 -9999 0 -0.59 26 26
MMP1 -0.12 0.23 -9999 0 -0.51 39 39
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.14 0.28 -10000 0 -0.56 43 43
IHH -0.015 0.089 -10000 0 -0.36 2 2
SHH Np/Cholesterol/GAS1 -0.045 0.14 -10000 0 -0.32 30 30
LRPAP1 0.03 0.009 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.045 0.14 0.32 30 -10000 0 30
SMO/beta Arrestin2 -0.12 0.23 -10000 0 -0.58 20 20
SMO -0.13 0.24 -10000 0 -0.6 21 21
AKT1 -0.093 0.21 -10000 0 -0.73 12 12
ARRB2 0.03 0.008 -10000 0 -10000 0 0
BOC 0.022 0.027 -10000 0 -10000 0 0
ADRBK1 0.032 0.005 -10000 0 -10000 0 0
heart looping -0.13 0.24 -10000 0 -0.59 21 21
STIL -0.077 0.16 -10000 0 -0.46 11 11
DHH N/PTCH2 0.047 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 -0.05 0.16 -10000 0 -0.3 42 42
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
DHH 0.032 0.003 -10000 0 -10000 0 0
PTHLH -0.25 0.45 -10000 0 -0.96 43 43
determination of left/right symmetry -0.13 0.24 -10000 0 -0.59 21 21
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
skeletal system development -0.24 0.44 -10000 0 -0.94 43 43
IHH N/Hhip -0.055 0.16 -10000 0 -0.42 21 21
DHH N/Hhip -0.024 0.14 -10000 0 -0.37 19 19
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.24 -10000 0 -0.59 21 21
pancreas development -0.058 0.18 -10000 0 -0.51 20 20
HHAT -0.007 0.14 -10000 0 -0.51 11 11
PI3K 0.004 0.075 -10000 0 -0.37 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.056 0.19 -10000 0 -0.51 22 22
somite specification -0.13 0.24 -10000 0 -0.59 21 21
SHH Np/Cholesterol/PTCH1 -0.069 0.16 -10000 0 -0.37 19 19
SHH Np/Cholesterol/PTCH2 0.007 0.086 -10000 0 -0.29 12 12
SHH Np/Cholesterol/Megalin 0.001 0.091 -10000 0 -0.29 13 13
SHH -0.013 0.1 -10000 0 -0.37 12 12
catabolic process -0.07 0.17 -10000 0 -0.34 43 43
SMO/Vitamin D3 -0.1 0.2 -10000 0 -0.52 19 19
SHH Np/Cholesterol/Hhip -0.043 0.13 -10000 0 -0.3 29 29
LRP2 0.02 0.052 -10000 0 -0.51 1 1
receptor-mediated endocytosis -0.1 0.2 -10000 0 -0.51 18 18
SHH Np/Cholesterol/BOC -0.001 0.085 -10000 0 -0.29 12 12
SHH Np/Cholesterol/CDO 0.006 0.087 -10000 0 -0.29 12 12
mesenchymal cell differentiation 0.043 0.13 0.3 29 -10000 0 29
mol:Vitamin D3 -0.07 0.16 -10000 0 -0.37 19 19
IHH N/PTCH2 0.015 0.06 -10000 0 -0.32 1 1
CDON 0.028 0.02 -10000 0 -10000 0 0
IHH N/PTCH1 -0.063 0.18 -10000 0 -0.34 43 43
Megalin/LRPAP1 0.034 0.044 -10000 0 -0.37 1 1
PTCH2 0.032 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.004 0.082 -10000 0 -0.28 12 12
PTCH1 -0.07 0.17 -10000 0 -0.34 43 43
HHIP -0.058 0.18 -10000 0 -0.51 20 20
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.002 0.11 -10000 0 -0.51 7 7
EPHB2 -0.021 0.15 -10000 0 -0.51 13 13
EFNB1 -0.031 0.13 -10000 0 -0.37 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.024 0.15 -10000 0 -0.3 29 29
Ephrin B2/EPHB1-2 -0.019 0.12 -10000 0 -0.3 21 21
neuron projection morphogenesis -0.034 0.13 -10000 0 -0.28 29 29
Ephrin B1/EPHB1-2/Tiam1 -0.034 0.15 -10000 0 -0.31 31 31
DNM1 0.027 0.046 -10000 0 -0.51 1 1
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.076 0.21 0.24 1 -0.59 21 22
YES1 -0.1 0.3 -10000 0 -0.82 22 22
Ephrin B1/EPHB1-2/NCK2 -0.035 0.15 -10000 0 -0.31 31 31
PI3K -0.066 0.23 -10000 0 -0.63 19 19
mol:GDP -0.034 0.15 -10000 0 -0.3 31 31
ITGA2B 0.032 0.004 -10000 0 -10000 0 0
endothelial cell proliferation 0.011 0.1 -10000 0 -0.38 9 9
FYN -0.1 0.3 -10000 0 -0.81 22 22
MAP3K7 -0.082 0.22 -10000 0 -0.61 22 22
FGR -0.096 0.29 -10000 0 -0.8 22 22
TIAM1 0.032 0.005 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
RGS3 0.032 0.005 -10000 0 -10000 0 0
cell adhesion -0.067 0.21 -10000 0 -0.59 19 19
LYN -0.1 0.29 -10000 0 -0.81 22 22
Ephrin B1/EPHB1-2/Src Family Kinases -0.1 0.27 -10000 0 -0.75 22 22
Ephrin B1/EPHB1-2 -0.088 0.24 -10000 0 -0.65 22 22
SRC -0.096 0.29 -10000 0 -0.8 22 22
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
EPHB1 -0.012 0.11 -10000 0 -0.51 6 6
EPHB4 0.012 0.097 -10000 0 -0.51 5 5
RAC1 0.032 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.011 0.1 -10000 0 -0.38 9 9
alphaIIb/beta3 Integrin 0.041 0.039 -10000 0 -0.37 1 1
BLK -0.11 0.29 -10000 0 -0.81 22 22
HCK -0.1 0.3 -10000 0 -0.81 22 22
regulation of stress fiber formation 0.035 0.15 0.31 31 -10000 0 31
MAPK8 -0.07 0.2 -10000 0 -0.57 20 20
Ephrin B1/EPHB1-2/RGS3 -0.034 0.15 -10000 0 -0.31 31 31
endothelial cell migration -0.086 0.22 -10000 0 -0.53 26 26
NCK2 0.032 0.004 -10000 0 -10000 0 0
PTPN13 -0.031 0.19 -10000 0 -0.63 14 14
regulation of focal adhesion formation 0.035 0.15 0.31 31 -10000 0 31
chemotaxis 0.035 0.15 0.31 31 -10000 0 31
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
Rac1/GTP -0.028 0.14 -10000 0 -0.29 29 29
angiogenesis -0.087 0.23 -10000 0 -0.65 22 22
LCK -0.11 0.3 -10000 0 -0.82 22 22
Endothelins

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
AKT1 -0.012 0.2 0.28 16 -0.45 17 33
PTK2B 0.028 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.079 0.28 -10000 0 -0.83 14 14
EDN1 -0.021 0.21 0.24 10 -0.51 20 30
EDN3 0.013 0.069 -10000 0 -0.51 2 2
EDN2 -0.15 0.23 -10000 0 -0.51 43 43
HRAS/GDP -0.053 0.2 -10000 0 -0.46 20 20
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.039 0.18 -10000 0 -0.41 18 18
ADCY4 -0.022 0.17 0.35 1 -0.48 12 13
ADCY5 -0.024 0.15 0.27 1 -0.46 11 12
ADCY6 -0.016 0.17 0.31 2 -0.46 11 13
ADCY7 -0.02 0.17 0.31 2 -0.48 11 13
ADCY1 -0.019 0.17 0.31 2 -0.46 11 13
ADCY2 -0.022 0.16 0.31 2 -0.45 11 13
ADCY3 -0.023 0.17 0.31 2 -0.45 12 14
ADCY8 -0.025 0.16 0.35 1 -0.43 12 13
ADCY9 -0.02 0.17 0.31 2 -0.44 12 14
arachidonic acid secretion -0.11 0.23 -10000 0 -0.49 32 32
ETB receptor/Endothelin-1/Gq/GTP -0.056 0.16 -10000 0 -0.33 28 28
GNAO1 0.031 0.011 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
ETA receptor/Endothelin-1/G12/GTP 0.033 0.21 0.38 18 -0.4 17 35
ETA receptor/Endothelin-1/Gs/GTP 0.012 0.2 0.35 14 -0.42 15 29
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.038 0.26 0.35 1 -0.6 20 21
EDNRB 0.001 0.096 -10000 0 -0.4 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.005 0.19 0.35 1 -0.55 9 10
CYSLTR1 -0.009 0.2 0.35 1 -0.55 10 11
SLC9A1 0.003 0.12 0.2 17 -0.29 11 28
mol:GDP -0.063 0.2 -10000 0 -0.47 20 20
SLC9A3 -0.11 0.32 -10000 0 -0.7 29 29
RAF1 -0.074 0.2 -10000 0 -0.45 23 23
JUN -0.089 0.31 -10000 0 -0.8 19 19
JAK2 -0.012 0.19 0.28 13 -0.41 18 31
mol:IP3 -0.047 0.17 -10000 0 -0.38 22 22
ETA receptor/Endothelin-1 0.02 0.25 0.43 19 -0.48 19 38
PLCB1 0.013 0.096 -10000 0 -0.51 5 5
PLCB2 0.03 0.01 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.028 0.12 -10000 0 -0.38 7 7
FOS -0.11 0.31 -10000 0 -0.87 19 19
Gai/GDP -0.053 0.24 -10000 0 -0.72 15 15
CRK 0.03 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.061 0.24 -10000 0 -0.59 20 20
BCAR1 0.031 0.007 -10000 0 -10000 0 0
PRKCB1 -0.048 0.17 -10000 0 -0.38 21 21
GNAQ -0.001 0.006 -10000 0 -10000 0 0
GNAZ 0.003 0.11 -10000 0 -0.51 7 7
GNAL 0.008 0.098 -10000 0 -0.51 5 5
Gs family/GDP -0.062 0.19 -10000 0 -0.44 19 19
ETA receptor/Endothelin-1/Gq/GTP -0.044 0.2 0.22 1 -0.4 23 24
MAPK14 -0.05 0.15 -10000 0 -0.38 16 16
TRPC6 -0.087 0.3 -10000 0 -0.9 14 14
GNAI2 0.028 0.017 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 -0.001 0.13 -10000 0 -0.51 9 9
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.05 0.16 -10000 0 -0.35 22 22
ETB receptor/Endothelin-2 -0.11 0.19 -10000 0 -0.38 46 46
ETB receptor/Endothelin-3 0.009 0.089 -10000 0 -0.38 6 6
ETB receptor/Endothelin-1 -0.017 0.18 -10000 0 -0.38 25 25
MAPK3 -0.1 0.28 -10000 0 -0.76 19 19
MAPK1 -0.11 0.29 -10000 0 -0.81 19 19
Rac1/GDP -0.047 0.19 -10000 0 -0.44 19 19
cAMP biosynthetic process 0.001 0.16 0.33 3 -0.46 9 12
MAPK8 -0.079 0.29 -10000 0 -0.68 21 21
SRC 0.031 0.011 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.042 0.16 -10000 0 -0.4 16 16
p130Cas/CRK/Src/PYK2 -0.072 0.21 -10000 0 -0.53 19 19
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.046 0.19 -10000 0 -0.44 19 19
COL1A2 -0.054 0.29 -10000 0 -0.8 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.096 0.2 -10000 0 -0.38 46 46
mol:DAG -0.047 0.17 -10000 0 -0.38 22 22
MAP2K2 -0.089 0.22 -10000 0 -0.6 19 19
MAP2K1 -0.089 0.23 -10000 0 -0.58 21 21
EDNRA 0.029 0.14 0.24 17 -0.48 7 24
positive regulation of muscle contraction -0.012 0.18 0.23 13 -0.5 10 23
Gq family/GDP -0.065 0.19 -10000 0 -0.43 24 24
HRAS/GTP -0.061 0.18 -10000 0 -0.42 20 20
PRKCH -0.056 0.18 -10000 0 -0.43 20 20
RAC1 0.032 0.005 -10000 0 -10000 0 0
PRKCA -0.046 0.16 -10000 0 -0.41 17 17
PRKCB -0.048 0.17 -10000 0 -0.38 21 21
PRKCE -0.035 0.16 0.26 3 -0.41 14 17
PRKCD -0.054 0.16 -10000 0 -0.41 17 17
PRKCG -0.05 0.16 -10000 0 -0.43 15 15
regulation of vascular smooth muscle contraction -0.14 0.36 -10000 0 -1 19 19
PRKCQ -0.061 0.18 -10000 0 -0.44 19 19
PLA2G4A -0.12 0.26 -10000 0 -0.54 32 32
GNA14 0.009 0.08 -10000 0 -0.51 3 3
GNA15 -0.019 0.15 -10000 0 -0.51 13 13
GNA12 0.032 0.006 -10000 0 -10000 0 0
GNA11 0.021 0.063 -10000 0 -0.51 2 2
Rac1/GTP 0.033 0.21 0.38 19 -0.39 18 37
MMP1 -0.24 0.4 0.53 1 -0.91 39 40
EPHB forward signaling

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
Ephrin A5/EPHB2 0.005 0.1 -10000 0 -0.31 13 13
cell-cell adhesion 0.067 0.13 0.3 32 -10000 0 32
Ephrin B/EPHB2/RasGAP -0.016 0.17 -10000 0 -0.31 34 34
ITSN1 0.032 0.003 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
SHC1 0.031 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.039 0.14 -10000 0 -0.36 22 22
Ephrin B1/EPHB1 -0.029 0.13 -10000 0 -0.34 21 21
HRAS/GDP -0.11 0.17 -10000 0 -0.4 25 25
Ephrin B/EPHB1/GRB7 -0.01 0.15 -10000 0 -0.32 24 24
Endophilin/SYNJ1 -0.055 0.13 -10000 0 -0.29 34 34
KRAS 0.016 0.086 -10000 0 -0.51 4 4
Ephrin B/EPHB1/Src -0.009 0.14 -10000 0 -0.31 23 23
endothelial cell migration -0.005 0.1 -10000 0 -0.36 9 9
GRB2 0.032 0.005 -10000 0 -10000 0 0
GRB7 0.032 0.006 -10000 0 -10000 0 0
PAK1 -0.033 0.15 -10000 0 -0.31 28 28
HRAS 0.024 0.062 -10000 0 -0.51 2 2
RRAS -0.061 0.14 -10000 0 -0.3 36 36
DNM1 0.027 0.046 -10000 0 -0.51 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.025 0.14 -10000 0 -0.3 24 24
lamellipodium assembly -0.067 0.13 -10000 0 -0.3 32 32
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.025 0.11 -10000 0 -0.39 6 6
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
EPHB2 -0.021 0.15 -10000 0 -0.51 13 13
EPHB3 -0.026 0.14 -10000 0 -0.51 12 12
EPHB1 -0.012 0.11 -10000 0 -0.51 6 6
EPHB4 0.012 0.097 -10000 0 -0.51 5 5
mol:GDP -0.1 0.16 -10000 0 -0.42 22 22
Ephrin B/EPHB2 -0.023 0.16 -10000 0 -0.31 33 33
Ephrin B/EPHB3 -0.034 0.15 -10000 0 -0.34 24 24
JNK cascade -0.017 0.2 0.36 19 -0.32 32 51
Ephrin B/EPHB1 -0.019 0.14 -10000 0 -0.32 24 24
RAP1/GDP -0.089 0.16 -10000 0 -0.38 23 23
EFNB2 0.002 0.11 -10000 0 -0.51 7 7
EFNB3 0.03 0.008 -10000 0 -10000 0 0
EFNB1 -0.032 0.17 -10000 0 -0.51 18 18
Ephrin B2/EPHB1-2 -0.02 0.12 -10000 0 -0.3 21 21
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
CDC42/GTP -0.052 0.17 -10000 0 -0.35 30 30
Rap1/GTP -0.057 0.13 -10000 0 -0.36 14 14
axon guidance 0.005 0.099 -10000 0 -0.31 13 13
MAPK3 -0.025 0.094 -10000 0 -0.37 5 5
MAPK1 -0.022 0.1 -10000 0 -0.35 6 6
Rac1/GDP -0.095 0.16 -10000 0 -0.39 22 22
actin cytoskeleton reorganization -0.098 0.12 -10000 0 -0.34 23 23
CDC42/GDP -0.096 0.16 -10000 0 -0.39 22 22
PI3K -0.003 0.11 -10000 0 -0.36 9 9
EFNA5 0.03 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.011 0.1 -10000 0 -0.38 9 9
Ephrin B/EPHB2/Intersectin/N-WASP -0.052 0.15 -10000 0 -0.3 35 35
CDC42 0.032 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.066 0.14 -10000 0 -0.38 17 17
PTK2 0.05 0.17 0.62 11 -0.49 1 12
MAP4K4 -0.018 0.2 0.36 19 -0.32 32 51
SRC 0.031 0.011 -10000 0 -10000 0 0
KALRN 0.026 0.019 -10000 0 -10000 0 0
Intersectin/N-WASP 0.036 0.067 -10000 0 -0.37 4 4
neuron projection morphogenesis -0.036 0.16 0.31 11 -0.4 11 22
MAP2K1 -0.026 0.1 -10000 0 -0.37 6 6
WASL 0.018 0.086 -10000 0 -0.51 4 4
Ephrin B1/EPHB1-2/NCK1 -0.035 0.16 -10000 0 -0.33 31 31
cell migration -0.03 0.13 0.3 1 -0.37 9 10
NRAS 0.025 0.047 -10000 0 -0.51 1 1
SYNJ1 -0.056 0.14 -10000 0 -0.3 34 34
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.066 0.12 -10000 0 -0.29 29 29
HRAS/GTP -0.047 0.15 -10000 0 -0.31 33 33
Ephrin B1/EPHB1-2 -0.042 0.15 -10000 0 -0.33 30 30
cell adhesion mediated by integrin 0.023 0.13 0.32 18 -0.19 1 19
RAC1 0.032 0.005 -10000 0 -10000 0 0
mol:GTP -0.045 0.15 -10000 0 -0.3 34 34
RAC1-CDC42/GTP -0.067 0.13 -10000 0 -0.42 11 11
RASA1 0.026 0.044 -10000 0 -0.51 1 1
RAC1-CDC42/GDP -0.086 0.16 -10000 0 -0.39 19 19
ruffle organization -0.059 0.15 0.32 2 -0.47 9 11
NCK1 0.02 0.062 -10000 0 -0.51 2 2
receptor internalization -0.072 0.13 -10000 0 -0.3 31 31
Ephrin B/EPHB2/KALRN -0.016 0.16 -10000 0 -0.31 30 30
ROCK1 0.038 0.18 0.19 66 -0.33 22 88
RAS family/GDP -0.1 0.13 -10000 0 -0.37 21 21
Rac1/GTP -0.066 0.14 -10000 0 -0.32 32 32
Ephrin B/EPHB1/Src/Paxillin -0.033 0.12 -10000 0 -0.41 7 7
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.002 0.12 -10000 0 -0.51 8 8
GNB1/GNG2 -0.063 0.08 -10000 0 -0.18 42 42
AKT1 -0.041 0.12 -10000 0 -0.27 7 7
EGF -0.032 0.15 -10000 0 -0.51 13 13
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.015 0.055 0.21 1 -10000 0 1
mol:Ca2+ -0.068 0.16 -10000 0 -0.3 44 44
LYN 0.014 0.057 0.21 1 -0.24 1 2
RhoA/GTP -0.027 0.072 -10000 0 -0.14 13 13
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.088 0.18 -10000 0 -0.35 44 44
GNG2 0.032 0.005 -10000 0 -10000 0 0
ARRB2 0.03 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.029 0.16 -10000 0 -0.41 19 19
G beta5/gamma2 -0.082 0.11 -10000 0 -0.24 41 41
PRKCH -0.088 0.19 -10000 0 -0.37 43 43
DNM1 0.027 0.046 -10000 0 -0.51 1 1
TXA2/TP beta/beta Arrestin3 0.015 0.099 -10000 0 -0.55 4 4
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.027 0.023 -10000 0 -10000 0 0
G12 family/GTP -0.076 0.16 -10000 0 -0.3 42 42
ADRBK1 0.032 0.005 -10000 0 -10000 0 0
ADRBK2 0.022 0.063 -10000 0 -0.51 2 2
RhoA/GTP/ROCK1 0.039 0.013 -10000 0 -10000 0 0
mol:GDP 0.027 0.11 0.46 3 -10000 0 3
mol:NADP 0.028 0.021 -10000 0 -10000 0 0
RAB11A 0.032 0.003 -10000 0 -10000 0 0
PRKG1 0.028 0.019 -10000 0 -10000 0 0
mol:IP3 -0.09 0.2 -10000 0 -0.38 44 44
cell morphogenesis 0.039 0.013 -10000 0 -10000 0 0
PLCB2 -0.13 0.26 -10000 0 -0.52 44 44
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.008 0.064 0.21 1 -0.24 3 4
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.003 0.075 0.21 1 -0.24 7 8
RHOA 0.03 0.009 -10000 0 -10000 0 0
PTGIR 0.025 0.062 -10000 0 -0.51 2 2
PRKCB1 -0.092 0.2 -10000 0 -0.38 45 45
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.028 0.021 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.13 0.27 -10000 0 -0.53 44 44
LCK 0.002 0.072 0.21 1 -0.23 6 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.039 0.042 -10000 0 -0.22 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.084 -10000 0 -0.38 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.038 0.043 -10000 0 -0.22 2 2
MAPK14 -0.055 0.12 -10000 0 -0.23 41 41
TGM2/GTP -0.11 0.22 -10000 0 -0.43 43 43
MAPK11 -0.054 0.12 -10000 0 -0.23 41 41
ARHGEF1 -0.039 0.098 -10000 0 -0.18 40 40
GNAI2 0.028 0.017 -10000 0 -10000 0 0
JNK cascade -0.092 0.2 -10000 0 -0.38 44 44
RAB11/GDP 0.032 0.003 -10000 0 -10000 0 0
ICAM1 -0.069 0.16 -10000 0 -0.3 43 43
cAMP biosynthetic process -0.085 0.18 -10000 0 -0.35 45 45
Gq family/GTP/EBP50 -0.043 0.13 -10000 0 -0.28 30 30
actin cytoskeleton reorganization 0.039 0.013 -10000 0 -10000 0 0
SRC 0.015 0.055 0.21 1 -10000 0 1
GNB5 0.018 0.086 -10000 0 -0.51 4 4
GNB1 0.032 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.014 0.1 0.2 3 -0.32 8 11
VCAM1 -0.073 0.17 -10000 0 -0.31 44 44
TP beta/Gq family/GDP/G beta5/gamma2 -0.029 0.16 -10000 0 -0.41 19 19
platelet activation -0.07 0.16 -10000 0 -0.3 43 43
PGI2/IP 0.018 0.045 -10000 0 -0.37 2 2
PRKACA 0.016 0.033 -10000 0 -0.25 2 2
Gq family/GDP/G beta5/gamma2 -0.024 0.14 -10000 0 -0.37 19 19
TXA2/TP beta/beta Arrestin2 0.015 0.063 -10000 0 -0.41 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.031 -10000 0 -0.24 2 2
mol:DAG -0.1 0.22 -10000 0 -0.43 44 44
EGFR -0.033 0.17 -10000 0 -0.51 17 17
TXA2/TP alpha -0.12 0.25 -10000 0 -0.47 45 45
Gq family/GTP -0.022 0.086 -10000 0 -0.24 19 19
YES1 0.013 0.054 0.21 1 -0.24 1 2
GNAI2/GTP 0.019 0.043 -10000 0 -0.22 2 2
PGD2/DP 0.02 0.015 -10000 0 -10000 0 0
SLC9A3R1 -0.035 0.17 -10000 0 -0.51 18 18
FYN 0.013 0.065 0.21 1 -0.32 2 3
mol:NO 0.028 0.021 -10000 0 -10000 0 0
GNA15 -0.015 0.15 -10000 0 -0.51 13 13
PGK/cGMP 0.035 0.023 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.038 0.086 -10000 0 -0.28 8 8
NOS3 0.028 0.021 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
PRKCA -0.083 0.19 -10000 0 -0.35 45 45
PRKCB -0.086 0.19 -10000 0 -0.36 45 45
PRKCE -0.077 0.19 -10000 0 -0.36 38 38
PRKCD -0.099 0.2 -10000 0 -0.39 44 44
PRKCG -0.094 0.2 -10000 0 -0.39 44 44
muscle contraction -0.12 0.25 -10000 0 -0.49 44 44
PRKCZ -0.081 0.18 -10000 0 -0.34 44 44
ARR3 0.032 0.005 -10000 0 -10000 0 0
TXA2/TP beta 0.035 0.052 -10000 0 -0.23 3 3
PRKCQ -0.095 0.19 -10000 0 -0.37 44 44
MAPKKK cascade -0.11 0.23 -10000 0 -0.45 45 45
SELE -0.094 0.2 -10000 0 -0.38 44 44
TP beta/GNAI2/GDP/G beta/gamma 0.055 0.046 -10000 0 -10000 0 0
ROCK1 0.032 0.005 -10000 0 -10000 0 0
GNA14 0.014 0.079 -10000 0 -0.51 3 3
chemotaxis -0.16 0.3 -10000 0 -0.62 43 43
GNA12 0.032 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.044 -10000 0 -0.51 1 1
GNA11 0.025 0.061 -10000 0 -0.51 2 2
Rac1/GTP 0.023 0.004 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.097 0.21 -10000 0 -0.5 26 26
IKBKB -0.004 0.12 -10000 0 -0.31 11 11
AKT1 -0.004 0.14 0.24 15 -0.26 20 35
IKBKG -0.009 0.12 0.21 1 -0.3 10 11
CALM1 -0.071 0.24 0.32 1 -0.64 20 21
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
MAP3K1 -0.13 0.28 -10000 0 -0.67 28 28
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.077 0.26 0.34 1 -0.65 22 23
DOK1 0.032 0.006 -10000 0 -10000 0 0
AP-1 -0.052 0.12 0.19 1 -0.28 25 26
LYN 0.027 0.044 -10000 0 -0.51 1 1
BLNK 0.013 0.096 -10000 0 -0.51 5 5
SHC1 0.031 0.007 -10000 0 -10000 0 0
BCR complex -0.052 0.2 -10000 0 -0.47 26 26
CD22 -0.12 0.31 -10000 0 -0.83 21 21
CAMK2G -0.061 0.22 0.31 2 -0.59 20 22
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.17 -10000 0 -0.37 28 28
GO:0007205 -0.081 0.27 0.34 1 -0.67 22 23
SYK 0.009 0.1 -10000 0 -0.51 6 6
ELK1 -0.074 0.25 0.32 1 -0.66 20 21
NFATC1 -0.12 0.28 -10000 0 -0.63 28 28
B-cell antigen/BCR complex -0.052 0.2 -10000 0 -0.47 26 26
PAG1/CSK 0.027 0.082 -10000 0 -0.37 6 6
NFKBIB 0.016 0.052 0.12 1 -0.12 5 6
HRAS -0.067 0.23 0.27 1 -0.55 23 24
NFKBIA 0.016 0.051 0.12 1 -0.12 6 7
NF-kappa-B/RelA/I kappa B beta 0.023 0.045 0.13 1 -10000 0 1
RasGAP/Csk -0.036 0.22 -10000 0 -0.43 31 31
mol:GDP -0.074 0.26 0.33 1 -0.63 22 23
PTEN 0.025 0.045 -10000 0 -0.51 1 1
CD79B -0.051 0.19 -10000 0 -0.51 22 22
NF-kappa-B/RelA/I kappa B alpha 0.023 0.045 0.13 1 -10000 0 1
GRB2 0.032 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.12 0.26 -10000 0 -0.63 27 27
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
mol:IP3 -0.082 0.28 0.34 1 -0.69 22 23
CSK 0.032 0.003 -10000 0 -10000 0 0
FOS -0.09 0.23 0.31 1 -0.61 21 22
CHUK -0.016 0.13 -10000 0 -0.33 13 13
IBTK 0.029 0.044 -10000 0 -0.51 1 1
CARD11/BCL10/MALT1/TAK1 -0.041 0.22 0.3 1 -0.57 18 19
PTPN6 -0.11 0.28 -10000 0 -0.76 21 21
RELA 0.033 0 -10000 0 -10000 0 0
BCL2A1 0.009 0.043 -10000 0 -0.12 2 2
VAV2 -0.17 0.37 -10000 0 -0.82 31 31
ubiquitin-dependent protein catabolic process 0.019 0.051 0.13 1 -0.12 5 6
BTK -0.098 0.35 -10000 0 -1.2 14 14
CD19 -0.16 0.36 -10000 0 -0.9 25 25
MAP4K1 0.029 0.01 -10000 0 -10000 0 0
CD72 -0.036 0.17 -10000 0 -0.51 18 18
PAG1 0.008 0.1 -10000 0 -0.51 6 6
MAPK14 -0.1 0.23 -10000 0 -0.55 27 27
SH3BP5 0.026 0.046 -10000 0 -0.51 1 1
PIK3AP1 -0.095 0.29 -10000 0 -0.73 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.12 0.36 -10000 0 -0.77 27 27
RAF1 -0.063 0.21 0.26 1 -0.55 20 21
RasGAP/p62DOK/SHIP -0.04 0.2 -10000 0 -0.4 31 31
CD79A -0.022 0.15 -10000 0 -0.51 13 13
re-entry into mitotic cell cycle -0.052 0.12 0.2 1 -0.28 25 26
RASA1 0.026 0.044 -10000 0 -0.51 1 1
MAPK3 -0.051 0.17 0.24 1 -0.47 18 19
MAPK1 -0.043 0.17 0.33 3 -0.46 17 20
CD72/SHP1 -0.095 0.31 0.35 2 -0.72 25 27
NFKB1 0.031 0.007 -10000 0 -10000 0 0
MAPK8 -0.1 0.23 -10000 0 -0.55 27 27
actin cytoskeleton organization -0.14 0.29 0.35 1 -0.66 30 31
NF-kappa-B/RelA 0.046 0.089 0.24 1 -0.24 1 2
Calcineurin -0.035 0.22 0.3 1 -0.57 19 20
PI3K -0.11 0.21 -10000 0 -0.56 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.088 0.3 0.37 1 -0.7 23 24
SOS1 0.032 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.16 0.37 -10000 0 -0.86 32 32
DAPP1 -0.21 0.44 -10000 0 -1 33 33
cytokine secretion -0.11 0.25 -10000 0 -0.57 28 28
mol:DAG -0.082 0.28 0.34 1 -0.69 22 23
PLCG2 0.013 0.096 -10000 0 -0.51 5 5
MAP2K1 -0.058 0.19 0.25 1 -0.53 18 19
B-cell antigen/BCR complex/FcgammaRIIB -0.061 0.24 -10000 0 -0.5 30 30
mol:PI-3-4-5-P3 -0.047 0.16 0.24 7 -0.36 20 27
ETS1 -0.056 0.2 0.29 2 -0.52 21 23
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.025 0.21 -10000 0 -0.41 30 30
B-cell antigen/BCR complex/LYN -0.12 0.33 -10000 0 -0.86 22 22
MALT1 0.03 0.012 -10000 0 -10000 0 0
TRAF6 0.021 0.075 -10000 0 -0.51 3 3
RAC1 -0.15 0.32 -10000 0 -0.73 30 30
B-cell antigen/BCR complex/LYN/SYK -0.07 0.31 0.38 1 -0.74 22 23
CARD11 -0.074 0.25 0.32 1 -0.65 21 22
FCGR2B -0.025 0.16 -10000 0 -0.51 16 16
PPP3CA 0.028 0.044 -10000 0 -0.51 1 1
BCL10 0.028 0.045 -10000 0 -0.51 1 1
IKK complex 0.015 0.06 0.13 6 -0.13 3 9
PTPRC -0.024 0.16 -10000 0 -0.51 15 15
PDPK1 -0.015 0.13 0.22 12 -0.25 16 28
PPP3CB 0.031 0.008 -10000 0 -10000 0 0
PPP3CC 0.022 0.062 -10000 0 -0.51 2 2
POU2F2 0.019 0.032 -10000 0 -10000 0 0
FOXM1 transcription factor 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
NFATC3 -0.13 0.48 -9999 0 -1.2 17 17
PLK1 0.04 0.12 -9999 0 -1.3 1 1
BIRC5 -0.047 0.38 -9999 0 -1.5 10 10
HSPA1B -0.14 0.48 -9999 0 -1.1 21 21
MAP2K1 0.018 0.055 -9999 0 -10000 0 0
BRCA2 -0.16 0.52 -9999 0 -1.2 23 23
FOXM1 -0.24 0.81 -9999 0 -1.9 21 21
XRCC1 -0.13 0.49 -9999 0 -1.2 17 17
FOXM1B/p19 -0.25 0.5 -9999 0 -1.3 22 22
Cyclin D1/CDK4 -0.16 0.49 -9999 0 -1.1 23 23
CDC2 -0.15 0.52 -9999 0 -1.2 21 21
TGFA -0.16 0.48 -9999 0 -1 26 26
SKP2 -0.13 0.52 -9999 0 -1.2 20 20
CCNE1 0.018 0.065 -9999 0 -0.51 2 2
CKS1B -0.14 0.48 -9999 0 -1.1 21 21
RB1 -0.081 0.32 -9999 0 -1 11 11
FOXM1C/SP1 -0.17 0.59 -9999 0 -1.4 21 21
AURKB -0.017 0.26 -9999 0 -0.98 9 9
CENPF -0.16 0.52 -9999 0 -1.2 23 23
CDK4 0.022 0.031 -9999 0 -10000 0 0
MYC -0.13 0.44 -9999 0 -0.99 21 21
CHEK2 0.015 0.071 -9999 0 -0.56 1 1
ONECUT1 -0.16 0.49 -9999 0 -1.1 23 23
CDKN2A -0.047 0.16 -9999 0 -0.5 16 16
LAMA4 -0.14 0.5 -9999 0 -1.2 18 18
FOXM1B/HNF6 -0.22 0.62 -9999 0 -1.5 23 23
FOS -0.21 0.56 -9999 0 -1.2 30 30
SP1 0.025 0.062 -9999 0 -0.51 2 2
CDC25B -0.13 0.49 -9999 0 -1.2 17 17
response to radiation 0.003 0.032 -9999 0 -10000 0 0
CENPB -0.14 0.5 -9999 0 -1.2 18 18
CENPA -0.14 0.51 -9999 0 -1.2 18 18
NEK2 -0.17 0.54 -9999 0 -1.2 23 23
HIST1H2BA -0.14 0.5 -9999 0 -1.2 19 19
CCNA2 0.018 0.078 -9999 0 -0.52 3 3
EP300 0.003 0.12 -9999 0 -0.51 8 8
CCNB1/CDK1 -0.18 0.58 -9999 0 -1.5 18 18
CCNB2 -0.14 0.49 -9999 0 -1.2 17 17
CCNB1 -0.15 0.52 -9999 0 -1.3 18 18
ETV5 -0.11 0.59 -9999 0 -1.3 24 24
ESR1 -0.16 0.52 -9999 0 -1.2 21 21
CCND1 -0.17 0.5 -9999 0 -1.1 23 23
GSK3A 0.019 0.049 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.031 0.11 -9999 0 -0.47 4 4
CDK2 0.026 0.047 -9999 0 -0.52 1 1
G2/M transition of mitotic cell cycle 0.002 0.038 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.54 -9999 0 -1.2 25 25
GAS1 -0.22 0.6 -9999 0 -1.3 32 32
MMP2 -0.2 0.57 -9999 0 -1.2 29 29
RB1/FOXM1C -0.17 0.5 -9999 0 -1.1 24 24
CREBBP 0.031 0.007 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.032 0.004 -10000 0 -10000 0 0
PTK2 0.026 0.044 -10000 0 -0.51 1 1
CRKL -0.05 0.12 -10000 0 -0.3 25 25
GRB2/SOS1/SHC 0.059 0.02 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
IRS1/Crk -0.046 0.13 -10000 0 -0.28 32 32
IGF-1R heterotetramer/IGF1/PTP1B -0.026 0.15 -10000 0 -0.32 28 28
AKT1 0.006 0.16 0.25 2 -0.43 11 13
BAD 0.004 0.16 0.24 2 -0.42 10 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.054 0.13 -10000 0 -0.3 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.14 -10000 0 -0.3 29 29
RAF1 0.013 0.17 -10000 0 -0.41 13 13
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.013 0.14 -10000 0 -0.29 27 27
YWHAZ 0.02 0.075 -10000 0 -0.51 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.045 0.15 -10000 0 -0.3 33 33
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
RPS6KB1 0.012 0.16 0.26 3 -0.41 10 13
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.014 0.15 0.3 3 -0.35 11 14
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.033 0.12 -10000 0 -0.28 26 26
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.01 0.14 -10000 0 -0.27 25 25
IGF-1R heterotetramer -0.025 0.15 -10000 0 -0.54 11 11
IGF-1R heterotetramer/IGF1/IRS/Nck -0.028 0.14 -10000 0 -0.3 28 28
Crk/p130 Cas/Paxillin -0.015 0.14 -10000 0 -0.28 27 27
IGF1R -0.025 0.15 -10000 0 -0.54 11 11
IGF1 -0.062 0.19 -10000 0 -0.54 20 20
IRS2/Crk -0.062 0.15 -10000 0 -0.32 33 33
PI3K -0.034 0.13 -10000 0 -0.39 14 14
apoptosis -0.017 0.15 0.4 10 -0.26 1 11
HRAS/GDP 0.018 0.045 -10000 0 -0.37 2 2
PRKCD -0.06 0.15 -10000 0 -0.39 21 21
RAF1/14-3-3 E 0.017 0.17 0.28 1 -0.36 14 15
BAD/14-3-3 0.016 0.16 0.27 1 -0.42 10 11
PRKCZ 0.009 0.16 0.25 3 -0.36 14 17
Crk/p130 Cas/Paxillin/FAK1 0.013 0.14 -10000 0 -0.43 7 7
PTPN1 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.059 0.16 -10000 0 -0.37 28 28
BCAR1 0.031 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.024 0.16 -10000 0 -0.33 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.032 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.041 0.14 -10000 0 -0.3 28 28
GRB10 -0.003 0.13 -10000 0 -0.51 9 9
PTPN11 -0.056 0.13 -10000 0 -0.3 29 29
IRS1 -0.057 0.14 -10000 0 -0.3 33 33
IRS2 -0.072 0.16 -10000 0 -0.32 38 38
IGF-1R heterotetramer/IGF1 -0.055 0.18 -10000 0 -0.42 28 28
GRB2 0.032 0.005 -10000 0 -10000 0 0
PDPK1 0.017 0.17 0.26 3 -0.37 15 18
YWHAE 0.03 0.008 -10000 0 -10000 0 0
PRKD1 -0.07 0.18 0.21 2 -0.46 21 23
SHC1 0.031 0.007 -10000 0 -10000 0 0
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 -0.055 0.16 -10000 0 -0.4 18 18
CRKL -0.07 0.16 -10000 0 -0.42 20 20
HRAS -0.047 0.16 -10000 0 -0.4 17 17
mol:PIP3 -0.037 0.17 -10000 0 -0.44 13 13
SPRED1 0.024 0.063 -10000 0 -0.51 2 2
SPRED2 0.026 0.045 -10000 0 -0.51 1 1
GAB1 -0.076 0.17 -10000 0 -0.42 25 25
FOXO3 -0.067 0.17 -10000 0 -0.43 17 17
AKT1 -0.07 0.18 -10000 0 -0.44 21 21
BAD -0.067 0.17 -10000 0 -0.42 19 19
megakaryocyte differentiation -0.081 0.17 -10000 0 -0.42 23 23
GSK3B -0.044 0.18 0.37 1 -0.43 16 17
RAF1 -0.033 0.14 0.26 1 -0.33 14 15
SHC1 0.031 0.007 -10000 0 -10000 0 0
STAT3 -0.076 0.17 -10000 0 -0.43 24 24
STAT1 -0.17 0.39 -10000 0 -1 23 23
HRAS/SPRED1 -0.03 0.15 -10000 0 -0.34 16 16
cell proliferation -0.071 0.17 0.27 1 -0.42 23 24
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
TEC 0.029 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.068 0.18 -10000 0 -0.42 24 24
HRAS/SPRED2 -0.026 0.14 -10000 0 -0.33 15 15
LYN/TEC/p62DOK -0.038 0.18 -10000 0 -0.42 21 21
MAPK3 -0.022 0.1 0.23 1 -0.29 5 6
STAP1 -0.094 0.2 -10000 0 -0.47 26 26
GRAP2 0.031 0.007 -10000 0 -10000 0 0
JAK2 -0.14 0.32 -10000 0 -0.85 21 21
STAT1 (dimer) -0.17 0.38 -10000 0 -0.97 23 23
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.055 0.2 -10000 0 -0.45 24 24
actin filament polymerization -0.072 0.17 -10000 0 -0.42 24 24
LYN 0.027 0.044 -10000 0 -0.51 1 1
STAP1/STAT5A (dimer) -0.12 0.26 -10000 0 -0.62 25 25
PIK3R1 0.004 0.099 -10000 0 -0.51 5 5
CBL/CRKL/GRB2 -0.043 0.17 -10000 0 -0.4 18 18
PI3K -0.055 0.16 -10000 0 -0.46 13 13
PTEN 0.025 0.044 -10000 0 -0.51 1 1
SCF/KIT/EPO/EPOR -0.17 0.45 -10000 0 -1.3 18 18
MAPK8 -0.071 0.17 0.28 1 -0.43 23 24
STAT3 (dimer) -0.075 0.17 -10000 0 -0.42 24 24
positive regulation of transcription -0.016 0.088 0.22 1 -0.24 4 5
mol:GDP -0.047 0.16 -10000 0 -0.4 20 20
PIK3C2B -0.073 0.18 -10000 0 -0.45 22 22
CBL/CRKL -0.053 0.17 -10000 0 -0.4 19 19
FER -0.075 0.18 -10000 0 -0.44 24 24
SH2B3 -0.077 0.18 -10000 0 -0.43 24 24
PDPK1 -0.033 0.16 -10000 0 -0.41 14 14
SNAI2 -0.11 0.19 -10000 0 -0.42 33 33
positive regulation of cell proliferation -0.13 0.28 -10000 0 -0.72 23 23
KITLG -0.025 0.16 -10000 0 -0.53 13 13
cell motility -0.13 0.28 -10000 0 -0.72 23 23
PTPN6 0.03 0.045 -10000 0 -0.5 1 1
EPOR -0.035 0.18 -10000 0 -0.72 6 6
STAT5A (dimer) -0.1 0.24 -10000 0 -0.59 23 23
SOCS1 0.026 0.046 -10000 0 -0.51 1 1
cell migration 0.074 0.17 0.42 24 -10000 0 24
SOS1 0.032 0.005 -10000 0 -10000 0 0
EPO 0.019 0.027 -10000 0 -10000 0 0
VAV1 0.01 0.1 -10000 0 -0.51 6 6
GRB10 -0.089 0.19 -10000 0 -0.45 26 26
PTPN11 0.031 0.044 -10000 0 -0.51 1 1
SCF/KIT -0.076 0.18 -10000 0 -0.44 24 24
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.027 0.11 0.24 1 -0.3 7 8
CBL 0.032 0.005 -10000 0 -10000 0 0
KIT -0.18 0.45 -10000 0 -1.2 22 22
MAP2K2 -0.026 0.11 0.24 1 -0.3 7 8
SHC/Grb2/SOS1 -0.04 0.18 -10000 0 -0.42 21 21
STAT5A -0.11 0.24 -10000 0 -0.61 23 23
GRB2 0.032 0.005 -10000 0 -10000 0 0
response to radiation -0.1 0.19 -10000 0 -0.41 33 33
SHC/GRAP2 0.044 0.014 -10000 0 -10000 0 0
PTPRO -0.083 0.17 -10000 0 -0.43 23 23
SH2B2 -0.074 0.17 -10000 0 -0.42 24 24
DOK1 0.032 0.006 -10000 0 -10000 0 0
MATK -0.076 0.17 -10000 0 -0.43 24 24
CREBBP 0.011 0.062 -10000 0 -0.18 2 2
BCL2 -0.11 0.37 -10000 0 -1.2 14 14
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.03 0.011 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.083 -10000 0 -0.37 6 6
PTK2 -0.08 0.2 -10000 0 -0.43 32 32
positive regulation of JNK cascade -0.041 0.15 -10000 0 -0.32 26 26
CDC42/GDP -0.05 0.2 -10000 0 -0.43 29 29
Rac1/GDP -0.05 0.2 -10000 0 -0.43 27 27
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
CTNNB1 0.028 0.015 -10000 0 -10000 0 0
CDC42/GTP -0.043 0.18 -10000 0 -0.39 26 26
nectin-3/I-afadin -0.048 0.16 -10000 0 -0.37 29 29
RAPGEF1 -0.071 0.21 -10000 0 -0.46 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.088 0.23 -10000 0 -0.52 29 29
PDGFB-D/PDGFRB 0.03 0.011 -10000 0 -10000 0 0
TLN1 -0.028 0.074 -10000 0 -0.4 2 2
Rap1/GTP -0.052 0.15 -10000 0 -0.34 29 29
IQGAP1 0.032 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.044 -10000 0 -0.29 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.048 0.16 -10000 0 -0.37 29 29
PVR 0.024 0.062 -10000 0 -0.51 2 2
Necl-5(dimer) 0.024 0.061 -10000 0 -0.51 2 2
mol:GDP -0.08 0.24 -10000 0 -0.53 29 29
MLLT4 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
PI3K -0.014 0.12 -10000 0 -0.31 15 15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.013 0.11 -10000 0 -0.37 12 12
positive regulation of lamellipodium assembly -0.052 0.16 -10000 0 -0.35 25 25
PVRL1 -0.01 0.14 -10000 0 -0.51 12 12
PVRL3 -0.084 0.21 -10000 0 -0.51 29 29
PVRL2 0.027 0.045 -10000 0 -0.51 1 1
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
CDH1 0.005 0.11 -10000 0 -0.51 7 7
CLDN1 -0.089 0.2 -10000 0 -0.51 29 29
JAM-A/CLDN1 -0.079 0.18 -10000 0 -0.38 35 35
SRC -0.1 0.25 -10000 0 -0.58 29 29
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
nectin-1(dimer)/I-afadin/I-afadin 0.013 0.11 -10000 0 -0.37 12 12
FARP2 -0.07 0.24 -10000 0 -0.53 24 24
RAC1 0.032 0.005 -10000 0 -10000 0 0
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.03 0.15 -10000 0 -0.32 29 29
nectin-1/I-afadin 0.013 0.11 -10000 0 -0.37 12 12
nectin-2/I-afadin 0.042 0.036 -10000 0 -0.37 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.042 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.054 0.17 -10000 0 -0.34 38 38
CDC42/GTP/IQGAP1/filamentous actin 0.042 0.009 -10000 0 -10000 0 0
F11R 0.013 0.096 -10000 0 -0.51 5 5
positive regulation of filopodium formation -0.041 0.15 -10000 0 -0.32 26 26
alphaV/beta3 Integrin/Talin 0.012 0.12 0.34 2 -0.41 5 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.036 -10000 0 -0.37 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.042 0.036 -10000 0 -0.37 1 1
PIP5K1C -0.033 0.09 -10000 0 -0.51 2 2
VAV2 -0.096 0.26 -10000 0 -0.58 26 26
RAP1/GDP -0.046 0.19 -10000 0 -0.41 27 27
ITGAV 0.013 0.097 -10000 0 -0.51 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.028 0.14 -10000 0 -0.32 29 29
nectin-3(dimer)/I-afadin/I-afadin -0.048 0.16 -10000 0 -0.37 29 29
Rac1/GTP -0.061 0.2 -10000 0 -0.44 25 25
PTPRM -0.03 0.096 -10000 0 -0.22 27 27
E-cadherin/beta catenin/alpha catenin 0.038 0.12 -10000 0 -0.28 17 17
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.032 0.005 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.026 0.21 0.27 5 -0.51 21 26
FYN -0.064 0.27 0.26 4 -0.66 22 26
LAT/GRAP2/SLP76 -0.048 0.24 0.24 1 -0.58 21 22
IKBKB 0.029 0.01 -10000 0 -10000 0 0
AKT1 -0.042 0.19 0.22 4 -0.43 24 28
B2M 0.008 0.11 -10000 0 -0.52 6 6
IKBKG -0.007 0.06 0.11 3 -0.14 16 19
MAP3K8 -0.013 0.14 -10000 0 -0.51 12 12
mol:Ca2+ -0.017 0.017 -10000 0 -0.082 2 2
integrin-mediated signaling pathway 0.033 0.051 -10000 0 -0.31 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.072 0.27 0.25 4 -0.63 25 29
TRPV6 0.002 0.1 1.2 1 -10000 0 1
CD28 -0.009 0.14 -10000 0 -0.52 11 11
SHC1 -0.064 0.26 0.26 6 -0.63 22 28
receptor internalization -0.097 0.3 0.22 1 -0.69 27 28
PRF1 -0.11 0.36 -10000 0 -1.1 17 17
KRAS 0.016 0.086 -10000 0 -0.51 4 4
GRB2 0.032 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.033 0.18 0.21 4 -0.39 26 30
LAT -0.074 0.26 0.25 1 -0.63 23 24
EntrezGene:6955 0 0.005 -10000 0 -10000 0 0
CD3D -0.01 0.14 -10000 0 -0.52 11 11
CD3E 0.03 0.013 -10000 0 -10000 0 0
CD3G -0.06 0.2 -10000 0 -0.51 25 25
RASGRP2 0.002 0.025 -10000 0 -0.2 1 1
RASGRP1 -0.037 0.18 0.26 2 -0.42 21 23
HLA-A -0.001 0.006 -10000 0 -10000 0 0
RASSF5 0.027 0.045 -10000 0 -0.51 1 1
RAP1A/GTP/RAPL 0.034 0.051 -10000 0 -0.31 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.06 0.14 8 -0.11 13 21
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.034 0.085 -10000 0 -0.23 21 21
PRKCA -0.021 0.11 0.17 2 -0.27 21 23
GRAP2 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.05 0.17 -10000 0 -0.43 22 22
EntrezGene:6957 -0.001 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.073 0.24 -10000 0 -0.59 21 21
ORAI1 -0.009 0.097 -10000 0 -1 1 1
CSK -0.068 0.25 0.23 3 -0.62 23 26
B7 family/CD28 -0.079 0.31 -10000 0 -0.72 24 24
CHUK 0.028 0.044 -10000 0 -0.51 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.094 0.29 0.23 2 -0.71 24 26
PTPN6 -0.075 0.26 0.21 1 -0.62 24 25
VAV1 -0.08 0.27 0.22 3 -0.66 24 27
Monovalent TCR/CD3 -0.077 0.24 -10000 0 -0.54 27 27
CBL 0.032 0.005 -10000 0 -10000 0 0
LCK -0.068 0.28 0.25 4 -0.65 23 27
PAG1 -0.072 0.26 0.24 3 -0.63 23 26
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
TCR/CD3/MHC I/CD8/LCK -0.098 0.3 0.21 2 -0.72 24 26
CD80 0.024 0.022 -10000 0 -10000 0 0
CD86 -0.009 0.13 -10000 0 -0.52 10 10
PDK1/CARD11/BCL10/MALT1 -0.028 0.1 -10000 0 -0.28 18 18
HRAS 0.024 0.062 -10000 0 -0.51 2 2
GO:0035030 -0.083 0.23 -10000 0 -0.58 24 24
CD8A -0.001 0.006 -10000 0 -10000 0 0
CD8B 0.019 0.052 -10000 0 -0.52 1 1
PTPRC -0.025 0.16 -10000 0 -0.52 15 15
PDK1/PKC theta -0.06 0.22 0.25 1 -0.51 25 26
CSK/PAG1 -0.062 0.25 0.32 2 -0.59 23 25
SOS1 0.032 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.005 0.079 -10000 0 -0.38 6 6
GRAP2/SLP76 -0.055 0.28 0.25 2 -0.67 22 24
STIM1 -0.008 0.058 -10000 0 -0.51 2 2
RAS family/GTP 0.005 0.087 0.18 4 -0.17 18 22
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.11 0.33 0.23 1 -0.75 27 28
mol:DAG -0.058 0.14 -10000 0 -0.37 24 24
RAP1A/GDP 0.008 0.032 0.088 2 -0.1 3 5
PLCG1 0.032 0.005 -10000 0 -10000 0 0
CD247 -0.038 0.18 -10000 0 -0.51 18 18
cytotoxic T cell degranulation -0.11 0.34 -10000 0 -0.98 17 17
RAP1A/GTP 0.001 0.015 -10000 0 -0.085 3 3
mol:PI-3-4-5-P3 -0.053 0.22 0.24 4 -0.51 25 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.055 0.23 -10000 0 -0.56 22 22
NRAS 0.025 0.047 -10000 0 -0.51 1 1
ZAP70 0.03 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.058 0.23 -10000 0 -0.56 22 22
MALT1 0.03 0.012 -10000 0 -10000 0 0
TRAF6 0.021 0.075 -10000 0 -0.51 3 3
CD8 heterodimer 0.014 0.039 -10000 0 -0.38 1 1
CARD11 0.021 0.033 -10000 0 -10000 0 0
PRKCB -0.043 0.097 -10000 0 -0.25 24 24
PRKCE -0.023 0.1 -10000 0 -0.26 20 20
PRKCQ -0.071 0.25 0.24 2 -0.58 26 28
LCP2 -0.016 0.15 -10000 0 -0.51 13 13
BCL10 0.028 0.045 -10000 0 -0.51 1 1
regulation of survival gene product expression -0.032 0.16 0.21 4 -0.36 24 28
IKK complex 0.009 0.058 0.14 8 -0.11 14 22
RAS family/GDP -0.005 0.017 -10000 0 -0.059 7 7
MAP3K14 -0.026 0.14 0.18 4 -0.29 26 30
PDPK1 -0.038 0.18 0.22 4 -0.4 25 29
TCR/CD3/MHC I/CD8/Fyn -0.08 0.26 -10000 0 -0.66 22 22
EGFR-dependent Endothelin signaling events

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
HRAS 0.024 0.062 -9999 0 -0.51 2 2
EGFR -0.033 0.17 -9999 0 -0.51 17 17
EGF/EGFR -0.075 0.18 -9999 0 -0.35 40 40
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.003 0.15 -9999 0 -0.32 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.003 0.11 -9999 0 -0.51 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.032 0.15 -9999 0 -0.51 13 13
EGF/EGFR dimer/SHC -0.028 0.16 -9999 0 -0.37 23 23
mol:GDP -0.007 0.14 -9999 0 -0.32 22 22
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.045 0.18 -9999 0 -0.51 19 19
GRB2/SOS1 0.046 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.021 0.14 -9999 0 -0.31 23 23
SHC1 0.031 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.01 0.15 -9999 0 -0.32 23 23
FRAP1 -0.058 0.11 -9999 0 -0.31 22 22
EGF/EGFR dimer -0.052 0.18 -9999 0 -0.42 25 25
SOS1 0.032 0.005 -9999 0 -10000 0 0
GRB2 0.032 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.034 0.16 -9999 0 -0.4 23 23
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.006 0.16 -10000 0 -0.41 13 13
TBX21 -0.2 0.56 -10000 0 -1.4 25 25
B2M 0.009 0.1 -10000 0 -0.51 6 6
TYK2 0.023 0.036 -10000 0 -10000 0 0
IL12RB1 0.024 0.034 -10000 0 -10000 0 0
GADD45B -0.12 0.42 -10000 0 -1 22 22
IL12RB2 -0.054 0.18 -10000 0 -0.52 19 19
GADD45G -0.12 0.42 -10000 0 -1.1 19 19
natural killer cell activation 0.002 0.019 -10000 0 -0.04 15 15
RELB 0.02 0.076 -10000 0 -0.51 3 3
RELA 0.033 0 -10000 0 -10000 0 0
IL18 -0.015 0.15 -10000 0 -0.51 13 13
IL2RA -0.008 0.14 -10000 0 -0.51 11 11
IFNG -0.1 0.21 -10000 0 -0.51 32 32
STAT3 (dimer) -0.094 0.36 -10000 0 -0.88 22 22
HLA-DRB5 -0.002 0.007 -10000 0 -0.022 13 13
FASLG -0.17 0.53 -10000 0 -1.4 20 20
NF kappa B2 p52/RelB -0.13 0.46 -10000 0 -1.1 23 23
CD4 0.024 0.02 -10000 0 -10000 0 0
SOCS1 0.026 0.046 -10000 0 -0.51 1 1
EntrezGene:6955 -0.002 0.01 -10000 0 -0.028 18 18
CD3D -0.015 0.14 -10000 0 -0.51 11 11
CD3E 0.026 0.021 -10000 0 -10000 0 0
CD3G -0.064 0.2 -10000 0 -0.51 25 25
IL12Rbeta2/JAK2 -0.028 0.15 -10000 0 -0.4 19 19
CCL3 -0.14 0.45 -10000 0 -1.2 19 19
CCL4 -0.14 0.46 -10000 0 -1.2 19 19
HLA-A 0 0.007 -10000 0 -0.035 5 5
IL18/IL18R -0.029 0.21 -10000 0 -0.39 33 33
NOS2 -0.13 0.44 -10000 0 -1 25 25
IL12/IL12R/TYK2/JAK2/SPHK2 -0.003 0.15 -10000 0 -0.4 11 11
IL1R1 -0.16 0.49 -10000 0 -1.3 22 22
IL4 0.015 0.033 -10000 0 -10000 0 0
JAK2 0.018 0.056 -10000 0 -0.54 1 1
EntrezGene:6957 -0.002 0.01 -10000 0 -0.026 18 18
TCR/CD3/MHC I/CD8 -0.1 0.32 -10000 0 -0.79 21 21
RAB7A -0.066 0.35 -10000 0 -0.86 19 19
lysosomal transport -0.057 0.33 -10000 0 -0.8 19 19
FOS -0.19 0.46 -10000 0 -1 31 31
STAT4 (dimer) -0.11 0.42 -10000 0 -1 22 22
STAT5A (dimer) -0.18 0.46 -10000 0 -1.1 25 25
GZMA -0.13 0.43 -10000 0 -1.1 22 22
GZMB -0.14 0.47 -10000 0 -1.3 19 19
HLX 0.031 0.01 -10000 0 -10000 0 0
LCK -0.17 0.52 -10000 0 -1.2 24 24
TCR/CD3/MHC II/CD4 -0.075 0.2 -10000 0 -0.4 33 33
IL2/IL2R 0.027 0.13 -10000 0 -0.35 13 13
MAPK14 -0.12 0.43 -10000 0 -1 23 23
CCR5 -0.17 0.5 -10000 0 -1.2 24 24
IL1B -0.08 0.21 -10000 0 -0.52 28 28
STAT6 -0.02 0.16 -10000 0 -0.4 11 11
STAT4 0.012 0.097 -10000 0 -0.51 5 5
STAT3 0.032 0.005 -10000 0 -10000 0 0
STAT1 0.009 0.1 -10000 0 -0.51 6 6
NFKB1 0.031 0.007 -10000 0 -10000 0 0
NFKB2 0.031 0.01 -10000 0 -10000 0 0
IL12B 0.014 0.081 -10000 0 -0.51 3 3
CD8A 0 0.007 -10000 0 -0.035 5 5
CD8B 0.02 0.052 -10000 0 -0.51 1 1
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.006 0.16 0.41 13 -10000 0 13
IL2RB 0.015 0.087 -10000 0 -0.51 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.09 0.37 -10000 0 -0.9 22 22
IL2RG 0.02 0.065 -10000 0 -0.51 2 2
IL12 0.011 0.077 -10000 0 -0.37 4 4
STAT5A 0.031 0.01 -10000 0 -10000 0 0
CD247 -0.042 0.18 -10000 0 -0.52 18 18
IL2 0.031 0.007 -10000 0 -10000 0 0
SPHK2 0.032 0.009 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.069 -10000 0 -0.52 2 2
IL12/IL12R/TYK2/JAK2 -0.19 0.61 -10000 0 -1.5 22 22
MAP2K3 -0.13 0.44 -10000 0 -1.1 23 23
RIPK2 0.026 0.046 -10000 0 -0.51 1 1
MAP2K6 -0.13 0.44 -10000 0 -1.1 21 21
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.008 -10000 0 -0.026 13 13
IL18RAP -0.044 0.18 -10000 0 -0.52 20 20
IL12Rbeta1/TYK2 0.036 0.047 -10000 0 -10000 0 0
EOMES -0.075 0.29 -10000 0 -0.99 12 12
STAT1 (dimer) -0.16 0.39 -10000 0 -0.98 24 24
T cell proliferation -0.058 0.29 -10000 0 -0.73 19 19
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.12 -10000 0 -0.51 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.085 0.33 -10000 0 -0.76 24 24
ATF2 -0.1 0.38 -10000 0 -0.93 22 22
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.024 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.044 -10000 0 -0.51 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.086 0.21 -10000 0 -0.47 27 27
IRAK/TOLLIP 0.037 0.007 -10000 0 -10000 0 0
IKBKB 0.029 0.01 -10000 0 -10000 0 0
IKBKG 0.032 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.14 0.22 -10000 0 -0.44 51 51
IL1A -0.15 0.24 -10000 0 -0.51 45 45
IL1B -0.073 0.18 -10000 0 -0.42 30 30
IRAK/TRAF6/p62/Atypical PKCs 0.016 0.069 -10000 0 -0.26 7 7
IL1R2 -0.044 0.17 -10000 0 -0.51 18 18
IL1R1 -0.005 0.13 -10000 0 -0.51 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.037 0.17 0.26 3 -0.46 16 19
TOLLIP 0.032 0.005 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.01 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.072 -10000 0 -0.35 1 1
JUN -0.031 0.075 0.16 2 -0.25 14 16
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.063 0.21 -10000 0 -0.5 23 23
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.099 0.2 -10000 0 -0.46 31 31
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.095 0.2 -10000 0 -0.43 33 33
IL1 beta fragment/IL1R1/IL1RAP -0.078 0.21 -10000 0 -0.49 25 25
NFKB1 0.031 0.007 -10000 0 -10000 0 0
MAPK8 -0.018 0.056 0.17 2 -0.24 8 10
IRAK1 0.018 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.048 0.18 -10000 0 -0.42 28 28
IRAK4 0.021 0.075 -10000 0 -0.51 3 3
PRKCI -0.004 0.1 -10000 0 -0.51 6 6
TRAF6 0.021 0.075 -10000 0 -0.51 3 3
PI3K 0.004 0.075 -10000 0 -0.37 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.076 0.23 -10000 0 -0.47 30 30
CHUK 0.028 0.044 -10000 0 -0.51 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.078 0.21 -10000 0 -0.49 25 25
IL1 beta/IL1R2 -0.087 0.21 -10000 0 -0.41 39 39
IRAK/TRAF6/TAK1/TAB1/TAB2 0.04 0.043 -10000 0 -0.25 3 3
NF kappa B1 p50/RelA -0.06 0.19 -10000 0 -0.57 15 15
IRAK3 -0.028 0.16 -10000 0 -0.51 15 15
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.07 0.21 -10000 0 -0.47 26 26
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.1 0.22 -10000 0 -0.46 35 35
IL1 alpha/IL1R1/IL1RAP -0.11 0.22 -10000 0 -0.5 31 31
RELA 0.033 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.019 -10000 0 -10000 0 0
MYD88 0.03 0.009 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.048 0.047 -10000 0 -0.27 3 3
IL1RAP -0.05 0.17 -10000 0 -0.51 18 18
UBE2N 0.033 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.071 0.18 -10000 0 -0.41 27 27
CASP1 0.004 0.12 -10000 0 -0.51 8 8
IL1RN/IL1R2 -0.073 0.2 -10000 0 -0.44 32 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.069 0.21 -10000 0 -0.48 24 24
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.086 0.22 -10000 0 -0.5 27 27
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
IL1RN -0.059 0.19 -10000 0 -0.51 23 23
TRAF6/TAK1/TAB1/TAB2 0.04 0.043 -10000 0 -0.26 3 3
MAP2K6 0.004 0.063 -10000 0 -0.25 8 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.023 0.085 -10000 0 -0.35 8 8
NFATC2 -0.005 0.038 -10000 0 -10000 0 0
NFATC3 -0.004 0.037 -10000 0 -10000 0 0
CD40LG -0.14 0.26 0.34 1 -0.56 34 35
PTGS2 -0.18 0.3 0.34 1 -0.63 39 40
JUNB 0.009 0.098 -10000 0 -0.51 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.03 -10000 0 -10000 0 0
CaM/Ca2+ 0.004 0.03 -10000 0 -10000 0 0
CALM1 0.018 0.026 -10000 0 -10000 0 0
JUN -0.008 0.12 -10000 0 -0.52 7 7
mol:Ca2+ -0.007 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.013 -10000 0 -10000 0 0
FOSL1 0.025 0.027 -10000 0 -10000 0 0
CREM 0.031 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.067 0.16 -10000 0 -0.35 25 25
FOS -0.041 0.16 -10000 0 -0.52 14 14
IFNG -0.2 0.31 -10000 0 -0.63 44 44
AP-1/NFAT1-c-4 -0.16 0.34 -10000 0 -0.69 33 33
FASLG -0.16 0.3 0.34 1 -0.64 34 35
NFAT1-c-4/ICER1 -0.029 0.11 -10000 0 -0.31 10 10
IL2RA -0.16 0.29 0.34 1 -0.6 35 36
FKBP12/FK506 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.16 0.29 0.34 1 -0.6 36 37
JunB/Fra1/NFAT1-c-4 -0.021 0.13 -10000 0 -0.36 9 9
IL4 -0.14 0.26 0.34 1 -0.56 33 34
IL2 -0.026 0.23 -10000 0 -0.99 8 8
IL3 -0.012 0.18 -10000 0 -0.74 8 8
FKBP1A 0.032 0.006 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.037 0.01 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.12 -10000 0 -0.35 14 14
fibroblast growth factor receptor signaling pathway -0.003 0.12 -10000 0 -0.35 14 14
LAMA1 0.023 0.03 -10000 0 -10000 0 0
PRNP 0.017 0.087 -10000 0 -0.51 4 4
GPC1/SLIT2 -0.051 0.18 -10000 0 -0.39 30 30
SMAD2 -0.017 0.095 -10000 0 -0.29 16 16
GPC1/PrPc/Cu2+ -0.007 0.12 -10000 0 -0.33 18 18
GPC1/Laminin alpha1 -0.007 0.12 -10000 0 -0.37 15 15
TDGF1 0.028 0.017 -10000 0 -10000 0 0
CRIPTO/GPC1 -0.003 0.12 -10000 0 -0.37 15 15
APP/GPC1 -0.018 0.15 -10000 0 -0.39 20 20
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.021 0.1 -10000 0 -0.32 16 16
FLT1 0.003 0.12 -10000 0 -0.51 8 8
GPC1/TGFB/TGFBR1/TGFBR2 0.013 0.12 -10000 0 -0.32 16 16
SERPINC1 0.029 0.017 -10000 0 -10000 0 0
FYN -0.022 0.11 -10000 0 -0.32 17 17
FGR -0.018 0.1 -10000 0 -0.32 15 15
positive regulation of MAPKKK cascade -0.042 0.16 0.33 1 -0.37 22 23
SLIT2 -0.037 0.17 -10000 0 -0.51 18 18
GPC1/NRG -0.027 0.17 -10000 0 -0.48 17 17
NRG1 -0.008 0.13 -10000 0 -0.51 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.14 -10000 0 -0.33 23 23
LYN -0.016 0.097 -10000 0 -0.32 14 14
mol:Spermine -0.031 0.11 -10000 0 -0.37 15 15
cell growth -0.003 0.12 -10000 0 -0.35 14 14
BMP signaling pathway 0.026 0.16 0.51 15 -10000 0 15
SRC -0.018 0.1 -10000 0 -0.32 15 15
TGFBR1 0.032 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.001 0.12 -10000 0 -0.51 7 7
GPC1 -0.027 0.16 -10000 0 -0.51 15 15
TGFBR1 (dimer) 0.032 0.004 -10000 0 -10000 0 0
VEGFA 0.025 0.061 -10000 0 -0.51 2 2
BLK -0.03 0.11 -10000 0 -0.32 18 18
HCK -0.033 0.12 -10000 0 -0.32 22 22
FGF2 0.016 0.077 -10000 0 -0.51 3 3
FGFR1 0.017 0.063 -10000 0 -0.51 2 2
VEGFR1 homodimer 0.003 0.12 -10000 0 -0.51 8 8
TGFBR2 0.025 0.046 -10000 0 -0.51 1 1
cell death -0.018 0.15 -10000 0 -0.38 20 20
ATIII/GPC1 0 0.12 -10000 0 -0.37 14 14
PLA2G2A/GPC1 -0.022 0.15 -10000 0 -0.4 20 20
LCK -0.039 0.12 -10000 0 -0.32 25 25
neuron differentiation -0.027 0.17 -10000 0 -0.48 17 17
PrPc/Cu2+ 0.013 0.063 -10000 0 -0.37 4 4
APP 0.009 0.1 -10000 0 -0.51 6 6
TGFBR2 (dimer) 0.025 0.046 -10000 0 -0.51 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.007 0.066 0.21 5 -0.19 11 16
RFC1 -0.002 0.074 0.21 7 -0.23 8 15
PRKDC 0.003 0.087 0.22 12 -0.3 3 15
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP7 -0.039 0.18 -10000 0 -0.74 8 8
FASLG/FAS/FADD/FAF1 -0.027 0.13 0.22 7 -0.32 19 26
MAP2K4 -0.047 0.22 0.27 1 -0.59 14 15
mol:ceramide -0.062 0.19 -10000 0 -0.51 17 17
GSN -0.024 0.099 0.21 5 -0.3 12 17
FASLG/FAS/FADD/FAF1/Caspase 8 -0.042 0.17 0.26 1 -0.45 17 18
FAS -0.024 0.15 -10000 0 -0.51 13 13
BID -0.028 0.056 -10000 0 -0.33 5 5
MAP3K1 -0.005 0.2 0.26 3 -0.65 9 12
MAP3K7 0.031 0.01 -10000 0 -10000 0 0
RB1 -0.006 0.072 0.21 6 -0.24 5 11
CFLAR 0.012 0.1 -10000 0 -0.5 6 6
HGF/MET 0.012 0.12 -10000 0 -0.34 16 16
ARHGDIB -0.009 0.1 0.24 10 -0.29 8 18
FADD 0.024 0.018 -10000 0 -10000 0 0
actin filament polymerization 0.023 0.099 0.3 11 -0.21 5 16
NFKB1 -0.033 0.15 -10000 0 -0.7 5 5
MAPK8 -0.064 0.24 0.27 1 -0.53 23 24
DFFA -0.006 0.066 0.21 5 -0.2 4 9
DNA fragmentation during apoptosis -0.007 0.065 0.21 5 -0.2 4 9
FAS/FADD/MET 0.011 0.11 -10000 0 -0.34 11 11
CFLAR/RIP1 0.034 0.073 -10000 0 -0.35 5 5
FAIM3 0.032 0.01 -10000 0 -10000 0 0
FAF1 0.026 0.018 -10000 0 -10000 0 0
PARP1 -0.006 0.07 0.21 6 -0.2 4 10
DFFB -0.007 0.066 0.21 5 -0.19 11 16
CHUK -0.037 0.14 -10000 0 -0.58 7 7
FASLG -0.036 0.16 -10000 0 -0.51 15 15
FAS/FADD -0.003 0.11 -10000 0 -0.37 11 11
HGF 0.028 0.02 -10000 0 -10000 0 0
LMNA -0.003 0.067 0.2 6 -0.26 2 8
CASP6 -0.002 0.058 0.21 5 -0.21 3 8
CASP10 0.015 0.077 -10000 0 -0.51 3 3
CASP3 0.004 0.065 0.26 5 -0.22 5 10
PTPN13 -0.021 0.16 -10000 0 -0.51 14 14
CASP8 -0.029 0.051 -10000 0 -0.38 3 3
IL6 -0.15 0.42 -10000 0 -1.2 19 19
MET 0.02 0.076 -10000 0 -0.51 3 3
ICAD/CAD -0.008 0.06 0.18 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.063 0.2 -10000 0 -0.52 17 17
activation of caspase activity by cytochrome c -0.028 0.056 -10000 0 -0.33 5 5
PAK2 0.08 0.13 0.23 59 -0.24 3 62
BCL2 -0.006 0.12 -10000 0 -0.51 7 7
LPA receptor mediated 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
GNB1/GNG2 0.013 0.086 -10000 0 -0.23 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.088 -10000 0 -0.32 5 5
AP1 -0.053 0.12 -10000 0 -0.26 33 33
mol:PIP3 -0.052 0.12 -10000 0 -0.28 27 27
AKT1 -0.009 0.12 0.26 1 -0.36 7 8
PTK2B -0.034 0.094 -10000 0 -0.22 28 28
RHOA -0.028 0.094 -10000 0 -0.31 11 11
PIK3CB 0.014 0.076 -10000 0 -0.51 3 3
mol:Ca2+ -0.023 0.07 -10000 0 -0.26 9 9
MAGI3 0.022 0.063 -10000 0 -0.51 2 2
RELA 0.033 0 -10000 0 -10000 0 0
apoptosis -0.012 0.074 -10000 0 -0.23 16 16
HRAS/GDP 0.018 0.045 -10000 0 -0.37 2 2
positive regulation of microtubule depolymerization -0.009 0.096 0.18 14 -0.24 8 22
NF kappa B1 p50/RelA -0.039 0.095 -10000 0 -0.29 13 13
endothelial cell migration -0.051 0.19 -10000 0 -0.59 17 17
ADCY4 -0.026 0.1 -10000 0 -0.29 15 15
ADCY5 -0.023 0.09 -10000 0 -0.26 12 12
ADCY6 -0.022 0.094 -10000 0 -0.27 12 12
ADCY7 -0.025 0.1 -10000 0 -0.3 13 13
ADCY1 -0.02 0.092 -10000 0 -0.27 12 12
ADCY2 -0.029 0.096 -10000 0 -0.3 11 11
ADCY3 -0.028 0.1 -10000 0 -0.26 17 17
ADCY8 -0.029 0.094 -10000 0 -0.26 15 15
ADCY9 -0.021 0.092 -10000 0 -0.26 13 13
GSK3B -0.009 0.1 0.19 16 -0.2 22 38
arachidonic acid secretion -0.031 0.1 -10000 0 -0.28 16 16
GNG2 0.032 0.005 -10000 0 -10000 0 0
TRIP6 0.002 0.078 -10000 0 -0.37 6 6
GNAO1 -0.011 0.084 -10000 0 -0.25 16 16
HRAS 0.024 0.062 -10000 0 -0.51 2 2
NFKBIA -0.023 0.083 -10000 0 -0.3 8 8
GAB1 0.019 0.076 -10000 0 -0.51 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.024 0.16 -10000 0 -0.84 5 5
JUN 0.002 0.11 -10000 0 -0.51 7 7
LPA/LPA2/NHERF2 0.003 0.051 -10000 0 -0.12 15 15
TIAM1 0.004 0.18 -10000 0 -0.98 5 5
PIK3R1 0.004 0.099 -10000 0 -0.51 5 5
mol:IP3 -0.024 0.071 -10000 0 -0.27 9 9
PLCB3 -0.001 0.06 -10000 0 -0.3 4 4
FOS -0.031 0.16 -10000 0 -0.51 14 14
positive regulation of mitosis -0.031 0.1 -10000 0 -0.28 16 16
LPA/LPA1-2-3 -0.022 0.071 -10000 0 -0.22 17 17
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.031 0.007 -10000 0 -10000 0 0
stress fiber formation -0.011 0.079 -10000 0 -0.26 7 7
GNAZ -0.023 0.1 -10000 0 -0.28 20 20
EGFR/PI3K-beta/Gab1 -0.049 0.12 -10000 0 -0.29 27 27
positive regulation of dendritic cell cytokine production -0.022 0.07 -10000 0 -0.22 17 17
LPA/LPA2/MAGI-3 0.002 0.051 -10000 0 -0.15 8 8
ARHGEF1 -0.006 0.081 0.19 3 -0.22 17 20
GNAI2 -0.013 0.082 -10000 0 -0.25 16 16
GNAI3 -0.012 0.084 -10000 0 -0.24 17 17
GNAI1 -0.029 0.11 -10000 0 -0.29 23 23
LPA/LPA3 -0.011 0.035 -10000 0 -0.11 17 17
LPA/LPA2 -0.011 0.035 -10000 0 -0.11 17 17
LPA/LPA1 -0.027 0.094 -10000 0 -0.29 17 17
HB-EGF/EGFR -0.069 0.18 -10000 0 -0.39 34 34
HBEGF -0.05 0.14 -10000 0 -0.37 25 25
mol:DAG -0.024 0.071 -10000 0 -0.27 9 9
cAMP biosynthetic process -0.027 0.11 0.21 1 -0.28 16 17
NFKB1 0.031 0.007 -10000 0 -10000 0 0
SRC 0.031 0.011 -10000 0 -10000 0 0
GNB1 0.032 0.005 -10000 0 -10000 0 0
LYN -0.022 0.081 -10000 0 -0.29 8 8
GNAQ -0.009 0.028 -10000 0 -0.086 17 17
LPAR2 -0.001 0.001 -10000 0 -10000 0 0
LPAR3 0 0.001 -10000 0 -10000 0 0
LPAR1 -0.017 0.054 -10000 0 -0.17 17 17
IL8 -0.2 0.23 -10000 0 -0.48 57 57
PTK2 -0.007 0.073 -10000 0 -0.21 17 17
Rac1/GDP 0.024 0.003 -10000 0 -10000 0 0
CASP3 -0.012 0.075 -10000 0 -0.23 16 16
EGFR -0.033 0.17 -10000 0 -0.51 17 17
PLCG1 -0.013 0.059 -10000 0 -0.16 17 17
PLD2 -0.01 0.079 -10000 0 -0.21 19 19
G12/G13 0.01 0.089 -10000 0 -0.23 17 17
PI3K-beta -0.035 0.1 -10000 0 -0.36 8 8
cell migration 0.012 0.066 -10000 0 -0.25 5 5
SLC9A3R2 0.021 0.064 -10000 0 -0.51 2 2
PXN -0.011 0.08 -10000 0 -0.27 7 7
HRAS/GTP -0.032 0.1 -10000 0 -0.28 16 16
RAC1 0.032 0.005 -10000 0 -10000 0 0
MMP9 -0.015 0.15 -10000 0 -0.51 13 13
PRKCE 0.03 0.009 -10000 0 -10000 0 0
PRKCD -0.027 0.076 -10000 0 -0.34 6 6
Gi(beta/gamma) -0.025 0.11 -10000 0 -0.28 16 16
mol:LPA -0.017 0.054 -10000 0 -0.17 17 17
TRIP6/p130 Cas/FAK1/Paxillin 0.002 0.091 -10000 0 -0.28 7 7
MAPKKK cascade -0.031 0.1 -10000 0 -0.28 16 16
contractile ring contraction involved in cytokinesis -0.029 0.095 -10000 0 -0.3 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.005 0.052 -10000 0 -0.17 8 8
GNA15 -0.023 0.091 -10000 0 -0.3 13 13
GNA12 0.031 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.044 -10000 0 -0.51 1 1
MAPT -0.01 0.097 0.18 14 -0.24 8 22
GNA11 -0.002 0.048 -10000 0 -0.32 2 2
Rac1/GTP 0.024 0.17 -10000 0 -0.89 5 5
MMP2 -0.052 0.19 -10000 0 -0.59 17 17
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.062 0.2 -10000 0 -0.36 43 43
SMAD6-7/SMURF1 0.048 0.064 -10000 0 -0.32 4 4
NOG 0.031 0.013 -10000 0 -10000 0 0
SMAD9 -0.035 0.18 -10000 0 -0.63 10 10
SMAD4 0.021 0.075 -10000 0 -0.51 3 3
SMAD5 -0.046 0.15 -10000 0 -0.44 12 12
BMP7/USAG1 -0.16 0.24 -10000 0 -0.46 55 55
SMAD5/SKI -0.038 0.16 0.28 1 -0.42 12 13
SMAD1 0.01 0.095 -10000 0 -0.44 5 5
BMP2 -0.062 0.19 -10000 0 -0.51 24 24
SMAD1/SMAD1/SMAD4 0.014 0.11 -10000 0 -0.44 4 4
BMPR1A 0.024 0.062 -10000 0 -0.51 2 2
BMPR1B 0.026 0.024 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.022 0.11 -10000 0 -0.34 10 10
AHSG 0.017 0.018 -10000 0 -10000 0 0
CER1 0.03 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 -0.018 0.14 -10000 0 -0.33 24 24
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.066 0.17 -10000 0 -0.44 17 17
BMP2-4 (homodimer) -0.037 0.16 -10000 0 -0.39 25 25
RGMB 0.03 0.008 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.038 0.098 -10000 0 -0.32 8 8
RGMA -0.062 0.2 -10000 0 -0.51 25 25
SMURF1 0.021 0.075 -10000 0 -0.51 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.061 0.16 -10000 0 -0.42 17 17
BMP2-4/USAG1 -0.13 0.21 -10000 0 -0.38 57 57
SMAD6/SMURF1/SMAD5 -0.04 0.16 0.28 1 -0.41 13 14
SOSTDC1 -0.15 0.24 -10000 0 -0.51 46 46
BMP7/BMPR2/BMPR1A-1B -0.015 0.15 -10000 0 -0.3 32 32
SKI 0.032 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.005 0.099 -10000 0 -0.51 5 5
HFE2 0.022 0.062 -10000 0 -0.51 2 2
ZFYVE16 0.03 0.009 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
BMP2-4/CHRD -0.022 0.11 -10000 0 -0.33 14 14
SMAD5/SMAD5/SMAD4 -0.041 0.16 0.28 1 -0.42 14 15
MAPK1 0.026 0.044 -10000 0 -0.51 1 1
TAK1/TAB family -0.041 0.15 -10000 0 -0.39 15 15
BMP7 (homodimer) -0.077 0.21 -10000 0 -0.51 29 29
NUP214 0.032 0.003 -10000 0 -10000 0 0
BMP6/FETUA 0.009 0.069 -10000 0 -0.37 4 4
SMAD1/SKI 0.022 0.11 -10000 0 -0.44 6 6
SMAD6 0.032 0.009 -10000 0 -10000 0 0
CTDSP2 0.032 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA -0.02 0.11 -10000 0 -0.33 14 14
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.037 0.17 -10000 0 -0.51 18 18
BMPR2 (homodimer) 0.024 0.062 -10000 0 -0.51 2 2
GADD34/PP1CA 0.054 0.047 -10000 0 -0.31 2 2
BMPR1A-1B (homodimer) 0.034 0.054 -10000 0 -0.37 2 2
CHRDL1 0.025 0.048 -10000 0 -0.51 1 1
ENDOFIN/SMAD1 0.022 0.11 -10000 0 -0.44 6 6
SMAD6-7/SMURF1/SMAD1 0.037 0.12 -10000 0 -0.47 3 3
SMAD6/SMURF1 0.021 0.075 -10000 0 -0.51 3 3
BAMBI -0.007 0.13 -10000 0 -0.51 9 9
SMURF2 0.024 0.062 -10000 0 -0.51 2 2
BMP2-4/CHRDL1 -0.017 0.15 -10000 0 -0.34 23 23
BMP2-4/GREM1 -0.056 0.18 -10000 0 -0.38 35 35
SMAD7 0.026 0.045 -10000 0 -0.51 1 1
SMAD8A/SMAD8A/SMAD4 -0.032 0.18 -10000 0 -0.61 10 10
SMAD1/SMAD6 0.015 0.12 -10000 0 -0.44 6 6
TAK1/SMAD6 0.037 0.059 -10000 0 -0.37 3 3
BMP7 -0.077 0.21 -10000 0 -0.51 29 29
BMP6 0.005 0.099 -10000 0 -0.51 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.061 0.16 -10000 0 -0.43 16 16
PPM1A 0.032 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.019 0.12 -10000 0 -0.49 6 6
SMAD7/SMURF1 0.032 0.068 -10000 0 -0.37 4 4
CTDSPL 0.026 0.045 -10000 0 -0.51 1 1
PPP1CA 0.032 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.032 0.005 -10000 0 -10000 0 0
PPP1R15A 0.024 0.062 -10000 0 -0.51 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.12 0.23 -10000 0 -0.52 30 30
CHRD 0.016 0.018 -10000 0 -10000 0 0
BMPR2 0.024 0.062 -10000 0 -0.51 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.076 0.17 -10000 0 -0.48 17 17
BMP4 0.018 0.066 -10000 0 -0.51 2 2
FST -0.067 0.2 -10000 0 -0.51 26 26
BMP2-4/NOG -0.016 0.14 -10000 0 -0.33 24 24
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.009 0.16 -10000 0 -0.3 31 31
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.035 0.14 -10000 0 -0.28 35 35
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.013 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.038 0.18 0.3 1 -0.46 14 15
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.1 -10000 0 -0.33 9 9
antigen processing and presentation of peptide antigen via MHC class I -0.026 0.093 -10000 0 -0.3 10 10
CaM/Ca2+ -0.029 0.14 -10000 0 -0.26 33 33
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
STAT1 (dimer)/SHP2 -0.054 0.16 -10000 0 -0.32 32 32
AKT1 0.01 0.14 0.33 3 -0.38 5 8
MAP2K1 -0.061 0.13 0.29 1 -0.34 11 12
MAP3K11 -0.054 0.13 0.29 1 -0.27 34 35
IFNGR1 -0.008 0.12 -10000 0 -0.51 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.01 0.12 -10000 0 -0.49 5 5
Rap1/GTP -0.041 0.099 -10000 0 -0.36 4 4
CRKL/C3G 0.042 0.017 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.027 0.15 -10000 0 -0.28 34 34
CEBPB -0.044 0.17 0.31 1 -0.5 11 12
STAT3 0.032 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.035 0.2 -10000 0 -0.79 5 5
STAT1 -0.062 0.15 0.29 1 -0.32 32 33
CALM1 0.031 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.21 -10000 0 -0.51 32 32
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
STAT1 (dimer)/PIAS1 -0.048 0.16 0.29 1 -0.31 29 30
CEBPB/PTGES2/Cbp/p300 -0.018 0.14 -10000 0 -0.37 11 11
mol:Ca2+ -0.036 0.14 -10000 0 -0.27 35 35
MAPK3 -0.043 0.15 -10000 0 -0.59 3 3
STAT1 (dimer) -0.025 0.14 -10000 0 -0.45 9 9
MAPK1 -0.064 0.19 -10000 0 -0.65 9 9
JAK2 0.009 0.052 -10000 0 -0.49 1 1
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
JAK1 0.013 0.055 -10000 0 -0.54 1 1
CAMK2D 0.023 0.062 -10000 0 -0.51 2 2
DAPK1 -0.027 0.14 -10000 0 -0.57 5 5
SMAD7 0.014 0.073 0.23 1 -0.24 3 4
CBL/CRKL/C3G -0.021 0.12 0.29 1 -0.37 4 5
PI3K -0.028 0.11 -10000 0 -0.28 16 16
IFNG -0.1 0.22 -10000 0 -0.51 32 32
apoptosis -0.015 0.12 -10000 0 -0.46 4 4
CAMK2G 0.031 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.032 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.007 -10000 0 -10000 0 0
CAMK2B 0.02 0.052 -10000 0 -0.51 1 1
FRAP1 0.003 0.14 0.32 3 -0.35 5 8
PRKCD 0.013 0.14 0.34 3 -0.32 6 9
RAP1B 0.031 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.026 0.093 -10000 0 -0.3 10 10
PTPN2 0.032 0.005 -10000 0 -10000 0 0
EP300 0.003 0.12 -10000 0 -0.51 8 8
IRF1 -0.062 0.15 0.26 1 -0.49 11 12
STAT1 (dimer)/PIASy -0.051 0.15 0.29 1 -0.47 10 11
SOCS1 0.001 0.19 -10000 0 -1.2 4 4
mol:GDP -0.025 0.12 0.27 1 -0.36 4 5
CASP1 0.008 0.093 0.23 1 -0.28 9 10
PTGES2 0.032 0.003 -10000 0 -10000 0 0
IRF9 -0.001 0.067 0.17 1 -0.25 2 3
mol:PI-3-4-5-P3 -0.032 0.1 -10000 0 -0.27 16 16
RAP1/GDP -0.019 0.11 -10000 0 -0.41 3 3
CBL -0.054 0.13 0.28 1 -0.26 34 35
MAP3K1 -0.06 0.14 0.29 1 -0.28 37 38
PIAS1 0.032 0.003 -10000 0 -10000 0 0
PIAS4 0.032 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.026 0.093 -10000 0 -0.3 10 10
PTPN11 -0.053 0.13 0.3 1 -0.27 35 36
CREBBP 0.031 0.007 -10000 0 -10000 0 0
RAPGEF1 0.032 0.003 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.064 -10000 0 -0.39 3 3
PDGFRB 0.029 0.011 -10000 0 -10000 0 0
SPHK1 -0.056 0.22 -10000 0 -0.88 10 10
mol:S1P -0.074 0.21 -10000 0 -0.65 15 15
S1P1/S1P/Gi -0.096 0.21 -10000 0 -0.46 29 29
GNAO1 0.023 0.021 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.081 0.19 -10000 0 -0.44 25 25
PLCG1 -0.095 0.2 -10000 0 -0.44 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.011 -10000 0 -10000 0 0
GNAI2 0.02 0.024 -10000 0 -10000 0 0
GNAI3 0.024 0.018 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.52 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.009 0.05 -10000 0 -0.34 3 3
S1P1/S1P -0.072 0.17 -10000 0 -0.5 17 17
negative regulation of cAMP metabolic process -0.093 0.2 -10000 0 -0.44 29 29
MAPK3 -0.13 0.26 -10000 0 -0.64 27 27
calcium-dependent phospholipase C activity -0.002 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
KDR 0.02 0.064 -10000 0 -0.52 2 2
PLCB2 -0.055 0.16 0.2 1 -0.44 17 18
RAC1 0.032 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.057 0.14 -10000 0 -0.41 17 17
receptor internalization -0.067 0.16 -10000 0 -0.43 19 19
PTGS2 -0.19 0.39 -10000 0 -1 26 26
Rac1/GTP -0.057 0.15 -10000 0 -0.41 17 17
RHOA 0.03 0.009 -10000 0 -10000 0 0
VEGFA 0.022 0.063 -10000 0 -0.52 2 2
negative regulation of T cell proliferation -0.093 0.2 -10000 0 -0.44 29 29
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.003 0.11 -10000 0 -0.52 7 7
MAPK1 -0.12 0.25 -10000 0 -0.62 26 26
S1P1/S1P/PDGFB-D/PDGFRB -0.063 0.18 -10000 0 -0.48 17 17
ABCC1 -0.026 0.15 -10000 0 -0.51 12 12
TCGA08_p53

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
CDKN2A -0.039 0.11 -10000 0 -0.37 16 16
TP53 -0.026 0.085 0.19 1 -0.34 8 9
Senescence -0.033 0.091 0.19 1 -0.28 14 15
Apoptosis -0.033 0.091 0.19 1 -0.28 14 15
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.11 0.28 18 -0.37 1 19
MDM4 0.032 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.015 0.11 -10000 0 -0.29 18 18
epithelial cell differentiation 0.034 0.092 -10000 0 -0.27 12 12
CYFIP2 0.025 0.046 -10000 0 -0.51 1 1
ENAH -0.014 0.11 0.28 2 -0.33 6 8
EGFR -0.033 0.17 -10000 0 -0.51 17 17
EPHA2 -0.015 0.14 -10000 0 -0.51 12 12
MYO6 -0.01 0.094 0.36 1 -0.28 14 15
CTNNB1 0.028 0.015 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.051 -10000 0 -0.32 2 2
AQP5 -0.063 0.17 -10000 0 -0.48 20 20
CTNND1 0.015 0.096 -10000 0 -0.51 5 5
mol:PI-4-5-P2 -0.006 0.083 0.36 1 -0.26 13 14
regulation of calcium-dependent cell-cell adhesion -0.024 0.11 0.36 1 -0.28 19 20
EGF -0.032 0.15 -10000 0 -0.51 13 13
NCKAP1 0.025 0.047 -10000 0 -0.51 1 1
AQP3 -0.099 0.19 -10000 0 -0.47 29 29
cortical microtubule organization 0.034 0.092 -10000 0 -0.27 12 12
GO:0000145 -0.025 0.074 0.34 1 -0.24 13 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.039 0.095 -10000 0 -0.27 12 12
MLLT4 0.031 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.056 0.11 -10000 0 -0.42 8 8
ARF6 0.024 0.062 -10000 0 -0.51 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.12 -10000 0 -0.35 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.013 0.058 -10000 0 -0.27 1 1
PVRL2 0.027 0.045 -10000 0 -0.51 1 1
ZYX -0.011 0.081 -10000 0 -0.26 14 14
ARF6/GTP 0.022 0.13 -10000 0 -0.34 14 14
CDH1 0.005 0.11 -10000 0 -0.51 7 7
EGFR/EGFR/EGF/EGF -0.043 0.15 -10000 0 -0.32 32 32
RhoA/GDP 0.036 0.089 -10000 0 -0.26 12 12
actin cytoskeleton organization -0.034 0.094 -10000 0 -0.31 13 13
IGF-1R heterotetramer -0.008 0.14 -10000 0 -0.51 11 11
GIT1 0.024 0.062 -10000 0 -0.51 2 2
IGF1R -0.008 0.14 -10000 0 -0.51 11 11
IGF1 -0.049 0.18 -10000 0 -0.51 20 20
DIAPH1 0.013 0.17 -10000 0 -0.58 9 9
Wnt receptor signaling pathway -0.034 0.092 0.27 12 -10000 0 12
RHOA 0.03 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.052 0.1 -10000 0 -0.42 7 7
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
VCL -0.035 0.097 -10000 0 -0.32 13 13
EFNA1 0.019 0.075 -10000 0 -0.51 3 3
LPP -0.02 0.065 0.35 1 -0.26 3 4
Ephrin A1/EPHA2 0 0.13 -10000 0 -0.31 20 20
SEC6/SEC8 -0.007 0.067 -10000 0 -0.25 10 10
MGAT3 -0.024 0.11 0.36 1 -0.29 19 20
HGF/MET 0.021 0.093 -10000 0 -0.26 14 14
HGF 0.028 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.015 0.11 -10000 0 -0.29 18 18
actin cable formation 0.036 0.12 0.34 6 -0.29 5 11
KIAA1543 -0.024 0.073 0.34 1 -0.25 12 13
KIFC3 -0.003 0.079 0.36 1 -0.26 11 12
NCK1 0.02 0.062 -10000 0 -0.51 2 2
EXOC3 0.026 0.013 -10000 0 -10000 0 0
ACTN1 -0.004 0.082 0.36 1 -0.26 12 13
NCK1/GIT1 0.027 0.068 -10000 0 -0.37 4 4
mol:GDP 0.034 0.092 -10000 0 -0.27 12 12
EXOC4 0.032 0.005 -10000 0 -10000 0 0
STX4 0 0.076 0.36 1 -0.26 10 11
PIP5K1C -0.006 0.084 0.36 1 -0.26 13 14
LIMA1 0 0.13 -10000 0 -0.51 9 9
ABI1 0.032 0.006 -10000 0 -10000 0 0
ROCK1 -0.011 0.13 0.33 4 -0.39 6 10
adherens junction assembly -0.014 0.1 0.35 1 -0.48 3 4
IGF-1R heterotetramer/IGF1 -0.038 0.15 -10000 0 -0.29 36 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.036 -10000 0 -0.37 1 1
MET 0.02 0.076 -10000 0 -0.51 3 3
PLEKHA7 -0.004 0.081 0.36 1 -0.26 12 13
mol:GTP 0.02 0.12 -10000 0 -0.35 13 13
establishment of epithelial cell apical/basal polarity 0.015 0.11 0.44 3 -10000 0 3
cortical actin cytoskeleton stabilization -0.015 0.11 -10000 0 -0.29 18 18
regulation of cell-cell adhesion -0.034 0.094 -10000 0 -0.31 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.015 0.11 -10000 0 -0.29 18 18
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.011 0.16 0.29 1 -0.47 13 14
ACTA1 -0.033 0.16 0.27 3 -0.48 14 17
NUMA1 -0.024 0.19 0.29 1 -0.49 18 19
SPTAN1 -0.028 0.16 0.3 2 -0.5 12 14
LIMK1 -0.036 0.17 0.27 3 -0.54 12 15
BIRC3 -0.028 0.16 -10000 0 -0.51 14 14
BIRC2 0.031 0.01 -10000 0 -10000 0 0
BAX 0.032 0.003 -10000 0 -10000 0 0
CASP10 -0.04 0.11 -10000 0 -0.43 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -0.001 5 5
PTK2 -0.014 0.16 0.29 1 -0.44 15 16
DIABLO 0.033 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.028 0.16 0.27 3 -0.49 12 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.061 -10000 0 -0.51 2 2
GSN -0.044 0.18 0.27 3 -0.53 14 17
MADD 0.032 0.006 -10000 0 -10000 0 0
TFAP2A -0.009 0.15 -10000 0 -0.55 9 9
BID -0.02 0.092 -10000 0 -0.29 14 14
MAP3K1 -0.037 0.18 -10000 0 -0.55 14 14
TRADD 0.027 0.044 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.045 0.034 -10000 0 -0.37 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.034 0.2 0.27 3 -0.63 12 15
CASP9 0.032 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.062 0.2 2 -0.2 8 10
neuron apoptosis -0.028 0.2 -10000 0 -0.76 10 10
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.029 0.19 0.31 1 -0.56 13 14
APAF1 0.029 0.044 -10000 0 -0.51 1 1
CASP6 -0.026 0.23 -10000 0 -0.92 8 8
TRAF2 0.031 0.01 -10000 0 -10000 0 0
ICAD/CAD -0.029 0.15 0.28 2 -0.48 12 14
CASP7 0.023 0.087 0.28 11 -0.24 1 12
KRT18 -0.009 0.12 -10000 0 -0.56 6 6
apoptosis -0.032 0.17 0.29 2 -0.52 13 15
DFFA -0.028 0.16 0.27 3 -0.5 12 15
DFFB -0.028 0.16 0.27 3 -0.5 12 15
PARP1 0.015 0.062 0.2 8 -0.2 2 10
actin filament polymerization 0.029 0.17 0.49 12 -0.34 5 17
TNF 0.024 0.048 -10000 0 -0.51 1 1
CYCS -0.004 0.07 0.16 1 -0.24 8 9
SATB1 -0.033 0.22 -10000 0 -0.85 8 8
SLK -0.028 0.16 0.3 2 -0.49 12 14
p15 BID/BAX -0.003 0.1 0.2 1 -0.27 15 16
CASP2 -0.001 0.087 -10000 0 -0.34 5 5
JNK cascade 0.036 0.18 0.54 14 -10000 0 14
CASP3 -0.027 0.17 0.28 4 -0.52 12 16
LMNB2 -0.001 0.16 0.26 1 -0.54 7 8
RIPK1 0.032 0.005 -10000 0 -10000 0 0
CASP4 0.025 0.061 -10000 0 -0.51 2 2
Mammalian IAPs/DIABLO 0.02 0.1 -10000 0 -0.29 14 14
negative regulation of DNA binding -0.009 0.15 -10000 0 -0.54 9 9
stress fiber formation -0.027 0.15 0.27 3 -0.48 12 15
GZMB -0.022 0.13 -10000 0 -0.5 10 10
CASP1 -0.005 0.11 -10000 0 -0.43 8 8
LMNB1 -0.032 0.21 0.26 1 -0.56 14 15
APP -0.029 0.2 -10000 0 -0.77 10 10
TNFRSF1A 0.016 0.086 -10000 0 -0.51 4 4
response to stress 0 0 0.001 3 -0.001 4 7
CASP8 0.001 0.052 -10000 0 -0.37 3 3
VIM -0.03 0.17 0.3 2 -0.53 13 15
LMNA 0.005 0.12 0.26 1 -0.4 8 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.093 -10000 0 -0.36 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.028 0.16 0.27 3 -0.49 12 15
APAF-1/Caspase 9 0.022 0.11 -10000 0 -0.59 4 4
nuclear fragmentation during apoptosis -0.023 0.18 0.29 1 -0.48 18 19
CFL2 -0.031 0.17 0.34 5 -0.5 12 17
GAS2 -0.056 0.17 0.28 2 -0.47 15 17
positive regulation of apoptosis -0.01 0.17 0.27 1 -0.49 11 12
PRF1 -0.003 0.12 -10000 0 -0.51 8 8
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.008 0.12 -10000 0 -0.36 14 14
EPHB2 -0.021 0.15 -10000 0 -0.51 13 13
Syndecan-2/TACI 0.012 0.072 -10000 0 -0.31 7 7
LAMA1 0.023 0.03 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.022 0.16 -10000 0 -0.32 28 28
HRAS 0.024 0.062 -10000 0 -0.51 2 2
Syndecan-2/CASK -0.003 0.062 -10000 0 -0.3 6 6
ITGA5 0.023 0.063 -10000 0 -0.51 2 2
BAX -0.001 0.055 -10000 0 -10000 0 0
EPB41 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.065 -10000 0 -0.28 7 7
LAMA3 -0.022 0.16 -10000 0 -0.51 14 14
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.049 0.19 -10000 0 -0.51 23 23
Syndecan-2/MMP2 -0.022 0.13 -10000 0 -0.36 19 19
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.016 0.15 -10000 0 -0.39 20 20
dendrite morphogenesis -0.013 0.12 -10000 0 -0.34 16 16
Syndecan-2/GM-CSF -0.018 0.12 -10000 0 -0.34 15 15
determination of left/right symmetry -0.002 0.073 -10000 0 -0.36 6 6
Syndecan-2/PKC delta 0.013 0.072 -10000 0 -0.31 7 7
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
MAPK3 -0.016 0.11 0.2 6 -0.32 15 21
MAPK1 -0.02 0.11 0.2 5 -0.33 15 20
Syndecan-2/RACK1 0.026 0.072 -10000 0 -0.26 8 8
NF1 0.032 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.002 0.073 -10000 0 -0.36 6 6
ITGA2 -0.039 0.18 -10000 0 -0.51 19 19
MAPK8 0.001 0.062 -10000 0 -0.3 6 6
Syndecan-2/alpha2/beta1 Integrin -0.005 0.13 -10000 0 -0.29 22 22
Syndecan-2/Kininogen 0.009 0.046 -10000 0 -0.31 2 2
ITGB1 0.024 0.062 -10000 0 -0.51 2 2
SRC 0.013 0.071 -10000 0 -0.25 7 7
Syndecan-2/CASK/Protein 4.1 0.016 0.061 -10000 0 -0.28 6 6
extracellular matrix organization 0.017 0.067 -10000 0 -0.31 6 6
actin cytoskeleton reorganization -0.008 0.12 -10000 0 -0.35 14 14
Syndecan-2/Caveolin-2/Ras -0.015 0.13 -10000 0 -0.3 25 25
Syndecan-2/Laminin alpha3 -0.007 0.1 -10000 0 -0.31 15 15
Syndecan-2/RasGAP 0.035 0.078 -10000 0 -0.25 9 9
alpha5/beta1 Integrin 0.032 0.068 -10000 0 -0.37 4 4
PRKCD 0.026 0.045 -10000 0 -0.51 1 1
Syndecan-2 dimer -0.013 0.12 -10000 0 -0.34 16 16
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.021 0.068 -10000 0 -0.25 8 8
RHOA 0.03 0.009 -10000 0 -10000 0 0
SDCBP 0.027 0.044 -10000 0 -0.51 1 1
TNFRSF13B 0.026 0.046 -10000 0 -0.51 1 1
RASA1 0.026 0.044 -10000 0 -0.51 1 1
alpha2/beta1 Integrin -0.016 0.15 -10000 0 -0.39 20 20
Syndecan-2/Synbindin 0.016 0.068 -10000 0 -0.31 6 6
TGFB1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.073 0.2 6 -0.28 7 13
FN1 -0.011 0.13 -10000 0 -0.51 10 10
Syndecan-2/IL8 -0.073 0.16 -10000 0 -0.33 39 39
SDC2 -0.002 0.073 -10000 0 -0.36 6 6
KNG1 0.017 0.018 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.068 -10000 0 -0.31 6 6
TRAPPC4 0.032 0.005 -10000 0 -10000 0 0
CSF2 -0.025 0.14 -10000 0 -0.51 11 11
Syndecan-2/TGFB1 0.017 0.068 -10000 0 -0.31 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.066 -10000 0 -0.28 7 7
Syndecan-2/Ezrin 0.014 0.061 -10000 0 -0.28 6 6
PRKACA 0.016 0.068 0.2 8 -0.28 5 13
angiogenesis -0.072 0.16 -10000 0 -0.33 39 39
MMP2 -0.031 0.16 -10000 0 -0.51 16 16
IL8 -0.12 0.23 -10000 0 -0.51 38 38
calcineurin-NFAT signaling pathway 0.012 0.072 -10000 0 -0.31 7 7
Arf6 signaling events

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
CENTA1/KIF3B 0.02 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.007 0.092 -10000 0 -0.24 17 17
EGFR -0.033 0.17 -10000 0 -0.51 17 17
EPHA2 -0.015 0.14 -10000 0 -0.51 12 12
USP6 0.03 0.008 -10000 0 -10000 0 0
IQSEC1 0.03 0.008 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.052 0.18 -10000 0 -0.42 25 25
ARRB2 0.009 0.048 -10000 0 -0.32 3 3
mol:GTP 0.003 0.026 0.11 1 -0.18 2 3
ARRB1 0.027 0.022 -10000 0 -10000 0 0
FBXO8 0.03 0.012 -10000 0 -10000 0 0
TSHR 0.024 0.062 -10000 0 -0.51 2 2
EGF -0.032 0.15 -10000 0 -0.51 13 13
somatostatin receptor activity 0 0 0 1 -0.001 13 14
ARAP2 0 0 0 6 0 12 18
mol:GDP -0.011 0.091 -10000 0 -0.24 12 12
mol:PI-3-4-5-P3 0 0 0 4 -0.001 13 17
ITGA2B 0.032 0.004 -10000 0 -10000 0 0
ARF6 0.024 0.062 -10000 0 -0.51 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.12 -10000 0 -0.35 13 13
ADAP1 0 0 0 4 0 9 13
KIF13B 0.029 0.013 -10000 0 -10000 0 0
HGF/MET 0.035 0.061 -10000 0 -0.37 3 3
PXN 0.032 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.1 0.18 4 -0.24 14 18
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.031 0.16 -10000 0 -0.36 25 25
ADRB2 -0.044 0.18 -10000 0 -0.51 19 19
receptor agonist activity 0 0 0 6 0 11 17
actin filament binding 0 0 0 1 0 13 14
SRC 0.031 0.011 -10000 0 -10000 0 0
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
GNAQ 0 0 0.001 4 -0.001 10 14
EFA6/PI-4-5-P2 0 0 0.001 3 -0.001 10 13
ARF6/GDP 0.006 0.11 0.19 3 -0.36 7 10
ARF6/GDP/GULP/ACAP1 -0.04 0.15 -10000 0 -0.29 30 30
alphaIIb/beta3 Integrin/paxillin/GIT1 0.067 0.059 -10000 0 -0.29 3 3
ACAP1 0 0 0 2 -10000 0 2
ACAP2 0 0 0 6 0 13 19
LHCGR/beta Arrestin2 0.015 0.068 -10000 0 -0.44 3 3
EFNA1 0.019 0.075 -10000 0 -0.51 3 3
HGF 0.028 0.02 -10000 0 -10000 0 0
CYTH3 0 0 0.001 6 -0.001 11 17
CYTH2 -0.001 0.001 -10000 0 -0.004 14 14
NCK1 0.02 0.062 -10000 0 -0.51 2 2
fibronectin binding 0 0 0 4 0 12 16
endosomal lumen acidification 0 0 0 8 0 8 16
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.072 0.2 -10000 0 -0.51 26 26
GNAQ/ARNO 0 0.003 0.008 5 -0.006 9 14
mol:Phosphatidic acid 0 0 0 6 0 13 19
PIP3-E 0 0 0 3 0 18 21
MET 0.02 0.076 -10000 0 -0.51 3 3
GNA14 0.014 0.079 -10000 0 -0.51 3 3
GNA15 -0.015 0.15 -10000 0 -0.51 13 13
GIT1 0.024 0.062 -10000 0 -0.51 2 2
mol:PI-4-5-P2 0 0 0.001 4 -0.001 13 17
GNA11 0.025 0.062 -10000 0 -0.51 2 2
LHCGR 0.017 0.076 -10000 0 -0.51 3 3
AGTR1 0.008 0.077 -10000 0 -0.51 3 3
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.068 -10000 0 -0.44 3 3
IPCEF1/ARNO -0.029 0.12 -10000 0 -0.28 25 25
alphaIIb/beta3 Integrin 0.041 0.039 -10000 0 -0.37 1 1
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.18 -10000 0 -0.45 21 21
alphaM/beta2 Integrin/GPIbA 0.01 0.13 -10000 0 -0.39 12 12
alphaM/beta2 Integrin/proMMP-9 -0.013 0.17 -10000 0 -0.41 21 21
PLAUR -0.008 0.14 -10000 0 -0.51 11 11
HMGB1 0.024 0.024 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.018 0.12 -10000 0 -0.4 10 10
AGER -0.006 0.095 -10000 0 -0.52 4 4
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
SELPLG 0.018 0.087 -10000 0 -0.51 4 4
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.012 0.16 -10000 0 -0.38 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.015 0.15 -10000 0 -0.51 13 13
CYR61 -0.011 0.13 -10000 0 -0.51 10 10
TLN1 0.03 0.009 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.14 -10000 0 -0.48 9 9
RHOA 0.03 0.009 -10000 0 -10000 0 0
P-selectin oligomer -0.062 0.2 -10000 0 -0.51 25 25
MYH2 -0.004 0.14 -10000 0 -0.48 8 8
MST1R -0.008 0.13 -10000 0 -0.51 9 9
leukocyte activation during inflammatory response 0.023 0.11 -10000 0 -0.35 10 10
APOB 0.027 0.045 -10000 0 -0.51 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.031 0.16 -10000 0 -0.51 16 16
JAM3 0.017 0.066 -10000 0 -0.51 2 2
GP1BA 0.025 0.025 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.008 0.15 -10000 0 -0.41 14 14
alphaM/beta2 Integrin -0.008 0.15 -10000 0 -0.52 9 9
JAM3 homodimer 0.017 0.066 -10000 0 -0.51 2 2
ICAM2 0.026 0.047 -10000 0 -0.51 1 1
ICAM1 -0.001 0.12 -10000 0 -0.51 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.15 -10000 0 -0.51 9 9
cell adhesion 0.01 0.13 -10000 0 -0.38 12 12
NFKB1 -0.057 0.18 0.39 1 -0.45 19 20
THY1 0.018 0.077 -10000 0 -0.51 3 3
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
Lipoprotein(a) 0.037 0.033 -10000 0 -0.31 1 1
alphaM/beta2 Integrin/LRP/tPA -0.009 0.15 -10000 0 -0.36 20 20
IL6 -0.11 0.27 0.38 1 -0.8 17 18
ITGB2 -0.012 0.14 -10000 0 -0.52 10 10
elevation of cytosolic calcium ion concentration -0.038 0.22 -10000 0 -0.45 27 27
alphaM/beta2 Integrin/JAM2/JAM3 0.008 0.16 -10000 0 -0.41 16 16
JAM2 0.008 0.1 -10000 0 -0.51 6 6
alphaM/beta2 Integrin/ICAM1 -0.005 0.18 -10000 0 -0.39 22 22
alphaM/beta2 Integrin/uPA/Plg -0.016 0.17 -10000 0 -0.36 24 24
RhoA/GTP -0.032 0.13 -10000 0 -0.49 9 9
positive regulation of phagocytosis -0.007 0.18 -10000 0 -0.57 11 11
Ron/MSP 0.011 0.1 -10000 0 -0.37 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.037 0.22 -10000 0 -0.45 27 27
alphaM/beta2 Integrin/uPAR -0.004 0.18 -10000 0 -0.5 15 15
PLAU -0.041 0.17 -10000 0 -0.51 18 18
PLAT -0.026 0.14 -10000 0 -0.51 12 12
actin filament polymerization -0.003 0.13 -10000 0 -0.46 8 8
MST1 0.029 0.012 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.028 0.11 -10000 0 -0.35 10 10
TNF -0.063 0.17 0.38 1 -0.67 6 7
RAP1B 0.031 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.034 0.18 -10000 0 -0.4 25 25
fibrinolysis -0.017 0.17 -10000 0 -0.36 24 24
HCK 0.005 0.11 -10000 0 -0.51 7 7
dendritic cell antigen processing and presentation -0.008 0.15 -10000 0 -0.51 9 9
VTN 0.03 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.008 0.17 -10000 0 -0.45 16 16
LPA 0.03 0.014 -10000 0 -10000 0 0
LRP1 0.032 0.003 -10000 0 -10000 0 0
cell migration -0.049 0.2 -10000 0 -0.43 27 27
FN1 -0.011 0.13 -10000 0 -0.51 10 10
alphaM/beta2 Integrin/Thy1 0.007 0.14 -10000 0 -0.39 14 14
MPO 0.027 0.046 -10000 0 -0.51 1 1
KNG1 0.017 0.018 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.042 -10000 0 -0.31 2 2
ROCK1 -0.001 0.14 -10000 0 -0.49 8 8
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.01 -10000 0 -10000 0 0
CTGF 0.018 0.087 -10000 0 -0.51 4 4
alphaM/beta2 Integrin/Hck 0.002 0.16 -10000 0 -0.49 13 13
ITGAM 0.009 0.091 -10000 0 -0.53 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.031 0.21 -10000 0 -0.42 27 27
HP 0.007 0.098 -10000 0 -0.51 5 5
leukocyte adhesion -0.034 0.18 -10000 0 -0.53 13 13
SELP -0.062 0.2 -10000 0 -0.51 25 25
HIF-2-alpha transcription factor network

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
MMP14 0.004 0.23 -10000 0 -1.2 5 5
oxygen homeostasis 0.002 0.012 -10000 0 -10000 0 0
TCEB2 0.032 0.006 -10000 0 -10000 0 0
TCEB1 0.031 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.005 0.19 -10000 0 -0.5 12 12
EPO -0.003 0.24 -10000 0 -0.59 11 11
FIH (dimer) 0.03 0.023 -10000 0 -10000 0 0
APEX1 0.026 0.029 -10000 0 -10000 0 0
SERPINE1 -0.038 0.31 0.47 1 -0.66 20 21
FLT1 -0.06 0.33 -10000 0 -1 14 14
ADORA2A -0.017 0.26 0.41 3 -0.63 13 16
germ cell development -0.006 0.26 0.46 1 -0.61 13 14
SLC11A2 -0.009 0.28 0.47 1 -0.68 12 13
BHLHE40 -0.028 0.26 -10000 0 -0.59 18 18
HIF1AN 0.03 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.007 0.22 -10000 0 -0.5 14 14
ETS1 0.027 0.073 -10000 0 -0.34 4 4
CITED2 0.028 0.098 -10000 0 -0.84 1 1
KDR -0.023 0.23 -10000 0 -0.88 9 9
PGK1 -0.01 0.28 0.47 1 -0.7 13 14
SIRT1 0.032 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.003 0.33 -10000 0 -0.77 14 14
EPAS1 -0.04 0.18 -10000 0 -0.43 21 21
SP1 0.03 0.064 -10000 0 -0.51 2 2
ABCG2 -0.027 0.27 -10000 0 -0.65 15 15
EFNA1 -0.02 0.28 -10000 0 -0.71 13 13
FXN -0.016 0.26 0.4 4 -0.64 13 17
POU5F1 -0.009 0.27 0.47 1 -0.64 13 14
neuron apoptosis 0.001 0.32 0.74 14 -10000 0 14
EP300 0.003 0.12 -10000 0 -0.51 8 8
EGLN3 -0.066 0.2 -10000 0 -0.52 24 24
EGLN2 0.021 0.066 -10000 0 -0.52 2 2
EGLN1 0.022 0.067 -10000 0 -0.51 2 2
VHL/Elongin B/Elongin C 0.049 0.058 -10000 0 -0.32 3 3
VHL 0.018 0.076 -10000 0 -0.51 3 3
ARNT 0.026 0.029 -10000 0 -10000 0 0
SLC2A1 -0.051 0.3 0.38 2 -0.62 24 26
TWIST1 -0.055 0.31 0.4 4 -0.68 23 27
ELK1 0.039 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.005 0.23 -10000 0 -0.5 16 16
VEGFA -0.011 0.28 0.47 1 -0.71 12 13
CREBBP 0.031 0.007 -10000 0 -10000 0 0
IL27-mediated 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
TGFB1 0.04 0.005 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.12 0.21 0.64 14 -10000 0 14
IL27/IL27R/JAK1 -0.11 0.26 -10000 0 -1.3 5 5
TBX21 -0.18 0.26 -10000 0 -0.69 25 25
IL12B 0.008 0.077 -10000 0 -0.51 3 3
IL12A -0.004 0.044 -10000 0 -0.37 2 2
IL6ST 0.006 0.067 -10000 0 -0.52 2 2
IL27RA/JAK1 -0.053 0.24 -10000 0 -1.3 5 5
IL27 -0.07 0.19 -10000 0 -0.52 22 22
TYK2 0.011 0.032 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.006 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.12 0.21 0.64 14 -10000 0 14
T cell proliferation during immune response 0.12 0.21 0.64 14 -10000 0 14
MAPKKK cascade -0.12 0.21 -10000 0 -0.64 14 14
STAT3 0.032 0.005 -10000 0 -10000 0 0
STAT2 0.032 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.11 -10000 0 -0.52 6 6
IL12RB1 0.03 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.19 0.26 -10000 0 -0.62 32 32
IL27/IL27R/JAK2/TYK2 -0.12 0.22 -10000 0 -0.65 14 14
positive regulation of T cell mediated cytotoxicity -0.12 0.21 -10000 0 -0.64 14 14
STAT1 (dimer) -0.19 0.36 -10000 0 -0.98 18 18
JAK2 0.008 0.052 -10000 0 -0.52 1 1
JAK1 0.027 0.044 -10000 0 -0.51 1 1
STAT2 (dimer) -0.11 0.21 -10000 0 -0.64 13 13
T cell proliferation -0.14 0.23 -10000 0 -0.67 15 15
IL12/IL12R/TYK2/JAK2 -0.091 0.26 -10000 0 -0.82 14 14
IL17A 0.007 0.11 -10000 0 -10000 0 0
mast cell activation 0.12 0.21 0.64 14 -10000 0 14
IFNG -0.035 0.057 -10000 0 -0.12 38 38
T cell differentiation -0.01 0.011 -10000 0 -0.026 39 39
STAT3 (dimer) -0.11 0.21 -10000 0 -0.66 12 12
STAT5A (dimer) -0.11 0.21 -10000 0 -0.66 12 12
STAT4 (dimer) -0.12 0.22 -10000 0 -0.64 15 15
STAT4 0.012 0.097 -10000 0 -0.51 5 5
T cell activation -0.003 0.025 0.12 5 -10000 0 5
IL27R/JAK2/TYK2 -0.065 0.25 -10000 0 -1.3 5 5
GATA3 0.02 0.048 -10000 0 -10000 0 0
IL18 -0.028 0.1 -10000 0 -0.37 13 13
positive regulation of mast cell cytokine production -0.11 0.21 -10000 0 -0.64 12 12
IL27/EBI3 -0.045 0.14 -10000 0 -0.38 22 22
IL27RA -0.064 0.25 -10000 0 -1.4 5 5
IL6 -0.039 0.16 -10000 0 -0.5 16 16
STAT5A 0.031 0.01 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.004 -10000 0 -10000 0 0
IL2 0.021 0.089 0.48 5 -10000 0 5
IL1B -0.067 0.14 -10000 0 -0.37 28 28
EBI3 0.014 0.029 -10000 0 -10000 0 0
TNF 0.001 0.033 -10000 0 -0.37 1 1
Syndecan-4-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
PTK2 -0.034 0.17 -10000 0 -0.46 17 17
Syndecan-4/Syndesmos -0.024 0.17 -10000 0 -0.47 15 15
positive regulation of JNK cascade -0.065 0.23 -10000 0 -0.53 26 26
Syndecan-4/ADAM12 -0.048 0.2 -10000 0 -0.5 20 20
CCL5 -0.023 0.16 -10000 0 -0.51 15 15
Rac1/GDP 0.024 0.003 -10000 0 -10000 0 0
DNM2 0.032 0.006 -10000 0 -10000 0 0
ITGA5 0.023 0.063 -10000 0 -0.51 2 2
SDCBP 0.027 0.044 -10000 0 -0.51 1 1
PLG 0.03 0.019 -10000 0 -10000 0 0
ADAM12 -0.014 0.14 -10000 0 -0.51 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.03 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.016 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.028 0.17 -10000 0 -0.47 14 14
Syndecan-4/CXCL12/CXCR4 -0.069 0.25 -10000 0 -0.56 26 26
Syndecan-4/Laminin alpha3 -0.051 0.18 -10000 0 -0.5 13 13
MDK 0.004 0.11 -10000 0 -0.51 7 7
Syndecan-4/FZD7 -0.059 0.19 -10000 0 -0.5 16 16
Syndecan-4/Midkine -0.041 0.18 -10000 0 -0.46 16 16
FZD7 -0.045 0.18 -10000 0 -0.51 20 20
Syndecan-4/FGFR1/FGF -0.033 0.17 -10000 0 -0.48 12 12
THBS1 0.024 0.063 -10000 0 -0.51 2 2
integrin-mediated signaling pathway -0.046 0.18 -10000 0 -0.46 17 17
positive regulation of MAPKKK cascade -0.065 0.23 -10000 0 -0.53 26 26
Syndecan-4/TACI -0.028 0.17 -10000 0 -0.46 16 16
CXCR4 -0.036 0.17 -10000 0 -0.51 18 18
cell adhesion -0.011 0.1 0.2 1 -0.33 12 13
Syndecan-4/Dynamin -0.025 0.17 -10000 0 -0.46 16 16
Syndecan-4/TSP1 -0.03 0.18 -10000 0 -0.46 16 16
Syndecan-4/GIPC -0.029 0.17 -10000 0 -0.46 16 16
Syndecan-4/RANTES -0.05 0.22 -10000 0 -0.54 20 20
ITGB1 0.024 0.062 -10000 0 -0.51 2 2
LAMA1 0.023 0.03 -10000 0 -10000 0 0
LAMA3 -0.022 0.16 -10000 0 -0.51 14 14
RAC1 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.015 0.13 0.85 3 -0.48 1 4
Syndecan-4/alpha-Actinin -0.027 0.17 -10000 0 -0.46 16 16
TFPI 0.001 0.11 -10000 0 -0.51 7 7
F2 0.026 0.023 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.032 0.068 -10000 0 -0.37 4 4
positive regulation of cell adhesion -0.053 0.17 -10000 0 -0.49 13 13
ACTN1 0.03 0.013 -10000 0 -10000 0 0
TNC -0.02 0.14 -10000 0 -0.51 11 11
Syndecan-4/CXCL12 -0.052 0.2 -10000 0 -0.5 22 22
FGF6 0.009 0.1 -10000 0 -0.51 6 6
RHOA 0.03 0.009 -10000 0 -10000 0 0
CXCL12 -0.025 0.16 -10000 0 -0.51 14 14
TNFRSF13B 0.026 0.046 -10000 0 -0.51 1 1
FGF2 0.016 0.077 -10000 0 -0.51 3 3
FGFR1 0.017 0.063 -10000 0 -0.51 2 2
Syndecan-4/PI-4-5-P2 -0.043 0.16 -10000 0 -0.46 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.013 0.13 -10000 0 -0.5 10 10
cell migration -0.014 0.012 -10000 0 -10000 0 0
PRKCD 0.023 0.046 -10000 0 -0.49 1 1
vasculogenesis -0.028 0.17 -10000 0 -0.45 16 16
SDC4 -0.038 0.17 -10000 0 -0.48 16 16
Syndecan-4/Tenascin C -0.048 0.19 -10000 0 -0.48 17 17
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.027 0.18 -10000 0 -0.46 17 17
MMP9 -0.015 0.15 -10000 0 -0.51 13 13
Rac1/GTP -0.012 0.1 0.2 1 -0.34 12 13
cytoskeleton organization -0.023 0.17 -10000 0 -0.45 15 15
GIPC1 0.028 0.044 -10000 0 -0.51 1 1
Syndecan-4/TFPI -0.042 0.19 -10000 0 -0.48 18 18
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.022 0.14 0.22 1 -0.38 10 11
adherens junction organization -0.006 0.14 -10000 0 -0.35 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.16 0.23 2 -0.39 11 13
FMN1 0 0.13 -10000 0 -0.32 16 16
mol:IP3 -0.018 0.089 -10000 0 -0.34 8 8
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.003 0.14 -10000 0 -0.34 16 16
CTNNB1 0.03 0.016 -10000 0 -10000 0 0
AKT1 -0.024 0.11 -10000 0 -0.41 8 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.18 -10000 0 -0.57 10 10
CTNND1 0.018 0.098 -10000 0 -0.52 5 5
mol:PI-4-5-P2 -0.001 0.13 -10000 0 -0.32 16 16
VASP -0.004 0.14 -10000 0 -0.34 17 17
ZYX -0.005 0.14 -10000 0 -0.34 17 17
JUB 0 0.13 -10000 0 -0.32 16 16
EGFR(dimer) -0.018 0.17 -10000 0 -0.4 19 19
E-cadherin/beta catenin-gamma catenin 0.012 0.12 -10000 0 -0.31 16 16
mol:PI-3-4-5-P3 -0.014 0.11 -10000 0 -0.35 10 10
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
PI3K -0.014 0.11 -10000 0 -0.36 10 10
FYN 0.023 0.12 0.22 1 -0.33 6 7
mol:Ca2+ -0.017 0.087 -10000 0 -0.33 8 8
JUP -0.002 0.13 -10000 0 -0.51 10 10
PIK3R1 0.007 0.099 -10000 0 -0.51 5 5
mol:DAG -0.018 0.089 -10000 0 -0.34 8 8
CDH1 0.007 0.11 -10000 0 -0.51 7 7
RhoA/GDP 0.024 0.16 0.23 2 -0.4 10 12
establishment of polarity of embryonic epithelium -0.003 0.14 -10000 0 -0.33 17 17
SRC 0.031 0.011 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
RHOA 0.03 0.009 -10000 0 -10000 0 0
EGFR -0.033 0.17 -10000 0 -0.51 17 17
CASR 0.023 0.11 0.22 1 -0.32 8 9
RhoA/GTP 0.042 0.12 -10000 0 -0.32 7 7
AKT2 -0.022 0.096 -10000 0 -0.34 9 9
actin cable formation -0.006 0.14 -10000 0 -0.33 17 17
apoptosis -0.02 0.14 0.36 11 -0.22 1 12
CTNNA1 0.034 0.01 -10000 0 -10000 0 0
mol:GDP 0.004 0.16 -10000 0 -0.4 12 12
PIP5K1A -0.001 0.13 -10000 0 -0.32 16 16
PLCG1 -0.018 0.091 -10000 0 -0.34 8 8
Rac1/GTP -0.008 0.16 -10000 0 -0.42 14 14
homophilic cell adhesion 0.002 0.005 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.039 0.16 -10000 0 -0.51 16 16
positive regulation of NF-kappaB transcription factor activity -0.023 0.12 -10000 0 -0.37 16 16
MAP2K4 0.018 0.11 -10000 0 -0.4 3 3
IKBKB 0.029 0.01 -10000 0 -10000 0 0
TNFRSF10B 0.019 0.075 -10000 0 -0.51 3 3
TNFRSF10A 0.017 0.076 -10000 0 -0.51 3 3
SMPD1 -0.016 0.069 -10000 0 -0.21 17 17
IKBKG 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.02 0.063 -10000 0 -0.51 2 2
TRAIL/TRAILR2 -0.026 0.14 -10000 0 -0.4 17 17
TRAIL/TRAILR3 -0.03 0.13 -10000 0 -0.39 17 17
TRAIL/TRAILR1 -0.026 0.14 -10000 0 -0.41 16 16
TRAIL/TRAILR4 -0.023 0.12 -10000 0 -0.37 16 16
TRAIL/TRAILR1/DAP3/GTP -0.011 0.11 -10000 0 -0.32 16 16
IKK complex -0.004 0.065 -10000 0 -0.43 2 2
RIPK1 0.032 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.023 0.005 -10000 0 -10000 0 0
MAPK3 -0.029 0.11 -10000 0 -0.37 15 15
MAP3K1 -0.017 0.11 -10000 0 -0.46 5 5
TRAILR4 (trimer) 0.02 0.063 -10000 0 -0.51 2 2
TRADD 0.027 0.044 -10000 0 -0.51 1 1
TRAILR1 (trimer) 0.017 0.076 -10000 0 -0.51 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.019 0.1 -10000 0 -0.51 3 3
CFLAR 0.01 0.1 -10000 0 -0.51 6 6
MAPK1 -0.029 0.12 -10000 0 -0.39 14 14
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.11 -10000 0 -0.31 14 14
mol:ceramide -0.016 0.069 -10000 0 -0.21 17 17
FADD 0.029 0.01 -10000 0 -10000 0 0
MAPK8 0.021 0.11 0.27 1 -0.38 3 4
TRAF2 0.031 0.01 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.009 0.088 -10000 0 -0.51 4 4
CHUK 0.028 0.044 -10000 0 -0.51 1 1
TRAIL/TRAILR1/FADD -0.015 0.12 -10000 0 -0.35 15 15
DAP3 0.031 0.007 -10000 0 -10000 0 0
CASP10 0.02 0.18 0.41 2 -0.44 14 16
JNK cascade -0.023 0.12 -10000 0 -0.37 16 16
TRAIL (trimer) -0.039 0.16 -10000 0 -0.51 16 16
TNFRSF10C 0.009 0.089 -10000 0 -0.51 4 4
TRAIL/TRAILR1/DAP3/GTP/FADD -0.007 0.11 -10000 0 -0.31 15 15
TRAIL/TRAILR2/FADD -0.016 0.12 -10000 0 -0.35 16 16
cell death -0.016 0.069 -10000 0 -0.21 17 17
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.019 0.098 -10000 0 -0.28 16 16
TRAILR2 (trimer) 0.019 0.075 -10000 0 -0.51 3 3
CASP8 -0.01 0.14 -10000 0 -0.72 5 5
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.11 -10000 0 -0.3 16 16
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.013 0.12 -9999 0 -0.33 16 16
E-cadherin/beta catenin 0.022 0.088 -9999 0 -0.37 7 7
CTNNB1 0.028 0.015 -9999 0 -10000 0 0
JUP -0.004 0.13 -9999 0 -0.51 10 10
CDH1 0.005 0.11 -9999 0 -0.51 7 7
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.012 0.14 -9999 0 -0.51 11 11
PLK4 0.03 0.011 -9999 0 -10000 0 0
regulation of centriole replication -0.014 0.1 -9999 0 -0.37 11 11
Signaling events mediated by PTP1B

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
PDGFRB 0.03 0.011 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.025 0.15 -10000 0 -0.45 13 13
PTP1B/AKT1 -0.049 0.14 -10000 0 -0.36 17 17
FYN 0.024 0.062 -10000 0 -0.51 2 2
p210 bcr-abl/PTP1B -0.066 0.14 -10000 0 -0.33 21 21
EGFR -0.038 0.17 -10000 0 -0.52 17 17
EGF/EGFR -0.088 0.19 -10000 0 -0.4 32 32
CSF1 0.03 0.014 -10000 0 -10000 0 0
AKT1 0.023 0.063 -10000 0 -0.52 2 2
INSR 0.028 0.044 -10000 0 -0.51 1 1
PTP1B/N-cadherin -0.055 0.14 -10000 0 -0.35 20 20
Insulin Receptor/Insulin -0.023 0.14 -10000 0 -0.4 10 10
HCK 0.005 0.11 -10000 0 -0.51 7 7
CRK 0.03 0.008 -10000 0 -10000 0 0
TYK2 -0.063 0.13 0.21 1 -0.33 19 20
EGF -0.037 0.15 -10000 0 -0.52 13 13
YES1 0.027 0.044 -10000 0 -0.51 1 1
CAV1 -0.086 0.18 0.2 1 -0.39 28 29
TXN 0.023 0.048 -10000 0 -0.52 1 1
PTP1B/IRS1/GRB2 -0.05 0.15 -10000 0 -0.35 20 20
cell migration 0.066 0.14 0.33 21 -10000 0 21
STAT3 0.032 0.005 -10000 0 -10000 0 0
PRLR 0.021 0.051 -10000 0 -0.51 1 1
ITGA2B 0.031 0.004 -10000 0 -10000 0 0
CSF1R 0.031 0.007 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.036 0.047 -10000 0 -0.37 1 1
FGR 0.031 0.01 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.05 0.14 -10000 0 -0.33 19 19
Crk/p130 Cas -0.037 0.14 -10000 0 -0.36 13 13
DOK1 -0.051 0.13 -10000 0 -0.34 17 17
JAK2 -0.037 0.15 -10000 0 -0.49 12 12
Jak2/Leptin Receptor/Leptin -0.027 0.16 -10000 0 -0.43 11 11
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
PTPN1 -0.066 0.14 -10000 0 -0.34 21 21
LYN 0.027 0.044 -10000 0 -0.51 1 1
CDH2 0.006 0.081 -10000 0 -0.51 3 3
SRC 0.003 0.069 -10000 0 -0.6 1 1
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
CAT1/PTP1B -0.055 0.18 -10000 0 -0.51 13 13
CAPN1 0.012 0.098 -10000 0 -0.52 5 5
CSK 0.032 0.003 -10000 0 -10000 0 0
PI3K -0.026 0.13 -10000 0 -0.46 8 8
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.023 0.16 -10000 0 -0.43 10 10
negative regulation of transcription -0.037 0.15 -10000 0 -0.48 12 12
FCGR2A -0.012 0.14 -10000 0 -0.51 12 12
FER 0.021 0.048 -10000 0 -0.52 1 1
alphaIIb/beta3 Integrin 0.038 0.039 -10000 0 -0.38 1 1
BLK 0.009 0.079 -10000 0 -0.51 3 3
Insulin Receptor/Insulin/Shc 0.056 0.037 -10000 0 -0.32 1 1
RHOA 0.028 0.009 -10000 0 -10000 0 0
LEPR 0.021 0.064 -10000 0 -0.51 2 2
BCAR1 0.031 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.005 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.013 0.18 -10000 0 -0.59 8 8
PRL 0.033 0.017 -10000 0 -10000 0 0
SOCS3 0.003 0.2 -10000 0 -1.4 3 3
SPRY2 -0.015 0.14 -10000 0 -0.52 10 10
Insulin Receptor/Insulin/IRS1 0.038 0.087 -10000 0 -0.32 8 8
CSF1/CSF1R -0.039 0.14 -10000 0 -0.35 14 14
Ras protein signal transduction 0.03 0.11 0.66 4 -10000 0 4
IRS1 0.004 0.11 -10000 0 -0.51 7 7
INS 0.032 0.006 -10000 0 -10000 0 0
LEP 0.015 0.055 -10000 0 -0.51 1 1
STAT5B -0.048 0.14 -10000 0 -0.37 15 15
STAT5A -0.049 0.14 -10000 0 -0.37 15 15
GRB2 0.032 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.051 0.14 -10000 0 -0.32 20 20
CSN2 0.045 0.058 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
LAT -0.044 0.18 -10000 0 -0.61 13 13
YBX1 0.038 0.012 -10000 0 -10000 0 0
LCK -0.006 0.13 -10000 0 -0.51 10 10
SHC1 0.031 0.007 -10000 0 -10000 0 0
NOX4 -0.05 0.19 -10000 0 -0.52 21 21
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.052 0.3 -10000 0 -1.1 11 11
regulation of axonogenesis 0.017 0.1 0.54 4 -10000 0 4
myoblast fusion -0.008 0.14 0.47 11 -10000 0 11
mol:GTP 0.002 0.093 -10000 0 -0.28 12 12
regulation of calcium-dependent cell-cell adhesion -0.044 0.099 0.28 11 -10000 0 11
ARF1/GTP 0.023 0.08 -10000 0 -0.38 3 3
mol:GM1 -0.004 0.071 -10000 0 -0.23 10 10
mol:Choline -0.022 0.11 -10000 0 -0.42 9 9
lamellipodium assembly -0.019 0.16 -10000 0 -0.52 12 12
MAPK3 0.001 0.11 -10000 0 -0.38 11 11
ARF6/GTP/NME1/Tiam1 0.045 0.1 -10000 0 -0.28 11 11
ARF1 0.032 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.008 0.15 -10000 0 -0.47 11 11
ARF1/GDP 0.011 0.14 -10000 0 -0.41 13 13
ARF6 0.021 0.094 -10000 0 -0.7 2 2
RAB11A 0.032 0.003 -10000 0 -10000 0 0
TIAM1 0.03 0.017 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.12 -10000 0 -0.4 11 11
actin filament bundle formation -0.008 0.14 0.41 13 -10000 0 13
KALRN -0.011 0.11 -10000 0 -0.39 10 10
RAB11FIP3/RAB11A 0.045 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.14 -10000 0 -0.41 13 13
NME1 0.03 0.018 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.14 -10000 0 -0.41 13 13
substrate adhesion-dependent cell spreading 0.002 0.093 -10000 0 -0.28 12 12
cortical actin cytoskeleton organization -0.019 0.16 -10000 0 -0.53 12 12
RAC1 0.032 0.005 -10000 0 -10000 0 0
liver development 0.002 0.093 -10000 0 -0.28 12 12
ARF6/GTP 0.002 0.093 -10000 0 -0.28 12 12
RhoA/GTP 0.021 0.08 -10000 0 -0.23 10 10
mol:GDP -0.022 0.14 -10000 0 -0.44 13 13
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.077 -10000 0 -0.43 2 2
RHOA 0.03 0.009 -10000 0 -10000 0 0
PLD1 -0.021 0.12 -10000 0 -0.37 12 12
RAB11FIP3 0.03 0.014 -10000 0 -10000 0 0
tube morphogenesis -0.019 0.16 -10000 0 -0.52 12 12
ruffle organization -0.017 0.1 -10000 0 -0.54 4 4
regulation of epithelial cell migration 0.002 0.093 -10000 0 -0.28 12 12
PLD2 0.003 0.083 -10000 0 -0.25 12 12
PIP5K1A -0.017 0.1 -10000 0 -0.55 4 4
mol:Phosphatidic acid -0.022 0.11 -10000 0 -0.42 9 9
Rac1/GTP -0.02 0.16 -10000 0 -0.53 12 12
PDGFR-alpha signaling pathway

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
PDGFRA -0.01 0.13 -9999 0 -0.51 9 9
PDGF/PDGFRA/CRKL 0.012 0.091 -9999 0 -0.36 8 8
positive regulation of JUN kinase activity 0.047 0.082 -9999 0 -0.27 8 8
CRKL 0.028 0.013 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.012 0.095 -9999 0 -0.36 9 9
AP1 -0.11 0.28 -9999 0 -0.86 17 17
mol:IP3 -0.013 0.084 -9999 0 -0.38 7 7
PLCG1 -0.013 0.084 -9999 0 -0.38 7 7
PDGF/PDGFRA/alphaV Integrin -0.002 0.12 -9999 0 -0.39 13 13
RAPGEF1 0.032 0.003 -9999 0 -10000 0 0
CRK 0.03 0.008 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.084 -9999 0 -0.38 7 7
CAV3 0.03 0.008 -9999 0 -10000 0 0
CAV1 -0.029 0.16 -9999 0 -0.51 15 15
SHC/Grb2/SOS1 0.049 0.083 -9999 0 -0.28 8 8
PDGF/PDGFRA/Shf 0.002 0.12 -9999 0 -0.39 12 12
FOS -0.12 0.27 -9999 0 -0.84 17 17
JUN -0.044 0.083 -9999 0 -0.4 7 7
oligodendrocyte development -0.002 0.12 -9999 0 -0.39 13 13
GRB2 0.032 0.005 -9999 0 -10000 0 0
PIK3R1 0.004 0.098 -9999 0 -0.51 5 5
mol:DAG -0.013 0.084 -9999 0 -0.38 7 7
PDGF/PDGFRA -0.01 0.13 -9999 0 -0.51 9 9
actin cytoskeleton reorganization 0.005 0.1 -9999 0 -0.34 11 11
SRF 0.018 0.012 -9999 0 -10000 0 0
SHC1 0.031 0.007 -9999 0 -10000 0 0
PI3K -0.002 0.087 -9999 0 -0.31 9 9
PDGF/PDGFRA/Crk/C3G 0.034 0.086 -9999 0 -0.3 9 9
JAK1 -0.013 0.089 -9999 0 -0.36 9 9
ELK1/SRF -0.002 0.076 -9999 0 -0.29 6 6
SHB 0.017 0.076 -9999 0 -0.51 3 3
SHF 0.017 0.087 -9999 0 -0.51 4 4
CSNK2A1 0.034 0.021 -9999 0 -10000 0 0
GO:0007205 -0.019 0.086 -9999 0 -0.4 7 7
SOS1 0.032 0.005 -9999 0 -10000 0 0
Ras protein signal transduction 0.047 0.082 -9999 0 -0.27 8 8
PDGF/PDGFRA/SHB 0.005 0.1 -9999 0 -0.34 11 11
PDGF/PDGFRA/Caveolin-1 -0.027 0.16 -9999 0 -0.44 18 18
ITGAV 0.013 0.097 -9999 0 -0.51 5 5
ELK1 -0.024 0.077 -9999 0 -0.35 7 7
PIK3CA 0.009 0.062 -9999 0 -0.51 2 2
PDGF/PDGFRA/Crk 0.012 0.096 -9999 0 -0.36 9 9
JAK-STAT cascade -0.013 0.089 -9999 0 -0.36 9 9
cell proliferation 0.002 0.12 -9999 0 -0.39 12 12
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.061 -10000 0 -0.37 3 3
alphaV beta3 Integrin 0.029 0.095 -10000 0 -0.32 9 9
PTK2 0.001 0.14 0.3 1 -0.55 6 7
IGF1R -0.008 0.14 -10000 0 -0.51 11 11
PI4KB 0.031 0.007 -10000 0 -10000 0 0
MFGE8 0.028 0.044 -10000 0 -0.51 1 1
SRC 0.031 0.011 -10000 0 -10000 0 0
CDKN1B 0.016 0.039 -10000 0 -10000 0 0
VEGFA 0.025 0.061 -10000 0 -0.51 2 2
ILK 0.017 0.039 -10000 0 -10000 0 0
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.011 0.05 -10000 0 -0.28 2 2
PTK2B 0.009 0.093 -10000 0 -0.34 7 7
alphaV/beta3 Integrin/JAM-A 0.023 0.11 -10000 0 -0.3 13 13
CBL 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.039 0.079 -10000 0 -0.31 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.028 0.17 -10000 0 -0.32 34 34
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.004 0.088 -10000 0 -0.36 6 6
alphaV/beta3 Integrin/Syndecan-1 0.014 0.13 -10000 0 -0.35 15 15
PI4KA 0.029 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.066 0.19 -10000 0 -0.36 38 38
PI4 Kinase 0.042 0.017 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
alphaV/beta3 Integrin/Osteopontin -0.052 0.16 -10000 0 -0.34 34 34
RPS6KB1 -0.094 0.16 -10000 0 -0.48 16 16
TLN1 0.03 0.009 -10000 0 -10000 0 0
MAPK3 -0.058 0.19 -10000 0 -0.63 12 12
GPR124 0.026 0.017 -10000 0 -10000 0 0
MAPK1 -0.059 0.19 -10000 0 -0.64 12 12
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
alphaV/beta3 Integrin/Tumstatin 0.04 0.083 -10000 0 -0.32 7 7
cell adhesion 0.018 0.085 -10000 0 -0.28 9 9
ANGPTL3 0.026 0.046 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.059 -10000 0 -0.32 3 3
IGF-1R heterotetramer -0.008 0.14 -10000 0 -0.51 11 11
Rac1/GDP 0.024 0.003 -10000 0 -10000 0 0
TGFBR2 0.025 0.046 -10000 0 -0.51 1 1
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
IGF1 -0.049 0.18 -10000 0 -0.51 20 20
RAC1 0.032 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.033 0.073 -10000 0 -0.31 5 5
apoptosis 0.013 0.096 -10000 0 -0.51 5 5
CD47 0.013 0.087 -10000 0 -0.51 4 4
alphaV/beta3 Integrin/CD47 0.025 0.092 -10000 0 -0.32 9 9
VCL 0.024 0.062 -10000 0 -0.51 2 2
alphaV/beta3 Integrin/Del1 -0.013 0.14 -10000 0 -0.37 18 18
CSF1 0.03 0.014 -10000 0 -10000 0 0
PIK3C2A 0.011 0.068 -10000 0 -0.47 2 2
PI4 Kinase/Pyk2 0.009 0.09 -10000 0 -0.36 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.1 -10000 0 -0.36 7 7
FAK1/Vinculin 0.017 0.13 0.29 1 -0.42 7 8
alphaV beta3/Integrin/ppsTEM5 0.034 0.074 -10000 0 -0.31 5 5
RHOA 0.03 0.009 -10000 0 -10000 0 0
VTN 0.03 0.014 -10000 0 -10000 0 0
BCAR1 0.031 0.007 -10000 0 -10000 0 0
FGF2 0.016 0.077 -10000 0 -0.51 3 3
F11R -0.007 0.086 -10000 0 -0.37 8 8
alphaV/beta3 Integrin/Lactadherin 0.041 0.078 -10000 0 -0.32 6 6
alphaV/beta3 Integrin/TGFBR2 0.037 0.089 -10000 0 -0.36 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.061 0.07 -10000 0 -0.28 5 5
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.038 0.071 -10000 0 -0.28 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.011 0.13 -10000 0 -0.51 10 10
alphaV/beta3 Integrin/Pyk2 0.034 0.097 -10000 0 -0.34 7 7
SDC1 -0.008 0.14 -10000 0 -0.51 11 11
VAV3 -0.05 0.13 -10000 0 -0.29 31 31
PTPN11 0.029 0.044 -10000 0 -0.51 1 1
IRS1 0.004 0.11 -10000 0 -0.51 7 7
FAK1/Paxillin 0.02 0.12 0.29 1 -0.43 6 7
cell migration 0.013 0.12 0.26 2 -0.38 7 9
ITGAV 0.013 0.097 -10000 0 -0.51 5 5
PI3K -0.004 0.1 -10000 0 -0.31 11 11
SPP1 -0.1 0.22 -10000 0 -0.51 33 33
KDR 0.021 0.062 -10000 0 -0.51 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.096 -10000 0 -0.51 5 5
COL4A3 0.028 0.044 -10000 0 -0.51 1 1
angiogenesis -0.05 0.2 -10000 0 -0.64 12 12
Rac1/GTP -0.038 0.13 -10000 0 -0.27 30 30
EDIL3 -0.041 0.16 -10000 0 -0.51 15 15
cell proliferation 0.037 0.088 -10000 0 -0.36 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.013 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.009 0.17 -10000 0 -0.51 10 10
NEF -0.011 0.046 -10000 0 -0.27 3 3
NFKBIA 0.012 0.064 -10000 0 -0.6 1 1
BIRC3 -0.029 0.17 -10000 0 -0.52 15 15
CYCS -0.028 0.14 0.19 2 -0.38 13 15
RIPK1 0.032 0.005 -10000 0 -10000 0 0
CD247 -0.054 0.21 -10000 0 -0.6 19 19
MAP2K7 -0.014 0.17 -10000 0 -0.61 7 7
protein ubiquitination 0.016 0.088 -10000 0 -0.32 4 4
CRADD 0.026 0.061 -10000 0 -0.51 2 2
DAXX 0.032 0.005 -10000 0 -10000 0 0
FAS -0.019 0.15 -10000 0 -0.51 13 13
BID -0.032 0.15 0.19 4 -0.38 16 20
NF-kappa-B/RelA/I kappa B alpha 0.026 0.11 -10000 0 -0.3 12 12
TRADD 0.027 0.044 -10000 0 -0.51 1 1
MAP3K5 0.021 0.075 -10000 0 -0.51 3 3
CFLAR 0.01 0.1 -10000 0 -0.51 6 6
FADD 0.029 0.01 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.026 0.11 -10000 0 -0.31 12 12
MAPK8 -0.011 0.16 -10000 0 -0.6 6 6
APAF1 0.029 0.044 -10000 0 -0.51 1 1
TRAF1 0.023 0.064 -10000 0 -0.51 2 2
TRAF2 0.031 0.01 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.03 0.15 0.2 4 -0.33 25 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.019 0.1 -10000 0 -0.36 4 4
CHUK 0.017 0.092 -10000 0 -0.35 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.032 0.12 -10000 0 -0.29 15 15
TCRz/NEF -0.049 0.19 -10000 0 -0.54 19 19
TNF 0.024 0.048 -10000 0 -0.51 1 1
FASLG -0.074 0.24 -10000 0 -0.65 20 20
NFKB1 0.016 0.041 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.062 -10000 0 -0.32 3 3
CASP6 -0.022 0.21 -10000 0 -0.68 11 11
CASP7 -0.045 0.22 -10000 0 -0.58 17 17
RELA 0.016 0.045 -10000 0 -0.16 2 2
CASP2 0.032 0.004 -10000 0 -10000 0 0
CASP3 -0.051 0.22 -10000 0 -0.58 18 18
TNFRSF1A 0.016 0.086 -10000 0 -0.51 4 4
TNFR1A/BAG4 0.028 0.061 -10000 0 -0.37 3 3
CASP8 0.021 0.075 -10000 0 -0.51 3 3
CASP9 0.032 0.005 -10000 0 -10000 0 0
MAP3K14 0.019 0.1 -10000 0 -0.39 4 4
APAF-1/Caspase 9 -0.038 0.16 -10000 0 -0.46 14 14
BCL2 -0.023 0.16 -10000 0 -0.55 7 7
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.04 0.041 0.41 1 -10000 0 1
AES 0.039 0.035 0.38 1 -10000 0 1
FBXW11 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.037 0.051 -10000 0 -0.37 2 2
SMAD4 0.021 0.075 -10000 0 -0.51 3 3
DKK2 0.01 0.089 -10000 0 -0.51 4 4
TLE1 0.026 0.079 0.28 1 -0.5 3 4
MACF1 0.021 0.075 -10000 0 -0.51 3 3
CTNNB1 0.018 0.12 0.3 2 -0.38 5 7
WIF1 -0.063 0.18 -10000 0 -0.51 21 21
beta catenin/RanBP3 0.031 0.18 0.44 17 -0.37 3 20
KREMEN2 -0.099 0.21 -10000 0 -0.51 30 30
DKK1 -0.094 0.2 -10000 0 -0.51 29 29
beta catenin/beta TrCP1 0.033 0.12 0.3 2 -0.37 4 6
FZD1 0.027 0.045 -10000 0 -0.51 1 1
AXIN2 -0.047 0.27 0.8 1 -1.4 5 6
AXIN1 0.031 0.011 -10000 0 -10000 0 0
RAN 0.033 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.015 0.12 -10000 0 -0.58 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.14 -10000 0 -0.45 7 7
Axin1/APC/GSK3 0.031 0.061 0.25 1 -0.27 2 3
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.1 -10000 0 -0.38 4 4
HNF1A 0.035 0.041 0.25 2 -10000 0 2
CTBP1 0.036 0.033 0.25 2 -10000 0 2
MYC -0.001 0.35 0.59 15 -1.4 6 21
RANBP3 0.032 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.054 0.15 -10000 0 -0.32 35 35
NKD1 0.026 0.025 -10000 0 -10000 0 0
TCF4 0.006 0.12 -10000 0 -0.46 9 9
TCF3 0.035 0.045 0.28 1 -0.39 1 2
WNT1/LRP6/FZD1/Axin1 0.064 0.054 -10000 0 -0.29 2 2
Ran/GTP 0.025 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.19 0.5 14 -0.43 3 17
LEF1 0.022 0.094 0.38 1 -0.5 4 5
DVL1 0.034 0.078 0.25 1 -0.45 2 3
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.001 0.17 -10000 0 -0.52 10 10
DKK1/LRP6/Kremen 2 -0.12 0.19 -10000 0 -0.36 53 53
LRP6 0.027 0.045 -10000 0 -0.51 1 1
CSNK1A1 0.036 0.06 0.41 1 -0.51 1 2
NLK 0.03 0.01 -10000 0 -10000 0 0
CCND1 -0.068 0.45 0.6 5 -1.5 12 17
WNT1 0.033 0.004 -10000 0 -10000 0 0
GSK3A 0.032 0.005 -10000 0 -10000 0 0
GSK3B 0.028 0.012 -10000 0 -10000 0 0
FRAT1 0.03 0.01 -10000 0 -10000 0 0
PPP2R5D 0.033 0.058 0.2 1 -0.26 3 4
APC 0.035 0.068 -10000 0 -0.28 2 2
WNT1/LRP6/FZD1 0.05 0.086 0.24 18 -0.27 2 20
CREBBP 0.037 0.032 0.25 2 -10000 0 2
IL6-mediated signaling events

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
BCL2L1 -0.026 0.24 -10000 0 -0.7 7 7
CRP -0.031 0.24 -10000 0 -0.72 6 6
cell cycle arrest -0.053 0.27 -10000 0 -0.7 13 13
TIMP1 -0.051 0.27 -10000 0 -0.87 8 8
IL6ST 0.022 0.064 -10000 0 -0.5 2 2
Rac1/GDP -0.026 0.17 0.33 1 -0.48 10 11
AP1 0.024 0.14 -10000 0 -0.46 4 4
GAB2 0.032 0.014 -10000 0 -10000 0 0
TNFSF11 -0.077 0.32 -10000 0 -1 11 11
HSP90B1 0.038 0.099 -10000 0 -1.1 1 1
GAB1 0.02 0.076 -10000 0 -0.51 3 3
MAPK14 -0.036 0.16 0.3 1 -0.86 3 4
AKT1 0.039 0.096 0.28 1 -0.47 3 4
FOXO1 0.031 0.1 -10000 0 -0.43 4 4
MAP2K6 -0.037 0.16 0.33 1 -0.6 5 6
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.029 0.18 0.34 1 -0.5 12 13
MITF -0.023 0.15 0.29 2 -0.46 8 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.013 -10000 0 -10000 0 0
A2M -0.024 0.23 -10000 0 -1.4 4 4
CEBPB 0.035 0.045 -10000 0 -0.51 1 1
GRB2/SOS1/GAB family/SHP2 0.022 0.099 -10000 0 -0.45 1 1
STAT3 -0.056 0.28 -10000 0 -0.75 13 13
STAT1 -0.026 0.22 -10000 0 -0.95 8 8
CEBPD -0.048 0.28 -10000 0 -0.78 12 12
PIK3CA 0.01 0.062 -10000 0 -0.51 2 2
PI3K 0.005 0.076 -10000 0 -0.37 5 5
JUN 0.002 0.11 -10000 0 -0.51 7 7
PIAS3/MITF -0.018 0.15 -10000 0 -0.47 7 7
MAPK11 -0.034 0.16 0.3 1 -0.86 3 4
STAT3 (dimer)/FOXO1 -0.022 0.26 -10000 0 -0.64 11 11
GRB2/SOS1/GAB family 0.003 0.18 -10000 0 -0.55 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.046 0.18 -10000 0 -0.48 13 13
GRB2 0.033 0.006 -10000 0 -10000 0 0
JAK2 0.024 0.046 -10000 0 -0.51 1 1
LBP -0.007 0.2 -10000 0 -0.64 4 4
PIK3R1 0.005 0.098 -10000 0 -0.51 5 5
JAK1 0.029 0.046 -10000 0 -0.52 1 1
MYC -0.045 0.3 -10000 0 -0.84 12 12
FGG -0.069 0.28 -10000 0 -0.82 11 11
macrophage differentiation -0.053 0.27 -10000 0 -0.7 13 13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.016 0.16 -10000 0 -0.32 26 26
JUNB -0.055 0.27 -10000 0 -0.84 10 10
FOS -0.03 0.16 -10000 0 -0.51 14 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.16 0.32 2 -0.43 11 13
STAT1/PIAS1 -0.017 0.18 0.34 2 -0.46 12 14
GRB2/SOS1/GAB family/SHP2/PI3K 0.041 0.082 -10000 0 -0.35 3 3
STAT3 (dimer) -0.058 0.28 -10000 0 -0.74 13 13
PRKCD -0.031 0.21 0.36 1 -0.55 13 14
IL6R 0.016 0.089 -10000 0 -0.52 4 4
SOCS3 -0.041 0.2 -10000 0 -1.2 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.024 0.12 -10000 0 -0.31 14 14
Rac1/GTP -0.028 0.18 0.33 1 -0.49 11 12
HCK 0.005 0.11 -10000 0 -0.51 7 7
MAPKKK cascade 0.045 0.094 -10000 0 -0.43 2 2
bone resorption -0.069 0.3 -10000 0 -0.92 11 11
IRF1 -0.065 0.3 -10000 0 -0.88 12 12
mol:GDP -0.036 0.17 0.34 1 -0.47 11 12
SOS1 0.033 0.007 -10000 0 -10000 0 0
VAV1 -0.037 0.17 0.34 1 -0.48 11 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.036 0.18 -10000 0 -1 3 3
PTPN11 0.02 0.08 -10000 0 -0.91 1 1
IL6/IL6RA -0.025 0.14 -10000 0 -0.38 19 19
gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.11 -10000 0 -0.31 13 13
gp130 (dimer)/JAK2/JAK2/LMO4 0.018 0.11 -10000 0 -0.31 14 14
IL6 -0.046 0.16 -10000 0 -0.51 16 16
PIAS3 0.03 0.009 -10000 0 -10000 0 0
PTPRE -0.002 0.11 -10000 0 -0.51 6 6
PIAS1 0.032 0.003 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.03 0.14 0.27 3 -0.37 9 12
LMO4 -0.012 0.14 -10000 0 -0.51 11 11
STAT3 (dimer)/PIAS3 -0.048 0.26 -10000 0 -0.69 13 13
MCL1 0.049 0.099 -10000 0 -0.48 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.001 0.12 -10000 0 -0.51 8 8
HSPA8 0.028 0.044 -10000 0 -0.51 1 1
SMAD3/SMAD4/ER alpha 0.01 0.15 -10000 0 -0.37 13 13
AKT1 -0.004 0.077 -10000 0 -0.51 2 2
GSC -0.016 0.18 -10000 0 -1.4 2 2
NKX2-5 -0.002 0.014 -10000 0 -10000 0 0
muscle cell differentiation 0.026 0.16 0.39 18 -10000 0 18
SMAD2-3/SMAD4/SP1 -0.002 0.18 -10000 0 -0.46 10 10
SMAD4 -0.004 0.1 -10000 0 -0.59 3 3
CBFB 0.031 0.007 -10000 0 -10000 0 0
SAP18 0.031 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.037 0.091 -10000 0 -0.32 8 8
SMAD3/SMAD4/VDR 0.021 0.16 -10000 0 -0.35 16 16
MYC 0.019 0.094 -10000 0 -0.48 5 5
CDKN2B -0.4 0.69 -10000 0 -1.6 35 35
AP1 -0.031 0.19 -10000 0 -0.44 18 18
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.037 0.1 -10000 0 -0.42 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.073 0.17 -10000 0 -0.36 31 31
SP3 0.032 0.013 -10000 0 -10000 0 0
CREB1 0.025 0.061 -10000 0 -0.51 2 2
FOXH1 0.02 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.021 0.12 -10000 0 -0.35 8 8
GATA3 0.03 0.027 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.018 0.082 -10000 0 -0.37 5 5
MEF2C/TIF2 -0.002 0.14 0.33 2 -0.51 7 9
endothelial cell migration 0.097 0.39 1.3 14 -10000 0 14
MAX 0.034 0.015 -10000 0 -10000 0 0
RBBP7 0.031 0.011 -10000 0 -10000 0 0
RBBP4 0.028 0.044 -10000 0 -0.51 1 1
RUNX2 0.025 0.061 -10000 0 -0.51 2 2
RUNX3 -0.004 0.13 -10000 0 -0.51 10 10
RUNX1 0.02 0.075 -10000 0 -0.51 3 3
CTBP1 0.03 0.009 -10000 0 -10000 0 0
NR3C1 0.033 0.017 -10000 0 -10000 0 0
VDR -0.002 0.13 -10000 0 -0.51 9 9
CDKN1A -0.037 0.22 -10000 0 -1.1 5 5
KAT2B 0 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.012 0.097 -10000 0 -0.27 8 8
DCP1A 0.03 0.009 -10000 0 -10000 0 0
SKI 0.032 0.005 -10000 0 -10000 0 0
SERPINE1 -0.099 0.4 -10000 0 -1.3 14 14
SMAD3/SMAD4/ATF2 0.017 0.12 -10000 0 -0.34 9 9
SMAD3/SMAD4/ATF3 -0.001 0.14 -10000 0 -0.35 14 14
SAP30 0.03 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.037 0.09 -10000 0 -0.32 7 7
JUN -0.042 0.18 -10000 0 -0.48 15 15
SMAD3/SMAD4/IRF7 0.02 0.13 -10000 0 -0.33 12 12
TFE3 0.025 0.037 -10000 0 -10000 0 0
COL1A2 -0.069 0.28 -10000 0 -0.91 14 14
mesenchymal cell differentiation -0.013 0.13 0.37 10 -10000 0 10
DLX1 0.025 0.027 -10000 0 -10000 0 0
TCF3 0.028 0.044 -10000 0 -0.51 1 1
FOS -0.037 0.16 -10000 0 -0.53 14 14
SMAD3/SMAD4/Max 0.023 0.12 -10000 0 -0.35 8 8
Cbp/p300/SNIP1 0.037 0.088 -10000 0 -0.32 8 8
ZBTB17 0.033 0.014 -10000 0 -10000 0 0
LAMC1 -0.019 0.14 -10000 0 -0.66 5 5
TGIF2/HDAC complex/SMAD3/SMAD4 0.014 0.12 -10000 0 -0.37 9 9
IRF7 0.029 0.047 -10000 0 -0.5 1 1
ESR1 0.005 0.11 -10000 0 -0.47 7 7
HNF4A 0.031 0.01 -10000 0 -10000 0 0
MEF2C -0.007 0.14 0.33 2 -0.51 7 9
SMAD2-3/SMAD4 0.002 0.13 -10000 0 -0.31 11 11
Cbp/p300/Src-1 0.038 0.09 -10000 0 -0.32 8 8
IGHV3OR16-13 -0.006 0.095 -10000 0 -0.61 3 3
TGIF2/HDAC complex 0.027 0.045 -10000 0 -0.51 1 1
CREBBP 0.029 0.018 -10000 0 -10000 0 0
SKIL 0 0.095 -10000 0 -0.51 5 5
HDAC1 0.031 0.01 -10000 0 -10000 0 0
HDAC2 0.032 0.009 -10000 0 -10000 0 0
SNIP1 0.031 0.007 -10000 0 -10000 0 0
GCN5L2 0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.14 -10000 0 -0.35 12 12
MSG1/HSC70 0.042 0.038 -10000 0 -0.37 1 1
SMAD2 0.002 0.064 -10000 0 -0.35 2 2
SMAD3 -0.011 0.12 -10000 0 -0.51 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0 0.088 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 -0.013 0.073 0.16 3 -0.27 6 9
NCOR1 0.031 0.008 -10000 0 -10000 0 0
NCOA2 0.024 0.062 -10000 0 -0.51 2 2
NCOA1 0.032 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.024 0.093 -10000 0 -0.37 8 8
SMAD2-3/SMAD4/SP1/MIZ-1 0.004 0.18 -10000 0 -0.48 9 9
IFNB1 -0.008 0.11 -10000 0 -0.41 6 6
SMAD3/SMAD4/MEF2C -0.005 0.16 -10000 0 -0.48 8 8
CITED1 0.03 0.016 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.013 0.12 -10000 0 -0.31 6 6
RBL1 0.03 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.11 0.25 -10000 0 -0.54 35 35
RUNX1-3/PEBPB2 0.029 0.11 -10000 0 -0.37 10 10
SMAD7 -0.046 0.2 -10000 0 -0.63 10 10
MYC/MIZ-1 0.039 0.077 -10000 0 -0.33 5 5
SMAD3/SMAD4 -0.029 0.18 0.32 1 -0.47 18 19
IL10 -0.002 0.09 -10000 0 -0.36 3 3
PIASy/HDAC complex 0.03 0.014 -10000 0 -10000 0 0
PIAS3 0.029 0.013 -10000 0 -10000 0 0
CDK2 0.026 0.048 -10000 0 -0.52 1 1
IL5 -0.004 0.095 -10000 0 -0.42 3 3
CDK4 0.03 0.018 -10000 0 -10000 0 0
PIAS4 0.03 0.014 -10000 0 -10000 0 0
ATF3 0.004 0.11 -10000 0 -0.51 6 6
SMAD3/SMAD4/SP1 -0.005 0.17 -10000 0 -0.42 13 13
FOXG1 0.02 0.033 -10000 0 -10000 0 0
FOXO3 -0.017 0.072 -10000 0 -0.37 3 3
FOXO1 -0.024 0.092 -10000 0 -0.4 6 6
FOXO4 -0.015 0.066 -10000 0 -0.37 2 2
heart looping -0.007 0.14 0.33 2 -0.5 7 9
CEBPB 0.011 0.054 -10000 0 -0.51 1 1
SMAD3/SMAD4/DLX1 0.014 0.12 -10000 0 -0.35 9 9
MYOD1 0.007 0.11 -10000 0 -0.51 7 7
SMAD3/SMAD4/HNF4 0.017 0.12 -10000 0 -0.34 9 9
SMAD3/SMAD4/GATA3 0.025 0.12 -10000 0 -0.35 8 8
SnoN/SIN3/HDAC complex/NCoR1 0 0.095 -10000 0 -0.51 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.022 0.16 -10000 0 -0.41 12 12
SMAD3/SMAD4/SP1-3 0.015 0.17 -10000 0 -0.54 7 7
MED15 0.028 0.013 -10000 0 -10000 0 0
SP1 0.003 0.09 -10000 0 -0.46 3 3
SIN3B 0.032 0.005 -10000 0 -10000 0 0
SIN3A 0.032 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.012 0.1 -10000 0 -0.28 11 11
ITGB5 -0.025 0.16 -10000 0 -0.65 6 6
TGIF/SIN3/HDAC complex/CtBP 0.026 0.065 -10000 0 -0.41 2 2
SMAD3/SMAD4/AR 0.004 0.13 -10000 0 -0.36 12 12
AR 0.012 0.08 -10000 0 -0.51 3 3
negative regulation of cell growth -0.013 0.11 -10000 0 -0.35 8 8
SMAD3/SMAD4/MYOD 0 0.14 -10000 0 -0.36 15 15
E2F5 0.014 0.087 -10000 0 -0.51 4 4
E2F4 0.031 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.031 0.12 -10000 0 -0.3 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 -0.075 0.18 -10000 0 -0.4 32 32
TFDP1 0.031 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.017 0.2 -10000 0 -0.51 14 14
SMAD3/SMAD4/RUNX2 0.013 0.13 -10000 0 -0.37 10 10
TGIF2 0.027 0.045 -10000 0 -0.51 1 1
TGIF1 0.027 0.044 -10000 0 -0.51 1 1
ATF2 0.032 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.031 0.01 -10000 0 -10000 0 0
HDAC2 0.032 0.009 -10000 0 -10000 0 0
GNB1/GNG2 0.002 0.14 -10000 0 -0.32 23 23
forebrain development -0.081 0.23 -10000 0 -0.65 15 15
GNAO1 0.03 0.011 -10000 0 -10000 0 0
SMO/beta Arrestin2 -0.025 0.15 -10000 0 -0.37 24 24
SMO -0.055 0.2 -10000 0 -0.51 24 24
ARRB2 0.03 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.004 0.16 0.28 1 -0.48 7 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.012 -10000 0 -10000 0 0
GNAI2 0.027 0.018 -10000 0 -10000 0 0
SIN3/HDAC complex 0.076 0.026 -10000 0 -10000 0 0
GNAI1 -0.001 0.13 -10000 0 -0.51 9 9
XPO1 0.026 0.017 -10000 0 -10000 0 0
GLI1/Su(fu) -0.091 0.23 -10000 0 -0.64 15 15
SAP30 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.055 0.2 -10000 0 -0.51 24 24
MIM/GLI2A -0.025 0.14 -10000 0 -0.48 11 11
IFT88 0.027 0.044 -10000 0 -0.51 1 1
GNAI3 0.031 0.007 -10000 0 -10000 0 0
GLI2 -0.011 0.12 -10000 0 -0.43 5 5
GLI3 -0.008 0.16 0.26 2 -0.47 8 10
CSNK1D 0.032 0.006 -10000 0 -10000 0 0
CSNK1E 0.028 0.044 -10000 0 -0.51 1 1
SAP18 0.031 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.044 -10000 0 -0.51 1 1
GNG2 0.032 0.005 -10000 0 -10000 0 0
Gi family/GTP -0.046 0.16 -10000 0 -0.34 28 28
SIN3B 0.032 0.005 -10000 0 -10000 0 0
SIN3A 0.032 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) -0.008 0.15 -10000 0 -0.44 10 10
GLI2/Su(fu) -0.027 0.15 -10000 0 -0.47 6 6
FOXA2 -0.16 0.39 -10000 0 -0.98 26 26
neural tube patterning -0.081 0.23 -10000 0 -0.65 15 15
SPOP 0.032 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.004 0.1 -10000 0 -0.66 1 1
GNB1 0.032 0.005 -10000 0 -10000 0 0
CSNK1G2 0.032 0.005 -10000 0 -10000 0 0
CSNK1G3 0.03 0.008 -10000 0 -10000 0 0
MTSS1 -0.025 0.14 -10000 0 -0.48 11 11
embryonic limb morphogenesis -0.081 0.23 -10000 0 -0.65 15 15
SUFU -0.011 0.095 -10000 0 -0.71 1 1
LGALS3 0.02 0.075 -10000 0 -0.51 3 3
catabolic process -0.016 0.18 -10000 0 -0.54 9 9
GLI3A/CBP -0.007 0.11 -10000 0 -0.37 12 12
KIF3A 0.023 0.062 -10000 0 -0.51 2 2
GLI1 -0.083 0.23 -10000 0 -0.67 15 15
RAB23 0.027 0.045 -10000 0 -0.51 1 1
CSNK1A1 0.028 0.044 -10000 0 -0.51 1 1
IFT172 0.03 0.016 -10000 0 -10000 0 0
RBBP7 0.031 0.011 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.007 0.11 -10000 0 -0.42 5 5
GNAZ 0.003 0.11 -10000 0 -0.51 7 7
RBBP4 0.028 0.044 -10000 0 -0.51 1 1
CSNK1G1 0.032 0.003 -10000 0 -10000 0 0
PIAS1 0.032 0.003 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0 0.12 -10000 0 -0.41 5 5
STK36 0.025 0.046 -10000 0 -0.51 1 1
Gi family/GNB1/GNG2/GDP -0.042 0.15 -10000 0 -0.43 14 14
PTCH1 -0.077 0.22 -10000 0 -0.69 12 12
MIM/GLI1 -0.1 0.26 -10000 0 -0.62 25 25
CREBBP -0.007 0.11 -10000 0 -0.37 12 12
Su(fu)/SIN3/HDAC complex 0.014 0.081 -10000 0 -0.4 4 4
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.12 -10000 0 -0.46 7 7
HDAC1 0.033 0.016 -10000 0 -10000 0 0
AES 0.032 0.007 -10000 0 -10000 0 0
FBXW11 0.031 0.007 -10000 0 -10000 0 0
DTX1 0.028 0.044 -10000 0 -0.51 1 1
LRP6/FZD1 0.037 0.05 -10000 0 -0.37 2 2
TLE1 0.021 0.074 -10000 0 -0.5 3 3
AP1 -0.023 0.1 -10000 0 -0.28 19 19
NCSTN 0.031 0.007 -10000 0 -10000 0 0
ADAM10 0.032 0.009 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.017 0.19 -10000 0 -0.83 6 6
NICD/RBPSUH 0.027 0.12 -10000 0 -0.44 8 8
WIF1 -0.063 0.18 -10000 0 -0.51 21 21
NOTCH1 0.003 0.11 -10000 0 -0.46 8 8
PSENEN 0.03 0.009 -10000 0 -10000 0 0
KREMEN2 -0.099 0.21 -10000 0 -0.51 30 30
DKK1 -0.094 0.2 -10000 0 -0.51 29 29
beta catenin/beta TrCP1 0.011 0.084 -10000 0 -0.3 4 4
APH1B 0.029 0.044 -10000 0 -0.51 1 1
APH1A 0.013 0.096 -10000 0 -0.51 5 5
AXIN1 0.001 0.1 -10000 0 -0.54 4 4
CtBP/CBP/TCF1/TLE1/AES 0.02 0.073 0.26 2 -0.34 1 3
PSEN1 0.028 0.044 -10000 0 -0.51 1 1
FOS -0.03 0.16 -10000 0 -0.51 14 14
JUN 0.002 0.11 -10000 0 -0.51 7 7
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
CTNNB1 -0.003 0.082 -10000 0 -0.3 6 6
MAPK3 0.032 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.055 0.15 -10000 0 -0.32 35 35
HNF1A 0.028 0.024 -10000 0 -10000 0 0
CTBP1 0.03 0.011 -10000 0 -10000 0 0
MYC -0.034 0.29 -10000 0 -1.5 6 6
NKD1 0.026 0.024 -10000 0 -10000 0 0
FZD1 0.026 0.045 -10000 0 -0.51 1 1
NOTCH1 precursor/Deltex homolog 1 0.028 0.12 -10000 0 -0.44 8 8
apoptosis -0.023 0.1 -10000 0 -0.28 19 19
Delta 1/NOTCHprecursor 0.024 0.12 -10000 0 -0.46 7 7
DLL1 0.019 0.076 -10000 0 -0.51 3 3
PPARD 0.024 0.031 -10000 0 -10000 0 0
Gamma Secretase 0.065 0.083 -10000 0 -0.32 5 5
APC -0.009 0.13 -10000 0 -0.49 8 8
DVL1 0.007 0.055 -10000 0 -0.32 3 3
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.19 -10000 0 -0.36 53 53
LRP6 0.027 0.045 -10000 0 -0.51 1 1
CSNK1A1 0.027 0.044 -10000 0 -0.51 1 1
NLK 0.019 0.015 -10000 0 -10000 0 0
CCND1 -0.099 0.39 -10000 0 -1.4 12 12
WNT1 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.006 0.12 -10000 0 -0.43 8 8
DKK2 0.01 0.089 -10000 0 -0.51 4 4
NOTCH1 precursor/DVL1 0.013 0.13 -10000 0 -0.48 8 8
GSK3B 0.028 0.012 -10000 0 -10000 0 0
FRAT1 0.031 0.011 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.029 0.12 -10000 0 -0.45 8 8
PPP2R5D 0.017 0.049 -10000 0 -0.34 2 2
MAPK1 0.026 0.044 -10000 0 -0.51 1 1
WNT1/LRP6/FZD1 -0.001 0.12 -10000 0 -0.29 21 21
RBPJ 0.03 0.008 -10000 0 -10000 0 0
CREBBP 0.031 0.012 -10000 0 -10000 0 0
Reelin 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
CDK5R1/CDK5 0.045 0.016 -10000 0 -10000 0 0
VLDLR -0.013 0.13 -10000 0 -0.51 10 10
CRKL 0.028 0.013 -10000 0 -10000 0 0
LRPAP1 0.03 0.009 -10000 0 -10000 0 0
FYN 0.024 0.062 -10000 0 -0.51 2 2
ITGA3 -0.006 0.12 -10000 0 -0.51 7 7
RELN/VLDLR/Fyn 0.013 0.11 -10000 0 -0.32 12 12
MAPK8IP1/MKK7/MAP3K11/JNK1 0.077 0.049 -10000 0 -0.27 1 1
AKT1 -0.026 0.11 -10000 0 -0.52 5 5
MAP2K7 0.029 0.018 -10000 0 -10000 0 0
RAPGEF1 0.032 0.003 -10000 0 -10000 0 0
DAB1 0.031 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.025 0.096 -10000 0 -0.29 12 12
LRPAP1/LRP8 0.008 0.11 -10000 0 -0.37 12 12
RELN/LRP8/DAB1/Fyn 0.033 0.11 -10000 0 -0.3 13 13
DAB1/alpha3/beta1 Integrin -0.027 0.14 -10000 0 -0.3 27 27
long-term memory 0.039 0.12 -10000 0 -0.3 14 14
DAB1/LIS1 0.01 0.13 -10000 0 -0.29 20 20
DAB1/CRLK/C3G -0.002 0.12 -10000 0 -0.29 19 19
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
DAB1/NCK2 0.011 0.13 -10000 0 -0.3 20 20
ARHGEF2 0.028 0.044 -10000 0 -0.51 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.006 -10000 0 -10000 0 0
CDK5R1 0.03 0.016 -10000 0 -10000 0 0
RELN 0.029 0.017 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
RELN/LRP8/Fyn 0.021 0.12 -10000 0 -0.34 13 13
GRIN2A/RELN/LRP8/DAB1/Fyn 0.045 0.11 -10000 0 -0.3 13 13
MAPK8 0.031 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.018 0.091 -10000 0 -0.29 10 10
ITGB1 0.024 0.062 -10000 0 -0.51 2 2
MAP1B -0.073 0.17 -10000 0 -0.32 39 39
RELN/LRP8 0.022 0.1 -10000 0 -0.32 12 12
GRIN2B/RELN/LRP8/DAB1/Fyn 0.039 0.12 -10000 0 -0.31 14 14
PI3K 0.004 0.075 -10000 0 -0.37 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.009 0.1 -10000 0 -0.37 9 9
RAP1A -0.023 0.13 0.35 3 -0.44 4 7
PAFAH1B1 0.03 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.03 0.014 -10000 0 -10000 0 0
CRLK/C3G 0.042 0.017 -10000 0 -10000 0 0
GRIN2B 0.023 0.062 -10000 0 -0.51 2 2
NCK2 0.032 0.004 -10000 0 -10000 0 0
neuron differentiation 0.014 0.077 -10000 0 -0.31 2 2
neuron adhesion -0.04 0.15 0.33 4 -0.49 5 9
LRP8 -0.015 0.14 -10000 0 -0.51 12 12
GSK3B -0.004 0.12 -10000 0 -0.5 5 5
RELN/VLDLR/DAB1/Fyn 0.024 0.099 -10000 0 -0.27 12 12
MAP3K11 0.033 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.019 0.1 -10000 0 -0.39 8 8
CDK5 0.032 0.004 -10000 0 -10000 0 0
MAPT 0.005 0.055 0.67 1 -10000 0 1
neuron migration -0.001 0.13 -10000 0 -0.43 5 5
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.014 0.077 -10000 0 -0.31 2 2
RELN/VLDLR 0 0.14 -10000 0 -0.32 20 20
Glypican 2 network

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
MDK 0.004 0.11 -9999 0 -0.51 7 7
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.002 0.083 -9999 0 -0.31 9 9
neuron projection morphogenesis 0.002 0.083 -9999 0 -0.31 9 9
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 0.031 -10000 0 -0.37 1 1
GNB1/GNG2 0.043 0.056 -10000 0 -0.29 3 3
regulation of S phase of mitotic cell cycle -0.002 0.053 -10000 0 -0.24 5 5
GNAO1 0.031 0.011 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
SHBG/T-DHT 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.004 0.043 -10000 0 -0.37 2 2
MAP2K1 -0.013 0.072 -10000 0 -0.26 5 5
T-DHT/AR 0.009 0.057 -10000 0 -0.37 3 3
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 18 18
GNAI2 0.027 0.017 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 -0.001 0.13 -10000 0 -0.51 9 9
mol:GDP -0.015 0.061 -10000 0 -0.3 4 4
cell proliferation -0.045 0.15 -10000 0 -0.41 18 18
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
FOS -0.08 0.26 -10000 0 -0.8 16 16
mol:Ca2+ -0.006 0.024 -10000 0 -0.067 16 16
MAPK3 -0.034 0.1 -10000 0 -0.29 15 15
MAPK1 -0.026 0.13 -10000 0 -0.55 6 6
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
mol:IP3 0 0.001 -10000 0 -0.004 17 17
cAMP biosynthetic process 0 0.016 -10000 0 -10000 0 0
GNG2 0.032 0.005 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 17 17
HRAS/GTP 0.027 0.071 -10000 0 -0.27 5 5
actin cytoskeleton reorganization 0.009 0.057 -10000 0 -0.26 5 5
SRC 0.03 0.011 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 17 17
PI3K 0.005 0.064 -10000 0 -0.32 5 5
apoptosis 0.041 0.16 0.44 18 -10000 0 18
T-DHT/AR/PELP1 0.026 0.054 -10000 0 -0.32 3 3
HRAS/GDP -0.002 0.076 -10000 0 -0.3 5 5
CREB1 -0.045 0.17 -10000 0 -0.47 18 18
RAC1-CDC42/GTP 0.014 0.061 -10000 0 -0.26 5 5
AR 0.012 0.08 -10000 0 -0.51 3 3
GNB1 0.032 0.005 -10000 0 -10000 0 0
RAF1 -0.003 0.07 -10000 0 -0.27 5 5
RAC1-CDC42/GDP 0.052 0.089 -10000 0 -0.31 3 3
T-DHT/AR/PELP1/Src 0.039 0.057 -10000 0 -0.29 3 3
MAP2K2 -0.011 0.071 -10000 0 -0.28 4 4
T-DHT/AR/PELP1/Src/PI3K -0.002 0.053 -10000 0 -0.24 5 5
GNAZ 0.003 0.11 -10000 0 -0.51 7 7
SHBG 0.03 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.01 0.15 -10000 0 -0.57 7 7
mol:T-DHT 0 0.001 -10000 0 -0.003 12 12
RAC1 0.032 0.005 -10000 0 -10000 0 0
GNRH1 -0.012 0.084 -10000 0 -0.37 8 8
Gi family/GTP -0.018 0.092 -10000 0 -0.25 17 17
CDC42 0.032 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.046 0.078 -10000 0 -0.27 7 7
ER alpha/Gai/GDP/Gbeta gamma -0.035 0.17 -10000 0 -0.58 9 9
AKT1 -0.046 0.22 -10000 0 -0.82 10 10
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.045 0.22 -10000 0 -0.83 10 10
mol:Ca2+ -0.033 0.1 -10000 0 -0.32 11 11
IGF1R -0.008 0.14 -10000 0 -0.51 11 11
E2/ER alpha (dimer)/Striatin 0.013 0.086 -10000 0 -0.31 9 9
SHC1 0.031 0.007 -10000 0 -10000 0 0
apoptosis 0.044 0.2 0.77 10 -10000 0 10
RhoA/GTP -0.007 0.083 -10000 0 -0.25 15 15
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.01 0.16 -10000 0 -0.48 10 10
regulation of stress fiber formation 0.024 0.099 0.4 2 -0.28 1 3
E2/ERA-ERB (dimer) 0.018 0.077 -10000 0 -0.31 7 7
KRAS 0.016 0.086 -10000 0 -0.51 4 4
G13/GTP 0.016 0.074 -10000 0 -0.28 8 8
pseudopodium formation -0.024 0.099 0.28 1 -0.4 2 3
E2/ER alpha (dimer)/PELP1 0.018 0.077 -10000 0 -0.31 7 7
GRB2 0.032 0.005 -10000 0 -10000 0 0
GNG2 0.032 0.005 -10000 0 -10000 0 0
GNAO1 0.031 0.011 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.027 0.16 -10000 0 -0.52 11 11
E2/ER beta (dimer) 0.023 0.007 -10000 0 -10000 0 0
mol:GDP -0.011 0.098 -10000 0 -0.4 7 7
mol:NADP -0.027 0.16 -10000 0 -0.52 11 11
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
mol:IP3 -0.034 0.11 -10000 0 -0.33 11 11
IGF-1R heterotetramer -0.008 0.14 -10000 0 -0.51 11 11
PLCB1 -0.028 0.11 -10000 0 -0.29 17 17
PLCB2 -0.024 0.11 -10000 0 -0.31 15 15
IGF1 -0.049 0.18 -10000 0 -0.51 20 20
mol:L-citrulline -0.027 0.16 -10000 0 -0.52 11 11
RHOA 0.03 0.009 -10000 0 -10000 0 0
Gai/GDP -0.042 0.22 -10000 0 -0.66 15 15
JNK cascade 0.023 0.007 -10000 0 -10000 0 0
BCAR1 0.031 0.007 -10000 0 -10000 0 0
ESR2 0.031 0.01 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.002 0.12 -10000 0 -0.51 7 7
Gq family/GDP/Gbeta gamma -0.034 0.18 -10000 0 -0.5 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.061 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.16 -10000 0 -0.46 11 11
GNAZ 0.003 0.11 -10000 0 -0.51 7 7
E2/ER alpha (dimer) 0 0.083 -10000 0 -0.37 7 7
STRN 0.02 0.076 -10000 0 -0.51 3 3
GNAL 0.008 0.098 -10000 0 -0.51 5 5
PELP1 0.03 0.008 -10000 0 -10000 0 0
MAPK11 0.017 0.007 -10000 0 -10000 0 0
GNAI2 0.028 0.017 -10000 0 -10000 0 0
GNAI3 0.031 0.006 -10000 0 -10000 0 0
GNAI1 -0.001 0.13 -10000 0 -0.51 9 9
HBEGF -0.061 0.2 0.35 2 -0.52 16 18
cAMP biosynthetic process 0.004 0.08 -10000 0 -0.26 12 12
SRC -0.031 0.17 0.27 2 -0.52 10 12
PI3K 0.004 0.075 -10000 0 -0.37 5 5
GNB1 0.032 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.019 0.1 -10000 0 -0.34 8 8
SOS1 0.032 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.067 0.15 -10000 0 -0.4 18 18
Gs family/GTP 0.011 0.084 -10000 0 -0.26 12 12
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.076 -10000 0 -0.29 7 7
vasodilation -0.024 0.16 -10000 0 -0.5 11 11
mol:DAG -0.034 0.11 -10000 0 -0.33 11 11
Gs family/GDP/Gbeta gamma -0.011 0.1 -10000 0 -0.33 9 9
MSN -0.026 0.1 0.29 1 -0.43 2 3
Gq family/GTP -0.021 0.12 -10000 0 -0.33 15 15
mol:PI-3-4-5-P3 -0.042 0.21 -10000 0 -0.79 10 10
NRAS 0.025 0.047 -10000 0 -0.51 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.024 0.16 0.5 11 -10000 0 11
GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.1 -10000 0 -0.38 7 7
NOS3 -0.029 0.17 -10000 0 -0.55 11 11
GNA11 0.025 0.061 -10000 0 -0.51 2 2
MAPKKK cascade -0.008 0.18 0.33 1 -0.56 11 12
E2/ER alpha (dimer)/PELP1/Src -0.014 0.17 -10000 0 -0.48 12 12
ruffle organization -0.024 0.099 0.28 1 -0.4 2 3
ROCK2 -0.013 0.092 0.31 1 -10000 0 1
GNA14 0.014 0.079 -10000 0 -0.51 3 3
GNA15 -0.015 0.15 -10000 0 -0.51 13 13
GNA13 0.028 0.044 -10000 0 -0.51 1 1
MMP9 -0.04 0.19 0.38 2 -0.53 13 15
MMP2 -0.047 0.18 0.44 1 -0.52 12 13
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.004 0.17 -10000 0 -0.62 10 10
VEGFR1 homodimer/NRP1 -0.024 0.16 -10000 0 -0.62 10 10
mol:DAG -0.023 0.15 -10000 0 -0.56 10 10
VEGFR1 homodimer/NRP1/VEGFR 121 -0.007 0.16 -10000 0 -0.56 11 11
CaM/Ca2+ -0.006 0.15 -10000 0 -0.6 8 8
HIF1A 0.01 0.12 -10000 0 -0.42 10 10
GAB1 0.019 0.076 -10000 0 -0.51 3 3
AKT1 0.019 0.18 0.33 1 -0.53 11 12
PLCG1 -0.023 0.15 -10000 0 -0.56 10 10
NOS3 0.012 0.14 -10000 0 -0.54 8 8
CBL 0.032 0.005 -10000 0 -10000 0 0
mol:NO 0.018 0.15 0.55 1 -0.52 8 9
FLT1 -0.021 0.18 -10000 0 -0.74 9 9
PGF 0.02 0.051 -10000 0 -0.51 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.003 0.18 -10000 0 -0.66 9 9
CALM1 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
eNOS/Hsp90 0.024 0.15 -10000 0 -0.49 9 9
endothelial cell proliferation -0.019 0.15 -10000 0 -0.58 9 9
mol:Ca2+ -0.023 0.15 -10000 0 -0.55 10 10
MAPK3 -0.04 0.13 0.35 1 -0.56 8 9
MAPK1 -0.04 0.13 0.35 1 -0.54 8 9
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
PLGF homodimer 0.02 0.051 -10000 0 -0.51 1 1
PRKACA 0.031 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.029 0.16 -10000 0 -0.51 15 15
VEGFA homodimer 0.025 0.061 -10000 0 -0.51 2 2
VEGFR1 homodimer/VEGFA homodimer -0.007 0.18 -10000 0 -0.6 11 11
platelet activating factor biosynthetic process -0.037 0.13 0.34 1 -0.53 8 9
PI3K -0.016 0.14 -10000 0 -0.53 9 9
PRKCA -0.032 0.14 -10000 0 -0.59 8 8
PRKCB -0.032 0.14 -10000 0 -0.55 9 9
VEGFR1 homodimer/PLGF homodimer -0.011 0.17 -10000 0 -0.6 11 11
VEGFA 0.025 0.061 -10000 0 -0.51 2 2
VEGFB 0.033 0 -10000 0 -10000 0 0
mol:IP3 -0.023 0.15 -10000 0 -0.56 10 10
RASA1 -0.019 0.16 -10000 0 -0.66 8 8
NRP2 0.02 0.076 -10000 0 -0.51 3 3
VEGFR1 homodimer -0.021 0.18 -10000 0 -0.74 9 9
VEGFB homodimer 0.033 0 -10000 0 -10000 0 0
NCK1 0.02 0.062 -10000 0 -0.51 2 2
eNOS/Caveolin-1 0 0.18 0.46 1 -0.52 11 12
PTPN11 0.029 0.044 -10000 0 -0.51 1 1
mol:PI-3-4-5-P3 -0.016 0.14 -10000 0 -0.52 9 9
mol:L-citrulline 0.018 0.15 0.55 1 -0.52 8 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.028 0.17 -10000 0 -0.64 8 8
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.005 0.15 -10000 0 -0.58 8 8
CD2AP 0.032 0.005 -10000 0 -10000 0 0
PI3K/GAB1 -0.014 0.15 -10000 0 -0.51 10 10
PDPK1 0.035 0.17 0.35 1 -0.5 9 10
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.009 0.17 -10000 0 -0.67 8 8
mol:NADP 0.018 0.15 0.55 1 -0.52 8 9
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.16 -10000 0 -0.63 8 8
VEGFR1 homodimer/NRP2 -0.012 0.18 -10000 0 -0.55 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0.004 0.12 -9999 0 -0.51 8 8
SVIL 0.004 0.12 -9999 0 -0.51 8 8
ZNF318 0.028 0.01 -9999 0 -10000 0 0
JMJD2C 0.007 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.012 0.086 -9999 0 -0.27 6 6
CARM1 0.032 0.006 -9999 0 -10000 0 0
PRDX1 0.013 0.079 -9999 0 -0.51 3 3
PELP1 0.03 0.008 -9999 0 -10000 0 0
CTNNB1 0.029 0.015 -9999 0 -10000 0 0
AKT1 0.023 0.062 -9999 0 -0.51 2 2
PTK2B 0.029 0.016 -9999 0 -10000 0 0
MED1 0.02 0.075 -9999 0 -0.51 3 3
MAK 0.026 0.018 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.033 0.01 -9999 0 -10000 0 0
GSN 0 0.13 -9999 0 -0.51 9 9
NCOA2 0.024 0.062 -9999 0 -0.51 2 2
NCOA6 0.026 0.062 -9999 0 -0.51 2 2
DNA-PK 0.054 0.036 -9999 0 -0.32 1 1
NCOA4 0.031 0.008 -9999 0 -10000 0 0
PIAS3 0.031 0.009 -9999 0 -10000 0 0
cell proliferation -0.006 0.055 -9999 0 -0.53 1 1
XRCC5 0.031 0.004 -9999 0 -10000 0 0
UBE3A 0.034 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.026 0.076 -9999 0 -0.2 12 12
FHL2 -0.15 0.36 -9999 0 -0.97 24 24
RANBP9 0.033 0.006 -9999 0 -10000 0 0
JMJD1A -0.025 0.057 -9999 0 -0.13 32 32
CDK6 0.009 0.1 -9999 0 -0.51 6 6
TGFB1I1 0.029 0.045 -9999 0 -0.51 1 1
T-DHT/AR/CyclinD1 -0.036 0.12 -9999 0 -0.36 15 15
XRCC6 0.031 0.006 -9999 0 -10000 0 0
T-DHT/AR -0.04 0.13 -9999 0 -0.3 12 12
CTDSP1 0.032 0.005 -9999 0 -10000 0 0
CTDSP2 0.03 0.003 -9999 0 -10000 0 0
BRCA1 0.03 0.044 -9999 0 -0.51 1 1
TCF4 -0.002 0.13 -9999 0 -0.51 9 9
CDKN2A -0.047 0.16 -9999 0 -0.51 16 16
SRF 0.003 0.069 -9999 0 -10000 0 0
NKX3-1 -0.058 0.099 -9999 0 -0.23 35 35
KLK3 0.024 0.049 -9999 0 -10000 0 0
TMF1 0.026 0.045 -9999 0 -0.51 1 1
HNRNPA1 0.031 0.004 -9999 0 -10000 0 0
AOF2 0.002 0 -9999 0 -10000 0 0
APPL1 0.006 0.054 -9999 0 -0.37 3 3
T-DHT/AR/Caspase 8 -0.02 0.097 -9999 0 -0.32 8 8
AR -0.021 0.095 -9999 0 -0.56 3 3
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.026 0.044 -9999 0 -0.51 1 1
PAWR 0.019 0.086 -9999 0 -0.51 4 4
PRKDC 0.026 0.044 -9999 0 -0.51 1 1
PA2G4 0.031 0.003 -9999 0 -10000 0 0
UBE2I 0.031 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.011 0.079 -9999 0 -0.22 8 8
RPS6KA3 0.029 0.045 -9999 0 -0.51 1 1
T-DHT/AR/ARA70 -0.013 0.085 -9999 0 -0.39 3 3
LATS2 0.023 0.062 -9999 0 -0.51 2 2
T-DHT/AR/PRX1 -0.02 0.092 -9999 0 -0.31 8 8
Cyclin D3/CDK11 p58 0.023 0.008 -9999 0 -10000 0 0
VAV3 -0.091 0.22 -9999 0 -0.51 32 32
KLK2 -0.007 0.047 -9999 0 -10000 0 0
CASP8 0.021 0.075 -9999 0 -0.51 3 3
T-DHT/AR/TIF2/CARM1 0 0.094 -9999 0 -0.35 5 5
TMPRSS2 -0.2 0.39 -9999 0 -0.92 33 33
CCND1 -0.015 0.14 -9999 0 -0.51 12 12
PIAS1 0.034 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.021 0.034 -9999 0 -0.067 51 51
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.022 0.1 -9999 0 -0.3 12 12
CMTM2 0.024 0.026 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.001 0.05 -9999 0 -10000 0 0
CCND3 0.031 0.013 -9999 0 -10000 0 0
TGIF1 0.026 0.044 -9999 0 -0.51 1 1
FKBP4 0.028 0.044 -9999 0 -0.51 1 1
Sphingosine 1-phosphate (S1P) 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 0.032 0.009 -9999 0 -10000 0 0
SPHK1 -0.007 0.13 -9999 0 -0.51 10 10
GNAI2 0.028 0.017 -9999 0 -10000 0 0
mol:S1P -0.027 0.12 -9999 0 -0.35 16 16
GNAO1 0.031 0.011 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.011 0.096 -9999 0 -0.37 10 10
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.001 0.11 -9999 0 -0.27 17 17
GNAI3 0.031 0.006 -9999 0 -10000 0 0
G12/G13 0.043 0.036 -9999 0 -0.37 1 1
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.03 0.11 -9999 0 -0.31 16 16
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.001 0.13 -9999 0 -0.51 9 9
S1P/S1P5/G12 -0.012 0.11 -9999 0 -0.28 16 16
S1P/S1P3/Gq -0.036 0.14 -9999 0 -0.39 17 17
S1P/S1P4/Gi -0.024 0.12 -9999 0 -0.38 11 11
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.003 0.11 -9999 0 -0.51 7 7
GNA14 0.014 0.079 -9999 0 -0.51 3 3
GNA15 -0.015 0.15 -9999 0 -0.51 13 13
GNA12 0.032 0.006 -9999 0 -10000 0 0
GNA13 0.028 0.044 -9999 0 -0.51 1 1
GNA11 0.025 0.061 -9999 0 -0.51 2 2
ABCC1 -0.025 0.15 -9999 0 -0.51 12 12
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.04 0.06 -10000 0 -0.27 5 5
RGS9BP -0.004 0.12 -10000 0 -0.51 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + -0.006 0.11 -10000 0 -0.32 15 15
mol:ADP 0.004 0.031 -10000 0 -0.37 1 1
GNAT2 0.026 0.045 -10000 0 -0.51 1 1
RGS9-1/Gbeta5/R9AP 0.01 0.12 -10000 0 -0.32 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.037 0.032 -10000 0 -0.31 1 1
GRK7 0.02 0.046 -10000 0 -0.51 1 1
CNGB3 -0.024 0.14 -10000 0 -0.51 12 12
Cone Metarhodopsin II/X-Arrestin 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.1 0.19 7 -0.29 15 22
Cone PDE6 0.026 0.12 -10000 0 -0.28 17 17
Cone Metarhodopsin II 0.013 0.026 -10000 0 -0.28 1 1
Na + (4 Units) 0.006 0.1 -10000 0 -0.29 15 15
GNAT2/GDP 0.018 0.11 -10000 0 -0.27 16 16
GNB5 0.018 0.086 -10000 0 -0.51 4 4
mol:GMP (4 units) 0.02 0.056 0.19 7 -0.29 3 10
Cone Transducin 0.043 0.065 -10000 0 -0.29 5 5
SLC24A2 0.029 0.012 -10000 0 -10000 0 0
GNB3/GNGT2 0.033 0.068 -10000 0 -0.37 4 4
GNB3 0.03 0.008 -10000 0 -10000 0 0
GNAT2/GTP 0.02 0.032 -10000 0 -0.37 1 1
CNGA3 0.017 0.077 -10000 0 -0.51 3 3
ARR3 0.032 0.005 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.006 0.11 -10000 0 -0.32 15 15
mol:Pi 0.01 0.12 -10000 0 -0.32 15 15
Cone CNG Channel 0.013 0.11 -10000 0 -0.27 18 18
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.029 0.012 -10000 0 -10000 0 0
RGS9 0.013 0.088 -10000 0 -0.51 4 4
PDE6C 0.024 0.062 -10000 0 -0.51 2 2
GNGT2 0.018 0.087 -10000 0 -0.51 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.007 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.031 0.075 -9999 0 -0.37 5 5
Necdin/E2F1 -0.003 0.12 -9999 0 -0.37 15 15
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.034 0.09 -9999 0 -0.27 10 10
NGF (dimer)/p75(NTR)/BEX1 0.018 0.047 -9999 0 -0.31 1 1
NT-4/5 (dimer)/p75(NTR) 0.017 0.022 -9999 0 -10000 0 0
IKBKB 0.029 0.01 -9999 0 -10000 0 0
AKT1 0.066 0.12 -9999 0 -0.31 6 6
IKBKG 0.032 0.005 -9999 0 -10000 0 0
BDNF -0.024 0.15 -9999 0 -0.51 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.019 0.094 -9999 0 -0.32 9 9
FURIN 0.013 0.097 -9999 0 -0.51 5 5
proBDNF (dimer)/p75(NTR)/Sortilin 0.005 0.11 -9999 0 -0.32 14 14
LINGO1 0.024 0.029 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.016 0.079 -9999 0 -0.28 9 9
proBDNF (dimer) -0.024 0.15 -9999 0 -0.51 12 12
NTRK1 0.031 0.011 -9999 0 -10000 0 0
RTN4R -0.003 0.13 -9999 0 -0.51 9 9
neuron apoptosis -0.031 0.13 -9999 0 -0.54 5 5
IRAK1 0.032 0.004 -9999 0 -10000 0 0
SHC1 0.011 0.018 -9999 0 -10000 0 0
ARHGDIA 0.032 0.005 -9999 0 -10000 0 0
RhoA/GTP 0.022 0.007 -9999 0 -10000 0 0
Gamma Secretase 0.065 0.083 -9999 0 -0.32 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.035 0.075 -9999 0 -0.35 4 4
MAGEH1 0.018 0.077 -9999 0 -0.51 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.001 0.12 -9999 0 -0.3 18 18
Mammalian IAPs/DIABLO 0.02 0.1 -9999 0 -0.29 14 14
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.017 0.087 -9999 0 -0.51 4 4
APP 0.009 0.1 -9999 0 -0.51 6 6
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.028 0.044 -9999 0 -0.51 1 1
RhoA/GDP/RHOGDI 0.032 0.027 -9999 0 -10000 0 0
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.01 0.034 -9999 0 -0.26 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.047 -9999 0 -0.25 4 4
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.028 0.056 -9999 0 -0.32 3 3
NCSTN 0.031 0.007 -9999 0 -10000 0 0
mol:GTP 0.03 0.039 -9999 0 -0.31 1 1
PSENEN 0.03 0.009 -9999 0 -10000 0 0
mol:ceramide 0.008 0.038 -9999 0 -0.28 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.002 0.048 -9999 0 -0.23 1 1
p75(NTR)/beta APP 0.017 0.087 -9999 0 -0.38 6 6
BEX1 0.01 0.059 -9999 0 -0.51 1 1
mol:GDP -0.001 0.013 -9999 0 -10000 0 0
NGF (dimer) 0 0.13 -9999 0 -0.3 24 24
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.032 0.094 -9999 0 -0.29 9 9
PIK3R1 0.004 0.098 -9999 0 -0.51 5 5
RAC1/GTP 0.03 0.022 -9999 0 -10000 0 0
MYD88 0.03 0.009 -9999 0 -10000 0 0
CHUK 0.028 0.044 -9999 0 -0.51 1 1
NGF (dimer)/p75(NTR)/PKA 0.03 0.039 -9999 0 -0.31 1 1
RHOB 0.017 0.077 -9999 0 -0.51 3 3
RHOA 0.03 0.009 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.045 0.017 -9999 0 -10000 0 0
NT3 (dimer) -0.007 0.12 -9999 0 -0.51 7 7
TP53 -0.034 0.11 -9999 0 -0.28 19 19
PRDM4 0.008 0.039 -9999 0 -0.29 2 2
BDNF (dimer) -0.12 0.19 -9999 0 -0.34 61 61
PIK3CA 0.009 0.062 -9999 0 -0.51 2 2
SORT1 0.024 0.062 -9999 0 -0.51 2 2
activation of caspase activity 0.029 0.087 -9999 0 -0.27 10 10
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.037 0.069 -9999 0 -0.29 5 5
RHOC 0.031 0.007 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.038 0.1 -9999 0 -0.36 6 6
DIABLO 0.033 0 -9999 0 -10000 0 0
SMPD2 0.009 0.038 -9999 0 -0.29 2 2
APH1B 0.029 0.044 -9999 0 -0.51 1 1
APH1A 0.013 0.096 -9999 0 -0.51 5 5
proNGF (dimer)/p75(NTR)/Sortilin 0.028 0.048 -9999 0 -0.31 2 2
PSEN1 0.028 0.044 -9999 0 -0.51 1 1
APAF-1/Pro-Caspase 9 0.044 0.034 -9999 0 -0.37 1 1
NT3 (dimer)/p75(NTR) 0.006 0.092 -9999 0 -0.37 7 7
MAPK8 -0.026 0.097 -9999 0 -0.35 5 5
MAPK9 -0.03 0.095 -9999 0 -0.35 5 5
APAF1 0.029 0.044 -9999 0 -0.51 1 1
NTF3 -0.007 0.12 -9999 0 -0.51 7 7
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.035 0.17 -9999 0 -0.51 17 17
RAC1/GDP 0.024 0.003 -9999 0 -10000 0 0
RhoA-B-C/GDP 0.038 0.063 -9999 0 -0.25 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.082 -9999 0 -0.29 7 7
RhoA-B-C/GTP 0.03 0.039 -9999 0 -0.31 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.12 -9999 0 -0.28 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.012 0.12 -9999 0 -0.3 17 17
PRKACB 0.027 0.045 -9999 0 -0.51 1 1
proBDNF (dimer)/p75 ECD -0.002 0.12 -9999 0 -0.37 13 13
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.027 0.16 -9999 0 -0.51 14 14
BIRC2 0.031 0.01 -9999 0 -10000 0 0
neuron projection morphogenesis -0.029 0.066 -9999 0 -0.32 2 2
BAD -0.035 0.098 -9999 0 -0.36 5 5
RIPK2 0.026 0.046 -9999 0 -0.51 1 1
NGFR 0.021 0.033 -9999 0 -10000 0 0
CYCS 0 0.065 -9999 0 -0.32 5 5
ADAM17 0.027 0.045 -9999 0 -0.51 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.038 0.064 -9999 0 -0.29 4 4
BCL2L11 -0.034 0.097 -9999 0 -0.36 5 5
BDNF (dimer)/p75(NTR) -0.006 0.12 -9999 0 -0.38 12 12
PI3K 0.005 0.065 -9999 0 -0.29 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.052 -9999 0 -0.29 2 2
NDNL2 0.032 0.004 -9999 0 -10000 0 0
YWHAE 0.03 0.008 -9999 0 -10000 0 0
PRKCI -0.004 0.1 -9999 0 -0.51 6 6
NGF (dimer)/p75(NTR) 0.017 0.022 -9999 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.034 0.079 -9999 0 -0.34 5 5
TRAF6 0.021 0.075 -9999 0 -0.51 3 3
RAC1 0.032 0.005 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.031 0.01 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.015 0.087 -9999 0 -0.28 14 14
SQSTM1 0.028 0.019 -9999 0 -10000 0 0
NGFRAP1 0.003 0.12 -9999 0 -0.51 8 8
CASP3 -0.035 0.096 -9999 0 -0.34 6 6
E2F1 0.031 0.007 -9999 0 -10000 0 0
CASP9 0.032 0.005 -9999 0 -10000 0 0
IKK complex 0.057 0.066 -9999 0 -10000 0 0
NGF (dimer)/TRKA 0.023 0.007 -9999 0 -10000 0 0
MMP7 -0.046 0.19 -9999 0 -0.51 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.045 0.076 -9999 0 -0.28 6 6
MMP3 -0.13 0.22 -9999 0 -0.51 39 39
APAF-1/Caspase 9 -0.025 0.089 -9999 0 -0.43 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.021 0.24 -10000 0 -0.78 5 5
PCK1 0.029 0.18 -10000 0 -0.66 1 1
HNF4A 0.04 0.24 -10000 0 -0.79 3 3
KCNJ11 0.027 0.28 -10000 0 -0.86 8 8
AKT1 0.047 0.16 -10000 0 -0.59 2 2
response to starvation 0.005 0.004 -10000 0 -10000 0 0
DLK1 0.026 0.28 0.67 2 -0.81 6 8
NKX2-1 0.062 0.18 0.38 17 -0.38 4 21
ACADM 0.024 0.25 -10000 0 -0.76 7 7
TAT 0.033 0.17 -10000 0 -0.57 3 3
CEBPB 0.032 0.045 -10000 0 -0.51 1 1
CEBPA 0.016 0.098 -10000 0 -0.51 5 5
TTR -0.028 0.25 -10000 0 -0.82 6 6
PKLR 0.038 0.24 -10000 0 -0.72 6 6
APOA1 0.036 0.28 -10000 0 -0.92 4 4
CPT1C -0.038 0.34 -10000 0 -0.83 18 18
ALAS1 0.033 0.15 -10000 0 -10000 0 0
TFRC -0.063 0.45 -10000 0 -1.3 16 16
FOXF1 0.02 0.065 -10000 0 -0.51 2 2
NF1 0.038 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.038 0.042 -10000 0 -0.2 1 1
CPT1A 0.028 0.24 -10000 0 -0.78 6 6
HMGCS1 0.03 0.29 -10000 0 -0.85 9 9
NR3C1 0.04 0.021 -10000 0 -10000 0 0
CPT1B 0.019 0.25 -10000 0 -0.79 7 7
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.028 0.067 -10000 0 -0.41 3 3
GCK 0.022 0.25 -10000 0 -0.82 6 6
CREB1 0.031 0.064 -10000 0 -0.5 2 2
IGFBP1 0.037 0.14 -10000 0 -10000 0 0
PDX1 0.03 0.24 -10000 0 -1.2 3 3
UCP2 0 0.3 -10000 0 -0.84 12 12
ALDOB 0.032 0.27 -10000 0 -0.8 6 6
AFP -0.047 0.15 -10000 0 -0.62 3 3
BDH1 0.076 0.33 0.59 1 -0.97 7 8
HADH 0.023 0.27 -10000 0 -0.85 6 6
F2 0.032 0.28 -10000 0 -0.97 3 3
HNF1A 0.038 0.042 -10000 0 -0.2 1 1
G6PC 0.026 0.11 -10000 0 -0.64 1 1
SLC2A2 0.043 0.22 -10000 0 -0.83 3 3
INS -0.003 0.023 -10000 0 -10000 0 0
FOXA1 -0.064 0.2 -10000 0 -0.5 27 27
FOXA3 0.012 0.12 -10000 0 -0.47 5 5
FOXA2 0.049 0.32 -10000 0 -0.9 6 6
ABCC8 0.023 0.28 -10000 0 -0.85 7 7
ALB -0.046 0.15 -10000 0 -1.1 1 1
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.082 0.4 1 -0.28 11 12
FRAP1 0.048 0.075 0.23 1 -0.45 1 2
AKT1 0.05 0.13 0.34 5 -0.26 11 16
INSR 0.028 0.044 -10000 0 -0.51 1 1
Insulin Receptor/Insulin 0.039 0.031 -10000 0 -0.31 1 1
mol:GTP 0.076 0.13 0.29 12 -0.38 2 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.041 -10000 0 -0.21 2 2
TSC2 0.027 0.044 -10000 0 -0.51 1 1
RHEB/GDP -0.007 0.066 -10000 0 -0.35 2 2
TSC1 0.029 0.044 -10000 0 -0.51 1 1
Insulin Receptor/IRS1 0.009 0.086 -10000 0 -0.3 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.003 0.053 -10000 0 -0.24 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.031 0.01 -10000 0 -10000 0 0
RPS6KB1 0.073 0.1 0.26 16 -0.24 1 17
MAP3K5 -0.003 0.057 0.18 1 -0.29 5 6
PIK3R1 0.005 0.098 -10000 0 -0.51 5 5
apoptosis -0.003 0.057 0.18 1 -0.29 5 6
mol:LY294002 0 0 0.001 1 -0.001 10 11
EIF4B 0.07 0.097 0.25 13 -10000 0 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.081 0.094 0.26 12 -10000 0 12
eIF4E/eIF4G1/eIF4A1 0 0.046 -10000 0 -0.28 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.087 -10000 0 -0.29 12 12
mTOR/RHEB/GTP/Raptor/GBL 0.056 0.086 0.22 15 -0.21 2 17
FKBP1A 0.033 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.068 0.11 0.26 10 -0.35 2 12
mol:Amino Acids 0 0 0.001 1 -0.001 10 11
FKBP12/Rapamycin 0.026 0.007 -10000 0 -10000 0 0
PDPK1 0.025 0.11 0.2 6 -0.26 11 17
EIF4E 0.031 0.007 -10000 0 -10000 0 0
ASK1/PP5C 0.05 0.14 -10000 0 -0.57 6 6
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.051 -10000 0 -10000 0 0
TSC1/TSC2 0.083 0.14 0.31 12 -0.41 2 14
tumor necrosis factor receptor activity 0 0 0.001 10 -0.001 1 11
RPS6 0.03 0.012 -10000 0 -10000 0 0
PPP5C 0.028 0.044 -10000 0 -0.51 1 1
EIF4G1 0.002 0.085 -10000 0 -0.51 4 4
IRS1 -0.008 0.082 -10000 0 -0.33 9 9
INS 0.032 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.044 -10000 0 -0.51 1 1
PDK2 0.024 0.11 0.21 5 -0.26 11 16
EIF4EBP1 -0.019 0.18 -10000 0 -1.1 4 4
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
PPP2R5D 0.047 0.076 0.25 1 -0.4 1 2
peptide biosynthetic process 0.018 0.028 0.19 1 -0.28 1 2
RHEB 0.032 0.005 -10000 0 -10000 0 0
EIF4A1 0.03 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.005 19 -0.003 2 21
EEF2 0.018 0.029 0.19 1 -0.29 1 2
eIF4E/4E-BP1 -0.003 0.17 -10000 0 -0.99 4 4
Retinoic acid receptors-mediated signaling

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
HDAC1 0.031 0.01 -10000 0 -10000 0 0
HDAC3 0.031 0.007 -10000 0 -10000 0 0
VDR -0.002 0.13 -10000 0 -0.51 9 9
Cbp/p300/PCAF 0.022 0.08 -10000 0 -0.31 8 8
EP300 0.003 0.12 -10000 0 -0.51 8 8
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.007 0.096 -10000 0 -0.4 5 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.009 -10000 0 -10000 0 0
AKT1 -0.005 0.11 0.21 12 -0.28 10 22
RAR alpha/9cRA/Cyclin H 0.041 0.089 -10000 0 -0.41 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.013 0.1 -10000 0 -0.24 21 21
CDC2 0 0.004 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.027 0.033 -10000 0 -10000 0 0
NCOR2 0.026 0.061 -10000 0 -0.51 2 2
VDR/VDR/Vit D3 -0.001 0.092 -10000 0 -0.37 9 9
RXRs/RARs/NRIP1/9cRA -0.011 0.18 -10000 0 -0.55 12 12
NCOA2 0.024 0.062 -10000 0 -0.51 2 2
NCOA3 0.025 0.062 -10000 0 -0.51 2 2
NCOA1 0.032 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA -0.002 0.13 -10000 0 -0.51 9 9
RARG 0.024 0.062 -10000 0 -0.51 2 2
RAR gamma1/9cRA 0.037 0.042 -10000 0 -0.31 2 2
MAPK3 0.03 0.013 -10000 0 -10000 0 0
MAPK1 0.026 0.044 -10000 0 -0.51 1 1
MAPK8 0.029 0.015 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.016 0.14 -10000 0 -0.41 10 10
RARA 0.02 0.03 -10000 0 -0.23 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.017 0.11 -10000 0 -0.34 11 11
PRKCA 0.025 0.049 -10000 0 -0.51 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.021 0.18 -10000 0 -0.58 12 12
RXRG 0.02 0.038 -10000 0 -0.31 1 1
RXRA 0.01 0.078 -10000 0 -0.43 3 3
RXRB 0.021 0.036 -10000 0 -0.31 1 1
VDR/Vit D3/DNA -0.001 0.092 -10000 0 -0.37 9 9
RBP1 -0.054 0.19 -10000 0 -0.51 22 22
CRBP1/9-cic-RA -0.039 0.14 -10000 0 -0.37 22 22
RARB -0.026 0.16 -10000 0 -0.51 14 14
PRKCG 0.029 0.022 -10000 0 -10000 0 0
MNAT1 0.031 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.15 0.28 1 -0.53 6 7
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.004 0.12 -10000 0 -0.43 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.096 -10000 0 -0.3 9 9
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.022 0.18 -10000 0 -0.58 12 12
positive regulation of DNA binding 0.031 0.081 -10000 0 -0.38 3 3
NRIP1 -0.05 0.31 -10000 0 -1.1 10 10
RXRs/RARs -0.016 0.16 -10000 0 -0.45 14 14
RXRs/RXRs/DNA/9cRA 0.008 0.11 -10000 0 -0.38 9 9
PRKACA 0.031 0.006 -10000 0 -10000 0 0
CDK7 0.03 0.009 -10000 0 -10000 0 0
TFIIH 0.058 0.022 -10000 0 -10000 0 0
RAR alpha/9cRA 0.059 0.046 -10000 0 -10000 0 0
CCNH 0.029 0.012 -10000 0 -10000 0 0
CREBBP 0.031 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.052 0.037 -10000 0 -0.26 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.029 0.01 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.039 0.15 -9999 0 -0.53 4 4
Syndecan-3/Neurocan 0.028 0.092 -9999 0 -0.5 4 4
POMC -0.022 0.16 -9999 0 -0.51 14 14
EGFR -0.033 0.17 -9999 0 -0.51 17 17
Syndecan-3/EGFR -0.002 0.12 -9999 0 -0.51 3 3
AGRP 0.027 0.022 -9999 0 -10000 0 0
NCSTN 0.031 0.007 -9999 0 -10000 0 0
PSENEN 0.03 0.009 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.029 0.044 -9999 0 -0.51 1 1
APH1A 0.013 0.096 -9999 0 -0.51 5 5
NCAN 0.032 0.005 -9999 0 -10000 0 0
long-term memory 0.035 0.093 -9999 0 -0.47 4 4
Syndecan-3/IL8 -0.051 0.15 -9999 0 -0.52 5 5
PSEN1 0.028 0.044 -9999 0 -0.51 1 1
Src/Cortactin 0.041 0.018 -9999 0 -10000 0 0
FYN 0.024 0.062 -9999 0 -0.51 2 2
limb bud formation -0.001 0.087 -9999 0 -0.51 4 4
MC4R 0.023 0.062 -9999 0 -0.51 2 2
SRC 0.031 0.011 -9999 0 -10000 0 0
PTN -0.13 0.23 -9999 0 -0.51 39 39
FGFR/FGF/Syndecan-3 -0.001 0.088 -9999 0 -0.52 4 4
neuron projection morphogenesis -0.037 0.15 -9999 0 -0.51 4 4
Syndecan-3/AgRP 0.025 0.092 -9999 0 -0.5 4 4
Syndecan-3/AgRP/MC4R 0.033 0.099 -9999 0 -0.48 4 4
Fyn/Cortactin 0.038 0.04 -9999 0 -0.37 1 1
SDC3 -0.001 0.088 -9999 0 -0.52 4 4
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.053 0.14 -9999 0 -0.51 5 5
IL8 -0.12 0.23 -9999 0 -0.51 38 38
Syndecan-3/Fyn/Cortactin 0.036 0.096 -9999 0 -0.48 4 4
Syndecan-3/CASK -0.002 0.084 -9999 0 -0.5 4 4
alpha-MSH/MC4R -0.002 0.13 -9999 0 -0.37 16 16
Gamma Secretase 0.065 0.083 -9999 0 -0.32 5 5
IL2 signaling events mediated by PI3K

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
BCL2L1 0.032 0.11 -10000 0 -0.48 1 1
UGCG 0.004 0.13 -10000 0 -0.77 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.17 -10000 0 -0.5 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.005 0.13 -10000 0 -0.76 4 4
mol:DAG -0.033 0.2 -10000 0 -0.9 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.2 -10000 0 -0.55 12 12
FRAP1 -0.016 0.23 -10000 0 -0.63 13 13
FOXO3 -0.003 0.2 0.31 1 -0.59 11 12
AKT1 -0.005 0.22 -10000 0 -0.62 12 12
GAB2 0.03 0.014 -10000 0 -10000 0 0
SMPD1 0.011 0.1 -10000 0 -0.67 3 3
SGMS1 -0.014 0.17 -10000 0 -0.7 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.059 -10000 0 -0.32 5 5
CALM1 0.031 0.006 -10000 0 -10000 0 0
cell proliferation 0.005 0.17 -10000 0 -0.52 8 8
EIF3A 0.031 0.01 -10000 0 -10000 0 0
PI3K 0.005 0.077 -10000 0 -0.38 5 5
RPS6KB1 0.007 0.066 -10000 0 -10000 0 0
mol:sphingomyelin -0.033 0.2 -10000 0 -0.9 8 8
natural killer cell activation 0 0.003 -10000 0 -0.014 1 1
JAK3 0.033 0.006 -10000 0 -10000 0 0
PIK3R1 0.006 0.099 -10000 0 -0.51 5 5
JAK1 0.03 0.044 -10000 0 -0.51 1 1
NFKB1 0.031 0.007 -10000 0 -10000 0 0
MYC 0.006 0.25 -10000 0 -0.97 7 7
MYB -0.087 0.35 -10000 0 -1.3 12 12
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.013 0.16 -10000 0 -0.46 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.074 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.014 0.15 -10000 0 -0.45 10 10
Rac1/GDP 0 0.058 -10000 0 -0.29 5 5
T cell proliferation 0.011 0.15 -10000 0 -0.42 10 10
SHC1 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.004 0.02 -10000 0 -0.066 12 12
PRKCZ 0.012 0.15 -10000 0 -0.44 10 10
NF kappa B1 p50/RelA 0.009 0.2 -10000 0 -0.62 9 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.1 -10000 0 -0.37 5 5
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
RELA 0.033 0 -10000 0 -10000 0 0
IL2RA -0.008 0.14 -10000 0 -0.51 11 11
IL2RB 0.017 0.088 -10000 0 -0.51 4 4
TERT 0.021 0.047 -10000 0 -0.51 1 1
E2F1 -0.012 0.12 -10000 0 -0.42 12 12
SOS1 0.031 0.007 -10000 0 -10000 0 0
RPS6 0.03 0.012 -10000 0 -10000 0 0
mol:cAMP 0.002 0.009 0.032 12 -10000 0 12
PTPN11 0.028 0.044 -10000 0 -0.51 1 1
IL2RG 0.022 0.065 -10000 0 -0.51 2 2
actin cytoskeleton organization 0.011 0.15 -10000 0 -0.42 10 10
GRB2 0.031 0.007 -10000 0 -10000 0 0
IL2 0.033 0.008 -10000 0 -10000 0 0
PIK3CA 0.01 0.062 -10000 0 -0.51 2 2
Rac1/GTP 0.012 0.064 -10000 0 -0.28 5 5
LCK -0.004 0.13 -10000 0 -0.51 10 10
BCL2 -0.032 0.25 -10000 0 -0.77 13 13
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.083 -10000 0 -0.37 6 6
AKT1 0.011 0.19 0.36 3 -0.57 10 13
PTK2B -0.002 0.14 0.36 1 -0.55 6 7
VEGFR2 homodimer/Frs2 0.002 0.12 -10000 0 -0.41 9 9
CAV1 -0.029 0.16 -10000 0 -0.51 15 15
CALM1 0.031 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.012 0.12 -10000 0 -0.43 8 8
endothelial cell proliferation 0.032 0.16 0.38 3 -0.46 8 11
mol:Ca2+ 0.003 0.14 0.37 1 -0.51 5 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.043 0.13 -10000 0 -0.5 5 5
RP11-342D11.1 -0.009 0.13 -10000 0 -0.51 5 5
CDH5 0.024 0.062 -10000 0 -0.51 2 2
VEGFA homodimer 0.051 0.092 -10000 0 -0.33 7 7
SHC1 0.031 0.007 -10000 0 -10000 0 0
SHC2 0.025 0.026 -10000 0 -10000 0 0
HRAS/GDP 0.009 0.11 -10000 0 -0.42 5 5
SH2D2A 0.016 0.087 -10000 0 -0.51 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.022 0.14 -10000 0 -0.48 7 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.007 0.13 -10000 0 -0.39 10 10
VEGFR1 homodimer 0.003 0.12 -10000 0 -0.51 8 8
SHC/GRB2/SOS1 0.048 0.13 -10000 0 -0.45 4 4
GRB10 -0.015 0.18 0.37 1 -0.55 13 14
PTPN11 0.029 0.044 -10000 0 -0.51 1 1
GRB2 0.032 0.005 -10000 0 -10000 0 0
PAK1 0.026 0.046 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.044 0.14 -10000 0 -0.5 6 6
HRAS 0.024 0.062 -10000 0 -0.51 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.14 -10000 0 -0.61 5 5
HIF1A 0.02 0.075 -10000 0 -0.51 3 3
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.027 0.12 -10000 0 -0.5 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.031 0.008 -10000 0 -10000 0 0
Nck/Pak 0.03 0.06 -10000 0 -0.37 3 3
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.14 -10000 0 -0.53 6 6
mol:GDP 0.021 0.12 -10000 0 -0.44 4 4
mol:NADP 0.026 0.13 0.34 2 -0.44 6 8
eNOS/Hsp90 0.035 0.13 0.34 2 -0.41 6 8
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
mol:IP3 0.003 0.14 0.37 1 -0.52 5 6
HIF1A/ARNT 0.035 0.061 -10000 0 -0.37 3 3
SHB 0.017 0.076 -10000 0 -0.51 3 3
VEGFA 0.02 0.066 -10000 0 -0.51 2 2
VEGFC 0.004 0.11 -10000 0 -0.51 6 6
FAK1/Vinculin 0.018 0.17 0.33 1 -0.62 7 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.03 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.027 0.16 -10000 0 -0.58 6 6
PTPN6 0.027 0.044 -10000 0 -0.51 1 1
EPAS1 0 0.14 -10000 0 -0.51 9 9
mol:L-citrulline 0.026 0.13 0.34 2 -0.44 6 8
ITGAV 0.013 0.097 -10000 0 -0.51 5 5
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.042 0.13 -10000 0 -0.5 5 5
VEGFR2 homodimer/VEGFA homodimer 0.008 0.14 -10000 0 -0.55 5 5
VEGFR2/3 heterodimer 0.003 0.12 -10000 0 -0.41 9 9
VEGFB 0.033 0 -10000 0 -10000 0 0
MAPK11 -0.007 0.14 0.34 3 -0.49 5 8
VEGFR2 homodimer -0.01 0.12 -10000 0 -0.49 8 8
FLT1 0.003 0.12 -10000 0 -0.51 8 8
NEDD4 0.021 0.066 -10000 0 -0.51 2 2
MAPK3 -0.004 0.14 0.33 4 -0.49 5 9
MAPK1 -0.004 0.14 0.3 8 -0.53 4 12
VEGFA145/NRP2 0.03 0.084 -10000 0 -0.44 4 4
VEGFR1/2 heterodimer -0.01 0.15 -10000 0 -0.45 12 12
KDR -0.011 0.12 -10000 0 -0.49 8 8
VEGFA165/NRP1/VEGFR2 homodimer 0.006 0.14 -10000 0 -0.55 5 5
SRC 0.031 0.011 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.003 0.14 0.37 3 -0.53 4 7
PI3K -0.024 0.14 -10000 0 -0.53 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.009 0.12 -10000 0 -0.45 6 6
FES -0.001 0.14 0.37 1 -0.52 5 6
GAB1 -0.012 0.17 -10000 0 -0.51 10 10
VEGFR2 homodimer/VEGFA homodimer/Src 0.012 0.12 -10000 0 -0.53 5 5
CTNNB1 0.028 0.015 -10000 0 -10000 0 0
SOS1 0.032 0.005 -10000 0 -10000 0 0
ARNT 0.031 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.15 0.36 1 -0.42 8 9
VEGFR2 homodimer/VEGFA homodimer/Yes 0.012 0.12 -10000 0 -0.42 7 7
PI3K/GAB1 0.005 0.18 -10000 0 -0.49 10 10
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.041 0.12 -10000 0 -0.52 3 3
PRKACA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.003 0.13 -10000 0 -0.38 12 12
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
CDC42 0.004 0.14 0.37 1 -0.52 5 6
actin cytoskeleton reorganization 0.007 0.13 -10000 0 -0.39 10 10
PTK2 -0.005 0.17 0.33 1 -0.66 7 8
EDG1 -0.009 0.13 -10000 0 -0.51 5 5
mol:DAG 0.003 0.14 0.37 1 -0.52 5 6
CaM/Ca2+ 0.015 0.13 -10000 0 -0.48 5 5
MAP2K3 -0.013 0.096 -10000 0 -0.4 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.007 0.18 -10000 0 -0.56 13 13
PLCG1 0.003 0.14 0.37 1 -0.52 5 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.034 0.13 -10000 0 -0.53 4 4
IQGAP1 0.032 0.005 -10000 0 -10000 0 0
YES1 0.027 0.044 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.013 0.13 -10000 0 -0.53 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.009 0.13 -10000 0 -0.44 9 9
cell migration 0.025 0.16 0.31 2 -0.61 6 8
mol:PI-3-4-5-P3 -0.021 0.14 -10000 0 -0.49 8 8
FYN 0.024 0.062 -10000 0 -0.51 2 2
VEGFB/NRP1 0.008 0.13 -10000 0 -0.48 5 5
mol:NO 0.026 0.13 0.34 2 -0.44 6 8
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.008 0.1 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.018 0.18 -10000 0 -0.56 13 13
VHL 0.018 0.076 -10000 0 -0.51 3 3
ITGB3 0.024 0.048 -10000 0 -0.51 1 1
NOS3 0.025 0.14 0.34 2 -0.49 6 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.01 0.12 -10000 0 -0.49 6 6
RAC1 0.032 0.005 -10000 0 -10000 0 0
PRKCA -0.006 0.14 0.37 1 -0.53 5 6
PRKCB -0.007 0.13 0.36 1 -0.48 5 6
VCL 0.024 0.062 -10000 0 -0.51 2 2
VEGFA165/NRP1 0.01 0.14 -10000 0 -0.51 5 5
VEGFR1/2 heterodimer/VEGFA homodimer -0.001 0.16 -10000 0 -0.47 11 11
VEGFA165/NRP2 0.03 0.084 -10000 0 -0.44 4 4
MAPKKK cascade -0.013 0.15 -10000 0 -0.48 12 12
NRP2 0.02 0.076 -10000 0 -0.51 3 3
VEGFC homodimer 0.004 0.11 -10000 0 -0.51 6 6
NCK1 0.02 0.062 -10000 0 -0.51 2 2
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.024 0.17 0.33 1 -0.61 7 8
MAP3K13 -0.009 0.1 -10000 0 -0.42 5 5
PDPK1 -0.023 0.12 -10000 0 -0.47 8 8
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.023 0.13 -10000 0 -0.4 14 14
KLHL20 -0.007 0.11 0.21 1 -0.31 9 10
CYFIP2 0.025 0.046 -10000 0 -0.51 1 1
Rac1/GDP 0.001 0.1 -10000 0 -0.3 1 1
ENAH -0.023 0.14 -10000 0 -0.4 15 15
AP1M1 0.032 0.006 -10000 0 -10000 0 0
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
CTNNB1 0.028 0.015 -10000 0 -10000 0 0
CDC42/GTP 0.01 0.074 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.031 0.058 -10000 0 -0.2 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.052 0.082 -10000 0 -0.29 7 7
RAPGEF1 -0.016 0.12 -10000 0 -0.4 8 8
CTNND1 0.015 0.096 -10000 0 -0.51 5 5
regulation of calcium-dependent cell-cell adhesion -0.019 0.15 -10000 0 -0.41 15 15
CRK -0.016 0.13 -10000 0 -0.4 11 11
E-cadherin/gamma catenin/alpha catenin 0.017 0.12 -10000 0 -0.33 16 16
alphaE/beta7 Integrin 0.045 0.012 -10000 0 -10000 0 0
IQGAP1 0.032 0.005 -10000 0 -10000 0 0
NCKAP1 0.025 0.047 -10000 0 -0.51 1 1
Rap1/GTP/I-afadin 0.051 0.044 -10000 0 -0.29 2 2
DLG1 -0.018 0.11 -10000 0 -0.38 9 9
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.043 -10000 0 -0.25 2 2
MLLT4 0.031 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.053 0.044 -10000 0 -0.29 2 2
PI3K -0.01 0.057 -10000 0 -0.33 2 2
ARF6 0.024 0.062 -10000 0 -0.51 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.14 -10000 0 -0.39 16 16
TIAM1 0.032 0.005 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.039 0.095 -10000 0 -0.27 12 12
AKT1 0.005 0.054 0.16 1 -0.22 3 4
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
CDH1 0.005 0.11 -10000 0 -0.51 7 7
RhoA/GDP 0.005 0.1 0.25 1 -0.28 2 3
actin cytoskeleton organization -0.003 0.079 0.16 2 -0.22 8 10
CDC42/GDP 0.003 0.1 0.25 1 -0.29 2 3
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.015 0.1 -10000 0 -0.27 20 20
ITGB7 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.043 0.1 -10000 0 -0.29 12 12
E-cadherin/Ca2+/beta catenin/alpha catenin 0.035 0.07 -10000 0 -0.27 7 7
mol:GDP -0.014 0.11 -10000 0 -0.32 5 5
CDC42/GTP/IQGAP1 0.042 0.009 -10000 0 -10000 0 0
JUP -0.004 0.13 -10000 0 -0.51 10 10
p120 catenin/RhoA/GDP 0.008 0.11 0.26 1 -0.29 1 2
RAC1/GTP/IQGAP1 0.042 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.042 0.037 -10000 0 -0.37 1 1
RHOA 0.03 0.009 -10000 0 -10000 0 0
CDC42 0.032 0.005 -10000 0 -10000 0 0
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.076 0.13 1 -0.23 12 13
NME1 0.032 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.025 0.14 -10000 0 -0.4 15 15
regulation of cell-cell adhesion 0 0.061 -10000 0 -10000 0 0
WASF2 -0.002 0.045 -10000 0 -0.14 6 6
Rap1/GTP 0.009 0.082 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.043 0.12 -10000 0 -0.29 16 16
CCND1 -0.011 0.093 0.15 1 -0.29 12 13
VAV2 -0.041 0.22 -10000 0 -0.67 12 12
RAP1/GDP 0.013 0.092 0.26 1 -10000 0 1
adherens junction assembly -0.024 0.14 -10000 0 -0.39 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.032 0.006 -10000 0 -10000 0 0
PIP5K1C 0.027 0.045 -10000 0 -0.51 1 1
regulation of heterotypic cell-cell adhesion 0.025 0.11 -10000 0 -0.28 16 16
E-cadherin/beta catenin -0.004 0.083 -10000 0 -0.35 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.025 0.14 -10000 0 -0.4 15 15
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
Rac1/GTP -0.062 0.15 -10000 0 -0.53 10 10
E-cadherin/beta catenin/alpha catenin 0.039 0.082 -10000 0 -0.31 7 7
ITGAE 0.031 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.15 -10000 0 -0.42 15 15
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.014 -10000 0 -10000 0 0
ELF1 0.011 0.1 -10000 0 -0.35 11 11
CCNA2 0.02 0.075 -10000 0 -0.51 3 3
PIK3CA 0.01 0.062 -10000 0 -0.51 2 2
JAK3 0.032 0.005 -10000 0 -10000 0 0
PIK3R1 0.005 0.098 -10000 0 -0.51 5 5
JAK1 0.029 0.044 -10000 0 -0.51 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.13 -10000 0 -0.44 6 6
SHC1 0.032 0.007 -10000 0 -10000 0 0
SP1 -0.013 0.12 -10000 0 -0.37 15 15
IL2RA -0.033 0.21 -10000 0 -0.78 11 11
IL2RB 0.015 0.087 -10000 0 -0.51 4 4
SOS1 0.032 0.005 -10000 0 -10000 0 0
IL2RG 0.02 0.065 -10000 0 -0.51 2 2
G1/S transition of mitotic cell cycle -0.071 0.28 -10000 0 -0.73 20 20
PTPN11 0.03 0.044 -10000 0 -0.51 1 1
CCND2 -0.062 0.23 -10000 0 -0.72 15 15
LCK -0.005 0.13 -10000 0 -0.51 10 10
GRB2 0.032 0.005 -10000 0 -10000 0 0
IL2 0.032 0.007 -10000 0 -10000 0 0
CDK6 0.009 0.1 -10000 0 -0.51 6 6
CCND3 0.025 0.12 0.4 1 -0.45 2 3
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.028 0.013 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.004 0.078 -10000 0 -0.28 8 8
NT3 (dimer)/TRKC 0.013 0.09 -10000 0 -0.37 7 7
NT3 (dimer)/TRKB -0.091 0.18 -10000 0 -0.34 47 47
SHC/Grb2/SOS1/GAB1/PI3K 0 0.068 -10000 0 -0.29 6 6
RAPGEF1 0.032 0.003 -10000 0 -10000 0 0
BDNF -0.024 0.15 -10000 0 -0.51 12 12
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
DYNLT1 0.032 0.005 -10000 0 -10000 0 0
NTRK1 0.031 0.011 -10000 0 -10000 0 0
NTRK2 -0.14 0.24 -10000 0 -0.51 46 46
NTRK3 0.031 0.013 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB -0.081 0.16 -10000 0 -0.32 46 46
neuron apoptosis 0.031 0.14 0.35 8 -0.25 1 9
SHC 2-3/Grb2 -0.034 0.15 0.26 1 -0.38 8 9
SHC1 0.031 0.007 -10000 0 -10000 0 0
SHC2 -0.027 0.13 0.24 1 -0.43 6 7
SHC3 -0.041 0.14 0.24 1 -0.4 10 11
STAT3 (dimer) -0.002 0.11 -10000 0 -0.36 12 12
NT3 (dimer)/TRKA 0.021 0.086 -10000 0 -0.32 7 7
RIN/GDP 0.052 0.075 0.24 4 -10000 0 4
GIPC1 0.028 0.044 -10000 0 -0.51 1 1
KRAS 0.016 0.086 -10000 0 -0.51 4 4
DNAJA3 0.028 0.061 0.24 2 -10000 0 2
RIN/GTP 0.02 0.032 -10000 0 -0.37 1 1
CCND1 -0.041 0.21 -10000 0 -0.77 12 12
MAGED1 0.017 0.087 -10000 0 -0.51 4 4
PTPN11 0.029 0.044 -10000 0 -0.51 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.059 0.02 -10000 0 -10000 0 0
GRB2 0.032 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.037 0.033 -10000 0 -0.31 1 1
TRKA/NEDD4-2 0.041 0.037 -10000 0 -0.37 1 1
ELMO1 0.027 0.045 -10000 0 -0.51 1 1
RhoG/GTP/ELMO1/DOCK1 0.039 0.031 -10000 0 -0.31 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
DOCK1 0.032 0.006 -10000 0 -10000 0 0
GAB2 0.03 0.014 -10000 0 -10000 0 0
RIT2 0.027 0.044 -10000 0 -0.51 1 1
RIT1 0.017 0.077 -10000 0 -0.51 3 3
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 0.027 0.046 -10000 0 -0.51 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.039 0.064 0.25 2 -10000 0 2
mol:GDP 0.054 0.091 0.34 2 -10000 0 2
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.02 0.032 -10000 0 -0.37 1 1
RIT1/GDP 0.043 0.075 0.19 2 -0.29 1 3
TIAM1 0.032 0.005 -10000 0 -10000 0 0
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
BDNF (dimer)/TRKB -0.094 0.2 -10000 0 -0.36 50 50
KIDINS220/CRKL/C3G 0.042 0.017 -10000 0 -10000 0 0
SHC/RasGAP 0.039 0.037 -10000 0 -0.37 1 1
FRS2 family/SHP2 0.062 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.064 0.059 -10000 0 -0.29 3 3
RIT1/GTP 0.013 0.055 -10000 0 -0.37 3 3
NT3 (dimer) -0.007 0.12 -10000 0 -0.51 7 7
RAP1/GDP 0.036 0.054 -10000 0 -10000 0 0
KIDINS220/CRKL 0.028 0.013 -10000 0 -10000 0 0
BDNF (dimer) -0.024 0.15 -10000 0 -0.51 12 12
ubiquitin-dependent protein catabolic process 0.037 0.032 -10000 0 -0.31 1 1
Schwann cell development -0.02 0.025 -10000 0 -10000 0 0
EHD4 0.031 0.01 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.076 0.025 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.028 0.042 -10000 0 -10000 0 0
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.024 0.062 -10000 0 -0.51 2 2
CDC42/GTP -0.081 0.16 -10000 0 -0.29 51 51
ABL1 0.032 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.032 0.11 -10000 0 -0.54 2 2
STAT3 -0.002 0.11 -10000 0 -0.36 12 12
axon guidance -0.089 0.15 -10000 0 -0.28 51 51
MAPK3 0.022 0.043 0.19 6 -0.29 1 7
MAPK1 0.016 0.043 0.19 3 -0.29 2 5
CDC42/GDP 0.055 0.074 0.24 4 -10000 0 4
NTF3 -0.007 0.12 -10000 0 -0.51 7 7
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.032 0.034 -10000 0 -0.31 1 1
PI3K 0.004 0.075 -10000 0 -0.37 5 5
FRS3 0.032 0.003 -10000 0 -10000 0 0
FAIM 0.023 0.045 -10000 0 -0.51 1 1
GAB1 0.019 0.076 -10000 0 -0.51 3 3
RASGRF1 0.018 0.068 0.24 2 -0.25 1 3
SOS1 0.032 0.005 -10000 0 -10000 0 0
MCF2L -0.005 0.071 -10000 0 -0.31 7 7
RGS19 0.028 0.044 -10000 0 -0.51 1 1
CDC42 0.032 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.057 0.088 0.39 1 -0.35 1 2
Rac1/GDP 0.054 0.073 0.26 3 -10000 0 3
NGF (dimer)/TRKA/GRIT 0.021 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.021 0.17 -10000 0 -0.86 4 4
NGF (dimer)/TRKA/NEDD4-2 0.037 0.032 -10000 0 -0.31 1 1
MAP2K1 0.024 0.062 -10000 0 -0.27 3 3
NGFR 0.021 0.033 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.023 0.041 -10000 0 -0.25 3 3
RAS family/GTP/PI3K -0.01 0.073 -10000 0 -0.27 9 9
FRS2 family/SHP2/GRB2/SOS1 0.087 0.032 -10000 0 -10000 0 0
NRAS 0.025 0.047 -10000 0 -0.51 1 1
GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
PRKCI -0.004 0.1 -10000 0 -0.51 6 6
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.002 0.052 -10000 0 -0.39 1 1
RASA1 0.026 0.044 -10000 0 -0.51 1 1
TRKA/c-Abl 0.046 0.013 -10000 0 -10000 0 0
SQSTM1 0.028 0.019 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.078 0.19 -10000 0 -0.33 49 49
NGF (dimer)/TRKA/p62/Atypical PKCs 0.015 0.064 -10000 0 -0.27 6 6
MATK 0.026 0.046 -10000 0 -0.51 1 1
NEDD4L 0.026 0.045 -10000 0 -0.51 1 1
RAS family/GDP -0.01 0.035 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0 0.045 0.27 2 -10000 0 2
Rac1/GTP -0.014 0.05 -10000 0 -0.24 2 2
FRS2 family/SHP2/CRK family 0.075 0.043 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.032 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.033 -10000 0 -0.37 1 1
Metarhodopsin II/Arrestin 0.035 0.033 -10000 0 -0.31 1 1
PDE6G/GNAT1/GTP 0.035 0.034 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.025 0.046 -10000 0 -0.51 1 1
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.02 0.086 -10000 0 -0.26 11 11
mol:Na + 0.026 0.089 -10000 0 -0.33 6 6
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.01 0.12 -10000 0 -0.32 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.037 0.097 -10000 0 -0.34 6 6
CNGB1 0.032 0.006 -10000 0 -10000 0 0
RDH5 0.031 0.013 -10000 0 -10000 0 0
SAG 0.028 0.045 -10000 0 -0.51 1 1
mol:Ca2+ 0.012 0.11 0.33 4 -0.67 1 5
Na + (4 Units) 0.019 0.082 -10000 0 -0.33 5 5
RGS9 0.013 0.088 -10000 0 -0.51 4 4
GNB1/GNGT1 -0.037 0.16 -10000 0 -0.37 27 27
GNAT1/GDP 0.016 0.11 -10000 0 -0.28 16 16
GUCY2D 0.027 0.044 -10000 0 -0.51 1 1
GNGT1 -0.073 0.2 -10000 0 -0.51 27 27
GUCY2F 0.023 0.063 -10000 0 -0.51 2 2
GNB5 0.018 0.086 -10000 0 -0.51 4 4
mol:GMP (4 units) 0.007 0.072 -10000 0 -0.27 9 9
mol:11-cis-retinal 0.031 0.013 -10000 0 -10000 0 0
mol:cGMP 0.037 0.08 -10000 0 -0.34 5 5
GNB1 0.032 0.005 -10000 0 -10000 0 0
Rhodopsin 0.041 0.018 -10000 0 -10000 0 0
SLC24A1 0.032 0.003 -10000 0 -10000 0 0
CNGA1 0.016 0.067 -10000 0 -0.51 2 2
Metarhodopsin II 0.018 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.079 -10000 0 -0.3 6 6
RGS9BP -0.004 0.12 -10000 0 -0.51 7 7
Metarhodopsin II/Transducin -0.032 0.11 -10000 0 -0.27 24 24
GCAP Family/Ca ++ 0.038 0.067 -10000 0 -0.29 5 5
PDE6A/B 0.013 0.095 -10000 0 -0.37 8 8
mol:Pi 0.01 0.12 -10000 0 -0.32 15 15
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.016 0.14 -10000 0 -0.3 27 27
PDE6B 0.002 0.11 -10000 0 -0.51 6 6
PDE6A 0.023 0.063 -10000 0 -0.51 2 2
PDE6G 0.03 0.013 -10000 0 -10000 0 0
RHO 0.028 0.011 -10000 0 -10000 0 0
PDE6 0.008 0.13 -10000 0 -0.29 21 21
GUCA1A 0.021 0.075 -10000 0 -0.51 3 3
GC2/GCAP Family 0.05 0.077 -10000 0 -0.3 5 5
GUCA1C 0.018 0.063 -10000 0 -0.51 2 2
GUCA1B 0.031 0.01 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.006 -10000 0 -10000 0 0
SMARCC1 0.001 0.16 -10000 0 -1.3 2 2
REL 0.002 0.11 -10000 0 -0.51 7 7
HDAC7 -0.033 0.11 0.23 2 -0.32 8 10
JUN 0.003 0.11 -10000 0 -0.51 7 7
EP300 0.003 0.12 -10000 0 -0.51 8 8
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.006 0.072 -10000 0 -0.37 5 5
FOXO1 0.014 0.096 -10000 0 -0.51 5 5
T-DHT/AR -0.008 0.14 -10000 0 -0.34 8 8
MAP2K6 0.003 0.098 -10000 0 -0.51 5 5
BRM/BAF57 0.037 0.043 -10000 0 -0.37 1 1
MAP2K4 0.017 0.048 -10000 0 -0.51 1 1
SMARCA2 0.023 0.047 -10000 0 -0.51 1 1
PDE9A -0.056 0.26 -10000 0 -1 9 9
NCOA2 0.024 0.062 -10000 0 -0.51 2 2
CEBPA 0.012 0.096 -10000 0 -0.51 5 5
EHMT2 0.032 0.006 -10000 0 -10000 0 0
cell proliferation -0.001 0.15 0.36 4 -0.36 7 11
NR0B1 -0.19 0.23 -10000 0 -0.51 51 51
EGR1 -0.022 0.15 -10000 0 -0.51 13 13
RXRs/9cRA 0.052 0.046 -10000 0 -0.3 2 2
AR/RACK1/Src 0.011 0.094 0.3 3 -0.28 4 7
AR/GR 0.015 0.082 0.21 1 -0.35 3 4
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
PKN1 0.031 0.006 -10000 0 -10000 0 0
RCHY1 0.023 0.062 -10000 0 -0.51 2 2
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.038 -10000 0 -0.36 1 1
T-DHT/AR/TIF2/CARM1 0.017 0.1 -10000 0 -0.34 5 5
SRC -0.02 0.072 0.2 6 -0.27 6 12
NR3C1 0.03 0.011 -10000 0 -10000 0 0
KLK3 -0.013 0.12 -10000 0 -10000 0 0
APPBP2 0.02 0.025 -10000 0 -10000 0 0
TRIM24 0.021 0.075 -10000 0 -0.51 3 3
T-DHT/AR/TIP60 -0.026 0.068 -10000 0 -0.27 7 7
TMPRSS2 -0.21 0.44 -10000 0 -1 33 33
RXRG 0.03 0.014 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.024 0.063 -10000 0 -0.51 2 2
RXRB 0.032 0.005 -10000 0 -10000 0 0
CARM1 0.032 0.006 -10000 0 -10000 0 0
NR2C2 0.027 0.044 -10000 0 -0.51 1 1
KLK2 0.016 0.082 -10000 0 -0.4 1 1
AR -0.007 0.071 -10000 0 -0.34 4 4
SENP1 0.033 0.003 -10000 0 -10000 0 0
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
MDM2 0.026 0.044 -10000 0 -0.51 1 1
SRY -0.001 0 -10000 0 -10000 0 0
GATA2 0.025 0.045 -10000 0 -0.51 1 1
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.097 0.22 -10000 0 -0.51 34 34
T-DHT/AR/RACK1/Src 0.007 0.095 0.31 3 -0.29 4 7
positive regulation of transcription 0.025 0.045 -10000 0 -0.51 1 1
DNAJA1 0.018 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.048 -10000 0 -0.32 3 3
NCOA1 0.04 0.031 -10000 0 -0.17 2 2
SPDEF 0.026 0.029 -10000 0 -10000 0 0
T-DHT/AR/TIF2 0.002 0.09 0.22 1 -0.35 4 5
T-DHT/AR/Hsp90 -0.001 0.085 0.24 1 -0.29 5 6
GSK3B 0.027 0.012 -10000 0 -10000 0 0
NR2C1 0.032 0 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.067 0.23 1 -0.29 6 7
SIRT1 0.031 0.006 -10000 0 -10000 0 0
ZMIZ2 0.03 0.01 -10000 0 -10000 0 0
POU2F1 0.002 0.063 -10000 0 -0.18 3 3
T-DHT/AR/DAX-1 -0.11 0.14 -10000 0 -0.29 46 46
CREBBP 0.031 0.007 -10000 0 -10000 0 0
SMARCE1 0.033 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.001 0.14 -9999 0 -0.36 16 16
MAP3K8 -0.014 0.14 -9999 0 -0.51 12 12
FOS 0 0.1 -9999 0 -0.39 5 5
PRKCA 0.023 0.047 -9999 0 -0.52 1 1
PTPN7 0.025 0.023 -9999 0 -10000 0 0
HRAS 0.024 0.062 -9999 0 -0.51 2 2
PRKCB -0.001 0.005 -9999 0 -0.016 15 15
NRAS 0.025 0.047 -9999 0 -0.51 1 1
RAS family/GTP 0.032 0.076 -9999 0 -0.29 7 7
MAPK3 0.017 0.057 -9999 0 -0.37 1 1
MAP2K1 -0.007 0.086 -9999 0 -0.36 5 5
ELK1 0.026 0.02 -9999 0 -10000 0 0
BRAF -0.002 0.074 -9999 0 -0.38 5 5
mol:GTP -0.001 0.002 -9999 0 -0.004 17 17
MAPK1 0.004 0.11 -9999 0 -0.5 5 5
RAF1 0.004 0.054 -9999 0 -0.4 2 2
KRAS 0.016 0.086 -9999 0 -0.51 4 4
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.008 0.036 -10000 0 -0.32 2 2
RAS family/GTP 0.015 0.1 -10000 0 -0.33 3 3
NFATC4 -0.02 0.075 -10000 0 -0.27 4 4
ERBB2IP 0.03 0.01 -10000 0 -10000 0 0
HSP90 (dimer) 0.031 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.094 -10000 0 -0.3 10 10
JUN 0.018 0.069 -10000 0 -10000 0 0
HRAS 0.024 0.062 -10000 0 -0.51 2 2
DOCK7 -0.015 0.089 -10000 0 -0.29 9 9
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.099 -10000 0 -0.32 9 9
AKT1 0.002 0.043 -10000 0 -0.37 2 2
BAD -0.008 0.036 -10000 0 -0.32 2 2
MAPK10 -0.021 0.057 -10000 0 -0.23 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.002 0.1 -10000 0 -0.32 10 10
RAF1 0.006 0.1 0.26 1 -0.31 4 5
ErbB2/ErbB3/neuregulin 2 0.026 0.053 -10000 0 -0.31 3 3
STAT3 0.012 0.15 -10000 0 -0.91 4 4
cell migration -0.012 0.054 -10000 0 -0.21 1 1
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.028 0.21 -10000 0 -0.59 11 11
FOS -0.031 0.19 -10000 0 -0.46 20 20
NRAS 0.025 0.047 -10000 0 -0.51 1 1
mol:Ca2+ -0.001 0.094 -10000 0 -0.3 10 10
MAPK3 -0.013 0.17 -10000 0 -0.5 7 7
MAPK1 -0.023 0.19 -10000 0 -0.57 9 9
JAK2 -0.02 0.091 -10000 0 -0.3 10 10
NF2 0.009 0.055 -10000 0 -0.56 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.007 0.074 -10000 0 -0.28 7 7
NRG1 -0.008 0.13 -10000 0 -0.51 9 9
GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
MAPK8 -0.003 0.095 -10000 0 -0.29 9 9
MAPK9 -0.012 0.059 0.29 1 -0.23 1 2
ERBB2 -0.026 0.043 -10000 0 -0.39 2 2
ERBB3 0.028 0.045 -10000 0 -0.51 1 1
SHC1 0.031 0.007 -10000 0 -10000 0 0
RAC1 0.032 0.005 -10000 0 -10000 0 0
apoptosis 0.004 0.041 0.36 2 -10000 0 2
STAT3 (dimer) 0.014 0.15 -10000 0 -0.89 4 4
RNF41 -0.01 0.033 -10000 0 -0.29 2 2
FRAP1 -0.006 0.035 -10000 0 -0.31 2 2
RAC1-CDC42/GTP -0.015 0.062 -10000 0 -0.24 4 4
ErbB2/ErbB2/HSP90 (dimer) 0.007 0.043 -10000 0 -0.33 2 2
CHRNA1 -0.002 0.15 -10000 0 -0.42 6 6
myelination -0.008 0.091 0.29 3 -0.32 2 5
PPP3CB -0.013 0.085 -10000 0 -0.27 9 9
KRAS 0.016 0.086 -10000 0 -0.51 4 4
RAC1-CDC42/GDP 0.033 0.084 -10000 0 -0.25 6 6
NRG2 0.028 0.019 -10000 0 -10000 0 0
mol:GDP 0.007 0.074 -10000 0 -0.27 7 7
SOS1 0.032 0.005 -10000 0 -10000 0 0
MAP2K2 0.001 0.1 0.24 2 -0.35 3 5
SRC 0.031 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.026 0.089 -10000 0 -0.29 9 9
MAP2K1 -0.019 0.17 -10000 0 -0.51 6 6
heart morphogenesis -0.001 0.094 -10000 0 -0.3 10 10
RAS family/GDP 0.023 0.1 -10000 0 -0.33 3 3
GRB2 0.032 0.005 -10000 0 -10000 0 0
PRKACA 0.008 0.068 -10000 0 -0.58 2 2
CHRNE 0.012 0.017 -10000 0 -10000 0 0
HSP90AA1 0.031 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.002 0.043 0.37 2 -10000 0 2
nervous system development -0.001 0.094 -10000 0 -0.3 10 10
CDC42 0.032 0.005 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.003 0.14 -10000 0 -0.39 13 13
epithelial cell differentiation 0.004 0.12 -10000 0 -0.58 3 3
ITCH 0.032 0.021 -10000 0 -10000 0 0
WWP1 0.008 0.17 -10000 0 -1.4 2 2
FYN 0.024 0.062 -10000 0 -0.51 2 2
EGFR -0.033 0.17 -10000 0 -0.51 17 17
PRL 0.03 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis 0.005 0.087 -10000 0 -0.42 3 3
PTPRZ1 -0.086 0.22 -10000 0 -0.51 33 33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.04 0.097 -10000 0 -0.37 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.005 0.11 -10000 0 -0.5 4 4
ADAM17 0.027 0.05 -10000 0 -0.34 2 2
ErbB4/ErbB4 0.016 0.1 -10000 0 -0.77 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.022 0.1 -10000 0 -0.45 5 5
NCOR1 0.031 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.003 0.12 -10000 0 -0.53 5 5
GRIN2B -0.011 0.12 -10000 0 -0.5 5 5
ErbB4/ErbB2/betacellulin 0.001 0.12 -10000 0 -0.54 4 4
STAT1 0.009 0.1 -10000 0 -0.51 6 6
HBEGF -0.025 0.16 -10000 0 -0.51 15 15
PRLR 0.018 0.05 -10000 0 -0.51 1 1
E4ICDs/ETO2 0.022 0.1 -10000 0 -0.49 4 4
axon guidance 0.017 0.12 0.33 2 -0.74 2 4
NEDD4 0.024 0.065 -10000 0 -0.51 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.03 0.043 -10000 0 -0.37 1 1
CBFA2T3 0.017 0.067 -10000 0 -0.51 2 2
ErbB4/ErbB2/HBEGF -0.004 0.14 -10000 0 -0.48 7 7
MAPK3 0.013 0.088 -10000 0 -0.36 4 4
STAT1 (dimer) 0.018 0.12 -10000 0 -0.49 6 6
MAPK1 0.009 0.091 -10000 0 -0.43 3 3
JAK2 0.024 0.046 -10000 0 -0.51 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.009 0.12 -10000 0 -0.6 4 4
NRG1 -0.013 0.097 -10000 0 -0.37 10 10
NRG3 0.02 0.075 -10000 0 -0.51 3 3
NRG2 0.028 0.019 -10000 0 -10000 0 0
NRG4 -0.028 0.15 -10000 0 -0.51 13 13
heart development 0.017 0.12 0.33 2 -0.74 2 4
neural crest cell migration -0.008 0.12 -10000 0 -0.59 4 4
ERBB2 0.008 0.065 -10000 0 -0.51 2 2
WWOX/E4ICDs 0.029 0.095 -10000 0 -0.71 2 2
SHC1 0.031 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.024 0.16 -10000 0 -0.57 6 6
apoptosis -0.012 0.1 0.46 5 -10000 0 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.027 0.097 -10000 0 -0.71 2 2
ErbB4/ErbB2/epiregulin 0.008 0.11 -10000 0 -0.54 4 4
ErbB4/ErbB4/betacellulin/betacellulin 0 0.13 -10000 0 -0.34 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.019 0.14 -10000 0 -0.54 4 4
MDM2 0.017 0.1 0.26 6 -0.56 3 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.005 0.1 -10000 0 -0.44 4 4
STAT5A 0.016 0.12 0.33 1 -0.71 2 3
ErbB4/EGFR/neuregulin 1 beta -0.027 0.16 -10000 0 -0.52 10 10
DLG4 0.03 0.012 -10000 0 -10000 0 0
GRB2/SHC 0.045 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.026 0.09 -10000 0 -0.67 2 2
STAT5A (dimer) 0.012 0.14 -10000 0 -0.65 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.035 0.12 0.32 1 -0.71 2 3
LRIG1 -0.014 0.14 -10000 0 -0.51 12 12
EREG -0.003 0.092 -10000 0 -0.51 4 4
BTC -0.021 0.15 -10000 0 -0.51 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.013 0.12 0.3 1 -0.75 2 3
ERBB4 0.016 0.1 -10000 0 -0.77 2 2
STAT5B 0.032 0.005 -10000 0 -10000 0 0
YAP1 0 0.12 -10000 0 -0.62 5 5
GRB2 0.032 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.004 0.13 -10000 0 -0.6 4 4
glial cell differentiation -0.025 0.089 0.66 2 -10000 0 2
WWOX 0.03 0.008 -10000 0 -10000 0 0
cell proliferation -0.052 0.16 -10000 0 -0.55 9 9
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.031 0.007 -9999 0 -10000 0 0
VLDLR -0.013 0.13 -9999 0 -0.51 10 10
LRPAP1 0.03 0.009 -9999 0 -10000 0 0
NUDC 0.032 0.005 -9999 0 -10000 0 0
RELN/LRP8 0.022 0.1 -9999 0 -0.32 12 12
CaM/Ca2+ 0.023 0.005 -9999 0 -10000 0 0
KATNA1 0.032 0.006 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.001 0.094 -9999 0 -0.29 12 12
IQGAP1/CaM 0.046 0.011 -9999 0 -10000 0 0
DAB1 0.031 0.01 -9999 0 -10000 0 0
IQGAP1 0.032 0.005 -9999 0 -10000 0 0
PLA2G7 -0.052 0.19 -9999 0 -0.51 22 22
CALM1 0.031 0.006 -9999 0 -10000 0 0
DYNLT1 0.032 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.008 0.11 -9999 0 -0.37 12 12
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.026 0.061 -9999 0 -0.51 2 2
CDK5R1 0.03 0.016 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.004 -9999 0 -10000 0 0
CDK5R2 0.032 0.005 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 0.018 0.099 -9999 0 -0.32 10 10
YWHAE 0.03 0.008 -9999 0 -10000 0 0
NDEL1/14-3-3 E 0.018 0.085 -9999 0 -10000 0 0
MAP1B -0.059 0.12 -9999 0 -0.28 33 33
RAC1 0.016 0.007 -9999 0 -10000 0 0
p35/CDK5 0.009 0.089 -9999 0 -0.26 12 12
RELN 0.029 0.017 -9999 0 -10000 0 0
PAFAH/LIS1 -0.02 0.12 -9999 0 -0.32 21 21
LIS1/CLIP170 0.029 0.041 -9999 0 -0.32 2 2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.026 0.07 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.003 0.097 -9999 0 -0.28 10 10
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.003 0.083 -9999 0 -10000 0 0
LIS1/IQGAP1 0.033 0.012 -9999 0 -10000 0 0
RHOA 0.016 0.007 -9999 0 -10000 0 0
PAFAH1B1 0.016 0.005 -9999 0 -10000 0 0
PAFAH1B3 0.032 0.005 -9999 0 -10000 0 0
PAFAH1B2 0.028 0.045 -9999 0 -0.51 1 1
MAP1B/LIS1/Dynein heavy chain -0.024 0.093 -9999 0 -0.31 3 3
NDEL1/Katanin 60/Dynein heavy chain 0.029 0.088 -9999 0 -10000 0 0
LRP8 -0.015 0.14 -9999 0 -0.51 12 12
NDEL1/Katanin 60 0.013 0.088 -9999 0 -10000 0 0
P39/CDK5 0.01 0.089 -9999 0 -0.26 12 12
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.012 -9999 0 -10000 0 0
CDK5 -0.021 0.086 -9999 0 -0.28 12 12
PPP2R5D 0.029 0.044 -9999 0 -0.51 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.035 -9999 0 -0.27 2 2
CSNK2A1 0.031 0.008 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.023 0.091 -9999 0 -0.28 10 10
RELN/VLDLR 0 0.14 -9999 0 -0.32 20 20
CDC42 0.017 0.006 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.035 0.1 -10000 0 -0.29 12 12
MAP4K1 0.029 0.01 -10000 0 -10000 0 0
MAP3K8 -0.013 0.14 -10000 0 -0.51 12 12
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.028 0.044 -10000 0 -0.51 1 1
CRKL 0.028 0.013 -10000 0 -10000 0 0
MAP3K1 0.001 0.078 -10000 0 -0.33 2 2
JUN -0.022 0.14 -10000 0 -0.44 11 11
MAP3K7 0.003 0.078 -10000 0 -0.33 2 2
GRAP2 0.031 0.007 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
MAP2K4 -0.008 0.11 0.24 1 -0.37 7 8
LAT 0.03 0.018 -10000 0 -10000 0 0
LCP2 -0.016 0.15 -10000 0 -0.51 13 13
MAPK8 -0.007 0.14 -10000 0 -0.75 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.012 0.08 -10000 0 -0.35 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55 0.044 0.1 -10000 0 -0.27 12 12
Cellular roles of Anthrax toxin

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
ANTXR1 0.01 0.097 -10000 0 -0.51 5 5
ANTXR2 0.026 0.046 -10000 0 -0.51 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.013 -10000 0 -0.069 6 6
monocyte activation -0.02 0.13 -10000 0 -0.4 14 14
MAP2K2 0.003 0.093 -10000 0 -0.56 4 4
MAP2K1 -0.005 0.012 -10000 0 -10000 0 0
MAP2K7 -0.006 0.012 -10000 0 -10000 0 0
MAP2K6 -0.014 0.048 -10000 0 -0.27 5 5
CYAA -0.016 0.051 -10000 0 -0.27 6 6
MAP2K4 -0.007 0.028 -10000 0 -0.33 1 1
IL1B -0.057 0.11 -10000 0 -0.28 29 29
Channel 0.021 0.065 -10000 0 -0.28 6 6
NLRP1 -0.011 0.037 -10000 0 -0.25 3 3
CALM1 0.031 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.004 0.057 -10000 0 -0.39 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.013 0.069 6 -10000 0 6
MAPK3 -0.005 0.012 -10000 0 -10000 0 0
MAPK1 -0.004 0.031 0.13 2 -0.33 1 3
PGR -0.008 0.034 0.13 1 -0.27 2 3
PA/Cellular Receptors 0.022 0.072 -10000 0 -0.31 6 6
apoptosis -0.004 0.013 -10000 0 -0.069 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.062 -10000 0 -0.27 6 6
macrophage activation -0.006 0.03 0.12 2 -0.32 1 3
TNF 0.024 0.048 -10000 0 -0.51 1 1
VCAM1 -0.022 0.13 -10000 0 -0.41 14 14
platelet activation 0.004 0.057 -10000 0 -0.39 3 3
MAPKKK cascade 0.003 0.029 0.14 2 -0.13 1 3
IL18 -0.03 0.088 -10000 0 -0.3 14 14
negative regulation of macrophage activation -0.004 0.013 -10000 0 -0.069 6 6
LEF -0.004 0.013 -10000 0 -0.069 6 6
CASP1 -0.008 0.037 -10000 0 -0.13 9 9
mol:cAMP 0.004 0.058 -10000 0 -0.39 3 3
necrosis -0.004 0.013 -10000 0 -0.069 6 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.062 -10000 0 -0.27 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.059 -10000 0 -0.37 3 3
CRKL 0.001 0.15 0.25 3 -0.44 12 15
mol:PIP3 0.013 0.051 0.46 1 -10000 0 1
AKT1 0.007 0.065 0.34 2 -10000 0 2
PTK2B 0.028 0.015 -10000 0 -10000 0 0
RAPGEF1 0.001 0.14 0.24 3 -0.42 12 15
RANBP10 0.027 0.044 -10000 0 -0.51 1 1
PIK3CA 0.009 0.062 -10000 0 -0.51 2 2
HGF/MET/SHIP2 0.045 0.066 -10000 0 -0.32 4 4
MAP3K5 0.007 0.14 -10000 0 -0.43 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS 0.053 0.079 -10000 0 -0.29 6 6
AP1 -0.024 0.14 -10000 0 -0.37 18 18
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.031 0.007 -10000 0 -10000 0 0
apoptosis -0.097 0.29 -10000 0 -0.76 23 23
STAT3 (dimer) 0.015 0.063 -10000 0 -0.28 1 1
GAB1/CRKL/SHP2/PI3K -0.004 0.13 -10000 0 -0.46 6 6
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.008 0.13 -10000 0 -0.42 12 12
PTPN11 0.029 0.044 -10000 0 -0.51 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.044 -10000 0 -0.51 1 1
ELK1 -0.003 0.075 0.27 8 -0.19 2 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.054 -10000 0 -0.22 3 3
PAK1 0.008 0.077 0.33 1 -0.53 1 2
HGF/MET/RANBP10 0.048 0.065 -10000 0 -0.32 4 4
HRAS 0.01 0.11 -10000 0 -0.57 4 4
DOCK1 0.003 0.14 0.24 3 -0.42 12 15
GAB1 -0.009 0.14 -10000 0 -0.46 12 12
CRK -0.011 0.13 -10000 0 -0.44 12 12
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.097 -10000 0 -0.52 4 4
JUN 0.002 0.11 -10000 0 -0.51 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.046 -10000 0 -0.26 4 4
PIK3R1 0.004 0.098 -10000 0 -0.51 5 5
cell morphogenesis 0.078 0.15 0.35 11 -0.35 2 13
GRB2/SHC 0.04 0.05 -10000 0 -0.23 3 3
FOS -0.03 0.16 -10000 0 -0.51 14 14
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.003 0.075 0.27 8 -0.19 2 10
HGF/MET/MUC20 0.032 0.052 -10000 0 -0.31 3 3
cell migration 0.039 0.05 -10000 0 -0.23 3 3
GRB2 0.032 0.005 -10000 0 -10000 0 0
CBL 0.032 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.033 0.069 -10000 0 -0.38 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.018 0.051 -10000 0 -0.23 5 5
MET/MUC20 0.015 0.055 -10000 0 -0.37 3 3
RAP1B 0.006 0.14 -10000 0 -0.42 10 10
RAP1A -0.004 0.13 -10000 0 -0.42 10 10
HGF/MET/RANBP9 0.05 0.058 -10000 0 -0.32 3 3
RAF1 0.012 0.1 -10000 0 -0.54 4 4
STAT3 0.015 0.064 -10000 0 -0.28 1 1
cell proliferation 0.022 0.083 0.26 2 -0.39 2 4
RPS6KB1 0.014 0.021 -10000 0 -10000 0 0
MAPK3 -0.016 0.077 0.66 1 -10000 0 1
MAPK1 0.009 0.15 0.7 6 -10000 0 6
RANBP9 0.032 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.14 -10000 0 -0.47 6 6
SRC 0.004 0.052 -10000 0 -10000 0 0
PI3K 0.003 0.068 -10000 0 -0.25 8 8
MET/Glomulin 0.017 0.053 -10000 0 -0.32 3 3
SOS1 0.032 0.005 -10000 0 -10000 0 0
MAP2K1 0.012 0.097 -10000 0 -0.5 4 4
MET 0.02 0.076 -10000 0 -0.51 3 3
MAP4K1 0.011