Lung Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 37 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
FOXA2 and FOXA3 transcription factor networks 63
TCGA08_retinoblastoma 57
IL4-mediated signaling events 52
Signaling events mediated by the Hedgehog family 49
Glypican 2 network 44
IL23-mediated signaling events 35
Visual signal transduction: Cones 34
HIF-1-alpha transcription factor network 31
BMP receptor signaling 31
Syndecan-1-mediated signaling events 30
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXA2 and FOXA3 transcription factor networks 63 2906 46 -0.6 0.015 1000 -1000 -0.13 -1000
TCGA08_retinoblastoma 57 458 8 -0.19 0.072 1000 -1000 -0.024 -1000
IL4-mediated signaling events 52 4759 91 -0.82 0.72 1000 -1000 -0.18 -1000
Signaling events mediated by the Hedgehog family 49 2599 52 -0.25 0.19 1000 -1000 -0.098 -1000
Glypican 2 network 44 177 4 -0.064 -1000 1000 -1000 -0.031 -1000
IL23-mediated signaling events 35 2140 60 -0.34 0.013 1000 -1000 -0.19 -1000
Visual signal transduction: Cones 34 1324 38 -0.22 0.012 1000 -1000 -0.059 -1000
HIF-1-alpha transcription factor network 31 2414 76 -0.49 0.019 1000 -1000 -0.23 -1000
BMP receptor signaling 31 2541 81 -0.25 0.025 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 30 1032 34 -0.18 0.012 1000 -1000 -0.07 -1000
Endothelins 30 2888 96 -0.19 0.012 1000 -1000 -0.1 -1000
Wnt signaling 30 213 7 -0.12 0.004 1000 -1000 -0.037 -1000
Visual signal transduction: Rods 30 1604 52 -0.22 0.012 1000 -1000 -0.089 -1000
Nephrin/Neph1 signaling in the kidney podocyte 29 1017 34 -0.095 0.012 1000 -1000 -0.062 -1000
Signaling events regulated by Ret tyrosine kinase 29 2378 82 -0.2 0.012 1000 -1000 -0.1 -1000
Effects of Botulinum toxin 29 771 26 -0.14 0.012 1000 -1000 -0.074 -1000
Ephrin A reverse signaling 28 200 7 -0.05 0 1000 -1000 -0.035 -1000
amb2 Integrin signaling 28 2350 82 -0.25 0.012 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 27 3484 125 -0.25 0.028 1000 -1000 -0.13 -1000
TCGA08_p53 27 195 7 -0.14 0.071 1000 -1000 -0.024 -1000
Glypican 1 network 26 1292 48 -0.15 0.017 1000 -1000 -0.055 -1000
Calcium signaling in the CD4+ TCR pathway 26 816 31 -0.27 0.012 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 24 1685 68 -0.32 0.076 1000 -1000 -0.14 -1000
Arf6 signaling events 23 1457 62 -0.12 0.012 1000 -1000 -0.078 -1000
Fc-epsilon receptor I signaling in mast cells 23 2273 97 -0.18 0.032 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 23 2695 114 -0.42 0.18 1000 -1000 -0.079 -1000
Ephrin B reverse signaling 23 1140 48 -0.12 0.08 1000 -1000 -0.079 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 23 1798 78 -0.13 0.057 1000 -1000 -0.095 -1000
FOXM1 transcription factor network 22 1147 51 -0.23 0.029 1000 -1000 -0.22 -1000
IL12-mediated signaling events 21 1848 87 -0.23 0.035 1000 -1000 -0.16 -1000
Osteopontin-mediated events 21 810 38 -0.12 0.014 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 21 546 26 -0.12 0.012 1000 -1000 -0.073 -1000
Signaling mediated by p38-alpha and p38-beta 21 962 44 -0.19 0.012 1000 -1000 -0.064 -1000
EGFR-dependent Endothelin signaling events 21 441 21 -0.12 0.018 1000 -1000 -0.086 -1000
Syndecan-2-mediated signaling events 20 1385 69 -0.14 0.034 1000 -1000 -0.068 -1000
Syndecan-4-mediated signaling events 20 1383 67 -0.15 0.014 1000 -1000 -0.091 -1000
Neurotrophic factor-mediated Trk receptor signaling 20 2457 120 -0.18 0.17 1000 -1000 -0.093 -1000
LPA4-mediated signaling events 17 211 12 -0.065 0.015 1000 -1000 -0.038 -1000
ErbB4 signaling events 17 1218 69 -0.28 0.074 1000 -1000 -0.098 -1000
Signaling events mediated by PTP1B 17 1359 76 -0.17 0.02 1000 -1000 -0.089 -1000
TCR signaling in naïve CD8+ T cells 17 1587 93 -0.15 0.084 1000 -1000 -0.1 -1000
Canonical Wnt signaling pathway 17 874 51 -0.27 0.07 1000 -1000 -0.082 -1000
EPHB forward signaling 17 1525 85 -0.16 0.097 1000 -1000 -0.11 -1000
IL6-mediated signaling events 17 1308 75 -0.43 0.048 1000 -1000 -0.1 -1000
BCR signaling pathway 17 1758 99 -0.16 0.029 1000 -1000 -0.12 -1000
Thromboxane A2 receptor signaling 16 1689 105 -0.12 0.028 1000 -1000 -0.081 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 16 1362 85 -0.1 0.012 1000 -1000 -0.093 -1000
Nectin adhesion pathway 16 1021 63 -0.07 0.018 1000 -1000 -0.089 -1000
Reelin signaling pathway 16 938 56 -0.17 0.018 1000 -1000 -0.099 -1000
Nongenotropic Androgen signaling 16 842 52 -0.1 0.012 1000 -1000 -0.076 -1000
IL27-mediated signaling events 16 863 51 -0.13 0.051 1000 -1000 -0.081 -1000
LPA receptor mediated events 16 1730 102 -0.15 0.035 1000 -1000 -0.11 -1000
Plasma membrane estrogen receptor signaling 16 1427 86 -0.078 0.042 1000 -1000 -0.1 -1000
Presenilin action in Notch and Wnt signaling 15 958 61 -0.27 0.023 1000 -1000 -0.088 -1000
S1P1 pathway 15 548 36 -0.17 0.012 1000 -1000 -0.068 -1000
Coregulation of Androgen receptor activity 14 1136 76 -0.19 0.021 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 14 735 52 -0.15 0.024 1000 -1000 -0.083 -1000
Angiopoietin receptor Tie2-mediated signaling 14 1291 88 -0.097 0.025 1000 -1000 -0.15 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 14 463 33 -0.19 0.029 1000 -1000 -0.078 -1000
Class IB PI3K non-lipid kinase events 14 42 3 -0.014 -1000 1000 -1000 -0.02 -1000
Aurora B signaling 14 981 67 -0.14 0.012 1000 -1000 -0.092 -1000
Integrins in angiogenesis 13 1146 84 -0.12 0.018 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 12 931 74 -0.094 0.015 1000 -1000 -0.057 -1000
FAS signaling pathway (CD95) 12 601 47 -0.15 0.015 1000 -1000 -0.067 -1000
Syndecan-3-mediated signaling events 12 434 35 -0.082 0.018 1000 -1000 -0.073 -1000
Regulation of Androgen receptor activity 12 908 70 -0.22 0.022 1000 -1000 -0.087 -1000
PDGFR-alpha signaling pathway 10 440 44 -0.066 0.021 1000 -1000 -0.087 -1000
IL1-mediated signaling events 10 680 62 -0.14 0.05 1000 -1000 -0.12 -1000
Sphingosine 1-phosphate (S1P) pathway 9 252 28 -0.068 0.019 1000 -1000 -0.046 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 9 487 54 -0.14 0.024 1000 -1000 -0.13 -1000
Signaling events mediated by HDAC Class III 9 388 40 -0.14 0.021 1000 -1000 -0.051 -1000
HIF-2-alpha transcription factor network 9 412 43 -0.093 0.034 1000 -1000 -0.12 -1000
Signaling mediated by p38-gamma and p38-delta 9 144 15 -0.019 0.02 1000 -1000 -0.048 -1000
Regulation of Telomerase 9 1013 102 -0.15 0.04 1000 -1000 -0.12 -1000
ErbB2/ErbB3 signaling events 8 540 65 -0.084 0.022 1000 -1000 -0.08 -1000
PLK2 and PLK4 events 8 26 3 -0.003 0.002 1000 -1000 -0.02 -1000
Cellular roles of Anthrax toxin 8 338 39 -0.06 0.016 1000 -1000 -0.036 -1000
Hedgehog signaling events mediated by Gli proteins 8 547 65 -0.24 0.052 1000 -1000 -0.074 -1000
Aurora C signaling 8 57 7 -0.028 0 1000 -1000 -0.035 -1000
S1P5 pathway 8 150 17 -0.068 0.049 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 8 479 54 -0.15 0.03 1000 -1000 -0.079 -1000
S1P4 pathway 8 212 25 -0.068 0.019 1000 -1000 -0.068 -1000
p38 MAPK signaling pathway 8 355 44 -0.13 0.022 1000 -1000 -0.086 -1000
Ras signaling in the CD4+ TCR pathway 8 138 17 -0.025 0.022 1000 -1000 -0.061 -1000
Regulation of nuclear SMAD2/3 signaling 7 1012 136 -0.2 0.051 1000 -1000 -0.092 -1000
PLK1 signaling events 7 602 85 -0.043 0.018 1000 -1000 -0.061 -1000
Ceramide signaling pathway 7 581 76 -0.12 0.039 1000 -1000 -0.082 -1000
Signaling events mediated by VEGFR1 and VEGFR2 7 883 125 -0.061 0.043 1000 -1000 -0.11 -1000
Stabilization and expansion of the E-cadherin adherens junction 7 560 74 -0.18 0.051 1000 -1000 -0.11 -1000
IL2 signaling events mediated by STAT5 7 157 22 -0.033 0.036 1000 -1000 -0.072 -1000
IGF1 pathway 7 455 57 -0.043 0.026 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 7 245 34 -0.1 0.023 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 6 110 17 -0.034 0.022 1000 -1000 -0.075 -1000
a4b1 and a4b7 Integrin signaling 6 30 5 0 0.008 1000 -1000 -0.028 -1000
Aurora A signaling 6 385 60 -0.068 0.032 1000 -1000 -0.079 -1000
TRAIL signaling pathway 6 332 48 -0.029 0.033 1000 -1000 -0.085 -1000
TCGA08_rtk_signaling 6 161 26 -0.09 0.033 1000 -1000 -0.029 -1000
Insulin Pathway 6 462 74 -0.097 0.029 1000 -1000 -0.094 -1000
S1P3 pathway 6 288 42 -0.067 0.023 1000 -1000 -0.052 -1000
IFN-gamma pathway 5 394 68 -0.13 0.033 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 5 189 37 -0.034 0.023 1000 -1000 -0.07 -1000
Retinoic acid receptors-mediated signaling 5 336 58 -0.093 0.03 1000 -1000 -0.089 -1000
IL2 signaling events mediated by PI3K 5 333 58 -0.093 0.04 1000 -1000 -0.11 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 5 245 45 -0.06 0.033 1000 -1000 -0.12 -1000
Rapid glucocorticoid signaling 5 105 20 -0.03 0.012 1000 -1000 -0.049 -1000
Signaling events mediated by HDAC Class II 4 353 75 -0.076 0.029 1000 -1000 -0.068 -1000
Arf6 downstream pathway 4 205 43 -0.021 0.021 1000 -1000 -0.051 -1000
ceramide signaling pathway 4 199 49 -0.06 0.025 1000 -1000 -0.073 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 337 83 -0.039 0.048 1000 -1000 -0.092 -1000
Class I PI3K signaling events 4 364 73 -0.12 0.037 1000 -1000 -0.083 -1000
E-cadherin signaling events 4 22 5 -0.012 0.01 1000 -1000 -0.063 -1000
BARD1 signaling events 3 189 57 -0.025 0.045 1000 -1000 -0.087 -1000
E-cadherin signaling in the nascent adherens junction 3 243 76 -0.026 0.046 1000 -1000 -0.1 -1000
VEGFR1 specific signals 3 197 56 -0.023 0.039 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 3 341 97 -0.093 0.048 1000 -1000 -0.1 -1000
Canonical NF-kappaB pathway 2 113 39 -0.06 0.066 1000 -1000 -0.11 -1000
Circadian rhythm pathway 2 61 22 -0.026 0.036 1000 -1000 -0.066 -1000
EPO signaling pathway 2 144 55 -0.014 0.051 1000 -1000 -0.11 -1000
mTOR signaling pathway 2 110 53 -0.011 0.025 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class I 2 251 104 -0.074 0.046 1000 -1000 -0.094 -1000
FoxO family signaling 2 142 64 -0.062 0.1 1000 -1000 -0.088 -1000
Paxillin-dependent events mediated by a4b1 2 101 36 -0.023 0.029 1000 -1000 -0.09 -1000
Arf6 trafficking events 2 188 71 -0.032 0.039 1000 -1000 -0.09 -1000
E-cadherin signaling in keratinocytes 2 121 43 -0.036 0.037 1000 -1000 -0.088 -1000
Insulin-mediated glucose transport 1 42 32 -0.014 0.033 1000 -1000 -0.08 -1000
Class I PI3K signaling events mediated by Akt 1 103 68 -0.033 0.045 1000 -1000 -0.066 -1000
Atypical NF-kappaB pathway 1 49 31 -0.004 0.038 1000 -1000 -0.056 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 22 23 -0.004 0.038 1000 -1000 -0.084 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 16 27 -0.003 0.029 1000 -1000 -0.065 -1000
Arf1 pathway 0 42 54 -0.01 0.023 1000 -1000 -0.048 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.018 1000 -1000 -0.085 -1000
Total 1869 107949 7203 -17 -2000 131000 -131000 -11 -131000
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.42 0.45 -10000 0 -1.1 86 86
PCK1 -0.35 0.38 -10000 0 -0.94 74 74
HNF4A -0.6 0.58 -10000 0 -1.2 130 130
KCNJ11 -0.5 0.54 -10000 0 -1.2 106 106
AKT1 -0.15 0.17 -10000 0 -0.45 4 4
response to starvation -0.004 0.013 -10000 0 -10000 0 0
DLK1 -0.52 0.54 -10000 0 -1.2 106 106
NKX2-1 -0.32 0.55 0.49 1 -1.7 45 46
ACADM -0.42 0.45 -10000 0 -1 88 88
TAT -0.38 0.44 -10000 0 -1 83 83
CEBPB 0.008 0.03 -10000 0 -0.55 1 1
CEBPA -0.034 0.17 -10000 0 -0.67 23 23
TTR -0.38 0.39 -10000 0 -1 68 68
PKLR -0.44 0.47 -10000 0 -1.1 88 88
APOA1 -0.55 0.56 -10000 0 -1.3 99 99
CPT1C -0.46 0.48 -10000 0 -1.1 100 100
ALAS1 -0.18 0.19 -10000 0 -1 1 1
TFRC -0.39 0.4 -10000 0 -1.1 51 51
FOXF1 0.009 0.11 -10000 0 -0.72 6 6
NF1 0.014 0.054 -10000 0 -0.71 2 2
HNF1A (dimer) -0.13 0.24 -10000 0 -0.59 73 73
CPT1A -0.43 0.46 -10000 0 -1 95 95
HMGCS1 -0.42 0.45 -10000 0 -1 89 89
NR3C1 -0.019 0.083 -10000 0 -0.77 2 2
CPT1B -0.45 0.49 -10000 0 -1.1 96 96
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.014 0.056 -10000 0 -10000 0 0
GCK -0.46 0.49 -10000 0 -1.1 98 98
CREB1 0.003 0.03 -10000 0 -10000 0 0
IGFBP1 -0.31 0.43 -10000 0 -1 66 66
PDX1 -0.44 0.54 -10000 0 -1.3 78 78
UCP2 -0.43 0.46 -10000 0 -1.1 88 88
ALDOB -0.53 0.54 -10000 0 -1.2 121 121
AFP -0.16 0.24 -10000 0 -0.84 22 22
BDH1 -0.44 0.47 -10000 0 -1.1 90 90
HADH -0.44 0.47 -10000 0 -1.1 85 85
F2 -0.56 0.56 -10000 0 -1.3 105 105
HNF1A -0.13 0.24 -10000 0 -0.59 73 73
G6PC -0.16 0.19 -10000 0 -0.42 84 84
SLC2A2 -0.29 0.28 -10000 0 -0.64 98 98
INS 0.015 0.051 -10000 0 -10000 0 0
FOXA1 -0.05 0.17 -10000 0 -0.66 18 18
FOXA3 -0.23 0.32 -10000 0 -0.7 99 99
FOXA2 -0.51 0.54 -10000 0 -1.2 108 108
ABCC8 -0.52 0.53 -10000 0 -1.2 115 115
ALB -0.22 0.32 -10000 0 -0.94 41 41
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 -0.025 0.15 -10000 0 -0.66 18 18
CDKN2C 0.025 0.038 -10000 0 -0.48 1 1
CDKN2A -0.19 0.3 -10000 0 -0.63 110 110
CCND2 0.059 0.11 0.26 65 -0.16 2 67
RB1 -0.056 0.13 -10000 0 -0.28 64 64
CDK4 0.072 0.13 0.29 68 -10000 0 68
CDK6 0.066 0.13 0.29 64 -0.18 2 66
G1/S progression 0.056 0.13 0.28 64 -10000 0 64
IL4-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
BCL2L1 -0.62 0.53 -10000 0 -1.3 104 104
STAT6 (cleaved dimer) -0.65 0.54 -10000 0 -1.2 144 144
IGHG1 -0.2 0.15 -10000 0 -0.49 2 2
IGHG3 -0.61 0.51 -10000 0 -1.1 138 138
AKT1 -0.27 0.26 -10000 0 -0.97 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.26 -10000 0 -1.3 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.29 -10000 0 -0.98 23 23
THY1 -0.63 0.54 -10000 0 -1.3 109 109
MYB -0.021 0.14 -10000 0 -0.63 18 18
HMGA1 -0.003 0.094 -10000 0 -0.58 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.32 -10000 0 -0.76 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.29 0.3 -10000 0 -1.1 20 20
SP1 0.018 0.004 -10000 0 -10000 0 0
INPP5D -0.004 0.1 -10000 0 -0.69 8 8
SOCS5 0.028 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.63 0.53 -10000 0 -1.2 126 126
SOCS1 -0.38 0.32 -10000 0 -0.79 79 79
SOCS3 -0.29 0.26 -10000 0 -1 15 15
FCER2 -0.58 0.54 -10000 0 -1.3 99 99
PARP14 0.006 0.054 -10000 0 -0.71 2 2
CCL17 -0.71 0.61 -10000 0 -1.4 118 118
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.23 0.24 -10000 0 -0.98 15 15
T cell proliferation -0.62 0.56 -10000 0 -1.3 109 109
IL4R/JAK1 -0.62 0.54 -10000 0 -1.3 104 104
EGR2 -0.65 0.56 -10000 0 -1.3 114 114
JAK2 -0.02 0.025 -10000 0 -10000 0 0
JAK3 0.013 0.054 -10000 0 -0.69 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.001 0.039 -10000 0 -0.71 1 1
COL1A2 -0.21 0.26 -10000 0 -1.2 14 14
CCL26 -0.72 0.61 -10000 0 -1.4 127 127
IL4R -0.67 0.57 -10000 0 -1.4 107 107
PTPN6 0.025 0.04 -10000 0 -0.69 1 1
IL13RA2 -0.73 0.61 -10000 0 -1.4 131 131
IL13RA1 -0.02 0.025 -10000 0 -10000 0 0
IRF4 -0.23 0.41 -10000 0 -1.2 43 43
ARG1 -0.16 0.18 -10000 0 -0.81 14 14
CBL -0.33 0.3 -10000 0 -0.83 41 41
GTF3A 0.015 0.038 -10000 0 -0.64 1 1
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.027 0.033 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.37 -10000 0 -1.2 36 36
CD40LG -0.049 0.2 -10000 0 -0.69 32 32
MAPK14 -0.33 0.3 -10000 0 -0.93 29 29
mitosis -0.26 0.24 -10000 0 -0.88 17 17
STAT6 -0.75 0.72 -10000 0 -1.5 137 137
SPI1 -0.006 0.12 -10000 0 -0.69 10 10
RPS6KB1 -0.25 0.24 -10000 0 -0.86 16 16
STAT6 (dimer) -0.76 0.73 -10000 0 -1.5 137 137
STAT6 (dimer)/PARP14 -0.69 0.61 -10000 0 -1.3 141 141
mast cell activation 0.015 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.3 -10000 0 -1.1 21 21
FRAP1 -0.27 0.26 -10000 0 -0.97 17 17
LTA -0.64 0.55 -10000 0 -1.3 110 110
FES 0.004 0.076 -10000 0 -0.71 4 4
T-helper 1 cell differentiation 0.72 0.64 1.4 137 -10000 0 137
CCL11 -0.69 0.58 -10000 0 -1.4 128 128
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.29 -10000 0 -0.97 23 23
IL2RG -0.007 0.12 -10000 0 -0.66 12 12
IL10 -0.64 0.56 -10000 0 -1.4 104 104
IRS1 -0.009 0.12 -10000 0 -0.71 10 10
IRS2 -0.018 0.13 -10000 0 -0.58 18 18
IL4 -0.14 0.1 -10000 0 -0.25 21 21
IL5 -0.63 0.53 -10000 0 -1.2 137 137
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.49 0.37 -10000 0 -0.91 114 114
COL1A1 -0.26 0.34 -10000 0 -1.3 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.64 0.56 -10000 0 -1.4 104 104
IL2R gamma/JAK3 -0.002 0.11 -10000 0 -0.52 13 13
TFF3 -0.82 0.64 -10000 0 -1.5 148 148
ALOX15 -0.78 0.63 -10000 0 -1.5 129 129
MYBL1 -0.006 0.1 -10000 0 -0.58 11 11
T-helper 2 cell differentiation -0.52 0.42 -10000 0 -0.97 123 123
SHC1 0.009 0.042 -10000 0 -0.55 2 2
CEBPB 0.012 0.032 -10000 0 -0.55 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.28 0.28 -10000 0 -0.99 21 21
mol:PI-3-4-5-P3 -0.27 0.26 -10000 0 -0.97 17 17
PI3K -0.29 0.29 -10000 0 -1.1 17 17
DOK2 -0.008 0.12 -10000 0 -0.69 10 10
ETS1 0.025 0.03 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.22 0.23 -10000 0 -0.96 14 14
ITGB3 -0.66 0.56 -10000 0 -1.3 114 114
PIGR -0.78 0.66 -10000 0 -1.5 136 136
IGHE 0.049 0.046 0.3 2 -10000 0 2
MAPKKK cascade -0.21 0.22 -10000 0 -0.92 14 14
BCL6 0.013 0.005 -10000 0 -10000 0 0
OPRM1 -0.63 0.53 -10000 0 -1.2 137 137
RETNLB -0.63 0.53 -10000 0 -1.2 137 137
SELP -0.66 0.58 -10000 0 -1.4 111 111
AICDA -0.64 0.54 -10000 0 -1.3 120 120
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.14 0.3 -10000 0 -0.79 46 46
IHH -0.12 0.26 -10000 0 -0.65 64 64
SHH Np/Cholesterol/GAS1 -0.097 0.22 -10000 0 -0.49 64 64
LRPAP1 0.01 0.038 -10000 0 -0.71 1 1
dorsoventral neural tube patterning 0.096 0.21 0.49 64 -10000 0 64
SMO/beta Arrestin2 -0.1 0.23 -10000 0 -0.66 32 32
SMO -0.12 0.25 -10000 0 -0.69 34 34
AKT1 -0.031 0.1 -10000 0 -0.36 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.003 0.099 -10000 0 -0.65 8 8
ADRBK1 0.012 0 -10000 0 -10000 0 0
heart looping -0.11 0.24 -10000 0 -0.68 34 34
STIL -0.14 0.25 -10000 0 -0.62 50 50
DHH N/PTCH2 -0.029 0.15 -10000 0 -0.51 31 31
DHH N/PTCH1 -0.1 0.21 -10000 0 -0.66 24 24
PIK3CA 0.012 0 -10000 0 -10000 0 0
DHH -0.018 0.14 -10000 0 -0.68 15 15
PTHLH -0.18 0.37 -10000 0 -0.98 46 46
determination of left/right symmetry -0.11 0.24 -10000 0 -0.68 34 34
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.18 0.36 -10000 0 -0.96 46 46
IHH N/Hhip -0.22 0.3 -10000 0 -0.58 129 129
DHH N/Hhip -0.16 0.25 -10000 0 -0.49 119 119
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.24 -10000 0 -0.68 34 34
pancreas development -0.19 0.3 -10000 0 -0.64 110 110
HHAT -0.013 0.13 -10000 0 -0.71 12 12
PI3K 0.018 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.036 0.17 -10000 0 -0.62 27 27
somite specification -0.11 0.24 -10000 0 -0.68 34 34
SHH Np/Cholesterol/PTCH1 -0.15 0.26 -10000 0 -0.61 59 59
SHH Np/Cholesterol/PTCH2 -0.089 0.2 -10000 0 -0.45 67 67
SHH Np/Cholesterol/Megalin -0.21 0.26 -10000 0 -0.52 116 116
SHH -0.096 0.22 -10000 0 -0.51 77 77
catabolic process -0.1 0.22 -10000 0 -0.55 45 45
SMO/Vitamin D3 -0.15 0.27 -10000 0 -0.66 53 53
SHH Np/Cholesterol/Hhip -0.19 0.26 -10000 0 -0.51 108 108
LRP2 -0.23 0.32 -10000 0 -0.64 130 130
receptor-mediated endocytosis -0.25 0.28 -10000 0 -0.69 78 78
SHH Np/Cholesterol/BOC -0.079 0.19 -10000 0 -0.45 59 59
SHH Np/Cholesterol/CDO -0.087 0.21 -10000 0 -0.47 63 63
mesenchymal cell differentiation 0.19 0.26 0.5 108 -10000 0 108
mol:Vitamin D3 -0.15 0.26 -10000 0 -0.62 59 59
IHH N/PTCH2 -0.089 0.2 -10000 0 -0.44 77 77
CDON -0.019 0.14 -10000 0 -0.62 17 17
IHH N/PTCH1 -0.1 0.22 -10000 0 -0.55 45 45
Megalin/LRPAP1 -0.16 0.24 -10000 0 -0.48 130 130
PTCH2 -0.02 0.14 -10000 0 -0.65 17 17
SHH Np/Cholesterol -0.088 0.17 -10000 0 -0.41 77 77
PTCH1 -0.1 0.22 -10000 0 -0.55 45 45
HHIP -0.19 0.3 -10000 0 -0.64 110 110
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.026 0.16 -9999 0 -0.69 19 19
GPC2 -0.061 0.2 -9999 0 -0.6 42 42
GPC2/Midkine -0.064 0.19 -9999 0 -0.48 58 58
neuron projection morphogenesis -0.064 0.19 -9999 0 -0.48 58 58
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.27 0.49 -10000 0 -1.2 51 51
IL23A -0.29 0.53 -10000 0 -1.3 51 51
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.44 -10000 0 -1.1 62 62
positive regulation of T cell mediated cytotoxicity -0.31 0.57 -10000 0 -1.3 64 64
ITGA3 -0.28 0.52 -10000 0 -1.2 56 56
IL17F -0.17 0.33 -10000 0 -0.73 49 49
IL12B -0.04 0.19 -10000 0 -0.7 26 26
STAT1 (dimer) -0.29 0.54 -10000 0 -1.2 62 62
CD4 -0.26 0.48 -10000 0 -1.2 46 46
IL23 -0.3 0.51 -10000 0 -1.2 57 57
IL23R -0.029 0.16 -10000 0 -1.1 4 4
IL1B -0.3 0.55 -10000 0 -1.4 52 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.29 0.51 -10000 0 -1.2 57 57
TYK2 0.007 0.022 -10000 0 -10000 0 0
STAT4 -0.01 0.12 -10000 0 -0.7 11 11
STAT3 0.012 0.001 -10000 0 -10000 0 0
IL18RAP -0.037 0.17 -10000 0 -0.65 25 25
IL12RB1 -0.017 0.14 -10000 0 -0.73 12 12
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.012 0.11 -10000 0 -0.56 12 12
IL23R/JAK2 -0.03 0.16 -10000 0 -1 4 4
positive regulation of chronic inflammatory response -0.31 0.57 -10000 0 -1.3 64 64
natural killer cell activation 0.003 0.011 0.057 6 -10000 0 6
JAK2 0.013 0.027 -10000 0 -10000 0 0
PIK3R1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0.011 0.004 -10000 0 -10000 0 0
RELA 0.011 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.28 0.48 -10000 0 -1.1 57 57
ALOX12B -0.34 0.55 -10000 0 -1.3 62 62
CXCL1 -0.32 0.56 -10000 0 -1.3 70 70
T cell proliferation -0.31 0.57 -10000 0 -1.3 64 64
NFKBIA 0.011 0.004 -10000 0 -10000 0 0
IL17A -0.12 0.28 -10000 0 -0.61 26 26
PI3K -0.34 0.45 -10000 0 -1.2 65 65
IFNG -0.025 0.052 0.13 2 -0.12 50 52
STAT3 (dimer) -0.32 0.43 -10000 0 -1.1 62 62
IL18R1 -0.009 0.11 -10000 0 -0.66 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.31 -10000 0 -0.82 26 26
IL18/IL18R -0.044 0.18 -10000 0 -0.48 43 43
macrophage activation -0.017 0.018 -10000 0 -0.046 33 33
TNF -0.3 0.56 -10000 0 -1.4 49 49
STAT3/STAT4 -0.34 0.46 -10000 0 -1.2 65 65
STAT4 (dimer) -0.3 0.54 -10000 0 -1.3 61 61
IL18 -0.023 0.15 -10000 0 -0.7 16 16
IL19 -0.27 0.48 -10000 0 -1.2 49 49
STAT5A (dimer) -0.29 0.54 -10000 0 -1.2 62 62
STAT1 0.012 0 -10000 0 -10000 0 0
SOCS3 0.007 0.057 -10000 0 -0.6 3 3
CXCL9 -0.34 0.57 -10000 0 -1.3 72 72
MPO -0.28 0.5 -10000 0 -1.2 55 55
positive regulation of humoral immune response -0.31 0.57 -10000 0 -1.3 64 64
IL23/IL23R/JAK2/TYK2 -0.34 0.67 -10000 0 -1.5 64 64
IL6 -0.3 0.53 -10000 0 -1.3 56 56
STAT5A 0.01 0.038 -10000 0 -0.71 1 1
IL2 -0.002 0.067 -10000 0 -0.55 5 5
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.011 0.057 6 -10000 0 6
CD3E -0.27 0.5 -10000 0 -1.2 50 50
keratinocyte proliferation -0.31 0.57 -10000 0 -1.3 64 64
NOS2 -0.29 0.51 -10000 0 -1.2 57 57
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.037 0.12 -9999 0 -0.39 33 33
RGS9BP -0.031 0.16 -9999 0 -0.61 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.032 0.14 -9999 0 -0.55 24 24
mol:Na + -0.22 0.24 -9999 0 -0.44 171 171
mol:ADP -0.019 0.11 -9999 0 -0.4 27 27
GNAT2 0.004 0.064 -9999 0 -0.59 4 4
RGS9-1/Gbeta5/R9AP -0.046 0.13 -9999 0 -0.45 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.04 -9999 0 -0.37 4 4
GRK7 0.003 0.051 -9999 0 -0.55 3 3
CNGB3 -0.12 0.25 -9999 0 -0.62 69 69
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.22 0.25 -9999 0 -0.47 144 144
Cone PDE6 -0.04 0.11 -9999 0 -0.39 24 24
Cone Metarhodopsin II -0.015 0.085 -9999 0 -0.31 27 27
Na + (4 Units) -0.22 0.24 -9999 0 -0.51 116 116
GNAT2/GDP -0.043 0.12 -9999 0 -0.4 25 25
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.037 -9999 0 -0.34 4 4
Cone Transducin -0.019 0.13 -9999 0 -0.41 33 33
SLC24A2 -0.044 0.17 -9999 0 -0.61 30 30
GNB3/GNGT2 -0.029 0.15 -9999 0 -0.51 31 31
GNB3 -0.027 0.16 -9999 0 -0.68 20 20
GNAT2/GTP 0.003 0.047 -9999 0 -0.43 4 4
CNGA3 -0.22 0.31 -9999 0 -0.62 128 128
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.22 0.24 -9999 0 -0.45 171 171
mol:Pi -0.046 0.13 -9999 0 -0.45 24 24
Cone CNG Channel -0.18 0.21 -9999 0 -0.45 101 101
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.044 0.17 -9999 0 -0.6 30 30
RGS9 -0.022 0.15 -9999 0 -0.69 17 17
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.011 0.12 -9999 0 -0.66 12 12
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.34 0.52 -9999 0 -1.3 39 39
HDAC7 0.013 0.004 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.36 -9999 0 -1 31 31
SMAD4 0.013 0.002 -9999 0 -10000 0 0
ID2 -0.34 0.53 -9999 0 -1.3 43 43
AP1 -0.021 0.14 -9999 0 -0.47 28 28
ABCG2 -0.35 0.54 -9999 0 -1.4 44 44
HIF1A -0.035 0.076 -9999 0 -10000 0 0
TFF3 -0.47 0.6 -9999 0 -1.4 72 72
GATA2 -0.022 0.15 -9999 0 -0.7 17 17
AKT1 -0.041 0.087 -9999 0 -10000 0 0
response to hypoxia -0.06 0.092 -9999 0 -10000 0 0
MCL1 -0.34 0.52 -9999 0 -1.4 37 37
NDRG1 -0.34 0.53 -9999 0 -1.3 42 42
SERPINE1 -0.36 0.55 -9999 0 -1.4 42 42
FECH -0.34 0.52 -9999 0 -1.4 37 37
FURIN -0.35 0.53 -9999 0 -1.3 41 41
NCOA2 -0.004 0.11 -9999 0 -0.71 8 8
EP300 -0.038 0.13 -9999 0 -0.36 12 12
HMOX1 -0.34 0.53 -9999 0 -1.4 37 37
BHLHE40 -0.34 0.53 -9999 0 -1.3 41 41
BHLHE41 -0.35 0.54 -9999 0 -1.3 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.039 0.065 -9999 0 -0.48 1 1
ENG 0.002 0.1 -9999 0 -0.81 1 1
JUN 0.006 0.063 -9999 0 -0.66 3 3
RORA -0.34 0.53 -9999 0 -1.3 41 41
ABCB1 -0.11 0.22 -9999 0 -1.1 14 14
TFRC -0.35 0.53 -9999 0 -1.3 41 41
CXCR4 -0.34 0.53 -9999 0 -1.3 41 41
TF -0.46 0.6 -9999 0 -1.4 73 73
CITED2 -0.34 0.53 -9999 0 -1.3 41 41
HIF1A/ARNT -0.46 0.66 -9999 0 -1.6 55 55
LDHA -0.043 0.059 -9999 0 -10000 0 0
ETS1 -0.34 0.52 -9999 0 -1.3 41 41
PGK1 -0.34 0.52 -9999 0 -1.3 41 41
NOS2 -0.37 0.54 -9999 0 -1.3 53 53
ITGB2 -0.35 0.54 -9999 0 -1.3 44 44
ALDOA -0.34 0.52 -9999 0 -1.3 41 41
Cbp/p300/CITED2 -0.36 0.53 -9999 0 -1.4 38 38
FOS -0.034 0.17 -9999 0 -0.62 26 26
HK2 -0.35 0.54 -9999 0 -1.3 45 45
SP1 0.019 0.009 -9999 0 -10000 0 0
GCK -0.16 0.35 -9999 0 -1.3 22 22
HK1 -0.34 0.52 -9999 0 -1.3 39 39
NPM1 -0.34 0.52 -9999 0 -1.3 39 39
EGLN1 -0.34 0.52 -9999 0 -1.3 39 39
CREB1 0.019 0.001 -9999 0 -10000 0 0
PGM1 -0.34 0.52 -9999 0 -1.3 41 41
SMAD3 0.009 0.048 -9999 0 -0.62 2 2
EDN1 -0.11 0.35 -9999 0 -1.2 26 26
IGFBP1 -0.42 0.56 -9999 0 -1.4 56 56
VEGFA -0.2 0.37 -9999 0 -0.94 18 18
HIF1A/JAB1 -0.026 0.037 -9999 0 -0.43 1 1
CP -0.4 0.58 -9999 0 -1.4 58 58
CXCL12 -0.35 0.54 -9999 0 -1.3 47 47
COPS5 0.011 0.03 -9999 0 -0.55 1 1
SMAD3/SMAD4 -0.003 0.035 -9999 0 -0.46 2 2
BNIP3 -0.35 0.53 -9999 0 -1.3 42 42
EGLN3 -0.39 0.56 -9999 0 -1.4 52 52
CA9 -0.49 0.58 -9999 0 -1.3 73 73
TERT -0.39 0.56 -9999 0 -1.4 50 50
ENO1 -0.34 0.52 -9999 0 -1.4 37 37
PFKL -0.34 0.52 -9999 0 -1.3 41 41
NCOA1 0.01 0.038 -9999 0 -0.71 1 1
ADM -0.37 0.55 -9999 0 -1.3 50 50
ARNT -0.036 0.075 -9999 0 -10000 0 0
HNF4A -0.2 0.29 -9999 0 -0.6 123 123
ADFP -0.37 0.51 -9999 0 -1.3 45 45
SLC2A1 -0.21 0.4 -9999 0 -1 25 25
LEP -0.38 0.55 -9999 0 -1.4 47 47
HIF1A/ARNT/Cbp/p300 -0.3 0.37 -9999 0 -1 36 36
EPO -0.16 0.3 -9999 0 -0.97 7 7
CREBBP -0.038 0.13 -9999 0 -0.38 9 9
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.37 -9999 0 -1 34 34
PFKFB3 -0.35 0.53 -9999 0 -1.3 44 44
NT5E -0.38 0.56 -9999 0 -1.4 50 50
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.2 0.24 -9999 0 -0.66 46 46
SMAD6-7/SMURF1 -0.007 0.056 -9999 0 -0.43 6 6
NOG -0.1 0.25 -9999 0 -0.64 61 61
SMAD9 -0.057 0.17 -9999 0 -0.61 23 23
SMAD4 0.012 0 -9999 0 -10000 0 0
SMAD5 -0.072 0.16 -9999 0 -0.5 20 20
BMP7/USAG1 -0.25 0.29 -9999 0 -0.51 177 177
SMAD5/SKI -0.062 0.16 -9999 0 -0.51 14 14
SMAD1 0.019 0.043 -9999 0 -10000 0 0
BMP2 -0.069 0.22 -9999 0 -0.66 43 43
SMAD1/SMAD1/SMAD4 -0.009 0.043 -9999 0 -10000 0 0
BMPR1A 0.012 0 -9999 0 -10000 0 0
BMPR1B -0.11 0.26 -9999 0 -0.67 62 62
BMPR1A-1B/BAMBI -0.14 0.21 -9999 0 -0.5 71 71
AHSG -0.041 0.15 -9999 0 -0.55 30 30
CER1 0 0 -9999 0 -10000 0 0
BMP2-4/CER1 -0.094 0.2 -9999 0 -0.47 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.068 0.17 -9999 0 -0.56 17 17
BMP2-4 (homodimer) -0.094 0.23 -9999 0 -0.54 71 71
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.091 0.21 -9999 0 -0.49 59 59
RGMA -0.046 0.18 -9999 0 -0.61 33 33
SMURF1 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.077 0.17 -9999 0 -0.49 29 29
BMP2-4/USAG1 -0.22 0.26 -9999 0 -0.56 95 95
SMAD6/SMURF1/SMAD5 -0.062 0.16 -9999 0 -0.5 15 15
SOSTDC1 -0.19 0.3 -9999 0 -0.62 114 114
BMP7/BMPR2/BMPR1A-1B -0.14 0.22 -9999 0 -0.47 83 83
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.076 0.21 -9999 0 -0.58 53 53
HFE2 -0.014 0.1 -9999 0 -0.55 13 13
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.13 0.24 -9999 0 -0.59 61 61
SMAD5/SMAD5/SMAD4 -0.062 0.16 -9999 0 -0.51 14 14
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.082 0.13 -9999 0 -0.48 17 17
BMP7 (homodimer) -0.15 0.28 -9999 0 -0.61 93 93
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.086 0.19 -9999 0 -0.42 80 80
SMAD1/SKI 0.025 0.041 -9999 0 -10000 0 0
SMAD6 0.004 0.076 -9999 0 -0.71 4 4
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.12 0.22 -9999 0 -0.57 53 53
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.14 0.28 -9999 0 -0.67 78 78
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.073 0.2 -9999 0 -0.5 62 62
CHRDL1 -0.099 0.25 -9999 0 -0.66 58 58
ENDOFIN/SMAD1 0.025 0.041 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.011 0.049 -9999 0 -10000 0 0
SMAD6/SMURF1 0.012 0 -9999 0 -10000 0 0
BAMBI -0.094 0.24 -9999 0 -0.61 60 60
SMURF2 0.01 0.03 -9999 0 -0.55 1 1
BMP2-4/CHRDL1 -0.16 0.27 -9999 0 -0.6 75 75
BMP2-4/GREM1 -0.18 0.25 -9999 0 -0.53 102 102
SMAD7 0.008 0.048 -9999 0 -0.63 2 2
SMAD8A/SMAD8A/SMAD4 -0.047 0.16 -9999 0 -0.6 21 21
SMAD1/SMAD6 0.025 0.041 -9999 0 -10000 0 0
TAK1/SMAD6 0.018 0 -9999 0 -10000 0 0
BMP7 -0.15 0.28 -9999 0 -0.61 93 93
BMP6 -0.076 0.21 -9999 0 -0.58 53 53
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.064 0.16 -9999 0 -0.46 27 27
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.024 0.043 -9999 0 -10000 0 0
SMAD7/SMURF1 0.015 0.036 -9999 0 -0.46 2 2
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.12 0.21 -9999 0 -0.54 46 46
CHRD -0.055 0.2 -9999 0 -0.63 37 37
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.087 0.19 -9999 0 -0.51 36 36
BMP4 -0.059 0.21 -9999 0 -0.65 38 38
FST -0.098 0.23 -9999 0 -0.58 65 65
BMP2-4/NOG -0.16 0.26 -9999 0 -0.59 74 74
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.14 0.2 -9999 0 -0.44 83 83
Syndecan-1-mediated signaling events

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
TGFB1 0.006 0.066 -9999 0 -0.71 3 3
CCL5 -0.016 0.13 -9999 0 -0.6 16 16
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.24 -9999 0 -0.65 37 37
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 -0.13 0.24 -9999 0 -0.65 41 41
Syndecan-1/Syntenin -0.12 0.23 -9999 0 -0.66 33 33
MAPK3 -0.097 0.21 -9999 0 -0.64 28 28
HGF/MET -0.093 0.22 -9999 0 -0.51 74 74
TGFB1/TGF beta receptor Type II 0.006 0.066 -9999 0 -0.71 3 3
BSG 0.01 0.038 -9999 0 -0.71 1 1
keratinocyte migration -0.13 0.23 -9999 0 -0.63 41 41
Syndecan-1/RANTES -0.13 0.23 -9999 0 -0.64 39 39
Syndecan-1/CD147 -0.11 0.22 -9999 0 -0.64 34 34
Syndecan-1/Syntenin/PIP2 -0.12 0.22 -9999 0 -0.64 33 33
LAMA5 -0.011 0.12 -9999 0 -0.67 12 12
positive regulation of cell-cell adhesion -0.13 0.2 -9999 0 -0.62 33 33
MMP7 -0.14 0.28 -9999 0 -0.62 86 86
HGF -0.035 0.17 -9999 0 -0.66 25 25
Syndecan-1/CASK -0.13 0.23 -9999 0 -0.63 37 37
Syndecan-1/HGF/MET -0.18 0.28 -9999 0 -0.67 60 60
regulation of cell adhesion -0.087 0.2 -9999 0 -0.65 25 25
HPSE -0.003 0.1 -9999 0 -0.67 8 8
positive regulation of cell migration -0.13 0.24 -9999 0 -0.65 37 37
SDC1 -0.13 0.24 -9999 0 -0.66 37 37
Syndecan-1/Collagen -0.13 0.24 -9999 0 -0.65 37 37
PPIB 0.01 0.03 -9999 0 -0.55 1 1
MET -0.09 0.24 -9999 0 -0.65 54 54
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.058 0.2 -9999 0 -0.64 38 38
MAPK1 -0.097 0.21 -9999 0 -0.68 25 25
homophilic cell adhesion -0.13 0.23 -9999 0 -0.64 37 37
MMP1 -0.16 0.29 -9999 0 -0.63 97 97
Endothelins

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.005 0.21 -10000 0 -0.51 30 30
PTK2B 0.004 0.077 -10000 0 -0.71 4 4
mol:Ca2+ -0.055 0.31 -10000 0 -0.85 34 34
EDN1 -0.018 0.21 -10000 0 -0.64 26 26
EDN3 -0.045 0.16 -10000 0 -0.55 33 33
EDN2 -0.15 0.28 -10000 0 -0.62 90 90
HRAS/GDP -0.031 0.23 -10000 0 -0.63 31 31
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.028 0.21 -10000 0 -0.55 35 35
ADCY4 -0.028 0.2 -10000 0 -0.56 22 22
ADCY5 -0.093 0.25 -10000 0 -0.56 54 54
ADCY6 -0.028 0.19 -10000 0 -0.59 18 18
ADCY7 -0.029 0.2 -10000 0 -0.6 19 19
ADCY1 -0.05 0.22 -10000 0 -0.61 26 26
ADCY2 -0.084 0.24 -10000 0 -0.61 39 39
ADCY3 -0.028 0.2 -10000 0 -0.53 26 26
ADCY8 -0.051 0.2 -10000 0 -0.56 27 27
ADCY9 -0.033 0.2 -10000 0 -0.55 23 23
arachidonic acid secretion -0.048 0.24 -10000 0 -0.63 32 32
ETB receptor/Endothelin-1/Gq/GTP -0.029 0.19 -10000 0 -0.54 31 31
GNAO1 -0.033 0.17 -10000 0 -0.65 24 24
HRAS 0.012 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.003 0.22 0.34 63 -0.54 17 80
ETA receptor/Endothelin-1/Gs/GTP -0.025 0.23 0.31 61 -0.48 39 100
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.031 0.27 -10000 0 -0.73 29 29
EDNRB -0.015 0.13 -10000 0 -0.64 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.025 0.26 -10000 0 -0.8 21 21
CYSLTR1 -0.029 0.26 -10000 0 -0.77 22 22
SLC9A1 -0.012 0.12 0.2 30 -0.36 8 38
mol:GDP -0.042 0.26 -10000 0 -0.66 36 36
SLC9A3 -0.066 0.28 -10000 0 -0.73 40 40
RAF1 -0.04 0.24 -10000 0 -0.68 28 28
JUN -0.019 0.23 -10000 0 -0.71 21 21
JAK2 -0.005 0.21 -10000 0 -0.51 30 30
mol:IP3 -0.041 0.24 -10000 0 -0.61 39 39
ETA receptor/Endothelin-1 -0.014 0.27 0.39 68 -0.56 36 104
PLCB1 -0.034 0.17 -10000 0 -0.69 23 23
PLCB2 -0.009 0.12 -10000 0 -0.71 10 10
ETA receptor/Endothelin-3 -0.04 0.16 -10000 0 -0.42 37 37
FOS -0.032 0.25 -10000 0 -0.91 15 15
Gai/GDP -0.044 0.21 -10000 0 -0.89 16 16
CRK 0.012 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.05 0.29 -10000 0 -0.73 37 37
BCAR1 0.004 0.076 -10000 0 -0.71 4 4
PRKCB1 -0.04 0.23 -10000 0 -0.58 39 39
GNAQ 0.01 0.039 -10000 0 -0.71 1 1
GNAZ -0.068 0.22 -10000 0 -0.64 43 43
GNAL -0.03 0.16 -10000 0 -0.62 23 23
Gs family/GDP -0.1 0.21 -10000 0 -0.58 42 42
ETA receptor/Endothelin-1/Gq/GTP -0.017 0.21 -10000 0 -0.54 32 32
MAPK14 -0.03 0.19 -10000 0 -0.58 26 26
TRPC6 -0.062 0.33 -10000 0 -0.97 31 31
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.095 -10000 0 -0.66 7 7
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.039 0.2 -10000 0 -0.57 32 32
ETB receptor/Endothelin-2 -0.12 0.23 -10000 0 -0.47 101 101
ETB receptor/Endothelin-3 -0.045 0.15 -10000 0 -0.43 46 46
ETB receptor/Endothelin-1 -0.026 0.2 -10000 0 -0.52 35 35
MAPK3 -0.036 0.26 -10000 0 -0.85 19 19
MAPK1 -0.036 0.26 -10000 0 -0.85 19 19
Rac1/GDP -0.031 0.23 -10000 0 -0.63 31 31
cAMP biosynthetic process -0.067 0.23 -10000 0 -0.58 36 36
MAPK8 -0.033 0.26 -10000 0 -0.67 35 35
SRC 0.012 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.037 0.18 -10000 0 -0.56 23 23
p130Cas/CRK/Src/PYK2 -0.047 0.26 -10000 0 -0.7 34 34
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.031 0.23 -10000 0 -0.63 31 31
COL1A2 -0.028 0.28 -10000 0 -0.79 26 26
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.23 -10000 0 -0.48 91 91
mol:DAG -0.041 0.24 -10000 0 -0.61 39 39
MAP2K2 -0.034 0.24 -10000 0 -0.69 25 25
MAP2K1 -0.034 0.24 -10000 0 -0.69 25 25
EDNRA 0.009 0.16 -10000 0 -0.58 13 13
positive regulation of muscle contraction 0.002 0.18 -10000 0 -0.57 12 12
Gq family/GDP -0.098 0.22 -10000 0 -0.68 35 35
HRAS/GTP -0.047 0.25 -10000 0 -0.63 38 38
PRKCH -0.033 0.23 -10000 0 -0.62 33 33
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.044 0.24 -10000 0 -0.63 35 35
PRKCB -0.043 0.25 -10000 0 -0.64 38 38
PRKCE -0.034 0.23 -10000 0 -0.62 33 33
PRKCD -0.033 0.23 -10000 0 -0.61 34 34
PRKCG -0.058 0.24 -10000 0 -0.6 40 40
regulation of vascular smooth muscle contraction -0.041 0.28 -10000 0 -1.1 16 16
PRKCQ -0.06 0.26 -10000 0 -0.63 44 44
PLA2G4A -0.057 0.26 -10000 0 -0.71 32 32
GNA14 -0.047 0.2 -10000 0 -0.71 29 29
GNA15 0 0.094 -10000 0 -0.71 6 6
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.006 0.066 -10000 0 -0.71 3 3
Rac1/GTP -0.003 0.22 0.34 63 -0.47 30 93
MMP1 -0.19 0.4 -10000 0 -0.8 93 93
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.11 0.23 -9999 0 -0.64 32 32
FZD6 0.004 0.076 -9999 0 -0.71 4 4
WNT6 -0.051 0.19 -9999 0 -0.61 35 35
WNT4 -0.12 0.26 -9999 0 -0.64 70 70
FZD3 -0.002 0.098 -9999 0 -0.69 7 7
WNT5A -0.024 0.16 -9999 0 -0.7 18 18
WNT11 -0.073 0.22 -9999 0 -0.63 47 47
Visual signal transduction: Rods

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
mol:K + 0.01 0.038 -9999 0 -0.71 1 1
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.002 0.025 -9999 0 -0.34 2 2
PDE6G/GNAT1/GTP -0.017 0.083 -9999 0 -0.41 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0 -9999 0 -10000 0 0
GRK1 -0.032 0.14 -9999 0 -0.55 24 24
CNG Channel -0.2 0.23 -9999 0 -0.49 102 102
mol:Na + -0.21 0.23 -9999 0 -0.47 123 123
mol:ADP -0.032 0.14 -9999 0 -0.55 24 24
RGS9-1/Gbeta5/R9AP -0.046 0.13 -9999 0 -0.45 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.22 0.24 -9999 0 -0.49 123 123
CNGB1 -0.15 0.28 -9999 0 -0.64 88 88
RDH5 -0.019 0.13 -9999 0 -0.57 19 19
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.24 -9999 0 -0.62 51 51
Na + (4 Units) -0.2 0.22 -9999 0 -0.6 51 51
RGS9 -0.022 0.15 -9999 0 -0.69 17 17
GNB1/GNGT1 -0.051 0.17 -9999 0 -0.5 45 45
GNAT1/GDP -0.04 0.11 -9999 0 -0.39 24 24
GUCY2D -0.058 0.2 -9999 0 -0.64 38 38
GNGT1 -0.079 0.23 -9999 0 -0.67 45 45
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.055 0.17 -9999 0 -0.48 34 34
mol:11-cis-retinal -0.019 0.13 -9999 0 -0.57 19 19
mol:cGMP -0.085 0.19 -9999 0 -0.43 61 61
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.013 0.11 -9999 0 -0.43 20 20
SLC24A1 0.01 0.038 -9999 0 -0.71 1 1
CNGA1 -0.1 0.24 -9999 0 -0.6 65 65
Metarhodopsin II -0.016 0.084 -9999 0 -0.31 26 26
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.09 0.2 -9999 0 -0.4 93 93
RGS9BP -0.031 0.16 -9999 0 -0.61 24 24
Metarhodopsin II/Transducin -0.027 0.1 -9999 0 -0.32 34 34
GCAP Family/Ca ++ -0.057 0.16 -9999 0 -0.39 61 61
PDE6A/B -0.065 0.19 -9999 0 -0.48 59 59
mol:Pi -0.046 0.13 -9999 0 -0.45 24 24
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.039 0.14 -9999 0 -0.39 45 45
PDE6B -0.03 0.17 -9999 0 -0.69 21 21
PDE6A -0.058 0.19 -9999 0 -0.59 41 41
PDE6G -0.015 0.13 -9999 0 -0.63 15 15
RHO 0.002 0.042 -9999 0 -0.55 2 2
PDE6 -0.1 0.2 -9999 0 -0.73 18 18
GUCA1A -0.073 0.22 -9999 0 -0.64 45 45
GC2/GCAP Family -0.057 0.16 -9999 0 -0.39 61 61
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B -0.025 0.15 -9999 0 -0.67 19 19
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.095 0.21 0.51 66 -10000 0 66
KIRREL -0.034 0.17 -10000 0 -0.73 19 19
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.095 0.21 -10000 0 -0.51 66 66
PLCG1 0.01 0.03 -10000 0 -0.55 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.071 0.16 -10000 0 -0.46 38 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.031 0.14 -10000 0 -0.38 38 38
FYN -0.054 0.16 -10000 0 -0.45 39 39
mol:Ca2+ -0.072 0.16 -10000 0 -0.45 39 39
mol:DAG -0.072 0.16 -10000 0 -0.45 39 39
NPHS2 -0.01 0.026 -10000 0 -10000 0 0
mol:IP3 -0.072 0.16 -10000 0 -0.45 39 39
regulation of endocytosis -0.044 0.15 -10000 0 -0.42 39 39
Nephrin/NEPH1/podocin/Cholesterol -0.073 0.16 -10000 0 -0.39 66 66
establishment of cell polarity -0.095 0.21 -10000 0 -0.51 66 66
Nephrin/NEPH1/podocin/NCK1-2 -0.065 0.15 -10000 0 -0.43 38 38
Nephrin/NEPH1/beta Arrestin2 -0.044 0.16 -10000 0 -0.42 39 39
NPHS1 -0.087 0.23 -10000 0 -0.63 52 52
Nephrin/NEPH1/podocin -0.057 0.16 -10000 0 -0.45 39 39
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.01 0.038 -10000 0 -0.71 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.072 0.16 -10000 0 -0.46 39 39
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.071 0.16 -10000 0 -0.46 38 38
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.091 0.19 -10000 0 -0.42 74 74
cytoskeleton organization -0.039 0.17 -10000 0 -0.47 38 38
Nephrin/NEPH1 -0.07 0.16 -10000 0 -0.37 66 66
Nephrin/NEPH1/ZO-1 -0.077 0.17 -10000 0 -0.49 38 38
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.04 0.053 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.45 26 26
JUN -0.068 0.16 -9999 0 -0.49 23 23
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.24 -9999 0 -0.54 72 72
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 -0.001 0.083 -9999 0 -0.55 8 8
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.14 0.24 -9999 0 -0.54 66 66
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.09 0.18 -9999 0 -0.44 51 51
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.48 68 68
GRB7 -0.001 0.092 -9999 0 -0.64 7 7
RET51/GFRalpha1/GDNF -0.14 0.23 -9999 0 -0.53 66 66
MAPKKK cascade -0.12 0.18 -9999 0 -0.59 22 22
BCAR1 0.004 0.076 -9999 0 -0.71 4 4
RET9/GFRalpha1/GDNF/IRS1 -0.1 0.19 -9999 0 -0.43 66 66
lamellipodium assembly -0.095 0.13 -9999 0 -0.41 26 26
RET51/GFRalpha1/GDNF/SHC -0.14 0.23 -9999 0 -0.53 67 67
PIK3CA 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.09 0.18 -9999 0 -0.44 50 50
RET9/GFRalpha1/GDNF/Shank3 -0.09 0.18 -9999 0 -0.44 51 51
MAPK3 -0.12 0.21 -9999 0 -0.6 29 29
DOK1 0.008 0.054 -9999 0 -0.71 2 2
DOK6 -0.024 0.15 -9999 0 -0.63 20 20
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.11 0.2 -9999 0 -0.56 33 33
DOK5 -0.091 0.24 -9999 0 -0.62 57 57
GFRA1 -0.14 0.28 -9999 0 -0.64 81 81
MAPK8 -0.075 0.17 -9999 0 -0.52 22 22
HRAS/GTP -0.14 0.2 -9999 0 -0.63 29 29
tube development -0.096 0.16 -9999 0 -0.41 51 51
MAPK1 -0.12 0.21 -9999 0 -0.6 29 29
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.052 0.13 -9999 0 -0.32 50 50
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.008 0.048 -9999 0 -0.63 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.23 -9999 0 -0.53 75 75
SHC1 0.009 0.042 -9999 0 -0.55 2 2
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.24 -9999 0 -0.54 68 68
RET51/GFRalpha1/GDNF/Dok5 -0.2 0.27 -9999 0 -0.57 92 92
PRKCA -0.009 0.12 -9999 0 -0.65 11 11
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.068 0.16 -9999 0 -0.39 49 49
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.049 0.13 -9999 0 -0.31 50 50
RET51/GFRalpha1/GDNF/Grb7 -0.15 0.24 -9999 0 -0.54 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.099 0.23 -9999 0 -0.58 66 66
DOK4 -0.004 0.097 -9999 0 -0.6 9 9
JNK cascade -0.066 0.16 -9999 0 -0.48 23 23
RET9/GFRalpha1/GDNF/FRS2 -0.095 0.18 -9999 0 -0.45 50 50
SHANK3 0.01 0.038 -9999 0 -0.71 1 1
RASA1 0.01 0.038 -9999 0 -0.71 1 1
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.049 0.13 -9999 0 -0.33 26 26
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.087 0.16 -9999 0 -0.46 29 29
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.086 0.17 -9999 0 -0.55 21 21
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.088 0.18 -9999 0 -0.53 26 26
PI3K -0.11 0.22 -9999 0 -0.59 37 37
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.096 0.16 -9999 0 -0.41 51 51
GRB10 -0.008 0.12 -9999 0 -0.69 10 10
activation of MAPKK activity -0.077 0.15 -9999 0 -0.46 21 21
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.24 -9999 0 -0.53 67 67
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 -0.009 0.12 -9999 0 -0.71 10 10
IRS2 -0.018 0.13 -9999 0 -0.58 18 18
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.088 0.18 -9999 0 -0.51 29 29
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.24 -9999 0 -0.54 72 72
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.026 0.13 -9999 0 -0.55 21 21
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.16 0.24 -9999 0 -0.53 75 75
Rac1/GTP -0.11 0.16 -9999 0 -0.5 26 26
RET9/GFRalpha1/GDNF -0.11 0.19 -9999 0 -0.41 98 98
GFRalpha1/GDNF -0.12 0.23 -9999 0 -0.48 98 98
Effects of Botulinum toxin

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
STX1A -0.009 0.095 -9999 0 -0.46 15 15
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.097 0.21 -9999 0 -0.46 84 84
STXBP1 -0.005 0.1 -9999 0 -0.64 9 9
ACh/CHRNA1 -0.087 0.18 -9999 0 -0.44 72 72
RAB3GAP2/RIMS1/UNC13B -0.093 0.17 -9999 0 -0.46 42 42
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.14 0.27 -9999 0 -0.62 83 83
mol:ACh -0.008 0.04 -9999 0 -0.098 51 51
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.097 0.15 -9999 0 -0.48 18 18
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.087 0.18 -9999 0 -0.44 72 72
UNC13B 0.008 0.048 -9999 0 -0.63 2 2
CHRNA1 -0.12 0.26 -9999 0 -0.63 72 72
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.095 0.18 -9999 0 -0.42 82 82
SNAP25 -0.024 0.083 -9999 0 -0.23 45 45
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.13 0.26 -9999 0 -0.61 82 82
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.011 0.1 -9999 0 -0.39 24 24
STX1A/SNAP25 fragment 1/VAMP2 -0.097 0.15 -9999 0 -0.48 18 18
Ephrin A reverse 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
MAPKKK cascade -0.05 0.14 -9999 0 -0.4 44 44
EFNA5 -0.028 0.16 -9999 0 -0.7 20 20
FYN -0.031 0.14 -9999 0 -0.44 22 22
neuron projection morphogenesis -0.05 0.14 -9999 0 -0.4 44 44
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.05 0.14 -9999 0 -0.4 44 44
EPHA5 -0.033 0.14 -9999 0 -0.55 26 26
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.059 0.2 -9999 0 -0.71 25 25
alphaM/beta2 Integrin/GPIbA -0.073 0.2 -9999 0 -0.59 38 38
alphaM/beta2 Integrin/proMMP-9 -0.089 0.23 -9999 0 -0.65 39 39
PLAUR -0.004 0.1 -9999 0 -0.69 8 8
HMGB1 0.006 0.033 -9999 0 -0.55 1 1
alphaM/beta2 Integrin/Talin -0.048 0.18 -9999 0 -0.73 19 19
AGER -0.19 0.3 -9999 0 -0.64 109 109
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG -0.002 0.1 -9999 0 -0.71 7 7
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.18 0.25 -9999 0 -0.69 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.058 0.2 -9999 0 -0.64 38 38
CYR61 0.002 0.082 -9999 0 -0.68 5 5
TLN1 0.01 0.038 -9999 0 -0.71 1 1
Rap1/GTP -0.12 0.18 -9999 0 -0.59 31 31
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.044 0.19 -9999 0 -0.7 28 28
MYH2 -0.16 0.22 -9999 0 -0.55 58 58
MST1R -0.009 0.12 -9999 0 -0.66 11 11
leukocyte activation during inflammatory response -0.11 0.2 -9999 0 -0.56 41 41
APOB -0.11 0.24 -9999 0 -0.6 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.01 0.12 -9999 0 -0.68 11 11
JAM3 -0.001 0.086 -9999 0 -0.57 8 8
GP1BA -0.031 0.17 -9999 0 -0.67 22 22
alphaM/beta2 Integrin/CTGF -0.064 0.19 -9999 0 -0.62 31 31
alphaM/beta2 Integrin -0.13 0.23 -9999 0 -0.53 56 56
JAM3 homodimer -0.001 0.086 -9999 0 -0.56 8 8
ICAM2 0.008 0.054 -9999 0 -0.71 2 2
ICAM1 -0.018 0.14 -9999 0 -0.69 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.13 0.22 -9999 0 -0.52 56 56
cell adhesion -0.073 0.2 -9999 0 -0.58 38 38
NFKB1 -0.17 0.31 -9999 0 -0.77 47 47
THY1 -0.008 0.12 -9999 0 -0.68 10 10
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.085 0.16 -9999 0 -0.38 79 79
alphaM/beta2 Integrin/LRP/tPA -0.098 0.23 -9999 0 -0.76 25 25
IL6 -0.18 0.34 -9999 0 -0.85 52 52
ITGB2 -0.021 0.14 -9999 0 -0.71 14 14
elevation of cytosolic calcium ion concentration -0.096 0.23 -9999 0 -0.68 34 34
alphaM/beta2 Integrin/JAM2/JAM3 -0.053 0.18 -9999 0 -0.7 21 21
JAM2 0.004 0.076 -9999 0 -0.71 4 4
alphaM/beta2 Integrin/ICAM1 -0.081 0.22 -9999 0 -0.66 36 36
alphaM/beta2 Integrin/uPA/Plg -0.091 0.21 -9999 0 -0.59 39 39
RhoA/GTP -0.15 0.22 -9999 0 -0.57 49 49
positive regulation of phagocytosis -0.12 0.21 -9999 0 -0.78 25 25
Ron/MSP -0.024 0.14 -9999 0 -0.48 30 30
alphaM/beta2 Integrin/uPAR/uPA -0.097 0.23 -9999 0 -0.69 34 34
alphaM/beta2 Integrin/uPAR -0.056 0.19 -9999 0 -0.68 25 25
PLAU -0.075 0.22 -9999 0 -0.61 49 49
PLAT -0.088 0.22 -9999 0 -0.57 61 61
actin filament polymerization -0.15 0.21 -9999 0 -0.52 58 58
MST1 -0.023 0.14 -9999 0 -0.61 20 20
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.21 -9999 0 -0.57 41 41
TNF -0.18 0.35 -9999 0 -0.89 50 50
RAP1B 0.002 0.072 -9999 0 -0.55 6 6
alphaM/beta2 Integrin/uPA -0.098 0.23 -9999 0 -0.63 40 40
fibrinolysis -0.09 0.21 -9999 0 -0.58 39 39
HCK -0.012 0.13 -9999 0 -0.68 12 12
dendritic cell antigen processing and presentation -0.13 0.22 -9999 0 -0.52 56 56
VTN -0.066 0.21 -9999 0 -0.6 45 45
alphaM/beta2 Integrin/CYR61 -0.053 0.18 -9999 0 -0.67 23 23
LPA -0.015 0.1 -9999 0 -0.55 12 12
LRP1 0.002 0.085 -9999 0 -0.71 5 5
cell migration -0.068 0.25 -9999 0 -0.66 38 38
FN1 -0.024 0.15 -9999 0 -0.63 20 20
alphaM/beta2 Integrin/Thy1 -0.058 0.2 -9999 0 -0.71 25 25
MPO -0.027 0.15 -9999 0 -0.59 23 23
KNG1 -0.045 0.16 -9999 0 -0.55 32 32
RAP1/GDP -0.006 0.043 -9999 0 -0.33 6 6
ROCK1 -0.14 0.21 -9999 0 -0.53 48 48
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0 -9999 0 -10000 0 0
CTGF -0.015 0.14 -9999 0 -0.68 14 14
alphaM/beta2 Integrin/Hck -0.06 0.22 -9999 0 -0.84 22 22
ITGAM -0.033 0.16 -9999 0 -0.67 21 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.08 0.24 -9999 0 -0.62 41 41
HP -0.25 0.32 -9999 0 -0.64 143 143
leukocyte adhesion -0.16 0.25 -9999 0 -0.79 29 29
SELP -0.044 0.19 -9999 0 -0.7 28 28
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.015 0.041 -9999 0 -0.53 2 2
Necdin/E2F1 0 0.094 -9999 0 -0.48 13 13
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.13 0.19 -9999 0 -0.72 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.2 0.24 -9999 0 -0.56 76 76
NT-4/5 (dimer)/p75(NTR) -0.081 0.21 -9999 0 -0.5 67 67
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 -0.095 0.19 -9999 0 -0.63 10 10
IKBKG 0.008 0.054 -9999 0 -0.71 2 2
BDNF -0.1 0.24 -9999 0 -0.62 63 63
MGDIs/NGR/p75(NTR)/LINGO1 -0.094 0.18 -9999 0 -0.49 36 36
FURIN -0.011 0.11 -9999 0 -0.56 14 14
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.2 -9999 0 -0.53 48 48
LINGO1 -0.055 0.19 -9999 0 -0.58 40 40
Sortilin/TRAF6/NRIF -0.005 0.036 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.24 -9999 0 -0.62 63 63
NTRK1 -0.034 0.17 -9999 0 -0.66 24 24
RTN4R -0.01 0.12 -9999 0 -0.7 11 11
neuron apoptosis -0.1 0.2 -9999 0 -0.61 21 21
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.13 0.22 -9999 0 -0.51 52 52
ARHGDIA 0.01 0.038 -9999 0 -0.71 1 1
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase -0.003 0.031 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.12 0.21 -9999 0 -0.48 55 55
MAGEH1 0.004 0.072 -9999 0 -0.67 4 4
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.12 0.22 -9999 0 -0.49 57 57
Mammalian IAPs/DIABLO 0.005 0.098 -9999 0 -0.41 14 14
proNGF (dimer) -0.16 0.28 -9999 0 -0.6 99 99
MAGED1 0.01 0.03 -9999 0 -0.55 1 1
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.054 0.2 -9999 0 -0.67 34 34
ZNF274 0.012 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.1 0.19 -9999 0 -0.44 53 53
NGF -0.16 0.28 -9999 0 -0.6 99 99
cell cycle arrest -0.11 0.19 -9999 0 -0.64 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.059 0.14 -9999 0 -0.48 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.081 0.18 -9999 0 -0.48 44 44
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.15 0.21 -9999 0 -0.52 54 54
PSENEN 0.007 0.051 -9999 0 -0.55 3 3
mol:ceramide -0.11 0.2 -9999 0 -0.46 53 53
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.12 -9999 0 -0.4 11 11
p75(NTR)/beta APP -0.033 0.15 -9999 0 -0.46 37 37
BEX1 -0.085 0.22 -9999 0 -0.58 57 57
mol:GDP -0.14 0.21 -9999 0 -0.4 127 127
NGF (dimer) -0.18 0.24 -9999 0 -0.52 80 80
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.062 0.18 -9999 0 -0.46 36 36
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.12 0.18 -9999 0 -0.44 52 52
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.15 0.21 -9999 0 -0.52 54 54
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.011 0.056 -9999 0 -0.45 5 5
NT3 (dimer) -0.068 0.22 -9999 0 -0.64 43 43
TP53 -0.061 0.18 -9999 0 -0.64 12 12
PRDM4 -0.11 0.2 -9999 0 -0.47 53 53
BDNF (dimer) -0.25 0.29 -9999 0 -0.56 124 124
PIK3CA 0.012 0 -9999 0 -10000 0 0
SORT1 0.008 0.054 -9999 0 -0.71 2 2
activation of caspase activity -0.13 0.19 -9999 0 -0.71 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.2 -9999 0 -0.47 53 53
RHOC 0.01 0.03 -9999 0 -0.55 1 1
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 -0.12 0.21 -9999 0 -0.58 32 32
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 -0.11 0.2 -9999 0 -0.47 53 53
APH1B 0.01 0.038 -9999 0 -0.71 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.15 0.21 -9999 0 -0.51 53 53
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.017 0.022 -9999 0 -0.39 1 1
NT3 (dimer)/p75(NTR) -0.09 0.23 -9999 0 -0.54 68 68
MAPK8 -0.096 0.19 -9999 0 -0.56 19 19
MAPK9 -0.095 0.19 -9999 0 -0.56 19 19
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.068 0.22 -9999 0 -0.64 43 43
NTF4 -0.054 0.2 -9999 0 -0.67 34 34
NDN -0.003 0.1 -9999 0 -0.67 8 8
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.12 0.17 -9999 0 -0.65 11 11
p75 CTF/Sortilin/TRAF6/NRIF 0.028 0.033 -9999 0 -0.41 2 2
RhoA-B-C/GTP -0.15 0.21 -9999 0 -0.52 54 54
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.093 0.17 -9999 0 -0.68 11 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.2 -9999 0 -0.48 48 48
PRKACB -0.003 0.096 -9999 0 -0.63 8 8
proBDNF (dimer)/p75 ECD -0.067 0.18 -9999 0 -0.46 63 63
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.031 0.16 -9999 0 -0.65 23 23
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.11 0.2 -9999 0 -0.48 51 51
BAD -0.095 0.19 -9999 0 -0.56 21 21
RIPK2 0.012 0 -9999 0 -10000 0 0
NGFR -0.055 0.2 -9999 0 -0.63 37 37
CYCS -0.099 0.19 -9999 0 -0.67 11 11
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.11 0.2 -9999 0 -0.46 52 52
BCL2L11 -0.095 0.19 -9999 0 -0.56 21 21
BDNF (dimer)/p75(NTR) -0.11 0.24 -9999 0 -0.5 90 90
PI3K -0.11 0.2 -9999 0 -0.46 52 52
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.11 0.2 -9999 0 -0.47 53 53
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.03 -9999 0 -0.55 1 1
NGF (dimer)/p75(NTR) -0.16 0.25 -9999 0 -0.47 127 127
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.11 0.2 -9999 0 -0.47 53 53
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ -0.002 0.09 -9999 0 -0.59 8 8
PLG 0 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.15 0.23 -9999 0 -0.59 43 43
SQSTM1 0.01 0.03 -9999 0 -0.55 1 1
NGFRAP1 -0.011 0.12 -9999 0 -0.71 11 11
CASP3 -0.086 0.18 -9999 0 -0.51 21 21
E2F1 0.003 0.074 -9999 0 -0.61 5 5
CASP9 0.01 0.03 -9999 0 -0.55 1 1
IKK complex -0.11 0.15 -9999 0 -0.53 11 11
NGF (dimer)/TRKA -0.14 0.23 -9999 0 -0.46 119 119
MMP7 -0.14 0.28 -9999 0 -0.62 86 86
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.12 0.18 -9999 0 -0.68 10 10
MMP3 -0.2 0.3 -9999 0 -0.63 115 115
APAF-1/Caspase 9 -0.1 0.15 -9999 0 -0.53 23 23
TCGA08_p53

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
CDKN2A -0.14 0.23 -10000 0 -0.48 110 110
TP53 -0.044 0.091 0.34 1 -0.44 4 5
Senescence -0.044 0.091 0.34 1 -0.44 4 5
Apoptosis -0.044 0.091 0.34 1 -0.44 4 5
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.071 0.14 0.3 61 -0.39 8 69
MDM4 0.01 0.038 -10000 0 -0.71 1 1
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.047 0.15 -10000 0 -0.54 19 19
fibroblast growth factor receptor signaling pathway -0.047 0.15 -10000 0 -0.54 19 19
LAMA1 -0.083 0.22 -10000 0 -0.6 55 55
PRNP 0.002 0.082 -10000 0 -0.68 5 5
GPC1/SLIT2 -0.045 0.18 -10000 0 -0.54 40 40
SMAD2 0.009 0.095 -10000 0 -0.43 13 13
GPC1/PrPc/Cu2+ -0.024 0.11 -10000 0 -0.48 18 18
GPC1/Laminin alpha1 -0.073 0.2 -10000 0 -0.48 65 65
TDGF1 -0.074 0.21 -10000 0 -0.6 49 49
CRIPTO/GPC1 -0.068 0.19 -10000 0 -0.46 63 63
APP/GPC1 -0.004 0.11 -10000 0 -0.5 15 15
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.05 0.16 -10000 0 -0.46 29 29
FLT1 0.006 0.066 -10000 0 -0.71 3 3
GPC1/TGFB/TGFBR1/TGFBR2 -0.021 0.097 -10000 0 -0.48 13 13
SERPINC1 -0.014 0.11 -10000 0 -0.55 15 15
FYN -0.052 0.17 -10000 0 -0.49 29 29
FGR -0.059 0.18 -10000 0 -0.48 34 34
positive regulation of MAPKKK cascade -0.079 0.21 -10000 0 -0.54 41 41
SLIT2 -0.042 0.19 -10000 0 -0.7 27 27
GPC1/NRG -0.075 0.2 -10000 0 -0.49 64 64
NRG1 -0.084 0.23 -10000 0 -0.63 53 53
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.024 0.1 -10000 0 -0.45 16 16
LYN -0.051 0.16 -10000 0 -0.47 29 29
mol:Spermine -0.012 0.11 -10000 0 -0.51 15 15
cell growth -0.047 0.15 -10000 0 -0.54 19 19
BMP signaling pathway 0.017 0.14 0.68 15 -10000 0 15
SRC -0.049 0.16 -10000 0 -0.46 28 28
TGFBR1 0.009 0.042 -10000 0 -0.55 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.15 0.28 -10000 0 -0.63 90 90
GPC1 -0.017 0.14 -10000 0 -0.68 15 15
TGFBR1 (dimer) 0.009 0.042 -10000 0 -0.55 2 2
VEGFA 0.008 0.048 -10000 0 -0.63 2 2
BLK -0.13 0.22 -10000 0 -0.49 73 73
HCK -0.064 0.18 -10000 0 -0.49 36 36
FGF2 -0.02 0.14 -10000 0 -0.62 18 18
FGFR1 -0.005 0.1 -10000 0 -0.6 10 10
VEGFR1 homodimer 0.006 0.066 -10000 0 -0.71 3 3
TGFBR2 0.01 0.038 -10000 0 -0.71 1 1
cell death -0.004 0.1 -10000 0 -0.5 15 15
ATIII/GPC1 -0.023 0.13 -10000 0 -0.46 29 29
PLA2G2A/GPC1 -0.13 0.23 -10000 0 -0.48 101 101
LCK -0.059 0.17 -10000 0 -0.48 34 34
neuron differentiation -0.075 0.2 -10000 0 -0.49 64 64
PrPc/Cu2+ 0.002 0.062 -10000 0 -0.51 5 5
APP 0.012 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.01 0.038 -10000 0 -0.71 1 1
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.014 0.067 -9999 0 -0.49 5 5
NFATC2 -0.042 0.13 -9999 0 -0.5 25 25
NFATC3 -0.007 0.035 -9999 0 -10000 0 0
CD40LG -0.22 0.34 -9999 0 -0.85 54 54
PTGS2 -0.27 0.36 -9999 0 -0.79 84 84
JUNB 0.004 0.072 -9999 0 -0.67 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.013 0.015 -9999 0 -10000 0 0
CALM1 0.005 0.011 -9999 0 -10000 0 0
JUN -0.001 0.062 -9999 0 -0.65 3 3
mol:Ca2+ -0.013 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.11 0.25 -9999 0 -0.61 67 67
CREM 0.012 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.15 0.19 -9999 0 -0.63 29 29
FOS -0.042 0.17 -9999 0 -0.62 26 26
IFNG -0.26 0.36 -9999 0 -0.78 86 86
AP-1/NFAT1-c-4 -0.25 0.38 -9999 0 -0.85 72 72
FASLG -0.23 0.34 -9999 0 -0.81 63 63
NFAT1-c-4/ICER1 -0.085 0.14 -9999 0 -0.54 22 22
IL2RA -0.22 0.33 -9999 0 -0.84 54 54
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.27 0.37 -9999 0 -0.8 86 86
JunB/Fra1/NFAT1-c-4 -0.14 0.18 -9999 0 -0.53 40 40
IL4 -0.21 0.3 -9999 0 -0.67 73 73
IL2 -0.009 0.056 -9999 0 -0.47 3 3
IL3 -0.029 0.077 -9999 0 -1 2 2
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 -0.017 0.13 -9999 0 -0.62 16 16
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.008 0.054 -9999 0 -0.71 2 2
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.018 0.15 -10000 0 -0.79 12 12
NFATC2 -0.066 0.28 -10000 0 -0.84 29 29
NFATC3 -0.014 0.069 -10000 0 -10000 0 0
CD40LG -0.27 0.42 -10000 0 -1.1 50 50
ITCH -0.023 0.12 -10000 0 -10000 0 0
CBLB -0.023 0.12 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.44 -10000 0 -1.3 44 44
JUNB 0.004 0.072 -10000 0 -0.67 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.071 0.13 -10000 0 -10000 0 0
T cell anergy -0.073 0.2 -10000 0 -0.49 45 45
TLE4 -0.046 0.26 -10000 0 -0.86 23 23
Jun/NFAT1-c-4/p21SNFT -0.17 0.37 -10000 0 -1.2 26 26
AP-1/NFAT1-c-4 -0.3 0.48 -10000 0 -1.3 44 44
IKZF1 -0.04 0.25 -10000 0 -0.84 21 21
T-helper 2 cell differentiation -0.071 0.24 -10000 0 -0.72 29 29
AP-1/NFAT1 -0.12 0.22 -10000 0 -0.69 31 31
CALM1 -0.018 0.081 -10000 0 -10000 0 0
EGR2 -0.095 0.36 -10000 0 -1.5 14 14
EGR3 -0.11 0.4 -10000 0 -1.7 16 16
NFAT1/FOXP3 -0.066 0.29 -10000 0 -0.86 31 31
EGR1 -0.018 0.13 -10000 0 -0.62 16 16
JUN -0.014 0.065 -10000 0 -0.65 3 3
EGR4 -0.1 0.24 -10000 0 -0.61 64 64
mol:Ca2+ -0.032 0.085 -10000 0 -10000 0 0
GBP3 -0.091 0.33 -10000 0 -0.89 44 44
FOSL1 -0.11 0.25 -10000 0 -0.61 67 67
NFAT1-c-4/MAF/IRF4 -0.15 0.35 -10000 0 -1.2 25 25
DGKA -0.036 0.23 -10000 0 -0.79 19 19
CREM 0.012 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.38 -10000 0 -1.2 28 28
CTLA4 -0.08 0.33 -10000 0 -1 33 33
NFAT1-c-4 (dimer)/EGR1 -0.14 0.38 -10000 0 -1.3 23 23
NFAT1-c-4 (dimer)/EGR4 -0.19 0.38 -10000 0 -1.2 26 26
FOS -0.055 0.17 -10000 0 -0.63 26 26
IFNG -0.26 0.44 -10000 0 -1.1 64 64
T cell activation -0.088 0.22 -10000 0 -0.87 10 10
MAF 0.008 0.054 -10000 0 -0.71 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.076 0.28 1.1 14 -10000 0 14
TNF -0.2 0.39 -10000 0 -1.1 39 39
FASLG -0.19 0.48 -10000 0 -1.5 35 35
TBX21 -0.041 0.16 -10000 0 -0.66 22 22
BATF3 -0.016 0.13 -10000 0 -0.62 16 16
PRKCQ -0.041 0.18 -10000 0 -0.71 25 25
PTPN1 -0.031 0.21 -10000 0 -0.81 15 15
NFAT1-c-4/ICER1 -0.14 0.34 -10000 0 -1.2 22 22
GATA3 -0.003 0.091 -10000 0 -0.56 9 9
T-helper 1 cell differentiation -0.22 0.44 -10000 0 -1 64 64
IL2RA -0.22 0.38 -10000 0 -1.1 43 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.031 0.21 -10000 0 -0.76 18 18
E2F1 0.008 0.075 -10000 0 -0.6 5 5
PPARG -0.066 0.22 -10000 0 -0.69 39 39
SLC3A2 -0.031 0.21 -10000 0 -0.76 18 18
IRF4 -0.047 0.19 -10000 0 -0.62 33 33
PTGS2 -0.32 0.44 -10000 0 -1.1 62 62
CSF2 -0.32 0.44 -10000 0 -1.1 60 60
JunB/Fra1/NFAT1-c-4 -0.17 0.35 -10000 0 -1.2 22 22
IL4 -0.075 0.25 -10000 0 -0.76 29 29
IL5 -0.25 0.38 -10000 0 -1 44 44
IL2 -0.09 0.23 -10000 0 -0.89 10 10
IL3 -0.058 0.089 -10000 0 -1 2 2
RNF128 -0.13 0.33 -10000 0 -0.73 81 81
NFATC1 -0.077 0.29 -10000 0 -1.2 14 14
CDK4 0.05 0.17 0.77 4 -10000 0 4
PTPRK -0.031 0.21 -10000 0 -0.76 18 18
IL8 -0.29 0.42 -10000 0 -1.1 51 51
POU2F1 0.008 0.054 -10000 0 -0.71 2 2
Arf6 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
CENTA1/KIF3B -0.023 0.096 -9999 0 -0.42 19 19
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.58 5 5
EGFR -0.036 0.17 -9999 0 -0.62 27 27
EPHA2 -0.015 0.14 -9999 0 -0.68 14 14
USP6 0.012 0 -9999 0 -10000 0 0
IQSEC1 0.01 0.038 -9999 0 -0.71 1 1
EGFR/EGFR/EGF/EGF -0.12 0.24 -9999 0 -0.52 89 89
ARRB2 -0.023 0.1 -9999 0 -0.29 40 40
mol:GTP 0.008 0.042 -9999 0 -0.28 3 3
ARRB1 0.006 0.066 -9999 0 -0.71 3 3
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR -0.062 0.21 -9999 0 -0.64 40 40
EGF -0.12 0.28 -9999 0 -0.69 68 68
somatostatin receptor activity 0 0 -9999 0 -0.001 36 36
ARAP2 -0.013 0.13 -9999 0 -0.71 12 12
mol:GDP -0.063 0.13 -9999 0 -0.35 37 37
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 29 29
ITGA2B -0.087 0.23 -9999 0 -0.61 56 56
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.007 0.097 -9999 0 -0.41 16 16
ADAP1 -0.008 0.11 -9999 0 -0.64 11 11
KIF13B -0.004 0.1 -9999 0 -0.69 8 8
HGF/MET -0.096 0.22 -9999 0 -0.51 74 74
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.071 0.13 -9999 0 -0.34 38 38
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.11 0.2 -9999 0 -0.49 67 67
ADRB2 -0.032 0.17 -9999 0 -0.7 22 22
receptor agonist activity 0 0 -9999 0 0 36 36
actin filament binding 0 0 -9999 0 -0.001 36 36
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.06 0.2 -9999 0 -0.59 42 42
GNAQ 0.01 0.038 -9999 0 -0.71 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 29 29
ARF6/GDP -0.009 0.11 -9999 0 -0.49 10 10
ARF6/GDP/GULP/ACAP1 -0.08 0.14 -9999 0 -0.5 25 25
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.068 0.18 -9999 0 -0.46 37 37
ACAP1 -0.006 0.11 -9999 0 -0.69 9 9
ACAP2 0.01 0.03 -9999 0 -0.55 1 1
LHCGR/beta Arrestin2 -0.042 0.14 -9999 0 -0.42 40 40
EFNA1 0 0.09 -9999 0 -0.68 6 6
HGF -0.036 0.17 -9999 0 -0.66 25 25
CYTH3 0.007 0.038 -9999 0 -0.4 3 3
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 34 34
endosomal lumen acidification 0 0 -9999 0 -0.001 33 33
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.016 0.14 -9999 0 -0.66 15 15
GNAQ/ARNO 0.01 0.022 -9999 0 -0.39 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 13 13
MET -0.09 0.24 -9999 0 -0.65 54 54
GNA14 -0.047 0.2 -9999 0 -0.71 29 29
GNA15 0 0.093 -9999 0 -0.71 6 6
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 32 32
GNA11 0.006 0.066 -9999 0 -0.71 3 3
LHCGR -0.063 0.2 -9999 0 -0.6 40 40
AGTR1 -0.072 0.22 -9999 0 -0.63 46 46
desensitization of G-protein coupled receptor protein signaling pathway -0.041 0.14 -9999 0 -0.42 40 40
IPCEF1/ARNO -0.077 0.17 -9999 0 -0.66 6 6
alphaIIb/beta3 Integrin -0.11 0.22 -9999 0 -0.47 90 90
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0.051 -9999 0 -0.55 3 3
LAT2 -0.089 0.23 -9999 0 -0.67 34 34
AP1 -0.12 0.21 -9999 0 -0.66 36 36
mol:PIP3 -0.097 0.24 -9999 0 -0.64 39 39
IKBKB -0.039 0.13 -9999 0 -0.32 31 31
AKT1 -0.089 0.21 -9999 0 -0.6 28 28
IKBKG -0.04 0.13 -9999 0 -0.32 30 30
MS4A2 -0.089 0.24 -9999 0 -0.66 52 52
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.001 -9999 0 -10000 0 0
MAP3K1 -0.054 0.19 -9999 0 -0.54 33 33
mol:Ca2+ -0.066 0.18 -9999 0 -0.44 39 39
LYN 0.006 0.056 -9999 0 -0.73 2 2
CBLB -0.081 0.21 -9999 0 -0.62 31 31
SHC1 0.009 0.042 -9999 0 -0.55 2 2
RasGAP/p62DOK 0.004 0.087 -9999 0 -0.42 12 12
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.004 0.1 -9999 0 -0.69 8 8
PLD2 -0.13 0.24 -9999 0 -0.63 42 42
PTPN13 -0.11 0.24 -9999 0 -0.65 41 41
PTPN11 0.007 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.041 0.16 -9999 0 -0.4 27 27
SYK 0 0.088 -9999 0 -0.73 5 5
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.22 -9999 0 -0.65 41 41
LAT -0.086 0.22 -9999 0 -0.63 33 33
PAK2 -0.069 0.22 -9999 0 -0.61 35 35
NFATC2 -0.1 0.22 -9999 0 -0.83 24 24
HRAS -0.086 0.25 -9999 0 -0.69 37 37
GAB2 0.002 0.082 -9999 0 -0.68 5 5
PLA2G1B 0.016 0.029 -9999 0 -10000 0 0
Fc epsilon R1 -0.18 0.27 -9999 0 -0.59 87 87
Antigen/IgE/Fc epsilon R1 -0.17 0.25 -9999 0 -0.54 88 88
mol:GDP -0.095 0.26 -9999 0 -0.74 37 37
JUN 0.006 0.062 -9999 0 -0.66 3 3
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.001 -9999 0 -10000 0 0
FOS -0.034 0.16 -9999 0 -0.62 26 26
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.093 0.22 -9999 0 -0.6 38 38
CHUK -0.039 0.13 -9999 0 -0.32 30 30
KLRG1 -0.086 0.21 -9999 0 -0.61 33 33
VAV1 -0.096 0.24 -9999 0 -0.63 41 41
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.081 0.21 -9999 0 -0.62 31 31
negative regulation of mast cell degranulation -0.08 0.22 -9999 0 -0.62 33 33
BTK -0.1 0.28 -9999 0 -0.79 36 36
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.28 -9999 0 -0.84 31 31
GAB2/PI3K/SHP2 -0.14 0.21 -9999 0 -0.61 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.092 0.22 -9999 0 -0.68 29 29
RAF1 0.023 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.28 -9999 0 -0.75 45 45
FCER1G -0.01 0.13 -9999 0 -0.71 11 11
FCER1A -0.18 0.3 -9999 0 -0.64 102 102
Antigen/IgE/Fc epsilon R1/Fyn -0.16 0.24 -9999 0 -0.52 87 87
MAPK3 0.032 0.021 -9999 0 -10000 0 0
MAPK1 0.032 0.021 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.003 0.067 -9999 0 -0.63 1 1
DUSP1 -0.014 0.13 -9999 0 -0.65 14 14
NF-kappa-B/RelA -0.041 0.061 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.077 0.2 -9999 0 -0.63 27 27
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.21 -9999 0 -0.64 33 33
FER -0.081 0.21 -9999 0 -0.62 31 31
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.048 0.13 -9999 0 -0.59 17 17
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.094 0.26 -9999 0 -0.73 37 37
cytokine secretion -0.03 0.044 -9999 0 -10000 0 0
SPHK1 -0.1 0.23 -9999 0 -0.59 46 46
PTK2 -0.081 0.22 -9999 0 -0.68 27 27
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.15 0.24 -9999 0 -0.69 40 40
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.091 0.23 -9999 0 -0.62 38 38
MAP2K2 0.028 0.021 -9999 0 -10000 0 0
MAP2K1 0.028 0.021 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.1 0.19 -9999 0 -0.58 32 32
MAP2K4 0.015 0.011 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.18 0.27 -9999 0 -0.56 93 93
mol:Choline -0.12 0.24 -9999 0 -0.61 42 42
SHC/Grb2/SOS1 -0.097 0.18 -9999 0 -0.62 25 25
FYN 0.006 0.066 -9999 0 -0.71 3 3
DOK1 0.008 0.054 -9999 0 -0.71 2 2
PXN -0.068 0.2 -9999 0 -0.62 25 25
HCLS1 -0.087 0.24 -9999 0 -0.68 32 32
PRKCB -0.066 0.18 -9999 0 -0.44 39 39
FCGR2B -0.024 0.15 -9999 0 -0.66 19 19
IGHE -0.003 0.008 -9999 0 -10000 0 0
KLRG1/SHIP -0.083 0.22 -9999 0 -0.64 33 33
LCP2 -0.002 0.098 -9999 0 -0.69 7 7
PLA2G4A -0.14 0.26 -9999 0 -0.6 61 61
RASA1 0.01 0.038 -9999 0 -0.71 1 1
mol:Phosphatidic acid -0.12 0.24 -9999 0 -0.61 42 42
IKK complex -0.017 0.1 -9999 0 -0.26 9 9
WIPF1 0.008 0.054 -9999 0 -0.71 2 2
Glucocorticoid receptor regulatory network

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
PCK2 0.011 0.099 -10000 0 -0.95 1 1
SMARCC2 0.013 0.004 -10000 0 -10000 0 0
SMARCC1 0.013 0.004 -10000 0 -10000 0 0
TBX21 -0.078 0.24 -10000 0 -0.77 26 26
SUMO2 0.012 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.02 0 -10000 0 -10000 0 0
FKBP4 0.01 0.03 -10000 0 -0.55 1 1
FKBP5 -0.012 0.12 -10000 0 -0.63 13 13
GR alpha/HSP90/FKBP51/HSP90 0.06 0.14 0.34 10 -0.42 8 18
PRL -0.062 0.16 -10000 0 -0.65 4 4
cortisol/GR alpha (dimer)/TIF2 0.15 0.29 0.6 53 -0.61 4 57
RELA -0.01 0.089 -10000 0 -10000 0 0
FGG -0.16 0.4 0.53 18 -0.63 123 141
GR beta/TIF2 0.062 0.15 0.36 14 -0.5 9 23
IFNG -0.32 0.45 -10000 0 -1 81 81
apoptosis -0.005 0.18 0.5 10 -0.79 3 13
CREB1 -0.012 0.071 -10000 0 -0.38 2 2
histone acetylation 0.05 0.16 0.4 29 -0.41 5 34
BGLAP -0.042 0.19 -10000 0 -1.2 5 5
GR/PKAc 0.065 0.12 0.33 10 -0.43 4 14
NF kappa B1 p50/RelA -0.02 0.16 -10000 0 -0.5 7 7
SMARCD1 0.012 0.03 -10000 0 -0.54 1 1
MDM2 0.054 0.11 0.28 20 -0.28 7 27
GATA3 -0.002 0.095 -10000 0 -0.57 9 9
AKT1 0.002 0.011 -10000 0 -10000 0 0
CSF2 -0.21 0.49 -10000 0 -1.3 58 58
GSK3B 0.012 0.007 -10000 0 -10000 0 0
NR1I3 0.012 0.19 0.49 8 -0.81 6 14
CSN2 0.076 0.19 0.37 43 -0.32 10 53
BRG1/BAF155/BAF170/BAF60A 0.024 0.076 -10000 0 -0.42 9 9
NFATC1 0.002 0.085 -10000 0 -0.71 5 5
POU2F1 0.006 0.059 -10000 0 -0.71 2 2
CDKN1A 0.012 0.15 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN -0.014 0.13 -10000 0 -0.7 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.048 0.15 0.34 7 -0.45 10 17
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.002 0.2 0.48 7 -0.9 7 14
JUN -0.19 0.21 -10000 0 -0.56 47 47
IL4 -0.058 0.15 -10000 0 -0.37 40 40
CDK5R1 0.002 0.076 -10000 0 -0.57 6 6
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.24 0.26 0.25 3 -0.6 91 94
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.066 0.13 0.34 8 -0.41 5 13
cortisol/GR alpha (monomer) 0.18 0.33 0.71 57 -10000 0 57
NCOA2 -0.004 0.11 -10000 0 -0.71 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.18 -10000 0 -0.67 26 26
AP-1/NFAT1-c-4 -0.35 0.36 -10000 0 -0.82 98 98
AFP -0.15 0.25 -10000 0 -1.1 13 13
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.1 0.16 0.48 12 -10000 0 12
TP53 0.019 0.091 -10000 0 -0.6 7 7
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.37 0.51 -10000 0 -1.1 90 90
KRT14 -0.34 0.5 -10000 0 -1.1 85 85
TBP 0.017 0.038 -10000 0 -0.36 3 3
CREBBP 0.097 0.11 0.34 31 -10000 0 31
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC2 0.027 0.034 -10000 0 -10000 0 0
AP-1 -0.36 0.36 -10000 0 -0.82 101 101
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.057 0.2 -10000 0 -0.65 37 37
MAPK11 0.004 0.073 -10000 0 -0.67 4 4
KRT5 -0.42 0.55 -10000 0 -1.2 102 102
interleukin-1 receptor activity 0.015 0.034 -10000 0 -10000 0 0
NCOA1 0.012 0.039 -10000 0 -0.7 1 1
STAT1 0.02 0 -10000 0 -10000 0 0
CGA -0.1 0.23 -10000 0 -0.69 23 23
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.23 0.51 85 -10000 0 85
MAPK3 0.012 0.008 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.11 0.3 -10000 0 -0.89 31 31
NFKB1 -0.01 0.089 -10000 0 -10000 0 0
MAPK8 -0.13 0.18 -10000 0 -0.46 45 45
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.011 0.19 0.51 10 -0.85 3 13
BAX 0.023 0.06 -10000 0 -10000 0 0
POMC -0.15 0.35 -10000 0 -1.5 15 15
EP300 0.098 0.11 0.33 39 -10000 0 39
cortisol/GR alpha (dimer)/p53 0.16 0.28 0.61 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.086 0.25 4 -0.25 6 10
SGK1 0.13 0.16 -10000 0 -1.5 1 1
IL13 -0.17 0.22 -10000 0 -0.73 18 18
IL6 -0.14 0.35 -10000 0 -1 36 36
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.14 0.18 -10000 0 -0.44 54 54
IL2 -0.2 0.25 -10000 0 -0.7 35 35
CDK5 0.012 0.004 -10000 0 -10000 0 0
PRKACB -0.003 0.096 -10000 0 -0.63 8 8
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.16 0.38 -10000 0 -1 47 47
CDK5R1/CDK5 0.001 0.057 -10000 0 -0.41 6 6
NF kappa B1 p50/RelA/PKAc -0.003 0.13 -10000 0 -0.48 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.26 0.57 51 -10000 0 51
SMARCA4 -0.005 0.12 -10000 0 -0.71 9 9
chromatin remodeling 0.1 0.16 0.41 25 -0.66 1 26
NF kappa B1 p50/RelA/Cbp 0.082 0.18 0.4 22 -0.44 1 23
JUN (dimer) -0.19 0.21 -10000 0 -0.56 47 47
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.11 0.32 -10000 0 -1 33 33
NR3C1 0.1 0.2 0.48 37 -0.53 2 39
NR4A1 -0.061 0.2 -10000 0 -0.59 38 38
TIF2/SUV420H1 0.005 0.082 -10000 0 -0.53 8 8
MAPKKK cascade -0.005 0.18 0.5 10 -0.79 3 13
cortisol/GR alpha (dimer)/Src-1 0.16 0.28 0.61 52 -10000 0 52
PBX1 -0.02 0.14 -10000 0 -0.7 15 15
POU1F1 -0.003 0.026 -10000 0 -10000 0 0
SELE -0.14 0.35 -10000 0 -0.98 36 36
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.16 0.41 24 -0.67 1 25
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.26 0.57 51 -10000 0 51
mol:cortisol 0.091 0.2 0.4 68 -0.24 9 77
MMP1 -0.32 0.5 -10000 0 -1.1 90 90
Ephrin B reverse signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.003 0.078 -10000 0 -0.64 5 5
EPHB2 -0.026 0.16 -10000 0 -0.66 20 20
EFNB1 -0.011 0.12 -10000 0 -0.45 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.086 0.19 -10000 0 -0.69 18 18
Ephrin B2/EPHB1-2 -0.073 0.17 -10000 0 -0.52 25 25
neuron projection morphogenesis -0.088 0.18 -10000 0 -0.66 18 18
Ephrin B1/EPHB1-2/Tiam1 -0.074 0.22 -10000 0 -0.55 39 39
DNM1 -0.013 0.13 -10000 0 -0.66 13 13
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.052 0.2 -10000 0 -0.74 27 27
YES1 -0.088 0.26 -10000 0 -0.97 27 27
Ephrin B1/EPHB1-2/NCK2 -0.061 0.19 -10000 0 -0.54 29 29
PI3K -0.052 0.21 -10000 0 -0.74 27 27
mol:GDP -0.092 0.2 -10000 0 -0.54 39 39
ITGA2B -0.087 0.23 -10000 0 -0.61 56 56
endothelial cell proliferation -0.005 0.06 -10000 0 -0.42 7 7
FYN -0.089 0.26 -10000 0 -0.97 27 27
MAP3K7 -0.073 0.21 -10000 0 -0.78 27 27
FGR -0.091 0.26 -10000 0 -0.98 27 27
TIAM1 -0.015 0.13 -10000 0 -0.66 14 14
PIK3R1 0.012 0 -10000 0 -10000 0 0
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.26 -10000 0 -0.74 36 36
LYN -0.089 0.26 -10000 0 -0.97 27 27
Ephrin B1/EPHB1-2/Src Family Kinases -0.084 0.24 -10000 0 -0.91 27 27
Ephrin B1/EPHB1-2 -0.083 0.23 -10000 0 -0.84 27 27
SRC -0.088 0.26 -10000 0 -0.97 27 27
ITGB3 -0.06 0.2 -10000 0 -0.59 42 42
EPHB1 -0.085 0.22 -10000 0 -0.58 58 58
EPHB4 0.008 0.054 -10000 0 -0.71 2 2
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.061 -10000 0 -0.42 7 7
alphaIIb/beta3 Integrin -0.11 0.22 -10000 0 -0.47 90 90
BLK -0.12 0.27 -10000 0 -0.93 31 31
HCK -0.092 0.26 -10000 0 -0.98 27 27
regulation of stress fiber formation 0.08 0.18 0.54 29 -10000 0 29
MAPK8 -0.044 0.19 -10000 0 -0.69 27 27
Ephrin B1/EPHB1-2/RGS3 -0.06 0.19 -10000 0 -0.67 15 15
endothelial cell migration -0.068 0.19 -10000 0 -0.67 30 30
NCK2 0.01 0.038 -10000 0 -0.71 1 1
PTPN13 -0.094 0.25 -10000 0 -0.68 53 53
regulation of focal adhesion formation 0.08 0.18 0.54 29 -10000 0 29
chemotaxis 0.079 0.18 0.66 15 -10000 0 15
PIK3CA 0.012 0 -10000 0 -10000 0 0
Rac1/GTP -0.091 0.18 -10000 0 -0.68 18 18
angiogenesis -0.082 0.22 -10000 0 -0.84 27 27
LCK -0.092 0.26 -10000 0 -0.97 27 27
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.035 0.17 -10000 0 -0.46 36 36
CRKL -0.033 0.17 -10000 0 -0.46 34 34
HRAS -0.021 0.17 -10000 0 -0.56 16 16
mol:PIP3 -0.047 0.16 -10000 0 -0.45 36 36
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.042 0.17 -10000 0 -0.49 34 34
FOXO3 -0.032 0.16 -10000 0 -0.43 32 32
AKT1 -0.042 0.17 -10000 0 -0.47 34 34
BAD -0.033 0.16 -10000 0 -0.43 33 33
megakaryocyte differentiation -0.059 0.2 -10000 0 -0.5 46 46
GSK3B -0.032 0.16 -10000 0 -0.43 32 32
RAF1 -0.006 0.14 -10000 0 -0.44 14 14
SHC1 0.009 0.042 -10000 0 -0.55 2 2
STAT3 -0.041 0.17 -10000 0 -0.49 34 34
STAT1 -0.097 0.35 -10000 0 -1 37 37
HRAS/SPRED1 -0.009 0.14 -10000 0 -0.44 14 14
cell proliferation -0.041 0.17 -10000 0 -0.47 36 36
PIK3CA 0.012 0 -10000 0 -10000 0 0
TEC 0.008 0.054 -10000 0 -0.71 2 2
RPS6KB1 -0.044 0.17 -10000 0 -0.47 39 39
HRAS/SPRED2 -0.009 0.14 -10000 0 -0.44 14 14
LYN/TEC/p62DOK -0.071 0.15 -10000 0 -0.47 33 33
MAPK3 0.009 0.1 -10000 0 -0.32 10 10
STAP1 -0.084 0.22 -10000 0 -0.52 58 58
GRAP2 -0.009 0.12 -10000 0 -0.71 10 10
JAK2 -0.13 0.28 -10000 0 -0.89 37 37
STAT1 (dimer) -0.094 0.34 -10000 0 -1 37 37
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.08 0.17 -10000 0 -0.5 37 37
actin filament polymerization -0.045 0.17 -10000 0 -0.46 39 39
LYN 0.008 0.054 -10000 0 -0.71 2 2
STAP1/STAT5A (dimer) -0.089 0.26 -10000 0 -0.69 44 44
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.018 0.15 -10000 0 -0.61 7 7
PI3K -0.031 0.17 -10000 0 -0.46 34 34
PTEN 0.012 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.42 -10000 0 -1.3 35 35
MAPK8 -0.043 0.17 -10000 0 -0.48 36 36
STAT3 (dimer) -0.04 0.17 -10000 0 -0.48 34 34
positive regulation of transcription 0.012 0.087 -10000 0 -0.29 2 2
mol:GDP -0.075 0.16 -10000 0 -0.59 18 18
PIK3C2B -0.047 0.19 -10000 0 -0.51 37 37
CBL/CRKL -0.024 0.16 -10000 0 -0.44 32 32
FER -0.041 0.17 -10000 0 -0.49 34 34
SH2B3 -0.044 0.18 -10000 0 -0.5 35 35
PDPK1 -0.037 0.15 -10000 0 -0.42 34 34
SNAI2 -0.065 0.2 -10000 0 -0.54 38 38
positive regulation of cell proliferation -0.068 0.27 -10000 0 -0.77 37 37
KITLG -0.008 0.12 -10000 0 -0.74 10 10
cell motility -0.068 0.27 -10000 0 -0.77 37 37
PTPN6 0.011 0.039 -10000 0 -0.7 1 1
EPOR -0.005 0.13 -10000 0 -1.5 1 1
STAT5A (dimer) -0.054 0.23 -10000 0 -0.65 36 36
SOCS1 0.008 0.048 -10000 0 -0.63 2 2
cell migration 0.057 0.19 0.49 48 -10000 0 48
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.002 0.073 -10000 0 -0.55 6 6
VAV1 -0.017 0.14 -10000 0 -0.71 14 14
GRB10 -0.052 0.18 -10000 0 -0.48 42 42
PTPN11 0.013 0.006 -10000 0 -10000 0 0
SCF/KIT -0.051 0.18 -10000 0 -0.49 39 39
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.005 0.11 -10000 0 -0.35 10 10
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.13 0.42 -10000 0 -1.3 35 35
MAP2K2 0.005 0.11 -10000 0 -0.35 10 10
SHC/Grb2/SOS1 -0.066 0.15 -10000 0 -0.46 33 33
STAT5A -0.057 0.23 -10000 0 -0.67 36 36
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.063 0.19 -10000 0 -0.53 38 38
SHC/GRAP2 0 0.096 -10000 0 -0.51 12 12
PTPRO -0.061 0.2 -10000 0 -0.51 46 46
SH2B2 -0.047 0.18 -10000 0 -0.47 39 39
DOK1 0.008 0.054 -10000 0 -0.71 2 2
MATK -0.059 0.2 -10000 0 -0.5 48 48
CREBBP 0.028 0.015 -10000 0 -10000 0 0
BCL2 -0.024 0.21 -10000 0 -1.2 8 8
FOXM1 transcription factor network

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
NFATC3 -0.019 0.45 -9999 0 -1.2 21 21
PLK1 -0.02 0.34 -9999 0 -1.6 16 16
BIRC5 -0.088 0.46 -9999 0 -1.5 32 32
HSPA1B -0.023 0.46 -9999 0 -1.2 22 22
MAP2K1 0.029 0.036 -9999 0 -10000 0 0
BRCA2 -0.026 0.46 -9999 0 -1.3 23 23
FOXM1 -0.089 0.67 -9999 0 -1.9 28 28
XRCC1 -0.019 0.45 -9999 0 -1.2 21 21
FOXM1B/p19 -0.23 0.38 -9999 0 -1.2 33 33
Cyclin D1/CDK4 -0.095 0.48 -9999 0 -1.1 27 27
CDC2 -0.031 0.48 -9999 0 -1.2 28 28
TGFA -0.11 0.5 -9999 0 -1.1 32 32
SKP2 -0.025 0.46 -9999 0 -1.2 23 23
CCNE1 -0.02 0.15 -9999 0 -0.63 19 19
CKS1B -0.022 0.45 -9999 0 -1.2 21 21
RB1 -0.12 0.23 -9999 0 -1 14 14
FOXM1C/SP1 -0.051 0.52 -9999 0 -1.4 28 28
AURKB -0.023 0.34 -9999 0 -1.6 15 15
CENPF -0.051 0.5 -9999 0 -1.2 33 33
CDK4 0.012 0.051 -9999 0 -0.52 3 3
MYC -0.009 0.42 -9999 0 -1.1 24 24
CHEK2 0.023 0.072 -9999 0 -0.56 4 4
ONECUT1 -0.1 0.51 -9999 0 -1.2 34 34
CDKN2A -0.2 0.3 -9999 0 -0.64 110 110
LAMA4 -0.025 0.46 -9999 0 -1.3 23 23
FOXM1B/HNF6 -0.14 0.6 -9999 0 -1.5 33 33
FOS -0.052 0.49 -9999 0 -1.2 32 32
SP1 0.013 0.001 -9999 0 -10000 0 0
CDC25B -0.019 0.45 -9999 0 -1.2 21 21
response to radiation 0.013 0.034 -9999 0 -10000 0 0
CENPB -0.019 0.45 -9999 0 -1.3 20 20
CENPA -0.071 0.55 -9999 0 -1.4 38 38
NEK2 -0.052 0.52 -9999 0 -1.4 31 31
HIST1H2BA -0.027 0.45 -9999 0 -1.2 28 28
CCNA2 -0.007 0.12 -9999 0 -0.68 11 11
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.053 0.54 -9999 0 -1.5 28 28
CCNB2 -0.033 0.49 -9999 0 -1.4 23 23
CCNB1 -0.032 0.48 -9999 0 -1.3 26 26
ETV5 -0.028 0.47 -9999 0 -1.2 24 24
ESR1 -0.077 0.52 -9999 0 -1.3 37 37
CCND1 -0.097 0.5 -9999 0 -1.2 29 29
GSK3A 0.027 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.003 0.15 -9999 0 -0.56 17 17
CDK2 0.015 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.039 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.19 0.39 -9999 0 -1.3 29 29
GAS1 -0.05 0.5 -9999 0 -1.3 32 32
MMP2 -0.034 0.48 -9999 0 -1.3 27 27
RB1/FOXM1C -0.086 0.49 -9999 0 -1.2 27 27
CREBBP 0.012 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.036 0.18 -10000 0 -0.58 15 15
TBX21 -0.11 0.42 -10000 0 -1.1 42 42
B2M 0.012 0.007 -10000 0 -10000 0 0
TYK2 0.015 0.019 -10000 0 -10000 0 0
IL12RB1 -0.009 0.14 -10000 0 -0.73 12 12
GADD45B -0.064 0.33 -10000 0 -0.98 22 22
IL12RB2 -0.063 0.21 -10000 0 -0.6 47 47
GADD45G -0.11 0.41 -10000 0 -1.1 36 36
natural killer cell activation 0.004 0.021 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 -0.018 0.15 -10000 0 -0.7 16 16
IL2RA -0.038 0.18 -10000 0 -0.67 26 26
IFNG -0.12 0.26 -10000 0 -0.62 72 72
STAT3 (dimer) -0.069 0.32 -10000 0 -0.79 41 41
HLA-DRB5 -0.078 0.22 -10000 0 -0.62 50 50
FASLG -0.14 0.46 -10000 0 -1.1 49 49
NF kappa B2 p52/RelB -0.17 0.33 -10000 0 -0.96 43 43
CD4 -0.002 0.1 -10000 0 -0.71 7 7
SOCS1 0.008 0.048 -10000 0 -0.63 2 2
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.014 0.13 -10000 0 -0.65 14 14
CD3E -0.01 0.12 -10000 0 -0.68 11 11
CD3G -0.033 0.17 -10000 0 -0.68 23 23
IL12Rbeta2/JAK2 -0.035 0.16 -10000 0 -0.44 47 47
CCL3 -0.12 0.44 -10000 0 -1.2 41 41
CCL4 -0.1 0.4 -10000 0 -1.1 37 37
HLA-A 0.004 0.077 -10000 0 -0.71 4 4
IL18/IL18R -0.014 0.19 -10000 0 -0.48 41 41
NOS2 -0.11 0.42 -10000 0 -1.1 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 -0.037 0.17 -10000 0 -0.5 21 21
IL1R1 -0.096 0.39 -10000 0 -1 37 37
IL4 -0.004 0.021 -10000 0 -10000 0 0
JAK2 0.015 0.019 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.066 0.36 -10000 0 -1.2 23 23
RAB7A -0.051 0.3 -10000 0 -0.81 21 21
lysosomal transport -0.046 0.29 -10000 0 -0.76 21 21
FOS -0.088 0.35 -10000 0 -1.2 22 22
STAT4 (dimer) -0.085 0.37 -10000 0 -0.91 42 42
STAT5A (dimer) -0.23 0.37 -10000 0 -0.97 56 56
GZMA -0.12 0.45 -10000 0 -1.2 40 40
GZMB -0.13 0.45 -10000 0 -1.2 45 45
HLX 0.002 0.082 -10000 0 -0.68 5 5
LCK -0.11 0.43 -10000 0 -1.1 41 41
TCR/CD3/MHC II/CD4 -0.061 0.26 -10000 0 -0.7 32 32
IL2/IL2R -0.031 0.19 -10000 0 -0.61 24 24
MAPK14 -0.082 0.36 -10000 0 -0.88 38 38
CCR5 -0.077 0.36 -10000 0 -1.2 22 22
IL1B -0.049 0.2 -10000 0 -0.66 34 34
STAT6 -0.008 0.14 -10000 0 -1.5 1 1
STAT4 -0.01 0.12 -10000 0 -0.7 11 11
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B -0.034 0.18 -10000 0 -0.68 26 26
CD8A -0.026 0.16 -10000 0 -0.64 21 21
CD8B -0.04 0.18 -10000 0 -0.63 29 29
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.035 0.18 0.56 16 -10000 0 16
IL2RB -0.008 0.12 -10000 0 -0.68 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.071 0.34 -10000 0 -0.82 40 40
IL2RG -0.011 0.12 -10000 0 -0.67 12 12
IL12 -0.036 0.17 -10000 0 -0.5 42 42
STAT5A 0.01 0.038 -10000 0 -0.71 1 1
CD247 0 0.091 -10000 0 -0.69 6 6
IL2 -0.001 0.066 -10000 0 -0.55 5 5
SPHK2 0.006 0.066 -10000 0 -0.71 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.014 0.14 -10000 0 -0.65 16 16
IL12/IL12R/TYK2/JAK2 -0.12 0.46 -10000 0 -1.1 45 45
MAP2K3 -0.078 0.36 -10000 0 -0.88 37 37
RIPK2 0.012 0 -10000 0 -10000 0 0
MAP2K6 -0.097 0.38 -10000 0 -0.9 44 44
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.026 0.16 -10000 0 -0.7 19 19
IL18RAP -0.032 0.17 -10000 0 -0.64 25 25
IL12Rbeta1/TYK2 0.003 0.11 -10000 0 -0.56 12 12
EOMES -0.049 0.27 -10000 0 -1.4 11 11
STAT1 (dimer) -0.12 0.36 -10000 0 -0.8 56 56
T cell proliferation -0.046 0.28 -10000 0 -0.68 30 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.004 0.11 -10000 0 -0.67 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.25 -10000 0 -0.76 32 32
ATF2 -0.067 0.33 -10000 0 -0.89 27 27
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.075 0.2 -9999 0 -0.59 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.2 -9999 0 -0.65 16 16
alphaV/beta3 Integrin/Osteopontin/Src -0.098 0.19 -9999 0 -0.47 73 73
AP1 -0.078 0.24 -9999 0 -0.78 19 19
ILK -0.082 0.21 -9999 0 -0.59 26 26
bone resorption -0.065 0.21 -9999 0 -0.73 15 15
PTK2B 0.004 0.076 -9999 0 -0.71 4 4
PYK2/p130Cas -0.11 0.19 -9999 0 -0.68 18 18
ITGAV 0.014 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.007 0.077 -9999 0 -0.53 7 7
alphaV/beta3 Integrin/Osteopontin -0.12 0.21 -9999 0 -0.54 53 53
MAP3K1 -0.084 0.21 -9999 0 -0.5 53 53
JUN 0.006 0.062 -9999 0 -0.65 3 3
MAPK3 -0.079 0.21 -9999 0 -0.63 25 25
MAPK1 -0.079 0.21 -9999 0 -0.63 25 25
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.072 0.21 -9999 0 -0.59 26 26
ITGB3 -0.058 0.2 -9999 0 -0.59 42 42
NFKBIA -0.073 0.22 -9999 0 -0.64 25 25
FOS -0.034 0.16 -9999 0 -0.62 26 26
CD44 0.006 0.066 -9999 0 -0.71 3 3
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.12 0.34 -9999 0 -1 32 32
NF kappa B1 p50/RelA -0.1 0.17 -9999 0 -0.67 16 16
BCAR1 0.004 0.076 -9999 0 -0.71 4 4
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.051 0.14 -9999 0 -0.43 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.089 0.22 -9999 0 -0.5 56 56
VAV3 -0.099 0.23 -9999 0 -0.64 31 31
MAP3K14 -0.087 0.22 -9999 0 -0.62 26 26
ROCK2 0.004 0.076 -9999 0 -0.71 4 4
SPP1 -0.12 0.27 -9999 0 -0.64 73 73
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.12 0.19 -9999 0 -0.65 23 23
MMP2 -0.062 0.21 -9999 0 -0.7 19 19
Noncanonical Wnt signaling 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
NFATC2 -0.039 0.18 -9999 0 -0.7 25 25
GNB1/GNG2 -0.087 0.21 -9999 0 -0.64 26 26
mol:DAG -0.072 0.19 -9999 0 -0.61 21 21
PLCG1 -0.076 0.2 -9999 0 -0.64 21 21
YES1 -0.096 0.22 -9999 0 -0.66 27 27
FZD3 -0.002 0.098 -9999 0 -0.69 7 7
FZD6 0.004 0.076 -9999 0 -0.71 4 4
G protein -0.077 0.2 -9999 0 -0.6 26 26
MAP3K7 -0.059 0.17 -9999 0 -0.61 12 12
mol:Ca2+ -0.07 0.18 -9999 0 -0.58 21 21
mol:IP3 -0.072 0.19 -9999 0 -0.61 21 21
NLK -0.005 0.008 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.071 0.18 -9999 0 -0.58 22 22
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.23 -9999 0 -0.64 32 32
CSNK1A1 0.01 0.038 -9999 0 -0.71 1 1
GNAS -0.095 0.22 -9999 0 -0.66 26 26
GO:0007205 -0.071 0.18 -9999 0 -0.59 21 21
WNT6 -0.051 0.19 -9999 0 -0.61 35 35
WNT4 -0.12 0.26 -9999 0 -0.64 70 70
NFAT1/CK1 alpha -0.095 0.22 -9999 0 -0.63 34 34
GNG2 0.008 0.054 -9999 0 -0.71 2 2
WNT5A -0.024 0.16 -9999 0 -0.7 18 18
WNT11 -0.073 0.22 -9999 0 -0.63 47 47
CDC42 -0.084 0.2 -9999 0 -0.62 27 27
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.19 0.42 -9999 0 -1.2 46 46
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.05 0.13 -9999 0 -0.41 7 7
ATF2/c-Jun -0.03 0.14 -9999 0 -0.77 5 5
MAPK11 -0.059 0.15 -9999 0 -0.59 10 10
MITF -0.058 0.18 -9999 0 -0.55 15 15
MAPKAPK5 -0.053 0.16 -9999 0 -0.52 11 11
KRT8 -0.056 0.17 -9999 0 -0.53 13 13
MAPKAPK3 0.01 0.038 -9999 0 -0.71 1 1
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.081 0.2 -9999 0 -0.48 58 58
CEBPB -0.054 0.16 -9999 0 -0.49 13 13
SLC9A1 -0.055 0.16 -9999 0 -0.52 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.05 0.17 -9999 0 -0.54 13 13
p38alpha-beta/MNK1 -0.053 0.17 -9999 0 -0.57 11 11
JUN -0.03 0.14 -9999 0 -0.76 5 5
PPARGC1A -0.14 0.24 -9999 0 -0.57 56 56
USF1 -0.053 0.16 -9999 0 -0.38 58 58
RAB5/GDP/GDI1 -0.059 0.1 -9999 0 -0.4 10 10
NOS2 -0.098 0.29 -9999 0 -1 22 22
DDIT3 -0.057 0.17 -9999 0 -0.55 12 12
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.041 0.15 -9999 0 -0.49 13 13
p38alpha-beta/HBP1 -0.053 0.17 -9999 0 -0.57 11 11
CREB1 -0.054 0.17 -9999 0 -0.4 57 57
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.041 0.15 -9999 0 -0.52 10 10
RPS6KA4 -0.053 0.16 -9999 0 -0.38 58 58
PLA2G4A -0.11 0.22 -9999 0 -0.57 47 47
GDI1 -0.053 0.16 -9999 0 -0.49 13 13
TP53 -0.075 0.2 -9999 0 -0.48 59 59
RPS6KA5 -0.059 0.18 -9999 0 -0.53 16 16
ESR1 -0.1 0.22 -9999 0 -0.54 43 43
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.061 0.18 -9999 0 -0.4 61 61
MEF2A -0.053 0.16 -9999 0 -0.52 11 11
EIF4EBP1 -0.057 0.17 -9999 0 -0.4 58 58
KRT19 -0.071 0.19 -9999 0 -0.55 24 24
ELK4 -0.053 0.16 -9999 0 -0.52 11 11
ATF6 -0.053 0.16 -9999 0 -0.49 13 13
ATF1 -0.054 0.17 -9999 0 -0.4 57 57
p38alpha-beta/MAPKAPK2 -0.053 0.17 -9999 0 -0.57 11 11
p38alpha-beta/MAPKAPK3 -0.055 0.17 -9999 0 -0.56 12 12
EGFR-dependent Endothelin signaling events

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.036 0.17 -9999 0 -0.62 27 27
EGF/EGFR -0.12 0.2 -9999 0 -0.44 87 87
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.096 0.17 -9999 0 -0.7 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.007 0.11 -9999 0 -0.66 10 10
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.12 0.28 -9999 0 -0.69 68 68
EGF/EGFR dimer/SHC -0.11 0.2 -9999 0 -0.49 67 67
mol:GDP -0.095 0.17 -9999 0 -0.69 7 7
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.033 0.17 -9999 0 -0.68 23 23
GRB2/SOS1 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.087 0.16 -9999 0 -0.65 7 7
SHC1 0.009 0.042 -9999 0 -0.55 2 2
HRAS/GDP -0.089 0.16 -9999 0 -0.65 7 7
FRAP1 -0.067 0.18 -9999 0 -0.67 7 7
EGF/EGFR dimer -0.12 0.24 -9999 0 -0.52 89 89
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.031 0.15 -9999 0 -0.5 33 33
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.006 0.11 -9999 0 -0.41 23 23
EPHB2 -0.026 0.16 -9999 0 -0.65 20 20
Syndecan-2/TACI -0.061 0.17 -9999 0 -0.4 69 69
LAMA1 -0.083 0.22 -9999 0 -0.6 55 55
Syndecan-2/alpha2 ITGB1 -0.071 0.2 -9999 0 -0.46 57 57
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.005 0.046 -9999 0 -0.43 4 4
ITGA5 -0.003 0.094 -9999 0 -0.58 9 9
BAX 0.031 0.049 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.004 0.041 -9999 0 -0.38 4 4
LAMA3 -0.11 0.26 -9999 0 -0.65 64 64
EZR 0.01 0.038 -9999 0 -0.71 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.027 0.16 -9999 0 -0.67 20 20
Syndecan-2/MMP2 0.004 0.097 -9999 0 -0.46 14 14
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.03 0.15 -9999 0 -0.49 33 33
dendrite morphogenesis -0.007 0.12 -9999 0 -0.44 22 22
Syndecan-2/GM-CSF -0.082 0.2 -9999 0 -0.43 82 82
determination of left/right symmetry 0.012 0.055 -9999 0 -0.5 4 4
Syndecan-2/PKC delta 0.018 0.047 -9999 0 -0.42 4 4
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.066 0.18 -9999 0 -0.43 56 56
MAPK1 -0.066 0.18 -9999 0 -0.43 56 56
Syndecan-2/RACK1 0.023 0.041 -9999 0 -0.39 3 3
NF1 0.008 0.054 -9999 0 -0.71 2 2
FGFR/FGF/Syndecan-2 0.012 0.055 -9999 0 -0.5 4 4
ITGA2 -0.049 0.2 -9999 0 -0.66 32 32
MAPK8 0.025 0.054 -9999 0 -0.45 4 4
Syndecan-2/alpha2/beta1 Integrin -0.057 0.18 -9999 0 -0.44 40 40
Syndecan-2/Kininogen -0.025 0.11 -9999 0 -0.35 35 35
ITGB1 0.01 0.03 -9999 0 -0.55 1 1
SRC 0.029 0.039 -9999 0 -0.36 3 3
Syndecan-2/CASK/Protein 4.1 -0.004 0.041 -9999 0 -0.38 4 4
extracellular matrix organization 0.014 0.077 -9999 0 -0.59 5 5
actin cytoskeleton reorganization -0.006 0.11 -9999 0 -0.41 23 23
Syndecan-2/Caveolin-2/Ras 0.001 0.1 -9999 0 -0.41 18 18
Syndecan-2/Laminin alpha3 -0.06 0.17 -9999 0 -0.41 68 68
Syndecan-2/RasGAP -0.005 0.041 -9999 0 -0.37 4 4
alpha5/beta1 Integrin 0.006 0.077 -9999 0 -0.46 9 9
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.007 0.12 -9999 0 -0.44 22 22
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.034 0.044 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.11 0.26 -9999 0 -0.64 65 65
RASA1 0.01 0.038 -9999 0 -0.71 1 1
alpha2/beta1 Integrin -0.03 0.15 -9999 0 -0.49 33 33
Syndecan-2/Synbindin 0.018 0.047 -9999 0 -0.42 4 4
TGFB1 0.006 0.066 -9999 0 -0.71 3 3
CASP3 0.025 0.043 -9999 0 -0.41 3 3
FN1 -0.024 0.15 -9999 0 -0.63 20 20
Syndecan-2/IL8 -0.042 0.15 -9999 0 -0.39 55 55
SDC2 0.012 0.055 -9999 0 -0.5 4 4
KNG1 -0.045 0.16 -9999 0 -0.55 32 32
Syndecan-2/Neurofibromin 0.015 0.059 -9999 0 -0.43 6 6
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.14 0.28 -9999 0 -0.66 81 81
Syndecan-2/TGFB1 0.014 0.078 -9999 0 -0.59 5 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.004 0.041 -9999 0 -0.38 4 4
Syndecan-2/Ezrin 0.023 0.049 -9999 0 -0.41 4 4
PRKACA 0.022 0.054 -9999 0 -0.41 5 5
angiogenesis -0.042 0.15 -9999 0 -0.39 55 55
MMP2 -0.01 0.12 -9999 0 -0.68 11 11
IL8 -0.08 0.23 -9999 0 -0.63 51 51
calcineurin-NFAT signaling pathway -0.061 0.17 -9999 0 -0.4 69 69
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.01 0.12 -9999 0 -0.62 10 10
Syndecan-4/Syndesmos -0.058 0.18 -9999 0 -0.62 24 24
positive regulation of JNK cascade -0.063 0.19 -9999 0 -0.59 27 27
Syndecan-4/ADAM12 -0.1 0.25 -9999 0 -0.72 35 35
CCL5 -0.016 0.13 -9999 0 -0.6 16 16
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 -0.003 0.094 -9999 0 -0.58 9 9
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG 0.001 0.009 -9999 0 -10000 0 0
ADAM12 -0.081 0.24 -9999 0 -0.67 48 48
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.024 0.039 -9999 0 -0.13 14 14
Syndecan-4/Laminin alpha1 -0.1 0.23 -9999 0 -0.63 37 37
Syndecan-4/CXCL12/CXCR4 -0.067 0.2 -9999 0 -0.63 27 27
Syndecan-4/Laminin alpha3 -0.12 0.24 -9999 0 -0.62 43 43
MDK -0.026 0.16 -9999 0 -0.69 19 19
Syndecan-4/FZD7 -0.062 0.19 -9999 0 -0.63 25 25
Syndecan-4/Midkine -0.077 0.21 -9999 0 -0.66 27 27
FZD7 0.002 0.082 -9999 0 -0.68 5 5
Syndecan-4/FGFR1/FGF -0.098 0.18 -9999 0 -0.62 26 26
THBS1 -0.02 0.14 -9999 0 -0.65 17 17
integrin-mediated signaling pathway -0.11 0.23 -9999 0 -0.65 37 37
positive regulation of MAPKKK cascade -0.063 0.19 -9999 0 -0.59 27 27
Syndecan-4/TACI -0.12 0.23 -9999 0 -0.62 44 44
CXCR4 0.008 0.048 -9999 0 -0.63 2 2
cell adhesion -0.004 0.11 -9999 0 -0.51 11 11
Syndecan-4/Dynamin -0.058 0.18 -9999 0 -0.62 24 24
Syndecan-4/TSP1 -0.073 0.21 -9999 0 -0.65 29 29
Syndecan-4/GIPC -0.059 0.18 -9999 0 -0.62 24 24
Syndecan-4/RANTES -0.071 0.19 -9999 0 -0.62 26 26
ITGB1 0.01 0.03 -9999 0 -0.55 1 1
LAMA1 -0.083 0.22 -9999 0 -0.6 55 55
LAMA3 -0.11 0.26 -9999 0 -0.65 64 64
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.002 0.11 -9999 0 -0.59 11 11
Syndecan-4/alpha-Actinin -0.059 0.19 -9999 0 -0.63 24 24
TFPI -0.04 0.18 -9999 0 -0.64 28 28
F2 -0.075 0.2 -9999 0 -0.56 50 50
alpha5/beta1 Integrin 0.006 0.077 -9999 0 -0.46 9 9
positive regulation of cell adhesion -0.15 0.26 -9999 0 -0.7 40 40
ACTN1 0.008 0.048 -9999 0 -0.63 2 2
TNC -0.1 0.25 -9999 0 -0.67 58 58
Syndecan-4/CXCL12 -0.074 0.2 -9999 0 -0.65 27 27
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.02 0.15 -9999 0 -0.69 16 16
TNFRSF13B -0.11 0.26 -9999 0 -0.64 65 65
FGF2 -0.02 0.14 -9999 0 -0.62 18 18
FGFR1 -0.005 0.1 -9999 0 -0.6 10 10
Syndecan-4/PI-4-5-P2 -0.065 0.18 -9999 0 -0.61 26 26
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.022 0.15 -9999 0 -0.62 20 20
cell migration -0.007 0.014 -9999 0 -10000 0 0
PRKCD 0.014 0.009 -9999 0 -10000 0 0
vasculogenesis -0.07 0.2 -9999 0 -0.62 29 29
SDC4 -0.068 0.19 -9999 0 -0.64 26 26
Syndecan-4/Tenascin C -0.11 0.24 -9999 0 -0.69 37 37
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.031 -9999 0 -0.11 7 7
Syndecan-4/Syntenin -0.058 0.18 -9999 0 -0.62 24 24
MMP9 -0.059 0.2 -9999 0 -0.64 38 38
Rac1/GTP -0.005 0.12 -9999 0 -0.53 11 11
cytoskeleton organization -0.055 0.18 -9999 0 -0.59 24 24
GIPC1 0.01 0.038 -9999 0 -0.71 1 1
Syndecan-4/TFPI -0.083 0.22 -9999 0 -0.69 29 29
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.01 0.03 -10000 0 -0.55 1 1
RAS family/GTP/Tiam1 -0.029 0.12 -10000 0 -0.4 13 13
NT3 (dimer)/TRKC -0.1 0.24 -10000 0 -0.53 78 78
NT3 (dimer)/TRKB -0.14 0.25 -10000 0 -0.57 71 71
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.014 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.1 0.24 -10000 0 -0.62 63 63
PIK3CA 0.012 0 -10000 0 -10000 0 0
DYNLT1 0.01 0.03 -10000 0 -0.55 1 1
NTRK1 -0.034 0.17 -10000 0 -0.66 24 24
NTRK2 -0.083 0.23 -10000 0 -0.63 52 52
NTRK3 -0.073 0.22 -10000 0 -0.66 45 45
NT-4/5 (dimer)/TRKB -0.14 0.24 -10000 0 -0.55 69 69
neuron apoptosis 0.17 0.22 0.62 51 -10000 0 51
SHC 2-3/Grb2 -0.17 0.26 -10000 0 -0.71 51 51
SHC1 0.009 0.042 -10000 0 -0.55 2 2
SHC2 -0.15 0.24 -10000 0 -0.75 35 35
SHC3 -0.18 0.27 -10000 0 -0.72 56 56
STAT3 (dimer) 0.004 0.074 -10000 0 -0.37 12 12
NT3 (dimer)/TRKA -0.12 0.22 -10000 0 -0.52 63 63
RIN/GDP -0.025 0.09 -10000 0 -0.28 6 6
GIPC1 0.01 0.038 -10000 0 -0.71 1 1
KRAS 0.01 0.03 -10000 0 -0.55 1 1
DNAJA3 -0.099 0.14 -10000 0 -0.45 26 26
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.009 0.18 -10000 0 -0.84 15 15
MAGED1 0.01 0.03 -10000 0 -0.55 1 1
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.054 0.2 -10000 0 -0.67 34 34
SHC/GRB2/SOS1 -0.002 0.024 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.22 -10000 0 -0.53 62 62
TRKA/NEDD4-2 -0.02 0.14 -10000 0 -0.49 26 26
ELMO1 0.001 0.083 -10000 0 -0.63 6 6
RhoG/GTP/ELMO1/DOCK1 -0.008 0.057 -10000 0 -0.41 7 7
NGF -0.16 0.28 -10000 0 -0.6 99 99
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.01 0.038 -10000 0 -0.71 1 1
GAB2 0.002 0.082 -10000 0 -0.68 5 5
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 -0.001 0.083 -10000 0 -0.55 8 8
DNM1 -0.013 0.13 -10000 0 -0.66 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.1 0.15 -10000 0 -0.46 30 30
mol:GDP -0.038 0.13 -10000 0 -0.41 10 10
NGF (dimer) -0.16 0.28 -10000 0 -0.6 99 99
RhoG/GDP 0.001 0.062 -10000 0 -0.47 6 6
RIT1/GDP -0.02 0.091 -10000 0 -0.3 3 3
TIAM1 -0.015 0.13 -10000 0 -0.66 14 14
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.12 0.22 -10000 0 -0.44 100 100
KIDINS220/CRKL/C3G 0.017 0.022 -10000 0 -0.39 1 1
SHC/RasGAP 0.014 0.042 -10000 0 -0.44 3 3
FRS2 family/SHP2 -0.007 0.048 -10000 0 -0.32 8 8
SHC/GRB2/SOS1/GAB1 0.029 0.024 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.068 0.22 -10000 0 -0.64 43 43
RAP1/GDP -0.039 0.065 -10000 0 -10000 0 0
KIDINS220/CRKL 0.01 0.03 -10000 0 -0.55 1 1
BDNF (dimer) -0.1 0.24 -10000 0 -0.62 63 63
ubiquitin-dependent protein catabolic process -0.13 0.19 -10000 0 -0.48 52 52
Schwann cell development -0.04 0.036 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.024 0.047 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.042 -10000 0 -0.42 1 1
RAP1B 0.002 0.072 -10000 0 -0.55 6 6
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.18 0.26 -10000 0 -0.71 49 49
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
Rap1/GTP -0.046 0.076 -10000 0 -10000 0 0
STAT3 0.004 0.074 -10000 0 -0.37 12 12
axon guidance -0.17 0.24 -10000 0 -0.67 49 49
MAPK3 -0.12 0.21 -10000 0 -0.48 62 62
MAPK1 -0.12 0.21 -10000 0 -0.48 62 62
CDC42/GDP -0.02 0.091 -10000 0 -0.3 3 3
NTF3 -0.068 0.22 -10000 0 -0.64 43 43
NTF4 -0.054 0.2 -10000 0 -0.67 34 34
NGF (dimer)/TRKA/FAIM -0.13 0.19 -10000 0 -0.48 51 51
PI3K 0.018 0 -10000 0 -10000 0 0
FRS3 0.012 0 -10000 0 -10000 0 0
FAIM 0.012 0 -10000 0 -10000 0 0
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.18 0.22 -10000 0 -0.51 84 84
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.097 0.22 -10000 0 -0.52 62 62
RGS19 0.012 0 -10000 0 -10000 0 0
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.083 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.091 -10000 0 -0.3 3 3
NGF (dimer)/TRKA/GRIT -0.13 0.19 -10000 0 -0.4 119 119
neuron projection morphogenesis -0.074 0.15 -10000 0 -0.53 9 9
NGF (dimer)/TRKA/NEDD4-2 -0.13 0.2 -10000 0 -0.48 52 52
MAP2K1 0.034 0.022 -10000 0 -10000 0 0
NGFR -0.055 0.2 -10000 0 -0.63 37 37
NGF (dimer)/TRKA/GIPC/GAIP -0.065 0.15 -10000 0 -0.58 9 9
RAS family/GTP/PI3K 0.028 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.006 0.039 -10000 0 -10000 0 0
NRAS 0.012 0 -10000 0 -10000 0 0
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
PRKCI 0.01 0.03 -10000 0 -0.55 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ -0.002 0.09 -10000 0 -0.59 8 8
MAPKKK cascade -0.14 0.23 -10000 0 -0.65 50 50
RASA1 0.01 0.038 -10000 0 -0.71 1 1
TRKA/c-Abl -0.017 0.13 -10000 0 -0.48 24 24
SQSTM1 0.01 0.03 -10000 0 -0.55 1 1
BDNF (dimer)/TRKB/GIPC -0.093 0.21 -10000 0 -0.49 56 56
NGF (dimer)/TRKA/p62/Atypical PKCs -0.12 0.17 -10000 0 -0.62 9 9
MATK -0.02 0.15 -10000 0 -0.7 16 16
NEDD4L 0.007 0.051 -10000 0 -0.55 3 3
RAS family/GDP -0.033 0.059 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.11 0.15 -10000 0 -0.37 68 68
Rac1/GTP -0.12 0.13 -10000 0 -0.38 42 42
FRS2 family/SHP2/CRK family -0.007 0.042 -10000 0 -10000 0 0
LPA4-mediated 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
ADCY4 0.014 0.051 -9999 0 -0.6 2 2
ADCY5 -0.065 0.17 -9999 0 -0.39 72 72
ADCY6 0.015 0.036 -9999 0 -0.46 2 2
ADCY7 0.014 0.044 -9999 0 -0.46 3 3
ADCY1 -0.011 0.11 -9999 0 -0.41 24 24
ADCY2 -0.054 0.16 -9999 0 -0.4 61 61
ADCY3 0.015 0.036 -9999 0 -0.46 2 2
ADCY8 -0.012 0.09 -9999 0 -0.34 25 25
PRKCE 0.009 0.029 -9999 0 -0.54 1 1
ADCY9 0.009 0.065 -9999 0 -0.44 7 7
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.033 0.11 -9999 0 -0.44 12 12
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.005 0.09 -10000 0 -0.52 5 5
epithelial cell differentiation -0.086 0.13 -10000 0 -0.56 6 6
ITCH 0.02 0.016 -10000 0 -10000 0 0
WWP1 0.003 0.063 -10000 0 -10000 0 0
FYN 0.006 0.066 -10000 0 -0.71 3 3
EGFR -0.036 0.17 -10000 0 -0.62 27 27
PRL -0.018 0.11 -10000 0 -0.55 14 14
neuron projection morphogenesis -0.007 0.13 -10000 0 -10000 0 0
PTPRZ1 -0.25 0.32 -10000 0 -0.62 147 147
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.12 -10000 0 -0.46 11 11
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.046 0.15 -10000 0 -0.45 31 31
ADAM17 0.02 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.08 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.026 0.11 -10000 0 -0.44 13 13
NCOR1 0.01 0.038 -10000 0 -0.71 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.041 0.15 -10000 0 -0.51 17 17
GRIN2B -0.038 0.15 -10000 0 -0.43 30 30
ErbB4/ErbB2/betacellulin -0.015 0.14 -10000 0 -0.54 15 15
STAT1 0.012 0 -10000 0 -10000 0 0
HBEGF 0.002 0.082 -10000 0 -0.68 5 5
PRLR -0.17 0.29 -10000 0 -0.63 99 99
E4ICDs/ETO2 -0.02 0.12 -10000 0 -0.48 12 12
axon guidance 0.049 0.091 -10000 0 -10000 0 0
NEDD4 0.013 0.066 -10000 0 -0.58 4 4
Prolactin receptor/Prolactin receptor/Prolactin -0.14 0.23 -10000 0 -0.48 108 108
CBFA2T3 -0.022 0.15 -10000 0 -0.65 18 18
ErbB4/ErbB2/HBEGF 0.005 0.085 -10000 0 -0.47 5 5
MAPK3 -0.014 0.13 -10000 0 -0.43 11 11
STAT1 (dimer) 0.001 0.067 -10000 0 -10000 0 0
MAPK1 -0.014 0.13 -10000 0 -10000 0 0
JAK2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.043 0.15 -10000 0 -0.43 32 32
NRG1 -0.048 0.18 -10000 0 -0.46 53 53
NRG3 -0.03 0.15 -10000 0 -0.6 23 23
NRG2 -0.052 0.19 -10000 0 -0.59 37 37
NRG4 -0.1 0.24 -10000 0 -0.58 68 68
heart development 0.049 0.091 -10000 0 -10000 0 0
neural crest cell migration -0.042 0.15 -10000 0 -0.42 32 32
ERBB2 0.019 0.061 -10000 0 -0.48 5 5
WWOX/E4ICDs 0 0.069 -10000 0 -10000 0 0
SHC1 0.009 0.042 -10000 0 -0.55 2 2
ErbB4/EGFR/neuregulin 4 -0.085 0.18 -10000 0 -0.54 22 22
apoptosis 0.074 0.099 0.47 8 -10000 0 8
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.038 0.13 -10000 0 -0.45 16 16
ErbB4/ErbB2/epiregulin -0.15 0.18 -10000 0 -0.47 17 17
ErbB4/ErbB4/betacellulin/betacellulin -0.027 0.14 -10000 0 -0.53 20 20
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.12 0.16 -10000 0 -0.51 18 18
MDM2 -0.005 0.087 -10000 0 -0.47 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.062 0.13 -10000 0 -0.43 26 26
STAT5A 0.051 0.089 -10000 0 -0.55 1 1
ErbB4/EGFR/neuregulin 1 beta -0.064 0.18 -10000 0 -0.56 20 20
DLG4 0.012 0 -10000 0 -10000 0 0
GRB2/SHC 0.015 0.031 -10000 0 -0.39 2 2
E4ICDs/TAB2/NCoR1 -0.025 0.056 -10000 0 -0.55 1 1
STAT5A (dimer) -0.091 0.14 -10000 0 -0.61 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.049 0.08 -10000 0 -10000 0 0
LRIG1 0.004 0.076 -10000 0 -0.71 4 4
EREG -0.28 0.31 -10000 0 -0.6 170 170
BTC -0.034 0.17 -10000 0 -0.69 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.049 0.091 -10000 0 -10000 0 0
ERBB4 -0.005 0.08 -10000 0 -10000 0 0
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.012 0.05 -10000 0 -0.51 3 3
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.055 0.15 -10000 0 -0.52 8 8
glial cell differentiation 0.025 0.056 0.55 1 -10000 0 1
WWOX 0.01 0.03 -10000 0 -0.55 1 1
cell proliferation -0.035 0.18 -10000 0 -0.6 15 15
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.008 0.054 -10000 0 -0.71 2 2
Jak2/Leptin Receptor -0.077 0.12 -10000 0 -0.46 16 16
PTP1B/AKT1 -0.012 0.076 -10000 0 -0.35 6 6
FYN 0.006 0.066 -10000 0 -0.71 3 3
p210 bcr-abl/PTP1B -0.02 0.084 -10000 0 -0.36 9 9
EGFR -0.038 0.17 -10000 0 -0.62 27 27
EGF/EGFR -0.11 0.19 -10000 0 -0.45 69 69
CSF1 -0.003 0.099 -10000 0 -0.65 8 8
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.006 0.066 -10000 0 -0.71 3 3
PTP1B/N-cadherin -0.085 0.17 -10000 0 -0.42 56 56
Insulin Receptor/Insulin -0.028 0.06 -10000 0 -0.37 5 5
HCK -0.012 0.13 -10000 0 -0.68 12 12
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.012 0.08 -10000 0 -0.36 7 7
EGF -0.12 0.28 -10000 0 -0.69 68 68
YES1 0.01 0.038 -10000 0 -0.71 1 1
CAV1 -0.038 0.12 -10000 0 -0.4 17 17
TXN 0.004 0.051 -10000 0 -0.54 3 3
PTP1B/IRS1/GRB2 -0.016 0.11 -10000 0 -0.44 13 13
cell migration 0.02 0.084 0.36 9 -10000 0 9
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.17 0.29 -10000 0 -0.63 99 99
ITGA2B -0.088 0.23 -10000 0 -0.61 56 56
CSF1R -0.017 0.14 -10000 0 -0.68 15 15
Prolactin Receptor/Prolactin -0.14 0.23 -10000 0 -0.48 108 108
FGR -0.004 0.1 -10000 0 -0.69 8 8
PTP1B/p130 Cas -0.017 0.091 -10000 0 -0.39 10 10
Crk/p130 Cas -0.01 0.088 -10000 0 -0.4 7 7
DOK1 -0.007 0.084 -10000 0 -0.42 5 5
JAK2 -0.059 0.12 -10000 0 -0.34 28 28
Jak2/Leptin Receptor/Leptin -0.076 0.12 -10000 0 -0.49 11 11
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.02 0.085 -10000 0 -0.36 9 9
LYN 0.008 0.054 -10000 0 -0.71 2 2
CDH2 -0.12 0.26 -10000 0 -0.61 78 78
SRC 0.007 0.033 -10000 0 -10000 0 0
ITGB3 -0.061 0.2 -10000 0 -0.59 42 42
CAT1/PTP1B -0.075 0.18 -10000 0 -0.6 24 24
CAPN1 0.012 0.002 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.02 0.054 -10000 0 -0.4 1 1
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.067 0.11 -10000 0 -0.44 11 11
negative regulation of transcription -0.059 0.12 -10000 0 -0.33 28 28
FCGR2A -0.004 0.1 -10000 0 -0.69 8 8
FER 0.009 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.12 0.22 -10000 0 -0.47 90 90
BLK -0.12 0.27 -10000 0 -0.65 70 70
Insulin Receptor/Insulin/Shc -0.005 0.049 -10000 0 -0.41 5 5
RHOA 0.012 0.002 -10000 0 -10000 0 0
LEPR -0.016 0.13 -10000 0 -0.6 16 16
BCAR1 0.004 0.076 -10000 0 -0.71 4 4
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.083 0.21 -10000 0 -0.69 24 24
PRL -0.018 0.11 -10000 0 -0.55 14 14
SOCS3 0.012 0.086 -10000 0 -1.4 1 1
SPRY2 0.004 0.062 -10000 0 -0.66 3 3
Insulin Receptor/Insulin/IRS1 -0.016 0.088 -10000 0 -0.46 13 13
CSF1/CSF1R -0.028 0.15 -10000 0 -0.6 14 14
Ras protein signal transduction 0.02 0.025 -10000 0 -10000 0 0
IRS1 -0.009 0.12 -10000 0 -0.71 10 10
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.075 0.21 -10000 0 -0.59 50 50
STAT5B -0.033 0.086 -10000 0 -0.32 11 11
STAT5A -0.034 0.087 -10000 0 -0.32 12 12
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.015 0.091 -10000 0 -0.44 7 7
CSN2 -0.042 0.079 -10000 0 -0.16 99 99
PIK3CA 0.012 0 -10000 0 -10000 0 0
LAT -0.01 0.11 -10000 0 -0.61 9 9
YBX1 0.018 0.002 -10000 0 -10000 0 0
LCK -0.004 0.1 -10000 0 -0.69 8 8
SHC1 0.009 0.042 -10000 0 -0.55 2 2
NOX4 -0.016 0.13 -10000 0 -0.69 13 13
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.055 0.15 -10000 0 -0.63 18 18
FYN -0.019 0.23 -10000 0 -0.85 20 20
LAT/GRAP2/SLP76 -0.049 0.19 -10000 0 -0.71 21 21
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.002 0.15 -10000 0 -0.52 18 18
B2M 0.012 0.004 -10000 0 -10000 0 0
IKBKG -0.019 0.045 -10000 0 -0.19 10 10
MAP3K8 0.006 0.062 -10000 0 -0.66 3 3
mol:Ca2+ -0.03 0.048 -10000 0 -0.11 75 75
integrin-mediated signaling pathway -0.004 0.042 -10000 0 -0.46 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.017 0.22 -10000 0 -0.74 23 23
TRPV6 -0.15 0.27 -10000 0 -0.6 91 91
CD28 -0.017 0.14 -10000 0 -0.72 14 14
SHC1 -0.021 0.22 -10000 0 -0.81 20 20
receptor internalization -0.029 0.24 -10000 0 -0.82 23 23
PRF1 -0.028 0.24 -10000 0 -0.91 18 18
KRAS 0.01 0.03 -10000 0 -0.55 1 1
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.01 0.13 -10000 0 -0.42 18 18
LAT -0.024 0.22 -10000 0 -0.81 21 21
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.014 0.13 -10000 0 -0.66 14 14
CD3E -0.009 0.12 -10000 0 -0.69 11 11
CD3G -0.032 0.17 -10000 0 -0.68 23 23
RASGRP2 -0.001 0.033 -10000 0 -0.17 8 8
RASGRP1 -0.002 0.17 -10000 0 -0.51 25 25
HLA-A 0.004 0.077 -10000 0 -0.71 4 4
RASSF5 0.006 0.066 -10000 0 -0.71 3 3
RAP1A/GTP/RAPL -0.004 0.042 -10000 0 -0.46 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.053 -10000 0 -0.14 15 15
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.033 0.076 -10000 0 -0.28 21 21
PRKCA -0.026 0.095 -10000 0 -0.32 20 20
GRAP2 -0.009 0.12 -10000 0 -0.71 10 10
mol:IP3 0.002 0.17 0.23 72 -0.5 18 90
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.24 -10000 0 -0.89 19 19
ORAI1 0.084 0.14 0.32 91 -10000 0 91
CSK -0.022 0.22 -10000 0 -0.83 20 20
B7 family/CD28 -0.087 0.24 -10000 0 -0.94 22 22
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.036 0.27 -10000 0 -0.97 21 21
PTPN6 -0.022 0.23 -10000 0 -0.86 19 19
VAV1 -0.031 0.24 -10000 0 -0.8 24 24
Monovalent TCR/CD3 -0.025 0.21 -10000 0 -0.66 24 24
CBL 0.012 0 -10000 0 -10000 0 0
LCK -0.025 0.24 -10000 0 -0.92 19 19
PAG1 -0.026 0.23 -10000 0 -0.82 21 21
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.033 0.26 -10000 0 -1 19 19
CD80 -0.02 0.15 -10000 0 -0.7 16 16
CD86 -0.008 0.12 -10000 0 -0.7 10 10
PDK1/CARD11/BCL10/MALT1 -0.04 0.094 -10000 0 -0.34 23 23
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.021 0.2 -10000 0 -0.73 22 22
CD8A -0.025 0.15 -10000 0 -0.63 21 21
CD8B -0.039 0.18 -10000 0 -0.62 29 29
PTPRC -0.017 0.14 -10000 0 -0.72 14 14
PDK1/PKC theta -0.003 0.19 -10000 0 -0.64 21 21
CSK/PAG1 -0.02 0.22 -10000 0 -0.83 19 19
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.012 0.059 -10000 0 -0.53 4 4
GRAP2/SLP76 -0.058 0.22 -10000 0 -0.84 21 21
STIM1 0.043 0.069 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.067 -10000 0 -0.19 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.035 0.27 -10000 0 -0.92 23 23
mol:DAG -0.025 0.13 -10000 0 -0.44 20 20
RAP1A/GDP 0.01 0.023 -10000 0 -10000 0 0
PLCG1 0.01 0.03 -10000 0 -0.55 1 1
CD247 0.001 0.091 -10000 0 -0.69 6 6
cytotoxic T cell degranulation -0.025 0.22 -10000 0 -0.85 18 18
RAP1A/GTP -0.003 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.18 -10000 0 -0.6 21 21
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.21 0.25 69 -0.66 20 89
NRAS 0.012 0 -10000 0 -10000 0 0
ZAP70 -0.028 0.16 -10000 0 -0.66 21 21
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.053 0.18 -10000 0 -0.64 23 23
MALT1 0.009 0.042 -10000 0 -0.55 2 2
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.045 0.2 -10000 0 -0.59 37 37
CARD11 -0.039 0.18 -10000 0 -0.71 25 25
PRKCB -0.024 0.1 -10000 0 -0.35 22 22
PRKCE -0.02 0.088 -10000 0 -0.31 18 18
PRKCQ -0.016 0.22 -10000 0 -0.73 23 23
LCP2 -0.002 0.098 -10000 0 -0.69 7 7
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.007 0.13 -10000 0 -0.44 17 17
IKK complex 0.027 0.052 -10000 0 -0.13 6 6
RAS family/GDP -0.003 0.009 -10000 0 -0.085 1 1
MAP3K14 0.017 0.097 -10000 0 -0.32 15 15
PDPK1 0.006 0.14 -10000 0 -0.5 17 17
TCR/CD3/MHC I/CD8/Fyn -0.035 0.26 -10000 0 -0.96 21 21
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0.027 -10000 0 -10000 0 0
AES 0.014 0.021 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.004 0.062 -10000 0 -0.46 6 6
SMAD4 0.012 0 -10000 0 -10000 0 0
DKK2 -0.029 0.17 -10000 0 -0.71 20 20
TLE1 0.01 0.042 -10000 0 -0.66 1 1
MACF1 0.004 0.076 -10000 0 -0.71 4 4
CTNNB1 0.043 0.11 0.28 4 -10000 0 4
WIF1 -0.24 0.32 -10000 0 -0.63 138 138
beta catenin/RanBP3 0.014 0.12 0.43 21 -10000 0 21
KREMEN2 -0.076 0.21 -10000 0 -0.58 52 52
DKK1 -0.27 0.32 -10000 0 -0.62 156 156
beta catenin/beta TrCP1 0.047 0.099 -10000 0 -10000 0 0
FZD1 0.003 0.074 -10000 0 -0.61 5 5
AXIN2 -0.043 0.29 -10000 0 -1.5 12 12
AXIN1 0.012 0.001 -10000 0 -10000 0 0
RAN 0.009 0.042 -10000 0 -0.55 2 2
Axin1/APC/GSK3/beta catenin 0.013 0.039 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.1 -10000 0 -0.55 3 3
Axin1/APC/GSK3 0.015 0.061 0.26 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.031 0.1 -10000 0 -0.55 2 2
HNF1A -0.11 0.23 -10000 0 -0.55 73 73
CTBP1 0.008 0.025 -10000 0 -10000 0 0
MYC -0.017 0.22 -10000 0 -1.6 6 6
RANBP3 0.012 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.077 0.18 -10000 0 -0.54 31 31
NKD1 -0.056 0.2 -10000 0 -0.65 36 36
TCF4 0.003 0.063 -10000 0 -0.62 3 3
TCF3 0.008 0.025 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.022 0.1 -10000 0 -0.46 11 11
Ran/GTP 0 0.031 -10000 0 -0.4 2 2
CtBP/CBP/TCF/TLE1/AES 0.009 0.15 0.5 20 -0.57 1 21
LEF1 -0.006 0.1 -10000 0 -0.66 8 8
DVL1 0.045 0.065 -10000 0 -0.39 2 2
CSNK2A1 0.012 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.029 0.12 -10000 0 -0.64 4 4
DKK1/LRP6/Kremen 2 -0.22 0.24 -10000 0 -0.52 100 100
LRP6 0.01 0.038 -10000 0 -0.71 1 1
CSNK1A1 0.008 0.045 -10000 0 -0.69 1 1
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 -0.041 0.29 -10000 0 -1.6 12 12
WNT1 -0.03 0.16 -10000 0 -0.6 24 24
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.048 -10000 0 -0.63 2 2
PPP2R5D 0.056 0.093 0.32 35 -10000 0 35
APC 0.008 0.1 -10000 0 -0.45 7 7
WNT1/LRP6/FZD1 0.07 0.12 0.26 65 -10000 0 65
CREBBP 0.008 0.025 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.049 0.15 -10000 0 -0.46 38 38
cell-cell adhesion 0.097 0.17 0.59 25 -10000 0 25
Ephrin B/EPHB2/RasGAP -0.074 0.17 -10000 0 -0.71 11 11
ITSN1 0.01 0.038 -10000 0 -0.71 1 1
PIK3CA 0.012 0 -10000 0 -10000 0 0
SHC1 0.009 0.042 -10000 0 -0.55 2 2
Ephrin B1/EPHB3 -0.021 0.085 -10000 0 -0.36 20 20
Ephrin B1/EPHB1 -0.068 0.14 -10000 0 -0.35 68 68
HRAS/GDP -0.089 0.17 -10000 0 -0.61 20 20
Ephrin B/EPHB1/GRB7 -0.11 0.19 -10000 0 -0.68 20 20
Endophilin/SYNJ1 -0.041 0.17 -10000 0 -0.45 37 37
KRAS 0.01 0.03 -10000 0 -0.55 1 1
Ephrin B/EPHB1/Src -0.1 0.18 -10000 0 -0.52 38 38
endothelial cell migration -0.007 0.049 -10000 0 -0.38 5 5
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.001 0.092 -10000 0 -0.64 7 7
PAK1 -0.046 0.19 -10000 0 -0.7 15 15
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS -0.044 0.17 -10000 0 -0.46 39 39
DNM1 -0.013 0.13 -10000 0 -0.66 13 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.071 0.19 -10000 0 -0.64 19 19
lamellipodium assembly -0.097 0.17 -10000 0 -0.59 25 25
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.035 0.13 -10000 0 -0.46 16 16
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 -0.026 0.16 -10000 0 -0.65 20 20
EPHB3 -0.006 0.11 -10000 0 -0.63 10 10
EPHB1 -0.085 0.22 -10000 0 -0.58 58 58
EPHB4 0.008 0.054 -10000 0 -0.71 2 2
mol:GDP -0.085 0.17 -10000 0 -0.61 21 21
Ephrin B/EPHB2 -0.075 0.17 -10000 0 -0.48 37 37
Ephrin B/EPHB3 -0.064 0.15 -10000 0 -0.45 31 31
JNK cascade -0.047 0.16 -10000 0 -0.48 23 23
Ephrin B/EPHB1 -0.1 0.19 -10000 0 -0.53 38 38
RAP1/GDP -0.076 0.15 -10000 0 -0.55 19 19
EFNB2 0.003 0.078 -10000 0 -0.64 5 5
EFNB3 -0.07 0.22 -10000 0 -0.64 44 44
EFNB1 -0.004 0.093 -10000 0 -0.55 10 10
Ephrin B2/EPHB1-2 -0.06 0.17 -10000 0 -0.52 25 25
RAP1B 0.002 0.072 -10000 0 -0.55 6 6
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.63 25 25
Rap1/GTP -0.099 0.18 -10000 0 -0.6 25 25
axon guidance -0.049 0.14 -10000 0 -0.45 38 38
MAPK3 -0.018 0.12 -10000 0 -0.42 15 15
MAPK1 -0.018 0.12 -10000 0 -0.44 10 10
Rac1/GDP -0.046 0.17 -10000 0 -0.58 17 17
actin cytoskeleton reorganization -0.076 0.14 -10000 0 -0.49 21 21
CDC42/GDP -0.046 0.17 -10000 0 -0.58 17 17
PI3K -0.007 0.05 -10000 0 -0.39 5 5
EFNA5 -0.028 0.16 -10000 0 -0.7 20 20
Ephrin B2/EPHB4 -0.008 0.06 -10000 0 -0.42 7 7
Ephrin B/EPHB2/Intersectin/N-WASP -0.025 0.14 -10000 0 -0.54 12 12
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.094 0.17 -10000 0 -0.61 20 20
PTK2 0.018 0.035 -10000 0 -10000 0 0
MAP4K4 -0.048 0.16 -10000 0 -0.48 23 23
SRC 0.012 0 -10000 0 -10000 0 0
KALRN -0.009 0.11 -10000 0 -0.61 12 12
Intersectin/N-WASP 0.016 0.029 -10000 0 -0.53 1 1
neuron projection morphogenesis -0.036 0.17 -10000 0 -0.51 19 19
MAP2K1 -0.026 0.12 -10000 0 -0.44 15 15
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.056 0.17 -10000 0 -0.52 22 22
cell migration -0.026 0.14 -10000 0 -0.5 15 15
NRAS 0.012 0 -10000 0 -10000 0 0
SYNJ1 -0.042 0.17 -10000 0 -0.46 37 37
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.16 0.24 -10000 0 -0.69 35 35
HRAS/GTP -0.1 0.18 -10000 0 -0.63 24 24
Ephrin B1/EPHB1-2 -0.064 0.17 -10000 0 -0.36 80 80
cell adhesion mediated by integrin 0.05 0.14 0.44 28 -10000 0 28
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.11 0.2 -10000 0 -0.69 24 24
RAC1-CDC42/GTP -0.1 0.18 -10000 0 -0.61 26 26
RASA1 0.01 0.038 -10000 0 -0.71 1 1
RAC1-CDC42/GDP -0.072 0.14 -10000 0 -0.57 15 15
ruffle organization -0.059 0.2 -10000 0 -0.64 21 21
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.046 0.18 -10000 0 -0.67 14 14
Ephrin B/EPHB2/KALRN -0.084 0.19 -10000 0 -0.51 43 43
ROCK1 0.003 0.081 -10000 0 -0.42 5 5
RAS family/GDP -0.074 0.14 -10000 0 -0.5 20 20
Rac1/GTP -0.1 0.19 -10000 0 -0.64 25 25
Ephrin B/EPHB1/Src/Paxillin -0.044 0.14 -10000 0 -0.49 19 19
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.17 0.27 -10000 0 -0.74 20 20
CRP -0.18 0.27 -10000 0 -0.76 24 24
cell cycle arrest -0.2 0.31 0.51 1 -0.77 41 42
TIMP1 -0.14 0.24 0.46 1 -0.75 15 16
IL6ST -0.017 0.13 -10000 0 -0.72 12 12
Rac1/GDP -0.073 0.18 -10000 0 -0.59 23 23
AP1 -0.005 0.12 -10000 0 -0.56 6 6
GAB2 0.003 0.082 -10000 0 -0.68 5 5
TNFSF11 -0.25 0.38 -10000 0 -0.99 48 48
HSP90B1 -0.004 0.054 -10000 0 -10000 0 0
GAB1 0.013 0.002 -10000 0 -10000 0 0
MAPK14 -0.048 0.17 -10000 0 -0.64 11 11
AKT1 0.042 0.035 -10000 0 -10000 0 0
FOXO1 0.045 0.045 -10000 0 -10000 0 0
MAP2K6 -0.071 0.18 -10000 0 -0.55 22 22
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.096 0.2 -10000 0 -0.63 22 22
MITF -0.058 0.16 0.3 1 -0.54 21 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.012 0 -10000 0 -10000 0 0
A2M -0.018 0.23 -10000 0 -1.5 8 8
CEBPB 0.016 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 -0.007 0.095 -10000 0 -0.62 4 4
STAT3 -0.21 0.32 0.52 1 -0.82 41 42
STAT1 -0.004 0.021 -10000 0 -10000 0 0
CEBPD -0.18 0.28 -10000 0 -0.78 25 25
PIK3CA 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0 -10000 0 -10000 0 0
JUN 0.006 0.062 -10000 0 -0.66 3 3
PIAS3/MITF -0.048 0.16 -10000 0 -0.56 16 16
MAPK11 -0.052 0.18 -10000 0 -0.66 12 12
STAT3 (dimer)/FOXO1 -0.12 0.26 0.55 1 -0.76 17 18
GRB2/SOS1/GAB family -0.053 0.15 -10000 0 -0.61 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.052 0.18 -10000 0 -0.52 32 32
GRB2 0.013 0.002 -10000 0 -10000 0 0
JAK2 0.012 0 -10000 0 -10000 0 0
LBP -0.18 0.29 0.46 1 -0.75 38 39
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.008 0.039 -10000 0 -0.71 1 1
MYC -0.18 0.29 -10000 0 -0.88 19 19
FGG -0.43 0.5 -10000 0 -1 132 132
macrophage differentiation -0.2 0.31 0.51 1 -0.77 41 42
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.068 0.17 -10000 0 -0.51 32 32
JUNB -0.17 0.27 -10000 0 -0.74 25 25
FOS -0.034 0.16 -10000 0 -0.62 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.065 0.16 0.33 1 -0.52 25 26
STAT1/PIAS1 -0.073 0.16 0.4 1 -0.49 25 26
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.038 -10000 0 -10000 0 0
STAT3 (dimer) -0.21 0.32 0.52 1 -0.84 37 38
PRKCD -0.12 0.23 -10000 0 -0.66 21 21
IL6R -0.014 0.13 -10000 0 -0.72 12 12
SOCS3 -0.032 0.17 -10000 0 -0.75 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.008 0.1 -10000 0 -0.46 16 16
Rac1/GTP -0.087 0.19 -10000 0 -0.62 23 23
HCK -0.012 0.13 -10000 0 -0.68 12 12
MAPKKK cascade 0.008 0.096 -10000 0 -0.72 4 4
bone resorption -0.23 0.35 -10000 0 -0.9 48 48
IRF1 -0.17 0.27 -10000 0 -0.72 24 24
mol:GDP -0.075 0.18 0.31 1 -0.54 32 33
SOS1 0.013 0.004 -10000 0 -10000 0 0
VAV1 -0.076 0.19 0.31 1 -0.58 28 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.03 0.16 -10000 0 -0.57 18 18
PTPN11 -0.004 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.068 0.19 -10000 0 -0.5 54 54
gp130 (dimer)/TYK2/TYK2/LMO4 -0.007 0.096 -10000 0 -0.46 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 -0.007 0.096 -10000 0 -0.46 15 15
IL6 -0.073 0.21 -10000 0 -0.61 46 46
PIAS3 0.012 0 -10000 0 -10000 0 0
PTPRE 0.003 0.11 -10000 0 -0.7 8 8
PIAS1 0.012 0 -10000 0 -10000 0 0
RAC1 0.011 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.046 0.14 0.29 1 -0.42 26 27
LMO4 0.002 0.063 -10000 0 -0.67 3 3
STAT3 (dimer)/PIAS3 -0.23 0.26 0.51 1 -0.77 36 37
MCL1 0.048 0.032 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.036 0.16 -10000 0 -0.5 24 24
IKBKB -0.008 0.083 -10000 0 -0.3 5 5
AKT1 -0.028 0.12 -10000 0 -0.29 22 22
IKBKG -0.009 0.092 -10000 0 -0.32 11 11
CALM1 -0.043 0.17 0.27 1 -0.65 20 21
PIK3CA 0.012 0 -10000 0 -10000 0 0
MAP3K1 -0.07 0.24 -10000 0 -0.66 36 36
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.19 0.27 1 -0.68 22 23
DOK1 0.008 0.054 -10000 0 -0.71 2 2
AP-1 -0.014 0.095 -10000 0 -0.29 17 17
LYN 0.008 0.054 -10000 0 -0.71 2 2
BLNK -0.006 0.11 -10000 0 -0.71 9 9
SHC1 0.009 0.042 -10000 0 -0.55 2 2
BCR complex -0.083 0.25 -10000 0 -0.62 56 56
CD22 -0.13 0.3 -10000 0 -0.97 30 30
CAMK2G -0.032 0.16 0.26 1 -0.6 19 20
CSNK2A1 0.012 0 -10000 0 -10000 0 0
INPP5D -0.004 0.1 -10000 0 -0.69 8 8
SHC/GRB2/SOS1 -0.078 0.19 -10000 0 -0.69 23 23
GO:0007205 -0.055 0.2 0.27 1 -0.7 22 23
SYK 0.002 0.085 -10000 0 -0.71 5 5
ELK1 -0.044 0.18 0.27 1 -0.67 20 21
NFATC1 -0.073 0.22 -10000 0 -0.61 38 38
B-cell antigen/BCR complex -0.083 0.25 -10000 0 -0.62 56 56
PAG1/CSK 0.01 0.059 -10000 0 -0.44 6 6
NFKBIB 0.007 0.029 -10000 0 -10000 0 0
HRAS -0.04 0.18 -10000 0 -0.67 19 19
NFKBIA 0.008 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.013 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.092 0.22 -10000 0 -0.76 24 24
mol:GDP -0.051 0.18 0.29 1 -0.65 22 23
PTEN 0.012 0 -10000 0 -10000 0 0
CD79B -0.031 0.16 -10000 0 -0.65 23 23
NF-kappa-B/RelA/I kappa B alpha 0.013 0.023 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.086 0.24 -10000 0 -0.63 41 41
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.056 0.2 0.28 1 -0.72 22 23
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.055 0.18 0.26 1 -0.63 22 23
CHUK -0.007 0.088 -10000 0 -0.3 9 9
IBTK 0.012 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.068 0.16 -10000 0 -0.57 26 26
PTPN6 -0.12 0.27 -10000 0 -0.89 30 30
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 0.009 0.033 -10000 0 -0.13 13 13
VAV2 -0.16 0.31 -10000 0 -0.86 44 44
ubiquitin-dependent protein catabolic process 0.011 0.028 -10000 0 -10000 0 0
BTK -0.049 0.23 0.41 1 -1.1 16 17
CD19 -0.16 0.34 -10000 0 -0.85 52 52
MAP4K1 -0.008 0.12 -10000 0 -0.69 10 10
CD72 0.003 0.078 -10000 0 -0.64 5 5
PAG1 0.002 0.08 -10000 0 -0.6 6 6
MAPK14 -0.05 0.2 -10000 0 -0.6 25 25
SH3BP5 0.01 0.03 -10000 0 -0.55 1 1
PIK3AP1 -0.061 0.23 -10000 0 -0.72 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.06 0.27 -10000 0 -0.69 37 37
RAF1 -0.031 0.16 -10000 0 -0.63 18 18
RasGAP/p62DOK/SHIP -0.097 0.23 -10000 0 -0.8 25 25
CD79A -0.086 0.24 -10000 0 -0.65 52 52
re-entry into mitotic cell cycle -0.014 0.095 -10000 0 -0.29 19 19
RASA1 0.01 0.038 -10000 0 -0.71 1 1
MAPK3 -0.011 0.13 -10000 0 -0.49 18 18
MAPK1 -0.011 0.13 -10000 0 -0.49 18 18
CD72/SHP1 -0.077 0.26 -10000 0 -0.83 29 29
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.05 0.2 -10000 0 -0.6 25 25
actin cytoskeleton organization -0.093 0.26 -10000 0 -0.7 39 39
NF-kappa-B/RelA 0.029 0.046 -10000 0 -10000 0 0
Calcineurin -0.047 0.13 -10000 0 -0.53 19 19
PI3K -0.13 0.22 -10000 0 -0.61 45 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.07 0.23 -10000 0 -0.81 22 22
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.096 0.31 -10000 0 -0.94 36 36
DAPP1 -0.14 0.34 -10000 0 -1.1 35 35
cytokine secretion -0.065 0.2 -10000 0 -0.55 38 38
mol:DAG -0.056 0.2 0.28 1 -0.72 22 23
PLCG2 0.002 0.085 -10000 0 -0.71 5 5
MAP2K1 -0.021 0.15 -10000 0 -0.56 18 18
B-cell antigen/BCR complex/FcgammaRIIB -0.11 0.25 -10000 0 -0.65 51 51
mol:PI-3-4-5-P3 -0.088 0.14 -10000 0 -0.41 41 41
ETS1 -0.023 0.14 -10000 0 -0.52 20 20
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.087 0.23 -10000 0 -0.8 23 23
B-cell antigen/BCR complex/LYN -0.098 0.28 -10000 0 -0.91 27 27
MALT1 0.009 0.042 -10000 0 -0.55 2 2
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.1 0.28 -10000 0 -0.78 39 39
B-cell antigen/BCR complex/LYN/SYK -0.12 0.28 -10000 0 -0.9 30 30
CARD11 -0.069 0.22 -10000 0 -0.61 37 37
FCGR2B -0.024 0.15 -10000 0 -0.66 19 19
PPP3CA 0.01 0.038 -10000 0 -0.71 1 1
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex 0.006 0.039 -10000 0 -10000 0 0
PTPRC -0.017 0.14 -10000 0 -0.71 14 14
PDPK1 -0.031 0.11 -10000 0 -0.3 19 19
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0.012 0 -10000 0 -10000 0 0
POU2F2 0.01 0.03 -10000 0 -0.12 10 10
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.008 0.11 -10000 0 -0.66 10 10
GNB1/GNG2 -0.034 0.064 -10000 0 -0.22 18 18
AKT1 0.008 0.096 -10000 0 -0.23 15 15
EGF -0.12 0.28 -10000 0 -0.69 68 68
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.021 0.092 -10000 0 -0.61 4 4
mol:Ca2+ -0.009 0.14 -10000 0 -0.33 37 37
LYN 0.026 0.073 -10000 0 -0.58 2 2
RhoA/GTP -0.022 0.043 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.009 0.15 -10000 0 -0.38 36 36
GNG2 0.008 0.054 -10000 0 -0.71 2 2
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.005 0.1 -10000 0 -0.51 9 9
G beta5/gamma2 -0.043 0.085 -10000 0 -0.3 18 18
PRKCH -0.012 0.15 -10000 0 -0.37 37 37
DNM1 -0.013 0.13 -10000 0 -0.66 13 13
TXA2/TP beta/beta Arrestin3 -0.011 0.048 -10000 0 -0.25 12 12
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.014 0.13 -10000 0 -0.64 14 14
G12 family/GTP -0.053 0.1 -10000 0 -0.32 35 35
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.008 0.054 -10000 0 -0.71 2 2
RhoA/GTP/ROCK1 0.01 0.008 -10000 0 -10000 0 0
mol:GDP -0.002 0.096 0.42 6 -10000 0 6
mol:NADP -0.044 0.18 -10000 0 -0.59 33 33
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.034 0.18 -10000 0 -0.7 23 23
mol:IP3 -0.018 0.17 -10000 0 -0.42 37 37
cell morphogenesis 0.008 0.008 -10000 0 -10000 0 0
PLCB2 -0.037 0.22 -10000 0 -0.58 37 37
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.033 0.15 -10000 0 -0.55 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.018 0.098 -10000 0 -0.61 4 4
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.002 0.085 -10000 0 -0.71 5 5
PRKCB1 -0.018 0.16 -10000 0 -0.4 39 39
GNAQ 0.01 0.038 -10000 0 -0.71 1 1
mol:L-citrulline -0.044 0.18 -10000 0 -0.59 33 33
TXA2/TXA2-R family -0.033 0.22 -10000 0 -0.56 37 37
LCK 0.021 0.091 -10000 0 -0.55 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.014 0.07 -10000 0 -0.65 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.029 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.014 0.069 -10000 0 -0.65 2 2
MAPK14 0.005 0.11 -10000 0 -0.27 19 19
TGM2/GTP -0.025 0.19 -10000 0 -0.48 38 38
MAPK11 0.003 0.11 -10000 0 -0.28 19 19
ARHGEF1 0.003 0.083 -10000 0 -0.21 5 5
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.015 0.16 -10000 0 -0.41 37 37
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.009 0.14 -10000 0 -0.34 35 35
cAMP biosynthetic process -0.019 0.16 -10000 0 -0.39 37 37
Gq family/GTP/EBP50 -0.005 0.1 -10000 0 -0.41 11 11
actin cytoskeleton reorganization 0.008 0.008 -10000 0 -10000 0 0
SRC 0.028 0.068 -10000 0 -0.58 2 2
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.12 -10000 0 -0.44 12 12
VCAM1 -0.011 0.14 -10000 0 -0.34 38 38
TP beta/Gq family/GDP/G beta5/gamma2 0.005 0.1 -10000 0 -0.51 9 9
platelet activation 0.006 0.14 -10000 0 -0.32 34 34
PGI2/IP -0.001 0.065 -10000 0 -0.54 5 5
PRKACA 0.002 0.082 -10000 0 -0.38 12 12
Gq family/GDP/G beta5/gamma2 0.004 0.1 -10000 0 -0.49 9 9
TXA2/TP beta/beta Arrestin2 -0.019 0.099 -10000 0 -0.61 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.086 -10000 0 -0.38 12 12
mol:DAG -0.022 0.18 -10000 0 -0.45 39 39
EGFR -0.036 0.17 -10000 0 -0.62 27 27
TXA2/TP alpha -0.033 0.21 -10000 0 -0.54 37 37
Gq family/GTP -0.029 0.1 -10000 0 -0.3 36 36
YES1 0.027 0.071 -10000 0 -0.58 2 2
GNAI2/GTP -0.014 0.07 -10000 0 -0.71 2 2
PGD2/DP -0.012 0.096 -10000 0 -0.48 14 14
SLC9A3R1 0.007 0.051 -10000 0 -0.55 3 3
FYN 0.025 0.078 -10000 0 -0.56 3 3
mol:NO -0.044 0.18 -10000 0 -0.59 33 33
GNA15 0 0.093 -10000 0 -0.71 6 6
PGK/cGMP -0.062 0.16 -10000 0 -0.41 54 54
RhoA/GDP 0.012 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.024 0.096 -10000 0 -0.74 3 3
NOS3 -0.044 0.18 -10000 0 -0.59 33 33
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.39 38 38
PRKCB -0.016 0.16 -10000 0 -0.4 38 38
PRKCE -0.011 0.15 -10000 0 -0.38 37 37
PRKCD -0.014 0.16 -10000 0 -0.39 35 35
PRKCG -0.026 0.17 -10000 0 -0.42 41 41
muscle contraction -0.027 0.2 -10000 0 -0.53 37 37
PRKCZ -0.011 0.15 -10000 0 -0.37 36 36
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.016 0.082 -10000 0 -0.84 2 2
PRKCQ -0.026 0.17 -10000 0 -0.42 39 39
MAPKKK cascade -0.029 0.2 -10000 0 -0.51 37 37
SELE -0.017 0.15 -10000 0 -0.35 40 40
TP beta/GNAI2/GDP/G beta/gamma -0.016 0.076 -10000 0 -0.64 3 3
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.047 0.2 -10000 0 -0.71 29 29
chemotaxis -0.039 0.23 -10000 0 -0.62 37 37
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 0.006 0.066 -10000 0 -0.71 3 3
Rac1/GTP 0.006 0.005 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.059 0.18 -9999 0 -0.48 54 54
CRKL -0.023 0.12 -9999 0 -0.47 5 5
mol:PIP3 -0.017 0.006 -9999 0 -10000 0 0
AKT1 0.002 0.004 -9999 0 -10000 0 0
PTK2B 0.004 0.076 -9999 0 -0.71 4 4
RAPGEF1 -0.015 0.12 -9999 0 -0.5 3 3
RANBP10 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.091 0.18 -9999 0 -0.48 51 51
MAP3K5 -0.013 0.13 -9999 0 -0.52 7 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.059 0.18 -9999 0 -0.44 52 52
AP1 -0.038 0.13 -9999 0 -0.44 28 28
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.009 0.042 -9999 0 -0.55 2 2
apoptosis -0.036 0.17 -9999 0 -0.84 13 13
STAT3 (dimer) -0.026 0.14 -9999 0 -0.59 6 6
GAB1/CRKL/SHP2/PI3K -0.044 0.095 -9999 0 -0.53 2 2
INPP5D -0.004 0.1 -9999 0 -0.69 8 8
CBL/CRK -0.014 0.12 -9999 0 -0.46 4 4
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.01 0.03 -9999 0 -0.55 1 1
PTEN 0.012 0 -9999 0 -10000 0 0
ELK1 -0.035 0.084 -9999 0 -0.23 54 54
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.033 0.071 -9999 0 -0.35 4 4
PAK1 0.009 0.004 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.091 0.18 -9999 0 -0.48 51 51
HRAS -0.07 0.24 -9999 0 -0.7 37 37
DOCK1 -0.016 0.12 -9999 0 -0.52 4 4
GAB1 -0.03 0.13 -9999 0 -0.34 38 38
CRK -0.022 0.12 -9999 0 -0.49 4 4
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.1 0.23 -9999 0 -0.64 50 50
JUN 0.006 0.062 -9999 0 -0.66 3 3
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.045 0.12 -9999 0 -0.32 51 51
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell morphogenesis -0.002 0.14 -9999 0 -0.63 3 3
GRB2/SHC -0.027 0.11 -9999 0 -0.45 5 5
FOS -0.034 0.16 -9999 0 -0.62 26 26
GLMN 0 0.011 -9999 0 -10000 0 0
cell motility -0.035 0.084 -9999 0 -0.23 54 54
HGF/MET/MUC20 -0.093 0.19 -9999 0 -0.44 74 74
cell migration -0.027 0.11 -9999 0 -0.44 5 5
GRB2 0.012 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
MET/RANBP10 -0.059 0.18 -9999 0 -0.48 54 54
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.034 0.14 -9999 0 -0.62 6 6
MET/MUC20 -0.067 0.18 -9999 0 -0.49 54 54
RAP1B -0.012 0.12 -9999 0 -0.52 2 2
RAP1A -0.007 0.11 -9999 0 -0.52 2 2
HGF/MET/RANBP9 -0.091 0.18 -9999 0 -0.48 51 51
RAF1 -0.059 0.22 -9999 0 -0.65 37 37
STAT3 -0.026 0.14 -9999 0 -0.6 6 6
cell proliferation -0.036 0.18 -9999 0 -0.47 38 38
RPS6KB1 -0.01 0.048 -9999 0 -0.22 1 1
MAPK3 -0.037 0.076 -9999 0 -0.23 35 35
MAPK1 -0.037 0.076 -9999 0 -10000 0 0
RANBP9 0.012 0 -9999 0 -10000 0 0
MAPK8 0.006 0.11 -9999 0 -0.42 6 6
SRC -0.024 0.14 -9999 0 -0.58 6 6
PI3K -0.026 0.11 -9999 0 -0.43 4 4
MET/Glomulin -0.057 0.16 -9999 0 -0.44 54 54
SOS1 0.012 0 -9999 0 -10000 0 0
MAP2K1 -0.047 0.2 -9999 0 -0.59 37 37
MET -0.09 0.24 -9999 0 -0.65 54 54
MAP4K1 -0.02 0.13 -9999 0 -0.5 8 8
PTK2 0.012 0 -9999 0 -10000 0 0
MAP2K2 -0.047 0.2 -9999 0 -0.59 37 37
BAD 0.007 0.021 -9999 0 -0.39 1 1
MAP2K4 -0.005 0.12 -9999 0 -0.47 7 7
SHP2/GRB2/SOS1/GAB1 -0.065 0.14 -9999 0 -0.44 37 37
INPPL1 0.012 0 -9999 0 -10000 0 0
PXN 0.012 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0.03 -9999 0 -0.55 1 1
HGS -0.036 0.12 -9999 0 -0.32 38 38
PLCgamma1/PKC 0.008 0.022 -9999 0 -0.4 1 1
HGF -0.035 0.17 -9999 0 -0.66 25 25
RASA1 0.01 0.038 -9999 0 -0.71 1 1
NCK1 0.012 0 -9999 0 -10000 0 0
PTPRJ 0.012 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.026 0.11 -9999 0 -0.45 4 4
PDPK1 -0.006 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.1 0.21 -9999 0 -0.53 52 52
Nectin adhesion 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
PDGFRB 0.008 0.054 -9999 0 -0.71 2 2
alphaV beta3 Integrin -0.036 0.15 -9999 0 -0.43 42 42
PTK2 -0.07 0.16 -9999 0 -0.5 31 31
positive regulation of JNK cascade -0.033 0.09 -9999 0 -0.32 30 30
CDC42/GDP -0.003 0.14 -9999 0 -0.44 29 29
Rac1/GDP -0.001 0.14 -9999 0 -0.43 29 29
RAP1B 0.002 0.072 -9999 0 -0.55 6 6
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.03 -9999 0 -0.55 1 1
CDC42/GTP -0.041 0.11 -9999 0 -0.39 30 30
nectin-3/I-afadin -0.037 0.16 -9999 0 -0.5 37 37
RAPGEF1 -0.01 0.15 -9999 0 -0.48 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.021 0.17 -9999 0 -0.56 29 29
PDGFB-D/PDGFRB 0.008 0.054 -9999 0 -0.71 2 2
TLN1 0.004 0.077 -9999 0 -0.39 3 3
Rap1/GTP -0.037 0.097 -9999 0 -0.34 29 29
IQGAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.018 0.041 -9999 0 -0.3 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.037 0.16 -9999 0 -0.5 37 37
PVR 0.012 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.013 0.17 -9999 0 -0.54 29 29
MLLT4 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
PI3K -0.039 0.12 -9999 0 -0.77 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.1 -9999 0 -0.47 16 16
positive regulation of lamellipodium assembly -0.035 0.096 -9999 0 -0.34 29 29
PVRL1 -0.018 0.14 -9999 0 -0.64 16 16
PVRL3 -0.06 0.21 -9999 0 -0.67 37 37
PVRL2 0.01 0.03 -9999 0 -0.55 1 1
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.002 0.085 -9999 0 -0.71 5 5
CLDN1 -0.061 0.21 -9999 0 -0.66 38 38
JAM-A/CLDN1 -0.056 0.19 -9999 0 -0.48 50 50
SRC -0.065 0.17 -9999 0 -0.62 29 29
ITGB3 -0.06 0.2 -9999 0 -0.59 42 42
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.1 -9999 0 -0.47 16 16
FARP2 -0.017 0.16 -9999 0 -0.52 30 30
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.045 0.13 -9999 0 -0.45 29 29
nectin-1/I-afadin -0.004 0.1 -9999 0 -0.47 16 16
nectin-2/I-afadin 0.017 0.022 -9999 0 -0.39 1 1
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.063 0.15 -9999 0 -0.45 38 38
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.01 0.038 -9999 0 -0.71 1 1
positive regulation of filopodium formation -0.033 0.09 -9999 0 -0.32 30 30
alphaV/beta3 Integrin/Talin -0.02 0.13 -9999 0 -0.59 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.017 0.022 -9999 0 -0.39 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.017 0.022 -9999 0 -0.39 1 1
PIP5K1C -0.002 0.079 -9999 0 -0.43 2 2
VAV2 -0.02 0.17 -9999 0 -0.55 30 30
RAP1/GDP -0.042 0.11 -9999 0 -0.4 29 29
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.046 0.13 -9999 0 -0.45 29 29
nectin-3(dimer)/I-afadin/I-afadin -0.037 0.16 -9999 0 -0.5 37 37
Rac1/GTP -0.043 0.12 -9999 0 -0.42 29 29
PTPRM -0.012 0.087 -9999 0 -0.27 31 31
E-cadherin/beta catenin/alpha catenin -0.021 0.089 -9999 0 -0.74 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
Reelin 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
CDK5R1/CDK5 0.01 0.056 -9999 0 -0.41 6 6
VLDLR -0.013 0.13 -9999 0 -0.71 12 12
CRKL 0.01 0.03 -9999 0 -0.55 1 1
LRPAP1 0.01 0.038 -9999 0 -0.71 1 1
FYN 0.006 0.066 -9999 0 -0.71 3 3
ITGA3 -0.018 0.14 -9999 0 -0.7 15 15
RELN/VLDLR/Fyn -0.081 0.18 -9999 0 -0.44 66 66
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.015 0.078 -9999 0 -0.77 1 1
AKT1 -0.023 0.12 -9999 0 -0.57 4 4
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.01 0.096 -9999 0 -0.55 11 11
RELN/LRP8/DAB1 -0.06 0.17 -9999 0 -0.46 36 36
LRPAP1/LRP8 0.003 0.083 -9999 0 -0.45 11 11
RELN/LRP8/DAB1/Fyn -0.074 0.16 -9999 0 -0.45 37 37
DAB1/alpha3/beta1 Integrin -0.091 0.18 -9999 0 -0.63 21 21
long-term memory -0.14 0.23 -9999 0 -0.68 29 29
DAB1/LIS1 -0.079 0.16 -9999 0 -0.65 10 10
DAB1/CRLK/C3G -0.076 0.16 -9999 0 -0.66 10 10
PIK3CA 0.012 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.08 0.16 -9999 0 -0.66 10 10
ARHGEF2 0.01 0.03 -9999 0 -0.55 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.17 0.28 -9999 0 -0.6 105 105
CDK5R1 0.002 0.076 -9999 0 -0.57 6 6
RELN -0.091 0.24 -9999 0 -0.63 57 57
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.077 0.17 -9999 0 -0.49 34 34
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 -9999 0 -0.7 29 29
MAPK8 0.01 0.038 -9999 0 -0.71 1 1
RELN/VLDLR/DAB1 -0.065 0.18 -9999 0 -0.45 46 46
ITGB1 0.01 0.03 -9999 0 -0.55 1 1
MAP1B -0.08 0.21 -9999 0 -0.54 44 44
RELN/LRP8 -0.074 0.16 -9999 0 -0.47 34 34
GRIN2B/RELN/LRP8/DAB1/Fyn -0.074 0.16 -9999 0 -0.45 37 37
PI3K 0.018 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.006 0.11 -9999 0 -0.54 15 15
RAP1A -0.033 0.16 -9999 0 -0.61 10 10
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 -0.012 0.13 -9999 0 -0.68 12 12
CRLK/C3G 0.017 0.022 -9999 0 -0.39 1 1
GRIN2B 0 0 -9999 0 -10000 0 0
NCK2 0.01 0.038 -9999 0 -0.71 1 1
neuron differentiation -0.014 0.12 -9999 0 -0.52 9 9
neuron adhesion -0.034 0.18 -9999 0 -0.6 16 16
LRP8 -0.006 0.1 -9999 0 -0.61 10 10
GSK3B -0.015 0.11 -9999 0 -0.54 4 4
RELN/VLDLR/DAB1/Fyn -0.078 0.16 -9999 0 -0.46 40 40
MAP3K11 0.01 0.038 -9999 0 -0.71 1 1
RELN/VLDLR/DAB1/P13K -0.032 0.12 -9999 0 -0.34 39 39
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.057 0.19 -9999 0 -0.56 41 41
neuron migration -0.02 0.16 -9999 0 -0.56 9 9
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.12 -9999 0 -0.52 9 9
RELN/VLDLR -0.056 0.18 -9999 0 -0.46 42 42
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.047 0.15 -10000 0 -0.43 34 34
regulation of S phase of mitotic cell cycle -0.018 0.1 -10000 0 -0.3 33 33
GNAO1 -0.033 0.17 -10000 0 -0.65 24 24
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.011 0.07 -10000 0 -0.42 10 10
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.018 0.13 -10000 0 -0.44 5 5
T-DHT/AR -0.077 0.19 -10000 0 -0.47 62 62
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.005 24 24
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.095 -10000 0 -0.66 7 7
mol:GDP -0.07 0.16 -10000 0 -0.54 33 33
cell proliferation -0.015 0.15 -10000 0 -0.57 9 9
PIK3CA 0.012 0 -10000 0 -10000 0 0
FOS -0.019 0.18 -10000 0 -0.84 12 12
mol:Ca2+ -0.018 0.031 -10000 0 -0.097 31 31
MAPK3 -0.016 0.14 -10000 0 -0.56 6 6
MAPK1 -0.001 0.073 -10000 0 -0.29 6 6
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 26 26
cAMP biosynthetic process 0.005 0.074 -10000 0 -0.39 10 10
GNG2 0.008 0.054 -10000 0 -0.71 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 26 26
HRAS/GTP -0.057 0.12 -10000 0 -0.38 33 33
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 26 26
PI3K 0.001 0.004 -10000 0 -10000 0 0
apoptosis 0.008 0.13 0.5 12 -10000 0 12
T-DHT/AR/PELP1 -0.07 0.16 -10000 0 -0.4 62 62
HRAS/GDP -0.065 0.15 -10000 0 -0.5 33 33
CREB1 -0.01 0.14 -10000 0 -0.54 12 12
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.1 0.25 -10000 0 -0.63 62 62
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 -0.025 0.13 -10000 0 -0.43 5 5
RAC1-CDC42/GDP -0.062 0.15 -10000 0 -0.48 33 33
T-DHT/AR/PELP1/Src -0.063 0.14 -10000 0 -0.41 35 35
MAP2K2 -0.018 0.13 -10000 0 -0.44 5 5
T-DHT/AR/PELP1/Src/PI3K -0.018 0.1 -10000 0 -0.3 33 33
GNAZ -0.068 0.22 -10000 0 -0.64 43 43
SHBG -0.008 0.11 -10000 0 -0.64 10 10
Gi family/GNB1/GNG2/GDP -0.027 0.14 -10000 0 -0.49 17 17
mol:T-DHT 0 0.001 0.002 1 -0.002 18 19
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 -0.006 0.094 -10000 0 -0.53 11 11
Gi family/GTP -0.051 0.14 -10000 0 -0.41 31 31
CDC42 0.012 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0.081 -10000 0 -0.76 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.051 0.18 0.62 20 -0.33 1 21
IL27/IL27R/JAK1 -0.098 0.25 -10000 0 -1.1 14 14
TBX21 -0.07 0.24 -10000 0 -0.66 36 36
IL12B -0.041 0.18 -10000 0 -0.68 26 26
IL12A -0.013 0.1 -10000 0 -0.48 16 16
IL6ST -0.015 0.13 -10000 0 -0.72 12 12
IL27RA/JAK1 -0.029 0.23 -10000 0 -1.4 10 10
IL27 -0.024 0.14 -10000 0 -0.62 18 18
TYK2 0.011 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.042 0.15 -10000 0 -0.8 2 2
T-helper 2 cell differentiation 0.051 0.18 0.62 20 -0.33 1 21
T cell proliferation during immune response 0.051 0.18 0.62 20 -0.33 1 21
MAPKKK cascade -0.051 0.18 0.33 1 -0.62 20 21
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.012 0.002 -10000 0 -10000 0 0
IL12RB1 -0.014 0.13 -10000 0 -0.7 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.089 0.26 -10000 0 -0.69 38 38
IL27/IL27R/JAK2/TYK2 -0.051 0.19 0.33 1 -0.63 20 21
positive regulation of T cell mediated cytotoxicity -0.051 0.18 0.33 1 -0.62 20 21
STAT1 (dimer) -0.13 0.28 -10000 0 -0.95 25 25
JAK2 0.011 0.008 -10000 0 -10000 0 0
JAK1 0.01 0.038 -10000 0 -0.71 1 1
STAT2 (dimer) -0.043 0.18 -10000 0 -0.63 17 17
T cell proliferation -0.088 0.22 -10000 0 -0.63 31 31
IL12/IL12R/TYK2/JAK2 -0.085 0.25 -10000 0 -0.91 22 22
IL17A -0.047 0.15 -10000 0 -0.8 2 2
mast cell activation 0.051 0.18 0.62 20 -0.33 1 21
IFNG -0.019 0.05 0.082 4 -0.11 61 65
T cell differentiation -0.006 0.009 0.019 4 -0.023 54 58
STAT3 (dimer) -0.043 0.18 -10000 0 -0.63 17 17
STAT5A (dimer) -0.044 0.18 -10000 0 -0.65 17 17
STAT4 (dimer) -0.054 0.2 -10000 0 -0.65 21 21
STAT4 -0.01 0.12 -10000 0 -0.7 11 11
T cell activation -0.004 0.023 0.13 10 -10000 0 10
IL27R/JAK2/TYK2 -0.051 0.22 -10000 0 -1.1 12 12
GATA3 0.009 0.1 -10000 0 -1.4 1 1
IL18 -0.015 0.11 -10000 0 -0.53 16 16
positive regulation of mast cell cytokine production -0.042 0.17 -10000 0 -0.62 17 17
IL27/EBI3 -0.039 0.15 -10000 0 -0.5 32 32
IL27RA -0.041 0.24 -10000 0 -1.4 10 10
IL6 -0.075 0.22 -10000 0 -0.62 46 46
STAT5A 0.01 0.038 -10000 0 -0.71 1 1
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.013 0.093 0.49 10 -10000 0 10
IL1B -0.038 0.15 -10000 0 -0.49 34 34
EBI3 -0.02 0.14 -10000 0 -0.7 15 15
TNF -0.044 0.16 -10000 0 -0.49 38 38
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.018 0.084 -9999 0 -0.48 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.071 0.12 -9999 0 -0.45 9 9
AP1 -0.11 0.17 -9999 0 -0.6 14 14
mol:PIP3 -0.1 0.16 -9999 0 -0.53 18 18
AKT1 0.035 0.07 -9999 0 -0.46 2 2
PTK2B -0.009 0.084 -9999 0 -0.38 10 10
RHOA 0.021 0.041 -9999 0 -10000 0 0
PIK3CB 0.008 0.054 -9999 0 -0.71 2 2
mol:Ca2+ -0.055 0.15 -9999 0 -0.49 12 12
MAGI3 0.004 0.072 -9999 0 -0.67 4 4
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.068 0.16 -9999 0 -0.39 47 47
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.03 0.13 -9999 0 -0.43 17 17
NF kappa B1 p50/RelA -0.09 0.15 -9999 0 -0.52 14 14
endothelial cell migration -0.008 0.15 -9999 0 -0.67 16 16
ADCY4 -0.021 0.15 -9999 0 -0.57 15 15
ADCY5 -0.052 0.18 -9999 0 -0.54 30 30
ADCY6 -0.02 0.14 -9999 0 -0.54 15 15
ADCY7 -0.021 0.14 -9999 0 -0.53 16 16
ADCY1 -0.03 0.15 -9999 0 -0.52 20 20
ADCY2 -0.049 0.17 -9999 0 -0.52 29 29
ADCY3 -0.02 0.14 -9999 0 -0.54 15 15
ADCY8 -0.029 0.15 -9999 0 -0.54 18 18
ADCY9 -0.023 0.15 -9999 0 -0.55 17 17
GSK3B -0.002 0.08 -9999 0 -0.41 6 6
arachidonic acid secretion -0.015 0.14 -9999 0 -0.51 16 16
GNG2 0.008 0.054 -9999 0 -0.71 2 2
TRIP6 0.003 0.092 -9999 0 -0.48 12 12
GNAO1 -0.023 0.14 -9999 0 -0.45 31 31
HRAS 0.012 0 -9999 0 -10000 0 0
NFKBIA -0.05 0.16 -9999 0 -0.5 13 13
GAB1 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.03 0.16 -9999 0 -0.95 11 11
JUN 0.006 0.062 -9999 0 -0.66 3 3
LPA/LPA2/NHERF2 -0.012 0.065 -9999 0 -0.43 8 8
TIAM1 -0.036 0.2 -9999 0 -1.1 11 11
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.056 0.15 -9999 0 -0.5 12 12
PLCB3 0.014 0.063 -9999 0 -0.41 6 6
FOS -0.034 0.16 -9999 0 -0.62 26 26
positive regulation of mitosis -0.015 0.14 -9999 0 -0.51 16 16
LPA/LPA1-2-3 -0.1 0.17 -9999 0 -0.44 47 47
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.004 0.076 -9999 0 -0.71 4 4
stress fiber formation -0.027 0.11 -9999 0 -0.41 10 10
GNAZ -0.045 0.17 -9999 0 -0.41 56 56
EGFR/PI3K-beta/Gab1 -0.1 0.16 -9999 0 -0.56 18 18
positive regulation of dendritic cell cytokine production -0.1 0.17 -9999 0 -0.44 47 47
LPA/LPA2/MAGI-3 -0.008 0.051 -9999 0 -0.41 5 5
ARHGEF1 0.017 0.082 -9999 0 -0.41 8 8
GNAI2 0.006 0.089 -9999 0 -0.46 8 8
GNAI3 0.006 0.089 -9999 0 -0.46 8 8
GNAI1 -0.002 0.11 -9999 0 -0.49 14 14
LPA/LPA3 -0.12 0.2 -9999 0 -0.46 90 90
LPA/LPA2 -0.005 0.029 -9999 0 -0.4 1 1
LPA/LPA1 -0.022 0.098 -9999 0 -0.44 16 16
HB-EGF/EGFR -0.06 0.18 -9999 0 -0.51 35 35
HBEGF -0.04 0.17 -9999 0 -0.48 42 42
mol:DAG -0.056 0.15 -9999 0 -0.5 12 12
cAMP biosynthetic process -0.035 0.16 -9999 0 -0.55 21 21
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
LYN -0.052 0.17 -9999 0 -0.52 15 15
GNAQ -0.062 0.15 -9999 0 -0.38 42 42
LPAR2 0.01 0.03 -9999 0 -0.55 1 1
LPAR3 -0.15 0.28 -9999 0 -0.62 90 90
LPAR1 -0.005 0.11 -9999 0 -0.69 8 8
IL8 -0.11 0.21 -9999 0 -0.5 50 50
PTK2 -0.071 0.17 -9999 0 -0.41 47 47
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.069 0.16 -9999 0 -0.39 47 47
EGFR -0.037 0.17 -9999 0 -0.62 27 27
PLCG1 -0.071 0.16 -9999 0 -0.41 49 49
PLD2 -0.071 0.17 -9999 0 -0.41 47 47
G12/G13 -0.016 0.075 -9999 0 -0.46 6 6
PI3K-beta -0.016 0.066 -9999 0 -0.54 2 2
cell migration -0.042 0.073 -9999 0 -0.28 11 11
SLC9A3R2 -0.002 0.098 -9999 0 -0.69 7 7
PXN -0.027 0.11 -9999 0 -0.42 10 10
HRAS/GTP -0.016 0.14 -9999 0 -0.53 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.058 0.2 -9999 0 -0.64 38 38
PRKCE 0.01 0.038 -9999 0 -0.71 1 1
PRKCD -0.047 0.15 -9999 0 -0.49 10 10
Gi(beta/gamma) -0.016 0.14 -9999 0 -0.51 17 17
mol:LPA -0.002 0.034 -9999 0 -0.21 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.09 0.15 -9999 0 -0.54 13 13
MAPKKK cascade -0.015 0.14 -9999 0 -0.51 16 16
contractile ring contraction involved in cytokinesis 0.021 0.041 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.095 0.2 -9999 0 -0.45 63 63
GNA15 -0.068 0.15 -9999 0 -0.39 46 46
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.032 0.14 -9999 0 -0.46 15 15
GNA11 -0.064 0.15 -9999 0 -0.37 45 45
Rac1/GTP -0.032 0.18 -9999 0 -1 11 11
MMP2 -0.008 0.15 -9999 0 -0.67 16 16
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.05 0.12 -10000 0 -0.42 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.051 0.19 -10000 0 -0.58 27 27
AKT1 -0.038 0.21 -10000 0 -0.87 20 20
PIK3CA 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.042 0.22 -10000 0 -0.89 20 20
mol:Ca2+ -0.056 0.21 -10000 0 -0.55 42 42
IGF1R 0.001 0.087 -10000 0 -0.66 6 6
E2/ER alpha (dimer)/Striatin -0.057 0.14 -10000 0 -0.39 52 52
SHC1 0.009 0.042 -10000 0 -0.55 2 2
apoptosis 0.035 0.2 0.82 20 -10000 0 20
RhoA/GTP -0.039 0.098 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.077 0.16 -10000 0 -0.57 26 26
regulation of stress fiber formation -0.002 0.11 0.52 5 -10000 0 5
E2/ERA-ERB (dimer) -0.058 0.14 -10000 0 -0.39 52 52
KRAS 0.01 0.03 -10000 0 -0.55 1 1
G13/GTP -0.036 0.13 -10000 0 -0.35 50 50
pseudopodium formation 0.002 0.11 -10000 0 -0.52 5 5
E2/ER alpha (dimer)/PELP1 -0.054 0.14 -10000 0 -0.38 50 50
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.008 0.054 -10000 0 -0.71 2 2
GNAO1 -0.033 0.17 -10000 0 -0.65 24 24
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.045 0.18 -10000 0 -0.6 26 26
E2/ER beta (dimer) 0.005 0.046 -10000 0 -0.49 3 3
mol:GDP -0.049 0.13 -10000 0 -0.49 22 22
mol:NADP -0.045 0.18 -10000 0 -0.6 26 26
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.06 0.22 -10000 0 -0.58 42 42
IGF-1R heterotetramer 0.001 0.087 -10000 0 -0.65 6 6
PLCB1 -0.059 0.21 -10000 0 -0.54 47 47
PLCB2 -0.045 0.2 -10000 0 -0.57 36 36
IGF1 -0.034 0.17 -10000 0 -0.64 25 25
mol:L-citrulline -0.045 0.18 -10000 0 -0.6 26 26
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.07 0.19 -10000 0 -0.86 16 16
JNK cascade 0.005 0.046 -10000 0 -0.49 3 3
BCAR1 0.004 0.076 -10000 0 -0.71 4 4
ESR2 0.006 0.062 -10000 0 -0.66 3 3
GNAQ 0.01 0.038 -10000 0 -0.71 1 1
ESR1 -0.076 0.22 -10000 0 -0.61 50 50
Gq family/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.62 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.004 0.09 -10000 0 -0.34 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.075 0.16 -10000 0 -0.58 23 23
GNAZ -0.068 0.22 -10000 0 -0.64 43 43
E2/ER alpha (dimer) -0.057 0.16 -10000 0 -0.46 50 50
STRN 0.008 0.054 -10000 0 -0.71 2 2
GNAL -0.03 0.16 -10000 0 -0.62 23 23
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.008 0.062 -10000 0 -0.42 7 7
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.095 -10000 0 -0.66 7 7
HBEGF -0.054 0.19 -10000 0 -0.63 19 19
cAMP biosynthetic process -0.067 0.14 -10000 0 -0.42 31 31
SRC -0.042 0.18 -10000 0 -0.56 24 24
PI3K 0.018 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.045 0.12 -10000 0 -0.44 22 22
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.077 0.14 -10000 0 -0.58 15 15
Gs family/GTP -0.068 0.14 -10000 0 -0.43 31 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.017 -10000 0 -10000 0 0
vasodilation -0.042 0.17 -10000 0 -0.56 26 26
mol:DAG -0.06 0.22 -10000 0 -0.58 42 42
Gs family/GDP/Gbeta gamma -0.057 0.13 -10000 0 -0.45 23 23
MSN 0 0.12 -10000 0 -0.57 5 5
Gq family/GTP -0.044 0.18 -10000 0 -0.58 31 31
mol:PI-3-4-5-P3 -0.039 0.21 -10000 0 -0.85 20 20
NRAS 0.012 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.042 0.17 0.56 26 -10000 0 26
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
RhoA/GDP -0.045 0.12 -10000 0 -0.45 22 22
NOS3 -0.048 0.2 -10000 0 -0.64 26 26
GNA11 0.006 0.066 -10000 0 -0.71 3 3
MAPKKK cascade -0.027 0.18 -10000 0 -0.65 22 22
E2/ER alpha (dimer)/PELP1/Src -0.078 0.17 -10000 0 -0.58 27 27
ruffle organization 0.002 0.11 -10000 0 -0.52 5 5
ROCK2 -0.003 0.11 -10000 0 -0.56 1 1
GNA14 -0.047 0.2 -10000 0 -0.71 29 29
GNA15 0 0.093 -10000 0 -0.71 6 6
GNA13 0.012 0 -10000 0 -10000 0 0
MMP9 -0.067 0.2 -10000 0 -0.64 22 22
MMP2 -0.042 0.19 -10000 0 -0.7 16 16
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.026 0.11 -10000 0 -0.71 5 5
HDAC1 0.01 0.01 -10000 0 -10000 0 0
AES 0.012 0.004 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 -0.002 0.09 -10000 0 -0.59 8 8
LRP6/FZD1 0.01 0.063 -10000 0 -0.46 6 6
TLE1 0.01 0.038 -10000 0 -0.7 1 1
AP1 -0.029 0.13 -10000 0 -0.38 31 31
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.012 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.002 0.09 -10000 0 -0.46 4 4
NICD/RBPSUH -0.009 0.085 -10000 0 -0.7 5 5
WIF1 -0.24 0.32 -10000 0 -0.63 138 138
NOTCH1 -0.011 0.089 -10000 0 -0.75 5 5
PSENEN 0.007 0.051 -10000 0 -0.55 3 3
KREMEN2 -0.075 0.21 -10000 0 -0.58 52 52
DKK1 -0.27 0.32 -10000 0 -0.62 156 156
beta catenin/beta TrCP1 0.023 0.062 -10000 0 -10000 0 0
APH1B 0.01 0.038 -10000 0 -0.71 1 1
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.039 0.26 2 -10000 0 2
CtBP/CBP/TCF1/TLE1/AES -0.014 0.088 0.28 2 -10000 0 2
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.034 0.16 -10000 0 -0.62 26 26
JUN 0.006 0.062 -10000 0 -0.66 3 3
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
CTNNB1 0.017 0.065 0.27 1 -10000 0 1
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.078 0.18 -10000 0 -0.54 31 31
HNF1A -0.1 0.23 -10000 0 -0.55 73 73
CTBP1 0.012 0.004 -10000 0 -10000 0 0
MYC -0.005 0.2 -10000 0 -1.5 6 6
NKD1 -0.055 0.2 -10000 0 -0.65 36 36
FZD1 0.003 0.074 -10000 0 -0.61 5 5
NOTCH1 precursor/Deltex homolog 1 -0.015 0.095 -10000 0 -0.66 6 6
apoptosis -0.028 0.13 -10000 0 -0.38 31 31
Delta 1/NOTCHprecursor -0.025 0.11 -10000 0 -0.7 5 5
DLL1 -0.021 0.14 -10000 0 -0.6 19 19
PPARD 0.021 0.022 -10000 0 -10000 0 0
Gamma Secretase -0.003 0.032 -10000 0 -10000 0 0
APC -0.004 0.039 0.26 2 -10000 0 2
DVL1 -0.03 0.066 -10000 0 -0.58 4 4
CSNK2A1 0.012 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.22 0.23 -10000 0 -0.52 100 100
LRP6 0.01 0.038 -10000 0 -0.71 1 1
CSNK1A1 0.01 0.038 -10000 0 -0.71 1 1
NLK 0.014 0.01 -10000 0 -10000 0 0
CCND1 -0.031 0.28 -10000 0 -1.5 12 12
WNT1 -0.031 0.16 -10000 0 -0.6 24 24
Axin1/APC/beta catenin 0.018 0.063 0.33 1 -0.36 1 2
DKK2 -0.029 0.17 -10000 0 -0.71 20 20
NOTCH1 precursor/DVL1 -0.023 0.093 -10000 0 -0.6 8 8
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.048 -10000 0 -0.63 2 2
NOTCH/Deltex homolog 1 -0.017 0.095 -10000 0 -0.66 6 6
PPP2R5D 0.016 0.094 0.29 35 -10000 0 35
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.22 -10000 0 -0.45 79 79
RBPJ 0.01 0.03 -10000 0 -0.55 1 1
CREBBP 0.014 0.003 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.1 -9999 0 -0.46 17 17
PDGFRB 0.006 0.055 -9999 0 -0.72 2 2
SPHK1 -0.053 0.17 -9999 0 -0.86 14 14
mol:S1P -0.053 0.16 -9999 0 -0.74 15 15
S1P1/S1P/Gi -0.085 0.2 -9999 0 -0.61 23 23
GNAO1 -0.035 0.17 -9999 0 -0.65 24 24
PDGFB-D/PDGFRB/PLCgamma1 -0.07 0.18 -9999 0 -0.56 22 22
PLCG1 -0.076 0.19 -9999 0 -0.58 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.055 -9999 0 -0.72 2 2
GNAI2 0.01 0.006 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GNAI1 -0.004 0.095 -9999 0 -0.67 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.007 0.089 -9999 0 -0.39 17 17
S1P1/S1P -0.063 0.14 -9999 0 -0.52 21 21
negative regulation of cAMP metabolic process -0.082 0.19 -9999 0 -0.59 23 23
MAPK3 -0.11 0.24 -9999 0 -0.61 48 48
calcium-dependent phospholipase C activity -0.002 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR -0.016 0.13 -9999 0 -0.62 15 15
PLCB2 -0.039 0.15 -9999 0 -0.47 27 27
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.053 0.11 -9999 0 -0.43 21 21
receptor internalization -0.059 0.12 -9999 0 -0.47 23 23
PTGS2 -0.17 0.38 -9999 0 -1.1 46 46
Rac1/GTP -0.053 0.11 -9999 0 -0.43 21 21
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.007 0.048 -9999 0 -0.63 2 2
negative regulation of T cell proliferation -0.082 0.19 -9999 0 -0.59 23 23
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.07 0.22 -9999 0 -0.65 43 43
MAPK1 -0.11 0.24 -9999 0 -0.61 48 48
S1P1/S1P/PDGFB-D/PDGFRB -0.039 0.15 -9999 0 -0.51 21 21
ABCC1 0.009 0.03 -9999 0 -0.56 1 1
Coregulation of Androgen receptor activity

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
NRIP1 0.008 0.054 -10000 0 -0.71 2 2
SVIL 0.006 0.066 -10000 0 -0.71 3 3
ZNF318 0.012 0 -10000 0 -10000 0 0
JMJD2C -0.004 0.025 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.069 0.18 -10000 0 -0.43 62 62
CARM1 0.012 0 -10000 0 -10000 0 0
PRDX1 0.009 0.042 -10000 0 -0.55 2 2
PELP1 0.012 0 -10000 0 -10000 0 0
CTNNB1 0.01 0.03 -10000 0 -0.55 1 1
AKT1 0.012 0 -10000 0 -10000 0 0
PTK2B 0.004 0.076 -10000 0 -0.71 4 4
MED1 0.012 0 -10000 0 -10000 0 0
MAK -0.034 0.16 -10000 0 -0.61 26 26
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0 0.093 -10000 0 -0.71 6 6
GSN 0.009 0.042 -10000 0 -0.55 2 2
NCOA2 -0.004 0.11 -10000 0 -0.71 8 8
NCOA6 0.012 0 -10000 0 -10000 0 0
DNA-PK -0.003 0.034 -10000 0 -0.45 2 2
NCOA4 0.012 0 -10000 0 -10000 0 0
PIAS3 0.012 0 -10000 0 -10000 0 0
cell proliferation -0.057 0.16 -10000 0 -0.54 26 26
XRCC5 0.012 0 -10000 0 -10000 0 0
UBE3A 0.012 0 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.089 0.2 -10000 0 -0.46 75 75
FHL2 -0.069 0.29 -10000 0 -1.2 21 21
RANBP9 0.012 0 -10000 0 -10000 0 0
JMJD1A -0.007 0.055 -10000 0 -0.16 33 33
CDK6 -0.013 0.12 -10000 0 -0.62 14 14
TGFB1I1 0.005 0.068 -10000 0 -0.63 4 4
T-DHT/AR/CyclinD1 -0.087 0.2 -10000 0 -0.45 74 74
XRCC6 0.012 0 -10000 0 -10000 0 0
T-DHT/AR -0.078 0.21 -10000 0 -0.53 46 46
CTDSP1 0.012 0 -10000 0 -10000 0 0
CTDSP2 0.012 0 -10000 0 -10000 0 0
BRCA1 0.008 0.048 -10000 0 -0.63 2 2
TCF4 0.006 0.062 -10000 0 -0.66 3 3
CDKN2A -0.19 0.3 -10000 0 -0.64 110 110
SRF 0.012 0.031 -10000 0 -10000 0 0
NKX3-1 -0.094 0.27 -10000 0 -1.1 21 21
KLK3 0.02 0.041 0.18 6 -10000 0 6
TMF1 0.012 0 -10000 0 -10000 0 0
HNRNPA1 0.012 0 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 0.021 0 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.07 0.18 -10000 0 -0.43 63 63
AR -0.11 0.26 -10000 0 -0.65 62 62
UBA3 0.012 0 -10000 0 -10000 0 0
PATZ1 0.01 0.03 -10000 0 -0.55 1 1
PAWR 0.01 0.038 -10000 0 -0.71 1 1
PRKDC 0.008 0.054 -10000 0 -0.71 2 2
PA2G4 0.012 0 -10000 0 -10000 0 0
UBE2I 0.012 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.064 0.16 -10000 0 -0.39 64 64
RPS6KA3 0.012 0 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.069 0.18 -10000 0 -0.43 62 62
LATS2 0.012 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.064 0.16 -10000 0 -0.4 64 64
Cyclin D3/CDK11 p58 0.006 0.036 -10000 0 -0.47 2 2
VAV3 -0.032 0.15 -10000 0 -0.56 27 27
KLK2 -0.072 0.14 -10000 0 -0.53 26 26
CASP8 0.01 0.038 -10000 0 -0.71 1 1
T-DHT/AR/TIF2/CARM1 -0.064 0.18 -10000 0 -0.46 47 47
TMPRSS2 -0.14 0.37 -10000 0 -1.2 36 36
CCND1 -0.017 0.14 -10000 0 -0.68 15 15
PIAS1 0.012 0 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.033 -10000 0 -10000 0 0
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.012 0 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.085 0.19 -10000 0 -0.43 75 75
CMTM2 -0.016 0.13 -10000 0 -0.63 15 15
SNURF -0.019 0.15 -10000 0 -0.71 15 15
ZMIZ1 0.002 0.052 -10000 0 -0.81 1 1
CCND3 0.008 0.048 -10000 0 -0.63 2 2
TGIF1 0.01 0.038 -10000 0 -0.71 1 1
FKBP4 0.01 0.03 -10000 0 -0.55 1 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.005 0.13 -10000 0 -1.4 3 3
VDR 0.001 0.087 -10000 0 -0.66 6 6
FAM120B 0.012 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.038 0.14 -10000 0 -0.46 7 7
RXRs/LXRs/DNA/Oxysterols -0.032 0.16 -10000 0 -0.52 6 6
MED1 0.012 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.016 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.003 0.11 -10000 0 -0.6 2 2
RXRs/NUR77 -0.087 0.19 -10000 0 -0.42 60 60
RXRs/PPAR -0.064 0.16 -10000 0 -0.46 19 19
NCOR2 0.01 0.038 -10000 0 -0.71 1 1
VDR/VDR/Vit D3 0 0.065 -10000 0 -0.49 6 6
RARs/VDR/DNA/Vit D3 -0.013 0.067 -10000 0 -0.39 8 8
RARA 0.01 0.038 -10000 0 -0.71 1 1
NCOA1 0.01 0.038 -10000 0 -0.71 1 1
VDR/VDR/DNA 0.001 0.087 -10000 0 -0.65 6 6
RARs/RARs/DNA/9cRA 0.014 0.055 -10000 0 -0.4 4 4
RARG 0.007 0.051 -10000 0 -0.55 3 3
RPS6KB1 0.024 0.058 -10000 0 -0.42 3 3
RARs/THRs/DNA/SMRT -0.003 0.11 -10000 0 -0.6 2 2
THRA 0.012 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0 0.065 -10000 0 -0.49 6 6
RXRs/PPAR/9cRA/PGJ2/DNA -0.067 0.17 0.3 1 -0.41 53 54
NR1H4 -0.072 0.19 -10000 0 -0.55 50 50
RXRs/LXRs/DNA -0.049 0.17 -10000 0 -0.5 7 7
NR1H2 0.012 0.04 -10000 0 -0.71 1 1
NR1H3 0.012 0.032 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 -0.063 0.17 -10000 0 -0.39 55 55
NR4A1 -0.035 0.16 -10000 0 -0.6 27 27
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.056 0.12 -10000 0 -0.33 11 11
RXRG -0.15 0.28 -10000 0 -0.64 86 86
RXR alpha/CCPG 0.019 0.008 -10000 0 -10000 0 0
RXRA 0.014 0.012 -10000 0 -10000 0 0
RXRB 0.013 0.014 -10000 0 -10000 0 0
THRB -0.056 0.21 -10000 0 -0.71 33 33
PPARG -0.066 0.22 -10000 0 -0.69 39 39
PPARD 0.012 0 -10000 0 -10000 0 0
TNF -0.086 0.33 -10000 0 -1.1 28 28
mol:Oxysterols 0.001 0.014 -10000 0 -10000 0 0
cholesterol transport -0.032 0.16 -10000 0 -0.52 6 6
PPARA 0.012 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.004 0.072 -10000 0 -0.67 4 4
RXRs/NUR77/BCL2 -0.064 0.14 -10000 0 -0.32 63 63
SREBF1 -0.024 0.16 -10000 0 -0.87 2 2
RXRs/RXRs/DNA/9cRA -0.067 0.17 0.29 1 -0.41 53 54
ABCA1 -0.021 0.14 -10000 0 -10000 0 0
RARs/THRs -0.043 0.13 -10000 0 -0.77 2 2
RXRs/FXR -0.11 0.19 -10000 0 -0.44 55 55
BCL2 -0.011 0.12 -10000 0 -0.61 13 13
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.007 0.26 -10000 0 -0.94 19 19
NCK1/PAK1/Dok-R -0.042 0.11 -10000 0 -0.44 19 19
NCK1/Dok-R -0.036 0.29 -10000 0 -1.2 19 19
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.004 0.054 0.25 13 -10000 0 13
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.009 0.042 -10000 0 -0.55 2 2
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.072 0.2 -10000 0 -0.56 49 49
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.071 0.24 -10000 0 -1.1 19 19
FN1 -0.024 0.15 -10000 0 -0.63 20 20
PLD2 -0.016 0.3 -10000 0 -1.2 19 19
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.097 0.25 -10000 0 -0.65 58 58
ELK1 -0.001 0.27 -10000 0 -1.1 19 19
GRB7 -0.001 0.092 -10000 0 -0.64 7 7
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.094 0.27 -10000 0 -1.1 20 20
CDKN1A 0.02 0.23 -10000 0 -0.69 23 23
ITGA5 -0.003 0.094 -10000 0 -0.58 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.037 0.29 -10000 0 -1.2 19 19
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO 0.002 0.22 -10000 0 -0.69 19 19
PLG -0.023 0.3 -10000 0 -1.2 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.004 0.24 -10000 0 -0.9 19 19
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.002 -10000 0 -10000 0 0
ANGPT2 -0.019 0.26 -10000 0 -0.9 21 21
BMX -0.051 0.33 -10000 0 -1.3 19 19
ANGPT1 -0.036 0.31 -10000 0 -1.4 15 15
tube development 0.014 0.24 -10000 0 -0.76 23 23
ANGPT4 -0.002 0.077 -10000 0 -0.55 7 7
response to hypoxia -0.002 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.079 0.33 -10000 0 -1.2 21 21
alpha5/beta1 Integrin 0.006 0.077 -10000 0 -0.46 9 9
FGF2 -0.021 0.14 -10000 0 -0.62 18 18
STAT5A (dimer) 0.009 0.27 -10000 0 -0.86 23 23
mol:L-citrulline 0.002 0.22 -10000 0 -0.69 19 19
AGTR1 -0.071 0.22 -10000 0 -0.63 46 46
MAPK14 -0.013 0.3 -10000 0 -1.2 19 19
Tie2/SHP2 -0.04 0.18 -10000 0 -1.3 7 7
TEK -0.01 0.22 -10000 0 -1.4 7 7
RPS6KB1 0.012 0.25 -10000 0 -0.89 19 19
Angiotensin II/AT1 -0.052 0.16 -10000 0 -0.47 46 46
Tie2/Ang1/GRB2 -0.021 0.31 -10000 0 -1.2 19 19
MAPK3 -0.006 0.27 -10000 0 -1.1 19 19
MAPK1 -0.006 0.27 -10000 0 -1.1 19 19
Tie2/Ang1/GRB7 -0.028 0.32 -10000 0 -1.2 19 19
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.018 0.3 -10000 0 -1.2 19 19
PI3K -0.003 0.29 -10000 0 -1.1 19 19
FES -0.017 0.3 -10000 0 -1.2 19 19
Crk/Dok-R -0.036 0.29 -10000 0 -1.2 19 19
Tie2/Ang1/ABIN2 -0.021 0.31 -10000 0 -1.2 19 19
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.013 0.24 -10000 0 -0.83 19 19
STAT5A 0.01 0.038 -10000 0 -0.71 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.012 0.25 -10000 0 -0.89 19 19
Tie2/Ang2 -0.011 0.32 -10000 0 -1.1 22 22
Tie2/Ang1 -0.027 0.33 -10000 0 -1.3 19 19
FOXO1 0.012 0.25 -10000 0 -0.82 22 22
ELF1 0.017 0.017 -10000 0 -10000 0 0
ELF2 -0.019 0.3 -10000 0 -1.2 19 19
mol:Choline -0.013 0.28 -10000 0 -1.1 19 19
cell migration -0.028 0.063 -10000 0 -0.26 3 3
FYN 0.006 0.27 -10000 0 -0.89 22 22
DOK2 -0.008 0.12 -10000 0 -0.69 10 10
negative regulation of cell cycle 0.024 0.21 -10000 0 -0.62 23 23
ETS1 0.007 0.059 -10000 0 -0.53 1 1
PXN 0.025 0.21 -10000 0 -0.72 19 19
ITGB1 0.01 0.03 -10000 0 -0.55 1 1
NOS3 -0.005 0.24 -10000 0 -0.8 19 19
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.064 0.22 -10000 0 -0.66 38 38
MAPKKK cascade -0.013 0.28 -10000 0 -1.1 19 19
RASA1 0.01 0.038 -10000 0 -0.71 1 1
Tie2/Ang1/Shc -0.022 0.31 -10000 0 -1.2 19 19
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis 0.007 0.2 -10000 0 -0.61 19 19
mol:Phosphatidic acid -0.013 0.28 -10000 0 -1.1 19 19
mol:Angiotensin II 0 0.006 -10000 0 -10000 0 0
mol:NADP 0.002 0.22 -10000 0 -0.69 19 19
Rac1/GTP -0.068 0.2 -10000 0 -0.83 19 19
MMP2 -0.028 0.31 -10000 0 -1.2 19 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.14 0.28 -9999 0 -0.62 87 87
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.038 -9999 0 -0.71 1 1
TCEB1 0.009 0.042 -9999 0 -0.55 2 2
HIF1A/p53 0.007 0.059 -9999 0 -0.4 4 4
HIF1A 0.005 0.041 -9999 0 -10000 0 0
COPS5 0.01 0.03 -9999 0 -0.55 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.028 -9999 0 -0.38 1 1
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.19 0.3 -9999 0 -0.64 110 110
ARNT/IPAS -0.099 0.21 -9999 0 -0.46 87 87
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.012 0.04 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.009 0.042 -9999 0 -0.55 2 2
RACK1/Elongin B/Elongin C -0.003 0.034 -9999 0 -0.45 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.012 0.04 -9999 0 -10000 0 0
PHD1-3/OS9 -0.035 0.15 -9999 0 -0.42 33 33
HIF1A/RACK1/Elongin B/Elongin C -0.012 0.037 -9999 0 -0.43 1 1
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.011 0.042 -9999 0 -10000 0 0
EGLN3 -0.094 0.24 -9999 0 -0.63 58 58
EGLN2 0.01 0.038 -9999 0 -0.71 1 1
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.004 0.076 -9999 0 -0.71 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.023 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.093 0.17 -9999 0 -0.37 70 70
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.014 0.13 0.64 14 -10000 0 14
PI3K Class IB/PDE3B -0.014 0.13 -10000 0 -0.64 14 14
PDE3B -0.014 0.13 -10000 0 -0.64 14 14
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.012 0.16 -9999 0 -0.72 14 14
STMN1 -0.014 0.13 -9999 0 -0.5 24 24
Aurora B/RasGAP/Survivin -0.06 0.21 -9999 0 -0.65 33 33
Chromosomal passenger complex/Cul3 protein complex -0.035 0.16 -9999 0 -0.62 17 17
BIRC5 -0.056 0.22 -9999 0 -0.73 33 33
DES -0.14 0.31 -9999 0 -0.76 57 57
Aurora C/Aurora B/INCENP -0.031 0.12 -9999 0 -0.45 22 22
Aurora B/TACC1 -0.024 0.12 -9999 0 -0.46 22 22
Aurora B/PP2A -0.024 0.12 -9999 0 -0.5 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.004 0.044 -9999 0 -0.19 15 15
mitotic metaphase/anaphase transition -0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.042 0.21 -9999 0 -0.64 34 34
Cul3 protein complex -0.044 0.13 -9999 0 -0.48 16 16
KIF2C -0.047 0.24 -9999 0 -0.67 33 33
PEBP1 0.011 0.004 -9999 0 -10000 0 0
KIF20A -0.013 0.13 -9999 0 -0.7 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.025 0.12 -9999 0 -0.5 22 22
SEPT1 -0.002 0.098 -9999 0 -0.69 7 7
SMC2 0.012 0 -9999 0 -10000 0 0
SMC4 0.012 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.019 0.2 -9999 0 -0.93 15 15
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B -0.006 0.092 -9999 0 -0.36 21 21
AURKB -0.027 0.16 -9999 0 -0.68 21 21
AURKC -0.014 0.13 -9999 0 -0.64 14 14
CDCA8 -0.001 0.094 -9999 0 -0.71 6 6
cytokinesis -0.087 0.26 -9999 0 -0.93 26 26
Aurora B/Septin1 -0.075 0.25 -9999 0 -0.96 21 21
AURKA -0.003 0.1 -9999 0 -0.65 8 8
INCENP 0.011 0.006 -9999 0 -10000 0 0
KLHL13 -0.053 0.19 -9999 0 -0.6 37 37
BUB1 -0.029 0.16 -9999 0 -0.7 20 20
hSgo1/Aurora B/Survivin -0.075 0.25 -9999 0 -0.75 36 36
EVI5 0.012 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.07 0.24 -9999 0 -0.79 27 27
SGOL1 -0.026 0.16 -9999 0 -0.69 19 19
CENPA -0.057 0.28 -9999 0 -0.71 38 38
NCAPG -0.014 0.13 -9999 0 -0.68 13 13
Aurora B/HC8 Proteasome -0.024 0.12 -9999 0 -0.5 21 21
NCAPD2 0.01 0.03 -9999 0 -0.55 1 1
Aurora B/PP1-gamma -0.024 0.12 -9999 0 -0.5 21 21
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH -0.028 0.16 -9999 0 -0.68 20 20
NPM1 -0.032 0.15 -9999 0 -0.71 15 15
RASA1 0.01 0.038 -9999 0 -0.71 1 1
KLHL9 0.004 0.076 -9999 0 -0.71 4 4
mitotic prometaphase -0.001 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.023 0.12 -9999 0 -0.49 21 21
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.081 0.28 -9999 0 -0.87 29 29
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.032 0.15 -9999 0 -0.71 15 15
MYLK -0.012 0.11 -9999 0 -0.42 20 20
KIF23 -0.022 0.15 -9999 0 -0.69 17 17
VIM -0.015 0.14 -9999 0 -0.5 25 25
RACGAP1 0.009 0.039 -9999 0 -0.73 1 1
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.032 0.15 -9999 0 -0.71 15 15
Chromosomal passenger complex -0.044 0.26 -9999 0 -0.76 31 31
Chromosomal passenger complex/EVI5 -0.05 0.22 -9999 0 -0.88 17 17
TACC1 0.006 0.066 -9999 0 -0.71 3 3
PPP2R5D 0.012 0 -9999 0 -10000 0 0
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.005 0.1 -9999 0 -0.46 17 17
alphaV beta3 Integrin -0.062 0.15 -9999 0 -0.5 18 18
PTK2 -0.06 0.19 -9999 0 -0.61 21 21
IGF1R 0.001 0.087 -9999 0 -0.66 6 6
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.006 0.066 -9999 0 -0.71 3 3
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.066 0.14 -9999 0 -0.55 18 18
VEGFA 0.008 0.048 -9999 0 -0.63 2 2
ILK -0.065 0.14 -9999 0 -0.55 17 17
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.034 0.14 -9999 0 -0.51 17 17
PTK2B -0.025 0.15 -9999 0 -0.46 22 22
alphaV/beta3 Integrin/JAM-A -0.065 0.18 -9999 0 -0.66 10 10
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.063 0.14 -9999 0 -0.48 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.015 0.14 -9999 0 -0.47 25 25
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.018 0.11 -9999 0 -0.46 8 8
alphaV/beta3 Integrin/Syndecan-1 -0.047 0.12 -9999 0 -0.45 15 15
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.099 0.2 -9999 0 -0.76 16 16
PI4 Kinase 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.12 0.21 -9999 0 -0.54 53 53
RPS6KB1 -0.054 0.2 -9999 0 -0.69 16 16
TLN1 0.01 0.038 -9999 0 -0.71 1 1
MAPK3 -0.053 0.2 -9999 0 -0.71 19 19
GPR124 0.004 0.076 -9999 0 -0.71 4 4
MAPK1 -0.053 0.2 -9999 0 -0.71 19 19
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.12 0.2 -9999 0 -0.48 60 60
cell adhesion -0.056 0.12 -9999 0 -0.44 12 12
ANGPTL3 -0.026 0.13 -9999 0 -0.55 21 21
VEGFR2 homodimer/VEGFA homodimer/Src -0.019 0.084 -9999 0 -0.38 17 17
IGF-1R heterotetramer 0.001 0.087 -9999 0 -0.65 6 6
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.01 0.038 -9999 0 -0.71 1 1
ITGB3 -0.06 0.2 -9999 0 -0.59 42 42
IGF1 -0.034 0.17 -9999 0 -0.64 25 25
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.048 0.13 -9999 0 -0.51 14 14
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.006 0.066 -9999 0 -0.71 3 3
alphaV/beta3 Integrin/CD47 -0.047 0.12 -9999 0 -0.45 15 15
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.088 0.2 -9999 0 -0.58 36 36
CSF1 -0.003 0.099 -9999 0 -0.65 8 8
PIK3C2A -0.065 0.14 -9999 0 -0.55 17 17
PI4 Kinase/Pyk2 -0.09 0.16 -9999 0 -0.59 20 20
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.029 0.15 -9999 0 -0.47 20 20
FAK1/Vinculin -0.04 0.15 -9999 0 -0.48 17 17
alphaV beta3/Integrin/ppsTEM5 -0.048 0.13 -9999 0 -0.51 14 14
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.066 0.21 -9999 0 -0.6 45 45
BCAR1 0.004 0.076 -9999 0 -0.71 4 4
FGF2 -0.02 0.14 -9999 0 -0.62 18 18
F11R -0.005 0.11 -9999 0 -0.46 19 19
alphaV/beta3 Integrin/Lactadherin -0.047 0.12 -9999 0 -0.45 15 15
alphaV/beta3 Integrin/TGFBR2 -0.044 0.12 -9999 0 -0.45 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.017 0.075 -9999 0 -0.41 9 9
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.02 0.12 -9999 0 -0.45 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.024 0.15 -9999 0 -0.63 20 20
alphaV/beta3 Integrin/Pyk2 -0.025 0.15 -9999 0 -0.49 17 17
SDC1 0.006 0.066 -9999 0 -0.71 3 3
VAV3 -0.001 0.12 -9999 0 -0.71 4 4
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 -0.009 0.12 -9999 0 -0.71 10 10
FAK1/Paxillin -0.04 0.15 -9999 0 -0.48 16 16
cell migration -0.029 0.14 -9999 0 -0.47 10 10
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.081 0.15 -9999 0 -0.6 10 10
SPP1 -0.12 0.27 -9999 0 -0.64 73 73
KDR -0.015 0.13 -9999 0 -0.62 15 15
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.12 0.27 -9999 0 -0.66 69 69
angiogenesis -0.055 0.2 -9999 0 -0.7 19 19
Rac1/GTP -0.03 0.1 -9999 0 -0.65 4 4
EDIL3 -0.064 0.21 -9999 0 -0.64 41 41
cell proliferation -0.044 0.12 -9999 0 -0.45 13 13
Caspase cascade in apoptosis

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
TOP1 -0.009 0.12 -10000 0 -0.4 22 22
ACTA1 -0.028 0.15 -10000 0 -0.5 22 22
NUMA1 -0.011 0.12 -10000 0 -0.4 24 24
SPTAN1 -0.02 0.15 -10000 0 -0.48 24 24
LIMK1 -0.018 0.14 -10000 0 -0.49 22 22
BIRC3 -0.031 0.16 -10000 0 -0.65 23 23
BIRC2 0.012 0 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.039 0.17 -10000 0 -0.54 29 29
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 -0.009 0.12 -10000 0 -0.4 22 22
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.14 -10000 0 -0.47 24 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0.03 -10000 0 -0.55 1 1
GSN -0.02 0.15 -10000 0 -0.5 21 21
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.094 0.26 -10000 0 -0.67 53 53
BID -0.007 0.081 -10000 0 -0.26 24 24
MAP3K1 0.001 0.053 -10000 0 -0.23 1 1
TRADD 0.01 0.038 -10000 0 -0.71 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0.022 -10000 0 -0.39 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.022 0.15 -10000 0 -0.48 26 26
CASP9 0.01 0.03 -10000 0 -0.55 1 1
DNA repair -0.005 0.049 -10000 0 -0.21 7 7
neuron apoptosis 0.015 0.031 -10000 0 -0.45 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.012 0.14 -10000 0 -0.46 24 24
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.003 0.082 -10000 0 -0.48 2 2
TRAF2 0.008 0.054 -10000 0 -0.71 2 2
ICAD/CAD -0.011 0.14 -10000 0 -0.48 21 21
CASP7 0.01 0.074 0.31 15 -0.24 1 16
KRT18 0.008 0.029 -10000 0 -10000 0 0
apoptosis -0.006 0.13 -10000 0 -0.42 22 22
DFFA -0.018 0.14 -10000 0 -0.49 22 22
DFFB -0.018 0.14 -10000 0 -0.49 22 22
PARP1 0.005 0.049 0.21 7 -10000 0 7
actin filament polymerization 0.01 0.13 0.46 21 -10000 0 21
TNF -0.06 0.21 -10000 0 -0.65 38 38
CYCS -0.005 0.065 -10000 0 -0.23 11 11
SATB1 0.002 0.1 -10000 0 -0.57 4 4
SLK -0.018 0.14 -10000 0 -0.49 22 22
p15 BID/BAX 0 0.073 -10000 0 -0.34 3 3
CASP2 0.006 0.1 -10000 0 -0.51 6 6
JNK cascade -0.001 0.052 0.23 1 -10000 0 1
CASP3 -0.026 0.15 -10000 0 -0.52 22 22
LMNB2 0.012 0.077 -10000 0 -0.45 2 2
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.008 0.054 -10000 0 -0.71 2 2
Mammalian IAPs/DIABLO 0.002 0.098 -10000 0 -0.41 14 14
negative regulation of DNA binding -0.092 0.26 -10000 0 -0.66 53 53
stress fiber formation -0.017 0.14 -10000 0 -0.48 22 22
GZMB -0.046 0.19 -10000 0 -0.53 43 43
CASP1 0.01 0.05 -10000 0 -0.4 5 5
LMNB1 0.01 0.084 -10000 0 -0.44 5 5
APP 0.015 0.032 -10000 0 -0.46 1 1
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.029 -10000 0 -0.54 1 1
VIM -0.011 0.13 -10000 0 -0.42 22 22
LMNA 0.009 0.096 -10000 0 -0.61 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.001 0.11 -10000 0 -0.55 6 6
LRDD 0.006 0.066 -10000 0 -0.71 3 3
SREBF1 -0.019 0.15 -10000 0 -0.51 22 22
APAF-1/Caspase 9 0 0.037 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.01 0.12 -10000 0 -0.4 24 24
CFL2 -0.01 0.14 -10000 0 -0.47 21 21
GAS2 -0.076 0.2 -10000 0 -0.51 44 44
positive regulation of apoptosis 0.013 0.087 -10000 0 -0.47 5 5
PRF1 -0.017 0.13 -10000 0 -0.58 17 17
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.063 0.34 5 -0.44 2 7
RFC1 0.011 0.053 0.34 5 -10000 0 5
PRKDC 0.008 0.059 0.34 5 -0.37 2 7
RIPK1 0.012 0.003 -10000 0 -10000 0 0
CASP7 -0.015 0.094 0.26 2 -1.6 1 3
FASLG/FAS/FADD/FAF1 -0.007 0.12 0.25 21 -0.33 22 43
MAP2K4 -0.01 0.14 -10000 0 -0.53 9 9
mol:ceramide -0.024 0.14 -10000 0 -0.48 21 21
GSN 0.009 0.058 0.34 5 -0.32 2 7
FASLG/FAS/FADD/FAF1/Caspase 8 0.002 0.13 -10000 0 -0.41 16 16
FAS -0.017 0.14 -10000 0 -0.7 14 14
BID 0.004 0.047 0.31 5 -0.46 1 6
MAP3K1 0.004 0.1 -10000 0 -1.2 1 1
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
RB1 0.008 0.063 0.34 5 -0.44 2 7
CFLAR 0.012 0.003 -10000 0 -10000 0 0
HGF/MET -0.15 0.23 -10000 0 -0.53 71 71
ARHGDIB 0.006 0.071 0.34 5 -0.44 4 9
FADD 0.011 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.009 0.058 0.32 2 -0.34 5 7
NFKB1 -0.03 0.061 -10000 0 -10000 0 0
MAPK8 -0.016 0.16 -10000 0 -0.61 8 8
DFFA 0.011 0.053 0.34 5 -10000 0 5
DNA fragmentation during apoptosis 0.011 0.053 0.34 5 -10000 0 5
FAS/FADD/MET -0.064 0.19 -10000 0 -0.49 44 44
CFLAR/RIP1 0.015 0.006 -10000 0 -10000 0 0
FAIM3 -0.003 0.099 -10000 0 -0.65 8 8
FAF1 0.012 0.005 -10000 0 -10000 0 0
PARP1 0.011 0.053 0.34 5 -10000 0 5
DFFB 0.011 0.053 0.34 5 -10000 0 5
CHUK -0.025 0.053 -10000 0 -10000 0 0
FASLG -0.057 0.2 -10000 0 -0.61 39 39
FAS/FADD -0.005 0.11 -10000 0 -0.52 14 14
HGF -0.035 0.17 -10000 0 -0.66 25 25
LMNA 0.008 0.056 0.3 5 -0.4 2 7
CASP6 0.011 0.053 0.34 5 -10000 0 5
CASP10 -0.001 0.094 -10000 0 -0.71 6 6
CASP3 0.013 0.066 0.36 8 -10000 0 8
PTPN13 -0.084 0.23 -10000 0 -0.63 53 53
CASP8 0.007 0.063 0.37 8 -0.55 1 9
IL6 -0.08 0.32 -10000 0 -1.3 18 18
MET -0.09 0.24 -10000 0 -0.65 54 54
ICAD/CAD 0.01 0.048 0.31 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.15 -10000 0 -0.48 21 21
activation of caspase activity by cytochrome c 0.004 0.047 0.31 5 -0.46 1 6
PAK2 0.011 0.052 0.34 5 -10000 0 5
BCL2 -0.011 0.12 -10000 0 -0.61 13 13
Syndecan-3-mediated signaling events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.045 0.11 -9999 0 -0.96 1 1
Syndecan-3/Neurocan -0.012 0.061 -9999 0 -0.51 2 2
POMC -0.056 0.19 -9999 0 -0.6 39 39
EGFR -0.036 0.17 -9999 0 -0.62 27 27
Syndecan-3/EGFR -0.027 0.1 -9999 0 -0.44 12 12
AGRP -0.061 0.2 -9999 0 -0.62 40 40
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.007 0.051 -9999 0 -0.55 3 3
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.01 0.038 -9999 0 -0.71 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.011 0.1 -9999 0 -0.55 12 12
long-term memory -0.005 0.047 -9999 0 -0.42 4 4
Syndecan-3/IL8 -0.049 0.12 -9999 0 -0.4 27 27
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.018 0 -9999 0 -10000 0 0
FYN 0.006 0.066 -9999 0 -0.71 3 3
limb bud formation -0.003 0.038 -9999 0 -0.7 1 1
MC4R -0.03 0.14 -9999 0 -0.55 24 24
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.082 0.23 -9999 0 -0.62 52 52
FGFR/FGF/Syndecan-3 -0.003 0.038 -9999 0 -0.71 1 1
neuron projection morphogenesis -0.051 0.12 -9999 0 -0.75 2 2
Syndecan-3/AgRP -0.038 0.11 -9999 0 -0.4 19 19
Syndecan-3/AgRP/MC4R -0.054 0.12 -9999 0 -0.43 19 19
Fyn/Cortactin 0.013 0.05 -9999 0 -0.53 3 3
SDC3 -0.003 0.039 -9999 0 -0.72 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.049 0.12 -9999 0 -0.39 27 27
IL8 -0.08 0.23 -9999 0 -0.63 51 51
Syndecan-3/Fyn/Cortactin -0.005 0.048 -9999 0 -0.43 4 4
Syndecan-3/CASK -0.003 0.037 -9999 0 -0.68 1 1
alpha-MSH/MC4R -0.062 0.18 -9999 0 -0.45 58 58
Gamma Secretase -0.003 0.031 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.021 0 -9999 0 -10000 0 0
SMARCC1 0.005 0.024 -9999 0 -10000 0 0
REL -0.002 0.1 -9999 0 -0.71 7 7
HDAC7 -0.018 0.15 -9999 0 -0.6 7 7
JUN 0.006 0.062 -9999 0 -0.66 3 3
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.012 0 -9999 0 -10000 0 0
KAT5 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.15 -9999 0 -0.47 34 34
FOXO1 0.007 0.057 -9999 0 -0.6 3 3
T-DHT/AR -0.023 0.16 -9999 0 -0.64 7 7
MAP2K6 -0.052 0.19 -9999 0 -0.64 34 34
BRM/BAF57 0.013 0.05 -9999 0 -0.53 3 3
MAP2K4 0.011 0.007 -9999 0 -10000 0 0
SMARCA2 0.006 0.066 -9999 0 -0.71 3 3
PDE9A -0.13 0.35 -9999 0 -1.3 29 29
NCOA2 -0.005 0.11 -9999 0 -0.71 8 8
CEBPA -0.032 0.17 -9999 0 -0.67 23 23
EHMT2 0.012 0 -9999 0 -10000 0 0
cell proliferation -0.01 0.17 -9999 0 -0.55 15 15
NR0B1 -0.2 0.3 -9999 0 -0.62 117 117
EGR1 -0.017 0.13 -9999 0 -0.62 16 16
RXRs/9cRA -0.072 0.17 -9999 0 -0.42 49 49
AR/RACK1/Src -0.036 0.12 -9999 0 -0.51 8 8
AR/GR -0.035 0.14 -9999 0 -0.5 17 17
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.017 0.032 -9999 0 -0.53 1 1
T-DHT/AR/TIF2/CARM1 -0.024 0.15 -9999 0 -0.53 14 14
SRC -0.005 0.12 -9999 0 -0.42 8 8
NR3C1 0.008 0.054 -9999 0 -0.71 2 2
KLK3 -0.091 0.15 -9999 0 -0.44 33 33
APPBP2 0.011 0.006 -9999 0 -10000 0 0
TRIM24 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.022 0.14 -9999 0 -0.55 8 8
TMPRSS2 -0.15 0.39 -9999 0 -1.2 40 40
RXRG -0.15 0.28 -9999 0 -0.64 86 86
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.012 0 -9999 0 -10000 0 0
RXRB 0.012 0 -9999 0 -10000 0 0
CARM1 0.011 0.003 -9999 0 -10000 0 0
NR2C2 0.012 0 -9999 0 -10000 0 0
KLK2 -0.03 0.16 -9999 0 -0.53 10 10
AR -0.041 0.15 -9999 0 -0.41 31 31
SENP1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 -0.002 0.088 -9999 0 -0.55 9 9
SRY 0 0 -9999 0 -10000 0 0
GATA2 -0.022 0.15 -9999 0 -0.7 17 17
MYST2 0.012 0 -9999 0 -10000 0 0
HOXB13 -0.22 0.31 -9999 0 -0.64 120 120
T-DHT/AR/RACK1/Src -0.016 0.13 -9999 0 -0.53 8 8
positive regulation of transcription -0.022 0.15 -9999 0 -0.7 17 17
DNAJA1 0.011 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.031 -9999 0 -10000 0 0
NCOA1 0.014 0.04 -9999 0 -0.74 1 1
SPDEF -0.084 0.24 -9999 0 -0.69 48 48
T-DHT/AR/TIF2 0.005 0.094 -9999 0 -0.4 3 3
T-DHT/AR/Hsp90 -0.022 0.14 -9999 0 -0.55 8 8
GSK3B 0.011 0.004 -9999 0 -10000 0 0
NR2C1 0.012 0 -9999 0 -10000 0 0
mol:T-DHT -0.012 0.12 -9999 0 -0.42 20 20
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0 -9999 0 -10000 0 0
POU2F1 0.009 0.065 -9999 0 -0.71 2 2
T-DHT/AR/DAX-1 -0.15 0.2 -9999 0 -0.54 39 39
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 0.012 0 -9999 0 -10000 0 0
PDGFR-alpha 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
PDGFRA -0.01 0.12 -9999 0 -0.68 11 11
PDGF/PDGFRA/CRKL 0 0.092 -9999 0 -0.48 12 12
positive regulation of JUN kinase activity -0.013 0.068 -9999 0 -0.39 9 9
CRKL 0.01 0.03 -9999 0 -0.55 1 1
PDGF/PDGFRA/Caveolin-3 -0.026 0.13 -9999 0 -0.44 31 31
AP1 -0.066 0.21 -9999 0 -1 13 13
mol:IP3 0.003 0.099 -9999 0 -0.53 11 11
PLCG1 0.003 0.099 -9999 0 -0.53 11 11
PDGF/PDGFRA/alphaV Integrin 0.002 0.089 -9999 0 -0.49 11 11
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.099 -9999 0 -0.53 11 11
CAV3 -0.025 0.13 -9999 0 -0.55 20 20
CAV1 -0.023 0.14 -9999 0 -0.57 21 21
SHC/Grb2/SOS1 -0.012 0.068 -9999 0 -0.39 9 9
PDGF/PDGFRA/Shf -0.02 0.14 -9999 0 -0.48 27 27
FOS -0.028 0.22 -9999 0 -0.98 13 13
JUN -0.009 0.049 -9999 0 -0.51 3 3
oligodendrocyte development 0.002 0.089 -9999 0 -0.49 11 11
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG 0.003 0.099 -9999 0 -0.53 11 11
PDGF/PDGFRA -0.01 0.12 -9999 0 -0.68 11 11
actin cytoskeleton reorganization 0 0.094 -9999 0 -0.5 12 12
SRF 0.02 0.006 -9999 0 -10000 0 0
SHC1 0.009 0.042 -9999 0 -0.55 2 2
PI3K -0.012 0.072 -9999 0 -0.44 9 9
PDGF/PDGFRA/Crk/C3G -0.012 0.073 -9999 0 -0.44 9 9
JAK1 0.003 0.094 -9999 0 -0.5 12 12
ELK1/SRF 0.021 0.075 -9999 0 -0.41 9 9
SHB 0.01 0.038 -9999 0 -0.71 1 1
SHF -0.018 0.13 -9999 0 -0.6 17 17
CSNK2A1 0.005 0.015 -9999 0 -10000 0 0
GO:0007205 0.003 0.1 -9999 0 -0.54 11 11
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.013 0.068 -9999 0 -0.39 9 9
PDGF/PDGFRA/SHB 0 0.094 -9999 0 -0.5 12 12
PDGF/PDGFRA/Caveolin-1 -0.024 0.14 -9999 0 -0.46 31 31
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 0.009 0.09 -9999 0 -0.5 9 9
PIK3CA 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk 0.002 0.089 -9999 0 -0.49 11 11
JAK-STAT cascade 0.003 0.094 -9999 0 -0.5 12 12
cell proliferation -0.02 0.14 -9999 0 -0.48 27 27
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.01 0.031 -9999 0 -0.39 2 2
PRKCZ -0.002 0.09 -9999 0 -0.59 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.01 0.038 -9999 0 -0.71 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.077 -9999 0 -0.48 4 4
IRAK/TOLLIP 0.024 0.024 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.008 0.054 -9999 0 -0.71 2 2
IL1 alpha/IL1R2 -0.14 0.26 -9999 0 -0.51 107 107
IL1A -0.13 0.27 -9999 0 -0.62 77 77
IL1B -0.032 0.16 -9999 0 -0.5 36 36
IRAK/TRAF6/p62/Atypical PKCs -0.009 0.047 -9999 0 -10000 0 0
IL1R2 -0.067 0.21 -9999 0 -0.63 43 43
IL1R1 0.004 0.076 -9999 0 -0.71 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.019 0.086 -9999 0 -0.53 3 3
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.006 0.066 -9999 0 -0.71 3 3
MAP3K3 0.01 0.038 -9999 0 -0.71 1 1
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.05 0.049 -9999 0 -10000 0 0
JUN 0.006 0.1 -9999 0 -0.57 1 1
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.041 0.13 -9999 0 -0.82 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.06 0.18 -9999 0 -0.45 40 40
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.077 0.16 -9999 0 -0.89 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.15 -9999 0 -0.48 27 27
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.001 0.1 -9999 0 -10000 0 0
IRAK1 0.019 0.026 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.032 0.16 -9999 0 -0.52 33 33
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.03 -9999 0 -0.55 1 1
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.1 -9999 0 -0.61 4 4
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.15 -9999 0 -0.48 27 27
IL1 beta/IL1R2 -0.071 0.2 -9999 0 -0.54 43 43
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.018 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.037 0.12 -9999 0 -0.74 4 4
IRAK3 -0.019 0.14 -9999 0 -0.63 17 17
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.044 0.13 -9999 0 -0.82 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.029 0.14 -9999 0 -0.85 3 3
IL1 alpha/IL1R1/IL1RAP -0.093 0.18 -9999 0 -0.5 40 40
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.01 0.03 -9999 0 -0.55 1 1
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.03 0.032 -9999 0 -10000 0 0
IL1RAP 0.006 0.066 -9999 0 -0.71 3 3
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.037 0.11 -9999 0 -0.67 4 4
CASP1 0.006 0.066 -9999 0 -0.71 3 3
IL1RN/IL1R2 -0.082 0.23 -9999 0 -0.54 64 64
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.011 0.15 -9999 0 -0.45 26 26
TMEM189-UBE2V1 0.002 0.042 -9999 0 -0.55 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.11 -9999 0 -0.74 3 3
PIK3CA 0.012 0 -9999 0 -10000 0 0
IL1RN -0.047 0.19 -9999 0 -0.64 32 32
TRAF6/TAK1/TAB1/TAB2 -0.001 0.019 -9999 0 -10000 0 0
MAP2K6 -0.005 0.1 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.006 0.066 -9999 0 -0.71 3 3
SPHK1 -0.028 0.16 -9999 0 -0.66 21 21
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.088 -9999 0 -0.36 16 16
GNAO1 -0.033 0.17 -9999 0 -0.65 24 24
mol:Sphinganine-1-P -0.014 0.13 -9999 0 -0.51 23 23
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.019 0.068 -9999 0 -0.65 1 1
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.018 0 -9999 0 -10000 0 0
S1PR3 0.008 0.048 -9999 0 -0.63 2 2
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.018 0.073 -9999 0 -0.32 16 16
S1PR5 -0.02 0.14 -9999 0 -0.58 19 19
S1PR4 -0.004 0.11 -9999 0 -0.71 8 8
GNAI1 -0.001 0.095 -9999 0 -0.66 7 7
S1P/S1P5/G12 -0.006 0.11 -9999 0 -0.56 6 6
S1P/S1P3/Gq -0.011 0.12 -9999 0 -0.53 9 9
S1P/S1P4/Gi -0.028 0.15 -9999 0 -0.53 14 14
GNAQ 0.01 0.038 -9999 0 -0.71 1 1
GNAZ -0.068 0.22 -9999 0 -0.64 43 43
GNA14 -0.047 0.2 -9999 0 -0.71 29 29
GNA15 0 0.093 -9999 0 -0.71 6 6
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.006 0.066 -9999 0 -0.71 3 3
ABCC1 0.01 0.03 -9999 0 -0.55 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.013 0.13 -9999 0 -0.71 12 12
LRPAP1 0.01 0.038 -9999 0 -0.71 1 1
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.074 0.16 -9999 0 -0.47 34 34
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.042 0.15 -9999 0 -0.42 34 34
IQGAP1/CaM 0.018 0 -9999 0 -10000 0 0
DAB1 -0.01 0.096 -9999 0 -0.55 11 11
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 -0.02 0.14 -9999 0 -0.65 17 17
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.01 0.03 -9999 0 -0.55 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.003 0.083 -9999 0 -0.45 11 11
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 0.002 0.076 -9999 0 -0.57 6 6
LIS1/Poliovirus Protein 3A 0.015 0 -9999 0 -10000 0 0
CDK5R2 -0.14 0.28 -9999 0 -0.63 84 84
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.088 0.18 -9999 0 -0.49 46 46
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.065 0.17 -9999 0 -0.55 14 14
MAP1B -0.022 0.078 -9999 0 -0.35 15 15
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.028 0.15 -9999 0 -0.53 5 5
RELN -0.091 0.24 -9999 0 -0.63 57 57
PAFAH/LIS1 0.004 0.094 -9999 0 -0.45 11 11
LIS1/CLIP170 0.024 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.075 0.11 -9999 0 -0.53 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.027 0.13 -9999 0 -0.64 5 5
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.076 0.18 -9999 0 -0.58 15 15
LIS1/IQGAP1 0.024 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.021 0 -9999 0 -10000 0 0
PAFAH1B3 0.004 0.072 -9999 0 -0.67 4 4
PAFAH1B2 0.01 0.038 -9999 0 -0.71 1 1
MAP1B/LIS1/Dynein heavy chain 0.008 0.055 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.088 0.14 -9999 0 -0.59 7 7
LRP8 -0.006 0.1 -9999 0 -0.61 10 10
NDEL1/Katanin 60 -0.065 0.17 -9999 0 -0.55 14 14
P39/CDK5 -0.11 0.2 -9999 0 -0.62 18 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0 -9999 0 -10000 0 0
CDK5 -0.032 0.14 -9999 0 -0.59 2 2
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.047 0.17 -9999 0 -0.67 7 7
RELN/VLDLR -0.056 0.18 -9999 0 -0.46 42 42
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.012 0 -10000 0 -10000 0 0
HDAC4 0.007 0.051 -10000 0 -0.55 3 3
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.005 0.08 0.42 12 -10000 0 12
CDKN1A -0.007 0.084 -10000 0 -0.76 4 4
KAT2B 0.012 0 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.007 0.057 -10000 0 -0.6 3 3
FOXO4 0.021 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT -0.076 0.22 -10000 0 -0.6 50 50
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0 -10000 0 -10000 0 0
PPARGC1A -0.14 0.27 -10000 0 -0.61 88 88
FHL2 -0.031 0.17 -10000 0 -0.7 21 21
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.015 -10000 0 -10000 0 0
HIST2H4A 0.005 0.08 -10000 0 -0.42 12 12
SIRT1/FOXO3a 0.001 0.014 -10000 0 -10000 0 0
SIRT1 0.002 0.02 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.033 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.012 0.059 -10000 0 -0.28 12 12
apoptosis -0.001 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.094 0.17 -10000 0 -0.38 88 88
p53/SIRT1 -0.002 0.07 0.42 3 -0.53 4 7
SIRT1/FOXO4 0.002 0.016 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.026 0.11 -10000 0 -0.45 20 20
HIST1H1E 0.003 0.072 -10000 0 -0.34 12 12
SIRT1/p300 0.002 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.002 0.014 -10000 0 -10000 0 0
TP53 -0.006 0.078 -10000 0 -0.71 4 4
KU70/SIRT1/BAX 0.001 0.014 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.061 0.16 -10000 0 -0.44 50 50
ACSS2 0.017 0.038 -10000 0 -0.46 2 2
SIRT1/PCAF/MYOD 0.002 0.014 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.015 0.11 -10000 0 -1.1 3 3
oxygen homeostasis 0.001 0.016 -10000 0 -10000 0 0
TCEB2 0.01 0.038 -10000 0 -0.71 1 1
TCEB1 0.009 0.042 -10000 0 -0.55 2 2
VHL/Elongin B/Elongin C/HIF2A -0.05 0.11 -10000 0 -0.46 8 8
EPO -0.011 0.25 -10000 0 -0.8 8 8
FIH (dimer) 0.014 0.015 -10000 0 -10000 0 0
APEX1 0.013 0.015 -10000 0 -10000 0 0
SERPINE1 -0.046 0.32 -10000 0 -0.93 19 19
FLT1 -0.017 0.13 -10000 0 -1.3 3 3
ADORA2A -0.021 0.27 -10000 0 -0.8 13 13
germ cell development -0.086 0.34 -10000 0 -0.86 24 24
SLC11A2 -0.023 0.28 -10000 0 -0.83 13 13
BHLHE40 -0.023 0.28 -10000 0 -0.83 14 14
HIF1AN 0.014 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.075 0.13 -10000 0 -0.54 14 14
ETS1 0.022 0.033 -10000 0 -0.54 1 1
CITED2 -0.011 0.055 -10000 0 -10000 0 0
KDR -0.037 0.19 -10000 0 -1.3 7 7
PGK1 -0.023 0.28 -10000 0 -0.83 13 13
SIRT1 0.012 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.036 0.33 -10000 0 -0.95 19 19
EPAS1 -0.012 0.16 -10000 0 -0.45 18 18
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 -0.035 0.3 -10000 0 -0.86 18 18
EFNA1 -0.029 0.29 -10000 0 -0.88 14 14
FXN -0.021 0.27 -10000 0 -0.8 13 13
POU5F1 -0.092 0.36 -10000 0 -0.9 26 26
neuron apoptosis 0.034 0.32 0.9 19 -10000 0 19
EP300 0.012 0 -10000 0 -10000 0 0
EGLN3 -0.093 0.24 -10000 0 -0.64 58 58
EGLN2 0.012 0.04 -10000 0 -0.7 1 1
EGLN1 0.014 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.034 -10000 0 -0.45 1 1
VHL 0.012 0 -10000 0 -10000 0 0
ARNT 0.013 0.015 -10000 0 -10000 0 0
SLC2A1 -0.041 0.3 -10000 0 -0.87 21 21
TWIST1 -0.09 0.36 -10000 0 -0.88 34 34
ELK1 0.019 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.072 0.13 -10000 0 -0.54 13 13
VEGFA -0.025 0.28 -10000 0 -0.83 14 14
CREBBP 0.012 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.024 0.036 -9999 0 -0.45 2 2
SNTA1 0.003 0.078 -9999 0 -0.64 5 5
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.02 0.052 -9999 0 -0.45 2 2
MAPK12 -0.012 0.12 -9999 0 -0.41 20 20
CCND1 -0.014 0.11 -9999 0 -0.52 12 12
p38 gamma/SNTA1 -0.01 0.12 -9999 0 -0.39 23 23
MAP2K3 0.012 0 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.012 0.12 -9999 0 -0.4 20 20
MAP2K6 -0.019 0.12 -9999 0 -0.39 35 35
MAPT -0.018 0.11 -9999 0 -0.37 22 22
MAPK13 0.018 0.042 -9999 0 -0.53 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.022 -9999 0 -0.41 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.14 0.35 -9999 0 -1.1 31 31
RAD9A 0.012 0 -9999 0 -10000 0 0
AP1 -0.022 0.13 -9999 0 -0.47 28 28
IFNAR2 0.011 0.006 -9999 0 -10000 0 0
AKT1 -0.021 0.088 -9999 0 -0.3 13 13
ER alpha/Oestrogen -0.058 0.16 -9999 0 -0.46 50 50
NFX1/SIN3/HDAC complex 0.036 0.018 -9999 0 -10000 0 0
EGF -0.12 0.28 -9999 0 -0.69 68 68
SMG5 0.012 0 -9999 0 -10000 0 0
SMG6 0.012 0 -9999 0 -10000 0 0
SP3/HDAC2 0.016 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.15 0.31 -9999 0 -1.1 29 29
SAP18 0.011 0.003 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.12 0.26 -9999 0 -0.65 67 67
WRN 0.012 0 -9999 0 -10000 0 0
SP1 0.011 0.009 -9999 0 -10000 0 0
SP3 0.01 0.005 -9999 0 -10000 0 0
TERF2IP 0.012 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.26 -9999 0 -0.93 28 28
Mad/Max 0.015 0.023 -9999 0 -0.39 1 1
TERT -0.15 0.37 -9999 0 -1.2 29 29
CCND1 -0.14 0.35 -9999 0 -1.1 37 37
MAX 0.01 0.005 -9999 0 -10000 0 0
RBBP7 0.011 0.003 -9999 0 -10000 0 0
RBBP4 0.011 0.003 -9999 0 -10000 0 0
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.01 0.03 -9999 0 -0.55 1 1
SIN3A 0.011 0.003 -9999 0 -10000 0 0
Telomerase/911 0.02 0.038 -9999 0 -10000 0 0
CDKN1B -0.053 0.17 -9999 0 -0.45 32 32
RAD1 0.012 0 -9999 0 -10000 0 0
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
SAP30 0.011 0.003 -9999 0 -10000 0 0
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.01 0.005 -9999 0 -10000 0 0
JUN 0.005 0.062 -9999 0 -0.65 3 3
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.006 -9999 0 -10000 0 0
FOS -0.036 0.17 -9999 0 -0.62 26 26
IFN-gamma/IRF1 -0.074 0.19 -9999 0 -0.44 73 73
PARP2 0.012 0 -9999 0 -10000 0 0
BLM 0.005 0.064 -9999 0 -0.59 4 4
Telomerase -0.006 0.1 -9999 0 -0.48 10 10
IRF1 0.013 0.013 -9999 0 -10000 0 0
ESR1 -0.077 0.22 -9999 0 -0.61 50 50
KU/TER 0.018 0 -9999 0 -10000 0 0
ATM/TRF2 0.017 0.026 -9999 0 -0.47 1 1
ubiquitin-dependent protein catabolic process 0.04 0.02 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.04 0.02 -9999 0 -10000 0 0
HDAC1 0.011 0.003 -9999 0 -10000 0 0
HDAC2 0.011 0.008 -9999 0 -10000 0 0
ATM -0.001 0.027 -9999 0 -0.51 1 1
SMAD3 0.015 0.062 -9999 0 -0.5 5 5
ABL1 0.012 0 -9999 0 -10000 0 0
MXD1 0.009 0.03 -9999 0 -0.55 1 1
MRE11A 0.012 0 -9999 0 -10000 0 0
HUS1 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.012 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.3 -9999 0 -1 29 29
NR2F2 0.014 0.009 -9999 0 -10000 0 0
MAPK3 0.009 0.049 -9999 0 -0.39 5 5
MAPK1 0.009 0.049 -9999 0 -0.39 5 5
TGFB1/TGF beta receptor Type II 0.006 0.066 -9999 0 -0.71 3 3
NFKB1 0.012 0 -9999 0 -10000 0 0
HNRNPC 0.012 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.027 -9999 0 -0.5 1 1
NBN 0.012 0 -9999 0 -10000 0 0
EGFR -0.037 0.17 -9999 0 -0.62 27 27
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.12 0.24 -9999 0 -0.52 89 89
MYC -0.003 0.098 -9999 0 -0.69 7 7
IL2 -0.003 0.067 -9999 0 -0.55 5 5
KU 0.018 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
TGFB1 0.006 0.066 -9999 0 -0.71 3 3
TRF2/BLM -0.004 0.043 -9999 0 -0.4 4 4
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.12 0.32 -9999 0 -1.1 29 29
SP1/HDAC2 0.017 0.015 -9999 0 -10000 0 0
PINX1 0.007 0.057 -9999 0 -0.6 3 3
Telomerase/EST1A -0.14 0.26 -9999 0 -0.93 28 28
Smad3/Myc 0.01 0.083 -9999 0 -0.45 10 10
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.11 0.25 -9999 0 -0.61 72 72
Telomerase/PinX1 -0.14 0.26 -9999 0 -0.93 28 28
Telomerase/AKT1/mTOR/p70S6K -0.008 0.079 -9999 0 -10000 0 0
SIN3B 0.011 0.003 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.14 0.26 -9999 0 -0.93 28 28
response to DNA damage stimulus 0.003 0.008 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.005 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.26 -9999 0 -0.93 28 28
E2F1 0.002 0.075 -9999 0 -0.62 5 5
ZNFX1 0.011 0.003 -9999 0 -10000 0 0
PIF1 -0.018 0.14 -9999 0 -0.65 16 16
NCL 0.012 0 -9999 0 -10000 0 0
DKC1 0.012 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.017 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.11 -10000 0 -0.51 3 3
NFATC4 -0.011 0.11 -10000 0 -0.44 3 3
ERBB2IP 0.012 0.003 -10000 0 -10000 0 0
HSP90 (dimer) 0.012 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.13 -10000 0 -0.58 2 2
JUN 0.003 0.11 -10000 0 -0.35 19 19
HRAS 0.012 0.001 -10000 0 -10000 0 0
DOCK7 -0.023 0.13 -10000 0 -0.54 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.053 0.16 -10000 0 -0.42 39 39
AKT1 0.01 0.003 -10000 0 -10000 0 0
BAD 0.016 0.026 -10000 0 -0.46 1 1
MAPK10 -0.042 0.099 -10000 0 -0.37 18 18
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.033 0.14 -10000 0 -0.64 2 2
RAF1 -0.006 0.12 -10000 0 -0.5 3 3
ErbB2/ErbB3/neuregulin 2 -0.053 0.14 -10000 0 -0.48 24 24
STAT3 0.001 0.002 -10000 0 -10000 0 0
cell migration 0 0.091 -10000 0 -0.29 14 14
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.06 0.25 -10000 0 -0.62 41 41
FOS -0.03 0.18 -10000 0 -0.44 26 26
NRAS 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.031 0.13 -10000 0 -0.58 2 2
MAPK3 -0.042 0.21 -10000 0 -0.6 15 15
MAPK1 -0.042 0.21 -10000 0 -0.6 15 15
JAK2 -0.023 0.13 -10000 0 -0.54 2 2
NF2 -0.002 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.028 0.12 -10000 0 -0.34 37 37
NRG1 -0.084 0.23 -10000 0 -0.63 53 53
GRB2/SOS1 0.014 0.008 -10000 0 -10000 0 0
MAPK8 -0.015 0.11 -10000 0 -0.33 13 13
MAPK9 -0.021 0.06 -10000 0 -0.26 1 1
ERBB2 -0.007 0.059 -10000 0 -0.49 5 5
ERBB3 -0.011 0.13 -10000 0 -0.71 11 11
SHC1 0.008 0.042 -10000 0 -0.55 2 2
RAC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.003 0.02 0.33 1 -10000 0 1
STAT3 (dimer) 0.017 0.006 -10000 0 -10000 0 0
RNF41 0.022 0.008 -10000 0 -10000 0 0
FRAP1 0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.037 0.08 -10000 0 -0.37 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.049 -10000 0 -0.41 5 5
CHRNA1 -0.067 0.26 -10000 0 -0.65 45 45
myelination -0.007 0.11 -10000 0 -0.41 3 3
PPP3CB -0.021 0.12 -10000 0 -0.5 2 2
KRAS 0.01 0.03 -10000 0 -0.55 1 1
RAC1-CDC42/GDP -0.011 0.11 -10000 0 -0.46 3 3
NRG2 -0.052 0.19 -10000 0 -0.59 37 37
mol:GDP -0.028 0.12 -10000 0 -0.34 37 37
SOS1 0.012 0.001 -10000 0 -10000 0 0
MAP2K2 -0.005 0.12 -10000 0 -0.53 2 2
SRC 0.012 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.024 0.12 -10000 0 -0.54 2 2
MAP2K1 -0.041 0.19 -10000 0 -0.52 21 21
heart morphogenesis -0.031 0.13 -10000 0 -0.58 2 2
RAS family/GDP -0.01 0.11 -10000 0 -0.51 3 3
GRB2 0.012 0.001 -10000 0 -10000 0 0
PRKACA -0.004 0.008 -10000 0 -10000 0 0
CHRNE 0.002 0.053 -10000 0 -0.21 19 19
HSP90AA1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.003 -10000 0 -10000 0 0
nervous system development -0.031 0.13 -10000 0 -0.58 2 2
CDC42 0.012 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.003 0.096 -9999 0 -0.63 8 8
PLK4 0.002 0.082 -9999 0 -0.68 5 5
regulation of centriole replication 0.002 0.095 -9999 0 -0.48 13 13
Cellular roles of Anthrax toxin

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
ANTXR1 0.001 0.087 -10000 0 -0.66 6 6
ANTXR2 0.006 0.066 -10000 0 -0.71 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.014 -10000 0 -0.085 9 9
monocyte activation -0.046 0.19 -10000 0 -0.57 32 32
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.002 0.011 -10000 0 -10000 0 0
MAP2K7 -0.002 0.011 -10000 0 -10000 0 0
MAP2K6 -0.036 0.11 -10000 0 -0.36 34 34
CYAA 0.004 0.061 -10000 0 -0.37 9 9
MAP2K4 -0.002 0.011 -10000 0 -10000 0 0
IL1B -0.026 0.12 -10000 0 -0.36 36 36
Channel 0.005 0.065 -10000 0 -0.4 9 9
NLRP1 -0.011 0.061 -10000 0 -0.4 8 8
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.014 0.085 9 -10000 0 9
MAPK3 -0.002 0.011 -10000 0 -10000 0 0
MAPK1 -0.002 0.011 -10000 0 -10000 0 0
PGR -0.026 0.093 -10000 0 -0.37 23 23
PA/Cellular Receptors -0.011 0.069 -10000 0 -0.43 9 9
apoptosis -0.002 0.014 -10000 0 -0.085 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.005 0.061 -10000 0 -0.37 9 9
macrophage activation 0.016 0.013 -10000 0 -10000 0 0
TNF -0.06 0.21 -10000 0 -0.65 38 38
VCAM1 -0.047 0.19 -10000 0 -0.58 32 32
platelet activation -0.003 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.004 0.03 0.18 1 -10000 0 1
IL18 -0.009 0.1 -10000 0 -0.43 17 17
negative regulation of macrophage activation -0.002 0.014 -10000 0 -0.085 9 9
LEF -0.002 0.014 -10000 0 -0.086 9 9
CASP1 -0.007 0.039 -10000 0 -0.22 9 9
mol:cAMP -0.003 0.016 -10000 0 -10000 0 0
necrosis -0.002 0.014 -10000 0 -0.085 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.005 0.062 -10000 0 -0.38 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.012 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0 0.092 -9999 0 -0.44 13 13
forebrain development -0.059 0.23 -9999 0 -0.7 27 27
GNAO1 -0.034 0.17 -9999 0 -0.65 24 24
SMO/beta Arrestin2 -0.002 0.099 -9999 0 -0.48 14 14
SMO -0.015 0.13 -9999 0 -0.65 14 14
ARRB2 0.011 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.036 0.07 -9999 0 -0.67 1 1
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.012 0 -9999 0 -10000 0 0
GNAI2 0.011 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0.008 0.016 -9999 0 -10000 0 0
GNAI1 -0.003 0.095 -9999 0 -0.66 7 7
XPO1 0.012 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.085 0.19 -9999 0 -0.73 17 17
SAP30 0.012 0.001 -9999 0 -10000 0 0
mol:GDP -0.015 0.13 -9999 0 -0.65 14 14
MIM/GLI2A -0.008 0.11 -9999 0 -0.64 9 9
IFT88 0.012 0 -9999 0 -10000 0 0
GNAI3 0.011 0.004 -9999 0 -10000 0 0
GLI2 0.032 0.046 -9999 0 -10000 0 0
GLI3 0.031 0.074 -9999 0 -0.72 1 1
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
SAP18 0.012 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.012 0 -9999 0 -10000 0 0
GNG2 0.008 0.054 -9999 0 -0.71 2 2
Gi family/GTP -0.036 0.16 -9999 0 -0.4 39 39
SIN3B 0.012 0.001 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.036 0.06 -9999 0 -0.45 2 2
GLI2/Su(fu) 0.031 0.065 -9999 0 -10000 0 0
FOXA2 -0.24 0.49 -9999 0 -1.2 65 65
neural tube patterning -0.059 0.23 -9999 0 -0.7 27 27
SPOP 0.012 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.016 0.05 -9999 0 -0.42 1 1
GNB1 0.012 0 -9999 0 -10000 0 0
CSNK1G2 0.006 0.066 -9999 0 -0.71 3 3
CSNK1G3 0.012 0 -9999 0 -10000 0 0
MTSS1 -0.008 0.11 -9999 0 -0.64 9 9
embryonic limb morphogenesis -0.059 0.23 -9999 0 -0.7 27 27
SUFU 0.012 0.055 -9999 0 -0.46 1 1
LGALS3 0.006 0.066 -9999 0 -0.71 3 3
catabolic process 0.052 0.072 -9999 0 -0.56 1 1
GLI3A/CBP -0.014 0.1 -9999 0 -0.37 23 23
KIF3A 0.012 0 -9999 0 -10000 0 0
GLI1 -0.061 0.24 -9999 0 -0.73 27 27
RAB23 0.01 0.038 -9999 0 -0.71 1 1
CSNK1A1 0.01 0.038 -9999 0 -0.71 1 1
IFT172 0.008 0.054 -9999 0 -0.71 2 2
RBBP7 0.012 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.013 0.063 -9999 0 -0.41 4 4
GNAZ -0.069 0.22 -9999 0 -0.65 43 43
RBBP4 0.012 0.001 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GLI2/SPOP 0.036 0.043 -9999 0 -10000 0 0
STK36 0.01 0.039 -9999 0 -0.71 1 1
Gi family/GNB1/GNG2/GDP -0.024 0.14 -9999 0 -0.57 11 11
PTCH1 -0.051 0.23 -9999 0 -0.84 17 17
MIM/GLI1 -0.11 0.32 -9999 0 -0.67 73 73
CREBBP -0.014 0.1 -9999 0 -0.37 23 23
Su(fu)/SIN3/HDAC complex 0.044 0.016 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.016 0.12 -9999 0 -0.44 22 22
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.033 -9999 0 -10000 0 0
AURKB -0.028 0.16 -9999 0 -0.66 21 21
AURKC -0.014 0.13 -9999 0 -0.64 14 14
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.049 0.1 0.43 9 -10000 0 9
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.019 0.082 -10000 0 -0.36 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.033 0.17 -10000 0 -0.65 24 24
RhoA/GTP -0.05 0.1 -10000 0 -0.44 9 9
negative regulation of cAMP metabolic process -0.031 0.13 -10000 0 -0.47 10 10
GNAZ -0.068 0.22 -10000 0 -0.64 43 43
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 -0.02 0.14 -10000 0 -0.58 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.031 0.13 -10000 0 -0.47 10 10
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.095 -10000 0 -0.66 7 7
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 -0.001 0.025 -9999 0 -0.46 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.051 0.19 -9999 0 -0.64 34 34
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.025 0.086 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.01 0.038 -9999 0 -0.71 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.01 0.038 -9999 0 -0.71 1 1
FYN 0.006 0.066 -9999 0 -0.71 3 3
MAP3K12 0.012 0 -9999 0 -10000 0 0
FGR -0.004 0.1 -9999 0 -0.69 8 8
p38 alpha/TAB1 -0.042 0.097 -9999 0 -0.38 17 17
PRKG1 -0.034 0.18 -9999 0 -0.7 23 23
DUSP8 -0.002 0.1 -9999 0 -0.71 7 7
PGK/cGMP/p38 alpha -0.06 0.13 -9999 0 -0.44 28 28
apoptosis -0.041 0.093 -9999 0 -0.37 16 16
RAL/GTP -0.001 0.018 -9999 0 -0.33 1 1
LYN 0.008 0.054 -9999 0 -0.71 2 2
DUSP1 -0.014 0.13 -9999 0 -0.65 14 14
PAK1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.03 0.023 -9999 0 -0.41 1 1
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.032 0.16 -9999 0 -0.51 22 22
BLK -0.12 0.27 -9999 0 -0.65 70 70
HCK -0.012 0.13 -9999 0 -0.68 12 12
MAP2K3 0.012 0 -9999 0 -10000 0 0
DUSP16 0.01 0.038 -9999 0 -0.71 1 1
DUSP10 0.01 0.038 -9999 0 -0.71 1 1
TRAF6/MEKK3 0.014 0.023 -9999 0 -0.42 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.011 0.12 -9999 0 -0.42 16 16
positive regulation of innate immune response -0.028 0.17 -9999 0 -0.56 19 19
LCK -0.004 0.1 -9999 0 -0.69 8 8
p38alpha-beta/MKP7 -0.022 0.16 -9999 0 -0.53 18 18
p38alpha-beta/MKP5 -0.022 0.16 -9999 0 -0.56 15 15
PGK/cGMP -0.026 0.13 -9999 0 -0.53 23 23
PAK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.032 0.18 -9999 0 -0.55 21 21
CDC42 0.012 0 -9999 0 -10000 0 0
RALB 0.01 0.03 -9999 0 -0.55 1 1
RALA 0.012 0 -9999 0 -10000 0 0
PAK3 -0.15 0.27 -9999 0 -0.59 94 94
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.033 0.17 -9999 0 -0.65 24 24
CDC42/GTP -0.048 0.12 -9999 0 -0.59 8 8
PLCG1 -0.02 0.14 -9999 0 -0.6 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.018 0 -9999 0 -10000 0 0
cell migration -0.047 0.11 -9999 0 -0.57 8 8
S1PR5 -0.02 0.14 -9999 0 -0.58 19 19
S1PR4 -0.004 0.11 -9999 0 -0.71 8 8
MAPK3 -0.019 0.13 -9999 0 -0.6 8 8
MAPK1 -0.019 0.13 -9999 0 -0.6 8 8
S1P/S1P5/Gi -0.031 0.13 -9999 0 -0.47 10 10
GNAI1 -0.001 0.095 -9999 0 -0.66 7 7
CDC42/GDP 0.009 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.019 0.082 -9999 0 -0.36 19 19
RHOA 0.019 0.062 -9999 0 -0.38 8 8
S1P/S1P4/Gi -0.028 0.14 -9999 0 -0.41 25 25
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.068 0.22 -9999 0 -0.64 43 43
S1P/S1P4/G12/G13 0.013 0.065 -9999 0 -0.42 8 8
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.011 0.022 -10000 0 -0.4 1 1
TRAF2/ASK1 -0.004 0.042 -10000 0 -0.46 3 3
ATM 0.01 0.038 -10000 0 -0.71 1 1
MAP2K3 0.014 0.05 -10000 0 -0.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.001 0.081 -10000 0 -0.36 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.037 0.17 -10000 0 -0.65 26 26
TXN 0.006 0.023 -10000 0 -0.24 3 3
CALM1 0.012 0 -10000 0 -10000 0 0
GADD45A -0.004 0.1 -10000 0 -0.62 9 9
GADD45B 0.007 0.057 -10000 0 -0.6 3 3
MAP3K1 0.012 0 -10000 0 -10000 0 0
MAP3K6 0.01 0.038 -10000 0 -0.71 1 1
MAP3K7 0.012 0 -10000 0 -10000 0 0
MAP3K4 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.015 0.041 -10000 0 -0.53 2 2
TAK1/TAB family 0.002 0.02 0.2 3 -10000 0 3
RAC1/OSM/MEKK3 0.022 0.023 -10000 0 -0.42 1 1
TRAF2 0.008 0.054 -10000 0 -0.71 2 2
RAC1/OSM/MEKK3/MKK3 -0.008 0.028 -10000 0 -10000 0 0
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.13 0.26 -10000 0 -0.59 85 85
CCM2 0.012 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.089 0.16 -10000 0 -0.37 85 85
MAPK11 0.004 0.072 -10000 0 -0.67 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.063 0.15 -10000 0 -0.33 86 86
OSM/MEKK3 0.016 0.029 -10000 0 -0.53 1 1
TAOK1 0.009 0.054 -10000 0 -0.4 6 6
TAOK2 0.015 0.022 -10000 0 -0.4 1 1
TAOK3 0.015 0.022 -10000 0 -0.4 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.012 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0.038 -10000 0 -0.71 1 1
MAP3K10 0.006 0.066 -10000 0 -0.71 3 3
MAP3K3 0.01 0.038 -10000 0 -0.71 1 1
TRX/ASK1 0.012 0.032 -10000 0 -0.45 1 1
GADD45/MTK1/MTK1 -0.036 0.12 -10000 0 -0.45 20 20
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.006 0.15 -9999 0 -0.62 10 10
MAP3K8 0.006 0.062 -9999 0 -0.66 3 3
FOS 0.006 0.13 -9999 0 -0.62 10 10
PRKCA -0.009 0.12 -9999 0 -0.65 11 11
PTPN7 -0.003 0.11 -9999 0 -0.71 8 8
HRAS 0.012 0.001 -9999 0 -10000 0 0
PRKCB -0.009 0.12 -9999 0 -0.65 11 11
NRAS 0.012 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.022 0.018 -9999 0 -10000 0 0
MAPK3 0.006 0.11 -9999 0 -0.63 8 8
MAP2K1 0.008 0.11 -9999 0 -0.51 14 14
ELK1 0.011 0.005 -9999 0 -10000 0 0
BRAF -0.025 0.1 -9999 0 -0.49 14 14
mol:GTP 0 0.001 -9999 0 -0.005 26 26
MAPK1 0.006 0.11 -9999 0 -0.63 8 8
RAF1 -0.025 0.1 -9999 0 -0.49 14 14
KRAS 0.01 0.03 -9999 0 -0.55 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.015 0.012 -10000 0 -10000 0 0
HSPA8 0.007 0.054 -10000 0 -0.7 2 2
SMAD3/SMAD4/ER alpha -0.054 0.16 -10000 0 -0.51 23 23
AKT1 0.011 0.017 -10000 0 -10000 0 0
GSC -0.098 0.32 -10000 0 -1.2 19 19
NKX2-5 -0.039 0.15 -10000 0 -0.55 28 28
muscle cell differentiation 0.034 0.082 0.46 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.036 0.086 -10000 0 -0.46 2 2
SMAD4 0.009 0.044 -10000 0 -10000 0 0
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.036 0.13 -10000 0 -0.43 17 17
SMAD3/SMAD4/VDR 0.003 0.075 -10000 0 -0.48 3 3
MYC -0.001 0.096 -10000 0 -0.66 7 7
CDKN2B -0.037 0.31 -10000 0 -1.5 16 16
AP1 0.016 0.12 -10000 0 -0.63 5 5
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.046 0.034 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.009 0.099 -10000 0 -0.47 5 5
SP3 0.014 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.056 0.18 -10000 0 -0.58 36 36
SMAD3/SMAD4/GR -0.005 0.063 -10000 0 -0.45 4 4
GATA3 -0.009 0.097 -10000 0 -0.56 9 9
SKI/SIN3/HDAC complex/NCoR1 0.037 0.022 -10000 0 -10000 0 0
MEF2C/TIF2 -0.039 0.17 -10000 0 -0.66 13 13
endothelial cell migration 0.051 0.28 1.4 12 -10000 0 12
MAX 0.013 0.011 -10000 0 -10000 0 0
RBBP7 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.001 -10000 0 -10000 0 0
RUNX2 0.01 0.03 -10000 0 -0.55 1 1
RUNX3 -0.002 0.098 -10000 0 -0.69 7 7
RUNX1 0.012 0 -10000 0 -10000 0 0
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.009 0.056 -10000 0 -0.71 2 2
VDR 0.001 0.087 -10000 0 -0.66 6 6
CDKN1A 0.039 0.14 -10000 0 -1.4 3 3
KAT2B 0.013 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.033 0.14 -10000 0 -0.46 14 14
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.001 -10000 0 -10000 0 0
SERPINE1 -0.052 0.28 -10000 0 -1.5 12 12
SMAD3/SMAD4/ATF2 -0.004 0.058 -10000 0 -0.44 3 3
SMAD3/SMAD4/ATF3 -0.021 0.097 -10000 0 -0.48 6 6
SAP30 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.02 0.036 -10000 0 -10000 0 0
JUN 0.017 0.12 -10000 0 -0.63 5 5
SMAD3/SMAD4/IRF7 -0.009 0.073 -10000 0 -0.46 5 5
TFE3 0.014 0.032 -10000 0 -0.53 1 1
COL1A2 -0.014 0.19 -10000 0 -0.76 16 16
mesenchymal cell differentiation 0.005 0.055 0.43 2 -10000 0 2
DLX1 -0.022 0.12 -10000 0 -0.55 19 19
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.03 0.16 -10000 0 -0.61 26 26
SMAD3/SMAD4/Max -0.002 0.053 -10000 0 -0.43 2 2
Cbp/p300/SNIP1 0.008 0.018 -10000 0 -10000 0 0
ZBTB17 0.008 0.056 -10000 0 -0.71 2 2
LAMC1 0.035 0.066 -10000 0 -0.64 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.004 0.057 -10000 0 -0.44 3 3
IRF7 0.005 0.073 -10000 0 -0.67 4 4
ESR1 -0.076 0.22 -10000 0 -0.61 50 50
HNF4A -0.2 0.29 -10000 0 -0.6 123 123
MEF2C -0.039 0.17 -10000 0 -0.71 10 10
SMAD2-3/SMAD4 -0.012 0.059 -10000 0 -0.42 3 3
Cbp/p300/Src-1 0.011 0.035 -10000 0 -0.45 1 1
IGHV3OR16-13 -0.003 0.016 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0.03 -10000 0 -0.55 1 1
CREBBP 0.014 0.009 -10000 0 -10000 0 0
SKIL 0.01 0.038 -10000 0 -0.71 1 1
HDAC1 0.012 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.001 -10000 0 -10000 0 0
SNIP1 0.011 0.003 -10000 0 -10000 0 0
GCN5L2 0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.069 -10000 0 -0.44 1 1
MSG1/HSC70 -0.049 0.16 -10000 0 -0.43 51 51
SMAD2 0.003 0.043 -10000 0 -0.56 1 1
SMAD3 0.012 0.065 -10000 0 -0.67 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.032 0.049 -10000 0 -0.36 1 1
SMAD2/SMAD2/SMAD4 0.013 0.024 -10000 0 -10000 0 0
NCOR1 0.01 0.038 -10000 0 -0.71 1 1
NCOA2 -0.004 0.11 -10000 0 -0.71 8 8
NCOA1 0.01 0.038 -10000 0 -0.71 1 1
MYOD/E2A 0.009 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.041 0.088 -10000 0 -0.45 1 1
IFNB1 0.021 0.083 -10000 0 -0.48 4 4
SMAD3/SMAD4/MEF2C -0.028 0.17 -10000 0 -0.72 10 10
CITED1 -0.072 0.21 -10000 0 -0.59 49 49
SMAD2-3/SMAD4/ARC105 0.026 0.071 -10000 0 -0.47 1 1
RBL1 0.008 0.054 -10000 0 -0.71 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.12 -10000 0 -0.51 16 16
RUNX1-3/PEBPB2 -0.009 0.061 -10000 0 -0.45 6 6
SMAD7 0.041 0.12 -10000 0 -0.71 3 3
MYC/MIZ-1 -0.006 0.085 -10000 0 -0.49 9 9
SMAD3/SMAD4 0.015 0.12 0.3 5 -0.46 7 12
IL10 -0.01 0.19 -10000 0 -0.74 18 18
PIASy/HDAC complex 0.011 0.009 -10000 0 -10000 0 0
PIAS3 0.013 0.005 -10000 0 -10000 0 0
CDK2 0.014 0.008 -10000 0 -10000 0 0
IL5 0.009 0.1 -10000 0 -0.47 4 4
CDK4 0.01 0.052 -10000 0 -0.55 3 3
PIAS4 0.011 0.009 -10000 0 -10000 0 0
ATF3 -0.017 0.13 -10000 0 -0.58 17 17
SMAD3/SMAD4/SP1 0.034 0.081 -10000 0 -0.46 3 3
FOXG1 -0.063 0.18 -10000 0 -0.56 41 41
FOXO3 0.02 0.022 -10000 0 -10000 0 0
FOXO1 0.016 0.05 -10000 0 -0.47 3 3
FOXO4 0.02 0.022 -10000 0 -10000 0 0
heart looping -0.038 0.17 -10000 0 -0.7 10 10
CEBPB 0.01 0.031 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 -0.022 0.1 -10000 0 -0.48 8 8
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.14 0.19 -10000 0 -0.47 50 50
SMAD3/SMAD4/GATA3 -0.024 0.1 -10000 0 -0.53 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.038 -10000 0 -0.71 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.005 0.079 -10000 0 -0.5 4 4
SMAD3/SMAD4/SP1-3 0.045 0.073 -10000 0 -0.43 1 1
MED15 0.01 0.038 -10000 0 -0.71 1 1
SP1 0.014 0.028 -10000 0 -10000 0 0
SIN3B 0.012 0.001 -10000 0 -10000 0 0
SIN3A 0.012 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.049 0.16 -10000 0 -0.6 9 9
ITGB5 0.047 0.064 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.076 0.17 -10000 0 -0.49 37 37
AR -0.1 0.25 -10000 0 -0.63 62 62
negative regulation of cell growth 0.032 0.062 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.006 0.053 -10000 0 -0.41 3 3
E2F5 0.009 0.042 -10000 0 -0.55 2 2
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.011 0.11 -10000 0 -0.47 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.027 0.092 -10000 0 -0.5 2 2
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.019 0.12 -10000 0 -0.64 5 5
SMAD3/SMAD4/RUNX2 -0.004 0.056 -10000 0 -0.43 2 2
TGIF2 0.01 0.03 -10000 0 -0.55 1 1
TGIF1 0.01 0.038 -10000 0 -0.71 1 1
ATF2 0.01 0.038 -10000 0 -0.71 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.006 0.069 0.29 19 -10000 0 19
BUB1B 0 0.1 -10000 0 -0.46 14 14
PLK1 0.009 0.038 -10000 0 -0.16 13 13
PLK1S1 0.011 0.018 -10000 0 -0.12 1 1
KIF2A 0.014 0.041 -10000 0 -0.27 4 4
regulation of mitotic centrosome separation 0.009 0.038 -10000 0 -0.16 13 13
GOLGA2 0.01 0.038 -10000 0 -0.71 1 1
Hec1/SPC24 -0.031 0.18 -10000 0 -0.53 34 34
WEE1 0.016 0.035 -10000 0 -0.32 1 1
cytokinesis 0.002 0.13 -10000 0 -0.64 12 12
PP2A-alpha B56 -0.008 0.17 -10000 0 -0.74 18 18
AURKA 0.006 0.047 -10000 0 -0.35 5 5
PICH/PLK1 0.017 0.085 -10000 0 -0.47 8 8
CENPE -0.006 0.11 -10000 0 -0.42 21 21
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.041 -10000 0 -0.27 4 4
PPP2CA 0.012 0 -10000 0 -10000 0 0
FZR1 0.008 0.054 -10000 0 -0.71 2 2
TPX2 -0.009 0.086 -10000 0 -0.34 22 22
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 -0.037 0.18 -10000 0 -0.68 25 25
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN -0.01 0.092 -10000 0 -0.33 24 24
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase -0.001 0.005 -10000 0 -0.023 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.018 -10000 0 -0.081 12 12
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 5 5
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.017 -10000 0 -10000 0 0
spindle elongation 0.009 0.038 -10000 0 -0.16 13 13
ODF2 0.011 0.002 -10000 0 -10000 0 0
BUB1 -0.043 0.18 -10000 0 -0.82 18 18
TPT1 0.01 0.024 -10000 0 -0.28 1 1
CDC25C -0.027 0.14 -10000 0 -0.46 30 30
CDC25B 0.012 0.002 -10000 0 -10000 0 0
SGOL1 -0.006 0.069 -10000 0 -0.29 19 19
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.01 0.058 -10000 0 -0.51 4 4
CDC14B 0.009 0.022 -10000 0 -0.41 1 1
CDC20 -0.031 0.17 -10000 0 -0.68 22 22
PLK1/PBIP1 -0.014 0.065 -10000 0 -0.39 8 8
mitosis 0.001 0.006 0.037 8 -10000 0 8
FBXO5 0.015 0.029 -10000 0 -0.19 3 3
CDC2 0.001 0.003 -10000 0 -0.021 4 4
NDC80 -0.036 0.17 -10000 0 -0.66 25 25
metaphase plate congression 0.009 0.025 -10000 0 -0.17 1 1
ERCC6L -0.015 0.079 -10000 0 -0.49 8 8
NLP/gamma Tubulin 0.009 0.02 -10000 0 -0.11 4 4
microtubule cytoskeleton organization 0.01 0.024 -10000 0 -0.28 1 1
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.012 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.006 0.11 -10000 0 -0.55 12 12
GRASP65/GM130/RAB1/GTP/PLK1 -0.006 0.029 -10000 0 -0.35 1 1
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.029 -10000 0 -0.22 1 1
mitotic prometaphase -0.001 0.003 -10000 0 -0.014 12 12
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.053 -10000 0 -10000 0 0
microtubule-based process 0.001 0.1 -10000 0 -0.49 13 13
Golgi organization 0.009 0.038 -10000 0 -0.16 13 13
Cohesin/SA2 -0.007 0.031 -10000 0 -0.23 3 3
PPP1CB/MYPT1 0.017 0.003 -10000 0 -10000 0 0
KIF20A -0.012 0.13 -10000 0 -0.7 12 12
APC/C/CDC20 -0.01 0.12 -10000 0 -0.47 22 22
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation -0.013 0.064 -10000 0 -0.38 8 8
PRC1 0.008 0.054 -10000 0 -0.71 2 2
ECT2 0.013 0.047 -10000 0 -0.35 3 3
C13orf34 0.013 0.029 -10000 0 -0.22 1 1
NUDC 0.009 0.025 -10000 0 -0.17 1 1
regulation of attachment of spindle microtubules to kinetochore 0 0.099 -10000 0 -0.46 14 14
spindle assembly 0.01 0.029 -10000 0 -0.17 4 4
spindle stabilization 0.011 0.018 -10000 0 -0.12 1 1
APC/C/HCDH1 0.013 0.041 -10000 0 -0.42 3 3
MKLP2/PLK1 0.001 0.1 -10000 0 -0.49 13 13
CCNB1 0.003 0.083 -10000 0 -0.68 5 5
PPP1CB 0.012 0.001 -10000 0 -10000 0 0
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.011 0.058 -10000 0 -0.47 4 4
TUBG1 0.011 0.018 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.057 -10000 0 -0.5 4 4
MLF1IP 0.001 0.07 -10000 0 -0.53 6 6
INCENP 0.011 0.003 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.003 0.11 -10000 0 -0.5 16 16
MAP4K4 0 0.12 -10000 0 -0.71 5 5
BAG4 0.01 0.03 -10000 0 -0.55 1 1
PKC zeta/ceramide -0.016 0.068 -10000 0 -0.33 8 8
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 -0.031 0.16 -10000 0 -0.65 23 23
BAX -0.001 0.025 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.019 0.012 -10000 0 -10000 0 0
BAD -0.01 0.049 0.18 8 -0.24 1 9
SMPD1 -0.001 0.075 -10000 0 -0.24 26 26
RB1 -0.012 0.057 0.18 9 -0.4 2 11
FADD/Caspase 8 0.011 0.12 -10000 0 -0.78 4 4
MAP2K4 -0.002 0.046 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.065 -10000 0 -0.32 7 7
EGF -0.12 0.28 -10000 0 -0.69 68 68
mol:ceramide -0.018 0.053 0.19 9 -10000 0 9
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0 0.1 -10000 0 -0.5 14 14
ASAH1 0.01 0.038 -10000 0 -0.71 1 1
negative regulation of cell cycle -0.012 0.057 0.18 9 -0.4 2 11
cell proliferation -0.015 0.087 -10000 0 -0.32 14 14
BID 0.002 0.078 -10000 0 -0.41 5 5
MAP3K1 -0.009 0.049 0.18 9 -10000 0 9
EIF2A 0.004 0.044 -10000 0 -10000 0 0
TRADD 0.01 0.038 -10000 0 -0.71 1 1
CRADD 0.01 0.03 -10000 0 -0.55 1 1
MAPK3 0.001 0.061 -10000 0 -0.35 3 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.061 -10000 0 -0.35 3 3
Cathepsin D/ceramide -0.011 0.053 -10000 0 -0.32 2 2
FADD 0.002 0.12 -10000 0 -0.75 4 4
KSR1 -0.017 0.068 0.18 9 -0.32 8 17
MAPK8 -0.002 0.053 -10000 0 -0.28 2 2
PRKRA -0.009 0.049 0.19 1 -10000 0 1
PDGFA -0.013 0.13 -10000 0 -0.67 13 13
TRAF2 0.008 0.054 -10000 0 -0.71 2 2
IGF1 -0.034 0.17 -10000 0 -0.64 25 25
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.018 0.052 0.19 9 -10000 0 9
CTSD 0.008 0.054 -10000 0 -0.71 2 2
regulation of nitric oxide biosynthetic process 0.018 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.094 -10000 0 -0.34 13 13
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ -0.002 0.09 -10000 0 -0.59 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0 0.1 -10000 0 -0.5 14 14
RelA/NF kappa B1 0.018 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0.038 -10000 0 -0.71 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.12 -10000 0 -0.8 4 4
TNFR1A/BAG4/TNF-alpha -0.045 0.13 -10000 0 -0.45 25 25
mol:Sphingosine-1-phosphate -0.003 0.11 -10000 0 -0.5 16 16
MAP2K1 -0.002 0.062 -10000 0 -0.36 3 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS 0 0.043 0.22 4 -10000 0 4
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.017 0.022 -10000 0 -0.39 1 1
EIF2AK2 -0.002 0.046 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.044 0.13 -10000 0 -0.45 25 25
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.094 -10000 0 -1.4 1 1
MAP2K2 -0.002 0.062 -10000 0 -0.36 3 3
SMPD3 -0.022 0.13 -10000 0 -0.47 14 14
TNF -0.06 0.21 -10000 0 -0.65 38 38
PKC zeta/PAR4 0.006 0.073 -10000 0 -0.44 9 9
mol:PHOSPHOCHOLINE 0.039 0.11 0.26 59 -10000 0 59
NF kappa B1/RelA/I kappa B alpha -0.008 0.048 -10000 0 -10000 0 0
AIFM1 0 0.043 0.22 4 -10000 0 4
BCL2 -0.011 0.12 -10000 0 -0.61 13 13
Signaling events me