Kidney Renal Clear Cell Carcinoma: 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 42 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 122
Syndecan-4-mediated signaling events 104
Ephrin A reverse signaling 90
Nephrin/Neph1 signaling in the kidney podocyte 83
Glypican 2 network 78
PDGFR-alpha signaling pathway 76
IL23-mediated signaling events 69
IL4-mediated signaling events 68
Syndecan-1-mediated signaling events 63
Signaling events mediated by the Hedgehog family 63
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 122 5637 46 -1.1 0.036 1000 -1000 -0.11 -1000
Syndecan-4-mediated signaling events 104 6997 67 -0.56 0.096 1000 -1000 -0.12 -1000
Ephrin A reverse signaling 90 636 7 -0.2 0 1000 -1000 -0.053 -1000
Nephrin/Neph1 signaling in the kidney podocyte 83 2833 34 -0.25 0.015 1000 -1000 -0.098 -1000
Glypican 2 network 78 315 4 -0.13 -0.054 1000 -1000 -0.058 -1000
PDGFR-alpha signaling pathway 76 3354 44 -0.24 0.03 1000 -1000 -0.086 -1000
IL23-mediated signaling events 69 4140 60 -0.55 0.015 1000 -1000 -0.19 -1000
IL4-mediated signaling events 68 6278 91 -0.78 0.58 1000 -1000 -0.17 -1000
Syndecan-1-mediated signaling events 63 2175 34 -0.3 0.015 1000 -1000 -0.097 -1000
Signaling events mediated by the Hedgehog family 63 3288 52 -0.42 0.17 1000 -1000 -0.13 -1000
LPA4-mediated signaling events 56 680 12 -0.25 0.021 1000 -1000 -0.043 -1000
amb2 Integrin signaling 53 4363 82 -0.43 0.015 1000 -1000 -0.13 -1000
IL6-mediated signaling events 48 3641 75 -0.65 0.05 1000 -1000 -0.13 -1000
BMP receptor signaling 47 3841 81 -0.37 0.027 1000 -1000 -0.14 -1000
Wnt signaling 47 334 7 -0.14 0.011 1000 -1000 -0.049 -1000
Glypican 1 network 45 2191 48 -0.19 0.027 1000 -1000 -0.077 -1000
Endothelins 45 4355 96 -0.31 0.016 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 41 2808 68 -0.45 0.11 1000 -1000 -0.19 -1000
HIF-1-alpha transcription factor network 40 3078 76 -0.43 0.048 1000 -1000 -0.19 -1000
TCR signaling in naïve CD8+ T cells 40 3756 93 -0.21 0.04 1000 -1000 -0.13 -1000
IL12-mediated signaling events 38 3373 87 -0.31 0.11 1000 -1000 -0.16 -1000
p75(NTR)-mediated signaling 38 4826 125 -0.55 0.015 1000 -1000 -0.16 -1000
EGFR-dependent Endothelin signaling events 36 772 21 -0.22 0.015 1000 -1000 -0.11 -1000
IL27-mediated signaling events 35 1823 51 -0.23 0.094 1000 -1000 -0.13 -1000
EPO signaling pathway 34 1913 55 -0.41 0.015 1000 -1000 -0.15 -1000
Effects of Botulinum toxin 34 903 26 -0.23 0.015 1000 -1000 -0.1 -1000
Reelin signaling pathway 33 1870 56 -0.36 0.015 1000 -1000 -0.13 -1000
Calcium signaling in the CD4+ TCR pathway 33 1037 31 -0.34 0.015 1000 -1000 -0.15 -1000
Angiopoietin receptor Tie2-mediated signaling 33 2935 88 -0.37 0.076 1000 -1000 -0.17 -1000
Visual signal transduction: Rods 33 1740 52 -0.18 0.015 1000 -1000 -0.13 -1000
Glucocorticoid receptor regulatory network 32 3666 114 -0.48 0.12 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 30 799 26 -0.17 0.015 1000 -1000 -0.13 -1000
LPA receptor mediated events 30 3122 102 -0.18 0.015 1000 -1000 -0.13 -1000
VEGFR1 specific signals 30 1735 56 -0.16 0.015 1000 -1000 -0.12 -1000
Arf6 signaling events 29 1852 62 -0.22 0.015 1000 -1000 -0.097 -1000
Signaling events regulated by Ret tyrosine kinase 27 2236 82 -0.21 0.015 1000 -1000 -0.13 -1000
Nongenotropic Androgen signaling 26 1373 52 -0.096 0.019 1000 -1000 -0.1 -1000
Signaling events mediated by VEGFR1 and VEGFR2 26 3336 125 -0.16 0.027 1000 -1000 -0.16 -1000
Neurotrophic factor-mediated Trk receptor signaling 26 3213 120 -0.25 0.16 1000 -1000 -0.12 -1000
Integrins in angiogenesis 25 2109 84 -0.35 0.019 1000 -1000 -0.14 -1000
Visual signal transduction: Cones 24 914 38 -0.16 0.015 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 24 2603 105 -0.22 0.028 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 23 855 37 -0.42 0.015 1000 -1000 -0.088 -1000
EPHB forward signaling 23 1987 85 -0.2 0.095 1000 -1000 -0.15 -1000
FOXM1 transcription factor network 23 1184 51 -0.12 0.19 1000 -1000 -0.21 -1000
HIF-2-alpha transcription factor network 22 971 43 -0.29 0.09 1000 -1000 -0.13 -1000
BCR signaling pathway 22 2196 99 -0.19 0.035 1000 -1000 -0.14 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 22 1723 78 -0.41 0.04 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 21 1488 69 -0.23 0.04 1000 -1000 -0.084 -1000
Signaling events mediated by PTP1B 21 1617 76 -0.23 0.023 1000 -1000 -0.11 -1000
S1P1 pathway 21 789 36 -0.092 0.015 1000 -1000 -0.081 -1000
JNK signaling in the CD4+ TCR pathway 20 355 17 -0.1 0.015 1000 -1000 -0.093 -1000
Canonical Wnt signaling pathway 20 1040 51 -0.18 0.052 1000 -1000 -0.089 -1000
Aurora B signaling 20 1358 67 -0.26 0.015 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 19 1035 54 -0.2 0.031 1000 -1000 -0.15 -1000
Fc-epsilon receptor I signaling in mast cells 19 1858 97 -0.16 0.032 1000 -1000 -0.14 -1000
Presenilin action in Notch and Wnt signaling 18 1158 61 -0.18 0.047 1000 -1000 -0.1 -1000
TCGA08_retinoblastoma 18 145 8 -0.03 0.019 1000 -1000 -0.029 -1000
Class IB PI3K non-lipid kinase events 18 54 3 -0.015 -1000 1000 -1000 -0.018 -1000
IL1-mediated signaling events 17 1114 62 -0.22 0.067 1000 -1000 -0.15 -1000
E-cadherin signaling events 17 89 5 -0.037 0.015 1000 -1000 -0.07 -1000
Ras signaling in the CD4+ TCR pathway 17 291 17 -0.049 0.015 1000 -1000 -0.074 -1000
Ephrin B reverse signaling 16 784 48 -0.11 0.1 1000 -1000 -0.11 -1000
Signaling mediated by p38-gamma and p38-delta 16 246 15 -0.05 0.02 1000 -1000 -0.05 -1000
Coregulation of Androgen receptor activity 15 1144 76 -0.29 0.024 1000 -1000 -0.076 -1000
IL2 signaling events mediated by PI3K 15 873 58 -0.097 0.03 1000 -1000 -0.12 -1000
Signaling mediated by p38-alpha and p38-beta 15 664 44 -0.22 0.015 1000 -1000 -0.079 -1000
Regulation of Telomerase 15 1550 102 -0.4 0.046 1000 -1000 -0.15 -1000
ErbB2/ErbB3 signaling events 14 953 65 -0.14 0.027 1000 -1000 -0.11 -1000
ErbB4 signaling events 14 1028 69 -0.16 0.07 1000 -1000 -0.14 -1000
Osteopontin-mediated events 14 534 38 -0.1 0.021 1000 -1000 -0.16 -1000
Cellular roles of Anthrax toxin 14 551 39 -0.08 0.018 1000 -1000 -0.049 -1000
PDGFR-beta signaling pathway 14 1408 97 -0.11 0.034 1000 -1000 -0.13 -1000
Caspase cascade in apoptosis 13 1013 74 -0.14 0.022 1000 -1000 -0.084 -1000
FAS signaling pathway (CD95) 13 629 47 -0.28 0.016 1000 -1000 -0.074 -1000
Syndecan-3-mediated signaling events 12 421 35 -0.14 0.015 1000 -1000 -0.11 -1000
IL2 signaling events mediated by STAT5 12 283 22 -0.086 0.016 1000 -1000 -0.072 -1000
Plasma membrane estrogen receptor signaling 12 1090 86 -0.071 0.043 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 11 1618 136 -0.14 0.14 1000 -1000 -0.11 -1000
Aurora A signaling 11 696 60 -0.21 0.033 1000 -1000 -0.09 -1000
IFN-gamma pathway 11 768 68 -0.24 0.027 1000 -1000 -0.14 -1000
Ceramide signaling pathway 11 841 76 -0.22 0.065 1000 -1000 -0.11 -1000
S1P3 pathway 11 481 42 -0.055 0.02 1000 -1000 -0.082 -1000
Regulation of Androgen receptor activity 11 770 70 -0.28 0.035 1000 -1000 -0.1 -1000
Sphingosine 1-phosphate (S1P) pathway 10 295 28 -0.045 0.015 1000 -1000 -0.084 -1000
PLK2 and PLK4 events 10 30 3 -0.004 0.007 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 10 54 5 -0.029 0.002 1000 -1000 -0.054 -1000
Regulation of p38-alpha and p38-beta 10 545 54 -0.16 0.015 1000 -1000 -0.096 -1000
TCGA08_rtk_signaling 10 267 26 -0.22 0.036 1000 -1000 -0.032 -1000
p38 MAPK signaling pathway 10 447 44 -0.18 0.021 1000 -1000 -0.093 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 9 821 85 -0.096 0.043 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 9 636 65 -0.33 0.062 1000 -1000 -0.086 -1000
Aurora C signaling 9 67 7 -0.047 0 1000 -1000 -0.069 -1000
PLK1 signaling events 9 834 85 -0.044 0.019 1000 -1000 -0.081 -1000
Insulin-mediated glucose transport 9 311 32 -0.19 0.032 1000 -1000 -0.1 -1000
Nectin adhesion pathway 9 614 63 -0.055 0.05 1000 -1000 -0.11 -1000
S1P5 pathway 9 168 17 -0.035 0.034 1000 -1000 -0.074 -1000
RXR and RAR heterodimerization with other nuclear receptor 9 504 52 -0.11 0.03 1000 -1000 -0.098 -1000
FoxO family signaling 9 577 64 -0.47 0.12 1000 -1000 -0.11 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 421 45 -0.089 0.046 1000 -1000 -0.14 -1000
Stabilization and expansion of the E-cadherin adherens junction 9 690 74 -0.22 0.068 1000 -1000 -0.14 -1000
Insulin Pathway 9 717 74 -0.084 0.032 1000 -1000 -0.13 -1000
TRAIL signaling pathway 8 421 48 -0.038 0.042 1000 -1000 -0.1 -1000
TCGA08_p53 8 62 7 -0.022 0.018 1000 -1000 -0.021 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 272 33 -0.095 0.035 1000 -1000 -0.09 -1000
Signaling events mediated by PRL 8 301 34 -0.073 0.019 1000 -1000 -0.07 -1000
BARD1 signaling events 7 411 57 -0.031 0.05 1000 -1000 -0.099 -1000
Signaling events mediated by HDAC Class III 7 299 40 -0.087 0.027 1000 -1000 -0.068 -1000
ceramide signaling pathway 7 372 49 -0.08 0.033 1000 -1000 -0.08 -1000
E-cadherin signaling in the nascent adherens junction 7 589 76 -0.042 0.049 1000 -1000 -0.13 -1000
Class I PI3K signaling events 7 566 73 -0.14 0.034 1000 -1000 -0.11 -1000
IGF1 pathway 7 428 57 -0.053 0.03 1000 -1000 -0.14 -1000
E-cadherin signaling in keratinocytes 7 322 43 -0.14 0.034 1000 -1000 -0.1 -1000
S1P4 pathway 7 198 25 -0.031 0.022 1000 -1000 -0.08 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 570 83 -0.19 0.056 1000 -1000 -0.12 -1000
Canonical NF-kappaB pathway 5 204 39 -0.08 0.085 1000 -1000 -0.14 -1000
Atypical NF-kappaB pathway 5 158 31 -0.041 0.036 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 4 343 75 -0.035 0.033 1000 -1000 -0.1 -1000
Circadian rhythm pathway 4 88 22 -0.015 0.041 1000 -1000 -0.097 -1000
mTOR signaling pathway 4 262 53 -0.018 0.03 1000 -1000 -0.086 -1000
Class I PI3K signaling events mediated by Akt 4 276 68 -0.19 0.054 1000 -1000 -0.096 -1000
Retinoic acid receptors-mediated signaling 4 252 58 -0.032 0.041 1000 -1000 -0.12 -1000
Paxillin-dependent events mediated by a4b1 4 174 36 -0.064 0.026 1000 -1000 -0.1 -1000
Arf6 trafficking events 4 328 71 -0.055 0.047 1000 -1000 -0.12 -1000
Alternative NF-kappaB pathway 4 56 13 -0.022 0.015 1000 -1000 -0.099 -1000
Arf6 downstream pathway 3 168 43 -0.025 0.025 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class I 3 412 104 -0.08 0.062 1000 -1000 -0.11 -1000
Rapid glucocorticoid signaling 3 78 20 -0.019 0.015 1000 -1000 -0.065 -1000
Arf1 pathway 2 126 54 -0.014 0.032 1000 -1000 -0.075 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 36 23 -0.01 0.051 1000 -1000 -0.11 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 11 27 -0.002 0.033 1000 -1000 -0.088 -1000
Total 2961 168283 7203 -25 -990 131000 -131000 -14 -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 -0.73 0.57 -10000 0 -1.3 189 189
PCK1 -0.76 0.68 -10000 0 -1.5 197 197
HNF4A -0.94 0.66 -10000 0 -1.5 221 221
KCNJ11 -0.73 0.64 -10000 0 -1.4 185 185
AKT1 -0.17 0.19 -10000 0 -1.3 2 2
response to starvation -0.027 0.047 -10000 0 -10000 0 0
DLK1 -0.74 0.61 -10000 0 -1.3 191 191
NKX2-1 -0.13 0.21 0.41 9 -0.45 51 60
ACADM -0.73 0.57 -10000 0 -1.3 188 188
TAT -0.43 0.33 -10000 0 -0.98 85 85
CEBPB -0.028 0.12 -10000 0 -0.74 13 13
CEBPA -0.04 0.16 -10000 0 -0.81 19 19
TTR -0.61 0.42 -10000 0 -1 188 188
PKLR -0.82 0.65 -10000 0 -1.5 198 198
APOA1 -0.88 0.63 -10000 0 -1.5 210 210
CPT1C -0.74 0.59 -10000 0 -1.3 198 198
ALAS1 -0.27 0.21 -10000 0 -1.1 9 9
TFRC -0.48 0.36 -10000 0 -1 93 93
FOXF1 -0.027 0.18 -10000 0 -0.81 24 24
NF1 0.022 0.01 -10000 0 -10000 0 0
HNF1A (dimer) -0.076 0.24 -10000 0 -0.89 35 35
CPT1A -0.73 0.57 -10000 0 -1.3 190 190
HMGCS1 -0.73 0.56 -10000 0 -1.3 189 189
NR3C1 -0.022 0.072 -10000 0 -0.78 1 1
CPT1B -0.8 0.63 -10000 0 -1.4 206 206
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.015 0 -10000 0 -10000 0 0
GCK -0.78 0.61 -10000 0 -1.4 206 206
CREB1 -0.037 0.069 -10000 0 -10000 0 0
IGFBP1 -0.57 0.54 -10000 0 -1.2 178 178
PDX1 -0.32 0.3 -10000 0 -0.76 93 93
UCP2 -0.73 0.57 -10000 0 -1.3 190 190
ALDOB -0.94 0.72 -10000 0 -1.5 242 242
AFP -0.37 0.4 -10000 0 -0.94 112 112
BDH1 -0.77 0.6 -10000 0 -1.4 189 189
HADH -0.71 0.6 -10000 0 -1.4 171 171
F2 -1.1 0.7 -10000 0 -1.6 270 270
HNF1A -0.076 0.24 -10000 0 -0.89 35 35
G6PC -0.6 0.66 -10000 0 -1.4 172 172
SLC2A2 -0.6 0.7 -10000 0 -1.8 104 104
INS 0.036 0.067 -10000 0 -10000 0 0
FOXA1 -0.33 0.38 -10000 0 -0.81 170 170
FOXA3 -0.24 0.33 -10000 0 -0.83 94 94
FOXA2 -0.84 0.75 -10000 0 -1.5 206 206
ABCC8 -0.74 0.61 -10000 0 -1.4 178 178
ALB -0.44 0.5 -10000 0 -1.1 136 136
Syndecan-4-mediated signaling events

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.063 0.15 -9999 0 -0.57 32 32
Syndecan-4/Syndesmos -0.48 0.36 -9999 0 -0.8 217 217
positive regulation of JNK cascade -0.44 0.31 -9999 0 -0.78 176 176
Syndecan-4/ADAM12 -0.56 0.4 -9999 0 -0.87 257 257
CCL5 -0.072 0.24 -9999 0 -0.75 53 53
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.011 0.056 -9999 0 -0.85 2 2
ITGA5 0 0.11 -9999 0 -0.85 8 8
SDCBP 0.013 0.033 -9999 0 -0.69 1 1
PLG -0.42 0.39 -9999 0 -0.75 265 265
ADAM12 -0.18 0.34 -9999 0 -0.75 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.065 -9999 0 -0.8 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.056 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.51 0.37 -9999 0 -0.82 234 234
Syndecan-4/CXCL12/CXCR4 -0.47 0.36 -9999 0 -0.86 175 175
Syndecan-4/Laminin alpha3 -0.49 0.36 -9999 0 -0.81 227 227
MDK -0.097 0.27 -9999 0 -0.76 68 68
Syndecan-4/FZD7 -0.48 0.36 -9999 0 -0.8 217 217
Syndecan-4/Midkine -0.53 0.38 -9999 0 -0.83 242 242
FZD7 0.005 0.083 -9999 0 -0.72 6 6
Syndecan-4/FGFR1/FGF -0.45 0.32 -9999 0 -0.76 202 202
THBS1 -0.007 0.13 -9999 0 -0.82 12 12
integrin-mediated signaling pathway -0.48 0.35 -9999 0 -0.79 227 227
positive regulation of MAPKKK cascade -0.44 0.31 -9999 0 -0.78 176 176
Syndecan-4/TACI -0.53 0.38 -9999 0 -0.84 242 242
CXCR4 -0.015 0.16 -9999 0 -0.85 16 16
cell adhesion -0.005 0.14 -9999 0 -0.68 14 14
Syndecan-4/Dynamin -0.47 0.36 -9999 0 -0.8 217 217
Syndecan-4/TSP1 -0.48 0.36 -9999 0 -0.81 222 222
Syndecan-4/GIPC -0.48 0.36 -9999 0 -0.8 217 217
Syndecan-4/RANTES -0.51 0.38 -9999 0 -0.83 232 232
ITGB1 0.015 0 -9999 0 -10000 0 0
LAMA1 -0.066 0.25 -9999 0 -0.83 45 45
LAMA3 -0.023 0.16 -9999 0 -0.73 24 24
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.096 0.1 -9999 0 -0.59 7 7
Syndecan-4/alpha-Actinin -0.48 0.36 -9999 0 -0.8 218 218
TFPI -0.081 0.27 -9999 0 -0.83 53 53
F2 -0.37 0.39 -9999 0 -0.76 234 234
alpha5/beta1 Integrin -0.011 0.085 -9999 0 -0.66 8 8
positive regulation of cell adhesion -0.5 0.36 -9999 0 -0.84 201 201
ACTN1 0.006 0.086 -9999 0 -0.82 5 5
TNC -0.069 0.24 -9999 0 -0.78 49 49
Syndecan-4/CXCL12 -0.49 0.37 -9999 0 -0.82 223 223
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CXCL12 -0.023 0.17 -9999 0 -0.79 22 22
TNFRSF13B -0.11 0.28 -9999 0 -0.76 74 74
FGF2 -0.012 0.15 -9999 0 -0.82 15 15
FGFR1 0.013 0.033 -9999 0 -0.69 1 1
Syndecan-4/PI-4-5-P2 -0.48 0.35 -9999 0 -0.8 218 218
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.028 0.19 -9999 0 -0.73 32 32
cell migration -0.03 0.021 -9999 0 -10000 0 0
PRKCD 0.008 0.11 -9999 0 -0.67 11 11
vasculogenesis -0.46 0.34 -9999 0 -0.76 222 222
SDC4 -0.52 0.39 -9999 0 -0.87 217 217
Syndecan-4/Tenascin C -0.51 0.38 -9999 0 -0.84 227 227
Syndecan-4/PI-4-5-P2/PKC alpha -0.082 0.044 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.47 0.36 -9999 0 -0.8 217 217
MMP9 -0.18 0.33 -9999 0 -0.74 118 118
Rac1/GTP -0.014 0.15 -9999 0 -0.71 14 14
cytoskeleton organization -0.45 0.33 -9999 0 -0.76 217 217
GIPC1 0.008 0.076 -9999 0 -0.81 4 4
Syndecan-4/TFPI -0.52 0.38 -9999 0 -0.83 240 240
Ephrin A reverse signaling

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.16 0.25 -9999 0 -0.54 136 136
EFNA5 -0.2 0.36 -9999 0 -0.79 126 126
FYN -0.13 0.25 -9999 0 -0.56 85 85
neuron projection morphogenesis -0.16 0.25 -9999 0 -0.54 136 136
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.16 0.25 -9999 0 -0.55 136 136
EPHA5 -0.02 0.13 -9999 0 -0.69 17 17
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.23 0.31 0.64 166 -10000 0 166
KIRREL -0.057 0.2 -10000 0 -0.87 25 25
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.23 0.31 -10000 0 -0.64 166 166
PLCG1 0.015 0 -10000 0 -10000 0 0
ARRB2 0.013 0.033 -10000 0 -0.69 1 1
WASL 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.24 0.3 -10000 0 -0.63 141 141
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.14 0.23 -10000 0 -0.55 57 57
FYN -0.21 0.29 -10000 0 -0.59 141 141
mol:Ca2+ -0.24 0.29 -10000 0 -0.62 140 140
mol:DAG -0.24 0.29 -10000 0 -0.62 140 140
NPHS2 -0.15 0.29 -10000 0 -0.75 88 88
mol:IP3 -0.24 0.29 -10000 0 -0.62 140 140
regulation of endocytosis -0.21 0.26 -10000 0 -0.71 59 59
Nephrin/NEPH1/podocin/Cholesterol -0.24 0.3 -10000 0 -0.63 140 140
establishment of cell polarity -0.23 0.31 -10000 0 -0.64 166 166
Nephrin/NEPH1/podocin/NCK1-2 -0.22 0.27 -10000 0 -0.76 57 57
Nephrin/NEPH1/beta Arrestin2 -0.2 0.27 -10000 0 -0.73 59 59
NPHS1 -0.25 0.37 -10000 0 -0.79 148 148
Nephrin/NEPH1/podocin -0.22 0.28 -10000 0 -0.6 141 141
TJP1 0.015 0 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
NCK2 0.013 0.04 -10000 0 -0.85 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.24 0.3 -10000 0 -0.62 140 140
CD2AP 0.011 0.052 -10000 0 -0.77 2 2
Nephrin/NEPH1/podocin/GRB2 -0.24 0.3 -10000 0 -0.62 140 140
GRB2 0.015 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.23 0.32 -10000 0 -0.62 151 151
cytoskeleton organization -0.19 0.29 -10000 0 -0.64 92 92
Nephrin/NEPH1 -0.17 0.24 -10000 0 -0.48 166 166
Nephrin/NEPH1/ZO-1 -0.19 0.26 -10000 0 -0.52 166 166
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 -0.097 0.27 -9999 0 -0.76 68 68
GPC2 -0.054 0.22 -9999 0 -0.77 41 41
GPC2/Midkine -0.13 0.26 -9999 0 -0.6 103 103
neuron projection morphogenesis -0.13 0.26 -9999 0 -0.6 103 103
PDGFR-alpha signaling pathway

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
PDGFRA -0.22 0.36 -9999 0 -0.77 142 142
PDGF/PDGFRA/CRKL -0.17 0.26 -9999 0 -0.57 142 142
positive regulation of JUN kinase activity -0.13 0.2 -9999 0 -0.49 69 69
CRKL 0.015 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.18 0.27 -9999 0 -0.58 142 142
AP1 -0.24 0.38 -9999 0 -1 69 69
mol:IP3 -0.16 0.28 -9999 0 -0.59 142 142
PLCG1 -0.16 0.28 -9999 0 -0.59 142 142
PDGF/PDGFRA/alphaV Integrin -0.17 0.27 -9999 0 -0.57 143 143
RAPGEF1 0.013 0.04 -9999 0 -0.85 1 1
CRK 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ -0.16 0.28 -9999 0 -0.58 142 142
CAV3 0 0 -9999 0 -10000 0 0
CAV1 -0.001 0.12 -9999 0 -0.83 9 9
SHC/Grb2/SOS1 -0.13 0.2 -9999 0 -0.5 69 69
PDGF/PDGFRA/Shf -0.18 0.27 -9999 0 -0.58 145 145
FOS -0.21 0.39 -9999 0 -0.98 69 69
JUN -0.027 0.086 -9999 0 -0.7 7 7
oligodendrocyte development -0.17 0.26 -9999 0 -0.57 143 143
GRB2 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
mol:DAG -0.16 0.28 -9999 0 -0.59 142 142
PDGF/PDGFRA -0.22 0.36 -9999 0 -0.77 142 142
actin cytoskeleton reorganization -0.17 0.26 -9999 0 -0.57 142 142
SRF 0.03 0.033 -9999 0 -0.65 1 1
SHC1 0.013 0.033 -9999 0 -0.69 1 1
PI3K -0.15 0.23 -9999 0 -0.54 87 87
PDGF/PDGFRA/Crk/C3G -0.15 0.23 -9999 0 -0.54 82 82
JAK1 -0.16 0.28 -9999 0 -0.57 143 143
ELK1/SRF -0.096 0.22 -9999 0 -0.58 12 12
SHB 0.015 0 -9999 0 -10000 0 0
SHF 0.006 0.083 -9999 0 -0.79 5 5
CSNK2A1 0.02 0.024 -9999 0 -10000 0 0
GO:0007205 -0.16 0.28 -9999 0 -0.58 142 142
SOS1 0.015 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.13 0.2 -9999 0 -0.49 69 69
PDGF/PDGFRA/SHB -0.17 0.26 -9999 0 -0.57 142 142
PDGF/PDGFRA/Caveolin-1 -0.18 0.28 -9999 0 -0.58 148 148
ITGAV 0.013 0.033 -9999 0 -0.69 1 1
ELK1 -0.14 0.25 -9999 0 -0.58 82 82
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
PDGF/PDGFRA/Crk -0.17 0.26 -9999 0 -0.57 142 142
JAK-STAT cascade -0.16 0.28 -9999 0 -0.57 143 143
cell proliferation -0.18 0.27 -9999 0 -0.58 145 145
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.44 0.56 -10000 0 -1.2 114 114
IL23A -0.42 0.55 -10000 0 -1.3 101 101
NF kappa B1 p50/RelA/I kappa B alpha -0.45 0.49 -10000 0 -1.2 108 108
positive regulation of T cell mediated cytotoxicity -0.47 0.63 -10000 0 -1.4 117 117
ITGA3 -0.4 0.53 -10000 0 -1.2 93 93
IL17F -0.26 0.35 -10000 0 -0.79 68 68
IL12B -0.11 0.29 -10000 0 -0.79 71 71
STAT1 (dimer) -0.45 0.6 -10000 0 -1.3 112 112
CD4 -0.4 0.52 -10000 0 -1.2 94 94
IL23 -0.44 0.55 -10000 0 -1.2 111 111
IL23R -0.055 0.16 -10000 0 -0.78 13 13
IL1B -0.44 0.58 -10000 0 -1.3 103 103
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.42 0.54 -10000 0 -1.2 109 109
TYK2 0.004 0.061 -10000 0 -0.88 2 2
STAT4 -0.014 0.16 -10000 0 -0.84 16 16
STAT3 0.015 0.001 -10000 0 -10000 0 0
IL18RAP -0.031 0.18 -10000 0 -0.8 24 24
IL12RB1 -0.031 0.18 -10000 0 -0.83 22 22
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
IL12Rbeta1/TYK2 -0.028 0.15 -10000 0 -0.68 23 23
IL23R/JAK2 -0.059 0.17 -10000 0 -0.75 12 12
positive regulation of chronic inflammatory response -0.47 0.63 -10000 0 -1.4 117 117
natural killer cell activation 0.006 0.012 0.059 15 -10000 0 15
JAK2 0.013 0.026 -10000 0 -10000 0 0
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
NFKB1 0.013 0.004 -10000 0 -10000 0 0
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.42 0.51 -10000 0 -1.2 111 111
ALOX12B -0.47 0.59 -10000 0 -1.3 123 123
CXCL1 -0.55 0.63 -10000 0 -1.3 150 150
T cell proliferation -0.47 0.63 -10000 0 -1.4 117 117
NFKBIA 0.011 0.04 -10000 0 -0.86 1 1
IL17A -0.19 0.28 -10000 0 -0.6 61 61
PI3K -0.47 0.51 -10000 0 -1.2 117 117
IFNG -0.041 0.064 0.12 8 -0.13 98 106
STAT3 (dimer) -0.44 0.48 -10000 0 -1.2 111 111
IL18R1 -0.035 0.19 -10000 0 -0.85 25 25
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.38 -10000 0 -0.99 58 58
IL18/IL18R -0.062 0.26 -10000 0 -0.8 43 43
macrophage activation -0.022 0.018 -10000 0 -0.045 63 63
TNF -0.45 0.59 -10000 0 -1.3 109 109
STAT3/STAT4 -0.47 0.52 -10000 0 -1.2 118 118
STAT4 (dimer) -0.45 0.6 -10000 0 -1.3 115 115
IL18 -0.021 0.15 -10000 0 -0.76 19 19
IL19 -0.4 0.51 -10000 0 -1.1 118 118
STAT5A (dimer) -0.45 0.59 -10000 0 -1.3 111 111
STAT1 0.008 0.069 -10000 0 -0.73 4 4
SOCS3 -0.034 0.19 -10000 0 -0.78 29 29
CXCL9 -0.44 0.57 -10000 0 -1.3 115 115
MPO -0.45 0.56 -10000 0 -1.2 118 118
positive regulation of humoral immune response -0.47 0.63 -10000 0 -1.4 117 117
IL23/IL23R/JAK2/TYK2 -0.54 0.79 -10000 0 -1.6 116 116
IL6 -0.54 0.62 -10000 0 -1.3 148 148
STAT5A 0.011 0.056 -10000 0 -0.85 2 2
IL2 -0.015 0.12 -10000 0 -0.7 14 14
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.012 0.059 15 -10000 0 15
CD3E -0.43 0.56 -10000 0 -1.3 106 106
keratinocyte proliferation -0.47 0.63 -10000 0 -1.4 117 117
NOS2 -0.44 0.56 -10000 0 -1.3 111 111
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.57 -10000 0 -1.3 118 118
STAT6 (cleaved dimer) -0.57 0.57 -10000 0 -1.2 166 166
IGHG1 -0.16 0.2 -10000 0 -0.62 14 14
IGHG3 -0.49 0.55 -10000 0 -1.1 155 155
AKT1 -0.24 0.35 -10000 0 -0.93 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.38 -10000 0 -1.2 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.37 -10000 0 -0.96 58 58
THY1 -0.51 0.6 -10000 0 -1.4 108 108
MYB -0.068 0.24 -10000 0 -0.75 51 51
HMGA1 -0.009 0.13 -10000 0 -0.73 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.48 -10000 0 -1 98 98
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.37 -10000 0 -0.99 49 49
SP1 0.022 0.011 -10000 0 -10000 0 0
INPP5D 0.009 0.069 -10000 0 -0.85 3 3
SOCS5 0.026 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.57 -10000 0 -1.2 161 161
SOCS1 -0.32 0.38 -10000 0 -0.85 100 100
SOCS3 -0.29 0.4 -10000 0 -1.1 59 59
FCER2 -0.46 0.53 -10000 0 -1.2 112 112
PARP14 0.012 0.041 -10000 0 -0.85 1 1
CCL17 -0.58 0.65 -10000 0 -1.4 137 137
GRB2 0.015 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.31 -10000 0 -0.94 39 39
T cell proliferation -0.52 0.61 -10000 0 -1.3 142 142
IL4R/JAK1 -0.5 0.58 -10000 0 -1.3 130 130
EGR2 -0.55 0.62 -10000 0 -1.4 127 127
JAK2 -0.003 0.031 -10000 0 -10000 0 0
JAK3 -0.02 0.18 -10000 0 -0.81 22 22
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
JAK1 0.005 0.042 -10000 0 -0.85 1 1
COL1A2 -0.21 0.38 -10000 0 -1.2 46 46
CCL26 -0.6 0.67 -10000 0 -1.4 157 157
IL4R -0.54 0.63 -10000 0 -1.4 132 132
PTPN6 0.022 0.057 -10000 0 -0.83 2 2
IL13RA2 -0.59 0.66 -10000 0 -1.4 157 157
IL13RA1 -0.003 0.031 -10000 0 -10000 0 0
IRF4 -0.22 0.46 -10000 0 -1.2 64 64
ARG1 -0.13 0.24 -10000 0 -0.92 20 20
CBL -0.31 0.42 -10000 0 -1.1 62 62
GTF3A 0.016 0.039 -10000 0 -0.69 1 1
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
IL13RA1/JAK2 -0.009 0.047 -10000 0 -10000 0 0
IRF4/BCL6 -0.21 0.41 -10000 0 -1.1 62 62
CD40LG -0.036 0.21 -10000 0 -0.83 31 31
MAPK14 -0.32 0.45 -10000 0 -1.1 67 67
mitosis -0.23 0.32 -10000 0 -0.86 53 53
STAT6 -0.62 0.77 -10000 0 -1.5 149 149
SPI1 0 0.12 -10000 0 -0.82 10 10
RPS6KB1 -0.21 0.31 -10000 0 -0.86 47 47
STAT6 (dimer) -0.62 0.78 -10000 0 -1.5 149 149
STAT6 (dimer)/PARP14 -0.56 0.64 -10000 0 -1.4 143 143
mast cell activation 0.011 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.42 -10000 0 -1.1 55 55
FRAP1 -0.24 0.35 -10000 0 -0.93 55 55
LTA -0.54 0.62 -10000 0 -1.4 133 133
FES 0.007 0.08 -10000 0 -0.85 4 4
T-helper 1 cell differentiation 0.58 0.69 1.4 150 -10000 0 150
CCL11 -0.65 0.65 -10000 0 -1.4 178 178
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.41 -10000 0 -1.1 57 57
IL2RG -0.044 0.21 -10000 0 -0.77 37 37
IL10 -0.55 0.62 -10000 0 -1.4 137 137
IRS1 -0.023 0.16 -10000 0 -0.73 24 24
IRS2 -0.054 0.21 -10000 0 -0.7 45 45
IL4 -0.11 0.13 -10000 0 -10000 0 0
IL5 -0.51 0.57 -10000 0 -1.3 130 130
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.42 -10000 0 -0.9 133 133
COL1A1 -0.31 0.52 -10000 0 -1.3 78 78
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.6 -10000 0 -1.3 129 129
IL2R gamma/JAK3 -0.051 0.24 -10000 0 -0.73 47 47
TFF3 -0.55 0.63 -10000 0 -1.4 132 132
ALOX15 -0.51 0.58 -10000 0 -1.4 102 102
MYBL1 -0.015 0.14 -10000 0 -0.69 20 20
T-helper 2 cell differentiation -0.43 0.49 -10000 0 -1 143 143
SHC1 0.013 0.033 -10000 0 -0.69 1 1
CEBPB -0.002 0.12 -10000 0 -0.72 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.37 -10000 0 -0.93 59 59
mol:PI-3-4-5-P3 -0.24 0.35 -10000 0 -0.93 55 55
PI3K -0.26 0.39 -10000 0 -1 55 55
DOK2 -0.011 0.14 -10000 0 -0.84 14 14
ETS1 0.005 0.13 -10000 0 -0.81 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.3 -10000 0 -0.9 39 39
ITGB3 -0.52 0.59 -10000 0 -1.3 118 118
PIGR -0.78 0.72 -10000 0 -1.5 210 210
IGHE 0.028 0.073 -10000 0 -0.4 1 1
MAPKKK cascade -0.18 0.29 -10000 0 -0.86 39 39
BCL6 0.009 0.077 -10000 0 -0.81 4 4
OPRM1 -0.51 0.57 -10000 0 -1.2 154 154
RETNLB -0.51 0.57 -10000 0 -1.2 154 154
SELP -0.54 0.63 -10000 0 -1.5 112 112
AICDA -0.56 0.62 -10000 0 -1.4 125 125
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.001 0.12 -9999 0 -0.83 9 9
CCL5 -0.072 0.24 -9999 0 -0.75 53 53
SDCBP 0.013 0.033 -9999 0 -0.69 1 1
FGFR/FGF2/Syndecan-1 -0.27 0.28 -9999 0 -0.68 100 100
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 -0.26 0.29 -9999 0 -0.69 96 96
Syndecan-1/Syntenin -0.25 0.27 -9999 0 -0.67 92 92
MAPK3 -0.22 0.26 -9999 0 -0.7 64 64
HGF/MET -0.063 0.19 -9999 0 -0.62 48 48
TGFB1/TGF beta receptor Type II -0.001 0.12 -9999 0 -0.83 9 9
BSG 0.005 0.083 -9999 0 -0.72 6 6
keratinocyte migration -0.25 0.28 -9999 0 -0.67 96 96
Syndecan-1/RANTES -0.3 0.31 -9999 0 -0.71 120 120
Syndecan-1/CD147 -0.24 0.27 -9999 0 -0.75 65 65
Syndecan-1/Syntenin/PIP2 -0.26 0.25 -9999 0 -0.65 92 92
LAMA5 -0.003 0.12 -9999 0 -0.82 10 10
positive regulation of cell-cell adhesion -0.25 0.24 -9999 0 -0.62 92 92
MMP7 -0.28 0.38 -9999 0 -0.76 178 178
HGF -0.059 0.23 -9999 0 -0.77 44 44
Syndecan-1/CASK -0.26 0.27 -9999 0 -0.66 100 100
Syndecan-1/HGF/MET -0.28 0.31 -9999 0 -0.77 95 95
regulation of cell adhesion -0.2 0.25 -9999 0 -0.83 31 31
HPSE -0.029 0.19 -9999 0 -0.81 25 25
positive regulation of cell migration -0.27 0.28 -9999 0 -0.68 100 100
SDC1 -0.27 0.29 -9999 0 -0.7 100 100
Syndecan-1/Collagen -0.27 0.28 -9999 0 -0.68 100 100
PPIB 0.013 0.033 -9999 0 -0.69 1 1
MET 0.002 0.1 -9999 0 -0.75 8 8
PRKACA 0.015 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.74 118 118
MAPK1 -0.22 0.25 -9999 0 -0.68 65 65
homophilic cell adhesion -0.27 0.28 -9999 0 -0.67 100 100
MMP1 -0.25 0.38 -9999 0 -0.78 157 157
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.26 0.35 -10000 0 -0.87 67 67
IHH -0.22 0.36 -10000 0 -0.83 119 119
SHH Np/Cholesterol/GAS1 -0.071 0.18 -10000 0 -0.5 67 67
LRPAP1 0.009 0.069 -10000 0 -0.85 3 3
dorsoventral neural tube patterning 0.07 0.18 0.49 67 -10000 0 67
SMO/beta Arrestin2 -0.17 0.27 -10000 0 -0.74 46 46
SMO -0.19 0.28 -10000 0 -0.76 53 53
AKT1 -0.068 0.15 -10000 0 -0.91 5 5
ARRB2 0.013 0.033 -10000 0 -0.69 1 1
BOC 0 0.11 -10000 0 -0.85 8 8
ADRBK1 0.009 0.069 -10000 0 -0.85 3 3
heart looping -0.19 0.28 -10000 0 -0.75 53 53
STIL -0.17 0.26 -10000 0 -0.68 55 55
DHH N/PTCH2 -0.1 0.24 -10000 0 -0.62 77 77
DHH N/PTCH1 -0.21 0.29 -10000 0 -0.75 66 66
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
DHH -0.063 0.24 -10000 0 -0.79 45 45
PTHLH -0.42 0.54 -10000 0 -1.2 114 114
determination of left/right symmetry -0.19 0.28 -10000 0 -0.75 53 53
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
skeletal system development -0.42 0.52 -10000 0 -1.2 114 114
IHH N/Hhip -0.29 0.36 -10000 0 -0.68 192 192
DHH N/Hhip -0.2 0.3 -10000 0 -0.62 153 153
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.19 0.28 -10000 0 -0.75 53 53
pancreas development -0.18 0.34 -10000 0 -0.75 122 122
HHAT 0.008 0.073 -10000 0 -0.77 4 4
PI3K -0.009 0.07 -10000 0 -0.57 7 7
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.018 0.16 -10000 0 -0.75 20 20
somite specification -0.19 0.28 -10000 0 -0.75 53 53
SHH Np/Cholesterol/PTCH1 -0.19 0.27 -10000 0 -0.69 67 67
SHH Np/Cholesterol/PTCH2 -0.088 0.2 -10000 0 -0.57 45 45
SHH Np/Cholesterol/Megalin -0.13 0.26 -10000 0 -0.57 109 109
SHH -0.042 0.2 -10000 0 -0.61 51 51
catabolic process -0.19 0.27 -10000 0 -0.62 95 95
SMO/Vitamin D3 -0.19 0.29 -10000 0 -0.76 57 57
SHH Np/Cholesterol/Hhip -0.17 0.26 -10000 0 -0.52 141 141
LRP2 -0.12 0.31 -10000 0 -0.84 73 73
receptor-mediated endocytosis -0.25 0.29 -10000 0 -0.82 68 68
SHH Np/Cholesterol/BOC -0.061 0.17 -10000 0 -0.5 58 58
SHH Np/Cholesterol/CDO -0.072 0.2 -10000 0 -0.53 63 63
mesenchymal cell differentiation 0.17 0.26 0.51 152 -10000 0 152
mol:Vitamin D3 -0.19 0.28 -10000 0 -0.7 67 67
IHH N/PTCH2 -0.18 0.3 -10000 0 -0.64 122 122
CDON -0.018 0.16 -10000 0 -0.84 18 18
IHH N/PTCH1 -0.19 0.27 -10000 0 -0.63 95 95
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.64 76 76
PTCH2 -0.046 0.21 -10000 0 -0.78 36 36
SHH Np/Cholesterol -0.053 0.16 -10000 0 -0.49 51 51
PTCH1 -0.19 0.27 -10000 0 -0.62 95 95
HHIP -0.18 0.34 -10000 0 -0.75 122 122
LPA4-mediated signaling events

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
ADCY4 -0.006 0.14 -9999 0 -0.59 23 23
ADCY5 -0.044 0.19 -9999 0 -0.58 52 52
ADCY6 0.021 0.035 -9999 0 -0.51 2 2
ADCY7 0.016 0.065 -9999 0 -0.56 6 6
ADCY1 -0.016 0.15 -9999 0 -0.53 33 33
ADCY2 -0.21 0.27 -9999 0 -0.51 204 204
ADCY3 0.018 0.059 -9999 0 -0.55 5 5
ADCY8 -0.25 0.28 -9999 0 -0.52 237 237
PRKCE 0.011 0.04 -9999 0 -0.6 2 2
ADCY9 0.021 0.035 -9999 0 -0.51 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.2 0.21 -9999 0 -0.5 114 114
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.071 0.22 -9999 0 -0.7 41 41
alphaM/beta2 Integrin/GPIbA -0.063 0.19 -9999 0 -0.7 35 35
alphaM/beta2 Integrin/proMMP-9 -0.16 0.29 -9999 0 -0.64 92 92
PLAUR -0.023 0.17 -9999 0 -0.73 24 24
HMGB1 0.001 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.044 0.17 -9999 0 -0.8 20 20
AGER -0.075 0.23 -9999 0 -0.78 45 45
RAP1A 0.015 0 -9999 0 -10000 0 0
SELPLG -0.004 0.12 -9999 0 -0.85 10 10
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.14 0.24 -9999 0 -0.86 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.74 118 118
CYR61 -0.032 0.19 -9999 0 -0.79 27 27
TLN1 0.013 0.04 -9999 0 -0.85 1 1
Rap1/GTP -0.2 0.23 -9999 0 -0.73 47 47
RHOA 0.015 0 -9999 0 -10000 0 0
P-selectin oligomer -0.051 0.23 -9999 0 -0.82 37 37
MYH2 -0.26 0.29 -9999 0 -0.64 129 129
MST1R -0.058 0.23 -9999 0 -0.76 44 44
leukocyte activation during inflammatory response -0.25 0.28 -9999 0 -0.63 108 108
APOB -0.33 0.39 -9999 0 -0.77 204 204
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.029 0.18 -9999 0 -0.75 27 27
JAM3 -0.005 0.13 -9999 0 -0.84 11 11
GP1BA -0.016 0.16 -9999 0 -0.82 17 17
alphaM/beta2 Integrin/CTGF -0.065 0.21 -9999 0 -0.75 33 33
alphaM/beta2 Integrin -0.23 0.29 -9999 0 -0.62 117 117
JAM3 homodimer -0.005 0.13 -9999 0 -0.83 11 11
ICAM2 0.006 0.086 -9999 0 -0.82 5 5
ICAM1 -0.011 0.14 -9999 0 -0.84 14 14
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.28 -9999 0 -0.61 116 116
cell adhesion -0.062 0.19 -9999 0 -0.69 35 35
NFKB1 -0.16 0.31 -9999 0 -0.88 42 42
THY1 -0.019 0.16 -9999 0 -0.82 19 19
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.26 0.27 -9999 0 -0.52 231 231
alphaM/beta2 Integrin/LRP/tPA -0.06 0.23 -9999 0 -0.86 28 28
IL6 -0.27 0.44 -9999 0 -1 90 90
ITGB2 -0.027 0.15 -9999 0 -0.86 15 15
elevation of cytosolic calcium ion concentration -0.078 0.24 -9999 0 -0.89 29 29
alphaM/beta2 Integrin/JAM2/JAM3 -0.062 0.2 -9999 0 -0.67 37 37
JAM2 -0.01 0.14 -9999 0 -0.83 14 14
alphaM/beta2 Integrin/ICAM1 -0.12 0.29 -9999 0 -0.94 36 36
alphaM/beta2 Integrin/uPA/Plg -0.32 0.3 -9999 0 -0.6 168 168
RhoA/GTP -0.28 0.31 -9999 0 -0.7 129 129
positive regulation of phagocytosis -0.17 0.22 -9999 0 -0.82 32 32
Ron/MSP -0.099 0.25 -9999 0 -0.65 71 71
alphaM/beta2 Integrin/uPAR/uPA -0.079 0.25 -9999 0 -0.91 29 29
alphaM/beta2 Integrin/uPAR -0.067 0.21 -9999 0 -0.8 28 28
PLAU -0.025 0.17 -9999 0 -0.73 25 25
PLAT -0.008 0.14 -9999 0 -0.81 13 13
actin filament polymerization -0.25 0.27 -9999 0 -0.6 129 129
MST1 -0.048 0.22 -9999 0 -0.78 37 37
alphaM/beta2 Integrin/lipoprotein(a) -0.26 0.29 -9999 0 -0.64 108 108
TNF -0.18 0.37 -9999 0 -1 56 56
RAP1B 0.013 0.033 -9999 0 -0.69 1 1
alphaM/beta2 Integrin/uPA -0.067 0.22 -9999 0 -0.67 40 40
fibrinolysis -0.31 0.29 -9999 0 -0.59 168 168
HCK 0 0.11 -9999 0 -0.83 8 8
dendritic cell antigen processing and presentation -0.23 0.28 -9999 0 -0.61 116 116
VTN -0.16 0.32 -9999 0 -0.73 110 110
alphaM/beta2 Integrin/CYR61 -0.072 0.22 -9999 0 -0.72 41 41
LPA -0.048 0.19 -9999 0 -0.69 36 36
LRP1 -0.005 0.13 -9999 0 -0.85 11 11
cell migration -0.17 0.31 -9999 0 -0.77 63 63
FN1 -0.038 0.2 -9999 0 -0.76 32 32
alphaM/beta2 Integrin/Thy1 -0.064 0.22 -9999 0 -0.81 30 30
MPO -0.088 0.26 -9999 0 -0.76 62 62
KNG1 -0.23 0.35 -9999 0 -0.74 151 151
RAP1/GDP -0.001 0.021 -9999 0 -0.45 1 1
ROCK1 -0.26 0.29 -9999 0 -0.69 108 108
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.43 0.39 -9999 0 -0.76 265 265
CTGF -0.02 0.17 -9999 0 -0.8 20 20
alphaM/beta2 Integrin/Hck -0.051 0.21 -9999 0 -0.92 21 21
ITGAM -0.021 0.14 -9999 0 -0.84 12 12
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.085 0.26 -9999 0 -0.75 46 46
HP -0.3 0.38 -9999 0 -0.75 195 195
leukocyte adhesion -0.14 0.26 -9999 0 -1 26 26
SELP -0.051 0.23 -9999 0 -0.82 37 37
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.38 0.31 -9999 0 -0.83 78 78
CRP -0.48 0.41 -9999 0 -0.99 143 143
cell cycle arrest -0.46 0.37 -9999 0 -0.9 138 138
TIMP1 -0.32 0.28 -9999 0 -0.79 59 59
IL6ST -0.062 0.23 -9999 0 -0.86 36 36
Rac1/GDP -0.19 0.24 -9999 0 -0.73 47 47
AP1 -0.085 0.18 -9999 0 -0.61 18 18
GAB2 0.014 0.033 -9999 0 -0.7 1 1
TNFSF11 -0.48 0.41 -9999 0 -1 136 136
HSP90B1 -0.041 0.086 -9999 0 -1.2 1 1
GAB1 0.012 0.056 -9999 0 -0.85 2 2
MAPK14 -0.13 0.25 -9999 0 -0.75 44 44
AKT1 0.041 0.062 -9999 0 -0.61 3 3
FOXO1 0.047 0.07 -9999 0 -0.61 3 3
MAP2K6 -0.16 0.24 -9999 0 -0.7 46 46
mol:GTP -0.003 0.003 -9999 0 -10000 0 0
MAP2K4 -0.23 0.25 -9999 0 -0.77 45 45
MITF -0.17 0.22 -9999 0 -0.67 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.011 0.056 -9999 0 -0.85 2 2
A2M -0.014 0.26 -9999 0 -1.6 12 12
CEBPB 0 0.12 -9999 0 -0.7 13 13
GRB2/SOS1/GAB family/SHP2 -0.046 0.079 -9999 0 -0.43 1 1
STAT3 -0.48 0.42 -9999 0 -0.98 139 139
STAT1 -0.021 0.07 -9999 0 -0.7 3 3
CEBPD -0.39 0.32 -9999 0 -0.86 80 80
PIK3CA 0.015 0.04 -9999 0 -0.85 1 1
PI3K 0.015 0.073 -9999 0 -0.57 7 7
JUN 0.002 0.1 -9999 0 -0.83 7 7
PIAS3/MITF -0.15 0.21 -9999 0 -0.72 28 28
MAPK11 -0.14 0.27 -9999 0 -0.78 49 49
STAT3 (dimer)/FOXO1 -0.3 0.28 -9999 0 -0.74 62 62
GRB2/SOS1/GAB family -0.12 0.18 -9999 0 -0.7 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.22 -9999 0 -0.73 30 30
GRB2 0.015 0.002 -9999 0 -10000 0 0
JAK2 0.015 0 -9999 0 -10000 0 0
LBP -0.53 0.4 -9999 0 -0.9 208 208
PIK3R1 0.006 0.086 -9999 0 -0.75 6 6
JAK1 0.009 0.041 -9999 0 -0.86 1 1
MYC -0.39 0.32 -9999 0 -0.86 84 84
FGG -0.65 0.48 -9999 0 -1 245 245
macrophage differentiation -0.46 0.37 -9999 0 -0.9 138 138
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.2 0.28 -9999 0 -0.81 35 35
JUNB -0.37 0.3 -9999 0 -0.8 90 90
FOS -0.097 0.28 -9999 0 -0.77 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.19 0.24 -9999 0 -0.58 85 85
STAT1/PIAS1 -0.21 0.21 -9999 0 -0.62 53 53
GRB2/SOS1/GAB family/SHP2/PI3K 0.016 0.052 -9999 0 -0.77 1 1
STAT3 (dimer) -0.48 0.42 -9999 0 -0.98 137 137
PRKCD -0.29 0.29 -9999 0 -0.84 52 52
IL6R -0.02 0.16 -9999 0 -0.84 17 17
SOCS3 -0.12 0.32 -9999 0 -1.1 33 33
gp130 (dimer)/JAK1/JAK1/LMO4 -0.041 0.16 -9999 0 -0.58 37 37
Rac1/GTP -0.22 0.25 -9999 0 -0.71 59 59
HCK 0 0.11 -9999 0 -0.83 8 8
MAPKKK cascade -0.022 0.07 -9999 0 -0.67 1 1
bone resorption -0.45 0.37 -9999 0 -0.9 139 139
IRF1 -0.38 0.32 -9999 0 -0.83 88 88
mol:GDP -0.2 0.25 -9999 0 -0.7 59 59
SOS1 0.013 0.007 -9999 0 -10000 0 0
VAV1 -0.2 0.26 -9999 0 -0.72 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.12 0.26 -9999 0 -0.77 39 39
PTPN11 -0.015 0.021 -9999 0 -10000 0 0
IL6/IL6RA -0.21 0.3 -9999 0 -0.61 162 162
gp130 (dimer)/TYK2/TYK2/LMO4 -0.041 0.16 -9999 0 -0.58 38 38
gp130 (dimer)/JAK2/JAK2/LMO4 -0.039 0.16 -9999 0 -0.58 36 36
IL6 -0.24 0.37 -9999 0 -0.78 149 149
PIAS3 0.015 0 -9999 0 -10000 0 0
PTPRE 0.018 0.09 -9999 0 -0.83 5 5
PIAS1 0.015 0 -9999 0 -10000 0 0
RAC1 0.013 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.15 0.21 -9999 0 -0.51 77 77
LMO4 0.004 0.01 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.46 0.34 -9999 0 -0.88 135 135
MCL1 0.05 0.055 -9999 0 -0.59 2 2
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.37 0.37 -9999 0 -0.91 117 117
SMAD6-7/SMURF1 -0.006 0.056 -9999 0 -0.57 4 4
NOG -0.29 0.39 -9999 0 -0.78 179 179
SMAD9 -0.1 0.22 -9999 0 -0.76 39 39
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD5 -0.11 0.22 -9999 0 -0.63 34 34
BMP7/USAG1 -0.34 0.36 -9999 0 -0.68 236 236
SMAD5/SKI -0.1 0.21 -9999 0 -0.63 33 33
SMAD1 0.019 0.054 -9999 0 -10000 0 0
BMP2 -0.016 0.16 -9999 0 -0.84 17 17
SMAD1/SMAD1/SMAD4 -0.006 0.054 -9999 0 -0.6 1 1
BMPR1A 0.015 0 -9999 0 -10000 0 0
BMPR1B -0.27 0.38 -9999 0 -0.77 171 171
BMPR1A-1B/BAMBI -0.22 0.27 -9999 0 -0.61 106 106
AHSG -0.043 0.18 -9999 0 -0.69 33 33
CER1 0 0 -9999 0 -10000 0 0
BMP2-4/CER1 -0.061 0.19 -9999 0 -0.59 48 48
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.098 0.21 -9999 0 -0.65 35 35
BMP2-4 (homodimer) -0.069 0.21 -9999 0 -0.67 48 48
RGMB 0.012 0.046 -9999 0 -0.69 2 2
BMP6/BMPR2/BMPR1A-1B -0.18 0.24 -9999 0 -0.55 93 93
RGMA -0.051 0.22 -9999 0 -0.8 38 38
SMURF1 0.013 0.033 -9999 0 -0.69 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.22 -9999 0 -0.6 46 46
BMP2-4/USAG1 -0.23 0.3 -9999 0 -0.66 109 109
SMAD6/SMURF1/SMAD5 -0.098 0.2 -9999 0 -0.61 31 31
SOSTDC1 -0.26 0.38 -9999 0 -0.77 163 163
BMP7/BMPR2/BMPR1A-1B -0.28 0.31 -9999 0 -0.66 141 141
SKI 0.009 0.069 -9999 0 -0.85 3 3
BMP6 (homodimer) -0.011 0.14 -9999 0 -0.81 15 15
HFE2 -0.041 0.19 -9999 0 -0.69 35 35
ZFYVE16 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.1 0.26 -9999 0 -0.77 49 49
SMAD5/SMAD5/SMAD4 -0.097 0.2 -9999 0 -0.6 32 32
MAPK1 0.015 0 -9999 0 -10000 0 0
TAK1/TAB family -0.11 0.16 -9999 0 -0.6 27 27
BMP7 (homodimer) -0.18 0.33 -9999 0 -0.74 122 122
NUP214 0.013 0.04 -9999 0 -0.85 1 1
BMP6/FETUA -0.056 0.17 -9999 0 -0.56 47 47
SMAD1/SKI 0.024 0.07 -9999 0 -0.59 3 3
SMAD6 0.007 0.08 -9999 0 -0.85 4 4
CTDSP2 0.015 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.09 0.22 -9999 0 -0.69 36 36
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.34 0.4 -9999 0 -0.78 208 208
BMPR2 (homodimer) 0.013 0.04 -9999 0 -0.85 1 1
GADD34/PP1CA -0.005 0.063 -9999 0 -0.63 4 4
BMPR1A-1B (homodimer) -0.21 0.28 -9999 0 -0.58 171 171
CHRDL1 -0.36 0.4 -9999 0 -0.77 223 223
ENDOFIN/SMAD1 0.027 0.051 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.009 0.054 -9999 0 -0.55 1 1
SMAD6/SMURF1 0.013 0.033 -9999 0 -0.69 1 1
BAMBI -0.039 0.21 -9999 0 -0.82 30 30
SMURF2 0.013 0.033 -9999 0 -0.69 1 1
BMP2-4/CHRDL1 -0.3 0.31 -9999 0 -0.67 136 136
BMP2-4/GREM1 -0.28 0.32 -9999 0 -0.57 231 231
SMAD7 0.015 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.069 0.22 -9999 0 -0.71 39 39
SMAD1/SMAD6 0.026 0.058 -9999 0 -0.6 1 1
TAK1/SMAD6 -0.001 0.024 -9999 0 -0.52 1 1
BMP7 -0.19 0.34 -9999 0 -0.75 122 122
BMP6 -0.011 0.14 -9999 0 -0.81 15 15
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.087 0.19 -9999 0 -0.56 35 35
PPM1A 0.015 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.055 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.024 -9999 0 -0.52 1 1
CTDSPL 0.01 0.057 -9999 0 -0.69 3 3
PPP1CA 0.011 0.056 -9999 0 -0.85 2 2
XIAP 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.011 0.056 -9999 0 -0.85 2 2
PPP1R15A 0.01 0.061 -9999 0 -0.75 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.3 -9999 0 -0.75 77 77
CHRD -0.053 0.23 -9999 0 -0.8 39 39
BMPR2 0.013 0.04 -9999 0 -0.85 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.12 0.22 -9999 0 -0.64 45 45
BMP4 -0.047 0.22 -9999 0 -0.79 36 36
FST -0.2 0.35 -9999 0 -0.76 128 128
BMP2-4/NOG -0.25 0.32 -9999 0 -0.68 125 125
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.26 0.29 -9999 0 -0.82 60 60
Wnt signaling

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.14 0.24 -9999 0 -0.62 55 55
FZD6 0.011 0.052 -9999 0 -0.77 2 2
WNT6 -0.14 0.31 -9999 0 -0.78 89 89
WNT4 -0.14 0.31 -9999 0 -0.76 94 94
FZD3 0.011 0.052 -9999 0 -0.77 2 2
WNT5A -0.032 0.18 -9999 0 -0.74 29 29
WNT11 -0.088 0.26 -9999 0 -0.75 63 63
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.024 0.12 -10000 0 -0.62 18 18
fibroblast growth factor receptor signaling pathway -0.024 0.12 -10000 0 -0.62 18 18
LAMA1 -0.066 0.25 -10000 0 -0.83 45 45
PRNP 0.011 0.052 -10000 0 -0.77 2 2
GPC1/SLIT2 -0.11 0.23 -10000 0 -0.6 86 86
SMAD2 0.027 0.082 -10000 0 -0.51 10 10
GPC1/PrPc/Cu2+ -0.008 0.066 -10000 0 -0.54 7 7
GPC1/Laminin alpha1 -0.068 0.2 -10000 0 -0.65 49 49
TDGF1 -0.13 0.29 -10000 0 -0.72 92 92
CRIPTO/GPC1 -0.11 0.22 -10000 0 -0.54 97 97
APP/GPC1 -0.008 0.071 -10000 0 -0.63 6 6
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.071 0.2 -10000 0 -0.46 97 97
FLT1 -0.055 0.24 -10000 0 -0.85 38 38
GPC1/TGFB/TGFBR1/TGFBR2 -0.013 0.084 -10000 0 -0.57 10 10
SERPINC1 -0.078 0.25 -10000 0 -0.74 57 57
FYN -0.075 0.22 -10000 0 -0.48 97 97
FGR -0.082 0.22 -10000 0 -0.48 103 103
positive regulation of MAPKKK cascade -0.098 0.27 -10000 0 -0.7 53 53
SLIT2 -0.12 0.3 -10000 0 -0.77 82 82
GPC1/NRG -0.073 0.2 -10000 0 -0.62 55 55
NRG1 -0.074 0.26 -10000 0 -0.82 50 50
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.081 0.26 -10000 0 -0.8 47 47
LYN -0.073 0.21 -10000 0 -0.47 98 98
mol:Spermine 0.007 0.067 -10000 0 -0.64 5 5
cell growth -0.024 0.12 -10000 0 -0.62 18 18
BMP signaling pathway -0.006 0.086 0.82 5 -10000 0 5
SRC -0.073 0.21 -10000 0 -0.47 97 97
TGFBR1 0.015 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.19 0.34 -10000 0 -0.75 124 124
GPC1 0.006 0.086 -10000 0 -0.82 5 5
TGFBR1 (dimer) 0.015 0 -10000 0 -10000 0 0
VEGFA -0.033 0.2 -10000 0 -0.85 26 26
BLK -0.17 0.3 -10000 0 -0.55 163 163
HCK -0.08 0.22 -10000 0 -0.48 102 102
FGF2 -0.012 0.15 -10000 0 -0.82 15 15
FGFR1 0.013 0.033 -10000 0 -0.69 1 1
VEGFR1 homodimer -0.055 0.24 -10000 0 -0.85 38 38
TGFBR2 0.004 0.097 -10000 0 -0.85 6 6
cell death -0.008 0.071 -10000 0 -0.63 6 6
ATIII/GPC1 -0.074 0.19 -10000 0 -0.56 62 62
PLA2G2A/GPC1 -0.16 0.26 -10000 0 -0.57 128 128
LCK -0.11 0.27 -10000 0 -0.56 109 109
neuron differentiation -0.073 0.2 -10000 0 -0.62 55 55
PrPc/Cu2+ -0.003 0.039 -10000 0 -0.6 2 2
APP 0.013 0.04 -10000 0 -0.85 1 1
TGFBR2 (dimer) 0.004 0.097 -10000 0 -0.85 6 6
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.086 0.4 -10000 0 -0.89 66 66
PTK2B 0.014 0.033 -10000 0 -0.69 1 1
mol:Ca2+ -0.001 0.31 -10000 0 -1 32 32
EDN1 -0.08 0.33 -10000 0 -0.91 54 54
EDN3 -0.072 0.22 -10000 0 -0.69 54 54
EDN2 -0.21 0.36 -10000 0 -0.79 133 133
HRAS/GDP -0.032 0.32 -10000 0 -0.95 42 42
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.042 0.31 -10000 0 -0.89 42 42
ADCY4 -0.1 0.38 -10000 0 -1 50 50
ADCY5 -0.13 0.4 -10000 0 -1 59 59
ADCY6 -0.084 0.34 -10000 0 -0.94 46 46
ADCY7 -0.086 0.34 -10000 0 -0.96 47 47
ADCY1 -0.11 0.38 -10000 0 -1 52 52
ADCY2 -0.27 0.4 -10000 0 -0.84 107 107
ADCY3 -0.086 0.34 -10000 0 -0.96 46 46
ADCY8 -0.31 0.39 -10000 0 -0.85 108 108
ADCY9 -0.084 0.34 -10000 0 -0.94 46 46
arachidonic acid secretion -0.019 0.28 -10000 0 -0.76 43 43
ETB receptor/Endothelin-1/Gq/GTP -0.046 0.28 -10000 0 -0.85 41 41
GNAO1 -0.029 0.18 -10000 0 -0.74 27 27
HRAS 0.008 0.069 -10000 0 -0.85 3 3
ETA receptor/Endothelin-1/G12/GTP -0.065 0.4 0.41 53 -1.1 42 95
ETA receptor/Endothelin-1/Gs/GTP -0.075 0.4 0.38 52 -1 48 100
mol:GTP 0.002 0.004 -10000 0 -10000 0 0
COL3A1 -0.12 0.47 -10000 0 -1.1 63 63
EDNRB -0.044 0.22 -10000 0 -0.84 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.18 0.49 -10000 0 -0.96 99 99
CYSLTR1 -0.097 0.42 -10000 0 -1.2 45 45
SLC9A1 -0.037 0.18 -10000 0 -0.44 39 39
mol:GDP -0.047 0.37 -10000 0 -1.1 43 43
SLC9A3 -0.22 0.47 -10000 0 -0.95 107 107
RAF1 -0.051 0.34 -10000 0 -0.97 42 42
JUN 0.007 0.29 -10000 0 -0.97 27 27
JAK2 -0.084 0.4 -10000 0 -0.9 63 63
mol:IP3 -0.056 0.34 -10000 0 -0.99 43 43
ETA receptor/Endothelin-1 -0.087 0.48 0.49 54 -0.99 67 121
PLCB1 -0.037 0.2 -10000 0 -0.85 28 28
PLCB2 -0.02 0.16 -10000 0 -0.82 19 19
ETA receptor/Endothelin-3 -0.072 0.24 -10000 0 -0.58 70 70
FOS -0.066 0.35 -10000 0 -0.86 57 57
Gai/GDP 0.009 0.17 -10000 0 -1 9 9
CRK 0.015 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.46 -10000 0 -1.2 58 58
BCAR1 0.009 0.069 -10000 0 -0.85 3 3
PRKCB1 -0.051 0.31 -10000 0 -0.92 43 43
GNAQ 0.016 0.007 -10000 0 -10000 0 0
GNAZ 0.001 0.1 -10000 0 -0.79 8 8
GNAL -0.008 0.13 -10000 0 -0.75 14 14
Gs family/GDP -0.11 0.27 -10000 0 -0.89 44 44
ETA receptor/Endothelin-1/Gq/GTP -0.027 0.29 -10000 0 -0.83 37 37
MAPK14 -0.044 0.29 -10000 0 -0.87 43 43
TRPC6 -0.008 0.34 -10000 0 -1.1 32 32
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.009 0.069 -10000 0 -0.85 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.056 0.3 -10000 0 -0.92 44 44
ETB receptor/Endothelin-2 -0.21 0.33 -10000 0 -0.67 147 147
ETB receptor/Endothelin-3 -0.1 0.24 -10000 0 -0.6 80 80
ETB receptor/Endothelin-1 -0.11 0.35 -10000 0 -0.91 62 62
MAPK3 -0.063 0.35 -10000 0 -0.87 57 57
MAPK1 -0.062 0.35 -10000 0 -0.86 57 57
Rac1/GDP -0.028 0.32 -10000 0 -0.94 40 40
cAMP biosynthetic process -0.22 0.35 -10000 0 -0.88 75 75
MAPK8 -0.019 0.36 -10000 0 -1.1 36 36
SRC 0.011 0.056 -10000 0 -0.85 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.24 -10000 0 -0.74 33 33
p130Cas/CRK/Src/PYK2 -0.021 0.35 -10000 0 -1 41 41
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.029 0.32 -10000 0 -0.95 40 40
COL1A2 -0.14 0.51 -10000 0 -1.2 73 73
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.18 0.34 -10000 0 -0.67 139 139
mol:DAG -0.056 0.34 -10000 0 -0.99 43 43
MAP2K2 -0.051 0.33 -10000 0 -0.94 39 39
MAP2K1 -0.049 0.32 -10000 0 -0.91 39 39
EDNRA -0.01 0.22 -10000 0 -0.93 17 17
positive regulation of muscle contraction -0.068 0.36 -10000 0 -1 41 41
Gq family/GDP -0.1 0.3 -10000 0 -1 40 40
HRAS/GTP -0.056 0.35 -10000 0 -1 43 43
PRKCH -0.047 0.33 -10000 0 -0.99 41 41
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.048 0.32 -10000 0 -0.98 41 41
PRKCB -0.058 0.36 -10000 0 -1 44 44
PRKCE -0.044 0.32 -10000 0 -0.96 40 40
PRKCD -0.05 0.33 -10000 0 -0.99 43 43
PRKCG -0.062 0.33 -10000 0 -0.95 46 46
regulation of vascular smooth muscle contraction -0.085 0.4 -10000 0 -1.1 53 53
PRKCQ -0.06 0.34 -10000 0 -0.97 47 47
PLA2G4A -0.03 0.31 -10000 0 -0.86 44 44
GNA14 -0.015 0.16 -10000 0 -0.84 17 17
GNA15 -0.004 0.13 -10000 0 -0.83 11 11
GNA12 0.013 0.033 -10000 0 -0.69 1 1
GNA11 0.004 0.095 -10000 0 -0.83 6 6
Rac1/GTP -0.064 0.4 0.41 54 -1 43 97
MMP1 -0.27 0.52 -10000 0 -0.98 150 150
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.16 0.35 -10000 0 -0.87 87 87
NFATC2 -0.11 0.35 -10000 0 -0.92 55 55
NFATC3 -0.018 0.094 -10000 0 -10000 0 0
CD40LG -0.31 0.5 -10000 0 -1.2 72 72
ITCH 0.04 0.074 -10000 0 -10000 0 0
CBLB 0.04 0.074 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.45 0.55 -10000 0 -1.2 128 128
JUNB -0.001 0.11 -10000 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.076 -10000 0 -10000 0 0
T cell anergy 0 0.15 -10000 0 -0.67 15 15
TLE4 -0.066 0.28 -10000 0 -0.91 29 29
Jun/NFAT1-c-4/p21SNFT -0.27 0.42 -10000 0 -1.3 46 46
AP-1/NFAT1-c-4 -0.37 0.61 -10000 0 -1.5 70 70
IKZF1 -0.084 0.34 -10000 0 -1.1 33 33
T-helper 2 cell differentiation -0.16 0.31 -10000 0 -0.81 64 64
AP-1/NFAT1 -0.19 0.33 -10000 0 -0.88 59 59
CALM1 0.021 0.047 -10000 0 -10000 0 0
EGR2 -0.18 0.46 -10000 0 -1.4 43 43
EGR3 -0.18 0.46 -10000 0 -1.3 40 40
NFAT1/FOXP3 -0.23 0.44 -10000 0 -0.95 101 101
EGR1 -0.1 0.28 -10000 0 -0.76 69 69
JUN -0.008 0.1 -10000 0 -0.83 7 7
EGR4 -0.04 0.18 -10000 0 -0.7 32 32
mol:Ca2+ 0.006 0.051 -10000 0 -10000 0 0
GBP3 -0.14 0.4 -10000 0 -1.1 63 63
FOSL1 -0.086 0.26 -10000 0 -0.75 62 62
NFAT1-c-4/MAF/IRF4 -0.27 0.42 -10000 0 -1.3 47 47
DGKA -0.077 0.31 -10000 0 -1 33 33
CREM 0.013 0.033 -10000 0 -0.69 1 1
NFAT1-c-4/PPARG -0.23 0.38 -10000 0 -1.2 37 37
CTLA4 -0.26 0.5 -10000 0 -1.1 112 112
NFAT1-c-4 (dimer)/EGR1 -0.29 0.45 -10000 0 -1.3 55 55
NFAT1-c-4 (dimer)/EGR4 -0.26 0.4 -10000 0 -1.2 45 45
FOS -0.11 0.28 -10000 0 -0.78 66 66
IFNG -0.42 0.56 -10000 0 -1.3 105 105
T cell activation -0.12 0.3 -10000 0 -0.99 25 25
MAF -0.004 0.12 -10000 0 -0.85 10 10
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.11 0.29 1.2 12 -10000 0 12
TNF -0.28 0.48 -10000 0 -1.2 65 65
FASLG -0.27 0.59 -10000 0 -1.6 53 53
TBX21 -0.051 0.19 -10000 0 -0.85 23 23
BATF3 -0.029 0.19 -10000 0 -0.82 25 25
PRKCQ -0.021 0.17 -10000 0 -0.8 20 20
PTPN1 -0.065 0.27 -10000 0 -0.9 28 28
NFAT1-c-4/ICER1 -0.23 0.38 -10000 0 -1.2 40 40
GATA3 -0.056 0.22 -10000 0 -0.74 44 44
T-helper 1 cell differentiation -0.38 0.55 -10000 0 -1.3 106 106
IL2RA -0.39 0.47 -10000 0 -1.1 115 115
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.065 0.27 -10000 0 -0.96 24 24
E2F1 0.014 0.08 -10000 0 -0.75 5 5
PPARG 0.011 0.056 -10000 0 -0.85 2 2
SLC3A2 -0.072 0.3 -10000 0 -0.95 32 32
IRF4 -0.082 0.26 -10000 0 -0.76 59 59
PTGS2 -0.33 0.52 -10000 0 -1.2 84 84
CSF2 -0.3 0.48 -10000 0 -1.2 73 73
JunB/Fra1/NFAT1-c-4 -0.26 0.42 -10000 0 -1.2 49 49
IL4 -0.17 0.33 -10000 0 -0.87 63 63
IL5 -0.3 0.46 -10000 0 -1.2 66 66
IL2 -0.12 0.31 -10000 0 -1 24 24
IL3 -0.065 0.12 -10000 0 -1.1 4 4
RNF128 0.006 0.21 -10000 0 -0.86 26 26
NFATC1 -0.11 0.3 -10000 0 -1.2 12 12
CDK4 0.087 0.2 0.69 5 -10000 0 5
PTPRK -0.066 0.28 -10000 0 -0.9 29 29
IL8 -0.36 0.52 -10000 0 -1.2 96 96
POU2F1 0.008 0.076 -10000 0 -0.81 4 4
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.2 0.57 -9999 0 -1.6 48 48
HDAC7 0.012 0.069 -9999 0 -0.85 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -9999 0 -1.1 56 56
SMAD4 0.016 0.005 -9999 0 -10000 0 0
ID2 -0.2 0.57 -9999 0 -1.6 48 48
AP1 -0.09 0.23 -9999 0 -0.63 68 68
ABCG2 -0.22 0.6 -9999 0 -1.6 52 52
HIF1A -0.011 0.088 -9999 0 -0.82 1 1
TFF3 -0.24 0.61 -9999 0 -1.6 60 60
GATA2 -0.026 0.18 -9999 0 -0.81 24 24
AKT1 -0.01 0.11 -9999 0 -0.98 2 2
response to hypoxia -0.027 0.1 -9999 0 -10000 0 0
MCL1 -0.2 0.57 -9999 0 -1.6 48 48
NDRG1 -0.21 0.58 -9999 0 -1.6 49 49
SERPINE1 -0.25 0.61 -9999 0 -1.6 61 61
FECH -0.2 0.57 -9999 0 -1.6 48 48
FURIN -0.2 0.57 -9999 0 -1.6 48 48
NCOA2 -0.04 0.18 -9999 0 -0.86 22 22
EP300 0.02 0.17 -9999 0 -0.43 6 6
HMOX1 -0.22 0.59 -9999 0 -1.6 50 50
BHLHE40 -0.21 0.57 -9999 0 -1.6 49 49
BHLHE41 -0.21 0.58 -9999 0 -1.6 49 49
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.033 0.094 -9999 0 -0.54 4 4
ENG 0.048 0.2 -9999 0 -0.9 14 14
JUN 0.002 0.1 -9999 0 -0.83 7 7
RORA -0.2 0.57 -9999 0 -1.6 48 48
ABCB1 -0.22 0.47 -9999 0 -1.3 67 67
TFRC -0.21 0.57 -9999 0 -1.6 48 48
CXCR4 -0.21 0.58 -9999 0 -1.6 48 48
TF -0.33 0.62 -9999 0 -1.5 69 69
CITED2 -0.21 0.57 -9999 0 -1.5 50 50
HIF1A/ARNT -0.42 1 -9999 0 -2.5 63 63
LDHA -0.04 0.15 -9999 0 -1.6 4 4
ETS1 -0.21 0.58 -9999 0 -1.6 48 48
PGK1 -0.2 0.57 -9999 0 -1.6 48 48
NOS2 -0.24 0.6 -9999 0 -1.6 56 56
ITGB2 -0.21 0.58 -9999 0 -1.6 48 48
ALDOA -0.2 0.57 -9999 0 -1.6 48 48
Cbp/p300/CITED2 -0.24 0.58 -9999 0 -1.5 58 58
FOS -0.096 0.28 -9999 0 -0.77 66 66
HK2 -0.21 0.59 -9999 0 -1.6 48 48
SP1 0.013 0.04 -9999 0 -10000 0 0
GCK -0.11 0.5 -9999 0 -1.3 54 54
HK1 -0.2 0.57 -9999 0 -1.6 48 48
NPM1 -0.2 0.57 -9999 0 -1.6 48 48
EGLN1 -0.2 0.57 -9999 0 -1.6 48 48
CREB1 0.024 0.002 -9999 0 -10000 0 0
PGM1 -0.2 0.57 -9999 0 -1.6 48 48
SMAD3 0.016 0.005 -9999 0 -10000 0 0
EDN1 -0.14 0.5 -9999 0 -1.4 58 58
IGFBP1 -0.36 0.63 -9999 0 -1.5 69 69
VEGFA -0.14 0.45 -9999 0 -1.2 36 36
HIF1A/JAB1 -0.017 0.041 -9999 0 -0.64 1 1
CP -0.31 0.64 -9999 0 -1.6 65 65
CXCL12 -0.22 0.58 -9999 0 -1.6 48 48
COPS5 0.002 0.018 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.005 -9999 0 -10000 0 0
BNIP3 -0.21 0.58 -9999 0 -1.6 48 48
EGLN3 -0.22 0.6 -9999 0 -1.7 48 48
CA9 -0.22 0.6 -9999 0 -1.7 49 49
TERT -0.25 0.59 -9999 0 -1.6 53 53
ENO1 -0.2 0.57 -9999 0 -1.6 48 48
PFKL -0.2 0.57 -9999 0 -1.6 48 48
NCOA1 0.008 0.011 -9999 0 -10000 0 0
ADM -0.21 0.58 -9999 0 -1.6 49 49
ARNT -0.007 0.078 -9999 0 -10000 0 0
HNF4A -0.1 0.29 -9999 0 -0.86 61 61
ADFP -0.21 0.57 -9999 0 -1.5 53 53
SLC2A1 -0.13 0.44 -9999 0 -1.2 37 37
LEP -0.25 0.6 -9999 0 -1.5 57 57
HIF1A/ARNT/Cbp/p300 -0.22 0.42 -9999 0 -1.1 57 57
EPO -0.43 0.56 -9999 0 -1.1 150 150
CREBBP 0.02 0.17 -9999 0 -0.4 8 8
HIF1A/ARNT/Cbp/p300/HDAC7 -0.25 0.44 -9999 0 -1.3 55 55
PFKFB3 -0.21 0.58 -9999 0 -1.6 49 49
NT5E -0.21 0.59 -9999 0 -1.6 51 51
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.66 62 62
FYN -0.1 0.36 -10000 0 -0.86 72 72
LAT/GRAP2/SLP76 -0.14 0.26 -10000 0 -0.7 70 70
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.046 0.22 -10000 0 -0.52 65 65
B2M 0.012 0.041 -10000 0 -0.86 1 1
IKBKG -0.035 0.06 -10000 0 -0.22 17 17
MAP3K8 0.008 0.073 -10000 0 -0.77 4 4
mol:Ca2+ -0.02 0.043 -10000 0 -0.14 53 53
integrin-mediated signaling pathway -0.011 0.079 -10000 0 -0.57 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.094 0.33 -10000 0 -0.79 71 71
TRPV6 -0.076 0.23 -10000 0 -0.74 50 50
CD28 -0.028 0.19 -10000 0 -0.83 24 24
SHC1 -0.11 0.35 -10000 0 -0.86 71 71
receptor internalization -0.13 0.39 -10000 0 -0.88 84 84
PRF1 -0.11 0.39 -10000 0 -1 58 58
KRAS 0.015 0 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
COT/AKT1 -0.026 0.18 -10000 0 -0.41 54 54
LAT -0.13 0.37 -10000 0 -0.9 75 75
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.09 0.27 -10000 0 -0.77 63 63
CD3E -0.073 0.25 -10000 0 -0.78 52 52
CD3G -0.085 0.27 -10000 0 -0.81 57 57
RASGRP2 -0.003 0.046 -10000 0 -0.18 21 21
RASGRP1 -0.042 0.23 -10000 0 -0.53 61 61
HLA-A 0.014 0.007 -10000 0 -10000 0 0
RASSF5 -0.002 0.12 -10000 0 -0.85 9 9
RAP1A/GTP/RAPL -0.011 0.079 -10000 0 -0.58 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.072 -10000 0 -0.15 15 15
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.062 0.1 -10000 0 -0.33 31 31
PRKCA -0.061 0.12 -10000 0 -0.33 49 49
GRAP2 -0.015 0.16 -10000 0 -0.85 16 16
mol:IP3 -0.085 0.2 0.27 30 -0.52 57 87
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.5 -10000 0 -1.1 78 78
ORAI1 0.04 0.13 0.4 11 -0.66 3 14
CSK -0.12 0.36 -10000 0 -0.86 77 77
B7 family/CD28 -0.19 0.35 -10000 0 -0.94 68 68
CHUK 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.15 0.44 -10000 0 -1 81 81
PTPN6 -0.12 0.37 -10000 0 -0.89 74 74
VAV1 -0.11 0.37 -10000 0 -0.88 73 73
Monovalent TCR/CD3 -0.12 0.4 -10000 0 -0.88 75 75
CBL 0.015 0 -10000 0 -10000 0 0
LCK -0.12 0.4 -10000 0 -0.93 76 76
PAG1 -0.12 0.37 -10000 0 -0.9 72 72
RAP1A 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.15 0.44 -10000 0 -1 80 80
CD80 -0.05 0.22 -10000 0 -0.81 37 37
CD86 -0.011 0.15 -10000 0 -0.86 14 14
PDK1/CARD11/BCL10/MALT1 -0.076 0.13 -10000 0 -0.38 45 45
HRAS 0.009 0.069 -10000 0 -0.85 3 3
GO:0035030 -0.093 0.3 -10000 0 -0.72 68 68
CD8A -0.14 0.32 -10000 0 -0.77 94 94
CD8B -0.16 0.33 -10000 0 -0.77 104 104
PTPRC -0.018 0.16 -10000 0 -0.84 17 17
PDK1/PKC theta -0.061 0.28 -10000 0 -0.65 65 65
CSK/PAG1 -0.11 0.36 -10000 0 -0.86 73 73
SOS1 0.015 0 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.034 -10000 0 -0.67 1 1
GRAP2/SLP76 -0.15 0.31 -10000 0 -0.81 72 72
STIM1 0.025 0.06 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.097 -10000 0 -0.25 3 3
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.15 0.45 -10000 0 -1 84 84
mol:DAG -0.087 0.17 -10000 0 -0.45 64 64
RAP1A/GDP 0.008 0.031 -10000 0 -10000 0 0
PLCG1 0.015 0 -10000 0 -10000 0 0
CD247 -0.017 0.16 -10000 0 -0.83 18 18
cytotoxic T cell degranulation -0.1 0.36 -10000 0 -0.95 60 60
RAP1A/GTP -0.005 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.066 0.26 -10000 0 -0.62 71 71
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.12 0.26 0.3 28 -0.7 59 87
NRAS 0.015 0 -10000 0 -10000 0 0
ZAP70 -0.064 0.24 -10000 0 -0.79 46 46
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.13 0.25 -10000 0 -0.68 69 69
MALT1 0.011 0.056 -10000 0 -0.85 2 2
TRAF6 0.013 0.04 -10000 0 -0.85 1 1
CD8 heterodimer -0.21 0.43 -10000 0 -0.95 111 111
CARD11 -0.076 0.25 -10000 0 -0.76 55 55
PRKCB -0.066 0.14 -10000 0 -0.38 47 47
PRKCE -0.06 0.12 -10000 0 -0.32 47 47
PRKCQ -0.086 0.32 -10000 0 -0.75 71 71
LCP2 0.002 0.1 -10000 0 -0.85 7 7
BCL10 0.015 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.032 0.19 -10000 0 -0.43 65 65
IKK complex 0.024 0.072 -10000 0 -10000 0 0
RAS family/GDP -0.006 0.012 -10000 0 -0.11 3 3
MAP3K14 -0.016 0.16 -10000 0 -0.4 35 35
PDPK1 -0.038 0.21 -10000 0 -0.49 61 61
TCR/CD3/MHC I/CD8/Fyn -0.17 0.47 -10000 0 -1.1 78 78
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.11 0.26 -10000 0 -0.66 48 48
TBX21 -0.13 0.49 -10000 0 -1.3 49 49
B2M 0.013 0.041 -10000 0 -0.85 1 1
TYK2 0.018 0.062 -10000 0 -0.88 2 2
IL12RB1 -0.018 0.18 -10000 0 -0.83 22 22
GADD45B -0.084 0.41 -10000 0 -1.2 33 33
IL12RB2 -0.17 0.33 -10000 0 -0.71 124 124
GADD45G -0.1 0.45 -10000 0 -1.2 49 49
natural killer cell activation 0.01 0.025 -10000 0 -10000 0 0
RELB 0.011 0.056 -10000 0 -0.85 2 2
RELA 0.015 0 -10000 0 -10000 0 0
IL18 -0.013 0.16 -10000 0 -0.77 19 19
IL2RA -0.098 0.28 -10000 0 -0.76 68 68
IFNG -0.24 0.37 -10000 0 -0.76 154 154
STAT3 (dimer) -0.087 0.37 -10000 0 -0.93 48 48
HLA-DRB5 -0.047 0.21 -10000 0 -0.76 37 37
FASLG -0.16 0.52 -10000 0 -1.4 58 58
NF kappa B2 p52/RelB -0.21 0.4 -10000 0 -1.1 61 61
CD4 0.001 0.1 -10000 0 -0.85 7 7
SOCS1 -0.022 0.16 -10000 0 -0.74 23 23
EntrezGene:6955 -0.002 0.012 -10000 0 -10000 0 0
CD3D -0.091 0.27 -10000 0 -0.77 63 63
CD3E -0.074 0.25 -10000 0 -0.78 52 52
CD3G -0.087 0.27 -10000 0 -0.82 57 57
IL12Rbeta2/JAK2 -0.11 0.25 -10000 0 -0.53 124 124
CCL3 -0.15 0.51 -10000 0 -1.3 60 60
CCL4 -0.13 0.48 -10000 0 -1.3 50 50
HLA-A 0.015 0.007 -10000 0 -10000 0 0
IL18/IL18R -0.013 0.28 -10000 0 -0.8 44 44
NOS2 -0.15 0.53 -10000 0 -1.4 57 57
IL12/IL12R/TYK2/JAK2/SPHK2 -0.096 0.25 -10000 0 -0.65 45 45
IL1R1 -0.12 0.45 -10000 0 -1.2 44 44
IL4 -0.01 0.025 -10000 0 -10000 0 0
JAK2 0.021 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.26 0.67 -10000 0 -1.4 89 89
RAB7A -0.042 0.34 -10000 0 -0.94 28 28
lysosomal transport -0.035 0.32 -10000 0 -0.87 28 28
FOS -0.18 0.5 -10000 0 -1.1 86 86
STAT4 (dimer) -0.1 0.44 -10000 0 -1.1 52 52
STAT5A (dimer) -0.31 0.44 -10000 0 -1 100 100
GZMA -0.14 0.5 -10000 0 -1.3 57 57
GZMB -0.13 0.48 -10000 0 -1.3 48 48
HLX -0.019 0.17 -10000 0 -0.83 19 19
LCK -0.16 0.54 -10000 0 -1.3 62 62
TCR/CD3/MHC II/CD4 -0.13 0.41 -10000 0 -1 58 58
IL2/IL2R -0.14 0.28 -10000 0 -0.74 63 63
MAPK14 -0.081 0.42 -10000 0 -1.1 44 44
CCR5 -0.12 0.48 -10000 0 -1.3 47 47
IL1B -0.054 0.24 -10000 0 -0.79 44 44
STAT6 -0.003 0.13 -10000 0 -10000 0 0
STAT4 -0.014 0.16 -10000 0 -0.84 16 16
STAT3 0.015 0 -10000 0 -10000 0 0
STAT1 0.008 0.069 -10000 0 -0.73 4 4
NFKB1 0.015 0 -10000 0 -10000 0 0
NFKB2 0.004 0.097 -10000 0 -0.85 6 6
IL12B -0.095 0.29 -10000 0 -0.77 71 71
CD8A -0.14 0.32 -10000 0 -0.77 94 94
CD8B -0.16 0.33 -10000 0 -0.77 104 104
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.25 0.65 49 -10000 0 49
IL2RB -0.026 0.18 -10000 0 -0.82 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.084 0.39 -10000 0 -0.96 52 52
IL2RG -0.047 0.21 -10000 0 -0.77 37 37
IL12 -0.094 0.27 -10000 0 -0.62 94 94
STAT5A 0.011 0.056 -10000 0 -0.85 2 2
CD247 -0.019 0.16 -10000 0 -0.83 18 18
IL2 -0.012 0.12 -10000 0 -0.69 14 14
SPHK2 0.009 0.069 -10000 0 -0.85 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.028 0.2 -10000 0 -0.83 27 27
IL12/IL12R/TYK2/JAK2 -0.19 0.68 -10000 0 -1.6 62 62
MAP2K3 -0.09 0.43 -10000 0 -1.1 49 49
RIPK2 0.012 0.046 -10000 0 -0.69 2 2
MAP2K6 -0.089 0.43 -10000 0 -1.1 49 49
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.14 -10000 0 -0.85 13 13
IL18RAP -0.023 0.18 -10000 0 -0.8 24 24
IL12Rbeta1/TYK2 -0.004 0.16 -10000 0 -0.67 23 23
EOMES -0.16 0.44 -10000 0 -1.1 72 72
STAT1 (dimer) -0.2 0.42 -10000 0 -0.92 79 79
T cell proliferation -0.028 0.32 0.51 1 -0.74 48 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.028 0.2 -10000 0 -0.86 25 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.17 0.28 -10000 0 -0.84 50 50
ATF2 -0.062 0.38 -10000 0 -1 36 36
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.006 0.06 -9999 0 -0.66 4 4
Necdin/E2F1 -0.051 0.18 -9999 0 -0.69 35 35
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.1 0.26 -9999 0 -0.97 27 27
NGF (dimer)/p75(NTR)/BEX1 -0.32 0.37 -9999 0 -0.78 125 125
NT-4/5 (dimer)/p75(NTR) -0.079 0.22 -9999 0 -0.66 56 56
IKBKB 0.015 0 -9999 0 -10000 0 0
AKT1 -0.067 0.28 -9999 0 -0.99 26 26
IKBKG 0.009 0.069 -9999 0 -0.85 3 3
BDNF -0.13 0.32 -9999 0 -0.79 86 86
MGDIs/NGR/p75(NTR)/LINGO1 -0.1 0.28 -9999 0 -0.71 69 69
FURIN 0.01 0.065 -9999 0 -0.8 3 3
proBDNF (dimer)/p75(NTR)/Sortilin -0.15 0.29 -9999 0 -0.69 80 80
LINGO1 -0.037 0.2 -9999 0 -0.83 29 29
Sortilin/TRAF6/NRIF -0.007 0.05 -9999 0 -10000 0 0
proBDNF (dimer) -0.13 0.31 -9999 0 -0.79 86 86
NTRK1 -0.076 0.25 -9999 0 -0.75 55 55
RTN4R -0.019 0.16 -9999 0 -0.74 21 21
neuron apoptosis -0.091 0.3 -9999 0 -0.93 36 36
IRAK1 0.013 0.04 -9999 0 -0.85 1 1
SHC1 -0.088 0.29 -9999 0 -0.76 63 63
ARHGDIA 0.011 0.056 -9999 0 -0.85 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.004 0.039 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.27 -9999 0 -0.72 63 63
MAGEH1 0.015 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.14 0.32 -9999 0 -0.78 79 79
Mammalian IAPs/DIABLO -0.026 0.11 -9999 0 -0.52 20 20
proNGF (dimer) -0.086 0.27 -9999 0 -0.81 57 57
MAGED1 0.01 0.057 -9999 0 -0.69 3 3
APP 0.013 0.04 -9999 0 -0.85 1 1
NT-4/5 (dimer) -0.02 0.13 -9999 0 -0.69 17 17
ZNF274 0.015 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.1 0.25 -9999 0 -0.68 63 63
NGF -0.086 0.27 -9999 0 -0.82 57 57
cell cycle arrest -0.034 0.29 -9999 0 -0.95 26 26
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.041 0.22 -9999 0 -0.76 27 27
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.069 0.2 -9999 0 -0.58 56 56
NCSTN 0.015 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.28 -9999 0 -0.75 63 63
PSENEN 0.013 0.033 -9999 0 -0.69 1 1
mol:ceramide -0.076 0.28 -9999 0 -0.72 63 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.022 0.19 -9999 0 -0.66 26 26
p75(NTR)/beta APP -0.062 0.19 -9999 0 -0.64 45 45
BEX1 -0.31 0.38 -9999 0 -0.75 201 201
mol:GDP -0.098 0.29 -9999 0 -0.71 77 77
NGF (dimer) -0.48 0.35 -9999 0 -0.76 225 225
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.098 0.27 -9999 0 -0.75 53 53
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
RAC1/GTP -0.1 0.25 -9999 0 -0.68 63 63
MYD88 0.004 0.097 -9999 0 -0.85 6 6
CHUK 0.015 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.28 -9999 0 -0.76 63 63
RHOB -0.02 0.17 -9999 0 -0.84 19 19
RHOA 0.015 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.006 0.059 -9999 0 -0.57 5 5
NT3 (dimer) -0.06 0.24 -9999 0 -0.8 43 43
TP53 -0.08 0.26 -9999 0 -0.95 18 18
PRDM4 -0.075 0.28 -9999 0 -0.72 63 63
BDNF (dimer) -0.55 0.37 -9999 0 -0.82 246 246
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
SORT1 0.009 0.069 -9999 0 -0.85 3 3
activation of caspase activity -0.1 0.25 -9999 0 -0.95 27 27
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.27 -9999 0 -0.72 64 64
RHOC 0.013 0.04 -9999 0 -0.85 1 1
XIAP 0.015 0 -9999 0 -10000 0 0
MAPK10 -0.069 0.26 -9999 0 -0.78 38 38
DIABLO 0.015 0 -9999 0 -10000 0 0
SMPD2 -0.078 0.29 -9999 0 -0.73 63 63
APH1B 0.011 0.056 -9999 0 -0.85 2 2
APH1A 0.015 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.12 0.29 -9999 0 -0.78 63 63
PSEN1 0.013 0.033 -9999 0 -0.69 1 1
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.11 0.29 -9999 0 -0.78 67 67
MAPK8 -0.069 0.26 -9999 0 -0.76 40 40
MAPK9 -0.068 0.26 -9999 0 -0.77 38 38
APAF1 0.015 0 -9999 0 -10000 0 0
NTF3 -0.061 0.24 -9999 0 -0.81 43 43
NTF4 -0.02 0.13 -9999 0 -0.69 17 17
NDN -0.046 0.22 -9999 0 -0.84 33 33
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.11 0.27 -9999 0 -0.97 32 32
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.047 -9999 0 -0.52 4 4
RhoA-B-C/GTP -0.11 0.27 -9999 0 -0.75 63 63
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.13 0.25 -9999 0 -0.99 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.14 0.26 -9999 0 -0.63 81 81
PRKACB 0.015 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.11 0.24 -9999 0 -0.6 86 86
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.03 0.19 -9999 0 -0.82 25 25
BIRC2 0.015 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.031 0.31 -9999 0 -0.78 51 51
BAD -0.057 0.25 -9999 0 -0.73 39 39
RIPK2 0.012 0.046 -9999 0 -0.69 2 2
NGFR -0.066 0.25 -9999 0 -0.83 45 45
CYCS -0.075 0.29 -9999 0 -0.98 32 32
ADAM17 0.015 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.11 0.26 -9999 0 -0.7 64 64
BCL2L11 -0.057 0.25 -9999 0 -0.73 38 38
BDNF (dimer)/p75(NTR) -0.17 0.31 -9999 0 -0.69 114 114
PI3K -0.11 0.27 -9999 0 -0.72 64 64
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.11 0.27 -9999 0 -0.72 63 63
NDNL2 0.015 0 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
PRKCI 0.012 0.046 -9999 0 -0.69 2 2
NGF (dimer)/p75(NTR) -0.13 0.31 -9999 0 -0.79 77 77
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.11 0.28 -9999 0 -0.74 63 63
TRAF6 0.013 0.04 -9999 0 -0.85 1 1
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCZ 0 0.11 -9999 0 -0.83 8 8
PLG -0.43 0.39 -9999 0 -0.76 265 265
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.14 0.35 -9999 0 -0.96 54 54
SQSTM1 0.015 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0.04 -9999 0 -0.85 1 1
CASP3 -0.047 0.23 -9999 0 -0.65 38 38
E2F1 0.007 0.08 -9999 0 -0.76 5 5
CASP9 0.015 0 -9999 0 -10000 0 0
IKK complex -0.12 0.25 -9999 0 -0.87 32 32
NGF (dimer)/TRKA -0.14 0.28 -9999 0 -0.66 98 98
MMP7 -0.28 0.38 -9999 0 -0.76 178 178
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.1 0.26 -9999 0 -0.98 26 26
MMP3 -0.075 0.23 -9999 0 -0.69 55 55
APAF-1/Caspase 9 -0.096 0.22 -9999 0 -0.74 39 39
EGFR-dependent Endothelin signaling events

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
HRAS 0.009 0.069 -9999 0 -0.85 3 3
EGFR -0.023 0.17 -9999 0 -0.8 22 22
EGF/EGFR -0.21 0.31 -9999 0 -0.64 125 125
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.15 0.22 -9999 0 -0.91 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.016 0.16 -9999 0 -0.83 17 17
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.22 0.36 -9999 0 -0.77 143 143
EGF/EGFR dimer/SHC -0.18 0.26 -9999 0 -0.52 160 160
mol:GDP -0.15 0.22 -9999 0 -0.89 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.081 0.27 -9999 0 -0.85 52 52
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.14 0.2 -9999 0 -0.82 7 7
SHC1 0.013 0.033 -9999 0 -0.69 1 1
HRAS/GDP -0.14 0.2 -9999 0 -0.83 7 7
FRAP1 -0.11 0.23 -9999 0 -0.86 6 6
EGF/EGFR dimer -0.21 0.3 -9999 0 -0.61 159 159
SOS1 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.093 0.26 -9999 0 -0.75 58 58
IL27-mediated 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
TGFB1 -0.001 0.12 -10000 0 -0.83 9 9
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.094 0.26 0.8 34 -10000 0 34
IL27/IL27R/JAK1 -0.14 0.31 -10000 0 -1.1 29 29
TBX21 -0.12 0.27 -10000 0 -0.75 41 41
IL12B -0.11 0.28 -10000 0 -0.77 71 71
IL12A -0.028 0.15 -10000 0 -0.64 27 27
IL6ST -0.057 0.23 -10000 0 -0.86 36 36
IL27RA/JAK1 -0.033 0.25 -10000 0 -1.4 13 13
IL27 -0.044 0.2 -10000 0 -0.77 32 32
TYK2 0.008 0.059 -10000 0 -0.87 2 2
T-helper cell lineage commitment -0.096 0.17 -10000 0 -0.32 155 155
T-helper 2 cell differentiation 0.094 0.26 0.8 34 -10000 0 34
T cell proliferation during immune response 0.094 0.26 0.8 34 -10000 0 34
MAPKKK cascade -0.094 0.26 -10000 0 -0.8 34 34
STAT3 0.015 0 -10000 0 -10000 0 0
STAT2 0.011 0.052 -10000 0 -0.77 2 2
STAT1 0.007 0.069 -10000 0 -0.73 4 4
IL12RB1 -0.027 0.17 -10000 0 -0.8 22 22
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.19 0.32 -10000 0 -0.73 74 74
IL27/IL27R/JAK2/TYK2 -0.097 0.27 -10000 0 -0.84 33 33
positive regulation of T cell mediated cytotoxicity -0.094 0.26 -10000 0 -0.8 34 34
STAT1 (dimer) -0.2 0.35 0.54 1 -1.1 42 43
JAK2 0.012 0.011 -10000 0 -10000 0 0
JAK1 0.012 0.04 -10000 0 -0.85 1 1
STAT2 (dimer) -0.084 0.25 -10000 0 -0.9 24 24
T cell proliferation -0.22 0.32 -10000 0 -0.74 82 82
IL12/IL12R/TYK2/JAK2 -0.16 0.32 -10000 0 -0.94 49 49
IL17A -0.096 0.17 -10000 0 -0.32 155 155
mast cell activation 0.094 0.26 0.8 34 -10000 0 34
IFNG -0.035 0.061 0.1 5 -0.12 124 129
T cell differentiation -0.009 0.011 0.024 7 -0.026 62 69
STAT3 (dimer) -0.082 0.25 -10000 0 -0.88 24 24
STAT5A (dimer) -0.084 0.26 -10000 0 -0.96 22 22
STAT4 (dimer) -0.096 0.29 -10000 0 -0.94 33 33
STAT4 -0.014 0.16 -10000 0 -0.84 16 16
T cell activation -0.007 0.023 0.13 13 -10000 0 13
IL27R/JAK2/TYK2 -0.094 0.28 -10000 0 -1.3 16 16
GATA3 -0.052 0.29 -10000 0 -1.3 17 17
IL18 -0.012 0.12 -10000 0 -0.59 19 19
positive regulation of mast cell cytokine production -0.08 0.24 -10000 0 -0.84 24 24
IL27/EBI3 -0.059 0.21 -10000 0 -0.68 45 45
IL27RA -0.043 0.26 -10000 0 -1.5 13 13
IL6 -0.23 0.36 -10000 0 -0.76 149 149
STAT5A 0.011 0.056 -10000 0 -0.85 2 2
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.006 0.12 0.53 3 -10000 0 3
IL1B -0.045 0.18 -10000 0 -0.6 44 44
EBI3 -0.026 0.17 -10000 0 -0.79 21 21
TNF -0.061 0.2 -10000 0 -0.6 56 56
EPO signaling pathway

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
BCL2L1 -0.13 0.22 -10000 0 -0.74 5 5
CRKL -0.17 0.21 -10000 0 -0.7 5 5
mol:DAG -0.17 0.23 -10000 0 -0.72 8 8
HRAS -0.12 0.19 -10000 0 -0.68 6 6
MAPK8 -0.22 0.24 -10000 0 -0.5 127 127
RAP1A -0.17 0.21 -10000 0 -0.7 5 5
GAB1 -0.18 0.22 -10000 0 -0.7 9 9
MAPK14 -0.22 0.24 -10000 0 -0.5 124 124
EPO -0.41 0.39 -10000 0 -0.76 257 257
PLCG1 -0.18 0.24 -10000 0 -0.76 8 8
EPOR/TRPC2/IP3 Receptors -0.013 0.091 -10000 0 -0.74 7 7
RAPGEF1 0.013 0.04 -10000 0 -0.85 1 1
EPO/EPOR (dimer)/SOCS3 -0.3 0.29 -10000 0 -0.61 143 143
GAB1/SHC/GRB2/SOS1 -0.17 0.16 -10000 0 -0.72 4 4
EPO/EPOR (dimer) -0.31 0.31 -10000 0 -0.58 260 260
IRS2 -0.21 0.24 -10000 0 -0.75 28 28
STAT1 -0.18 0.24 -10000 0 -0.76 11 11
STAT5B -0.18 0.24 -10000 0 -0.77 8 8
cell proliferation -0.2 0.23 -10000 0 -0.72 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.16 0.16 -10000 0 -0.75 7 7
TEC -0.17 0.21 -10000 0 -0.7 5 5
SOCS3 -0.034 0.19 -10000 0 -0.78 29 29
STAT1 (dimer) -0.17 0.24 -10000 0 -0.73 11 11
JAK2 -0.003 0.019 -10000 0 -10000 0 0
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
EPO/EPOR (dimer)/JAK2 -0.19 0.23 -10000 0 -0.69 7 7
EPO/EPOR -0.31 0.31 -10000 0 -0.58 260 260
LYN 0.012 0.057 -10000 0 -0.85 2 2
TEC/VAV2 -0.16 0.21 -10000 0 -0.67 5 5
elevation of cytosolic calcium ion concentration -0.013 0.091 -10000 0 -0.74 7 7
SHC1 0.013 0.033 -10000 0 -0.69 1 1
EPO/EPOR (dimer)/LYN -0.25 0.27 -10000 0 -0.55 128 128
mol:IP3 -0.17 0.23 -10000 0 -0.72 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.21 0.21 -10000 0 -0.71 33 33
SH2B3 -0.007 0.06 -10000 0 -0.87 2 2
NFKB1 -0.22 0.24 -10000 0 -0.5 124 124
EPO/EPOR (dimer)/JAK2/SOCS3 -0.18 0.18 0.33 1 -0.41 130 131
PTPN6 -0.19 0.22 -10000 0 -0.68 7 7
TEC/VAV2/GRB2 -0.15 0.2 -10000 0 -0.74 2 2
EPOR -0.013 0.091 -10000 0 -0.74 7 7
INPP5D 0.009 0.069 -10000 0 -0.85 3 3
mol:GDP -0.17 0.16 -10000 0 -0.74 4 4
SOS1 0.015 0 -10000 0 -10000 0 0
PLCG2 -0.018 0.15 -10000 0 -0.72 21 21
CRKL/CBL/C3G -0.15 0.2 -10000 0 -0.76 3 3
VAV2 -0.17 0.21 -10000 0 -0.7 5 5
CBL -0.17 0.21 -10000 0 -0.7 5 5
SHC/Grb2/SOS1 -0.18 0.17 -10000 0 -0.64 5 5
STAT5A -0.18 0.24 -10000 0 -0.78 9 9
GRB2 0.015 0 -10000 0 -10000 0 0
STAT5 (dimer) -0.15 0.23 -10000 0 -0.87 6 6
LYN/PLCgamma2 -0.026 0.13 -10000 0 -0.59 21 21
PTPN11 0.015 0 -10000 0 -10000 0 0
BTK -0.18 0.23 -10000 0 -0.77 11 11
BCL2 -0.15 0.26 -10000 0 -1 14 14
Effects of Botulinum toxin

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
STX1A -0.005 0.1 -9999 0 -0.56 15 15
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.053 0.16 -9999 0 -0.52 48 48
STXBP1 0.005 0.089 -9999 0 -0.77 6 6
ACh/CHRNA1 -0.17 0.26 -9999 0 -0.55 147 147
RAB3GAP2/RIMS1/UNC13B -0.045 0.13 -9999 0 -0.44 48 48
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 -0.061 0.21 -9999 0 -0.69 48 48
mol:ACh -0.014 0.061 -9999 0 -0.16 64 64
RAB3GAP2 0.015 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.071 0.15 -9999 0 -0.56 21 21
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.17 0.26 -9999 0 -0.55 147 147
UNC13B 0.015 0 -9999 0 -10000 0 0
CHRNA1 -0.23 0.36 -9999 0 -0.77 147 147
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.062 0.18 -9999 0 -0.56 54 54
SNAP25 -0.044 0.14 -9999 0 -0.38 63 63
VAMP2 0.008 0 -9999 0 -10000 0 0
SYT1 -0.074 0.25 -9999 0 -0.76 54 54
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.11 -9999 0 -0.51 20 20
STX1A/SNAP25 fragment 1/VAMP2 -0.071 0.15 -9999 0 -0.56 21 21
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.005 0.054 -9999 0 -0.58 4 4
VLDLR 0.004 0.092 -9999 0 -0.74 7 7
CRKL 0.015 0 -9999 0 -10000 0 0
LRPAP1 0.009 0.069 -9999 0 -0.85 3 3
FYN 0.007 0.08 -9999 0 -0.85 4 4
ITGA3 -0.003 0.12 -9999 0 -0.8 10 10
RELN/VLDLR/Fyn -0.15 0.24 -9999 0 -0.6 54 54
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.013 0.11 -9999 0 -1.4 2 2
AKT1 -0.074 0.17 -9999 0 -0.47 30 30
MAP2K7 0.011 0.056 -9999 0 -0.85 2 2
RAPGEF1 0.013 0.04 -9999 0 -0.85 1 1
DAB1 -0.065 0.22 -9999 0 -0.69 50 50
RELN/LRP8/DAB1 -0.19 0.26 -9999 0 -0.66 72 72
LRPAP1/LRP8 -0.029 0.12 -9999 0 -0.54 25 25
RELN/LRP8/DAB1/Fyn -0.18 0.26 -9999 0 -0.63 75 75
DAB1/alpha3/beta1 Integrin -0.17 0.24 -9999 0 -0.75 41 41
long-term memory -0.36 0.35 -9999 0 -0.85 124 124
DAB1/LIS1 -0.17 0.24 -9999 0 -0.75 35 35
DAB1/CRLK/C3G -0.17 0.23 -9999 0 -0.74 36 36
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
DAB1/NCK2 -0.17 0.24 -9999 0 -0.76 36 36
ARHGEF2 0.015 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.26 0.38 -9999 0 -0.77 168 168
CDK5R1 0.013 0.033 -9999 0 -0.69 1 1
RELN -0.2 0.35 -9999 0 -0.75 134 134
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
RELN/LRP8/Fyn -0.16 0.25 -9999 0 -0.63 57 57
GRIN2A/RELN/LRP8/DAB1/Fyn -0.33 0.34 -9999 0 -0.86 98 98
MAPK8 0.009 0.069 -9999 0 -0.85 3 3
RELN/VLDLR/DAB1 -0.18 0.25 -9999 0 -0.63 68 68
ITGB1 0.015 0 -9999 0 -10000 0 0
MAP1B -0.15 0.27 -9999 0 -0.77 40 40
RELN/LRP8 -0.16 0.24 -9999 0 -0.5 151 151
GRIN2B/RELN/LRP8/DAB1/Fyn -0.23 0.29 -9999 0 -0.82 57 57
PI3K -0.009 0.07 -9999 0 -0.57 7 7
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.013 0.089 -9999 0 -0.61 10 10
RAP1A -0.11 0.24 -9999 0 -0.68 36 36
PAFAH1B1 0.015 0 -9999 0 -10000 0 0
MAPK8IP1 0.003 0.097 -9999 0 -0.78 7 7
CRLK/C3G -0.001 0.03 -9999 0 -0.66 1 1
GRIN2B -0.08 0.24 -9999 0 -0.72 58 58
NCK2 0.013 0.04 -9999 0 -0.85 1 1
neuron differentiation -0.049 0.15 -9999 0 -0.52 19 19
neuron adhesion -0.1 0.25 -9999 0 -0.75 15 15
LRP8 -0.019 0.15 -9999 0 -0.71 22 22
GSK3B -0.062 0.16 -9999 0 -0.52 10 10
RELN/VLDLR/DAB1/Fyn -0.17 0.24 -9999 0 -0.6 71 71
MAP3K11 0.011 0.056 -9999 0 -0.85 2 2
RELN/VLDLR/DAB1/P13K -0.087 0.17 -9999 0 -0.43 51 51
CDK5 0.01 0.065 -9999 0 -0.8 3 3
MAPT -0.092 0.28 -9999 0 -0.8 65 65
neuron migration -0.078 0.22 -9999 0 -0.6 18 18
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.05 0.16 -9999 0 -0.53 19 19
RELN/VLDLR -0.15 0.23 -9999 0 -0.59 60 60
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0 0.066 -9999 0 -0.59 4 4
NFATC2 -0.051 0.18 -9999 0 -0.59 43 43
NFATC3 0.005 0.037 -9999 0 -10000 0 0
CD40LG -0.22 0.38 -9999 0 -0.93 67 67
PTGS2 -0.25 0.4 -9999 0 -0.91 86 86
JUNB -0.001 0.11 -9999 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.009 0.015 -9999 0 -10000 0 0
CALM1 0.01 0.011 -9999 0 -10000 0 0
JUN -0.003 0.1 -9999 0 -0.84 7 7
mol:Ca2+ -0.011 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.003 -9999 0 -10000 0 0
FOSL1 -0.086 0.26 -9999 0 -0.75 62 62
CREM 0.013 0.033 -9999 0 -0.69 1 1
Jun/NFAT1-c-4/p21SNFT -0.15 0.23 -9999 0 -0.79 33 33
FOS -0.1 0.28 -9999 0 -0.78 66 66
IFNG -0.32 0.44 -9999 0 -0.88 143 143
AP-1/NFAT1-c-4 -0.34 0.42 -9999 0 -1.1 82 82
FASLG -0.24 0.4 -9999 0 -0.91 88 88
NFAT1-c-4/ICER1 -0.086 0.16 -9999 0 -0.57 26 26
IL2RA -0.25 0.4 -9999 0 -0.91 87 87
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.22 0.36 -9999 0 -0.88 65 65
JunB/Fra1/NFAT1-c-4 -0.14 0.23 -9999 0 -0.72 46 46
IL4 -0.22 0.34 -9999 0 -0.8 76 76
IL2 -0.019 0.11 -9999 0 -0.62 14 14
IL3 -0.032 0.097 -9999 0 -1.2 3 3
FKBP1A 0.015 0 -9999 0 -10000 0 0
BATF3 -0.03 0.19 -9999 0 -0.82 25 25
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.008 0.076 -9999 0 -0.81 4 4
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.038 0.39 -10000 0 -1 45 45
NCK1/PAK1/Dok-R -0.054 0.14 -10000 0 -0.46 42 42
NCK1/Dok-R -0.14 0.4 -10000 0 -1.3 45 45
PIK3CA 0.012 0.04 -10000 0 -0.85 1 1
mol:beta2-estradiol 0.002 0.066 0.32 12 -10000 0 12
RELA 0.015 0 -10000 0 -10000 0 0
SHC1 0.014 0.033 -10000 0 -0.69 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.37 0.39 -10000 0 -0.77 222 222
TNIP2 0.009 0.069 -10000 0 -0.85 3 3
NF kappa B/RelA -0.12 0.35 -10000 0 -1.2 43 43
FN1 -0.038 0.2 -10000 0 -0.76 32 32
PLD2 -0.016 0.46 -10000 0 -1.4 44 44
PTPN11 0.015 0 -10000 0 -10000 0 0
GRB14 -0.067 0.24 -10000 0 -0.75 50 50
ELK1 0.008 0.4 -10000 0 -1.2 44 44
GRB7 -0.003 0.12 -10000 0 -0.84 10 10
PAK1 0.015 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.14 0.4 -10000 0 -1.3 46 46
CDKN1A 0.071 0.3 -10000 0 -0.71 46 46
ITGA5 0 0.11 -10000 0 -0.85 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.4 -10000 0 -1.3 45 45
CRK 0.015 0 -10000 0 -10000 0 0
mol:NO 0.063 0.3 -10000 0 -0.75 49 49
PLG -0.26 0.47 -10000 0 -1.5 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.035 0.32 -10000 0 -0.96 44 44
GRB2 0.015 0 -10000 0 -10000 0 0
PIK3R1 0.006 0.086 -10000 0 -0.75 6 6
ANGPT2 0.018 0.38 -10000 0 -1.1 35 35
BMX -0.087 0.5 -10000 0 -1.5 45 45
ANGPT1 0.019 0.4 -10000 0 -1.5 27 27
tube development 0.059 0.33 -10000 0 -0.81 48 48
ANGPT4 -0.087 0.27 -10000 0 -0.78 60 60
response to hypoxia -0.005 0.022 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.064 0.51 -10000 0 -1.5 45 45
alpha5/beta1 Integrin -0.011 0.085 -10000 0 -0.66 8 8
FGF2 -0.017 0.15 -10000 0 -0.82 15 15
STAT5A (dimer) 0.05 0.38 -10000 0 -0.95 48 48
mol:L-citrulline 0.063 0.3 -10000 0 -0.75 49 49
AGTR1 -0.18 0.34 -10000 0 -0.79 111 111
MAPK14 -0.005 0.46 -10000 0 -1.4 43 43
Tie2/SHP2 -0.11 0.36 -10000 0 -1.4 35 35
TEK -0.092 0.42 -10000 0 -1.5 35 35
RPS6KB1 0.046 0.36 -10000 0 -0.98 44 44
Angiotensin II/AT1 -0.13 0.27 -10000 0 -0.61 111 111
Tie2/Ang1/GRB2 -0.027 0.48 -10000 0 -1.5 43 43
MAPK3 0.001 0.41 -10000 0 -1.2 46 46
MAPK1 0.003 0.41 -10000 0 -1.2 44 44
Tie2/Ang1/GRB7 -0.035 0.49 -10000 0 -1.5 43 43
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 -0.015 0.46 -10000 0 -1.4 43 43
PI3K 0.017 0.44 -10000 0 -1.3 44 44
FES -0.008 0.46 -10000 0 -1.4 43 43
Crk/Dok-R -0.14 0.4 -10000 0 -1.3 45 45
Tie2/Ang1/ABIN2 -0.03 0.48 -10000 0 -1.5 43 43
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.05 0.34 -10000 0 -0.9 45 45
STAT5A 0.012 0.057 -10000 0 -0.85 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.046 0.36 -10000 0 -0.98 44 44
Tie2/Ang2 0.017 0.46 -10000 0 -1.2 47 47
Tie2/Ang1 -0.035 0.53 -10000 0 -1.6 43 43
FOXO1 0.048 0.36 -10000 0 -0.94 45 45
ELF1 0.019 0.029 -10000 0 -10000 0 0
ELF2 -0.017 0.46 -10000 0 -1.4 43 43
mol:Choline -0.007 0.43 -10000 0 -1.3 44 44
cell migration -0.031 0.078 -10000 0 -10000 0 0
FYN 0.046 0.38 -10000 0 -0.96 48 48
DOK2 -0.011 0.14 -10000 0 -0.84 14 14
negative regulation of cell cycle 0.076 0.28 -10000 0 -0.64 46 46
ETS1 -0.011 0.17 -10000 0 -0.97 12 12
PXN 0.067 0.3 -10000 0 -0.78 44 44
ITGB1 0.015 0 -10000 0 -10000 0 0
NOS3 0.051 0.35 -10000 0 -0.89 49 49
RAC1 0.015 0 -10000 0 -10000 0 0
TNF -0.082 0.26 -10000 0 -0.77 56 56
MAPKKK cascade -0.007 0.43 -10000 0 -1.3 44 44
RASA1 0.015 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.027 0.48 -10000 0 -1.5 43 43
NCK1 0.015 0 -10000 0 -10000 0 0
vasculogenesis 0.07 0.28 -10000 0 -0.66 49 49
mol:Phosphatidic acid -0.007 0.43 -10000 0 -1.3 44 44
mol:Angiotensin II 0 0.008 -10000 0 -10000 0 0
mol:NADP 0.063 0.3 -10000 0 -0.75 49 49
Rac1/GTP -0.097 0.27 -10000 0 -0.9 44 44
MMP2 -0.036 0.47 -10000 0 -1.4 45 45
Visual signal transduction: Rods

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
mol:K + 0.015 0 -9999 0 -10000 0 0
GNAT1/GTP -0.009 0.068 -9999 0 -0.53 8 8
Metarhodopsin II/Arrestin -0.017 0.085 -9999 0 -0.46 17 17
PDE6G/GNAT1/GTP -0.029 0.12 -9999 0 -0.47 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.006 0.091 -9999 0 -0.69 8 8
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.14 0.27 -9999 0 -0.88 36 36
mol:Na + -0.15 0.24 -9999 0 -0.79 28 28
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.16 0.26 -9999 0 -0.63 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.25 -9999 0 -0.83 28 28
CNGB1 -0.044 0.18 -9999 0 -0.69 35 35
RDH5 -0.05 0.22 -9999 0 -0.83 36 36
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.24 -9999 0 -0.76 28 28
Na + (4 Units) -0.14 0.22 -9999 0 -0.73 28 28
RGS9 -0.16 0.33 -9999 0 -0.79 100 100
GNB1/GNGT1 -0.15 0.27 -9999 0 -0.63 110 110
GNAT1/GDP -0.14 0.24 -9999 0 -0.57 81 81
GUCY2D -0.08 0.25 -9999 0 -0.74 57 57
GNGT1 -0.18 0.36 -9999 0 -0.83 110 110
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.045 0.2 -9999 0 -0.64 33 33
mol:11-cis-retinal -0.05 0.22 -9999 0 -0.83 36 36
mol:cGMP -0.082 0.19 -9999 0 -0.55 42 42
GNB1 0.015 0 -9999 0 -10000 0 0
Rhodopsin -0.068 0.19 -9999 0 -0.61 52 52
SLC24A1 0.015 0 -9999 0 -10000 0 0
CNGA1 -0.092 0.27 -9999 0 -0.78 63 63
Metarhodopsin II -0.015 0.078 -9999 0 -0.42 17 17
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.089 0.2 -9999 0 -0.53 58 58
RGS9BP -0.057 0.23 -9999 0 -0.76 43 43
Metarhodopsin II/Transducin -0.077 0.17 -9999 0 -0.38 95 95
GCAP Family/Ca ++ -0.036 0.13 -9999 0 -0.5 34 34
PDE6A/B -0.064 0.19 -9999 0 -0.62 48 48
mol:Pi -0.15 0.26 -9999 0 -0.63 80 80
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.13 0.22 -9999 0 -0.51 116 116
PDE6B -0.036 0.2 -9999 0 -0.84 28 28
PDE6A -0.022 0.15 -9999 0 -0.69 23 23
PDE6G -0.019 0.16 -9999 0 -0.73 21 21
RHO -0.016 0.13 -9999 0 -0.69 17 17
PDE6 -0.18 0.3 -9999 0 -0.92 45 45
GUCA1A -0.013 0.12 -9999 0 -0.69 13 13
GC2/GCAP Family -0.036 0.13 -9999 0 -0.5 34 34
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B -0.026 0.18 -9999 0 -0.81 23 23
Glucocorticoid receptor regulatory network

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
PCK2 -0.011 0.15 -10000 0 -0.98 7 7
SMARCC2 0.016 0.011 -10000 0 -10000 0 0
SMARCC1 0.016 0.011 -10000 0 -10000 0 0
TBX21 -0.058 0.29 -10000 0 -1 29 29
SUMO2 0.011 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.084 -10000 0 -0.62 7 7
FKBP4 0.015 0 -10000 0 -10000 0 0
FKBP5 -0.047 0.21 -10000 0 -0.75 38 38
GR alpha/HSP90/FKBP51/HSP90 0.013 0.19 0.38 8 -0.56 23 31
PRL -0.026 0.15 -10000 0 -0.66 6 6
cortisol/GR alpha (dimer)/TIF2 0.074 0.31 0.58 61 -0.63 15 76
RELA -0.052 0.1 -10000 0 -10000 0 0
FGG -0.29 0.47 0.54 22 -0.73 209 231
GR beta/TIF2 0.019 0.19 0.37 15 -0.63 23 38
IFNG -0.47 0.57 -10000 0 -1.3 133 133
apoptosis -0.095 0.23 0.61 8 -0.71 14 22
CREB1 0.015 0 -10000 0 -10000 0 0
histone acetylation 0.046 0.18 0.49 23 -0.49 15 38
BGLAP 0.002 0.13 -10000 0 -0.63 1 1
GR/PKAc 0.057 0.11 0.38 4 -0.63 1 5
NF kappa B1 p50/RelA -0.091 0.2 -10000 0 -0.57 15 15
SMARCD1 0.016 0.011 -10000 0 -10000 0 0
MDM2 0.043 0.1 0.29 25 -10000 0 25
GATA3 -0.052 0.22 -10000 0 -0.74 44 44
AKT1 -0.001 0.047 -10000 0 -0.68 2 2
CSF2 -0.006 0.16 -10000 0 -0.65 10 10
GSK3B 0.011 0.013 -10000 0 -10000 0 0
NR1I3 -0.065 0.23 0.72 4 -0.92 7 11
CSN2 0.036 0.21 0.38 47 -0.38 16 63
BRG1/BAF155/BAF170/BAF60A 0.03 0.054 -10000 0 -0.51 2 2
NFATC1 0.007 0.08 -10000 0 -0.85 4 4
POU2F1 0.008 0.08 -10000 0 -0.81 4 4
CDKN1A 0.036 0.14 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.009 -10000 0 -10000 0 0
SFN -0.19 0.34 -10000 0 -0.74 125 125
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.11 0.26 0.4 3 -0.64 35 38
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.31 0.68 4 -0.94 32 36
JUN -0.23 0.24 -10000 0 -0.67 56 56
IL4 -0.029 0.14 -10000 0 -0.38 37 37
CDK5R1 0.01 0.034 -10000 0 -0.71 1 1
PRKACA 0.015 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.36 0.32 0.31 1 -0.72 151 152
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.021 0.18 0.39 4 -0.66 9 13
cortisol/GR alpha (monomer) 0.12 0.35 0.7 70 -0.56 7 77
NCOA2 -0.026 0.18 -10000 0 -0.85 22 22
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.17 0.28 -10000 0 -0.84 66 66
AP-1/NFAT1-c-4 -0.47 0.4 -10000 0 -0.92 159 159
AFP -0.25 0.4 -10000 0 -1.3 45 45
SUV420H1 0.015 0 -10000 0 -10000 0 0
IRF1 0.056 0.22 0.53 9 -1.1 8 17
TP53 0.034 0.068 -10000 0 -0.74 3 3
PPP5C 0.011 0.056 -10000 0 -0.85 2 2
KRT17 -0.39 0.54 -10000 0 -1.3 106 106
KRT14 -0.24 0.49 -10000 0 -1.2 74 74
TBP 0.026 0.001 -10000 0 -10000 0 0
CREBBP 0.065 0.11 0.36 21 -10000 0 21
HDAC1 0.01 0.012 -10000 0 -10000 0 0
HDAC2 0.016 0.01 -10000 0 -10000 0 0
AP-1 -0.48 0.41 -10000 0 -0.94 158 158
MAPK14 0.011 0.009 -10000 0 -10000 0 0
MAPK10 0 0.098 -10000 0 -0.85 6 6
MAPK11 -0.009 0.13 -10000 0 -0.85 11 11
KRT5 -0.44 0.54 -10000 0 -1.1 141 141
interleukin-1 receptor activity 0.001 0.01 -10000 0 -10000 0 0
NCOA1 0.017 0.009 -10000 0 -10000 0 0
STAT1 0.014 0.084 -10000 0 -0.62 7 7
CGA -0.024 0.14 0.27 1 -0.36 36 37
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.06 0.16 0.42 29 -10000 0 29
MAPK3 0.007 0.057 -10000 0 -0.85 2 2
MAPK1 0.011 0.009 -10000 0 -10000 0 0
ICAM1 -0.13 0.34 -10000 0 -1 35 35
NFKB1 -0.052 0.1 -10000 0 -10000 0 0
MAPK8 -0.14 0.19 -10000 0 -0.55 38 38
MAPK9 0.011 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.1 0.24 0.67 6 -0.74 16 22
BAX 0.038 0.13 -10000 0 -1.8 2 2
POMC -0.11 0.34 -10000 0 -1.3 23 23
EP300 0.066 0.11 0.38 15 -10000 0 15
cortisol/GR alpha (dimer)/p53 0.12 0.29 0.61 56 -0.99 2 58
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.078 0.26 4 -10000 0 4
SGK1 0.091 0.23 -10000 0 -1.5 7 7
IL13 -0.21 0.29 -10000 0 -0.88 47 47
IL6 -0.33 0.56 -10000 0 -1.1 130 130
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.17 0.22 -10000 0 -0.74 32 32
IL2 -0.22 0.27 -10000 0 -0.87 31 31
CDK5 0.006 0.065 -10000 0 -0.8 3 3
PRKACB 0.015 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
IL8 -0.23 0.47 -10000 0 -1 98 98
CDK5R1/CDK5 -0.003 0.056 -10000 0 -0.59 4 4
NF kappa B1 p50/RelA/PKAc -0.044 0.14 -10000 0 -0.67 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.27 0.58 55 -0.91 1 56
SMARCA4 0.012 0.057 -10000 0 -0.85 2 2
chromatin remodeling 0.084 0.17 0.43 28 -0.64 2 30
NF kappa B1 p50/RelA/Cbp -0.007 0.2 0.44 4 -0.74 4 8
JUN (dimer) -0.23 0.24 -10000 0 -0.67 56 56
YWHAH 0.015 0 -10000 0 -10000 0 0
VIPR1 -0.11 0.35 -10000 0 -0.92 62 62
NR3C1 0.067 0.2 0.53 36 -0.98 1 37
NR4A1 -0.11 0.29 -10000 0 -0.74 79 79
TIF2/SUV420H1 -0.031 0.14 -10000 0 -0.66 22 22
MAPKKK cascade -0.095 0.23 0.61 8 -0.71 14 22
cortisol/GR alpha (dimer)/Src-1 0.11 0.29 0.6 64 -1.1 1 65
PBX1 -0.009 0.14 -10000 0 -0.86 13 13
POU1F1 0.003 0.04 -10000 0 -0.68 1 1
SELE -0.21 0.47 -10000 0 -1.2 69 69
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.084 0.17 0.44 27 -0.65 2 29
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.27 0.58 55 -0.91 1 56
mol:cortisol 0.051 0.21 0.42 66 -0.26 15 81
MMP1 -0.44 0.6 -10000 0 -1.3 139 139
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 -0.063 0.25 -9999 0 -0.84 43 43
GNB1/GNG2 -0.15 0.2 -9999 0 -0.65 40 40
mol:DAG -0.1 0.21 -9999 0 -0.65 25 25
PLCG1 -0.1 0.22 -9999 0 -0.68 25 25
YES1 -0.12 0.22 -9999 0 -0.65 37 37
FZD3 0.011 0.052 -9999 0 -0.77 2 2
FZD6 0.011 0.052 -9999 0 -0.77 2 2
G protein -0.14 0.2 -9999 0 -0.69 27 27
MAP3K7 -0.12 0.22 -9999 0 -0.66 33 33
mol:Ca2+ -0.096 0.2 -9999 0 -0.63 25 25
mol:IP3 -0.1 0.21 -9999 0 -0.65 25 25
NLK -0.007 0.01 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.14 0.24 -9999 0 -0.73 34 34
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.24 -9999 0 -0.62 55 55
CSNK1A1 0.015 0 -9999 0 -10000 0 0
GNAS -0.13 0.23 -9999 0 -0.66 39 39
GO:0007205 -0.097 0.2 -9999 0 -0.64 25 25
WNT6 -0.14 0.31 -9999 0 -0.78 89 89
WNT4 -0.14 0.31 -9999 0 -0.76 94 94
NFAT1/CK1 alpha -0.17 0.22 -9999 0 -0.7 44 44
GNG2 0.004 0.097 -9999 0 -0.85 6 6
WNT5A -0.032 0.18 -9999 0 -0.74 29 29
WNT11 -0.088 0.26 -9999 0 -0.75 63 63
CDC42 -0.11 0.21 -9999 0 -0.61 37 37
LPA receptor mediated events

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
GNB1/GNG2 -0.079 0.19 -9999 0 -0.56 53 53
NF kappa B1 p50/RelA/I kappa B alpha -0.047 0.12 -9999 0 -0.67 9 9
AP1 -0.14 0.25 -9999 0 -0.87 26 26
mol:PIP3 -0.097 0.19 -9999 0 -0.72 19 19
AKT1 -0.061 0.14 -9999 0 -0.64 12 12
PTK2B -0.021 0.14 -9999 0 -0.57 14 14
RHOA 0.002 0.091 -9999 0 -0.57 5 5
PIK3CB 0.011 0.056 -9999 0 -0.85 2 2
mol:Ca2+ 0.003 0.17 -9999 0 -0.74 16 16
MAGI3 -0.001 0.1 -9999 0 -0.71 10 10
RELA 0.015 0 -9999 0 -10000 0 0
apoptosis -0.045 0.16 -9999 0 -0.46 50 50
HRAS/GDP -0.004 0.053 -9999 0 -0.66 3 3
positive regulation of microtubule depolymerization -0.065 0.21 -9999 0 -0.5 73 73
NF kappa B1 p50/RelA -0.089 0.19 -9999 0 -0.76 17 17
endothelial cell migration -0.079 0.26 -9999 0 -0.66 69 69
ADCY4 -0.062 0.24 -9999 0 -0.62 61 61
ADCY5 -0.077 0.25 -9999 0 -0.63 64 64
ADCY6 -0.049 0.22 -9999 0 -0.61 54 54
ADCY7 -0.051 0.23 -9999 0 -0.6 57 57
ADCY1 -0.064 0.24 -9999 0 -0.62 61 61
ADCY2 -0.14 0.27 -9999 0 -0.72 69 69
ADCY3 -0.051 0.22 -9999 0 -0.61 54 54
ADCY8 -0.16 0.26 -9999 0 -0.7 66 66
ADCY9 -0.049 0.22 -9999 0 -0.61 54 54
GSK3B -0.011 0.14 -9999 0 -0.59 11 11
arachidonic acid secretion -0.043 0.22 -9999 0 -0.57 56 56
GNG2 0.004 0.097 -9999 0 -0.85 6 6
TRIP6 0.012 0.12 -9999 0 -1.1 4 4
GNAO1 -0.081 0.24 -9999 0 -0.56 81 81
HRAS 0.009 0.069 -9999 0 -0.85 3 3
NFKBIA -0.008 0.17 -9999 0 -0.68 17 17
GAB1 0.011 0.056 -9999 0 -0.85 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.015 0.14 -9999 0 -1 9 9
JUN 0.002 0.1 -9999 0 -0.83 7 7
LPA/LPA2/NHERF2 -0.031 0.14 -9999 0 -0.63 21 21
TIAM1 -0.021 0.18 -9999 0 -1.3 9 9
PIK3R1 0.005 0.086 -9999 0 -0.74 6 6
mol:IP3 0.002 0.18 -9999 0 -0.8 15 15
PLCB3 0 0.15 -9999 0 -0.66 19 19
FOS -0.096 0.28 -9999 0 -0.77 66 66
positive regulation of mitosis -0.043 0.22 -9999 0 -0.57 56 56
LPA/LPA1-2-3 -0.097 0.21 -9999 0 -0.58 56 56
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.009 0.069 -9999 0 -0.85 3 3
stress fiber formation -0.025 0.16 -9999 0 -0.59 14 14
GNAZ -0.062 0.22 -9999 0 -0.57 64 64
EGFR/PI3K-beta/Gab1 -0.1 0.2 -9999 0 -0.78 19 19
positive regulation of dendritic cell cytokine production -0.096 0.21 -9999 0 -0.58 56 56
LPA/LPA2/MAGI-3 -0.027 0.11 -9999 0 -0.53 21 21
ARHGEF1 -0.034 0.19 -9999 0 -0.52 49 49
GNAI2 -0.053 0.2 -9999 0 -0.56 57 57
GNAI3 -0.053 0.2 -9999 0 -0.56 57 57
GNAI1 -0.056 0.21 -9999 0 -0.57 59 59
LPA/LPA3 -0.022 0.092 -9999 0 -0.52 14 14
LPA/LPA2 -0.021 0.1 -9999 0 -0.66 11 11
LPA/LPA1 -0.094 0.22 -9999 0 -0.61 65 65
HB-EGF/EGFR -0.13 0.26 -9999 0 -0.64 54 54
HBEGF -0.13 0.27 -9999 0 -0.57 121 121
mol:DAG 0.002 0.18 -9999 0 -0.8 15 15
cAMP biosynthetic process -0.085 0.24 -9999 0 -0.65 57 57
NFKB1 0.015 0 -9999 0 -10000 0 0
SRC 0.011 0.056 -9999 0 -0.85 2 2
GNB1 0.015 0.001 -9999 0 -10000 0 0
LYN -0.009 0.18 -9999 0 -0.71 17 17
GNAQ 0 0.096 -9999 0 -0.47 11 11
LPAR2 -0.005 0.13 -9999 0 -0.82 11 11
LPAR3 -0.012 0.12 -9999 0 -0.7 14 14
LPAR1 -0.091 0.28 -9999 0 -0.82 57 57
IL8 -0.15 0.24 -9999 0 -0.52 89 89
PTK2 -0.055 0.21 -9999 0 -0.54 55 55
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.046 0.17 -9999 0 -0.46 50 50
EGFR -0.025 0.17 -9999 0 -0.8 22 22
PLCG1 0 0.12 -9999 0 -0.55 13 13
PLD2 -0.059 0.22 -9999 0 -0.56 59 59
G12/G13 -0.074 0.17 -9999 0 -0.54 47 47
PI3K-beta -0.07 0.16 -9999 0 -0.7 14 14
cell migration -0.031 0.073 -9999 0 -0.3 10 10
SLC9A3R2 -0.007 0.14 -9999 0 -0.85 12 12
PXN -0.026 0.17 -9999 0 -0.61 14 14
HRAS/GTP -0.045 0.22 -9999 0 -0.59 56 56
RAC1 0.015 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.74 118 118
PRKCE 0.011 0.052 -9999 0 -0.77 2 2
PRKCD 0.003 0.18 -9999 0 -0.73 17 17
Gi(beta/gamma) -0.046 0.22 -9999 0 -0.58 56 56
mol:LPA -0.006 0.044 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.079 0.19 -9999 0 -0.85 11 11
MAPKKK cascade -0.043 0.22 -9999 0 -0.57 56 56
contractile ring contraction involved in cytokinesis 0.002 0.09 -9999 0 -0.56 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.017 0.14 -9999 0 -0.52 24 24
GNA15 -0.01 0.13 -9999 0 -0.55 18 18
GNA12 0.013 0.033 -9999 0 -0.7 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
MAPT -0.069 0.22 -9999 0 -0.52 73 73
GNA11 -0.006 0.12 -9999 0 -0.6 12 12
Rac1/GTP -0.017 0.16 -9999 0 -1.1 9 9
MMP2 -0.079 0.26 -9999 0 -0.67 69 69
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.044 0.28 -9999 0 -0.98 38 38
VEGFR1 homodimer/NRP1 -0.08 0.27 -9999 0 -0.98 38 38
mol:DAG -0.13 0.35 -9999 0 -1.1 38 38
VEGFR1 homodimer/NRP1/VEGFR 121 -0.1 0.33 -9999 0 -1.1 44 44
CaM/Ca2+ -0.12 0.34 -9999 0 -1.1 38 38
HIF1A -0.011 0.12 -9999 0 -1.1 1 1
GAB1 0.011 0.056 -9999 0 -0.85 2 2
AKT1 -0.091 0.32 -9999 0 -0.98 41 41
PLCG1 -0.13 0.36 -9999 0 -1.2 38 38
NOS3 -0.093 0.34 -9999 0 -1.1 40 40
CBL 0.015 0 -9999 0 -10000 0 0
mol:NO -0.084 0.32 -9999 0 -0.98 40 40
FLT1 -0.054 0.31 -9999 0 -1.1 38 38
PGF -0.16 0.33 -9999 0 -0.76 107 107
VEGFR1 homodimer/NRP2/VEGFR121 -0.11 0.36 -9999 0 -1.2 38 38
CALM1 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
eNOS/Hsp90 -0.074 0.3 -9999 0 -0.93 41 41
endothelial cell proliferation -0.12 0.36 -9999 0 -1.1 40 40
mol:Ca2+ -0.13 0.34 -9999 0 -1.1 38 38
MAPK3 -0.1 0.32 -9999 0 -0.98 40 40
MAPK1 -0.1 0.32 -9999 0 -0.99 39 39
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
PLGF homodimer -0.16 0.32 -9999 0 -0.76 107 107
PRKACA 0.015 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.001 0.12 -9999 0 -0.83 9 9
VEGFA homodimer -0.033 0.2 -9999 0 -0.85 26 26
VEGFR1 homodimer/VEGFA homodimer -0.072 0.36 -9999 0 -1.1 44 44
platelet activating factor biosynthetic process -0.091 0.31 -9999 0 -0.94 40 40
PI3K -0.16 0.34 -9999 0 -1.1 39 39
PRKCA -0.12 0.34 -9999 0 -1.1 39 39
PRKCB -0.13 0.36 -9999 0 -1.1 40 40
VEGFR1 homodimer/PLGF homodimer -0.16 0.38 -9999 0 -1 60 60
VEGFA -0.033 0.2 -9999 0 -0.85 26 26
VEGFB 0.015 0 -9999 0 -10000 0 0
mol:IP3 -0.13 0.35 -9999 0 -1.1 38 38
RASA1 -0.029 0.26 -9999 0 -0.9 38 38
NRP2 -0.005 0.13 -9999 0 -0.84 11 11
VEGFR1 homodimer -0.054 0.31 -9999 0 -1.1 38 38
VEGFB homodimer 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.078 0.32 -9999 0 -0.98 40 40
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.16 0.32 -9999 0 -1.1 39 39
mol:L-citrulline -0.084 0.32 -9999 0 -0.98 40 40
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.097 0.32 -9999 0 -1.1 38 38
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.1 0.33 -9999 0 -1.2 38 38
CD2AP 0.011 0.052 -9999 0 -0.77 2 2
PI3K/GAB1 -0.16 0.32 -9999 0 -1.1 39 39
PDPK1 -0.1 0.32 -9999 0 -1 39 39
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.1 0.33 -9999 0 -1.2 38 38
mol:NADP -0.084 0.32 -9999 0 -0.98 40 40
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
ubiquitin-dependent protein catabolic process -0.094 0.3 -9999 0 -1.1 38 38
VEGFR1 homodimer/NRP2 -0.056 0.31 -9999 0 -1 41 41
Arf6 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
CENTA1/KIF3B -0.024 0.12 -9999 0 -0.56 20 20
ARNO/beta Arrestin1-2 -0.038 0.13 -9999 0 -0.9 6 6
EGFR -0.023 0.17 -9999 0 -0.8 22 22
EPHA2 -0.001 0.11 -9999 0 -0.82 9 9
USP6 -0.003 0.11 -9999 0 -0.69 12 12
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.3 -9999 0 -0.61 159 159
ARRB2 -0.018 0.097 -9999 0 -0.31 46 46
mol:GTP 0.012 0.054 -9999 0 -0.34 7 7
ARRB1 0.004 0.097 -9999 0 -0.85 6 6
FBXO8 0.015 0 -9999 0 -10000 0 0
TSHR -0.099 0.28 -9999 0 -0.8 65 65
EGF -0.22 0.36 -9999 0 -0.77 143 143
somatostatin receptor activity 0 0 -9999 0 -0.001 39 39
ARAP2 0.011 0.056 -9999 0 -0.85 2 2
mol:GDP -0.074 0.16 -9999 0 -0.41 58 58
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 29 29
ITGA2B -0.098 0.28 -9999 0 -0.77 67 67
ARF6 0.015 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.022 0.12 -9999 0 -0.58 16 16
ADAP1 -0.003 0.12 -9999 0 -0.75 11 11
KIF13B -0.005 0.12 -9999 0 -0.71 13 13
HGF/MET -0.064 0.19 -9999 0 -0.62 48 48
PXN 0.013 0.033 -9999 0 -0.69 1 1
ARF6/GTP -0.069 0.14 -9999 0 -0.38 42 42
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.26 -9999 0 -0.6 84 84
ADRB2 -0.007 0.13 -9999 0 -0.77 13 13
receptor agonist activity 0 0 -9999 0 0 40 40
actin filament binding 0 0 -9999 0 -0.001 39 39
SRC 0.011 0.056 -9999 0 -0.85 2 2
ITGB3 -0.015 0.15 -9999 0 -0.77 18 18
GNAQ 0.015 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 32 32
ARF6/GDP -0.009 0.15 -9999 0 -0.58 19 19
ARF6/GDP/GULP/ACAP1 -0.13 0.24 -9999 0 -0.69 59 59
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.085 0.19 -9999 0 -0.56 46 46
ACAP1 -0.045 0.21 -9999 0 -0.79 35 35
ACAP2 0.015 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.042 0.14 -9999 0 -0.46 45 45
EFNA1 -0.003 0.12 -9999 0 -0.84 10 10
HGF -0.059 0.23 -9999 0 -0.77 44 44
CYTH3 0.013 0 -9999 0 -10000 0 0
CYTH2 0.002 0.1 -9999 0 -1.3 3 3
NCK1 0.015 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 36 36
endosomal lumen acidification 0 0 -9999 0 -0.001 41 41
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.061 0.24 -9999 0 -0.79 44 44
GNAQ/ARNO 0.007 0.095 -9999 0 -1.2 3 3
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 11 11
MET 0.002 0.1 -9999 0 -0.75 8 8
GNA14 -0.016 0.16 -9999 0 -0.84 17 17
GNA15 -0.005 0.13 -9999 0 -0.82 11 11
GIT1 0.011 0.056 -9999 0 -0.85 2 2
mol:PI-4-5-P2 0 0 -9999 0 -0.001 36 36
GNA11 0.004 0.095 -9999 0 -0.82 6 6
LHCGR -0.062 0.21 -9999 0 -0.7 45 45
AGTR1 -0.18 0.34 -9999 0 -0.79 111 111
desensitization of G-protein coupled receptor protein signaling pathway -0.042 0.14 -9999 0 -0.46 45 45
IPCEF1/ARNO -0.14 0.23 -9999 0 -0.55 46 46
alphaIIb/beta3 Integrin -0.1 0.24 -9999 0 -0.62 80 80
Signaling events regulated by Ret tyrosine kinase

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 -0.039 0.058 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.12 0.16 -9999 0 -0.53 31 31
JUN -0.063 0.19 -9999 0 -0.64 24 24
HRAS 0.009 0.069 -9999 0 -0.85 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.27 -9999 0 -0.69 55 55
RAP1A 0.015 0 -9999 0 -10000 0 0
FRS2 0.015 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.27 -9999 0 -0.66 70 70
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.13 0.22 -9999 0 -0.59 46 46
RHOA 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.16 0.26 -9999 0 -0.88 29 29
GRB7 -0.003 0.12 -9999 0 -0.84 10 10
RET51/GFRalpha1/GDNF -0.17 0.26 -9999 0 -0.68 55 55
MAPKKK cascade -0.14 0.22 -9999 0 -0.76 31 31
BCAR1 0.009 0.069 -9999 0 -0.85 3 3
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.22 -9999 0 -0.58 49 49
lamellipodium assembly -0.11 0.15 -9999 0 -0.48 26 26
RET51/GFRalpha1/GDNF/SHC -0.17 0.26 -9999 0 -0.66 68 68
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
RET9/GFRalpha1/GDNF/SHC -0.12 0.21 -9999 0 -0.57 44 44
RET9/GFRalpha1/GDNF/Shank3 -0.13 0.24 -9999 0 -0.63 50 50
MAPK3 -0.12 0.26 -9999 0 -0.82 30 30
DOK1 0.007 0.08 -9999 0 -0.85 4 4
DOK6 -0.039 0.21 -9999 0 -0.83 30 30
PXN 0.013 0.033 -9999 0 -0.69 1 1
neurite development -0.11 0.26 -9999 0 -0.76 36 36
DOK5 -0.063 0.24 -9999 0 -0.76 47 47
GFRA1 -0.17 0.33 -9999 0 -0.76 114 114
MAPK8 -0.069 0.18 -9999 0 -0.62 22 22
HRAS/GTP -0.15 0.24 -9999 0 -0.88 25 25
tube development -0.12 0.22 -9999 0 -0.59 50 50
MAPK1 -0.12 0.26 -9999 0 -0.82 29 29
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.047 0.14 -9999 0 -0.58 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.011 0.056 -9999 0 -0.85 2 2
PDLIM7 0.001 0.1 -9999 0 -0.77 8 8
RET51/GFRalpha1/GDNF/Dok6 -0.19 0.3 -9999 0 -0.96 40 40
SHC1 0.013 0.033 -9999 0 -0.69 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.18 0.28 -9999 0 -0.71 69 69
RET51/GFRalpha1/GDNF/Dok5 -0.21 0.31 -9999 0 -0.74 81 81
PRKCA 0.004 0.089 -9999 0 -0.72 7 7
HRAS/GDP -0.004 0.053 -9999 0 -0.66 3 3
CREB1 -0.06 0.17 -9999 0 -0.56 16 16
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.05 0.15 -9999 0 -0.69 5 5
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.28 -9999 0 -0.69 73 73
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.076 0.25 -9999 0 -0.76 55 55
DOK4 -0.002 0.12 -9999 0 -0.85 9 9
JNK cascade -0.061 0.19 -9999 0 -0.62 24 24
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.21 -9999 0 -0.56 44 44
SHANK3 -0.007 0.14 -9999 0 -0.84 12 12
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.048 0.14 -9999 0 -0.38 34 34
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.075 0.18 -9999 0 -0.59 21 21
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.08 0.19 -9999 0 -0.63 24 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.08 0.2 -9999 0 -0.71 21 21
PI3K -0.12 0.27 -9999 0 -0.81 33 33
SOS1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.12 0.22 -9999 0 -0.59 50 50
GRB10 0.013 0.04 -9999 0 -0.85 1 1
activation of MAPKK activity -0.065 0.16 -9999 0 -0.54 18 18
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.26 -9999 0 -0.65 68 68
GAB1 0.011 0.056 -9999 0 -0.85 2 2
IRS1 -0.023 0.16 -9999 0 -0.73 24 24
IRS2 -0.054 0.21 -9999 0 -0.7 45 45
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.083 0.21 -9999 0 -0.74 23 23
RET51/GFRalpha1/GDNF/PKC alpha -0.18 0.27 -9999 0 -0.66 70 70
GRB2 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GDNF -0.011 0.11 -9999 0 -0.69 11 11
RAC1 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.19 0.27 -9999 0 -0.67 74 74
Rac1/GTP -0.13 0.18 -9999 0 -0.58 32 32
RET9/GFRalpha1/GDNF -0.13 0.23 -9999 0 -0.51 122 122
GFRalpha1/GDNF -0.15 0.26 -9999 0 -0.58 122 122
Nongenotropic Androgen 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
PTK2 0.013 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.073 0.19 -10000 0 -0.56 60 60
regulation of S phase of mitotic cell cycle -0.018 0.14 -10000 0 -0.63 4 4
GNAO1 -0.029 0.18 -10000 0 -0.74 27 27
HRAS 0.009 0.069 -10000 0 -0.85 3 3
SHBG/T-DHT -0.046 0.15 -10000 0 -0.52 41 41
PELP1 0.015 0.001 -10000 0 -10000 0 0
AKT1 0.011 0.044 -10000 0 -0.67 2 2
MAP2K1 -0.019 0.17 -10000 0 -0.57 16 16
T-DHT/AR -0.084 0.22 -10000 0 -0.66 60 60
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 66 66
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.009 0.069 -10000 0 -0.85 3 3
mol:GDP -0.086 0.22 -10000 0 -0.66 58 58
cell proliferation -0.025 0.21 -10000 0 -0.72 17 17
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
FOS -0.057 0.28 -10000 0 -0.68 66 66
mol:Ca2+ -0.011 0.026 -10000 0 -0.1 16 16
MAPK3 -0.022 0.2 -10000 0 -0.69 17 17
MAPK1 -0.002 0.097 -10000 0 -0.31 10 10
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
mol:IP3 0 0.002 -10000 0 -0.004 66 66
cAMP biosynthetic process -0.034 0.14 -10000 0 -0.49 41 41
GNG2 0.004 0.097 -10000 0 -0.85 6 6
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 66 66
HRAS/GTP -0.067 0.17 -10000 0 -0.5 60 60
actin cytoskeleton reorganization -0.006 0.049 -10000 0 -0.46 3 3
SRC 0.011 0.056 -10000 0 -0.85 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 66 66
PI3K -0.007 0.061 -10000 0 -0.5 7 7
apoptosis 0.019 0.17 0.46 40 -10000 0 40
T-DHT/AR/PELP1 -0.072 0.19 -10000 0 -0.57 60 60
HRAS/GDP -0.083 0.22 -10000 0 -0.63 60 60
CREB1 -0.023 0.18 -10000 0 -0.5 40 40
RAC1-CDC42/GTP -0.006 0.049 -10000 0 -0.47 3 3
AR -0.096 0.29 -10000 0 -0.85 60 60
GNB1 0.015 0 -10000 0 -10000 0 0
RAF1 -0.028 0.18 -10000 0 -0.59 16 16
RAC1-CDC42/GDP -0.077 0.2 -10000 0 -0.6 58 58
T-DHT/AR/PELP1/Src -0.068 0.18 -10000 0 -0.53 60 60
MAP2K2 -0.022 0.19 -10000 0 -0.69 12 12
T-DHT/AR/PELP1/Src/PI3K -0.018 0.14 -10000 0 -0.64 4 4
GNAZ 0.001 0.1 -10000 0 -0.79 8 8
SHBG -0.055 0.22 -10000 0 -0.77 41 41
Gi family/GNB1/GNG2/GDP 0.009 0.14 -10000 0 -0.78 6 6
mol:T-DHT 0 0.001 0.002 9 -0.003 52 61
RAC1 0.015 0 -10000 0 -10000 0 0
GNRH1 -0.044 0.18 -10000 0 -0.63 42 42
Gi family/GTP -0.045 0.11 -10000 0 -0.53 12 12
CDC42 0.015 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.024 0.12 -9999 0 -0.58 19 19
AKT1 0.011 0.27 -9999 0 -0.79 46 46
PTK2B -0.048 0.34 -9999 0 -1.1 40 40
VEGFR2 homodimer/Frs2 -0.048 0.32 -9999 0 -1.1 37 37
CAV1 -0.001 0.12 -9999 0 -0.83 9 9
CALM1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.35 -9999 0 -1.2 37 37
endothelial cell proliferation 0.027 0.26 -9999 0 -0.74 42 42
mol:Ca2+ -0.039 0.33 -9999 0 -1.1 40 40
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.1 0.33 -9999 0 -1.2 37 37
RP11-342D11.1 -0.048 0.33 -9999 0 -1.1 40 40
CDH5 -0.015 0.16 -9999 0 -0.85 16 16
VEGFA homodimer -0.033 0.13 -9999 0 -0.55 28 28
SHC1 0.013 0.033 -9999 0 -0.69 1 1
SHC2 -0.015 0.15 -9999 0 -0.8 17 17
HRAS/GDP -0.085 0.25 -9999 0 -0.87 41 41
SH2D2A -0.08 0.26 -9999 0 -0.78 56 56
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.082 0.24 -9999 0 -0.81 42 42
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.16 0.4 -9999 0 -1.3 43 43
VEGFR1 homodimer -0.055 0.24 -9999 0 -0.85 38 38
SHC/GRB2/SOS1 -0.098 0.3 -9999 0 -1 40 40
GRB10 -0.039 0.33 -9999 0 -1.1 40 40
PTPN11 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
PAK1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.11 0.36 -9999 0 -1.2 37 37
HRAS 0.009 0.069 -9999 0 -0.85 3 3
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.2 -9999 0 -0.69 25 25
HIF1A 0.013 0.033 -9999 0 -0.69 1 1
FRS2 0.015 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.099 0.32 -9999 0 -1.1 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.024 0.18 -9999 0 -0.85 21 21
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.36 -9999 0 -1.3 37 37
mol:GDP -0.091 0.28 -9999 0 -0.97 40 40
mol:NADP 0.015 0.23 -9999 0 -0.68 43 43
eNOS/Hsp90 0.022 0.22 -9999 0 -0.68 30 30
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
mol:IP3 -0.042 0.34 -9999 0 -1.1 40 40
HIF1A/ARNT -0.001 0.024 -9999 0 -0.52 1 1
SHB 0.015 0 -9999 0 -10000 0 0
VEGFA -0.03 0.2 -9999 0 -0.85 26 26
VEGFC 0.004 0.095 -9999 0 -0.82 6 6
FAK1/Vinculin -0.021 0.31 -9999 0 -0.97 41 41
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.12 0.36 -9999 0 -1.2 40 40
PTPN6 0.011 0.056 -9999 0 -0.85 2 2
EPAS1 -0.031 0.23 -9999 0 -1.2 14 14
mol:L-citrulline 0.015 0.23 -9999 0 -0.68 43 43
ITGAV 0.013 0.033 -9999 0 -0.69 1 1
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.1 0.33 -9999 0 -1.2 37 37
VEGFR2 homodimer/VEGFA homodimer -0.12 0.37 -9999 0 -1.2 40 40
VEGFR2/3 heterodimer -0.07 0.39 -9999 0 -1.3 37 37
VEGFB 0.015 0 -9999 0 -10000 0 0
MAPK11 -0.046 0.36 -9999 0 -1.1 45 45
VEGFR2 homodimer -0.057 0.35 -9999 0 -1.2 37 37
FLT1 -0.055 0.24 -9999 0 -0.85 38 38
NEDD4 0.003 0.11 -9999 0 -0.85 8 8
MAPK3 -0.027 0.3 -9999 0 -0.96 41 41
MAPK1 -0.026 0.3 -9999 0 -0.96 41 41
VEGFA145/NRP2 -0.05 0.19 -9999 0 -0.73 32 32
VEGFR1/2 heterodimer -0.088 0.43 -9999 0 -1.5 37 37
KDR -0.057 0.35 -9999 0 -1.2 37 37
VEGFA165/NRP1/VEGFR2 homodimer -0.11 0.35 -9999 0 -1.2 41 41
SRC 0.011 0.056 -9999 0 -0.85 2 2
platelet activating factor biosynthetic process -0.029 0.32 -9999 0 -1 41 41
PI3K -0.12 0.34 -9999 0 -1.1 45 45
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.35 -9999 0 -1.2 37 37
FES -0.049 0.36 -9999 0 -1.1 41 41
GAB1 -0.12 0.35 -9999 0 -1.2 44 44
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.35 -9999 0 -1.2 37 37
CTNNB1 0.015 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.018 0.23 -9999 0 -0.67 39 39
VEGFR2 homodimer/VEGFA homodimer/Yes -0.11 0.35 -9999 0 -1.2 37 37
PI3K/GAB1 0.009 0.28 -9999 0 -0.81 45 45
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.098 0.32 -9999 0 -1.1 37 37
PRKACA 0.015 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.11 0.37 -9999 0 -1.3 37 37
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
CDC42 -0.045 0.36 -9999 0 -1.1 40 40
actin cytoskeleton reorganization -0.16 0.38 -9999 0 -1.2 43 43
PTK2 -0.04 0.36 -9999 0 -1.1 42 42
EDG1 -0.048 0.33 -9999 0 -1.1 40 40
mol:DAG -0.042 0.34 -9999 0 -1.1 40 40
CaM/Ca2+ -0.092 0.28 -9999 0 -0.98 40 40
MAP2K3 -0.041 0.35 -9999 0 -1.1 43 43
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.11 0.35 -9999 0 -1.2 40 40
PLCG1 -0.045 0.36 -9999 0 -1.1 40 40
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.1 0.33 -9999 0 -1.2 37 37
IQGAP1 0.015 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.35 -9999 0 -1.2 37 37
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.35 -9999 0 -1.2 38 38
cell migration 0.02 0.26 -9999 0 -0.78 38 38
mol:PI-3-4-5-P3 -0.1 0.29 -9999 0 -0.96 45 45
FYN 0.007 0.08 -9999 0 -0.85 4 4
VEGFB/NRP1 -0.093 0.29 -9999 0 -0.99 40 40
mol:NO 0.015 0.23 -9999 0 -0.68 43 43
PXN 0.013 0.033 -9999 0 -0.69 1 1
HRAS/GTP -0.086 0.26 -9999 0 -0.87 41 41
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.049 0.37 -9999 0 -1.2 40 40
VHL 0.009 0.069 -9999 0 -0.85 3 3
ITGB3 -0.015 0.15 -9999 0 -0.77 18 18
NOS3 0.004 0.28 -9999 0 -0.82 43 43
VEGFR2 homodimer/VEGFA homodimer/Sck -0.12 0.38 -9999 0 -1.3 38 38
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA -0.03 0.32 -9999 0 -1 41 41
PRKCB -0.041 0.34 -9999 0 -1.1 41 41
VCL 0.015 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.054 0.35 -9999 0 -1.1 40 40
VEGFR1/2 heterodimer/VEGFA homodimer -0.14 0.45 -9999 0 -1.5 43 43
VEGFA165/NRP2 -0.05 0.19 -9999 0 -0.73 32 32
MAPKKK cascade -0.086 0.26 -9999 0 -0.88 41 41
NRP2 -0.005 0.13 -9999 0 -0.84 11 11
VEGFC homodimer 0.004 0.094 -9999 0 -0.82 6 6
NCK1 0.015 0 -9999 0 -10000 0 0
ROCK1 0.013 0.04 -9999 0 -0.85 1 1
FAK1/Paxillin -0.022 0.32 -9999 0 -0.99 40 40
MAP3K13 -0.055 0.38 -9999 0 -1.2 42 42
PDPK1 0.004 0.27 -9999 0 -0.79 45 45
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.015 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.057 0.12 -10000 0 -0.61 7 7
NT3 (dimer)/TRKC -0.15 0.32 -10000 0 -0.75 96 96
NT3 (dimer)/TRKB -0.2 0.36 -10000 0 -0.82 91 91
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.052 -10000 0 -0.69 1 1
RAPGEF1 0.013 0.04 -10000 0 -0.85 1 1
BDNF -0.13 0.32 -10000 0 -0.79 86 86
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
DYNLT1 0.013 0.033 -10000 0 -0.69 1 1
NTRK1 -0.076 0.25 -10000 0 -0.75 55 55
NTRK2 -0.15 0.33 -10000 0 -0.79 96 96
NTRK3 -0.12 0.31 -10000 0 -0.8 80 80
NT-4/5 (dimer)/TRKB -0.17 0.31 -10000 0 -0.64 127 127
neuron apoptosis 0.16 0.24 0.67 66 -10000 0 66
SHC 2-3/Grb2 -0.18 0.28 -10000 0 -0.78 66 66
SHC1 0.013 0.033 -10000 0 -0.69 1 1
SHC2 -0.16 0.3 -10000 0 -0.77 72 72
SHC3 -0.17 0.29 -10000 0 -0.73 73 73
STAT3 (dimer) 0.013 0.067 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.15 0.31 -10000 0 -0.67 108 108
RIN/GDP -0.001 0.12 -10000 0 -0.34 14 14
GIPC1 0.008 0.076 -10000 0 -0.81 4 4
KRAS 0.015 0 -10000 0 -10000 0 0
DNAJA3 -0.11 0.24 -10000 0 -0.71 49 49
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.006 0.18 -10000 0 -1.1 13 13
MAGED1 0.01 0.057 -10000 0 -0.69 3 3
PTPN11 0.015 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.13 -10000 0 -0.69 17 17
SHC/GRB2/SOS1 -0.001 0.02 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.14 0.28 -10000 0 -0.62 104 104
TRKA/NEDD4-2 -0.084 0.22 -10000 0 -0.6 66 66
ELMO1 0 0.11 -10000 0 -0.85 8 8
RhoG/GTP/ELMO1/DOCK1 -0.01 0.075 -10000 0 -0.58 8 8
NGF -0.086 0.27 -10000 0 -0.82 57 57
HRAS 0.009 0.069 -10000 0 -0.85 3 3
DOCK1 0.015 0 -10000 0 -10000 0 0
GAB2 0.013 0.033 -10000 0 -0.69 1 1
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.009 0.069 -10000 0 -0.85 3 3
FRS2 0.015 0 -10000 0 -10000 0 0
DNM1 -0.051 0.22 -10000 0 -0.8 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.11 0.25 -10000 0 -0.72 52 52
mol:GDP -0.009 0.18 -10000 0 -0.52 25 25
NGF (dimer) -0.086 0.27 -10000 0 -0.81 57 57
RhoG/GDP -0.011 0.086 -10000 0 -0.66 8 8
RIT1/GDP 0.005 0.12 -10000 0 -0.39 10 10
TIAM1 0 0.11 -10000 0 -0.85 8 8
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
BDNF (dimer)/TRKB -0.2 0.31 -10000 0 -0.6 155 155
KIDINS220/CRKL/C3G -0.001 0.03 -10000 0 -0.66 1 1
SHC/RasGAP -0.001 0.024 -10000 0 -0.52 1 1
FRS2 family/SHP2 -0.003 0.042 -10000 0 -0.57 2 2
SHC/GRB2/SOS1/GAB1 -0.003 0.038 -10000 0 -0.52 2 2
RIT1/GTP -0.004 0.053 -10000 0 -0.66 3 3
NT3 (dimer) -0.06 0.24 -10000 0 -0.8 43 43
RAP1/GDP -0.036 0.076 -10000 0 -0.4 1 1
KIDINS220/CRKL 0.015 0 -10000 0 -10000 0 0
BDNF (dimer) -0.13 0.31 -10000 0 -0.79 86 86
ubiquitin-dependent protein catabolic process -0.14 0.28 -10000 0 -0.75 60 60
Schwann cell development -0.037 0.041 -10000 0 -10000 0 0
EHD4 0.015 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.003 0.038 -10000 0 -0.52 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.045 0.038 -10000 0 -0.62 1 1
RAP1B 0.013 0.033 -10000 0 -0.69 1 1
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.25 0.36 -10000 0 -0.98 72 72
ABL1 0.011 0.056 -10000 0 -0.85 2 2
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.063 0.099 -10000 0 -0.89 1 1
STAT3 0.013 0.067 -10000 0 -10000 0 0
axon guidance -0.24 0.33 -10000 0 -0.89 72 72
MAPK3 -0.096 0.28 -10000 0 -0.71 60 60
MAPK1 -0.094 0.28 -10000 0 -0.69 60 60
CDC42/GDP 0.006 0.12 -10000 0 -0.35 8 8
NTF3 -0.061 0.24 -10000 0 -0.81 43 43
NTF4 -0.02 0.13 -10000 0 -0.69 17 17
NGF (dimer)/TRKA/FAIM -0.12 0.26 -10000 0 -0.59 98 98
PI3K -0.009 0.07 -10000 0 -0.57 7 7
FRS3 0.01 0.065 -10000 0 -0.8 3 3
FAIM 0.011 0.052 -10000 0 -0.77 2 2
GAB1 0.011 0.056 -10000 0 -0.85 2 2
RASGRF1 -0.14 0.28 -10000 0 -0.74 67 67
SOS1 0.015 0 -10000 0 -10000 0 0
MCF2L -0.12 0.33 -10000 0 -0.71 99 99
RGS19 0.011 0.056 -10000 0 -0.85 2 2
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.099 -10000 0 -0.68 2 2
Rac1/GDP 0.006 0.12 -10000 0 -0.34 10 10
NGF (dimer)/TRKA/GRIT -0.12 0.25 -10000 0 -0.59 98 98
neuron projection morphogenesis -0.066 0.23 -10000 0 -0.76 34 34
NGF (dimer)/TRKA/NEDD4-2 -0.14 0.29 -10000 0 -0.76 60 60
MAP2K1 0.044 0.039 -10000 0 -10000 0 0
NGFR -0.066 0.25 -10000 0 -0.83 45 45
NGF (dimer)/TRKA/GIPC/GAIP -0.069 0.24 -10000 0 -0.78 30 30
RAS family/GTP/PI3K 0.03 0.054 -10000 0 -0.67 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.003 0.035 -10000 0 -10000 0 0
NRAS 0.015 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.012 0.046 -10000 0 -0.69 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ 0 0.11 -10000 0 -0.83 8 8
MAPKKK cascade -0.13 0.28 -10000 0 -0.82 60 60
RASA1 0.015 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.069 0.19 -10000 0 -0.57 57 57
SQSTM1 0.015 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.19 0.29 -10000 0 -0.65 102 102
NGF (dimer)/TRKA/p62/Atypical PKCs -0.11 0.24 -10000 0 -0.95 18 18
MATK -0.013 0.15 -10000 0 -0.8 16 16
NEDD4L -0.012 0.14 -10000 0 -0.71 17 17
RAS family/GDP -0.034 0.072 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.12 0.25 -10000 0 -0.75 51 51
Rac1/GTP -0.087 0.15 -10000 0 -0.46 47 47
FRS2 family/SHP2/CRK family -0.003 0.035 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.084 0.26 -9999 0 -0.81 49 49
alphaV beta3 Integrin -0.037 0.14 -9999 0 -0.56 31 31
PTK2 -0.086 0.28 -9999 0 -0.79 45 45
IGF1R 0.009 0.069 -9999 0 -0.85 3 3
PI4KB 0.013 0.04 -9999 0 -0.85 1 1
MFGE8 -0.008 0.14 -9999 0 -0.83 13 13
SRC 0.011 0.056 -9999 0 -0.85 2 2
CDKN1B -0.11 0.19 -9999 0 -0.62 32 32
VEGFA -0.033 0.2 -9999 0 -0.85 26 26
ILK -0.11 0.19 -9999 0 -0.62 32 32
ROCK1 0.013 0.04 -9999 0 -0.85 1 1
AKT1 -0.099 0.18 -9999 0 -0.59 32 32
PTK2B -0.04 0.25 -9999 0 -1 19 19
alphaV/beta3 Integrin/JAM-A -0.13 0.21 -9999 0 -0.89 10 10
CBL 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.25 0.28 -9999 0 -0.53 224 224
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.052 0.14 -9999 0 -0.55 18 18
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.06 0.2 -9999 0 -0.63 34 34
alphaV/beta3 Integrin/Syndecan-1 -0.046 0.14 -9999 0 -0.57 20 20
PI4KA 0.013 0.04 -9999 0 -0.85 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.097 0.22 -9999 0 -0.85 24 24
PI4 Kinase -0.003 0.055 -9999 0 -1.2 1 1
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
alphaV/beta3 Integrin/Osteopontin -0.044 0.16 -9999 0 -0.56 37 37
RPS6KB1 -0.035 0.23 -9999 0 -0.77 24 24
TLN1 0.013 0.04 -9999 0 -0.85 1 1
MAPK3 -0.095 0.2 -9999 0 -0.83 25 25
GPR124 -0.018 0.17 -9999 0 -0.85 18 18
MAPK1 -0.094 0.2 -9999 0 -0.83 24 24
PXN 0.013 0.033 -9999 0 -0.69 1 1
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
alphaV/beta3 Integrin/Tumstatin -0.075 0.2 -9999 0 -0.62 47 47
cell adhesion -0.2 0.24 -9999 0 -0.86 23 23
ANGPTL3 -0.35 0.4 -9999 0 -0.78 218 218
VEGFR2 homodimer/VEGFA homodimer/Src -0.077 0.23 -9999 0 -0.71 51 51
IGF-1R heterotetramer 0.009 0.069 -9999 0 -0.85 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.004 0.097 -9999 0 -0.85 6 6
ITGB3 -0.015 0.15 -9999 0 -0.77 18 18
IGF1 -0.033 0.18 -9999 0 -0.74 30 30
RAC1 0.015 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.041 0.15 -9999 0 -0.57 34 34
apoptosis 0.013 0.033 -9999 0 -0.69 1 1
CD47 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.02 0.099 -9999 0 -0.5 19 19
VCL 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.081 0.21 -9999 0 -0.58 66 66
CSF1 0.002 0.1 -9999 0 -0.83 7 7
PIK3C2A -0.11 0.19 -9999 0 -0.62 32 32
PI4 Kinase/Pyk2 -0.15 0.26 -9999 0 -0.87 39 39
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.086 0.25 -9999 0 -0.72 54 54
FAK1/Vinculin -0.053 0.21 -9999 0 -0.58 38 38
alphaV beta3/Integrin/ppsTEM5 -0.042 0.16 -9999 0 -0.57 34 34
RHOA 0.015 0 -9999 0 -10000 0 0
VTN -0.16 0.32 -9999 0 -0.73 110 110
BCAR1 0.009 0.069 -9999 0 -0.85 3 3
FGF2 -0.012 0.15 -9999 0 -0.82 15 15
F11R 0.002 0.13 -9999 0 -0.66 17 17
alphaV/beta3 Integrin/Lactadherin -0.035 0.15 -9999 0 -0.58 28 28
alphaV/beta3 Integrin/TGFBR2 -0.027 0.12 -9999 0 -0.56 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.011 0.096 -9999 0 -0.71 7 7
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
alphaV/beta3 Integrin/Talin -0.02 0.099 -9999 0 -0.49 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.038 0.2 -9999 0 -0.76 32 32
alphaV/beta3 Integrin/Pyk2 -0.081 0.24 -9999 0 -1 19 19
SDC1 -0.025 0.17 -9999 0 -0.77 24 24
VAV3 0.019 0.13 -9999 0 -0.56 17 17
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 -0.023 0.16 -9999 0 -0.73 24 24
FAK1/Paxillin -0.054 0.21 -9999 0 -0.6 35 35
cell migration -0.037 0.2 -9999 0 -0.53 32 32
ITGAV 0.013 0.033 -9999 0 -0.69 1 1
PI3K -0.12 0.2 -9999 0 -0.83 13 13
SPP1 -0.023 0.17 -9999 0 -0.76 23 23
KDR -0.053 0.23 -9999 0 -0.85 37 37
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.033 -9999 0 -0.69 1 1
COL4A3 -0.072 0.25 -9999 0 -0.81 49 49
angiogenesis -0.065 0.23 -9999 0 -0.83 23 23
Rac1/GTP -0.024 0.11 -9999 0 -1 2 2
EDIL3 -0.081 0.26 -9999 0 -0.8 55 55
cell proliferation -0.027 0.12 -9999 0 -0.55 23 23
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.1 0.19 -9999 0 -0.52 53 53
RGS9BP -0.057 0.23 -9999 0 -0.76 43 43
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.031 0.12 -9999 0 -0.46 31 31
mol:ADP 0.004 0.055 -9999 0 -0.53 5 5
GNAT2 0.012 0.033 -9999 0 -0.69 1 1
RGS9-1/Gbeta5/R9AP -0.16 0.26 -9999 0 -0.63 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.002 0.029 -9999 0 -0.45 2 2
GRK7 0.004 0.073 -9999 0 -0.69 5 5
CNGB3 -0.015 0.12 -9999 0 -0.69 14 14
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.022 0.11 -9999 0 -0.43 31 31
Cone PDE6 -0.14 0.24 -9999 0 -0.87 18 18
Cone Metarhodopsin II -0.004 0.043 -9999 0 -0.42 5 5
Na + (4 Units) -0.028 0.11 -9999 0 -0.42 31 31
GNAT2/GDP -0.13 0.23 -9999 0 -0.55 80 80
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.059 -9999 0 -0.41 9 9
Cone Transducin -0.11 0.2 -9999 0 -0.54 53 53
SLC24A2 0 0 -9999 0 -10000 0 0
GNB3/GNGT2 -0.13 0.25 -9999 0 -0.6 104 104
GNB3 -0.15 0.32 -9999 0 -0.77 99 99
GNAT2/GTP -0.001 0.024 -9999 0 -0.53 1 1
CNGA3 -0.022 0.13 -9999 0 -0.69 18 18
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.031 0.12 -9999 0 -0.47 31 31
mol:Pi -0.15 0.26 -9999 0 -0.63 80 80
Cone CNG Channel -0.032 0.12 -9999 0 -0.72 5 5
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0 0 -9999 0 -10000 0 0
RGS9 -0.16 0.33 -9999 0 -0.79 100 100
PDE6C -0.004 0.085 -9999 0 -0.69 7 7
GNGT2 0.002 0.1 -9999 0 -0.85 7 7
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.033 -9999 0 -0.69 1 1
Thromboxane A2 receptor signaling

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
TGM2 -0.029 0.18 -10000 0 -0.81 24 24
GNB1/GNG2 -0.042 0.077 -10000 0 -0.23 34 34
AKT1 0.025 0.12 -10000 0 -0.34 5 5
EGF -0.22 0.36 -10000 0 -0.77 143 143
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.011 0.16 -10000 0 -0.69 18 18
mol:Ca2+ 0.007 0.17 -10000 0 -0.36 49 49
LYN 0.016 0.14 -10000 0 -0.63 16 16
RhoA/GTP -0.027 0.051 -10000 0 -0.21 4 4
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.008 0.19 -10000 0 -0.41 44 44
GNG2 0.004 0.097 -10000 0 -0.85 6 6
ARRB2 0.013 0.033 -10000 0 -0.69 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.009 0.15 -10000 0 -0.74 15 15
G beta5/gamma2 -0.055 0.1 -10000 0 -0.32 39 39
PRKCH 0 0.19 -10000 0 -0.44 44 44
DNM1 -0.051 0.22 -10000 0 -0.8 38 38
TXA2/TP beta/beta Arrestin3 -0.027 0.081 -10000 0 -0.3 37 37
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR -0.022 0.17 -10000 0 -0.82 21 21
G12 family/GTP -0.065 0.12 -10000 0 -0.34 47 47
ADRBK1 0.009 0.069 -10000 0 -0.85 3 3
ADRBK2 0.013 0.04 -10000 0 -0.85 1 1
RhoA/GTP/ROCK1 -0.001 0.027 -10000 0 -0.58 1 1
mol:GDP -0.002 0.15 0.46 33 -10000 0 33
mol:NADP -0.016 0.16 -10000 0 -0.85 17 17
RAB11A 0.015 0 -10000 0 -10000 0 0
PRKG1 -0.057 0.24 -10000 0 -0.85 39 39
mol:IP3 -0.004 0.21 -10000 0 -0.46 53 53
cell morphogenesis -0.001 0.027 -10000 0 -0.57 1 1
PLCB2 -0.029 0.27 -10000 0 -0.65 53 53
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.056 0.2 -10000 0 -0.64 22 22
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.012 0.16 -10000 0 -0.66 17 17
RHOA 0.015 0 -10000 0 -10000 0 0
PTGIR -0.026 0.18 -10000 0 -0.82 23 23
PRKCB1 -0.005 0.2 -10000 0 -0.41 72 72
GNAQ 0.015 0 -10000 0 -10000 0 0
mol:L-citrulline -0.016 0.16 -10000 0 -0.85 17 17
TXA2/TXA2-R family -0.023 0.27 -10000 0 -0.58 74 74
LCK -0.006 0.19 -10000 0 -0.74 21 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.046 0.16 -10000 0 -0.72 19 19
TXA2-R family/G12 family/GDP/G beta/gamma 0.023 0.057 -10000 0 -0.38 4 4
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.045 0.16 -10000 0 -0.89 12 12
MAPK14 0.023 0.13 -10000 0 -0.33 5 5
TGM2/GTP -0.015 0.24 -10000 0 -0.57 50 50
MAPK11 0.018 0.14 -10000 0 -0.41 16 16
ARHGEF1 0.017 0.11 -10000 0 -0.32 6 6
GNAI2 0.015 0 -10000 0 -10000 0 0
JNK cascade 0 0.2 -10000 0 -0.42 71 71
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 0.009 0.16 -10000 0 -0.36 33 33
cAMP biosynthetic process -0.005 0.2 -10000 0 -0.44 50 50
Gq family/GTP/EBP50 0.003 0.12 -10000 0 -0.42 23 23
actin cytoskeleton reorganization -0.001 0.027 -10000 0 -0.57 1 1
SRC 0.017 0.14 -10000 0 -0.64 15 15
GNB5 0.015 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.15 -10000 0 -0.48 25 25
VCAM1 -0.001 0.18 -10000 0 -0.41 56 56
TP beta/Gq family/GDP/G beta5/gamma2 0.009 0.15 -10000 0 -0.74 15 15
platelet activation 0.028 0.18 -10000 0 -0.36 34 34
PGI2/IP -0.031 0.14 -10000 0 -0.64 23 23
PRKACA -0.014 0.15 -10000 0 -0.52 30 30
Gq family/GDP/G beta5/gamma2 0.009 0.15 -10000 0 -0.71 15 15
TXA2/TP beta/beta Arrestin2 -0.049 0.17 -10000 0 -0.69 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.022 0.2 -10000 0 -0.86 19 19
mol:DAG -0.009 0.22 -10000 0 -0.47 72 72
EGFR -0.023 0.17 -10000 0 -0.8 22 22
TXA2/TP alpha -0.021 0.26 -10000 0 -0.62 53 53
Gq family/GTP -0.018 0.083 -10000 0 -0.32 28 28
YES1 0.018 0.14 -10000 0 -0.61 15 15
GNAI2/GTP -0.042 0.15 -10000 0 -0.75 15 15
PGD2/DP -0.029 0.13 -10000 0 -0.64 21 21
SLC9A3R1 -0.007 0.14 -10000 0 -0.84 12 12
FYN 0.015 0.15 -10000 0 -0.66 16 16
mol:NO -0.016 0.16 -10000 0 -0.85 17 17
GNA15 -0.005 0.13 -10000 0 -0.82 11 11
PGK/cGMP -0.067 0.22 -10000 0 -0.7 45 45
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.066 0.22 -10000 0 -0.99 20 20
NOS3 -0.017 0.16 -10000 0 -0.85 17 17
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA 0 0.19 -10000 0 -0.43 41 41
PRKCB -0.006 0.21 -10000 0 -0.48 48 48
PRKCE 0.003 0.19 -10000 0 -0.41 41 41
PRKCD -0.005 0.2 -10000 0 -0.44 68 68
PRKCG -0.011 0.21 -10000 0 -0.47 54 54
muscle contraction -0.014 0.25 -10000 0 -0.54 74 74
PRKCZ 0.006 0.19 -10000 0 -0.41 38 38
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.05 0.18 -10000 0 -0.91 15 15
PRKCQ -0.008 0.2 -10000 0 -0.46 49 49
MAPKKK cascade -0.019 0.25 -10000 0 -0.56 56 56
SELE -0.005 0.19 -10000 0 -0.4 64 64
TP beta/GNAI2/GDP/G beta/gamma -0.049 0.18 -10000 0 -0.93 14 14
ROCK1 0.013 0.04 -10000 0 -0.85 1 1
GNA14 -0.016 0.16 -10000 0 -0.84 17 17
chemotaxis -0.029 0.29 -10000 0 -0.64 70 70
GNA12 0.013 0.033 -10000 0 -0.69 1 1
GNA13 0.015 0 -10000 0 -10000 0 0
GNA11 0.004 0.095 -10000 0 -0.82 6 6
Rac1/GTP 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.011 0.13 -9999 0 -0.67 13 13
CRKL 0.015 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.015 0 -9999 0 -10000 0 0
ITGA4 -0.011 0.14 -9999 0 -0.84 14 14
alpha4/beta7 Integrin/MAdCAM1 -0.037 0.13 -9999 0 -0.57 18 18
EPO -0.42 0.39 -9999 0 -0.77 257 257
alpha4/beta7 Integrin -0.029 0.14 -9999 0 -0.7 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.64 14 14
EPO/EPOR (dimer) -0.32 0.3 -9999 0 -0.59 260 260
lamellipodium assembly -0.003 0.045 -9999 0 -0.47 3 3
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
PI3K -0.009 0.07 -9999 0 -0.57 7 7
ARF6 0.015 0 -9999 0 -10000 0 0
JAK2 -0.17 0.2 -9999 0 -0.77 11 11
PXN 0.013 0.033 -9999 0 -0.69 1 1
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
MADCAM1 -0.013 0.13 -9999 0 -0.69 17 17
cell adhesion -0.037 0.13 -9999 0 -0.57 18 18
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC -0.028 0.21 -9999 0 -0.63 47 47
ITGB7 0.002 0.1 -9999 0 -0.85 7 7
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.067 0.21 -9999 0 -0.67 47 47
p130Cas/Crk/Dock1 -0.001 0.19 -9999 0 -0.88 12 12
VCAM1 -0.064 0.25 -9999 0 -0.85 43 43
RHOA 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.018 0.098 -9999 0 -0.54 15 15
BCAR1 -0.019 0.21 -9999 0 -0.94 13 13
EPOR 0.004 0.089 -9999 0 -0.72 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.015 0 -9999 0 -10000 0 0
GIT1 0.011 0.056 -9999 0 -0.85 2 2
Rac1/GTP -0.003 0.047 -9999 0 -0.49 3 3
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.17 0.27 -10000 0 -0.56 146 146
cell-cell adhesion 0.095 0.2 0.75 26 -10000 0 26
Ephrin B/EPHB2/RasGAP -0.087 0.22 -10000 0 -1 14 14
ITSN1 0.013 0.04 -10000 0 -0.85 1 1
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
SHC1 0.013 0.033 -10000 0 -0.69 1 1
Ephrin B1/EPHB3 -0.046 0.17 -10000 0 -0.61 35 35
Ephrin B1/EPHB1 -0.048 0.15 -10000 0 -0.5 45 45
HRAS/GDP -0.087 0.2 -10000 0 -0.8 23 23
Ephrin B/EPHB1/GRB7 -0.1 0.24 -10000 0 -0.97 21 21
Endophilin/SYNJ1 -0.043 0.22 -10000 0 -0.92 14 14
KRAS 0.015 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.095 0.24 -10000 0 -1 18 18
endothelial cell migration -0.028 0.13 -10000 0 -0.57 21 21
GRB2 0.015 0 -10000 0 -10000 0 0
GRB7 -0.003 0.12 -10000 0 -0.84 10 10
PAK1 -0.04 0.23 -10000 0 -0.94 16 16
HRAS 0.009 0.069 -10000 0 -0.85 3 3
RRAS -0.051 0.24 -10000 0 -0.97 18 18
DNM1 -0.051 0.22 -10000 0 -0.8 38 38
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.051 0.23 -10000 0 -0.91 17 17
lamellipodium assembly -0.095 0.2 -10000 0 -0.75 26 26
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.02 0.17 -10000 0 -0.68 18 18
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
EPHB2 -0.037 0.2 -10000 0 -0.77 31 31
EPHB3 -0.044 0.22 -10000 0 -0.83 33 33
EPHB1 -0.05 0.21 -10000 0 -0.72 41 41
EPHB4 0.004 0.095 -10000 0 -0.82 6 6
mol:GDP -0.076 0.22 -10000 0 -0.74 28 28
Ephrin B/EPHB2 -0.089 0.22 -10000 0 -0.64 51 51
Ephrin B/EPHB3 -0.094 0.23 -10000 0 -0.62 60 60
JNK cascade -0.027 0.19 -10000 0 -0.61 25 25
Ephrin B/EPHB1 -0.095 0.23 -10000 0 -0.67 46 46
RAP1/GDP -0.062 0.18 -10000 0 -0.74 16 16
EFNB2 -0.015 0.16 -10000 0 -0.85 16 16
EFNB3 -0.054 0.23 -10000 0 -0.8 40 40
EFNB1 0.004 0.095 -10000 0 -0.82 6 6
Ephrin B2/EPHB1-2 -0.085 0.2 -10000 0 -0.64 37 37
RAP1B 0.013 0.033 -10000 0 -0.69 1 1
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.22 -10000 0 -0.82 26 26
Rap1/GTP -0.094 0.2 -10000 0 -0.77 26 26
axon guidance -0.17 0.27 -10000 0 -0.56 146 146
MAPK3 -0.001 0.16 -10000 0 -0.7 15 15
MAPK1 0.001 0.16 -10000 0 -0.67 14 14
Rac1/GDP -0.022 0.2 -10000 0 -0.7 22 22
actin cytoskeleton reorganization -0.074 0.16 -10000 0 -0.6 21 21
CDC42/GDP -0.022 0.2 -10000 0 -0.76 17 17
PI3K -0.029 0.13 -10000 0 -0.57 21 21
EFNA5 -0.2 0.36 -10000 0 -0.79 126 126
Ephrin B2/EPHB4 -0.027 0.12 -10000 0 -0.57 22 22
Ephrin B/EPHB2/Intersectin/N-WASP -0.025 0.18 -10000 0 -0.78 15 15
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP -0.093 0.2 -10000 0 -0.75 27 27
PTK2 0.015 0.037 -10000 0 -10000 0 0
MAP4K4 -0.027 0.19 -10000 0 -0.62 25 25
SRC 0.011 0.056 -10000 0 -0.85 2 2
KALRN 0.006 0.086 -10000 0 -0.82 5 5
Intersectin/N-WASP -0.001 0.03 -10000 0 -0.66 1 1
neuron projection morphogenesis -0.007 0.19 -10000 0 -0.62 15 15
MAP2K1 -0.009 0.16 -10000 0 -0.71 14 14
WASL 0.015 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.072 0.19 -10000 0 -0.65 25 25
cell migration -0.005 0.18 -10000 0 -0.76 15 15
NRAS 0.015 0 -10000 0 -10000 0 0
SYNJ1 -0.045 0.22 -10000 0 -0.95 14 14
PXN 0.013 0.033 -10000 0 -0.69 1 1
TF -0.18 0.3 -10000 0 -0.86 42 42
HRAS/GTP -0.1 0.23 -10000 0 -0.84 27 27
Ephrin B1/EPHB1-2 -0.073 0.19 -10000 0 -0.49 70 70
cell adhesion mediated by integrin 0.07 0.2 0.64 39 -10000 0 39
RAC1 0.015 0 -10000 0 -10000 0 0
mol:GTP -0.11 0.24 -10000 0 -0.92 25 25
RAC1-CDC42/GTP -0.12 0.23 -10000 0 -0.78 32 32
RASA1 0.015 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.18 -10000 0 -0.72 16 16
ruffle organization -0.039 0.24 -10000 0 -0.78 26 26
NCK1 0.015 0 -10000 0 -10000 0 0
receptor internalization -0.068 0.26 -10000 0 -0.94 24 24
Ephrin B/EPHB2/KALRN -0.092 0.23 -10000 0 -1 16 16
ROCK1 -0.015 0.17 -10000 0 -0.57 35 35
RAS family/GDP -0.073 0.16 -10000 0 -0.61 21 21
Rac1/GTP -0.1 0.23 -10000 0 -0.84 26 26
Ephrin B/EPHB1/Src/Paxillin -0.03 0.19 -10000 0 -0.76 18 18
FOXM1 transcription factor network

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
NFATC3 0.19 0.45 -10000 0 -1.2 26 26
PLK1 0.039 0.22 -10000 0 -0.82 24 24
BIRC5 0.011 0.3 -10000 0 -0.95 34 34
HSPA1B 0.18 0.46 -10000 0 -1.2 28 28
MAP2K1 0.06 0.041 -10000 0 -10000 0 0
BRCA2 0.17 0.49 -10000 0 -1.3 34 34
FOXM1 0.13 0.72 -10000 0 -2.1 32 32
XRCC1 0.19 0.46 -10000 0 -1.3 26 26
FOXM1B/p19 -0.12 0.36 0.46 1 -1.3 31 32
Cyclin D1/CDK4 0.16 0.45 -10000 0 -1.2 29 29
CDC2 0.18 0.48 -10000 0 -1.3 30 30
TGFA 0.16 0.47 -10000 0 -1.2 36 36
SKP2 0.19 0.46 -10000 0 -1.3 27 27
CCNE1 0.005 0.12 -10000 0 -0.72 12 12
CKS1B 0.19 0.45 -10000 0 -1.2 27 27
RB1 -0.056 0.16 -10000 0 -0.8 14 14
FOXM1C/SP1 0.15 0.53 -10000 0 -1.5 30 30
AURKB 0.003 0.33 -10000 0 -1.1 32 32
CENPF 0.18 0.47 -10000 0 -1.3 31 31
CDK4 0.031 0.018 -10000 0 -10000 0 0
MYC 0.18 0.42 -10000 0 -1.1 28 28
CHEK2 0.056 0.07 -10000 0 -0.82 2 2
ONECUT1 0.16 0.47 -10000 0 -1.3 30 30
CDKN2A -0.04 0.18 -10000 0 -0.8 26 26
LAMA4 0.18 0.48 -10000 0 -1.3 31 31
FOXM1B/HNF6 0.13 0.61 -10000 0 -1.8 31 31
FOS 0.11 0.56 -10000 0 -1.3 53 53
SP1 0.016 0.003 -10000 0 -10000 0 0
CDC25B 0.19 0.46 -10000 0 -1.3 26 26
response to radiation 0.039 0.038 -10000 0 -10000 0 0
CENPB 0.19 0.46 -10000 0 -1.3 27 27
CENPA 0.17 0.49 -10000 0 -1.3 34 34
NEK2 0.17 0.49 -10000 0 -1.4 32 32
HIST1H2BA 0.18 0.45 -10000 0 -1.2 30 30
CCNA2 0.01 0.1 -10000 0 -0.72 9 9
EP300 0.015 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.17 0.54 -10000 0 -1.6 29 29
CCNB2 0.18 0.48 -10000 0 -1.4 28 28
CCNB1 0.18 0.49 -10000 0 -1.4 28 28
ETV5 0.19 0.45 -10000 0 -1.3 24 24
ESR1 0.18 0.48 -10000 0 -1.3 29 29
CCND1 0.17 0.47 -10000 0 -1.3 31 31
GSK3A 0.051 0.07 -10000 0 -0.89 2 2
Cyclin A-E1/CDK1-2 0.05 0.13 -10000 0 -0.57 17 17
CDK2 0.024 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.045 0.044 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.36 -10000 0 -1.3 33 33
GAS1 0.17 0.48 -10000 0 -1.2 35 35
MMP2 0.16 0.5 -10000 0 -1.3 35 35
RB1/FOXM1C 0.17 0.47 -10000 0 -1.3 30 30
CREBBP 0.015 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.023 0.15 -10000 0 -1.2 7 7
oxygen homeostasis 0.004 0.019 -10000 0 -10000 0 0
TCEB2 0.009 0.069 -10000 0 -0.85 3 3
TCEB1 0.015 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.061 0.18 -10000 0 -0.66 30 30
EPO -0.29 0.45 -10000 0 -0.95 72 72
FIH (dimer) 0.019 0.017 -10000 0 -10000 0 0
APEX1 0.011 0.018 -10000 0 -10000 0 0
SERPINE1 -0.11 0.43 -10000 0 -1.1 52 52
FLT1 -0.14 0.46 -10000 0 -1.6 40 40
ADORA2A -0.053 0.38 -10000 0 -1.1 39 39
germ cell development -0.094 0.4 -10000 0 -1 47 47
SLC11A2 -0.059 0.37 -10000 0 -1.1 36 36
BHLHE40 -0.064 0.38 -10000 0 -1.1 36 36
HIF1AN 0.019 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.12 0.22 -10000 0 -0.81 32 32
ETS1 0.007 0.14 -10000 0 -0.87 12 12
CITED2 -0.019 0.1 -10000 0 -0.97 4 4
KDR -0.14 0.45 -10000 0 -1.6 40 40
PGK1 -0.061 0.37 -10000 0 -1.1 36 36
SIRT1 0.01 0.006 -10000 0 -10000 0 0
response to hypoxia -0.009 0.01 -10000 0 -10000 0 0
HIF2A/ARNT -0.12 0.58 -10000 0 -1.7 40 40
EPAS1 0.009 0.23 -10000 0 -0.7 33 33
SP1 0.024 0.003 -10000 0 -10000 0 0
ABCG2 -0.08 0.41 -10000 0 -1.1 42 42
EFNA1 -0.064 0.38 -10000 0 -1.1 38 38
FXN -0.049 0.37 -10000 0 -1 38 38
POU5F1 -0.11 0.44 -10000 0 -1.1 47 47
neuron apoptosis 0.09 0.47 1.4 40 -10000 0 40
EP300 0.015 0 -10000 0 -10000 0 0
EGLN3 -0.038 0.22 -10000 0 -0.87 31 31
EGLN2 0.014 0.072 -10000 0 -0.86 3 3
EGLN1 0.019 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.007 0.064 -10000 0 -0.57 6 6
VHL 0.009 0.069 -10000 0 -0.85 3 3
ARNT 0.011 0.018 -10000 0 -10000 0 0
SLC2A1 -0.058 0.39 -10000 0 -1.1 40 40
TWIST1 -0.077 0.41 -10000 0 -1.1 48 48
ELK1 0.019 0.057 -10000 0 -0.69 3 3
HIF2A/ARNT/Cbp/p300 -0.086 0.21 -10000 0 -0.78 32 32
VEGFA -0.073 0.41 -10000 0 -1.2 41 41
CREBBP 0.015 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.039 0.17 -10000 0 -0.53 25 25
IKBKB -0.01 0.087 -10000 0 -0.33 4 4
AKT1 -0.034 0.12 0.24 1 -0.32 11 12
IKBKG -0.01 0.098 -10000 0 -0.38 10 10
CALM1 -0.037 0.14 -10000 0 -0.65 14 14
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
MAP3K1 -0.076 0.23 -10000 0 -0.62 42 42
MAP3K7 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.15 -10000 0 -0.59 21 21
DOK1 0.007 0.08 -10000 0 -0.85 4 4
AP-1 -0.028 0.11 -10000 0 -0.31 18 18
LYN 0.011 0.056 -10000 0 -0.85 2 2
BLNK -0.002 0.12 -10000 0 -0.79 10 10
SHC1 0.013 0.033 -10000 0 -0.69 1 1
BCR complex -0.13 0.27 -10000 0 -0.62 102 102
CD22 -0.13 0.25 -10000 0 -0.78 44 44
CAMK2G -0.025 0.13 -10000 0 -0.64 11 11
CSNK2A1 0.015 0 -10000 0 -10000 0 0
INPP5D 0.009 0.069 -10000 0 -0.85 3 3
SHC/GRB2/SOS1 -0.097 0.2 -10000 0 -0.87 17 17
GO:0007205 -0.049 0.16 -10000 0 -0.61 21 21
SYK 0.004 0.094 -10000 0 -0.82 6 6
ELK1 -0.039 0.15 -10000 0 -0.67 15 15
NFATC1 -0.08 0.21 -10000 0 -0.62 28 28
B-cell antigen/BCR complex -0.13 0.27 -10000 0 -0.62 102 102
PAG1/CSK -0.015 0.1 -10000 0 -0.7 10 10
NFKBIB 0.009 0.032 -10000 0 -10000 0 0
HRAS -0.038 0.17 -10000 0 -0.69 18 18
NFKBIA 0.009 0.033 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.016 0.026 -10000 0 -10000 0 0
RasGAP/Csk -0.13 0.25 -10000 0 -0.92 25 25
mol:GDP -0.046 0.14 -10000 0 -0.56 21 21
PTEN 0.013 0.04 -10000 0 -0.85 1 1
CD79B -0.013 0.15 -10000 0 -0.8 16 16
NF-kappa-B/RelA/I kappa B alpha 0.016 0.026 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.1 0.23 -10000 0 -0.6 44 44
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
mol:IP3 -0.058 0.16 -10000 0 -0.62 21 21
CSK 0.009 0.069 -10000 0 -0.85 3 3
FOS -0.085 0.2 -10000 0 -0.55 49 49
CHUK -0.009 0.094 -10000 0 -0.33 9 9
IBTK 0.015 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.08 0.17 -10000 0 -0.64 25 25
PTPN6 -0.12 0.24 -10000 0 -0.87 30 30
RELA 0.015 0 -10000 0 -10000 0 0
BCL2A1 0.008 0.043 -10000 0 -0.13 17 17
VAV2 -0.17 0.28 -10000 0 -0.69 78 78
ubiquitin-dependent protein catabolic process 0.013 0.032 -10000 0 -10000 0 0
BTK -0.03 0.18 -10000 0 -1.2 10 10
CD19 -0.19 0.31 -10000 0 -0.67 110 110
MAP4K1 -0.054 0.23 -10000 0 -0.79 40 40
CD72 -0.035 0.19 -10000 0 -0.76 30 30
PAG1 0 0.11 -10000 0 -0.83 8 8
MAPK14 -0.053 0.19 -10000 0 -0.59 24 24
SH3BP5 -0.005 0.13 -10000 0 -0.84 11 11
PIK3AP1 -0.048 0.19 -10000 0 -0.78 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.074 0.26 -10000 0 -0.71 41 41
RAF1 -0.027 0.15 -10000 0 -0.72 13 13
RasGAP/p62DOK/SHIP -0.13 0.25 -10000 0 -0.91 26 26
CD79A -0.14 0.31 -10000 0 -0.74 97 97
re-entry into mitotic cell cycle -0.028 0.11 -10000 0 -0.31 18 18
RASA1 0.015 0 -10000 0 -10000 0 0
MAPK3 -0.005 0.13 -10000 0 -0.69 9 9
MAPK1 -0.004 0.12 -10000 0 -0.62 9 9
CD72/SHP1 -0.094 0.28 -10000 0 -0.79 46 46
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 -0.056 0.2 -10000 0 -0.59 26 26
actin cytoskeleton organization -0.11 0.25 -10000 0 -0.57 76 76
NF-kappa-B/RelA 0.035 0.059 -10000 0 -0.33 4 4
Calcineurin -0.042 0.1 -10000 0 -0.57 10 10
PI3K -0.15 0.21 -10000 0 -0.63 42 42
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.063 0.17 0.29 2 -0.71 20 22
SOS1 0.015 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.097 0.29 -10000 0 -0.89 42 42
DAPP1 -0.11 0.29 -10000 0 -1.1 31 31
cytokine secretion -0.073 0.19 -10000 0 -0.56 28 28
mol:DAG -0.058 0.16 -10000 0 -0.62 21 21
PLCG2 -0.018 0.15 -10000 0 -0.72 21 21
MAP2K1 -0.015 0.14 -10000 0 -0.68 11 11
B-cell antigen/BCR complex/FcgammaRIIB -0.15 0.28 -10000 0 -0.59 123 123
mol:PI-3-4-5-P3 -0.1 0.15 0.36 1 -0.43 32 33
ETS1 -0.024 0.15 -10000 0 -0.65 18 18
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.24 -10000 0 -1 16 16
B-cell antigen/BCR complex/LYN -0.11 0.24 -10000 0 -0.71 44 44
MALT1 0.011 0.056 -10000 0 -0.85 2 2
TRAF6 0.013 0.04 -10000 0 -0.85 1 1
RAC1 -0.12 0.27 -10000 0 -0.62 76 76
B-cell antigen/BCR complex/LYN/SYK -0.13 0.26 -10000 0 -0.9 32 32
CARD11 -0.085 0.22 -10000 0 -0.66 45 45
FCGR2B -0.047 0.22 -10000 0 -0.79 36 36
PPP3CA 0.015 0 -10000 0 -10000 0 0
BCL10 0.015 0 -10000 0 -10000 0 0
IKK complex 0.007 0.043 -10000 0 -0.14 3 3
PTPRC -0.016 0.16 -10000 0 -0.83 17 17
PDPK1 -0.037 0.12 0.24 1 -0.3 2 3
PPP3CB 0.015 0 -10000 0 -10000 0 0
PPP3CC 0.015 0 -10000 0 -10000 0 0
POU2F2 0.014 0.034 -10000 0 -0.14 14 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.044 0.2 -10000 0 -0.67 28 28
CRKL -0.018 0.14 -10000 0 -0.55 21 21
HRAS -0.014 0.18 -10000 0 -0.67 23 23
mol:PIP3 -0.035 0.13 -10000 0 -0.52 23 23
SPRED1 0.013 0.04 -10000 0 -0.85 1 1
SPRED2 0.015 0 -10000 0 -10000 0 0
GAB1 -0.028 0.15 -10000 0 -0.54 27 27
FOXO3 -0.01 0.13 -10000 0 -0.53 15 15
AKT1 -0.021 0.14 -10000 0 -0.52 23 23
BAD -0.013 0.14 -10000 0 -0.56 17 17
megakaryocyte differentiation -0.044 0.18 -10000 0 -0.58 40 40
GSK3B -0.01 0.13 -10000 0 -0.52 16 16
RAF1 0.003 0.15 -10000 0 -0.52 20 20
SHC1 0.013 0.033 -10000 0 -0.69 1 1
STAT3 -0.026 0.14 -10000 0 -0.52 25 25
STAT1 -0.087 0.28 -10000 0 -1.1 23 23
HRAS/SPRED1 -0.042 0.13 -10000 0 -0.52 23 23
cell proliferation -0.028 0.15 -10000 0 -0.52 28 28
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
TEC 0.015 0 -10000 0 -10000 0 0
RPS6KB1 -0.025 0.14 -10000 0 -0.5 29 29
HRAS/SPRED2 -0.042 0.13 -10000 0 -0.5 23 23
LYN/TEC/p62DOK -0.038 0.14 -10000 0 -0.64 15 15
MAPK3 0.018 0.11 -10000 0 -0.43 10 10
STAP1 -0.098 0.24 -10000 0 -0.55 83 83
GRAP2 -0.015 0.16 -10000 0 -0.85 16 16
JAK2 -0.11 0.22 -10000 0 -0.9 25 25
STAT1 (dimer) -0.084 0.28 -10000 0 -1.1 24 24
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.067 0.2 -10000 0 -0.66 35 35
actin filament polymerization -0.034 0.16 -10000 0 -0.57 28 28
LYN 0.011 0.056 -10000 0 -0.85 2 2
STAP1/STAT5A (dimer) -0.099 0.26 -10000 0 -0.71 50 50
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
CBL/CRKL/GRB2 -0.027 0.12 -10000 0 -0.61 8 8
PI3K -0.035 0.14 -10000 0 -0.53 23 23
PTEN 0.013 0.04 -10000 0 -0.85 1 1
SCF/KIT/EPO/EPOR -0.25 0.38 -10000 0 -1.3 32 32
MAPK8 -0.029 0.15 -10000 0 -0.54 28 28
STAT3 (dimer) -0.025 0.14 -10000 0 -0.51 25 25
positive regulation of transcription 0.021 0.093 -10000 0 -0.47 2 2
mol:GDP -0.064 0.18 -10000 0 -0.68 29 29
PIK3C2B -0.032 0.16 -10000 0 -0.6 26 26
CBL/CRKL -0.007 0.13 -10000 0 -0.61 10 10
FER -0.028 0.15 -10000 0 -0.53 27 27
SH2B3 -0.028 0.15 -10000 0 -0.56 22 22
PDPK1 -0.024 0.12 -10000 0 -0.52 16 16
SNAI2 -0.044 0.2 -10000 0 -0.67 32 32
positive regulation of cell proliferation -0.054 0.21 -10000 0 -0.8 23 23
KITLG -0.029 0.17 -10000 0 -0.8 22 22
cell motility -0.054 0.21 -10000 0 -0.8 23 23
PTPN6 0.008 0.056 -10000 0 -0.84 2 2
EPOR 0 0.14 -10000 0 -1.1 3 3
STAT5A (dimer) -0.044 0.18 -10000 0 -0.68 23 23
SOCS1 -0.022 0.16 -10000 0 -0.74 23 23
cell migration 0.04 0.18 0.58 34 -10000 0 34
SOS1 0.015 0 -10000 0 -10000 0 0
EPO -0.41 0.39 -10000 0 -0.77 257 257
VAV1 -0.018 0.16 -10000 0 -0.83 18 18
GRB10 -0.027 0.15 -10000 0 -0.57 21 21
PTPN11 0.015 0.005 -10000 0 -10000 0 0
SCF/KIT -0.038 0.15 -10000 0 -0.49 36 36
GO:0007205 0 0.007 -10000 0 -10000 0 0
MAP2K1 0.016 0.12 -10000 0 -0.42 9 9
CBL 0.015 0 -10000 0 -10000 0 0
KIT -0.043 0.29 -10000 0 -0.94 35 35
MAP2K2 0.014 0.12 -10000 0 -0.47 10 10
SHC/Grb2/SOS1 -0.033 0.12 -10000 0 -0.58 12 12
STAT5A -0.046 0.19 -10000 0 -0.71 23 23
GRB2 0.015 0 -10000 0 -10000 0 0
response to radiation -0.042 0.19 -10000 0 -0.65 32 32
SHC/GRAP2 -0.023 0.12 -10000 0 -0.65 17 17
PTPRO -0.046 0.19 -10000 0 -0.6 40 40
SH2B2 -0.035 0.17 -10000 0 -0.59 28 28
DOK1 0.007 0.08 -10000 0 -0.85 4 4
MATK -0.042 0.18 -10000 0 -0.6 34 34
CREBBP 0.036 0.013 -10000 0 -10000 0 0
BCL2 -0.02 0.27 -10000 0 -1.6 12 12
Syndecan-2-mediated signaling events

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.012 0.15 -9999 0 -0.52 34 34
EPHB2 -0.037 0.2 -9999 0 -0.77 31 31
Syndecan-2/TACI -0.062 0.2 -9999 0 -0.5 77 77
LAMA1 -0.066 0.25 -9999 0 -0.83 45 45
Syndecan-2/alpha2 ITGB1 -0.033 0.12 -9999 0 -0.51 16 16
HRAS 0.009 0.069 -9999 0 -0.85 3 3
Syndecan-2/CASK -0.005 0.054 -9999 0 -0.57 4 4
ITGA5 0 0.11 -9999 0 -0.85 8 8
BAX 0.035 0.12 -9999 0 -1.5 2 2
EPB41 0.004 0.089 -9999 0 -0.72 7 7
positive regulation of cell-cell adhesion -0.006 0.059 -9999 0 -0.61 4 4
LAMA3 -0.023 0.16 -9999 0 -0.73 24 24
EZR 0.011 0.052 -9999 0 -0.77 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.076 -9999 0 -0.81 4 4
Syndecan-2/MMP2 -0.006 0.13 -9999 0 -0.5 31 31
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.012 0.088 -9999 0 -0.64 9 9
dendrite morphogenesis -0.011 0.14 -9999 0 -0.52 34 34
Syndecan-2/GM-CSF -0.01 0.11 -9999 0 -0.48 21 21
determination of left/right symmetry 0.018 0.063 -9999 0 -0.65 4 4
Syndecan-2/PKC delta 0.013 0.093 -9999 0 -0.5 14 14
GNB2L1 0.01 0.065 -9999 0 -0.8 3 3
MAPK3 0.01 0.11 -9999 0 -0.8 4 4
MAPK1 0.012 0.1 -9999 0 -0.61 4 4
Syndecan-2/RACK1 -0.01 0.098 -9999 0 -0.82 5 5
NF1 0.015 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.018 0.063 -9999 0 -0.65 4 4
ITGA2 -0.001 0.12 -9999 0 -0.83 9 9
MAPK8 0.031 0.081 -9999 0 -0.57 8 8
Syndecan-2/alpha2/beta1 Integrin -0.058 0.18 -9999 0 -0.56 45 45
Syndecan-2/Kininogen -0.14 0.24 -9999 0 -0.49 152 152
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC 0.032 0.11 -9999 0 -0.93 5 5
Syndecan-2/CASK/Protein 4.1 -0.011 0.07 -9999 0 -0.46 11 11
extracellular matrix organization 0.013 0.11 -9999 0 -0.66 11 11
actin cytoskeleton reorganization -0.012 0.15 -9999 0 -0.52 34 34
Syndecan-2/Caveolin-2/Ras -0.012 0.096 -9999 0 -0.66 8 8
Syndecan-2/Laminin alpha3 -0.002 0.12 -9999 0 -0.48 28 28
Syndecan-2/RasGAP -0.01 0.093 -9999 0 -0.78 5 5
alpha5/beta1 Integrin -0.011 0.085 -9999 0 -0.66 8 8
PRKCD -0.002 0.11 -9999 0 -0.69 11 11
Syndecan-2 dimer -0.012 0.15 -9999 0 -0.52 34 34
GO:0007205 0.004 0.008 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.11 -9999 0 -1.2 3 3
RHOA 0.015 0 -9999 0 -10000 0 0
SDCBP 0.013 0.033 -9999 0 -0.69 1 1
TNFRSF13B -0.11 0.28 -9999 0 -0.76 74 74
RASA1 0.015 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.012 0.088 -9999 0 -0.64 9 9
Syndecan-2/Synbindin 0.023 0.056 -9999 0 -0.56 4 4
TGFB1 -0.001 0.12 -9999 0 -0.83 9 9
CASP3 0.023 0.094 -9999 0 -0.7 4 4
FN1 -0.038 0.2 -9999 0 -0.76 32 32
Syndecan-2/IL8 -0.078 0.22 -9999 0 -0.49 96 96
SDC2 0.018 0.064 -9999 0 -0.65 4 4
KNG1 -0.23 0.35 -9999 0 -0.74 151 151
Syndecan-2/Neurofibromin 0.023 0.056 -9999 0 -0.56 4 4
TRAPPC4 0.015 0 -9999 0 -10000 0 0
CSF2 -0.02 0.14 -9999 0 -0.69 18 18
Syndecan-2/TGFB1 0.013 0.11 -9999 0 -0.66 11 11
Syndecan-2/Syntenin/PI-4-5-P2 -0.006 0.06 -9999 0 -0.62 4 4
Syndecan-2/Ezrin -0.007 0.056 -9999 0 -0.54 4 4
PRKACA 0.034 0.052 -9999 0 -0.55 3 3
angiogenesis -0.078 0.21 -9999 0 -0.49 96 96
MMP2 -0.029 0.18 -9999 0 -0.75 27 27
IL8 -0.14 0.31 -9999 0 -0.74 94 94
calcineurin-NFAT signaling pathway -0.062 0.2 -9999 0 -0.5 77 77
Signaling events mediated by PTP1B

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
PDGFRB -0.024 0.18 -10000 0 -0.85 21 21
Jak2/Leptin Receptor -0.047 0.13 -10000 0 -0.58 15 15
PTP1B/AKT1 -0.012 0.11 -10000 0 -0.51 12 12
FYN 0.007 0.08 -10000 0 -0.85 4 4
p210 bcr-abl/PTP1B -0.019 0.11 -10000 0 -0.4 19 19
EGFR -0.027 0.17 -10000 0 -0.81 22 22
EGF/EGFR -0.16 0.23 -10000 0 -0.54 98 98
CSF1 0.002 0.1 -10000 0 -0.83 7 7
AKT1 0.011 0.057 -10000 0 -0.86 2 2
INSR -0.004 0.12 -10000 0 -0.85 10 10
PTP1B/N-cadherin -0.038 0.17 -10000 0 -0.58 32 32
Insulin Receptor/Insulin -0.037 0.11 -10000 0 -0.63 13 13
HCK 0 0.11 -10000 0 -0.83 8 8
CRK 0.015 0 -10000 0 -10000 0 0
TYK2 -0.011 0.11 -10000 0 -0.52 12 12
EGF -0.23 0.37 -10000 0 -0.77 143 143
YES1 0.015 0 -10000 0 -10000 0 0
CAV1 -0.043 0.15 -10000 0 -0.53 22 22
TXN 0.009 0.034 -10000 0 -0.7 1 1
PTP1B/IRS1/GRB2 -0.024 0.14 -10000 0 -0.51 20 20
cell migration 0.019 0.11 0.4 19 -10000 0 19
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.098 0.27 -10000 0 -0.75 69 69
ITGA2B -0.099 0.28 -10000 0 -0.78 67 67
CSF1R -0.015 0.16 -10000 0 -0.81 17 17
Prolactin Receptor/Prolactin -0.092 0.22 -10000 0 -0.57 77 77
FGR -0.003 0.12 -10000 0 -0.8 10 10
PTP1B/p130 Cas -0.013 0.12 -10000 0 -0.53 13 13
Crk/p130 Cas -0.007 0.11 -10000 0 -0.53 11 11
DOK1 -0.02 0.16 -10000 0 -0.55 27 27
JAK2 -0.028 0.12 -10000 0 -0.4 19 19
Jak2/Leptin Receptor/Leptin -0.1 0.19 -10000 0 -0.66 31 31
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
PTPN1 -0.019 0.11 -10000 0 -0.41 19 19
LYN 0.011 0.056 -10000 0 -0.85 2 2
CDH2 -0.033 0.2 -10000 0 -0.85 26 26
SRC 0.004 0.11 -10000 0 -1.2 3 3
ITGB3 -0.017 0.15 -10000 0 -0.78 18 18
CAT1/PTP1B -0.051 0.2 -10000 0 -0.69 27 27
CAPN1 0.009 0.07 -10000 0 -0.86 3 3
CSK 0.009 0.069 -10000 0 -0.85 3 3
PI3K -0.032 0.12 -10000 0 -0.62 14 14
mol:H2O2 -0.002 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.096 0.19 -10000 0 -0.67 29 29
negative regulation of transcription -0.027 0.11 -10000 0 -0.39 19 19
FCGR2A 0.002 0.1 -10000 0 -0.83 7 7
FER 0.007 0.057 -10000 0 -0.86 2 2
alphaIIb/beta3 Integrin -0.1 0.24 -10000 0 -0.62 80 80
BLK -0.14 0.31 -10000 0 -0.76 92 92
Insulin Receptor/Insulin/Shc -0.013 0.086 -10000 0 -0.56 11 11
RHOA 0.014 0.004 -10000 0 -10000 0 0
LEPR -0.004 0.12 -10000 0 -0.81 11 11
BCAR1 0.009 0.069 -10000 0 -0.85 3 3
p210 bcr-abl/Grb2 0.015 0 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.059 0.23 -10000 0 -0.79 26 26
PRL -0.008 0.096 -10000 0 -0.7 9 9
SOCS3 -0.053 0.3 -10000 0 -1.1 29 29
SPRY2 0.007 0.057 -10000 0 -0.86 2 2
Insulin Receptor/Insulin/IRS1 -0.037 0.14 -10000 0 -0.52 33 33
CSF1/CSF1R -0.027 0.17 -10000 0 -0.65 23 23
Ras protein signal transduction 0.023 0.031 -10000 0 -10000 0 0
IRS1 -0.023 0.16 -10000 0 -0.73 24 24
INS 0 0.003 -10000 0 -10000 0 0
LEP -0.095 0.26 -10000 0 -0.72 68 68
STAT5B -0.019 0.1 -10000 0 -0.4 16 16
STAT5A -0.02 0.1 -10000 0 -0.4 17 17
GRB2 0.015 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.033 0.16 -10000 0 -0.58 29 29
CSN2 -0.02 0.069 -10000 0 -0.18 68 68
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
LAT -0.028 0.16 -10000 0 -0.66 21 21
YBX1 0.023 0.003 -10000 0 -10000 0 0
LCK -0.041 0.21 -10000 0 -0.81 32 32
SHC1 0.013 0.033 -10000 0 -0.69 1 1
NOX4 -0.028 0.17 -10000 0 -0.81 22 22
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.085 0.26 -9999 0 -0.81 49 49
PDGFRB -0.024 0.18 -9999 0 -0.86 21 21
SPHK1 -0.044 0.15 -9999 0 -0.62 20 20
mol:S1P -0.043 0.14 -9999 0 -0.68 14 14
S1P1/S1P/Gi -0.04 0.23 -9999 0 -0.73 31 31
GNAO1 -0.029 0.18 -9999 0 -0.74 27 27
PDGFB-D/PDGFRB/PLCgamma1 -0.035 0.24 -9999 0 -0.84 25 25
PLCG1 -0.029 0.22 -9999 0 -0.73 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.024 0.18 -9999 0 -0.86 21 21
GNAI2 0.014 0.006 -9999 0 -10000 0 0
GNAI3 0.013 0.006 -9999 0 -10000 0 0
GNAI1 0.008 0.07 -9999 0 -0.86 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.056 0.24 -9999 0 -0.71 49 49
S1P1/S1P -0.092 0.22 -9999 0 -0.63 56 56
negative regulation of cAMP metabolic process -0.037 0.22 -9999 0 -0.69 31 31
MAPK3 -0.045 0.25 -9999 0 -0.69 42 42
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.054 0.23 -9999 0 -0.85 37 37
PLCB2 -0.05 0.23 -9999 0 -0.7 37 37
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.074 0.17 -9999 0 -0.6 35 35
receptor internalization -0.084 0.2 -9999 0 -0.57 56 56
PTGS2 -0.073 0.32 -9999 0 -0.97 38 38
Rac1/GTP -0.074 0.17 -9999 0 -0.6 35 35
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFA -0.034 0.2 -9999 0 -0.85 26 26
negative regulation of T cell proliferation -0.037 0.22 -9999 0 -0.69 31 31
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0 0.11 -9999 0 -0.8 8 8
MAPK1 -0.043 0.25 -9999 0 -0.7 40 40
S1P1/S1P/PDGFB-D/PDGFRB -0.059 0.28 -9999 0 -0.94 31 31
ABCC1 0.015 0.003 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.1 0.28 -9999 0 -0.84 47 47
MAP4K1 -0.054 0.23 -9999 0 -0.79 40 40
MAP3K8 0.008 0.073 -9999 0 -0.77 4 4
PRKCB -0.017 0.16 -9999 0 -0.82 18 18
DBNL 0.009 0.069 -9999 0 -0.85 3 3
CRKL 0.015 0 -9999 0 -10000 0 0
MAP3K1 -0.014 0.22 -9999 0 -0.89 21 21
JUN -0.009 0.23 -9999 0 -1 20 20
MAP3K7 -0.014 0.22 -9999 0 -0.89 21 21
GRAP2 -0.015 0.16 -9999 0 -0.85 16 16
CRK 0.015 0 -9999 0 -10000 0 0
MAP2K4 -0.004 0.21 -9999 0 -0.86 21 21
LAT -0.048 0.21 -9999 0 -0.75 39 39
LCP2 0.002 0.1 -9999 0 -0.85 7 7
MAPK8 -0.013 0.22 -9999 0 -1 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.026 0.23 -9999 0 -0.76 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.097 0.28 -9999 0 -0.83 47 47
Canonical Wnt signaling pathway

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
HDAC1 0.005 0.025 -10000 0 -10000 0 0
AES -0.001 0.07 -10000 0 -0.71 4 4
FBXW11 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.025 0.13 -10000 0 -0.66 18 18
SMAD4 0.015 0 -10000 0 -10000 0 0
DKK2 -0.16 0.33 -10000 0 -0.78 103 103
TLE1 0 0.068 -10000 0 -0.8 3 3
MACF1 0.013 0.04 -10000 0 -0.85 1 1
CTNNB1 -0.013 0.13 -10000 0 -0.48 7 7
WIF1 -0.039 0.18 -10000 0 -0.7 31 31
beta catenin/RanBP3 -0.028 0.13 0.44 11 -0.72 2 13
KREMEN2 -0.087 0.26 -10000 0 -0.76 61 61
DKK1 -0.099 0.28 -10000 0 -0.77 68 68
beta catenin/beta TrCP1 -0.003 0.12 -10000 0 -0.49 1 1
FZD1 -0.016 0.16 -10000 0 -0.85 17 17
AXIN2 0.013 0.14 -10000 0 -1.3 4 4
AXIN1 0.009 0.069 -10000 0 -0.85 3 3
RAN 0.015 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin -0.007 0.083 -10000 0 -1 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.01 0.18 -10000 0 -0.71 18 18
Axin1/APC/GSK3 0.002 0.1 -10000 0 -0.88 3 3
Axin1/APC/GSK3/beta catenin/Macf1 -0.001 0.17 -10000 0 -0.75 6 6
HNF1A -0.06 0.22 -10000 0 -0.84 35 35
CTBP1 0.005 0.022 -10000 0 -10000 0 0
MYC -0.007 0.24 -10000 0 -1.4 12 12
RANBP3 0.011 0.056 -10000 0 -0.85 2 2
DKK2/LRP6/Kremen 2 -0.18 0.27 -10000 0 -0.55 149 149
NKD1 -0.088 0.26 -10000 0 -0.76 62 62
TCF4 -0.017 0.13 -10000 0 -0.82 12 12
TCF3 0.005 0.022 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.062 0.16 -10000 0 -0.52 47 47
Ran/GTP 0.001 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.028 0.16 0.56 11 -0.63 7 18
LEF1 -0.098 0.26 -10000 0 -0.74 65 65
DVL1 0.004 0.062 -10000 0 -0.44 5 5
CSNK2A1 0.015 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.007 0.22 -10000 0 -0.84 20 20
DKK1/LRP6/Kremen 2 -0.14 0.26 -10000 0 -0.56 112 112
LRP6 0.013 0.04 -10000 0 -0.85 1 1
CSNK1A1 0.005 0.025 -10000 0 -10000 0 0
NLK 0.015 0.003 -10000 0 -10000 0 0
CCND1 -0.017 0.29 -10000 0 -1.7 13 13
WNT1 -0.053 0.22 -10000 0 -0.8 39 39
GSK3A 0.011 0.057 -10000 0 -0.85 2 2
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.046 -10000 0 -0.7 2 2
PPP2R5D 0.052 0.12 0.34 61 -0.92 1 62
APC -0.021 0.18 -10000 0 -0.61 8 8
WNT1/LRP6/FZD1 -0.004 0.12 0.26 1 -0.35 9 10
CREBBP 0.005 0.022 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.003 0.15 -9999 0 -0.7 15 15
STMN1 -0.017 0.17 -9999 0 -0.6 35 35
Aurora B/RasGAP/Survivin -0.049 0.23 -9999 0 -0.78 37 37
Chromosomal passenger complex/Cul3 protein complex -0.005 0.15 -9999 0 -0.55 28 28
BIRC5 -0.042 0.2 -9999 0 -0.76 35 35
DES -0.26 0.34 -9999 0 -0.7 137 137
Aurora C/Aurora B/INCENP -0.028 0.17 -9999 0 -0.54 32 32
Aurora B/TACC1 -0.026 0.14 -9999 0 -0.51 36 36
Aurora B/PP2A -0.03 0.16 -9999 0 -0.59 36 36
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.006 0.05 -9999 0 -0.21 14 14
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -10000 0 0
NDC80 -0.029 0.21 -9999 0 -0.69 38 38
Cul3 protein complex -0.011 0.075 -9999 0 -0.52 10 10
KIF2C -0.011 0.13 -9999 0 -0.47 28 28
PEBP1 0.014 0.005 -9999 0 -10000 0 0
KIF20A -0.041 0.2 -9999 0 -0.74 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.16 -9999 0 -0.57 35 35
SEPT1 -0.011 0.14 -9999 0 -0.74 16 16
SMC2 0.013 0.04 -9999 0 -0.85 1 1
SMC4 0.013 0.04 -9999 0 -0.85 1 1
NSUN2/NPM1/Nucleolin -0.013 0.19 -9999 0 -0.95 14 14
PSMA3 0.015 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B -0.007 0.11 -9999 0 -0.38 35 35
AURKB -0.038 0.21 -9999 0 -0.77 35 35
AURKC -0.002 0.12 -9999 0 -0.79 10 10
CDCA8 -0.005 0.12 -9999 0 -0.72 13 13
cytokinesis -0.094 0.24 -9999 0 -0.9 34 34
Aurora B/Septin1 -0.062 0.26 -9999 0 -0.88 35 35
AURKA -0.009 0.13 -9999 0 -0.7 15 15
INCENP 0.009 0.071 -9999 0 -0.87 3 3
KLHL13 -0.002 0.12 -9999 0 -0.79 10 10
BUB1 -0.038 0.19 -9999 0 -0.75 32 32
hSgo1/Aurora B/Survivin -0.066 0.26 -9999 0 -0.78 48 48
EVI5 0.015 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.064 0.21 -9999 0 -0.86 26 26
SGOL1 -0.021 0.16 -9999 0 -0.74 22 22
CENPA -0.025 0.19 -9999 0 -0.61 39 39
NCAPG -0.008 0.13 -9999 0 -0.74 14 14
Aurora B/HC8 Proteasome -0.027 0.16 -9999 0 -0.57 35 35
NCAPD2 0.008 0.069 -9999 0 -0.73 4 4
Aurora B/PP1-gamma -0.027 0.16 -9999 0 -0.57 35 35
RHOA 0.015 0 -9999 0 -10000 0 0
NCAPH -0.011 0.14 -9999 0 -0.73 16 16
NPM1 -0.031 0.16 -9999 0 -0.62 24 24
RASA1 0.015 0 -9999 0 -10000 0 0
KLHL9 0.015 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.16 -9999 0 -0.57 35 35
PPP1CC 0.015 0 -9999 0 -10000 0 0
Centraspindlin -0.073 0.24 -9999 0 -0.95 27 27
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.031 0.16 -9999 0 -0.79 14 14
MYLK -0.016 0.13 -9999 0 -0.41 42 42
KIF23 -0.009 0.13 -9999 0 -0.72 15 15
VIM -0.036 0.2 -9999 0 -0.63 47 47
RACGAP1 0.009 0.057 -9999 0 -0.7 3 3
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.031 0.16 -9999 0 -0.61 26 26
Chromosomal passenger complex -0.03 0.22 -9999 0 -0.68 40 40
Chromosomal passenger complex/EVI5 -0.035 0.26 -9999 0 -0.84 38 38
TACC1 0.011 0.056 -9999 0 -0.85 2 2
PPP2R5D 0.011 0.052 -9999 0 -0.77 2 2
CUL3 0.015 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0.04 -10000 0 -0.85 1 1
VLDLR 0.004 0.092 -10000 0 -0.74 7 7
LRPAP1 0.009 0.069 -10000 0 -0.85 3 3
NUDC 0.015 0 -10000 0 -10000 0 0
RELN/LRP8 -0.16 0.24 -10000 0 -0.5 151 151
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
KATNA1 0.015 0 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.12 0.24 -10000 0 -0.58 57 57
IQGAP1/CaM 0 0 -10000 0 -10000 0 0
DAB1 -0.065 0.22 -10000 0 -0.69 50 50
IQGAP1 0.015 0 -10000 0 -10000 0 0
PLA2G7 -0.084 0.26 -10000 0 -0.77 59 59
CALM1 0.015 0 -10000 0 -10000 0 0
DYNLT1 0.013 0.033 -10000 0 -0.69 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.029 0.12 -10000 0 -0.54 25 25
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.015 0 -10000 0 -10000 0 0
CDK5R1 0.013 0.033 -10000 0 -0.69 1 1
LIS1/Poliovirus Protein 3A 0 0 -10000 0 -10000 0 0
CDK5R2 -0.1 0.26 -10000 0 -0.72 72 72
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.27 -10000 0 -0.68 68 68
YWHAE 0.015 0 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.1 0.22 -10000 0 -0.69 16 16
MAP1B -0.005 0.053 0.3 2 -0.38 8 10
RAC1 0 0 -10000 0 -10000 0 0
p35/CDK5 -0.094 0.23 -10000 0 -0.84 11 11
RELN -0.2 0.35 -10000 0 -0.75 134 134
PAFAH/LIS1 -0.035 0.18 -10000 0 -0.5 59 59
LIS1/CLIP170 0.031 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.14 -10000 0 -0.64 5 5
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.081 0.18 -10000 0 -0.52 27 27
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.12 0.23 -10000 0 -0.65 31 31
LIS1/IQGAP1 0.031 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PAFAH1B1 0.027 0 -10000 0 -10000 0 0
PAFAH1B3 0.002 0.1 -10000 0 -0.75 8 8
PAFAH1B2 -0.002 0.12 -10000 0 -0.85 9 9
MAP1B/LIS1/Dynein heavy chain 0.024 0.043 -10000 0 -0.51 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.18 -10000 0 -0.65 17 17
LRP8 -0.019 0.15 -10000 0 -0.71 22 22
NDEL1/Katanin 60 -0.1 0.22 -10000 0 -0.69 16 16
P39/CDK5 -0.16 0.27 -10000 0 -0.79 31 31
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0 -10000 0 -10000 0 0
CDK5 -0.11 0.24 -10000 0 -0.56 57 57
PPP2R5D 0.011 0.052 -10000 0 -0.77 2 2
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.23 -10000 0 -0.78 24 24
RELN/VLDLR -0.15 0.23 -10000 0 -0.59 60 60
CDC42 0 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.007 0.14 -9999 0 -0.85 12 12
LAT2 -0.042 0.24 -9999 0 -0.85 25 25
AP1 -0.11 0.22 -9999 0 -0.7 43 43
mol:PIP3 -0.051 0.25 -9999 0 -0.75 34 34
IKBKB -0.005 0.14 -9999 0 -0.39 24 24
AKT1 -0.038 0.23 -9999 0 -0.77 22 22
IKBKG -0.007 0.14 -9999 0 -0.39 28 28
MS4A2 -0.066 0.25 -9999 0 -0.84 44 44
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
MAP3K1 -0.004 0.19 -9999 0 -0.63 27 27
mol:Ca2+ -0.027 0.18 -9999 0 -0.51 34 34
LYN 0.011 0.059 -9999 0 -0.89 2 2
CBLB -0.035 0.22 -9999 0 -0.8 22 22
SHC1 0.013 0.033 -9999 0 -0.7 1 1
RasGAP/p62DOK -0.022 0.11 -9999 0 -0.52 20 20
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.069 -9999 0 -0.85 3 3
PLD2 -0.079 0.27 -9999 0 -1 21 21
PTPN13 -0.026 0.2 -9999 0 -0.73 22 22
PTPN11 0.014 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.009 0.16 -9999 0 -0.46 18 18
SYK 0.004 0.098 -9999 0 -0.85 6 6
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.23 -9999 0 -0.79 34 34
LAT -0.07 0.26 -9999 0 -0.78 39 39
PAK2 -0.019 0.22 -9999 0 -0.74 28 28
NFATC2 -0.1 0.25 -9999 0 -0.84 43 43
HRAS -0.035 0.25 -9999 0 -0.84 30 30
GAB2 0.013 0.033 -9999 0 -0.69 1 1
PLA2G1B 0.024 0.042 -9999 0 -10000 0 0
Fc epsilon R1 -0.14 0.28 -9999 0 -0.71 70 70
Antigen/IgE/Fc epsilon R1 -0.13 0.27 -9999 0 -0.66 70 70
mol:GDP -0.043 0.26 -9999 0 -0.88 30 30
JUN 0.002 0.1 -9999 0 -0.83 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
FOS -0.096 0.28 -9999 0 -0.77 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.083 0.22 -9999 0 -0.76 28 28
CHUK -0.005 0.14 -9999 0 -0.39 25 25
KLRG1 -0.039 0.22 -9999 0 -0.82 22 22
VAV1 -0.052 0.26 -9999 0 -0.84 32 32
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.035 0.22 -9999 0 -0.8 22 22
negative regulation of mast cell degranulation -0.028 0.2 -9999 0 -0.75 22 22
BTK -0.089 0.24 -9999 0 -0.9 28 28
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.084 0.3 -9999 0 -0.99 32 32
GAB2/PI3K/SHP2 -0.1 0.22 -9999 0 -0.88 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.051 0.24 -9999 0 -0.96 21 21
RAF1 0.021 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.31 -9999 0 -1.1 32 32
FCER1G -0.001 0.12 -9999 0 -0.83 9 9
FCER1A -0.11 0.29 -9999 0 -0.79 71 71
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.26 -9999 0 -0.73 47 47
MAPK3 0.03 0.048 -9999 0 -0.6 2 2
MAPK1 0.032 0.03 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 0.014 0.087 -9999 0 -0.63 5 5
DUSP1 -0.015 0.16 -9999 0 -0.85 16 16
NF-kappa-B/RelA -0.033 0.062 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.031 0.19 -9999 0 -0.71 22 22
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.084 0.21 -9999 0 -0.78 29 29
FER -0.037 0.22 -9999 0 -0.78 24 24
RELA 0.015 0 -9999 0 -10000 0 0
ITK -0.05 0.16 -9999 0 -0.66 26 26
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG1 -0.038 0.26 -9999 0 -0.87 30 30
cytokine secretion -0.024 0.044 -9999 0 -10000 0 0
SPHK1 -0.065 0.26 -9999 0 -0.78 35 35
PTK2 -0.035 0.21 -9999 0 -0.77 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.23 -9999 0 -0.85 28 28
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.04 0.24 -9999 0 -0.75 31 31
MAP2K2 0.025 0.048 -9999 0 -0.51 3 3
MAP2K1 0.029 0.022 -9999 0 -10000 0 0
MAP2K7 0.011 0.056 -9999 0 -0.85 2 2
KLRG1/SHP2 -0.071 0.19 -9999 0 -0.76 22 22
MAP2K4 0.018 0.074 -9999 0 -1.1 2 2
Fc epsilon R1/FcgammaRIIB -0.16 0.32 -9999 0 -0.82 61 61
mol:Choline -0.077 0.26 -9999 0 -0.96 21 21
SHC/Grb2/SOS1 -0.068 0.18 -9999 0 -0.78 19 19
FYN 0.007 0.08 -9999 0 -0.85 4 4
DOK1 0.007 0.08 -9999 0 -0.85 4 4
PXN -0.022 0.19 -9999 0 -0.71 20 20
HCLS1 -0.041 0.24 -9999 0 -0.9 23 23
PRKCB -0.029 0.19 -9999 0 -0.55 35 35
FCGR2B -0.047 0.22 -9999 0 -0.79 36 36
IGHE -0.001 0.008 -9999 0 -10000 0 0
KLRG1/SHIP -0.03 0.22 -9999 0 -0.8 22 22
LCP2 0.002 0.1 -9999 0 -0.85 7 7
PLA2G4A -0.048 0.24 -9999 0 -0.8 28 28
RASA1 0.015 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.077 0.26 -9999 0 -0.96 21 21
IKK complex 0.015 0.11 -9999 0 -0.3 10 10
WIPF1 0.011 0.056 -9999 0 -0.85 2 2
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.026 0.12 -10000 0 -0.82 5 5
HDAC1 0.003 0.01 -10000 0 -10000 0 0
AES 0.007 0.072 -10000 0 -0.76 4 4
FBXW11 0.015 0 -10000 0 -10000 0 0
DTX1 -0.032 0.19 -10000 0 -0.8 27 27
LRP6/FZD1 -0.025 0.13 -10000 0 -0.66 18 18
TLE1 0.009 0.065 -10000 0 -0.8 3 3
AP1 -0.068 0.2 -10000 0 -0.5 55 55
NCSTN 0.015 0 -10000 0 -10000 0 0
ADAM10 0.009 0.069 -10000 0 -0.85 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.016 0.15 -10000 0 -0.72 13 13
NICD/RBPSUH -0.009 0.083 -10000 0 -0.8 5 5
WIF1 -0.038 0.18 -10000 0 -0.69 31 31
NOTCH1 -0.01 0.088 -10000 0 -0.85 5 5
PSENEN 0.013 0.033 -10000 0 -0.69 1 1
KREMEN2 -0.087 0.26 -10000 0 -0.76 61 61
DKK1 -0.099 0.28 -10000 0 -0.77 68 68
beta catenin/beta TrCP1 0.047 0.076 -10000 0 -0.6 1 1
APH1B 0.011 0.056 -10000 0 -0.85 2 2
APH1A 0.015 0 -10000 0 -10000 0 0
AXIN1 -0.006 0.056 0.28 1 -0.45 4 5
CtBP/CBP/TCF1/TLE1/AES -0.005 0.12 -10000 0 -0.73 5 5
PSEN1 0.013 0.033 -10000 0 -0.69 1 1
FOS -0.096 0.28 -10000 0 -0.77 66 66
JUN 0.002 0.1 -10000 0 -0.83 7 7
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
CTNNB1 0.041 0.081 0.28 1 -0.64 1 2
MAPK3 0.011 0.056 -10000 0 -0.85 2 2
DKK2/LRP6/Kremen 2 -0.18 0.27 -10000 0 -0.55 150 150
HNF1A -0.05 0.23 -10000 0 -0.85 35 35
CTBP1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.005 0.23 -10000 0 -1.4 12 12
NKD1 -0.088 0.26 -10000 0 -0.76 62 62
FZD1 -0.016 0.16 -10000 0 -0.85 17 17
NOTCH1 precursor/Deltex homolog 1 -0.034 0.14 -10000 0 -0.83 6 6
apoptosis -0.068 0.2 -10000 0 -0.5 55 55
Delta 1/NOTCHprecursor -0.026 0.12 -10000 0 -0.8 5 5
DLL1 -0.017 0.16 -10000 0 -0.81 18 18
PPARD 0.022 0.11 -10000 0 -1.6 2 2
Gamma Secretase -0.004 0.039 -10000 0 -0.49 2 2
APC -0.005 0.052 0.28 1 -0.44 3 4
DVL1 -0.016 0.058 -10000 0 -0.52 5 5
CSNK2A1 0.015 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.14 0.26 -10000 0 -0.56 113 113
LRP6 0.013 0.04 -10000 0 -0.85 1 1
CSNK1A1 0.015 0.003 -10000 0 -10000 0 0
NLK 0.017 0.009 -10000 0 -10000 0 0
CCND1 -0.015 0.27 -10000 0 -1.6 13 13
WNT1 -0.054 0.22 -10000 0 -0.8 39 39
Axin1/APC/beta catenin 0.046 0.08 0.34 1 -0.53 4 5
DKK2 -0.16 0.33 -10000 0 -0.78 103 103
NOTCH1 precursor/DVL1 -0.016 0.09 -10000 0 -0.78 5 5
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.011 0.046 -10000 0 -0.69 2 2
NOTCH/Deltex homolog 1 -0.034 0.14 -10000 0 -0.85 6 6
PPP2R5D 0.035 0.13 0.34 62 -0.95 1 63
MAPK1 0.015 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.086 0.18 -10000 0 -0.54 45 45
RBPJ 0.015 0 -10000 0 -10000 0 0
CREBBP 0.018 0.004 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.11 -10000 0 -0.82 8 8
CDKN2C 0.004 0.099 -10000 0 -0.79 7 7
CDKN2A -0.03 0.18 -10000 0 -0.78 26 26
CCND2 0.014 0.07 0.3 19 -0.18 2 21
RB1 -0.018 0.079 -10000 0 -0.32 21 21
CDK4 0.019 0.083 0.34 21 -10000 0 21
CDK6 0.018 0.083 0.34 20 -10000 0 20
G1/S progression -0.001 0.083 0.32 21 -10000 0 21
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.015 0.15 0.76 18 -10000 0 18
PI3K Class IB/PDE3B -0.015 0.15 -10000 0 -0.76 18 18
PDE3B -0.015 0.15 -10000 0 -0.76 18 18
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.003 0.041 -10000 0 -0.52 3 3
PRKCZ 0 0.11 -10000 0 -0.83 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.041 0.17 -10000 0 -1.2 7 7
IRAK/TOLLIP 0.03 0.042 -10000 0 -0.52 1 1
IKBKB 0.015 0 -10000 0 -10000 0 0
IKBKG 0.009 0.069 -10000 0 -0.85 3 3
IL1 alpha/IL1R2 -0.22 0.3 -10000 0 -0.6 171 171
IL1A -0.05 0.21 -10000 0 -0.72 40 40
IL1B -0.047 0.22 -10000 0 -0.65 51 51
IRAK/TRAF6/p62/Atypical PKCs -0.013 0.08 -10000 0 -0.84 2 2
IL1R2 -0.22 0.35 -10000 0 -0.75 145 145
IL1R1 0.008 0.076 -10000 0 -0.81 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.01 0.15 0.25 3 -1.1 6 9
TOLLIP 0.015 0 -10000 0 -10000 0 0
TICAM2 0.009 0.069 -10000 0 -0.85 3 3
MAP3K3 0.015 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.067 0.071 -10000 0 -0.8 2 2
JUN 0.039 0.088 -10000 0 -0.75 2 2
MAP3K7 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.066 0.19 -10000 0 -1.1 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.054 0.17 -10000 0 -0.73 15 15
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.051 0.16 -10000 0 -1 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.068 0.2 -10000 0 -0.66 34 34
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.038 0.069 -10000 0 -0.86 1 1
IRAK1 0.023 0.046 -10000 0 -0.58 1 1
IL1RN/IL1R1 -0.056 0.17 -10000 0 -0.57 46 46
IRAK4 0.015 0 -10000 0 -10000 0 0
PRKCI 0.012 0.046 -10000 0 -0.69 2 2
TRAF6 0.013 0.04 -10000 0 -0.85 1 1
PI3K -0.009 0.07 -10000 0 -0.57 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.001 0.18 -10000 0 -0.97 10 10
CHUK 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.068 0.2 -10000 0 -0.66 34 34
IL1 beta/IL1R2 -0.21 0.3 -10000 0 -0.56 173 173
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.004 0.04 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.058 0.17 -10000 0 -0.92 9 9
IRAK3 0.002 0.1 -10000 0 -0.85 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.063 0.19 -10000 0 -1 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.13 -10000 0 -0.86 6 6
IL1 alpha/IL1R1/IL1RAP -0.053 0.16 -10000 0 -0.62 14 14
RELA 0.015 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.015 0 -10000 0 -10000 0 0
MYD88 0.004 0.097 -10000 0 -0.85 6 6
IRAK/TRAF6/MEKK3 0.016 0.049 -10000 0 -10000 0 0
IL1RAP 0 0.11 -10000 0 -0.76 9 9
UBE2N 0.015 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.054 0.15 -10000 0 -0.83 8 8
CASP1 -0.007 0.14 -10000 0 -0.85 12 12
IL1RN/IL1R2 -0.22 0.3 -10000 0 -0.6 173 173
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.069 0.22 -10000 0 -1.2 10 10
TMEM189-UBE2V1 0.002 0.056 -10000 0 -0.69 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.12 -10000 0 -0.94 5 5
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
IL1RN -0.054 0.22 -10000 0 -0.73 43 43
TRAF6/TAK1/TAB1/TAB2 -0.003 0.036 -10000 0 -0.48 1 1
MAP2K6 0.033 0.052 -10000 0 -0.46 2 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.037 0.14 -9999 0 -0.57 30 30
E-cadherin/beta catenin -0.036 0.14 -9999 0 -0.62 27 27
CTNNB1 0.015 0 -9999 0 -10000 0 0
JUP 0.006 0.089 -9999 0 -0.85 5 5
CDH1 -0.033 0.19 -9999 0 -0.81 27 27
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.036 0.24 -9999 0 -0.82 26 26
MAP3K8 0.007 0.073 -9999 0 -0.77 4 4
FOS -0.024 0.22 -9999 0 -0.78 26 26
PRKCA 0.003 0.089 -9999 0 -0.72 7 7
PTPN7 -0.049 0.22 -9999 0 -0.78 38 38
HRAS 0.009 0.069 -9999 0 -0.85 3 3
PRKCB -0.018 0.16 -9999 0 -0.83 18 18
NRAS 0.015 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.003 0.042 -9999 0 -0.52 3 3
MAPK3 -0.02 0.19 -9999 0 -0.72 26 26
MAP2K1 0.013 0.13 -9999 0 -0.58 16 16
ELK1 0.009 0.057 -9999 0 -0.69 3 3
BRAF -0.028 0.12 -9999 0 -0.58 18 18
mol:GTP -0.001 0.002 -9999 0 -0.006 63 63
MAPK1 -0.018 0.19 -9999 0 -0.73 24 24
RAF1 -0.026 0.11 -9999 0 -0.58 16 16
KRAS 0.015 0.001 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 -0.015 0.16 -10000 0 -0.85 16 16
EPHB2 -0.037 0.2 -10000 0 -0.77 31 31
EFNB1 -0.032 0.2 -10000 0 -0.68 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.22 -10000 0 -0.96 16 16
Ephrin B2/EPHB1-2 -0.085 0.2 -10000 0 -0.62 41 41
neuron projection morphogenesis -0.094 0.21 -10000 0 -0.89 16 16
Ephrin B1/EPHB1-2/Tiam1 -0.1 0.26 -10000 0 -0.94 21 21
DNM1 -0.052 0.22 -10000 0 -0.8 38 38
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.015 0.09 -10000 0 -0.83 5 5
YES1 -0.01 0.11 -10000 0 -1.1 5 5
Ephrin B1/EPHB1-2/NCK2 -0.097 0.24 -10000 0 -0.73 32 32
PI3K 0.008 0.11 -10000 0 -0.72 8 8
mol:GDP -0.11 0.24 -10000 0 -0.85 24 24
ITGA2B -0.098 0.28 -10000 0 -0.77 67 67
endothelial cell proliferation -0.027 0.12 -10000 0 -0.57 22 22
FYN -0.012 0.11 -10000 0 -1.1 5 5
MAP3K7 -0.01 0.093 -10000 0 -0.89 5 5
FGR -0.014 0.11 -10000 0 -1.1 5 5
TIAM1 0 0.11 -10000 0 -0.85 8 8
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
RGS3 0.011 0.056 -10000 0 -0.85 2 2
cell adhesion -0.053 0.21 -10000 0 -0.8 14 14
LYN -0.011 0.12 -10000 0 -1.1 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.012 0.11 -10000 0 -1 5 5
Ephrin B1/EPHB1-2 -0.015 0.1 -10000 0 -0.96 5 5
SRC -0.011 0.11 -10000 0 -1.1 5 5
ITGB3 -0.015 0.15 -10000 0 -0.77 18 18
EPHB1 -0.05 0.21 -10000 0 -0.73 41 41
EPHB4 0.004 0.095 -10000 0 -0.82 6 6
RAC1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.027 0.12 -10000 0 -0.57 22 22
alphaIIb/beta3 Integrin -0.1 0.24 -10000 0 -0.62 80 80
BLK -0.037 0.13 -10000 0 -1.1 5 5
HCK -0.013 0.11 -10000 0 -1.1 5 5
regulation of stress fiber formation 0.1 0.23 0.71 32 -10000 0 32
MAPK8 0.02 0.094 -10000 0 -0.78 5 5
Ephrin B1/EPHB1-2/RGS3 -0.098 0.24 -10000 0 -0.97 17 17
endothelial cell migration -0.029 0.14 -10000 0 -0.58 25 25
NCK2 0.013 0.04 -10000 0 -0.85 1 1
PTPN13 0 0.1 -10000 0 -0.97 5 5
regulation of focal adhesion formation 0.1 0.23 0.71 32 -10000 0 32
chemotaxis 0.1 0.23 0.94 17 -10000 0 17
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
Rac1/GTP -0.098 0.22 -10000 0 -0.96 16 16
angiogenesis -0.015 0.098 -10000 0 -0.94 5 5
LCK -0.021 0.12 -10000 0 -1.1 5 5
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.017 0.11 -9999 0 -0.63 13 13
SNTA1 0.005 0.083 -9999 0 -0.72 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.02 0.1 -9999 0 -0.59 12 12
MAPK12 -0.011 0.15 -9999 0 -0.46 42 42
CCND1 -0.007 0.12 -9999 0 -0.6 13 13
p38 gamma/SNTA1 -0.008 0.16 -9999 0 -0.6 16 16
MAP2K3 0.011 0.056 -9999 0 -0.85 2 2
PKN1 0.009 0.069 -9999 0 -0.85 3 3
G2/M transition checkpoint -0.01 0.15 -9999 0 -0.46 42 42
MAP2K6 0.02 0.07 -9999 0 -0.49 8 8
MAPT -0.05 0.2 -9999 0 -0.47 72 72
MAPK13 0.011 0.11 -9999 0 -0.71 10 10
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.056 -9999 0 -0.44 7 7
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.065 -10000 0 -0.8 3 3
SVIL 0.015 0 -10000 0 -10000 0 0
ZNF318 0.015 0 -10000 0 -10000 0 0
JMJD2C -0.001 0.02 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.095 0.21 -10000 0 -0.62 60 60
CARM1 0.011 0.056 -10000 0 -0.85 2 2
PRDX1 0.015 0 -10000 0 -10000 0 0
PELP1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.015 0 -10000 0 -10000 0 0
AKT1 0.011 0.056 -10000 0 -0.85 2 2
PTK2B 0.013 0.033 -10000 0 -0.69 1 1
MED1 0.015 0 -10000 0 -10000 0 0
MAK -0.011 0.15 -10000 0 -0.85 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0 0.11 -10000 0 -0.85 8 8
GSN 0.009 0.069 -10000 0 -0.85 3 3
NCOA2 -0.026 0.18 -10000 0 -0.85 22 22
NCOA6 0.015 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
NCOA4 0.015 0 -10000 0 -10000 0 0
PIAS3 0.015 0 -10000 0 -10000 0 0
cell proliferation -0.052 0.18 -10000 0 -1 14 14
XRCC5 0.015 0 -10000 0 -10000 0 0
UBE3A 0.015 0 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.26 -10000 0 -0.67 78 78
FHL2 -0.091 0.32 -10000 0 -1.2 35 35
RANBP9 0.015 0 -10000 0 -10000 0 0
JMJD1A -0.027 0.071 -10000 0 -0.26 4 4
CDK6 0.01 0.061 -10000 0 -0.75 3 3
TGFB1I1 -0.009 0.14 -10000 0 -0.84 13 13
T-DHT/AR/CyclinD1 -0.11 0.24 -10000 0 -0.66 68 68
XRCC6 0.015 0 -10000 0 -10000 0 0
T-DHT/AR -0.1 0.24 -10000 0 -0.65 63 63
CTDSP1 0.011 0.056 -10000 0 -0.85 2 2
CTDSP2 0.015 0 -10000 0 -10000 0 0
BRCA1 0.004 0.092 -10000 0 -0.8 6 6
TCF4 -0.007 0.14 -10000 0 -0.85 12 12
CDKN2A -0.03 0.19 -10000 0 -0.8 26 26
SRF 0.014 0.051 -10000 0 -0.85 1 1
NKX3-1 -0.12 0.23 -10000 0 -1.2 15 15
KLK3 0.006 0.042 0.2 5 -0.3 2 7
TMF1 0.013 0.04 -10000 0 -0.85 1 1
HNRNPA1 0.015 0 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 0.024 0.044 -10000 0 -0.66 2 2
T-DHT/AR/Caspase 8 -0.095 0.21 -10000 0 -0.62 60 60
AR -0.11 0.29 -10000 0 -0.87 60 60
UBA3 0.015 0 -10000 0 -10000 0 0
PATZ1 0.015 0 -10000 0 -10000 0 0
PAWR 0.011 0.056 -10000 0 -0.85 2 2
PRKDC 0.015 0 -10000 0 -10000 0 0
PA2G4 0.015 0 -10000 0 -10000 0 0
UBE2I 0.015 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.073 0.2 -10000 0 -0.58 60 60
RPS6KA3 0.011 0.052 -10000 0 -0.77 2 2
T-DHT/AR/ARA70 -0.095 0.21 -10000 0 -0.62 60 60
LATS2 0.015 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.072 0.2 -10000 0 -0.57 60 60
Cyclin D3/CDK11 p58 -0.001 0.031 -10000 0 -0.66 1 1
VAV3 -0.013 0.15 -10000 0 -0.85 15 15
KLK2 -0.073 0.16 -10000 0 -0.75 21 21
CASP8 0.015 0 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.11 0.25 -10000 0 -0.68 68 68
TMPRSS2 -0.29 0.45 -10000 0 -0.93 138 138
CCND1 -0.009 0.14 -10000 0 -0.85 13 13
PIAS1 0.015 0 -10000 0 -10000 0 0
mol:T-DHT -0.019 0.04 -10000 0 -10000 0 0
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.011 0.056 -10000 0 -0.85 2 2
T-DHT/AR/CDK6 -0.098 0.22 -10000 0 -0.63 61 61
CMTM2 -0.03 0.18 -10000 0 -0.76 27 27
SNURF -0.035 0.2 -10000 0 -0.85 27 27
ZMIZ1 0 0.034 -10000 0 -10000 0 0
CCND3 0.013 0.04 -10000 0 -0.85 1 1
TGIF1 0.013 0.033 -10000 0 -0.69 1 1
FKBP4 0.015 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.002 0.24 -10000 0 -1 18 18
UGCG -0.017 0.072 -10000 0 -0.73 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT 0.006 0.17 -10000 0 -0.56 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.012 0.079 -10000 0 -0.72 4 4
mol:DAG -0.002 0.017 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.062 0.17 -10000 0 -0.7 22 22
FRAP1 0.005 0.25 -10000 0 -0.83 27 27
FOXO3 0.015 0.23 -10000 0 -0.86 21 21
AKT1 0.001 0.27 -10000 0 -0.98 23 23
GAB2 0.014 0.033 -10000 0 -0.69 1 1
SMPD1 -0.011 0.03 -10000 0 -10000 0 0
SGMS1 -0.011 0.03 -10000 0 -0.34 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.064 -10000 0 -0.5 7 7
CALM1 0.015 0 -10000 0 -10000 0 0
cell proliferation 0.024 0.094 -10000 0 -0.33 11 11
EIF3A 0.015 0 -10000 0 -10000 0 0
PI3K 0.017 0.074 -10000 0 -0.57 7 7
RPS6KB1 0.007 0.066 -10000 0 -0.26 6 6
mol:sphingomyelin -0.002 0.017 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.021 0.18 -10000 0 -0.82 22 22
PIK3R1 0.008 0.086 -10000 0 -0.74 6 6
JAK1 0.016 0.04 -10000 0 -0.85 1 1
NFKB1 0.015 0 -10000 0 -10000 0 0
MYC 0.015 0.23 -10000 0 -0.9 19 19
MYB -0.058 0.3 -10000 0 -0.84 51 51
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.015 0.28 -10000 0 -0.98 26 26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.068 -10000 0 -0.4 1 1
mol:PI-3-4-5-P3 -0.009 0.26 -10000 0 -0.91 26 26
Rac1/GDP 0.025 0.059 -10000 0 -0.44 7 7
T cell proliferation -0.002 0.24 -10000 0 -0.85 24 24
SHC1 0.014 0.033 -10000 0 -0.69 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0 0.02 -10000 0 -0.056 51 51
PRKCZ -0.006 0.26 -10000 0 -0.93 24 24
NF kappa B1 p50/RelA -0.06 0.17 -10000 0 -0.75 18 18
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.018 0.27 -10000 0 -0.94 30 30
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
RELA 0.015 0 -10000 0 -10000 0 0
IL2RA -0.097 0.28 -10000 0 -0.76 68 68
IL2RB -0.023 0.18 -10000 0 -0.82 23 23
TERT -0.08 0.23 -10000 0 -0.69 59 59
E2F1 -0.01 0.13 -10000 0 -0.35 53 53
SOS1 0.015 0.003 -10000 0 -10000 0 0
RPS6 0.01 0.057 -10000 0 -0.69 3 3
mol:cAMP 0 0.009 0.027 51 -10000 0 51
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.044 0.22 -10000 0 -0.77 37 37
actin cytoskeleton organization -0.002 0.24 -10000 0 -0.85 24 24
GRB2 0.015 0.003 -10000 0 -10000 0 0
IL2 -0.008 0.12 -10000 0 -0.69 14 14
PIK3CA 0.016 0.04 -10000 0 -0.85 1 1
Rac1/GTP 0.03 0.058 -10000 0 -0.42 7 7
LCK -0.038 0.21 -10000 0 -0.81 32 32
BCL2 0.015 0.23 -10000 0 -0.85 21 21
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.36 -9999 0 -1.2 30 30
MKNK1 0.015 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.12 -9999 0 -0.48 2 2
ATF2/c-Jun -0.02 0.18 -9999 0 -1 9 9
MAPK11 -0.049 0.19 -9999 0 -0.85 15 15
MITF -0.031 0.17 -9999 0 -0.64 11 11
MAPKAPK5 -0.031 0.17 -9999 0 -0.64 11 11
KRT8 -0.036 0.18 -9999 0 -0.61 18 18
MAPKAPK3 0.008 0.069 -9999 0 -0.73 4 4
MAPKAPK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.059 0.22 -9999 0 -0.81 17 17
CEBPB -0.041 0.19 -9999 0 -0.62 20 20
SLC9A1 -0.036 0.2 -9999 0 -0.71 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.027 0.18 -9999 0 -0.65 13 13
p38alpha-beta/MNK1 -0.034 0.18 -9999 0 -0.71 15 15
JUN -0.019 0.17 -9999 0 -0.98 9 9
PPARGC1A -0.09 0.26 -9999 0 -0.77 36 36
USF1 -0.032 0.18 -9999 0 -0.62 17 17
RAB5/GDP/GDI1 -0.055 0.13 -9999 0 -0.62 11 11
NOS2 -0.11 0.38 -9999 0 -1.4 30 30
DDIT3 -0.042 0.2 -9999 0 -0.67 21 21
RAB5A 0.015 0 -9999 0 -10000 0 0
HSPB1 -0.026 0.18 -9999 0 -0.69 16 16
p38alpha-beta/HBP1 -0.034 0.18 -9999 0 -0.8 10 10
CREB1 -0.033 0.19 -9999 0 -0.64 22 22
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.022 0.16 -9999 0 -0.73 10 10
RPS6KA4 -0.035 0.19 -9999 0 -0.7 17 17
PLA2G4A -0.037 0.2 -9999 0 -0.8 15 15
GDI1 -0.034 0.19 -9999 0 -0.66 17 17
TP53 -0.047 0.22 -9999 0 -0.76 18 18
RPS6KA5 -0.039 0.2 -9999 0 -0.66 22 22
ESR1 -0.047 0.21 -9999 0 -0.84 13 13
HBP1 0.015 0 -9999 0 -10000 0 0
MEF2C -0.044 0.22 -9999 0 -0.76 20 20
MEF2A -0.031 0.17 -9999 0 -0.64 11 11
EIF4EBP1 -0.041 0.21 -9999 0 -0.69 25 25
KRT19 -0.22 0.31 -9999 0 -0.8 63 63
ELK4 -0.031 0.17 -9999 0 -0.64 11 11
ATF6 -0.031 0.17 -9999 0 -0.57 17 17
ATF1 -0.033 0.19 -9999 0 -0.64 22 22
p38alpha-beta/MAPKAPK2 -0.034 0.18 -9999 0 -0.71 15 15
p38alpha-beta/MAPKAPK3 -0.038 0.2 -9999 0 -0.82 13 13
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.16 0.25 -9999 0 -0.75 40 40
RAD9A 0.008 0.073 -9999 0 -0.77 4 4
AP1 -0.084 0.23 -9999 0 -0.63 68 68
IFNAR2 0.007 0.08 -9999 0 -0.85 4 4
AKT1 0 0.088 -9999 0 -0.46 4 4
ER alpha/Oestrogen -0.02 0.11 -9999 0 -0.62 15 15
NFX1/SIN3/HDAC complex 0.041 0.055 -9999 0 -10000 0 0
EGF -0.23 0.36 -9999 0 -0.77 143 143
SMG5 0.015 0 -9999 0 -10000 0 0
SMG6 0.013 0.04 -9999 0 -0.85 1 1
SP3/HDAC2 0.012 0.013 -9999 0 -10000 0 0
TERT/c-Abl -0.16 0.23 -9999 0 -0.72 40 40
SAP18 0.014 0.003 -9999 0 -10000 0 0
MRN complex -0.002 0.033 -9999 0 -0.57 1 1
WT1 -0.4 0.4 -9999 0 -0.78 242 242
WRN 0.011 0.052 -9999 0 -0.77 2 2
SP1 0.015 0.006 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.015 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.2 -9999 0 -0.86 7 7
Mad/Max 0.007 0.012 -9999 0 -10000 0 0
TERT -0.16 0.26 -9999 0 -0.78 39 39
CCND1 -0.15 0.28 -9999 0 -1.3 15 15
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.014 0.004 -9999 0 -10000 0 0
RBBP4 0.014 0.003 -9999 0 -10000 0 0
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.015 0 -9999 0 -10000 0 0
SIN3A 0.014 0.003 -9999 0 -10000 0 0
Telomerase/911 0.018 0.051 -9999 0 -10000 0 0
CDKN1B -0.14 0.26 -9999 0 -0.57 73 73
RAD1 0.015 0 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
XRCC6 0.015 0 -9999 0 -10000 0 0
SAP30 -0.006 0.13 -9999 0 -0.85 11 11
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.013 0.005 -9999 0 -10000 0 0
JUN 0.001 0.1 -9999 0 -0.83 7 7
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.007 0.007 -9999 0 -10000 0 0
FOS -0.097 0.28 -9999 0 -0.77 66 66
IFN-gamma/IRF1 -0.19 0.28 -9999 0 -0.58 157 157
PARP2 0.015 0 -9999 0 -10000 0 0
BLM 0 0.1 -9999 0 -0.75 9 9
Telomerase 0.005 0.12 -9999 0 -0.53 9 9
IRF1 0.004 0.11 -9999 0 -0.82 8 8
ESR1 -0.012 0.14 -9999 0 -0.8 15 15
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.027 -9999 0 -0.58 1 1
ubiquitin-dependent protein catabolic process 0.046 0.052 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.046 0.053 -9999 0 -10000 0 0
HDAC1 0.014 0.003 -9999 0 -10000 0 0
HDAC2 0.015 0.006 -9999 0 -10000 0 0
ATM -0.001 0.027 -9999 0 -0.58 1 1
SMAD3 0.015 0.091 -9999 0 -0.64 9 9
ABL1 0.011 0.056 -9999 0 -0.85 2 2
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.015 0 -9999 0 -10000 0 0
HUS1 0.015 0 -9999 0 -10000 0 0
RPS6KB1 0.015 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.22 -9999 0 -0.81 13 13
NR2F2 0.016 0.007 -9999 0 -10000 0 0
MAPK3 0.002 0.1 -9999 0 -0.54 16 16
MAPK1 0.004 0.092 -9999 0 -0.52 14 14
TGFB1/TGF beta receptor Type II -0.001 0.12 -9999 0 -0.83 9 9
NFKB1 0.015 0 -9999 0 -10000 0 0
HNRNPC 0.015 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 -0.58 1 1
NBN 0.013 0.033 -9999 0 -0.69 1 1
EGFR -0.024 0.17 -9999 0 -0.8 22 22
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.21 0.3 -9999 0 -0.61 159 159
MYC -0.007 0.13 -9999 0 -0.81 12 12
IL2 -0.012 0.12 -9999 0 -0.7 14 14
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0.04 -9999 0 -0.85 1 1
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
TGFB1 -0.001 0.12 -9999 0 -0.83 9 9
TRF2/BLM -0.01 0.073 -9999 0 -0.53 9 9
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.15 0.22 -9999 0 -0.76 22 22
SP1/HDAC2 0.019 0.014 -9999 0 -10000 0 0
PINX1 0.013 0.04 -9999 0 -0.85 1 1
Telomerase/EST1A -0.13 0.2 -9999 0 -0.85 8 8
Smad3/Myc 0.007 0.13 -9999 0 -0.62 18 18
911 complex -0.004 0.047 -9999 0 -0.5 4 4
IFNG -0.24 0.36 -9999 0 -0.75 154 154
Telomerase/PinX1 -0.13 0.2 -9999 0 -0.85 8 8
Telomerase/AKT1/mTOR/p70S6K -0.007 0.084 -9999 0 -10000 0 0
SIN3B 0.01 0.056 -9999 0 -0.85 2 2
YWHAE 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.13 0.2 -9999 0 -0.86 7 7
response to DNA damage stimulus 0.004 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.002 0.028 -9999 0 -10000 0 0
TRF2/WRN -0.002 0.036 -9999 0 -0.55 2 2
Telomerase/hnRNP C1/C2 -0.13 0.2 -9999 0 -0.86 7 7
E2F1 0.006 0.08 -9999 0 -0.76 5 5
ZNFX1 0.014 0.003 -9999 0 -10000 0 0
PIF1 -0.042 0.2 -9999 0 -0.73 36 36
NCL 0.015 0 -9999 0 -10000 0 0
DKC1 0.013 0.033 -9999 0 -0.69 1 1
telomeric DNA binding 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.02 0.04 -10000 0 -0.58 2 2
RAS family/GTP -0.063 0.16 -10000 0 -0.9 11 11
NFATC4 -0.03 0.17 -10000 0 -0.59 19 19
ERBB2IP 0.015 0.003 -10000 0 -10000 0 0
HSP90 (dimer) 0.012 0.046 -10000 0 -0.69 2 2
mammary gland morphogenesis -0.069 0.17 -10000 0 -0.73 11 11
JUN 0.009 0.12 -10000 0 -0.5 14 14
HRAS 0.009 0.069 -10000 0 -0.85 3 3
DOCK7 -0.034 0.18 -10000 0 -0.69 12 12
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.086 0.22 -10000 0 -0.58 62 62
AKT1 0.01 0.045 -10000 0 -0.67 2 2
BAD 0.016 0.081 -10000 0 -0.8 4 4
MAPK10 -0.035 0.085 -10000 0 -0.44 5 5
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.048 0.2 -10000 0 -0.83 11 11
RAF1 -0.018 0.18 -10000 0 -0.85 10 10
ErbB2/ErbB3/neuregulin 2 -0.079 0.22 -10000 0 -0.67 44 44
STAT3 -0.004 0.074 -10000 0 -1.1 2 2
cell migration 0.019 0.099 -10000 0 -0.35 4 4
mol:PI-3-4-5-P3 -0.001 0.003 -10000 0 -10000 0 0
cell proliferation -0.12 0.31 -10000 0 -0.64 81 81
FOS -0.079 0.24 -10000 0 -0.5 59 59
NRAS 0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.17 -10000 0 -0.73 11 11
MAPK3 -0.091 0.26 -10000 0 -0.69 25 25
MAPK1 -0.09 0.26 -10000 0 -0.68 24 24
JAK2 -0.033 0.17 -10000 0 -0.68 11 11
NF2 -0.003 0.02 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.039 0.2 -10000 0 -0.49 59 59
NRG1 -0.075 0.26 -10000 0 -0.82 50 50
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 -0.02 0.15 -10000 0 -0.48 13 13
MAPK9 -0.031 0.075 -10000 0 -0.31 1 1
ERBB2 -0.004 0.054 -10000 0 -0.68 3 3
ERBB3 -0.042 0.21 -10000 0 -0.85 30 30
SHC1 0.013 0.033 -10000 0 -0.69 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
apoptosis 0.01 0.085 0.79 4 -10000 0 4
STAT3 (dimer) -0.004 0.071 -10000 0 -1.1 2 2
RNF41 0.027 0.038 -10000 0 -0.53 2 2
FRAP1 0.009 0.039 -10000 0 -0.59 2 2
RAC1-CDC42/GTP -0.045 0.11 -10000 0 -0.44 12 12
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.055 -10000 0 -0.53 5 5
CHRNA1 -0.14 0.31 -10000 0 -0.67 89 89
myelination -0.017 0.16 -10000 0 -0.54 19 19
PPP3CB -0.029 0.16 -10000 0 -0.61 11 11
KRAS 0.014 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.048 0.17 -10000 0 -0.96 10 10
NRG2 -0.056 0.22 -10000 0 -0.76 43 43
mol:GDP -0.039 0.2 -10000 0 -0.49 59 59
SOS1 0.014 0.001 -10000 0 -10000 0 0
MAP2K2 -0.018 0.18 -10000 0 -0.76 13 13
SRC 0.011 0.056 -10000 0 -0.85 2 2
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.033 0.17 -10000 0 -0.68 11 11
MAP2K1 -0.081 0.23 -10000 0 -0.62 32 32
heart morphogenesis -0.069 0.17 -10000 0 -0.73 11 11
RAS family/GDP -0.06 0.16 -10000 0 -0.9 11 11
GRB2 0.014 0.001 -10000 0 -10000 0 0
PRKACA -0.004 0.01 -10000 0 -10000 0 0
CHRNE 0.011 0.049 -10000 0 -0.24 14 14
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
activation of caspase activity -0.01 0.045 0.67 2 -10000 0 2
nervous system development -0.069 0.17 -10000 0 -0.73 11 11
CDC42 0.015 0 -10000 0 -10000 0 0
ErbB4 signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.01 0.1 -10000 0 -0.59 3 3
epithelial cell differentiation -0.072 0.14 -10000 0 -0.67 3 3
ITCH 0.027 0.02 -10000 0 -10000 0 0
WWP1 -0.001 0.082 -10000 0 -10000 0 0
FYN 0.007 0.08 -10000 0 -0.85 4 4
EGFR -0.023 0.17 -10000 0 -0.8 22 22
PRL -0.008 0.096 -10000 0 -0.69 9 9
neuron projection morphogenesis -0.003 0.17 -10000 0 -0.7 9 9
PTPRZ1 -0.086 0.25 -10000 0 -0.71 63 63
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.067 0.16 -10000 0 -0.74 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.047 0.18 -10000 0 -0.56 44 44
ADAM17 0.027 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.011 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.15 -10000 0 -0.62 21 21
NCOR1 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.075 0.17 -10000 0 -0.69 16 16
GRIN2B -0.081 0.22 -10000 0 -0.68 21 21
ErbB4/ErbB2/betacellulin -0.077 0.16 -10000 0 -0.61 12 12
STAT1 0.008 0.069 -10000 0 -0.73 4 4
HBEGF 0.005 0.086 -10000 0 -0.75 6 6
PRLR -0.098 0.27 -10000 0 -0.75 69 69
E4ICDs/ETO2 -0.014 0.12 -10000 0 -0.65 7 7
axon guidance 0.017 0.096 -10000 0 -10000 0 0
NEDD4 0.011 0.11 -10000 0 -0.84 8 8
Prolactin receptor/Prolactin receptor/Prolactin -0.094 0.22 -10000 0 -0.57 77 77
CBFA2T3 -0.001 0.11 -10000 0 -0.82 9 9
ErbB4/ErbB2/HBEGF -0.029 0.077 -10000 0 -0.6 3 3
MAPK3 -0.013 0.18 -10000 0 -0.73 9 9
STAT1 (dimer) -0.008 0.096 -10000 0 -0.65 1 1
MAPK1 -0.011 0.17 -10000 0 -0.69 7 7
JAK2 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.16 -10000 0 -0.62 16 16
NRG1 -0.037 0.21 -10000 0 -0.63 50 50
NRG3 -0.024 0.18 -10000 0 -0.82 22 22
NRG2 -0.056 0.22 -10000 0 -0.76 43 43
NRG4 -0.083 0.26 -10000 0 -0.75 59 59
heart development 0.017 0.096 -10000 0 -10000 0 0
neural crest cell migration -0.073 0.16 -10000 0 -0.61 16 16
ERBB2 0.03 0.056 -10000 0 -0.66 3 3
WWOX/E4ICDs -0.006 0.093 -10000 0 -0.71 1 1
SHC1 0.013 0.033 -10000 0 -0.69 1 1
ErbB4/EGFR/neuregulin 4 -0.11 0.19 -10000 0 -0.69 20 20
apoptosis 0.07 0.12 0.59 15 -10000 0 15
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.18 -10000 0 -0.61 33 33
ErbB4/ErbB2/epiregulin -0.12 0.18 -10000 0 -0.61 12 12
ErbB4/ErbB4/betacellulin/betacellulin -0.065 0.19 -10000 0 -0.57 49 49
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.094 0.17 -10000 0 -0.67 9 9
MDM2 0 0.088 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.067 0.16 -10000 0 -0.59 16 16
STAT5A 0.023 0.097 -10000 0 -0.57 2 2
ErbB4/EGFR/neuregulin 1 beta -0.091 0.2 -10000 0 -0.77 19 19
DLG4 0.004 0.095 -10000 0 -0.82 6 6
GRB2/SHC -0.001 0.024 -10000 0 -0.52 1 1
E4ICDs/TAB2/NCoR1 -0.033 0.062 -10000 0 -10000 0 0
STAT5A (dimer) -0.077 0.16 -10000 0 -0.74 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.022 0.087 -10000 0 -10000 0 0
LRIG1 0.013 0.04 -10000 0 -0.85 1 1
EREG -0.16 0.32 -10000 0 -0.75 106 106
BTC -0.079 0.26 -10000 0 -0.8 54 54
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.017 0.096 -10000 0 -10000 0 0
ERBB4 -0.011 0.1 -10000 0 -10000 0 0
STAT5B 0.015 0 -10000 0 -10000 0 0
YAP1 -0.01 0.021 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.078 0.16 -10000 0 -0.62 11 11
glial cell differentiation 0.033 0.062 -10000 0 -10000 0 0
WWOX 0.011 0.052 -10000 0 -0.77 2 2
cell proliferation -0.061 0.24 -10000 0 -0.81 24 24
Osteopontin-mediated events

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
IKK alpha homodimer 0.007 0.18 -9999 0 -0.79 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.049 0.16 -9999 0 -0.79 13 13
alphaV/beta3 Integrin/Osteopontin/Src -0.029 0.13 -9999 0 -0.57 24 24
AP1 -0.1 0.21 -9999 0 -0.85 21 21
ILK 0.014 0.15 -9999 0 -0.69 8 8
bone resorption -0.055 0.17 -9999 0 -0.76 15 15
PTK2B 0.013 0.033 -9999 0 -0.69 1 1
PYK2/p130Cas -0.044 0.15 -9999 0 -0.77 9 9
ITGAV 0.018 0.033 -9999 0 -0.68 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.13 -9999 0 -0.56 25 25
alphaV/beta3 Integrin/Osteopontin -0.043 0.15 -9999 0 -0.61 25 25
MAP3K1 0.013 0.15 -9999 0 -0.56 24 24
JUN 0.003 0.1 -9999 0 -0.83 7 7
MAPK3 0.009 0.2 -9999 0 -0.83 14 14
MAPK1 0.011 0.19 -9999 0 -0.79 13 13
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 0.021 0.15 -9999 0 -0.64 10 10
ITGB3 -0.011 0.15 -9999 0 -0.76 18 18
NFKBIA 0.017 0.21 -9999 0 -0.78 19 19
FOS -0.096 0.28 -9999 0 -0.77 66 66
CD44 -0.015 0.14 -9999 0 -0.71 19 19
CHUK 0.015 0 -9999 0 -10000 0 0
PLAU 0.004 0.25 -9999 0 -1.1 13 13
NF kappa B1 p50/RelA -0.049 0.15 -9999 0 -0.87 7 7
BCAR1 0.009 0.069 -9999 0 -0.85 3 3
RELA 0.015 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.023 0.11 -9999 0 -0.57 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.006 0.17 -9999 0 -0.6 28 28
VAV3 0 0.2 -9999 0 -0.71 19 19
MAP3K14 -0.001 0.2 -9999 0 -0.62 34 34
ROCK2 0.004 0.097 -9999 0 -0.85 6 6
SPP1 -0.019 0.17 -9999 0 -0.76 23 23
RAC1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.051 0.16 -9999 0 -0.75 12 12
MMP2 -0.024 0.25 -9999 0 -0.75 26 26
Cellular roles of Anthrax toxin

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
ANTXR1 -0.001 0.12 -10000 0 -0.83 9 9
ANTXR2 -0.005 0.13 -10000 0 -0.84 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.021 -10000 0 -0.11 17 17
monocyte activation -0.073 0.21 -10000 0 -0.52 68 68
MAP2K2 -0.007 0.073 -10000 0 -0.91 3 3
MAP2K1 -0.003 0.017 -10000 0 -10000 0 0
MAP2K7 -0.006 0.038 -10000 0 -0.52 2 2
MAP2K6 -0.006 0.045 -10000 0 -0.53 3 3
CYAA -0.003 0.12 -10000 0 -0.57 17 17
MAP2K4 -0.003 0.017 -10000 0 -10000 0 0
IL1B -0.035 0.16 -10000 0 -0.48 48 48
Channel -0.022 0.12 -10000 0 -0.61 17 17
NLRP1 -0.015 0.084 -10000 0 -0.52 12 12
CALM1 0.015 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.005 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.021 0.11 17 -10000 0 17
MAPK3 -0.006 0.038 -10000 0 -0.52 2 2
MAPK1 -0.003 0.017 -10000 0 -10000 0 0
PGR -0.042 0.14 -10000 0 -0.48 40 40
PA/Cellular Receptors -0.024 0.13 -10000 0 -0.65 17 17
apoptosis -0.004 0.021 -10000 0 -0.11 17 17
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.003 0.12 -10000 0 -0.57 17 17
macrophage activation 0.018 0.038 -10000 0 -0.49 2 2
TNF -0.08 0.26 -10000 0 -0.78 56 56
VCAM1 -0.074 0.21 -10000 0 -0.53 68 68
platelet activation -0.005 0.024 -10000 0 -10000 0 0
MAPKKK cascade -0.014 0.029 0.2 4 -10000 0 4
IL18 -0.01 0.13 -10000 0 -0.58 21 21
negative regulation of macrophage activation -0.004 0.021 -10000 0 -0.11 17 17
LEF -0.004 0.021 -10000 0 -0.11 17 17
CASP1 -0.014 0.074 -10000 0 -0.36 15 15
mol:cAMP -0.005 0.025 -10000 0 -10000 0 0
necrosis -0.004 0.021 -10000 0 -0.11 17 17
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.021 0.11 -10000 0 -0.58 17 17
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.058 0.18 -9999 0 -0.71 27 27
PDGFB-D/PDGFRB/SLAP -0.049 0.19 -9999 0 -0.7 33 33
PDGFB-D/PDGFRB/APS/CBL -0.035 0.14 -9999 0 -0.61 25 25
AKT1 0.024 0.16 -9999 0 -0.77 9 9
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.022 0.21 -9999 0 -0.75 27 27
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
FGR -0.038 0.19 -9999 0 -0.78 22 22
mol:Ca2+ -0.007 0.18 -9999 0 -0.79 21 21
MYC 0.014 0.17 -9999 0 -0.8 13 13
SHC1 0.013 0.033 -9999 0 -0.69 1 1
HRAS/GDP -0.02 0.11 -9999 0 -0.51 13 13
LRP1/PDGFRB/PDGFB -0.041 0.18 -9999 0 -0.72 27 27
GRB10 0.013 0.04 -9999 0 -0.85 1 1
PTPN11 0.015 0 -9999 0 -10000 0 0
GO:0007205 -0.008 0.18 -9999 0 -0.81 21 21
PTEN 0.013 0.04 -9999 0 -0.85 1 1
GRB2 0.015 0 -9999 0 -10000 0 0
GRB7 -0.003 0.12 -9999 0 -0.84 10 10
PDGFB-D/PDGFRB/SHP2 -0.029 0.14 -9999 0 -0.66 21 21
PDGFB-D/PDGFRB/GRB10 -0.031 0.14 -9999 0 -0.66 22 22
cell cycle arrest -0.049 0.19 -9999 0 -0.7 33 33
HRAS 0.009 0.069 -9999 0 -0.85 3 3
HIF1A 0.034 0.14 -9999 0 -0.63 10 10
GAB1 -0.017 0.2 -9999 0 -0.86 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.011 0.19 -9999 0 -0.77 23 23
PDGFB-D/PDGFRB -0.019 0.12 -9999 0 -0.58 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.029 0.14 -9999 0 -0.66 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.061 0.2 -9999 0 -0.75 27 27
positive regulation of MAPKKK cascade -0.029 0.14 -9999 0 -0.65 21 21
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
mol:IP3 -0.009 0.18 -9999 0 -0.82 21 21
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.009 0.068 -9999 0 -0.84 3 3
PDGFB-D/PDGFRB/GRB7 -0.043 0.17 -9999 0 -0.67 30 30
SHB 0.015 0 -9999 0 -10000 0 0
BLK -0.11 0.25 -9999 0 -0.72 55 55
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.029 0.14 -9999 0 -0.66 21 21
BCAR1 0.009 0.069 -9999 0 -0.85 3 3
VAV2 -0.013 0.22 -9999 0 -0.86 22 22
CBL 0.015 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.032 0.15 -9999 0 -0.69 22 22
LCK -0.066 0.24 -9999 0 -0.8 36 36
PDGFRB -0.024 0.18 -9999 0 -0.86 21 21
ACP1 0.015 0 -9999 0 -10000 0 0
HCK -0.032 0.15 -9999 0 -0.63 25 25
ABL1 -0.015 0.19 -9999 0 -0.76 22 22
PDGFB-D/PDGFRB/CBL -0.02 0.21 -9999 0 -0.92 21 21
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.015 0 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
STAT1 0.008 0.069 -9999 0 -0.73 4 4
cell proliferation 0.017 0.15 -9999 0 -0.69 13 13
SLA -0.013 0.15 -9999 0 -0.8 16 16
actin cytoskeleton reorganization 0.031 0.12 -9999 0 -0.9 2 2
SRC -0.027 0.14 -9999 0 -0.62 21 21
PI3K -0.046 0.15 -9999 0 -0.81 9 9
PDGFB-D/PDGFRB/GRB7/SHC -0.038 0.14 -9999 0 -0.58 30 30
SH2B2 -0.001 0.11 -9999 0 -0.8 9 9
PLCgamma1/SPHK1 -0.024 0.22 -9999 0 -0.8 26 26
LYN -0.026 0.14 -9999 0 -0.63 20 20
LRP1 -0.005 0.13 -9999 0 -0.85 11 11
SOS1 0.015 0 -9999 0 -10000 0 0
STAT5B 0.015 0 -9999 0 -10000 0 0
STAT5A 0.011 0.056 -9999 0 -0.85 2 2
NCK1-2/p130 Cas -0.022 0.11 -9999 0 -0.94 2 2
SPHK1 -0.042 0.2 -9999 0 -0.74 36 36
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.009 0.18 -9999 0 -0.82 21 21
PLCG1 -0.01 0.19 -9999 0 -0.86 21 21
NHERF/PDGFRB -0.054 0.18 -9999 0 -0.64 39 39
YES1 -0.023 0.12 -9999 0 -0.57 19 19
cell migration -0.053 0.18 -9999 0 -0.64 39 39
SHC/Grb2/SOS1 -0.019 0.098 -9999 0 -10000 0 0
SLC9A3R2 -0.007 0.14 -9999 0 -0.85 12 12
SLC9A3R1 -0.007 0.14 -9999 0 -0.84 12 12
NHERF1-2/PDGFRB/PTEN -0.05 0.18 -9999 0 -0.6 39 39
FYN -0.03 0.16 -9999 0 -0.72 20 20
DOK1 0.01 0.13 -9999 0 -0.56 23 23
HRAS/GTP -0.004 0.053 -9999 0 -0.66 3 3
PDGFB 0.009 0.069 -9999 0 -0.85 3 3
RAC1 0.002 0.21 -9999 0 -0.78 24 24
PRKCD 0.005 0.14 -9999 0 -0.6 21 21
FER 0.012 0.12 -9999 0 -0.52 23 23
MAPKKK cascade -0.02 0.095 -9999 0 -10000 0 0
RASA1 0.015 0.12 -9999 0 -0.52 21 21
NCK1 0.015 0 -9999 0 -10000 0 0
NCK2 0.013 0.04 -9999 0 -0.85 1 1
p62DOK/Csk -0.017 0.14 -9999 0 -0.65 14 14
PDGFB-D/PDGFRB/SHB -0.029 0.14 -9999 0 -0.66 21 21
chemotaxis -0.013 0.18 -9999 0 -0.72 22 22
STAT1-3-5/STAT1-3-5 -0.025 0.11 -9999 0 -0.9 2 2
Bovine Papilomavirus E5/PDGFRB -0.029 0.14 -9999 0 -0.67 21 21
PTPRJ 0.01 0.057 -9999 0 -0.69 3 3
Caspase cascade in apoptosis

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
TOP1 0.001 0.15 -10000 0 -0.62 20 20
ACTA1 -0.02 0.17 -10000 0 -0.72 21 21
NUMA1 0 0.15 -10000 0 -0.63 20 20
SPTAN1 -0.007 0.18 -10000 0 -0.74 20 20
LIMK1 -0.014 0.18 -10000 0 -0.73 23 23
BIRC3 -0.03 0.19 -10000 0 -0.82 25 25
BIRC2 0.015 0 -10000 0 -10000 0 0
BAX 0.011 0.056 -10000 0 -0.85 2 2
CASP10 -0.021 0.21 -10000 0 -0.72 34 34
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.015 0 -10000 0 -10000 0 0
PTK2 0.001 0.15 -10000 0 -0.62 20 20
DIABLO 0.015 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.006 0.17 -10000 0 -0.72 20 20
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0.04 -10000 0 -0.85 1 1
GSN -0.01 0.18 -10000 0 -0.72 22 22
MADD 0.013 0.04 -10000 0 -0.85 1 1
TFAP2A -0.14 0.28 -10000 0 -0.69 71 71
BID 0.004 0.098 -10000 0 -0.37 22 22
MAP3K1 0.008 0.054 -10000 0 -0.22 11 11
TRADD 0.011 0.056 -10000 0 -0.85 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.001 0.004 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.19 -10000 0 -0.81 20 20
CASP9 0.015 0 -10000 0 -10000 0 0
DNA repair -0.012 0.041 -10000 0 -0.23 7 7
neuron apoptosis 0.022 0.056 -10000 0 -1.1 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.18 -10000 0 -0.74 20 20
APAF1 0.015 0 -10000 0 -10000 0 0
CASP6 0.012 0.12 -10000 0 -0.58 12 12
TRAF2 0.011 0.056 -10000 0 -0.85 2 2
ICAD/CAD 0.001 0.18 -10000 0 -0.74 19 19
CASP7 0.007 0.086 0.38 22 -10000 0 22
KRT18 0.012 0.047 -10000 0 -0.46 2 2
apoptosis 0.003 0.17 -10000 0 -0.81 14 14
DFFA -0.007 0.17 -10000 0 -0.72 20 20
DFFB -0.008 0.18 -10000 0 -0.76 20 20
PARP1 0.012 0.041 0.23 7 -10000 0 7
actin filament polymerization 0.004 0.17 0.69 21 -10000 0 21
TNF -0.08 0.26 -10000 0 -0.78 56 56
CYCS 0.002 0.097 -10000 0 -0.42 17 17
SATB1 0.015 0.13 -10000 0 -0.75 9 9
SLK -0.008 0.17 -10000 0 -0.72 20 20
p15 BID/BAX 0.009 0.099 -10000 0 -0.45 13 13
CASP2 0.01 0.13 -10000 0 -0.64 7 7
JNK cascade -0.008 0.053 0.22 13 -10000 0 13
CASP3 -0.016 0.18 -10000 0 -0.77 20 20
LMNB2 0.017 0.12 -10000 0 -0.66 7 7
RIPK1 0.015 0 -10000 0 -10000 0 0
CASP4 0.015 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.026 0.11 -10000 0 -0.52 20 20
negative regulation of DNA binding -0.13 0.28 -10000 0 -0.68 71 71
stress fiber formation -0.007 0.17 -10000 0 -0.7 20 20
GZMB -0.035 0.23 -10000 0 -0.78 36 36
CASP1 0.008 0.076 -10000 0 -0.46 12 12
LMNB1 0.016 0.12 -10000 0 -0.68 8 8
APP 0.022 0.057 -10000 0 -1.1 1 1
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.014 0 -10000 0 -10000 0 0
VIM -0.003 0.17 -10000 0 -0.7 21 21
LMNA 0.018 0.12 -10000 0 -0.74 6 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.001 0.14 -10000 0 -0.7 7 7
LRDD -0.002 0.11 -10000 0 -0.76 10 10
SREBF1 -0.012 0.19 -10000 0 -0.76 21 21
APAF-1/Caspase 9 0.001 0.03 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.15 -10000 0 -0.61 20 20
CFL2 -0.005 0.18 -10000 0 -0.72 21 21
GAS2 -0.057 0.23 -10000 0 -0.77 28 28
positive regulation of apoptosis 0.019 0.12 -10000 0 -0.73 6 6
PRF1 -0.023 0.18 -10000 0 -0.84 21 21
FAS signaling pathway (CD95)

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
SPTAN1 0.01 0.072 0.39 9 -0.76 1 10
RFC1 0.012 0.064 0.36 12 -10000 0 12
PRKDC 0.012 0.064 0.36 12 -10000 0 12
RIPK1 0.016 0.005 -10000 0 -10000 0 0
CASP7 -0.019 0.046 0.29 1 -10000 0 1
FASLG/FAS/FADD/FAF1 -0.046 0.12 -10000 0 -0.43 24 24
MAP2K4 -0.045 0.16 -10000 0 -0.5 18 18
mol:ceramide -0.048 0.18 -10000 0 -0.69 16 16
GSN 0.008 0.081 0.36 12 -0.62 3 15
FASLG/FAS/FADD/FAF1/Caspase 8 -0.04 0.15 -10000 0 -0.53 24 24
FAS -0.002 0.1 -10000 0 -0.85 7 7
BID 0.006 0.047 0.33 7 -0.39 1 8
MAP3K1 -0.011 0.097 0.34 1 -10000 0 1
MAP3K7 0.011 0.007 -10000 0 -10000 0 0
RB1 0.009 0.066 0.35 11 -0.55 1 12
CFLAR 0.012 0.057 -10000 0 -0.85 2 2
HGF/MET -0.061 0.18 -10000 0 -0.56 51 51
ARHGDIB 0.005 0.075 0.35 11 -0.48 4 15
FADD 0.011 0.008 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.081 0.62 3 -0.36 12 15
NFKB1 -0.064 0.089 -10000 0 -10000 0 0
MAPK8 -0.077 0.22 -10000 0 -0.59 18 18
DFFA 0.012 0.064 0.36 12 -10000 0 12
DNA fragmentation during apoptosis 0.009 0.077 0.36 12 -0.65 2 14
FAS/FADD/MET -0.017 0.093 -10000 0 -0.53 15 15
CFLAR/RIP1 -0.003 0.043 -10000 0 -0.66 2 2
FAIM3 -0.003 0.12 -10000 0 -0.81 11 11
FAF1 0.011 0.008 -10000 0 -10000 0 0
PARP1 0.012 0.064 0.39 9 -10000 0 9
DFFB 0.009 0.077 0.36 12 -0.66 2 14
CHUK -0.054 0.078 -10000 0 -10000 0 0
FASLG -0.089 0.26 -10000 0 -0.78 60 60
FAS/FADD -0.01 0.08 -10000 0 -0.66 7 7
HGF -0.059 0.23 -10000 0 -0.77 44 44
LMNA 0.007 0.072 0.43 4 -0.61 2 6
CASP6 0.012 0.064 0.39 9 -10000 0 9
CASP10 0.009 0.04 -10000 0 -0.85 1 1
CASP3 0.014 0.081 0.46 12 -10000 0 12
PTPN13 0.006 0.089 -10000 0 -0.85 5 5
CASP8 0.01 0.067 0.44 11 -10000 0 11
IL6 -0.28 0.52 -10000 0 -1.3 74 74
MET 0.002 0.1 -10000 0 -0.75 8 8
ICAD/CAD 0.008 0.071 0.44 4 -0.61 2 6
FASLG/FAS/FADD/FAF1/Caspase 10 -0.049 0.18 -10000 0 -0.71 16 16
activation of caspase activity by cytochrome c 0.006 0.047 0.33 7 -0.39 1 8
PAK2 0.011 0.064 0.36 12 -10000 0 12
BCL2 -0.007 0.14 -10000 0 -0.85 12 12
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.015 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.068 0.17 -9999 0 -0.83 7 7
Syndecan-3/Neurocan -0.02 0.1 -9999 0 -0.76 5 5
POMC -0.011 0.14 -9999 0 -0.8 15 15
EGFR -0.023 0.17 -9999 0 -0.8 22 22
Syndecan-3/EGFR -0.03 0.13 -9999 0 -0.61 18 18
AGRP -0.002 0.086 -9999 0 -0.69 7 7
NCSTN 0.015 0 -9999 0 -10000 0 0
PSENEN 0.013 0.033 -9999 0 -0.69 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.011 0.056 -9999 0 -0.85 2 2
APH1A 0.015 0 -9999 0 -10000 0 0
NCAN -0.01 0.12 -9999 0 -0.69 14 14
long-term memory -0.012 0.096 -9999 0 -0.86 5 5
Syndecan-3/IL8 -0.09 0.19 -9999 0 -0.56 33 33
PSEN1 0.013 0.033 -9999 0 -0.69 1 1
Src/Cortactin -0.003 0.043 -9999 0 -0.66 2 2
FYN 0.007 0.08 -9999 0 -0.85 4 4
limb bud formation -0.01 0.082 -9999 0 -0.78 5 5
MC4R -0.015 0.12 -9999 0 -0.69 13 13
SRC 0.011 0.056 -9999 0 -0.85 2 2
PTN -0.1 0.28 -9999 0 -0.79 68 68
FGFR/FGF/Syndecan-3 -0.01 0.083 -9999 0 -0.8 5 5
neuron projection morphogenesis -0.074 0.17 -9999 0 -0.84 8 8
Syndecan-3/AgRP -0.015 0.09 -9999 0 -0.76 5 5
Syndecan-3/AgRP/MC4R -0.024 0.11 -9999 0 -0.73 6 6
Fyn/Cortactin -0.006 0.06 -9999 0 -0.66 4 4
SDC3 -0.01 0.085 -9999 0 -0.81 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.089 0.18 -9999 0 -0.55 33 33
IL8 -0.14 0.31 -9999 0 -0.74 94 94
Syndecan-3/Fyn/Cortactin -0.013 0.1 -9999 0 -0.9 5 5
Syndecan-3/CASK -0.009 0.08 -9999 0 -0.77 5 5
alpha-MSH/MC4R -0.034 0.14 -9999 0 -0.59 27 27
Gamma Secretase -0.004 0.039 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0.033 -9999 0 -0.69 1 1
ELF1 -0.027 0.13 -9999 0 -10000 0 0
CCNA2 0.001 0.1 -9999 0 -0.71 9 9
PIK3CA 0.014 0.04 -9999 0 -0.85 1 1
JAK3 -0.024 0.18 -9999 0 -0.82 22 22
PIK3R1 0.006 0.086 -9999 0 -0.75 6 6
JAK1 0.014 0.04 -9999 0 -0.85 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.008 0.25 -9999 0 -0.96 23 23
SHC1 0.014 0.033 -9999 0 -0.69 1 1
SP1 0.014 0.063 -9999 0 -10000 0 0
IL2RA -0.086 0.31 -9999 0 -0.82 68 68
IL2RB -0.025 0.18 -9999 0 -0.82 23 23
SOS1 0.016 0 -9999 0 -10000 0 0
IL2RG -0.046 0.21 -9999 0 -0.77 37 37
G1/S transition of mitotic cell cycle 0.015 0.2 -9999 0 -1.2 11 11
PTPN11 0.016 0.001 -9999 0 -10000 0 0
CCND2 0.01 0.16 -9999 0 -1 12 12
LCK -0.04 0.21 -9999 0 -0.81 32 32
GRB2 0.016 0 -9999 0 -10000 0 0
IL2 -0.011 0.12 -9999 0 -0.69 14 14
CDK6 0.01 0.061 -9999 0 -0.75 3 3
CCND3 0.011 0.2 -9999 0 -0.79 19 19
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.051 0.16 -10000 0 -0.58 23 23
ER alpha/Gai/GDP/Gbeta gamma 0.013 0.16 -10000 0 -0.83 11 11
AKT1 0.011 0.16 -10000 0 -0.94 11 11
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.01 0.16 -10000 0 -1 10 10
mol:Ca2+ -0.032 0.23 -10000 0 -0.74 33 33
IGF1R 0.009 0.069 -10000 0 -0.85 3 3
E2/ER alpha (dimer)/Striatin -0.039 0.14 -10000 0 -0.56 33 33
SHC1 0.013 0.033 -10000 0 -0.69 1 1
apoptosis -0.013 0.15 0.88 11 -10000 0 11
RhoA/GTP -0.015 0.077 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.034 0.14 -10000 0 -0.78 13 13
regulation of stress fiber formation -0.042 0.085 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.053 0.16 -10000 0 -0.52 48 48
KRAS 0.015 0 -10000 0 -10000 0 0
G13/GTP -0.016 0.087 -10000 0 -0.49 15 15
pseudopodium formation 0.042 0.085 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.017 0.094 -10000 0 -0.53 15 15
GRB2 0.015 0 -10000 0 -10000 0 0
GNG2 0.004 0.097 -10000 0 -0.85 6 6
GNAO1 -0.029 0.18 -10000 0 -0.74 27 27
HRAS 0.009 0.069 -10000 0 -0.85 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.003 0.17 -10000 0 -0.71 18 18
E2/ER beta (dimer) -0.042 0.15 -10000 0 -0.57 35 35
mol:GDP -0.042 0.13 -10000 0 -0.58 19 19
mol:NADP 0.003 0.17 -10000 0 -0.71 18 18
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
mol:IP3 -0.037 0.24 -10000 0 -0.79 33 33
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.85 3 3
PLCB1 -0.03 0.22 -10000 0 -0.67 40 40
PLCB2 -0.02 0.2 -10000 0 -0.66 33 33
IGF1 -0.033 0.18 -10000 0 -0.74 30 30
mol:L-citrulline 0.003 0.17 -10000 0 -0.71 18 18
RHOA 0.015 0 -10000 0 -10000 0 0
Gai/GDP -0.032 0.14 -10000 0 -0.91 9 9
JNK cascade -0.042 0.15 -10000 0 -0.56 35 35
BCAR1 0.009 0.069 -10000 0 -0.85 3 3
ESR2 -0.041 0.2 -10000 0 -0.74 35 35
GNAQ 0.015 0 -10000 0 -10000 0 0
ESR1 -0.011 0.14 -10000 0 -0.8 15 15
Gq family/GDP/Gbeta gamma 0.009 0.17 -10000 0 -0.78 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.034 0.064 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.032 0.13 -10000 0 -0.75 12 12
GNAZ 0.001 0.1 -10000 0 -0.79 8 8
E2/ER alpha (dimer) -0.02 0.11 -10000 0 -0.62 15 15
STRN -0.018 0.17 -10000 0 -0.85 18 18
GNAL -0.008 0.13 -10000 0 -0.75 14 14
PELP1 0.015 0 -10000 0 -10000 0 0
MAPK11 -0.029 0.16 -10000 0 -0.52 44 44
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.009 0.069 -10000 0 -0.85 3 3
HBEGF -0.03 0.2 -10000 0 -0.87 14 14
cAMP biosynthetic process -0.054 0.16 -10000 0 -0.59 24 24
SRC 0.021 0.15 -10000 0 -0.84 10 10
PI3K -0.009 0.07 -10000 0 -0.57 7 7
GNB1 0.015 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.041 0.13 -10000 0 -0.63 13 13
SOS1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.043 0.13 -10000 0 -0.64 14 14
Gs family/GTP -0.056 0.16 -10000 0 -0.6 24 24
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.042 -10000 0 -0.52 3 3
vasodilation 0.005 0.16 -10000 0 -0.66 18 18
mol:DAG -0.037 0.24 -10000 0 -0.79 33 33
Gs family/GDP/Gbeta gamma -0.046 0.14 -10000 0 -0.69 11 11
MSN 0.043 0.091 -10000 0 -10000 0 0
Gq family/GTP -0.047 0.15 -10000 0 -0.65 22 22
mol:PI-3-4-5-P3 0.011 0.15 -10000 0 -0.95 10 10
NRAS 0.015 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.16 0.66 18 -10000 0 18
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.039 0.12 -10000 0 -0.6 12 12
NOS3 0.001 0.18 -10000 0 -0.77 18 18
GNA11 0.004 0.095 -10000 0 -0.82 6 6
MAPKKK cascade 0.02 0.16 -10000 0 -0.74 13 13
E2/ER alpha (dimer)/PELP1/Src -0.034 0.14 -10000 0 -0.81 12 12
ruffle organization 0.042 0.085 -10000 0 -10000 0 0
ROCK2 0.036 0.096 -10000 0 -10000 0 0
GNA14 -0.016 0.16 -10000 0 -0.84 17 17
GNA15 -0.005 0.13 -10000 0 -0.82 11 11
GNA13 0.015 0 -10000 0 -10000 0 0
MMP9 -0.071 0.24 -10000 0 -0.75 21 21
MMP2 0.008 0.19 -10000 0 -0.85 16 16
Regulation of nuclear SMAD2/3 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
EP300 0.014 0.011 -10000 0 -10000 0 0
HSPA8 0.012 0.057 -10000 0 -0.85 2 2
SMAD3/SMAD4/ER alpha -0.007 0.12 -10000 0 -0.61 12 12
AKT1 0.014 0.058 -10000 0 -0.85 2 2
GSC -0.073 0.39 -10000 0 -1.3 36 36
NKX2-5 -0.039 0.17 -10000 0 -0.69 31 31
muscle cell differentiation 0.043 0.1 0.51 7 -10000 0 7
SMAD2-3/SMAD4/SP1 0.051 0.094 -10000 0 -0.51 2 2
SMAD4 0.016 0.051 -10000 0 -10000 0 0
CBFB 0.015 0 -10000 0 -10000 0 0
SAP18 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.01 0.091 -10000 0 -0.51 14 14
SMAD3/SMAD4/VDR -0.007 0.077 -10000 0 -0.5 1 1
MYC -0.008 0.13 -10000 0 -0.79 12 12
CDKN2B 0.023 0.21 -10000 0 -1.6 8 8
AP1 -0.011 0.21 -10000 0 -0.89 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.066 0.06 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.038 0.086 -10000 0 -0.5 4 4
SP3 0.018 0 -10000 0 -10000 0 0
CREB1 0.015 0 -10000 0 -10000 0 0
FOXH1 -0.063 0.24 -10000 0 -0.78 45 45
SMAD3/SMAD4/GR 0 0.051 -10000 0 -0.51 1 1
GATA3 -0.063 0.23 -10000 0 -0.77 44 44
SKI/SIN3/HDAC complex/NCoR1 0.048 0.054 -10000 0 -0.43 2 2
MEF2C/TIF2 -0.09 0.25 -10000 0 -0.87 29 29
endothelial cell migration 0.14 0.41 1 71 -10000 0 71
MAX 0.019 0.017 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.002 -10000 0 -10000 0 0
RUNX2 -0.008 0.14 -10000 0 -0.81 13 13
RUNX3 -0.017 0.16 -10000 0 -0.82 18 18
RUNX1 -0.005 0.13 -10000 0 -0.82 11 11
CTBP1 0.015 0 -10000 0 -10000 0 0
NR3C1 0.018 0.037 -10000 0 -0.7 1 1
VDR -0.007 0.13 -10000 0 -0.73 14 14
CDKN1A 0.056 0.13 -10000 0 -1.5 2 2
KAT2B 0.014 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.057 0.18 -10000 0 -0.61 31 31
DCP1A 0.015 0 -10000 0 -10000 0 0
SKI 0.009 0.069 -10000 0 -0.85 3 3
SERPINE1 -0.14 0.42 -10000 0 -1 71 71
SMAD3/SMAD4/ATF2 -0.006 0.058 -10000 0 -0.63 2 2
SMAD3/SMAD4/ATF3 -0.056 0.16 -10000 0 -0.54 39 39
SAP30 -0.005 0.13 -10000 0 -0.85 11 11
Cbp/p300/PIAS3 0.006 0.029 -10000 0 -10000 0 0
JUN -0.001 0.21 -10000 0 -0.9 11 11
SMAD3/SMAD4/IRF7 -0.016 0.093 -10000 0 -0.56 10 10
TFE3 0.017 0.017 -10000 0 -10000 0 0
COL1A2 -0.076 0.27 -10000 0 -0.85 45 45
mesenchymal cell differentiation 0.019 0.11 0.64 13 -10000 0 13
DLX1 -0.063 0.24 -10000 0 -0.81 44 44
TCF3 0.015 0 -10000 0 -10000 0 0
FOS -0.089 0.28 -10000 0 -0.77 66 66
SMAD3/SMAD4/Max 0.001 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.003 0.013 -10000 0 -10000 0 0
ZBTB17 0.007 0.07 -10000 0 -0.85 3 3
LAMC1 0.048 0.073 -10000 0 -1 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.003 0.042 -10000 0 -10000 0 0
IRF7 -0.003 0.12 -10000 0 -0.79 11 11
ESR1 -0.009 0.14 -10000 0 -0.78 15 15
HNF4A -0.097 0.29 -10000 0 -0.84 61 61
MEF2C -0.033 0.24 -10000 0 -0.85 24 24
SMAD2-3/SMAD4 -0.008 0.051 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.019 -10000 0 -10000 0 0
IGHV3OR16-13 -0.007 0.027 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.015 0 -10000 0 -10000 0 0
CREBBP 0.014 0.008 -10000 0 -10000 0 0
SKIL 0.013 0.033 -10000 0 -0.69 1 1
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.015 0.004 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.002 0.051 -10000 0 -0.59 1 1
MSG1/HSC70 -0.016 0.11 -10000 0 -0.6 16 16
SMAD2 0.016 0.03 -10000 0 -10000 0 0
SMAD3 0.018 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.043 0.057 -10000 0 -0.42 3 3
SMAD2/SMAD2/SMAD4 0.016 0.028 -10000 0 -10000 0 0
NCOR1 0.015 0.002 -10000 0 -10000 0 0
NCOA2 -0.026 0.18 -10000 0 -0.85 22 22
NCOA1 0.015 0 -10000 0 -10000 0 0
MYOD/E2A -0.024 0.11 -10000 0 -0.52 22 22
SMAD2-3/SMAD4/SP1/MIZ-1 0.057 0.1 -10000 0 -0.57 3 3
IFNB1 0.031 0.1 -10000 0 -0.57 7 7
SMAD3/SMAD4/MEF2C -0.025 0.24 -10000 0 -0.84 22 22
CITED1 -0.01 0.14 -10000 0 -0.78 14 14
SMAD2-3/SMAD4/ARC105 -0.005 0.056 -10000 0 -0.53 2 2
RBL1 0.009 0.069 -10000 0 -0.85 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.048 0.11 -10000 0 -0.64 8 8
RUNX1-3/PEBPB2 -0.033 0.15 -10000 0 -0.69 20 20
SMAD7 0.04 0.16 -10000 0 -0.9 4 4
MYC/MIZ-1 -0.017 0.11 -10000 0 -0.61 15 15
SMAD3/SMAD4 -0.028 0.14 0.31 5 -0.46 8 13
IL10 -0.047 0.3 -10000 0 -0.83 47 47
PIASy/HDAC complex 0.014 0.057 -10000 0 -0.85 2 2
PIAS3 0.013 0.006 -10000 0 -10000 0 0
CDK2 0.014 0.008 -10000 0 -10000 0 0
IL5 -0.012 0.19 -10000 0 -0.71 17 17
CDK4 0.014 0.009 -10000 0 -10000 0 0
PIAS4 0.014 0.057 -10000 0 -0.85 2 2
ATF3 -0.065 0.23 -10000 0 -0.74 50 50
SMAD3/SMAD4/SP1 -0.015 0.065 -10000 0 -0.48 1 1
FOXG1 -0.034 0.17 -10000 0 -0.72 27 27
FOXO3 0.028 0.047 -10000 0 -0.66 2 2
FOXO1 0.024 0.068 -10000 0 -0.56 6 6
FOXO4 0.028 0.047 -10000 0 -0.66 2 2
heart looping -0.032 0.24 -10000 0 -0.83 24 24
CEBPB -0.004 0.12 -10000 0 -0.71 13 13
SMAD3/SMAD4/DLX1 -0.057 0.18 -10000 0 -0.59 42 42
MYOD1 -0.027 0.15 -10000 0 -0.69 22 22
SMAD3/SMAD4/HNF4 -0.081 0.21 -10000 0 -0.61 61 61
SMAD3/SMAD4/GATA3 -0.069 0.19 -10000 0 -0.65 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.033 -10000 0 -0.69 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.028 0.15 -10000 0 -0.74 14 14
SMAD3/SMAD4/SP1-3 -0.002 0.059 -10000 0 -10000 0 0
MED15 0.011 0.056 -10000 0 -0.85 2 2
SP1 0.013 0.046 -10000 0 -10000 0 0
SIN3B 0.011 0.056 -10000 0 -0.85 2 2
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.059 0.22 -10000 0 -0.69 31 31
ITGB5 0.064 0.071 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.049 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.078 0.21 -10000 0 -0.61 59 59
AR -0.095 0.29 -10000 0 -0.84 60 60
negative regulation of cell growth 0.025 0.097 -10000 0 -0.5 2 2
SMAD3/SMAD4/MYOD -0.026 0.1 -10000 0 -0.45 21 21
E2F5 0.012 0.046 -10000 0 -0.69 2 2
E2F4 0.015 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.045 0.14 -10000 0 -0.59 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 0.051 0.084 -10000 0 -0.57 4 4
TFDP1 0.015 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.007 0.21 -10000 0 -0.9 12 12
SMAD3/SMAD4/RUNX2 -0.019 0.11 -10000 0 -0.64 13 13
TGIF2 0.015 0 -10000 0 -10000 0 0
TGIF1 0.013 0.033 -10000 0 -0.69 1 1
ATF2 0.011 0.056 -10000 0 -0.85 2 2
Aurora A signaling

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
Aurora A/GADD45A 0.019 0.062 -9999 0 -0.44 4 4
BIRC5 -0.041 0.2 -9999 0 -0.74 35 35
NFKBIA 0.027 0.054 -9999 0 -0.57 1 1
CPEB1 -0.21 0.35 -9999 0 -0.75 140 140
AKT1 0.026 0.061 -9999 0 -0.58 2 2
NDEL1 0.015 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.011 0.071 -9999 0 -0.55 6 6
NDEL1/TACC3 -0.011 0.074 -9999 0 -0.52 8 8
GADD45A 0.009 0.065 -9999 0 -0.69 4 4
GSK3B 0.014 0.008 -9999 0 -10000 0 0
PAK1/Aurora A 0.023 0.045 -9999 0 -10000 0 0
MDM2 0.015 0 -9999 0 -10000 0 0
JUB -0.002 0.12 -9999 0 -0.85 9 9
TPX2 0.009 0.099 -9999 0 -0.52 16 16
TP53 0.029 0.041 -9999 0 -0.57 1 1
DLG7 0.016 0.046 -9999 0 -10000 0 0
AURKAIP1 0.006 0.083 -9999 0 -0.79 5 5
ARHGEF7 0.015 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.012 0.078 -9999 0 -0.55 8 8
G2/M transition of mitotic cell cycle -0.011 0.07 -9999 0 -0.55 6 6
AURKA 0.02 0.055 -9999 0 -10000 0 0
AURKB -0.025 0.083 -9999 0 -0.32 30 30
CDC25B -0.01 0.061 -9999 0 -0.45 5 5
G2/M transition checkpoint -0.014 0.079 -9999 0 -0.52 9 9
mRNA polyadenylation -0.14 0.21 -9999 0 -0.46 138 138
Aurora A/CPEB -0.14 0.21 -9999 0 -0.46 138 138
Aurora A/TACC1/TRAP/chTOG -0.005 0.045 -9999 0 -0.48 2 2
BRCA1 0.004 0.092 -9999 0 -0.8 6 6
centrosome duplication 0.023 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.012 0.072 -9999 0 -0.52 8 8
spindle assembly -0.006 0.043 -9999 0 -0.48 2 2
TDRD7 0.015 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.039 0.13 -9999 0 -0.53 25 25
CENPA -0.022 0.078 -9999 0 -0.33 24 24
Aurora A/PP2A 0.021 0.057 -9999 0 -0.51 2 2
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.033 0.049 -9999 0 -0.5 1 1
negative regulation of DNA binding 0.029 0.041 -9999 0 -0.56 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.003 0.043 -9999 0 -0.66 2 2
RASA1 0.015 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.015 0.08 -9999 0 -0.52 9 9
mitotic prometaphase 0.006 0.023 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.055 -9999 0 -10000 0 0
TACC1 0.011 0.056 -9999 0 -0.85 2 2
TACC3 0.001 0.1 -9999 0 -0.77 8 8
Aurora A/Antizyme1 -0.009 0.06 -9999 0 -0.52 3 3
Aurora A/RasGAP 0.023 0.045 -9999 0 -10000 0 0
OAZ1 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.008 -9999 0 -10000 0 0
GIT1 0.011 0.056 -9999 0 -0.85 2 2
GIT1/beta-PIX/PAK1 -0.002 0.037 -9999 0 -0.57 2 2
Importin alpha/Importin beta/TPX2 0.009 0.098 -9999 0 -0.52 16 16
PPP2R5D 0.011 0.052 -9999 0 -0.77 2 2
Aurora A/TPX2 0.02 0.11 -9999 0 -0.59 14 14
PAK1 0.015 0 -9999 0 -10000 0 0
CKAP5 0.015 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.094 0.2 -9999 0 -0.55 4 4
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.11 0.16 -9999 0 -0.73 7 7
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.019 0.036 -9999 0 -0.57 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.082 0.11 -9999 0 -0.48 13 13
CaM/Ca2+ -0.11 0.17 -9999 0 -0.5 4 4
RAP1A 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.081 0.2 -9999 0 -0.62 7 7
AKT1 -0.063 0.18 -9999 0 -0.73 2 2
MAP2K1 -0.063 0.19 -9999 0 -10000 0 0
MAP3K11 -0.08 0.2 -9999 0 -0.56 6 6
IFNGR1 0.005 0.017 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.22 -9999 0 -0.71 42 42
Rap1/GTP -0.085 0.12 -9999 0 -0.67 1 1
CRKL/C3G -0.001 0.03 -9999 0 -0.66 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.13 0.19 -9999 0 -0.5 4 4
CEBPB -0.026 0.19 -9999 0 -0.76 4 4
STAT3 0.015 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.15 0.25 -9999 0 -1.1 15 15
STAT1 -0.081 0.2 -9999 0 -0.63 7 7
CALM1 0.015 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.24 0.37 -9999 0 -0.76 154 154
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
STAT1 (dimer)/PIAS1 -0.068 0.19 -9999 0 -0.66 3 3
CEBPB/PTGES2/Cbp/p300 -0.056 0.09 -9999 0 -0.51 5 5
mol:Ca2+ -0.12 0.18 -9999 0 -0.54 4 4
MAPK3 -0.041 0.18 -9999 0 -0.98 2 2
STAT1 (dimer) -0.11 0.16 -9999 0 -0.77 13 13
MAPK1 -0.037 0.17 -9999 0 -10000 0 0
JAK2 0.005 0.017 -9999 0 -10000 0 0
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
JAK1 0.003 0.043 -9999 0 -0.85 1 1
CAMK2D 0.015 0 -9999 0 -10000 0 0
DAPK1 0 0.14 -9999 0 -0.68 6 6
SMAD7 -0.003 0.084 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.1 0.15 -9999 0 -10000 0 0
PI3K -0.12 0.16 -9999 0 -10000 0 0
IFNG -0.24 0.37 -9999 0 -0.76 154 154
apoptosis -0.012 0.12 -9999 0 -0.5 6 6
CAMK2G 0.015 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.09 0.27 -9999 0 -0.76 63 63
CAMK2B -0.18 0.34 -9999 0 -0.75 122 122
FRAP1 -0.057 0.18 -9999 0 -0.66 2 2
PRKCD -0.068 0.2 -9999 0 -0.73 6 6
RAP1B 0.013 0.033 -9999 0 -0.69 1 1
negative regulation of cell growth -0.082 0.11 -9999 0 -0.48 13 13
PTPN2 0.015 0 -9999 0 -10000 0 0
EP300 0.015 0.001 -9999 0 -10000 0 0
IRF1 -0.036 0.2 -9999 0 -0.72 14 14
STAT1 (dimer)/PIASy -0.11 0.17 -9999 0 -0.59 9 9
SOCS1 -0.03 0.21 -9999 0 -0.92 19 19
mol:GDP -0.099 0.14 -9999 0 -10000 0 0
CASP1 -0.008 0.1 -9999 0 -0.41 12 12
PTGES2 0.007 0.08 -9999 0 -0.76 5 5
IRF9 0.027 0.068 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.11 0.16 -9999 0 -10000 0 0
RAP1/GDP -0.086 0.13 -9999 0 -0.7 1 1
CBL -0.079 0.19 -9999 0 -0.51 4 4
MAP3K1 -0.077 0.2 -9999 0 -0.51 4 4
PIAS1 0.015 0 -9999 0 -10000 0 0
PIAS4 0.011 0.056 -9999 0 -0.85 2 2
antigen processing and presentation of peptide antigen via MHC class II -0.082 0.11 -9999 0 -0.48 13 13
PTPN11 -0.092 0.2 -9999 0 -0.54 4 4
CREBBP 0.015 0.001 -9999 0 -10000 0 0
RAPGEF1 0.013 0.04 -9999 0 -0.85 1 1
Ceramide signaling 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
SPHK2 0.014 0.094 -10000 0 -0.66 9 9
MAP4K4 0.006 0.14 -10000 0 -0.8 8 8
BAG4 0.015 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.038 0.08 -10000 0 -0.49 8 8
NFKBIA 0.013 0.04 -10000 0 -0.85 1 1
BIRC3 -0.03 0.19 -10000 0 -0.82 25 25
BAX -0.012 0.035 -10000 0 -0.36 2 2
RIPK1 0.015 0 -10000 0 -10000 0 0
AKT1 0.026 0.054 -10000 0 -0.78 2 2
BAD -0.033 0.061 -10000 0 -0.36 4 4
SMPD1 0.001 0.088 -10000 0 -0.34 6 6
RB1 -0.031 0.065 0.23 1 -0.56 2 3
FADD/Caspase 8 0.021 0.13 -10000 0 -0.8 6 6
MAP2K4 -0.019 0.052 -10000 0 -10000 0 0
NSMAF 0.015 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.035 0.099 -10000 0 -0.51 14 14
EGF -0.22 0.36 -10000 0 -0.77 143 143
mol:ceramide -0.041 0.059 0.23 3 -10000 0 3
MADD 0.013 0.04 -10000 0 -0.85 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.093 -10000 0 -0.61 10 10
ASAH1 0.008 0.069 -10000 0 -0.73 4 4
negative regulation of cell cycle -0.031 0.064 0.23 1 -0.55 2 3
cell proliferation -0.055 0.15 -10000 0 -0.64 21 21
BID -0.003 0.12 -10000 0 -0.83 5 5
MAP3K1 -0.029 0.055 0.22 3 -10000 0 3
EIF2A -0.01 0.056 -10000 0 -0.54 1 1
TRADD 0.011 0.056 -10000 0 -0.85 2 2
CRADD 0.013 0.04 -10000 0 -0.85 1 1
MAPK3 -0.022 0.1 -10000 0 -0.52 13 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.02 0.094 -10000 0 -0.5 12 12
Cathepsin D/ceramide -0.036 0.07 -10000 0 -0.41 7 7
FADD 0.008 0.14 -10000 0 -0.81 7 7
KSR1 -0.045 0.1 -10000 0 -0.53 15 15
MAPK8 -0.019 0.063 -10000 0 -0.3 7 7
PRKRA -0.029 0.055 0.23 1 -10000 0 1
PDGFA 0.004 0.097 -10000 0 -0.85 6 6
TRAF2 0.011 0.056 -10000 0 -0.85 2 2
IGF1 -0.033 0.18 -10000 0 -0.74 30 30
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.041 0.058 0.23 3 -10000 0 3
CTSD 0.004 0.092 -10000 0 -0.74 7 7
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.036 0.17 -10000 0 -0.75 19 19
PRKCD -0.002 0.11 -10000 0 -0.69 11 11
PRKCZ 0 0.11 -10000 0 -0.83 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.093 -10000 0 -0.61 10 10
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.011 0.056 -10000 0 -0.85 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.002 0.15 -10000 0 -0.87 7 7
TNFR1A/BAG4/TNF-alpha -0.06 0.17 -10000 0 -0.51 56 56
mol:Sphingosine-1-phosphate 0.014 0.093 -10000 0 -0.65 9 9
MAP2K1 -0.024 0.094 -10000 0 -0.51 11 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
CYCS -0.02 0.06 0.21 6 -0.27 11 17
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
NFKB1 0.015 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.02 0.058 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/FAN -0.06 0.17 -10000 0 -0.51 56 56
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.073 -10000 0 -0.45 1 1
MAP2K2 -0.027 0.1 -10000 0 -0.53 12 12
SMPD3 -0.002 0.12 -10000 0 -0.55 9 9
TNF -0.08 0.26 -10000 0 -0.78 56 56
PKC zeta/PAR4 -0.013 0.099 -10000 0 -0.7 9 9
mol:PHOSPHOCHOLINE 0.065 0.13 0.25 136 -10000 0 136
NF kappa B1/RelA/I kappa B alpha -0.011 0.078 -10000 0 -0.96 1 1
AIFM1 -0.015 0.051 0.33 1 -0.37 2 3
BCL2 -0.007 0.14 -10000 0 -0.85 12 12
S1P3 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
PDGFRB -0.024 0.18 -9999 0 -0.85 21 21
mol:S1P 0.002 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.018 0.092 -9999 0 -0.49 8 8
GNAO1 -0.027 0.18 -9999 0 -0.74 27 27
S1P/S1P3/G12/G13 -0.026 0.11 -9999 0 -0.51 24 24
AKT1 -0.046 0.18 -9999 0 -0.8 23 23
AKT3 -0.013 0.25 -9999 0 -1.1 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.024 0.18 -9999 0 -0.85 21 21
GNAI2 0.017 0.003 -9999 0 -10000 0 0
GNAI3 0.017 0.002 -9999 0 -10000 0 0
GNAI1 0.011 0.069 -9999 0 -0.85 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.025 0.18 -9999 0 -0.84 23 23
S1PR2 0.004 0.092 -9999 0 -0.8 6 6
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.15 -9999 0 -0.79 10 10
MAPK3 0.015 0.15 -9999 0 -0.71 12 12
MAPK1 0.017 0.15 -9999 0 -0.76 10 10
JAK2 0.013 0.17 -9999 0 -0.73 15 15
CXCR4 0 0.19 -9999 0 -0.73 22 22
FLT1 -0.052 0.24 -9999 0 -0.85 38 38
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.015 0.15 -9999 0 -0.74 12 12
S1P/S1P3/Gi 0.008 0.16 -9999 0 -0.81 10 10
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.036 0.13 -9999 0 -0.73 10 10
VEGFA -0.03 0.2 -9999 0 -0.85 26 26
S1P/S1P2/Gi 0.02 0.11 -9999 0 -0.66 6 6
VEGFR1 homodimer/VEGFA homodimer -0.055 0.28 -9999 0 -0.9 44 44
RHOA 0.015 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.009 0.17 -9999 0 -0.51 38 38
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.003 0.1 -9999 0 -0.79 8 8
G12/G13 -0.001 0.024 -9999 0 -0.52 1 1
GNA14 -0.016 0.16 -9999 0 -0.84 17 17
GNA15 -0.005 0.13 -9999 0 -0.82 11 11
GNA12 0.013 0.033 -9999 0 -0.69 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.004 0.095 -9999 0 -0.82 6 6
Rac1/GTP -0.036 0.13 -9999 0 -0.73 10 10
Regulation of Androgen receptor activity

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
HDAC1 0.027 0 -9999 0 -10000 0 0
SMARCC1 0.01 0.013 -9999 0 -10000 0 0
REL -0.012 0.15 -9999 0 -0.84 15 15
HDAC7 0.005 0.14 -9999 0 -0.69 4 4
JUN 0.002 0.1 -9999 0 -0.83 7 7
EP300 0.015 0 -9999 0 -10000 0 0
KAT2B 0.015 0 -9999 0 -10000 0 0
KAT5 0.013 0.04 -9999 0 -0.85 1 1
MAPK14 0.019 0.054 -9999 0 -0.63 3 3
FOXO1 0.009 0.065 -9999 0 -0.69 4 4
T-DHT/AR 0.002 0.14 -9999 0 -0.75 2 2
MAP2K6 0.007 0.066 -9999 0 -0.81 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0.008 -9999 0 -10000 0 0
SMARCA2 0.015 0 -9999 0 -10000 0 0
PDE9A -0.076 0.22 -9999 0 -1.3 10 10
NCOA2 -0.026 0.18 -9999 0 -0.85 22 22
CEBPA -0.017 0.16 -9999 0 -0.78 19 19
EHMT2 0.011 0.056 -9999 0 -0.85 2 2
cell proliferation 0.012 0.17 -9999 0 -0.65 6 6
NR0B1 -0.048 0.18 -9999 0 -0.69 35 35
EGR1 -0.099 0.28 -9999 0 -0.76 69 69
RXRs/9cRA -0.018 0.086 -9999 0 -0.43 19 19
AR/RACK1/Src -0.017 0.1 -9999 0 -0.71 5 5
AR/GR -0.009 0.13 -9999 0 -0.7 5 5
GNB2L1 0.009 0.065 -9999 0 -0.8 3 3
PKN1 0.009 0.069 -9999 0 -0.85 3 3
RCHY1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.018 0.057 -9999 0 -0.67 3 3
T-DHT/AR/TIF2/CARM1 -0.037 0.15 -9999 0 -0.73 9 9
SRC 0.029 0.078 -9999 0 -0.56 3 3
NR3C1 0.013 0.033 -9999 0 -0.69 1 1
KLK3 -0.09 0.15 -9999 0 -0.47 37 37
APPBP2 0.012 0.008 -9999 0 -10000 0 0
TRIM24 0.015 0 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.012 0.099 -9999 0 -0.64 5 5
TMPRSS2 -0.28 0.47 -9999 0 -1.2 81 81
RXRG -0.016 0.14 -9999 0 -0.73 18 18
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.015 0 -9999 0 -10000 0 0
RXRB 0.013 0.04 -9999 0 -0.85 1 1
CARM1 0.011 0.056 -9999 0 -0.85 2 2
NR2C2 0.011 0.056 -9999 0 -0.85 2 2
KLK2 -0.004 0.17 -9999 0 -0.7 14 14
AR -0.016 0.15 -9999 0 -0.48 21 21
SENP1 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
MDM2 0.015 0 -9999 0 -10000 0 0
SRY 0 0 -9999 0 -10000 0 0
GATA2 -0.026 0.18 -9999 0 -0.79 24 24
MYST2 0.015 0 -9999 0 -10000 0 0
HOXB13 -0.22 0.35 -9999 0 -0.75 139 139
T-DHT/AR/RACK1/Src 0.016 0.11 -9999 0 -0.72 5 5
positive regulation of transcription -0.026 0.18 -9999 0 -0.79 24 24
DNAJA1 0.012 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0 -9999 0 -10000 0 0
NCOA1 0.02 0.004 -9999 0 -10000 0 0
SPDEF -0.17 0.33 -9999 0 -0.74 115 115
T-DHT/AR/TIF2 0.024 0.11 -9999 0 -0.54 4 4
T-DHT/AR/Hsp90 0.012 0.099 -9999 0 -0.65 4 4
GSK3B 0.014 0.005 -9999 0 -10000 0 0
NR2C1 0.015 0 -9999 0 -10000 0 0
mol:T-DHT 0.024 0.073 -9999 0 -0.54 5 5
SIRT1 0.015 0 -9999 0 -10000 0 0
ZMIZ2 0.008 0.076 -9999 0 -0.81 4 4
POU2F1 0.015 0.081 -9999 0 -0.83 4 4
T-DHT/AR/DAX-1 -0.046 0.14 -9999 0 -0.69 6 6
CREBBP 0.015 0 -9999 0 -10000 0 0
SMARCE1 0.015 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.009 0.069 -9999 0 -0.85 3 3
SPHK1 -0.043 0.2 -9999 0 -0.73 36 36
GNAI2 0.015 0 -9999 0 -10000 0 0
mol:S1P 0 0.11 -9999 0 -0.56 9 9
GNAO1 -0.029 0.18 -9999 0 -0.74 27 27
mol:Sphinganine-1-P -0.021 0.17 -9999 0 -0.6 36 36
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.023 0.11 -9999 0 -0.72 8 8
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.024 -9999 0 -0.52 1 1
S1PR3 -0.027 0.18 -9999 0 -0.84 23 23
S1PR2 0.004 0.092 -9999 0 -0.8 6 6
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.022 0.09 -9999 0 -0.5 9 9
S1PR5 -0.03 0.19 -9999 0 -0.82 25 25
S1PR4 -0.01 0.14 -9999 0 -0.83 14 14
GNAI1 0.009 0.069 -9999 0 -0.85 3 3
S1P/S1P5/G12 -0.045 0.16 -9999 0 -0.66 22 22
S1P/S1P3/Gq -0.01 0.18 -9999 0 -0.79 18 18
S1P/S1P4/Gi 0.007 0.14 -9999 0 -0.61 12 12
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.001 0.1 -9999 0 -0.79 8 8
GNA14 -0.016 0.16 -9999 0 -0.84 17 17
GNA15 -0.005 0.13 -9999 0 -0.82 11 11
GNA12 0.013 0.033 -9999 0 -0.69 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.004 0.095 -9999 0 -0.82 6 6
ABCC1 0.015 0 -9999 0 -10000 0 0
PLK2 and PLK4 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
PLK2 -0.004 0.12 -9999 0 -0.85 10 10
PLK4 0.007 0.073 -9999 0 -0.69 5 5
regulation of centriole replication 0.007 0.11 -9999 0 -0.61 15 15
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.015 0 -9999 0 -10000 0 0
ITGB7 0.002 0.1 -9999 0 -0.85 7 7
ITGA4 -0.011 0.14 -9999 0 -0.84 14 14
alpha4/beta7 Integrin -0.029 0.14 -9999 0 -0.7 19 19
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.64 14 14
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.01 0.065 -9999 0 -0.8 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.015 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.028 0.12 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.015 0 -9999 0 -10000 0 0
FYN 0.007 0.08 -9999 0 -0.85 4 4
MAP3K12 0.002 0.1 -9999 0 -0.85 7 7
FGR -0.003 0.12 -9999 0 -0.8 10 10
p38 alpha/TAB1 -0.039 0.12 -9999 0 -0.65 12 12
PRKG1 -0.057 0.24 -9999 0 -0.85 39 39
DUSP8 -0.011 0.14 -9999 0 -0.75 16 16
PGK/cGMP/p38 alpha -0.069 0.17 -9999 0 -0.52 46 46
apoptosis -0.037 0.11 -9999 0 -0.61 12 12
RAL/GTP -0.001 0.027 -9999 0 -0.58 1 1
LYN 0.011 0.056 -9999 0 -0.85 2 2
DUSP1 -0.015 0.16 -9999 0 -0.85 16 16
PAK1 0.015 0 -9999 0 -10000 0 0
SRC 0.011 0.056 -9999 0 -0.85 2 2
RAC1/OSM/MEKK3/MKK3 -0.005 0.07 -9999 0 -0.85 3 3
TRAF6 0.013 0.04 -9999 0 -0.85 1 1
RAC1 0.015 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 0.009 0.069 -9999 0 -0.85 3 3
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.013 0.19 -9999 0 -0.91 13 13
BLK -0.14 0.31 -9999 0 -0.76 92 92
HCK 0 0.11 -9999 0 -0.83 8 8
MAP2K3 0.011 0.056 -9999 0 -0.85 2 2
DUSP16 0.015 0 -9999 0 -10000 0 0
DUSP10 0.004 0.092 -9999 0 -0.8 6 6
TRAF6/MEKK3 -0.001 0.025 -9999 0 -0.53 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.006 0.15 -9999 0 -0.72 12 12
positive regulation of innate immune response -0.005 0.19 -9999 0 -0.9 13 13
LCK -0.041 0.21 -9999 0 -0.81 32 32
p38alpha-beta/MKP7 0.004 0.18 -9999 0 -0.85 12 12
p38alpha-beta/MKP5 0.001 0.19 -9999 0 -0.88 13 13
PGK/cGMP -0.055 0.18 -9999 0 -0.66 39 39
PAK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.01 0.2 -9999 0 -0.73 23 23
CDC42 0.015 0 -9999 0 -10000 0 0
RALB 0.013 0.04 -9999 0 -0.85 1 1
RALA 0.015 0 -9999 0 -10000 0 0
PAK3 -0.16 0.34 -9999 0 -0.8 101 101
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.36 -10000 0 -0.77 142 142
HRAS 0.009 0.069 -10000 0 -0.85 3 3
EGFR -0.023 0.17 -10000 0 -0.8 22 22
AKT 0.025 0.08 -10000 0 -0.67 4 4
FOXO3 0.015 0 -10000 0 -10000 0 0
AKT1 0.011 0.056 -10000 0 -0.85 2 2
FOXO1 0.009 0.065 -10000 0 -0.69 4 4
AKT3 0.004 0.097 -10000 0 -0.85 6 6
FOXO4 0.015 0 -10000 0 -10000 0 0
MET 0.002 0.1 -10000 0 -0.75 8 8
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
PIK3CB 0.011 0.056 -10000 0 -0.85 2 2
NRAS 0.015 0 -10000 0 -10000 0 0
PIK3CG -0.023 0.18 -10000 0 -0.84 21 21
PIK3R3 0.006 0.089 -10000 0 -0.85 5 5
PIK3R2 0.011 0.056 -10000 0 -0.85 2 2
NF1 0.015 0 -10000 0 -10000 0 0
RAS -0.035 0.1 -10000 0 -0.4 12 12
ERBB2 0.009 0.069 -10000 0 -0.85 3 3
proliferation/survival/translation -0.029 0.048 0.31 3 -10000 0 3
PI3K -0.026 0.1 -10000 0 -0.35 17 17
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
KRAS 0.015 0 -10000 0 -10000 0 0
FOXO 0.036 0.043 -10000 0 -0.44 1 1
AKT2 0.011 0.056 -10000 0 -0.85 2 2
PTEN 0.013 0.04 -10000 0 -0.85 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.028 -10000 0 -0.43 2 2
TRAF2/ASK1 -0.004 0.046 -10000 0 -0.58 3 3
ATM 0.013 0.04 -10000 0 -0.85 1 1
MAP2K3 0.014 0.082 -10000 0 -0.76 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.084 -10000 0 -0.63 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.042 0.2 -10000 0 -0.73 36 36
TXN 0.009 0.015 -10000 0 -0.32 1 1
CALM1 0.015 0 -10000 0 -10000 0 0
GADD45A 0.009 0.065 -10000 0 -0.69 4 4
GADD45B -0.006 0.12 -10000 0 -0.73 13 13
MAP3K1 0.015 0 -10000 0 -10000 0 0
MAP3K6 0.007 0.08 -10000 0 -0.85 4 4
MAP3K7 0.015 0 -10000 0 -10000 0 0
MAP3K4 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.007 0.067 -10000 0 -0.66 5 5
TAK1/TAB family 0.005 0.035 0.22 11 -0.22 1 12
RAC1/OSM/MEKK3 -0.003 0.042 -10000 0 -0.52 3 3
TRAF2 0.011 0.056 -10000 0 -0.85 2 2
RAC1/OSM/MEKK3/MKK3 -0.013 0.059 -10000 0 -0.59 4 4
TRAF6 0.009 0.022 -10000 0 -0.47 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.18 0.34 -10000 0 -0.75 122 122
CCM2 0.009 0.069 -10000 0 -0.85 3 3
CaM/Ca2+/CAMKIIB -0.13 0.22 -10000 0 -0.49 122 122
MAPK11 -0.005 0.13 -10000 0 -0.85 11 11
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.12 0.2 -10000 0 -0.52 45 45
OSM/MEKK3 -0.004 0.052 -10000 0 -0.66 3 3
TAOK1 -0.002 0.11 -10000 0 -0.5 20 20
TAOK2 0.017 0.038 -10000 0 -0.46 3 3
TAOK3 0.019 0.022 -10000 0 -0.46 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.015 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.013 0.04 -10000 0 -0.85 1 1
MAP3K10 0.009 0.069 -10000 0 -0.85 3 3
MAP3K3 0.015 0 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.03 -10000 0 -0.57 1 1
GADD45/MTK1/MTK1 -0.045 0.15 -10000 0 -0.68 14 14
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.01 0.074 -10000 0 -0.57 8 8
CRKL 0.016 0.11 -10000 0 -0.84 3 3
mol:PIP3 -0.023 0.034 0.71 1 -10000 0 1
AKT1 0 0.041 0.46 1 -0.53 2 3
PTK2B 0.013 0.033 -10000 0 -0.69 1 1
RAPGEF1 0.023 0.1 -10000 0 -0.69 4 4
RANBP10 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
HGF/MET/SHIP2 -0.057 0.17 -10000 0 -0.54 50 50
MAP3K5 0.014 0.13 -10000 0 -0.59 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.054 0.17 -10000 0 -0.64 26 26
AP1 -0.083 0.21 -10000 0 -0.56 68 68
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0.033 -10000 0 -0.69 1 1
apoptosis -0.057 0.23 -10000 0 -0.81 36 36
STAT3 (dimer) 0.017 0.1 -10000 0 -0.48 5 5
GAB1/CRKL/SHP2/PI3K -0.027 0.098 -10000 0 -0.75 5 5
INPP5D 0.009 0.069 -10000 0 -0.85 3 3
CBL/CRK 0.024 0.1 -10000 0 -0.77 3 3
PTPN11 0.015 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.015 0 -10000 0 -10000 0 0
PTEN 0.013 0.04 -10000 0 -0.85 1 1
ELK1 -0.003 0.044 0.32 2 -0.28 8 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.019 0.06 -10000 0 -0.36 6 6
PAK1 0.008 0.039 0.43 1 -0.5 2 3
HGF/MET/RANBP10 -0.055 0.17 -10000 0 -0.54 48 48
HRAS 0.001 0.14 -10000 0 -0.67 8 8
DOCK1 0.024 0.1 -10000 0 -0.77 3 3
GAB1 0.007 0.11 -10000 0 -0.55 9 9
CRK 0.016 0.11 -10000 0 -0.84 3 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.16 -10000 0 -0.63 26 26
JUN 0.002 0.1 -10000 0 -0.83 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.027 0.084 -10000 0 -0.31 30 30
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
cell morphogenesis 0.043 0.12 -10000 0 -0.69 5 5
GRB2/SHC 0.008 0.084 -10000 0 -0.51 3 3
FOS -0.096 0.28 -10000 0 -0.77 66 66
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.044 0.32 2 -0.28 8 10
HGF/MET/MUC20 -0.056 0.17 -10000 0 -0.55 48 48
cell migration -0.023 0.073 -10000 0 -0.5 3 3
GRB2 0.015 0 -10000 0 -10000 0 0
CBL 0.015 0 -10000 0 -10000 0 0
MET/RANBP10 -0.01 0.074 -10000 0 -0.57 8 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.009 0.11 -10000 0 -0.52 5 5
MET/MUC20 -0.01 0.075 -10000 0 -0.58 8 8
RAP1B 0.031 0.1 -10000 0 -0.71 4 4
RAP1A 0.032 0.098 -10000 0 -0.7 3 3
HGF/MET/RANBP9 -0.055 0.17 -10000 0 -0.54 48 48
RAF1 0.011 0.13 -10000 0 -0.64 7 7
STAT3 0.017 0.1 -10000 0 -0.48 5 5
cell proliferation 0.022 0.14 -10000 0 -0.65 4 4
RPS6KB1 0.006 0.033 -10000 0 -10000 0 0
MAPK3 -0.005 0.073 0.98 2 -0.26 3 5
MAPK1 -0.009 0.033 -10000 0 -0.25 8 8
RANBP9 0.015 0 -10000 0 -10000 0 0
MAPK8 0.034 0.12 -10000 0 -0.6 6 6
SRC 0.016 0.11 -10000 0 -0.53 4 4
PI3K 0.002 0.1 -10000 0 -0.47 12 12
MET/Glomulin 0.005 0.069 -10000 0 -0.52 8 8
SOS1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.02 0.12 -10000 0 -0.66 4 4
MET 0.002 0.1 -10000 0 -0.75 8 8
MAP4K1 0.005 0.14 -10000 0 -0.58 13 13
PTK2 0.015 0 -10000 0 -10000 0 0
MAP2K2 0.017 0.14 -10000 0 -0.75 6 6
BAD 0.004 0.073 0.43 1 -0.7 4 5
MAP2K4 0.023 0.12 -10000 0 -0.64 4 4
SHP2/GRB2/SOS1/GAB1 -0.025 0.092 -10000 0 -0.67 5 5
INPPL1 0.011 0.056 -10000 0 -0.85 2 2
PXN 0.013 0.033 -10000 0 -0.69 1 1
SH3KBP1 0.007 0.08 -10000 0 -0.85 4 4
HGS -0.003 0.093 -10000 0 -0.44 10 10
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.059 0.23 -10000 0 -0.77 44 44
RASA1 0.015 0 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
PTPRJ 0.01 0.057 -10000 0 -0.69 3 3
NCK/PLCgamma1 0.009 0.087 -10000 0 -0.44 5 5
PDPK1 -0.01 0.025 0.53 1 -10000 0 1
HGF/MET/SHIP -0.058 0.18 -10000 0 -0.57 48 48
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.017 0.1 -9999 0 -0.61 12 12
forebrain development -0.068 0.2 -9999 0 -0.55 38 38
GNAO1 -0.032 0.18 -9999 0 -0.74 27 27
SMO/beta Arrestin2 0.005 0.09 -9999 0 -0.63 9 9
SMO -0.003 0.11 -9999 0 -0.83 8 8
ARRB2 0.009 0.033 -9999 0 -0.69 1 1
GLI3/SPOP 0.046 0.075 -9999 0 -0.64 1 1
mol:GTP -0.001 0.004 -9999 0 -10000 0 0
GSK3B 0.015 0 -9999 0 -10000 0 0
GNAI2 0.011 0.007 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.09 -9999 0 -0.52 13 13
GNAI1 0.006 0.069 -9999 0 -0.85 3 3
XPO1 0.012 0.009 -9999 0 -10000 0 0
GLI1/Su(fu) -0.089 0.14 -9999 0 -0.7 11 11
SAP30 -0.005 0.13 -9999 0 -0.85 11 11
mol:GDP -0.003 0.11 -9999 0 -0.83 8 8
MIM/GLI2A -0.001 0.11 -9999 0 -0.79 9 9
IFT88 0.007 0.08 -9999 0 -0.85 4 4
GNAI3 0.011 0.007 -9999 0 -10000 0 0
GLI2 0.032 0.087 -9999 0 -0.66 3 3
GLI3 0.04 0.079 -9999 0 -0.46 6 6
CSNK1D 0.01 0.065 -9999 0 -0.8 3 3
CSNK1E 0.013 0.033 -9999 0 -0.69 1 1
SAP18 0.015 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.007 0.079 -9999 0 -0.85 4 4
GNG2 0.004 0.097 -9999 0 -0.85 6 6
Gi family/GTP 0.003 0.11 -9999 0 -0.54 9 9
SIN3B 0.012 0.056 -9999 0 -0.85 2 2
SIN3A 0.015 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.036 0.083 -9999 0 -0.71 2 2
GLI2/Su(fu) 0.027 0.096 -9999 0 -0.7 3 3
FOXA2 -0.33 0.5 -9999 0 -1.2 91 91
neural tube patterning -0.068 0.2 -9999 0 -0.55 38 38
SPOP 0.015 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.048 -9999 0 -0.51 1 1
GNB1 0.015 0 -9999 0 -10000 0 0
CSNK1G2 0.009 0.069 -9999 0 -0.85 3 3
CSNK1G3 0.015 0 -9999 0 -10000 0 0
MTSS1 -0.001 0.11 -9999 0 -0.8 9 9
embryonic limb morphogenesis -0.068 0.2 -9999 0 -0.55 38 38
SUFU 0.018 0.052 -9999 0 -0.56 1 1
LGALS3 -0.021 0.16 -9999 0 -0.72 23 23
catabolic process 0.062 0.1 -9999 0 -0.61 3 3
GLI3A/CBP -0.025 0.12 -9999 0 -0.39 32 32
KIF3A 0.015 0 -9999 0 -10000 0 0
GLI1 -0.069 0.2 -9999 0 -0.57 38 38
RAB23 0.013 0.033 -9999 0 -0.69 1 1
CSNK1A1 0.015 0 -9999 0 -10000 0 0
IFT172 0.013 0.04 -9999 0 -0.85 1 1
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0 0.12 -9999 0 -0.62 8 8
GNAZ -0.003 0.1 -9999 0 -0.79 8 8
RBBP4 0.015 0.001 -9999 0 -10000 0 0
CSNK1G1 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GLI2/SPOP 0.037 0.082 -9999 0 -0.62 3 3
STK36 0.012 0.009 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.007 0.12 -9999 0 -0.72 7 7
PTCH1 -0.053 0.19 -9999 0 -0.77 10 10
MIM/GLI1 -0.15 0.3 -9999 0 -0.61 95 95
CREBBP -0.025 0.12 -9999 0 -0.39 32 32
Su(fu)/SIN3/HDAC complex 0.053 0.056 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.009 0.069 -9999 0 -0.85 3 3
Aurora C/Aurora B/INCENP -0.047 0.16 -9999 0 -0.62 19 19
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.012 0.037 -9999 0 -10000 0 0
AURKB -0.043 0.2 -9999 0 -0.76 35 35
AURKC -0.002 0.12 -9999 0 -0.79 10 10
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0 0.06 0.26 22 -10000 0 22
BUB1B 0.009 0.093 -10000 0 -0.45 16 16
PLK1 0.013 0.041 -10000 0 -0.19 16 16
PLK1S1 0.014 0.025 -10000 0 -0.29 1 1
KIF2A 0.008 0.089 -10000 0 -0.44 15 15
regulation of mitotic centrosome separation 0.013 0.041 -10000 0 -0.19 16 16
GOLGA2 0.015 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.018 0.18 -10000 0 -0.57 39 39
WEE1 0.015 0.059 -10000 0 -0.35 1 1
cytokinesis -0.004 0.15 -10000 0 -0.5 34 34
PP2A-alpha B56 -0.036 0.15 -10000 0 -0.81 14 14
AURKA 0.01 0.045 -10000 0 -0.23 15 15
PICH/PLK1 0.011 0.16 -10000 0 -0.78 15 15
CENPE 0.003 0.11 -10000 0 -0.5 21 21
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.088 -10000 0 -0.43 15 15
PPP2CA 0.015 0 -10000 0 -10000 0 0
FZR1 0.009 0.069 -10000 0 -0.85 3 3
TPX2 0.009 0.046 -10000 0 -0.23 16 16
PAK1 0.014 0.001 -10000 0 -10000 0 0
SPC24 -0.044 0.21 -10000 0 -0.8 34 34
FBXW11 0.015 0 -10000 0 -10000 0 0
CLSPN 0.002 0.073 -10000 0 -0.34 19 19
GORASP1 0.015 0 -10000 0 -10000 0 0
metaphase -0.001 0.005 -10000 0 -0.02 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.02 -10000 0 -0.089 15 15
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.012 5 5
STAG2 0.011 0.056 -10000 0 -0.85 2 2
GRASP65/GM130/RAB1/GTP 0 0.008 -10000 0 -10000 0 0
spindle elongation 0.013 0.041 -10000 0 -0.19 16 16
ODF2 0.014 0.003 -10000 0 -10000 0 0
BUB1 -0.039 0.15 -10000 0 -0.83 14 14
TPT1 0.014 0.02 -10000 0 -10000 0 0
CDC25C -0.013 0.11 -10000 0 -0.35 41 41
CDC25B 0.003 0.093 -10000 0 -0.7 8 8
SGOL1 0 0.06 -10000 0 -0.26 22 22
RHOA 0.015 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.022 0.1 -10000 0 -0.54 14 14
CDC14B 0.012 0.032 -10000 0 -0.68 1 1
CDC20 -0.018 0.15 -10000 0 -0.71 21 21
PLK1/PBIP1 -0.011 0.057 -10000 0 -0.53 4 4
mitosis 0.001 0.005 0.029 11 -10000 0 11
FBXO5 0.019 0.041 -10000 0 -0.53 1 1
CDC2 0.001 0.004 -10000 0 -0.02 14 14
NDC80 -0.006 0.13 -10000 0 -0.78 12 12
metaphase plate congression 0.013 0.027 -10000 0 -10000 0 0
ERCC6L -0.029 0.14 -10000 0 -0.77 14 14
NLP/gamma Tubulin 0.012 0.026 -10000 0 -0.15 6 6
microtubule cytoskeleton organization 0.014 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.015 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.006 0.15 -10000 0 -0.52 34 34
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.023 -10000 0 -10000 0 0
RAB1A 0.015 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.018 0.034 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -10000 0 -0.013 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.051 -10000 0 -0.75 1 1
microtubule-based process -0.012 0.14 -10000 0 -0.5 34 34
Golgi organization 0.013 0.041 -10000 0 -0.19 16 16
Cohesin/SA2 -0.009 0.045 -10000 0 -0.5 2 2
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.04 0.2 -10000 0 -0.74 34 34
APC/C/CDC20 0.002 0.12 -10000 0 -0.54 21 21
PPP2R1A 0.011 0.056 -10000 0 -0.85 2 2
chromosome segregation -0.011 0.056 -10000 0 -0.52 4 4
PRC1 0.009 0.065 -10000 0 -0.69 4 4
ECT2 0.016 0.075 -10000 0 -0.54 7 7
C13orf34 0.019 0.034 -10000 0 -10000 0 0
NUDC 0.014 0.027 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.009 0.092 -10000 0 -0.45 16 16
spindle assembly 0.014 0.035 -10000 0 -0.16 13 13
spindle stabilization 0.014 0.024 -10000 0 -0.28 1 1
APC/C/HCDH1 0.015 0.055 -10000 0 -0.58 4 4
MKLP2/PLK1 -0.012 0.14 -10000 0 -0.5 34 34
CCNB1 -0.002 0.11 -10000 0 -0.7 11 11
PPP1CB 0.015 0.001 -10000 0 -10000 0 0
BTRC 0.015 0 -10000 0 -10000 0 0
ROCK2 0.016 0.068 -10000 0 -0.52 6 6
TUBG1 0.013 0.033 -10000 0 -0.39 2 2
G2/M transition of mitotic cell cycle -0.021 0.096 -10000 0 -0.52 14 14
MLF1IP 0.008 0.058 -10000 0 -0.61 4 4
INCENP 0.008 0.069 -10000 0 -0.85 3 3
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.032 0.099 -10000 0 -0.57 6 6
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.056 -10000 0 -0.85 2 2
AKT2 0.011 0.056 -10000 0 -0.85 2 2
STXBP4 0.013 0.04 -10000 0 -0.85 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.031 0.14 0.29 37 -0.55 8 45
YWHAZ 0.015 0 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.017 0.078 -10000 0 -0.57 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
SNARE/Synip -0.004 0.045 -10000 0 -0.57 3 3
YWHAG 0.015 0 -10000 0 -10000 0 0
ASIP -0.082 0.24 -10000 0 -0.72 60 60
PRKCI 0.012 0.046 -10000 0 -0.69 2 2
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0.033 -10000 0 -0.69 1 1
GYS1 0.032 0.09 -10000 0 -1.3 2 2
PRKCZ 0 0.11 -10000 0 -0.83 8 8
TRIP10 0.004 0.097 -10000 0 -0.85 6 6
TC10/GTP/CIP4/Exocyst -0.008 0.074 -10000 0 -0.64 6 6
AS160/14-3-3 -0.01 0.11 -10000 0 -0.44 4 4
VAMP2 0.015 0 -10000 0 -10000 0 0
SLC2A4 0.03 0.15 0.34 7 -0.64 8 15
STX4 0.011 0.056 -10000 0 -0.85 2 2
GSK3B 0.025 0.08 -10000 0 -1.2 2 2
SFN -0.19 0.34 -10000 0 -0.74 125 125
LNPEP -0.005 0.13 -10000 0 -0.85 11 11
YWHAE 0.015 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.024 0.18 -9999 0 -0.85 21 21
alphaV beta3 Integrin -0.024 0.12 -9999 0 -0.58 19 19
PTK2 -0.028 0.12 -9999 0 -0.63 14 14
positive regulation of JNK cascade -0.013 0.062 -9999 0 -0.35 14 14
CDC42/GDP 0.048 0.098 -9999 0 -0.48 13 13
Rac1/GDP 0.05 0.097 -9999 0 -0.47 13 13
RAP1B 0.013 0.033 -9999 0 -0.69 1 1
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.016 0.077 -9999 0 -0.44 14 14
nectin-3/I-afadin -0.017 0.1 -9999 0 -0.66 12 12
RAPGEF1 0.042 0.11 -9999 0 -0.55 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.034 0.12 -9999 0 -0.63 14 14
PDGFB-D/PDGFRB -0.024 0.18 -9999 0 -0.85 21 21
TLN1 0.018 0.1 -9999 0 -0.5 13 13
Rap1/GTP -0.013 0.068 -9999 0 -0.48 4 4
IQGAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.4 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.017 0.1 -9999 0 -0.66 12 12
PVR 0.01 0.057 -9999 0 -0.69 3 3
Necl-5(dimer) 0.01 0.056 -9999 0 -0.69 3 3
mol:GDP 0.045 0.12 -9999 0 -0.59 14 14
MLLT4 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
PI3K -0.04 0.14 -9999 0 -0.49 35 35
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.049 -9999 0 -0.61 3 3
positive regulation of lamellipodium assembly -0.013 0.062 -9999 0 -0.36 13 13
PVRL1 0.01 0.065 -9999 0 -0.8 3 3
PVRL3 -0.007 0.14 -9999 0 -0.85 12 12
PVRL2 0.011 0.056 -9999 0 -0.85 2 2
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
CDH1 -0.033 0.19 -9999 0 -0.81 27 27
CLDN1 -0.052 0.22 -9999 0 -0.79 39 39
JAM-A/CLDN1 -0.055 0.15 -9999 0 -0.52 38 38
SRC -0.026 0.13 -9999 0 -0.72 14 14
ITGB3 -0.015 0.15 -9999 0 -0.77 18 18
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.049 -9999 0 -0.61 3 3
FARP2 0.037 0.12 -9999 0 -0.59 15 15
RAC1 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.017 0.096 -9999 0 -0.54 15 15
nectin-1/I-afadin -0.004 0.049 -9999 0 -0.61 3 3
nectin-2/I-afadin -0.003 0.043 -9999 0 -0.66 2 2
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 -0.018 0.098 -9999 0 -0.56 15 15
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.009 0.069 -9999 0 -0.85 3 3
positive regulation of filopodium formation -0.013 0.062 -9999 0 -0.35 14 14
alphaV/beta3 Integrin/Talin 0.016 0.14 -9999 0 -0.85 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.043 -9999 0 -0.66 2 2
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.043 -9999 0 -0.66 2 2
PIP5K1C 0.01 0.098 -9999 0 -0.5 13 13
VAV2 0.038 0.12 -9999 0 -0.59 14 14
RAP1/GDP -0.016 0.079 -9999 0 -0.44 14 14
ITGAV 0.013 0.033 -9999 0 -0.69 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.017 0.097 -9999 0 -0.57 14 14
nectin-3(dimer)/I-afadin/I-afadin -0.017 0.1 -9999 0 -0.66 12 12
Rac1/GTP -0.016 0.077 -9999 0 -0.45 13 13
PTPRM -0.019 0.091 -9999 0 -0.41 22 22
E-cadherin/beta catenin/alpha catenin -0.029 0.12 -9999 0 -0.87 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.034 0.12 0.63 11 -10000 0 11
GNAI2 0.015 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.031 0.13 -10000 0 -0.55 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.029 0.18 -10000 0 -0.74 27 27
RhoA/GTP -0.035 0.12 -10000 0 -0.65 11 11
negative regulation of cAMP metabolic process -0.002 0.14 -10000 0 -0.48 28 28
GNAZ 0.001 0.1 -10000 0 -0.79 8 8
GNAI3 0.015 0 -10000 0 -10000 0 0
GNA12 0.013 0.033 -10000 0 -0.69 1 1
S1PR5 -0.03 0.19 -10000 0 -0.82 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.002 0.14 -10000 0 -0.49 28 28
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
GNAI1 0.009 0.069 -10000 0 -0.85 3 3
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.018 0.2 -9999 0 -1.4 9 9
VDR -0.007 0.13 -9999 0 -0.73 14 14
FAM120B 0.015 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.019 0.14 -9999 0 -0.68 6 6
RXRs/LXRs/DNA/Oxysterols 0.012 0.19 -9999 0 -0.8 7 7
MED1 0.015 0 -9999 0 -10000 0 0
mol:9cRA 0.001 0.02 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.008 0.13 -9999 0 -0.8 5 5
RXRs/NUR77 -0.052 0.2 -9999 0 -0.54 34 34
RXRs/PPAR 0.03 0.077 -9999 0 -0.71 1 1
NCOR2 0.009 0.069 -9999 0 -0.85 3 3
VDR/VDR/Vit D3 -0.017 0.095 -9999 0 -0.56 14 14
RARs/VDR/DNA/Vit D3 -0.027 0.12 -9999 0 -0.54 17 17
RARA 0.011 0.056 -9999 0 -0.85 2 2
NCOA1 0.015 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.007 0.13 -9999 0 -0.73 14 14
RARs/RARs/DNA/9cRA -0.016 0.093 -9999 0 -0.53 14 14
RARG 0.007 0.08 -9999 0 -0.85 4 4
RPS6KB1 0.004 0.064 -9999 0 -0.42 8 8
RARs/THRs/DNA/SMRT 0.005 0.16 -9999 0 -0.98 6 6
THRA 0.009 0.069 -9999 0 -0.85 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.017 0.095 -9999 0 -0.56 14 14
RXRs/PPAR/9cRA/PGJ2/DNA 0.015 0.11 -9999 0 -0.51 9 9
NR1H4 -0.028 0.19 -9999 0 -0.83 24 24
RXRs/LXRs/DNA 0.028 0.15 -9999 0 -1.1 3 3
NR1H2 0.013 0.071 -9999 0 -0.86 3 3
NR1H3 0.012 0.072 -9999 0 -0.86 3 3
RXRs/VDR/DNA/Vit D3 0.01 0.12 -9999 0 -0.5 10 10
NR4A1 -0.11 0.28 -9999 0 -0.75 76 76
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.006 0.11 -9999 0 -0.38 22 22
RXRG -0.014 0.14 -9999 0 -0.73 18 18
RXR alpha/CCPG 0.024 0.01 -9999 0 -10000 0 0
RXRA 0.018 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.043 -9999 0 -0.86 1 1
THRB -0.035 0.2 -9999 0 -0.8 29 29
PPARG 0.011 0.056 -9999 0 -0.85 2 2
PPARD 0.011 0.056 -9999 0 -0.85 2 2
TNF -0.051 0.36 -9999 0 -1.2 34 34
mol:Oxysterols 0.002 0.017 -9999 0 -10000 0 0
cholesterol transport 0.013 0.18 -9999 0 -0.76 7 7
PPARA 0.013 0.04 -9999 0 -0.85 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.002 0.12 -9999 0 -0.85 9 9
RXRs/NUR77/BCL2 -0.034 0.15 -9999 0 -0.65 10 10
SREBF1 0.019 0.18 -9999 0 -1.4 3 3
RXRs/RXRs/DNA/9cRA 0.015 0.11 -9999 0 -0.51 9 9
ABCA1 0.008 0.23 -9999 0 -1.2 11 11
RARs/THRs -0.046 0.16 -9999 0 -1 5 5
RXRs/FXR -0.003 0.16 -9999 0 -0.54 26 26
BCL2 -0.007 0.14 -9999 0 -0.85 12 12
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.47 0.64 -9999 0 -1.5 118 118
PLK1 0.05 0.27 -9999 0 -1 19 19
CDKN1B 0.053 0.14 -9999 0 -10000 0 0
FOXO3 0.063 0.22 -9999 0 -0.85 14 14
KAT2B 0.026 0.015 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.14 0.17 -9999 0 -0.53 2 2
CAT 0.065 0.22 -9999 0 -0.94 11 11
CTNNB1 0.015 0 -9999 0 -10000 0 0
AKT1 0.005 0.064 -9999 0 -0.86 2 2
FOXO1 -0.13 0.21 -9999 0 -0.42 117 117
MAPK10 0.03 0.069 -9999 0 -0.51 7 7
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.099 0.073 -9999 0 -10000 0 0
response to oxidative stress -0.01 0.034 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.028 0.18 -9999 0 -0.78 12 12
XPO1 0.016 0.001 -9999 0 -10000 0 0
EP300 -0.004 0.025 -9999 0 -10000 0 0
BCL2L11 0.037 0.035 -9999 0 -10000 0 0
FOXO1/SKP2 -0.12 0.2 -9999 0 -0.64 6 6
mol:GDP -0.01 0.034 -9999 0 -10000 0 0
RAN 0.017 0.002 -9999 0 -10000 0 0
GADD45A 0.12 0.11 -9999 0 -0.73 1 1
YWHAQ 0.015 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family -0.006 0.11 -9999 0 -0.75 3 3
MST1 -0.036 0.22 -9999 0 -0.78 37 37
CSNK1D 0.01 0.065 -9999 0 -0.8 3 3
CSNK1E 0.013 0.033 -9999 0 -0.69 1 1
FOXO4/14-3-3 family -0.002 0.13 -9999 0 -10000 0 0
YWHAB 0.015 0 -9999 0 -10000 0 0
MAPK8 0.034 0.054 -9999 0 -0.51 4 4
MAPK9 0.036 0.03 -9999 0 -0.51 1 1
YWHAG 0.015 0 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
YWHAZ 0.015 0 -9999 0 -10000 0 0
SIRT1 0.015 0.021 -9999 0 -10000 0 0
SOD2 0.046 0.2 -9999 0 -0.97 6 6
RBL2 0.088 0.16 -9999 0 -1.3 1 1
RAL/GDP 0.016 0.037 -9999 0 -0.6 1 1
CHUK 0.026 0.015 -9999 0 -10000 0 0
Ran/GTP 0.016 0.004 -9999 0 -10000 0 0
CSNK1G2 0.009 0.069 -9999 0 -0.85 3 3
RAL/GTP 0.03 0.035 -9999 0 -0.55 1 1
CSNK1G1 0.015 0 -9999 0 -10000 0 0
FASLG -0.096 0.42 -9999 0 -1.6 30 30
SKP2 0.008 0.073 -9999 0 -0.77 4 4
USP7 0.017 0.002 -9999 0 -10000 0 0
IKBKB 0.026 0.015 -9999 0 -10000 0 0
CCNB1 0.062 0.22 -9999 0 -0.91 15 15
FOXO1-3a-4/beta catenin -0.033 0.1 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.2 -9999 0 -0.64 6 6
CSNK1A1 0.015 0 -9999 0 -10000 0 0
SGK1 0.013 0.11 -9999 0 -0.87 7 7
CSNK1G3 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.006 -9999 0 -10000 0 0
ZFAND5 0.1 0.074 -9999 0 -10000 0 0
SFN -0.19 0.34 -9999 0 -0.74 125 125
CDK2 -0.018 0.039 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.014 0.13 -9999 0 -0.49 2 2
CREBBP -0.018 0.039 -9999 0 -10000 0 0
FBXO32 0.064 0.21 -9999 0 -0.84 13 13
BCL6 0.083 0.19 -9999 0 -1.2 4 4
RALB 0.015 0.04 -9999 0 -0.85 1 1
RALA 0.016 0.001 -9999 0 -10000 0 0
YWHAH 0.015 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.015 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.033 0.094 -9999 0 -0.56 7 7
NEF -0.016 0.062 -9999 0 -10000 0 0
NFKBIA 0.01 0.054 -9999 0 -0.98 1 1
BIRC3 0.007 0.2 -9999 0 -0.83 25 25
CYCS 0.011 0.15 -9999 0 -0.72 12 12
RIPK1 0.015 0 -9999 0 -10000 0 0
CD247 -0.037 0.2 -9999 0 -0.99 18 18
MAP2K7 0.02 0.12 -9999 0 -0.68 7 7
protein ubiquitination 0.039 0.12 -9999 0 -0.64 8 8
CRADD 0.013 0.04 -9999 0 -0.85 1 1
DAXX 0.015 0 -9999 0 -10000 0 0
FAS 0.002 0.1 -9999 0 -0.85 7 7
BID 0.012 0.12 -9999 0 -0.64 7 7
NF-kappa-B/RelA/I kappa B alpha -0.019 0.084 -9999 0 -0.93 1 1
TRADD 0.011 0.056 -9999 0 -0.85 2 2
MAP3K5 0.013 0.04 -9999 0 -0.85 1 1
CFLAR 0.011 0.056 -9999 0 -0.85 2 2
FADD 0.015 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.019 0.085 -9999 0 -0.94 1 1
MAPK8 0.026 0.12 -9999 0 -0.69 5 5
APAF1 0.015 0 -9999 0 -10000 0 0
TRAF1 0.004 0.092 -9999 0 -0.8 6 6
TRAF2 0.011 0.056 -9999 0 -0.85 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.004 0.12 -9999 0 -0.61 7 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.031 0.12 -9999 0 -0.76 4 4
CHUK 0.037 0.14 -9999 0 -0.73 8 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.008 0.062 -9999 0 -10000 0 0
TCRz/NEF -0.068 0.2 -9999 0 -0.68 34 34
TNF -0.08 0.26 -9999 0 -0.78 56 56
FASLG -0.089 0.33 -9999 0 -0.88 63 63
NFKB1 0.012 0.028 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.06 0.17 -9999 0 -0.51 56 56
CASP6 -0.022 0.076 -9999 0 -0.73 2 2
CASP7 0.046 0.18 -9999 0 -0.71 20 20
RELA 0.012 0.028 -9999 0 -10000 0 0
CASP2 0.015 0 -9999 0 -10000 0 0
CASP3 0.046 0.18 -9999 0 -0.71 20 20
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.015 0 -9999 0 -10000 0 0
CASP9 0.015 0 -9999 0 -10000 0 0
MAP3K14 0.028 0.16 -9999 0 -0.76 12 12
APAF-1/Caspase 9 -0.044 0.14 -9999 0 -0.64 19 19
BCL2 0.023 0.14 -9999 0 -0.7 7 7
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.015 0.087 -10000 0 -0.45 2 2
epithelial cell differentiation -0.026 0.11 -10000 0 -0.48 20 20
CYFIP2 0.001 0.11 -10000 0 -0.81 8 8
ENAH 0.047 0.11 -10000 0 -0.51 8 8
EGFR -0.023 0.17 -10000 0 -0.8 22 22
EPHA2 -0.001 0.11 -10000 0 -0.82 9 9
MYO6 0.015 0.12 -10000 0 -0.93 2 2
CTNNB1 0.015 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.009 0.07 -10000 0 -0.53 8 8
AQP5 -0.043 0.13 -10000 0 -0.7 9 9
CTNND1 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.12 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.2 -10000 0 -0.86 14 14
EGF -0.22 0.36 -10000 0 -0.77 143 143
NCKAP1 0.015 0 -10000 0 -10000 0 0
AQP3 -0.063 0.19 -10000 0 -0.72 29 29
cortical microtubule organization -0.026 0.11 -10000 0 -0.48 20 20
GO:0000145 0.015 0.11 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.026 0.11 -10000 0 -0.49 20 20
MLLT4 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.036 0.14 -10000 0 -0.77 10 10
ARF6 0.015 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.022 0.12 -10000 0 -0.58 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.028 0.12 -10000 0 -0.57 4 4
PVRL2 0.011 0.056 -10000 0 -0.85 2 2
ZYX 0.015 0.12 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.11 -10000 0 -1.3 1 1
CDH1 -0.033 0.19 -10000 0 -0.81 27 27
EGFR/EGFR/EGF/EGF -0.16 0.24 -10000 0 -0.91 17 17
RhoA/GDP -0.024 0.099 -10000 0 -10000 0 0
actin cytoskeleton organization 0.024 0.12 -10000 0 -0.84 2 2
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.85 3 3
GIT1 0.011 0.056 -10000 0 -0.85 2 2
IGF1R 0.009 0.069 -10000 0 -0.85 3 3
IGF1 -0.033 0.18 -10000 0 -0.74 30 30
DIAPH1 -0.013 0.094 -10000 0 -0.82 6 6
Wnt receptor signaling pathway 0.026 0.11 0.48 20 -10000 0 20
RHOA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP -0.036 0.14 -10000 0 -0.77 10 10
CTNNA1 0.015 0 -10000 0 -10000 0 0
VCL 0.023 0.12 -10000 0 -0.89 2 2
EFNA1 -0.003 0.12 -10000 0 -0.84 10 10
LPP 0.022 0.13 -10000 0 -0.8 5 5
Ephrin A1/EPHA2 -0.041 0.15 -10000 0 -0.88 10 10
SEC6/SEC8 -0.026 0.1 -10000 0 -0.82 2 2
MGAT3 -0.032 0.21 -10000 0 -0.89 14 14
HGF/MET -0.066 0.18 -10000 0 -0.83 12 12
HGF -0.059 0.23 -10000 0 -0.77 44 44
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.015 0.088 -10000 0 -0.46 2 2
actin cable formation 0.068 0.11 -10000 0 -0.48 6 6
KIAA1543 0.007 0.18 -10000 0 -1.1 7 7
KIFC3 0.01 0.14 -10000 0 -0.83 4 4
NCK1 0.015 0 -10000 0 -10000 0 0
EXOC3 0.008 0.073 -10000 0 -0.77 4 4
ACTN1 0.013 0.13 -10000 0 -0.82 4 4
NCK1/GIT1 -0.003 0.043 -10000 0 -0.66 2 2
mol:GDP -0.026 0.11 -10000 0 -0.48 20 20
EXOC4 0.015 0 -10000 0 -10000 0 0
STX4 0.016 0.12 -10000 0 -10000 0 0
PIP5K1C 0.015 0.12 -10000 0 -10000 0 0
LIMA1 0.009 0.065 -10000 0 -0.69 4 4
ABI1 0.015 0 -10000 0 -10000 0 0
ROCK1 -0.031 0.11 -10000 0 -0.62 10 10
adherens junction assembly 0.018 0.2 -10000 0 -0.95 14 14
IGF-1R heterotetramer/IGF1 -0.05 0.15 -10000 0 -0.75 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.043 -10000 0 -0.66 2 2
MET 0.002 0.1 -10000 0 -0.75 8 8
PLEKHA7 0.008 0.15 -10000 0 -0.93 6 6
mol:GTP -0.022 0.12 -10000 0 -0.57 16 16
establishment of epithelial cell apical/basal polarity 0.044 0.12 -10000 0 -1 2 2
cortical actin cytoskeleton stabilization 0.015 0.087 -10000 0 -0.45 2 2
regulation of cell-cell adhesion 0.024 0.12 -10000 0 -0.84 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.015 0.088 -10000 0 -0.46 2 2
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.046 0.14 -9999 0 -0.96 4 4
TC10/GTP -0.02 0.099 -9999 0 -1.2 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.033 0.12 -9999 0 -0.46 33 33
HRAS 0.009 0.069 -9999 0 -0.85 3 3
APS homodimer -0.001 0.11 -9999 0 -0.8 9 9
GRB14 -0.067 0.24 -9999 0 -0.75 50 50
FOXO3 -0.024 0.12 -9999 0 -1 7 7
AKT1 -0.015 0.18 -9999 0 -0.7 16 16
INSR -0.002 0.12 -9999 0 -0.85 10 10
Insulin Receptor/Insulin -0.01 0.065 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0.04 -9999 0 -0.85 1 1
SORBS1 -0.005 0.13 -9999 0 -0.85 11 11
CRK 0.015 0 -9999 0 -10000 0 0
PTPN1 0.032 0.07 -9999 0 -10000 0 0
CAV1 -0.01 0.14 -9999 0 -0.46 41 41
CBL/APS/CAP/Crk-II/C3G -0.021 0.1 -9999 0 -0.97 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.034 0.12 -9999 0 -0.47 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.12 -9999 0 -0.49 17 17
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.018 0.12 -9999 0 -0.7 10 10
RPS6KB1 -0.002 0.17 -9999 0 -0.62 16 16
PARD6A -0.005 0.12 -9999 0 -0.75 12 12
CBL 0.015 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.007 0.093 -9999 0 -1 4 4
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.059 0.15 -9999 0 -0.64 16 16
HRAS/GTP -0.03 0.11 -9999 0 -0.74 3 3
Insulin Receptor -0.002 0.12 -9999 0 -0.84 10 10
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.031 0.11 -9999 0 -0.58 5 5
PRKCI -0.025 0.1 -9999 0 -0.85 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.07 0.18 -9999 0 -0.77 15 15
SHC1 0.013 0.033 -9999 0 -0.69 1 1
negative regulation of MAPKKK cascade -0.006 0.08 -9999 0 -0.86 4 4
PI3K -0.035 0.12 -9999 0 -0.5 17 17
NCK2 0.013 0.04 -9999 0 -0.85 1 1
RHOQ 0.013 0.033 -9999 0 -0.69 1 1
mol:H2O2 -0.001 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.004 0.053 -9999 0 -0.66 3 3
AKT2 -0.015 0.18 -9999 0 -0.7 16 16
PRKCZ -0.035 0.14 -9999 0 -0.92 11 11
SH2B2 -0.001 0.11 -9999 0 -0.8 9 9
SHC/SHIP 0.005 0.13 -9999 0 -0.52 16 16
F2RL2 -0.084 0.26 -9999 0 -0.77 59 59
TRIP10 0.004 0.097 -9999 0 -0.85 6 6
Insulin Receptor/Insulin/Shc -0.012 0.075 -9999 0 -0.5 11 11
TC10/GTP/CIP4/Exocyst -0.008 0.074 -9999 0 -0.64 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.011 0.068 -9999 0 -0.46 10 10
RAPGEF1 0.013 0.04 -9999 0 -0.85 1 1
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.021 0.1 -9999 0 -0.52 17 17
TC10/GDP -0.001 0.024 -9999 0 -0.53 1 1
Insulin Receptor/Insulin/SHC/GRB10 -0.012 0.084 -9999 0 -0.54 10 10
INPP5D -0.004 0.14 -9999 0 -0.56 16 16
SOS1 0.015 0 -9999 0 -10000 0 0
SGK1 -0.023 0.15 -9999 0 -1.3 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 -0.023 0.16 -9999 0 -0.73 24 24
p62DOK/RasGAP -0.006 0.081 -9999 0 -0.87 4 4
INS 0.003 0.008 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.003 0.13 -9999 0 -0.55 16 16
GRB2 0.015 0 -9999 0 -10000 0 0
EIF4EBP1 -0.017 0.2 -9999 0 -0.69 24 24
PTPRA 0.016 0.006 -9999 0 -10000 0 0
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
TC10/GTP/CIP4 -0.008 0.074 -9999 0 -0.64 6 6
PDPK1 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.017 0.087 -9999 0 -0.7 1 1
Insulin Receptor/Insulin/IRS1 -0.033 0.12 -9999 0 -0.47 33 33
Insulin Receptor/Insulin/IRS3 -0.014 0.095 -9999 0 -0.66 10 10
Par3/Par6 -0.071 0.19 -9999 0 -0.6 34 34
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.012 0.15 -10000 0 -0.84 15 15
positive regulation of NF-kappaB transcription factor activity -0.026 0.13 -10000 0 -0.68 18 18
MAP2K4 0.038 0.092 -10000 0 -0.61 5 5
IKBKB 0.015 0 -10000 0 -10000 0 0
TNFRSF10B 0.013 0.04 -10000 0 -0.85 1 1
TNFRSF10A -0.004 0.12 -10000 0 -0.85 10 10
SMPD1 -0.011 0.057 -10000 0 -0.3 17 17
IKBKG 0.009 0.069 -10000 0 -0.85 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.007 0.08 -10000 0 -0.85 4 4
TRAIL/TRAILR2 -0.022 0.12 -10000 0 -0.65 16 16
TRAIL/TRAILR3 -0.038 0.16 -10000 0 -0.69 26 26
TRAIL/TRAILR1 -0.034 0.16 -10000 0 -0.72 22 22
TRAIL/TRAILR4 -0.026 0.13 -10000 0 -0.68 18 18
TRAIL/TRAILR1/DAP3/GTP -0.028 0.13 -10000 0 -0.6 21 21
IKK complex -0.014 0.079 -10000 0 -0.84 3 3
RIPK1 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.003 0.13 -10000 0 -0.65 17 17
MAP3K1 -0.017 0.087 -10000 0 -0.65 5 5
TRAILR4 (trimer) 0.007 0.079 -10000 0 -0.85 4 4
TRADD 0.011 0.056 -10000 0 -0.85 2 2
TRAILR1 (trimer) -0.004 0.12 -10000 0 -0.85 10 10
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.12 -10000 0 -0.82 5 5
CFLAR 0.011 0.056 -10000 0 -0.85 2 2
MAPK1 0.006 0.12 -10000 0 -0.64 15 15
TRAIL/TRAILR1/FADD/TRADD/RIP -0.027 0.13 -10000 0 -0.97 4 4
mol:ceramide -0.011 0.057 -10000 0 -0.3 17 17
FADD 0.015 0 -10000 0 -10000 0 0
MAPK8 0.042 0.096 -10000 0 -0.75 2 2
TRAF2 0.011 0.056 -10000 0 -0.85 2 2
TRAILR3 (trimer) -0.01 0.14 -10000 0 -0.76 15 15
CHUK 0.015 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.03 0.14 -10000 0 -0.64 21 21
DAP3 0.015 0 -10000 0 -10000 0 0
CASP10 -0.023 0.12 0.32 2 -0.63 14 16
JNK cascade -0.026 0.13 -10000 0 -0.68 18 18
TRAIL (trimer) -0.012 0.15 -10000 0 -0.84 15 15
TNFRSF10C -0.01 0.14 -10000 0 -0.76 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD -0.026 0.12 -10000 0 -0.56 21 21
TRAIL/TRAILR2/FADD -0.019 0.1 -10000 0 -0.56 16 16
cell death 0.011 0.061 -10000 0 -0.3 17 17
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.029 0.082 -10000 0 -0.69 2 2
TRAILR2 (trimer) 0.013 0.04 -10000 0 -0.85 1 1
CASP8 0.003 0.034 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.018 0.091 -10000 0 -10000 0 0
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.022 0.14 -10000 0 -0.62 26 26
TP53 -0.008 0.056 0.3 4 -0.55 1 5
Senescence -0.008 0.056 0.3 4 -0.55 1 5
Apoptosis -0.008 0.056 0.3 4 -0.55 1 5
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.018 0.073 0.34 17 -10000 0 17
MDM4 0.008 0.069 -10000 0 -0.73 4 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.095 0.28 -9999 0 -0.78 65 65
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.009 0.069 -9999 0 -0.85 3 3
TCEB1 0.015 0 -9999 0 -10000 0 0
HIF1A/p53 0.027 0.048 -9999 0 -0.58 1 1
HIF1A 0.02 0.041 -9999 0 -0.34 1 1
COPS5 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.008 0.065 -9999 0 -0.86 1 1
FIH (dimer) 0.015 0 -9999 0 -10000 0 0
CDKN2A -0.03 0.19 -9999 0 -0.8 26 26
ARNT/IPAS -0.082 0.21 -9999 0 -0.59 65 65
HIF1AN 0.015 0 -9999 0 -10000 0 0
GNB2L1 0.01 0.065 -9999 0 -0.8 3 3
HIF1A/ARNT 0.028 0.039 -9999 0 -10000 0 0
CUL2 0.015 0 -9999 0 -10000 0 0
OS9 0.015 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.007 0.078 -9999 0 -0.91 3 3
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.026 0.048 -9999 0 -0.47 1 1
PHD1-3/OS9 -0.037 0.13 -9999 0 -0.52 34 34
HIF1A/RACK1/Elongin B/Elongin C -0.011 0.069 -9999 0 -0.78 3 3
VHL 0.009 0.069 -9999 0 -0.85 3 3
HSP90AA1 0.012 0.046 -9999 0 -0.69 2 2
HIF1A/JAB1 0.028 0.039 -9999 0 -10000 0 0
EGLN3 -0.042 0.22 -9999 0 -0.85 31 31
EGLN2 0.009 0.069 -9999 0 -0.85 3 3
EGLN1 0.015 0 -9999 0 -10000 0 0
TP53 0.013 0.04 -9999 0 -0.85 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.065 -9999 0 -0.64 3 3
ARNT 0.015 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0.046 -9999 0 -0.69 2 2
HIF1A/p19ARF 0.003 0.12 -9999 0 -0.51 21 21
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.004 0.11 -10000 0 -0.71 12 12
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.005 0.13 -10000 0 -0.85 11 11
CDKN1A 0.006 0.088 -10000 0 -0.58 3 3
PRL-3/alpha Tubulin -0.008 0.071 -10000 0 -0.63 6 6
mol:Ca2+ -0.062 0.2 0.45 6 -0.63 50 56
AGT -0.073 0.26 -10000 0 -0.81 50 50
CCNA2 -0.025 0.18 -10000 0 -0.84 2 2
TUBA1B 0.015 0 -10000 0 -10000 0 0
EGR1 -0.059 0.21 -10000 0 -0.57 69 69
CDK2/Cyclin E1 0.011 0.1 -10000 0 -0.68 4 4
MAPK3 0.016 0.099 -10000 0 -0.81 6 6
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.074 -10000 0 -0.63 6 6
PTP4A1 -0.028 0.17 -10000 0 -10000 0 0
PTP4A3 0.004 0.095 -10000 0 -0.82 6 6
PTP4A2 0.015 0 -10000 0 -10000 0 0
ITGB1 0.019 0.074 -10000 0 -0.63 6 6
SRC 0.011 0.056 -10000 0 -0.85 2 2
RAC1 0.003 0.11 -10000 0 -0.72 5 5
Rab GGTase beta/Rab GGTase alpha -0.003 0.043 -10000 0 -0.66 2 2
PRL-1/ATF-5 -0.028 0.17 -10000 0 -10000 0 0
RABGGTA 0.011 0.056 -10000 0 -0.85 2 2
BCAR1 0 0.051 0.43 3 -0.46 3 6
RHOC 0.001 0.12 -10000 0 -0.87 5 5
RHOA 0.003 0.11 -10000 0 -0.72 5 5
cell motility 0.005 0.11 -10000 0 -0.77 5 5
PRL-1/alpha Tubulin -0.019 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.023 0.12 -10000 0 -0.65 17 17
ROCK1 0.005 0.12 -10000 0 -0.78 5 5
RABGGTB 0.015 0 -10000 0 -10000 0 0
CDK2 0.015 0 -10000 0 -10000 0 0
mitosis -0.028 0.17 -10000 0 -10000 0 0
ATF5 0 0.1 -10000 0 -0.69 10 10
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.02 0.11 -10000 0 -0.66 14 14
ATM 0.013 0.04 -10000 0 -0.85 1 1
UBE2D3 0.015 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
ATR 0.015 0 -10000 0 -10000 0 0
UBE2L3 0.015 0 -10000 0 -10000 0 0
FANCD2 0.025 0.046 -10000 0 -0.45 2 2
protein ubiquitination -0.03 0.12 -10000 0 -0.84 3 3
XRCC5 0.015 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
M/R/N Complex -0.002 0.033 -10000 0 -0.57 1 1
MRE11A 0.015 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.016 0.084 -10000 0 -0.85 3 3
FANCF 0.015 0 -10000 0 -10000 0 0
BRCA1 0.004 0.092 -10000 0 -0.8 6 6
CCNE1 -0.004 0.11 -10000 0 -0.71 12 12
CDK2/Cyclin E1 -0.013 0.083 -10000 0 -0.53 12 12
FANCG 0.013 0.04 -10000 0 -0.85 1 1
BRCA1/BACH1/BARD1 -0.027 0.13 -10000 0 -0.64 20 20
FANCE 0.01 0.065 -10000 0 -0.8 3 3
FANCC 0.011 0.052 -10000 0 -0.77 2 2
NBN 0.013 0.033 -10000 0 -0.69 1 1
FANCA -0.016 0.15 -10000 0 -0.75 19 19
DNA repair 0.05 0.14 -10000 0 -0.73 6 6
BRCA1/BARD1/ubiquitin -0.027 0.13 -10000 0 -0.64 20 20
BARD1/DNA-PK -0.015 0.088 -10000 0 -0.52 14 14
FANCL 0.015 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.02 0.11 0.65 14 -10000 0 14
BRCA1/BARD1/CTIP/M/R/N Complex 0.031 0.087 -10000 0 -0.64 3 3
BRCA1/BACH1/BARD1/TopBP1 -0.024 0.11 -10000 0 -0.56 20 20
BRCA1/BARD1/P53 -0.023 0.11 -10000 0 -0.54 19 19
BARD1/CSTF1/BRCA1 -0.024 0.11 -10000 0 -0.57 18 18
BRCA1/BACH1 0.004 0.092 -10000 0 -0.8 6 6
BARD1 -0.011 0.15 -10000 0 -0.85 14 14
PCNA 0.015 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.024 0.11 -10000 0 -0.57 18 18
BRCA1/BARD1/UbcH7 -0.024 0.11 -10000 0 -0.57 18 18
BRCA1/BARD1/RAD51/PCNA -0.026 0.12 -10000 0 -0.54 20 20
BARD1/DNA-PK/P53 -0.015 0.085 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.027 0.13 -10000 0 -0.64 20 20
BRCA1/BARD1/CTIP -0.024 0.12 -10000 0 -0.56 18 18
FA complex 0.031 0.083 -10000 0 -0.76 2 2
BARD1/EWS -0.02 0.11 -10000 0 -0.66 14 14
RBBP8 0.023 0.047 -10000 0 -0.56 3 3
TP53 0.013 0.04 -10000 0 -0.85 1 1
TOPBP1 0.015 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.022 0.11 0.53 19 -10000 0 19
BRCA1/BARD1 -0.031 0.12 -10000 0 -0.86 3 3
CSTF1 0.015 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.02 0.11 -10000 0 -0.66 14 14
CDK2 0.015 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.006 0.08 -10000 0 -0.69 6 6
RAD50 0.013 0.04 -10000 0 -0.85 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.027 0.13 -10000 0 -0.64 20 20
EWSR1 0.015 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.015 0 -10000 0 -10000 0 0
HDAC4 0.013 0.033 -10000 0 -0.69 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.02 0.049 0.5 4 -10000 0 4
CDKN1A -0.006 0.074 -10000 0 -0.76 4 4
KAT2B 0.015 0 -10000 0 -10000 0 0
BAX 0.011 0.056 -10000 0 -0.85 2 2
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.009 0.065 -10000 0 -0.69 4 4
FOXO4 0.027 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
TAT -0.03 0.17 -10000 0 -0.69 28 28
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.006 0.11 -10000 0 -0.52 22 22
PPARGC1A -0.087 0.27 -10000 0 -0.8 59 59
FHL2 -0.045 0.21 -10000 0 -0.81 34 34
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.013 -10000 0 -10000 0 0
HIST2H4A 0.02 0.049 -10000 0 -0.5 4 4
SIRT1/FOXO3a 0.001 0.012 -10000 0 -10000 0 0
SIRT1 0.002 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.033 -10000 0 -0.52 1 1
SIRT1/Histone H1b -0.018 0.069 -10000 0 -10000 0 0
apoptosis 0.001 0.037 0.54 2 -10000 0 2
SIRT1/PGC1A -0.066 0.18 -10000 0 -0.53 59 59
p53/SIRT1 0.002 0.047 0.44 2 -0.66 1 3
SIRT1/FOXO4 0.001 0.014 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.038 0.14 -10000 0 -0.57 25 25
HIST1H1E 0.001 0.088 -10000 0 -0.37 14 14
SIRT1/p300 0.001 0.013 -10000 0 -10000 0 0
muscle cell differentiation 0.019 0.093 -10000 0 -10000 0 0
TP53 0 0.043 -10000 0 -0.85 1 1
KU70/SIRT1/BAX -0.001 0.037 -10000 0 -0.54 2 2
CREBBP 0.015 0 -10000 0 -10000 0 0
MEF2D 0.013 0.04 -10000 0 -0.85 1 1
HIV-1 Tat/SIRT1 -0.03 0.12 -10000 0 -0.52 28 28
ACSS2 0.024 0.027 -10000 0 -0.52 1 1
SIRT1/PCAF/MYOD -0.019 0.094 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.011 0.14 -9999 0 -0.73 8 8
BAG4 0.015 0 -9999 0 -10000 0 0
BAD 0.017 0.07 -9999 0 -0.54 4 4
NFKBIA 0.013 0.04 -9999 0 -0.85 1 1
BIRC3 -0.03 0.19 -9999 0 -0.82 25 25
BAX 0.019 0.064 -9999 0 -0.68 2 2
EnzymeConsortium:3.1.4.12 0.006 0.035 -9999 0 -0.12 13 13
IKBKB 0.02 0.13 -9999 0 -0.66 8 8
MAP2K2 0.02 0.11 -9999 0 -0.54 11 11
MAP2K1 0.022 0.098 -9999 0 -0.5 9 9
SMPD1 0.012 0.037 -9999 0 -0.2 2 2
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.021 0.14 -9999 0 -0.68 7 7
MAP2K4 0.028 0.049 -9999 0 -10000 0 0
protein ubiquitination 0.021 0.14 -9999 0 -0.71 8 8
EnzymeConsortium:2.7.1.37 0.025 0.11 -9999 0 -0.48 15 15
response to UV 0 0.001 -9999 0 -0.003 10 10
RAF1 0.015 0.1 -9999 0 -0.49 15 15
CRADD 0.013 0.04 -9999 0 -0.85 1 1
mol:ceramide 0.013 0.05 -9999 0 -0.22 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.027 -9999 0 -0.58 1 1
MADD 0.013 0.04 -9999 0 -0.85 1 1
MAP3K1 0.021 0.049 -9999 0 -0.27 1 1
TRADD 0.011 0.057 -9999 0 -0.85 2 2
RELA/p50 0.015 0 -9999 0 -10000 0 0
MAPK3 0.023 0.11 -9999 0 -0.55 10 10
MAPK1 0.024 0.1 -9999 0 -0.5 10 10
p50/RELA/I-kappa-B-alpha -0.001 0.03 -9999 0 -0.66 1 1
FADD 0.012 0.14 -9999 0 -0.72 7 7
KSR1 0.007 0.11 -9999 0 -0.53 15 15
MAPK8 0.033 0.059 -9999 0 -0.41 3 3
TRAF2 0.011 0.056 -9999 0 -0.85 2 2
response to radiation 0 0.001 -9999 0 -0.003 1 1
CHUK 0.02 0.13 -9999 0 -0.66 8 8
TNF R/SODD 0 0 -9999 0 -10000 0 0
TNF -0.08 0.26 -9999 0 -0.78 56 56
CYCS 0.02 0.075 -9999 0 -0.38 8 8
IKBKG 0.018 0.15 -9999 0 -0.75 8 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.15 -9999 0 -0.79 7 7
RELA 0.015 0 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
AIFM1 0.023 0.067 -9999 0 -0.7 2 2
TNF/TNF R/SODD -0.06 0.16 -9999 0 -0.5 56 56
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
response to heat 0 0.001 -9999 0 -0.003 1 1
CASP8 0.024 0.033 -9999 0 -10000 0 0
NSMAF 0.012 0.14 -9999 0 -0.72 7 7
response to hydrogen peroxide 0 0.001 -9999 0 -0.003 10 10
BCL2 -0.007 0.14 -9999 0 -0.85 12 12
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0.14 -9999 0 -0.6 20 20
KLHL20 -0.017 0.059 -9999 0 -0.36 7 7
CYFIP2 0.001 0.11 -9999 0 -0.81 8 8
Rac1/GDP 0.049 0.097 -9999 0 -10000 0 0
ENAH 0.017 0.14 -9999 0 -0.6 20 20
AP1M1 0.013 0.04 -9999 0 -0.85 1 1
RAP1B 0.013 0.033 -9999 0 -0.69 1 1
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.018 0.07 -9999 0 -0.54 1 1
ABI1/Sra1/Nap1 -0.013 0.045 -9999 0 -0.24 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.038 0.16 -9999 0 -0.65 23 23
RAPGEF1 0.033 0.12 -9999 0 -0.5 21 21
CTNND1 0.015 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.13 -9999 0 -0.63 20 20
CRK 0.026 0.13 -9999 0 -0.55 20 20
E-cadherin/gamma catenin/alpha catenin -0.037 0.14 -9999 0 -0.61 23 23
alphaE/beta7 Integrin -0.013 0.094 -9999 0 -0.67 9 9
IQGAP1 0.015 0 -9999 0 -10000 0 0
NCKAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.4 1 1
DLG1 0.017 0.14 -9999 0 -0.6 20 20
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.055 -9999 0 -0.4 1 1
MLLT4 0.015 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.01 0.07 -9999 0 -0.51 9 9
PI3K -0.02 0.072 -9999 0 -0.56 1 1
ARF6 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.042 0.17 -9999 0 -0.66 30 30
TIAM1 0 0.11 -9999 0 -0.85 8 8
E-cadherin(dimer)/Ca2+ -0.026 0.11 -9999 0 -0.49 20 20
AKT1 -0.012 0.047 -9999 0 -0.47 2 2
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
CDH1 -0.033 0.19 -9999 0 -0.81 27 27
RhoA/GDP 0.048 0.096 -9999 0 -10000 0 0
actin cytoskeleton organization -0.012 0.043 -9999 0 -0.25 7 7
CDC42/GDP 0.048 0.096 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.096 -9999 0 -0.38 23 23
ITGB7 0.002 0.1 -9999 0 -0.85 7 7
RAC1 0.015 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.11 -9999 0 -0.52 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.11 -9999 0 -0.5 20 20
mol:GDP 0.043 0.11 -9999 0 -0.55 1 1
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.006 0.089 -9999 0 -0.85 5 5
p120 catenin/RhoA/GDP -0.02 0.08 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 -0.005 0.069 -9999 0 -0.83 3 3
RHOA 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.029 0.06 -9999 0 -0.28 13 13
NME1 0.013 0.033 -9999 0 -0.69 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.017 0.14 -9999 0 -0.6 20 20
regulation of cell-cell adhesion -0.016 0.061 -9999 0 -0.45 1 1
WASF2 -0.007 0.025 -9999 0 -0.27 1 1
Rap1/GTP -0.021 0.081 -9999 0 -0.64 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.04 0.17 -9999 0 -1 8 8
CCND1 0.033 0.074 -9999 0 -0.36 13 13
VAV2 0.031 0.13 -9999 0 -0.58 2 2
RAP1/GDP -0.019 0.081 -9999 0 -0.63 1 1
adherens junction assembly 0.019 0.13 -9999 0 -0.58 20 20
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.015 0 -9999 0 -10000 0 0
PIP5K1C 0.009 0.069 -9999 0 -0.85 3 3
regulation of heterotypic cell-cell adhesion -0.038 0.16 -9999 0 -0.98 8 8
E-cadherin/beta catenin -0.029 0.11 -9999 0 -0.45 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.015 0.14 -9999 0 -0.6 20 20
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
Rac1/GTP -0.028 0.11 -9999 0 -0.65 8 8
E-cadherin/beta catenin/alpha catenin -0.031 0.12 -9999 0 -0.57 20 20
ITGAE 0.01 0.057 -9999 0 -0.69 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.032 0.13 -9999 0 -0.64 20 20
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.011 0.087 -10000 0 -1 2 2
DAPP1 -0.03 0.23 -10000 0 -0.86 23 23
Src family/SYK family/BLNK-LAT/BTK-ITK -0.046 0.27 -10000 0 -0.9 31 31
mol:DAG 0.014 0.12 -10000 0 -0.35 18 18
HRAS 0.01 0.07 -10000 0 -0.86 3 3
RAP1A 0.015 0.004 -10000 0 -10000 0 0
ARF5/GDP 0.032 0.1 -10000 0 -0.59 10 10
PLCG2 -0.018 0.15 -10000 0 -0.72 21 21
PLCG1 0.015 0 -10000 0 -10000 0 0
ARF5 0.011 0.056 -10000 0 -0.85 2 2
mol:GTP -0.01 0.075 -10000 0 -0.89 1 1
ARF1/GTP -0.011 0.083 -10000 0 -0.76 3 3
RHOA 0.015 0 -10000 0 -10000 0 0
YES1 0.015 0 -10000 0 -10000 0 0
RAP1A/GTP -0.01 0.074 -10000 0 -0.87 1 1
ADAP1 -0.019 0.1 -10000 0 -1 2 2
ARAP3 -0.01 0.075 -10000 0 -0.88 1 1
INPPL1 0.011 0.056 -10000 0 -0.85 2 2
PREX1 0.006 0.089 -10000 0 -0.85 5 5
ARHGEF6 0.013 0.04 -10000 0 -0.85 1 1
ARHGEF7 0.015 0 -10000 0 -10000 0 0
ARF1 0.015 0 -10000 0 -10000 0 0
NRAS 0.015 0.004 -10000 0 -10000 0 0
FYN 0.007 0.08 -10000 0 -0.85 4 4
ARF6 0.015 0 -10000 0 -10000 0 0
FGR -0.003 0.12 -10000 0 -0.8 10 10
mol:Ca2+ 0.021 0.063 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0 0.11 -10000 0 -0.85 8 8
ZAP70 -0.064 0.24 -10000 0 -0.79 46 46
mol:IP3 0.022 0.085 -10000 0 -10000 0 0
LYN 0.011 0.056 -10000 0 -0.85 2 2
ARF1/GDP 0.034 0.097 -10000 0 -0.62 7 7
RhoA/GDP -0.015 0.086 -10000 0 -0.79 3 3
PDK1/Src/Hsp90 -0.004 0.047 -10000 0 -0.57 2 2
BLNK -0.002 0.12 -10000 0 -0.79 10 10
actin cytoskeleton reorganization 0.055 0.11 -10000 0 -0.78 3 3
SRC 0.011 0.056 -10000 0 -0.85 2 2
PLEKHA2 0.026 0.085 -10000 0 -0.64 7 7
RAC1 0.015 0 -10000 0 -10000 0 0
PTEN -0.001 0.039 -10000 0 -0.83 1 1
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
ARF6/GTP -0.012 0.093 -10000 0 -0.96 3 3
RhoA/GTP -0.01 0.07 -10000 0 -0.82 1 1
Src family/SYK family/BLNK-LAT -0.068 0.31 -10000 0 -0.97 36 36
BLK -0.14 0.31 -10000 0 -0.76 92 92
PDPK1 0.015 0 -10000 0 -10000 0 0
CYTH1 -0.01 0.07 -10000 0 -0.82 1 1
HCK 0 0.11 -10000 0 -0.83 8 8
CYTH3 -0.01 0.07 -10000 0 -0.82 1 1
CYTH2 -0.013 0.096 -10000 0 -0.99 3 3
KRAS 0.015 0.004 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.015 0.093 -10000 0 -0.64 9 9
SGK1 -0.017 0.1 -10000 0 -0.71 9 9
INPP5D 0.009 0.069 -10000 0 -0.85 3 3
mol:GDP 0.026 0.1 -10000 0 -0.6 9 9
SOS1 0.015 0 -10000 0 -10000 0 0
SYK 0.004 0.095 -10000 0 -0.82 6 6
ARF6/GDP -0.015 0.086 0.3 1 -0.79 3 4
mol:PI-3-4-5-P3 -0.01 0.076 0.38 1 -0.89 1 2
ARAP3/RAP1A/GTP -0.011 0.075 -10000 0 -0.89 1 1
VAV1 -0.018 0.16 -10000 0 -0.83 18 18
mol:PI-3-4-P2 0.02 0.07 -10000 0 -0.66 5 5
RAS family/GTP/PI3K Class I -0.011 0.075 -10000 0 -0.91 1 1
PLEKHA1 0.028 0.068 -10000 0 -0.57 6 6
Rac1/GDP 0.034 0.097 -10000 0 -0.62 7 7
LAT -0.048 0.21 -10000 0 -0.75 39 39
Rac1/GTP 0.027 0.12 -10000 0 -0.73 9 9
ITK -0.038 0.13 -10000 0 -0.85 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.005 0.16 -10000 0 -0.51 23 23
LCK -0.041 0.21 -10000 0 -0.81 32 32
BTK -0.02 0.1 -10000 0 -0.84 2 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0.04 -10000 0 -0.85 1 1
PTK2 0.015 0 -10000 0 -10000 0 0
CRKL -0.014 0.13 -10000 0 -0.49 13 13
GRB2/SOS1/SHC -0.001 0.02 -10000 0 -10000 0 0
HRAS 0.009 0.069 -10000 0 -0.85 3 3
IRS1/Crk -0.014 0.13 -10000 0 -0.49 13 13
IGF-1R heterotetramer/IGF1/PTP1B -0.034 0.12 -10000 0 -0.53 13 13
AKT1 0.007 0.13 -10000 0 -0.74 4 4
BAD 0.013 0.14 -10000 0 -0.84 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0.13 -10000 0 -0.49 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.042 0.12 -10000 0 -0.5 13 13
RAF1 0.022 0.12 -10000 0 -0.74 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.039 0.11 -10000 0 -0.64 2 2
YWHAZ 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.047 0.13 -10000 0 -0.43 35 35
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
RPS6KB1 0.009 0.12 -10000 0 -0.74 2 2
GNB2L1 0.01 0.065 -10000 0 -0.8 3 3
positive regulation of MAPKKK cascade 0.019 0.1 -10000 0 -0.59 3 3
PXN 0.013 0.033 -10000 0 -0.69 1 1
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.037 0.1 -10000 0 -0.61 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.026 0.091 -10000 0 -10000 0 0
IGF-1R heterotetramer 0 0.074 -10000 0 -0.86 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck -0.043 0.12 -10000 0 -0.5 14 14
Crk/p130 Cas/Paxillin -0.04 0.11 -10000 0 -0.65 3 3
IGF1R 0 0.074 -10000 0 -0.86 3 3
IGF1 -0.037 0.18 -10000 0 -0.74 30 30
IRS2/Crk -0.042 0.19 -10000 0 -0.72 17 17
PI3K -0.045 0.12 -10000 0 -0.5 15 15
apoptosis -0.022 0.12 0.72 4 -10000 0 4
HRAS/GDP -0.004 0.053 -10000 0 -0.66 3 3
PRKCD 0.005 0.14 -10000 0 -0.6 17 17
RAF1/14-3-3 E 0.03 0.11 -10000 0 -0.6 3 3
BAD/14-3-3 0.022 0.13 -10000 0 -0.8 4 4
PRKCZ 0.001 0.14 -10000 0 -0.73 6 6
Crk/p130 Cas/Paxillin/FAK1 -0.034 0.095 -10000 0 -0.64 3 3
PTPN1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.12 -10000 0 -0.52 14 14
BCAR1 0.009 0.069 -10000 0 -0.85 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.031 0.11 -10000 0 -0.5 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.015 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.016 0.13 -10000 0 -0.49 14 14
GRB10 0.013 0.04 -10000 0 -0.85 1 1
PTPN11 -0.014 0.13 -10000 0 -0.49 13 13
IRS1 -0.026 0.14 -10000 0 -0.43 35 35
IRS2 -0.053 0.2 -10000 0 -0.65 26 26
IGF-1R heterotetramer/IGF1 -0.045 0.15 -10000 0 -0.57 33 33
GRB2 0.015 0 -10000 0 -10000 0 0
PDPK1 -0.001 0.13 -10000 0 -0.81 2 2
YWHAE 0.015 0 -10000 0 -10000 0 0
PRKD1 0.011 0.12 -10000 0 -0.52 12 12
SHC1 0.013 0.033 -10000 0 -0.69 1 1
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.037 0.099 -10000 0 -0.69 5 5
adherens junction organization 0.012 0.12 -10000 0 -0.61 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.027 0.13 -10000 0 -0.66 6 6
FMN1 -0.021 0.17 -10000 0 -0.48 39 39
mol:IP3 -0.017 0.07 -10000 0 -0.55 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.019 0.1 -10000 0 -0.65 4 4
CTNNB1 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.034 0.1 -10000 0 -0.68 5 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.15 -10000 0 -0.63 22 22
CTNND1 0.016 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.095 -10000 0 -0.67 3 3
VASP 0.028 0.098 -10000 0 -0.69 3 3
ZYX 0.025 0.12 -10000 0 -0.82 5 5
JUB 0.019 0.13 -10000 0 -0.62 12 12
EGFR(dimer) 0.005 0.15 -10000 0 -0.59 17 17
E-cadherin/beta catenin-gamma catenin -0.035 0.14 -10000 0 -0.56 30 30
mol:PI-3-4-5-P3 -0.02 0.079 -10000 0 -0.56 6 6
PIK3CA 0.014 0.04 -10000 0 -0.85 1 1
PI3K -0.02 0.081 -10000 0 -0.57 6 6
FYN -0.11 0.2 -10000 0 -0.62 13 13
mol:Ca2+ -0.016 0.068 -10000 0 -0.53 4 4
JUP 0.006 0.089 -10000 0 -0.85 5 5
PIK3R1 0.006 0.086 -10000 0 -0.75 6 6
mol:DAG -0.017 0.07 -10000 0 -0.55 4 4
CDH1 -0.033 0.19 -10000 0 -0.81 27 27
RhoA/GDP 0.027 0.13 -10000 0 -0.66 6 6
establishment of polarity of embryonic epithelium 0.028 0.095 -10000 0 -0.67 3 3
SRC 0.011 0.056 -10000 0 -0.85 2 2
RAC1 0.015 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
EGFR -0.023 0.17 -10000 0 -0.8 22 22
CASR -0.14 0.23 -10000 0 -0.67 13 13
RhoA/GTP -0.015 0.061 -10000 0 -0.5 3 3
AKT2 0.034 0.1 -10000 0 -0.68 5 5
actin cable formation -0.012 0.17 -10000 0 -0.58 7 7
apoptosis 0.02 0.089 0.62 7 -10000 0 7
CTNNA1 0.016 0.002 -10000 0 -10000 0 0
mol:GDP 0.019 0.14 -10000 0 -0.73 6 6
PIP5K1A 0.028 0.098 -10000 0 -0.69 3 3
PLCG1 -0.017 0.072 -10000 0 -0.56 4 4
Rac1/GTP -0.036 0.12 -10000 0 -0.7 7 7
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.029 0.18 -9999 0 -0.74 27 27
CDC42/GTP -0.027 0.1 -9999 0 -0.8 4 4
PLCG1 0.016 0.12 -9999 0 -0.83 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.024 -9999 0 -0.52 1 1
cell migration -0.027 0.098 -9999 0 -0.76 4 4
S1PR5 -0.03 0.19 -9999 0 -0.82 25 25
S1PR4 -0.01 0.14 -9999 0 -0.83 14 14
MAPK3 0.014 0.12 -9999 0 -0.76 6 6
MAPK1 0.016 0.12 -9999 0 -0.83 4 4
S1P/S1P5/Gi -0.002 0.14 -9999 0 -0.49 28 28
GNAI1 0.009 0.069 -9999 0 -0.85 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.031 0.13 -9999 0 -0.55 26 26
RHOA 0.022 0.088 -9999 0 -0.49 12 12
S1P/S1P4/Gi 0.007 0.12 -9999 0 -0.45 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.1 -9999 0 -0.79 8 8
S1P/S1P4/G12/G13 -0.016 0.088 -9999 0 -0.52 12 12
GNA12 0.013 0.033 -9999 0 -0.69 1 1
GNA13 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.015 0 -10000 0 -10000 0 0
NFATC1 0.051 0.079 -10000 0 -0.7 2 2
NFATC2 0.015 0.08 -10000 0 -0.37 6 6
NFATC3 0.015 0.072 -10000 0 -0.55 7 7
YWHAE 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.004 0.14 -10000 0 -0.66 13 13
Exportin 1/Ran/NUP214 -0.001 0.026 -10000 0 -0.57 1 1
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.041 0.15 -10000 0 -0.82 14 14
BCL2/BAX -0.02 0.11 -10000 0 -0.66 14 14
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.007 -10000 0 -10000 0 0
BAX 0.011 0.056 -10000 0 -0.85 2 2
MAPK14 0.013 0.006 -10000 0 -10000 0 0
BAD 0.008 0.076 -10000 0 -0.81 4 4
CABIN1/MEF2D 0.009 0.13 -10000 0 -0.8 8 8
Calcineurin A alpha-beta B1/BCL2 -0.007 0.14 -10000 0 -0.85 12 12
FKBP8 0.009 0.069 -10000 0 -0.85 3 3
activation-induced cell death of T cells -0.009 0.13 0.7 10 -10000 0 10
KPNB1 0.015 0 -10000 0 -10000 0 0
KPNA2 0.006 0.08 -10000 0 -0.69 6 6
XPO1 0.015 0.001 -10000 0 -10000 0 0
SFN -0.19 0.34 -10000 0 -0.74 125 125
MAP3K8 0.006 0.073 -10000 0 -0.78 4 4
NFAT4/CK1 alpha -0.006 0.045 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.06 0.13 -10000 0 -0.56 10 10
CABIN1 0.004 0.14 -10000 0 -0.67 13 13
CALM1 0.013 0.006 -10000 0 -10000 0 0
RAN 0.015 0.001 -10000 0 -10000 0 0
MAP3K1 0.015 0 -10000 0 -10000 0 0
CAMK4 -0.011 0.14 -10000 0 -0.84 14 14
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.056 -10000 0 -0.85 2 2
YWHAH 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.02 0.11 -10000 0 -0.58 16 16
YWHAB 0.015 0 -10000 0 -10000 0 0
MAPK8 0.008 0.069 -10000 0 -0.85 3 3
MAPK9 0.015 0 -10000 0 -10000 0 0
YWHAG 0.015 0 -10000 0 -10000 0 0
FKBP1A 0.015 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.012 0.071 -10000 0 -0.64 3 3
PRKCH 0.004 0.097 -10000 0 -0.85 6 6
CABIN1/Cbp/p300 0 0.002 -10000 0 -10000 0 0
CASP3 0.011 0.033 -10000 0 -0.7 1 1
PIM1 0.01 0.057 -10000 0 -0.69 3 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.01 0.072 -10000 0 -0.97 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.096 -10000 0 -0.61 1 1
PRKCB -0.017 0.16 -10000 0 -0.82 18 18
PRKCE 0.011 0.052 -10000 0 -0.77 2 2
JNK2/NFAT4 0.02 0.066 -10000 0 -0.5 7 7
BAD/BCL-XL -0.005 0.057 -10000 0 -0.62 4 4
PRKCD -0.002 0.11 -10000 0 -0.69 11 11
NUP214 0.013 0.04 -10000 0 -0.85 1 1
PRKCZ -0.001 0.11 -10000 0 -0.83 8 8
PRKCA 0.004 0.089 -10000 0 -0.72 7 7
PRKCG -0.021 0.14 -10000 0 -0.69 19 19
PRKCQ -0.019 0.16 -10000 0 -0.79 20 20
FKBP38/BCL2 -0.021 0.12 -10000 0 -0.66 15 15
EP300 0.014 0.004 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.088 -10000 0 -0.71 2 2
CaM/Ca2+/FKBP38 -0.004 0.046 -10000 0 -0.58 3 3
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.021 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.017 0.097 -10000 0 -0.57 14 14
NFATc/ERK1 0.056 0.091 -10000 0 -0.96 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.04 0.15 -10000 0 -0.83 13 13
NR4A1 -0.047 0.28 -10000 0 -0.66 76 76
GSK3B 0.013 0.006 -10000 0 -10000 0 0
positive T cell selection 0.015 0.072 -10000 0 -0.55 7 7
NFAT1/CK1 alpha -0.019 0.049 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.007 0.058 -10000 0 -0.52 6 6
YWHAQ 0.015 0 -10000 0 -10000 0 0
PRKACA 0.013 0.006 -10000 0 -10000 0 0
AKAP5 -0.012 0.14 -10000 0 -0.76 16 16
MEF2D 0.012 0.041 -10000 0 -0.86 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.015 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.051 0.078 -10000 0 -0.82 1 1
CREBBP 0.014 0.004 -10000 0 -10000 0 0
BCL2 -0.007 0.14 -10000 0 -0.85 12 12
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.085 0.061 -9999 0 -10000 0 0
ERC1 0.015 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.039 0.15 -9999 0 -0.59 31 31
NFKBIA 0.054 0.042 -9999 0 -0.85 1 1
BIRC2 0.015 0 -9999 0 -10000 0 0
IKBKB 0.015 0 -9999 0 -10000 0 0
RIPK2 0.012 0.046 -9999 0 -0.69 2 2
IKBKG -0.018 0.071 -9999 0 -0.49 5 5
IKK complex/A20 -0.057 0.14 -9999 0 -0.74 5 5
NEMO/A20/RIP2 0.012 0.046 -9999 0 -0.69 2 2
XPO1 0.015 0 -9999 0 -10000 0 0
NEMO/ATM 0.038 0.084 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.014 0.057 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.004 0.045 -9999 0 -0.57 3 3
NOD2 -0.035 0.19 -9999 0 -0.79 29 29
NFKB1 0.019 0.006 -9999 0 -10000 0 0
RELA 0.019 0.006 -9999 0 -10000 0 0
MALT1 0.011 0.056 -9999 0 -0.85 2 2
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.013 0.04 -9999 0 -0.85 1 1
TNF/TNFR1A -0.07 0.19 -9999 0 -0.59 56 56
TRAF6 0.013 0.04 -9999 0 -0.85 1 1
PRKCA 0.004 0.089 -9999 0 -0.72 7 7
CHUK 0.015 0 -9999 0 -10000 0 0
UBE2D3 0.015 0 -9999 0 -10000 0 0
TNF -0.08 0.26 -9999 0 -0.78 56 56
NF kappa B1 p50/RelA -0.001 0.016 -9999 0 -10000 0 0
BCL10 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.054 0.041 -9999 0 -0.84 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.006 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
IKK complex -0.016 0.062 -9999 0 -10000 0 0
CYLD 0.015 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.02 0.079 -9999 0 -0.77 2 2
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.009 0.075 -9999 0 -0.62 7 7
FBXW11 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.012 0.1 -9999 0 -0.57 14 14
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.1 -9999 0 -0.69 5 5
NFKBIA 0.007 0.11 -9999 0 -0.66 8 8
MAPK14 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0 -9999 0 -10000 0 0
ARRB2 0.02 0.015 -9999 0 -10000 0 0
REL -0.012 0.15 -9999 0 -0.84 15 15
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.023 0.068 -9999 0 -0.57 5 5
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.04 -9999 0 -0.85 1 1
NF kappa B1 p50 dimer 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.005 0.086 -9999 0 -0.75 6 6
NFKB1 0.027 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.091 -9999 0 -0.54 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.036 0.099 -9999 0 -0.67 5 5
SRC 0.011 0.056 -9999 0 -0.85 2 2
PI3K -0.009 0.07 -9999 0 -0.57 7 7
NF kappa B1 p50/RelA 0.019 0.092 -9999 0 -0.54 5 5
IKBKB 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
SYK 0.004 0.095 -9999 0 -0.82 6 6
I kappa B alpha/PIK3R1 0.009 0.12 -9999 0 -0.68 9 9
cell death -0.019 0.081 -9999 0 -0.63 5 5
NF kappa B1 p105/c-Rel 0.012 0.1 -9999 0 -0.57 14 14
LCK -0.041 0.21 -9999 0 -0.81 32 32
BCL3 0.003 0.1 -9999 0 -0.81 7 7
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.013 0.099 -10000 0 -0.68 9 9
HDAC3 0.015 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.015 -10000 0 -10000 0 0
GATA1/HDAC4 -0.021 0.1 -10000 0 -0.52 19 19
GATA1/HDAC5 -0.024 0.11 -10000 0 -0.54 21 21
GATA2/HDAC5 -0.035 0.14 -10000 0 -0.61 27 27
HDAC5/BCL6/BCoR -0.009 0.072 -10000 0 -0.57 7 7
HDAC9 0.004 0.097 -10000 0 -0.85 6 6
Glucocorticoid receptor/Hsp90/HDAC6 -0.005 0.059 -10000 0 -0.6 4 4
HDAC4/ANKRA2 -0.001 0.024 -10000 0 -0.52 1 1
HDAC5/YWHAB -0.004 0.052 -10000 0 -0.66 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.024 0.025 -10000 0 -10000 0 0
GATA2 -0.026 0.18 -10000 0 -0.79 24 24
HDAC4/RFXANK -0.004 0.049 -10000 0 -0.61 3 3
BCOR 0.013 0.04 -10000 0 -0.85 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.009 0.069 -10000 0 -0.85 3 3
HDAC5 0.009 0.069 -10000 0 -0.85 3 3
GNB1/GNG2 -0.008 0.074 -10000 0 -0.66 6 6
Histones 0.03 0.15 -10000 0 -1.2 5 5
ADRBK1 0.009 0.069 -10000 0 -0.85 3 3
HDAC4 0.013 0.033 -10000 0 -0.69 1 1
XPO1 0.015 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.004 0.052 -10000 0 -0.66 3 3
HDAC4/Ubc9 -0.001 0.024 -10000 0 -0.52 1 1
HDAC7 0.009 0.069 -10000 0 -0.85 3 3
HDAC5/14-3-3 E -0.004 0.052 -10000 0 -0.66 3 3
TUBA1B 0.015 0 -10000 0 -10000 0 0
HDAC6 0.011 0.056 -10000 0 -0.85 2 2
HDAC5/RFXANK -0.006 0.083 -10000 0 -1 3 3
CAMK4 -0.011 0.14 -10000 0 -0.84 14 14
Tubulin/HDAC6 -0.016 0.092 -10000 0 -0.74 3 3
SUMO1 0.015 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
GATA1 -0.015 0.14 -10000 0 -0.69 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.015 0 -10000 0 -10000 0 0
NR3C1 0.013 0.033 -10000 0 -0.69 1 1
SUMO1/HDAC4 0.033 0.03 -10000 0 -0.36 1 1
SRF 0.013 0.04 -10000 0 -0.85 1 1
HDAC4/YWHAB -0.001 0.024 -10000 0 -0.52 1 1
Tubulin -0.016 0.092 -10000 0 -0.54 14 14
HDAC4/14-3-3 E -0.001 0.024 -10000 0 -0.52 1 1
GNB1 0.015 0 -10000 0 -10000 0 0
RANGAP1 0.009 0.069 -10000 0 -0.85 3 3
BCL6/BCoR -0.007 0.065 -10000 0 -0.63 5 5
HDAC4/HDAC3/SMRT (N-CoR2) -0.005 0.049 -10000 0 -0.53 4 4
HDAC4/SRF -0.019 0.1 -10000 0 -0.6 14 14
HDAC4/ER alpha -0.021 0.11 -10000 0 -0.6 16 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.14 -10000 0 -1.1 5 5
cell motility -0.016 0.092 -10000 0 -0.73 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.015 0 -10000 0 -10000 0 0
HDAC7/HDAC3 -0.004 0.052 -10000 0 -0.66 3 3
BCL6 0.008 0.076 -10000 0 -0.81 4 4
HDAC4/CaMK II delta B 0.013 0.033 -10000 0 -0.69 1 1
Hsp90/HDAC6 -0.005 0.054 -10000 0 -0.58 4 4
ESR1 -0.011 0.14 -10000 0 -0.8 15 15
HDAC6/HDAC11 -0.009 0.08 -10000 0 -0.67 6 6
Ran/GTP/Exportin 1 -0.002 0.019 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.004 0.12 -10000 0 -0.85 10 10
RAN 0.015 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.014 0.081 -10000 0 -10000 0 0
GNG2 0.004 0.097 -10000 0 -0.85 6 6
NCOR2 0.009 0.069 -10000 0 -0.85 3 3
TUBB2A -0.007 0.12 -10000 0 -0.72 14 14
HDAC11 0.007 0.08 -10000 0 -0.76 5 5
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
RANBP2 0.015 0 -10000 0 -10000 0 0
ANKRA2 0.015 0 -10000 0 -10000 0 0
RFXANK 0.011 0.056 -10000 0 -0.85 2 2
nuclear import 0.004 0.039 0.46 3 -10000 0 3
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.008 0.053 -10000 0 -0.73 1 1
CLOCK 0.007 0.097 -10000 0 -0.84 6 6
TIMELESS/CRY2 0.041 0.071 -10000 0 -0.72 3 3
DEC1/BMAL1 0 0.002 -10000 0 -10000 0 0
ATR 0.015 0 -10000 0 -10000 0 0
NR1D1 0.034 0.14 -10000 0 -1.4 4 4
ARNTL 0.018 0.005 -10000 0 -10000 0 0
TIMELESS 0.04 0.066 -10000 0 -0.71 2 2
NPAS2 -0.012 0.16 -10000 0 -0.83 17 17
CRY2 0.013 0.04 -10000 0 -0.85 1 1
mol:CO -0.015 0.016 0.14 5 -10000 0 5
CHEK1 0.012 0.046 -10000 0 -0.69 2 2
mol:HEME 0.015 0.016 -10000 0 -0.14 5 5
PER1 0.002 0.1 -10000 0 -0.85 7 7
BMAL/CLOCK/NPAS2 0.02 0.13 -10000 0 -0.58 20 20
BMAL1/CLOCK 0.037 0.13 -10000 0 -0.99 5 5
S phase of mitotic cell cycle -0.008 0.053 -10000 0 -0.73 1 1
TIMELESS/CHEK1/ATR -0.008 0.053 -10000 0 -0.75 1 1
mol:NADPH 0.015 0.016 -10000 0 -0.14 5 5
PER1/TIMELESS 0.034 0.094 -10000 0 -0.74 3 3
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.015 0 -10000 0 -10000 0 0
mol:PIP3 -0.017 0.075 0.34 1 -0.4 12 13
FRAP1 0.015 0.026 -10000 0 -10000 0 0
AKT1 -0.017 0.08 0.25 1 -0.6 5 6
INSR -0.004 0.12 -10000 0 -0.85 10 10
Insulin Receptor/Insulin -0.012 0.085 -10000 0 -0.59 10 10
mol:GTP -0.015 0.073 -10000 0 -0.7 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.018 -10000 0 -10000 0 0
TSC2 0.009 0.069 -10000 0 -0.85 3 3
RHEB/GDP -0.014 0.065 -10000 0 -0.61 3 3
TSC1 0.015 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.007 0.1 -10000 0 -0.52 14 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.015 0 -10000 0 -10000 0 0
RPS6KB1 0.023 0.05 -10000 0 -0.41 2 2
MAP3K5 0.012 0.022 -10000 0 -0.46 1 1
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
apoptosis 0.012 0.022 -10000 0 -0.46 1 1
mol:LY294002 0 0 0.001 1 -0.001 23 24
EIF4B 0.03 0.045 -10000 0 -0.41 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.009 0.039 -10000 0 -0.38 1 1
eIF4E/eIF4G1/eIF4A1 -0.002 0.015 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.008 0.084 -10000 0 -0.42 12 12
mTOR/RHEB/GTP/Raptor/GBL 0.029 0.038 -10000 0 -0.24 1 1
FKBP1A 0.015 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.013 0.063 -10000 0 -0.6 3 3
mol:Amino Acids 0 0 0.001 1 -0.001 23 24
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.015 0.068 0.27 1 -0.49 3 4
EIF4E 0.015 0 -10000 0 -10000 0 0
ASK1/PP5C 0.02 0.039 -10000 0 -0.64 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.015 -10000 0 -10000 0 0
TSC1/TSC2 -0.016 0.082 -10000 0 -0.81 3 3
tumor necrosis factor receptor activity 0 0 0.001 23 -0.001 1 24
RPS6 0.01 0.057 -10000 0 -0.69 3 3
PPP5C 0.011 0.056 -10000 0 -0.85 2 2
EIF4G1 0.015 0 -10000 0 -10000 0 0
IRS1 -0.006 0.071 -10000 0 -0.3 24 24
INS 0 0 -10000 0 -10000 0 0
PTEN 0.013 0.04 -10000 0 -0.85 1 1
PDK2 -0.018 0.081 0.27 1 -0.53 6 7
EIF4EBP1 -0.018 0.18 -10000 0 -1.2 10 10
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
PPP2R5D 0.021 0.033 -10000 0 -0.34 1 1
peptide biosynthetic process 0.005 0.09 -10000 0 -0.53 13 13
RHEB 0.013 0.033 -10000 0 -0.69 1 1
EIF4A1 0.015 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 1 -0.004 5 6
EEF2 0.005 0.091 -10000 0 -0.53 13 13
eIF4E/4E-BP1 -0.008 0.17 -10000 0 -1.1 10 10
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.004 0.045 -10000 0 -0.52 3 3
CDKN1B 0.041 0.049 -10000 0 -0.68 2 2
CDKN1A 0.037 0.072 -10000 0 -0.76 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
FOXO3 0.041 0.049 -10000 0 -0.68 2 2
AKT1 -0.004 0.049 -10000 0 -0.72 2 2
BAD 0.008 0.076 -10000 0 -0.81 4 4
AKT3 0.014 0.054 -10000 0 -0.46 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.041 0.049 -10000 0 -0.68 2 2
AKT1/ASK1 -0.004 0.049 -10000 0 -0.59 3 3
BAD/YWHAZ -0.005 0.049 -10000 0 -0.53 4 4
RICTOR 0.015 0 -10000 0 -10000 0 0
RAF1 0.015 0 -10000 0 -10000 0 0
JNK cascade 0.004 0.047 0.56 3 -10000 0 3
TSC1 0.041 0.049 -10000 0 -0.68 2 2
YWHAZ 0.015 0 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.049 -10000 0 -0.68 2 2
EP300 0.015 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.048 -10000 0 -0.71 2 2
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.038 0.083 -10000 0 -0.96 3 3
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.021 0.061 -10000 0 -0.44 8 8
MAP3K5 0.013 0.04 -10000 0 -0.85 1 1
MAPKAP1 0.015 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.07 0.41 1 -10000 0 1
YWHAH 0.015 0 -10000 0 -10000 0 0
AKT1S1 0.04 0.066 -10000 0 -0.89 2 2
CASP9 0.041 0.049 -10000 0 -0.68 2 2
YWHAB 0.015 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.048 0.047 -10000 0 -0.63 2 2
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.004 0.047 -10000 0 -0.57 2 2
YWHAE 0.015 0 -10000 0 -10000 0 0
SRC 0.011 0.056 -10000 0 -0.85 2 2
AKT2/p21CIP1 -0.007 0.072 -10000 0 -0.82 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.015 -10000 0 -10000 0 0
CHUK 0.041 0.049 -10000 0 -0.68 2 2
BAD/BCL-XL 0.052 0.078 -10000 0 -0.87 3 3
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.018 0.031 -10000 0 -0.46 2 2
FOXO1-3a-4/14-3-3 family 0.024 0.087 -10000 0 -0.74 1 1
PDPK1 0.015 0 -10000 0 -10000 0 0
MDM2 0.041 0.049 -10000 0 -0.68 2 2
MAPKKK cascade -0.039 0.048 0.66 2 -10000 0 2
MDM2/Cbp/p300 0.054 0.045 -10000 0 -0.74 1 1
TSC1/TSC2 0.045 0.08 -10000 0 -0.91 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.038 -10000 0 -0.57 2 2
glucose import -0.011 0.16 -10000 0 -0.56 27 27
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.035 0.032 -10000 0 -0.41 2 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.16 -10000 0 -0.57 27 27
GSK3A 0.039 0.077 -10000 0 -1.1 2 2
FOXO1 0.037 0.061 -10000 0 -0.68 2 2
GSK3B 0.041 0.049 -10000 0 -0.68 2 2
SFN -0.19 0.34 -10000 0 -0.74 125 125
G1/S transition of mitotic cell cycle 0.047 0.074 -10000 0 -1.1 2 2
p27Kip1/14-3-3 family -0.002 0.1 -10000 0 -10000 0 0
PRKACA 0.015 0 -10000 0 -10000 0 0
KPNA1 0.015 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0.046 -10000 0 -0.69 2 2
YWHAG 0.015 0 -10000 0 -10000 0 0
RHEB 0.013 0.033 -10000 0 -0.69 1 1
CREBBP 0.015 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -10000 0 -10000 0 0
HDAC3 0.015 0 -10000 0 -10000 0 0
VDR -0.007 0.13 -10000 0 -0.73 14 14
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.015 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.041 0.06 -10000 0 -0.42 3 3
KAT2B 0.015 0 -10000 0 -10000 0 0
MAPK14 0.015 0 -10000 0 -10000 0 0
AKT1 0.016 0.079 0.25 1 -0.44 10 11
RAR alpha/9cRA/Cyclin H -0.013 0.06 -10000 0 -0.51 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.037 0.065 -10000 0 -0.43 4 4
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.003 0.081 -10000 0 -0.63 5 5
NCOR2 0.009 0.069 -10000 0 -0.85 3 3
VDR/VDR/Vit D3 -0.017 0.095 -10000 0 -0.56 14 14
RXRs/RARs/NRIP1/9cRA 0.037 0.12 -10000 0 -0.75 4 4
NCOA2 -0.026 0.18 -10000 0 -0.85 22 22
NCOA3 0.015 0 -10000 0 -10000 0 0
NCOA1 0.015 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.007 0.13 -10000 0 -0.73 14 14
RARG 0.009 0.08 -10000 0 -0.85 4 4
RAR gamma1/9cRA -0.005 0.053 -10000 0 -0.58 4 4
MAPK3 0.012 0.057 -10000 0 -0.85 2 2
MAPK1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.011 0.069 -10000 0 -0.85 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.032 0.099 -10000 0 -0.57 5 5
RARA 0.016 0.073 -10000 0 -0.41 8 8
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.022 0.1 -10000 0 -0.57 6 6
PRKCA 0.008 0.089 -10000 0 -0.71 7 7
RXRs/RARs/NRIP1/9cRA/HDAC1 0.032 0.11 -10000 0 -0.66 5 5
RXRG -0.003 0.11 -10000 0 -0.5 8 8
RXRA 0.025 0.074 -10000 0 -0.47 5 5
RXRB 0.011 0.085 -10000 0 -0.53 4 4
VDR/Vit D3/DNA -0.017 0.095 -10000 0 -0.56 14 14
RBP1 0 0.11 -10000 0 -0.76 9 9
CRBP1/9-cic-RA -0.011 0.081 -10000 0 -0.59 9 9
RARB 0.001 0.12 -10000 0 -0.85 9 9
PRKCG -0.017 0.14 -10000 0 -0.69 19 19
MNAT1 0.015 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.032 0.11 -10000 0 -0.67 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.035 0.12 -10000 0 -0.74 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.073 -10000 0 -0.48 4 4
RXRs/RARs/NRIP1/9cRA/HDAC3 0.032 0.11 -10000 0 -0.66 5 5
positive regulation of DNA binding -0.013 0.057 -10000 0 -0.48 2 2
NRIP1 0.029 0.14 -10000 0 -1.1 4 4
RXRs/RARs 0.026 0.11 -10000 0 -0.61 5 5
RXRs/RXRs/DNA/9cRA -0.023 0.084 -10000 0 -0.55 6 6
PRKACA 0.015 0 -10000 0 -10000 0 0
CDK7 0.015 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.008 0.039 -10000 0 -10000 0 0
CCNH 0.015 0 -10000 0 -10000 0 0
CREBBP 0.015 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.004 0.041 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.015 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.013 -10000 0 -10000 0 0
DOCK1 0.015 0 -10000 0 -10000 0 0
ITGA4 -0.011 0.14 -10000 0 -0.84 14 14
RAC1 0.015 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.029 0.14 -10000 0 -0.7 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.017 0.095 -10000 0 -0.56 14 14
alpha4/beta7 Integrin/Paxillin -0.024 0.12 -10000 0 -0.57 18 18
lamellipodium assembly -0.006 0.06 -10000 0 -0.54 4 4
PIK3CA 0.013 0.04 -10000 0 -0.85 1 1
PI3K -0.009 0.07 -10000 0 -0.57 7 7
ARF6 0.015 0 -10000 0 -10000 0 0
TLN1 0.013 0.04 -10000 0 -0.85 1 1
PXN 0.026 0.025 -10000 0 -0.52 1 1
PIK3R1 0.005 0.086 -10000 0 -0.75 6 6
ARF6/GTP -0.015 0.084 -10000 0 -0.78 1 1
cell adhesion -0.016 0.084 -10000 0 -10000 0 0
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.016 0.088 -10000 0 -0.52 13 13
ITGB1 0.015 0 -10000 0 -10000 0 0
ITGB7 0.002 0.1 -10000 0 -0.85 7 7
ARF6/GDP 0.002 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.059 0.19 -10000 0 -0.96 11 11
p130Cas/Crk/Dock1 -0.004 0.045 -10000 0 -0.57 3 3
VCAM1 -0.064 0.25 -10000 0 -0.85 43 43
alpha4/beta1 Integrin/Paxillin/Talin -0.016 0.085 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.017 0.092 -10000 0 -0.86 1 1
BCAR1 0.009 0.069 -10000 0 -0.85 3 3
mol:GDP 0.017 0.091 0.84 1 -10000 0 1
CBL 0.015 0 -10000 0 -10000 0 0
PRKACA 0.015 0 -10000 0 -10000 0 0
GIT1 0.011 0.056 -10000 0 -0.85 2 2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.016 0.085 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.067 -10000 0 -0.62 4 4
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.05 0.22 -10000 0 -0.78 38 38
CLTC 0.035 0.028 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.028 0.041 -10000 0 -0.74 1 1
Dynamin 2/GTP -0.003 0.039 -10000 0 -0.48 3 3
EXOC4 0.015 0 -10000 0 -10000 0 0
CD59 0.032 0.02 -10000 0 -10000 0 0
CPE -0.03 0.16 -10000 0 -0.48 48 48
CTNNB1 0.015 0 -10000 0 -10000 0 0
membrane fusion -0.003 0.038 -10000 0 -0.71 1 1
CTNND1 0.035 0.039 -10000 0 -0.49 2 2
DNM2 0.011 0.056 -10000 0 -0.85 2 2
mol:PI-4-5-P2 0.033 0.063 -10000 0 -0.87 2 2
TSHR -0.055 0.2 -10000 0 -0.54 65 65
INS 0.013 0.014 -10000 0 -10000 0 0
BIN1 0.011 0.052 -10000 0 -0.77 2 2
mol:Choline -0.003 0.038 -10000 0 -0.71 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.022 -10000 0 -0.44 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.039 -10000 0 -0.48 3 3
JUP 0.029 0.045 -10000 0 -0.51 2 2
ASAP2/amphiphysin II -0.002 0.03 -10000 0 -0.46 2 2
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.016 0.07 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 -0.031 0.19 -10000 0 -0.81 26 26
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.015 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.047 0.053 -10000 0 -0.74 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.015 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.013 0.055 0.54 2 -10000 0 2
positive regulation of phagocytosis 0.022 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.03 0.12 -10000 0 -0.54 26 26
ACAP1 0.019 0.057 -10000 0 -0.46 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.017 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.039 0.049 -10000 0 -0.63 2 2
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.015 0 -10000 0 -10000 0 0
exocyst 0.047 0.054 -10000 0 -0.75 2 2
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.035 0.039 -10000 0 -0.49 2 2
NME1 0.021 0.022 -10000 0 -0.45 1 1
clathrin coat assembly 0.035 0.028 -10000 0 -10000 0 0
IL2RA -0.005 0.095 -10000 0 -0.39 2 2
VAMP3 0.022 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.035 0.12 -10000 0 -0.46 25 25
EXOC6 0.015 0 -10000 0 -10000 0 0
PLD1 -0.002 0.023 -10000 0 -0.35 2 2
PLD2 -0.004 0.047 -10000 0 -0.47 4 4
EXOC5 0.015 0 -10000 0 -10000 0 0
PIP5K1C 0.033 0.065 -10000 0 -0.9 2 2
SDC1 0.019 0.064 -10000 0 -0.39 2 2
ARF6/GDP 0.02 0.021 -10000 0 -0.44 1 1
EXOC7 0.011 0.056 -10000 0 -0.85 2 2
E-cadherin/beta catenin -0.013 0.057 -10000 0 -0.57 2 2
mol:Phosphatidic acid -0.003 0.038 -10000 0 -0.71 1 1
endocytosis 0.002 0.03 0.46 2 -10000 0 2
SCAMP2 0.013 0.04 -10000 0 -0.85 1 1
ADRB2 0.031 0.078 -10000 0 -0.45 7 7
EXOC3 0.008 0.073 -10000 0 -0.77 4 4
ASAP2 0.015 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.041 -10000 0 -0.48 3 3
KLC1 0.015 0 -10000 0 -10000 0 0
AVPR2 -0.015 0.16 -10000 0 -0.48 27 27
RALA 0.015 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.05 -10000 0 -0.56 1 1
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.019 0.11 -9999 0 -0.64 14 14
FBXW11 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.022 0.14 -9999 0 -1.1 6 6
NFKB1 0.015 0 -9999 0 -10000 0 0
MAP3K14 -0.011 0.14 -9999 0 -0.84 14 14
NF kappa B1 p50/RelB -0.003 0.043 -9999 0 -0.66 2 2
RELB 0.011 0.056 -9999 0 -0.85 2 2
NFKB2 0.004 0.097 -9999 0 -0.85 6 6
NF kappa B2 p52/RelB -0.01 0.088 -9999 0 -0.75 6 6
regulation of B cell activation -0.009 0.088 -9999 0 -0.74 6 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.008 0.21 -10000 0 -1.2 9 9
regulation of axonogenesis -0.025 0.05 0.37 2 -10000 0 2
myoblast fusion -0.004 0.095 0.58 7 -10000 0 7
mol:GTP -0.01 0.044 -10000 0 -0.3 4 4
regulation of calcium-dependent cell-cell adhesion -0.02 0.095 0.59 9 -10000 0 9
ARF1/GTP -0.007 0.03 -10000 0 -10000 0 0
mol:GM1 0.005 0.036 -10000 0 -0.25 2 2
mol:Choline 0.022 0.068 -10000 0 -0.57 5 5
lamellipodium assembly -0.016 0.08 -10000 0 -0.48 7 7
MAPK3 0.017 0.09 -10000 0 -0.66 4 4
ARF6/GTP/NME1/Tiam1 0.021 0.096 -10000 0 -0.6 9 9
ARF1 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.09 -10000 0 -0.58 7 7
ARF1/GDP 0.015 0.089 -10000 0 -0.63 5 5
ARF6 0.008 0.025 -10000 0 -10000 0 0
RAB11A 0.015 0 -10000 0 -10000 0 0
TIAM1 0.001 0.11 -10000 0 -0.85 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.066 -10000 0 -0.39 3 3
actin filament bundle formation 0.017 0.082 0.63 5 -10000 0 5
KALRN -0.016 0.088 -10000 0 -0.71 5 5
RAB11FIP3/RAB11A -0.004 0.049 -10000 0 -0.61 3 3
RhoA/GDP -0.017 0.083 -10000 0 -0.63 5 5
NME1 0.015 0.034 -10000 0 -0.72 1 1
Rac1/GDP -0.017 0.083 -10000 0 -0.63 5 5
substrate adhesion-dependent cell spreading -0.01 0.044 -10000 0 -0.3 4 4
cortical actin cytoskeleton organization -0.016 0.081 -10000 0 -0.49 7 7
RAC1 0.015 0 -10000 0 -10000 0 0
liver development -0.01 0.044 -10000 0 -0.3 4 4
ARF6/GTP -0.01 0.044 -10000 0 -0.3 4 4
RhoA/GTP -0.007 0.03 -10000 0 -10000 0 0
mol:GDP -0.017 0.092 -10000 0 -0.59 7 7
ARF6/GTP/RAB11FIP3/RAB11A -0.008 0.048 -10000 0 -0.57 2 2
RHOA 0.015 0 -10000 0 -10000 0 0
PLD1 0.016 0.046 -10000 0 -0.62 1 1
RAB11FIP3 0.01 0.065 -10000 0 -0.8 3 3
tube morphogenesis -0.016 0.08 -10000 0 -0.48 7 7
ruffle organization 0.025 0.05 -10000 0 -0.37 2 2
regulation of epithelial cell migration -0.01 0.044 -10000 0 -0.3 4 4
PLD2 0.012 0.07 -10000 0 -0.64 4 4
PIP5K1A 0.025 0.05 -10000 0 -0.38 2 2
mol:Phosphatidic acid 0.022 0.068 -10000 0 -0.57 5 5
Rac1/GTP -0.016 0.081 -10000 0 -0.49 7 7
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.051 0.14 -9999 0 -0.52 30 30
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.041 0.12 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
ZFPM1 0 0.11 -9999 0 -0.78 9 9
NPC/RanGAP1/SUMO1/Ubc9 0.024 0.025 -9999 0 -10000 0 0
FKBP3 0.015 0 -9999 0 -10000 0 0
Histones -0.021 0.059 -9999 0 -10000 0 0
YY1/LSF 0.037 0 -9999 0 -10000 0 0
SMG5 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.003 0.12 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.007 0.087 -9999 0 -0.48 1 1
SAP18 0.015 0 -9999 0 -10000 0 0
RELA 0.008 0.1 -9999 0 -0.32 30 30
HDAC1/Smad7 -0.001 0.02 -9999 0 -0.44 1 1
RANGAP1 0.009 0.069 -9999 0 -0.85 3 3
HDAC3/TR2 0.008 0.084 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.053 0.04 -9999 0 -0.6 1 1
NF kappa B1 p50/RelA 0.014 0.095 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.026 0.18 -9999 0 -0.79 24 24
GATA1 -0.015 0.14 -9999 0 -0.69 18 18
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.053 0.073 -9999 0 -0.56 4 4
RBBP7 0.015 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.015 0 -9999 0 -10000 0 0
MAX 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.015 0 -9999 0 -10000 0 0
NFKBIA -0.001 0.096 -9999 0 -0.53 1 1
KAT2B 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.043 0.051 -9999 0 -10000 0 0
SIN3 complex -0.014 0.085 -9999 0 -0.52 13 13
SMURF1 0.013 0.033 -9999 0 -0.69 1 1
CHD3 0.009 0.069 -9999 0 -0.85 3 3
SAP30 -0.005 0.13 -9999 0 -0.85 11 11
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0 -9999 0 -10000 0 0
YY1/HDAC3 0.024 0.078 -9999 0 -10000 0 0
YY1/HDAC2 0.037 0 -9999 0 -10000 0 0
YY1/HDAC1 0.037 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.055 0.021 -9999 0 -10000 0 0
PPARG -0.048 0.13 -9999 0 -0.47 30 30
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.004 0.096 -9999 0 -0.6 3 3
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.02 -9999 0 -0.44 1 1
CREBBP 0.015 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.056 0.046 -9999 0 -0.71 1 1
HDAC1 0.015 0 -9999 0 -10000 0 0
HDAC3 0 0.093 -9999 0 -10000 0 0
HDAC2 0.015 0 -9999 0 -10000 0 0
YY1 0.036 0 -9999 0 -10000 0 0
HDAC8 0.015 0 -9999 0 -10000 0 0
SMAD7 0.015 0 -9999 0 -10000 0 0
NCOR2 0.009 0.069 -9999 0 -0.85 3 3
MXD1 0.015 0 -9999 0 -10000 0 0
STAT3 0.031 0 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.012 0.076 -9999 0 -0.5 11 11
EP300 0.015 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.031 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.096 -9999 0 -0.53 1 1
histone deacetylation 0.055 0.021 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.02 0.078 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GATAD2B 0.015 0 -9999 0 -10000 0 0
GATAD2A 0.015 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.018 0.14 -9999 0 -0.54 17 17
GATA1/HDAC1 -0.02 0.099 -9999 0 -0.52 18 18
GATA1/HDAC3 -0.014 0.11 -9999 0 -0.65 1 1
CHD4 0.015 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.07 0.19 -9999 0 -0.59 56 56
SIN3/HDAC complex/Mad/Max 0.05 0.043 -9999 0 -10000 0 0
NuRD Complex 0.062 0.039 -9999 0 -0.49 1 1
positive regulation of chromatin silencing -0.021 0.058 -9999 0 -10000 0 0
SIN3B 0.011 0.056 -9999 0 -0.85 2 2
MTA2 0.015 0 -9999 0 -10000 0 0
SIN3A 0.015 0 -9999 0 -10000 0 0
XPO1 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.033 0.023 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.031 0.13 -9999 0 -0.54 27 27
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.08 0.26 -9999 0 -0.78 56 56
negative regulation of cell growth 0.049 0.043 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.055 0.021 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.002 0.019 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.044 0.12 -9999 0 -0.45 30 30
SIN3/HDAC complex/NCoR1 0.047 0.043 -9999 0 -10000 0 0
TFCP2 0.015 0 -9999 0 -10000 0 0
NR2C1 0.015 0 -9999 0 -10000 0 0
MBD3 0.007 0.08 -9999 0 -0.85 4 4
MBD2 0.015 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.019 0.096 -10000 0 -0.55 10 10
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.065 -10000 0 -0.58 6 6
GNB1 0.015 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
Gs family/GTP -0.014 0.079 -10000 0 -0.46 14 14
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0.018 0.11 14 -10000 0 14
GNAL -0.008 0.13 -10000 0 -0.75 14 14
GNG2 0.004 0.097 -10000 0 -0.85 6 6
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.038 -10000 0 -0.47 3 3
MAPK11 -0.001 0.073 -10000 0 -0.47 11 11
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.008 0.076 -9999 0 -0.55 7 7
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.023 -9999 0 -0.33 1 1
AP2 -0.006 0.083 -9999 0 -1 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP -0.001 0.028 -9999 0 -0.61 1 1
CLTB 0.009 0.069 -9999 0 -0.85 3 3
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0.033 -9999 0 -0.38 3 3
CD4 0.002 0.1 -9999 0 -0.85 7 7
CLTA 0.015 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.004 -9999 0 -10000 0 0
ARFGAP1 0.006 0.066 -9999 0 -0.57 6 6
mol:PI-4-5-P2 -0.004 0.038 -9999 0 -0.37 4 4
ARF1/GTP -0.004 0.044 -9999 0 -0.54 3 3
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0.063 -9999 0 -0.49 6 6
mol:Choline -0.004 0.038 -9999 0 -0.37 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0.003 -9999 0 -10000 0 0
DDEF1 -0.004 0.038 -9999 0 -0.37 4 4
ARF1/GDP -0.006 0.055 -9999 0 -0.47 6 6
AP2M1 0.011 0.056 -9999 0 -0.85 2 2
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.002 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.007 0.055 -9999 0 -0.45 7 7
ARFIP2 -0.001 0.038 -9999 0 -0.83 1 1
COPA 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0.031 -9999 0 -0.35 3 3
ARF1/GTP/ARHGAP10 0 0.003 -9999 0 -10000 0 0
GGA3 0.013 0.04 -9999 0 -0.85 1 1
ARF1/GTP/Membrin -0.002 0.017 -9999 0 -0.28 1 1
AP2A1 0.009 0.069 -9999 0 -0.85 3 3
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.026 0.066 -9999 0 -0.71 3 3
ARF1/GDP/Membrin -0.001 0.014 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP -0.001 0.027 -9999 0 -0.58 1 1
CYTH2 0.009 0.069 -9999 0 -0.85 3 3
ARF1/GTP/GGA3 -0.001 0.029 -9999 0 -0.63 1 1
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.032 0.084 -9999 0 -0.87 3 3
PLD2 -0.004 0.038 -9999 0 -0.38 4 4
ARF-GAP1/v-SNARE 0.006 0.066 -9999 0 -0.57 6 6
PIP5K1A -0.004 0.038 -9999 0 -0.37 4 4
ARF1/GTP/Membrin/GBF1/p115 -0.003 0.028 -9999 0 -0.47 1 1
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.038 -9999 0 -0.37 4 4
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.066 -9999 0 -0.57 6 6
GOSR2 -0.001 0.014 -9999 0 -0.22 1 1
USO1 -0.001 0.014 -9999 0 -0.22 1 1
GBF1 -0.001 0.014 -9999 0 -0.22 1 1
ARF1/GTP/Arfaptin 2 -0.002 0.03 -9999 0 -0.64 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.014 0.1 -9999 0 -0.67 10 10
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD2 0.014 0.022 -9999 0 -10000 0 0
SMAD3 0.045 0.057 -9999 0 -0.78 2 2
SMAD3/SMAD4 0.051 0.037 -9999 0 -0.51 1 1
SMAD4/Ubc9/PIASy -0.002 0.037 -9999 0 -0.57 2 2
SMAD2/SMAD2/SMAD4 -0.007 0.047 -9999 0 -0.6 1 1
PPM1A 0.015 0 -9999 0 -10000 0 0
CALM1 0.015 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0.02 -9999 0 -10000 0 0
MAP3K1 0.015 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.01 0.079 -9999 0 -0.66 7 7
MAPK3 0.011 0.056 -9999 0 -0.85 2 2
MAPK1 0.015 0 -9999 0 -10000 0 0
NUP214 0.013 0.04 -9999 0 -0.85 1 1
CTDSP1 0.011 0.056 -9999 0 -0.85 2 2
CTDSP2 0.015 0 -9999 0 -10000 0 0
CTDSPL 0.01 0.057 -9999 0 -0.69 3 3
KPNB1 0.015 0 -9999 0 -10000 0 0
TGFBRAP1 0.002 0.1 -9999 0 -0.85 7 7
UBE2I 0.015 0 -9999 0 -10000 0 0
NUP153 0.015 0 -9999 0 -10000 0 0
KPNA2 0.006 0.08 -9999 0 -0.69 6 6
PIAS4 0.011 0.056 -9999 0 -0.85 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.002 0.018 -9999 0 -10000 0 0
MDM2/SUMO1 0.033 0.023 -9999 0 -10000 0 0
HDAC4 0.013 0.033 -9999 0 -0.69 1 1
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.018 0.03 -9999 0 -0.36 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.032 0.024 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0.03 -9999 0 -0.36 1 1
SUMO1/HDAC1 0.033 0.023 -9999 0 -10000 0 0
RANGAP1 0.009 0.069 -9999 0 -0.85 3 3
MDM2/SUMO1/SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0.025 -9999 0 -0.29 3 3
Ran/GTP -0.002 0.02 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.015 0 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.002 0.019 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 469 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.DV.5576 TCGA.DV.5575 TCGA.DV.5574 TCGA.DV.5573
109_MAP3K5 -0.24 0.065 0.065 0.065
47_PPARGC1A 0.015 0.015 0.015 0.015
105_BMP4 0.015 0.015 0.015 0.015
105_BMP6 0.015 0.015 0.015 0.015
105_BMP7 -0.69 -0.85 -0.69 -0.69
105_BMP2 0.015 0.015 0.015 0.015
131_RELN/VLDLR 0 0 -0.39 0
30_TGFB1/TGF beta receptor Type II 0.015 0.014 0.015 0.014
84_STAT5B -0.019 0.053 -0.035 0.053
84_STAT5A -0.019 0.053 -0.035 0.053
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/2282321/0.mRNAseq_preprocessor.Finished/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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