PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1KS6Q6X
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1KS6Q6X
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 46 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
TCGA08_retinoblastoma 374
HIF-1-alpha transcription factor network 200
Nephrin/Neph1 signaling in the kidney podocyte 172
TCR signaling in naïve CD8+ T cells 146
TCGA08_p53 142
Aurora B signaling 120
Syndecan-4-mediated signaling events 118
FOXA2 and FOXA3 transcription factor networks 117
IL12-mediated signaling events 107
FOXM1 transcription factor network 106
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 518 . Pathway is significant if Significance.Ratio > 0.05 .

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 518 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.7220 374 2996 8 -0.84 0.22 1000 -1000 -0.035 -1000
HIF-1-alpha transcription factor network 0.3861 200 15233 76 -1.3 0.026 1000 -1000 -0.18 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.3320 172 5853 34 -0.61 0.016 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.2819 146 13655 93 -0.66 0.33 1000 -1000 -0.12 -1000
TCGA08_p53 0.2741 142 999 7 -0.65 0.31 1000 -1000 -0.018 -1000
Aurora B signaling 0.2317 120 8050 67 -0.41 0.016 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.2278 118 7939 67 -0.65 0.11 1000 -1000 -0.14 -1000
FOXA2 and FOXA3 transcription factor networks 0.2259 117 5387 46 -1.2 0.025 1000 -1000 -0.083 -1000
IL12-mediated signaling events 0.2066 107 9314 87 -0.7 0.16 1000 -1000 -0.16 -1000
FOXM1 transcription factor network 0.2046 106 5441 51 -0.82 0.04 1000 -1000 -0.19 -1000
Glypican 1 network 0.1988 103 4964 48 -0.56 0.045 1000 -1000 -0.08 -1000
PDGFR-alpha signaling pathway 0.1950 101 4486 44 -0.28 0.034 1000 -1000 -0.09 -1000
amb2 Integrin signaling 0.1622 84 6921 82 -0.56 0.016 1000 -1000 -0.11 -1000
JNK signaling in the CD4+ TCR pathway 0.1583 82 1401 17 -0.42 0.016 1000 -1000 -0.085 -1000
IL4-mediated signaling events 0.1467 76 6996 91 -0.84 0.54 1000 -1000 -0.17 -1000
EGFR-dependent Endothelin signaling events 0.1390 72 1522 21 -0.67 0.016 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 0.1332 69 5167 74 -0.33 0.16 1000 -1000 -0.083 -1000
Aurora C signaling 0.1332 69 489 7 -0.4 0.012 1000 -1000 -0.06 -1000
VEGFR1 specific signals 0.1332 69 3897 56 -0.47 0.046 1000 -1000 -0.12 -1000
Glypican 2 network 0.1313 68 272 4 -0.12 -1000 1000 -1000 -0.051 -1000
HIF-2-alpha transcription factor network 0.1274 66 2841 43 -0.76 0.34 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 0.1236 64 2186 34 -0.42 0.016 1000 -1000 -0.11 -1000
IL23-mediated signaling events 0.1139 59 3584 60 -0.4 0.021 1000 -1000 -0.19 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1139 59 1958 33 -0.83 0.016 1000 -1000 -0.085 -1000
BMP receptor signaling 0.1120 58 4741 81 -0.7 0.016 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.0927 48 2537 52 -0.44 0.12 1000 -1000 -0.13 -1000
Fc-epsilon receptor I signaling in mast cells 0.0849 44 4343 97 -0.32 0.04 1000 -1000 -0.13 -1000
IL27-mediated signaling events 0.0811 42 2144 51 -0.61 0.078 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.0792 41 1072 26 -0.37 0.016 1000 -1000 -0.087 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0792 41 2813 68 -0.55 0.064 1000 -1000 -0.18 -1000
Ephrin A reverse signaling 0.0753 39 277 7 -0.057 0 1000 -1000 -0.043 -1000
Arf6 signaling events 0.0714 37 2354 62 -0.67 0.016 1000 -1000 -0.09 -1000
p75(NTR)-mediated signaling 0.0714 37 4734 125 -0.42 0.016 1000 -1000 -0.15 -1000
Calcium signaling in the CD4+ TCR pathway 0.0714 37 1175 31 -0.46 0.016 1000 -1000 -0.15 -1000
IL2 signaling events mediated by STAT5 0.0656 34 760 22 -0.44 0.038 1000 -1000 -0.073 -1000
BCR signaling pathway 0.0656 34 3439 99 -0.34 0.035 1000 -1000 -0.13 -1000
LPA4-mediated signaling events 0.0637 33 402 12 -0.16 0.026 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0637 33 1948 58 -0.44 0.031 1000 -1000 -0.12 -1000
Coregulation of Androgen receptor activity 0.0579 30 2287 76 -0.92 0.033 1000 -1000 -0.071 -1000
PLK1 signaling events 0.0579 30 2603 85 -0.38 0.016 1000 -1000 -0.086 -1000
Glucocorticoid receptor regulatory network 0.0560 29 3405 114 -0.41 0.16 1000 -1000 -0.1 -1000
S1P1 pathway 0.0560 29 1056 36 -0.38 0.018 1000 -1000 -0.1 -1000
IL6-mediated signaling events 0.0560 29 2226 75 -0.28 0.076 1000 -1000 -0.12 -1000
Regulation of Telomerase 0.0560 29 2998 102 -0.67 0.051 1000 -1000 -0.15 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0541 28 1516 54 -0.66 0.031 1000 -1000 -0.13 -1000
Integrins in angiogenesis 0.0502 26 2264 84 -0.38 0.039 1000 -1000 -0.14 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0483 25 1965 78 -0.32 0.045 1000 -1000 -0.1 -1000
Aurora A signaling 0.0463 24 1458 60 -0.24 0.053 1000 -1000 -0.089 -1000
Visual signal transduction: Rods 0.0463 24 1253 52 -0.29 0.016 1000 -1000 -0.12 -1000
Reelin signaling pathway 0.0444 23 1296 56 -0.24 0.016 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0444 23 2043 88 -0.32 0.074 1000 -1000 -0.14 -1000
Signaling events mediated by PTP1B 0.0425 22 1725 76 -0.67 0.049 1000 -1000 -0.11 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0425 22 1000 45 -0.58 0.061 1000 -1000 -0.12 -1000
Syndecan-2-mediated signaling events 0.0386 20 1415 69 -0.56 0.054 1000 -1000 -0.089 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0386 20 2465 120 -0.17 0.14 1000 -1000 -0.12 -1000
Endothelins 0.0367 19 1908 96 -0.35 0.088 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 0.0328 17 2410 136 -0.45 0.1 1000 -1000 -0.11 -1000
EPO signaling pathway 0.0328 17 975 55 -0.29 0.018 1000 -1000 -0.15 -1000
Wnt signaling 0.0328 17 123 7 -0.07 0.016 1000 -1000 -0.077 -1000
Thromboxane A2 receptor signaling 0.0309 16 1730 105 -0.67 0.066 1000 -1000 -0.1 -1000
Presenilin action in Notch and Wnt signaling 0.0309 16 1011 61 -0.19 0.093 1000 -1000 -0.11 -1000
S1P3 pathway 0.0309 16 698 42 -0.38 0.062 1000 -1000 -0.084 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0290 15 590 37 -0.3 0.026 1000 -1000 -0.12 -1000
FoxO family signaling 0.0290 15 980 64 -0.57 0.12 1000 -1000 -0.1 -1000
LPA receptor mediated events 0.0290 15 1619 102 -0.4 0.061 1000 -1000 -0.12 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0270 14 402 28 -0.13 0.025 1000 -1000 -0.086 -1000
PLK2 and PLK4 events 0.0270 14 42 3 -0.015 0.011 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0270 14 1134 76 -0.67 0.23 1000 -1000 -0.099 -1000
Canonical Wnt signaling pathway 0.0270 14 727 51 -0.19 0.096 1000 -1000 -0.086 -1000
FAS signaling pathway (CD95) 0.0251 13 638 47 -0.43 0.028 1000 -1000 -0.069 -1000
Class I PI3K signaling events 0.0251 13 998 73 -0.46 0.036 1000 -1000 -0.11 -1000
E-cadherin signaling events 0.0251 13 68 5 -0.023 0.016 1000 -1000 -0.07 -1000
IFN-gamma pathway 0.0232 12 869 68 -0.38 0.017 1000 -1000 -0.14 -1000
Nongenotropic Androgen signaling 0.0232 12 637 52 -0.18 0.071 1000 -1000 -0.087 -1000
Regulation of Androgen receptor activity 0.0232 12 896 70 -0.96 0.04 1000 -1000 -0.11 -1000
ErbB4 signaling events 0.0212 11 818 69 -0.18 0.1 1000 -1000 -0.12 -1000
S1P5 pathway 0.0212 11 187 17 -0.13 0.045 1000 -1000 -0.081 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0212 11 1454 125 -0.39 0.044 1000 -1000 -0.15 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0212 11 845 74 -0.67 0.099 1000 -1000 -0.14 -1000
S1P4 pathway 0.0193 10 265 25 -0.13 0.035 1000 -1000 -0.076 -1000
Visual signal transduction: Cones 0.0174 9 355 38 -0.041 0.016 1000 -1000 -0.096 -1000
a4b1 and a4b7 Integrin signaling 0.0174 9 45 5 -0.019 0.016 1000 -1000 -0.053 -1000
Noncanonical Wnt signaling pathway 0.0154 8 213 26 -0.11 0.016 1000 -1000 -0.13 -1000
Signaling events regulated by Ret tyrosine kinase 0.0154 8 667 82 -0.064 0.027 1000 -1000 -0.12 -1000
TCGA08_rtk_signaling 0.0154 8 232 26 -0.28 0.041 1000 -1000 -0.036 -1000
Canonical NF-kappaB pathway 0.0116 6 268 39 -0.19 0.075 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class III 0.0116 6 240 40 -0.059 0.033 1000 -1000 -0.063 -1000
IL1-mediated signaling events 0.0116 6 385 62 -0.091 0.06 1000 -1000 -0.14 -1000
Signaling events mediated by PRL 0.0116 6 231 34 -0.056 0.046 1000 -1000 -0.088 -1000
Class IB PI3K non-lipid kinase events 0.0116 6 18 3 -0.006 0.006 1000 -1000 -0.022 -1000
p38 MAPK signaling pathway 0.0116 6 270 44 -0.1 0.049 1000 -1000 -0.089 -1000
ErbB2/ErbB3 signaling events 0.0097 5 382 65 -0.13 0.059 1000 -1000 -0.11 -1000
Insulin-mediated glucose transport 0.0097 5 183 32 -0.086 0.067 1000 -1000 -0.095 -1000
Ephrin B reverse signaling 0.0097 5 279 48 -0.027 0.032 1000 -1000 -0.11 -1000
Signaling mediated by p38-gamma and p38-delta 0.0097 5 82 15 0 0.037 1000 -1000 -0.05 -1000
Syndecan-3-mediated signaling events 0.0097 5 205 35 -0.04 0.016 1000 -1000 -0.11 -1000
E-cadherin signaling in the nascent adherens junction 0.0097 5 391 76 -0.026 0.068 1000 -1000 -0.12 -1000
Arf6 trafficking events 0.0097 5 397 71 -0.12 0.058 1000 -1000 -0.1 -1000
Ras signaling in the CD4+ TCR pathway 0.0097 5 85 17 -0.037 0.055 1000 -1000 -0.068 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0077 4 368 85 -0.037 0.079 1000 -1000 -0.11 -1000
Arf6 downstream pathway 0.0077 4 214 43 -0.033 0.033 1000 -1000 -0.059 -1000
Paxillin-dependent events mediated by a4b1 0.0077 4 146 36 -0.026 0.031 1000 -1000 -0.1 -1000
EPHB forward signaling 0.0077 4 360 85 -0.074 0.07 1000 -1000 -0.14 -1000
Plasma membrane estrogen receptor signaling 0.0077 4 345 86 -0.17 0.072 1000 -1000 -0.12 -1000
BARD1 signaling events 0.0058 3 218 57 -0.17 0.043 1000 -1000 -0.1 -1000
Cellular roles of Anthrax toxin 0.0058 3 119 39 -0.022 0.027 1000 -1000 -0.05 -1000
E-cadherin signaling in keratinocytes 0.0058 3 162 43 -0.29 0.054 1000 -1000 -0.12 -1000
Osteopontin-mediated events 0.0039 2 113 38 -0.03 0.099 1000 -1000 -0.15 -1000
Hedgehog signaling events mediated by Gli proteins 0.0039 2 130 65 -0.062 0.093 1000 -1000 -0.093 -1000
ceramide signaling pathway 0.0039 2 126 49 -0.12 0.054 1000 -1000 -0.071 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0039 2 128 52 -0.031 0.093 1000 -1000 -0.096 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0039 2 176 83 -0.086 0.081 1000 -1000 -0.11 -1000
Retinoic acid receptors-mediated signaling 0.0039 2 122 58 -0.026 0.063 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0039 2 148 54 -0.041 0.073 1000 -1000 -0.083 -1000
Insulin Pathway 0.0039 2 207 74 -0.034 0.055 1000 -1000 -0.14 -1000
PDGFR-beta signaling pathway 0.0039 2 272 97 -0.057 0.087 1000 -1000 -0.13 -1000
Signaling events mediated by HDAC Class II 0.0019 1 121 75 -0.027 0.051 1000 -1000 -0.095 -1000
Circadian rhythm pathway 0.0019 1 33 22 -0.019 0.064 1000 -1000 -0.095 -1000
mTOR signaling pathway 0.0019 1 70 53 -0.008 0.044 1000 -1000 -0.093 -1000
Class I PI3K signaling events mediated by Akt 0.0019 1 104 68 -0.086 0.06 1000 -1000 -0.099 -1000
Signaling events mediated by HDAC Class I 0.0019 1 202 104 -0.029 0.064 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 0.0019 1 52 31 -0.021 0.037 1000 -1000 -0.11 -1000
Signaling mediated by p38-alpha and p38-beta 0.0019 1 57 44 -0.043 0.051 1000 -1000 -0.082 -1000
IGF1 pathway 0.0019 1 92 57 -0.065 0.071 1000 -1000 -0.14 -1000
Alternative NF-kappaB pathway 0.0019 1 14 13 -0.005 0.016 1000 -1000 -0.091 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.062 1000 -1000 -0.096 -1000
Nectin adhesion pathway 0.0000 0 61 63 -0.015 0.08 1000 -1000 -0.12 -1000
TRAIL signaling pathway 0.0000 0 29 48 -0.002 0.071 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.081 -1000
Rapid glucocorticoid signaling 0.0000 0 12 20 -0.005 0.016 1000 -1000 -0.07 -1000
Arf1 pathway 0.0000 0 31 54 -0.01 0.043 1000 -1000 -0.071 -1000
Total NA 4156 218451 7203 -40 -990 131000 -131000 -14 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.01 0.093 -10000 0 -0.87 6 6
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.84 0.16 -10000 0 -0.88 499 499
CCND2 0.18 0.048 0.19 498 -10000 0 498
RB1 -0.2 0.05 -10000 0 -0.21 498 498
CDK4 0.22 0.051 0.22 498 -10000 0 498
CDK6 0.2 0.054 0.21 498 -0.18 1 499
G1/S progression 0.2 0.053 0.21 498 -10000 0 498
HIF-1-alpha transcription factor network

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
PKM2 -0.98 0.53 -9999 0 -1.4 303 303
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.91 309 309
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.98 0.53 -9999 0 -1.3 318 318
AP1 -0.014 0.088 -9999 0 -0.56 13 13
ABCG2 -0.98 0.53 -9999 0 -1.4 303 303
HIF1A -0.11 0.068 -9999 0 -0.89 2 2
TFF3 -0.99 0.53 -9999 0 -1.4 304 304
GATA2 0 0.12 -9999 0 -0.74 12 12
AKT1 -0.094 0.052 -9999 0 -10000 0 0
response to hypoxia -0.13 0.057 -9999 0 -10000 0 0
MCL1 -0.98 0.53 -9999 0 -1.4 294 294
NDRG1 -0.98 0.53 -9999 0 -1.4 298 298
SERPINE1 -1 0.56 -9999 0 -1.4 319 319
FECH -0.98 0.53 -9999 0 -1.4 302 302
FURIN -0.98 0.53 -9999 0 -1.4 302 302
NCOA2 -0.002 0.099 -9999 0 -0.75 9 9
EP300 -0.1 0.074 -9999 0 -0.36 6 6
HMOX1 -1 0.54 -9999 0 -1.4 305 305
BHLHE40 -0.98 0.53 -9999 0 -1.4 299 299
BHLHE41 -1.1 0.58 -9999 0 -1.5 320 320
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.079 0.056 -9999 0 -0.6 2 2
ENG -0.059 0.062 -9999 0 -10000 0 0
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.98 0.53 -9999 0 -1.4 299 299
ABCB1 -0.3 0.42 -9999 0 -1.3 68 68
TFRC -0.98 0.53 -9999 0 -1.4 294 294
CXCR4 -1.1 0.59 -9999 0 -1.5 321 321
TF -1 0.58 -9999 0 -1.4 308 308
CITED2 -0.98 0.53 -9999 0 -1.4 294 294
HIF1A/ARNT -1.3 0.85 -9999 0 -1.7 340 340
LDHA -0.086 0.063 -9999 0 -0.86 2 2
ETS1 -0.98 0.53 -9999 0 -1.4 302 302
PGK1 -0.98 0.53 -9999 0 -1.4 299 299
NOS2 -0.99 0.53 -9999 0 -1.4 296 296
ITGB2 -1 0.56 -9999 0 -1.4 323 323
ALDOA -0.98 0.53 -9999 0 -1.4 294 294
Cbp/p300/CITED2 -0.98 0.53 -9999 0 -1.4 295 295
FOS -0.003 0.12 -9999 0 -0.75 13 13
HK2 -1.2 0.58 -9999 0 -1.5 383 383
SP1 0.021 0.029 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.1 10 10
HK1 -0.98 0.53 -9999 0 -1.3 317 317
NPM1 -0.98 0.53 -9999 0 -1.4 294 294
EGLN1 -0.98 0.53 -9999 0 -1.4 297 297
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.98 0.53 -9999 0 -1.4 303 303
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.091 0.16 -9999 0 -0.8 18 18
IGFBP1 -1 0.57 -9999 0 -1.4 309 309
VEGFA -0.78 0.41 -9999 0 -1.2 235 235
HIF1A/JAB1 -0.055 0.047 -9999 0 -0.7 2 2
CP -1.2 0.58 -9999 0 -1.5 378 378
CXCL12 -0.99 0.53 -9999 0 -1.4 308 308
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.98 0.53 -9999 0 -1.4 294 294
EGLN3 -1.3 0.51 -9999 0 -1.5 402 402
CA9 -1.3 0.47 -9999 0 -1.5 414 414
TERT -1 0.55 -9999 0 -1.4 317 317
ENO1 -0.98 0.53 -9999 0 -1.4 298 298
PFKL -0.98 0.53 -9999 0 -1.4 299 299
NCOA1 0.015 0.003 -9999 0 -10000 0 0
ADM -1.1 0.56 -9999 0 -1.4 317 317
ARNT -0.1 0.046 -9999 0 -10000 0 0
HNF4A -0.045 0.21 -9999 0 -0.75 44 44
ADFP -0.99 0.52 -9999 0 -1.3 334 334
SLC2A1 -0.63 0.33 -9999 0 -0.97 171 171
LEP -1 0.54 -9999 0 -1.4 319 319
HIF1A/ARNT/Cbp/p300 -0.71 0.34 -9999 0 -0.93 310 310
EPO -0.61 0.39 -9999 0 -1.1 177 177
CREBBP -0.099 0.072 -9999 0 -0.35 3 3
HIF1A/ARNT/Cbp/p300/HDAC7 -0.75 0.38 -9999 0 -1 296 296
PFKFB3 -0.98 0.53 -9999 0 -1.3 317 317
NT5E -0.98 0.53 -9999 0 -1.4 299 299
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.48 0.26 0.62 402 -10000 0 402
KIRREL -0.055 0.11 -10000 0 -0.82 9 9
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.49 0.26 -10000 0 -0.62 402 402
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.53 0.31 -10000 0 -0.84 224 224
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.41 0.26 -10000 0 -0.66 224 224
FYN -0.5 0.3 -10000 0 -0.8 224 224
mol:Ca2+ -0.52 0.3 -10000 0 -0.83 224 224
mol:DAG -0.53 0.31 -10000 0 -0.83 224 224
NPHS2 -0.41 0.38 -10000 0 -0.81 248 248
mol:IP3 -0.53 0.31 -10000 0 -0.83 224 224
regulation of endocytosis -0.47 0.28 -10000 0 -0.75 224 224
Nephrin/NEPH1/podocin/Cholesterol -0.54 0.31 -10000 0 -0.85 225 225
establishment of cell polarity -0.48 0.26 -10000 0 -0.62 402 402
Nephrin/NEPH1/podocin/NCK1-2 -0.49 0.29 -10000 0 -0.78 224 224
Nephrin/NEPH1/beta Arrestin2 -0.48 0.28 -10000 0 -0.76 224 224
NPHS1 -0.61 0.33 -10000 0 -0.78 400 400
Nephrin/NEPH1/podocin -0.51 0.3 -10000 0 -0.8 224 224
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.033 -10000 0 -0.75 1 1
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.53 0.31 -10000 0 -0.84 224 224
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.53 0.31 -10000 0 -0.84 224 224
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.49 0.3 -10000 0 -0.79 224 224
cytoskeleton organization -0.53 0.32 -10000 0 -0.85 224 224
Nephrin/NEPH1 -0.36 0.2 -10000 0 -0.47 402 402
Nephrin/NEPH1/ZO-1 -0.39 0.22 -10000 0 -0.55 225 225
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.69 231 231
FYN -0.41 0.5 -10000 0 -0.92 237 237
LAT/GRAP2/SLP76 -0.36 0.39 -10000 0 -0.74 247 247
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.25 0.29 -10000 0 -0.53 245 245
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.08 0.072 -10000 0 -0.19 78 78
MAP3K8 0.012 0.055 -10000 0 -0.86 2 2
mol:Ca2+ -0.11 0.045 -10000 0 -0.14 291 291
integrin-mediated signaling pathway -0.018 0.1 -10000 0 -0.58 16 16
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.41 0.45 -10000 0 -0.85 250 250
TRPV6 -0.66 0.26 -10000 0 -0.76 448 448
CD28 -0.058 0.23 -10000 0 -0.87 39 39
SHC1 -0.44 0.49 -10000 0 -0.93 244 244
receptor internalization -0.52 0.56 -10000 0 -1.1 248 248
PRF1 -0.49 0.6 -10000 0 -1.1 242 242
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.18 0.22 -10000 0 -0.41 222 222
LAT -0.5 0.53 -10000 0 -1 257 257
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 234 234
CD3E -0.34 0.44 -10000 0 -0.88 208 208
CD3G -0.33 0.43 -10000 0 -0.87 202 202
RASGRP2 -0.023 0.029 -10000 0 -0.14 2 2
RASGRP1 -0.23 0.27 -10000 0 -0.5 236 236
HLA-A 0.005 0.056 -10000 0 -0.88 2 2
RASSF5 -0.011 0.15 -10000 0 -0.86 16 16
RAP1A/GTP/RAPL -0.018 0.1 -10000 0 -0.59 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.082 -10000 0 -0.14 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 104 104
PRKCA -0.14 0.17 -10000 0 -0.31 213 213
GRAP2 -0.043 0.22 -10000 0 -0.86 35 35
mol:IP3 -0.16 0.34 0.26 168 -0.5 230 398
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.53 0.63 -10000 0 -1.1 249 249
ORAI1 0.33 0.13 0.38 447 -10000 0 447
CSK -0.46 0.51 -10000 0 -0.97 243 243
B7 family/CD28 -0.52 0.52 -10000 0 -1 243 243
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.56 0.62 -10000 0 -1.2 250 250
PTPN6 -0.44 0.52 -10000 0 -0.99 234 234
VAV1 -0.49 0.53 -10000 0 -1 253 253
Monovalent TCR/CD3 -0.46 0.53 -10000 0 -0.99 238 238
CBL 0.014 0.033 -10000 0 -0.75 1 1
LCK -0.44 0.53 -10000 0 -0.98 240 240
PAG1 -0.46 0.51 -10000 0 -0.97 244 244
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.63 -10000 0 -1.2 242 242
CD80 -0.18 0.37 -10000 0 -0.87 115 115
CD86 -0.13 0.32 -10000 0 -0.87 81 81
PDK1/CARD11/BCL10/MALT1 -0.18 0.17 -10000 0 -0.36 186 186
HRAS 0.014 0.039 -10000 0 -0.86 1 1
GO:0035030 -0.36 0.42 -10000 0 -0.77 243 243
CD8A -0.39 0.44 -10000 0 -0.87 234 234
CD8B -0.31 0.43 -10000 0 -0.88 186 186
PTPRC -0.086 0.27 -10000 0 -0.87 56 56
PDK1/PKC theta -0.32 0.36 -10000 0 -0.68 242 242
CSK/PAG1 -0.44 0.49 -10000 0 -0.94 240 240
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.042 -10000 0 -0.68 2 2
GRAP2/SLP76 -0.44 0.44 -10000 0 -0.88 244 244
STIM1 0.17 0.065 -10000 0 -10000 0 0
RAS family/GTP -0.064 0.11 -10000 0 -0.25 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.59 0.65 -10000 0 -1.2 248 248
mol:DAG -0.2 0.26 -10000 0 -0.46 236 236
RAP1A/GDP -0.014 0.036 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 171 171
cytotoxic T cell degranulation -0.45 0.55 -10000 0 -0.99 242 242
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.32 0.35 -10000 0 -0.65 250 250
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.27 0.44 0.3 112 -0.7 236 348
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.46 0.44 -10000 0 -0.86 281 281
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.38 0.35 -10000 0 -0.72 248 248
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.5 0.57 -10000 0 -1.1 240 240
CARD11 -0.17 0.36 -10000 0 -0.86 110 110
PRKCB -0.14 0.17 -10000 0 -0.31 214 214
PRKCE -0.14 0.17 -10000 0 -0.31 213 213
PRKCQ -0.39 0.42 -10000 0 -0.8 249 249
LCP2 -0.04 0.22 -10000 0 -0.86 33 33
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.2 0.24 -10000 0 -0.44 241 241
IKK complex -0.028 0.085 -10000 0 -10000 0 0
RAS family/GDP -0.012 0.012 -10000 0 -0.11 1 1
MAP3K14 -0.13 0.18 -10000 0 -0.32 175 175
PDPK1 -0.23 0.27 -10000 0 -0.5 235 235
TCR/CD3/MHC I/CD8/Fyn -0.56 0.65 -10000 0 -1.2 239 239
TCGA08_p53

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
CDKN2A -0.65 0.13 -10000 0 -0.68 499 499
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.037 -10000 0 -10000 0 0
Apoptosis -0.17 0.037 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.061 0.32 499 -10000 0 499
MDM4 0.014 0.039 -10000 0 -0.86 1 1
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.24 0.32 -9999 0 -0.68 161 161
STMN1 -0.29 0.35 -9999 0 -0.66 243 243
Aurora B/RasGAP/Survivin -0.41 0.48 -9999 0 -0.88 249 249
Chromosomal passenger complex/Cul3 protein complex -0.17 0.23 -9999 0 -0.49 149 149
BIRC5 -0.26 0.41 -9999 0 -0.89 153 153
DES -0.38 0.34 -9999 0 -0.59 308 308
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 244 244
Aurora B/TACC1 -0.26 0.3 -9999 0 -0.58 243 243
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 243 243
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.073 0.09 -9999 0 -0.17 106 106
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.41 0.5 -9999 0 -0.89 247 247
Cul3 protein complex -0.016 0.085 -9999 0 -10000 0 0
KIF2C -0.15 0.18 -9999 0 -0.34 198 198
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.38 0.44 -9999 0 -0.87 234 234
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 244 244
SEPT1 -0.096 0.29 -9999 0 -0.86 66 66
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.18 0.24 -9999 0 -0.44 224 224
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.005 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 243 243
AURKB -0.4 0.44 -9999 0 -0.87 243 243
AURKC 0.012 0.055 -9999 0 -0.86 2 2
CDCA8 -0.025 0.17 -9999 0 -0.9 19 19
cytokinesis -0.35 0.37 -9999 0 -0.75 208 208
Aurora B/Septin1 -0.36 0.42 -9999 0 -0.83 206 206
AURKA 0.002 0.095 -9999 0 -0.87 6 6
INCENP 0.008 0.009 -9999 0 -10000 0 0
KLHL13 -0.009 0.14 -9999 0 -0.75 17 17
BUB1 -0.37 0.44 -9999 0 -0.87 227 227
hSgo1/Aurora B/Survivin -0.4 0.49 -9999 0 -0.86 250 250
EVI5 0.01 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.34 -9999 0 -0.72 188 188
SGOL1 -0.015 0.16 -9999 0 -0.86 18 18
CENPA -0.29 0.35 -9999 0 -0.62 253 253
NCAPG -0.28 0.42 -9999 0 -0.86 174 174
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 243 243
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 243 243
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.13 0.33 -9999 0 -0.86 87 87
NPM1 -0.22 0.24 -9999 0 -0.47 243 243
RASA1 0.014 0.033 -9999 0 -0.75 1 1
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 243 243
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.34 0.38 -9999 0 -0.78 198 198
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.22 0.24 -9999 0 -0.47 243 243
MYLK -0.17 0.21 -9999 0 -0.39 243 243
KIF23 -0.007 0.11 -9999 0 -0.88 8 8
VIM -0.35 0.4 -9999 0 -0.73 257 257
RACGAP1 0.004 0.055 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.22 0.24 -9999 0 -0.47 243 243
Chromosomal passenger complex -0.35 0.41 -9999 0 -0.74 248 248
Chromosomal passenger complex/EVI5 -0.37 0.48 -9999 0 -0.94 182 182
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-4-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
PTK2 -0.055 0.14 -9999 0 -0.54 38 38
Syndecan-4/Syndesmos -0.46 0.39 -9999 0 -0.85 233 233
positive regulation of JNK cascade -0.54 0.37 -9999 0 -0.84 281 281
Syndecan-4/ADAM12 -0.57 0.5 -9999 0 -1 257 257
CCL5 -0.36 0.44 -9999 0 -0.86 221 221
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 38 38
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.37 0.37 -9999 0 -0.72 269 269
ADAM12 -0.22 0.39 -9999 0 -0.86 140 140
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.48 0.4 -9999 0 -0.86 235 235
Syndecan-4/CXCL12/CXCR4 -0.59 0.43 -9999 0 -0.94 281 281
Syndecan-4/Laminin alpha3 -0.47 0.39 -9999 0 -0.85 238 238
MDK -0.05 0.23 -9999 0 -0.86 39 39
Syndecan-4/FZD7 -0.46 0.39 -9999 0 -0.84 234 234
Syndecan-4/Midkine -0.5 0.42 -9999 0 -0.88 246 246
FZD7 0.014 0.033 -9999 0 -0.75 1 1
Syndecan-4/FGFR1/FGF -0.44 0.34 -9999 0 -0.77 236 236
THBS1 0.011 0.058 -9999 0 -0.75 3 3
integrin-mediated signaling pathway -0.45 0.36 -9999 0 -0.79 239 239
positive regulation of MAPKKK cascade -0.54 0.37 -9999 0 -0.84 281 281
Syndecan-4/TACI -0.5 0.42 -9999 0 -0.9 246 246
CXCR4 -0.29 0.42 -9999 0 -0.86 178 178
cell adhesion -0.007 0.12 -9999 0 -0.51 14 14
Syndecan-4/Dynamin -0.46 0.39 -9999 0 -0.85 233 233
Syndecan-4/TSP1 -0.47 0.39 -9999 0 -0.85 235 235
Syndecan-4/GIPC -0.46 0.39 -9999 0 -0.84 234 234
Syndecan-4/RANTES -0.65 0.46 -9999 0 -1 289 289
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.007 0.13 -9999 0 -0.75 15 15
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.066 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.47 0.39 -9999 0 -0.85 234 234
TFPI 0.001 0.11 -9999 0 -0.81 9 9
F2 -0.32 0.42 -9999 0 -0.87 194 194
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.67 38 38
positive regulation of cell adhesion -0.45 0.38 -9999 0 -0.82 240 240
ACTN1 0.013 0.051 -9999 0 -0.8 2 2
TNC -0.003 0.12 -9999 0 -0.75 13 13
Syndecan-4/CXCL12 -0.47 0.39 -9999 0 -0.85 238 238
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 0 0.11 -9999 0 -0.75 11 11
TNFRSF13B -0.071 0.26 -9999 0 -0.86 50 50
FGF2 0.008 0.077 -9999 0 -0.77 5 5
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.47 0.39 -9999 0 -0.86 233 233
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.039 0.22 -9999 0 -0.83 38 38
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.045 -9999 0 -0.85 1 1
vasculogenesis -0.44 0.36 -9999 0 -0.79 235 235
SDC4 -0.51 0.43 -9999 0 -0.93 233 233
Syndecan-4/Tenascin C -0.47 0.39 -9999 0 -0.84 239 239
Syndecan-4/PI-4-5-P2/PKC alpha -0.08 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.46 0.39 -9999 0 -0.85 233 233
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
Rac1/GTP -0.008 0.12 -9999 0 -0.53 14 14
cytoskeleton organization -0.44 0.36 -9999 0 -0.8 233 233
GIPC1 0.014 0.033 -9999 0 -0.75 1 1
Syndecan-4/TFPI -0.47 0.39 -9999 0 -0.85 237 237
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.45 0.48 -10000 0 -1.2 111 111
PCK1 -0.94 0.71 -10000 0 -1.4 302 302
HNF4A -0.58 0.58 -10000 0 -1.3 142 142
KCNJ11 -0.45 0.51 -10000 0 -1.3 103 103
AKT1 -0.17 0.18 -10000 0 -10000 0 0
response to starvation -0.02 0.038 -10000 0 -10000 0 0
DLK1 -0.56 0.58 -10000 0 -1.3 161 161
NKX2-1 -0.057 0.21 0.58 1 -0.84 4 5
ACADM -0.45 0.48 -10000 0 -1.1 124 124
TAT -0.52 0.36 -10000 0 -0.97 144 144
CEBPB -0.024 0.14 -10000 0 -0.92 12 12
CEBPA -0.019 0.13 -10000 0 -0.9 10 10
TTR -0.89 0.48 -10000 0 -1.2 331 331
PKLR -0.5 0.56 -10000 0 -1.3 127 127
APOA1 -0.56 0.56 -10000 0 -1.3 142 142
CPT1C -0.45 0.48 -10000 0 -1.2 108 108
ALAS1 -0.17 0.19 -10000 0 -10000 0 0
TFRC -0.63 0.42 -10000 0 -1 202 202
FOXF1 -0.002 0.12 -10000 0 -0.84 10 10
NF1 0.025 0.001 -10000 0 -10000 0 0
HNF1A (dimer) -0.003 0.087 -10000 0 -0.79 5 5
CPT1A -0.45 0.48 -10000 0 -1.1 128 128
HMGCS1 -0.45 0.48 -10000 0 -1.2 115 115
NR3C1 0.003 0.065 -10000 0 -0.97 1 1
CPT1B -0.46 0.5 -10000 0 -1.2 116 116
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.017 0.005 -10000 0 -10000 0 0
GCK -0.46 0.49 -10000 0 -1.2 122 122
CREB1 -0.028 0.066 -10000 0 -10000 0 0
IGFBP1 -0.32 0.42 -10000 0 -1 119 119
PDX1 -0.19 0.22 -10000 0 -1 6 6
UCP2 -0.45 0.48 -10000 0 -1.2 116 116
ALDOB -0.94 0.62 -10000 0 -1.2 398 398
AFP -0.71 0.5 -10000 0 -0.97 319 319
BDH1 -0.6 0.57 -10000 0 -1.2 197 197
HADH -0.44 0.49 -10000 0 -1.2 102 102
F2 -0.66 0.62 -10000 0 -1.3 192 192
HNF1A -0.002 0.087 -10000 0 -0.79 5 5
G6PC -0.81 0.66 -10000 0 -1.5 248 248
SLC2A2 -0.32 0.48 -10000 0 -1.7 47 47
INS 0.01 0.055 -10000 0 -10000 0 0
FOXA1 -0.37 0.39 -10000 0 -0.96 136 136
FOXA3 -0.61 0.37 -10000 0 -0.89 296 296
FOXA2 -0.52 0.57 -10000 0 -1.3 130 130
ABCC8 -0.44 0.49 -10000 0 -1.2 110 110
ALB -1.2 0.49 -10000 0 -1.4 445 445
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.17 0.26 -10000 0 -0.65 70 70
TBX21 -0.55 0.68 -10000 0 -1.3 214 214
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.022 -10000 0 -10000 0 0
IL12RB1 -0.27 0.43 -10000 0 -0.91 159 159
GADD45B -0.3 0.43 -10000 0 -0.83 143 143
IL12RB2 -0.11 0.31 -10000 0 -0.87 74 74
GADD45G -0.31 0.43 -10000 0 -0.81 167 167
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.002 0.1 -10000 0 -0.87 7 7
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IFNG -0.39 0.44 -10000 0 -0.86 237 237
STAT3 (dimer) -0.37 0.47 -10000 0 -0.88 200 200
HLA-DRB5 -0.038 0.21 -10000 0 -0.86 32 32
FASLG -0.61 0.7 -10000 0 -1.3 229 229
NF kappa B2 p52/RelB -0.52 0.53 -10000 0 -1.1 219 219
CD4 0.001 0.12 -10000 0 -0.86 9 9
SOCS1 0.006 0.094 -10000 0 -0.86 6 6
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 234 234
CD3E -0.34 0.43 -10000 0 -0.87 208 208
CD3G -0.33 0.43 -10000 0 -0.87 202 202
IL12Rbeta2/JAK2 -0.085 0.25 -10000 0 -0.68 74 74
CCL3 -0.49 0.63 -10000 0 -1.2 196 196
CCL4 -0.5 0.66 -10000 0 -1.3 192 192
HLA-A 0.007 0.055 -10000 0 -0.86 2 2
IL18/IL18R -0.13 0.3 -10000 0 -0.6 145 145
NOS2 -0.36 0.5 -10000 0 -0.95 171 171
IL12/IL12R/TYK2/JAK2/SPHK2 -0.16 0.26 -10000 0 -0.65 67 67
IL1R1 -0.45 0.59 -10000 0 -1.2 179 179
IL4 0.014 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.022 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.7 0.82 -10000 0 -1.4 258 258
RAB7A -0.24 0.37 -10000 0 -0.78 53 53
lysosomal transport -0.22 0.36 -10000 0 -0.73 56 56
FOS -0.38 0.5 -10000 0 -0.95 200 200
STAT4 (dimer) -0.41 0.53 -10000 0 -0.97 206 206
STAT5A (dimer) -0.66 0.61 -10000 0 -1.2 248 248
GZMA -0.57 0.7 -10000 0 -1.3 217 217
GZMB -0.54 0.67 -10000 0 -1.3 205 205
HLX -0.088 0.28 -10000 0 -0.86 61 61
LCK -0.52 0.69 -10000 0 -1.2 217 217
TCR/CD3/MHC II/CD4 -0.38 0.47 -10000 0 -0.86 228 228
IL2/IL2R -0.42 0.42 -10000 0 -0.71 306 306
MAPK14 -0.3 0.44 -10000 0 -0.82 162 162
CCR5 -0.45 0.59 -10000 0 -1.1 200 200
IL1B 0.002 0.096 -10000 0 -0.86 6 6
STAT6 -0.084 0.15 -10000 0 -10000 0 0
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.039 -10000 0 -0.86 1 1
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.092 0.29 -10000 0 -0.89 60 60
CD8A -0.38 0.44 -10000 0 -0.87 234 234
CD8B -0.3 0.42 -10000 0 -0.87 186 186
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.16 0.26 0.64 70 -10000 0 70
IL2RB -0.45 0.44 -10000 0 -0.86 272 272
proteasomal ubiquitin-dependent protein catabolic process -0.36 0.47 -10000 0 -0.86 203 203
IL2RG -0.042 0.22 -10000 0 -0.86 34 34
IL12 -0.07 0.24 -10000 0 -0.71 61 61
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 171 171
IL2 -0.007 0.12 -10000 0 -0.86 10 10
SPHK2 0.013 0.047 -10000 0 -0.75 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.046 -10000 0 -0.91 1 1
IL12/IL12R/TYK2/JAK2 -0.58 0.78 -10000 0 -1.4 220 220
MAP2K3 -0.31 0.44 -10000 0 -0.81 180 180
RIPK2 0.014 0.039 -10000 0 -0.86 1 1
MAP2K6 -0.31 0.44 -10000 0 -0.83 167 167
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.077 -10000 0 -0.86 4 4
IL18RAP -0.21 0.39 -10000 0 -0.87 133 133
IL12Rbeta1/TYK2 -0.21 0.34 -10000 0 -0.72 159 159
EOMES -0.3 0.37 -10000 0 -0.74 213 213
STAT1 (dimer) -0.45 0.51 -10000 0 -0.96 233 233
T cell proliferation -0.26 0.37 -10000 0 -0.67 178 178
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.81 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.37 0.33 -10000 0 -0.75 182 182
ATF2 -0.27 0.41 -10000 0 -0.78 137 137
FOXM1 transcription factor network

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
NFATC3 -0.19 0.68 -10000 0 -1.2 122 122
PLK1 -0.1 0.41 -10000 0 -0.8 128 128
BIRC5 -0.14 0.43 -10000 0 -0.79 153 153
HSPA1B -0.19 0.68 -10000 0 -1.2 118 118
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.2 0.68 -10000 0 -1.2 123 123
FOXM1 -0.37 0.99 -10000 0 -1.8 133 133
XRCC1 -0.19 0.68 -10000 0 -1.2 118 118
FOXM1B/p19 -0.5 0.49 0.51 1 -1.2 131 132
Cyclin D1/CDK4 -0.18 0.61 -10000 0 -1.1 117 117
CDC2 -0.22 0.72 -10000 0 -1.3 133 133
TGFA -0.16 0.6 -10000 0 -1.1 114 114
SKP2 -0.19 0.68 -10000 0 -1.2 118 118
CCNE1 0.003 0.1 -10000 0 -0.88 7 7
CKS1B -0.19 0.68 -10000 0 -1.2 122 122
RB1 -0.19 0.26 -10000 0 -0.69 93 93
FOXM1C/SP1 -0.28 0.78 -10000 0 -1.5 130 130
AURKB -0.25 0.46 -10000 0 -0.74 243 243
CENPF -0.21 0.72 -10000 0 -1.3 124 124
CDK4 0.02 0.022 -10000 0 -10000 0 0
MYC -0.16 0.6 -10000 0 -1 121 121
CHEK2 0.038 0.063 -10000 0 -0.91 1 1
ONECUT1 -0.19 0.65 -10000 0 -1.2 122 122
CDKN2A -0.82 0.17 -10000 0 -0.86 499 499
LAMA4 -0.28 0.69 -10000 0 -1.3 134 134
FOXM1B/HNF6 -0.28 0.79 -10000 0 -1.5 123 123
FOS -0.2 0.69 -10000 0 -1.2 124 124
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.19 0.68 -10000 0 -1.2 118 118
response to radiation 0.013 0.05 -10000 0 -10000 0 0
CENPB -0.19 0.68 -10000 0 -1.2 121 121
CENPA -0.28 0.78 -10000 0 -1.4 144 144
NEK2 -0.24 0.75 -10000 0 -1.4 129 129
HIST1H2BA -0.2 0.68 -10000 0 -1.2 123 123
CCNA2 -0.16 0.36 -10000 0 -0.88 101 101
EP300 0.014 0.033 -10000 0 -0.75 1 1
CCNB1/CDK1 -0.28 0.81 -10000 0 -1.5 123 123
CCNB2 -0.24 0.76 -10000 0 -1.4 133 133
CCNB1 -0.21 0.72 -10000 0 -1.3 122 122
ETV5 -0.19 0.68 -10000 0 -1.2 121 121
ESR1 -0.19 0.68 -10000 0 -1.2 123 123
CCND1 -0.18 0.63 -10000 0 -1.1 118 118
GSK3A 0.036 0.041 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.082 0.28 -10000 0 -0.64 102 102
CDK2 0.015 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.58 -10000 0 -1.3 137 137
GAS1 -0.23 0.7 -10000 0 -1.2 132 132
MMP2 -0.19 0.68 -10000 0 -1.2 119 119
RB1/FOXM1C -0.21 0.67 -10000 0 -1.2 122 122
CREBBP 0.016 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.053 -10000 0 -0.49 6 6
fibroblast growth factor receptor signaling pathway -0.006 0.053 -10000 0 -0.49 6 6
LAMA1 -0.007 0.13 -10000 0 -0.75 15 15
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.56 111 111
SMAD2 0.045 0.021 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.021 -10000 0 -0.49 1 1
GPC1/Laminin alpha1 -0.017 0.098 -10000 0 -0.57 16 16
TDGF1 -0.56 0.32 -10000 0 -0.75 390 390
CRIPTO/GPC1 -0.42 0.24 -10000 0 -0.56 390 390
APP/GPC1 -0.002 0.035 -10000 0 -0.56 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.35 0.22 -10000 0 -0.48 390 390
FLT1 0.007 0.086 -10000 0 -0.86 5 5
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.021 -10000 0 -10000 0 0
SERPINC1 -0.054 0.22 -10000 0 -0.76 45 45
FYN -0.35 0.22 -10000 0 -0.48 390 390
FGR -0.35 0.22 -10000 0 -0.48 390 390
positive regulation of MAPKKK cascade -0.36 0.24 -10000 0 -0.73 52 52
SLIT2 -0.15 0.31 -10000 0 -0.75 110 110
GPC1/NRG -0.018 0.1 -10000 0 -0.56 17 17
NRG1 -0.008 0.13 -10000 0 -0.75 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.26 0.3 -10000 0 -0.59 234 234
LYN -0.35 0.22 -10000 0 -0.48 390 390
mol:Spermine 0.014 0.026 -10000 0 -0.57 1 1
cell growth -0.006 0.053 -10000 0 -0.49 6 6
BMP signaling pathway -0.014 0.033 0.74 1 -10000 0 1
SRC -0.35 0.22 -10000 0 -0.48 390 390
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.062 0.24 -10000 0 -0.86 43 43
GPC1 0.014 0.033 -10000 0 -0.75 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.38 0.44 -10000 0 -0.86 233 233
BLK -0.39 0.26 -10000 0 -0.52 395 395
HCK -0.38 0.24 -10000 0 -0.5 400 400
FGF2 0.008 0.077 -10000 0 -0.77 5 5
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.086 -10000 0 -0.86 5 5
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.035 -10000 0 -0.56 2 2
ATIII/GPC1 -0.051 0.16 -10000 0 -0.58 46 46
PLA2G2A/GPC1 -0.056 0.18 -10000 0 -0.66 44 44
LCK -0.37 0.24 -10000 0 -0.5 398 398
neuron differentiation -0.018 0.099 -10000 0 -0.56 17 17
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.033 -10000 0 -0.75 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.28 0.37 -9999 0 -0.74 199 199
PDGF/PDGFRA/CRKL -0.21 0.26 -9999 0 -0.54 199 199
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.52 1 1
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.56 202 202
AP1 -0.16 0.24 -9999 0 -1.2 13 13
mol:IP3 -0.19 0.29 -9999 0 -0.56 199 199
PLCG1 -0.19 0.29 -9999 0 -0.56 199 199
PDGF/PDGFRA/alphaV Integrin -0.21 0.26 -9999 0 -0.54 199 199
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.56 199 199
CAV3 -0.001 0.066 -9999 0 -0.86 3 3
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/Shf -0.21 0.26 -9999 0 -0.54 200 200
FOS -0.12 0.27 -9999 0 -1.2 13 13
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.26 -9999 0 -0.54 199 199
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
mol:DAG -0.19 0.29 -9999 0 -0.56 199 199
PDGF/PDGFRA -0.27 0.37 -9999 0 -0.74 199 199
actin cytoskeleton reorganization -0.21 0.26 -9999 0 -0.54 199 199
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
PI3K -0.18 0.22 -9999 0 -0.46 200 200
PDGF/PDGFRA/Crk/C3G -0.18 0.22 -9999 0 -0.46 199 199
JAK1 -0.19 0.28 -9999 0 -0.54 199 199
ELK1/SRF -0.15 0.19 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.033 -9999 0 -0.75 1 1
CSNK2A1 0.017 0.022 -9999 0 -10000 0 0
GO:0007205 -0.2 0.3 -9999 0 -0.57 199 199
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/SHB -0.21 0.26 -9999 0 -0.54 199 199
PDGF/PDGFRA/Caveolin-1 -0.26 0.3 -9999 0 -0.58 228 228
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.26 -9999 0 -0.49 199 199
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PDGF/PDGFRA/Crk -0.21 0.26 -9999 0 -0.54 199 199
JAK-STAT cascade -0.19 0.28 -9999 0 -0.54 199 199
cell proliferation -0.21 0.26 -9999 0 -0.54 200 200
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin/GPIbA -0.13 0.28 -9999 0 -0.68 101 101
alphaM/beta2 Integrin/proMMP-9 -0.4 0.43 -9999 0 -0.75 275 275
PLAUR -0.028 0.19 -9999 0 -0.86 26 26
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.28 -9999 0 -0.68 100 100
AGER -0.14 0.33 -9999 0 -0.86 90 90
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.042 0.22 -9999 0 -0.86 34 34
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.23 0.34 -9999 0 -0.66 167 167
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
CYR61 0.007 0.082 -9999 0 -0.75 6 6
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.56 114 114
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.018 0.16 -9999 0 -0.74 23 23
MYH2 -0.34 0.26 -9999 0 -0.64 186 186
MST1R 0.005 0.092 -9999 0 -0.78 7 7
leukocyte activation during inflammatory response -0.28 0.35 -9999 0 -0.63 220 220
APOB -0.27 0.41 -9999 0 -0.86 169 169
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.006 0.092 -9999 0 -0.84 6 6
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.033 -9999 0 -0.75 1 1
alphaM/beta2 Integrin/CTGF -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.54 222 222
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.003 0.13 -9999 0 -0.86 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.25 -9999 0 -0.53 222 222
cell adhesion -0.13 0.28 -9999 0 -0.67 101 101
NFKB1 -0.17 0.37 -9999 0 -0.95 62 62
THY1 0.014 0.033 -9999 0 -0.75 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.28 -9999 0 -0.59 170 170
alphaM/beta2 Integrin/LRP/tPA -0.13 0.27 -9999 0 -0.63 102 102
IL6 -0.2 0.41 -9999 0 -0.91 99 99
ITGB2 -0.15 0.34 -9999 0 -0.86 98 98
elevation of cytosolic calcium ion concentration -0.15 0.3 -9999 0 -0.64 120 120
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.26 -9999 0 -0.62 100 100
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.14 0.28 -9999 0 -0.85 41 41
alphaM/beta2 Integrin/uPA/Plg -0.35 0.34 -9999 0 -0.77 138 138
RhoA/GTP -0.37 0.27 -9999 0 -0.68 185 185
positive regulation of phagocytosis -0.25 0.27 -9999 0 -0.69 111 111
Ron/MSP -0.018 0.1 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.15 0.3 -9999 0 -0.64 120 120
alphaM/beta2 Integrin/uPAR -0.16 0.32 -9999 0 -0.71 116 116
PLAU 0.003 0.1 -9999 0 -0.75 9 9
PLAT -0.005 0.12 -9999 0 -0.75 14 14
actin filament polymerization -0.33 0.24 -9999 0 -0.61 186 186
MST1 0.002 0.11 -9999 0 -0.85 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.28 0.36 -9999 0 -0.64 220 220
TNF -0.15 0.34 -9999 0 -0.84 66 66
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.14 0.28 -9999 0 -0.66 109 109
fibrinolysis -0.35 0.34 -9999 0 -0.76 138 138
HCK -0.032 0.2 -9999 0 -0.86 28 28
dendritic cell antigen processing and presentation -0.3 0.25 -9999 0 -0.53 222 222
VTN -0.1 0.28 -9999 0 -0.76 79 79
alphaM/beta2 Integrin/CYR61 -0.14 0.28 -9999 0 -0.67 106 106
LPA 0.002 0.067 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.4 -9999 0 -0.7 277 277
FN1 -0.049 0.23 -9999 0 -0.86 38 38
alphaM/beta2 Integrin/Thy1 -0.13 0.28 -9999 0 -0.68 101 101
MPO -0.014 0.16 -9999 0 -0.86 17 17
KNG1 -0.56 0.33 -9999 0 -0.75 386 386
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.33 0.26 -9999 0 -0.64 176 176
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.38 0.38 -9999 0 -0.75 269 269
CTGF 0.005 0.088 -9999 0 -0.75 7 7
alphaM/beta2 Integrin/Hck -0.16 0.35 -9999 0 -0.79 104 104
ITGAM -0.021 0.17 -9999 0 -0.86 21 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.34 -9999 0 -0.75 109 109
HP -0.2 0.38 -9999 0 -0.86 129 129
leukocyte adhesion -0.18 0.27 -9999 0 -0.78 60 60
SELP -0.018 0.16 -9999 0 -0.75 23 23
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.42 0.54 -9999 0 -0.9 238 238
MAP4K1 -0.34 0.43 -9999 0 -0.86 211 211
MAP3K8 0.012 0.055 -9999 0 -0.86 2 2
PRKCB 0.008 0.082 -9999 0 -0.82 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.15 0.3 -9999 0 -0.62 121 121
JUN 0.001 0.08 -9999 0 -0.56 5 5
MAP3K7 -0.15 0.3 -9999 0 -0.62 121 121
GRAP2 -0.043 0.22 -9999 0 -0.86 35 35
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.14 0.29 -9999 0 -0.59 121 121
LAT -0.23 0.4 -9999 0 -0.86 145 145
LCP2 -0.04 0.22 -9999 0 -0.86 33 33
MAPK8 -0.01 0.084 -9999 0 -0.6 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.2 0.29 -9999 0 -0.67 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.39 0.51 -9999 0 -0.85 238 238
IL4-mediated signaling events

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
BCL2L1 -0.48 0.48 -10000 0 -1.2 107 107
STAT6 (cleaved dimer) -0.58 0.49 -10000 0 -1.1 181 181
IGHG1 -0.17 0.19 -10000 0 -0.66 12 12
IGHG3 -0.48 0.46 -10000 0 -1.1 143 143
AKT1 -0.28 0.33 -10000 0 -0.84 83 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.24 0.32 -10000 0 -0.83 83 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.79 68 68
THY1 -0.48 0.48 -10000 0 -1.2 113 113
MYB -0.22 0.39 -10000 0 -0.86 139 139
HMGA1 0.014 0.039 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.42 -10000 0 -1 117 117
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.79 67 67
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.009 0.077 -10000 0 -0.86 4 4
SOCS5 0.027 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.48 -10000 0 -1.2 155 155
SOCS1 -0.33 0.34 -10000 0 -0.8 81 81
SOCS3 -0.3 0.34 -10000 0 -0.92 67 67
FCER2 -0.41 0.44 -10000 0 -1.1 84 84
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.5 0.5 -10000 0 -1.2 113 113
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.28 -10000 0 -0.77 58 58
T cell proliferation -0.5 0.51 -10000 0 -1.2 131 131
IL4R/JAK1 -0.48 0.47 -10000 0 -1.2 111 111
EGR2 -0.49 0.5 -10000 0 -1.2 116 116
JAK2 0.007 0.023 -10000 0 -10000 0 0
JAK3 -0.16 0.36 -10000 0 -0.87 105 105
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
JAK1 0.007 0.016 -10000 0 -10000 0 0
COL1A2 -0.21 0.3 -10000 0 -0.89 66 66
CCL26 -0.49 0.49 -10000 0 -1.2 112 112
IL4R -0.51 0.51 -10000 0 -1.2 112 112
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.55 0.56 -10000 0 -1.3 136 136
IL13RA1 0.007 0.023 -10000 0 -10000 0 0
IRF4 -0.27 0.42 -10000 0 -0.99 116 116
ARG1 -0.18 0.26 -10000 0 -0.76 50 50
CBL -0.36 0.4 -10000 0 -0.96 110 110
GTF3A 0.011 0.029 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
IL13RA1/JAK2 -0.006 0.043 -10000 0 -10000 0 0
IRF4/BCL6 -0.27 0.38 -10000 0 -0.93 114 114
CD40LG -0.074 0.28 -10000 0 -0.92 53 53
MAPK14 -0.35 0.39 -10000 0 -0.99 97 97
mitosis -0.26 0.31 -10000 0 -0.79 82 82
STAT6 -0.55 0.56 -10000 0 -1.3 127 127
SPI1 -0.098 0.3 -10000 0 -0.86 70 70
RPS6KB1 -0.24 0.3 -10000 0 -0.78 70 70
STAT6 (dimer) -0.55 0.56 -10000 0 -1.3 127 127
STAT6 (dimer)/PARP14 -0.51 0.51 -10000 0 -1.2 126 126
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.36 -10000 0 -0.91 95 95
FRAP1 -0.28 0.33 -10000 0 -0.84 83 83
LTA -0.6 0.56 -10000 0 -1.3 161 161
FES 0.013 0.047 -10000 0 -0.75 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 127 -10000 0 127
CCL11 -0.7 0.61 -10000 0 -1.3 228 228
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.29 0.34 -10000 0 -0.87 91 91
IL2RG -0.037 0.22 -10000 0 -0.86 34 34
IL10 -0.5 0.5 -10000 0 -1.2 116 116
IRS1 0.01 0.067 -10000 0 -0.75 4 4
IRS2 0.002 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 109 109
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.37 -10000 0 -0.88 108 108
COL1A1 -0.41 0.43 -10000 0 -0.92 198 198
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.48 -10000 0 -1.2 103 103
IL2R gamma/JAK3 -0.16 0.37 -10000 0 -0.83 109 109
TFF3 -0.5 0.5 -10000 0 -1.2 121 121
ALOX15 -0.48 0.48 -10000 0 -1.2 112 112
MYBL1 -0.045 0.22 -10000 0 -0.86 36 36
T-helper 2 cell differentiation -0.43 0.41 -10000 0 -0.96 129 129
SHC1 0.014 0.039 -10000 0 -0.86 1 1
CEBPB 0 0.14 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.3 -10000 0 -0.78 69 69
mol:PI-3-4-5-P3 -0.28 0.33 -10000 0 -0.84 83 83
PI3K -0.3 0.36 -10000 0 -0.91 83 83
DOK2 -0.037 0.21 -10000 0 -0.86 31 31
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.27 -10000 0 -0.75 58 58
ITGB3 -0.48 0.49 -10000 0 -1.2 113 113
PIGR -0.84 0.7 -10000 0 -1.5 267 267
IGHE 0.028 0.09 0.29 12 -0.38 3 15
MAPKKK cascade -0.2 0.27 -10000 0 -0.73 58 58
BCL6 0.014 0.005 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 111 111
RETNLB -0.49 0.48 -10000 0 -1.2 106 106
SELP -0.51 0.52 -10000 0 -1.3 117 117
AICDA -0.62 0.55 -10000 0 -1.2 189 189
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EGF/EGFR -0.38 0.16 -9999 0 -0.86 26 26
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.36 0.14 -9999 0 -0.9 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.055 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 466 466
EGF/EGFR dimer/SHC -0.44 0.16 -9999 0 -0.49 467 467
mol:GDP -0.36 0.14 -9999 0 -0.88 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.013 0.16 -9999 0 -0.86 17 17
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.33 0.13 -9999 0 -0.82 10 10
SHC1 0.014 0.039 -9999 0 -0.86 1 1
HRAS/GDP -0.33 0.13 -9999 0 -0.83 10 10
FRAP1 -0.34 0.14 -9999 0 -0.85 9 9
EGF/EGFR dimer -0.51 0.18 -9999 0 -0.57 467 467
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.024 0.12 -9999 0 -0.66 19 19
Caspase cascade in apoptosis

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
TOP1 -0.13 0.27 -10000 0 -0.49 167 167
ACTA1 -0.19 0.36 -10000 0 -0.67 168 168
NUMA1 -0.13 0.27 -10000 0 -0.52 144 144
SPTAN1 -0.19 0.36 -10000 0 -0.67 167 167
LIMK1 -0.19 0.36 -10000 0 -0.67 168 168
BIRC3 -0.12 0.32 -10000 0 -0.86 80 80
BIRC2 0.012 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.46 -10000 0 -0.87 185 185
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.015 0.003 -10000 0 -10000 0 0
PTK2 -0.13 0.27 -10000 0 -0.49 167 167
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.35 -10000 0 -0.65 167 167
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.19 0.36 -10000 0 -0.67 167 167
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.3 0.28 -10000 0 -0.54 283 283
BID -0.091 0.17 -10000 0 -0.37 104 104
MAP3K1 -0.044 0.11 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.19 0.36 -10000 0 -0.67 167 167
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.013 0.094 -10000 0 -0.21 35 35
neuron apoptosis 0.011 0.045 -10000 0 -0.62 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.34 -10000 0 -0.64 167 167
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.05 0.15 -10000 0 -0.52 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.34 -10000 0 -0.77 104 104
CASP7 0.051 0.13 0.34 80 -10000 0 80
KRT18 -0.002 0.046 -10000 0 -0.3 2 2
apoptosis -0.18 0.32 -10000 0 -0.69 111 111
DFFA -0.19 0.36 -10000 0 -0.67 167 167
DFFB -0.19 0.36 -10000 0 -0.67 167 167
PARP1 -0.013 0.095 0.21 35 -10000 0 35
actin filament polymerization 0.16 0.33 0.72 105 -10000 0 105
TNF 0.003 0.1 -10000 0 -0.8 8 8
CYCS -0.069 0.13 -10000 0 -0.28 105 105
SATB1 -0.037 0.15 -10000 0 -0.48 3 3
SLK -0.19 0.36 -10000 0 -0.67 167 167
p15 BID/BAX -0.074 0.15 -10000 0 -10000 0 0
CASP2 0.031 0.089 -10000 0 -10000 0 0
JNK cascade 0.044 0.11 -10000 0 -10000 0 0
CASP3 -0.21 0.37 -10000 0 -0.71 167 167
LMNB2 0.011 0.085 -10000 0 -0.41 3 3
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.081 0.19 -10000 0 -0.52 80 80
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.54 283 283
stress fiber formation -0.18 0.35 -10000 0 -0.65 167 167
GZMB -0.33 0.51 -10000 0 -0.97 185 185
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.008 0.09 -10000 0 -0.37 7 7
APP 0.01 0.045 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.66 112 112
LMNA 0.011 0.085 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.03 0.073 -10000 0 -0.41 7 7
LRDD 0.004 0.1 -10000 0 -0.85 7 7
SREBF1 -0.19 0.36 -10000 0 -0.67 166 166
APAF-1/Caspase 9 -0.009 0.063 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.13 0.26 -10000 0 -0.48 167 167
CFL2 -0.17 0.34 -10000 0 -0.75 105 105
GAS2 -0.2 0.36 -10000 0 -0.66 178 178
positive regulation of apoptosis 0.015 0.085 -10000 0 -0.4 3 3
PRF1 -0.21 0.38 -10000 0 -0.86 131 131
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.25 0.27 -9999 0 -0.54 244 244
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.068 -9999 0 -10000 0 0
AURKB -0.4 0.44 -9999 0 -0.86 243 243
AURKC 0.012 0.055 -9999 0 -0.86 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.072 -9999 0 -0.68 5 5
VEGFR1 homodimer/NRP1 -0.008 0.073 -9999 0 -0.62 7 7
mol:DAG -0.26 0.29 -9999 0 -0.52 287 287
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 234 234
CaM/Ca2+ -0.27 0.25 -9999 0 -0.92 7 7
HIF1A 0.02 0.058 -9999 0 -0.72 2 2
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.23 0.21 -9999 0 -0.95 6 6
PLCG1 -0.27 0.29 -9999 0 -0.52 287 287
NOS3 -0.18 0.24 -9999 0 -0.85 6 6
CBL 0.014 0.033 -9999 0 -0.75 1 1
mol:NO -0.17 0.24 -9999 0 -0.8 6 6
FLT1 0.031 0.087 -9999 0 -0.71 7 7
PGF -0.47 0.44 -9999 0 -0.86 286 286
VEGFR1 homodimer/NRP2/VEGFR121 -0.25 0.27 -9999 0 -0.53 239 239
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.76 6 6
endothelial cell proliferation -0.2 0.26 -9999 0 -0.86 8 8
mol:Ca2+ -0.26 0.29 -9999 0 -0.52 287 287
MAPK3 -0.21 0.26 -9999 0 -0.88 6 6
MAPK1 -0.21 0.26 -9999 0 -0.88 6 6
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
PLGF homodimer -0.47 0.44 -9999 0 -0.86 286 286
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
VEGFA homodimer -0.38 0.44 -9999 0 -0.86 233 233
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 234 234
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.85 6 6
PI3K -0.27 0.25 -9999 0 -0.99 7 7
PRKCA -0.24 0.27 -9999 0 -0.89 7 7
PRKCB -0.24 0.28 -9999 0 -0.91 9 9
VEGFR1 homodimer/PLGF homodimer -0.32 0.3 -9999 0 -0.58 287 287
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.52 287 287
RASA1 0.046 0.079 -9999 0 -0.65 6 6
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.031 0.087 -9999 0 -0.71 7 7
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.8 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.25 -9999 0 -0.96 7 7
mol:L-citrulline -0.17 0.24 -9999 0 -0.8 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.94 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -0.53 235 235
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.99 6 6
PDPK1 -0.22 0.27 -9999 0 -1 6 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -0.53 234 234
mol:NADP -0.17 0.24 -9999 0 -0.8 6 6
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.25 -9999 0 -0.92 6 6
VEGFR1 homodimer/NRP2 -0.016 0.097 -9999 0 -0.61 12 12
Glypican 2 network

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
MDK -0.05 0.23 -9999 0 -0.86 39 39
GPC2 -0.085 0.28 -9999 0 -0.86 59 59
GPC2/Midkine -0.12 0.28 -9999 0 -0.74 87 87
neuron projection morphogenesis -0.12 0.28 -9999 0 -0.73 87 87
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.027 0.08 -10000 0 -0.73 6 6
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.011 0.064 -10000 0 -0.82 3 3
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.45 38 38
EPO -0.4 0.41 -10000 0 -0.9 147 147
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.014 -10000 0 -10000 0 0
SERPINE1 -0.34 0.41 -10000 0 -0.93 118 118
FLT1 -0.019 0.078 -10000 0 -0.76 5 5
ADORA2A -0.3 0.34 -10000 0 -0.82 81 81
germ cell development -0.4 0.44 -10000 0 -0.89 203 203
SLC11A2 -0.29 0.34 -10000 0 -0.81 81 81
BHLHE40 -0.29 0.34 -10000 0 -0.81 81 81
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.52 214 214
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.023 0.057 -10000 0 -1.2 1 1
KDR -0.015 0.066 -10000 0 -1.4 1 1
PGK1 -0.29 0.34 -10000 0 -0.81 81 81
SIRT1 0.014 0.005 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.35 0.42 -10000 0 -1 81 81
EPAS1 -0.27 0.19 -10000 0 -0.44 217 217
SP1 0.026 0.005 -10000 0 -10000 0 0
ABCG2 -0.29 0.35 -10000 0 -0.81 82 82
EFNA1 -0.29 0.35 -10000 0 -0.81 82 82
FXN -0.3 0.34 -10000 0 -0.82 81 81
POU5F1 -0.43 0.48 -10000 0 -0.95 203 203
neuron apoptosis 0.34 0.4 0.96 81 -10000 0 81
EP300 0.014 0.033 -10000 0 -0.75 1 1
EGLN3 -0.76 0.29 -10000 0 -0.87 456 456
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.004 0.046 -10000 0 -0.53 4 4
VHL 0.014 0.033 -10000 0 -0.75 1 1
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.32 0.37 -10000 0 -0.89 86 86
TWIST1 -0.31 0.35 -10000 0 -0.83 84 84
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.56 82 82
VEGFA -0.47 0.49 -10000 0 -0.94 240 240
CREBBP 0.016 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.007 0.086 -9999 0 -0.86 5 5
CCL5 -0.36 0.44 -9999 0 -0.86 221 221
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.59 91 91
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 -0.2 0.22 -9999 0 -0.56 91 91
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.56 91 91
MAPK3 -0.16 0.2 -9999 0 -0.7 15 15
HGF/MET -0.033 0.15 -9999 0 -0.66 26 26
TGFB1/TGF beta receptor Type II 0.007 0.086 -9999 0 -0.86 5 5
BSG 0.014 0.039 -9999 0 -0.86 1 1
keratinocyte migration -0.2 0.21 -9999 0 -0.55 91 91
Syndecan-1/RANTES -0.42 0.33 -9999 0 -0.68 275 275
Syndecan-1/CD147 -0.2 0.19 -9999 0 -0.57 59 59
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 91 91
LAMA5 0.014 0.033 -9999 0 -0.75 1 1
positive regulation of cell-cell adhesion -0.21 0.18 -9999 0 -0.52 91 91
MMP7 -0.12 0.3 -9999 0 -0.76 93 93
HGF -0.021 0.17 -9999 0 -0.8 23 23
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.57 91 91
Syndecan-1/HGF/MET -0.23 0.22 -9999 0 -0.63 75 75
regulation of cell adhesion -0.15 0.2 -9999 0 -0.67 15 15
HPSE 0.013 0.047 -9999 0 -0.75 2 2
positive regulation of cell migration -0.22 0.23 -9999 0 -0.59 91 91
SDC1 -0.22 0.23 -9999 0 -0.6 91 91
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.59 91 91
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
MAPK1 -0.16 0.2 -9999 0 -0.7 15 15
homophilic cell adhesion -0.22 0.22 -9999 0 -0.58 91 91
MMP1 -0.15 0.34 -9999 0 -0.83 102 102
IL23-mediated 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
CCL2 -0.25 0.48 -10000 0 -1.1 68 68
IL23A -0.24 0.47 -10000 0 -1.1 46 46
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.39 -10000 0 -1 76 76
positive regulation of T cell mediated cytotoxicity -0.29 0.53 -10000 0 -1.1 88 88
ITGA3 -0.24 0.47 -10000 0 -1.1 62 62
IL17F -0.15 0.34 -10000 0 -0.74 39 39
IL12B -0.085 0.29 -10000 0 -0.89 60 60
STAT1 (dimer) -0.28 0.5 -10000 0 -1.1 82 82
CD4 -0.25 0.48 -10000 0 -1.1 65 65
IL23 -0.28 0.48 -10000 0 -1.2 63 63
IL23R -0.012 0.15 -10000 0 -0.8 10 10
IL1B -0.25 0.48 -10000 0 -1.1 66 66
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.25 0.47 -10000 0 -1.1 66 66
TYK2 0.016 0.025 -10000 0 -10000 0 0
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.22 0.39 -10000 0 -0.88 133 133
IL12RB1 -0.26 0.42 -10000 0 -0.89 159 159
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
IL12Rbeta1/TYK2 -0.2 0.34 -10000 0 -0.7 159 159
IL23R/JAK2 -0.011 0.16 -10000 0 -0.78 9 9
positive regulation of chronic inflammatory response -0.29 0.53 -10000 0 -1.1 88 88
natural killer cell activation 0.002 0.012 0.063 10 -10000 0 10
JAK2 0.021 0.035 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
NFKB1 0.01 0.034 -10000 0 -0.74 1 1
RELA 0.011 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.46 -10000 0 -1.1 63 63
ALOX12B -0.31 0.5 -10000 0 -1.1 83 83
CXCL1 -0.29 0.52 -10000 0 -1.2 77 77
T cell proliferation -0.29 0.53 -10000 0 -1.1 88 88
NFKBIA 0.011 0.009 -10000 0 -10000 0 0
IL17A -0.1 0.29 -10000 0 -0.59 11 11
PI3K -0.33 0.4 -10000 0 -1 89 89
IFNG -0.053 0.07 0.13 4 -0.12 215 219
STAT3 (dimer) -0.32 0.38 -10000 0 -0.99 84 84
IL18R1 -0.004 0.1 -10000 0 -0.81 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.38 -10000 0 -0.85 64 64
IL18/IL18R -0.17 0.28 -10000 0 -0.62 145 145
macrophage activation -0.017 0.018 -10000 0 -0.045 7 7
TNF -0.26 0.49 -10000 0 -1.1 68 68
STAT3/STAT4 -0.36 0.43 -10000 0 -1.1 98 98
STAT4 (dimer) -0.3 0.53 -10000 0 -1.2 91 91
IL18 -0.003 0.1 -10000 0 -0.86 7 7
IL19 -0.25 0.46 -10000 0 -1 75 75
STAT5A (dimer) -0.28 0.5 -10000 0 -1.1 87 87
STAT1 0.014 0.039 -10000 0 -0.86 1 1
SOCS3 0.012 0.055 -10000 0 -0.86 2 2
CXCL9 -0.4 0.59 -10000 0 -1.1 162 162
MPO -0.26 0.48 -10000 0 -1.1 70 70
positive regulation of humoral immune response -0.29 0.53 -10000 0 -1.1 88 88
IL23/IL23R/JAK2/TYK2 -0.3 0.55 -10000 0 -1.2 88 88
IL6 -0.3 0.53 -10000 0 -1.2 90 90
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.016 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 10 -10000 0 10
CD3E -0.39 0.6 -10000 0 -1.1 162 162
keratinocyte proliferation -0.29 0.53 -10000 0 -1.1 88 88
NOS2 -0.25 0.47 -10000 0 -1.1 67 67
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.006 0.13 -9999 0 -0.78 14 14
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.064 -9999 0 -0.82 3 3
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.047 -9999 0 -0.39 1 1
HIF1A -0.099 0.039 -9999 0 -0.42 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.039 -9999 0 -0.49 2 2
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.16 -9999 0 -0.86 499 499
ARNT/IPAS -0.016 0.096 -9999 0 -0.59 14 14
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.047 -9999 0 -0.39 1 1
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.048 -9999 0 -0.55 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.047 -9999 0 -0.39 1 1
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 455 455
HIF1A/RACK1/Elongin B/Elongin C -0.067 0.05 -9999 0 -0.54 4 4
VHL 0.014 0.033 -9999 0 -0.75 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.047 -9999 0 -0.39 1 1
EGLN3 -0.76 0.29 -9999 0 -0.86 456 456
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.003 0.035 -9999 0 -0.61 1 1
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.56 0.11 -9999 0 -0.57 499 499
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.6 0.31 -9999 0 -0.85 277 277
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.31 -9999 0 -0.84 82 82
SMAD9 -0.064 0.083 -9999 0 -0.57 10 10
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.52 18 18
BMP7/USAG1 -0.7 0.34 -9999 0 -0.8 452 452
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 14 14
SMAD1 0.002 0.042 -9999 0 -10000 0 0
BMP2 0.01 0.069 -9999 0 -0.78 4 4
SMAD1/SMAD1/SMAD4 0 0.001 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.35 -9999 0 -0.75 355 355
BMPR1A-1B/BAMBI -0.33 0.23 -9999 0 -0.85 5 5
AHSG -0.013 0.13 -9999 0 -0.86 12 12
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.007 0.058 -9999 0 -0.5 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.49 18 18
BMP2-4 (homodimer) -0.008 0.067 -9999 0 -0.57 7 7
RGMB 0.012 0.055 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.85 4 4
RGMA 0.008 0.074 -9999 0 -0.75 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.13 -9999 0 -0.56 18 18
BMP2-4/USAG1 -0.31 0.24 -9999 0 -0.48 335 335
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 14 14
SOSTDC1 -0.48 0.36 -9999 0 -0.75 334 334
BMP7/BMPR2/BMPR1A-1B -0.58 0.3 -9999 0 -0.86 257 257
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.094 -9999 0 -0.74 8 8
HFE2 -0.018 0.16 -9999 0 -0.86 18 18
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.017 0.099 -9999 0 -0.56 16 16
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.5 14 14
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.5 14 14
BMP7 (homodimer) -0.5 0.35 -9999 0 -0.74 350 350
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.024 0.12 -9999 0 -0.62 20 20
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.02 0.1 -9999 0 -0.55 19 19
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.18 0.33 -9999 0 -0.76 128 128
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.26 -9999 0 -0.56 355 355
CHRDL1 -0.38 0.38 -9999 0 -0.75 271 271
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.005 0.088 -9999 0 -0.75 7 7
SMURF2 0.014 0.033 -9999 0 -0.75 1 1
BMP2-4/CHRDL1 -0.26 0.25 -9999 0 -0.48 273 273
BMP2-4/GREM1 -0.13 0.22 -9999 0 -0.49 133 133
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.088 -9999 0 -0.53 10 10
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.5 0.35 -9999 0 -0.75 350 350
BMP6 0.004 0.094 -9999 0 -0.75 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.13 -9999 0 -0.46 18 18
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.18 -9999 0 -0.6 62 62
CHRD -0.001 0.12 -9999 0 -0.78 11 11
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 18 18
BMP4 0.011 0.058 -9999 0 -0.75 3 3
FST -0.074 0.25 -9999 0 -0.77 59 59
BMP2-4/NOG -0.095 0.21 -9999 0 -0.56 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.55 0.29 -9999 0 -0.81 257 257
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.25 0.26 -10000 0 -0.74 32 32
IHH -0.099 0.23 -10000 0 -0.82 47 47
SHH Np/Cholesterol/GAS1 -0.037 0.12 -10000 0 -0.45 42 42
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.12 0.45 42 -10000 0 42
SMO/beta Arrestin2 -0.15 0.15 -10000 0 -0.6 33 33
SMO -0.13 0.19 -10000 0 -0.64 33 33
AKT1 -0.042 0.093 -10000 0 -0.46 1 1
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.13 0.19 -10000 0 -0.62 33 33
STIL -0.095 0.17 -10000 0 -0.67 10 10
DHH N/PTCH2 -0.044 0.16 -10000 0 -0.63 36 36
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.62 36 36
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
DHH -0.001 0.11 -10000 0 -0.75 11 11
PTHLH -0.44 0.41 -10000 0 -0.74 322 322
determination of left/right symmetry -0.13 0.19 -10000 0 -0.62 33 33
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
skeletal system development -0.44 0.4 -10000 0 -0.73 322 322
IHH N/Hhip -0.2 0.31 -10000 0 -0.65 160 160
DHH N/Hhip -0.15 0.26 -10000 0 -0.57 138 138
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.19 -10000 0 -0.62 33 33
pancreas development -0.18 0.33 -10000 0 -0.75 129 129
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.032 0.18 -10000 0 -0.75 32 32
somite specification -0.13 0.19 -10000 0 -0.62 33 33
SHH Np/Cholesterol/PTCH1 -0.14 0.14 -10000 0 -0.67 10 10
SHH Np/Cholesterol/PTCH2 -0.035 0.13 -10000 0 -0.51 36 36
SHH Np/Cholesterol/Megalin -0.048 0.15 -10000 0 -0.48 51 51
SHH 0.018 0.087 -10000 0 -0.57 11 11
catabolic process -0.16 0.19 -10000 0 -0.65 32 32
SMO/Vitamin D3 -0.11 0.18 -10000 0 -0.72 7 7
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.46 135 135
LRP2 -0.051 0.22 -10000 0 -0.75 45 45
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.77 19 19
SHH Np/Cholesterol/BOC -0.009 0.064 -10000 0 -0.45 11 11
SHH Np/Cholesterol/CDO -0.07 0.18 -10000 0 -0.53 69 69
mesenchymal cell differentiation 0.12 0.21 0.46 135 -10000 0 135
mol:Vitamin D3 -0.11 0.17 -10000 0 -0.67 10 10
IHH N/PTCH2 -0.084 0.22 -10000 0 -0.62 70 70
CDON -0.084 0.28 -10000 0 -0.86 59 59
IHH N/PTCH1 -0.16 0.2 -10000 0 -0.66 32 32
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.56 45 45
PTCH2 -0.027 0.19 -10000 0 -0.86 25 25
SHH Np/Cholesterol -0.01 0.066 -10000 0 -0.46 11 11
PTCH1 -0.16 0.19 -10000 0 -0.66 32 32
HHIP -0.18 0.33 -10000 0 -0.76 129 129
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.16 0.23 -9999 0 -0.7 61 61
AP1 -0.16 0.21 -9999 0 -0.56 83 83
mol:PIP3 -0.23 0.34 -9999 0 -0.7 143 143
IKBKB -0.088 0.17 -9999 0 -0.34 84 84
AKT1 -0.17 0.21 -9999 0 -0.73 22 22
IKBKG -0.088 0.17 -9999 0 -0.34 82 82
MS4A2 -0.18 0.36 -9999 0 -0.86 114 114
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.034 -9999 0 -0.75 1 1
MAP3K1 -0.12 0.26 -9999 0 -0.58 90 90
mol:Ca2+ -0.16 0.24 -9999 0 -0.48 143 143
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.12 0.15 -9999 0 -0.54 21 21
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.002 0.03 -9999 0 -0.48 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
PLD2 -0.18 0.28 -9999 0 -0.92 20 20
PTPN13 -0.069 0.16 -9999 0 -0.5 17 17
PTPN11 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.044 0.17 -9999 0 -0.4 9 9
SYK 0.008 0.048 -9999 0 -0.76 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.3 0.32 -9999 0 -0.76 141 141
LAT -0.25 0.3 -9999 0 -0.65 155 155
PAK2 -0.15 0.29 -9999 0 -0.64 114 114
NFATC2 -0.069 0.095 -9999 0 -0.74 3 3
HRAS -0.18 0.32 -9999 0 -0.7 121 121
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.04 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.32 -9999 0 -0.62 213 213
Antigen/IgE/Fc epsilon R1 -0.24 0.3 -9999 0 -0.58 213 213
mol:GDP -0.21 0.36 -9999 0 -0.77 128 128
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.034 -9999 0 -0.75 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.13 0.16 -9999 0 -0.58 21 21
CHUK -0.088 0.17 -9999 0 -0.34 82 82
KLRG1 -0.12 0.15 -9999 0 -0.55 21 21
VAV1 -0.2 0.32 -9999 0 -0.69 135 135
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.15 -9999 0 -0.55 22 22
negative regulation of mast cell degranulation -0.11 0.15 -9999 0 -0.56 23 23
BTK -0.18 0.24 -9999 0 -0.63 94 94
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.22 -9999 0 -0.58 85 85
GAB2/PI3K/SHP2 -0.18 0.24 -9999 0 -0.82 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.15 -9999 0 -0.55 21 21
RAF1 0.026 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.31 0.39 -9999 0 -0.96 99 99
FCER1G -0.16 0.34 -9999 0 -0.87 97 97
FCER1A -0.022 0.16 -9999 0 -0.77 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.28 -9999 0 -0.55 199 199
MAPK3 0.04 0.026 -9999 0 -10000 0 0
MAPK1 0.04 0.026 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
MAPK8 -0.012 0.076 -9999 0 -0.68 1 1
DUSP1 0.014 0.039 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.07 0.074 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.074 0.16 -9999 0 -0.48 21 21
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.22 0.29 -9999 0 -0.72 115 115
FER -0.12 0.16 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.15 0.19 -9999 0 -0.42 161 161
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.2 0.36 -9999 0 -0.75 131 131
cytokine secretion -0.051 0.053 -9999 0 -10000 0 0
SPHK1 -0.16 0.22 -9999 0 -0.64 58 58
PTK2 -0.077 0.16 -9999 0 -0.5 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.25 0.31 -9999 0 -0.77 109 109
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.31 -9999 0 -0.68 111 111
MAP2K2 0.034 0.031 -9999 0 -0.42 1 1
MAP2K1 0.035 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.53 21 21
MAP2K4 0.017 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.32 0.41 -9999 0 -0.73 224 224
mol:Choline -0.17 0.28 -9999 0 -0.89 20 20
SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.52 16 16
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.062 0.15 -9999 0 -0.47 13 13
HCLS1 -0.13 0.18 -9999 0 -0.67 29 29
PRKCB -0.14 0.23 -9999 0 -0.47 124 124
FCGR2B -0.14 0.34 -9999 0 -0.86 95 95
IGHE -0.005 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.16 -9999 0 -0.58 23 23
LCP2 -0.041 0.22 -9999 0 -0.87 33 33
PLA2G4A -0.12 0.16 -9999 0 -0.56 25 25
RASA1 0.014 0.033 -9999 0 -0.75 1 1
mol:Phosphatidic acid -0.17 0.28 -9999 0 -0.89 20 20
IKK complex -0.048 0.13 -9999 0 -0.28 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.009 0.086 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.078 0.2 0.63 27 -0.44 3 30
IL27/IL27R/JAK1 -0.083 0.35 0.58 1 -0.86 57 58
TBX21 -0.21 0.41 0.5 1 -0.76 155 156
IL12B -0.093 0.28 -10000 0 -0.87 60 60
IL12A 0.008 0.032 -10000 0 -0.69 1 1
IL6ST -0.014 0.14 -10000 0 -0.76 17 17
IL27RA/JAK1 0.01 0.062 -10000 0 -0.7 1 1
IL27 -0.045 0.21 -10000 0 -0.88 32 32
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.078 0.2 0.63 27 -0.44 3 30
T cell proliferation during immune response 0.078 0.2 0.63 27 -0.44 3 30
MAPKKK cascade -0.078 0.2 0.44 3 -0.63 27 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.86 1 1
IL12RB1 -0.26 0.41 -10000 0 -0.87 159 159
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.72 95 96
IL27/IL27R/JAK2/TYK2 -0.08 0.2 0.44 3 -0.64 27 30
positive regulation of T cell mediated cytotoxicity -0.078 0.2 0.44 3 -0.63 27 30
STAT1 (dimer) -0.07 0.51 0.54 118 -1 68 186
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.082 0.18 0.39 3 -0.63 22 25
T cell proliferation -0.12 0.25 -10000 0 -0.71 48 48
IL12/IL12R/TYK2/JAK2 -0.18 0.27 -10000 0 -0.75 45 45
IL17A -0.025 0.13 -10000 0 -0.74 2 2
mast cell activation 0.078 0.2 0.63 27 -0.44 3 30
IFNG -0.041 0.066 0.13 3 -0.11 235 238
T cell differentiation -0.011 0.011 0.03 3 -0.026 139 142
STAT3 (dimer) -0.082 0.18 0.39 3 -0.63 22 25
STAT5A (dimer) -0.082 0.18 0.39 3 -0.62 23 26
STAT4 (dimer) -0.11 0.24 0.39 2 -0.77 42 44
STAT4 -0.035 0.2 -10000 0 -0.86 30 30
T cell activation -0.012 0.007 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.043 0.1 -10000 0 -0.71 1 1
GATA3 -0.61 0.68 -10000 0 -1.3 251 251
IL18 0.005 0.08 -10000 0 -0.68 7 7
positive regulation of mast cell cytokine production -0.082 0.18 0.38 3 -0.62 22 25
IL27/EBI3 -0.12 0.33 -10000 0 -0.83 85 85
IL27RA -0.003 0.063 -10000 0 -0.76 1 1
IL6 -0.087 0.28 -10000 0 -0.82 65 65
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0 0.088 -10000 0 -0.6 10 10
IL1B 0.006 0.073 -10000 0 -0.66 6 6
EBI3 -0.12 0.31 -10000 0 -0.88 75 75
TNF 0.004 0.079 -10000 0 -0.63 8 8
Effects of Botulinum toxin

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
STX1A 0.007 0.073 -9999 0 -0.66 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.021 0.12 -9999 0 -0.67 16 16
STXBP1 0.014 0.033 -9999 0 -0.75 1 1
ACh/CHRNA1 -0.27 0.31 -9999 0 -0.63 226 226
RAB3GAP2/RIMS1/UNC13B -0.018 0.1 -9999 0 -0.58 16 16
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 -0.015 0.15 -9999 0 -0.86 16 16
mol:ACh -0.009 0.053 -9999 0 -0.13 80 80
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.27 0.31 -9999 0 -0.63 226 226
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.37 0.44 -9999 0 -0.86 226 226
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.083 0.2 -9999 0 -0.53 84 84
SNAP25 -0.039 0.12 -9999 0 -0.33 76 76
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.75 84 84
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.065 -9999 0 -0.56 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.1 -9999 0 -0.62 4 4
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.36 -10000 0 -1.1 69 69
NFATC2 -0.079 0.23 -10000 0 -0.68 29 29
NFATC3 -0.021 0.064 -10000 0 -10000 0 0
CD40LG -0.24 0.44 -10000 0 -1.2 56 56
ITCH 0.054 0.058 -10000 0 -10000 0 0
CBLB 0.054 0.058 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.55 0.56 -10000 0 -1.2 197 197
JUNB 0.013 0.047 -10000 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.058 -10000 0 -10000 0 0
T cell anergy 0.023 0.095 -10000 0 -0.53 2 2
TLE4 -0.03 0.17 -10000 0 -0.7 7 7
Jun/NFAT1-c-4/p21SNFT -0.24 0.28 -10000 0 -1 24 24
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -1.2 38 38
IKZF1 -0.13 0.36 -10000 0 -0.88 91 91
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.72 110 110
AP-1/NFAT1 -0.093 0.16 -10000 0 -0.68 12 12
CALM1 0.028 0.036 -10000 0 -10000 0 0
EGR2 -0.11 0.29 -10000 0 -1.4 9 9
EGR3 -0.11 0.29 -10000 0 -1.4 8 8
NFAT1/FOXP3 -0.28 0.4 -10000 0 -0.94 116 116
EGR1 0.001 0.11 -10000 0 -0.74 11 11
JUN 0.005 0.022 -10000 0 -10000 0 0
EGR4 0.006 0.077 -10000 0 -0.86 4 4
mol:Ca2+ 0.009 0.04 -10000 0 -10000 0 0
GBP3 -0.034 0.18 -10000 0 -0.79 9 9
FOSL1 -0.027 0.19 -10000 0 -0.86 25 25
NFAT1-c-4/MAF/IRF4 -0.27 0.36 -10000 0 -0.94 84 84
DGKA -0.034 0.19 -10000 0 -1 7 7
CREM 0.015 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.21 -10000 0 -1.1 7 7
CTLA4 -0.44 0.58 -10000 0 -1 237 237
NFAT1-c-4 (dimer)/EGR1 -0.17 0.24 -10000 0 -1.1 11 11
NFAT1-c-4 (dimer)/EGR4 -0.17 0.23 -10000 0 -1.2 7 7
FOS -0.014 0.12 -10000 0 -0.76 13 13
IFNG -0.5 0.52 -10000 0 -1 232 232
T cell activation -0.049 0.22 -10000 0 -0.83 16 16
MAF 0.016 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.064 0.2 0.91 3 -10000 0 3
TNF -0.095 0.28 -10000 0 -1.1 13 13
FASLG -0.34 0.48 -10000 0 -1.2 19 19
TBX21 -0.31 0.44 -10000 0 -0.93 169 169
BATF3 -0.061 0.25 -10000 0 -0.86 45 45
PRKCQ -0.034 0.13 -10000 0 -0.75 15 15
PTPN1 -0.03 0.17 -10000 0 -0.7 7 7
NFAT1-c-4/ICER1 -0.17 0.21 -10000 0 -1.2 6 6
GATA3 -0.35 0.38 -10000 0 -0.75 251 251
T-helper 1 cell differentiation -0.49 0.5 -10000 0 -1 233 233
IL2RA -0.39 0.46 -10000 0 -1.1 128 128
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.03 0.17 -10000 0 -0.72 6 6
E2F1 -0.081 0.28 -10000 0 -0.85 62 62
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.03 0.17 -10000 0 -0.7 7 7
IRF4 -0.18 0.37 -10000 0 -0.86 118 118
PTGS2 -0.21 0.4 -10000 0 -1.1 35 35
CSF2 -0.21 0.4 -10000 0 -1.1 33 33
JunB/Fra1/NFAT1-c-4 -0.18 0.22 -10000 0 -1 10 10
IL4 -0.36 0.29 -10000 0 -0.76 108 108
IL5 -0.2 0.37 -10000 0 -1.1 25 25
IL2 -0.05 0.22 -10000 0 -0.85 16 16
IL3 -0.05 0.049 -10000 0 -10000 0 0
RNF128 0.033 0.16 -10000 0 -0.79 19 19
NFATC1 -0.064 0.2 -10000 0 -0.91 3 3
CDK4 0.035 0.18 0.57 1 -10000 0 1
PTPRK -0.03 0.17 -10000 0 -0.7 7 7
IL8 -0.22 0.42 -10000 0 -1.1 41 41
POU2F1 0.016 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.056 0.17 -9999 0 -0.53 55 55
EFNA5 -0.057 0.22 -9999 0 -0.75 49 49
FYN -0.026 0.16 -9999 0 -0.48 55 55
neuron projection morphogenesis -0.056 0.17 -9999 0 -0.53 55 55
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.056 0.17 -9999 0 -0.53 55 55
EPHA5 -0.008 0.11 -9999 0 -0.86 8 8
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.043 -9999 0 -0.49 4 4
ARNO/beta Arrestin1-2 -0.018 0.063 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.75 1 1
USP6 0.014 0.039 -9999 0 -0.86 1 1
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.51 0.18 -9999 0 -0.57 467 467
ARRB2 -0.014 0.11 -9999 0 -0.39 38 38
mol:GTP -0.011 0.048 -9999 0 -0.29 1 1
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.085 0.28 -9999 0 -0.86 59 59
EGF -0.67 0.23 -9999 0 -0.75 466 466
somatostatin receptor activity 0 0 -9999 0 -0.001 11 11
ARAP2 0.013 0.047 -9999 0 -0.75 2 2
mol:GDP -0.057 0.095 -9999 0 -0.34 22 22
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 4 4
ITGA2B -0.015 0.16 -9999 0 -0.86 18 18
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
ADAP1 0.01 0.067 -9999 0 -0.75 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.033 0.15 -9999 0 -0.66 26 26
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.087 0.09 -9999 0 -0.35 16 16
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.44 0.16 -9999 0 -0.48 467 467
ADRB2 0.013 0.047 -9999 0 -0.75 2 2
receptor agonist activity 0 0 -9999 0 0 11 11
actin filament binding 0 0 -9999 0 -0.001 11 11
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
GNAQ 0.015 0.001 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 10 10
ARF6/GDP -0.068 0.14 -9999 0 -0.4 6 6
ARF6/GDP/GULP/ACAP1 -0.23 0.26 -9999 0 -0.53 198 198
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.021 0.1 -9999 0 -0.52 17 17
ACAP1 -0.32 0.43 -9999 0 -0.86 196 196
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.043 0.15 -9999 0 -0.59 38 38
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
HGF -0.021 0.17 -9999 0 -0.8 23 23
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
fibronectin binding 0 0 -9999 0 -0.001 10 10
endosomal lumen acidification 0 0 -9999 0 -0.001 17 17
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.011 0.14 -9999 0 -0.75 18 18
GNAQ/ARNO 0.009 0.01 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 10 10
GNA11 0.011 0.058 -9999 0 -0.75 3 3
LHCGR -0.057 0.22 -9999 0 -0.86 37 37
AGTR1 -0.027 0.18 -9999 0 -0.75 29 29
desensitization of G-protein coupled receptor protein signaling pathway -0.043 0.15 -9999 0 -0.59 38 38
IPCEF1/ARNO -0.34 0.13 -9999 0 -0.82 8 8
alphaIIb/beta3 Integrin -0.027 0.13 -9999 0 -0.64 22 22
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.025 -9999 0 -0.56 1 1
Necdin/E2F1 -0.083 0.22 -9999 0 -0.68 63 63
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.081 0.2 -9999 0 -0.54 76 76
NGF (dimer)/p75(NTR)/BEX1 -0.27 0.31 -9999 0 -0.56 249 249
NT-4/5 (dimer)/p75(NTR) -0.054 0.18 -9999 0 -0.67 42 42
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.034 0.22 -9999 0 -0.95 9 9
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.1 0.3 -9999 0 -0.86 69 69
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.2 -9999 0 -0.61 61 61
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.25 -9999 0 -0.61 99 99
LINGO1 -0.022 0.18 -9999 0 -0.86 22 22
Sortilin/TRAF6/NRIF -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.3 -9999 0 -0.86 69 69
NTRK1 -0.045 0.21 -9999 0 -0.76 40 40
RTN4R 0.004 0.1 -9999 0 -0.85 7 7
neuron apoptosis -0.067 0.23 -9999 0 -0.67 30 30
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.062 0.24 -9999 0 -0.63 78 78
ARHGDIA 0.014 0.033 -9999 0 -0.75 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.086 0.21 -9999 0 -0.58 76 76
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.089 0.22 -9999 0 -0.58 77 77
Mammalian IAPs/DIABLO -0.081 0.19 -9999 0 -0.52 80 80
proNGF (dimer) -0.067 0.26 -9999 0 -0.86 49 49
MAGED1 0.014 0.039 -9999 0 -0.86 1 1
APP 0.014 0.033 -9999 0 -0.75 1 1
NT-4/5 (dimer) -0.004 0.093 -9999 0 -0.86 6 6
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.081 0.2 -9999 0 -0.54 76 76
NGF -0.067 0.26 -9999 0 -0.86 49 49
cell cycle arrest -0.014 0.25 -9999 0 -0.56 76 76
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.046 0.11 -9999 0 -0.57 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.047 0.16 -9999 0 -0.58 42 42
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.093 0.23 -9999 0 -0.62 77 77
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.046 0.22 -9999 0 -0.57 76 76
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.035 0.087 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.047 0.17 -9999 0 -0.66 37 37
BEX1 -0.27 0.37 -9999 0 -0.75 191 191
mol:GDP -0.074 0.24 -9999 0 -0.64 77 77
NGF (dimer) -0.35 0.3 -9999 0 -0.84 88 88
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.066 0.19 -9999 0 -0.56 61 61
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RAC1/GTP -0.082 0.21 -9999 0 -0.56 77 77
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.093 0.23 -9999 0 -0.63 77 77
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.08 0.22 -9999 0 -0.67 62 62
NT3 (dimer) 0.005 0.092 -9999 0 -0.78 7 7
TP53 -0.042 0.22 -9999 0 -0.91 7 7
PRDM4 -0.047 0.23 -9999 0 -0.57 76 76
BDNF (dimer) -0.42 0.36 -9999 0 -0.86 144 144
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
SORT1 0.014 0.033 -9999 0 -0.75 1 1
activation of caspase activity -0.079 0.2 -9999 0 -0.53 76 76
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.086 0.21 -9999 0 -0.58 76 76
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.025 0.21 -9999 0 -0.64 22 22
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.047 0.23 -9999 0 -0.57 76 76
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.094 0.23 -9999 0 -0.63 78 78
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.054 0.18 -9999 0 -0.67 42 42
MAPK8 -0.023 0.2 -9999 0 -0.63 21 21
MAPK9 -0.022 0.2 -9999 0 -0.64 20 20
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.092 -9999 0 -0.78 7 7
NTF4 -0.004 0.093 -9999 0 -0.86 6 6
NDN 0.011 0.058 -9999 0 -0.75 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.073 0.18 -9999 0 -0.91 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.019 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.092 0.23 -9999 0 -0.62 77 77
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.099 0.21 -9999 0 -0.52 97 97
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.23 -9999 0 -0.56 97 97
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.088 0.22 -9999 0 -0.66 69 69
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 80 80
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.006 0.24 -9999 0 -0.53 60 60
BAD -0.011 0.2 -9999 0 -0.6 21 21
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
NGFR -0.045 0.22 -9999 0 -0.86 36 36
CYCS -0.036 0.22 -9999 0 -0.97 9 9
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.086 0.21 -9999 0 -0.58 77 77
BCL2L11 -0.011 0.2 -9999 0 -0.6 21 21
BDNF (dimer)/p75(NTR) -0.13 0.28 -9999 0 -0.7 99 99
PI3K -0.087 0.22 -9999 0 -0.58 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.086 0.21 -9999 0 -0.58 76 76
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.26 -9999 0 -0.72 77 77
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.087 0.21 -9999 0 -0.58 77 77
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.058 -9999 0 -0.75 3 3
PLG -0.38 0.38 -9999 0 -0.75 269 269
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.13 0.23 -9999 0 -0.67 44 44
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.005 0.18 -9999 0 -0.53 21 21
E2F1 -0.09 0.29 -9999 0 -0.86 62 62
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.071 0.15 -9999 0 -0.6 11 11
NGF (dimer)/TRKA -0.11 0.24 -9999 0 -0.63 87 87
MMP7 -0.12 0.3 -9999 0 -0.76 93 93
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.081 0.2 -9999 0 -0.54 76 76
MMP3 -0.071 0.25 -9999 0 -0.86 47 47
APAF-1/Caspase 9 -0.11 0.18 -9999 0 -0.69 11 11
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.014 0.047 -9999 0 -10000 0 0
NFATC2 -0.017 0.064 -9999 0 -0.59 3 3
NFATC3 -0.014 0.047 -9999 0 -10000 0 0
CD40LG -0.31 0.42 -9999 0 -0.93 102 102
PTGS2 -0.29 0.39 -9999 0 -0.86 96 96
JUNB 0.013 0.047 -9999 0 -0.75 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.02 0.018 -9999 0 -10000 0 0
CALM1 0.006 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.027 0.19 -9999 0 -0.86 25 25
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.73 36 36
FOS -0.014 0.12 -9999 0 -0.76 13 13
IFNG -0.44 0.52 -9999 0 -0.98 224 224
AP-1/NFAT1-c-4 -0.41 0.41 -9999 0 -1.1 94 94
FASLG -0.46 0.52 -9999 0 -0.98 227 227
NFAT1-c-4/ICER1 -0.081 0.081 -9999 0 -0.58 3 3
IL2RA -0.34 0.44 -9999 0 -1 105 105
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.29 0.38 -9999 0 -0.87 92 92
JunB/Fra1/NFAT1-c-4 -0.094 0.12 -9999 0 -0.63 8 8
IL4 -0.28 0.37 -9999 0 -0.83 90 90
IL2 -0.012 0.11 -9999 0 -0.77 10 10
IL3 -0.028 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.061 0.25 -9999 0 -0.86 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.046 0.14 -9999 0 -0.72 1 1
CCNA2 -0.16 0.35 -9999 0 -0.86 101 101
PIK3CA 0.015 0.033 -9999 0 -0.75 1 1
JAK3 -0.16 0.35 -9999 0 -0.86 105 105
PIK3R1 0.015 0.033 -9999 0 -0.74 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.25 -9999 0 -0.66 59 59
SHC1 0.015 0.039 -9999 0 -0.86 1 1
SP1 0.025 0.022 -9999 0 -10000 0 0
IL2RA -0.12 0.33 -9999 0 -0.77 105 105
IL2RB -0.44 0.44 -9999 0 -0.86 272 272
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.041 0.22 -9999 0 -0.86 34 34
G1/S transition of mitotic cell cycle -0.046 0.2 -9999 0 -0.53 17 17
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.051 -9999 0 -0.78 2 2
LCK -0.02 0.18 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.006 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.033 -9999 0 -0.75 1 1
CCND3 -0.078 0.21 -9999 0 -0.66 28 28
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.054 0.17 -10000 0 -0.42 38 38
IKBKB -0.023 0.1 -10000 0 -0.28 2 2
AKT1 -0.023 0.13 -10000 0 -0.31 9 9
IKBKG -0.023 0.11 -10000 0 -0.3 2 2
CALM1 -0.042 0.1 -10000 0 -0.46 4 4
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
MAP3K1 -0.11 0.25 -10000 0 -0.63 71 71
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 0.27 1 -0.5 4 5
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.011 0.09 -10000 0 -10000 0 0
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.033 -10000 0 -0.75 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
BCR complex -0.17 0.3 -10000 0 -0.68 127 127
CD22 -0.15 0.23 -10000 0 -0.68 51 51
CAMK2G -0.029 0.098 -10000 0 -0.5 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.077 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.1 0.19 -10000 0 -0.85 4 4
GO:0007205 -0.055 0.11 0.27 1 -0.51 4 5
SYK 0.013 0.047 -10000 0 -0.75 2 2
ELK1 -0.043 0.1 -10000 0 -0.51 3 3
NFATC1 -0.071 0.2 -10000 0 -0.5 66 66
B-cell antigen/BCR complex -0.17 0.3 -10000 0 -0.68 127 127
PAG1/CSK -0.003 0.041 -10000 0 -0.67 2 2
NFKBIB 0.005 0.039 -10000 0 -0.13 1 1
HRAS -0.038 0.12 -10000 0 -0.49 4 4
NFKBIA 0.005 0.038 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.013 0.032 -10000 0 -0.18 1 1
RasGAP/Csk -0.21 0.32 -10000 0 -0.62 175 175
mol:GDP -0.051 0.1 0.29 1 -0.47 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.011 0.067 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.013 0.032 -10000 0 -0.19 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.079 0.22 -10000 0 -0.57 64 64
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
mol:IP3 -0.066 0.1 0.27 1 -0.51 4 5
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.04 0.11 -10000 0 -0.48 6 6
CHUK -0.023 0.11 -10000 0 -0.3 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.13 0.2 -10000 0 -0.54 84 84
PTPN6 -0.14 0.21 -10000 0 -0.68 39 39
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.011 0.068 -10000 0 -0.14 105 105
VAV2 -0.17 0.28 -10000 0 -0.8 74 74
ubiquitin-dependent protein catabolic process 0.011 0.037 -10000 0 -0.12 1 1
BTK -0.088 0.17 0.46 1 -0.42 106 107
CD19 -0.19 0.33 -10000 0 -0.82 91 91
MAP4K1 -0.34 0.43 -10000 0 -0.86 211 211
CD72 -0.19 0.37 -10000 0 -0.86 122 122
PAG1 0.012 0.055 -10000 0 -0.86 2 2
MAPK14 -0.084 0.21 -10000 0 -0.52 67 67
SH3BP5 0.014 0.033 -10000 0 -0.75 1 1
PIK3AP1 -0.037 0.11 -10000 0 -0.55 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.23 -10000 0 -0.58 77 77
RAF1 -0.025 0.11 -10000 0 -0.54 2 2
RasGAP/p62DOK/SHIP -0.2 0.32 -10000 0 -0.97 48 48
CD79A -0.2 0.38 -10000 0 -0.86 127 127
re-entry into mitotic cell cycle -0.012 0.09 -10000 0 -10000 0 0
RASA1 0.014 0.033 -10000 0 -0.75 1 1
MAPK3 -0.001 0.1 -10000 0 -10000 0 0
MAPK1 -0.001 0.1 -10000 0 -10000 0 0
CD72/SHP1 -0.23 0.33 -10000 0 -0.83 99 99
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MAPK8 -0.085 0.22 -10000 0 -0.52 68 68
actin cytoskeleton organization -0.096 0.26 -10000 0 -0.65 73 73
NF-kappa-B/RelA 0.035 0.059 -10000 0 -10000 0 0
Calcineurin -0.042 0.07 -10000 0 -0.44 2 2
PI3K -0.14 0.22 -10000 0 -0.6 69 69
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.062 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.27 0.32 -10000 0 -0.74 133 133
DAPP1 -0.11 0.18 -10000 0 -0.61 36 36
cytokine secretion -0.064 0.19 -10000 0 -0.46 66 66
mol:DAG -0.066 0.1 0.27 1 -0.51 4 5
PLCG2 0.003 0.1 -10000 0 -0.82 8 8
MAP2K1 -0.013 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.24 0.37 -10000 0 -0.72 175 175
mol:PI-3-4-5-P3 -0.097 0.15 -10000 0 -0.4 65 65
ETS1 -0.017 0.092 -10000 0 -0.44 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.22 -10000 0 -0.5 126 126
B-cell antigen/BCR complex/LYN -0.14 0.22 -10000 0 -0.57 71 71
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.11 0.28 -10000 0 -0.71 73 73
B-cell antigen/BCR complex/LYN/SYK -0.16 0.25 -10000 0 -0.67 64 64
CARD11 -0.15 0.26 -10000 0 -0.62 110 110
FCGR2B -0.14 0.34 -10000 0 -0.86 95 95
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.005 0.048 -10000 0 -10000 0 0
PTPRC -0.079 0.27 -10000 0 -0.86 56 56
PDPK1 -0.061 0.1 -10000 0 -0.31 9 9
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0 0.058 -10000 0 -0.14 66 66
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.026 0.023 -9999 0 -0.49 1 1
ADCY5 0.006 0.1 -9999 0 -0.49 22 22
ADCY6 0.026 0.042 -9999 0 -0.93 1 1
ADCY7 0.009 0.11 -9999 0 -0.58 16 16
ADCY1 0.014 0.083 -9999 0 -0.5 13 13
ADCY2 -0.13 0.27 -9999 0 -0.58 135 135
ADCY3 0.026 0.023 -9999 0 -0.49 1 1
ADCY8 -0.16 0.28 -9999 0 -0.59 160 160
PRKCE 0.014 0.026 -9999 0 -0.57 1 1
ADCY9 0.026 0.023 -9999 0 -0.49 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.091 0.17 -9999 0 -0.51 51 51
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.12 0.24 -10000 0 -0.78 35 35
UGCG -0.023 0.047 -10000 0 -0.84 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.081 0.19 -10000 0 -0.5 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.057 -10000 0 -0.83 1 1
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.16 -10000 0 -0.53 45 45
FRAP1 -0.085 0.23 -10000 0 -0.62 49 49
FOXO3 -0.075 0.22 -10000 0 -0.65 35 35
AKT1 -0.093 0.24 -10000 0 -0.64 52 52
GAB2 0.016 0.003 -10000 0 -10000 0 0
SMPD1 -0.021 0.03 -10000 0 -10000 0 0
SGMS1 -0.021 0.03 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.032 -10000 0 -0.48 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.022 0.099 -10000 0 -0.58 1 1
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
RPS6KB1 -0.028 0.087 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 105 105
PIK3R1 0.017 0.034 -10000 0 -0.74 1 1
JAK1 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MYC -0.076 0.22 -10000 0 -0.63 43 43
MYB -0.19 0.34 -10000 0 -0.74 139 139
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.12 0.26 -10000 0 -0.68 62 62
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.035 0.067 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 -0.12 0.25 -10000 0 -0.66 62 62
Rac1/GDP 0.012 0.033 -10000 0 -0.43 2 2
T cell proliferation -0.097 0.24 -10000 0 -0.65 47 47
SHC1 0.014 0.039 -10000 0 -0.86 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.05 139 139
PRKCZ -0.1 0.25 -10000 0 -0.69 47 47
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.58 30 30
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.15 0.26 -10000 0 -0.58 102 102
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IL2RB -0.44 0.44 -10000 0 -0.86 272 272
TERT -0.11 0.3 -10000 0 -0.86 73 73
E2F1 -0.1 0.2 -10000 0 -0.38 165 165
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.012 0.055 -10000 0 -0.86 2 2
mol:cAMP 0.004 0.013 0.025 139 -10000 0 139
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.039 0.22 -10000 0 -0.86 34 34
actin cytoskeleton organization -0.097 0.24 -10000 0 -0.65 47 47
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 -0.005 0.12 -10000 0 -0.86 10 10
PIK3CA 0.017 0.034 -10000 0 -0.74 1 1
Rac1/GTP 0.031 0.035 -10000 0 -0.41 2 2
LCK -0.018 0.18 -10000 0 -0.85 22 22
BCL2 -0.052 0.18 -10000 0 -0.53 24 24
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.036 -9999 0 -0.78 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.023 -9999 0 -10000 0 0
JMJD2C -0.001 0.021 -9999 0 -0.11 18 18
T-DHT/AR/Ubc9 -0.077 0.11 -9999 0 -0.55 24 24
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.014 0.009 -9999 0 -10000 0 0
MAK 0.015 0.045 -9999 0 -0.86 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.009 0.069 -9999 0 -0.77 4 4
GSN 0.015 0.008 -9999 0 -10000 0 0
NCOA2 0.002 0.1 -9999 0 -0.75 9 9
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.027 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.028 0.036 -9999 0 -0.61 1 1
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.092 0.14 -9999 0 -0.58 37 37
FHL2 -0.04 0.11 -9999 0 -1.1 5 5
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.055 -9999 0 -0.14 449 449
CDK6 0.014 0.033 -9999 0 -0.74 1 1
TGFB1I1 0.013 0.039 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.15 -9999 0 -0.6 44 44
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.59 24 24
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.018 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 499 499
SRF 0.026 0.012 -9999 0 -10000 0 0
NKX3-1 -0.19 0.069 -9999 0 -10000 0 0
KLK3 0.023 0.15 -9999 0 -0.71 21 21
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.013 -9999 0 -10000 0 0
AOF2 -0.002 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.11 -9999 0 -0.54 24 24
AR -0.068 0.16 -9999 0 -0.79 24 24
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.013 -9999 0 -10000 0 0
PAWR 0.014 0.034 -9999 0 -0.75 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.068 0.099 -9999 0 -0.5 24 24
RPS6KA3 0.013 0.036 -9999 0 -0.79 1 1
T-DHT/AR/ARA70 -0.078 0.11 -9999 0 -0.55 24 24
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.068 0.099 -9999 0 -0.5 24 24
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.005 0.12 -9999 0 -0.75 14 14
KLK2 -0.084 0.14 -9999 0 -0.8 18 18
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.067 0.12 -9999 0 -0.56 27 27
TMPRSS2 -0.92 0.35 -9999 0 -1.1 449 449
CCND1 -0.019 0.17 -9999 0 -0.86 20 20
PIAS1 0.014 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.027 -9999 0 -0.072 446 446
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.56 24 24
CMTM2 -0.005 0.13 -9999 0 -0.86 12 12
SNURF -0.008 0.13 -9999 0 -0.75 16 16
ZMIZ1 -0.032 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.013 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0 0.057 0.29 18 -10000 0 18
BUB1B -0.023 0.12 -10000 0 -0.51 26 26
PLK1 -0.012 0.059 -10000 0 -0.2 10 10
PLK1S1 0.001 0.031 -10000 0 -10000 0 0
KIF2A -0.003 0.073 -10000 0 -0.56 4 4
regulation of mitotic centrosome separation -0.012 0.059 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.33 -10000 0 -0.72 126 126
WEE1 -0.001 0.056 -10000 0 -0.3 5 5
cytokinesis -0.2 0.27 -10000 0 -0.5 234 234
PP2A-alpha B56 -0.14 0.16 -10000 0 -10000 0 0
AURKA -0.002 0.045 -10000 0 -0.3 6 6
PICH/PLK1 -0.045 0.16 -10000 0 -0.84 18 18
CENPE -0.063 0.21 -10000 0 -0.63 60 60
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.072 -10000 0 -0.55 4 4
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.033 -10000 0 -0.75 1 1
TPX2 -0.05 0.12 -10000 0 -0.25 125 125
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.076 0.27 -10000 0 -0.86 54 54
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.025 0.096 -10000 0 -0.28 59 59
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.009 -10000 0 -0.02 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.012 0.059 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.16 0.19 -10000 0 -0.46 7 7
TPT1 0.001 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 238 238
CDC25B 0.007 0.088 -10000 0 -0.88 5 5
SGOL1 0 0.057 -10000 0 -0.29 18 18
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.024 0.1 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.056 0.24 -10000 0 -0.86 42 42
PLK1/PBIP1 -0.041 0.11 -10000 0 -0.59 18 18
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.003 0.045 -10000 0 -0.21 2 2
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.17 0.36 -10000 0 -0.86 109 109
metaphase plate congression -0.005 0.041 -10000 0 -10000 0 0
ERCC6L -0.037 0.16 -10000 0 -0.82 18 18
NLP/gamma Tubulin -0.003 0.035 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0.001 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.26 0.29 -10000 0 -0.57 234 234
GRASP65/GM130/RAB1/GTP/PLK1 -0.013 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.038 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 120 120
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.043 -10000 0 -10000 0 0
microtubule-based process -0.25 0.31 -10000 0 -0.58 234 234
Golgi organization -0.012 0.059 -10000 0 -0.2 10 10
Cohesin/SA2 -0.024 0.045 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.38 0.44 -10000 0 -0.86 234 234
APC/C/CDC20 -0.045 0.18 -10000 0 -0.64 42 42
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.04 0.11 -10000 0 -0.58 18 18
PRC1 0.006 0.094 -10000 0 -0.86 6 6
ECT2 0.001 0.053 -10000 0 -10000 0 0
C13orf34 0.003 0.043 -10000 0 -10000 0 0
NUDC -0.005 0.041 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.023 0.12 -10000 0 -0.5 26 26
spindle assembly -0.006 0.048 -10000 0 -0.18 6 6
spindle stabilization 0.001 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.022 -10000 0 -0.49 1 1
MKLP2/PLK1 -0.25 0.31 -10000 0 -0.59 234 234
CCNB1 0.002 0.11 -10000 0 -0.88 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.005 0.053 -10000 0 -0.46 3 3
TUBG1 0.001 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.098 -10000 0 -0.71 9 9
MLF1IP -0.012 0.13 -10000 0 -0.69 18 18
INCENP 0.009 0.008 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.25 0.41 -10000 0 -0.82 172 172
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.054 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.004 0.1 -10000 0 -0.85 7 7
GR alpha/HSP90/FKBP51/HSP90 0.055 0.13 0.39 5 -0.59 7 12
PRL -0.014 0.11 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.56 87 -0.62 2 89
RELA 0.004 0.076 -10000 0 -10000 0 0
FGG -0.15 0.43 0.57 13 -0.73 149 162
GR beta/TIF2 0.052 0.14 0.42 6 -0.55 7 13
IFNG -0.41 0.44 -10000 0 -0.86 219 219
apoptosis -0.093 0.21 0.43 1 -0.62 10 11
CREB1 -0.015 0.1 -10000 0 -0.39 6 6
histone acetylation 0.018 0.13 0.39 10 -0.42 8 18
BGLAP -0.008 0.13 -10000 0 -0.74 3 3
GR/PKAc 0.065 0.1 0.37 4 -0.6 1 5
NF kappa B1 p50/RelA 0.01 0.15 -10000 0 -0.58 7 7
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.047 0.093 0.3 15 -10000 0 15
GATA3 -0.35 0.38 -10000 0 -0.74 251 251
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.027 0.16 -10000 0 -0.68 17 17
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.057 0.22 -10000 0 -0.83 12 12
CSN2 0.044 0.19 0.46 8 -0.66 1 9
BRG1/BAF155/BAF170/BAF60A 0.003 0.013 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.02 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.053 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 62 62
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.005 0.21 0.38 2 -0.58 25 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.22 -10000 0 -0.84 12 12
JUN -0.22 0.25 -10000 0 -0.64 74 74
IL4 -0.023 0.12 -10000 0 -0.58 2 2
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 0.31 2 -0.68 85 87
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.061 0.12 0.41 2 -0.6 4 6
cortisol/GR alpha (monomer) 0.15 0.34 0.65 100 -0.81 1 101
NCOA2 0.003 0.1 -10000 0 -0.75 9 9
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.055 0.14 -10000 0 -0.83 13 13
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.82 107 107
AFP -0.35 0.56 -10000 0 -1.4 109 109
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.084 0.15 0.51 8 -0.62 1 9
TP53 0.044 0.021 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.25 0.41 -10000 0 -1.1 70 70
KRT14 -0.15 0.3 -10000 0 -0.83 75 75
TBP 0.028 0.01 -10000 0 -10000 0 0
CREBBP 0.047 0.081 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.33 0.34 -10000 0 -0.82 108 108
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 0.004 0.075 -10000 0 -0.75 5 5
MAPK11 0.009 0.04 -10000 0 -0.88 1 1
KRT5 -0.26 0.39 -10000 0 -0.9 112 112
interleukin-1 receptor activity 0 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.054 -10000 0 -1.2 1 1
CGA -0.13 0.37 -10000 0 -1.2 51 51
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.15 0.45 36 -10000 0 36
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.049 0.23 -10000 0 -0.81 24 24
NFKB1 0.003 0.086 -10000 0 -0.9 1 1
MAPK8 -0.14 0.2 -10000 0 -0.51 49 49
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.098 0.22 0.43 1 -0.64 12 13
BAX 0.052 0.028 -10000 0 -10000 0 0
POMC -0.037 0.17 -10000 0 -0.81 7 7
EP300 0.045 0.085 -10000 0 -0.6 1 1
cortisol/GR alpha (dimer)/p53 0.16 0.29 0.57 99 -0.7 1 100
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.071 0.27 3 -10000 0 3
SGK1 0.1 0.096 -10000 0 -10000 0 0
IL13 -0.36 0.28 -10000 0 -0.76 110 110
IL6 -0.12 0.38 -10000 0 -0.98 72 72
PRKACG 0.003 0.007 -10000 0 -10000 0 0
IL5 -0.29 0.21 -10000 0 -0.7 40 40
IL2 -0.17 0.25 -10000 0 -0.86 26 26
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.078 0.3 -10000 0 -0.9 46 46
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.11 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.54 83 -0.65 1 84
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.15 0.39 43 -10000 0 43
NF kappa B1 p50/RelA/Cbp 0.063 0.14 -10000 0 -0.94 1 1
JUN (dimer) -0.21 0.25 -10000 0 -0.63 75 75
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.058 0.22 -10000 0 -0.82 24 24
NR3C1 0.08 0.19 0.49 35 -0.95 1 36
NR4A1 0.002 0.13 -10000 0 -0.73 16 16
TIF2/SUV420H1 -0.01 0.073 -10000 0 -0.56 9 9
MAPKKK cascade -0.093 0.21 0.43 1 -0.62 10 11
cortisol/GR alpha (dimer)/Src-1 0.15 0.28 0.56 97 -0.8 1 98
PBX1 -0.003 0.13 -10000 0 -0.74 15 15
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.097 0.37 -10000 0 -1.2 43 43
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.4 42 -10000 0 42
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.54 83 -0.65 1 84
mol:cortisol 0.063 0.2 0.36 93 -0.26 26 119
MMP1 -0.23 0.39 -10000 0 -0.97 102 102
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 233 233
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.03 0.1 -9999 0 -0.36 43 43
mol:S1P -0.024 0.095 -9999 0 -0.41 6 6
S1P1/S1P/Gi -0.047 0.14 -9999 0 -0.51 13 13
GNAO1 0.01 0.084 -9999 0 -0.84 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.054 0.087 -9999 0 -0.63 2 2
PLCG1 -0.028 0.13 -9999 0 -0.51 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.25 0.3 -9999 0 -0.58 233 233
S1P1/S1P -0.21 0.21 -9999 0 -0.63 23 23
negative regulation of cAMP metabolic process -0.046 0.14 -9999 0 -0.5 13 13
MAPK3 -0.038 0.16 -9999 0 -0.57 25 25
calcium-dependent phospholipase C activity 0 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 0.014 0.034 -9999 0 -0.75 1 1
PLCB2 -0.2 0.26 -9999 0 -0.67 59 59
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.17 0.17 -9999 0 -0.52 22 22
receptor internalization -0.2 0.2 -9999 0 -0.57 23 23
PTGS2 -0.048 0.24 -9999 0 -0.99 26 26
Rac1/GTP -0.17 0.17 -9999 0 -0.52 22 22
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
negative regulation of T cell proliferation -0.046 0.14 -9999 0 -0.5 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
MAPK1 -0.038 0.16 -9999 0 -0.57 25 25
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.64 22 22
ABCC1 0.016 0.002 -9999 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.3 -9999 0 -0.76 36 36
CRP -0.2 0.39 -9999 0 -0.9 91 91
cell cycle arrest -0.18 0.35 -9999 0 -0.78 83 83
TIMP1 -0.15 0.33 -9999 0 -0.77 70 70
IL6ST -0.013 0.14 -9999 0 -0.74 17 17
Rac1/GDP -0.14 0.26 -9999 0 -0.59 88 88
AP1 0.021 0.11 -9999 0 -0.58 2 2
GAB2 0.011 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.37 -9999 0 -0.85 77 77
HSP90B1 0.004 0.088 -9999 0 -10000 0 0
GAB1 0.014 0.006 -9999 0 -10000 0 0
MAPK14 0.017 0.13 -9999 0 -0.69 3 3
AKT1 0.06 0.035 -9999 0 -10000 0 0
FOXO1 0.076 0.024 -9999 0 -10000 0 0
MAP2K6 -0.017 0.14 -9999 0 -0.63 5 5
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.28 -9999 0 -0.65 69 69
MITF -0.024 0.14 -9999 0 -0.6 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.002 0.13 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0.001 0.069 -9999 0 -10000 0 0
STAT3 -0.18 0.36 -9999 0 -0.82 83 83
STAT1 -0.005 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.31 -9999 0 -0.75 40 40
PIK3CA 0.017 0.034 -9999 0 -0.74 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.018 0.13 -9999 0 -0.75 2 2
MAPK11 0.016 0.13 -9999 0 -0.7 4 4
STAT3 (dimer)/FOXO1 -0.071 0.27 -9999 0 -0.64 21 21
GRB2/SOS1/GAB family -0.046 0.11 -9999 0 -0.67 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.038 0.15 -9999 0 -0.63 12 12
GRB2 0.014 0.006 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.28 0.44 -9999 0 -0.88 159 159
PIK3R1 0.016 0.033 -9999 0 -0.74 1 1
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.32 -9999 0 -0.77 55 55
FGG -0.28 0.43 -9999 0 -0.87 129 129
macrophage differentiation -0.18 0.35 -9999 0 -0.78 83 83
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.069 0.17 -9999 0 -0.54 34 34
JUNB -0.14 0.3 -9999 0 -0.76 37 37
FOS -0.009 0.12 -9999 0 -0.76 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.035 0.15 -9999 0 -0.43 28 28
STAT1/PIAS1 -0.047 0.16 -9999 0 -0.49 19 19
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.038 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.82 83 83
PRKCD -0.15 0.3 -9999 0 -0.69 67 67
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.032 0.12 -9999 0 -0.63 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.09 -9999 0 -0.47 17 17
Rac1/GTP -0.18 0.23 -9999 0 -0.6 96 96
HCK -0.032 0.2 -9999 0 -0.86 28 28
MAPKKK cascade 0.026 0.06 -9999 0 -10000 0 0
bone resorption -0.18 0.35 -9999 0 -0.79 77 77
IRF1 -0.14 0.31 -9999 0 -0.75 41 41
mol:GDP -0.15 0.27 -9999 0 -0.55 133 133
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.56 133 133
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.003 0.12 -9999 0 -0.64 3 3
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.078 0.21 -9999 0 -0.63 65 65
gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.085 -9999 0 -0.47 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.085 -9999 0 -0.47 17 17
IL6 -0.092 0.28 -9999 0 -0.82 65 65
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.017 0.017 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.13 -9999 0 -0.42 14 14
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.29 -9999 0 -0.75 82 82
MCL1 0.075 0.023 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.28 -9999 0 -0.86 73 73
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.014 0.089 -9999 0 -0.57 13 13
IFNAR2 0.015 0.007 -9999 0 -10000 0 0
AKT1 0.014 0.069 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.005 0.053 -9999 0 -0.6 4 4
NFX1/SIN3/HDAC complex 0.045 0.054 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.75 466 466
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.79 73 73
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.38 -9999 0 -0.75 242 242
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.23 -9999 0 -0.72 62 62
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.24 0.29 -9999 0 -0.89 73 73
CCND1 -0.22 0.27 -9999 0 -0.79 78 78
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.034 -9999 0 -0.75 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0.003 0.027 -9999 0 -10000 0 0
CDKN1B -0.23 0.3 -9999 0 -0.55 237 237
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.017 0.16 -9999 0 -0.86 18 18
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.005 0.12 -9999 0 -0.76 13 13
IFN-gamma/IRF1 -0.3 0.32 -9999 0 -0.65 237 237
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.003 0.13 -9999 0 -0.86 11 11
Telomerase -0.019 0.16 -9999 0 -0.4 45 45
IRF1 0.016 0.039 -9999 0 -0.86 1 1
ESR1 0.007 0.07 -9999 0 -0.78 4 4
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.022 -9999 0 -0.49 1 1
ubiquitin-dependent protein catabolic process 0.051 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.006 0.033 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM -0.001 0.023 -9999 0 -0.52 1 1
SMAD3 0.025 0.068 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.25 -9999 0 -0.76 63 63
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.009 0.096 -9999 0 -0.67 10 10
MAPK1 0.009 0.096 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.008 0.086 -9999 0 -0.86 5 5
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.023 -9999 0 -0.52 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR 0 0.11 -9999 0 -0.85 9 9
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.51 0.18 -9999 0 -0.57 467 467
MYC -0.018 0.16 -9999 0 -0.86 19 19
IL2 -0.008 0.12 -9999 0 -0.87 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.008 0.086 -9999 0 -0.86 5 5
TRF2/BLM -0.013 0.09 -9999 0 -0.63 11 11
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.21 0.26 -9999 0 -0.79 72 72
SP1/HDAC2 0.007 0.014 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.18 0.23 -9999 0 -0.72 61 61
Smad3/Myc -0.02 0.13 -9999 0 -0.6 23 23
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.85 237 237
Telomerase/PinX1 -0.18 0.23 -9999 0 -0.72 61 61
Telomerase/AKT1/mTOR/p70S6K -0.013 0.079 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.18 0.23 -9999 0 -0.72 61 61
response to DNA damage stimulus 0.004 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.23 -9999 0 -0.74 51 51
E2F1 -0.091 0.29 -9999 0 -0.87 62 62
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.14 0.33 -9999 0 -0.86 89 89
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 173 173
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.11 0.22 -9999 0 -0.52 6 6
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.66 0.37 -9999 0 -0.86 397 397
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.67 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.86 66 66
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.24 -9999 0 -0.49 183 183
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.16 -9999 0 -0.59 16 16
MAP1B -0.001 0.02 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.17 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 172 172
PAFAH/LIS1 -0.44 0.24 -9999 0 -0.58 397 397
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.098 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.7 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.13 0.19 -9999 0 -0.64 16 16
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.033 -9999 0 -0.75 1 1
PAFAH1B2 0.014 0.033 -9999 0 -0.75 1 1
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 -9999 0 -0.56 16 16
LRP8 0.014 0.039 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.13 0.16 -9999 0 -0.59 16 16
P39/CDK5 -0.18 0.23 -9999 0 -0.86 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.094 0.21 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.2 -9999 0 -0.51 17 17
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
CDC42 0 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 233 233
alphaV beta3 Integrin -0.008 0.069 -9999 0 -0.54 8 8
PTK2 -0.15 0.23 -9999 0 -0.55 46 46
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.039 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.083 0.19 -9999 0 -0.53 79 79
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
ILK -0.083 0.19 -9999 0 -0.53 79 79
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.076 0.17 -9999 0 -0.49 71 71
PTK2B -0.19 0.27 -9999 0 -0.88 1 1
alphaV/beta3 Integrin/JAM-A -0.069 0.15 -9999 0 -0.81 1 1
CBL 0.014 0.033 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.48 243 243
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.067 -9999 0 -0.52 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.14 -9999 0 -0.47 44 44
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.065 -9999 0 -0.48 10 10
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.14 -9999 0 -0.8 4 4
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Osteopontin -0.007 0.059 -9999 0 -0.48 8 8
RPS6KB1 -0.043 0.13 -9999 0 -0.73 4 4
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.042 0.097 -9999 0 -0.82 3 3
GPR124 0.012 0.055 -9999 0 -0.86 2 2
MAPK1 -0.042 0.097 -9999 0 -0.82 3 3
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
alphaV/beta3 Integrin/Tumstatin -0.057 0.16 -9999 0 -0.48 61 61
cell adhesion -0.17 0.18 -9999 0 -0.83 1 1
ANGPTL3 -0.34 0.38 -9999 0 -0.75 239 239
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 233 233
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
IGF1 0.006 0.094 -9999 0 -0.86 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.006 0.054 -9999 0 -0.51 6 6
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.004 0.042 -9999 0 -0.48 4 4
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.017 0.095 -9999 0 -0.54 16 16
CSF1 0.014 0.033 -9999 0 -0.75 1 1
PIK3C2A -0.085 0.2 -9999 0 -0.54 80 80
PI4 Kinase/Pyk2 -0.23 0.24 -9999 0 -0.76 45 45
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 233 233
FAK1/Vinculin -0.11 0.18 -9999 0 -0.56 3 3
alphaV beta3/Integrin/ppsTEM5 -0.006 0.055 -9999 0 -0.51 6 6
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.1 0.28 -9999 0 -0.76 79 79
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
FGF2 0.008 0.077 -9999 0 -0.77 5 5
F11R 0.025 0.06 -9999 0 -0.58 5 5
alphaV/beta3 Integrin/Lactadherin -0.005 0.049 -9999 0 -0.5 5 5
alphaV/beta3 Integrin/TGFBR2 -0.004 0.042 -9999 0 -0.48 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.042 -9999 0 -0.85 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.003 0.038 -9999 0 -0.44 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.049 0.23 -9999 0 -0.86 38 38
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.88 1 1
SDC1 0.007 0.082 -9999 0 -0.75 6 6
VAV3 0.039 0.084 -9999 0 -0.8 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.067 -9999 0 -0.75 4 4
FAK1/Paxillin -0.11 0.18 -9999 0 -0.56 3 3
cell migration -0.09 0.17 -9999 0 -0.52 2 2
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.061 0.14 -9999 0 -1.1 1 1
SPP1 0.01 0.067 -9999 0 -0.75 4 4
KDR 0.014 0.033 -9999 0 -0.75 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.07 0.24 -9999 0 -0.75 58 58
angiogenesis 0.004 0.15 -9999 0 -0.8 3 3
Rac1/GTP -0.012 0.067 -9999 0 -0.73 1 1
EDIL3 -0.005 0.13 -9999 0 -0.79 13 13
cell proliferation -0.004 0.041 -9999 0 -0.47 4 4
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.17 0.27 -10000 0 -0.54 92 92
CRKL 0.017 0.12 -10000 0 -0.57 8 8
HRAS -0.044 0.18 -10000 0 -0.51 41 41
mol:PIP3 -0.004 0.11 -10000 0 -0.45 21 21
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.014 0.033 -10000 0 -0.75 1 1
GAB1 0.006 0.12 -10000 0 -0.5 21 21
FOXO3 0.024 0.11 -10000 0 -0.51 8 8
AKT1 0.014 0.11 -10000 0 -0.46 21 21
BAD 0.022 0.11 -10000 0 -0.59 6 6
megakaryocyte differentiation -0.071 0.21 -10000 0 -0.45 111 111
GSK3B 0.024 0.11 -10000 0 -0.48 10 10
RAF1 -0.012 0.15 -10000 0 -0.54 3 3
SHC1 0.014 0.039 -10000 0 -0.86 1 1
STAT3 0.007 0.12 -10000 0 -0.5 21 21
STAT1 -0.016 0.24 -10000 0 -1 21 21
HRAS/SPRED1 -0.068 0.12 -10000 0 -0.43 19 19
cell proliferation 0.006 0.12 -10000 0 -0.5 21 21
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.12 -10000 0 -0.44 30 30
HRAS/SPRED2 -0.068 0.12 -10000 0 -0.43 20 20
LYN/TEC/p62DOK -0.018 0.1 -10000 0 -0.66 5 5
MAPK3 0.011 0.12 -10000 0 -0.37 2 2
STAP1 -0.32 0.22 -10000 0 -0.48 198 198
GRAP2 -0.043 0.22 -10000 0 -0.86 35 35
JAK2 -0.067 0.19 -10000 0 -0.91 21 21
STAT1 (dimer) -0.014 0.23 -10000 0 -1 21 21
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.13 0.22 -10000 0 -0.56 48 48
actin filament polymerization 0.001 0.13 -10000 0 -0.48 27 27
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.29 0.23 -10000 0 -0.87 30 30
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
CBL/CRKL/GRB2 -0.014 0.093 -10000 0 -0.59 5 5
PI3K -0.02 0.11 -10000 0 -0.46 22 22
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.34 -10000 0 -1.3 23 23
MAPK8 0.006 0.13 -10000 0 -0.52 21 21
STAT3 (dimer) 0.007 0.12 -10000 0 -0.49 21 21
positive regulation of transcription 0.014 0.099 -10000 0 -0.31 1 1
mol:GDP -0.11 0.19 -10000 0 -0.62 44 44
PIK3C2B 0.007 0.12 -10000 0 -0.5 21 21
CBL/CRKL 0.026 0.11 -10000 0 -0.62 5 5
FER 0.005 0.13 -10000 0 -0.5 23 23
SH2B3 0.007 0.12 -10000 0 -0.5 21 21
PDPK1 0.006 0.1 -10000 0 -0.49 9 9
SNAI2 0.006 0.13 -10000 0 -0.5 23 23
positive regulation of cell proliferation 0 0.19 -10000 0 -0.7 28 28
KITLG 0 0.11 -10000 0 -0.77 10 10
cell motility 0 0.19 -10000 0 -0.7 28 28
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.04 0.071 -10000 0 -10000 0 0
STAT5A (dimer) 0.003 0.16 -10000 0 -0.59 29 29
SOCS1 0.006 0.094 -10000 0 -0.86 6 6
cell migration 0.044 0.2 0.51 68 -10000 0 68
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.29 0.42 -10000 0 -0.86 182 182
VAV1 -0.2 0.38 -10000 0 -0.86 124 124
GRB10 0.006 0.12 -10000 0 -0.5 21 21
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.035 0.12 -10000 0 -0.46 33 33
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.005 0.13 -10000 0 -0.42 2 2
CBL 0.014 0.033 -10000 0 -0.75 1 1
KIT -0.01 0.28 -10000 0 -1.2 28 28
MAP2K2 0.004 0.13 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.019 0.1 -10000 0 -0.66 5 5
STAT5A 0.002 0.17 -10000 0 -0.61 29 29
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.006 0.12 -10000 0 -0.49 23 23
SHC/GRAP2 -0.046 0.17 -10000 0 -0.66 36 36
PTPRO -0.073 0.22 -10000 0 -0.46 111 111
SH2B2 0.001 0.13 -10000 0 -0.49 27 27
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.045 0.2 -10000 0 -0.52 68 68
CREBBP 0.045 0.012 -10000 0 -10000 0 0
BCL2 0.042 0.069 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.019 0.045 -9999 0 -10000 0 0
BIRC5 -0.24 0.4 -9999 0 -0.86 153 153
NFKBIA 0.047 0.04 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.76 104 104
AKT1 0.047 0.04 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.017 0.041 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.076 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.014 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.019 0.045 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.011 0.058 -9999 0 -0.75 3 3
TPX2 -0.14 0.3 -9999 0 -0.67 125 125
TP53 0.025 0.037 -9999 0 -10000 0 0
DLG7 0.02 0.043 -9999 0 -0.29 6 6
AURKAIP1 0.011 0.061 -9999 0 -0.78 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.079 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.017 0.04 -9999 0 -10000 0 0
AURKA 0.027 0.055 -9999 0 -0.34 6 6
AURKB -0.14 0.15 -9999 0 -0.29 243 243
CDC25B 0.018 0.062 -9999 0 -0.58 2 2
G2/M transition checkpoint 0.015 0.053 -9999 0 -0.44 3 3
mRNA polyadenylation -0.074 0.19 -9999 0 -0.44 104 104
Aurora A/CPEB -0.074 0.19 -9999 0 -0.45 104 104
Aurora A/TACC1/TRAP/chTOG 0.021 0.044 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.019 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.006 0.065 -9999 0 -0.73 4 4
spindle assembly -0.002 0.023 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.22 -9999 0 -0.47 153 153
CENPA -0.12 0.14 -9999 0 -0.3 168 168
Aurora A/PP2A 0.019 0.045 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.053 0.035 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.037 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.75 1 1
Ajuba/Aurora A 0.015 0.053 -9999 0 -0.44 3 3
mitotic prometaphase 0.037 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -9999 0 -0.34 6 6
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.009 0.077 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.017 0.061 -9999 0 -0.49 3 3
Aurora A/RasGAP 0.018 0.05 -9999 0 -0.47 1 1
OAZ1 0.014 0.039 -9999 0 -0.86 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.67 125 125
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.088 0.24 -9999 0 -0.52 125 125
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.009 0.078 -9999 0 -0.68 7 7
Metarhodopsin II/Arrestin -0.018 0.1 -9999 0 -0.59 16 16
PDE6G/GNAT1/GTP -0.013 0.084 -9999 0 -0.56 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.005 0.1 -9999 0 -0.86 7 7
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.95 12 12
mol:Na + -0.11 0.21 -9999 0 -0.81 21 21
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.037 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.85 21 21
CNGB1 -0.009 0.13 -9999 0 -0.86 11 11
RDH5 -0.004 0.13 -9999 0 -0.84 12 12
SAG 0.001 0.038 -9999 0 -0.86 1 1
mol:Ca2+ -0.068 0.22 -9999 0 -0.78 21 21
Na + (4 Units) -0.1 0.2 -9999 0 -0.75 21 21
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
GNB1/GNGT1 -0.23 0.32 -9999 0 -0.67 179 179
GNAT1/GDP -0.038 0.13 -9999 0 -0.53 15 15
GUCY2D -0.03 0.19 -9999 0 -0.86 25 25
GNGT1 -0.29 0.42 -9999 0 -0.86 179 179
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.15 -9999 0 -0.6 28 28
mol:11-cis-retinal -0.004 0.13 -9999 0 -0.83 12 12
mol:cGMP -0.041 0.14 -9999 0 -0.53 38 38
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.034 0.15 -9999 0 -0.66 27 27
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.12 0.3 -9999 0 -0.75 95 95
Metarhodopsin II -0.016 0.093 -9999 0 -0.55 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.15 -9999 0 -0.56 38 38
RGS9BP -0.019 0.16 -9999 0 -0.75 23 23
Metarhodopsin II/Transducin -0.12 0.16 -9999 0 -0.62 11 11
GCAP Family/Ca ++ -0.017 0.1 -9999 0 -0.56 16 16
PDE6A/B -0.036 0.15 -9999 0 -0.66 28 28
mol:Pi -0.036 0.13 -9999 0 -0.5 38 38
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.27 -9999 0 -0.55 181 181
PDE6B 0.007 0.082 -9999 0 -0.75 6 6
PDE6A -0.025 0.18 -9999 0 -0.86 23 23
PDE6G 0.008 0.077 -9999 0 -0.77 5 5
RHO -0.015 0.15 -9999 0 -0.86 15 15
PDE6 -0.057 0.16 -9999 0 -0.83 8 8
GUCA1A -0.01 0.12 -9999 0 -0.86 10 10
GC2/GCAP Family -0.017 0.099 -9999 0 -0.56 16 16
GUCA1C 0.001 0.047 -9999 0 -0.75 2 2
GUCA1B 0.007 0.086 -9999 0 -0.86 5 5
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.012 0.055 -9999 0 -0.86 2 2
RELN/VLDLR/Fyn -0.16 0.23 -9999 0 -0.48 172 172
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.043 -9999 0 -0.81 1 1
AKT1 -0.067 0.16 -9999 0 -0.57 2 2
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.01 0.13 -9999 0 -0.86 12 12
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.45 184 184
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.67 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 18 18
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.82 1 1
long-term memory -0.21 0.25 -9999 0 -0.88 24 24
DAB1/LIS1 -0.14 0.18 -9999 0 -0.86 1 1
DAB1/CRLK/C3G -0.13 0.18 -9999 0 -0.82 1 1
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
DAB1/NCK2 -0.14 0.18 -9999 0 -0.86 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.3 -9999 0 -0.84 76 76
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 172 172
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RELN/LRP8/Fyn -0.16 0.23 -9999 0 -0.48 173 173
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.26 -9999 0 -0.9 24 24
MAPK8 0.014 0.033 -9999 0 -0.75 1 1
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.45 183 183
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.51 18 18
RELN/LRP8 -0.16 0.23 -9999 0 -0.48 173 173
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.9 2 2
PI3K -0.002 0.035 -9999 0 -0.56 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.041 -9999 0 -0.67 2 2
RAP1A -0.11 0.17 -9999 0 -0.76 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.047 -9999 0 -0.75 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.055 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.029 0.12 -9999 0 -0.53 3 3
neuron adhesion -0.05 0.19 -9999 0 -0.71 1 1
LRP8 0.014 0.039 -9999 0 -0.86 1 1
GSK3B -0.053 0.15 -9999 0 -0.54 2 2
RELN/VLDLR/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 17 17
MAP3K11 0.014 0.033 -9999 0 -0.75 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.61 2 2
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.015 0.083 -9999 0 -0.69 6 6
neuron migration -0.059 0.21 -9999 0 -0.61 1 1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.057 0.1 -9999 0 -0.54 3 3
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.085 0.31 -10000 0 -0.91 29 29
NCK1/PAK1/Dok-R -0.083 0.11 -10000 0 -0.42 27 27
NCK1/Dok-R -0.084 0.27 -10000 0 -1.1 31 31
PIK3CA 0.005 0.034 -10000 0 -0.74 1 1
mol:beta2-estradiol -0.006 0.039 0.32 5 -10000 0 5
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.006 0.039 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.32 0.42 -10000 0 -0.85 194 194
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.058 0.23 -10000 0 -0.96 30 30
FN1 -0.049 0.23 -10000 0 -0.86 38 38
PLD2 0.032 0.3 -10000 0 -1.1 30 30
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.025 0.17 -10000 0 -0.75 28 28
ELK1 0.061 0.27 -10000 0 -0.97 30 30
GRB7 0.005 0.088 -10000 0 -0.75 7 7
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.3 -10000 0 -1 44 44
CDKN1A -0.11 0.31 -10000 0 -0.66 24 24
ITGA5 -0.049 0.23 -10000 0 -0.86 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.084 0.27 -10000 0 -1.1 31 31
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.05 0.26 -10000 0 -0.65 29 29
PLG -0.19 0.35 -10000 0 -1.3 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.21 -10000 0 -0.85 29 29
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.034 -10000 0 -0.75 1 1
ANGPT2 -0.21 0.38 -10000 0 -0.65 162 162
BMX -0.037 0.34 -10000 0 -1.1 30 30
ANGPT1 0.074 0.2 -10000 0 -1.2 8 8
tube development -0.13 0.34 -10000 0 -0.74 24 24
ANGPT4 -0.019 0.15 -10000 0 -0.87 16 16
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.025 0.32 -10000 0 -1.2 30 30
alpha5/beta1 Integrin -0.049 0.17 -10000 0 -0.67 38 38
FGF2 0.01 0.079 -10000 0 -0.77 5 5
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 25 25
mol:L-citrulline -0.05 0.26 -10000 0 -0.65 29 29
AGTR1 -0.038 0.18 -10000 0 -0.75 29 29
MAPK14 -0.004 0.31 -10000 0 -1.2 29 29
Tie2/SHP2 -0.061 0.25 -10000 0 -1.1 28 28
TEK -0.046 0.29 -10000 0 -1.2 28 28
RPS6KB1 -0.048 0.28 -10000 0 -0.86 29 29
Angiotensin II/AT1 -0.045 0.13 -10000 0 -0.58 29 29
Tie2/Ang1/GRB2 -0.005 0.3 -10000 0 -1.1 30 30
MAPK3 0.045 0.28 -10000 0 -0.99 30 30
MAPK1 0.045 0.28 -10000 0 -0.99 30 30
Tie2/Ang1/GRB7 -0.009 0.31 -10000 0 -1.2 30 30
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
MAPK8 0.032 0.3 -10000 0 -1.1 30 30
PI3K -0.071 0.32 -10000 0 -1.1 29 29
FES -0.009 0.31 -10000 0 -1.1 30 30
Crk/Dok-R -0.083 0.26 -10000 0 -1.1 30 30
Tie2/Ang1/ABIN2 -0.005 0.3 -10000 0 -1.1 30 30
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.074 0.29 -10000 0 -0.8 29 29
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.048 0.28 -10000 0 -0.86 29 29
Tie2/Ang2 -0.19 0.4 -10000 0 -1 25 25
Tie2/Ang1 0.024 0.33 -10000 0 -1.2 30 30
FOXO1 -0.11 0.31 -10000 0 -0.81 29 29
ELF1 0.023 0.036 -10000 0 -0.73 1 1
ELF2 0.028 0.31 -10000 0 -1.1 30 30
mol:Choline 0.035 0.28 -10000 0 -1 30 30
cell migration -0.055 0.071 -10000 0 -10000 0 0
FYN -0.15 0.36 -10000 0 -0.86 24 24
DOK2 -0.037 0.21 -10000 0 -0.86 31 31
negative regulation of cell cycle -0.097 0.3 -10000 0 -0.6 24 24
ETS1 0.028 0.037 -10000 0 -10000 0 0
PXN -0.026 0.25 -10000 0 -0.7 29 29
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.061 0.28 -10000 0 -0.75 29 29
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.009 0.11 -10000 0 -0.8 8 8
MAPKKK cascade 0.035 0.28 -10000 0 -1 30 30
RASA1 0.014 0.033 -10000 0 -0.75 1 1
Tie2/Ang1/Shc -0.004 0.3 -10000 0 -1.1 30 30
NCK1 0.014 0.033 -10000 0 -0.75 1 1
vasculogenesis -0.041 0.24 -10000 0 -0.58 29 29
mol:Phosphatidic acid 0.035 0.28 -10000 0 -1 30 30
mol:Angiotensin II -0.017 0.022 -10000 0 -10000 0 0
mol:NADP -0.05 0.26 -10000 0 -0.65 29 29
Rac1/GTP -0.13 0.19 -10000 0 -0.8 29 29
MMP2 0.027 0.31 -10000 0 -1.1 30 30
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.048 0.1 -10000 0 -0.55 5 5
PTP1B/AKT1 -0.031 0.047 -10000 0 -0.39 3 3
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.049 0.053 -10000 0 -0.37 6 6
EGFR -0.013 0.11 -10000 0 -0.87 9 9
EGF/EGFR -0.37 0.14 -10000 0 -0.41 466 466
CSF1 0.014 0.033 -10000 0 -0.75 1 1
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.049 0.087 -10000 0 -0.45 18 18
Insulin Receptor/Insulin -0.008 0.034 -10000 0 -10000 0 0
HCK -0.032 0.2 -10000 0 -0.86 28 28
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.035 0.05 -10000 0 -0.42 3 3
EGF -0.67 0.23 -10000 0 -0.75 466 466
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 40 40
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.033 0.055 -10000 0 -0.45 6 6
cell migration 0.049 0.053 0.37 6 -10000 0 6
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.09 0.26 -10000 0 -0.75 68 68
ITGA2B -0.022 0.16 -10000 0 -0.86 18 18
CSF1R 0.004 0.1 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.074 0.19 -10000 0 -0.57 68 68
FGR 0.011 0.067 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.052 -10000 0 -0.41 4 4
Crk/p130 Cas -0.03 0.042 -10000 0 -0.42 2 2
DOK1 -0.018 0.046 -10000 0 -0.38 2 2
JAK2 -0.054 0.11 -10000 0 -0.49 10 10
Jak2/Leptin Receptor/Leptin -0.052 0.13 -10000 0 -0.52 9 9
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
PTPN1 -0.049 0.053 -10000 0 -0.37 6 6
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.008 0.13 -10000 0 -0.75 16 16
SRC 0 0.021 -10000 0 -10000 0 0
ITGB3 0.002 0.067 -10000 0 -0.75 4 4
CAT1/PTP1B -0.23 0.13 -10000 0 -0.58 36 36
CAPN1 0.002 0.005 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.009 0.043 -10000 0 -0.63 1 1
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.034 0.12 -10000 0 -0.61 3 3
negative regulation of transcription -0.053 0.11 -10000 0 -0.48 10 10
FCGR2A -0.023 0.18 -10000 0 -0.86 23 23
FER -0.001 0.047 -10000 0 -0.76 2 2
alphaIIb/beta3 Integrin -0.027 0.13 -10000 0 -0.64 22 22
BLK -0.041 0.22 -10000 0 -0.86 33 33
Insulin Receptor/Insulin/Shc -0.001 0.026 -10000 0 -0.59 1 1
RHOA 0.002 0.005 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.75 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.22 0.15 -10000 0 -0.55 60 60
PRL 0.003 0.007 -10000 0 -10000 0 0
SOCS3 0.028 0.049 -10000 0 -0.73 2 2
SPRY2 0.001 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.043 -10000 0 -0.49 4 4
CSF1/CSF1R -0.037 0.075 -10000 0 -0.53 10 10
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.01 0.067 -10000 0 -0.75 4 4
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.073 0.26 -10000 0 -0.86 50 50
STAT5B -0.045 0.068 -10000 0 -0.46 5 5
STAT5A -0.045 0.068 -10000 0 -0.46 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.05 -10000 0 -0.42 3 3
CSN2 -0.008 0.069 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
LAT -0.1 0.17 -10000 0 -0.35 146 146
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.021 0.18 -10000 0 -0.85 22 22
SHC1 0.014 0.039 -10000 0 -0.86 1 1
NOX4 -0.006 0.074 -10000 0 -0.76 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.033 -9999 0 -0.75 1 1
Caspase 8 (4 units) -0.098 0.092 -9999 0 -10000 0 0
NEF -0.058 0.084 -9999 0 -10000 0 0
NFKBIA 0.001 0.045 -9999 0 -10000 0 0
BIRC3 -0.072 0.31 -9999 0 -0.79 80 80
CYCS -0.079 0.14 -9999 0 -0.43 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.37 0.48 -9999 0 -1 171 171
MAP2K7 -0.041 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.06 0.071 -9999 0 -0.44 1 1
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.093 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.051 0.12 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.051 0.12 -9999 0 -10000 0 0
MAPK8 -0.03 0.1 -9999 0 -0.51 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.039 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.14 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.048 0.067 -9999 0 -10000 0 0
CHUK 0.061 0.075 -9999 0 -0.49 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.4 0.44 -9999 0 -0.75 279 279
TNF 0.003 0.1 -9999 0 -0.8 8 8
FASLG -0.58 0.61 -9999 0 -1.1 279 279
NFKB1 0 0.055 -9999 0 -0.74 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -9999 0 -0.52 9 9
CASP6 -0.048 0.052 -9999 0 -10000 0 0
CASP7 -0.062 0.21 -9999 0 -0.55 54 54
RELA 0.001 0.045 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.062 0.21 -9999 0 -0.55 54 54
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.025 -9999 0 -0.56 1 1
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.08 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.56 54 54
BCL2 -0.017 0.098 -9999 0 -0.46 1 1
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.042 0.15 -9999 0 -0.58 38 38
EPHB2 0.001 0.11 -9999 0 -0.77 10 10
Syndecan-2/TACI -0.056 0.17 -9999 0 -0.58 50 50
LAMA1 -0.007 0.13 -9999 0 -0.75 15 15
Syndecan-2/alpha2 ITGB1 -0.01 0.068 -9999 0 -0.49 7 7
HRAS 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 38 38
BAX 0.054 0.02 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.002 0.11 -9999 0 -0.86 8 8
Syndecan-2/MMP2 -0.007 0.06 -9999 0 -0.56 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.005 0.055 -9999 0 -0.56 5 5
dendrite morphogenesis -0.01 0.068 -9999 0 -0.5 10 10
Syndecan-2/GM-CSF -0.017 0.097 -9999 0 -0.58 15 15
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.025 -9999 0 -0.58 1 1
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
MAPK3 0.022 0.094 -9999 0 -0.52 15 15
MAPK1 0.022 0.094 -9999 0 -0.52 15 15
Syndecan-2/RACK1 -0.002 0.031 -9999 0 -0.5 2 2
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.008 0.074 -9999 0 -0.75 5 5
MAPK8 0.046 0.023 -9999 0 -0.47 1 1
Syndecan-2/alpha2/beta1 Integrin -0.016 0.082 -9999 0 -0.65 2 2
Syndecan-2/Kininogen -0.36 0.21 -9999 0 -0.48 386 386
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.048 0.032 -9999 0 -0.46 2 2
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.006 0.056 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.042 0.15 -9999 0 -0.57 38 38
Syndecan-2/Caveolin-2/Ras -0.009 0.069 -9999 0 -0.52 9 9
Syndecan-2/Laminin alpha3 -0.008 0.067 -9999 0 -0.58 7 7
Syndecan-2/RasGAP -0.003 0.043 -9999 0 -0.67 2 2
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.67 38 38
PRKCD 0.014 0.039 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.069 -9999 0 -0.5 10 10
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.041 -9999 0 -0.83 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.071 0.26 -9999 0 -0.86 50 50
RASA1 0.014 0.033 -9999 0 -0.75 1 1
alpha2/beta1 Integrin -0.005 0.055 -9999 0 -0.56 5 5
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.086 -9999 0 -0.86 5 5
CASP3 0.043 0.025 -9999 0 -0.52 1 1
FN1 -0.049 0.23 -9999 0 -0.86 38 38
Syndecan-2/IL8 -0.037 0.14 -9999 0 -0.56 34 34
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.56 0.33 -9999 0 -0.75 386 386
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.018 0.15 -9999 0 -0.86 15 15
Syndecan-2/TGFB1 -0.006 0.057 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.044 0 -9999 0 -10000 0 0
angiogenesis -0.036 0.14 -9999 0 -0.56 34 34
MMP2 0.006 0.092 -9999 0 -0.84 6 6
IL8 -0.04 0.21 -9999 0 -0.84 34 34
calcineurin-NFAT signaling pathway -0.056 0.17 -9999 0 -0.57 50 50
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.059 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.041 0.16 -10000 0 -0.61 35 35
NT3 (dimer)/TRKB -0.14 0.25 -10000 0 -0.54 131 131
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.022 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.1 0.3 -10000 0 -0.86 69 69
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.045 0.21 -10000 0 -0.76 40 40
NTRK2 -0.13 0.3 -10000 0 -0.75 99 99
NTRK3 -0.03 0.18 -10000 0 -0.75 31 31
NT-4/5 (dimer)/TRKB -0.14 0.25 -10000 0 -0.56 129 129
neuron apoptosis 0.14 0.18 0.62 36 -10000 0 36
SHC 2-3/Grb2 -0.16 0.2 -10000 0 -0.71 35 35
SHC1 0.014 0.039 -10000 0 -0.86 1 1
SHC2 -0.098 0.14 -10000 0 -0.53 31 31
SHC3 -0.16 0.24 -10000 0 -0.64 87 87
STAT3 (dimer) 0.012 0.068 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.2 -10000 0 -0.56 78 78
RIN/GDP 0.048 0.064 -10000 0 -0.32 1 1
GIPC1 0.014 0.033 -10000 0 -0.75 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.07 0.14 -10000 0 -0.63 13 13
RIN/GTP -0.001 0.03 -10000 0 -0.68 1 1
CCND1 0.009 0.16 -10000 0 -0.78 20 20
MAGED1 0.014 0.039 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.093 -10000 0 -0.86 6 6
SHC/GRB2/SOS1 -0.001 0.025 -10000 0 -0.58 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.27 -10000 0 -0.6 129 129
TRKA/NEDD4-2 -0.045 0.16 -10000 0 -0.58 40 40
ELMO1 0.012 0.055 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.042 -10000 0 -0.55 3 3
NGF -0.067 0.26 -10000 0 -0.86 49 49
HRAS 0.014 0.039 -10000 0 -0.86 1 1
DOCK1 0.014 0.033 -10000 0 -0.75 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.039 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.07 0.14 -10000 0 -0.6 15 15
mol:GDP 0.062 0.087 -10000 0 -0.48 2 2
NGF (dimer) -0.067 0.26 -10000 0 -0.86 49 49
RhoG/GDP -0.003 0.042 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.063 -10000 0 -0.31 1 1
TIAM1 0.014 0.033 -10000 0 -0.75 1 1
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
BDNF (dimer)/TRKB -0.17 0.26 -10000 0 -0.55 156 156
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.038 -10000 0 -0.61 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.023 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.092 -10000 0 -0.78 7 7
RAP1/GDP -0.008 0.031 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.1 0.3 -10000 0 -0.86 69 69
ubiquitin-dependent protein catabolic process -0.092 0.21 -10000 0 -0.55 87 87
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.24 -10000 0 -0.82 31 31
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.05 0.078 -10000 0 -10000 0 0
STAT3 0.012 0.068 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.76 31 31
MAPK3 -0.1 0.26 -10000 0 -0.58 95 95
MAPK1 -0.1 0.26 -10000 0 -0.58 95 95
CDC42/GDP 0.055 0.063 -10000 0 -0.31 1 1
NTF3 0.005 0.092 -10000 0 -0.78 7 7
NTF4 -0.004 0.093 -10000 0 -0.86 6 6
NGF (dimer)/TRKA/FAIM -0.091 0.21 -10000 0 -0.55 87 87
PI3K -0.002 0.035 -10000 0 -0.56 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.08 0.16 -10000 0 -0.62 23 23
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0 0.14 -10000 0 -0.52 35 35
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.063 -10000 0 -0.31 1 1
NGF (dimer)/TRKA/GRIT -0.093 0.21 -10000 0 -0.56 87 87
neuron projection morphogenesis -0.022 0.14 -10000 0 -0.54 13 13
NGF (dimer)/TRKA/NEDD4-2 -0.092 0.21 -10000 0 -0.55 87 87
MAP2K1 0.053 0.024 -10000 0 -10000 0 0
NGFR -0.045 0.22 -10000 0 -0.86 36 36
NGF (dimer)/TRKA/GIPC/GAIP -0.054 0.12 -10000 0 -0.59 3 3
RAS family/GTP/PI3K -0.002 0.029 -10000 0 -0.6 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.058 -10000 0 -0.75 3 3
MAPKKK cascade -0.096 0.18 -10000 0 -0.61 45 45
RASA1 0.014 0.033 -10000 0 -0.75 1 1
TRKA/c-Abl -0.044 0.15 -10000 0 -0.57 40 40
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.15 0.24 -10000 0 -0.5 157 157
NGF (dimer)/TRKA/p62/Atypical PKCs -0.079 0.18 -10000 0 -0.87 3 3
MATK -0.073 0.26 -10000 0 -0.86 52 52
NEDD4L 0.014 0.033 -10000 0 -0.75 1 1
RAS family/GDP -0.008 0.032 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.076 0.16 -10000 0 -0.47 38 38
Rac1/GTP -0.045 0.085 -10000 0 -0.42 7 7
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 0.009 0.22 -10000 0 -0.56 18 18
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.086 0.12 -10000 0 -0.76 2 2
EDN1 -0.015 0.19 -10000 0 -0.77 18 18
EDN3 -0.019 0.16 -10000 0 -0.86 17 17
EDN2 -0.091 0.28 -10000 0 -0.82 66 66
HRAS/GDP 0.052 0.17 -10000 0 -0.7 9 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.022 0.15 -10000 0 -0.51 15 15
ADCY4 0.01 0.17 -10000 0 -0.74 3 3
ADCY5 -0.007 0.2 -10000 0 -0.69 14 14
ADCY6 0.009 0.17 -10000 0 -0.74 3 3
ADCY7 -0.005 0.19 -10000 0 -0.73 7 7
ADCY1 0 0.18 -10000 0 -0.74 4 4
ADCY2 -0.12 0.27 -10000 0 -0.71 29 29
ADCY3 0.01 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.27 -10000 0 -0.74 33 33
ADCY9 0.01 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.078 0.15 -10000 0 -0.57 7 7
ETB receptor/Endothelin-1/Gq/GTP 0.035 0.11 -10000 0 -0.46 11 11
GNAO1 0.007 0.084 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
ETA receptor/Endothelin-1/G12/GTP -0.013 0.22 0.38 72 -0.83 3 75
ETA receptor/Endothelin-1/Gs/GTP -0.013 0.21 0.36 72 -0.79 3 75
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.042 0.34 -10000 0 -0.95 52 52
EDNRB 0.007 0.069 -10000 0 -0.78 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.041 0.3 -10000 0 -0.75 48 48
CYSLTR1 0.008 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.013 0.11 -10000 0 -0.39 2 2
mol:GDP 0.045 0.18 -10000 0 -0.68 12 12
SLC9A3 -0.35 0.3 -10000 0 -0.53 324 324
RAF1 0.048 0.17 -10000 0 -0.71 9 9
JUN 0.088 0.12 -10000 0 -0.57 1 1
JAK2 0.009 0.22 -10000 0 -0.88 3 3
mol:IP3 0.018 0.17 -10000 0 -0.57 17 17
ETA receptor/Endothelin-1 -0.026 0.27 0.45 72 -0.57 53 125
PLCB1 0.003 0.1 -10000 0 -0.75 9 9
PLCB2 -0.081 0.28 -10000 0 -0.86 58 58
ETA receptor/Endothelin-3 -0.022 0.15 -10000 0 -0.68 19 19
FOS 0.06 0.2 -10000 0 -0.86 15 15
Gai/GDP 0.039 0.07 -10000 0 -0.63 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.003 0.24 -10000 0 -0.77 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
PRKCB1 0.02 0.16 -10000 0 -0.54 17 17
GNAQ 0.02 0.004 -10000 0 -10000 0 0
GNAZ 0.011 0.058 -10000 0 -0.75 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.044 0.11 -10000 0 -0.61 11 11
ETA receptor/Endothelin-1/Gq/GTP 0.045 0.14 -10000 0 -0.5 9 9
MAPK14 0.024 0.13 -10000 0 -0.6 8 8
TRPC6 0.086 0.13 -10000 0 -0.81 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.058 -10000 0 -0.75 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.14 -10000 0 -0.54 14 14
ETB receptor/Endothelin-2 -0.086 0.21 -10000 0 -0.62 69 69
ETB receptor/Endothelin-3 -0.029 0.13 -10000 0 -0.66 20 20
ETB receptor/Endothelin-1 -0.032 0.16 -10000 0 -0.63 19 19
MAPK3 0.06 0.19 -10000 0 -0.72 17 17
MAPK1 0.06 0.19 -10000 0 -0.72 17 17
Rac1/GDP 0.052 0.17 -10000 0 -0.71 8 8
cAMP biosynthetic process -0.06 0.19 -10000 0 -0.61 13 13
MAPK8 0.08 0.13 -10000 0 -0.59 3 3
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.03 0.091 -10000 0 -0.57 3 3
p130Cas/CRK/Src/PYK2 0.073 0.17 -10000 0 -0.7 8 8
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.052 0.17 -10000 0 -0.71 8 8
COL1A2 -0.1 0.34 -10000 0 -0.89 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.23 -10000 0 -0.63 68 68
mol:DAG 0.018 0.17 -10000 0 -0.57 17 17
MAP2K2 0.057 0.18 -10000 0 -0.7 10 10
MAP2K1 0.058 0.17 -10000 0 -0.7 9 9
EDNRA -0.008 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.02 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.035 0.14 -10000 0 -0.7 15 15
HRAS/GTP 0.036 0.17 -10000 0 -0.67 12 12
PRKCH 0.03 0.16 -10000 0 -0.6 12 12
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.03 0.16 -10000 0 -0.64 10 10
PRKCB 0.025 0.18 -10000 0 -0.71 13 13
PRKCE 0.028 0.16 -10000 0 -0.59 13 13
PRKCD 0.029 0.16 -10000 0 -0.64 10 10
PRKCG 0.003 0.2 -10000 0 -0.73 20 20
regulation of vascular smooth muscle contraction 0.059 0.23 -10000 0 -1 15 15
PRKCQ 0.017 0.18 -10000 0 -0.69 14 14
PLA2G4A 0.077 0.16 -10000 0 -0.63 7 7
GNA14 0.009 0.088 -10000 0 -0.75 7 7
GNA15 -0.007 0.15 -10000 0 -0.86 15 15
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.058 -10000 0 -0.74 3 3
Rac1/GTP -0.013 0.22 0.38 72 -0.83 3 75
MMP1 -0.13 0.37 -10000 0 -0.85 102 102
Regulation of nuclear SMAD2/3 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
EP300 0.014 0.034 -10000 0 -0.73 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.021 0.087 -10000 0 -0.52 4 4
AKT1 0.02 0.006 -10000 0 -10000 0 0
GSC -0.027 0.22 -10000 0 -0.76 43 43
NKX2-5 -0.048 0.22 -10000 0 -0.86 34 34
muscle cell differentiation 0.035 0.11 0.58 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.04 0.08 -10000 0 -10000 0 0
SMAD4 0.032 0.029 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.003 0.046 -10000 0 -0.53 3 3
SMAD3/SMAD4/VDR 0.011 0.05 -10000 0 -10000 0 0
MYC -0.031 0.16 -10000 0 -0.86 19 19
CDKN2B 0.056 0.091 -10000 0 -0.68 6 6
AP1 0.06 0.075 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.013 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.044 0.069 -10000 0 -0.48 2 2
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.06 0.25 -10000 0 -0.88 44 44
SMAD3/SMAD4/GR 0.009 0.044 -10000 0 -0.6 1 1
GATA3 -0.35 0.38 -10000 0 -0.74 251 251
SKI/SIN3/HDAC complex/NCoR1 0.055 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 -0.075 0.19 -10000 0 -0.81 20 20
endothelial cell migration 0.097 0.26 0.74 74 -10000 0 74
MAX 0.019 0.016 -10000 0 -10000 0 0
RBBP7 0.015 0.005 -10000 0 -10000 0 0
RBBP4 0.014 0.034 -10000 0 -0.75 1 1
RUNX2 -0.008 0.14 -10000 0 -0.86 14 14
RUNX3 -0.37 0.44 -10000 0 -0.86 225 225
RUNX1 -0.047 0.23 -10000 0 -0.86 37 37
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.017 0.042 -10000 0 -0.87 1 1
VDR 0.011 0.058 -10000 0 -0.75 3 3
CDKN1A 0.083 0.075 -10000 0 -0.64 2 2
KAT2B 0.013 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.054 0.18 -10000 0 -0.61 44 44
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.004 -10000 0 -10000 0 0
SERPINE1 -0.099 0.26 -10000 0 -0.74 74 74
SMAD3/SMAD4/ATF2 0.008 0.037 -10000 0 -0.48 1 1
SMAD3/SMAD4/ATF3 0.005 0.054 -10000 0 -0.49 4 4
SAP30 -0.016 0.16 -10000 0 -0.86 18 18
Cbp/p300/PIAS3 0.007 0.035 -10000 0 -0.45 1 1
JUN 0.075 0.072 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.012 0.11 -10000 0 -0.56 18 18
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.094 0.25 -10000 0 -0.75 66 66
mesenchymal cell differentiation 0.007 0.1 0.59 14 -10000 0 14
DLX1 -0.45 0.44 -10000 0 -0.86 275 275
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.006 0.12 -10000 0 -0.74 13 13
SMAD3/SMAD4/Max 0.011 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.02 -10000 0 -0.46 1 1
ZBTB17 -0.001 0.045 -10000 0 -0.72 2 2
LAMC1 0.071 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.031 -10000 0 -10000 0 0
IRF7 -0.014 0.16 -10000 0 -0.85 19 19
ESR1 0.002 0.071 -10000 0 -0.76 4 4
HNF4A -0.049 0.21 -10000 0 -0.75 44 44
MEF2C -0.007 0.22 -10000 0 -0.8 20 20
SMAD2-3/SMAD4 0.005 0.032 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.029 -10000 0 -0.46 1 1
IGHV3OR16-13 -0.051 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.004 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.01 0.036 -10000 0 -10000 0 0
MSG1/HSC70 0.002 0.044 -10000 0 -0.67 2 2
SMAD2 0.022 0.019 -10000 0 -10000 0 0
SMAD3 0.033 0.026 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.062 0.034 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.032 -10000 0 -0.52 1 1
NCOR1 0.015 0.005 -10000 0 -10000 0 0
NCOA2 0.003 0.1 -10000 0 -0.75 9 9
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.037 0.15 -10000 0 -0.67 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.085 -10000 0 -10000 0 0
IFNB1 0.045 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.012 0.21 -10000 0 -0.82 15 15
CITED1 0.011 0.055 -10000 0 -0.86 2 2
SMAD2-3/SMAD4/ARC105 0.007 0.031 -10000 0 -10000 0 0
RBL1 0.016 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.077 0.065 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.29 0.32 -10000 0 -0.61 247 247
SMAD7 0.1 0.08 -10000 0 -10000 0 0
MYC/MIZ-1 -0.026 0.13 -10000 0 -0.65 21 21
SMAD3/SMAD4 -0.021 0.12 -10000 0 -10000 0 0
IL10 -0.19 0.31 -10000 0 -0.99 31 31
PIASy/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.25 -10000 0 -0.75 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.01 -10000 0 -10000 0 0
ATF3 0.01 0.067 -10000 0 -0.75 4 4
SMAD3/SMAD4/SP1 -0.012 0.053 -10000 0 -10000 0 0
FOXG1 -0.026 0.17 -10000 0 -0.87 20 20
FOXO3 0.037 0.009 -10000 0 -10000 0 0
FOXO1 0.037 0.008 -10000 0 -10000 0 0
FOXO4 0.037 0.008 -10000 0 -10000 0 0
heart looping -0.007 0.22 -10000 0 -0.79 20 20
CEBPB -0.003 0.13 -10000 0 -0.87 12 12
SMAD3/SMAD4/DLX1 -0.31 0.3 -10000 0 -0.58 275 275
MYOD1 -0.043 0.2 -10000 0 -0.86 29 29
SMAD3/SMAD4/HNF4 -0.034 0.14 -10000 0 -0.5 41 41
SMAD3/SMAD4/GATA3 -0.23 0.25 -10000 0 -0.84 15 15
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.24 0.28 -10000 0 -0.67 51 51
SMAD3/SMAD4/SP1-3 -0.005 0.043 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.013 0.05 -10000 0 -10000 0 0
SIN3B 0.015 0.005 -10000 0 -10000 0 0
SIN3A 0.015 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.078 0.22 -10000 0 -0.64 55 55
ITGB5 0.085 0.064 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.014 0.11 -10000 0 -0.5 19 19
AR -0.02 0.16 -10000 0 -0.75 24 24
negative regulation of cell growth 0.066 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.025 0.14 -10000 0 -0.6 29 29
E2F5 0.014 0.033 -10000 0 -0.75 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.042 0.15 -10000 0 -0.66 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 0.077 0.043 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.007 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 14 14
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.014 0.033 -10000 0 -0.75 1 1
EPO signaling pathway

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
BCL2L1 -0.02 0.18 -9999 0 -10000 0 0
CRKL -0.094 0.22 -9999 0 -10000 0 0
mol:DAG -0.12 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -0.7 1 1
MAPK8 -0.14 0.25 -9999 0 -10000 0 0
RAP1A -0.094 0.22 -9999 0 -10000 0 0
GAB1 -0.094 0.22 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -10000 0 0
EPO -0.29 0.42 -9999 0 -0.85 182 182
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.19 0.26 -9999 0 -0.55 183 183
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.31 -9999 0 -0.65 182 182
IRS2 -0.1 0.23 -9999 0 -0.88 2 2
STAT1 -0.065 0.21 -9999 0 -10000 0 0
STAT5B -0.07 0.21 -9999 0 -10000 0 0
cell proliferation -0.12 0.24 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.11 0.15 -9999 0 -0.71 1 1
TEC -0.094 0.22 -9999 0 -10000 0 0
SOCS3 0.012 0.055 -9999 0 -0.86 2 2
STAT1 (dimer) -0.063 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -10000 0 0
EPO/EPOR -0.23 0.31 -9999 0 -0.65 182 182
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.081 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 182 182
mol:IP3 -0.12 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.14 0.26 -9999 0 -0.91 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 1 1
PTPN6 -0.11 0.23 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.12 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.13 0.17 -9999 0 -0.73 1 1
VAV2 -0.094 0.22 -9999 0 -10000 0 0
CBL -0.095 0.22 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.13 0.17 -9999 0 -10000 0 0
STAT5A -0.07 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.045 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.01 0.077 -9999 0 -0.62 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.29 -9999 0 -0.88 29 29
BCL2 -0.02 0.18 -9999 0 -10000 0 0
Wnt signaling

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.013 0.16 -9999 0 -0.86 17 17
WNT4 -0.07 0.24 -9999 0 -0.75 58 58
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.058 -9999 0 -0.75 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 37 37
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.005 0.13 -10000 0 -0.86 11 11
GNB1/GNG2 -0.035 0.063 -10000 0 -0.22 15 15
AKT1 0.054 0.1 -10000 0 -0.25 1 1
EGF -0.67 0.23 -10000 0 -0.75 466 466
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.033 0.081 -10000 0 -0.61 2 2
mol:Ca2+ 0.04 0.14 -10000 0 -0.33 28 28
LYN -0.03 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.038 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.049 0.16 -10000 0 -0.37 25 25
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.039 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.42 7 7
G beta5/gamma2 -0.046 0.084 -10000 0 -0.3 16 16
PRKCH 0.042 0.16 -10000 0 -0.39 21 21
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
TXA2/TP beta/beta Arrestin3 -0.013 0.041 -10000 0 -0.32 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.31 -10000 0 -0.86 77 77
G12 family/GTP -0.043 0.092 -10000 0 -0.32 25 25
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.11 0.31 12 -10000 0 12
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.003 0.12 -10000 0 -0.75 13 13
mol:IP3 0.037 0.17 -10000 0 -0.42 28 28
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.027 0.22 -10000 0 -0.59 28 28
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.055 0.13 -10000 0 -0.61 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.051 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.013 0.051 -10000 0 -0.8 2 2
PRKCB1 0.036 0.16 -10000 0 -0.38 42 42
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.034 0.21 -10000 0 -0.53 44 44
LCK -0.047 0.12 -10000 0 -0.6 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.041 0.097 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.041 0.096 -10000 0 -0.43 1 1
MAPK14 0.054 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.035 0.19 -10000 0 -0.48 30 30
MAPK11 0.053 0.11 -10000 0 -0.38 2 2
ARHGEF1 0.041 0.089 -10000 0 -0.33 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.043 0.17 -10000 0 -0.39 44 44
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.044 0.14 -10000 0 -0.35 20 20
cAMP biosynthetic process 0.034 0.16 -10000 0 -0.38 32 32
Gq family/GTP/EBP50 0.025 0.06 -10000 0 -0.28 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.03 0.071 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.086 0.1 -10000 0 -0.41 15 15
VCAM1 0.043 0.14 -10000 0 -0.35 25 25
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.42 7 7
platelet activation 0.066 0.15 -10000 0 -0.34 15 15
PGI2/IP -0.002 0.039 -10000 0 -0.62 2 2
PRKACA -0.052 0.12 -10000 0 -0.34 79 79
Gq family/GDP/G beta5/gamma2 0.024 0.079 -10000 0 -0.41 7 7
TXA2/TP beta/beta Arrestin2 -0.013 0.059 -10000 0 -0.41 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.13 -10000 0 -10000 0 0
mol:DAG 0.036 0.18 -10000 0 -0.44 42 42
EGFR 0.001 0.11 -10000 0 -0.85 9 9
TXA2/TP alpha 0.032 0.21 -10000 0 -0.54 32 32
Gq family/GTP -0.005 0.053 -10000 0 -0.26 7 7
YES1 -0.03 0.071 -10000 0 -10000 0 0
GNAI2/GTP -0.035 0.083 -10000 0 -10000 0 0
PGD2/DP -0.1 0.24 -10000 0 -0.68 77 77
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.03 0.071 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.01 0.15 -10000 0 -0.86 15 15
PGK/cGMP -0.012 0.076 -10000 0 -0.49 13 13
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.048 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.042 0.16 -10000 0 -0.39 21 21
PRKCB 0.04 0.16 -10000 0 -0.43 22 22
PRKCE 0.043 0.16 -10000 0 -0.4 21 21
PRKCD 0.04 0.16 -10000 0 -0.41 22 22
PRKCG 0.028 0.19 -10000 0 -0.49 32 32
muscle contraction 0.042 0.2 -10000 0 -0.49 44 44
PRKCZ 0.049 0.16 -10000 0 -0.38 20 20
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.04 0.095 -10000 0 -10000 0 0
PRKCQ 0.034 0.17 -10000 0 -0.43 23 23
MAPKKK cascade 0.034 0.19 -10000 0 -0.49 29 29
SELE 0.036 0.16 -10000 0 -0.41 40 40
TP beta/GNAI2/GDP/G beta/gamma -0.038 0.091 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.005 0.088 -10000 0 -0.75 7 7
chemotaxis 0.034 0.23 -10000 0 -0.61 43 43
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.011 0.058 -10000 0 -0.75 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.029 -10000 0 -0.66 1 1
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.005 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.055 0.22 -10000 0 -0.75 48 48
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.097 0.16 -10000 0 -0.34 147 147
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.014 0.033 -10000 0 -0.74 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH -0.001 0.028 -10000 0 -0.64 1 1
WIF1 0.001 0.077 -10000 0 -0.77 5 5
NOTCH1 -0.001 0.03 -10000 0 -0.68 1 1
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.09 0.28 -10000 0 -0.86 62 62
DKK1 -0.019 0.17 -10000 0 -0.83 21 21
beta catenin/beta TrCP1 0.084 0.084 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.008 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.004 0.12 -10000 0 -0.76 13 13
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.008 -10000 0 -10000 0 0
CTNNB1 0.08 0.091 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.22 -10000 0 -0.57 86 86
HNF1A -0.002 0.074 -10000 0 -0.75 5 5
CTBP1 0.005 0.008 -10000 0 -10000 0 0
MYC 0.004 0.14 -10000 0 -0.73 19 19
NKD1 -0.19 0.34 -10000 0 -0.75 138 138
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.037 0.12 -10000 0 -0.64 1 1
apoptosis -0.097 0.16 -10000 0 -0.34 147 147
Delta 1/NOTCHprecursor -0.001 0.028 -10000 0 -0.64 1 1
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.029 0.023 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.005 0.032 -10000 0 -0.47 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.62 76 76
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.015 0.013 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -0.73 20 20
WNT1 -0.028 0.19 -10000 0 -0.86 25 25
Axin1/APC/beta catenin 0.081 0.052 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 25 25
NOTCH1 precursor/DVL1 -0.003 0.034 -10000 0 -0.58 1 1
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.012 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.037 0.12 -10000 0 -0.66 1 1
PPP2R5D 0.093 0.16 0.36 137 -10000 0 137
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.03 0.12 -10000 0 -0.52 26 26
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.044 -9999 0 -10000 0 0
GNAO1 0.01 0.084 -9999 0 -0.84 5 5
S1P/S1P3/G12/G13 -0.001 0.019 -9999 0 -0.44 1 1
AKT1 -0.002 0.013 -9999 0 -10000 0 0
AKT3 -0.025 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.058 -9999 0 -0.74 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.054 0.049 -9999 0 -0.54 1 1
MAPK3 0.062 0.047 -9999 0 -0.5 1 1
MAPK1 0.062 0.047 -9999 0 -0.5 1 1
JAK2 -0.023 0.13 -9999 0 -0.48 2 2
CXCR4 -0.12 0.26 -9999 0 -0.47 179 179
FLT1 0.01 0.086 -9999 0 -0.86 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.047 -9999 0 -0.5 1 1
S1P/S1P3/Gi 0.054 0.049 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.036 -9999 0 -0.49 1 1
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
S1P/S1P2/Gi 0.049 0.044 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 234 234
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.072 -9999 0 -10000 0 0
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.058 -9999 0 -0.74 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.058 -9999 0 -0.75 3 3
Rac1/GTP -0.005 0.036 -9999 0 -0.49 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.015 0.087 -9999 0 -0.52 15 15
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.033 -9999 0 -0.75 1 1
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin/MAdCAM1 -0.027 0.12 -9999 0 -0.52 27 27
EPO -0.3 0.42 -9999 0 -0.86 182 182
alpha4/beta7 Integrin -0.019 0.11 -9999 0 -0.67 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.67 15 15
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.67 182 182
lamellipodium assembly 0 0.036 -9999 0 -0.53 2 2
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.12 0.17 -9999 0 -0.66 5 5
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
MADCAM1 -0.007 0.13 -9999 0 -0.86 12 12
cell adhesion -0.027 0.12 -9999 0 -0.52 27 27
CRKL/CBL -0.001 0.025 -9999 0 -0.56 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.015 0.13 -9999 0 -0.52 24 24
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.031 0.13 -9999 0 -0.56 29 29
p130Cas/Crk/Dock1 -0.024 0.1 -9999 0 -0.8 1 1
VCAM1 -0.007 0.14 -9999 0 -0.82 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.015 0.088 -9999 0 -0.52 15 15
BCAR1 0.026 0.12 -9999 0 -0.89 1 1
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.75 1 1
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.037 -9999 0 -0.55 2 2
FoxO family signaling

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
G6PC -0.57 0.68 -9999 0 -1.3 242 242
PLK1 -0.12 0.37 -9999 0 -0.8 93 93
CDKN1B 0.062 0.16 -9999 0 -10000 0 0
FOXO3 -0.038 0.23 -9999 0 -0.66 14 14
KAT2B 0.012 0.04 -9999 0 -0.78 1 1
FOXO1/SIRT1 -0.14 0.21 -9999 0 -0.4 2 2
CAT -0.026 0.23 -9999 0 -0.89 7 7
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.007 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 242 242
MAPK10 0.033 0.049 -9999 0 -0.43 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.047 -9999 0 -10000 0 0
response to oxidative stress -0.029 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.028 0.2 -9999 0 -0.58 13 13
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 -0.006 0.042 -9999 0 -0.75 1 1
BCL2L11 0.012 0.044 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -10000 0 0
mol:GDP -0.029 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.098 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.086 -9999 0 -10000 0 0
MST1 0 0.11 -9999 0 -0.86 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.097 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.037 0.028 -9999 0 -0.43 1 1
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.036 0.028 -9999 0 -10000 0 0
SOD2 0.014 0.2 -9999 0 -0.71 6 6
RBL2 0.023 0.17 -9999 0 -1.3 1 1
RAL/GDP 0.009 0.024 -9999 0 -10000 0 0
CHUK 0.013 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.004 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.75 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.34 0.39 -9999 0 -0.73 262 262
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.002 -9999 0 -10000 0 0
IKBKB 0.013 0.02 -9999 0 -10000 0 0
CCNB1 -0.029 0.23 -9999 0 -0.92 10 10
FOXO1-3a-4/beta catenin -0.07 0.1 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.013 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.043 -9999 0 -10000 0 0
SFN -0.086 0.28 -9999 0 -0.83 62 62
CDK2 -0.018 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.012 0.099 -9999 0 -10000 0 0
CREBBP -0.018 0.041 -9999 0 -10000 0 0
FBXO32 -0.026 0.22 -9999 0 -0.79 8 8
BCL6 0.025 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.021 0.088 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
AP1 -0.03 0.1 -9999 0 -0.6 1 1
mol:PIP3 -0.026 0.091 -9999 0 -0.55 1 1
AKT1 -0.014 0.057 -9999 0 -10000 0 0
PTK2B 0.033 0.059 -9999 0 -10000 0 0
RHOA 0.037 0.035 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.051 0.052 -9999 0 -0.45 2 2
MAGI3 0.013 0.047 -9999 0 -0.75 2 2
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.021 0.085 -9999 0 -0.37 26 26
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
positive regulation of microtubule depolymerization 0.046 0.069 -9999 0 -0.38 3 3
NF kappa B1 p50/RelA -0.018 0.073 -9999 0 -10000 0 0
endothelial cell migration 0.007 0.13 -9999 0 -0.54 28 28
ADCY4 0.032 0.12 -9999 0 -0.47 24 24
ADCY5 0.023 0.13 -9999 0 -0.49 27 27
ADCY6 0.032 0.12 -9999 0 -0.47 24 24
ADCY7 0.027 0.12 -9999 0 -0.48 24 24
ADCY1 0.027 0.12 -9999 0 -0.48 25 25
ADCY2 -0.017 0.14 -9999 0 -0.52 25 25
ADCY3 0.032 0.12 -9999 0 -0.47 24 24
ADCY8 -0.027 0.14 -9999 0 -0.48 24 24
ADCY9 0.032 0.12 -9999 0 -0.47 24 24
GSK3B 0.042 0.056 -9999 0 -10000 0 0
arachidonic acid secretion 0.039 0.11 -9999 0 -0.44 22 22
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0.001 0.008 -9999 0 -10000 0 0
GNAO1 0.007 0.12 -9999 0 -0.48 27 27
HRAS 0.014 0.039 -9999 0 -0.86 1 1
NFKBIA 0.061 0.062 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.054 -9999 0 -0.86 2 2
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.48 1 1
TIAM1 -0.003 0.063 -9999 0 -1 2 2
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.051 0.053 -9999 0 -0.48 1 1
PLCB3 0.037 0.023 -9999 0 -0.43 1 1
FOS -0.004 0.12 -9999 0 -0.76 13 13
positive regulation of mitosis 0.039 0.11 -9999 0 -0.44 22 22
LPA/LPA1-2-3 -0.025 0.1 -9999 0 -0.44 26 26
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
stress fiber formation 0.04 0.076 -9999 0 -10000 0 0
GNAZ 0.01 0.12 -9999 0 -0.48 25 25
EGFR/PI3K-beta/Gab1 -0.027 0.095 -9999 0 -0.57 1 1
positive regulation of dendritic cell cytokine production -0.025 0.099 -9999 0 -0.44 26 26
LPA/LPA2/MAGI-3 -0.003 0.031 -9999 0 -0.48 2 2
ARHGEF1 0.031 0.095 -9999 0 -0.49 1 1
GNAI2 0.013 0.11 -9999 0 -0.47 22 22
GNAI3 0.013 0.11 -9999 0 -0.47 22 22
GNAI1 0.01 0.12 -9999 0 -0.48 25 25
LPA/LPA3 -0.007 0.06 -9999 0 -0.67 4 4
LPA/LPA2 -0.001 0.013 -9999 0 -10000 0 0
LPA/LPA1 -0.027 0.12 -9999 0 -0.51 28 28
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 253 253
HBEGF -0.3 0.35 -9999 0 -0.67 247 247
mol:DAG 0.051 0.053 -9999 0 -0.48 1 1
cAMP biosynthetic process 0.02 0.12 -9999 0 -0.46 26 26
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.061 0.062 -9999 0 -10000 0 0
GNAQ -0.004 0.036 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.003 0.077 -9999 0 -0.86 4 4
LPAR1 -0.012 0.15 -9999 0 -0.73 22 22
IL8 -0.08 0.2 -9999 0 -0.49 44 44
PTK2 0.024 0.1 -9999 0 -0.48 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.085 -9999 0 -0.38 26 26
EGFR 0 0.11 -9999 0 -0.85 9 9
PLCG1 0.019 0.054 -9999 0 -0.41 4 4
PLD2 0.024 0.1 -9999 0 -0.48 4 4
G12/G13 -0.021 0.088 -9999 0 -0.42 22 22
PI3K-beta -0.016 0.067 -9999 0 -0.52 1 1
cell migration -0.009 0.034 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.75 1 1
PXN 0.04 0.077 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.098 -9999 0 -0.45 22 22
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 247 247
PRKCE 0.013 0.034 -9999 0 -0.75 1 1
PRKCD 0.059 0.055 -9999 0 -10000 0 0
Gi(beta/gamma) -0.025 0.097 -9999 0 -0.44 24 24
mol:LPA 0.004 0.023 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.017 0.081 -9999 0 -10000 0 0
MAPKKK cascade 0.039 0.11 -9999 0 -0.44 22 22
contractile ring contraction involved in cytokinesis 0.037 0.035 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.009 0.059 -9999 0 -0.4 11 11
GNA15 -0.016 0.079 -9999 0 -0.42 18 18
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.046 0.07 -9999 0 -0.39 3 3
GNA11 -0.006 0.046 -9999 0 -0.39 7 7
Rac1/GTP -0.002 0.057 -9999 0 -0.91 2 2
MMP2 0.007 0.13 -9999 0 -0.54 28 28
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0.047 -9999 0 -0.75 2 2
SPHK1 -0.057 0.24 -9999 0 -0.86 43 43
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.095 -9999 0 -0.31 45 45
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
mol:Sphinganine-1-P -0.029 0.2 -9999 0 -0.66 45 45
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.055 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.033 -9999 0 -0.75 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.023 0.074 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
S1PR4 -0.028 0.19 -9999 0 -0.86 26 26
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
S1P/S1P5/G12 -0.11 0.21 -9999 0 -0.54 88 88
S1P/S1P3/Gq 0.023 0.097 -9999 0 -0.42 16 16
S1P/S1P4/Gi 0.025 0.096 -9999 0 -0.38 12 12
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
GNA14 0.005 0.088 -9999 0 -0.75 7 7
GNA15 -0.01 0.15 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.058 -9999 0 -0.75 3 3
ABCC1 0.016 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.015 0.16 -9999 0 -0.86 18 18
PLK4 0.011 0.067 -9999 0 -0.86 3 3
regulation of centriole replication 0.003 0.14 -9999 0 -0.67 21 21
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.045 -10000 0 -0.56 3 3
MAP4K4 0.025 0.094 -10000 0 -0.48 1 1
BAG4 0.014 0.033 -10000 0 -0.75 1 1
PKC zeta/ceramide -0.099 0.047 -10000 0 -0.48 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.32 -10000 0 -0.86 80 80
BAX -0.042 0.018 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.046 0.008 -10000 0 -10000 0 0
BAD -0.098 0.043 -10000 0 -0.45 2 2
SMPD1 0.026 0.042 -10000 0 -0.28 1 1
RB1 -0.096 0.038 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.088 -10000 0 -10000 0 0
MAP2K4 -0.081 0.036 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.085 0.057 -10000 0 -0.59 4 4
EGF -0.67 0.23 -10000 0 -0.75 466 466
mol:ceramide -0.12 0.04 0.2 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.026 -10000 0 -0.56 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.095 0.037 -10000 0 -10000 0 0
cell proliferation -0.052 0.06 -10000 0 -0.46 10 10
BID -0.012 0.066 -10000 0 -10000 0 0
MAP3K1 -0.096 0.038 -10000 0 -10000 0 0
EIF2A -0.067 0.034 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.065 0.052 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.065 0.052 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.097 0.036 -10000 0 -0.26 1 1
FADD 0.025 0.094 -10000 0 -0.48 1 1
KSR1 -0.1 0.06 -10000 0 -0.63 4 4
MAPK8 -0.076 0.04 -10000 0 -0.35 3 3
PRKRA -0.096 0.038 -10000 0 -10000 0 0
PDGFA 0.014 0.033 -10000 0 -0.75 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.006 0.094 -10000 0 -0.86 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.04 0.2 2 -10000 0 2
CTSD 0.014 0.033 -10000 0 -0.75 1 1
regulation of nitric oxide biosynthetic process -0.001 0.024 -10000 0 -0.56 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.055 0.066 -10000 0 -0.5 10 10
PRKCD 0.014 0.039 -10000 0 -0.86 1 1
PRKCZ 0.011 0.058 -10000 0 -0.75 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.026 -10000 0 -0.56 1 1
RelA/NF kappa B1 -0.001 0.025 -10000 0 -0.56 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.033 -10000 0 -0.75 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.034 0.078 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -10000 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0.027 0.045 -10000 0 -0.56 3 3
MAP2K1 -0.071 0.054 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.063 0.023 -10000 0 -0.23 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.75 1 1
TNFR1A/BAG4 -0.001 0.025 -10000 0 -0.56 1 1
EIF2AK2 -0.081 0.036 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.008 0.065 -10000 0 -0.53 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.037 -10000 0 -10000 0 0
MAP2K2 -0.071 0.054 -10000 0 -0.55 4 4
SMPD3 0.026 0.052 -10000 0 -0.33 2 2
TNF 0.003 0.1 -10000 0 -0.8 8 8
PKC zeta/PAR4 -0.004 0.049 -10000 0 -0.56 4 4
mol:PHOSPHOCHOLINE 0.23 0.083 0.26 468 -10000 0 468
NF kappa B1/RelA/I kappa B alpha -0.004 0.038 -10000 0 -10000 0 0
AIFM1 -0.063 0.025 -10000 0 -0.23 1 1
BCL2 0.016 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.005 0.019 -10000 0 -10000 0 0
AES 0.005 0.016 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.025 0.18 -10000 0 -0.83 25 25
TLE1 0.005 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.048 0.1 -10000 0 -0.45 1 1
WIF1 -0.001 0.076 -10000 0 -0.77 5 5
beta catenin/RanBP3 0.004 0.1 0.36 19 -10000 0 19
KREMEN2 -0.09 0.28 -10000 0 -0.86 62 62
DKK1 -0.019 0.17 -10000 0 -0.83 21 21
beta catenin/beta TrCP1 0.056 0.094 -10000 0 -10000 0 0
FZD1 0.016 0.003 -10000 0 -10000 0 0
AXIN2 0.009 0.1 -10000 0 -1.4 2 2
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.018 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.073 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.04 0.083 0.25 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.003 0.075 -10000 0 -0.74 5 5
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.008 0.15 -10000 0 -0.75 19 19
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.22 -10000 0 -0.57 86 86
NKD1 -0.19 0.34 -10000 0 -0.75 138 138
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.025 0.11 -10000 0 -0.52 25 25
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.11 0.36 39 -10000 0 39
LEF1 -0.02 0.15 -10000 0 -0.87 15 15
DVL1 0.003 0.034 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.082 0.07 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.62 76 76
LRP6 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.005 0.019 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.009 0.15 -10000 0 -0.75 20 20
WNT1 -0.028 0.19 -10000 0 -0.86 25 25
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.002 -10000 0 -10000 0 0
FRAT1 0.014 0.004 -10000 0 -10000 0 0
PPP2R5D 0.096 0.16 0.35 137 -10000 0 137
APC -0.017 0.11 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.012 0.064 0.27 5 -10000 0 5
CREBBP 0.005 0.017 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.043 -10000 0 -10000 0 0
RFC1 0.012 0.043 -10000 0 -10000 0 0
PRKDC 0.012 0.043 -10000 0 -10000 0 0
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.024 0.066 0.25 6 -10000 0 6
FASLG/FAS/FADD/FAF1 -0.14 0.16 -10000 0 -0.35 22 22
MAP2K4 -0.086 0.16 -10000 0 -0.43 23 23
mol:ceramide -0.15 0.2 -10000 0 -0.48 32 32
GSN 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.17 0.18 -10000 0 -0.44 22 22
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.018 0.066 -10000 0 -10000 0 0
MAP3K1 -0.036 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.012 0.043 -10000 0 -10000 0 0
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.037 0.15 -10000 0 -0.58 33 33
ARHGDIB 0.012 0.043 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.043 -10000 0 -10000 0 0
NFKB1 -0.066 0.077 -10000 0 -0.71 1 1
MAPK8 -0.085 0.18 -10000 0 -0.52 24 24
DFFA 0.012 0.043 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.043 -10000 0 -10000 0 0
FAS/FADD/MET -0.006 0.056 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.045 0.22 -10000 0 -0.86 36 36
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.012 0.043 -10000 0 -10000 0 0
DFFB 0.012 0.043 -10000 0 -10000 0 0
CHUK -0.053 0.067 -10000 0 -0.65 1 1
FASLG -0.43 0.44 -10000 0 -0.87 262 262
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.021 0.17 -10000 0 -0.8 23 23
LMNA 0.01 0.047 -10000 0 -0.52 1 1
CASP6 0.012 0.043 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.014 0.05 -10000 0 -10000 0 0
PTPN13 0.003 0.1 -10000 0 -0.75 9 9
CASP8 0.028 0.1 0.4 36 -10000 0 36
IL6 -0.13 0.34 -10000 0 -0.96 65 65
MET 0.007 0.086 -10000 0 -0.86 5 5
ICAD/CAD 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.15 0.2 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c 0.018 0.066 -10000 0 -10000 0 0
PAK2 0.012 0.043 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
Class I PI3K signaling 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
ARF5/GTP -0.001 0.017 -9999 0 -10000 0 0
DAPP1 0.03 0.11 -9999 0 -0.54 9 9
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.26 -9999 0 -0.74 53 53
mol:DAG -0.07 0.15 -9999 0 -0.32 61 61
HRAS 0.015 0.038 -9999 0 -0.86 1 1
RAP1A 0.017 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.018 0.074 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.019 -9999 0 -10000 0 0
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
ADAP1 -0.004 0.037 -9999 0 -10000 0 0
ARAP3 -0.001 0.019 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.011 0.067 -9999 0 -0.86 3 3
mol:Ca2+ -0.022 0.078 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.033 -9999 0 -0.75 1 1
ZAP70 -0.46 0.44 -9999 0 -0.86 281 281
mol:IP3 -0.036 0.11 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.018 0.074 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.017 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.021 -9999 0 -0.48 1 1
BLNK 0.014 0.033 -9999 0 -0.75 1 1
actin cytoskeleton reorganization 0.045 0.082 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.054 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.017 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.018 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.2 0.24 -9999 0 -0.56 129 129
BLK -0.041 0.22 -9999 0 -0.86 33 33
PDPK1 0.014 0.033 -9999 0 -0.75 1 1
CYTH1 -0.001 0.018 -9999 0 -10000 0 0
HCK -0.032 0.2 -9999 0 -0.86 28 28
CYTH3 -0.001 0.018 -9999 0 -10000 0 0
CYTH2 -0.001 0.018 -9999 0 -10000 0 0
KRAS 0.017 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.024 -9999 0 -0.55 1 1
SGK1 -0.001 0.026 -9999 0 -0.6 1 1
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
mol:GDP 0.01 0.078 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.047 -9999 0 -0.75 2 2
ARF6/GDP -0.004 0.017 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.019 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
VAV1 -0.2 0.38 -9999 0 -0.86 124 124
mol:PI-3-4-P2 0.025 0.061 -9999 0 -0.67 4 4
RAS family/GTP/PI3K Class I -0.001 0.019 -9999 0 -10000 0 0
PLEKHA1 0.036 0.054 -9999 0 -0.57 4 4
Rac1/GDP 0.018 0.074 -9999 0 -10000 0 0
LAT -0.23 0.4 -9999 0 -0.86 145 145
Rac1/GTP -0.001 0.1 -9999 0 -10000 0 0
ITK -0.14 0.21 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.11 0.21 -9999 0 -0.46 77 77
LCK -0.021 0.18 -9999 0 -0.85 22 22
BTK -0.097 0.19 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.022 0.1 -9999 0 -0.5 23 23
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.56 21 21
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.058 -9999 0 -0.75 3 3
CDH1 -0.015 0.15 -9999 0 -0.75 21 21
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.2 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.16 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.029 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.11 0.09 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.13 0.22 -9999 0 -10000 0 0
MAP3K11 -0.15 0.23 -9999 0 -0.81 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.28 0.29 -9999 0 -0.74 113 113
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.07 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.2 0.22 -9999 0 -1 2 2
STAT1 -0.15 0.24 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.38 0.43 -9999 0 -0.85 237 237
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.076 0.084 -9999 0 -0.47 1 1
mol:Ca2+ -0.2 0.21 -9999 0 -10000 0 0
MAPK3 -0.091 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.091 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.026 0.15 -9999 0 -0.63 3 3
SMAD7 -0.021 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.18 0.19 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.86 237 237
apoptosis -0.038 0.12 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.36 -9999 0 -0.75 173 173
CAMK2B -0.1 0.28 -9999 0 -0.76 78 78
FRAP1 -0.11 0.2 -9999 0 -10000 0 0
PRKCD -0.12 0.22 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.11 0.09 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.033 -9999 0 -0.74 1 1
IRF1 -0.061 0.19 -9999 0 -0.93 1 1
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.011 0.083 -9999 0 -0.73 6 6
mol:GDP -0.16 0.17 -9999 0 -10000 0 0
CASP1 -0.021 0.082 -9999 0 -10000 0 0
PTGES2 0.013 0.047 -9999 0 -0.75 2 2
IRF9 0.017 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.15 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.11 0.09 -9999 0 -0.37 1 1
PTPN11 -0.17 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.02 0.092 -10000 0 -0.44 24 24
regulation of S phase of mitotic cell cycle -0.014 0.068 -10000 0 -0.62 1 1
GNAO1 0.008 0.084 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
SHBG/T-DHT -0.051 0.15 -10000 0 -0.5 53 53
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.047 0.091 -10000 0 -10000 0 0
T-DHT/AR -0.027 0.12 -10000 0 -0.57 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 13 13
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.058 -10000 0 -0.75 3 3
mol:GDP -0.026 0.12 -10000 0 -0.56 24 24
cell proliferation 0.071 0.11 -10000 0 -0.64 4 4
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
FOS 0.056 0.15 -10000 0 -0.81 13 13
mol:Ca2+ -0.003 0.014 -10000 0 -0.11 4 4
MAPK3 0.063 0.1 -10000 0 -0.57 4 4
MAPK1 0.045 0.054 -10000 0 -0.29 4 4
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process -0.046 0.15 -10000 0 -0.48 53 53
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.019 0.085 -10000 0 -0.45 5 5
actin cytoskeleton reorganization -0.001 0.024 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K -0.002 0.03 -10000 0 -0.49 2 2
apoptosis -0.061 0.095 0.43 12 -10000 0 12
T-DHT/AR/PELP1 -0.023 0.1 -10000 0 -0.49 24 24
HRAS/GDP -0.025 0.12 -10000 0 -0.53 25 25
CREB1 0.061 0.1 -10000 0 -0.47 12 12
RAC1-CDC42/GTP -0.001 0.024 -10000 0 -10000 0 0
AR -0.019 0.16 -10000 0 -0.75 24 24
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.036 0.093 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.023 0.1 -10000 0 -0.49 24 24
T-DHT/AR/PELP1/Src -0.02 0.092 -10000 0 -0.44 24 24
MAP2K2 0.047 0.093 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.015 0.068 -10000 0 -0.63 1 1
GNAZ 0.011 0.058 -10000 0 -0.75 3 3
SHBG -0.063 0.23 -10000 0 -0.75 53 53
Gi family/GNB1/GNG2/GDP -0.008 0.045 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.18 0.31 -10000 0 -0.68 142 142
Gi family/GTP -0.013 0.058 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.031 0.002 -9999 0 -10000 0 0
SMARCC1 0.026 0.01 -9999 0 -10000 0 0
REL 0.009 0.058 -9999 0 -0.74 3 3
HDAC7 -0.097 0.087 -9999 0 -0.67 3 3
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.014 0.034 -9999 0 -0.75 1 1
KAT2B 0.014 0.034 -9999 0 -0.75 1 1
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0 0.047 -9999 0 -0.59 3 3
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.089 -9999 0 -0.68 4 4
MAP2K6 -0.002 0.059 -9999 0 -0.77 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -1.2 5 5
NCOA2 0.002 0.1 -9999 0 -0.75 9 9
CEBPA -0.001 0.12 -9999 0 -0.86 10 10
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.092 0.095 -9999 0 -0.55 2 2
NR0B1 -0.053 0.22 -9999 0 -0.86 34 34
EGR1 -0.001 0.11 -9999 0 -0.75 11 11
RXRs/9cRA -0.004 0.047 -9999 0 -0.54 4 4
AR/RACK1/Src -0.015 0.061 -9999 0 -0.58 2 2
AR/GR 0.002 0.084 -9999 0 -0.72 3 3
GNB2L1 0.014 0.039 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.003 0.029 -9999 0 -0.59 1 1
T-DHT/AR/TIF2/CARM1 -0.019 0.089 -9999 0 -0.81 3 3
SRC 0.003 0.047 -9999 0 -10000 0 0
NR3C1 0.014 0.039 -9999 0 -0.86 1 1
KLK3 -0.053 0.19 -9999 0 -0.72 27 27
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.025 0.054 -9999 0 -0.62 2 2
TMPRSS2 -0.96 0.38 -9999 0 -1.1 449 449
RXRG 0.006 0.077 -9999 0 -0.87 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.014 0.034 -9999 0 -0.75 1 1
KLK2 -0.023 0.13 -9999 0 -0.63 20 20
AR -0.009 0.084 -9999 0 -0.42 12 12
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 -0.002 0.12 -9999 0 -0.75 12 12
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.17 0.35 -9999 0 -0.86 104 104
T-DHT/AR/RACK1/Src -0.015 0.059 -9999 0 -0.6 2 2
positive regulation of transcription -0.002 0.11 -9999 0 -0.74 12 12
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.18 0.36 -9999 0 -0.86 112 112
T-DHT/AR/TIF2 0.02 0.07 -9999 0 -0.67 3 3
T-DHT/AR/Hsp90 -0.026 0.053 -9999 0 -0.59 3 3
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.011 0.05 -9999 0 -0.51 2 2
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.014 0.008 -9999 0 -10000 0 0
POU2F1 0.005 0.014 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.067 0.14 -9999 0 -0.61 27 27
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.071 -10000 0 -10000 0 0
epithelial cell differentiation -0.051 0.11 -10000 0 -0.57 1 1
ITCH 0.055 0.018 -10000 0 -10000 0 0
WWP1 -0.096 0.067 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.08 -10000 0 -0.57 1 1
PTPRZ1 -0.082 0.25 -10000 0 -0.76 63 63
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.073 -10000 0 -0.6 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.083 0.094 -10000 0 -0.57 9 9
ADAM17 0.055 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.086 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.63 11 11
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.076 0.077 -10000 0 -0.54 9 9
GRIN2B -0.057 0.091 -10000 0 -0.61 3 3
ErbB4/ErbB2/betacellulin -0.13 0.16 -10000 0 -0.52 70 70
STAT1 0.014 0.039 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.084 0.26 -10000 0 -0.75 68 68
E4ICDs/ETO2 -0.11 0.08 -10000 0 -0.6 3 3
axon guidance -0.017 0.072 -10000 0 -10000 0 0
NEDD4 0.052 0.052 -10000 0 -0.73 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.074 0.19 -10000 0 -0.57 68 68
CBFA2T3 0.012 0.055 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.064 0.038 -10000 0 -0.52 1 1
MAPK3 -0.029 0.082 -10000 0 -0.6 1 1
STAT1 (dimer) -0.11 0.073 -10000 0 -0.54 1 1
MAPK1 -0.029 0.082 -10000 0 -0.6 1 1
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.077 0.081 -10000 0 -0.53 10 10
NRG1 0.036 0.11 -10000 0 -0.56 16 16
NRG3 -0.003 0.13 -10000 0 -0.86 11 11
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
NRG4 -0.057 0.22 -10000 0 -0.77 47 47
heart development -0.017 0.072 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.08 -10000 0 -0.53 10 10
ERBB2 0.052 0.04 -10000 0 -0.56 2 2
WWOX/E4ICDs -0.11 0.075 -10000 0 -0.7 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.15 0.15 -10000 0 -0.57 51 51
apoptosis 0.1 0.063 0.39 7 -10000 0 7
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.089 -10000 0 -0.52 11 11
ErbB4/ErbB2/epiregulin -0.098 0.13 -10000 0 -0.57 34 34
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.18 -10000 0 -0.59 78 78
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.14 -10000 0 -0.73 1 1
MDM2 -0.1 0.074 -10000 0 -0.4 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.077 -10000 0 -0.52 9 9
STAT5A -0.005 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.084 0.1 -10000 0 -0.56 17 17
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.029 -10000 0 -0.67 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.048 -10000 0 -0.38 1 1
STAT5A (dimer) -0.054 0.12 -10000 0 -0.62 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.064 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.041 0.21 -10000 0 -0.86 33 33
BTC -0.098 0.27 -10000 0 -0.75 77 77
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.017 0.072 -10000 0 -10000 0 0
ERBB4 -0.14 0.086 -10000 0 -0.47 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.11 0.13 -10000 0 -0.51 44 44
glial cell differentiation 0.1 0.048 0.37 1 -10000 0 1
WWOX 0.014 0.039 -10000 0 -0.86 1 1
cell proliferation -0.075 0.16 -10000 0 -0.59 14 14
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.045 0.092 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 88 88
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
RhoA/GTP -0.046 0.094 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.014 0.12 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.004 0.049 -9999 0 -0.56 4 4
AKT1 -0.055 0.2 -9999 0 -0.71 3 3
PTK2B -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.002 0.041 -9999 0 -0.83 1 1
CAV1 -0.047 0.23 -9999 0 -0.86 37 37
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.23 0.25 -9999 0 -1.2 1 1
endothelial cell proliferation -0.041 0.2 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.039 -9999 0 -0.86 1 1
VEGFA homodimer -0.24 0.26 -9999 0 -0.52 233 233
SHC1 0.014 0.039 -9999 0 -0.86 1 1
SHC2 0.008 0.082 -9999 0 -0.82 5 5
HRAS/GDP -0.17 0.19 -9999 0 -0.83 2 2
SH2D2A -0.27 0.41 -9999 0 -0.86 168 168
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.39 0.34 -9999 0 -1 66 66
VEGFR1 homodimer 0.007 0.086 -9999 0 -0.86 5 5
SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.014 0.039 -9999 0 -0.86 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.085 0.094 -9999 0 -0.58 1 1
HIF1A 0.013 0.047 -9999 0 -0.75 2 2
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.001 0.025 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.23 0.25 -9999 0 -1.2 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.063 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.053 0.18 -9999 0 -0.57 1 1
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
mol:IP3 -0.16 0.27 -9999 0 -1.1 1 1
HIF1A/ARNT -0.002 0.035 -9999 0 -0.56 2 2
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 233 233
VEGFC 0.014 0.039 -9999 0 -0.86 1 1
FAK1/Vinculin -0.1 0.22 -9999 0 -1 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.22 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.037 -9999 0 -0.72 1 1
mol:L-citrulline -0.063 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2/3 heterodimer -0.002 0.041 -9999 0 -0.83 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -0.84 2 2
VEGFR2 homodimer 0.044 0.05 -9999 0 -0.73 2 2
FLT1 0.007 0.086 -9999 0 -0.86 5 5
NEDD4 0.015 0.047 -9999 0 -0.74 2 2
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.3 0.33 -9999 0 -0.66 238 238
VEGFR1/2 heterodimer -0.008 0.069 -9999 0 -0.61 6 6
KDR 0.044 0.05 -9999 0 -0.73 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -0.78 2 2
PI3K -0.16 0.18 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.2 1 1
FES -0.17 0.27 -9999 0 -1 2 2
GAB1 -0.17 0.19 -9999 0 -0.81 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.23 0.25 -9999 0 -1.2 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.083 0.2 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.23 0.25 -9999 0 -1.2 1 1
PI3K/GAB1 -0.055 0.2 -9999 0 -0.69 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.1 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.044 -9999 0 -0.77 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.16 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.39 0.33 -9999 0 -1 66 66
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.27 -9999 0 -1.1 1 1
CaM/Ca2+ -0.19 0.2 -9999 0 -1 1 1
MAP2K3 -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.16 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.23 0.25 -9999 0 -1.2 1 1
cell migration -0.052 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.7 6 6
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.063 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.19 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.014 0.033 -9999 0 -0.75 1 1
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
NOS3 -0.074 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -1.1 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.15 0.25 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.22 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 5 5
VEGFA165/NRP2 -0.3 0.33 -9999 0 -0.66 238 238
MAPKKK cascade -0.16 0.18 -9999 0 -0.8 2 2
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.039 -9999 0 -0.86 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.1 0.22 -9999 0 -1 1 1
MAP3K13 -0.16 0.27 -9999 0 -1.2 1 1
PDPK1 -0.073 0.2 -9999 0 -0.65 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.058 -9999 0 -10000 0 0
epithelial cell differentiation -0.016 0.079 -9999 0 -10000 0 0
CYFIP2 0.004 0.094 -9999 0 -0.75 8 8
ENAH 0.079 0.065 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.75 1 1
MYO6 0.032 0.097 -9999 0 -0.78 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.059 -9999 0 -0.48 8 8
AQP5 -0.17 0.24 -9999 0 -0.52 159 159
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.035 0.083 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.12 -9999 0 -0.49 15 15
EGF -0.67 0.23 -9999 0 -0.75 466 466
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.051 0.16 -9999 0 -0.57 38 38
cortical microtubule organization -0.016 0.079 -9999 0 -10000 0 0
GO:0000145 0.035 0.079 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.08 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.014 0.063 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.035 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.051 0.084 -9999 0 -0.58 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.035 0.084 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.032 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.75 21 21
EGFR/EGFR/EGF/EGF -0.35 0.14 -9999 0 -0.77 27 27
RhoA/GDP -0.015 0.073 -9999 0 -10000 0 0
actin cytoskeleton organization 0.042 0.092 -9999 0 -0.72 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.006 0.094 -9999 0 -0.86 6 6
DIAPH1 -0.01 0.086 -9999 0 -0.7 8 8
Wnt receptor signaling pathway 0.016 0.079 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.063 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.042 0.094 -9999 0 -0.74 2 2
EFNA1 0.014 0.039 -9999 0 -0.86 1 1
LPP 0.044 0.089 -9999 0 -0.8 1 1
Ephrin A1/EPHA2 -0.016 0.074 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.062 -9999 0 -10000 0 0
MGAT3 0.018 0.12 -9999 0 -0.5 15 15
HGF/MET -0.037 0.13 -9999 0 -0.96 4 4
HGF -0.021 0.17 -9999 0 -0.8 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.099 0.07 -9999 0 -10000 0 0
KIAA1543 0.037 0.12 -9999 0 -0.86 6 6
KIFC3 0.034 0.086 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.033 0.093 -9999 0 -0.87 1 1
NCK1/GIT1 -0.001 0.025 -9999 0 -0.56 1 1
mol:GDP -0.016 0.079 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.035 0.084 -9999 0 -10000 0 0
PIP5K1C 0.035 0.084 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.055 -9999 0 -10000 0 0
adherens junction assembly 0.059 0.12 -9999 0 -0.79 7 7
IGF-1R heterotetramer/IGF1 -0.02 0.084 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PLEKHA7 0.032 0.1 -9999 0 -0.78 3 3
mol:GTP -0.003 0.035 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.071 0.076 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.058 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.042 0.092 -9999 0 -0.72 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
S1P4 pathway

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.007 0.084 -9999 0 -0.84 5 5
CDC42/GTP -0.017 0.061 -9999 0 -10000 0 0
PLCG1 0.035 0.077 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.017 0.06 -9999 0 -10000 0 0
S1PR5 -0.13 0.33 -9999 0 -0.86 88 88
S1PR4 -0.028 0.19 -9999 0 -0.86 26 26
MAPK3 0.035 0.077 -9999 0 -10000 0 0
MAPK1 0.035 0.077 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.058 -9999 0 -0.75 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 88 88
RHOA 0.016 0.12 -9999 0 -0.49 26 26
S1P/S1P4/Gi -0.019 0.07 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
S1P/S1P4/G12/G13 -0.027 0.12 -9999 0 -0.53 26 26
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.031 0.12 -9999 0 -0.51 32 32
RGS9BP -0.019 0.16 -9999 0 -0.75 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.013 0.085 -9999 0 -0.59 11 11
mol:ADP 0.012 0.044 -9999 0 -0.68 2 2
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.037 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.026 -9999 0 -0.59 1 1
GRK7 0.008 0.055 -9999 0 -0.86 2 2
CNGB3 -0.007 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.12 -9999 0 -0.64 15 15
Cone PDE6 -0.034 0.12 -9999 0 -0.58 5 5
Cone Metarhodopsin II -0.002 0.034 -9999 0 -0.55 2 2
Na + (4 Units) -0.019 0.11 -9999 0 -0.64 15 15
GNAT2/GDP -0.031 0.11 -9999 0 -0.5 9 9
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.043 -9999 0 -0.54 3 3
Cone Transducin -0.033 0.13 -9999 0 -0.54 32 32
SLC24A2 -0.009 0.1 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.041 0.16 -9999 0 -0.67 32 32
GNB3 -0.038 0.21 -9999 0 -0.86 31 31
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.066 -9999 0 -0.86 3 3
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.013 0.086 -9999 0 -0.6 11 11
mol:Pi -0.036 0.13 -9999 0 -0.5 38 38
Cone CNG Channel -0.013 0.085 -9999 0 -0.55 9 9
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.1 -9999 0 -0.86 7 7
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
PDE6C 0.004 0.055 -9999 0 -0.86 2 2
GNGT2 0.014 0.039 -9999 0 -0.86 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.039 -9999 0 -0.86 1 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
alpha4/beta7 Integrin -0.019 0.11 -9999 0 -0.67 15 15
alpha4/beta1 Integrin -0.019 0.11 -9999 0 -0.67 15 15
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.011 0.061 -9999 0 -0.78 3 3
GNB1/GNG2 -0.054 0.11 -9999 0 -0.53 8 8
mol:DAG 0.01 0.13 -9999 0 -10000 0 0
PLCG1 0.009 0.13 -9999 0 -10000 0 0
YES1 -0.011 0.14 -9999 0 -0.56 8 8
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.05 0.1 -9999 0 -10000 0 0
MAP3K7 -0.095 0.22 -9999 0 -0.69 7 7
mol:Ca2+ 0.01 0.13 -9999 0 -10000 0 0
mol:IP3 0.01 0.13 -9999 0 -10000 0 0
NLK -0.007 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.24 -9999 0 -0.61 48 48
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.011 0.14 -9999 0 -0.56 8 8
GO:0007205 0.011 0.13 -9999 0 -10000 0 0
WNT6 -0.013 0.16 -9999 0 -0.86 17 17
WNT4 -0.07 0.24 -9999 0 -0.75 58 58
NFAT1/CK1 alpha -0.049 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.058 -9999 0 -0.75 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 37 37
CDC42 0 0.14 -9999 0 -0.52 8 8
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.036 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.035 0.096 -9999 0 -0.48 7 7
JUN 0.027 0.11 -9999 0 -0.55 7 7
HRAS 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.051 0.16 -9999 0 -0.7 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.051 0.16 -9999 0 -0.7 11 11
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.13 -9999 0 -0.47 44 44
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.045 0.14 -9999 0 -0.83 5 5
GRB7 0.005 0.088 -9999 0 -0.75 7 7
RET51/GFRalpha1/GDNF -0.051 0.16 -9999 0 -0.68 12 12
MAPKKK cascade -0.041 0.12 -9999 0 -0.71 6 6
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.039 0.13 -9999 0 -0.47 43 43
lamellipodium assembly -0.033 0.091 -9999 0 -0.44 7 7
RET51/GFRalpha1/GDNF/SHC -0.052 0.16 -9999 0 -0.67 13 13
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC -0.037 0.12 -9999 0 -0.46 41 41
RET9/GFRalpha1/GDNF/Shank3 -0.036 0.12 -9999 0 -0.46 40 40
MAPK3 0.007 0.15 -9999 0 -0.77 5 5
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.002 0.12 -9999 0 -0.75 12 12
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.042 0.13 -9999 0 -0.73 5 5
DOK5 -0.007 0.13 -9999 0 -0.76 15 15
GFRA1 -0.039 0.2 -9999 0 -0.76 37 37
MAPK8 0.016 0.12 -9999 0 -0.58 7 7
HRAS/GTP -0.047 0.14 -9999 0 -0.84 6 6
tube development -0.033 0.11 -9999 0 -0.5 6 6
MAPK1 0.007 0.15 -9999 0 -0.77 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.08 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.077 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.057 0.17 -9999 0 -0.87 12 12
SHC1 0.014 0.039 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.051 0.16 -9999 0 -0.7 11 11
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.19 -9999 0 -0.8 19 19
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
CREB1 -0.031 0.097 -9999 0 -0.54 5 5
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.081 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.057 0.18 -9999 0 -0.8 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.013 0.15 -9999 0 -0.76 19 19
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.027 0.11 -9999 0 -0.53 7 7
RET9/GFRalpha1/GDNF/FRS2 -0.036 0.12 -9999 0 -0.46 40 40
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.75 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.082 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.1 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.035 0.11 -9999 0 -0.61 6 6
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.11 -9999 0 -0.77 5 5
PI3K -0.05 0.14 -9999 0 -0.74 7 7
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.033 0.11 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.03 0.092 -9999 0 -0.53 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.051 0.16 -9999 0 -0.7 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.067 -9999 0 -0.75 4 4
IRS2 0.002 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.11 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF/PKC alpha -0.051 0.16 -9999 0 -0.7 11 11
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.066 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.054 0.16 -9999 0 -0.7 13 13
Rac1/GTP -0.039 0.11 -9999 0 -0.54 7 7
RET9/GFRalpha1/GDNF -0.039 0.14 -9999 0 -0.51 40 40
GFRalpha1/GDNF -0.045 0.16 -9999 0 -0.58 40 40
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.28 0.37 -9999 0 -0.75 199 199
HRAS 0.014 0.039 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
AKT 0.035 0.03 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.086 -9999 0 -0.86 5 5
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.011 0.067 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.041 0.097 -9999 0 -0.38 5 5
ERBB2 0.013 0.047 -9999 0 -0.75 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.022 0.092 -9999 0 -0.29 6 6
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.075 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.16 0.29 -9999 0 -0.67 123 123
NFKBIA 0.063 0.02 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.039 -9999 0 -0.86 1 1
IKBKG -0.047 0.085 -9999 0 -10000 0 0
IKK complex/A20 -0.041 0.08 -9999 0 -0.59 2 2
NEMO/A20/RIP2 0.014 0.039 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.043 0.078 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.035 0.062 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.19 0.37 -9999 0 -0.86 123 123
NFKB1 0.019 0.033 -9999 0 -0.74 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.033 -9999 0 -0.75 1 1
TNF/TNFR1A -0.009 0.076 -9999 0 -0.61 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
NF kappa B1 p50/RelA -0.001 0.02 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.039 0.07 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.036 0.064 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.033 -10000 0 -0.75 1 1
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.043 0.67 2 -10000 0 2
CDKN1A -0.003 0.04 -10000 0 -0.65 2 2
KAT2B 0.014 0.033 -10000 0 -0.75 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0.001 0.023 0.53 1 -10000 0 1
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.03 0.016 -10000 0 -0.33 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.006 0.13 -10000 0 -0.86 11 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.16 -10000 0 -0.66 30 30
PPARGC1A -0.059 0.23 -10000 0 -0.75 51 51
FHL2 0.008 0.077 -10000 0 -0.77 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.008 -10000 0 -10000 0 0
HIST2H4A 0.025 0.043 -10000 0 -0.67 2 2
SIRT1/FOXO3a 0.001 0.016 0.32 1 -10000 0 1
SIRT1 0.001 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.001 0.019 -10000 0 -10000 0 0
apoptosis 0 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.048 0.14 -10000 0 -0.49 51 51
p53/SIRT1 0.001 0.023 0.38 2 -10000 0 2
SIRT1/FOXO4 0 0.015 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.004 0.046 -10000 0 -0.46 5 5
HIST1H1E 0.029 0.022 -10000 0 -0.32 2 2
SIRT1/p300 -0.001 0.026 -10000 0 -0.56 1 1
muscle cell differentiation 0.033 0.13 0.57 30 -10000 0 30
TP53 0.001 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.014 0.097 -10000 0 -0.67 11 11
ACSS2 0.028 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.033 0.13 -10000 0 -0.57 30 30
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.058 -9999 0 -0.75 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.03 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.085 0.22 -9999 0 -0.62 71 71
IL1A -0.007 0.13 -9999 0 -0.86 12 12
IL1B 0.023 0.073 -9999 0 -0.65 6 6
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -10000 0 0
IL1R2 -0.077 0.26 -9999 0 -0.79 60 60
IL1R1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.025 -9999 0 -10000 0 0
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.016 0.001 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.04 0.047 -9999 0 -10000 0 0
JUN 0.06 0.034 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.07 -9999 0 -0.78 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.09 -9999 0 -0.52 15 15
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.015 0.083 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.01 0.069 -9999 0 -0.52 8 8
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
MAPK8 0.051 0.036 -9999 0 -10000 0 0
IRAK1 0.031 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -9999 0 -0.67 17 17
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.035 -9999 0 -0.56 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.032 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.01 0.069 -9999 0 -0.52 8 8
IL1 beta/IL1R2 -0.066 0.17 -9999 0 -0.52 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.07 -9999 0 -1 1 1
IRAK3 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.009 0.061 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.048 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.018 0.099 -9999 0 -0.57 16 16
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.009 0.075 -9999 0 -0.84 4 4
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.007 0.049 -9999 0 -10000 0 0
CASP1 0.016 0 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.091 0.22 -9999 0 -0.63 75 75
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.009 0.065 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.007 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.032 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
IL1RN -0.013 0.16 -9999 0 -0.86 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.043 0.032 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.004 0.1 -10000 0 -0.86 7 7
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0 -10000 0 -10000 0 0
CDKN1A 0.04 0.034 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.023 0.12 -10000 0 -0.67 18 18
mol:Ca2+ -0.016 0.16 0.41 18 -0.65 24 42
AGT -0.023 0.18 -10000 0 -0.82 24 24
CCNA2 -0.056 0.23 -10000 0 -0.88 6 6
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 0.02 0.084 -10000 0 -0.55 11 11
CDK2/Cyclin E1 -0.01 0.057 -10000 0 -0.47 7 7
MAPK3 0.007 0.13 -10000 0 -0.67 18 18
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.13 -10000 0 -0.67 18 18
PTP4A1 0.042 0.067 -10000 0 -10000 0 0
PTP4A3 -0.015 0.16 -10000 0 -0.86 18 18
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.007 0.13 -10000 0 -0.67 18 18
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.031 0.061 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.002 0.035 -10000 0 -0.56 2 2
PRL-1/ATF-5 0.043 0.074 -10000 0 -10000 0 0
RABGGTA 0.013 0.047 -10000 0 -0.75 2 2
BCAR1 0.013 0.079 0.41 18 -0.58 1 19
RHOC 0.031 0.061 -10000 0 -10000 0 0
RHOA 0.031 0.061 -10000 0 -10000 0 0
cell motility 0.036 0.063 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.046 0.062 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.023 0.12 -10000 0 -0.67 18 18
ROCK1 0.036 0.064 -10000 0 -10000 0 0
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.041 0.067 -10000 0 -10000 0 0
ATF5 0.011 0.067 -10000 0 -0.86 3 3
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.006 0.086 0.78 6 -10000 0 6
PI3K Class IB/PDE3B 0.006 0.086 -10000 0 -0.78 6 6
PDE3B 0.006 0.086 -10000 0 -0.78 6 6
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.014 0.033 -10000 0 -0.75 1 1
MAP2K3 0.038 0.044 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.049 0.045 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.003 0.12 -10000 0 -0.85 11 11
TXN 0.011 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
GADD45A 0.016 0 -10000 0 -10000 0 0
GADD45B 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
MAP3K6 0.014 0.033 -10000 0 -0.75 1 1
MAP3K7 0.016 0 -10000 0 -10000 0 0
MAP3K4 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.001 0.025 -10000 0 -0.56 1 1
TAK1/TAB family 0 0.009 0.2 1 -10000 0 1
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.014 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.1 0.28 -10000 0 -0.76 78 78
CCM2 0.016 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.075 0.18 -10000 0 -0.5 78 78
MAPK11 0.014 0.039 -10000 0 -0.86 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.067 0.16 -10000 0 -0.45 78 78
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 0.017 0.05 -10000 0 -0.41 7 7
TAOK2 0.022 0.019 -10000 0 -0.41 1 1
TAOK3 0.022 0.019 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.016 0 -10000 0 -10000 0 0
MAP3K10 0.014 0.033 -10000 0 -0.75 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TRX/ASK1 0 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.01 0.071 -10000 0 -0.5 10 10
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.074 -10000 0 -0.72 3 3
NFATC4 0.047 0.077 -10000 0 -0.54 2 2
ERBB2IP 0.008 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.017 0.077 -10000 0 -0.64 1 1
JUN 0.037 0.079 -10000 0 -0.41 2 2
HRAS 0.013 0.039 -10000 0 -0.87 1 1
DOCK7 0.02 0.091 -10000 0 -0.62 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.022 0.1 -10000 0 -0.87 2 2
AKT1 0.016 0.002 -10000 0 -10000 0 0
BAD 0.026 0.036 -10000 0 -0.54 2 2
MAPK10 -0.011 0.045 -10000 0 -0.39 1 1
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.083 -10000 0 -0.72 1 1
RAF1 0.039 0.095 -10000 0 -0.68 3 3
ErbB2/ErbB3/neuregulin 2 -0.02 0.097 -10000 0 -0.49 21 21
STAT3 0 0.002 -10000 0 -10000 0 0
cell migration 0.059 0.056 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.089 0.26 -10000 0 -0.6 9 9
FOS -0.038 0.19 -10000 0 -0.48 15 15
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.077 -10000 0 -0.64 1 1
MAPK3 -0.058 0.21 -10000 0 -0.56 8 8
MAPK1 -0.058 0.21 -10000 0 -0.56 8 8
JAK2 0.02 0.088 -10000 0 -0.6 1 1
NF2 -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.09 -10000 0 -0.82 2 2
NRG1 -0.014 0.13 -10000 0 -0.75 16 16
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.024 0.084 -10000 0 -0.44 2 2
MAPK9 -0.008 0.036 -10000 0 -10000 0 0
ERBB2 -0.002 0.036 -10000 0 -0.58 2 2
ERBB3 -0.004 0.099 -10000 0 -0.75 9 9
SHC1 0.007 0.039 -10000 0 -0.86 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.002 0.022 0.35 2 -10000 0 2
STAT3 (dimer) 0 0.002 -10000 0 -10000 0 0
RNF41 0.038 0.005 -10000 0 -10000 0 0
FRAP1 0.014 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.012 0.053 -10000 0 -0.41 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.03 -10000 0 -0.49 2 2
CHRNA1 -0.13 0.28 -10000 0 -0.45 226 226
myelination 0.051 0.074 -10000 0 -0.49 2 2
PPP3CB 0.02 0.082 -10000 0 -0.55 1 1
KRAS 0.015 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.014 0.069 -10000 0 -0.72 2 2
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
mol:GDP 0.007 0.089 -10000 0 -0.82 2 2
SOS1 0.009 0.008 -10000 0 -10000 0 0
MAP2K2 0.045 0.097 -10000 0 -0.7 2 2
SRC 0.016 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.02 0.087 -10000 0 -0.6 1 1
MAP2K1 -0.041 0.18 -10000 0 -0.57 8 8
heart morphogenesis -0.017 0.077 -10000 0 -0.64 1 1
RAS family/GDP -0.015 0.073 -10000 0 -0.72 3 3
GRB2 0.009 0.008 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.021 0.027 -10000 0 -0.24 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.016 0.002 -10000 0 -10000 0 0
nervous system development -0.017 0.077 -10000 0 -0.64 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.006 0.035 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.065 0.089 0.32 33 -0.36 1 34
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.031 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.069 0.25 -10000 0 -0.86 48 48
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.043 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.058 -10000 0 -0.75 3 3
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.032 0.084 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.067 0.093 0.33 33 -0.4 1 34
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.034 0 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 62 62
LNPEP 0.013 0.047 -10000 0 -0.75 2 2
YWHAE 0.016 0 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0 -10000 0 -10000 0 0
EPHB2 0.001 0.11 -10000 0 -0.77 10 10
EFNB1 0.018 0.096 -10000 0 -0.66 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.095 -10000 0 -0.74 3 3
Ephrin B2/EPHB1-2 -0.011 0.081 -10000 0 -0.54 11 11
neuron projection morphogenesis -0.018 0.091 -10000 0 -0.71 3 3
Ephrin B1/EPHB1-2/Tiam1 -0.021 0.1 -10000 0 -0.81 3 3
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.023 0.093 -10000 0 -0.67 9 9
YES1 -0.015 0.12 -10000 0 -0.9 9 9
Ephrin B1/EPHB1-2/NCK2 -0.02 0.099 -10000 0 -0.81 2 2
PI3K -0.012 0.098 -10000 0 -0.69 10 10
mol:GDP -0.02 0.1 -10000 0 -0.79 3 3
ITGA2B -0.015 0.16 -10000 0 -0.86 18 18
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.015 0.12 -10000 0 -0.9 9 9
MAP3K7 -0.012 0.094 -10000 0 -0.72 9 9
FGR -0.016 0.12 -10000 0 -0.89 9 9
TIAM1 0.014 0.033 -10000 0 -0.75 1 1
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion 0.018 0.14 -10000 0 -0.73 9 9
LYN -0.015 0.12 -10000 0 -0.9 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.11 -10000 0 -0.84 9 9
Ephrin B1/EPHB1-2 -0.016 0.1 -10000 0 -0.78 9 9
SRC -0.015 0.12 -10000 0 -0.89 9 9
ITGB3 0.01 0.067 -10000 0 -0.75 4 4
EPHB1 0.011 0.061 -10000 0 -0.79 3 3
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.027 0.13 -10000 0 -0.64 22 22
BLK -0.022 0.12 -10000 0 -0.89 9 9
HCK -0.021 0.12 -10000 0 -0.94 9 9
regulation of stress fiber formation 0.02 0.097 0.79 2 -10000 0 2
MAPK8 0.032 0.091 -10000 0 -0.63 9 9
Ephrin B1/EPHB1-2/RGS3 -0.02 0.099 -10000 0 -0.81 2 2
endothelial cell migration -0.009 0.081 -10000 0 -0.61 9 9
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.01 0.11 -10000 0 -0.85 9 9
regulation of focal adhesion formation 0.02 0.097 0.79 2 -10000 0 2
chemotaxis 0.02 0.097 0.79 2 -10000 0 2
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
Rac1/GTP -0.019 0.094 -10000 0 -0.74 3 3
angiogenesis -0.016 0.1 -10000 0 -0.77 9 9
LCK -0.02 0.12 -10000 0 -0.91 9 9
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.036 0.053 -9999 0 -0.5 5 5
SNTA1 0.013 0.051 -9999 0 -0.8 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.037 0.045 -9999 0 -0.48 4 4
MAPK12 0.028 0.085 -9999 0 -0.49 13 13
CCND1 0.013 0.071 -9999 0 -0.3 20 20
p38 gamma/SNTA1 0.033 0.089 -9999 0 -0.51 11 11
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.028 0.085 -9999 0 -0.49 13 13
MAP2K6 0.03 0.041 -9999 0 -0.47 3 3
MAPT 0.033 0.068 -9999 0 -0.5 6 6
MAPK13 0.026 0.052 -9999 0 -0.56 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.018 -9999 0 -0.39 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 0.07 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.011 0.073 -9999 0 -0.48 12 12
POMC 0.012 0.051 -9999 0 -0.8 2 2
EGFR 0.001 0.11 -9999 0 -0.85 9 9
Syndecan-3/EGFR -0.009 0.065 -9999 0 -0.47 10 10
AGRP 0.007 0.047 -9999 0 -0.75 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.007 0.13 -9999 0 -0.86 11 11
long-term memory -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.032 0.12 -9999 0 -0.47 35 35
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.019 -9999 0 -0.43 1 1
MC4R -0.01 0.11 -9999 0 -0.86 9 9
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.012 0.14 -9999 0 -0.75 19 19
FGFR/FGF/Syndecan-3 -0.001 0.019 -9999 0 -0.43 1 1
neuron projection morphogenesis -0.022 0.089 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.002 0.03 -9999 0 -0.4 3 3
Syndecan-3/AgRP/MC4R -0.01 0.067 -9999 0 -0.47 9 9
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.019 -9999 0 -0.43 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.031 0.12 -9999 0 -0.46 35 35
IL8 -0.04 0.21 -9999 0 -0.84 34 34
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.018 -9999 0 -0.41 1 1
alpha-MSH/MC4R -0.014 0.095 -9999 0 -0.66 11 11
Gamma Secretase 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.1 -9999 0 -0.51 21 21
KLHL20 -0.013 0.046 -9999 0 -0.35 2 2
CYFIP2 0.004 0.094 -9999 0 -0.75 8 8
Rac1/GDP 0.068 0.076 -9999 0 -10000 0 0
ENAH -0.021 0.1 -9999 0 -0.51 21 21
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.046 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -9999 0 -0.22 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.084 -9999 0 -10000 0 0
RAPGEF1 0.054 0.099 -9999 0 -10000 0 0
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.11 -9999 0 -0.54 21 21
CRK 0.043 0.11 -9999 0 -0.49 1 1
E-cadherin/gamma catenin/alpha catenin -0.022 0.1 -9999 0 -0.5 23 23
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.021 0.1 -9999 0 -0.51 21 21
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.035 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.019 -9999 0 -0.44 1 1
PI3K -0.01 0.044 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.026 0.12 -9999 0 -0.58 23 23
TIAM1 0.014 0.033 -9999 0 -0.75 1 1
E-cadherin(dimer)/Ca2+ -0.016 0.08 -9999 0 -10000 0 0
AKT1 -0.005 0.025 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
CDH1 -0.016 0.15 -9999 0 -0.75 21 21
RhoA/GDP 0.067 0.075 -9999 0 -10000 0 0
actin cytoskeleton organization -0.01 0.034 -9999 0 -0.24 2 2
CDC42/GDP 0.067 0.075 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.068 -9999 0 -0.32 23 23
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.017 0.084 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.017 0.082 -9999 0 -0.41 21 21
mol:GDP 0.063 0.086 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.058 -9999 0 -0.75 3 3
p120 catenin/RhoA/GDP -0.012 0.06 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.035 0.064 -9999 0 -0.26 20 20
NME1 0.016 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.021 0.1 -9999 0 -0.51 21 21
regulation of cell-cell adhesion -0.008 0.041 -9999 0 -10000 0 0
WASF2 -0.005 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.054 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.087 -9999 0 -0.81 1 1
CCND1 -0.016 0.065 -9999 0 -0.33 20 20
VAV2 0.049 0.1 -9999 0 -0.5 1 1
RAP1/GDP -0.011 0.056 -9999 0 -10000 0 0
adherens junction assembly 0.033 0.11 -9999 0 -0.49 21 21
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.081 -9999 0 -0.77 1 1
E-cadherin/beta catenin -0.018 0.09 -9999 0 -0.45 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.021 0.1 -9999 0 -0.51 21 21
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
Rac1/GTP -0.02 0.072 -9999 0 -0.6 1 1
E-cadherin/beta catenin/alpha catenin -0.019 0.094 -9999 0 -0.48 21 21
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.11 -9999 0 -0.55 21 21
Arf6 trafficking events

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
SLC2A4 -0.003 0.12 -9999 0 -0.82 12 12
CLTC 0.043 0 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.036 0 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
CD59 0.039 0 -9999 0 -10000 0 0
CPE -0.001 0.12 -9999 0 -0.58 22 22
CTNNB1 0.016 0 -9999 0 -10000 0 0
membrane fusion 0 0 -9999 0 -10000 0 0
CTNND1 0.044 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.045 0 -9999 0 -10000 0 0
TSHR -0.045 0.2 -9999 0 -0.59 59 59
INS 0.017 0.001 -9999 0 -10000 0 0
BIN1 0.016 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.025 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.038 0.021 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 0.028 0.055 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 -0.05 0.23 -9999 0 -0.86 39 39
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.016 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.058 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.03 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.025 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 -0.044 0.16 -9999 0 -0.59 39 39
ACAP1 -0.019 0.024 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.032 0.012 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.043 0.011 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.016 0 -9999 0 -10000 0 0
exocyst 0 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.044 0 -9999 0 -10000 0 0
NME1 0.025 0 -9999 0 -10000 0 0
clathrin coat assembly 0.043 0 -9999 0 -10000 0 0
IL2RA -0.015 0.11 -9999 0 -10000 0 0
VAMP3 0.025 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.06 -9999 0 -0.4 11 11
EXOC6 0.016 0 -9999 0 -10000 0 0
PLD1 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.045 0 -9999 0 -10000 0 0
SDC1 0.036 0.03 -9999 0 -10000 0 0
ARF6/GDP 0 0 -9999 0 -10000 0 0
EXOC7 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.006 0.031 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.016 0 -9999 0 -10000 0 0
ADRB2 0.05 0.026 -9999 0 -10000 0 0
EXOC3 0.016 0 -9999 0 -10000 0 0
ASAP2 0.016 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0 0 -9999 0 -10000 0 0
KLC1 0.016 0 -9999 0 -10000 0 0
AVPR2 -0.12 0.21 -9999 0 -0.37 215 215
RALA 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.025 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.049 0.12 -9999 0 -0.68 5 5
MAP3K8 0.013 0.055 -9999 0 -0.86 2 2
FOS 0.041 0.11 -9999 0 -0.57 5 5
PRKCA 0.017 0.003 -9999 0 -10000 0 0
PTPN7 -0.037 0.21 -9999 0 -0.86 33 33
HRAS 0.014 0.039 -9999 0 -0.86 1 1
PRKCB 0.009 0.083 -9999 0 -0.83 5 5
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.023 -9999 0 -0.53 1 1
MAPK3 0.029 0.085 -9999 0 -0.52 3 3
MAP2K1 0.055 0.056 -9999 0 -0.48 5 5
ELK1 0.017 0.003 -9999 0 -10000 0 0
BRAF -0.004 0.044 -9999 0 -0.44 5 5
mol:GTP 0 0.001 -9999 0 -0.006 12 12
MAPK1 0.029 0.085 -9999 0 -0.52 3 3
RAF1 -0.004 0.044 -9999 0 -0.44 5 5
KRAS 0.016 0.001 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.006 0.065 -9999 0 -0.67 5 5
CRKL 0.04 0.065 -9999 0 -0.46 2 2
mol:PIP3 -0.03 0.003 -9999 0 -10000 0 0
AKT1 0 0.02 -9999 0 -0.45 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.049 0.062 -9999 0 -0.43 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
HGF/MET/SHIP2 -0.029 0.13 -9999 0 -0.57 26 26
MAP3K5 -0.024 0.12 -9999 0 -0.41 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.027 0.12 -9999 0 -0.61 15 15
AP1 -0.014 0.082 -9999 0 -0.52 13 13
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.039 -9999 0 -0.86 1 1
apoptosis 0.004 0.11 -9999 0 -0.7 12 12
STAT3 (dimer) 0.041 0.078 -9999 0 -0.53 3 3
GAB1/CRKL/SHP2/PI3K -0.011 0.055 -9999 0 -0.59 2 2
INPP5D 0.009 0.077 -9999 0 -0.86 4 4
CBL/CRK 0.047 0.068 -9999 0 -0.51 3 3
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 0.001 0.03 -9999 0 -0.29 5 5
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.008 0.039 -9999 0 -0.34 2 2
PAK1 0.01 0.019 -9999 0 -0.42 1 1
HGF/MET/RANBP10 -0.029 0.13 -9999 0 -0.57 26 26
HRAS 0.031 0.098 -9999 0 -0.71 3 3
DOCK1 0.048 0.069 -9999 0 -0.51 3 3
GAB1 0.031 0.068 -9999 0 -0.44 3 3
CRK 0.04 0.065 -9999 0 -0.46 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.023 0.1 -9999 0 -0.54 14 14
JUN 0.016 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.013 0.06 -9999 0 -0.4 5 5
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
cell morphogenesis 0.079 0.085 -9999 0 -0.65 2 2
GRB2/SHC -0.012 0.057 -9999 0 -0.54 3 3
FOS -0.004 0.12 -9999 0 -0.76 13 13
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0.001 0.03 -9999 0 -0.29 5 5
HGF/MET/MUC20 -0.029 0.13 -9999 0 -0.58 26 26
cell migration -0.011 0.056 -9999 0 -0.52 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.75 1 1
MET/RANBP10 -0.006 0.065 -9999 0 -0.67 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.072 -9999 0 -0.58 3 3
MET/MUC20 -0.007 0.066 -9999 0 -0.68 5 5
RAP1B 0.058 0.059 -9999 0 -10000 0 0
RAP1A 0.058 0.059 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.029 0.13 -9999 0 -0.57 26 26
RAF1 0.041 0.093 -9999 0 -0.66 3 3
STAT3 -0.015 0.066 -9999 0 -0.54 3 3
cell proliferation 0.054 0.1 -9999 0 -0.62 4 4
RPS6KB1 -0.004 0.02 -9999 0 -10000 0 0
MAPK3 -0.006 0.027 -9999 0 -0.27 5 5
MAPK1 -0.006 0.027 -9999 0 -0.27 5 5
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.012 0.097 -9999 0 -0.56 1 1
SRC 0.042 0.079 -9999 0 -0.55 3 3
PI3K -0.012 0.061 -9999 0 -0.54 4 4
MET/Glomulin 0.009 0.061 -9999 0 -0.61 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.05 0.088 -9999 0 -0.6 3 3
MET 0.007 0.086 -9999 0 -0.86 5 5
MAP4K1 -0.037 0.12 -9999 0 -0.4 12 12
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.049 0.089 -9999 0 -0.6 3 3
BAD 0.008 0.045 -9999 0 -0.67 2 2
MAP2K4 -0.012 0.11 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.056 -9999 0 -0.57 2 2
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.012 0.054 -9999 0 -0.49 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.021 0.17 -9999 0 -0.8 23 23
RASA1 0.014 0.033 -9999 0 -0.75 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.013 0.059 -9999 0 -0.53 3 3
PDPK1 -0.014 0.021 -9999 0 -0.49 1 1
HGF/MET/SHIP -0.033 0.14 -9999 0 -0.59 29 29
Arf6 downstream pathway

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
PLAUR 0.02 0.17 -10000 0 -0.72 26 26
regulation of axonogenesis -0.033 0.034 -10000 0 -10000 0 0
myoblast fusion 0.016 0.07 0.32 26 -10000 0 26
mol:GTP -0.01 0.043 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.041 0.45 1 -10000 0 1
ARF1/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.035 -10000 0 -10000 0 0
mol:Choline 0.033 0.03 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.073 -10000 0 -0.33 26 26
MAPK3 0.024 0.068 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.041 -10000 0 -0.45 1 1
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.07 -10000 0 -0.32 26 26
ARF1/GDP 0.02 0.07 -10000 0 -10000 0 0
ARF6 0.009 0.024 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.016 0.034 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.068 -10000 0 -10000 0 0
actin filament bundle formation 0.014 0.062 -10000 0 -10000 0 0
KALRN -0.012 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.025 -10000 0 -0.56 1 1
RhoA/GDP -0.014 0.062 -10000 0 -10000 0 0
NME1 0.017 0.004 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.062 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.01 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.016 0.073 -10000 0 -0.33 26 26
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.01 0.043 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.043 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GDP -0.016 0.07 -10000 0 -0.32 26 26
ARF6/GTP/RAB11FIP3/RAB11A -0.006 0.029 -10000 0 -0.46 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.021 0.035 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.033 -10000 0 -0.75 1 1
tube morphogenesis -0.016 0.073 -10000 0 -0.33 26 26
ruffle organization 0.033 0.034 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.043 -10000 0 -10000 0 0
PLD2 0.021 0.035 -10000 0 -10000 0 0
PIP5K1A 0.033 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.033 0.03 -10000 0 -10000 0 0
Rac1/GTP -0.017 0.073 -10000 0 -0.33 26 26
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.002 0.012 -9999 0 -10000 0 0
DOCK1 0.014 0.033 -9999 0 -0.75 1 1
ITGA4 -0.01 0.15 -9999 0 -0.86 15 15
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.019 0.11 -9999 0 -0.67 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.017 0.097 -9999 0 -0.58 15 15
alpha4/beta7 Integrin/Paxillin -0.015 0.088 -9999 0 -0.52 15 15
lamellipodium assembly -0.001 0.043 -9999 0 -0.77 1 1
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PI3K -0.002 0.035 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
TLN1 0.016 0 -9999 0 -10000 0 0
PXN 0.031 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
ARF6/GTP -0.013 0.074 -9999 0 -10000 0 0
cell adhesion -0.014 0.081 -9999 0 -0.48 15 15
CRKL/CBL -0.001 0.025 -9999 0 -0.56 1 1
alpha4/beta1 Integrin/Paxillin -0.015 0.088 -9999 0 -0.52 15 15
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ARF6/GDP 0.002 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.026 0.11 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 -0.002 0.029 -9999 0 -0.48 2 2
VCAM1 -0.007 0.14 -9999 0 -0.82 14 14
alpha4/beta1 Integrin/Paxillin/Talin -0.014 0.082 -9999 0 -0.49 15 15
alpha4/beta1 Integrin/Paxillin/GIT1 -0.014 0.082 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
mol:GDP 0.014 0.081 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.75 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.014 0.082 -9999 0 -0.49 15 15
Rac1/GTP -0.001 0.051 -9999 0 -0.93 1 1
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.056 0.16 -10000 0 -0.5 59 59
cell-cell adhesion 0.013 0.073 0.63 3 -10000 0 3
Ephrin B/EPHB2/RasGAP -0.015 0.08 -10000 0 -0.59 3 3
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
SHC1 0.014 0.039 -10000 0 -0.86 1 1
Ephrin B1/EPHB3 -0.013 0.08 -10000 0 -0.49 14 14
Ephrin B1/EPHB1 -0.003 0.04 -10000 0 -0.52 3 3
HRAS/GDP -0.008 0.053 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.014 0.073 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.035 0.086 -10000 0 -0.75 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.009 0.058 -10000 0 -10000 0 0
endothelial cell migration -0.002 0.025 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 0.005 0.088 -10000 0 -0.75 7 7
PAK1 0.047 0.084 -10000 0 -0.76 1 1
HRAS 0.014 0.039 -10000 0 -0.86 1 1
RRAS 0.036 0.087 -10000 0 -0.54 4 4
DNM1 -0.001 0.12 -10000 0 -0.86 10 10
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.043 0.063 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.073 -10000 0 -0.63 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.006 0.037 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
EPHB2 0.001 0.11 -10000 0 -0.77 10 10
EPHB3 -0.005 0.12 -10000 0 -0.75 14 14
EPHB1 0.011 0.061 -10000 0 -0.78 3 3
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.06 -10000 0 -10000 0 0
Ephrin B/EPHB2 -0.014 0.08 -10000 0 -0.6 3 3
Ephrin B/EPHB3 -0.017 0.09 -10000 0 -0.71 3 3
JNK cascade 0.041 0.083 -10000 0 -0.78 2 2
Ephrin B/EPHB1 -0.009 0.06 -10000 0 -0.5 1 1
RAP1/GDP -0.003 0.052 -10000 0 -10000 0 0
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 0.004 0.094 -10000 0 -0.75 8 8
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.011 0.081 -10000 0 -0.54 11 11
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.015 0.08 -10000 0 -0.71 3 3
Rap1/GTP -0.013 0.073 -10000 0 -0.64 3 3
axon guidance -0.056 0.16 -10000 0 -0.49 59 59
MAPK3 0.065 0.041 -10000 0 -10000 0 0
MAPK1 0.065 0.041 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.055 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.011 0.058 -10000 0 -0.49 2 2
CDC42/GDP -0.003 0.055 -10000 0 -10000 0 0
PI3K -0.002 0.025 -10000 0 -10000 0 0
EFNA5 -0.057 0.22 -10000 0 -0.75 49 49
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.056 -10000 0 -0.6 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.014 0.076 -10000 0 -0.64 4 4
PTK2 0.002 0.017 -10000 0 -10000 0 0
MAP4K4 0.042 0.084 -10000 0 -0.8 2 2
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.011 0.058 -10000 0 -0.49 3 3
MAP2K1 0.057 0.043 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.012 0.082 -10000 0 -0.66 5 5
cell migration 0.067 0.049 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.035 0.088 -10000 0 -0.77 1 1
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.074 0.23 -10000 0 -0.79 3 3
HRAS/GTP -0.016 0.085 -10000 0 -0.72 4 4
Ephrin B1/EPHB1-2 -0.011 0.081 -10000 0 -0.54 11 11
cell adhesion mediated by integrin 0.01 0.065 0.46 8 -10000 0 8
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.016 0.086 -10000 0 -0.75 3 3
RAC1-CDC42/GTP -0.022 0.099 -10000 0 -0.77 5 5
RASA1 0.014 0.033 -10000 0 -0.75 1 1
RAC1-CDC42/GDP -0.003 0.052 -10000 0 -10000 0 0
ruffle organization 0.07 0.088 -10000 0 -0.64 3 3
NCK1 0.014 0.033 -10000 0 -0.75 1 1
receptor internalization 0.036 0.11 -10000 0 -0.72 1 1
Ephrin B/EPHB2/KALRN -0.014 0.079 -10000 0 -0.59 3 3
ROCK1 0.021 0.077 -10000 0 -0.44 14 14
RAS family/GDP -0.011 0.058 -10000 0 -0.53 1 1
Rac1/GTP -0.014 0.078 -10000 0 -0.69 3 3
Ephrin B/EPHB1/Src/Paxillin -0.006 0.042 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.01 0.066 -10000 0 -0.5 6 6
ER alpha/Gai/GDP/Gbeta gamma 0.054 0.055 -10000 0 -10000 0 0
AKT1 0.046 0.073 -10000 0 -0.65 5 5
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.041 0.073 -10000 0 -0.73 4 4
mol:Ca2+ -0.015 0.19 -10000 0 -0.68 12 12
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.008 0.069 -10000 0 -0.56 7 7
SHC1 0.014 0.039 -10000 0 -0.86 1 1
apoptosis -0.046 0.07 0.62 5 -10000 0 5
RhoA/GTP -0.004 0.037 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.007 0.045 -10000 0 -10000 0 0
regulation of stress fiber formation -0.067 0.047 0.54 1 -10000 0 1
E2/ERA-ERB (dimer) -0.012 0.079 -10000 0 -0.54 11 11
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.004 0.041 -10000 0 -0.47 4 4
pseudopodium formation 0.067 0.047 -10000 0 -0.54 1 1
E2/ER alpha (dimer)/PELP1 -0.004 0.045 -10000 0 -0.51 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
GNAO1 0.007 0.084 -10000 0 -0.84 5 5
HRAS 0.014 0.039 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.063 0.061 -10000 0 -0.46 4 4
E2/ER beta (dimer) -0.009 0.075 -10000 0 -0.65 7 7
mol:GDP -0.009 0.06 -10000 0 -0.47 4 4
mol:NADP 0.063 0.061 -10000 0 -0.46 4 4
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
mol:IP3 -0.017 0.19 -10000 0 -0.72 12 12
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 -0.023 0.098 -10000 0 -0.58 9 9
PLCB2 -0.068 0.17 -10000 0 -0.49 64 64
IGF1 0.006 0.094 -10000 0 -0.86 6 6
mol:L-citrulline 0.063 0.061 -10000 0 -0.46 4 4
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.048 -10000 0 -0.63 1 1
JNK cascade -0.009 0.075 -10000 0 -0.65 7 7
BCAR1 0.014 0.033 -10000 0 -0.75 1 1
ESR2 0.004 0.098 -10000 0 -0.83 7 7
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 0.01 0.069 -10000 0 -0.78 4 4
Gq family/GDP/Gbeta gamma -0.016 0.074 -10000 0 -0.56 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.052 0.032 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.046 -10000 0 -10000 0 0
GNAZ 0.011 0.058 -10000 0 -0.75 3 3
E2/ER alpha (dimer) -0.005 0.053 -10000 0 -0.6 4 4
STRN 0.01 0.067 -10000 0 -0.75 4 4
GNAL 0.016 0 -10000 0 -10000 0 0
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.016 0.072 -10000 0 -0.56 8 8
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.058 -10000 0 -0.75 3 3
HBEGF -0.042 0.14 -10000 0 -0.5 7 7
cAMP biosynthetic process -0.009 0.064 -10000 0 -0.44 11 11
SRC 0.063 0.052 -10000 0 -10000 0 0
PI3K -0.002 0.035 -10000 0 -0.56 2 2
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.008 0.052 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.009 0.05 -10000 0 -10000 0 0
Gs family/GTP -0.009 0.065 -10000 0 -0.45 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.023 -10000 0 -0.53 1 1
vasodilation 0.063 0.059 -10000 0 -0.44 4 4
mol:DAG -0.017 0.19 -10000 0 -0.72 12 12
Gs family/GDP/Gbeta gamma -0.007 0.047 -10000 0 -10000 0 0
MSN 0.069 0.051 -10000 0 -0.6 1 1
Gq family/GTP -0.019 0.078 -10000 0 -0.46 10 10
mol:PI-3-4-5-P3 0.042 0.07 -10000 0 -0.7 4 4
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.063 0.059 0.44 4 -10000 0 4
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.008 0.056 -10000 0 -0.45 3 3
NOS3 0.064 0.063 -10000 0 -0.48 4 4
GNA11 0.011 0.058 -10000 0 -0.75 3 3
MAPKKK cascade 0.072 0.071 -10000 0 -0.59 4 4
E2/ER alpha (dimer)/PELP1/Src -0.007 0.046 -10000 0 -0.48 3 3
ruffle organization 0.067 0.047 -10000 0 -0.54 1 1
ROCK2 -0.005 0.048 -10000 0 -0.68 1 1
GNA14 0.005 0.088 -10000 0 -0.75 7 7
GNA15 -0.01 0.15 -10000 0 -0.86 15 15
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.17 0.25 -10000 0 -0.66 8 8
MMP2 0.066 0.08 -10000 0 -0.66 3 3
BARD1 signaling events

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
BARD1/CSTF1 -0.004 0.049 -10000 0 -0.56 4 4
ATM 0.014 0.033 -10000 0 -0.75 1 1
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.034 0.019 -10000 0 -0.4 1 1
protein ubiquitination -0.01 0.072 -10000 0 -0.88 1 1
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.034 0.068 -10000 0 -0.52 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.016 0 -10000 0 -10000 0 0
CCNE1 0.004 0.1 -10000 0 -0.86 7 7
CDK2/Cyclin E1 -0.009 0.077 -10000 0 -0.67 7 7
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.049 -10000 0 -0.56 4 4
FANCE 0.014 0.039 -10000 0 -0.86 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.17 0.36 -10000 0 -0.86 109 109
DNA repair 0.043 0.14 -10000 0 -0.67 5 5
BRCA1/BARD1/ubiquitin -0.004 0.049 -10000 0 -0.56 4 4
BARD1/DNA-PK -0.003 0.037 -10000 0 -10000 0 0
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.004 0.049 0.56 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex -0.004 0.042 -10000 0 -0.78 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/P53 -0.003 0.037 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BACH1 0.016 0 -10000 0 -10000 0 0
BARD1 0.01 0.067 -10000 0 -0.75 4 4
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/UbcH7 -0.004 0.042 -10000 0 -0.48 4 4
BRCA1/BARD1/RAD51/PCNA -0.017 0.092 -10000 0 -0.52 14 14
BARD1/DNA-PK/P53 -0.003 0.034 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.049 -10000 0 -0.56 4 4
BRCA1/BARD1/CTIP -0.005 0.053 -10000 0 -0.86 1 1
FA complex -0.057 0.11 -10000 0 -0.57 1 1
BARD1/EWS -0.004 0.049 -10000 0 -0.56 4 4
RBBP8 0.029 0.046 -10000 0 -1 1 1
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.037 -10000 0 -10000 0 0
BRCA1/BARD1 -0.01 0.073 -10000 0 -0.9 1 1
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.004 0.05 -10000 0 -0.57 4 4
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.008 0.14 -10000 0 -0.86 14 14
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.049 -10000 0 -0.56 4 4
EWSR1 0.016 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.033 -10000 0 -0.75 1 1
ANTXR2 0.014 0.033 -10000 0 -0.75 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.006 -10000 0 -0.094 2 2
monocyte activation 0.006 0.085 -10000 0 -0.37 21 21
MAP2K2 -0.002 0.035 -10000 0 -0.8 1 1
MAP2K1 0 0.005 -10000 0 -10000 0 0
MAP2K7 0 0.005 -10000 0 -10000 0 0
MAP2K6 -0.003 0.033 -10000 0 -0.43 3 3
CYAA 0.02 0.027 -10000 0 -0.42 2 2
MAP2K4 0 0.005 -10000 0 -10000 0 0
IL1B 0.017 0.06 -10000 0 -0.49 6 6
Channel -0.002 0.028 -10000 0 -0.45 2 2
NLRP1 -0.005 0.052 -10000 0 -0.52 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.006 0.094 2 -10000 0 2
MAPK3 0 0.005 -10000 0 -10000 0 0
MAPK1 0 0.005 -10000 0 -10000 0 0
PGR -0.016 0.081 -10000 0 -0.44 18 18
PA/Cellular Receptors -0.002 0.03 -10000 0 -0.49 2 2
apoptosis 0 0.006 -10000 0 -0.094 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.026 -10000 0 -0.42 2 2
macrophage activation 0.027 0.006 -10000 0 -10000 0 0
TNF 0.003 0.1 -10000 0 -0.8 8 8
VCAM1 -0.015 0.081 -10000 0 -0.37 21 21
platelet activation 0 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.01 -10000 0 -10000 0 0
IL18 0.015 0.067 -10000 0 -0.52 7 7
negative regulation of macrophage activation 0 0.006 -10000 0 -0.094 2 2
LEF 0 0.006 -10000 0 -0.094 2 2
CASP1 -0.003 0.023 -10000 0 -0.23 5 5
mol:cAMP 0 0.007 -10000 0 -10000 0 0
necrosis 0 0.006 -10000 0 -0.094 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.026 -10000 0 -0.42 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.057 0.052 -10000 0 -0.46 1 1
adherens junction organization 0.04 0.08 -10000 0 -0.53 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.06 -10000 0 -10000 0 0
FMN1 0.023 0.12 -10000 0 -0.39 28 28
mol:IP3 -0.008 0.04 -10000 0 -0.48 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.065 -10000 0 -0.71 1 1
CTNNB1 0.001 0.006 -10000 0 -10000 0 0
AKT1 0.054 0.057 -10000 0 -0.51 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.11 -10000 0 -0.53 21 21
CTNND1 0.016 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.074 -10000 0 -0.56 2 2
VASP 0.045 0.072 -10000 0 -0.66 1 1
ZYX 0.045 0.072 -10000 0 -0.66 1 1
JUB 0.042 0.08 -10000 0 -0.58 2 2
EGFR(dimer) -0.02 0.082 -10000 0 -0.48 9 9
E-cadherin/beta catenin-gamma catenin -0.021 0.1 -10000 0 -0.48 23 23
mol:PI-3-4-5-P3 -0.01 0.048 -10000 0 -0.54 1 1
PIK3CA 0.015 0.033 -10000 0 -0.74 1 1
PI3K -0.01 0.049 -10000 0 -0.56 1 1
FYN -0.24 0.13 -10000 0 -0.62 2 2
mol:Ca2+ -0.008 0.039 -10000 0 -0.47 1 1
JUP -0.003 0.057 -10000 0 -0.74 3 3
PIK3R1 0.015 0.033 -10000 0 -0.74 1 1
mol:DAG -0.008 0.04 -10000 0 -0.48 1 1
CDH1 -0.03 0.15 -10000 0 -0.74 21 21
RhoA/GDP -0.013 0.06 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.045 0.071 -10000 0 -0.64 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
CASR -0.29 0.15 -10000 0 -0.54 18 18
RhoA/GTP -0.007 0.035 -10000 0 -10000 0 0
AKT2 0.054 0.057 -10000 0 -0.51 1 1
actin cable formation 0.033 0.12 -10000 0 -0.64 2 2
apoptosis 0.009 0.043 0.49 1 -10000 0 1
CTNNA1 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.015 0.066 -10000 0 -0.49 1 1
PIP5K1A 0.044 0.076 -10000 0 -0.58 2 2
PLCG1 -0.008 0.041 -10000 0 -0.49 1 1
Rac1/GTP -0.018 0.074 -10000 0 -0.6 1 1
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.01 0.061 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.057 -9999 0 -0.68 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.048 -9999 0 -0.55 4 4
AP1 -0.018 0.088 -9999 0 -0.7 5 5
ILK 0.062 0.06 -9999 0 -10000 0 0
bone resorption -0.025 0.1 -9999 0 -0.74 3 3
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.007 0.05 -9999 0 -10000 0 0
ITGAV 0.022 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.14 -9999 0 -0.65 24 24
alphaV/beta3 Integrin/Osteopontin -0.007 0.056 -9999 0 -0.49 2 2
MAP3K1 0.062 0.06 -9999 0 -10000 0 0
JUN 0.016 0.002 -9999 0 -10000 0 0
MAPK3 0.074 0.078 -9999 0 -10000 0 0
MAPK1 0.074 0.078 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
MAPK8 0.074 0.067 -9999 0 -0.78 1 1
ITGB3 0.016 0.067 -9999 0 -0.74 4 4
NFKBIA 0.087 0.078 -9999 0 -10000 0 0
FOS -0.003 0.12 -9999 0 -0.76 13 13
CD44 -0.02 0.17 -9999 0 -0.86 21 21
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU 0.086 0.17 -9999 0 -1.1 9 9
NF kappa B1 p50/RelA -0.011 0.059 -9999 0 -0.64 1 1
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.004 0.048 -9999 0 -0.55 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.058 0.066 -9999 0 -10000 0 0
VAV3 0.057 0.099 -9999 0 -0.78 1 1
MAP3K14 0.06 0.079 -9999 0 -0.5 4 4
ROCK2 0.011 0.058 -9999 0 -0.75 3 3
SPP1 0.016 0.067 -9999 0 -0.74 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.074 -9999 0 -0.71 1 1
MMP2 0.099 0.12 -9999 0 -0.76 6 6
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.016 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.021 -9999 0 -10000 0 0
forebrain development 0.055 0.095 -9999 0 -0.5 2 2
GNAO1 0.008 0.084 -9999 0 -0.84 5 5
SMO/beta Arrestin2 -0.002 0.038 -9999 0 -0.61 2 2
SMO 0.016 0.034 -9999 0 -0.74 1 1
ARRB2 0.014 0.039 -9999 0 -0.86 1 1
GLI3/SPOP 0.061 0.025 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex -0.018 0.096 -9999 0 -0.52 18 18
GNAI1 0.011 0.058 -9999 0 -0.74 3 3
XPO1 0.019 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.014 0.062 -9999 0 -10000 0 0
SAP30 -0.015 0.16 -9999 0 -0.86 18 18
mol:GDP 0.016 0.034 -9999 0 -0.74 1 1
MIM/GLI2A 0.023 0.008 -9999 0 -10000 0 0
IFT88 0.014 0.033 -9999 0 -0.75 1 1
GNAI3 0.016 0.004 -9999 0 -10000 0 0
GLI2 0.058 0.031 -9999 0 -10000 0 0
GLI3 0.055 0.026 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0.033 -9999 0 -0.74 1 1
GNG2 0.016 0 -9999 0 -10000 0 0
Gi family/GTP 0.044 0.052 -9999 0 -0.55 1 1
SIN3B 0.016 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.058 0.044 -9999 0 -10000 0 0
GLI2/Su(fu) 0.075 0.037 -9999 0 -10000 0 0
FOXA2 -0.062 0.22 -9999 0 -0.83 38 38
neural tube patterning 0.055 0.095 -9999 0 -0.5 2 2
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.014 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.75 1 1
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.023 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.055 0.095 -9999 0 -0.5 2 2
SUFU 0.038 0.021 -9999 0 -10000 0 0
LGALS3 -0.005 0.13 -9999 0 -0.86 12 12
catabolic process 0.093 0.031 -9999 0 -10000 0 0
GLI3A/CBP 0.017 0.057 -9999 0 -10000 0 0
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 0.055 0.096 -9999 0 -0.51 2 2
RAB23 0.016 0 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.016 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.013 0.082 -9999 0 -0.54 12 12
GNAZ 0.011 0.058 -9999 0 -0.75 3 3
RBBP4 0.014 0.033 -9999 0 -0.75 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.061 0.029 -9999 0 -10000 0 0
STK36 0.019 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.052 0.047 -9999 0 -0.48 1 1
PTCH1 0.062 0.1 -9999 0 -1.1 1 1
MIM/GLI1 0.051 0.15 -9999 0 -0.72 1 1
CREBBP 0.017 0.057 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.057 0.047 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.027 0.1 -9999 0 -10000 0 0
BAG4 0.014 0.033 -9999 0 -0.75 1 1
BAD 0.03 0.046 -9999 0 -0.42 2 2
NFKBIA 0.016 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 80 80
BAX 0.032 0.036 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.027 -9999 0 -10000 0 0
IKBKB 0.037 0.097 -9999 0 -10000 0 0
MAP2K2 0.046 0.053 -9999 0 -0.38 4 4
MAP2K1 0.047 0.05 -9999 0 -10000 0 0
SMPD1 0.019 0.028 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.038 0.098 -9999 0 -10000 0 0
MAP2K4 0.041 0.035 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.098 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.054 0.052 -9999 0 -0.38 4 4
response to UV 0.001 0 -9999 0 -10000 0 0
RAF1 0.039 0.053 -9999 0 -0.42 4 4
CRADD 0.016 0.001 -9999 0 -10000 0 0
mol:ceramide 0.022 0.038 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.016 0.001 -9999 0 -10000 0 0
MAP3K1 0.032 0.036 -9999 0 -10000 0 0
TRADD 0.016 0.001 -9999 0 -10000 0 0
RELA/p50 0.016 0 -9999 0 -10000 0 0
MAPK3 0.05 0.05 -9999 0 -0.37 4 4
MAPK1 0.05 0.05 -9999 0 -0.37 4 4
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.027 0.1 -9999 0 -10000 0 0
KSR1 0.029 0.055 -9999 0 -0.45 4 4
MAPK8 0.049 0.037 -9999 0 -10000 0 0
TRAF2 0.016 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.037 0.097 -9999 0 -10000 0 0
TNF R/SODD -0.001 0.025 -9999 0 -0.56 1 1
TNF 0.003 0.1 -9999 0 -0.8 8 8
CYCS 0.032 0.038 -9999 0 -10000 0 0
IKBKG 0.037 0.097 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.1 -9999 0 -0.44 1 1
RELA 0.016 0 -9999 0 -10000 0 0
RIPK1 0.016 0.001 -9999 0 -10000 0 0
AIFM1 0.033 0.038 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.009 0.068 -9999 0 -0.52 9 9
TNFRSF1A 0.016 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.028 0.03 -9999 0 -10000 0 0
NSMAF 0.028 0.099 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -10000 0 0
BCL2 0.016 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.005 0.073 -9999 0 -0.73 5 5
VDR 0.011 0.058 -9999 0 -0.75 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.077 0.05 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.087 0.062 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.009 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.02 0.073 -9999 0 -10000 0 0
RXRs/NUR77 -0.008 0.088 -9999 0 -0.5 5 5
RXRs/PPAR 0.058 0.03 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.043 -9999 0 -0.57 3 3
RARs/VDR/DNA/Vit D3 -0.004 0.039 -9999 0 -10000 0 0
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.058 -9999 0 -0.74 3 3
RARs/RARs/DNA/9cRA -0.001 0.026 -9999 0 -0.41 2 2
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.035 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.02 0.073 -9999 0 -10000 0 0
THRA 0.014 0.033 -9999 0 -0.75 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.003 0.043 -9999 0 -0.57 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.005 0.057 -9999 0 -0.5 4 4
NR1H4 -0.01 0.14 -9999 0 -0.75 17 17
RXRs/LXRs/DNA 0.008 0.057 -9999 0 -10000 0 0
NR1H2 0.023 0.034 -9999 0 -0.74 1 1
NR1H3 0.025 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.005 0.053 -9999 0 -0.48 4 4
NR4A1 -0.007 0.13 -9999 0 -0.75 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.041 0.068 -9999 0 -0.41 2 2
RXRG 0.015 0.077 -9999 0 -0.85 4 4
RXR alpha/CCPG 0 0.004 -9999 0 -10000 0 0
RXRA 0.024 0.005 -9999 0 -10000 0 0
RXRB 0.025 0.006 -9999 0 -10000 0 0
THRB -0.031 0.18 -9999 0 -0.75 32 32
PPARG 0.016 0 -9999 0 -10000 0 0
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.084 0.13 -9999 0 -0.87 8 8
mol:Oxysterols 0.009 0.007 -9999 0 -10000 0 0
cholesterol transport 0.087 0.062 -9999 0 -10000 0 0
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0.047 -9999 0 -0.75 2 2
RXRs/NUR77/BCL2 -0.01 0.055 -9999 0 -10000 0 0
SREBF1 0.093 0.065 -9999 0 -0.66 1 1
RXRs/RXRs/DNA/9cRA 0.005 0.057 -9999 0 -0.5 4 4
ABCA1 0.092 0.072 -9999 0 -0.66 2 2
RARs/THRs -0.027 0.099 -9999 0 -10000 0 0
RXRs/FXR -0.009 0.093 -9999 0 -0.5 7 7
BCL2 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.076 0.027 -10000 0 -10000 0 0
NFATC2 0.054 0.033 -10000 0 -0.32 1 1
NFATC3 0.029 0.04 -10000 0 -0.49 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.032 0.072 -10000 0 -0.46 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.013 0.054 -10000 0 -0.52 2 2
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.001 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0.003 -10000 0 -10000 0 0
BAD 0.013 0.051 -10000 0 -0.8 2 2
CABIN1/MEF2D 0.037 0.068 -10000 0 -0.45 3 3
Calcineurin A alpha-beta B1/BCL2 0.016 0 -10000 0 -10000 0 0
FKBP8 0.014 0.033 -10000 0 -0.75 1 1
activation-induced cell death of T cells -0.037 0.067 0.44 3 -10000 0 3
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
SFN -0.086 0.28 -10000 0 -0.83 62 62
MAP3K8 0.013 0.055 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.002 0.024 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.01 0.056 -10000 0 -10000 0 0
CABIN1 0.032 0.073 -10000 0 -0.47 4 4
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0.013 0.047 -10000 0 -0.75 2 2
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.035 -10000 0 -0.56 2 2
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.015 0.034 -10000 0 -0.75 1 1
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.028 -10000 0 -10000 0 0
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.024 -10000 0 -0.56 1 1
CASP3 0.016 0.003 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.02 -10000 0 -0.4 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.077 -10000 0 -0.47 2 2
PRKCB 0.008 0.082 -10000 0 -0.82 5 5
PRKCE 0.014 0.033 -10000 0 -0.75 1 1
JNK2/NFAT4 -0.003 0.033 -10000 0 -0.44 3 3
BAD/BCL-XL -0.002 0.038 -10000 0 -0.61 2 2
PRKCD 0.014 0.039 -10000 0 -0.86 1 1
NUP214 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.058 -10000 0 -0.75 3 3
PRKCA 0.016 0 -10000 0 -10000 0 0
PRKCG -0.031 0.18 -10000 0 -0.86 23 23
PRKCQ -0.006 0.13 -10000 0 -0.75 15 15
FKBP38/BCL2 -0.001 0.025 -10000 0 -0.56 1 1
EP300 0.015 0.033 -10000 0 -0.74 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.08 0.034 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.022 -10000 0 -0.5 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.03 -10000 0 -0.49 2 2
NFATc/ERK1 0.081 0.026 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.013 0.054 -10000 0 -0.52 2 2
NR4A1 0.073 0.13 -10000 0 -0.67 15 15
GSK3B 0.016 0.003 -10000 0 -10000 0 0
positive T cell selection 0.029 0.04 -10000 0 -0.49 3 3
NFAT1/CK1 alpha -0.003 0.017 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0.003 -10000 0 -10000 0 0
AKAP5 0.013 0.047 -10000 0 -0.75 2 2
MEF2D 0.016 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.081 0.029 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.011 0.058 -10000 0 -0.75 3 3
Cbp/p300/PCAF -0.002 0.04 -10000 0 -0.92 1 1
EP300 0.014 0.033 -10000 0 -0.75 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.056 0.034 -10000 0 -0.43 1 1
KAT2B 0.014 0.033 -10000 0 -0.75 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.03 0.038 0.24 1 -0.3 2 3
RAR alpha/9cRA/Cyclin H -0.009 0.038 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.052 0.037 -10000 0 -0.48 1 1
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.002 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.01 0.047 -10000 0 -0.59 1 1
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.043 -10000 0 -0.57 3 3
RXRs/RARs/NRIP1/9cRA 0.063 0.083 -10000 0 -0.52 1 1
NCOA2 0.003 0.1 -10000 0 -0.75 9 9
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.058 -10000 0 -0.74 3 3
RARG 0.017 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.001 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.016 0.033 -10000 0 -0.74 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.018 0.074 -10000 0 -10000 0 0
RARA 0.025 0.059 -10000 0 -0.28 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.047 0.063 -10000 0 -0.61 2 2
PRKCA 0.021 0.001 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.054 0.084 -10000 0 -0.57 1 1
RXRG 0.012 0.092 -10000 0 -0.38 27 27
RXRA 0.036 0.056 -10000 0 -10000 0 0
RXRB 0.017 0.085 -10000 0 -0.37 23 23
VDR/Vit D3/DNA -0.003 0.043 -10000 0 -0.57 3 3
RBP1 0.009 0.075 -10000 0 -0.84 4 4
CRBP1/9-cic-RA -0.005 0.057 -10000 0 -0.65 4 4
RARB 0.016 0.047 -10000 0 -0.75 2 2
PRKCG -0.026 0.18 -10000 0 -0.86 23 23
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.053 0.084 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.061 0.075 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.047 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.054 0.084 -10000 0 -0.57 1 1
positive regulation of DNA binding -0.008 0.036 -10000 0 -10000 0 0
NRIP1 0.053 0.092 -10000 0 -1.2 1 1
RXRs/RARs 0.046 0.082 -10000 0 -0.41 1 1
RXRs/RXRs/DNA/9cRA -0.017 0.074 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.006 0.026 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.011 0.058 -9999 0 -0.75 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.006 0.038 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 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 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
MAP3K12 0.014 0.033 -9999 0 -0.75 1 1
FGR 0.011 0.067 -9999 0 -0.86 3 3
p38 alpha/TAB1 -0.012 0.038 -9999 0 -0.31 2 2
PRKG1 -0.003 0.12 -9999 0 -0.75 13 13
DUSP8 0.014 0.033 -9999 0 -0.75 1 1
PGK/cGMP/p38 alpha -0.019 0.063 -9999 0 -0.44 3 3
apoptosis -0.012 0.037 -9999 0 -0.3 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 0.014 0.039 -9999 0 -0.86 1 1
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 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 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.056 0.084 -9999 0 -0.42 2 2
BLK -0.041 0.22 -9999 0 -0.86 33 33
HCK -0.032 0.2 -9999 0 -0.86 28 28
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.011 0.067 -9999 0 -0.86 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.057 0.066 -9999 0 -0.34 2 2
positive regulation of innate immune response 0.068 0.091 -9999 0 -0.44 2 2
LCK -0.021 0.18 -9999 0 -0.85 22 22
p38alpha-beta/MKP7 0.073 0.088 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.071 0.093 -9999 0 -10000 0 0
PGK/cGMP -0.014 0.089 -9999 0 -0.57 13 13
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.072 0.089 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.008 0.14 -9999 0 -0.83 14 14
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.01 0.062 -9999 0 -10000 0 0
TC10/GTP -0.006 0.052 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.039 -9999 0 -10000 0 0
HRAS 0.014 0.039 -9999 0 -0.86 1 1
APS homodimer 0.006 0.094 -9999 0 -0.86 6 6
GRB14 -0.025 0.17 -9999 0 -0.75 28 28
FOXO3 -0.003 0.013 -9999 0 -10000 0 0
AKT1 -0.022 0.085 -9999 0 -0.66 2 2
INSR 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
SORBS1 0.014 0.033 -9999 0 -0.75 1 1
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.049 0.001 -9999 0 -10000 0 0
CAV1 -0.006 0.15 -9999 0 -0.51 37 37
CBL/APS/CAP/Crk-II/C3G -0.007 0.057 -9999 0 -0.49 6 6
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.039 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.041 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.002 0.024 -9999 0 -10000 0 0
RPS6KB1 0.055 0.096 -9999 0 -0.58 2 2
PARD6A 0.011 0.058 -9999 0 -0.75 3 3
CBL 0.014 0.033 -9999 0 -0.75 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.019 0.074 -9999 0 -0.59 2 2
HRAS/GTP -0.007 0.056 -9999 0 -0.73 1 1
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.004 0.042 -9999 0 -0.5 1 1
PRKCI -0.005 0.019 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.024 0.093 -9999 0 -0.73 2 2
SHC1 0.014 0.039 -9999 0 -0.86 1 1
negative regulation of MAPKKK cascade -0.001 0.036 -9999 0 -0.82 1 1
PI3K -0.005 0.042 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.03 -9999 0 -0.68 1 1
AKT2 -0.022 0.085 -9999 0 -0.66 2 2
PRKCZ -0.009 0.056 -9999 0 -0.7 3 3
SH2B2 0.006 0.094 -9999 0 -0.86 6 6
SHC/SHIP -0.008 0.063 -9999 0 -0.55 5 5
F2RL2 -0.034 0.2 -9999 0 -0.86 29 29
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.024 -9999 0 -0.55 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.022 -9999 0 -0.5 1 1
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.75 1 1
NCK1 0.014 0.033 -9999 0 -0.75 1 1
CBL/APS/CAP/Crk-II -0.008 0.062 -9999 0 -0.52 6 6
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.024 -9999 0 -0.54 1 1
INPP5D 0.029 0.068 -9999 0 -0.61 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.001 0.006 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.067 -9999 0 -0.75 4 4
p62DOK/RasGAP -0.002 0.037 -9999 0 -0.84 1 1
INS 0.005 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.029 0.067 -9999 0 -0.6 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.032 0.15 -9999 0 -0.73 6 6
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.75 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.003 0.028 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.04 -9999 0 -0.46 4 4
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.03 0.12 -9999 0 -0.5 29 29
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.036 0.12 -9999 0 -0.46 18 18
PDGFB-D/PDGFRB/SLAP -0.031 0.14 -9999 0 -0.67 24 24
PDGFB-D/PDGFRB/APS/CBL -0.008 0.065 -9999 0 -0.56 7 7
AKT1 -0.002 0.022 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0.14 -9999 0 -0.48 18 18
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
FGR -0.004 0.029 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.041 -9999 0 -10000 0 0
MYC 0.043 0.13 -9999 0 -0.57 19 19
SHC1 0.014 0.039 -9999 0 -0.86 1 1
HRAS/GDP -0.002 0.039 -9999 0 -0.88 1 1
LRP1/PDGFRB/PDGFB 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.038 0.041 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.005 0.088 -9999 0 -0.75 7 7
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.031 0.14 -9999 0 -0.67 24 24
HRAS 0.014 0.039 -9999 0 -0.86 1 1
HIF1A 0.087 0.041 -9999 0 -0.6 1 1
GAB1 0.033 0.076 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.036 0.082 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.038 0.12 -9999 0 -0.51 10 10
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
mol:IP3 0.038 0.041 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.065 -9999 0 -0.57 7 7
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.023 0.087 -9999 0 -0.46 1 1
PTPN2 0.016 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.75 1 1
VAV2 0.035 0.088 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.75 1 1
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.018 0.082 -9999 0 -0.64 2 2
PDGFRB 0.016 0.006 -9999 0 -10000 0 0
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.02 0.082 -9999 0 -10000 0 0
ABL1 0.033 0.06 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.033 0.071 -9999 0 -10000 0 0
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.014 0.039 -9999 0 -0.86 1 1
cell proliferation 0.044 0.12 -9999 0 -0.52 19 19
SLA -0.025 0.18 -9999 0 -0.86 24 24
actin cytoskeleton reorganization 0.001 0.025 -9999 0 -10000 0 0
SRC -0.001 0.013 -9999 0 -10000 0 0
PI3K -0.002 0.025 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.008 0.061 -9999 0 -0.49 8 8
SH2B2 0.006 0.094 -9999 0 -0.86 6 6
PLCgamma1/SPHK1 0.012 0.14 -9999 0 -0.49 18 18
LYN -0.001 0.014 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.023 -9999 0 -10000 0 0
SPHK1 -0.057 0.24 -9999 0 -0.86 43 43
EDG1 0.001 0.003 -9999 0 -10000 0 0
mol:DAG 0.038 0.041 -9999 0 -10000 0 0
PLCG1 0.039 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.021 -9999 0 -0.48 1 1
YES1 -0.001 0.014 -9999 0 -10000 0 0
cell migration -0.001 0.021 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 -0.001 0.02 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.75 1 1
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.019 -9999 0 -10000 0 0
FYN -0.001 0.013 -9999 0 -10000 0 0
DOK1 0.044 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.03 -9999 0 -0.68 1 1
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 0.045 0.1 -9999 0 -0.5 2 2
PRKCD 0.042 0.028 -9999 0 -0.53 1 1
FER 0.041 0.033 -9999 0 -10000 0 0
MAPKKK cascade 0 0.022 -9999 0 -10000 0 0
RASA1 0.042 0.025 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.75 1 1
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.018 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.033 0.059 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.001 0.02 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.019 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 -0.026 0.13 -10000 0 -0.67 20 20
GATA1/HDAC5 -0.027 0.13 -10000 0 -0.66 21 21
GATA2/HDAC5 -0.014 0.088 -10000 0 -0.56 13 13
HDAC5/BCL6/BCoR -0.001 0.021 -10000 0 -0.48 1 1
HDAC9 0.016 0 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.025 -10000 0 -0.58 1 1
HDAC4/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC5/YWHAB -0.001 0.025 -10000 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.002 0.12 -10000 0 -0.75 12 12
HDAC4/RFXANK -0.001 0.029 -10000 0 -0.67 1 1
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.033 -10000 0 -0.75 1 1
HDAC5 0.014 0.033 -10000 0 -0.75 1 1
GNB1/GNG2 0 0 -10000 0 -10000 0 0
Histones -0.003 0.04 -10000 0 -0.84 1 1
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.025 -10000 0 -0.56 1 1
HDAC4/Ubc9 0 0 -10000 0 -10000 0 0
HDAC7 0.016 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.025 -10000 0 -0.56 1 1
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.002 0.038 -10000 0 -0.61 2 2
CAMK4 0.013 0.047 -10000 0 -0.75 2 2
Tubulin/HDAC6 -0.001 0.021 -10000 0 -0.48 1 1
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 -0.021 0.17 -10000 0 -0.86 20 20
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0 -10000 0 -10000 0 0
NR3C1 0.014 0.039 -10000 0 -0.86 1 1
SUMO1/HDAC4 0 0 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0 0 -10000 0 -10000 0 0
Tubulin -0.001 0.025 -10000 0 -0.56 1 1
HDAC4/14-3-3 E 0 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.016 0 -10000 0 -10000 0 0
BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -10000 0 -10000 0 0
HDAC4/SRF -0.002 0.029 -10000 0 -0.48 2 2
HDAC4/ER alpha -0.005 0.051 -10000 0 -0.59 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.051 0.043 -10000 0 -0.82 1 1
cell motility -0.001 0.021 -10000 0 -0.47 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 0.016 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 0.01 0.069 -10000 0 -0.78 4 4
HDAC6/HDAC11 -0.002 0.035 -10000 0 -0.56 2 2
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0.016 0 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.014 0.033 -10000 0 -0.75 1 1
HDAC11 0.013 0.047 -10000 0 -0.75 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.014 0.039 -10000 0 -0.86 1 1
nuclear import 0.001 0.017 0.39 1 -10000 0 1
Circadian rhythm pathway

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
chromatin modification -0.001 0.016 -10000 0 -10000 0 0
CLOCK 0.019 0.033 -10000 0 -0.74 1 1
TIMELESS/CRY2 0.056 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.029 -10000 0 -0.66 1 1
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.053 0.07 -10000 0 -1 2 2
ARNTL 0.02 0.003 -10000 0 -10000 0 0
TIMELESS 0.056 0.028 -10000 0 -10000 0 0
NPAS2 0.006 0.1 -10000 0 -0.74 10 10
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.019 0.009 0.12 2 -10000 0 2
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.019 0.009 -10000 0 -0.12 2 2
PER1 0.016 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.075 -10000 0 -0.46 11 11
BMAL1/CLOCK 0.064 0.056 -10000 0 -0.82 1 1
S phase of mitotic cell cycle -0.001 0.016 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.002 0.016 -10000 0 -10000 0 0
mol:NADPH 0.019 0.009 -10000 0 -0.12 2 2
PER1/TIMELESS 0.056 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.039 -10000 0 -0.86 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.037 -10000 0 -0.4 2 2
FRAP1 0.02 0.013 -10000 0 -10000 0 0
AKT1 -0.004 0.037 -10000 0 -0.47 2 2
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.029 -10000 0 -0.46 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.009 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.025 -10000 0 -0.42 1 1
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.036 -10000 0 -0.39 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.036 0.024 -10000 0 -0.34 1 1
MAP3K5 0.014 0.001 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
apoptosis 0.014 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 4 4
EIF4B 0.044 0.022 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.032 -10000 0 -0.45 2 2
eIF4E/eIF4G1/eIF4A1 0 0.005 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.039 -10000 0 -0.36 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.042 0.018 -10000 0 -10000 0 0
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.025 -10000 0 -0.41 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 4 4
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.044 -10000 0 -0.75 1 1
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.008 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.023 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.031 -10000 0 -0.5 1 1
tumor necrosis factor receptor activity 0 0 0.002 4 -10000 0 4
RPS6 0.012 0.055 -10000 0 -0.86 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.008 0.038 -10000 0 -0.42 4 4
INS 0 0.001 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.004 0.034 -10000 0 -0.37 2 2
EIF4EBP1 -0.008 0.1 -10000 0 -0.46 25 25
PIK3CA 0.014 0.034 -10000 0 -0.75 1 1
PPP2R5D 0.029 0.012 -10000 0 -10000 0 0
peptide biosynthetic process 0.023 0.001 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.004 1 1
EEF2 0.023 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.002 0.091 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.031 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.002 0.03 -9999 0 -0.52 1 1
CDKN1B 0.051 0.007 -9999 0 -10000 0 0
CDKN1A 0.049 0.033 -9999 0 -0.47 2 2
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.051 0.007 -9999 0 -10000 0 0
AKT1 0 0.006 -9999 0 -10000 0 0
BAD 0.013 0.051 -9999 0 -0.8 2 2
AKT3 0.022 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.051 0.007 -9999 0 -10000 0 0
AKT1/ASK1 0 0.005 -9999 0 -10000 0 0
BAD/YWHAZ -0.002 0.033 -9999 0 -0.53 2 2
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.016 0 -9999 0 -10000 0 0
JNK cascade 0 0.005 -9999 0 -10000 0 0
TSC1 0.051 0.007 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0.005 -9999 0 -10000 0 0
EP300 0.014 0.033 -9999 0 -0.75 1 1
mol:GDP 0 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.051 0.007 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.033 0.017 -9999 0 -0.34 1 1
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.041 0.052 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.051 0.007 -9999 0 -10000 0 0
CASP9 0.051 0.007 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.058 0.007 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.021 -9999 0 -0.48 1 1
YWHAE 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.002 0.03 -9999 0 -0.45 2 2
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.002 -9999 0 -10000 0 0
CHUK 0.051 0.007 -9999 0 -10000 0 0
BAD/BCL-XL -0.002 0.029 -9999 0 -0.56 1 1
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.022 0.019 -9999 0 -0.41 1 1
FOXO1-3a-4/14-3-3 family 0.059 0.06 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.75 1 1
MDM2 0.051 0.007 -9999 0 -10000 0 0
MAPKKK cascade 0 0.005 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.001 0.021 -9999 0 -0.48 1 1
TSC1/TSC2 0.059 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.02 -9999 0 -0.46 1 1
glucose import 0.03 0.08 -9999 0 -0.48 12 12
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.043 0.005 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.03 0.081 -9999 0 -0.48 12 12
GSK3A 0.051 0.007 -9999 0 -10000 0 0
FOXO1 0.051 0.007 -9999 0 -10000 0 0
GSK3B 0.051 0.007 -9999 0 -10000 0 0
SFN -0.086 0.28 -9999 0 -0.83 62 62
G1/S transition of mitotic cell cycle 0.06 0.007 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.036 0.079 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.008 0.059 -9999 0 -0.55 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.048 -9999 0 -0.54 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.058 -9999 0 -0.75 3 3
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.032 -9999 0 -0.72 1 1
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.04 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.003 0.027 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.046 0.042 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.003 0.027 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.063 0.025 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA 0.048 0.048 -9999 0 -0.65 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.002 0.12 -9999 0 -0.75 12 12
GATA1 -0.021 0.17 -9999 0 -0.86 20 20
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.045 -9999 0 -0.53 2 2
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.014 0.033 -9999 0 -0.75 1 1
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.032 -9999 0 -10000 0 0
KAT2B 0.014 0.033 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.007 0.038 -9999 0 -10000 0 0
SIN3 complex -0.018 0.096 -9999 0 -0.52 18 18
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 -0.015 0.16 -9999 0 -0.86 18 18
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.004 0.036 -9999 0 -0.64 1 1
YY1/HDAC2 -0.001 0.032 -9999 0 -0.72 1 1
YY1/HDAC1 -0.001 0.032 -9999 0 -0.72 1 1
NuRD/MBD2 Complex (MeCP1) 0.064 0.01 -9999 0 -10000 0 0
PPARG -0.006 0.047 -9999 0 -10000 0 0
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.003 0.027 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.024 -9999 0 -0.52 1 1
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.032 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.039 0.037 -9999 0 -0.81 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.034 0.019 -9999 0 -0.4 1 1
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.03 -9999 0 -0.67 1 1
YY1/SAP30/HDAC1 -0.019 0.097 -9999 0 -0.52 19 19
EP300 0.014 0.033 -9999 0 -0.75 1 1
STAT3 (dimer non-phopshorylated) 0.034 0.019 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.032 -9999 0 -10000 0 0
histone deacetylation 0.064 0.01 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.026 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.013 0.069 -9999 0 -0.42 12 12
GATA1/HDAC1 -0.026 0.13 -9999 0 -0.67 20 20
GATA1/HDAC3 -0.023 0.1 -9999 0 -0.52 20 20
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.009 0.076 -9999 0 -0.61 8 8
SIN3/HDAC complex/Mad/Max 0.056 0.04 -9999 0 -10000 0 0
NuRD Complex -0.001 0.02 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.022 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.019 -9999 0 -10000 0 0
GATA1/Fog1 -0.029 0.14 -9999 0 -0.65 23 23
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
negative regulation of cell growth 0.056 0.04 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.064 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.045 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 -0.006 0.029 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.013 0.051 -9999 0 -0.8 2 2
MBD2 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.003 0.041 -9999 0 -0.67 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.004 0.042 -9999 0 -0.48 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
NFKBIA 0.028 0.056 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.021 -9999 0 -0.48 1 1
ARRB2 0.022 0.018 -9999 0 -0.39 1 1
REL 0.011 0.058 -9999 0 -0.75 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.003 0.041 -9999 0 -0.54 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.021 -9999 0 -0.48 1 1
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
NF kappa B1 p50 dimer 0.025 0.026 -9999 0 -0.56 1 1
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
NFKB1 0.03 0.026 -9999 0 -0.56 1 1
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.055 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.008 0.037 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.035 -9999 0 -0.56 2 2
NF kappa B1 p50/RelA 0.037 0.055 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.047 -9999 0 -0.75 2 2
I kappa B alpha/PIK3R1 0.034 0.055 -9999 0 -0.39 1 1
cell death -0.008 0.036 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.004 0.042 -9999 0 -0.48 4 4
LCK -0.021 0.18 -9999 0 -0.85 22 22
BCL3 0.012 0.055 -9999 0 -0.86 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.008 0.25 -9999 0 -1.1 26 26
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.023 0.073 -9999 0 -10000 0 0
ATF2/c-Jun 0.044 0.063 -9999 0 -0.61 1 1
MAPK11 0.022 0.082 -9999 0 -0.84 1 1
MITF 0.044 0.09 -9999 0 -10000 0 0
MAPKAPK5 0.044 0.09 -9999 0 -10000 0 0
KRT8 0.043 0.092 -9999 0 -10000 0 0
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.032 0.11 -9999 0 -0.62 1 1
CEBPB 0.034 0.11 -9999 0 -10000 0 0
SLC9A1 0.044 0.09 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.051 0.095 -9999 0 -0.82 1 1
p38alpha-beta/MNK1 -0.019 0.073 -9999 0 -10000 0 0
JUN 0.045 0.063 -9999 0 -0.6 1 1
PPARGC1A 0.001 0.15 -9999 0 -0.75 2 2
USF1 0.044 0.09 -9999 0 -10000 0 0
RAB5/GDP/GDI1 -0.013 0.05 -9999 0 -10000 0 0
NOS2 0.039 0.13 -9999 0 -0.84 7 7
DDIT3 0.041 0.095 -9999 0 -10000 0 0
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 0.047 0.085 -9999 0 -0.67 2 2
p38alpha-beta/HBP1 -0.019 0.073 -9999 0 -10000 0 0
CREB1 0.049 0.093 -9999 0 -10000 0 0
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.048 0.078 -9999 0 -10000 0 0
RPS6KA4 0.044 0.09 -9999 0 -10000 0 0
PLA2G4A 0.043 0.099 -9999 0 -0.79 2 2
GDI1 0.044 0.09 -9999 0 -10000 0 0
TP53 0.046 0.11 -9999 0 -0.5 1 1
RPS6KA5 0.044 0.09 -9999 0 -10000 0 0
ESR1 0.04 0.097 -9999 0 -10000 0 0
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C 0.044 0.09 -9999 0 -10000 0 0
MEF2A 0.044 0.09 -9999 0 -10000 0 0
EIF4EBP1 0.043 0.098 -9999 0 -0.46 2 2
KRT19 -0.043 0.21 -9999 0 -0.88 9 9
ELK4 0.044 0.09 -9999 0 -10000 0 0
ATF6 0.044 0.09 -9999 0 -10000 0 0
ATF1 0.049 0.093 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK2 -0.019 0.073 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 -0.019 0.073 -9999 0 -0.5 1 1
IGF1 pathway

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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL 0.029 0.056 -10000 0 -10000 0 0
GRB2/SOS1/SHC -0.001 0.025 -10000 0 -0.58 1 1
HRAS 0.014 0.039 -10000 0 -0.86 1 1
IRS1/Crk -0.007 0.051 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.056 -10000 0 -0.52 6 6
AKT1 0.054 0.062 -10000 0 -0.71 1 1
BAD 0.062 0.072 -10000 0 -1.1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.056 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.052 -10000 0 -10000 0 0
RAF1 0.067 0.058 -10000 0 -0.7 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.007 0.048 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.008 0.057 -10000 0 -0.45 6 6
PIK3CA 0.014 0.033 -10000 0 -0.75 1 1
RPS6KB1 0.054 0.062 -10000 0 -0.71 1 1
GNB2L1 0.014 0.039 -10000 0 -0.86 1 1
positive regulation of MAPKKK cascade 0.059 0.05 -10000 0 -0.57 1 1
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.75 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.049 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.049 -10000 0 -0.51 1 1
IGF-1R heterotetramer 0.015 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.052 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.007 0.047 -10000 0 -10000 0 0
IGF1R 0.015 0.012 -10000 0 -10000 0 0
IGF1 0.006 0.093 -10000 0 -0.85 6 6
IRS2/Crk 0.029 0.084 -10000 0 -0.49 8 8
PI3K -0.008 0.053 -10000 0 -10000 0 0
apoptosis -0.065 0.06 0.79 1 -10000 0 1
HRAS/GDP -0.001 0.03 -10000 0 -0.68 1 1
PRKCD 0.05 0.057 -10000 0 -0.82 1 1
RAF1/14-3-3 E 0.071 0.051 -10000 0 -0.57 1 1
BAD/14-3-3 0.068 0.065 -10000 0 -0.89 1 1
PRKCZ 0.052 0.069 -10000 0 -0.71 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.007 0.044 -10000 0 -0.57 1 1
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.042 0.048 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.75 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.006 0.054 -10000 0 -0.47 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.007 0.051 -10000 0 -10000 0 0
GRB10 0.016 0 -10000 0 -10000 0 0
PTPN11 0.029 0.056 -10000 0 -10000 0 0
IRS1 0.018 0.06 -10000 0 -0.45 6 6
IRS2 0.02 0.088 -10000 0 -0.47 14 14
IGF-1R heterotetramer/IGF1 -0.008 0.07 -10000 0 -0.66 6 6
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 0.044 0.065 -10000 0 -0.77 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 0.05 0.049 -10000 0 -10000 0 0
SHC1 0.014 0.039 -10000 0 -0.86 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 -0.005 0.058 -9999 0 -0.67 4 4
FBXW11 0.016 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 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.043 -9999 0 -0.49 4 4
NFKB1 0.014 0.033 -9999 0 -0.75 1 1
MAP3K14 0.009 0.077 -9999 0 -0.86 4 4
NF kappa B1 p50/RelB -0.001 0.025 -9999 0 -0.56 1 1
RELB 0.016 0 -9999 0 -10000 0 0
NFKB2 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.019 0 -9999 0 -10000 0 0
SMAD3 0.057 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.062 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.027 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.025 -9999 0 -0.56 1 1
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.014 0.033 -9999 0 -0.75 1 1
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.004 0.049 -9999 0 -0.56 4 4
PTK2 -0.003 0.03 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.002 0.022 -9999 0 -10000 0 0
CDC42/GDP 0.077 0.032 -9999 0 -10000 0 0
Rac1/GDP 0.08 0.032 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.002 0.027 -9999 0 -10000 0 0
nectin-3/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
RAPGEF1 0.075 0.033 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.068 0.037 -9999 0 -0.51 2 2
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 0.046 0.015 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.019 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.079 0.038 -9999 0 -0.48 2 2
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.75 1 1
PI3K -0.003 0.035 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.001 0.019 -9999 0 -10000 0 0
PVRL1 0.016 0 -9999 0 -10000 0 0
PVRL3 0.013 0.047 -9999 0 -0.75 2 2
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.75 1 1
CDH1 -0.015 0.15 -9999 0 -0.75 21 21
CLDN1 0.008 0.079 -9999 0 -0.79 5 5
JAM-A/CLDN1 -0.006 0.053 -9999 0 -0.52 2 2
SRC -0.003 0.036 -9999 0 -0.57 2 2
ITGB3 0.01 0.067 -9999 0 -0.75 4 4
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.069 0.044 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.002 0.029 -9999 0 -0.48 2 2
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
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 -0.002 0.029 -9999 0 -0.48 2 2
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.002 0.022 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.003 0.033 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.001 0.014 -9999 0 -10000 0 0
VAV2 0.069 0.036 -9999 0 -0.48 2 2
RAP1/GDP -0.002 0.023 -9999 0 -10000 0 0
ITGAV 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.002 0.029 -9999 0 -0.48 2 2
nectin-3(dimer)/I-afadin/I-afadin -0.002 0.035 -9999 0 -0.56 2 2
Rac1/GTP -0.002 0.023 -9999 0 -10000 0 0
PTPRM -0.001 0.016 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.015 0.073 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.014 0.033 -9999 0 -0.75 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.024 -9999 0 -0.56 1 1
MAP2K4 0.063 0.017 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
TNFRSF10B 0.014 0.039 -9999 0 -0.86 1 1
TNFRSF10A 0.014 0.033 -9999 0 -0.75 1 1
SMPD1 -0.001 0.017 -9999 0 -0.27 1 1
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.002 0.038 -9999 0 -0.61 2 2
TRAIL/TRAILR3 -0.002 0.038 -9999 0 -0.61 2 2
TRAIL/TRAILR1 -0.002 0.035 -9999 0 -0.56 2 2
TRAIL/TRAILR4 -0.001 0.025 -9999 0 -0.56 1 1
TRAIL/TRAILR1/DAP3/GTP -0.002 0.027 -9999 0 -0.44 2 2
IKK complex -0.001 0.009 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.03 0.026 -9999 0 -0.56 1 1
MAP3K1 -0.001 0.014 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.018 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
MAPK1 0.03 0.026 -9999 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.024 -9999 0 -10000 0 0
mol:ceramide -0.001 0.017 -9999 0 -0.27 1 1
FADD 0.016 0 -9999 0 -10000 0 0
MAPK8 0.071 0.025 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.039 -9999 0 -0.86 1 1
CHUK 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.029 -9999 0 -0.48 2 2
DAP3 0.016 0 -9999 0 -10000 0 0
CASP10 -0.002 0.025 -9999 0 -0.45 1 1
JNK cascade -0.001 0.024 -9999 0 -0.56 1 1
TRAIL (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TNFRSF10C 0.014 0.039 -9999 0 -0.86 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.025 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD -0.002 0.033 -9999 0 -0.53 2 2
cell death -0.001 0.016 -9999 0 -0.27 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.017 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.014 0.039 -9999 0 -0.86 1 1
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.027 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.039 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0 0 -9999 0 -10000 0 0
MAPK9 0.011 0 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.003 0.067 -9999 0 -0.68 5 5
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.011 0 -9999 0 -10000 0 0
Gs family/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.016 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
CRH -0.005 0.085 -9999 0 -0.86 5 5
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0.019 -9999 0 -0.42 1 1
MAPK11 0.011 0.018 -9999 0 -0.4 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.023 -9999 0 -0.52 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.009 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.002 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 0 0.12 -9999 0 -0.86 9 9
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.014 0.026 -9999 0 -0.57 1 1
mol:PI-4-5-P2 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.021 -9999 0 -0.47 1 1
mol:Choline -0.001 0.017 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.017 -9999 0 -0.39 1 1
ARF1/GDP -0.001 0.021 -9999 0 -0.47 1 1
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.018 -9999 0 -0.42 1 1
ARFIP2 0 0.003 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.035 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.006 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.011 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.006 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
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 0.043 0.034 -9999 0 -10000 0 0
PLD2 -0.001 0.017 -9999 0 -0.38 1 1
ARF-GAP1/v-SNARE 0.014 0.026 -9999 0 -0.57 1 1
PIP5K1A -0.001 0.017 -9999 0 -0.39 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.009 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.017 -9999 0 -0.38 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.026 -9999 0 -0.57 1 1
GOSR2 0 0.007 -9999 0 -10000 0 0
USO1 0 0.007 -9999 0 -10000 0 0
GBF1 0 0.007 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.01 0.075 -9999 0 -0.58 9 9
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 518 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MW.A4EC TCGA.MM.A564 TCGA.GK.A6C7 TCGA.G6.A5PC
109_MAP3K5 0.074 0.074 0.074 -0.13
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 -3e-15 -0.75 -0.75 0
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR -0.43 -0.43 -0.43 -0.43
30_TGFB1/TGF beta receptor Type II 0.015 0.021 0.015 0.015
84_STAT5B -0.031 -0.14 -0.031 -0.26
84_STAT5A -0.031 -0.14 -0.031 -0.26
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/8100468/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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