PARADIGM pathway analysis of mRNASeq expression data
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C12J69NQ
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/C12J69NQ
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 34 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
Signaling events mediated by the Hedgehog family 166
Angiopoietin receptor Tie2-mediated signaling 157
Aurora B signaling 132
FOXM1 transcription factor network 109
Aurora C signaling 100
Endothelins 77
Glypican 2 network 61
TCGA08_retinoblastoma 60
amb2 Integrin signaling 59
Fc-epsilon receptor I signaling in mast cells 52
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 489 . 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 ( 489 ).

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
Signaling events mediated by the Hedgehog family 0.3395 166 8679 52 -0.65 0.35 1000 -1000 -0.093 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3211 157 13894 88 -0.77 0.06 1000 -1000 -0.11 -1000
Aurora B signaling 0.2699 132 8844 67 -0.62 0.005 1000 -1000 -0.08 -1000
FOXM1 transcription factor network 0.2229 109 5577 51 -0.71 0.002 1000 -1000 -0.21 -1000
Aurora C signaling 0.2045 100 704 7 -0.41 0 1000 -1000 -0.045 -1000
Endothelins 0.1575 77 7413 96 -0.45 0.038 1000 -1000 -0.1 -1000
Glypican 2 network 0.1247 61 245 4 -0.085 -0.07 1000 -1000 -0.044 -1000
TCGA08_retinoblastoma 0.1227 60 480 8 -0.28 0.085 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.1207 59 4845 82 -0.68 0 1000 -1000 -0.099 -1000
Fc-epsilon receptor I signaling in mast cells 0.1063 52 5047 97 -0.25 0.033 1000 -1000 -0.11 -1000
Thromboxane A2 receptor signaling 0.1002 49 5169 105 -0.18 0.039 1000 -1000 -0.082 -1000
IL4-mediated signaling events 0.1002 49 4500 91 -0.8 0.44 1000 -1000 -0.19 -1000
Glucocorticoid receptor regulatory network 0.0941 46 5251 114 -0.56 0.37 1000 -1000 -0.093 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0941 46 2423 52 -0.38 0.057 1000 -1000 -0.078 -1000
Signaling events regulated by Ret tyrosine kinase 0.0920 45 3690 82 -0.2 0 1000 -1000 -0.1 -1000
PLK1 signaling events 0.0859 42 3587 85 -0.36 0.071 1000 -1000 -0.063 -1000
Visual signal transduction: Cones 0.0798 39 1507 38 -0.28 0.009 1000 -1000 -0.072 -1000
BMP receptor signaling 0.0798 39 3202 81 -0.39 0.033 1000 -1000 -0.1 -1000
Glypican 1 network 0.0757 37 1799 48 -0.22 0.03 1000 -1000 -0.057 -1000
Nectin adhesion pathway 0.0757 37 2343 63 -0.28 0 1000 -1000 -0.087 -1000
Arf6 signaling events 0.0736 36 2278 62 -0.3 0.015 1000 -1000 -0.073 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0736 36 2814 78 -0.12 0.035 1000 -1000 -0.1 -1000
Signaling mediated by p38-alpha and p38-beta 0.0695 34 1504 44 -0.13 0 1000 -1000 -0.064 -1000
Nongenotropic Androgen signaling 0.0695 34 1780 52 -0.15 0.046 1000 -1000 -0.071 -1000
TCGA08_p53 0.0675 33 234 7 -0.19 0.097 1000 -1000 -0.025 -1000
HIF-1-alpha transcription factor network 0.0634 31 2416 76 -0.44 0.016 1000 -1000 -0.2 -1000
Integrins in angiogenesis 0.0634 31 2615 84 -0.46 0.002 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.0573 28 1319 46 -0.78 0.073 1000 -1000 -0.13 -1000
Canonical Wnt signaling pathway 0.0552 27 1398 51 -0.47 0.16 1000 -1000 -0.077 -1000
LPA4-mediated signaling events 0.0532 26 314 12 -0.14 0.017 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 0.0532 26 2047 76 -0.4 0.029 1000 -1000 -0.06 -1000
Syndecan-3-mediated signaling events 0.0532 26 914 35 -0.34 0 1000 -1000 -0.084 -1000
IL23-mediated signaling events 0.0532 26 1593 60 -0.24 0.018 1000 -1000 -0.19 -1000
IL6-mediated signaling events 0.0511 25 1931 75 -0.47 0.05 1000 -1000 -0.11 -1000
Presenilin action in Notch and Wnt signaling 0.0491 24 1522 61 -0.47 0.013 1000 -1000 -0.084 -1000
Reelin signaling pathway 0.0491 24 1398 56 -0.13 0.003 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0491 24 1639 68 -0.23 0.015 1000 -1000 -0.18 -1000
ErbB4 signaling events 0.0470 23 1606 69 -0.39 0.2 1000 -1000 -0.098 -1000
Regulation of Androgen receptor activity 0.0450 22 1541 70 -0.42 0.018 1000 -1000 -0.085 -1000
Syndecan-1-mediated signaling events 0.0429 21 746 34 -0.35 0 1000 -1000 -0.075 -1000
Aurora A signaling 0.0429 21 1295 60 -0.49 0.029 1000 -1000 -0.064 -1000
Calcium signaling in the CD4+ TCR pathway 0.0429 21 669 31 -0.21 0.012 1000 -1000 -0.15 -1000
Visual signal transduction: Rods 0.0429 21 1117 52 -0.18 0 1000 -1000 -0.098 -1000
IL12-mediated signaling events 0.0409 20 1777 87 -0.15 0.017 1000 -1000 -0.15 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0409 20 2593 125 -0.21 0 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0409 20 661 33 -0.27 0 1000 -1000 -0.073 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0389 19 1046 54 -0.15 0.02 1000 -1000 -0.11 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0389 19 2299 120 -0.27 0.13 1000 -1000 -0.1 -1000
Osteopontin-mediated events 0.0368 18 697 38 -0.3 0 1000 -1000 -0.13 -1000
Wnt signaling 0.0368 18 127 7 -0.095 0 1000 -1000 -0.061 -1000
Plasma membrane estrogen receptor signaling 0.0368 18 1559 86 -0.18 0.032 1000 -1000 -0.097 -1000
HIF-2-alpha transcription factor network 0.0348 17 773 43 -0.37 0.2 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0327 16 1520 93 -0.063 0.036 1000 -1000 -0.1 -1000
p75(NTR)-mediated signaling 0.0307 15 1931 125 -0.34 0 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.0307 15 665 44 -0.21 0.014 1000 -1000 -0.081 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0286 14 1207 85 -0.15 0.01 1000 -1000 -0.089 -1000
Ephrin A reverse signaling 0.0266 13 91 7 -0.023 0.003 1000 -1000 -0.043 -1000
EGFR-dependent Endothelin signaling events 0.0245 12 264 21 -0.063 0 1000 -1000 -0.085 -1000
Caspase cascade in apoptosis 0.0225 11 861 74 -0.069 0.035 1000 -1000 -0.068 -1000
Regulation of nuclear SMAD2/3 signaling 0.0225 11 1516 136 -0.33 0.093 1000 -1000 -0.095 -1000
JNK signaling in the CD4+ TCR pathway 0.0225 11 194 17 -0.039 0.023 1000 -1000 -0.073 -1000
FAS signaling pathway (CD95) 0.0225 11 552 47 -0.2 0.009 1000 -1000 -0.056 -1000
Noncanonical Wnt signaling pathway 0.0204 10 269 26 -0.1 0 1000 -1000 -0.1 -1000
Syndecan-2-mediated signaling events 0.0204 10 702 69 -0.17 0.033 1000 -1000 -0.075 -1000
Effects of Botulinum toxin 0.0204 10 271 26 -0.074 0.005 1000 -1000 -0.072 -1000
Ras signaling in the CD4+ TCR pathway 0.0204 10 184 17 -0.054 0.008 1000 -1000 -0.075 -1000
S1P1 pathway 0.0184 9 359 36 -0.061 0.01 1000 -1000 -0.093 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0184 9 702 74 -0.17 0.068 1000 -1000 -0.096 -1000
BCR signaling pathway 0.0184 9 946 99 -0.11 0.039 1000 -1000 -0.11 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0164 8 305 34 -0.028 0 1000 -1000 -0.074 -1000
Hedgehog signaling events mediated by Gli proteins 0.0164 8 576 65 -0.6 0.043 1000 -1000 -0.087 -1000
IL2 signaling events mediated by STAT5 0.0164 8 177 22 -0.15 0.059 1000 -1000 -0.066 -1000
Syndecan-4-mediated signaling events 0.0164 8 595 67 -0.17 0.009 1000 -1000 -0.11 -1000
S1P4 pathway 0.0164 8 218 25 -0.066 0.002 1000 -1000 -0.067 -1000
Signaling events mediated by PTP1B 0.0143 7 535 76 -0.1 0.033 1000 -1000 -0.094 -1000
Signaling events mediated by HDAC Class III 0.0143 7 293 40 -0.15 0.051 1000 -1000 -0.051 -1000
TRAIL signaling pathway 0.0143 7 351 48 -0.097 0.046 1000 -1000 -0.079 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0123 6 187 28 -0.18 0.02 1000 -1000 -0.066 -1000
Cellular roles of Anthrax toxin 0.0123 6 257 39 -0.09 0.017 1000 -1000 -0.034 -1000
Retinoic acid receptors-mediated signaling 0.0123 6 369 58 -0.22 0.034 1000 -1000 -0.094 -1000
Regulation of p38-alpha and p38-beta 0.0123 6 326 54 -0.095 0.037 1000 -1000 -0.086 -1000
IL27-mediated signaling events 0.0123 6 307 51 -0.12 0.011 1000 -1000 -0.092 -1000
S1P3 pathway 0.0123 6 257 42 -0.18 0.042 1000 -1000 -0.067 -1000
Signaling events mediated by PRL 0.0123 6 209 34 -0.13 0.029 1000 -1000 -0.069 -1000
BARD1 signaling events 0.0102 5 288 57 -0.13 0.022 1000 -1000 -0.084 -1000
IL1-mediated signaling events 0.0102 5 328 62 -0.058 0.042 1000 -1000 -0.12 -1000
IL2 signaling events mediated by PI3K 0.0102 5 300 58 -0.22 0.073 1000 -1000 -0.098 -1000
LPA receptor mediated events 0.0102 5 597 102 -0.1 0.034 1000 -1000 -0.1 -1000
IGF1 pathway 0.0102 5 291 57 -0.02 0.04 1000 -1000 -0.13 -1000
Insulin Pathway 0.0102 5 442 74 -0.1 0.031 1000 -1000 -0.11 -1000
ErbB2/ErbB3 signaling events 0.0082 4 287 65 -0.077 0.054 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class II 0.0082 4 328 75 -0.079 0 1000 -1000 -0.073 -1000
Ephrin B reverse signaling 0.0082 4 212 48 -0.07 0.04 1000 -1000 -0.079 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0082 4 362 83 -0.07 0.049 1000 -1000 -0.093 -1000
Signaling events mediated by HDAC Class I 0.0082 4 442 104 -0.079 0.041 1000 -1000 -0.079 -1000
Arf6 trafficking events 0.0082 4 301 71 -0.087 0.032 1000 -1000 -0.077 -1000
a4b1 and a4b7 Integrin signaling 0.0061 3 17 5 -0.008 -0.002 1000 -1000 -0.048 -1000
IFN-gamma pathway 0.0061 3 250 68 -0.068 0.065 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0061 3 313 85 -0.07 0.032 1000 -1000 -0.11 -1000
TCGA08_rtk_signaling 0.0061 3 79 26 -0.066 0.038 1000 -1000 -0.038 -1000
Class I PI3K signaling events 0.0061 3 270 73 -0.05 0.026 1000 -1000 -0.084 -1000
Regulation of Telomerase 0.0061 3 405 102 -0.12 0.025 1000 -1000 -0.11 -1000
VEGFR1 specific signals 0.0061 3 212 56 -0.21 0.044 1000 -1000 -0.087 -1000
p38 MAPK signaling pathway 0.0061 3 159 44 -0.068 0.034 1000 -1000 -0.08 -1000
Circadian rhythm pathway 0.0041 2 56 22 -0.03 0.038 1000 -1000 -0.07 -1000
Ceramide signaling pathway 0.0041 2 182 76 -0.025 0.04 1000 -1000 -0.078 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0041 2 90 37 -0.01 0.027 1000 -1000 -0.09 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0041 2 116 45 -0.027 0.061 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0041 2 216 97 -0.04 0.054 1000 -1000 -0.1 -1000
E-cadherin signaling in keratinocytes 0.0041 2 91 43 -0.022 0.042 1000 -1000 -0.087 -1000
Class IB PI3K non-lipid kinase events 0.0041 2 6 3 -0.003 -1000 1000 -1000 -0.034 -1000
PLK2 and PLK4 events 0.0020 1 4 3 -0.002 0.018 1000 -1000 -0.028 -1000
EPO signaling pathway 0.0020 1 62 55 -0.008 0.065 1000 -1000 -0.11 -1000
Insulin-mediated glucose transport 0.0020 1 52 32 -0.057 0.034 1000 -1000 -0.066 -1000
S1P5 pathway 0.0020 1 26 17 -0.01 0.006 1000 -1000 -0.066 -1000
FoxO family signaling 0.0020 1 95 64 -0.089 0.08 1000 -1000 -0.1 -1000
Signaling mediated by p38-gamma and p38-delta 0.0020 1 15 15 -0.001 0.027 1000 -1000 -0.06 -1000
Paxillin-dependent events mediated by a4b1 0.0020 1 65 36 -0.008 0.02 1000 -1000 -0.074 -1000
Rapid glucocorticoid signaling 0.0020 1 35 20 -0.008 0.007 1000 -1000 -0.043 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 0 23 0 0.036 1000 -1000 -0.075 -1000
Canonical NF-kappaB pathway 0.0000 0 33 39 -0.019 0.071 1000 -1000 -0.1 -1000
Arf6 downstream pathway 0.0000 0 19 43 -0.024 0.025 1000 -1000 -0.046 -1000
mTOR signaling pathway 0.0000 0 7 53 -0.003 0.03 1000 -1000 -0.072 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 57 68 -0.057 0.043 1000 -1000 -0.075 -1000
ceramide signaling pathway 0.0000 0 45 49 -0.013 0.043 1000 -1000 -0.065 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 -0.002 0.03 1000 -1000 -0.085 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 50 76 -0.023 0.053 1000 -1000 -0.095 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 -0.001 0.025 1000 -1000 -0.066 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0 1000 -1000 -0.047 -1000
Arf1 pathway 0.0000 0 48 54 -0.023 0.022 1000 -1000 -0.05 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 -0.001 0 1000 -1000 -0.079 -1000
Total NA 2590 159884 7203 -25 -990 131000 -131000 -11 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.43 0.29 -10000 0 -0.69 228 228
IHH -0.47 0.38 -10000 0 -0.81 273 273
SHH Np/Cholesterol/GAS1 -0.07 0.16 -10000 0 -0.46 71 71
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.069 0.16 0.45 71 -10000 0 71
SMO/beta Arrestin2 -0.36 0.25 -10000 0 -0.59 236 236
SMO -0.38 0.27 -10000 0 -0.6 278 278
AKT1 -0.15 0.11 -10000 0 -0.34 1 1
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.005 0.06 -10000 0 -0.66 4 4
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.37 0.27 -10000 0 -0.59 278 278
STIL -0.33 0.25 -10000 0 -0.53 254 254
DHH N/PTCH2 -0.045 0.15 -10000 0 -0.56 39 39
DHH N/PTCH1 -0.36 0.24 -10000 0 -0.57 241 241
PIK3CA 0 0 -10000 0 -10000 0 0
DHH -0.051 0.19 -10000 0 -0.74 34 34
PTHLH -0.58 0.36 -10000 0 -0.92 228 228
determination of left/right symmetry -0.37 0.27 -10000 0 -0.59 278 278
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.57 0.35 -10000 0 -0.9 228 228
IHH N/Hhip -0.65 0.38 -10000 0 -0.82 389 389
DHH N/Hhip -0.41 0.29 -10000 0 -0.59 335 335
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.37 0.27 -10000 0 -0.59 278 278
pancreas development -0.49 0.35 -10000 0 -0.74 327 327
HHAT 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.012 0.094 -10000 0 -0.74 8 8
somite specification -0.37 0.27 -10000 0 -0.59 278 278
SHH Np/Cholesterol/PTCH1 -0.35 0.25 -10000 0 -0.55 256 256
SHH Np/Cholesterol/PTCH2 -0.068 0.16 -10000 0 -0.44 69 69
SHH Np/Cholesterol/Megalin -0.29 0.27 -10000 0 -0.5 280 280
SHH -0.064 0.2 -10000 0 -0.54 72 72
catabolic process -0.37 0.25 -10000 0 -0.57 282 282
SMO/Vitamin D3 -0.37 0.26 -10000 0 -0.59 251 251
SHH Np/Cholesterol/Hhip -0.36 0.26 -10000 0 -0.5 345 345
LRP2 -0.38 0.37 -10000 0 -0.74 251 251
receptor-mediated endocytosis -0.5 0.31 -10000 0 -0.72 285 285
SHH Np/Cholesterol/BOC -0.066 0.16 -10000 0 -0.45 66 66
SHH Np/Cholesterol/CDO -0.067 0.16 -10000 0 -0.44 70 70
mesenchymal cell differentiation 0.35 0.26 0.5 345 -10000 0 345
mol:Vitamin D3 -0.35 0.26 -10000 0 -0.56 252 252
IHH N/PTCH2 -0.31 0.27 -10000 0 -0.54 273 273
CDON -0.008 0.074 -10000 0 -0.74 5 5
IHH N/PTCH1 -0.38 0.26 -10000 0 -0.58 282 282
Megalin/LRPAP1 -0.29 0.28 -10000 0 -0.56 251 251
PTCH2 -0.008 0.076 -10000 0 -0.68 6 6
SHH Np/Cholesterol -0.064 0.15 -10000 0 -0.43 72 72
PTCH1 -0.37 0.25 -10000 0 -0.57 282 282
HHIP -0.49 0.35 -10000 0 -0.74 327 327
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.53 0.53 -10000 0 -1 266 266
NCK1/PAK1/Dok-R -0.25 0.23 -10000 0 -0.45 266 266
NCK1/Dok-R -0.69 0.66 -10000 0 -1.3 266 266
PIK3CA 0.007 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.06 0.1 0.25 105 -10000 0 105
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.002 0.004 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.053 0.13 -10000 0 -0.57 9 9
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.61 0.58 -10000 0 -1.1 266 266
FN1 -0.017 0.11 -10000 0 -0.74 11 11
PLD2 -0.68 0.71 -10000 0 -1.3 266 266
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.047 0.18 -10000 0 -0.73 31 31
ELK1 -0.58 0.61 -10000 0 -1.1 266 266
GRB7 -0.005 0.052 -10000 0 -0.57 4 4
PAK1 -0.001 0.026 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.65 0.62 -10000 0 -1.2 266 266
CDKN1A -0.36 0.35 -10000 0 -0.68 254 254
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.69 0.66 -10000 0 -1.3 266 266
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.36 0.38 -10000 0 -0.71 266 266
PLG -0.68 0.71 -10000 0 -1.3 266 266
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.51 0.48 -10000 0 -0.95 266 266
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 0.002 0.004 -10000 0 -10000 0 0
ANGPT2 -0.34 0.34 -10000 0 -0.75 171 171
BMX -0.75 0.75 -10000 0 -1.4 266 266
ANGPT1 -0.37 0.62 -10000 0 -1.4 126 126
tube development -0.42 0.4 -10000 0 -0.78 264 264
ANGPT4 -0.33 0.37 -10000 0 -0.74 220 220
response to hypoxia -0.035 0.036 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.75 0.72 -10000 0 -1.4 266 266
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.017 0.13 -10000 0 -0.74 15 15
STAT5A (dimer) -0.48 0.47 -10000 0 -0.91 262 262
mol:L-citrulline -0.36 0.38 -10000 0 -0.71 266 266
AGTR1 -0.29 0.37 -10000 0 -0.74 199 199
MAPK14 -0.7 0.7 -10000 0 -1.3 266 266
Tie2/SHP2 -0.6 0.62 -10000 0 -1.2 232 232
TEK -0.68 0.69 -10000 0 -1.4 232 232
RPS6KB1 -0.5 0.51 -10000 0 -0.96 266 266
Angiotensin II/AT1 -0.23 0.28 -10000 0 -0.56 199 199
Tie2/Ang1/GRB2 -0.73 0.72 -10000 0 -1.3 266 266
MAPK3 -0.6 0.63 -10000 0 -1.2 266 266
MAPK1 -0.6 0.63 -10000 0 -1.2 266 266
Tie2/Ang1/GRB7 -0.73 0.72 -10000 0 -1.3 266 266
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.68 0.71 -10000 0 -1.3 266 266
PI3K -0.63 0.63 -10000 0 -1.2 266 266
FES -0.7 0.7 -10000 0 -1.3 266 266
Crk/Dok-R -0.69 0.66 -10000 0 -1.3 266 266
Tie2/Ang1/ABIN2 -0.73 0.72 -10000 0 -1.3 266 266
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.46 0.46 -10000 0 -0.88 266 266
STAT5A 0 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.5 0.51 -10000 0 -0.96 266 266
Tie2/Ang2 -0.62 0.59 -10000 0 -1.1 264 264
Tie2/Ang1 -0.77 0.82 -10000 0 -1.5 266 266
FOXO1 -0.46 0.47 -10000 0 -0.89 266 266
ELF1 -0.034 0.052 -10000 0 -10000 0 0
ELF2 -0.69 0.72 -10000 0 -1.3 266 266
mol:Choline -0.63 0.66 -10000 0 -1.2 266 266
cell migration -0.13 0.12 -10000 0 -0.26 67 67
FYN -0.49 0.47 -10000 0 -0.91 264 264
DOK2 -0.066 0.21 -10000 0 -0.74 44 44
negative regulation of cell cycle -0.32 0.32 -10000 0 -0.61 254 254
ETS1 -0.063 0.16 -10000 0 -0.83 13 13
PXN -0.39 0.41 -10000 0 -0.77 266 266
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.42 0.44 -10000 0 -0.82 266 266
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.062 0.16 -10000 0 -0.81 13 13
MAPKKK cascade -0.63 0.66 -10000 0 -1.2 266 266
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.72 0.73 -10000 0 -1.4 266 266
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.32 0.34 -10000 0 -0.63 266 266
mol:Phosphatidic acid -0.63 0.66 -10000 0 -1.2 266 266
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.36 0.38 -10000 0 -0.71 266 266
Rac1/GTP -0.48 0.44 -10000 0 -0.88 266 266
MMP2 -0.68 0.71 -10000 0 -1.3 266 266
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.18 0.14 -9999 0 -0.4 77 77
STMN1 -0.29 0.19 -9999 0 -0.41 351 351
Aurora B/RasGAP/Survivin -0.5 0.22 -9999 0 -0.62 357 357
Chromosomal passenger complex/Cul3 protein complex -0.2 0.1 -9999 0 -0.33 128 128
BIRC5 -0.49 0.21 -9999 0 -0.58 415 415
DES -0.56 0.38 -9999 0 -0.83 315 315
Aurora C/Aurora B/INCENP -0.22 0.15 -9999 0 -0.32 218 218
Aurora B/TACC1 -0.24 0.16 -9999 0 -0.34 351 351
Aurora B/PP2A -0.29 0.19 -9999 0 -0.4 351 351
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.059 0.044 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.003 -9999 0 -10000 0 0
NDC80 -0.41 0.29 -9999 0 -0.55 367 367
Cul3 protein complex -0.011 0.065 -9999 0 -0.48 3 3
KIF2C -0.17 0.086 -9999 0 -0.24 252 252
PEBP1 -0.002 0.048 -9999 0 -0.76 2 2
KIF20A -0.3 0.29 -9999 0 -0.58 253 253
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.29 0.19 -9999 0 -0.4 351 351
SEPT1 -0.001 0.026 -9999 0 -0.57 1 1
SMC2 0 0 -9999 0 -10000 0 0
SMC4 0 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.1 0.066 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.15 0.1 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.57 351 351
AURKC -0.003 0.042 -9999 0 -0.66 2 2
CDCA8 -0.16 0.26 -9999 0 -0.58 134 134
cytokinesis -0.32 0.16 -9999 0 -0.49 174 174
Aurora B/Septin1 -0.3 0.16 -9999 0 -0.47 167 167
AURKA -0.016 0.12 -9999 0 -0.58 22 22
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.014 0.089 -9999 0 -0.57 12 12
BUB1 -0.049 0.17 -9999 0 -0.58 45 45
hSgo1/Aurora B/Survivin -0.62 0.31 -9999 0 -0.79 356 356
EVI5 0.005 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.18 -9999 0 -0.49 151 151
SGOL1 -0.3 0.29 -9999 0 -0.57 255 255
CENPA -0.24 0.12 -9999 0 -0.31 340 340
NCAPG -0.1 0.22 -9999 0 -0.57 88 88
Aurora B/HC8 Proteasome -0.29 0.19 -9999 0 -0.4 351 351
NCAPD2 -0.001 0.026 -9999 0 -0.57 1 1
Aurora B/PP1-gamma -0.29 0.19 -9999 0 -0.4 351 351
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.29 0.29 -9999 0 -0.57 249 249
NPM1 -0.13 0.083 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.005 0.058 -9999 0 -0.74 3 3
mitotic prometaphase -0.012 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.29 0.19 -9999 0 -0.4 351 351
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.2 -9999 0 -0.51 179 179
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.13 0.083 -9999 0 -10000 0 0
MYLK -0.15 0.1 -9999 0 -0.21 341 341
KIF23 -0.12 0.23 -9999 0 -0.58 98 98
VIM -0.3 0.21 -9999 0 -0.42 351 351
RACGAP1 0.001 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.13 0.083 -9999 0 -10000 0 0
Chromosomal passenger complex -0.27 0.14 -9999 0 -0.35 335 335
Chromosomal passenger complex/EVI5 -0.49 0.25 -9999 0 -0.63 343 343
TACC1 -0.003 0.047 -9999 0 -0.74 2 2
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.58 0.43 -9999 0 -1.1 109 109
PLK1 -0.19 0.2 -9999 0 -10000 0 0
BIRC5 -0.32 0.16 -9999 0 -10000 0 0
HSPA1B -0.58 0.43 -9999 0 -1 135 135
MAP2K1 -0.012 0.023 -9999 0 -10000 0 0
BRCA2 -0.58 0.43 -9999 0 -1 135 135
FOXM1 -0.7 0.55 -9999 0 -1.2 180 180
XRCC1 -0.58 0.43 -9999 0 -1.1 109 109
FOXM1B/p19 -0.6 0.43 -9999 0 -1 169 169
Cyclin D1/CDK4 -0.54 0.4 -9999 0 -0.99 114 114
CDC2 -0.61 0.45 -9999 0 -1.1 172 172
TGFA -0.52 0.38 -9999 0 -0.97 91 91
SKP2 -0.58 0.43 -9999 0 -1 136 136
CCNE1 -0.13 0.24 -9999 0 -0.58 108 108
CKS1B -0.58 0.43 -9999 0 -1 134 134
RB1 -0.26 0.15 -9999 0 -0.48 23 23
FOXM1C/SP1 -0.65 0.45 -9999 0 -1.1 180 180
AURKB -0.28 0.19 -9999 0 -10000 0 0
CENPF -0.64 0.47 -9999 0 -1.1 204 204
CDK4 0.002 0.028 -9999 0 -0.59 1 1
MYC -0.51 0.38 -9999 0 -0.91 122 122
CHEK2 -0.012 0.023 -9999 0 -10000 0 0
ONECUT1 -0.57 0.42 -9999 0 -1 145 145
CDKN2A -0.26 0.29 -9999 0 -0.56 229 229
LAMA4 -0.58 0.43 -9999 0 -1 134 134
FOXM1B/HNF6 -0.65 0.5 -9999 0 -1.2 145 145
FOS -0.63 0.5 -9999 0 -1.2 147 147
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.58 0.43 -9999 0 -1 136 136
response to radiation -0.024 0.023 -9999 0 -10000 0 0
CENPB -0.58 0.43 -9999 0 -1 134 134
CENPA -0.71 0.46 -9999 0 -1.1 219 219
NEK2 -0.69 0.48 -9999 0 -1.1 202 202
HIST1H2BA -0.58 0.43 -9999 0 -1 134 134
CCNA2 -0.15 0.26 -9999 0 -0.59 126 126
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.66 0.5 -9999 0 -1.2 146 146
CCNB2 -0.66 0.48 -9999 0 -1.1 214 214
CCNB1 -0.62 0.46 -9999 0 -1.1 139 139
ETV5 -0.58 0.44 -9999 0 -1.1 134 134
ESR1 -0.6 0.45 -9999 0 -1.1 139 139
CCND1 -0.55 0.41 -9999 0 -1 117 117
GSK3A -0.004 0.019 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.17 0.24 -9999 0 -0.44 193 193
CDK2 0.002 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.64 0.42 -9999 0 -1 199 199
GAS1 -0.58 0.44 -9999 0 -1.1 138 138
MMP2 -0.58 0.43 -9999 0 -1 135 135
RB1/FOXM1C -0.58 0.44 -9999 0 -1 150 150
CREBBP 0 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.23 0.14 -9999 0 -0.32 351 351
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.04 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.57 351 351
AURKC -0.003 0.042 -9999 0 -0.66 2 2
Endothelins

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
AKT1 -0.029 0.23 -9999 0 -0.57 52 52
PTK2B 0.002 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.081 0.29 -9999 0 -0.87 39 39
EDN1 -0.042 0.25 -9999 0 -0.78 42 42
EDN3 -0.089 0.24 -9999 0 -0.7 62 62
EDN2 -0.085 0.21 -9999 0 -0.59 71 71
HRAS/GDP -0.18 0.3 -9999 0 -0.64 124 124
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.054 0.2 -9999 0 -0.48 61 61
ADCY4 -0.078 0.22 -9999 0 -0.65 42 42
ADCY5 -0.09 0.23 -9999 0 -0.55 74 74
ADCY6 -0.054 0.19 -9999 0 -0.57 36 36
ADCY7 -0.053 0.18 -9999 0 -0.59 31 31
ADCY1 -0.054 0.18 -9999 0 -0.56 35 35
ADCY2 -0.085 0.21 -9999 0 -0.59 46 46
ADCY3 -0.053 0.18 -9999 0 -0.58 33 33
ADCY8 -0.18 0.24 -9999 0 -0.58 73 73
ADCY9 -0.054 0.18 -9999 0 -0.58 34 34
arachidonic acid secretion -0.15 0.27 -9999 0 -0.6 92 92
ETB receptor/Endothelin-1/Gq/GTP -0.32 0.35 -9999 0 -0.7 176 176
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
HRAS 0.002 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.038 0.26 -9999 0 -0.54 52 52
ETA receptor/Endothelin-1/Gs/GTP 0.031 0.25 -9999 0 -0.52 55 55
mol:GTP 0 0.004 -9999 0 -10000 0 0
COL3A1 -0.045 0.25 -9999 0 -0.7 31 31
EDNRB -0.45 0.36 -9999 0 -0.74 301 301
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.044 0.27 -9999 0 -0.78 37 37
CYSLTR1 -0.092 0.36 -9999 0 -0.87 71 71
SLC9A1 -0.007 0.12 -9999 0 -0.36 19 19
mol:GDP -0.21 0.33 -9999 0 -0.7 127 127
SLC9A3 -0.37 0.39 -9999 0 -0.68 252 252
RAF1 -0.21 0.32 -9999 0 -0.66 136 136
JUN -0.058 0.23 -9999 0 -0.66 30 30
JAK2 -0.029 0.23 -9999 0 -0.57 52 52
mol:IP3 -0.21 0.3 -9999 0 -0.67 129 129
ETA receptor/Endothelin-1 0.018 0.32 -9999 0 -0.66 52 52
PLCB1 0.003 0.005 -9999 0 -10000 0 0
PLCB2 -0.005 0.095 -9999 0 -0.74 8 8
ETA receptor/Endothelin-3 -0.056 0.21 -9999 0 -0.54 67 67
FOS -0.2 0.36 -9999 0 -0.86 85 85
Gai/GDP -0.007 0.067 -9999 0 -0.95 1 1
CRK 0.002 0.004 -9999 0 -10000 0 0
mol:Ca ++ -0.25 0.36 -9999 0 -0.76 139 139
BCAR1 0.007 0.005 -9999 0 -10000 0 0
PRKCB1 -0.2 0.29 -9999 0 -0.64 128 128
GNAQ 0.008 0.034 -9999 0 -0.74 1 1
GNAZ -0.009 0.081 -9999 0 -0.74 6 6
GNAL -0.006 0.067 -9999 0 -0.74 4 4
Gs family/GDP -0.21 0.27 -9999 0 -0.62 125 125
ETA receptor/Endothelin-1/Gq/GTP -0.066 0.23 -9999 0 -0.54 64 64
MAPK14 -0.24 0.29 -9999 0 -0.66 128 128
TRPC6 -0.089 0.31 -9999 0 -0.96 38 38
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.033 -9999 0 -0.74 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.26 0.3 -9999 0 -0.66 144 144
ETB receptor/Endothelin-2 -0.4 0.29 -9999 0 -0.58 332 332
ETB receptor/Endothelin-3 -0.4 0.3 -9999 0 -0.6 327 327
ETB receptor/Endothelin-1 -0.38 0.34 -9999 0 -0.61 314 314
MAPK3 -0.22 0.36 -9999 0 -0.79 109 109
MAPK1 -0.22 0.36 -9999 0 -0.79 109 109
Rac1/GDP -0.18 0.3 -9999 0 -0.64 123 123
cAMP biosynthetic process -0.077 0.21 -9999 0 -0.59 44 44
MAPK8 -0.08 0.27 -9999 0 -0.62 67 67
SRC 0 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.17 -9999 0 -0.49 47 47
p130Cas/CRK/Src/PYK2 -0.19 0.32 -9999 0 -0.68 123 123
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.18 0.3 -9999 0 -0.64 124 124
COL1A2 -0.26 0.31 -9999 0 -0.75 94 94
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.049 0.19 -9999 0 -0.46 74 74
mol:DAG -0.21 0.31 -9999 0 -0.67 129 129
MAP2K2 -0.2 0.32 -9999 0 -0.68 123 123
MAP2K1 -0.2 0.32 -9999 0 -0.65 140 140
EDNRA 0.015 0.14 -9999 0 -0.66 9 9
positive regulation of muscle contraction -0.031 0.2 -9999 0 -0.6 29 29
Gq family/GDP -0.2 0.3 -9999 0 -0.7 116 116
HRAS/GTP -0.22 0.32 -9999 0 -0.69 128 128
PRKCH -0.2 0.29 -9999 0 -0.66 118 118
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.2 0.29 -9999 0 -0.66 119 119
PRKCB -0.22 0.32 -9999 0 -0.71 125 125
PRKCE -0.2 0.29 -9999 0 -0.66 116 116
PRKCD -0.2 0.29 -9999 0 -0.65 120 120
PRKCG -0.22 0.3 -9999 0 -0.68 125 125
regulation of vascular smooth muscle contraction -0.24 0.42 -9999 0 -1 86 86
PRKCQ -0.23 0.34 -9999 0 -0.73 132 132
PLA2G4A -0.16 0.3 -9999 0 -0.66 92 92
GNA14 -0.17 0.32 -9999 0 -0.74 117 117
GNA15 0.008 0.005 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.005 -9999 0 -10000 0 0
Rac1/GTP 0.038 0.26 -9999 0 -0.58 39 39
MMP1 -0.23 0.24 -9999 0 -0.44 254 254
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.012 0.081 -9999 0 -0.57 10 10
GPC2 -0.085 0.2 -9999 0 -0.57 73 73
GPC2/Midkine -0.07 0.16 -9999 0 -0.42 81 81
neuron projection morphogenesis -0.07 0.16 -9999 0 -0.42 81 81
TCGA08_retinoblastoma

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
CDKN2B -0.06 0.2 -10000 0 -0.71 41 41
CDKN2C 0.03 0.032 -10000 0 -10000 0 0
CDKN2A -0.28 0.3 -10000 0 -0.59 229 229
CCND2 0.073 0.081 0.26 42 -10000 0 42
RB1 -0.079 0.084 -10000 0 -0.26 42 42
CDK4 0.085 0.087 0.26 42 -10000 0 42
CDK6 0.081 0.089 0.29 42 -10000 0 42
G1/S progression 0.072 0.091 0.26 42 -10000 0 42
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.062 0.22 -9999 0 -0.72 42 42
alphaM/beta2 Integrin/GPIbA -0.063 0.21 -9999 0 -0.7 43 43
alphaM/beta2 Integrin/proMMP-9 -0.076 0.21 -9999 0 -0.67 44 44
PLAUR 0 0 -9999 0 -10000 0 0
HMGB1 0 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.058 0.2 -9999 0 -0.69 41 41
AGER -0.68 0.2 -9999 0 -0.74 449 449
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG -0.048 0.18 -9999 0 -0.74 32 32
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.48 0.26 -9999 0 -0.52 449 449
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 26 26
CYR61 -0.039 0.17 -9999 0 -0.74 26 26
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.21 0.29 -9999 0 -0.63 115 115
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.32 -9999 0 -0.74 124 124
MYH2 -0.32 0.36 -9999 0 -0.71 173 173
MST1R -0.045 0.18 -9999 0 -0.74 30 30
leukocyte activation during inflammatory response -0.087 0.22 -9999 0 -0.58 65 65
APOB -0.049 0.18 -9999 0 -0.72 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.006 0.067 -9999 0 -0.74 4 4
JAM3 0 0 -9999 0 -10000 0 0
GP1BA -0.007 0.071 -9999 0 -0.71 5 5
alphaM/beta2 Integrin/CTGF -0.075 0.24 -9999 0 -0.73 50 50
alphaM/beta2 Integrin -0.26 0.38 -9999 0 -0.77 119 119
JAM3 homodimer 0 0 -9999 0 -10000 0 0
ICAM2 -0.05 0.18 -9999 0 -0.74 33 33
ICAM1 -0.065 0.21 -9999 0 -0.74 43 43
phagocytosis triggered by activation of immune response cell surface activating receptor -0.24 0.37 -9999 0 -0.74 119 119
cell adhesion -0.062 0.21 -9999 0 -0.7 43 43
NFKB1 -0.46 0.3 -9999 0 -0.92 112 112
THY1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.045 0.14 -9999 0 -0.45 48 48
alphaM/beta2 Integrin/LRP/tPA -0.057 0.19 -9999 0 -0.64 41 41
IL6 -0.49 0.38 -9999 0 -1.1 114 114
ITGB2 -0.031 0.15 -9999 0 -0.74 20 20
elevation of cytosolic calcium ion concentration -0.072 0.2 -9999 0 -0.64 41 41
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.28 -9999 0 -0.63 92 92
JAM2 -0.11 0.26 -9999 0 -0.74 74 74
alphaM/beta2 Integrin/ICAM1 -0.11 0.28 -9999 0 -0.64 84 84
alphaM/beta2 Integrin/uPA/Plg -0.075 0.2 -9999 0 -0.65 41 41
RhoA/GTP -0.3 0.37 -9999 0 -0.86 117 117
positive regulation of phagocytosis -0.18 0.27 -9999 0 -0.74 71 71
Ron/MSP -0.035 0.14 -9999 0 -0.55 31 31
alphaM/beta2 Integrin/uPAR/uPA -0.072 0.2 -9999 0 -0.64 41 41
alphaM/beta2 Integrin/uPAR -0.058 0.2 -9999 0 -0.69 41 41
PLAU -0.035 0.14 -9999 0 -0.57 30 30
PLAT -0.007 0.063 -9999 0 -0.57 6 6
actin filament polymerization -0.3 0.32 -9999 0 -0.66 174 174
MST1 -0.001 0.026 -9999 0 -0.57 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.089 0.22 -9999 0 -0.59 65 65
TNF -0.42 0.28 -9999 0 -0.84 112 112
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.079 0.21 -9999 0 -0.68 44 44
fibrinolysis -0.074 0.2 -9999 0 -0.64 41 41
HCK -0.008 0.074 -9999 0 -0.74 5 5
dendritic cell antigen processing and presentation -0.24 0.37 -9999 0 -0.74 119 119
VTN -0.29 0.36 -9999 0 -0.74 192 192
alphaM/beta2 Integrin/CYR61 -0.082 0.25 -9999 0 -0.72 56 56
LPA -0.021 0.11 -9999 0 -0.57 18 18
LRP1 0 0 -9999 0 -10000 0 0
cell migration -0.073 0.21 -9999 0 -0.66 42 42
FN1 -0.017 0.11 -9999 0 -0.74 11 11
alphaM/beta2 Integrin/Thy1 -0.058 0.2 -9999 0 -0.69 41 41
MPO -0.033 0.15 -9999 0 -0.74 22 22
KNG1 -0.014 0.089 -9999 0 -0.57 12 12
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.26 0.34 -9999 0 -0.79 111 111
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.045 -9999 0 -0.57 3 3
CTGF -0.027 0.14 -9999 0 -0.74 18 18
alphaM/beta2 Integrin/Hck -0.063 0.22 -9999 0 -0.71 43 43
ITGAM -0.061 0.2 -9999 0 -0.74 40 40
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.36 -9999 0 -0.66 139 139
HP -0.23 0.34 -9999 0 -0.74 153 153
leukocyte adhesion -0.44 0.3 -9999 0 -0.8 147 147
SELP -0.19 0.32 -9999 0 -0.74 124 124
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -9999 0 -10000 0 0
LAT2 -0.16 0.25 -9999 0 -0.67 71 71
AP1 -0.19 0.26 -9999 0 -0.64 104 104
mol:PIP3 -0.16 0.29 -9999 0 -0.66 83 83
IKBKB -0.07 0.16 -9999 0 -0.34 75 75
AKT1 -0.17 0.24 -9999 0 -0.67 68 68
IKBKG -0.069 0.16 -9999 0 -0.34 75 75
MS4A2 -0.17 0.31 -9999 0 -0.74 110 110
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.002 -9999 0 -10000 0 0
MAP3K1 -0.099 0.23 -9999 0 -0.54 78 78
mol:Ca2+ -0.11 0.21 -9999 0 -0.46 83 83
LYN 0.005 0.05 -9999 0 -0.77 2 2
CBLB -0.16 0.24 -9999 0 -0.64 70 70
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.057 0.15 -9999 0 -0.44 63 63
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.002 0.033 -9999 0 -0.74 1 1
PLD2 -0.21 0.28 -9999 0 -0.56 149 149
PTPN13 -0.12 0.24 -9999 0 -0.6 71 71
PTPN11 0.005 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.08 0.19 -9999 0 -0.42 71 71
SYK 0.006 0.036 -9999 0 -0.77 1 1
GRB2 0 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.2 0.27 -9999 0 -0.69 84 84
LAT -0.16 0.24 -9999 0 -0.64 70 70
PAK2 -0.12 0.26 -9999 0 -0.61 82 82
NFATC2 -0.18 0.32 -9999 0 -0.94 67 67
HRAS -0.14 0.29 -9999 0 -0.68 84 84
GAB2 -0.02 0.12 -9999 0 -0.74 13 13
PLA2G1B -0.002 0.037 -9999 0 -10000 0 0
Fc epsilon R1 -0.25 0.34 -9999 0 -0.63 196 196
Antigen/IgE/Fc epsilon R1 -0.24 0.32 -9999 0 -0.59 196 196
mol:GDP -0.16 0.31 -9999 0 -0.74 85 85
JUN 0 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0 0.002 -9999 0 -10000 0 0
FOS -0.085 0.24 -9999 0 -0.74 56 56
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.17 0.25 -9999 0 -0.54 117 117
CHUK -0.069 0.16 -9999 0 -0.34 73 73
KLRG1 -0.15 0.23 -9999 0 -0.63 71 71
VAV1 -0.16 0.25 -9999 0 -0.67 71 71
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.16 0.24 -9999 0 -0.64 70 70
negative regulation of mast cell degranulation -0.14 0.22 -9999 0 -0.58 70 70
BTK -0.2 0.33 -9999 0 -0.8 88 88
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.2 0.31 -9999 0 -0.88 68 68
GAB2/PI3K/SHP2 -0.19 0.27 -9999 0 -0.75 68 68
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.17 0.25 -9999 0 -0.69 72 72
RAF1 0.025 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.22 0.32 -9999 0 -0.86 69 69
FCER1G -0.016 0.13 -9999 0 -0.76 14 14
FCER1A -0.22 0.35 -9999 0 -0.75 144 144
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.3 -9999 0 -0.55 196 196
MAPK3 0.033 0.023 -9999 0 -10000 0 0
MAPK1 0.033 0.023 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.021 0.07 -9999 0 -10000 0 0
DUSP1 -0.095 0.25 -9999 0 -0.74 63 63
NF-kappa-B/RelA -0.059 0.075 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.13 0.24 -9999 0 -0.63 69 69
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.15 0.24 -9999 0 -0.63 78 78
FER -0.16 0.24 -9999 0 -0.64 70 70
RELA 0 0 -9999 0 -10000 0 0
ITK -0.077 0.18 -9999 0 -0.66 37 37
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.16 0.31 -9999 0 -0.74 85 85
cytokine secretion -0.043 0.054 -9999 0 -10000 0 0
SPHK1 -0.16 0.24 -9999 0 -0.64 70 70
PTK2 -0.14 0.26 -9999 0 -0.67 69 69
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.21 0.28 -9999 0 -0.73 84 84
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.15 0.28 -9999 0 -0.64 83 83
MAP2K2 0.03 0.024 -9999 0 -10000 0 0
MAP2K1 0.03 0.024 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.14 0.22 -9999 0 -0.58 71 71
MAP2K4 0.009 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.24 0.33 -9999 0 -0.59 197 197
mol:Choline -0.2 0.28 -9999 0 -0.55 149 149
SHC/Grb2/SOS1 -0.14 0.22 -9999 0 -0.6 69 69
FYN -0.002 0.033 -9999 0 -0.74 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.12 0.24 -9999 0 -0.6 69 69
HCLS1 -0.16 0.24 -9999 0 -0.64 70 70
PRKCB -0.11 0.22 -9999 0 -0.49 83 83
FCGR2B -0.014 0.099 -9999 0 -0.74 9 9
IGHE -0.004 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.14 0.22 -9999 0 -0.6 70 70
LCP2 -0.011 0.088 -9999 0 -0.74 7 7
PLA2G4A -0.16 0.24 -9999 0 -0.65 72 72
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.2 0.28 -9999 0 -0.55 149 149
IKK complex -0.038 0.12 -9999 0 -0.28 24 24
WIPF1 0 0 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.059 0.21 -10000 0 -0.74 43 43
GNB1/GNG2 -0.07 0.09 -10000 0 -0.22 59 59
AKT1 -0.035 0.13 -10000 0 -0.23 28 28
EGF -0.014 0.098 -10000 0 -0.69 10 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.037 0.13 -10000 0 -0.59 17 17
mol:Ca2+ -0.074 0.18 -10000 0 -0.31 168 168
LYN -0.017 0.076 -10000 0 -0.53 7 7
RhoA/GTP -0.047 0.059 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.082 0.2 -10000 0 -0.35 165 165
GNG2 -0.008 0.074 -10000 0 -0.74 5 5
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.018 0.1 -10000 0 -0.57 5 5
G beta5/gamma2 -0.091 0.12 -10000 0 -0.29 68 68
PRKCH -0.088 0.21 -10000 0 -0.36 155 155
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
TXA2/TP beta/beta Arrestin3 -0.002 0.014 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.023 0.13 -10000 0 -0.74 15 15
G12 family/GTP -0.12 0.14 -10000 0 -0.31 165 165
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.002 0.033 -10000 0 -0.74 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.13 0.41 20 -10000 0 20
mol:NADP -0.006 0.067 -10000 0 -0.74 4 4
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.06 0.2 -10000 0 -0.74 40 40
mol:IP3 -0.1 0.22 -10000 0 -0.39 168 168
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.15 0.3 -10000 0 -0.54 168 168
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.03 0.1 -10000 0 -0.49 12 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.019 0.085 -10000 0 -0.56 8 8
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.02 0.12 -10000 0 -0.74 13 13
PRKCB1 -0.1 0.22 -10000 0 -0.39 167 167
GNAQ -0.002 0.033 -10000 0 -0.74 1 1
mol:L-citrulline -0.006 0.067 -10000 0 -0.74 4 4
TXA2/TXA2-R family -0.15 0.3 -10000 0 -0.55 167 167
LCK -0.016 0.075 -10000 0 -0.52 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.019 0.09 -10000 0 -0.65 6 6
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.044 -10000 0 -0.42 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.019 0.089 -10000 0 -0.65 6 6
MAPK14 -0.043 0.14 -10000 0 -0.26 37 37
TGM2/GTP -0.12 0.26 -10000 0 -0.51 102 102
MAPK11 -0.043 0.14 -10000 0 -0.26 39 39
ARHGEF1 -0.035 0.11 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.099 0.23 -10000 0 -0.4 167 167
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.076 0.19 -10000 0 -0.32 164 164
cAMP biosynthetic process -0.095 0.21 -10000 0 -0.39 111 111
Gq family/GTP/EBP50 -0.036 0.11 -10000 0 -0.53 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.015 0.072 -10000 0 -0.52 6 6
GNB5 0 0 -10000 0 -10000 0 0
GNB1 -0.002 0.033 -10000 0 -0.74 1 1
EGF/EGFR 0.023 0.095 -10000 0 -0.39 13 13
VCAM1 -0.069 0.17 -10000 0 -0.3 165 165
TP beta/Gq family/GDP/G beta5/gamma2 -0.018 0.1 -10000 0 -0.57 5 5
platelet activation -0.06 0.19 -10000 0 -0.33 81 81
PGI2/IP -0.015 0.091 -10000 0 -0.57 13 13
PRKACA -0.022 0.1 -10000 0 -0.44 24 24
Gq family/GDP/G beta5/gamma2 -0.021 0.1 -10000 0 -0.59 5 5
TXA2/TP beta/beta Arrestin2 -0.002 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.11 -10000 0 -0.43 25 25
mol:DAG -0.11 0.25 -10000 0 -0.44 166 166
EGFR -0.022 0.12 -10000 0 -0.63 17 17
TXA2/TP alpha -0.14 0.28 -10000 0 -0.5 173 173
Gq family/GTP -0.066 0.12 -10000 0 -0.28 117 117
YES1 -0.015 0.072 -10000 0 -0.52 6 6
GNAI2/GTP -0.018 0.084 -10000 0 -0.62 6 6
PGD2/DP -0.017 0.098 -10000 0 -0.57 15 15
SLC9A3R1 -0.005 0.052 -10000 0 -0.57 4 4
FYN -0.016 0.076 -10000 0 -0.56 6 6
mol:NO -0.006 0.067 -10000 0 -0.74 4 4
GNA15 0 0 -10000 0 -10000 0 0
PGK/cGMP -0.044 0.14 -10000 0 -0.51 42 42
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.054 0.17 -10000 0 -0.76 17 17
NOS3 -0.006 0.067 -10000 0 -0.74 4 4
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.089 0.21 -10000 0 -0.37 156 156
PRKCB -0.098 0.22 -10000 0 -0.39 156 156
PRKCE -0.088 0.21 -10000 0 -0.37 155 155
PRKCD -0.097 0.22 -10000 0 -0.39 164 164
PRKCG -0.11 0.23 -10000 0 -0.41 164 164
muscle contraction -0.13 0.28 -10000 0 -0.5 167 167
PRKCZ -0.081 0.2 -10000 0 -0.35 165 165
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.02 0.096 -10000 0 -0.67 7 7
PRKCQ -0.11 0.23 -10000 0 -0.4 171 171
MAPKKK cascade -0.13 0.27 -10000 0 -0.48 169 169
SELE -0.11 0.23 -10000 0 -0.42 162 162
TP beta/GNAI2/GDP/G beta/gamma -0.023 0.1 -10000 0 -0.73 7 7
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 117 117
chemotaxis -0.17 0.34 -10000 0 -0.63 165 165
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.39 0.54 -10000 0 -1.2 105 105
STAT6 (cleaved dimer) -0.45 0.48 -10000 0 -1.1 136 136
IGHG1 -0.12 0.19 -10000 0 -0.4 6 6
IGHG3 -0.38 0.51 -10000 0 -1.1 124 124
AKT1 -0.14 0.26 -10000 0 -0.92 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.22 -10000 0 -1.1 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.27 -10000 0 -1 9 9
THY1 -0.39 0.54 -10000 0 -1.2 100 100
MYB -0.021 0.11 -10000 0 -0.59 17 17
HMGA1 -0.004 0.045 -10000 0 -0.57 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.31 -10000 0 -0.68 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.27 -10000 0 -1 9 9
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D -0.002 0.033 -10000 0 -0.74 1 1
SOCS5 0.019 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.44 0.48 -10000 0 -1.2 111 111
SOCS1 -0.23 0.35 -10000 0 -0.78 70 70
SOCS3 -0.16 0.27 -10000 0 -1 8 8
FCER2 -0.34 0.5 -10000 0 -1.3 66 66
PARP14 0.007 0.006 -10000 0 -10000 0 0
CCL17 -0.46 0.62 -10000 0 -1.4 125 125
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.22 -10000 0 -0.9 7 7
T cell proliferation -0.38 0.54 -10000 0 -1.2 107 107
IL4R/JAK1 -0.39 0.53 -10000 0 -1.2 105 105
EGR2 -0.41 0.56 -10000 0 -1.3 108 108
JAK2 -0.004 0.034 -10000 0 -10000 0 0
JAK3 0.013 0.007 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.009 0.014 -10000 0 -10000 0 0
COL1A2 -0.1 0.18 -10000 0 -0.65 2 2
CCL26 -0.42 0.55 -10000 0 -1.2 117 117
IL4R -0.42 0.57 -10000 0 -1.3 105 105
PTPN6 0.019 0.014 -10000 0 -10000 0 0
IL13RA2 -0.42 0.57 -10000 0 -1.3 114 114
IL13RA1 -0.004 0.034 -10000 0 -10000 0 0
IRF4 -0.17 0.36 -10000 0 -0.93 72 72
ARG1 -0.12 0.24 -10000 0 -0.8 30 30
CBL -0.18 0.29 -10000 0 -0.68 37 37
GTF3A 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.05 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.31 -10000 0 -0.86 72 72
CD40LG -0.12 0.29 -10000 0 -0.74 86 86
MAPK14 -0.18 0.3 -10000 0 -0.94 12 12
mitosis -0.14 0.25 -10000 0 -0.84 9 9
STAT6 -0.46 0.63 -10000 0 -1.4 118 118
SPI1 -0.044 0.19 -10000 0 -0.74 35 35
RPS6KB1 -0.13 0.24 -10000 0 -0.88 7 7
STAT6 (dimer) -0.46 0.63 -10000 0 -1.3 120 120
STAT6 (dimer)/PARP14 -0.43 0.58 -10000 0 -1.3 108 108
mast cell activation 0.008 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.3 -10000 0 -0.82 33 33
FRAP1 -0.14 0.26 -10000 0 -0.92 9 9
LTA -0.39 0.54 -10000 0 -1.2 104 104
FES -0.002 0.033 -10000 0 -0.74 1 1
T-helper 1 cell differentiation 0.44 0.61 1.3 120 -10000 0 120
CCL11 -0.39 0.52 -10000 0 -1.2 107 107
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.26 -10000 0 -1.1 9 9
IL2RG 0 0.095 -10000 0 -0.73 8 8
IL10 -0.39 0.54 -10000 0 -1.2 106 106
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.005 0.058 -10000 0 -0.74 3 3
IL4 -0.079 0.14 -10000 0 -10000 0 0
IL5 -0.4 0.53 -10000 0 -1.2 104 104
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.42 -10000 0 -0.9 105 105
COL1A1 -0.14 0.23 -10000 0 -0.65 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.4 0.55 -10000 0 -1.3 103 103
IL2R gamma/JAK3 -0.004 0.071 -10000 0 -0.55 8 8
TFF3 -0.44 0.62 -10000 0 -1.4 111 111
ALOX15 -0.63 0.76 -10000 0 -1.5 183 183
MYBL1 -0.001 0.026 -10000 0 -0.57 1 1
T-helper 2 cell differentiation -0.32 0.43 -10000 0 -0.93 107 107
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.26 -10000 0 -1 9 9
mol:PI-3-4-5-P3 -0.14 0.26 -10000 0 -0.92 9 9
PI3K -0.15 0.28 -10000 0 -1 9 9
DOK2 -0.066 0.21 -10000 0 -0.74 44 44
ETS1 -0.001 0.12 -10000 0 -0.7 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.22 -10000 0 -0.87 7 7
ITGB3 -0.4 0.55 -10000 0 -1.2 103 103
PIGR -0.8 0.83 -10000 0 -1.6 258 258
IGHE 0.029 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.11 0.21 -10000 0 -0.85 7 7
BCL6 0.001 0.004 -10000 0 -10000 0 0
OPRM1 -0.4 0.53 -10000 0 -1.2 103 103
RETNLB -0.4 0.53 -10000 0 -1.2 104 104
SELP -0.57 0.74 -10000 0 -1.6 150 150
AICDA -0.38 0.51 -10000 0 -1.2 103 103
Glucocorticoid receptor regulatory network

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
PCK2 0.06 0.099 0.37 1 -10000 0 1
SMARCC2 0.011 0 -10000 0 -10000 0 0
SMARCC1 0.011 0 -10000 0 -10000 0 0
TBX21 -0.2 0.35 -10000 0 -1 66 66
SUMO2 0.002 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0 -10000 0 -10000 0 0
FKBP4 -0.001 0.026 -10000 0 -0.57 1 1
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.13 0.1 0.33 48 -10000 0 48
PRL -0.085 0.12 -10000 0 -0.54 3 3
cortisol/GR alpha (dimer)/TIF2 0.31 0.25 0.59 157 -10000 0 157
RELA -0.046 0.1 -10000 0 -10000 0 0
FGG -0.13 0.47 0.52 67 -0.62 228 295
GR beta/TIF2 0.14 0.12 0.36 56 -0.39 1 57
IFNG -0.35 0.24 -10000 0 -0.8 56 56
apoptosis 0.028 0.12 0.46 2 -0.55 1 3
CREB1 0.001 0.028 -10000 0 -10000 0 0
histone acetylation -0.012 0.15 0.32 4 -0.38 24 28
BGLAP -0.096 0.14 -10000 0 -0.51 13 13
GR/PKAc 0.12 0.099 0.32 42 -10000 0 42
NF kappa B1 p50/RelA -0.083 0.18 -10000 0 -0.48 38 38
SMARCD1 0.011 0 -10000 0 -10000 0 0
MDM2 0.11 0.098 0.29 57 -0.31 1 58
GATA3 -0.013 0.13 -10000 0 -0.71 17 17
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.18 0.42 -10000 0 -1.3 54 54
GSK3B 0.002 0.006 -10000 0 -10000 0 0
NR1I3 0.047 0.11 0.47 1 -10000 0 1
CSN2 0.17 0.16 0.42 55 -10000 0 55
BRG1/BAF155/BAF170/BAF60A 0 0 -10000 0 -10000 0 0
NFATC1 0.001 0.034 -10000 0 -0.74 1 1
POU2F1 0.005 0.014 -10000 0 -10000 0 0
CDKN1A 0.026 0.015 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 48 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.14 0.33 39 -10000 0 39
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.035 0.16 0.46 1 -0.9 9 10
JUN -0.29 0.16 -10000 0 -0.54 83 83
IL4 -0.11 0.15 -10000 0 -0.53 13 13
CDK5R1 -0.01 0.081 -10000 0 -0.57 10 10
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.44 0.23 -10000 0 -0.62 236 236
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.099 0.33 40 -10000 0 40
cortisol/GR alpha (monomer) 0.37 0.32 0.71 168 -10000 0 168
NCOA2 -0.002 0.033 -10000 0 -0.74 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.17 0.24 -10000 0 -0.83 56 56
AP-1/NFAT1-c-4 -0.53 0.24 -10000 0 -0.77 170 170
AFP -0.19 0.15 -10000 0 -0.68 13 13
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.18 0.15 0.46 51 -10000 0 51
TP53 0.029 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.54 0.25 -10000 0 -0.71 262 262
KRT14 -0.37 0.22 -10000 0 -0.62 130 130
TBP 0.017 0 -10000 0 -10000 0 0
CREBBP 0.11 0.066 0.34 1 -10000 0 1
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.011 0.031 -10000 0 -10000 0 0
AP-1 -0.53 0.25 -10000 0 -0.77 173 173
MAPK14 0.002 0.005 -10000 0 -10000 0 0
MAPK10 -0.01 0.094 -10000 0 -0.74 8 8
MAPK11 0.002 0.006 -10000 0 -10000 0 0
KRT5 -0.56 0.26 -10000 0 -0.72 267 267
interleukin-1 receptor activity 0.008 0.029 -10000 0 -10000 0 0
NCOA1 0.013 0.002 -10000 0 -10000 0 0
STAT1 0.017 0 -10000 0 -10000 0 0
CGA -0.12 0.16 -10000 0 -0.58 19 19
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.19 0.48 108 -10000 0 108
MAPK3 0.002 0.006 -10000 0 -10000 0 0
MAPK1 0.002 0.005 -10000 0 -10000 0 0
ICAM1 -0.27 0.45 -10000 0 -1.2 72 72
NFKB1 -0.046 0.1 -10000 0 -0.31 3 3
MAPK8 -0.24 0.17 -10000 0 -0.48 110 110
MAPK9 0.002 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.026 0.12 0.46 2 -0.58 1 3
BAX 0.026 0.015 -10000 0 -10000 0 0
POMC -0.21 0.24 -10000 0 -0.61 84 84
EP300 0.11 0.067 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.33 0.25 0.61 156 -10000 0 156
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.074 0.26 11 -0.27 1 12
SGK1 0.17 0.076 -10000 0 -10000 0 0
IL13 -0.27 0.2 -10000 0 -0.76 41 41
IL6 -0.34 0.53 -10000 0 -1.3 103 103
PRKACG -0.001 0.026 -10000 0 -0.57 1 1
IL5 -0.24 0.17 -10000 0 -0.78 21 21
IL2 -0.34 0.2 -10000 0 -0.78 42 42
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.2 0.28 -10000 0 -0.71 75 75
CDK5R1/CDK5 -0.007 0.059 -10000 0 -0.41 10 10
NF kappa B1 p50/RelA/PKAc -0.058 0.12 -10000 0 -0.47 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 153 -10000 0 153
SMARCA4 0.011 0 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.14 0.4 104 -10000 0 104
NF kappa B1 p50/RelA/Cbp 0.036 0.18 0.37 14 -0.5 3 17
JUN (dimer) -0.29 0.16 -10000 0 -0.54 83 83
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.42 0.51 -10000 0 -1.1 177 177
NR3C1 0.2 0.2 0.5 102 -10000 0 102
NR4A1 -0.098 0.26 -10000 0 -0.72 68 68
TIF2/SUV420H1 -0.001 0.025 -10000 0 -0.56 1 1
MAPKKK cascade 0.028 0.12 0.46 2 -0.55 1 3
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.6 158 -10000 0 158
PBX1 0 0.06 -10000 0 -0.74 3 3
POU1F1 -0.002 0.047 -10000 0 -0.57 3 3
SELE -0.47 0.61 -10000 0 -1.3 155 155
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.14 0.4 104 -10000 0 104
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 153 -10000 0 153
mol:cortisol 0.2 0.2 0.42 161 -0.23 3 164
MMP1 -0.33 0.19 -10000 0 -0.5 164 164
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.032 0.03 -9999 0 -10000 0 0
VDR -0.002 0.033 -9999 0 -0.74 1 1
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.13 0.18 -9999 0 -0.54 10 10
RXRs/LXRs/DNA/Oxysterols -0.098 0.16 -9999 0 -0.58 13 13
MED1 0 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.012 0.059 -9999 0 -10000 0 0
RXRs/NUR77 -0.28 0.26 -9999 0 -0.49 282 282
RXRs/PPAR -0.18 0.2 -9999 0 -0.5 57 57
NCOR2 -0.002 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.026 -9999 0 -0.56 1 1
RARs/VDR/DNA/Vit D3 -0.003 0.032 -9999 0 -0.41 3 3
RARA 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.033 -9999 0 -0.74 1 1
RARs/RARs/DNA/9cRA -0.002 0.026 -9999 0 -0.41 2 2
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.057 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.013 0.061 -9999 0 -10000 0 0
THRA 0 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.026 -9999 0 -0.56 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.23 0.21 -9999 0 -0.43 258 258
NR1H4 -0.005 0.052 -9999 0 -0.57 4 4
RXRs/LXRs/DNA -0.21 0.2 -9999 0 -0.56 10 10
NR1H2 0.015 0.004 -9999 0 -10000 0 0
NR1H3 0.014 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.21 0.2 -9999 0 -0.4 259 259
NR4A1 -0.098 0.25 -9999 0 -0.74 65 65
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.12 0.14 -9999 0 -0.26 258 258
RXRG -0.38 0.37 -9999 0 -0.74 258 258
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.004 -9999 0 -10000 0 0
RXRB 0.014 0.005 -9999 0 -10000 0 0
THRB -0.026 0.14 -9999 0 -0.74 17 17
PPARG -0.088 0.24 -9999 0 -0.74 58 58
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.1 0.23 -9999 0 -1.2 13 13
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.097 0.16 -9999 0 -0.58 13 13
PPARA 0 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.003 0.047 -9999 0 -0.74 2 2
RXRs/NUR77/BCL2 -0.2 0.2 -9999 0 -0.36 282 282
SREBF1 -0.082 0.15 -9999 0 -0.6 9 9
RXRs/RXRs/DNA/9cRA -0.23 0.21 -9999 0 -0.43 258 258
ABCA1 -0.082 0.15 -9999 0 -0.6 9 9
RARs/THRs -0.016 0.078 -9999 0 -0.4 19 19
RXRs/FXR -0.23 0.22 -9999 0 -0.43 258 258
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.044 0.056 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.099 0.14 -9999 0 -0.43 21 21
JUN -0.063 0.14 -9999 0 -0.41 18 18
HRAS 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.22 -9999 0 -0.48 126 126
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.22 -9999 0 -0.48 126 126
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.16 0.22 -9999 0 -0.48 121 121
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.66 22 22
GRB7 -0.005 0.052 -9999 0 -0.57 4 4
RET51/GFRalpha1/GDNF -0.17 0.22 -9999 0 -0.48 126 126
MAPKKK cascade -0.13 0.18 -9999 0 -0.59 20 20
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.48 121 121
lamellipodium assembly -0.095 0.13 -9999 0 -0.4 21 21
RET51/GFRalpha1/GDNF/SHC -0.17 0.22 -9999 0 -0.48 126 126
PIK3CA 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.48 121 121
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.22 -9999 0 -0.49 121 121
MAPK3 -0.14 0.19 -9999 0 -0.62 22 22
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.065 0.21 -9999 0 -0.74 43 43
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.14 0.18 -9999 0 -0.55 41 41
DOK5 -0.005 0.06 -9999 0 -0.66 4 4
GFRA1 -0.18 0.32 -9999 0 -0.74 121 121
MAPK8 -0.096 0.13 -9999 0 -0.44 18 18
HRAS/GTP -0.14 0.2 -9999 0 -0.62 22 22
tube development -0.15 0.21 -9999 0 -0.46 121 121
MAPK1 -0.14 0.19 -9999 0 -0.62 22 22
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.33 121 121
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.19 0.25 -9999 0 -0.77 43 43
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.22 -9999 0 -0.48 126 126
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.23 -9999 0 -0.49 126 126
PRKCA -0.003 0.047 -9999 0 -0.74 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.16 -9999 0 -0.36 121 121
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.33 121 121
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.22 -9999 0 -0.49 127 127
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.02 0.11 -9999 0 -0.58 17 17
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.062 0.14 -9999 0 -0.41 18 18
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.48 121 121
SHANK3 -0.003 0.047 -9999 0 -0.74 2 2
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.34 121 121
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.47 18 18
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.14 -9999 0 -0.47 18 18
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.48 18 18
PI3K -0.14 0.2 -9999 0 -0.52 52 52
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.21 -9999 0 -0.46 121 121
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.1 0.14 -9999 0 -0.47 18 18
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.22 -9999 0 -0.48 126 126
GAB1 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
IRS2 -0.005 0.058 -9999 0 -0.74 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.48 18 18
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.49 127 127
GRB2 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.094 0.21 -9999 0 -0.57 80 80
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.22 -9999 0 -0.48 126 126
Rac1/GTP -0.11 0.16 -9999 0 -0.48 21 21
RET9/GFRalpha1/GDNF -0.18 0.24 -9999 0 -0.47 185 185
GFRalpha1/GDNF -0.2 0.27 -9999 0 -0.54 185 185
PLK1 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
regulation of centriole-centriole cohesion 0.071 0.074 0.14 255 -10000 0 255
BUB1B -0.13 0.098 -10000 0 -0.22 203 203
PLK1 -0.014 0.036 -10000 0 -0.13 8 8
PLK1S1 -0.003 0.02 -10000 0 -10000 0 0
KIF2A -0.004 0.033 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.014 0.036 -10000 0 -0.13 8 8
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.21 0.23 -10000 0 -0.42 241 241
WEE1 -0.006 0.038 -10000 0 -10000 0 0
cytokinesis -0.11 0.12 -10000 0 -0.29 35 35
PP2A-alpha B56 -0.007 0.022 -10000 0 -10000 0 0
AURKA -0.006 0.029 -10000 0 -0.12 8 8
PICH/PLK1 -0.11 0.17 -10000 0 -0.5 40 40
CENPE -0.041 0.11 -10000 0 -0.35 54 54
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.033 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.06 0.049 -10000 0 -0.12 19 19
PAK1 0.002 0.026 -10000 0 -0.57 1 1
SPC24 -0.17 0.26 -10000 0 -0.57 147 147
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.013 0.039 -10000 0 -0.15 5 5
GORASP1 0 0 -10000 0 -10000 0 0
metaphase -0.001 0.003 -10000 0 -0.012 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.02 -10000 0 -0.066 4 4
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.001 0.008 -10000 0 -10000 0 0
spindle elongation -0.014 0.036 -10000 0 -0.13 8 8
ODF2 0.004 0.005 -10000 0 -10000 0 0
BUB1 -0.005 0.032 -10000 0 -10000 0 0
TPT1 -0.003 0.02 -10000 0 -10000 0 0
CDC25C -0.077 0.057 -10000 0 -10000 0 0
CDC25B 0.009 0.003 -10000 0 -10000 0 0
SGOL1 -0.071 0.074 -10000 0 -0.14 255 255
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.028 0.079 -10000 0 -0.29 4 4
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.36 0.28 -10000 0 -0.57 312 312
PLK1/PBIP1 -0.03 0.063 -10000 0 -0.33 18 18
mitosis -0.001 0.005 0.022 14 -0.018 8 22
FBXO5 -0.004 0.031 -10000 0 -10000 0 0
CDC2 -0.001 0.004 -10000 0 -0.012 14 14
NDC80 -0.2 0.27 -10000 0 -0.57 172 172
metaphase plate congression -0.007 0.025 -10000 0 -10000 0 0
ERCC6L -0.11 0.16 -10000 0 -0.49 36 36
NLP/gamma Tubulin -0.005 0.021 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0 0 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.2 0.2 -10000 0 -0.37 260 260
GRASP65/GM130/RAB1/GTP/PLK1 -0.008 0.015 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.043 0.035 -10000 0 -10000 0 0
microtubule-based process -0.18 0.17 -10000 0 -0.34 253 253
Golgi organization -0.014 0.036 -10000 0 -0.13 8 8
Cohesin/SA2 -0.019 0.024 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.3 0.29 -10000 0 -0.57 253 253
APC/C/CDC20 -0.22 0.16 -10000 0 -0.34 312 312
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.029 0.062 -10000 0 -0.32 18 18
PRC1 -0.056 0.17 -10000 0 -0.57 48 48
ECT2 -0.016 0.072 -10000 0 -0.35 18 18
C13orf34 -0.003 0.028 -10000 0 -10000 0 0
NUDC -0.007 0.025 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.13 0.098 -10000 0 -0.21 203 203
spindle assembly -0.008 0.03 -10000 0 -10000 0 0
spindle stabilization -0.003 0.02 -10000 0 -10000 0 0
APC/C/HCDH1 0 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.18 0.17 -10000 0 -0.34 253 253
CCNB1 -0.057 0.18 -10000 0 -0.57 57 57
PPP1CB 0 0 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.001 0.025 -10000 0 -10000 0 0
TUBG1 -0.003 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.076 -10000 0 -0.29 4 4
MLF1IP -0.01 0.082 -10000 0 -0.43 18 18
INCENP 0.004 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.021 0.086 -9999 0 -0.37 27 27
RGS9BP -0.015 0.1 -9999 0 -0.74 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.037 -9999 0 -0.57 2 2
mol:Na + -0.18 0.18 -9999 0 -0.35 242 242
mol:ADP -0.009 0.093 -9999 0 -0.42 24 24
GNAT2 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.49 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.026 0.12 -9999 0 -0.57 22 22
CNGB3 -0.28 0.29 -9999 0 -0.57 240 240
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.21 0.2 -9999 0 -0.57 53 53
Cone PDE6 -0.053 0.14 -9999 0 -0.42 61 61
Cone Metarhodopsin II -0.016 0.07 -9999 0 -0.32 24 24
Na + (4 Units) -0.22 0.2 -9999 0 -0.57 53 53
GNAT2/GDP -0.053 0.14 -9999 0 -0.42 61 61
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.005 -9999 0 -10000 0 0
Cone Transducin -0.022 0.091 -9999 0 -0.39 27 27
SLC24A2 -0.11 0.23 -9999 0 -0.57 94 94
GNB3/GNGT2 -0.028 0.12 -9999 0 -0.5 27 27
GNB3 -0.012 0.081 -9999 0 -0.57 10 10
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.002 0.037 -9999 0 -0.57 2 2
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.18 0.18 -9999 0 -0.35 242 242
mol:Pi -0.061 0.16 -9999 0 -0.49 61 61
Cone CNG Channel -0.14 0.14 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.22 -9999 0 -0.57 94 94
RGS9 -0.08 0.23 -9999 0 -0.74 53 53
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.026 0.14 -9999 0 -0.74 17 17
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.21 -9999 0 -0.56 73 73
SMAD6-7/SMURF1 -0.052 0.15 -9999 0 -0.48 53 53
NOG -0.028 0.14 -9999 0 -0.73 19 19
SMAD9 -0.1 0.22 -9999 0 -0.59 73 73
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.023 0.13 -9999 0 -0.47 23 23
BMP7/USAG1 -0.25 0.27 -9999 0 -0.5 240 240
SMAD5/SKI -0.049 0.11 -9999 0 -0.44 23 23
SMAD1 0.033 0.026 -9999 0 -10000 0 0
BMP2 -0.098 0.25 -9999 0 -0.74 65 65
SMAD1/SMAD1/SMAD4 -0.034 0.095 -9999 0 -10000 0 0
BMPR1A 0 0 -9999 0 -10000 0 0
BMPR1B -0.056 0.2 -9999 0 -0.74 37 37
BMPR1A-1B/BAMBI -0.04 0.13 -9999 0 -0.48 40 40
AHSG -0.019 0.1 -9999 0 -0.57 16 16
CER1 -0.002 0.037 -9999 0 -0.57 2 2
BMP2-4/CER1 -0.075 0.18 -9999 0 -0.5 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.067 0.14 -9999 0 -0.59 17 17
BMP2-4 (homodimer) -0.085 0.21 -9999 0 -0.57 72 72
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.044 0.14 -9999 0 -0.45 48 48
RGMA -0.063 0.18 -9999 0 -0.57 54 54
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.13 -9999 0 -0.45 30 30
BMP2-4/USAG1 -0.16 0.27 -9999 0 -0.55 143 143
SMAD6/SMURF1/SMAD5 -0.049 0.11 -9999 0 -0.47 18 18
SOSTDC1 -0.14 0.29 -9999 0 -0.74 93 93
BMP7/BMPR2/BMPR1A-1B -0.14 0.19 -9999 0 -0.53 43 43
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.02 0.12 -9999 0 -0.74 13 13
HFE2 -0.002 0.037 -9999 0 -0.57 2 2
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.075 0.18 -9999 0 -0.5 72 72
SMAD5/SMAD5/SMAD4 -0.049 0.11 -9999 0 -0.46 19 19
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.05 0.1 -9999 0 -0.45 17 17
BMP7 (homodimer) -0.2 0.28 -9999 0 -0.58 171 171
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.028 0.12 -9999 0 -0.48 29 29
SMAD1/SKI -0.004 0.012 -9999 0 -10000 0 0
SMAD6 -0.079 0.23 -9999 0 -0.74 52 52
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.084 0.19 -9999 0 -0.51 71 71
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.34 0.28 -9999 0 -0.57 293 293
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.042 0.15 -9999 0 -0.56 37 37
CHRDL1 -0.39 0.37 -9999 0 -0.74 256 256
ENDOFIN/SMAD1 -0.004 0.012 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.039 0.11 -9999 0 -0.4 9 9
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.007 0.068 -9999 0 -0.67 5 5
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.3 -9999 0 -0.55 282 282
BMP2-4/GREM1 -0.28 0.22 -9999 0 -0.62 71 71
SMAD7 -0.002 0.033 -9999 0 -0.74 1 1
SMAD8A/SMAD8A/SMAD4 -0.096 0.2 -9999 0 -0.55 73 73
SMAD1/SMAD6 -0.004 0.012 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.2 0.28 -9999 0 -0.58 171 171
BMP6 -0.02 0.12 -9999 0 -0.74 13 13
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.058 0.12 -9999 0 -0.41 31 31
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.004 0.012 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.025 -9999 0 -0.56 1 1
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.084 0.14 -9999 0 -0.46 42 42
CHRD -0.004 0.054 -9999 0 -0.68 3 3
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.14 -9999 0 -0.49 30 30
BMP4 -0.015 0.1 -9999 0 -0.72 10 10
FST -0.093 0.21 -9999 0 -0.57 79 79
BMP2-4/NOG -0.09 0.21 -9999 0 -0.53 82 82
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.13 0.18 -9999 0 -0.7 14 14
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.034 0.11 -10000 0 -0.4 42 42
fibroblast growth factor receptor signaling pathway -0.034 0.11 -10000 0 -0.39 42 42
LAMA1 -0.17 0.26 -10000 0 -0.57 143 143
PRNP 0 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.15 0.25 -10000 0 -0.55 129 129
SMAD2 -0.025 0.14 -10000 0 -0.43 39 39
GPC1/PrPc/Cu2+ -0.019 0.079 -10000 0 -0.35 26 26
GPC1/Laminin alpha1 -0.14 0.22 -10000 0 -0.45 154 154
TDGF1 -0.004 0.045 -10000 0 -0.57 3 3
CRIPTO/GPC1 -0.025 0.098 -10000 0 -0.41 29 29
APP/GPC1 -0.022 0.093 -10000 0 -0.41 26 26
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.087 -10000 0 -0.34 29 29
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.056 0.15 -10000 0 -0.48 39 39
SERPINC1 -0.007 0.063 -10000 0 -0.57 6 6
FYN -0.001 0.09 -10000 0 -0.35 30 30
FGR -0.033 0.15 -10000 0 -0.42 61 61
positive regulation of MAPKKK cascade 0.001 0.11 -10000 0 -0.46 14 14
SLIT2 -0.17 0.31 -10000 0 -0.74 110 110
GPC1/NRG -0.038 0.13 -10000 0 -0.46 40 40
NRG1 -0.021 0.12 -10000 0 -0.74 14 14
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.018 0.077 -10000 0 -0.34 26 26
LYN -0.002 0.092 -10000 0 -0.35 31 31
mol:Spermine -0.013 0.097 -10000 0 -0.42 26 26
cell growth -0.034 0.11 -10000 0 -0.39 42 42
BMP signaling pathway 0.03 0.13 0.57 26 -10000 0 26
SRC 0 0.087 -10000 0 -0.34 29 29
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.22 0.34 -10000 0 -0.74 145 145
GPC1 -0.03 0.13 -10000 0 -0.57 26 26
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.023 0.13 -10000 0 -0.39 54 54
HCK -0.005 0.099 -10000 0 -0.36 34 34
FGF2 -0.023 0.13 -10000 0 -0.74 15 15
FGFR1 -0.002 0.033 -10000 0 -0.74 1 1
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 -0.059 0.2 -10000 0 -0.74 39 39
cell death -0.022 0.092 -10000 0 -0.41 26 26
ATIII/GPC1 -0.027 0.1 -10000 0 -0.41 32 32
PLA2G2A/GPC1 -0.18 0.27 -10000 0 -0.56 162 162
LCK -0.001 0.09 -10000 0 -0.35 30 30
neuron differentiation -0.038 0.13 -10000 0 -0.46 40 40
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.059 0.2 -10000 0 -0.74 39 39
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.033 -9999 0 -0.74 1 1
alphaV beta3 Integrin -0.009 0.071 -9999 0 -0.56 8 8
PTK2 -0.1 0.16 -9999 0 -0.59 37 37
positive regulation of JNK cascade -0.034 0.089 -9999 0 -0.34 37 37
CDC42/GDP -0.021 0.13 -9999 0 -0.46 37 37
Rac1/GDP -0.02 0.13 -9999 0 -0.46 37 37
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.041 0.11 -9999 0 -0.42 37 37
nectin-3/I-afadin -0.042 0.15 -9999 0 -0.56 37 37
RAPGEF1 -0.032 0.15 -9999 0 -0.53 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.045 0.17 -9999 0 -0.62 37 37
PDGFB-D/PDGFRB -0.002 0.033 -9999 0 -0.74 1 1
TLN1 -0.019 0.15 -9999 0 -0.5 31 31
Rap1/GTP -0.034 0.096 -9999 0 -0.36 37 37
IQGAP1 0 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 -0.042 0.15 -9999 0 -0.56 37 37
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.033 0.16 -9999 0 -0.58 37 37
MLLT4 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K -0.031 0.11 -9999 0 -0.4 38 38
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.41 237 237
positive regulation of lamellipodium assembly -0.037 0.096 -9999 0 -0.36 39 39
PVRL1 -0.28 0.29 -9999 0 -0.57 237 237
PVRL3 -0.056 0.2 -9999 0 -0.74 37 37
PVRL2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
CLDN1 -0.11 0.22 -9999 0 -0.58 91 91
JAM-A/CLDN1 -0.09 0.17 -9999 0 -0.49 38 38
SRC -0.076 0.18 -9999 0 -0.7 37 37
ITGB3 -0.012 0.094 -9999 0 -0.74 8 8
nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.41 237 237
FARP2 -0.036 0.16 -9999 0 -0.57 37 37
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.036 0.13 -9999 0 -0.48 37 37
nectin-1/I-afadin -0.2 0.21 -9999 0 -0.41 237 237
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 -0.2 0.21 -9999 0 -0.39 255 255
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.034 0.089 -9999 0 -0.34 37 37
alphaV/beta3 Integrin/Talin -0.046 0.14 -9999 0 -0.76 11 11
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 -0.049 0.15 -9999 0 -0.54 31 31
VAV2 -0.04 0.17 -9999 0 -0.58 40 40
RAP1/GDP -0.038 0.11 -9999 0 -0.43 37 37
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.036 0.13 -9999 0 -0.48 37 37
nectin-3(dimer)/I-afadin/I-afadin -0.042 0.15 -9999 0 -0.56 37 37
Rac1/GTP -0.044 0.12 -9999 0 -0.44 39 39
PTPRM -0.054 0.16 -9999 0 -0.43 61 61
E-cadherin/beta catenin/alpha catenin -0.13 0.13 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.017 0.093 -9999 0 -0.51 16 16
ARNO/beta Arrestin1-2 -0.17 0.24 -9999 0 -0.7 49 49
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EPHA2 -0.005 0.058 -9999 0 -0.74 3 3
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.026 0.12 -9999 0 -0.5 26 26
ARRB2 0.007 0.011 -9999 0 -0.21 1 1
mol:GTP 0.015 0.025 -9999 0 -0.15 8 8
ARRB1 -0.14 0.29 -9999 0 -0.74 93 93
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.019 0.1 -9999 0 -0.57 16 16
EGF -0.014 0.098 -9999 0 -0.69 10 10
somatostatin receptor activity 0 0 -9999 0 -0.001 121 121
ARAP2 -0.002 0.033 -9999 0 -0.74 1 1
mol:GDP -0.12 0.15 -9999 0 -0.33 133 133
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 76 76
ITGA2B -0.023 0.13 -9999 0 -0.74 15 15
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.43 3 3
ADAP1 -0.014 0.099 -9999 0 -0.74 9 9
KIF13B -0.012 0.094 -9999 0 -0.74 8 8
HGF/MET -0.12 0.23 -9999 0 -0.56 105 105
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.11 0.15 -9999 0 -0.31 144 144
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.022 0.099 -9999 0 -0.42 26 26
ADRB2 -0.21 0.34 -9999 0 -0.74 141 141
receptor agonist activity 0 0 -9999 0 0 146 146
actin filament binding 0 0 -9999 0 -0.001 144 144
SRC 0 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.094 -9999 0 -0.74 8 8
GNAQ -0.002 0.033 -9999 0 -0.74 1 1
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 103 103
ARF6/GDP -0.013 0.071 -9999 0 -0.35 3 3
ARF6/GDP/GULP/ACAP1 -0.11 0.14 -9999 0 -0.43 46 46
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.02 0.092 -9999 0 -0.43 23 23
ACAP1 -0.003 0.042 -9999 0 -0.66 2 2
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.014 -9999 0 -0.31 1 1
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.15 0.3 -9999 0 -0.74 102 102
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 103 103
endosomal lumen acidification 0 0 0 1 -0.001 91 92
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.014 0.099 -9999 0 -0.74 9 9
GNAQ/ARNO 0.004 0.02 -9999 0 -0.41 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 10 10
MET -0.004 0.054 -9999 0 -0.68 3 3
GNA14 -0.18 0.32 -9999 0 -0.74 117 117
GNA15 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 118 118
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.001 0.026 -9999 0 -0.57 1 1
AGTR1 -0.3 0.36 -9999 0 -0.74 199 199
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.014 -9999 0 -0.31 1 1
IPCEF1/ARNO -0.017 0.078 -9999 0 -0.74 1 1
alphaIIb/beta3 Integrin -0.026 0.12 -9999 0 -0.56 23 23
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.008 0.14 -10000 0 -0.38 59 59
CRKL -0.013 0.15 -10000 0 -0.41 60 60
HRAS -0.057 0.14 -10000 0 -0.62 11 11
mol:PIP3 -0.024 0.14 -10000 0 -0.39 59 59
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.021 0.15 -10000 0 -0.43 60 60
FOXO3 -0.006 0.14 -10000 0 -0.37 59 59
AKT1 -0.015 0.14 -10000 0 -0.4 60 60
BAD -0.006 0.14 -10000 0 -0.37 59 59
megakaryocyte differentiation -0.047 0.2 -10000 0 -0.48 79 79
GSK3B -0.006 0.14 -10000 0 -0.37 59 59
RAF1 0.007 0.13 -10000 0 -0.48 11 11
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.021 0.15 -10000 0 -0.43 60 60
STAT1 -0.072 0.35 -10000 0 -1 60 60
HRAS/SPRED1 -0.046 0.11 -10000 0 -0.48 11 11
cell proliferation -0.02 0.15 -10000 0 -0.42 60 60
PIK3CA 0 0 -10000 0 -10000 0 0
TEC -0.005 0.058 -10000 0 -0.74 3 3
RPS6KB1 -0.021 0.15 -10000 0 -0.43 60 60
HRAS/SPRED2 -0.046 0.11 -10000 0 -0.48 11 11
LYN/TEC/p62DOK -0.052 0.14 -10000 0 -0.42 61 61
MAPK3 0.019 0.098 -10000 0 -0.32 11 11
STAP1 -0.044 0.2 -10000 0 -0.49 74 74
GRAP2 -0.039 0.17 -10000 0 -0.74 26 26
JAK2 -0.1 0.28 -10000 0 -0.85 60 60
STAT1 (dimer) -0.069 0.34 -10000 0 -0.99 60 60
mol:Gleevec -0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.053 0.14 -10000 0 -0.4 60 60
actin filament polymerization -0.02 0.15 -10000 0 -0.42 60 60
LYN -0.003 0.047 -10000 0 -0.74 2 2
STAP1/STAT5A (dimer) -0.048 0.25 -10000 0 -0.67 60 60
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.044 0.12 -10000 0 -10000 0 0
PI3K -0.049 0.13 -10000 0 -0.4 60 60
PTEN -0.002 0.033 -10000 0 -0.74 1 1
SCF/KIT/EPO/EPOR -0.099 0.44 -10000 0 -1.3 60 60
MAPK8 -0.021 0.15 -10000 0 -0.43 60 60
STAT3 (dimer) -0.02 0.15 -10000 0 -0.42 60 60
positive regulation of transcription 0.021 0.083 -10000 0 -0.3 1 1
mol:GDP -0.061 0.15 -10000 0 -0.66 11 11
PIK3C2B -0.021 0.15 -10000 0 -0.43 60 60
CBL/CRKL -0.006 0.14 -10000 0 -0.38 60 60
FER -0.021 0.15 -10000 0 -0.43 60 60
SH2B3 -0.022 0.16 -10000 0 -0.43 62 62
PDPK1 -0.015 0.13 -10000 0 -0.36 59 59
SNAI2 -0.021 0.15 -10000 0 -0.43 60 60
positive regulation of cell proliferation -0.043 0.26 -10000 0 -0.74 60 60
KITLG 0.013 0.005 -10000 0 -10000 0 0
cell motility -0.043 0.26 -10000 0 -0.74 60 60
PTPN6 0.004 0.01 -10000 0 -10000 0 0
EPOR 0.01 0.1 -10000 0 -10000 0 0
STAT5A (dimer) -0.031 0.22 -10000 0 -0.61 60 60
SOCS1 -0.002 0.033 -10000 0 -0.74 1 1
cell migration 0.035 0.18 0.45 73 -10000 0 73
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.002 0.064 -10000 0 -0.57 6 6
VAV1 -0.008 0.074 -10000 0 -0.74 5 5
GRB10 -0.021 0.15 -10000 0 -0.43 60 60
PTPN11 0.003 0.008 -10000 0 -10000 0 0
SCF/KIT -0.057 0.15 -10000 0 -0.46 60 60
GO:0007205 0 0.008 -10000 0 -10000 0 0
MAP2K1 0.016 0.11 -10000 0 -0.36 11 11
CBL 0 0 -10000 0 -10000 0 0
KIT -0.12 0.46 -10000 0 -1.4 60 60
MAP2K2 0.016 0.11 -10000 0 -0.36 11 11
SHC/Grb2/SOS1 -0.049 0.13 -10000 0 -0.4 60 60
STAT5A -0.033 0.22 -10000 0 -0.63 60 60
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.02 0.15 -10000 0 -0.42 60 60
SHC/GRAP2 -0.03 0.12 -10000 0 -0.56 26 26
PTPRO -0.049 0.21 -10000 0 -0.5 79 79
SH2B2 -0.021 0.15 -10000 0 -0.43 60 60
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.037 0.18 -10000 0 -0.46 73 73
CREBBP 0.028 0.011 -10000 0 -10000 0 0
BCL2 0.011 0.1 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.39 -9999 0 -1.2 50 50
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.036 0.12 -9999 0 -0.43 8 8
ATF2/c-Jun -0.01 0.098 -9999 0 -0.43 3 3
MAPK11 -0.036 0.12 -9999 0 -0.43 8 8
MITF -0.041 0.16 -9999 0 -0.37 83 83
MAPKAPK5 -0.032 0.15 -9999 0 -0.53 8 8
KRT8 -0.032 0.15 -9999 0 -0.36 73 73
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.054 0.18 -9999 0 -0.46 73 73
CEBPB -0.032 0.15 -9999 0 -0.53 8 8
SLC9A1 -0.032 0.15 -9999 0 -0.36 73 73
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.026 0.15 -9999 0 -0.52 8 8
p38alpha-beta/MNK1 -0.065 0.13 -9999 0 -0.58 8 8
JUN -0.009 0.098 -9999 0 -0.42 3 3
PPARGC1A -0.13 0.28 -9999 0 -0.5 146 146
USF1 -0.032 0.15 -9999 0 -0.36 73 73
RAB5/GDP/GDI1 -0.045 0.095 -9999 0 -0.4 8 8
NOS2 -0.098 0.32 -9999 0 -1.2 31 31
DDIT3 -0.032 0.15 -9999 0 -0.53 8 8
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.018 0.12 -9999 0 -0.44 8 8
p38alpha-beta/HBP1 -0.065 0.13 -9999 0 -0.58 8 8
CREB1 -0.03 0.15 -9999 0 -0.38 73 73
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.021 0.13 -9999 0 -0.52 8 8
RPS6KA4 -0.032 0.15 -9999 0 -0.36 73 73
PLA2G4A -0.025 0.14 -9999 0 -0.53 13 13
GDI1 -0.032 0.15 -9999 0 -0.53 8 8
TP53 -0.044 0.18 -9999 0 -0.45 73 73
RPS6KA5 -0.032 0.15 -9999 0 -0.53 8 8
ESR1 -0.054 0.19 -9999 0 -0.42 88 88
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.042 0.17 -9999 0 -0.39 81 81
MEF2A -0.032 0.15 -9999 0 -0.36 73 73
EIF4EBP1 -0.032 0.16 -9999 0 -0.38 73 73
KRT19 -0.039 0.18 -9999 0 -0.4 75 75
ELK4 -0.032 0.15 -9999 0 -0.53 8 8
ATF6 -0.032 0.15 -9999 0 -0.36 73 73
ATF1 -0.03 0.15 -9999 0 -0.38 73 73
p38alpha-beta/MAPKAPK2 -0.065 0.13 -9999 0 -0.58 8 8
p38alpha-beta/MAPKAPK3 -0.065 0.13 -9999 0 -0.58 8 8
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.097 0.18 -10000 0 -0.44 108 108
regulation of S phase of mitotic cell cycle -0.064 0.13 -10000 0 -0.31 102 102
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.05 0.16 -10000 0 -0.46 17 17
T-DHT/AR -0.12 0.23 -10000 0 -0.57 102 102
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 56 56
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.033 -10000 0 -0.74 1 1
mol:GDP -0.12 0.22 -10000 0 -0.55 102 102
cell proliferation -0.056 0.2 -10000 0 -0.65 17 17
PIK3CA 0 0 -10000 0 -10000 0 0
FOS -0.085 0.29 -10000 0 -0.86 56 56
mol:Ca2+ -0.012 0.022 -10000 0 -0.085 8 8
MAPK3 -0.052 0.18 -10000 0 -0.58 17 17
MAPK1 -0.021 0.096 -10000 0 -0.3 17 17
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 56 56
cAMP biosynthetic process 0.011 0.021 -10000 0 -10000 0 0
GNG2 -0.008 0.074 -10000 0 -0.74 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 56 56
HRAS/GTP -0.086 0.16 -10000 0 -0.4 102 102
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 56 56
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.046 0.17 0.45 56 -10000 0 56
T-DHT/AR/PELP1 -0.1 0.2 -10000 0 -0.49 102 102
HRAS/GDP -0.11 0.21 -10000 0 -0.52 102 102
CREB1 -0.051 0.19 -10000 0 -0.48 56 56
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.15 0.3 -10000 0 -0.74 102 102
GNB1 -0.002 0.033 -10000 0 -0.74 1 1
RAF1 -0.057 0.17 -10000 0 -0.38 102 102
RAC1-CDC42/GDP -0.1 0.2 -10000 0 -0.5 102 102
T-DHT/AR/PELP1/Src -0.092 0.18 -10000 0 -0.44 102 102
MAP2K2 -0.05 0.16 -10000 0 -0.46 17 17
T-DHT/AR/PELP1/Src/PI3K -0.064 0.13 -10000 0 -0.31 102 102
GNAZ -0.009 0.081 -10000 0 -0.74 6 6
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.024 0.065 -10000 0 -0.62 3 3
mol:T-DHT 0 0.001 -10000 0 -0.003 39 39
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.007 0.037 -10000 0 -0.57 2 2
Gi family/GTP -0.043 0.085 -10000 0 -0.44 5 5
CDC42 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.19 0.22 -10000 0 -0.42 229 229
TP53 -0.051 0.056 -10000 0 -10000 0 0
Senescence -0.051 0.056 -10000 0 -10000 0 0
Apoptosis -0.051 0.056 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.097 0.11 0.31 4 -0.43 1 5
MDM4 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.2 0.43 -9999 0 -1.2 40 40
HDAC7 -0.007 0.013 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 -9999 0 -0.89 39 39
SMAD4 0 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.43 -9999 0 -1.2 39 39
AP1 -0.066 0.18 -9999 0 -0.56 56 56
ABCG2 -0.24 0.5 -9999 0 -1.3 60 60
HIF1A -0.023 0.07 -9999 0 -10000 0 0
TFF3 -0.24 0.47 -9999 0 -1.3 46 46
GATA2 -0.07 0.23 -9999 0 -0.74 52 52
AKT1 -0.033 0.058 -9999 0 -10000 0 0
response to hypoxia -0.047 0.064 -9999 0 -10000 0 0
MCL1 -0.2 0.43 -9999 0 -1.2 39 39
NDRG1 -0.2 0.44 -9999 0 -1.2 41 41
SERPINE1 -0.2 0.43 -9999 0 -1.2 39 39
FECH -0.2 0.43 -9999 0 -1.2 40 40
FURIN -0.2 0.43 -9999 0 -1.2 40 40
NCOA2 0.007 0.034 -9999 0 -0.74 1 1
EP300 -0.023 0.088 -9999 0 -10000 0 0
HMOX1 -0.2 0.43 -9999 0 -1.2 40 40
BHLHE40 -0.2 0.43 -9999 0 -1.2 39 39
BHLHE41 -0.2 0.45 -9999 0 -1.2 42 42
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.031 0.079 -9999 0 -0.51 5 5
ENG 0.003 0.13 -9999 0 -0.83 7 7
JUN 0.008 0.005 -9999 0 -10000 0 0
RORA -0.2 0.43 -9999 0 -1.2 39 39
ABCB1 -0.2 0.45 -9999 0 -1.4 61 61
TFRC -0.2 0.43 -9999 0 -1.2 39 39
CXCR4 -0.2 0.43 -9999 0 -1.2 40 40
TF -0.22 0.45 -9999 0 -1.2 46 46
CITED2 -0.2 0.44 -9999 0 -1.2 40 40
HIF1A/ARNT -0.24 0.49 -9999 0 -1.4 46 46
LDHA -0.034 0.047 -9999 0 -10000 0 0
ETS1 -0.21 0.45 -9999 0 -1.3 39 39
PGK1 -0.2 0.43 -9999 0 -1.2 40 40
NOS2 -0.24 0.48 -9999 0 -1.2 55 55
ITGB2 -0.21 0.46 -9999 0 -1.3 45 45
ALDOA -0.2 0.43 -9999 0 -1.2 39 39
Cbp/p300/CITED2 -0.24 0.43 -9999 0 -1.2 44 44
FOS -0.077 0.24 -9999 0 -0.74 56 56
HK2 -0.2 0.43 -9999 0 -1.2 39 39
SP1 0.011 0.024 -9999 0 -10000 0 0
GCK -0.029 0.14 -9999 0 -0.73 1 1
HK1 -0.2 0.43 -9999 0 -1.2 39 39
NPM1 -0.2 0.43 -9999 0 -1.2 39 39
EGLN1 -0.2 0.43 -9999 0 -1.2 39 39
CREB1 0.016 0 -9999 0 -10000 0 0
PGM1 -0.2 0.43 -9999 0 -1.2 39 39
SMAD3 0 0.002 -9999 0 -10000 0 0
EDN1 -0.16 0.4 -9999 0 -1.3 48 48
IGFBP1 -0.2 0.44 -9999 0 -1.2 42 42
VEGFA -0.23 0.31 -9999 0 -0.84 33 33
HIF1A/JAB1 -0.017 0.029 -9999 0 -10000 0 0
CP -0.22 0.46 -9999 0 -1.3 43 43
CXCL12 -0.23 0.48 -9999 0 -1.3 49 49
COPS5 0.009 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.004 -9999 0 -10000 0 0
BNIP3 -0.2 0.43 -9999 0 -1.2 40 40
EGLN3 -0.24 0.47 -9999 0 -1.2 50 50
CA9 -0.42 0.47 -9999 0 -1.2 68 68
TERT -0.3 0.49 -9999 0 -1.2 58 58
ENO1 -0.2 0.43 -9999 0 -1.2 39 39
PFKL -0.2 0.43 -9999 0 -1.2 39 39
NCOA1 0 0.001 -9999 0 -10000 0 0
ADM -0.2 0.43 -9999 0 -1.2 40 40
ARNT -0.023 0.07 -9999 0 -10000 0 0
HNF4A 0.002 0.075 -9999 0 -0.57 8 8
ADFP -0.2 0.43 -9999 0 -1.2 42 42
SLC2A1 -0.44 0.35 -9999 0 -0.94 90 90
LEP -0.25 0.47 -9999 0 -1.2 55 55
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -9999 0 -0.91 44 44
EPO -0.081 0.25 -9999 0 -0.83 3 3
CREBBP -0.023 0.088 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.26 0.37 -9999 0 -0.95 56 56
PFKFB3 -0.2 0.43 -9999 0 -1.2 39 39
NT5E -0.2 0.44 -9999 0 -1.2 40 40
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.03 0.12 -9999 0 -0.56 26 26
alphaV beta3 Integrin -0.022 0.1 -9999 0 -0.5 22 22
PTK2 -0.19 0.23 -9999 0 -0.7 40 40
IGF1R 0 0 -9999 0 -10000 0 0
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
CDKN1B -0.23 0.29 -9999 0 -0.58 190 190
VEGFA 0 0 -9999 0 -10000 0 0
ILK -0.23 0.29 -9999 0 -0.58 190 190
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.21 0.27 -9999 0 -0.54 190 190
PTK2B -0.028 0.12 -9999 0 -0.8 5 5
alphaV/beta3 Integrin/JAM-A -0.18 0.22 -9999 0 -0.84 13 13
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.011 0.068 -9999 0 -0.48 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.015 0.078 -9999 0 -0.43 16 16
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.16 -9999 0 -0.65 20 20
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.064 -9999 0 -0.48 9 9
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.038 0.14 -9999 0 -0.78 10 10
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.19 0.18 -9999 0 -0.6 8 8
RPS6KB1 -0.035 0.13 -9999 0 -0.72 10 10
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.1 0.18 -9999 0 -0.77 22 22
GPR124 0 0 -9999 0 -10000 0 0
MAPK1 -0.1 0.18 -9999 0 -0.77 22 22
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.31 0.24 -9999 0 -0.49 308 308
cell adhesion -0.011 0.066 -9999 0 -0.44 8 8
ANGPTL3 -0.005 0.052 -9999 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.025 0.11 -9999 0 -0.48 26 26
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.059 0.2 -9999 0 -0.74 39 39
ITGB3 -0.012 0.094 -9999 0 -0.74 8 8
IGF1 -0.025 0.13 -9999 0 -0.73 17 17
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.008 0.06 -9999 0 -0.48 8 8
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.005 0.058 -9999 0 -0.74 3 3
alphaV/beta3 Integrin/CD47 -0.011 0.071 -9999 0 -0.48 11 11
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.034 0.13 -9999 0 -0.5 33 33
CSF1 -0.006 0.067 -9999 0 -0.74 4 4
PIK3C2A -0.23 0.29 -9999 0 -0.58 190 190
PI4 Kinase/Pyk2 -0.16 0.21 -9999 0 -0.74 26 26
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.03 0.12 -9999 0 -0.5 29 29
FAK1/Vinculin -0.15 0.18 -9999 0 -0.55 31 31
alphaV beta3/Integrin/ppsTEM5 -0.008 0.061 -9999 0 -0.48 8 8
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.29 0.36 -9999 0 -0.74 192 192
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.023 0.13 -9999 0 -0.74 15 15
F11R 0.002 0.099 -9999 0 -0.56 15 15
alphaV/beta3 Integrin/Lactadherin -0.008 0.061 -9999 0 -0.48 8 8
alphaV/beta3 Integrin/TGFBR2 -0.045 0.16 -9999 0 -0.54 41 41
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.039 -9999 0 -0.43 4 4
HSP90AA1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.007 0.056 -9999 0 -0.44 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.017 0.11 -9999 0 -0.74 11 11
alphaV/beta3 Integrin/Pyk2 -0.028 0.12 -9999 0 -0.81 5 5
SDC1 -0.002 0.033 -9999 0 -0.74 1 1
VAV3 -0.004 0.04 -9999 0 -0.4 5 5
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.15 0.18 -9999 0 -0.55 31 31
cell migration -0.13 0.16 -9999 0 -0.48 30 30
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.16 0.2 -9999 0 -0.76 13 13
SPP1 -0.3 0.29 -9999 0 -0.57 256 256
KDR -0.039 0.17 -9999 0 -0.74 26 26
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.46 0.36 -9999 0 -0.74 308 308
angiogenesis -0.11 0.22 -9999 0 -0.76 24 24
Rac1/GTP -0.004 0.037 -9999 0 -10000 0 0
EDIL3 -0.041 0.17 -9999 0 -0.74 27 27
cell proliferation -0.045 0.16 -9999 0 -0.54 41 41
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.27 0.34 -10000 0 -0.84 51 51
PCK1 -0.14 0.21 -10000 0 -0.78 14 14
HNF4A -0.31 0.4 -10000 0 -1.1 42 42
KCNJ11 -0.28 0.39 -10000 0 -1 39 39
AKT1 -0.001 0.086 -10000 0 -10000 0 0
response to starvation -0.009 0.034 -10000 0 -10000 0 0
DLK1 -0.3 0.38 -10000 0 -0.94 49 49
NKX2-1 -0.78 0.79 -10000 0 -1.5 258 258
ACADM -0.27 0.34 -10000 0 -0.85 43 43
TAT -0.12 0.2 -10000 0 -0.76 10 10
CEBPB 0.003 0.006 -10000 0 -10000 0 0
CEBPA 0.002 0.035 -10000 0 -0.75 1 1
TTR -0.051 0.19 -10000 0 -0.78 16 16
PKLR -0.27 0.34 -10000 0 -0.88 42 42
APOA1 -0.43 0.55 -10000 0 -1.4 79 79
CPT1C -0.27 0.34 -10000 0 -0.86 39 39
ALAS1 -0.11 0.18 -10000 0 -10000 0 0
TFRC -0.16 0.25 -10000 0 -0.89 12 12
FOXF1 0.005 0.24 0.28 4 -0.62 54 58
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.014 0.082 -10000 0 -0.6 8 8
CPT1A -0.27 0.34 -10000 0 -0.84 50 50
HMGCS1 -0.27 0.34 -10000 0 -0.93 22 22
NR3C1 0.017 0.012 -10000 0 -10000 0 0
CPT1B -0.27 0.34 -10000 0 -0.84 51 51
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.006 0.03 -10000 0 -10000 0 0
GCK -0.27 0.34 -10000 0 -0.84 54 54
CREB1 0.007 0.016 -10000 0 -10000 0 0
IGFBP1 -0.12 0.17 -10000 0 -0.65 4 4
PDX1 -0.18 0.24 -10000 0 -0.68 20 20
UCP2 -0.27 0.34 -10000 0 -0.83 52 52
ALDOB -0.27 0.36 -10000 0 -0.95 24 24
AFP 0.018 0.13 -10000 0 -0.76 3 3
BDH1 -0.27 0.34 -10000 0 -0.84 51 51
HADH -0.27 0.36 -10000 0 -0.93 24 24
F2 -0.34 0.42 -10000 0 -1.1 40 40
HNF1A -0.014 0.083 -10000 0 -0.6 8 8
G6PC 0.009 0.086 -10000 0 -0.74 1 1
SLC2A2 -0.17 0.23 -10000 0 -0.78 3 3
INS -0.009 0.011 -10000 0 -10000 0 0
FOXA1 0.073 0.14 0.35 10 -0.57 11 21
FOXA3 -0.01 0.15 -10000 0 -0.72 18 18
FOXA2 -0.32 0.41 -10000 0 -0.92 66 66
ABCC8 -0.29 0.39 -10000 0 -1 42 42
ALB 0.026 0.12 -10000 0 -0.67 4 4
Canonical Wnt signaling pathway

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
HDAC1 0.004 0.019 -10000 0 -10000 0 0
AES 0.003 0.015 -10000 0 -10000 0 0
FBXW11 0 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 0 -10000 0 -10000 0 0
DKK2 -0.13 0.28 -10000 0 -0.74 87 87
TLE1 0.002 0.031 -10000 0 -0.61 1 1
MACF1 0.004 0.048 -10000 0 -0.74 2 2
CTNNB1 0.068 0.098 0.29 10 -10000 0 10
WIF1 -0.47 0.36 -10000 0 -0.74 311 311
beta catenin/RanBP3 0.003 0.093 0.39 22 -10000 0 22
KREMEN2 -0.37 0.27 -10000 0 -0.57 318 318
DKK1 -0.038 0.15 -10000 0 -0.62 30 30
beta catenin/beta TrCP1 0.069 0.092 0.28 10 -10000 0 10
FZD1 0.001 0.003 -10000 0 -10000 0 0
AXIN2 -0.04 0.29 -10000 0 -1.5 18 18
AXIN1 0.008 0.005 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.094 0.052 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.02 0.063 0.24 29 -10000 0 29
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.041 -10000 0 -10000 0 0
HNF1A -0.006 0.076 -10000 0 -0.58 8 8
CTBP1 0.004 0.018 -10000 0 -10000 0 0
MYC 0.007 0.05 -10000 0 -10000 0 0
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.3 0.25 -10000 0 -0.72 87 87
NKD1 -0.071 0.22 -10000 0 -0.72 48 48
TCF4 0.002 0.038 -10000 0 -0.74 1 1
TCF3 0.004 0.018 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.019 -10000 0 -10000 0 0
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.098 0.45 23 -10000 0 23
LEF1 0.003 0.031 -10000 0 -0.58 1 1
DVL1 0.08 0.061 0.21 1 -10000 0 1
CSNK2A1 0.001 0.003 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.068 -10000 0 -0.56 1 1
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.67 24 24
LRP6 0.003 0.005 -10000 0 -10000 0 0
CSNK1A1 0.004 0.019 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.009 0.17 -10000 0 -1.5 6 6
WNT1 0.004 0.037 -10000 0 -0.57 2 2
GSK3A 0.008 0.005 -10000 0 -10000 0 0
GSK3B 0.001 0.003 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
PPP2R5D 0.076 0.1 0.37 48 -10000 0 48
APC 0 0.019 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.16 0.12 0.26 309 -10000 0 309
CREBBP 0.004 0.018 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.015 0.13 -9999 0 -0.5 31 31
ADCY5 -0.029 0.15 -9999 0 -0.5 44 44
ADCY6 0.016 0.032 -9999 0 -0.48 2 2
ADCY7 0.017 0.023 -9999 0 -0.48 1 1
ADCY1 0.015 0.039 -9999 0 -0.49 3 3
ADCY2 -0.025 0.13 -9999 0 -0.4 49 49
ADCY3 0.017 0.023 -9999 0 -0.48 1 1
ADCY8 -0.14 0.23 -9999 0 -0.48 155 155
PRKCE 0.009 0.026 -9999 0 -0.57 1 1
ADCY9 0.016 0.032 -9999 0 -0.48 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.068 0.13 -9999 0 -0.44 25 25
Coregulation of Androgen receptor activity

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
NRIP1 0.002 0.004 -9999 0 -10000 0 0
SVIL 0.001 0.004 -9999 0 -10000 0 0
ZNF318 0 0.005 -9999 0 -10000 0 0
JMJD2C -0.004 0.026 -9999 0 -0.08 49 49
T-DHT/AR/Ubc9 -0.13 0.21 -9999 0 -0.52 102 102
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0 0.001 -9999 0 -10000 0 0
PELP1 0 0.001 -9999 0 -10000 0 0
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.001 0.004 -9999 0 -10000 0 0
MED1 0 0.002 -9999 0 -10000 0 0
MAK -0.052 0.19 -9999 0 -0.74 35 35
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.001 0.004 -9999 0 -10000 0 0
GSN 0.002 0.004 -9999 0 -10000 0 0
NCOA2 -0.002 0.033 -9999 0 -0.74 1 1
NCOA6 0.002 0.004 -9999 0 -10000 0 0
DNA-PK 0 0.006 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.094 0.24 -9999 0 -0.94 35 35
XRCC5 0 0.002 -9999 0 -10000 0 0
UBE3A 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.14 0.22 -9999 0 -0.54 112 112
FHL2 -0.055 0.081 -9999 0 -0.55 2 2
RANBP9 0.002 0.004 -9999 0 -10000 0 0
JMJD1A -0.034 0.07 -9999 0 -0.13 158 158
CDK6 -0.002 0.037 -9999 0 -0.57 2 2
TGFB1I1 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.14 0.22 -9999 0 -0.53 107 107
XRCC6 0 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.24 -9999 0 -0.55 103 103
CTDSP1 0.001 0.003 -9999 0 -10000 0 0
CTDSP2 0 0.004 -9999 0 -10000 0 0
BRCA1 0.001 0.004 -9999 0 -10000 0 0
TCF4 -0.001 0.034 -9999 0 -0.74 1 1
CDKN2A -0.27 0.29 -9999 0 -0.57 229 229
SRF 0.016 0.007 -9999 0 -10000 0 0
NKX3-1 -0.11 0.14 -9999 0 -0.95 2 2
KLK3 0.029 0.051 -9999 0 -10000 0 0
TMF1 0.001 0.003 -9999 0 -10000 0 0
HNRNPA1 0 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.13 0.21 -9999 0 -0.52 102 102
AR -0.17 0.31 -9999 0 -0.77 102 102
UBA3 0.001 0.003 -9999 0 -10000 0 0
PATZ1 0 0.002 -9999 0 -10000 0 0
PAWR 0.001 0.003 -9999 0 -10000 0 0
PRKDC 0 0.002 -9999 0 -10000 0 0
PA2G4 0 0.003 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.12 0.19 -9999 0 -0.48 102 102
RPS6KA3 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.21 -9999 0 -0.52 102 102
LATS2 -0.001 0.033 -9999 0 -0.74 1 1
T-DHT/AR/PRX1 -0.12 0.19 -9999 0 -0.48 102 102
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0 0.034 -9999 0 -0.74 1 1
KLK2 -0.094 0.14 -9999 0 -0.5 28 28
CASP8 0 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.48 103 103
TMPRSS2 -0.4 0.54 -9999 0 -1.2 158 158
CCND1 -0.01 0.085 -9999 0 -0.72 7 7
PIAS1 0.001 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.019 0.036 -9999 0 -0.078 115 115
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.001 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.52 104 104
CMTM2 -0.098 0.25 -9999 0 -0.74 65 65
SNURF -0.023 0.13 -9999 0 -0.74 15 15
ZMIZ1 -0.008 0.047 -9999 0 -0.8 1 1
CCND3 0 0.001 -9999 0 -10000 0 0
TGIF1 0 0.002 -9999 0 -10000 0 0
FKBP4 0 0.026 -9999 0 -0.57 1 1
Syndecan-3-mediated 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
CTTN 0 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.01 0.058 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.02 0.072 -9999 0 -10000 0 0
POMC -0.055 0.17 -9999 0 -0.58 46 46
EGFR -0.022 0.12 -9999 0 -0.63 17 17
Syndecan-3/EGFR -0.011 0.061 -9999 0 -0.4 6 6
AGRP -0.34 0.37 -9999 0 -0.74 226 226
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.04 0.15 -9999 0 -0.57 34 34
long-term memory -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/IL8 -0.013 0.062 -9999 0 -0.4 4 4
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN -0.002 0.033 -9999 0 -0.74 1 1
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.025 0.12 -9999 0 -0.57 21 21
SRC 0 0 -9999 0 -10000 0 0
PTN -0.02 0.12 -9999 0 -0.7 14 14
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.026 0.081 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.19 0.2 -9999 0 -0.4 226 226
Syndecan-3/AgRP/MC4R -0.19 0.2 -9999 0 -0.4 226 226
Fyn/Cortactin -0.001 0.025 -9999 0 -0.56 1 1
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.012 0.061 -9999 0 -0.4 4 4
IL8 -0.025 0.12 -9999 0 -0.61 20 20
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.057 0.15 -9999 0 -0.42 66 66
Gamma Secretase 0 0 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.13 0.43 -10000 0 -1.3 38 38
IL23A -0.14 0.43 -10000 0 -1.2 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.35 -10000 0 -1.1 47 47
positive regulation of T cell mediated cytotoxicity -0.14 0.46 -10000 0 -1.2 47 47
ITGA3 -0.13 0.42 -10000 0 -1.1 41 41
IL17F -0.063 0.28 -10000 0 -0.74 29 29
IL12B 0.016 0.025 -10000 0 -10000 0 0
STAT1 (dimer) -0.21 0.38 -10000 0 -1.2 47 47
CD4 -0.13 0.43 -10000 0 -1.2 40 40
IL23 -0.14 0.4 -10000 0 -1.2 36 36
IL23R 0.003 0.085 -10000 0 -10000 0 0
IL1B -0.14 0.44 -10000 0 -1.3 37 37
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.13 0.4 -10000 0 -1.1 40 40
TYK2 0.011 0.019 -10000 0 -10000 0 0
STAT4 -0.012 0.094 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.027 0.15 -10000 0 -0.74 22 22
IL12RB1 -0.037 0.19 -10000 0 -0.77 31 31
PIK3CA 0 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.026 0.15 -10000 0 -0.59 31 31
IL23R/JAK2 0.003 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.14 0.46 -10000 0 -1.2 47 47
natural killer cell activation 0 0.007 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
NFKB1 0.005 0.006 -10000 0 -10000 0 0
RELA 0.005 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.38 -10000 0 -1.1 36 36
ALOX12B -0.17 0.42 -10000 0 -1.2 38 38
CXCL1 -0.14 0.46 -10000 0 -1.2 52 52
T cell proliferation -0.14 0.46 -10000 0 -1.2 47 47
NFKBIA 0.005 0.006 -10000 0 -10000 0 0
IL17A -0.042 0.24 -10000 0 -0.59 22 22
PI3K -0.21 0.36 -10000 0 -1.1 47 47
IFNG 0 0.029 0.098 1 -0.13 8 9
STAT3 (dimer) -0.2 0.34 -10000 0 -1 47 47
IL18R1 -0.001 0.075 -10000 0 -0.74 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.06 0.28 -10000 0 -0.85 21 21
IL18/IL18R -0.028 0.13 -10000 0 -0.56 25 25
macrophage activation -0.012 0.017 -10000 0 -0.044 29 29
TNF -0.14 0.44 -10000 0 -1.3 40 40
STAT3/STAT4 -0.21 0.36 -10000 0 -1.1 47 47
STAT4 (dimer) -0.22 0.39 -10000 0 -1.2 47 47
IL18 0.003 0.058 -10000 0 -0.74 3 3
IL19 -0.13 0.4 -10000 0 -1.2 32 32
STAT5A (dimer) -0.21 0.38 -10000 0 -1.2 47 47
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.003 0.047 -10000 0 -0.74 2 2
CXCL9 -0.13 0.43 -10000 0 -1.2 37 37
MPO -0.15 0.46 -10000 0 -1.2 51 51
positive regulation of humoral immune response -0.14 0.46 -10000 0 -1.2 47 47
IL23/IL23R/JAK2/TYK2 -0.16 0.52 -10000 0 -1.4 47 47
IL6 -0.24 0.58 -10000 0 -1.3 96 96
STAT5A 0 0 -10000 0 -10000 0 0
IL2 0.006 0.008 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.007 -10000 0 -10000 0 0
CD3E -0.12 0.41 -10000 0 -1.2 32 32
keratinocyte proliferation -0.14 0.46 -10000 0 -1.2 47 47
NOS2 -0.17 0.48 -10000 0 -1.2 63 63
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.25 -9999 0 -0.73 13 13
CRP -0.15 0.25 -9999 0 -0.73 15 15
cell cycle arrest -0.17 0.27 -9999 0 -0.64 59 59
TIMP1 -0.1 0.21 -9999 0 -0.6 10 10
IL6ST -0.016 0.13 -9999 0 -0.74 16 16
Rac1/GDP -0.065 0.18 -9999 0 -0.69 19 19
AP1 -0.004 0.16 -9999 0 -0.52 13 13
GAB2 -0.003 0.12 -9999 0 -0.73 13 13
TNFSF11 -0.16 0.26 -9999 0 -0.67 34 34
HSP90B1 0 0.049 -9999 0 -10000 0 0
GAB1 0.014 0.008 -9999 0 -10000 0 0
MAPK14 -0.029 0.17 -9999 0 -0.73 15 15
AKT1 0.042 0.055 -9999 0 -10000 0 0
FOXO1 0.049 0.051 -9999 0 -10000 0 0
MAP2K6 -0.052 0.18 -9999 0 -0.73 16 16
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 -0.075 0.2 -9999 0 -0.72 16 16
MITF -0.069 0.19 -9999 0 -0.47 63 63
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M -0.46 0.69 -9999 0 -1.5 159 159
CEBPB 0.016 0.004 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.029 0.11 -9999 0 -0.53 6 6
STAT3 -0.18 0.29 -9999 0 -0.69 55 55
STAT1 -0.008 0.016 -9999 0 -10000 0 0
CEBPD -0.14 0.25 -9999 0 -0.8 13 13
PIK3CA 0.01 0.003 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
JUN 0 0.002 -9999 0 -10000 0 0
PIAS3/MITF -0.087 0.16 -9999 0 -0.63 24 24
MAPK11 -0.029 0.17 -9999 0 -0.73 15 15
STAT3 (dimer)/FOXO1 -0.19 0.31 -9999 0 -0.75 57 57
GRB2/SOS1/GAB family -0.031 0.17 -9999 0 -0.64 18 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.052 0.19 -9999 0 -0.54 38 38
GRB2 0.014 0.008 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
LBP -0.11 0.21 -9999 0 -0.64 6 6
PIK3R1 0.008 0.005 -9999 0 -10000 0 0
JAK1 0.01 0.005 -9999 0 -10000 0 0
MYC -0.14 0.25 -9999 0 -0.73 13 13
FGG -0.47 0.57 -9999 0 -1.1 228 228
macrophage differentiation -0.17 0.27 -9999 0 -0.64 59 59
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.2 -9999 0 -0.52 63 63
JUNB -0.14 0.24 -9999 0 -0.72 14 14
FOS -0.084 0.24 -9999 0 -0.74 56 56
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.19 -9999 0 -0.48 62 62
STAT1/PIAS1 -0.085 0.17 -9999 0 -0.46 56 56
GRB2/SOS1/GAB family/SHP2/PI3K 0.014 0.059 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.28 -9999 0 -0.67 59 59
PRKCD -0.09 0.22 -9999 0 -0.76 14 14
IL6R -0.008 0.12 -9999 0 -0.74 12 12
SOCS3 -0.015 0.17 -9999 0 -0.9 8 8
gp130 (dimer)/JAK1/JAK1/LMO4 -0.01 0.089 -9999 0 -0.47 17 17
Rac1/GTP -0.11 0.17 -9999 0 -0.5 52 52
HCK -0.003 0.075 -9999 0 -0.74 5 5
MAPKKK cascade 0.044 0.12 -9999 0 -0.54 13 13
bone resorption -0.15 0.25 -9999 0 -0.63 34 34
IRF1 -0.14 0.25 -9999 0 -0.73 13 13
mol:GDP -0.068 0.19 -9999 0 -0.48 58 58
SOS1 0.01 0.015 -9999 0 -10000 0 0
VAV1 -0.069 0.2 -9999 0 -0.49 58 58
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.047 0.18 -9999 0 -0.76 18 18
PTPN11 -0.006 0.013 -9999 0 -10000 0 0
IL6/IL6RA -0.1 0.24 -9999 0 -0.6 88 88
gp130 (dimer)/TYK2/TYK2/LMO4 -0.012 0.087 -9999 0 -0.47 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.087 -9999 0 -0.47 17 17
IL6 -0.12 0.28 -9999 0 -0.74 83 83
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.01 0.049 -9999 0 -0.73 2 2
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.077 0.17 -9999 0 -0.45 63 63
LMO4 0.007 0.029 -9999 0 -0.59 1 1
STAT3 (dimer)/PIAS3 -0.21 0.22 -9999 0 -0.66 55 55
MCL1 0.05 0.049 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.005 -10000 0 -10000 0 0
AES 0 0.002 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.002 0.037 -10000 0 -0.57 2 2
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 -0.001 0.033 -10000 0 -0.73 1 1
AP1 -0.077 0.18 -10000 0 -0.42 88 88
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.042 -10000 0 -0.55 1 1
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.47 0.36 -10000 0 -0.74 311 311
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 -0.37 0.27 -10000 0 -0.57 318 318
DKK1 -0.038 0.15 -10000 0 -0.62 30 30
beta catenin/beta TrCP1 0.007 0.06 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.026 0.3 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES -0.001 0.027 -10000 0 -10000 0 0
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.085 0.24 -10000 0 -0.74 56 56
JUN 0 0 -10000 0 -10000 0 0
MAP3K7 0 0.003 -10000 0 -10000 0 0
CTNNB1 0.01 0.065 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.3 0.25 -10000 0 -0.72 87 87
HNF1A -0.009 0.073 -10000 0 -0.57 8 8
CTBP1 0 0.002 -10000 0 -10000 0 0
MYC 0.002 0.012 -10000 0 -10000 0 0
NKD1 -0.071 0.22 -10000 0 -0.72 48 48
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
apoptosis -0.076 0.18 -10000 0 -0.42 88 88
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.002 0.012 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.026 0.3 1 -10000 0 1
DVL1 -0.045 0.043 -10000 0 -0.67 1 1
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 24 24
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.001 0.006 -10000 0 -10000 0 0
CCND1 -0.015 0.16 -10000 0 -1.4 6 6
WNT1 -0.002 0.037 -10000 0 -0.57 2 2
Axin1/APC/beta catenin 0.011 0.045 0.27 1 -0.36 1 2
DKK2 -0.13 0.28 -10000 0 -0.74 87 87
NOTCH1 precursor/DVL1 -0.022 0.029 -10000 0 -0.55 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
NOTCH/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
PPP2R5D 0.01 0.1 0.31 48 -10000 0 48
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.28 0.21 -10000 0 -0.43 310 310
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Reelin 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
CDK5R1/CDK5 -0.008 0.058 -9999 0 -0.41 10 10
VLDLR -0.003 0.047 -9999 0 -0.74 2 2
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.002 0.033 -9999 0 -0.74 1 1
ITGA3 -0.008 0.074 -9999 0 -0.74 5 5
RELN/VLDLR/Fyn -0.087 0.19 -9999 0 -0.48 88 88
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.001 0.022 -9999 0 -10000 0 0
AKT1 -0.056 0.12 -9999 0 -0.51 2 2
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.57 31 31
RELN/LRP8/DAB1 -0.1 0.18 -9999 0 -0.41 118 118
LRPAP1/LRP8 -0.003 0.032 -9999 0 -0.41 3 3
RELN/LRP8/DAB1/Fyn -0.093 0.17 -9999 0 -0.42 86 86
DAB1/alpha3/beta1 Integrin -0.087 0.16 -9999 0 -0.69 5 5
long-term memory -0.12 0.19 -9999 0 -0.73 15 15
DAB1/LIS1 -0.087 0.16 -9999 0 -0.63 4 4
DAB1/CRLK/C3G -0.083 0.15 -9999 0 -0.61 4 4
PIK3CA 0 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.088 0.16 -9999 0 -0.64 4 4
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.066 0.2 -9999 0 -0.65 49 49
CDK5R1 -0.012 0.081 -9999 0 -0.57 10 10
RELN -0.13 0.28 -9999 0 -0.73 87 87
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.087 0.18 -9999 0 -0.47 90 90
GRIN2A/RELN/LRP8/DAB1/Fyn -0.13 0.2 -9999 0 -0.45 103 103
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.099 0.18 -9999 0 -0.42 116 116
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.094 0.17 -9999 0 -0.42 88 88
RELN/LRP8 -0.086 0.18 -9999 0 -0.47 90 90
GRIN2B/RELN/LRP8/DAB1/Fyn -0.095 0.17 -9999 0 -0.42 87 87
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.006 0.056 -9999 0 -0.56 5 5
RAP1A -0.078 0.14 -9999 0 -0.57 4 4
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.003 0.042 -9999 0 -0.66 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.005 0.052 -9999 0 -0.57 4 4
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.015 0.096 -9999 0 -0.43 2 2
neuron adhesion -0.075 0.14 -9999 0 -0.6 5 5
LRP8 -0.004 0.045 -9999 0 -0.57 3 3
GSK3B -0.027 0.12 -9999 0 -0.48 2 2
RELN/VLDLR/DAB1/Fyn -0.093 0.17 -9999 0 -0.43 87 87
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.066 0.12 -9999 0 -0.32 87 87
CDK5 0 0 -9999 0 -10000 0 0
MAPT 0.003 0.084 -9999 0 -0.67 7 7
neuron migration -0.032 0.17 -9999 0 -0.55 5 5
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.082 -9999 0 -0.44 2 2
RELN/VLDLR -0.08 0.17 -9999 0 -0.44 85 85
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.001 0.093 -10000 0 -0.58 12 12
NFATC2 -0.054 0.3 -10000 0 -0.73 69 69
NFATC3 0.013 0.054 -10000 0 -10000 0 0
CD40LG -0.17 0.45 -10000 0 -1.1 68 68
ITCH -0.008 0.11 -10000 0 -10000 0 0
CBLB -0.008 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.28 -10000 0 -1.1 28 28
JUNB -0.002 0.033 -10000 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.053 0.12 -10000 0 -0.33 79 79
T cell anergy -0.061 0.18 -10000 0 -0.45 79 79
TLE4 -0.022 0.24 -10000 0 -0.8 23 23
Jun/NFAT1-c-4/p21SNFT -0.12 0.26 -10000 0 -1.1 20 20
AP-1/NFAT1-c-4 -0.23 0.39 -10000 0 -1.3 37 37
IKZF1 -0.031 0.28 -10000 0 -1 23 23
T-helper 2 cell differentiation -0.044 0.28 -10000 0 -0.86 36 36
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.67 50 50
CALM1 -0.028 0.065 -10000 0 -10000 0 0
EGR2 -0.017 0.3 -10000 0 -1.6 12 12
EGR3 -0.019 0.31 -10000 0 -1.5 14 14
NFAT1/FOXP3 -0.09 0.21 -10000 0 -0.73 25 25
EGR1 -0.005 0.1 -10000 0 -0.74 9 9
JUN 0.002 0.022 -10000 0 -10000 0 0
EGR4 -0.005 0.087 -10000 0 -0.57 11 11
mol:Ca2+ -0.032 0.073 -10000 0 -10000 0 0
GBP3 -0.04 0.28 -10000 0 -0.9 32 32
FOSL1 -0.002 0.037 -10000 0 -0.57 2 2
NFAT1-c-4/MAF/IRF4 -0.097 0.26 -10000 0 -1.2 17 17
DGKA -0.018 0.22 -10000 0 -0.76 21 21
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.29 -10000 0 -1.1 24 24
CTLA4 -0.018 0.21 -10000 0 -0.77 16 16
NFAT1-c-4 (dimer)/EGR1 -0.11 0.28 -10000 0 -1.2 21 21
NFAT1-c-4 (dimer)/EGR4 -0.11 0.27 -10000 0 -1.1 19 19
FOS -0.083 0.24 -10000 0 -0.75 56 56
IFNG -0.16 0.35 -10000 0 -1.1 47 47
T cell activation -0.04 0.24 -10000 0 -0.85 14 14
MAF 0 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 -0.004 0.19 0.85 11 -10000 0 11
TNF -0.037 0.3 -10000 0 -1 23 23
FASLG -0.086 0.44 -10000 0 -1.5 34 34
TBX21 -0.065 0.23 -10000 0 -0.74 51 51
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.06 0.22 -10000 0 -0.74 46 46
PTPN1 -0.018 0.22 -10000 0 -0.72 25 25
NFAT1-c-4/ICER1 -0.1 0.26 -10000 0 -1.1 19 19
GATA3 -0.023 0.13 -10000 0 -0.71 17 17
T-helper 1 cell differentiation -0.15 0.34 -10000 0 -1 49 49
IL2RA -0.14 0.28 -10000 0 -0.89 41 41
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.22 -10000 0 -0.8 18 18
E2F1 0.015 0.004 -10000 0 -10000 0 0
PPARG -0.088 0.24 -10000 0 -0.74 58 58
SLC3A2 -0.018 0.22 -10000 0 -0.76 21 21
IRF4 -0.009 0.081 -10000 0 -0.74 6 6
PTGS2 -0.15 0.41 -10000 0 -1.1 53 53
CSF2 -0.15 0.42 -10000 0 -1.1 46 46
JunB/Fra1/NFAT1-c-4 -0.096 0.25 -10000 0 -1.1 16 16
IL4 -0.049 0.3 -10000 0 -0.93 34 34
IL5 -0.12 0.36 -10000 0 -1 35 35
IL2 -0.041 0.24 -10000 0 -0.9 12 12
IL3 -0.037 0.049 -10000 0 -10000 0 0
RNF128 -0.097 0.31 -10000 0 -0.8 79 79
NFATC1 0.004 0.19 -10000 0 -0.88 10 10
CDK4 0.007 0.16 0.62 8 -10000 0 8
PTPRK -0.018 0.22 -10000 0 -0.71 26 26
IL8 -0.12 0.38 -10000 0 -1.1 36 36
POU2F1 0 0.003 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.08 0.12 -10000 0 -0.51 18 18
epithelial cell differentiation -0.036 0.1 -10000 0 -0.55 11 11
ITCH 0.023 0.027 -10000 0 -10000 0 0
WWP1 -0.039 0.088 -10000 0 -0.4 1 1
FYN -0.002 0.033 -10000 0 -0.74 1 1
EGFR -0.022 0.12 -10000 0 -0.63 17 17
PRL -0.009 0.073 -10000 0 -0.57 8 8
neuron projection morphogenesis 0.001 0.088 -10000 0 -10000 0 0
PTPRZ1 -0.39 0.27 -10000 0 -0.57 328 328
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.043 0.076 -10000 0 -0.48 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.057 0.096 -10000 0 -0.5 14 14
ADAM17 0.023 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.059 0.11 -10000 0 -0.49 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.18 0.22 -10000 0 -0.54 125 125
NCOR1 0 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.053 0.091 -10000 0 -0.48 15 15
GRIN2B -0.028 0.1 -10000 0 -0.52 8 8
ErbB4/ErbB2/betacellulin -0.074 0.13 -10000 0 -0.48 38 38
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.026 0.14 -10000 0 -0.74 17 17
PRLR -0.04 0.15 -10000 0 -0.63 31 31
E4ICDs/ETO2 -0.072 0.1 -10000 0 -0.6 8 8
axon guidance 0.053 0.073 -10000 0 -10000 0 0
NEDD4 0.022 0.043 -10000 0 -0.71 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.036 0.13 -10000 0 -0.46 38 38
CBFA2T3 -0.012 0.094 -10000 0 -0.74 8 8
ErbB4/ErbB2/HBEGF -0.056 0.092 -10000 0 -0.45 17 17
MAPK3 -0.038 0.071 -10000 0 -0.45 7 7
STAT1 (dimer) -0.064 0.079 -10000 0 -0.43 1 1
MAPK1 -0.038 0.071 -10000 0 -0.45 7 7
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.053 0.088 -10000 0 -0.46 14 14
NRG1 0.014 0.099 -10000 0 -0.56 14 14
NRG3 -0.19 0.32 -10000 0 -0.74 124 124
NRG2 -0.077 0.23 -10000 0 -0.74 51 51
NRG4 -0.07 0.19 -10000 0 -0.57 60 60
heart development 0.053 0.073 -10000 0 -10000 0 0
neural crest cell migration -0.053 0.087 -10000 0 -0.46 14 14
ERBB2 0.029 0.032 -10000 0 -0.42 2 2
WWOX/E4ICDs -0.064 0.079 -10000 0 -0.43 1 1
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.1 0.14 -10000 0 -0.47 35 35
apoptosis 0.2 0.26 0.57 125 -10000 0 125
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.17 -10000 0 -0.54 51 51
ErbB4/ErbB2/epiregulin -0.13 0.18 -10000 0 -0.47 97 97
ErbB4/ErbB4/betacellulin/betacellulin -0.1 0.15 -10000 0 -0.55 38 38
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.085 0.14 -10000 0 -0.59 20 20
MDM2 -0.043 0.098 -10000 0 -0.37 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.041 0.081 -10000 0 -0.46 14 14
STAT5A 0.057 0.068 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.064 0.12 -10000 0 -0.54 19 19
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.059 0.073 -10000 0 -0.4 1 1
STAT5A (dimer) -0.038 0.11 -10000 0 -0.6 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.045 0.068 -10000 0 -10000 0 0
LRIG1 -0.002 0.033 -10000 0 -0.74 1 1
EREG -0.15 0.29 -10000 0 -0.72 103 103
BTC -0.057 0.2 -10000 0 -0.74 38 38
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.053 0.073 -10000 0 -10000 0 0
ERBB4 -0.079 0.097 -10000 0 -0.49 1 1
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 -0.02 0.025 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.077 0.12 -10000 0 -0.42 29 29
glial cell differentiation 0.059 0.072 0.4 1 -10000 0 1
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.021 0.15 -10000 0 -0.59 13 13
Regulation 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
HDAC1 0.02 0 -9999 0 -10000 0 0
SMARCC1 0.006 0.008 -9999 0 -10000 0 0
REL 0 0.002 -9999 0 -10000 0 0
HDAC7 -0.03 0.12 -9999 0 -10000 0 0
JUN 0.001 0.003 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.002 0.033 -9999 0 -0.74 1 1
KAT5 0 0.001 -9999 0 -10000 0 0
MAPK14 0.011 0.026 -9999 0 -0.45 1 1
FOXO1 0 0 -9999 0 -10000 0 0
T-DHT/AR -0.037 0.13 -9999 0 -10000 0 0
MAP2K6 0.005 0.028 -9999 0 -0.6 1 1
BRM/BAF57 -0.001 0.025 -9999 0 -0.56 1 1
MAP2K4 0.007 0.007 -9999 0 -10000 0 0
SMARCA2 0 0.034 -9999 0 -0.74 1 1
PDE9A -0.11 0.23 -9999 0 -0.85 28 28
NCOA2 0.004 0.034 -9999 0 -0.74 1 1
CEBPA -0.001 0.033 -9999 0 -0.74 1 1
EHMT2 0.001 0.003 -9999 0 -10000 0 0
cell proliferation -0.047 0.17 -9999 0 -0.52 24 24
NR0B1 -0.18 0.27 -9999 0 -0.57 156 156
EGR1 -0.012 0.1 -9999 0 -0.74 9 9
RXRs/9cRA -0.23 0.22 -9999 0 -0.44 258 258
AR/RACK1/Src -0.015 0.074 -9999 0 -10000 0 0
AR/GR -0.064 0.12 -9999 0 -0.34 41 41
GNB2L1 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.012 0.016 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.014 0.074 -9999 0 -0.45 1 1
SRC 0.018 0.041 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
KLK3 -0.13 0.15 -9999 0 -0.6 13 13
APPBP2 0.007 0.006 -9999 0 -10000 0 0
TRIM24 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.037 0.053 -9999 0 -10000 0 0
TMPRSS2 -0.42 0.57 -9999 0 -1.2 157 157
RXRG -0.39 0.37 -9999 0 -0.74 258 258
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.006 0.005 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.02 0.13 -9999 0 -0.48 3 3
AR -0.053 0.15 -9999 0 -0.33 102 102
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
SRY -0.005 0.052 -9999 0 -0.57 4 4
GATA2 -0.079 0.23 -9999 0 -0.74 52 52
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.34 0.28 -9999 0 -0.57 287 287
T-DHT/AR/RACK1/Src -0.015 0.069 -9999 0 -10000 0 0
positive regulation of transcription -0.078 0.23 -9999 0 -0.74 52 52
DNAJA1 0.007 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -9999 0 -10000 0 0
NCOA1 0.014 0.004 -9999 0 -10000 0 0
SPDEF -0.097 0.25 -9999 0 -0.73 66 66
T-DHT/AR/TIF2 0.012 0.057 -9999 0 -0.37 1 1
T-DHT/AR/Hsp90 -0.037 0.053 -9999 0 -10000 0 0
GSK3B 0.007 0.005 -9999 0 -10000 0 0
NR2C1 0 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.012 0.043 -9999 0 -0.38 1 1
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0 0.002 -9999 0 -10000 0 0
POU2F1 -0.001 0.042 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.13 0.15 -9999 0 -0.47 20 20
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.001 0.003 -9999 0 -10000 0 0
Syndecan-1-mediated 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
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.014 0.099 -9999 0 -0.74 9 9
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.088 0.1 -9999 0 -0.42 4 4
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 -0.092 0.078 -9999 0 -0.4 5 5
Syndecan-1/Syntenin -0.091 0.077 -9999 0 -0.4 4 4
MAPK3 -0.058 0.087 -9999 0 -0.48 1 1
HGF/MET -0.12 0.23 -9999 0 -0.56 105 105
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.091 0.078 -9999 0 -0.39 5 5
Syndecan-1/RANTES -0.098 0.1 -9999 0 -0.52 12 12
Syndecan-1/CD147 -0.083 0.072 -9999 0 -0.43 2 2
Syndecan-1/Syntenin/PIP2 -0.087 0.075 -9999 0 -0.39 4 4
LAMA5 -0.002 0.033 -9999 0 -0.74 1 1
positive regulation of cell-cell adhesion -0.086 0.073 -9999 0 -0.38 4 4
MMP7 -0.038 0.15 -9999 0 -0.62 30 30
HGF -0.15 0.3 -9999 0 -0.74 102 102
Syndecan-1/CASK -0.084 0.094 -9999 0 -0.41 4 4
Syndecan-1/HGF/MET -0.17 0.17 -9999 0 -0.46 105 105
regulation of cell adhesion -0.049 0.085 -9999 0 -0.46 1 1
HPSE 0 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.088 0.1 -9999 0 -0.42 4 4
SDC1 -0.089 0.1 -9999 0 -0.43 4 4
Syndecan-1/Collagen -0.088 0.1 -9999 0 -0.42 4 4
PPIB 0 0 -9999 0 -10000 0 0
MET -0.004 0.054 -9999 0 -0.68 3 3
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 26 26
MAPK1 -0.058 0.087 -9999 0 -0.48 1 1
homophilic cell adhesion -0.088 0.099 -9999 0 -0.42 4 4
MMP1 -0.35 0.28 -9999 0 -0.57 302 302
Aurora A signaling

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
Aurora A/GADD45A 0.016 0.04 -9999 0 -10000 0 0
BIRC5 -0.49 0.2 -9999 0 -0.57 415 415
NFKBIA 0.018 0.041 -9999 0 -10000 0 0
CPEB1 -0.05 0.18 -9999 0 -0.74 33 33
AKT1 0.018 0.041 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.014 0.036 -9999 0 -10000 0 0
NDEL1/TACC3 0.018 0.039 -9999 0 -0.29 1 1
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.013 0.006 -9999 0 -10000 0 0
PAK1/Aurora A 0.015 0.043 -9999 0 -0.35 1 1
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.28 0.2 -9999 0 -0.41 340 340
TP53 0.019 0.028 -9999 0 -10000 0 0
DLG7 0.01 0.04 -9999 0 -10000 0 0
AURKAIP1 0 0 -9999 0 -10000 0 0
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.019 0.042 -9999 0 -0.31 1 1
G2/M transition of mitotic cell cycle 0.014 0.036 -9999 0 -10000 0 0
AURKA 0.016 0.05 -9999 0 -10000 0 0
AURKB -0.087 0.05 -9999 0 -0.16 21 21
CDC25B 0.02 0.034 -9999 0 -10000 0 0
G2/M transition checkpoint 0.014 0.036 -9999 0 -10000 0 0
mRNA polyadenylation -0.017 0.12 -9999 0 -0.44 33 33
Aurora A/CPEB -0.017 0.12 -9999 0 -0.44 33 33
Aurora A/TACC1/TRAP/chTOG 0.023 0.044 -9999 0 -0.4 2 2
BRCA1 0 0 -9999 0 -10000 0 0
centrosome duplication 0.015 0.043 -9999 0 -0.34 1 1
regulation of centrosome cycle 0.017 0.039 -9999 0 -0.29 1 1
spindle assembly 0.015 0.043 -9999 0 -0.4 2 2
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.24 0.1 -9999 0 -0.41 22 22
CENPA -0.075 0.041 -9999 0 -0.17 21 21
Aurora A/PP2A 0.016 0.04 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.029 0.031 -9999 0 -10000 0 0
negative regulation of DNA binding 0.019 0.028 -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 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.014 0.036 -9999 0 -10000 0 0
mitotic prometaphase 0.025 0.017 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.05 -9999 0 -10000 0 0
TACC1 -0.003 0.047 -9999 0 -0.74 2 2
TACC3 -0.002 0.037 -9999 0 -0.57 2 2
Aurora A/Antizyme1 0.02 0.036 -9999 0 -10000 0 0
Aurora A/RasGAP 0.016 0.04 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.006 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.016 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.28 0.2 -9999 0 -0.41 340 340
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.21 0.16 -9999 0 -0.46 22 22
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
CKAP5 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 0.011 0.037 -9999 0 -0.53 1 1
NFATC2 -0.06 0.18 -9999 0 -0.52 67 67
NFATC3 0.012 0.028 -9999 0 -10000 0 0
CD40LG -0.17 0.38 -9999 0 -0.84 89 89
PTGS2 -0.15 0.34 -9999 0 -0.81 65 65
JUNB -0.002 0.033 -9999 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 -0.001 0.003 -9999 0 -10000 0 0
JUN -0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.002 0.037 -9999 0 -0.57 2 2
CREM 0 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.1 0.18 -9999 0 -0.57 43 43
FOS -0.086 0.24 -9999 0 -0.74 56 56
IFNG -0.11 0.3 -9999 0 -0.83 26 26
AP-1/NFAT1-c-4 -0.21 0.3 -9999 0 -0.77 89 89
FASLG -0.12 0.32 -9999 0 -0.9 33 33
NFAT1-c-4/ICER1 -0.083 0.16 -9999 0 -0.51 46 46
IL2RA -0.11 0.3 -9999 0 -0.85 26 26
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.15 0.34 -9999 0 -0.82 59 59
JunB/Fra1/NFAT1-c-4 -0.08 0.16 -9999 0 -0.5 43 43
IL4 -0.12 0.29 -9999 0 -0.84 23 23
IL2 -0.004 0.014 -9999 0 -10000 0 0
IL3 -0.019 0.023 -9999 0 -10000 0 0
FKBP1A 0 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0 0.003 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.053 -9999 0 -0.42 8 8
Metarhodopsin II/Arrestin -0.001 0.023 -9999 0 -0.36 2 2
PDE6G/GNAT1/GTP -0.016 0.082 -9999 0 -0.43 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.009 0.073 -9999 0 -0.57 8 8
GRK1 -0.002 0.037 -9999 0 -0.57 2 2
CNG Channel -0.056 0.13 -9999 0 -0.58 6 6
mol:Na + -0.094 0.15 -9999 0 -0.52 23 23
mol:ADP -0.002 0.036 -9999 0 -0.57 2 2
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.49 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.097 0.15 -9999 0 -0.54 23 23
CNGB1 -0.052 0.16 -9999 0 -0.57 44 44
RDH5 -0.003 0.047 -9999 0 -0.74 2 2
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.09 0.14 -9999 0 -0.5 23 23
Na + (4 Units) -0.088 0.14 -9999 0 -0.49 23 23
RGS9 -0.08 0.23 -9999 0 -0.74 53 53
GNB1/GNGT1 -0.13 0.19 -9999 0 -0.41 151 151
GNAT1/GDP -0.058 0.15 -9999 0 -0.43 61 61
GUCY2D 0 0 -9999 0 -10000 0 0
GNGT1 -0.18 0.26 -9999 0 -0.57 150 150
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.033 0.11 -9999 0 -0.42 32 32
mol:11-cis-retinal -0.003 0.047 -9999 0 -0.74 2 2
mol:cGMP -0.079 0.13 -9999 0 -10000 0 0
GNB1 -0.002 0.033 -9999 0 -0.74 1 1
Rhodopsin -0.004 0.045 -9999 0 -0.49 4 4
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.007 0.063 -9999 0 -0.57 6 6
Metarhodopsin II -0.003 0.029 -9999 0 -0.32 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.084 0.14 -9999 0 -10000 0 0
RGS9BP -0.015 0.1 -9999 0 -0.74 10 10
Metarhodopsin II/Transducin -0.051 0.076 -9999 0 -0.37 2 2
GCAP Family/Ca ++ -0.086 0.14 -9999 0 -0.32 131 131
PDE6A/B -0.026 0.12 -9999 0 -0.54 24 24
mol:Pi -0.061 0.16 -9999 0 -0.49 61 61
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.15 -9999 0 -0.56 3 3
PDE6B -0.015 0.1 -9999 0 -0.72 10 10
PDE6A -0.02 0.12 -9999 0 -0.72 14 14
PDE6G -0.015 0.1 -9999 0 -0.74 10 10
RHO -0.002 0.037 -9999 0 -0.57 2 2
PDE6 -0.075 0.17 -9999 0 -0.8 10 10
GUCA1A -0.15 0.25 -9999 0 -0.57 131 131
GC2/GCAP Family -0.085 0.14 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.13 -10000 0 -0.4 23 23
TBX21 -0.095 0.5 -10000 0 -1.4 57 57
B2M 0.008 0.048 -10000 0 -0.74 2 2
TYK2 0.016 0.016 -10000 0 -10000 0 0
IL12RB1 -0.032 0.19 -10000 0 -0.77 31 31
GADD45B -0.034 0.37 -10000 0 -1.1 40 40
IL12RB2 -0.045 0.18 -10000 0 -0.57 52 52
GADD45G -0.017 0.33 -10000 0 -1 32 32
natural killer cell activation 0.006 0.019 -10000 0 -10000 0 0
RELB -0.001 0.026 -10000 0 -0.57 1 1
RELA 0 0 -10000 0 -10000 0 0
IL18 0.009 0.06 -10000 0 -0.75 3 3
IL2RA -0.008 0.073 -10000 0 -0.66 6 6
IFNG -0.008 0.076 -10000 0 -0.68 6 6
STAT3 (dimer) -0.005 0.29 -10000 0 -0.79 42 42
HLA-DRB5 -0.063 0.22 -10000 0 -0.74 47 47
FASLG -0.049 0.41 -10000 0 -1.2 42 42
NF kappa B2 p52/RelB -0.13 0.3 -10000 0 -1 40 40
CD4 -0.014 0.13 -10000 0 -0.74 15 15
SOCS1 -0.002 0.033 -10000 0 -0.74 1 1
EntrezGene:6955 -0.001 0.009 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.74 11 11
CD3E -0.003 0.1 -10000 0 -0.74 9 9
CD3G -0.035 0.18 -10000 0 -0.74 30 30
IL12Rbeta2/JAK2 -0.02 0.14 -10000 0 -0.41 52 52
CCL3 -0.028 0.35 -10000 0 -1.1 37 37
CCL4 -0.03 0.36 -10000 0 -1.1 37 37
HLA-A 0.009 0.034 -10000 0 -0.74 1 1
IL18/IL18R 0.017 0.15 -10000 0 -0.59 25 25
NOS2 -0.078 0.44 -10000 0 -1.1 59 59
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.13 -10000 0 -0.4 21 21
IL1R1 -0.026 0.35 -10000 0 -1 38 38
IL4 -0.004 0.019 -10000 0 -10000 0 0
JAK2 0.016 0.016 -10000 0 -10000 0 0
EntrezGene:6957 0 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.31 -10000 0 -1.3 22 22
RAB7A 0.007 0.28 -10000 0 -0.82 30 30
lysosomal transport 0.011 0.27 -10000 0 -0.77 31 31
FOS -0.15 0.49 -10000 0 -1.2 77 77
STAT4 (dimer) -0.009 0.34 -10000 0 -0.95 41 41
STAT5A (dimer) -0.13 0.3 -10000 0 -0.99 42 42
GZMA -0.033 0.37 -10000 0 -1.1 36 36
GZMB -0.035 0.37 -10000 0 -1.1 37 37
HLX 0 0 -10000 0 -10000 0 0
LCK -0.037 0.39 -10000 0 -1.1 40 40
TCR/CD3/MHC II/CD4 -0.084 0.32 -10000 0 -0.89 48 48
IL2/IL2R -0.014 0.1 -10000 0 -0.66 9 9
MAPK14 -0.016 0.34 -10000 0 -0.99 39 39
CCR5 -0.025 0.36 -10000 0 -1.1 35 35
IL1B 0 0.11 -10000 0 -0.77 10 10
STAT6 0.017 0.1 -10000 0 -10000 0 0
STAT4 -0.012 0.094 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.016 0.016 -10000 0 -10000 0 0
CD8A 0 0.09 -10000 0 -0.74 7 7
CD8B -0.011 0.12 -10000 0 -0.7 15 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.13 0.4 23 -10000 0 23
IL2RB -0.005 0.058 -10000 0 -0.74 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.31 -10000 0 -0.84 41 41
IL2RG -0.012 0.094 -10000 0 -0.74 8 8
IL12 0.017 0.081 -10000 0 -0.57 8 8
STAT5A 0 0 -10000 0 -10000 0 0
CD247 -0.006 0.11 -10000 0 -0.75 11 11
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.099 -10000 0 -0.75 8 8
IL12/IL12R/TYK2/JAK2 -0.052 0.45 -10000 0 -1.2 45 45
MAP2K3 -0.02 0.34 -10000 0 -1 39 39
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.02 0.34 -10000 0 -1 39 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.055 0.21 -10000 0 -0.74 42 42
IL18RAP -0.021 0.16 -10000 0 -0.75 22 22
IL12Rbeta1/TYK2 -0.015 0.15 -10000 0 -0.6 31 31
EOMES -0.023 0.22 -10000 0 -1.4 11 11
STAT1 (dimer) -0.003 0.29 -10000 0 -0.81 37 37
T cell proliferation 0.006 0.26 -10000 0 -0.69 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.077 -10000 0 -0.75 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.1 0.23 -10000 0 -0.76 41 41
ATF2 -0.003 0.31 -10000 0 -0.9 38 38
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.009 0.071 -9999 0 -0.56 8 8
AKT1 -0.011 0.2 -9999 0 -0.65 26 26
PTK2B -0.056 0.25 -9999 0 -0.88 28 28
VEGFR2 homodimer/Frs2 -0.11 0.26 -9999 0 -0.99 26 26
CAV1 -0.21 0.33 -9999 0 -0.74 137 137
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.1 0.24 -9999 0 -0.93 26 26
endothelial cell proliferation -0.007 0.2 -9999 0 -0.62 29 29
mol:Ca2+ -0.053 0.24 -9999 0 -0.84 26 26
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.098 0.23 -9999 0 -0.88 26 26
RP11-342D11.1 -0.06 0.24 -9999 0 -0.84 26 26
CDH5 -0.15 0.3 -9999 0 -0.74 97 97
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.005 0.058 -9999 0 -0.74 3 3
HRAS/GDP -0.079 0.18 -9999 0 -0.71 26 26
SH2D2A -0.002 0.033 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.075 0.18 -9999 0 -0.67 27 27
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.1 0.24 -9999 0 -0.93 26 26
VEGFR1 homodimer 0 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.088 0.21 -9999 0 -0.81 26 26
GRB10 -0.053 0.24 -9999 0 -0.84 26 26
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.17 0.32 -9999 0 -0.95 54 54
HRAS 0 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.055 0.12 -9999 0 -0.45 28 28
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.097 0.22 -9999 0 -0.86 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.036 0.16 -9999 0 -0.74 24 24
Nck/Pak -0.001 0.019 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.1 0.25 -9999 0 -0.94 26 26
mol:GDP -0.085 0.2 -9999 0 -0.77 26 26
mol:NADP -0.009 0.17 -9999 0 -0.55 27 27
eNOS/Hsp90 -0.003 0.16 -9999 0 -0.51 27 27
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.054 0.24 -9999 0 -0.86 26 26
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFC -0.003 0.047 -9999 0 -0.74 2 2
FAK1/Vinculin -0.042 0.24 -9999 0 -0.84 28 28
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.1 0.25 -9999 0 -0.94 28 28
PTPN6 0 0 -9999 0 -10000 0 0
EPAS1 -0.13 0.29 -9999 0 -0.71 92 92
mol:L-citrulline -0.009 0.17 -9999 0 -0.55 27 27
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.098 0.23 -9999 0 -0.88 26 26
VEGFR2 homodimer/VEGFA homodimer -0.1 0.24 -9999 0 -0.94 26 26
VEGFR2/3 heterodimer -0.14 0.3 -9999 0 -0.92 41 41
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 -0.052 0.25 -9999 0 -0.87 26 26
VEGFR2 homodimer -0.1 0.31 -9999 0 -0.69 92 92
FLT1 0 0 -9999 0 -10000 0 0
NEDD4 -0.002 0.033 -9999 0 -0.74 1 1
MAPK3 -0.047 0.23 -9999 0 -0.8 26 26
MAPK1 -0.047 0.23 -9999 0 -0.8 26 26
VEGFA145/NRP2 -0.005 0.05 -9999 0 -0.56 4 4
VEGFR1/2 heterodimer -0.11 0.26 -9999 0 -0.61 92 92
KDR -0.11 0.31 -9999 0 -0.7 92 92
VEGFA165/NRP1/VEGFR2 homodimer -0.097 0.23 -9999 0 -0.9 26 26
SRC 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.047 0.23 -9999 0 -0.82 26 26
PI3K -0.089 0.21 -9999 0 -0.82 26 26
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.1 0.24 -9999 0 -0.93 26 26
FES -0.056 0.25 -9999 0 -0.89 26 26
GAB1 -0.092 0.22 -9999 0 -0.84 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.1 0.24 -9999 0 -0.93 26 26
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.097 0.23 -9999 0 -0.57 60 60
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.24 -9999 0 -0.93 26 26
PI3K/GAB1 -0.012 0.2 -9999 0 -0.67 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.094 0.22 -9999 0 -0.86 26 26
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.28 -9999 0 -1.1 29 29
HSP90AA1 0 0 -9999 0 -10000 0 0
CDC42 -0.056 0.25 -9999 0 -0.88 26 26
actin cytoskeleton reorganization -0.1 0.24 -9999 0 -0.91 26 26
PTK2 -0.053 0.27 -9999 0 -0.94 28 28
EDG1 -0.06 0.24 -9999 0 -0.84 26 26
mol:DAG -0.054 0.24 -9999 0 -0.86 26 26
CaM/Ca2+ -0.087 0.2 -9999 0 -0.78 26 26
MAP2K3 -0.044 0.23 -9999 0 -0.82 26 26
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.098 0.23 -9999 0 -0.89 26 26
PLCG1 -0.056 0.25 -9999 0 -0.88 26 26
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.098 0.23 -9999 0 -0.88 26 26
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.1 0.24 -9999 0 -0.93 26 26
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.1 0.24 -9999 0 -0.93 26 26
cell migration -0.039 0.23 -9999 0 -0.75 28 28
mol:PI-3-4-5-P3 -0.082 0.19 -9999 0 -0.73 26 26
FYN -0.002 0.033 -9999 0 -0.74 1 1
VEGFB/NRP1 -0.089 0.21 -9999 0 -0.79 26 26
mol:NO -0.009 0.17 -9999 0 -0.55 27 27
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.079 0.18 -9999 0 -0.71 26 26
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.098 0.23 -9999 0 -0.89 26 26
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.094 -9999 0 -0.74 8 8
NOS3 -0.015 0.2 -9999 0 -0.64 27 27
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.25 -9999 0 -0.94 27 27
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.043 0.23 -9999 0 -0.8 27 27
PRKCB -0.063 0.26 -9999 0 -0.88 28 28
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.095 0.22 -9999 0 -0.85 26 26
VEGFR1/2 heterodimer/VEGFA homodimer -0.1 0.24 -9999 0 -0.93 26 26
VEGFA165/NRP2 -0.005 0.05 -9999 0 -0.56 4 4
MAPKKK cascade -0.078 0.18 -9999 0 -0.71 26 26
NRP2 -0.006 0.067 -9999 0 -0.74 4 4
VEGFC homodimer -0.003 0.047 -9999 0 -0.74 2 2
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.042 0.24 -9999 0 -0.84 28 28
MAP3K13 -0.056 0.25 -9999 0 -0.88 26 26
PDPK1 -0.013 0.19 -9999 0 -0.63 26 26
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.24 0.35 -9999 0 -0.74 162 162
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0 0 -9999 0 -10000 0 0
TCEB1 0 0 -9999 0 -10000 0 0
HIF1A/p53 -0.009 0.022 -9999 0 -10000 0 0
HIF1A -0.011 0.025 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.27 0.29 -9999 0 -0.57 229 229
ARNT/IPAS -0.18 0.26 -9999 0 -0.56 162 162
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.009 0.022 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.022 -9999 0 -10000 0 0
PHD1-3/OS9 -0.045 0.11 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.016 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.009 0.022 -9999 0 -10000 0 0
EGLN3 -0.084 0.2 -9999 0 -0.57 72 72
EGLN2 0 0 -9999 0 -10000 0 0
EGLN1 0 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.14 0.14 -9999 0 -0.35 36 36
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.003 0.047 -9999 0 -0.74 2 2
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.086 0.18 -9999 0 -0.47 90 90
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.054 0.18 -9999 0 -0.43 84 84
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.57 31 31
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.006 0.067 -9999 0 -0.74 4 4
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.003 0.032 -9999 0 -0.41 3 3
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.012 0.081 -9999 0 -0.57 10 10
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.15 0.25 -9999 0 -0.57 126 126
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.2 -9999 0 -0.46 116 116
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.092 0.14 -9999 0 -0.48 28 28
MAP1B -0.002 0.019 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.073 0.15 -9999 0 -0.62 3 3
RELN -0.13 0.28 -9999 0 -0.73 87 87
PAFAH/LIS1 -0.004 0.043 -9999 0 -0.48 4 4
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.069 0.11 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.063 0.12 -9999 0 -0.31 84 84
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.1 0.15 -9999 0 -0.51 28 28
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.02 0 -9999 0 -10000 0 0
PAFAH1B3 -0.006 0.061 -9999 0 -0.61 5 5
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.001 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.087 0.14 -9999 0 -0.46 28 28
LRP8 -0.004 0.045 -9999 0 -0.57 3 3
NDEL1/Katanin 60 -0.092 0.14 -9999 0 -0.48 28 28
P39/CDK5 -0.14 0.19 -9999 0 -0.65 26 26
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.042 0.16 -9999 0 -0.4 84 84
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.091 0.17 -9999 0 -0.42 87 87
RELN/VLDLR -0.08 0.17 -9999 0 -0.44 85 85
CDC42 0 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.064 0.1 -10000 0 -0.37 4 4
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.57 146 146
NT3 (dimer)/TRKB -0.12 0.19 -10000 0 -0.54 36 36
SHC/Grb2/SOS1/GAB1/PI3K 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.095 0.25 -10000 0 -0.74 63 63
PIK3CA 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.008 0.074 -10000 0 -0.74 5 5
NTRK2 -0.14 0.26 -10000 0 -0.62 108 108
NTRK3 -0.22 0.34 -10000 0 -0.74 143 143
NT-4/5 (dimer)/TRKB -0.12 0.19 -10000 0 -0.54 38 38
neuron apoptosis 0.13 0.19 0.47 87 -10000 0 87
SHC 2-3/Grb2 -0.14 0.21 -10000 0 -0.52 87 87
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.056 0.1 -10000 0 -0.55 9 9
SHC3 -0.16 0.26 -10000 0 -0.69 86 86
STAT3 (dimer) -0.005 0.042 -10000 0 -0.37 6 6
NT3 (dimer)/TRKA -0.041 0.12 -10000 0 -0.48 10 10
RIN/GDP -0.045 0.092 -10000 0 -0.27 2 2
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.023 0.067 -10000 0 -0.46 2 2
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.013 0.11 -10000 0 -0.88 7 7
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.094 -10000 0 -0.74 8 8
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.034 0.12 -10000 0 -0.48 33 33
TRKA/NEDD4-2 -0.006 0.056 -10000 0 -0.56 5 5
ELMO1 -0.017 0.11 -10000 0 -0.74 11 11
RhoG/GTP/ELMO1/DOCK1 -0.011 0.072 -10000 0 -0.48 11 11
NGF -0.017 0.11 -10000 0 -0.7 12 12
HRAS 0 0 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.02 0.12 -10000 0 -0.74 13 13
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.031 0.086 -10000 0 -0.4 13 13
mol:GDP -0.066 0.13 -10000 0 -0.38 5 5
NGF (dimer) -0.017 0.11 -10000 0 -0.7 12 12
RhoG/GDP -0.013 0.084 -10000 0 -0.56 11 11
RIT1/GDP -0.041 0.092 -10000 0 -0.27 2 2
TIAM1 -0.002 0.033 -10000 0 -0.74 1 1
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.23 -10000 0 -0.45 156 156
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.01 0.082 -10000 0 -0.69 7 7
RAP1/GDP -0.047 0.067 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.095 0.25 -10000 0 -0.74 63 63
ubiquitin-dependent protein catabolic process -0.016 0.083 -10000 0 -0.48 14 14
Schwann cell development -0.054 0.036 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.007 0.04 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.22 0.27 -10000 0 -0.72 75 75
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.077 -10000 0 -0.38 1 1
STAT3 -0.005 0.042 -10000 0 -0.37 6 6
axon guidance -0.21 0.25 -10000 0 -0.68 75 75
MAPK3 -0.004 0.12 -10000 0 -0.43 33 33
MAPK1 -0.004 0.12 -10000 0 -0.43 33 33
CDC42/GDP -0.041 0.092 -10000 0 -0.28 1 1
NTF3 -0.01 0.083 -10000 0 -0.69 7 7
NTF4 -0.012 0.094 -10000 0 -0.74 8 8
NGF (dimer)/TRKA/FAIM -0.016 0.084 -10000 0 -0.48 14 14
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.27 0.2 -10000 0 -0.42 307 307
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.13 0.24 -10000 0 -0.49 144 144
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.057 0.08 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.092 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.016 0.085 -10000 0 -0.46 17 17
neuron projection morphogenesis 0.004 0.072 -10000 0 -0.47 1 1
NGF (dimer)/TRKA/NEDD4-2 -0.016 0.084 -10000 0 -0.48 14 14
MAP2K1 0 0 -10000 0 -10000 0 0
NGFR -0.049 0.16 -10000 0 -0.57 42 42
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.053 -10000 0 -0.31 14 14
RAS family/GTP/PI3K 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.046 0.12 -10000 0 -0.67 14 14
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.056 -10000 0 -0.56 5 5
SQSTM1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.21 -10000 0 -0.51 81 81
NGF (dimer)/TRKA/p62/Atypical PKCs -0.013 0.07 -10000 0 -0.4 14 14
MATK -0.029 0.14 -10000 0 -0.74 19 19
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.042 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.025 0.073 -10000 0 -0.33 14 14
Rac1/GTP -0.18 0.13 -10000 0 -0.32 141 141
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.14 0.14 -9999 0 -0.66 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.11 -9999 0 -0.58 3 3
alphaV/beta3 Integrin/Osteopontin/Src -0.21 0.2 -9999 0 -0.4 256 256
AP1 -0.16 0.16 -9999 0 -0.6 31 31
ILK -0.14 0.17 -9999 0 -0.7 3 3
bone resorption -0.12 0.12 -9999 0 -0.6 4 4
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.14 0.13 -9999 0 -0.65 3 3
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.025 -9999 0 -0.56 1 1
alphaV/beta3 Integrin/Osteopontin -0.18 0.17 -9999 0 -0.58 8 8
MAP3K1 -0.14 0.17 -9999 0 -0.61 5 5
JUN 0 0 -9999 0 -10000 0 0
MAPK3 -0.12 0.17 -9999 0 -0.66 3 3
MAPK1 -0.12 0.17 -9999 0 -0.66 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.16 -9999 0 -0.58 5 5
ITGB3 -0.012 0.093 -9999 0 -0.74 8 8
NFKBIA -0.1 0.16 -9999 0 -0.64 3 3
FOS -0.085 0.24 -9999 0 -0.74 56 56
CD44 -0.002 0.033 -9999 0 -0.74 1 1
CHUK 0 0 -9999 0 -10000 0 0
PLAU -0.099 0.16 -9999 0 -0.58 4 4
NF kappa B1 p50/RelA -0.12 0.11 -9999 0 -0.56 3 3
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.009 0.07 -9999 0 -0.55 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.14 0.17 -9999 0 -0.52 9 9
VAV3 -0.12 0.17 -9999 0 -0.64 5 5
MAP3K14 -0.14 0.17 -9999 0 -0.6 5 5
ROCK2 0 0 -9999 0 -10000 0 0
SPP1 -0.3 0.28 -9999 0 -0.56 256 256
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.13 -9999 0 -0.73 3 3
MMP2 -0.1 0.17 -9999 0 -0.65 8 8
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.044 0.084 -9999 0 -0.49 1 1
FZD6 0 0 -9999 0 -10000 0 0
WNT6 -0.095 0.21 -9999 0 -0.57 81 81
WNT4 -0.011 0.084 -9999 0 -0.66 8 8
FZD3 0 0 -9999 0 -10000 0 0
WNT5A -0.012 0.084 -9999 0 -0.59 10 10
WNT11 -0.037 0.16 -9999 0 -0.68 27 27
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.023 0.1 -10000 0 -0.46 25 25
ER alpha/Gai/GDP/Gbeta gamma -0.026 0.11 -10000 0 -0.46 23 23
AKT1 -0.005 0.18 -10000 0 -0.82 22 22
PIK3CA 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.008 0.18 -10000 0 -0.83 22 22
mol:Ca2+ -0.089 0.23 -10000 0 -0.48 118 118
IGF1R 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.022 0.1 -10000 0 -0.48 22 22
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.003 0.17 0.78 22 -10000 0 22
RhoA/GTP -0.016 0.074 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.027 0.11 -10000 0 -0.52 23 23
regulation of stress fiber formation -0.032 0.071 0.58 1 -10000 0 1
E2/ERA-ERB (dimer) -0.022 0.1 -10000 0 -0.48 22 22
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.02 0.092 -10000 0 -0.44 22 22
pseudopodium formation 0.032 0.071 -10000 0 -0.58 1 1
E2/ER alpha (dimer)/PELP1 -0.022 0.1 -10000 0 -0.48 22 22
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.008 0.074 -10000 0 -0.74 5 5
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.015 0.13 -10000 0 -0.54 23 23
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.1 -10000 0 -0.5 22 22
mol:NADP 0.015 0.13 -10000 0 -0.54 23 23
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.094 0.24 -10000 0 -0.5 118 118
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.22 -10000 0 -0.51 117 117
PLCB2 -0.13 0.23 -10000 0 -0.51 122 122
IGF1 -0.025 0.13 -10000 0 -0.73 17 17
mol:L-citrulline 0.015 0.13 -10000 0 -0.54 23 23
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.046 -10000 0 -0.67 1 1
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0 0 -10000 0 -10000 0 0
GNAQ -0.002 0.033 -10000 0 -0.74 1 1
ESR1 -0.033 0.15 -10000 0 -0.74 22 22
Gq family/GDP/Gbeta gamma -0.074 0.14 -10000 0 -0.81 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.072 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.027 0.11 -10000 0 -0.52 23 23
GNAZ -0.009 0.081 -10000 0 -0.74 6 6
E2/ER alpha (dimer) -0.025 0.12 -10000 0 -0.56 22 22
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.006 0.067 -10000 0 -0.74 4 4
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.033 -10000 0 -0.74 1 1
HBEGF 0.014 0.12 -10000 0 -0.72 5 5
cAMP biosynthetic process -0.021 0.091 -10000 0 -0.41 25 25
SRC 0.019 0.11 -10000 0 -0.44 23 23
PI3K 0 0 -10000 0 -10000 0 0
GNB1 -0.002 0.033 -10000 0 -0.74 1 1
G13/GDP/Gbeta gamma -0.024 0.11 -10000 0 -0.48 22 22
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.11 -10000 0 -0.58 9 9
Gs family/GTP -0.021 0.093 -10000 0 -0.42 25 25
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.016 0.12 -10000 0 -0.51 23 23
mol:DAG -0.094 0.24 -10000 0 -0.5 118 118
Gs family/GDP/Gbeta gamma -0.024 0.1 -10000 0 -0.45 22 22
MSN 0.032 0.076 -10000 0 -0.64 1 1
Gq family/GTP -0.13 0.24 -10000 0 -0.54 117 117
mol:PI-3-4-5-P3 -0.007 0.17 -10000 0 -0.79 22 22
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.016 0.12 0.51 23 -10000 0 23
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.021 0.097 -10000 0 -0.47 22 22
NOS3 0.014 0.14 -10000 0 -0.56 23 23
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.019 0.14 -10000 0 -0.63 22 22
E2/ER alpha (dimer)/PELP1/Src -0.029 0.12 -10000 0 -0.55 23 23
ruffle organization 0.032 0.071 -10000 0 -0.58 1 1
ROCK2 -0.015 0.068 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 117 117
GNA15 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MMP9 0.01 0.12 -10000 0 -0.59 5 5
MMP2 0.022 0.12 -10000 0 -0.79 5 5
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.029 -10000 0 -10000 0 0
oxygen homeostasis -0.01 0.013 -10000 0 -10000 0 0
TCEB2 0 0 -10000 0 -10000 0 0
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.099 0.12 -10000 0 -0.42 17 17
EPO -0.15 0.21 -10000 0 -0.66 14 14
FIH (dimer) 0.003 0.009 -10000 0 -10000 0 0
APEX1 0.003 0.012 -10000 0 -10000 0 0
SERPINE1 -0.2 0.24 -10000 0 -0.78 14 14
FLT1 -0.039 0.16 -10000 0 -0.96 13 13
ADORA2A -0.19 0.23 -10000 0 -0.75 14 14
germ cell development -0.19 0.24 -10000 0 -0.74 18 18
SLC11A2 -0.2 0.24 -10000 0 -0.74 19 19
BHLHE40 -0.2 0.24 -10000 0 -0.78 14 14
HIF1AN 0.003 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.14 0.16 -10000 0 -0.48 41 41
ETS1 0.002 0.12 -10000 0 -0.75 13 13
CITED2 -0.032 0.16 -10000 0 -1.3 8 8
KDR -0.095 0.33 -10000 0 -1.3 34 34
PGK1 -0.2 0.24 -10000 0 -0.78 14 14
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.21 0.29 -10000 0 -0.8 38 38
EPAS1 -0.12 0.16 -10000 0 -0.4 76 76
SP1 0.016 0 -10000 0 -10000 0 0
ABCG2 -0.24 0.32 -10000 0 -0.96 57 57
EFNA1 -0.2 0.24 -10000 0 -0.74 19 19
FXN -0.19 0.23 -10000 0 -0.72 19 19
POU5F1 -0.2 0.24 -10000 0 -0.78 18 18
neuron apoptosis 0.2 0.28 0.77 39 -10000 0 39
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.084 0.21 -10000 0 -0.59 72 72
EGLN2 0.003 0.009 -10000 0 -10000 0 0
EGLN1 0.003 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.003 0.012 -10000 0 -10000 0 0
SLC2A1 -0.37 0.28 -10000 0 -0.78 77 77
TWIST1 -0.27 0.3 -10000 0 -0.76 66 66
ELK1 0.016 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.14 0.16 -10000 0 -0.48 39 39
VEGFA -0.2 0.24 -10000 0 -0.73 20 20
CREBBP 0 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.039 0.14 -10000 0 -0.6 25 25
FYN 0.002 0.23 -10000 0 -0.89 25 25
LAT/GRAP2/SLP76 -0.053 0.18 -10000 0 -0.68 31 31
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
AKT1 0.024 0.14 -10000 0 -0.48 29 29
B2M 0.007 0.049 -10000 0 -0.75 2 2
IKBKG -0.009 0.03 -10000 0 -0.18 1 1
MAP3K8 -0.003 0.047 -10000 0 -0.74 2 2
mol:Ca2+ -0.006 0.022 -10000 0 -0.13 9 9
integrin-mediated signaling pathway -0.001 0.022 -10000 0 -0.48 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.011 0.21 -10000 0 -0.75 29 29
TRPV6 -0.018 0.12 -10000 0 -0.69 14 14
CD28 0.002 0.076 -10000 0 -0.75 5 5
SHC1 0.006 0.21 -10000 0 -0.81 25 25
receptor internalization -0.009 0.23 -10000 0 -0.83 30 30
PRF1 -0.036 0.32 -10000 0 -1.3 29 29
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.027 0.11 -10000 0 -0.41 23 23
LAT 0.006 0.2 -10000 0 -0.81 25 25
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D -0.007 0.11 -10000 0 -0.75 11 11
CD3E -0.003 0.1 -10000 0 -0.75 9 9
CD3G -0.036 0.18 -10000 0 -0.75 30 30
RASGRP2 -0.013 0.065 -10000 0 -0.18 65 65
RASGRP1 0.025 0.14 -10000 0 -0.49 26 26
HLA-A 0.009 0.035 -10000 0 -0.75 1 1
RASSF5 -0.002 0.033 -10000 0 -0.74 1 1
RAP1A/GTP/RAPL -0.001 0.022 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.049 -10000 0 -0.13 26 26
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.017 0.054 -10000 0 -0.25 14 14
PRKCA -0.023 0.076 -10000 0 -0.31 23 23
GRAP2 -0.039 0.17 -10000 0 -0.74 26 26
mol:IP3 -0.033 0.13 0.25 10 -0.49 27 37
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.015 0.23 -10000 0 -0.86 26 26
ORAI1 0.01 0.063 0.35 14 -0.57 1 15
CSK 0.004 0.21 -10000 0 -0.82 25 25
B7 family/CD28 -0.063 0.23 -10000 0 -0.87 30 30
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.009 0.25 -10000 0 -1 25 25
PTPN6 0.002 0.21 -10000 0 -0.86 24 24
VAV1 0.004 0.21 -10000 0 -0.84 25 25
Monovalent TCR/CD3 -0.024 0.21 -10000 0 -0.64 36 36
CBL 0 0 -10000 0 -10000 0 0
LCK -0.001 0.23 -10000 0 -0.91 25 25
PAG1 0.001 0.22 -10000 0 -0.82 26 26
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.01 0.25 -10000 0 -0.97 26 26
CD80 -0.015 0.13 -10000 0 -0.74 16 16
CD86 0 0.083 -10000 0 -0.75 6 6
PDK1/CARD11/BCL10/MALT1 -0.02 0.065 -10000 0 -0.3 16 16
HRAS 0 0 -10000 0 -10000 0 0
GO:0035030 0.007 0.19 -10000 0 -0.67 30 30
CD8A 0 0.09 -10000 0 -0.75 7 7
CD8B -0.011 0.12 -10000 0 -0.7 15 15
PTPRC -0.039 0.19 -10000 0 -0.74 32 32
PDK1/PKC theta 0.018 0.18 -10000 0 -0.59 32 32
CSK/PAG1 0.007 0.2 -10000 0 -0.87 21 21
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.053 -10000 0 -0.8 2 2
GRAP2/SLP76 -0.062 0.21 -10000 0 -0.81 31 31
STIM1 0.007 0.031 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.058 -10000 0 -0.18 15 15
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.014 0.26 -10000 0 -0.92 30 30
mol:DAG -0.032 0.11 -10000 0 -0.44 27 27
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.007 0.11 -10000 0 -0.75 11 11
cytotoxic T cell degranulation -0.03 0.3 -10000 0 -1.2 29 29
RAP1A/GTP -0.009 0.022 -10000 0 -0.069 18 18
mol:PI-3-4-5-P3 0.019 0.17 -10000 0 -0.59 29 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.044 0.17 0.26 10 -0.66 27 37
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.012 0.094 -10000 0 -0.74 8 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.049 0.16 -10000 0 -0.66 28 28
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.023 0.13 -10000 0 -0.66 17 17
CARD11 -0.004 0.049 -10000 0 -0.63 3 3
PRKCB -0.033 0.1 -10000 0 -0.37 33 33
PRKCE -0.023 0.074 -10000 0 -0.3 23 23
PRKCQ 0.006 0.21 -10000 0 -0.69 33 33
LCP2 -0.01 0.088 -10000 0 -0.74 7 7
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.026 0.12 -10000 0 -0.4 29 29
IKK complex 0.035 0.046 -10000 0 -0.13 10 10
RAS family/GDP -0.003 0.007 -10000 0 -10000 0 0
MAP3K14 0.032 0.087 -10000 0 -0.31 20 20
PDPK1 0.027 0.13 -10000 0 -0.48 24 24
TCR/CD3/MHC I/CD8/Fyn -0.011 0.24 -10000 0 -1 22 22
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.007 0.061 -9999 0 -0.56 6 6
Necdin/E2F1 -0.008 0.066 -9999 0 -0.56 7 7
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.038 0.11 -9999 0 -0.44 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.097 0.19 -9999 0 -0.54 55 55
NT-4/5 (dimer)/p75(NTR) -0.045 0.13 -9999 0 -0.44 50 50
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
AKT1 -0.033 0.1 -9999 0 -0.68 2 2
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.095 0.25 -9999 0 -0.74 63 63
MGDIs/NGR/p75(NTR)/LINGO1 -0.062 0.14 -9999 0 -0.68 7 7
FURIN 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.096 0.19 -9999 0 -0.45 104 104
LINGO1 -0.052 0.16 -9999 0 -0.57 44 44
Sortilin/TRAF6/NRIF -0.004 0.038 -9999 0 -10000 0 0
proBDNF (dimer) -0.095 0.25 -9999 0 -0.74 63 63
NTRK1 -0.008 0.074 -9999 0 -0.74 5 5
RTN4R -0.003 0.042 -9999 0 -0.66 2 2
neuron apoptosis -0.031 0.16 -9999 0 -0.59 11 11
IRAK1 0 0 -9999 0 -10000 0 0
SHC1 -0.019 0.13 -9999 0 -0.55 9 9
ARHGDIA 0 0 -9999 0 -10000 0 0
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 -0.041 0.12 -9999 0 -0.47 15 15
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.048 0.13 -9999 0 -0.48 21 21
Mammalian IAPs/DIABLO -0.005 0.048 -9999 0 -0.43 6 6
proNGF (dimer) -0.017 0.11 -9999 0 -0.7 12 12
MAGED1 0 0 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.094 -9999 0 -0.74 8 8
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.034 0.1 -9999 0 -0.47 9 9
NGF -0.017 0.11 -9999 0 -0.7 12 12
cell cycle arrest -0.022 0.13 -9999 0 -0.44 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.019 0.06 -9999 0 -0.46 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.037 0.11 -9999 0 -0.48 8 8
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.04 0.12 -9999 0 -0.54 9 9
PSENEN 0 0 -9999 0 -10000 0 0
mol:ceramide -0.015 0.12 -9999 0 -0.47 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.014 0.046 -9999 0 -0.37 2 2
p75(NTR)/beta APP -0.035 0.12 -9999 0 -0.41 42 42
BEX1 -0.09 0.23 -9999 0 -0.68 64 64
mol:GDP -0.027 0.13 -9999 0 -0.39 52 52
NGF (dimer) -0.033 0.11 -9999 0 -0.5 17 17
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.055 0.13 -9999 0 -0.63 7 7
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.035 0.1 -9999 0 -0.48 9 9
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.04 0.12 -9999 0 -0.55 9 9
RHOB -0.002 0.033 -9999 0 -0.74 1 1
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.01 0.082 -9999 0 -0.69 7 7
TP53 -0.076 0.15 -9999 0 -0.67 7 7
PRDM4 -0.016 0.13 -9999 0 -0.47 15 15
BDNF (dimer) -0.27 0.24 -9999 0 -0.65 86 86
PIK3CA 0 0 -9999 0 -10000 0 0
SORT1 -0.009 0.081 -9999 0 -0.74 6 6
activation of caspase activity -0.038 0.11 -9999 0 -0.44 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.12 -9999 0 -0.47 15 15
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.14 -9999 0 -0.57 8 8
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.016 0.13 -9999 0 -0.47 15 15
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.046 0.13 -9999 0 -0.52 15 15
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.043 0.13 -9999 0 -0.43 49 49
MAPK8 -0.01 0.14 -9999 0 -0.56 6 6
MAPK9 -0.01 0.14 -9999 0 -0.56 6 6
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.01 0.083 -9999 0 -0.69 7 7
NTF4 -0.012 0.094 -9999 0 -0.74 8 8
NDN -0.011 0.088 -9999 0 -0.74 7 7
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.031 0.093 -9999 0 -0.65 2 2
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.048 -9999 0 -0.43 6 6
RhoA-B-C/GTP -0.04 0.12 -9999 0 -0.54 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.081 0.16 -9999 0 -0.43 68 68
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.087 0.18 -9999 0 -0.46 68 68
PRKACB 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.072 0.19 -9999 0 -0.56 63 63
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.081 -9999 0 -0.74 6 6
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.014 0.13 -9999 0 -0.44 14 14
BAD -0.003 0.14 -9999 0 -0.55 6 6
RIPK2 0 0 -9999 0 -10000 0 0
NGFR -0.049 0.16 -9999 0 -0.57 42 42
CYCS -0.038 0.11 -9999 0 -0.44 15 15
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.036 0.11 -9999 0 -0.5 9 9
BCL2L11 -0.003 0.14 -9999 0 -0.55 6 6
BDNF (dimer)/p75(NTR) -0.11 0.22 -9999 0 -0.52 99 99
PI3K -0.036 0.11 -9999 0 -0.5 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.041 0.12 -9999 0 -0.47 15 15
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.048 0.14 -9999 0 -0.45 52 52
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.041 0.12 -9999 0 -0.47 15 15
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG -0.004 0.045 -9999 0 -0.57 3 3
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.084 0.17 -9999 0 -0.62 17 17
SQSTM1 0 0 -9999 0 -10000 0 0
NGFRAP1 0 0 -9999 0 -10000 0 0
CASP3 0 0.13 -9999 0 -0.5 6 6
E2F1 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.018 0.07 -9999 0 -0.51 2 2
NGF (dimer)/TRKA -0.018 0.098 -9999 0 -0.53 17 17
MMP7 -0.038 0.15 -9999 0 -0.62 30 30
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -9999 0 -0.55 4 4
MMP3 -0.34 0.28 -9999 0 -0.57 294 294
APAF-1/Caspase 9 -0.03 0.084 -9999 0 -0.54 3 3
PDGFR-alpha signaling pathway

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0 0.074 -9999 0 -0.71 5 5
PDGF/PDGFRA/CRKL -0.006 0.053 -9999 0 -0.52 5 5
positive regulation of JUN kinase activity -0.004 0.04 -9999 0 -0.42 4 4
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.099 0.21 -9999 0 -0.57 84 84
AP1 -0.13 0.34 -9999 0 -1.1 56 56
mol:IP3 0.01 0.06 -9999 0 -0.54 5 5
PLCG1 0.01 0.06 -9999 0 -0.54 5 5
PDGF/PDGFRA/alphaV Integrin -0.006 0.053 -9999 0 -0.52 5 5
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.06 -9999 0 -0.54 5 5
CAV3 -0.12 0.27 -9999 0 -0.74 79 79
CAV1 -0.21 0.33 -9999 0 -0.74 137 137
SHC/Grb2/SOS1 -0.004 0.04 -9999 0 -0.42 4 4
PDGF/PDGFRA/Shf -0.006 0.053 -9999 0 -0.52 5 5
FOS -0.087 0.35 -9999 0 -1.1 56 56
JUN -0.007 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.006 0.053 -9999 0 -0.52 5 5
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0.01 0.06 -9999 0 -0.54 5 5
PDGF/PDGFRA 0 0.074 -9999 0 -0.71 5 5
actin cytoskeleton reorganization -0.006 0.053 -9999 0 -0.52 5 5
SRF 0.005 0.014 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.004 0.045 -9999 0 -0.47 4 4
PDGF/PDGFRA/Crk/C3G -0.004 0.045 -9999 0 -0.47 4 4
JAK1 0.013 0.055 -9999 0 -0.52 5 5
ELK1/SRF -0.006 0.04 -9999 0 -0.42 4 4
SHB 0 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0.018 -9999 0 -10000 0 0
GO:0007205 0.011 0.062 -9999 0 -0.54 5 5
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.004 0.04 -9999 0 -0.42 4 4
PDGF/PDGFRA/SHB -0.006 0.053 -9999 0 -0.52 5 5
PDGF/PDGFRA/Caveolin-1 -0.16 0.26 -9999 0 -0.57 140 140
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 0.014 0.061 -9999 0 -0.52 4 4
PIK3CA 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.006 0.053 -9999 0 -0.52 5 5
JAK-STAT cascade 0.013 0.055 -9999 0 -0.52 5 5
cell proliferation -0.006 0.053 -9999 0 -0.52 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.04 -10000 0 -0.51 3 3
CRKL -0.025 0.12 -10000 0 -0.43 2 2
mol:PIP3 -0.015 0.03 0.63 1 -10000 0 1
AKT1 0.003 0.02 0.42 1 -10000 0 1
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.017 0.11 -10000 0 -0.4 2 2
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.1 0.2 -10000 0 -0.48 104 104
MAP3K5 -0.009 0.11 -10000 0 -0.44 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.094 0.18 -10000 0 -0.44 104 104
AP1 -0.057 0.16 -10000 0 -0.5 56 56
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.073 0.24 -10000 0 -0.73 56 56
STAT3 (dimer) -0.033 0.13 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.044 0.086 -10000 0 -10000 0 0
INPP5D -0.002 0.033 -10000 0 -0.74 1 1
CBL/CRK -0.018 0.11 -10000 0 -0.4 2 2
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.033 -10000 0 -0.74 1 1
ELK1 -0.004 0.022 -10000 0 -0.24 3 3
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.038 0.076 -10000 0 -0.46 2 2
PAK1 0.01 0.022 0.39 1 -10000 0 1
HGF/MET/RANBP10 -0.1 0.2 -10000 0 -0.48 105 105
HRAS -0.079 0.15 -10000 0 -0.59 4 4
DOCK1 -0.017 0.11 -10000 0 -0.4 2 2
GAB1 -0.033 0.12 -10000 0 -0.39 4 4
CRK -0.025 0.12 -10000 0 -0.43 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.22 -10000 0 -0.54 104 104
JUN 0 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.053 0.1 -10000 0 -0.25 104 104
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.01 0.14 -10000 0 -10000 0 0
GRB2/SHC -0.044 0.087 -10000 0 -0.5 2 2
FOS -0.085 0.24 -10000 0 -0.74 56 56
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.004 0.022 -10000 0 -0.24 3 3
HGF/MET/MUC20 -0.1 0.2 -10000 0 -0.48 105 105
cell migration -0.044 0.086 -10000 0 -0.49 2 2
GRB2 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.003 0.04 -10000 0 -0.51 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.065 0.12 -10000 0 -10000 0 0
MET/MUC20 -0.003 0.041 -10000 0 -0.52 3 3
RAP1B -0.009 0.1 -10000 0 -0.37 2 2
RAP1A -0.009 0.1 -10000 0 -0.37 2 2
HGF/MET/RANBP9 -0.1 0.2 -10000 0 -0.48 104 104
RAF1 -0.043 0.16 -10000 0 -0.55 4 4
STAT3 -0.063 0.12 -10000 0 -10000 0 0
cell proliferation -0.046 0.18 -10000 0 -0.52 4 4
RPS6KB1 -0.018 0.036 -10000 0 -10000 0 0
MAPK3 -0.007 0.019 -10000 0 -0.23 2 2
MAPK1 -0.007 0.019 -10000 0 -0.22 3 3
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.095 -10000 0 -0.37 2 2
SRC -0.06 0.12 -10000 0 -10000 0 0
PI3K -0.044 0.087 -10000 0 -0.5 2 2
MET/Glomulin -0.003 0.036 -10000 0 -0.46 3 3
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.033 0.15 -10000 0 -0.5 4 4
MET -0.004 0.054 -10000 0 -0.68 3 3
MAP4K1 -0.018 0.12 -10000 0 -0.47 4 4
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.033 0.15 -10000 0 -0.5 4 4
BAD 0.01 0.018 0.39 1 -10000 0 1
MAP2K4 -0.001 0.1 -10000 0 -0.45 2 2
SHP2/GRB2/SOS1/GAB1 -0.046 0.09 -10000 0 -0.45 2 2
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 -0.003 0.047 -10000 0 -0.74 2 2
HGS -0.048 0.094 -10000 0 -0.42 4 4
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.15 0.3 -10000 0 -0.74 102 102
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ -0.003 0.047 -10000 0 -0.74 2 2
NCK/PLCgamma1 -0.05 0.098 -10000 0 -0.53 2 2
PDPK1 -0.005 0.023 0.48 1 -10000 0 1
HGF/MET/SHIP -0.1 0.2 -10000 0 -0.48 104 104
Ephrin A reverse 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
MAPKKK cascade -0.016 0.076 -9999 0 -0.36 22 22
EFNA5 -0.003 0.047 -9999 0 -0.74 2 2
FYN 0.003 0.074 -9999 0 -0.44 3 3
neuron projection morphogenesis -0.016 0.076 -9999 0 -0.36 22 22
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.016 0.076 -9999 0 -0.36 22 22
EPHA5 -0.023 0.11 -9999 0 -0.57 20 20
EGFR-dependent Endothelin signaling events

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
HRAS 0 0 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EGF/EGFR -0.056 0.15 -9999 0 -0.45 53 53
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.083 -9999 0 -0.44 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.008 0.074 -9999 0 -0.74 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.014 0.098 -9999 0 -0.69 10 10
EGF/EGFR dimer/SHC -0.022 0.099 -9999 0 -0.42 26 26
mol:GDP -0.019 0.082 -9999 0 -0.43 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.063 0.21 -9999 0 -0.74 42 42
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.075 -9999 0 -0.74 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.017 0.077 -9999 0 -0.75 1 1
FRAP1 -0.018 0.079 -9999 0 -0.42 12 12
EGF/EGFR dimer -0.026 0.12 -9999 0 -0.5 26 26
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.054 0.16 -9999 0 -0.56 47 47
Caspase cascade in apoptosis

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
TOP1 0 0.12 -10000 0 -0.48 25 25
ACTA1 -0.012 0.16 -10000 0 -0.64 25 25
NUMA1 0 0.12 -10000 0 -0.48 25 25
SPTAN1 -0.01 0.16 -10000 0 -0.64 25 25
LIMK1 -0.01 0.16 -10000 0 -0.64 25 25
BIRC3 -0.009 0.081 -10000 0 -0.74 6 6
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.011 0.16 -10000 0 -0.63 28 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0 0.12 -10000 0 -0.48 25 25
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.01 0.15 -10000 0 -0.62 25 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.01 0.16 -10000 0 -0.64 25 25
MADD 0 0 -10000 0 -10000 0 0
TFAP2A -0.069 0.12 -10000 0 -0.78 12 12
BID 0.004 0.074 -10000 0 -0.3 27 27
MAP3K1 0.004 0.046 -10000 0 -0.23 10 10
TRADD 0 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 -0.011 0.16 -10000 0 -0.63 26 26
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.034 0.17 8 -0.21 2 10
neuron apoptosis 0.019 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.004 0.15 -10000 0 -0.61 25 25
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.017 0.072 -10000 0 -0.51 2 2
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD -0.003 0.15 -10000 0 -0.61 25 25
CASP7 -0.005 0.042 0.36 6 -10000 0 6
KRT18 0.013 0.02 -10000 0 -10000 0 0
apoptosis -0.003 0.14 -10000 0 -0.56 25 25
DFFA -0.01 0.16 -10000 0 -0.64 25 25
DFFB -0.01 0.16 -10000 0 -0.64 25 25
PARP1 0.002 0.034 0.21 2 -0.17 8 10
actin filament polymerization 0.002 0.14 0.58 25 -10000 0 25
TNF -0.019 0.12 -10000 0 -0.73 13 13
CYCS 0.007 0.056 -10000 0 -0.26 12 12
SATB1 0.021 0.079 -10000 0 -0.54 3 3
SLK -0.01 0.16 -10000 0 -0.64 25 25
p15 BID/BAX -0.014 0.061 -10000 0 -0.34 10 10
CASP2 0.034 0.051 -10000 0 -0.44 1 1
JNK cascade -0.004 0.046 0.23 10 -10000 0 10
CASP3 -0.018 0.16 -10000 0 -0.68 25 25
LMNB2 0.032 0.049 -10000 0 -0.48 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.002 0.033 -10000 0 -0.74 1 1
Mammalian IAPs/DIABLO -0.005 0.048 -10000 0 -0.43 6 6
negative regulation of DNA binding -0.069 0.12 -10000 0 -0.77 12 12
stress fiber formation -0.01 0.15 -10000 0 -0.62 25 25
GZMB -0.022 0.18 -10000 0 -0.73 27 27
CASP1 0.012 0.051 -10000 0 -0.73 2 2
LMNB1 0.032 0.049 -10000 0 -0.48 1 1
APP 0.019 0.016 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.008 0.14 -10000 0 -0.55 25 25
LMNA 0.032 0.049 -10000 0 -0.48 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.047 -10000 0 -0.47 1 1
LRDD -0.002 0.033 -10000 0 -0.74 1 1
SREBF1 -0.01 0.16 -10000 0 -0.64 25 25
APAF-1/Caspase 9 -0.003 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0 0.12 -10000 0 -0.47 25 25
CFL2 -0.003 0.15 -10000 0 -0.6 25 25
GAS2 -0.063 0.21 -10000 0 -0.52 71 71
positive regulation of apoptosis 0.035 0.049 -10000 0 -0.47 1 1
PRF1 -0.038 0.16 -10000 0 -0.74 25 25
Regulation of nuclear SMAD2/3 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
EP300 0.007 0.013 -10000 0 -10000 0 0
HSPA8 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.025 0.11 -10000 0 -0.52 22 22
AKT1 0.006 0.021 -10000 0 -10000 0 0
GSC -0.038 0.13 -10000 0 -0.47 2 2
NKX2-5 -0.29 0.28 -10000 0 -0.57 251 251
muscle cell differentiation 0.093 0.098 0.44 6 -10000 0 6
SMAD2-3/SMAD4/SP1 -0.009 0.034 -10000 0 -10000 0 0
SMAD4 0.017 0.026 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.01 0.035 -10000 0 -0.46 1 1
SMAD3/SMAD4/VDR 0.009 0.032 -10000 0 -10000 0 0
MYC 0.007 0.024 -10000 0 -10000 0 0
CDKN2B -0.091 0.41 -10000 0 -1.4 41 41
AP1 -0.036 0.12 -10000 0 -0.46 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.028 0.087 -10000 0 -0.42 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.048 0.17 -10000 0 -0.58 45 45
SMAD3/SMAD4/GR -0.003 0.014 -10000 0 -10000 0 0
GATA3 -0.026 0.13 -10000 0 -0.71 17 17
SKI/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
MEF2C/TIF2 -0.17 0.19 -10000 0 -0.68 33 33
endothelial cell migration -0.013 0.023 -10000 0 -10000 0 0
MAX 0 0 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 0 0 -10000 0 -10000 0 0
RUNX3 0 0 -10000 0 -10000 0 0
RUNX1 0 0 -10000 0 -10000 0 0
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0 0 -10000 0 -10000 0 0
VDR -0.002 0.033 -10000 0 -0.74 1 1
CDKN1A 0.058 0.042 -10000 0 -10000 0 0
KAT2B 0.002 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.046 0.11 -10000 0 -0.47 13 13
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.013 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.001 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.002 0.029 -10000 0 -0.54 1 1
SAP30 0 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.031 -10000 0 -10000 0 0
JUN 0.007 0.13 -10000 0 -0.45 1 1
SMAD3/SMAD4/IRF7 -0.003 0.039 -10000 0 -0.54 2 2
TFE3 0.016 0.001 -10000 0 -10000 0 0
COL1A2 0.006 0.052 -10000 0 -0.4 4 4
mesenchymal cell differentiation 0.001 0.017 -10000 0 -10000 0 0
DLX1 -0.33 0.28 -10000 0 -0.57 282 282
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.071 0.24 -10000 0 -0.73 56 56
SMAD3/SMAD4/Max -0.003 0.014 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0.016 -10000 0 -0.34 1 1
ZBTB17 0.006 0.019 -10000 0 -10000 0 0
LAMC1 0.048 0.028 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.017 -10000 0 -10000 0 0
IRF7 -0.003 0.047 -10000 0 -0.74 2 2
ESR1 -0.033 0.15 -10000 0 -0.74 22 22
HNF4A -0.009 0.073 -10000 0 -0.57 8 8
MEF2C -0.16 0.22 -10000 0 -0.71 33 33
SMAD2-3/SMAD4 -0.009 0.029 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.011 0.021 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.001 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.005 0.01 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 -0.001 0.026 -10000 0 -0.58 1 1
GCN5L2 0.003 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.004 0.022 -10000 0 -10000 0 0
MSG1/HSC70 -0.002 0.032 -10000 0 -0.49 2 2
SMAD2 0.004 0.027 -10000 0 -10000 0 0
SMAD3 0.019 0.022 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.039 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.023 -10000 0 -0.42 1 1
NCOR1 0 0 -10000 0 -10000 0 0
NCOA2 -0.002 0.033 -10000 0 -0.74 1 1
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A -0.06 0.14 -10000 0 -0.41 71 71
SMAD2-3/SMAD4/SP1/MIZ-1 0.018 0.053 -10000 0 -10000 0 0
IFNB1 0.035 0.048 -10000 0 -0.48 3 3
SMAD3/SMAD4/MEF2C -0.17 0.19 -10000 0 -0.68 33 33
CITED1 -0.003 0.042 -10000 0 -0.66 2 2
SMAD2-3/SMAD4/ARC105 -0.007 0.023 -10000 0 -10000 0 0
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.15 -10000 0 -0.48 41 41
RUNX1-3/PEBPB2 0 0 -10000 0 -10000 0 0
SMAD7 -0.024 0.1 -10000 0 -1.1 1 1
MYC/MIZ-1 0.013 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.071 0.29 7 -10000 0 7
IL10 0.026 0.11 -10000 0 -0.61 8 8
PIASy/HDAC complex 0.006 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.007 -10000 0 -10000 0 0
CDK2 0.006 0.01 -10000 0 -10000 0 0
IL5 0.024 0.096 -10000 0 -0.52 4 4
CDK4 0.005 0.028 -10000 0 -0.57 1 1
PIAS4 0.006 0.005 -10000 0 -10000 0 0
ATF3 -0.002 0.033 -10000 0 -0.74 1 1
SMAD3/SMAD4/SP1 0.002 0.027 -10000 0 -10000 0 0
FOXG1 -0.062 0.18 -10000 0 -0.57 52 52
FOXO3 0.015 0.028 -10000 0 -10000 0 0
FOXO1 0.015 0.028 -10000 0 -10000 0 0
FOXO4 0.015 0.028 -10000 0 -10000 0 0
heart looping -0.16 0.22 -10000 0 -0.7 33 33
CEBPB 0.008 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.21 0.18 -10000 0 -0.4 56 56
MYOD1 -0.083 0.2 -10000 0 -0.57 71 71
SMAD3/SMAD4/HNF4 -0.007 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.02 0.093 -10000 0 -0.51 15 15
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.004 0.025 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.017 0.011 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.2 0.19 -10000 0 -0.65 34 34
ITGB5 0.056 0.034 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.1 0.2 -10000 0 -0.5 102 102
AR -0.15 0.3 -10000 0 -0.74 102 102
negative regulation of cell growth 0.004 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.053 0.13 -10000 0 -0.41 15 15
E2F5 0 0 -10000 0 -10000 0 0
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.032 0.088 -10000 0 -0.44 4 4
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.094 -10000 0 -0.36 1 1
TFDP1 -0.004 0.045 -10000 0 -0.57 3 3
SMAD3/SMAD4/AP1 -0.035 0.12 -10000 0 -0.46 1 1
SMAD3/SMAD4/RUNX2 -0.001 0.017 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.033 0.12 -9999 0 -0.47 34 34
MAP4K1 -0.006 0.067 -9999 0 -0.74 4 4
MAP3K8 -0.003 0.047 -9999 0 -0.74 2 2
PRKCB -0.038 0.16 -9999 0 -0.74 25 25
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.016 0.096 -9999 0 -0.72 3 3
JUN -0.005 0.16 -9999 0 -0.66 25 25
MAP3K7 0.016 0.096 -9999 0 -0.72 3 3
GRAP2 -0.039 0.17 -9999 0 -0.74 26 26
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.023 0.098 -9999 0 -0.76 3 3
LAT 0 0 -9999 0 -10000 0 0
LCP2 -0.011 0.088 -9999 0 -0.74 7 7
MAPK8 -0.013 0.16 -9999 0 -0.7 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.024 0.094 -9999 0 -0.76 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.03 0.12 -9999 0 -0.44 34 34
FAS signaling pathway (CD95)

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
SPTAN1 0.003 0.022 -10000 0 -10000 0 0
RFC1 0.003 0.022 -10000 0 -10000 0 0
PRKDC 0.003 0.022 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.012 0.039 0.26 2 -10000 0 2
FASLG/FAS/FADD/FAF1 -0.017 0.076 0.24 6 -0.34 20 26
MAP2K4 -0.012 0.13 -10000 0 -0.5 8 8
mol:ceramide -0.007 0.11 -10000 0 -0.44 21 21
GSN 0.003 0.022 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.09 0.22 4 -0.41 21 25
FAS 0.007 0.035 -10000 0 -0.76 1 1
BID 0.003 0.032 0.31 5 -10000 0 5
MAP3K1 0.004 0.08 0.22 2 -0.28 6 8
MAP3K7 0.008 0.004 -10000 0 -10000 0 0
RB1 0.003 0.022 -10000 0 -10000 0 0
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.2 -10000 0 -0.48 108 108
ARHGDIB 0.002 0.025 -10000 0 -0.32 1 1
FADD 0.009 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.003 0.022 -10000 0 -10000 0 0
NFKB1 -0.038 0.08 -10000 0 -0.29 7 7
MAPK8 -0.032 0.19 -10000 0 -0.44 81 81
DFFA 0.003 0.022 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.022 -10000 0 -10000 0 0
FAS/FADD/MET -0.004 0.041 -10000 0 -0.45 4 4
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.006 0.079 -10000 0 -0.71 6 6
FAF1 0.009 0.004 -10000 0 -10000 0 0
PARP1 0.003 0.022 -10000 0 -10000 0 0
DFFB 0.003 0.022 -10000 0 -10000 0 0
CHUK -0.034 0.07 -10000 0 -10000 0 0
FASLG -0.022 0.15 -10000 0 -0.74 20 20
FAS/FADD -0.002 0.026 -10000 0 -0.58 1 1
HGF -0.15 0.3 -10000 0 -0.74 102 102
LMNA 0.002 0.02 -10000 0 -10000 0 0
CASP6 0.003 0.022 -10000 0 -10000 0 0
CASP10 0.007 0.034 -10000 0 -0.74 1 1
CASP3 0.003 0.026 0.24 3 -10000 0 3
PTPN13 -0.006 0.067 -10000 0 -0.74 4 4
CASP8 0.005 0.045 0.43 5 -10000 0 5
IL6 -0.2 0.51 -10000 0 -1.3 83 83
MET -0.004 0.054 -10000 0 -0.68 3 3
ICAD/CAD 0.002 0.021 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.007 0.11 -10000 0 -0.44 21 21
activation of caspase activity by cytochrome c 0.003 0.032 0.31 5 -10000 0 5
PAK2 0.003 0.021 -10000 0 -10000 0 0
BCL2 0.001 0.026 -10000 0 -0.57 1 1
Noncanonical Wnt signaling pathway

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.1 0.25 -9999 0 -0.74 67 67
GNB1/GNG2 -0.041 0.086 -9999 0 -0.54 4 4
mol:DAG -0.002 0.095 -9999 0 -0.51 3 3
PLCG1 -0.037 0.079 -9999 0 -0.53 3 3
YES1 -0.039 0.076 -9999 0 -0.45 1 1
FZD3 0 0 -9999 0 -10000 0 0
FZD6 0 0 -9999 0 -10000 0 0
G protein -0.038 0.08 -9999 0 -0.55 3 3
MAP3K7 -0.014 0.13 -9999 0 -0.54 13 13
mol:Ca2+ -0.001 0.092 -9999 0 -0.5 3 3
mol:IP3 -0.002 0.095 -9999 0 -0.51 3 3
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 -0.002 0.033 -9999 0 -0.74 1 1
CAMK2A -0.024 0.14 -9999 0 -0.58 14 14
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.044 0.084 -9999 0 -0.49 1 1
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.039 0.076 -9999 0 -0.45 1 1
GO:0007205 -0.001 0.094 -9999 0 -0.51 3 3
WNT6 -0.095 0.21 -9999 0 -0.57 81 81
WNT4 -0.011 0.084 -9999 0 -0.66 8 8
NFAT1/CK1 alpha -0.079 0.14 -9999 0 -0.54 17 17
GNG2 -0.008 0.074 -9999 0 -0.74 5 5
WNT5A -0.012 0.084 -9999 0 -0.59 10 10
WNT11 -0.037 0.16 -9999 0 -0.68 27 27
CDC42 -0.003 0.087 -9999 0 -0.43 1 1
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.014 0.084 -9999 0 -0.51 13 13
EPHB2 -0.009 0.073 -9999 0 -0.57 8 8
Syndecan-2/TACI -0.013 0.071 -9999 0 -0.41 15 15
LAMA1 -0.17 0.26 -9999 0 -0.57 143 143
Syndecan-2/alpha2 ITGB1 -0.012 0.07 -9999 0 -0.4 15 15
HRAS 0 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.038 -9999 0 -0.48 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.033 0.035 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.003 0.034 -9999 0 -0.44 3 3
LAMA3 -0.018 0.11 -9999 0 -0.74 12 12
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.021 0.12 -9999 0 -0.74 14 14
Syndecan-2/MMP2 -0.007 0.063 -9999 0 -0.55 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis -0.009 0.057 -9999 0 -0.38 11 11
Syndecan-2/GM-CSF -0.054 0.15 -9999 0 -0.48 55 55
determination of left/right symmetry 0.014 0.045 -9999 0 -0.56 3 3
Syndecan-2/PKC delta -0.003 0.037 -9999 0 -0.48 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 -0.024 0.14 -9999 0 -0.43 55 55
MAPK1 -0.024 0.14 -9999 0 -0.43 55 55
Syndecan-2/RACK1 -0.003 0.032 -9999 0 -0.41 3 3
NF1 0 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.045 -9999 0 -0.56 3 3
ITGA2 0 0 -9999 0 -10000 0 0
MAPK8 0.027 0.039 -9999 0 -0.47 3 3
Syndecan-2/alpha2/beta1 Integrin -0.085 0.13 -9999 0 -0.5 3 3
Syndecan-2/Kininogen -0.011 0.065 -9999 0 -0.37 15 15
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.03 -9999 0 -0.38 3 3
Syndecan-2/CASK/Protein 4.1 -0.003 0.034 -9999 0 -0.44 3 3
extracellular matrix organization -0.003 0.037 -9999 0 -0.47 3 3
actin cytoskeleton reorganization -0.014 0.084 -9999 0 -0.51 13 13
Syndecan-2/Caveolin-2/Ras -0.015 0.084 -9999 0 -0.46 16 16
Syndecan-2/Laminin alpha3 -0.015 0.083 -9999 0 -0.48 15 15
Syndecan-2/RasGAP -0.002 0.03 -9999 0 -0.39 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.009 0.057 -9999 0 -0.38 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.029 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.015 0.098 -9999 0 -0.63 12 12
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.003 0.037 -9999 0 -0.48 3 3
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.025 0.036 -9999 0 -0.43 3 3
FN1 -0.017 0.11 -9999 0 -0.74 11 11
Syndecan-2/IL8 -0.018 0.086 -9999 0 -0.4 22 22
SDC2 0.014 0.045 -9999 0 -0.56 3 3
KNG1 -0.014 0.089 -9999 0 -0.57 12 12
Syndecan-2/Neurofibromin -0.003 0.037 -9999 0 -0.48 3 3
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.079 0.23 -9999 0 -0.74 52 52
Syndecan-2/TGFB1 -0.003 0.037 -9999 0 -0.48 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.003 0.034 -9999 0 -0.44 3 3
Syndecan-2/Ezrin -0.003 0.034 -9999 0 -0.43 3 3
PRKACA 0.025 0.036 -9999 0 -0.43 3 3
angiogenesis -0.018 0.086 -9999 0 -0.4 22 22
MMP2 -0.006 0.067 -9999 0 -0.74 4 4
IL8 -0.025 0.12 -9999 0 -0.61 20 20
calcineurin-NFAT signaling pathway -0.012 0.071 -9999 0 -0.41 15 15
Effects of Botulinum toxin

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
STX1A 0.006 0.039 -9999 0 -0.42 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.059 0.17 -9999 0 -0.56 51 51
STXBP1 -0.005 0.058 -9999 0 -0.74 3 3
ACh/CHRNA1 -0.015 0.073 -9999 0 -0.42 14 14
RAB3GAP2/RIMS1/UNC13B -0.05 0.15 -9999 0 -0.48 51 51
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 -0.074 0.22 -9999 0 -0.74 49 49
mol:ACh 0.005 0.024 -9999 0 -0.15 12 12
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.043 0.12 -9999 0 -0.65 3 3
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.073 -9999 0 -0.42 14 14
UNC13B -0.005 0.058 -9999 0 -0.74 3 3
CHRNA1 -0.018 0.11 -9999 0 -0.63 14 14
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.015 0.07 -9999 0 -0.39 16 16
SNAP25 -0.007 0.049 -9999 0 -0.32 11 11
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.019 0.1 -9999 0 -0.57 16 16
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.006 0.049 -9999 0 -0.41 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.043 0.12 -9999 0 -0.65 3 3
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.054 0.13 -9999 0 -0.56 6 6
MAP3K8 0.005 0.048 -9999 0 -0.74 2 2
FOS 0.002 0.1 -9999 0 -0.46 6 6
PRKCA 0.006 0.048 -9999 0 -0.74 2 2
PTPN7 0.008 0.043 -9999 0 -0.65 2 2
HRAS 0 0 -9999 0 -10000 0 0
PRKCB -0.029 0.16 -9999 0 -0.74 25 25
NRAS 0 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.008 0.061 -9999 0 -0.45 1 1
MAP2K1 -0.002 0.13 -9999 0 -0.52 26 26
ELK1 -0.001 0.004 -9999 0 -10000 0 0
BRAF -0.031 0.12 -9999 0 -0.52 26 26
mol:GTP -0.001 0.002 -9999 0 -0.006 56 56
MAPK1 0.008 0.061 -9999 0 -0.28 6 6
RAF1 -0.031 0.12 -9999 0 -0.52 26 26
KRAS 0 0 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.03 0.13 -9999 0 -0.56 26 26
PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.01 0.029 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.001 0.14 -9999 0 -0.59 7 7
GNAO1 0.006 0.051 -9999 0 -0.64 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.1 -9999 0 -0.5 8 8
PLCG1 0.006 0.13 -9999 0 -0.54 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.009 0.004 -9999 0 -10000 0 0
GNAI1 0.008 0.035 -9999 0 -0.75 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.012 0.11 -9999 0 -0.48 26 26
S1P1/S1P -0.032 0.091 -9999 0 -0.38 26 26
negative regulation of cAMP metabolic process 0 0.13 -9999 0 -0.57 7 7
MAPK3 -0.012 0.19 -9999 0 -0.55 50 50
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.039 0.17 -9999 0 -0.74 26 26
PLCB2 0.003 0.11 -9999 0 -0.44 9 9
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.027 0.077 -9999 0 -0.41 7 7
receptor internalization -0.03 0.086 -9999 0 -0.36 26 26
PTGS2 -0.061 0.34 -9999 0 -1.1 50 50
Rac1/GTP -0.027 0.077 -9999 0 -0.41 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA 0 0.001 -9999 0 -10000 0 0
negative regulation of T cell proliferation 0 0.13 -9999 0 -0.57 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0 0.083 -9999 0 -0.74 6 6
MAPK1 -0.012 0.19 -9999 0 -0.55 50 50
S1P1/S1P/PDGFB-D/PDGFRB 0.006 0.11 -9999 0 -0.55 7 7
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 -0.023 0.13 -9999 0 -0.74 15 15
ENAH 0.058 0.023 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
EPHA2 -0.005 0.058 -9999 0 -0.74 3 3
MYO6 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.082 -9999 0 -0.48 15 15
AQP5 -0.17 0.25 -9999 0 -0.55 152 152
CTNND1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.17 -9999 0 -0.38 136 136
EGF -0.014 0.098 -9999 0 -0.69 10 10
NCKAP1 0 0 -9999 0 -10000 0 0
AQP3 -0.079 0.19 -9999 0 -0.55 71 71
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.033 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GDP -0.002 0.025 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.43 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.044 0 -9999 0 -10000 0 0
PVRL2 0 0 -9999 0 -10000 0 0
ZYX 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.031 -9999 0 -0.4 3 3
CDH1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.076 -9999 0 -0.76 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
IGF1R 0 0 -9999 0 -10000 0 0
IGF1 -0.025 0.13 -9999 0 -0.73 17 17
DIAPH1 -0.02 0.11 -9999 0 -0.64 15 15
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.025 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
VCL 0.04 0 -9999 0 -10000 0 0
EFNA1 0 0 -9999 0 -10000 0 0
LPP 0.04 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.002 0.029 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.11 0.17 -9999 0 -0.39 136 136
HGF/MET -0.079 0.15 -9999 0 -10000 0 0
HGF -0.15 0.3 -9999 0 -0.74 102 102
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0 -9999 0 -10000 0 0
actin cable formation 0.068 0.028 -9999 0 -10000 0 0
KIAA1543 0.039 0.019 -9999 0 -10000 0 0
KIFC3 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
EXOC3 0 0 -9999 0 -10000 0 0
ACTN1 0 0 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
STX4 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
LIMA1 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
ROCK1 -0.002 0.022 -9999 0 -10000 0 0
adherens junction assembly 0.052 0.018 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.013 0.067 -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 -0.004 0.054 -9999 0 -0.68 3 3
PLEKHA7 0 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.034 -9999 0 -0.43 3 3
establishment of epithelial cell apical/basal polarity 0 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0 -9999 0 -10000 0 0
BCR 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
JUN 0.014 0.094 -10000 0 -0.47 10 10
IKBKB 0.015 0.051 -10000 0 -0.28 2 2
AKT1 0.003 0.084 -10000 0 -0.28 11 11
IKBKG 0.017 0.053 -10000 0 -0.3 2 2
CALM1 -0.009 0.097 -10000 0 -0.49 12 12
PIK3CA 0 0 -10000 0 -10000 0 0
MAP3K1 0.001 0.14 -10000 0 -0.7 11 11
MAP3K7 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.1 0.23 4 -0.53 12 16
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.001 0.08 0.18 2 -0.28 6 8
LYN -0.003 0.047 -10000 0 -0.74 2 2
BLNK -0.002 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.03 0.12 -10000 0 -0.52 28 28
CD22 -0.076 0.21 -10000 0 -0.84 26 26
CAMK2G -0.002 0.09 -10000 0 -0.45 12 12
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
SHC/GRB2/SOS1 -0.021 0.09 -10000 0 -0.74 3 3
GO:0007205 -0.018 0.1 0.23 4 -0.54 12 16
SYK -0.002 0.033 -10000 0 -0.74 1 1
ELK1 -0.01 0.099 -10000 0 -0.5 12 12
NFATC1 -0.006 0.12 -10000 0 -0.54 14 14
B-cell antigen/BCR complex -0.03 0.12 -10000 0 -0.52 28 28
PAG1/CSK -0.008 0.066 -10000 0 -0.56 7 7
NFKBIB 0.014 0.019 0.078 2 -10000 0 2
HRAS -0.002 0.093 -10000 0 -0.48 12 12
NFKBIA 0.014 0.019 0.078 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.018 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.029 0.12 -10000 0 -0.76 6 6
mol:GDP -0.019 0.1 -10000 0 -0.52 12 12
PTEN -0.002 0.033 -10000 0 -0.74 1 1
CD79B -0.005 0.063 -10000 0 -0.7 4 4
NF-kappa-B/RelA/I kappa B alpha 0.018 0.016 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.014 0.14 -10000 0 -0.56 18 18
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.026 0.1 0.23 4 -0.55 12 16
CSK 0 0 -10000 0 -10000 0 0
FOS -0.047 0.16 -10000 0 -0.41 60 60
CHUK 0.017 0.053 -10000 0 -0.3 2 2
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.022 0.081 -10000 0 -0.61 6 6
PTPN6 -0.07 0.2 -10000 0 -0.77 26 26
RELA 0 0.001 -10000 0 -10000 0 0
BCL2A1 0.015 0.023 -10000 0 -0.12 11 11
VAV2 -0.059 0.16 -10000 0 -0.83 13 13
ubiquitin-dependent protein catabolic process 0.018 0.019 0.081 2 -10000 0 2
BTK -0.11 0.33 -10000 0 -1.1 46 46
CD19 -0.065 0.17 -10000 0 -0.66 23 23
MAP4K1 -0.006 0.067 -10000 0 -0.74 4 4
CD72 -0.001 0.026 -10000 0 -0.57 1 1
PAG1 -0.011 0.088 -10000 0 -0.74 7 7
MAPK14 0.01 0.12 -10000 0 -0.59 10 10
SH3BP5 -0.011 0.088 -10000 0 -0.74 7 7
PIK3AP1 -0.012 0.13 0.26 4 -0.56 18 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.031 0.13 -10000 0 -0.6 18 18
RAF1 0.005 0.088 -10000 0 -0.57 6 6
RasGAP/p62DOK/SHIP -0.028 0.11 -10000 0 -0.74 7 7
CD79A -0.035 0.15 -10000 0 -0.66 26 26
re-entry into mitotic cell cycle -0.001 0.08 0.18 3 -0.29 6 9
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.019 0.074 -10000 0 -0.48 5 5
MAPK1 0.019 0.074 -10000 0 -0.48 5 5
CD72/SHP1 -0.065 0.18 -10000 0 -0.71 26 26
NFKB1 0 0.001 -10000 0 -10000 0 0
MAPK8 0.01 0.12 -10000 0 -0.59 10 10
actin cytoskeleton organization -0.013 0.15 -10000 0 -0.67 13 13
NF-kappa-B/RelA 0.039 0.031 0.16 2 -10000 0 2
Calcineurin -0.02 0.072 -10000 0 -0.57 5 5
PI3K -0.064 0.14 -10000 0 -0.6 17 17
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.022 0.1 0.26 4 -0.53 12 16
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.038 0.16 -10000 0 -0.91 12 12
DAPP1 -0.042 0.17 -10000 0 -1.1 11 11
cytokine secretion -0.005 0.11 -10000 0 -0.5 14 14
mol:DAG -0.026 0.1 0.23 4 -0.55 12 16
PLCG2 0 0 -10000 0 -10000 0 0
MAP2K1 0.012 0.081 -10000 0 -0.55 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.14 -10000 0 -0.59 21 21
mol:PI-3-4-5-P3 -0.046 0.098 -10000 0 -0.4 17 17
ETS1 -0.004 0.11 -10000 0 -0.5 17 17
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.025 0.11 -10000 0 -0.48 18 18
B-cell antigen/BCR complex/LYN -0.042 0.16 -10000 0 -0.89 12 12
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0.002 -10000 0 -10000 0 0
RAC1 -0.016 0.16 -10000 0 -0.73 13 13
B-cell antigen/BCR complex/LYN/SYK -0.068 0.19 -10000 0 -0.74 26 26
CARD11 -0.012 0.11 -10000 0 -0.55 12 12
FCGR2B -0.014 0.099 -10000 0 -0.74 9 9
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.016 0.026 -10000 0 -10000 0 0
PTPRC -0.048 0.18 -10000 0 -0.74 32 32
PDPK1 -0.031 0.067 -10000 0 -0.28 9 9
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.018 0.013 -10000 0 -0.1 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.028 0.11 0.44 31 -10000 0 31
KIRREL -0.003 0.091 -10000 0 -0.75 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.028 0.11 -10000 0 -0.44 31 31
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.022 0.084 -10000 0 -0.46 8 8
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.012 0.051 -10000 0 -0.34 7 7
FYN -0.02 0.08 -10000 0 -0.46 8 8
mol:Ca2+ -0.022 0.083 -10000 0 -0.45 8 8
mol:DAG -0.022 0.084 -10000 0 -0.46 8 8
NPHS2 -0.003 0.047 -10000 0 -0.58 3 3
mol:IP3 -0.022 0.084 -10000 0 -0.46 8 8
regulation of endocytosis -0.019 0.074 -10000 0 -0.43 8 8
Nephrin/NEPH1/podocin/Cholesterol -0.022 0.086 -10000 0 -0.46 8 8
establishment of cell polarity -0.028 0.11 -10000 0 -0.44 31 31
Nephrin/NEPH1/podocin/NCK1-2 -0.02 0.075 -10000 0 -0.42 8 8
Nephrin/NEPH1/beta Arrestin2 -0.019 0.075 -10000 0 -0.44 8 8
NPHS1 -0.022 0.12 -10000 0 -0.57 24 24
Nephrin/NEPH1/podocin -0.02 0.081 -10000 0 -0.46 8 8
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.022 0.084 -10000 0 -0.46 8 8
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.022 0.084 -10000 0 -0.46 8 8
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.022 0.14 -10000 0 -0.5 28 28
cytoskeleton organization -0.016 0.064 -10000 0 -0.42 8 8
Nephrin/NEPH1 -0.02 0.079 -10000 0 -0.32 31 31
Nephrin/NEPH1/ZO-1 -0.022 0.087 -10000 0 -0.46 8 8
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.006 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.057 -9999 0 -0.45 8 8
forebrain development -0.087 0.14 -9999 0 -0.49 9 9
GNAO1 0.001 0.05 -9999 0 -0.63 3 3
SMO/beta Arrestin2 -0.002 0.027 -9999 0 -0.42 2 2
SMO 0.003 0.038 -9999 0 -0.58 2 2
ARRB2 0.005 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.043 0.015 -9999 0 -10000 0 0
mol:GTP -0.003 0.004 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.005 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.034 -9999 0 -0.74 1 1
XPO1 0.006 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.11 0.11 -9999 0 -0.53 4 4
SAP30 0.006 0.006 -9999 0 -10000 0 0
mol:GDP 0.003 0.038 -9999 0 -0.58 2 2
MIM/GLI2A -0.033 0.05 -9999 0 -10000 0 0
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.005 0.005 -9999 0 -10000 0 0
GLI2 0.037 0.021 -9999 0 -10000 0 0
GLI3 0.04 0.016 -9999 0 -0.28 1 1
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.006 0.006 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.008 0.074 -9999 0 -0.74 5 5
Gi family/GTP 0.002 0.05 -9999 0 -0.32 5 5
SIN3B 0.006 0.006 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.001 0.009 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.032 -9999 0 -10000 0 0
FOXA2 -0.6 0.6 -9999 0 -1.2 245 245
neural tube patterning -0.087 0.14 -9999 0 -0.49 9 9
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.009 -9999 0 -10000 0 0
GNB1 -0.002 0.033 -9999 0 -0.74 1 1
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 -0.033 0.05 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.087 0.14 -9999 0 -0.49 9 9
SUFU 0.012 0.017 -9999 0 -10000 0 0
LGALS3 0 0 -9999 0 -10000 0 0
catabolic process -0.001 0.012 -9999 0 -10000 0 0
GLI3A/CBP 0.005 0.033 -9999 0 -0.38 1 1
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.089 0.15 -9999 0 -0.5 9 9
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.006 0.006 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.001 0.009 -9999 0 -10000 0 0
GNAZ -0.004 0.082 -9999 0 -0.74 6 6
RBBP4 0.006 0.006 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.002 0.014 -9999 0 -10000 0 0
STK36 0.006 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.055 -9999 0 -0.62 2 2
PTCH1 -0.08 0.16 -9999 0 -1 6 6
MIM/GLI1 -0.23 0.29 -9999 0 -0.52 245 245
CREBBP 0.005 0.033 -9999 0 -0.38 1 1
Su(fu)/SIN3/HDAC complex 0.029 0.029 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.01 0.12 -9999 0 -0.74 13 13
ELF1 -0.004 0.034 -9999 0 -0.37 3 3
CCNA2 -0.15 0.25 -9999 0 -0.57 126 126
PIK3CA 0.01 0.001 -9999 0 -10000 0 0
JAK3 0.01 0.001 -9999 0 -10000 0 0
PIK3R1 0.01 0.001 -9999 0 -10000 0 0
JAK1 0.01 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.055 0.074 -9999 0 -0.68 3 3
SHC1 0.01 0.001 -9999 0 -10000 0 0
SP1 -0.002 0.029 -9999 0 -0.37 3 3
IL2RA 0.018 0.084 -9999 0 -0.69 6 6
IL2RB 0.006 0.058 -9999 0 -0.74 3 3
SOS1 0.01 0.001 -9999 0 -10000 0 0
IL2RG -0.002 0.095 -9999 0 -0.74 8 8
G1/S transition of mitotic cell cycle -0.014 0.11 -9999 0 -0.93 3 3
PTPN11 0.01 0.001 -9999 0 -10000 0 0
CCND2 0.02 0.077 -9999 0 -0.95 3 3
LCK 0.009 0.034 -9999 0 -0.74 1 1
GRB2 0.01 0.001 -9999 0 -10000 0 0
IL2 0.005 0.005 -9999 0 -10000 0 0
CDK6 -0.002 0.037 -9999 0 -0.57 2 2
CCND3 0.059 0.064 -9999 0 -0.56 3 3
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0.094 -9999 0 -0.61 11 11
Syndecan-4/Syndesmos -0.014 0.062 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.045 0.12 -9999 0 -0.58 8 8
Syndecan-4/ADAM12 -0.087 0.13 -9999 0 -0.57 2 2
CCL5 -0.014 0.099 -9999 0 -0.74 9 9
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.005 0.045 -9999 0 -0.58 3 3
ADAM12 -0.16 0.26 -9999 0 -0.57 134 134
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.011 0.033 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.091 0.13 -9999 0 -0.57 1 1
Syndecan-4/CXCL12/CXCR4 -0.047 0.12 -9999 0 -0.62 8 8
Syndecan-4/Laminin alpha3 -0.024 0.087 -9999 0 -0.6 2 2
MDK -0.012 0.081 -9999 0 -0.57 10 10
Syndecan-4/FZD7 -0.015 0.063 -9999 0 -10000 0 0
Syndecan-4/Midkine -0.02 0.074 -9999 0 -0.57 1 1
FZD7 -0.001 0.026 -9999 0 -0.57 1 1
Syndecan-4/FGFR1/FGF -0.028 0.088 -9999 0 -0.59 3 3
THBS1 -0.011 0.088 -9999 0 -0.74 7 7
integrin-mediated signaling pathway -0.023 0.066 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.045 0.12 -9999 0 -0.58 8 8
Syndecan-4/TACI -0.02 0.077 -9999 0 -10000 0 0
CXCR4 0 0 -9999 0 -10000 0 0
cell adhesion -0.007 0.059 -9999 0 -0.36 13 13
Syndecan-4/Dynamin -0.014 0.062 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.02 0.091 -9999 0 -0.65 6 6
Syndecan-4/GIPC -0.014 0.062 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.021 0.084 -9999 0 -0.68 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.17 0.26 -9999 0 -0.57 143 143
LAMA3 -0.018 0.11 -9999 0 -0.74 12 12
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.05 -9999 0 -0.69 2 2
Syndecan-4/alpha-Actinin -0.014 0.062 -9999 0 -10000 0 0
TFPI -0.062 0.2 -9999 0 -0.74 41 41
F2 -0.013 0.096 -9999 0 -0.57 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.072 0.16 -9999 0 -0.64 5 5
ACTN1 0 0 -9999 0 -10000 0 0
TNC -0.011 0.08 -9999 0 -0.59 9 9
Syndecan-4/CXCL12 -0.045 0.13 -9999 0 -0.64 8 8
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.06 0.2 -9999 0 -0.74 40 40
TNFRSF13B -0.015 0.098 -9999 0 -0.63 12 12
FGF2 -0.023 0.13 -9999 0 -0.74 15 15
FGFR1 -0.002 0.033 -9999 0 -0.74 1 1
Syndecan-4/PI-4-5-P2 0.007 0.069 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.015 0.11 -9999 0 -0.73 11 11
cell migration -0.004 0.013 -9999 0 -10000 0 0
PRKCD 0.002 0.006 -9999 0 -10000 0 0
vasculogenesis -0.023 0.085 -9999 0 -0.62 6 6
SDC4 0.008 0.073 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.019 0.07 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.009 0.026 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.014 0.062 -9999 0 -10000 0 0
MMP9 -0.021 0.13 -9999 0 -0.57 26 26
Rac1/GTP -0.007 0.06 -9999 0 -0.37 13 13
cytoskeleton organization -0.018 0.058 -9999 0 -10000 0 0
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.046 0.13 -9999 0 -0.64 8 8
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
CDC42/GTP -0.029 0.087 -9999 0 -0.47 3 3
PLCG1 0.002 0.1 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.029 0.085 -9999 0 -0.46 3 3
S1PR5 -0.01 0.076 -9999 0 -0.59 8 8
S1PR4 -0.066 0.21 -9999 0 -0.74 44 44
MAPK3 0.002 0.1 -9999 0 -0.48 3 3
MAPK1 0.002 0.1 -9999 0 -0.48 3 3
S1P/S1P5/Gi -0.008 0.04 -9999 0 -10000 0 0
GNAI1 -0.002 0.033 -9999 0 -0.74 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.047 -9999 0 -0.37 8 8
RHOA -0.037 0.12 -9999 0 -0.41 44 44
S1P/S1P4/Gi -0.033 0.097 -9999 0 -0.32 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.009 0.081 -9999 0 -0.74 6 6
S1P/S1P4/G12/G13 -0.04 0.13 -9999 0 -0.44 44 44
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.033 -10000 0 -0.74 1 1
Jak2/Leptin Receptor -0.027 0.099 -10000 0 -0.38 29 29
PTP1B/AKT1 -0.006 0.024 -10000 0 -0.27 1 1
FYN -0.002 0.033 -10000 0 -0.74 1 1
p210 bcr-abl/PTP1B 0.024 0.037 -10000 0 -0.31 1 1
EGFR -0.012 0.12 -10000 0 -0.63 17 17
EGF/EGFR -0.02 0.084 -10000 0 -0.48 12 12
CSF1 -0.006 0.067 -10000 0 -0.74 4 4
AKT1 0.007 0.005 -10000 0 -10000 0 0
INSR 0.007 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.023 0.078 -10000 0 -0.34 18 18
Insulin Receptor/Insulin -0.004 0.018 -10000 0 -10000 0 0
HCK -0.008 0.074 -10000 0 -0.74 5 5
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.035 -10000 0 -0.29 1 1
EGF -0.005 0.1 -10000 0 -0.69 10 10
YES1 0 0 -10000 0 -10000 0 0
CAV1 -0.026 0.11 -10000 0 -0.47 11 11
TXN 0.007 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.005 0.022 -10000 0 -10000 0 0
cell migration -0.024 0.037 0.31 1 -10000 0 1
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.04 0.15 -10000 0 -0.63 31 31
ITGA2B -0.023 0.13 -10000 0 -0.74 15 15
CSF1R -0.014 0.099 -10000 0 -0.74 9 9
Prolactin Receptor/Prolactin -0.036 0.13 -10000 0 -0.46 38 38
FGR -0.05 0.18 -10000 0 -0.74 33 33
PTP1B/p130 Cas -0.006 0.025 -10000 0 -0.29 1 1
Crk/p130 Cas -0.005 0.022 -10000 0 -10000 0 0
DOK1 0.033 0.036 -10000 0 -0.33 1 1
JAK2 0.014 0.048 -10000 0 -0.32 1 1
Jak2/Leptin Receptor/Leptin -0.043 0.082 -10000 0 -0.48 3 3
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 0.024 0.037 -10000 0 -0.31 1 1
LYN -0.003 0.047 -10000 0 -0.74 2 2
CDH2 -0.036 0.14 -10000 0 -0.58 30 30
SRC 0.023 0.016 -10000 0 -10000 0 0
ITGB3 -0.012 0.094 -10000 0 -0.74 8 8
CAT1/PTP1B 0.017 0.12 -10000 0 -0.51 15 15
CAPN1 0.007 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.015 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.039 0.076 -10000 0 -0.54 2 2
negative regulation of transcription 0.014 0.048 -10000 0 -0.32 1 1
FCGR2A -0.017 0.11 -10000 0 -0.74 11 11
FER 0.007 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.026 0.12 -10000 0 -0.56 23 23
BLK -0.035 0.15 -10000 0 -0.66 26 26
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.005 -10000 0 -10000 0 0
LEPR -0.041 0.18 -10000 0 -0.74 29 29
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.001 0.14 -10000 0 -0.61 16 16
PRL -0.009 0.073 -10000 0 -0.57 8 8
SOCS3 0.002 0.092 -10000 0 -1.4 2 2
SPRY2 -0.004 0.058 -10000 0 -0.74 3 3
Insulin Receptor/Insulin/IRS1 0 0 -10000 0 -10000 0 0
CSF1/CSF1R -0.015 0.075 -10000 0 -0.46 11 11
Ras protein signal transduction 0.005 0.012 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.1 0.22 -10000 0 -0.57 86 86
STAT5B 0.022 0.037 -10000 0 -0.25 1 1
STAT5A 0.022 0.037 -10000 0 -0.25 1 1
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.033 -10000 0 -0.38 2 2
CSN2 -0.012 0.04 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
LAT 0.012 0.077 -10000 0 -0.48 11 11
YBX1 0.001 0.004 -10000 0 -10000 0 0
LCK -0.002 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.001 0.026 -10000 0 -0.57 1 1
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.047 0.41 6 -10000 0 6
CDKN1A 0 0 -10000 0 -10000 0 0
KAT2B -0.002 0.033 -10000 0 -0.74 1 1
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.019 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.002 0.037 -10000 0 -0.57 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.049 0.15 -10000 0 -0.42 72 72
PPARGC1A -0.15 0.3 -10000 0 -0.74 99 99
FHL2 -0.005 0.052 -10000 0 -0.57 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A 0.012 0.048 -10000 0 -0.41 6 6
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.011 0.036 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.098 0.2 -10000 0 -0.49 99 99
p53/SIRT1 0 0 -10000 0 -10000 0 0
SIRT1/FOXO4 0 0 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.028 -10000 0 -10000 0 0
HIST1H1E 0.004 0.051 -10000 0 -10000 0 0
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.051 0.12 0.48 1 -10000 0 1
TP53 0 0 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.026 -10000 0 -0.41 2 2
ACSS2 0.017 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.051 0.12 -10000 0 -0.48 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0 0 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity -0.027 0.12 -10000 0 -0.56 24 24
MAP2K4 0.041 0.011 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.003 0.047 -10000 0 -0.74 2 2
SMPD1 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.036 0.16 -10000 0 -0.74 24 24
TRAIL/TRAILR2 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.073 0.19 -10000 0 -0.56 64 64
TRAIL/TRAILR1 -0.002 0.036 -10000 0 -0.56 2 2
TRAIL/TRAILR4 -0.027 0.12 -10000 0 -0.56 24 24
TRAIL/TRAILR1/DAP3/GTP -0.002 0.028 -10000 0 -0.44 2 2
IKK complex -0.001 0.009 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.009 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.036 0.16 -10000 0 -0.74 24 24
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.003 0.047 -10000 0 -0.74 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.02 -10000 0 -10000 0 0
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.026 -10000 0 -0.4 2 2
mol:ceramide 0 0 -10000 0 -10000 0 0
FADD 0 0 -10000 0 -10000 0 0
MAPK8 0.046 0.01 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.097 0.25 -10000 0 -0.74 64 64
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.03 -10000 0 -0.48 2 2
DAP3 0 0 -10000 0 -10000 0 0
CASP10 0.013 0.066 0.29 23 -0.39 1 24
JNK cascade -0.027 0.12 -10000 0 -0.56 24 24
TRAIL (trimer) 0 0 -10000 0 -10000 0 0
TNFRSF10C -0.097 0.25 -10000 0 -0.74 64 64
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.026 -10000 0 -0.41 2 2
TRAIL/TRAILR2/FADD 0 0 -10000 0 -10000 0 0
cell death 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0 -10000 0 -10000 0 0
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0 0.003 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.019 0.008 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
mol:Sphinganine-1-P 0.02 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.004 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.006 -9999 0 -10000 0 0
S1PR5 -0.01 0.076 -9999 0 -0.59 8 8
S1PR4 -0.066 0.21 -9999 0 -0.74 44 44
GNAI1 -0.002 0.033 -9999 0 -0.74 1 1
S1P/S1P5/G12 -0.005 0.041 -9999 0 -0.43 1 1
S1P/S1P3/Gq -0.067 0.12 -9999 0 -0.64 2 2
S1P/S1P4/Gi -0.031 0.093 -9999 0 -0.5 3 3
GNAQ -0.002 0.033 -9999 0 -0.74 1 1
GNAZ -0.009 0.081 -9999 0 -0.74 6 6
GNA14 -0.18 0.32 -9999 0 -0.74 117 117
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.047 -10000 0 -0.74 2 2
ANTXR2 -0.011 0.088 -10000 0 -0.74 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.1 7 7
monocyte activation -0.002 0.081 -10000 0 -0.45 15 15
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.002 0.018 -10000 0 -0.31 1 1
CYAA 0.006 0.069 -10000 0 -0.53 7 7
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B 0.004 0.071 -10000 0 -0.45 11 11
Channel -0.008 0.071 -10000 0 -0.57 7 7
NLRP1 -0.004 0.038 -10000 0 -0.47 3 3
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.1 7 -10000 0 7
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.09 0.18 -10000 0 -0.44 101 101
PA/Cellular Receptors -0.009 0.076 -10000 0 -0.61 7 7
apoptosis -0.002 0.013 -10000 0 -0.1 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.067 -10000 0 -0.53 7 7
macrophage activation 0.017 0.012 -10000 0 -10000 0 0
TNF -0.019 0.12 -10000 0 -0.73 13 13
VCAM1 -0.015 0.079 -10000 0 -0.46 15 15
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.013 0.12 2 -10000 0 2
IL18 0.01 0.045 -10000 0 -0.36 6 6
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.1 7 7
LEF -0.002 0.013 -10000 0 -0.11 7 7
CASP1 -0.003 0.031 -10000 0 -0.28 4 4
mol:cAMP -0.002 0.015 -10000 0 -10000 0 0
necrosis -0.002 0.013 -10000 0 -0.1 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.068 -10000 0 -0.54 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 0 0 -9999 0 -10000 0 0
VDR -0.002 0.033 -9999 0 -0.74 1 1
Cbp/p300/PCAF -0.001 0.022 -9999 0 -0.48 1 1
EP300 0 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.026 -9999 0 -0.31 1 1
KAT2B -0.002 0.033 -9999 0 -0.74 1 1
MAPK14 0 0 -9999 0 -10000 0 0
AKT1 0.02 0.033 -9999 0 -0.31 2 2
RAR alpha/9cRA/Cyclin H -0.007 0.029 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.032 0.031 -9999 0 -0.41 1 1
CDC2 0.001 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.03 -9999 0 -10000 0 0
NCOR2 -0.002 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.026 -9999 0 -0.56 1 1
RXRs/RARs/NRIP1/9cRA -0.024 0.081 -9999 0 -0.6 2 2
NCOA2 -0.002 0.033 -9999 0 -0.74 1 1
NCOA3 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.033 -9999 0 -0.74 1 1
RARG 0.01 0.001 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.01 0.001 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0.001 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.065 0.072 -9999 0 -0.66 2 2
RARA 0.013 0.043 -9999 0 -0.29 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.033 -9999 0 -0.41 1 1
PRKCA 0.01 0.048 -9999 0 -0.74 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.041 0.09 -9999 0 -0.63 2 2
RXRG -0.22 0.22 -9999 0 -0.42 259 259
RXRA 0.021 0.041 -9999 0 -0.31 2 2
RXRB 0.006 0.065 -9999 0 -0.41 2 2
VDR/Vit D3/DNA -0.001 0.026 -9999 0 -0.56 1 1
RBP1 -0.02 0.1 -9999 0 -0.57 17 17
CRBP1/9-cic-RA -0.015 0.077 -9999 0 -0.42 17 17
RARB 0.009 0.048 -9999 0 -0.74 2 2
PRKCG -0.031 0.15 -9999 0 -0.57 35 35
MNAT1 0 0 -9999 0 -10000 0 0
RAR alpha/RXRs -0.031 0.081 -9999 0 -0.66 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.07 -9999 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.036 -9999 0 -0.4 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.041 0.09 -9999 0 -0.63 2 2
positive regulation of DNA binding -0.006 0.027 -9999 0 -10000 0 0
NRIP1 -0.037 0.084 -9999 0 -0.69 1 1
RXRs/RARs -0.048 0.091 -9999 0 -0.63 2 2
RXRs/RXRs/DNA/9cRA -0.07 0.075 -9999 0 -0.69 2 2
PRKACA 0 0 -9999 0 -10000 0 0
CDK7 0 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.005 0.017 -9999 0 -10000 0 0
CCNH 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.001 0.026 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.003 0.025 -9999 0 -0.26 4 4
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 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 0 -9999 0 -10000 0 0
FYN -0.002 0.033 -9999 0 -0.74 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.05 0.18 -9999 0 -0.74 33 33
p38 alpha/TAB1 -0.012 0.044 -9999 0 -0.33 2 2
PRKG1 -0.06 0.2 -9999 0 -0.74 40 40
DUSP8 -0.014 0.099 -9999 0 -0.74 9 9
PGK/cGMP/p38 alpha -0.039 0.11 -9999 0 -0.38 40 40
apoptosis -0.012 0.042 -9999 0 -0.32 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN -0.003 0.047 -9999 0 -0.74 2 2
DUSP1 -0.095 0.25 -9999 0 -0.74 63 63
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
SRC 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 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 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.031 0.079 -9999 0 -0.35 11 11
BLK -0.035 0.15 -9999 0 -0.66 26 26
HCK -0.008 0.074 -9999 0 -0.74 5 5
MAP2K3 0 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.002 0.033 -9999 0 -0.74 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.033 0.061 -9999 0 -0.36 2 2
positive regulation of innate immune response 0.037 0.087 -9999 0 -0.38 11 11
LCK -0.002 0.033 -9999 0 -0.74 1 1
p38alpha-beta/MKP7 -0.019 0.065 -9999 0 -0.38 6 6
p38alpha-beta/MKP5 -0.019 0.069 -9999 0 -0.48 3 3
PGK/cGMP -0.046 0.16 -9999 0 -0.56 40 40
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.13 -9999 0 -0.49 17 17
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.007 0.071 -9999 0 -0.71 5 5
IL27-mediated signaling events

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
TGFB1 0.003 0.026 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.068 -10000 0 -10000 0 0
IL27/IL27R/JAK1 -0.028 0.093 -10000 0 -0.58 1 1
TBX21 -0.029 0.22 -10000 0 -0.61 48 48
IL12B 0.009 0.004 -10000 0 -10000 0 0
IL12A 0.001 0.073 -10000 0 -0.57 8 8
IL6ST -0.015 0.14 -10000 0 -0.75 16 16
IL27RA/JAK1 -0.003 0.013 -10000 0 -10000 0 0
IL27 0.008 0.007 -10000 0 -10000 0 0
TYK2 0.011 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.062 0.14 -10000 0 -0.69 3 3
T-helper 2 cell differentiation -0.003 0.068 -10000 0 -10000 0 0
T cell proliferation during immune response -0.003 0.068 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.068 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.001 0.003 -10000 0 -10000 0 0
IL12RB1 -0.038 0.18 -10000 0 -0.74 31 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.019 0.19 -10000 0 -0.63 12 12
IL27/IL27R/JAK2/TYK2 0.002 0.068 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.003 0.068 -10000 0 -10000 0 0
STAT1 (dimer) -0.058 0.16 0.51 3 -0.75 7 10
JAK2 0.006 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.011 0.057 -10000 0 -10000 0 0
T cell proliferation -0.051 0.18 -10000 0 -0.52 23 23
IL12/IL12R/TYK2/JAK2 0.008 0.092 -10000 0 -0.59 2 2
IL17A -0.062 0.14 -10000 0 -0.69 3 3
mast cell activation -0.003 0.068 -10000 0 -10000 0 0
IFNG 0.006 0.019 -10000 0 -0.13 4 4
T cell differentiation -0.003 0.005 -10000 0 -0.023 3 3
STAT3 (dimer) -0.011 0.057 -10000 0 -10000 0 0
STAT5A (dimer) -0.011 0.057 -10000 0 -10000 0 0
STAT4 (dimer) -0.018 0.079 -10000 0 -0.48 6 6
STAT4 -0.012 0.094 -10000 0 -0.74 8 8
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.018 0.076 -10000 0 -10000 0 0
GATA3 -0.035 0.24 -10000 0 -1.4 14 14
IL18 0.006 0.045 -10000 0 -0.57 3 3
positive regulation of mast cell cytokine production -0.011 0.056 -10000 0 -10000 0 0
IL27/EBI3 -0.002 0.042 -10000 0 -0.52 3 3
IL27RA 0.007 0.017 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.74 83 83
STAT5A 0 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.006 -10000 0 -10000 0 0
IL1B -0.002 0.082 -10000 0 -0.57 10 10
EBI3 0.001 0.055 -10000 0 -0.69 3 3
TNF -0.005 0.091 -10000 0 -0.56 13 13
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.033 -9999 0 -0.74 1 1
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.006 0.039 -9999 0 -0.31 7 7
GNAO1 0.007 0.05 -9999 0 -0.63 3 3
S1P/S1P3/G12/G13 0 0.001 -9999 0 -10000 0 0
AKT1 -0.003 0.024 -9999 0 -0.46 1 1
AKT3 0.041 0.063 -9999 0 -1.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.033 -9999 0 -0.74 1 1
GNAI2 0.011 0.001 -9999 0 -10000 0 0
GNAI3 0.011 0.001 -9999 0 -10000 0 0
GNAI1 0.009 0.034 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.011 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.04 -9999 0 -10000 0 0
MAPK3 0.039 0.038 -9999 0 -10000 0 0
MAPK1 0.039 0.038 -9999 0 -10000 0 0
JAK2 0.042 0.038 -9999 0 -10000 0 0
CXCR4 0.039 0.038 -9999 0 -10000 0 0
FLT1 0.012 0.001 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.039 0.038 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.04 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.03 -9999 0 -10000 0 0
VEGFA 0.012 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.03 0.039 -9999 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer 0.022 0.003 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.076 0.14 -9999 0 -0.32 117 117
GNAQ -0.002 0.033 -9999 0 -0.74 1 1
GNAZ 0.002 0.082 -9999 0 -0.74 6 6
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.32 -9999 0 -0.74 117 117
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.005 0.03 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.13 0.24 -9999 0 -0.57 108 108
mol:Halofuginone 0 0 -9999 0 -10000 0 0
ITGA1 -0.008 0.074 -9999 0 -0.74 5 5
CDKN1A -0.003 0.022 -9999 0 -10000 0 0
PRL-3/alpha Tubulin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.03 0.13 -9999 0 -0.56 26 26
AGT -0.039 0.16 -9999 0 -0.73 26 26
CCNA2 -0.052 0.15 -9999 0 -0.68 3 3
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 0.01 0.077 -9999 0 -0.55 9 9
CDK2/Cyclin E1 -0.062 0.11 -9999 0 -0.43 2 2
MAPK3 0.02 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.02 0 -9999 0 -10000 0 0
PTP4A1 0.025 0.061 -9999 0 -0.42 9 9
PTP4A3 0 0 -9999 0 -10000 0 0
PTP4A2 0 0 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 -0.003 0.022 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.011 0.062 -9999 0 -10000 0 0
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC -0.003 0.022 -9999 0 -10000 0 0
RHOA -0.003 0.022 -9999 0 -10000 0 0
cell motility 0.029 0.028 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.007 0.052 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.006 0.056 -9999 0 -0.56 5 5
ROCK1 0.029 0.028 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis 0.025 0.061 -9999 0 -0.42 9 9
ATF5 -0.008 0.068 -9999 0 -0.57 7 7
BARD1 signaling events

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
BARD1/CSTF1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
UBE2L3 0 0 -9999 0 -10000 0 0
FANCD2 0.022 0 -9999 0 -10000 0 0
protein ubiquitination -0.061 0.12 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
M/R/N Complex 0 0 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
DNA-PK 0 0 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -9999 0 -10000 0 0
FANCF 0 0 -9999 0 -10000 0 0
BRCA1 0 0 -9999 0 -10000 0 0
CCNE1 -0.13 0.24 -9999 0 -0.57 108 108
CDK2/Cyclin E1 -0.091 0.17 -9999 0 -0.41 108 108
FANCG -0.002 0.037 -9999 0 -0.57 2 2
BRCA1/BACH1/BARD1 0 0 -9999 0 -10000 0 0
FANCE 0 0 -9999 0 -10000 0 0
FANCC 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
FANCA -0.002 0.037 -9999 0 -0.57 2 2
DNA repair 0.009 0.1 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0 0 -9999 0 -10000 0 0
BARD1/DNA-PK 0 0 -9999 0 -10000 0 0
FANCL -0.001 0.026 -9999 0 -0.57 1 1
mRNA polyadenylation 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0 0 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0 0 -9999 0 -10000 0 0
BRCA1/BACH1 0 0 -9999 0 -10000 0 0
BARD1 0 0 -9999 0 -10000 0 0
PCNA 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.042 0.1 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0 0 -9999 0 -10000 0 0
FA complex -0.001 0.016 -9999 0 -10000 0 0
BARD1/EWS 0 0 -9999 0 -10000 0 0
RBBP8 0.02 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
TOPBP1 0 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0 0 -9999 0 -10000 0 0
BRCA1/BARD1 -0.062 0.12 -9999 0 -10000 0 0
CSTF1 0 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.078 0.2 -9999 0 -0.57 67 67
RAD50 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0 0 -9999 0 -10000 0 0
EWSR1 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.034 -10000 0 -10000 0 0
IRAK/TOLLIP 0 0 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.058 0.16 -10000 0 -0.47 61 61
IL1A -0.052 0.18 -10000 0 -0.65 39 39
IL1B 0.005 0.089 -10000 0 -0.56 12 12
IRAK/TRAF6/p62/Atypical PKCs 0 0 -10000 0 -10000 0 0
IL1R2 -0.028 0.12 -10000 0 -0.57 24 24
IL1R1 -0.002 0.033 -10000 0 -0.74 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.041 0.22 9 -10000 0 9
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.009 0.081 -10000 0 -0.74 6 6
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.042 0.012 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.061 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.03 0.11 -10000 0 -0.45 19 19
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.028 0.099 -10000 0 -0.42 19 19
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.069 -10000 0 -0.43 13 13
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.036 0.013 -10000 0 -10000 0 0
IRAK1 0.022 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.007 0.064 -10000 0 -0.54 6 6
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.006 0.039 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.069 -10000 0 -0.43 13 13
IL1 beta/IL1R2 -0.029 0.11 -10000 0 -0.5 12 12
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.055 -10000 0 -10000 0 0
IRAK3 -0.02 0.12 -10000 0 -0.74 13 13
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.015 0.078 -10000 0 -0.78 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.069 -10000 0 -0.62 1 1
IL1 alpha/IL1R1/IL1RAP -0.034 0.12 -10000 0 -0.42 39 39
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.012 0.064 -10000 0 -0.64 1 1
CASP1 -0.003 0.047 -10000 0 -0.74 2 2
IL1RN/IL1R2 -0.026 0.1 -10000 0 -0.43 29 29
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.011 0.065 -10000 0 -10000 0 0
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.053 -10000 0 -0.61 1 1
PIK3CA 0 0 -10000 0 -10000 0 0
IL1RN -0.008 0.07 -10000 0 -0.63 6 6
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.012 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.049 0.058 -10000 0 -0.82 1 1
UGCG -0.002 0.009 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.034 0.066 -10000 0 -0.41 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.024 0.015 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.043 -10000 0 -0.48 3 3
FRAP1 0.071 0.067 -10000 0 -0.56 3 3
FOXO3 0.073 0.064 -10000 0 -0.55 3 3
AKT1 0.068 0.068 -10000 0 -0.6 3 3
GAB2 -0.01 0.12 -10000 0 -0.74 13 13
SMPD1 -0.002 0.009 -10000 0 -10000 0 0
SGMS1 -0.002 0.009 -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 0.02 0.001 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.044 0.029 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.026 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.012 0.001 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
JAK1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.071 0.059 -10000 0 -0.6 1 1
MYB 0.015 0.1 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.058 0.075 -10000 0 -0.68 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.058 0.073 -10000 0 -0.66 3 3
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation 0.064 0.068 -10000 0 -0.6 3 3
SHC1 0.01 0.002 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.008 -10000 0 -0.039 17 17
PRKCZ 0.064 0.07 -10000 0 -0.63 3 3
NF kappa B1 p50/RelA -0.007 0.042 -10000 0 -0.47 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.043 0.063 -10000 0 -0.64 3 3
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA 0.002 0.074 -10000 0 -0.66 6 6
IL2RB 0.008 0.059 -10000 0 -0.74 3 3
TERT -0.22 0.28 -10000 0 -0.57 192 192
E2F1 0.018 0.048 -10000 0 -0.45 2 2
SOS1 0.01 0.002 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.019 17 -10000 0 17
PTPN11 0.01 0.002 -10000 0 -10000 0 0
IL2RG 0 0.095 -10000 0 -0.74 8 8
actin cytoskeleton organization 0.064 0.068 -10000 0 -0.6 3 3
GRB2 0.01 0.002 -10000 0 -10000 0 0
IL2 0.007 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.005 -10000 0 -10000 0 0
LCK 0.011 0.034 -10000 0 -0.74 1 1
BCL2 0.073 0.057 -10000 0 -0.53 1 1
LPA receptor mediated 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
GNB1/GNG2 -0.009 0.081 -9999 0 -0.66 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.047 -9999 0 -10000 0 0
AP1 -0.054 0.13 -9999 0 -0.51 8 8
mol:PIP3 -0.02 0.077 -9999 0 -0.58 3 3
AKT1 -0.006 0.051 -9999 0 -0.57 3 3
PTK2B 0.017 0.038 -9999 0 -0.29 4 4
RHOA 0.027 0.02 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0.081 -9999 0 -0.45 3 3
MAGI3 -0.002 0.033 -9999 0 -0.74 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.011 0.058 -9999 0 -0.41 6 6
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.06 -9999 0 -0.39 8 8
NF kappa B1 p50/RelA -0.023 0.066 -9999 0 -0.64 1 1
endothelial cell migration 0.016 0.088 -9999 0 -0.82 5 5
ADCY4 0.017 0.097 -9999 0 -0.62 6 6
ADCY5 0.012 0.095 -9999 0 -0.66 4 4
ADCY6 0.031 0.07 -9999 0 -0.59 4 4
ADCY7 0.032 0.068 -9999 0 -0.66 3 3
ADCY1 0.031 0.069 -9999 0 -0.66 3 3
ADCY2 0.018 0.082 -9999 0 -0.6 4 4
ADCY3 0.032 0.068 -9999 0 -0.66 3 3
ADCY8 -0.037 0.12 -9999 0 -0.65 5 5
ADCY9 0.031 0.073 -9999 0 -0.65 4 4
GSK3B 0.023 0.036 -9999 0 -0.32 2 2
arachidonic acid secretion 0.034 0.07 -9999 0 -0.58 4 4
GNG2 -0.008 0.074 -9999 0 -0.74 5 5
TRIP6 0 0.004 -9999 0 -10000 0 0
GNAO1 0.017 0.063 -9999 0 -0.54 5 5
HRAS 0 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.074 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.059 -9999 0 -0.92 2 2
JUN 0 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.004 0.038 -9999 0 -0.48 3 3
TIAM1 -0.004 0.07 -9999 0 -1.1 2 2
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0 0.082 -9999 0 -0.46 3 3
PLCB3 0.021 0.037 -9999 0 -0.43 3 3
FOS -0.085 0.24 -9999 0 -0.74 56 56
positive regulation of mitosis 0.034 0.07 -9999 0 -0.58 4 4
LPA/LPA1-2-3 -0.014 0.072 -9999 0 -0.48 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.025 0.048 -9999 0 -0.42 2 2
GNAZ 0.014 0.074 -9999 0 -0.46 11 11
EGFR/PI3K-beta/Gab1 -0.02 0.081 -9999 0 -0.61 3 3
positive regulation of dendritic cell cytokine production -0.014 0.071 -9999 0 -0.48 6 6
LPA/LPA2/MAGI-3 -0.002 0.023 -9999 0 -0.48 1 1
ARHGEF1 -0.003 0.041 -9999 0 -0.54 2 2
GNAI2 0.02 0.05 -9999 0 -0.64 2 2
GNAI3 0.02 0.05 -9999 0 -0.47 4 4
GNAI1 0.019 0.065 -9999 0 -0.84 2 2
LPA/LPA3 -0.014 0.078 -9999 0 -0.46 14 14
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.005 0.055 -9999 0 -0.5 5 5
HB-EGF/EGFR -0.048 0.14 -9999 0 -0.52 23 23
HBEGF -0.023 0.14 -9999 0 -0.48 42 42
mol:DAG 0 0.082 -9999 0 -0.46 3 3
cAMP biosynthetic process 0.02 0.076 -9999 0 -0.66 4 4
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
GNB1 -0.002 0.033 -9999 0 -0.74 1 1
LYN 0.015 0.085 -9999 0 -0.46 6 6
GNAQ -0.009 0.05 -9999 0 -0.38 5 5
LPAR2 0 0 -9999 0 -10000 0 0
LPAR3 -0.018 0.1 -9999 0 -0.62 14 14
LPAR1 -0.005 0.055 -9999 0 -0.83 2 2
IL8 0.001 0.13 -9999 0 -0.44 18 18
PTK2 -0.012 0.066 -9999 0 -0.45 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.011 0.058 -9999 0 -0.41 6 6
EGFR -0.022 0.12 -9999 0 -0.63 17 17
PLCG1 -0.016 0.084 -9999 0 -0.36 10 10
PLD2 -0.012 0.066 -9999 0 -0.45 6 6
G12/G13 -0.004 0.044 -9999 0 -0.58 2 2
PI3K-beta -0.007 0.062 -9999 0 -0.69 3 3
cell migration 0.002 0.032 -9999 0 -0.26 2 2
SLC9A3R2 -0.005 0.058 -9999 0 -0.74 3 3
PXN 0.025 0.049 -9999 0 -0.43 2 2
HRAS/GTP -0.009 0.067 -9999 0 -0.61 4 4
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.03 0.13 -9999 0 -0.57 26 26
PRKCE 0.008 0.034 -9999 0 -0.74 1 1
PRKCD 0.007 0.079 -9999 0 -0.47 2 2
Gi(beta/gamma) -0.01 0.079 -9999 0 -0.65 5 5
mol:LPA -0.001 0.017 -9999 0 -0.21 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.002 0.06 -9999 0 -0.64 1 1
MAPKKK cascade 0.034 0.07 -9999 0 -0.58 4 4
contractile ring contraction involved in cytokinesis 0.027 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.17 -9999 0 -0.4 121 121
GNA15 -0.008 0.047 -9999 0 -0.38 4 4
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT 0.024 0.062 -9999 0 -0.41 8 8
GNA11 -0.008 0.047 -9999 0 -0.38 4 4
Rac1/GTP -0.004 0.063 -9999 0 -0.98 2 2
MMP2 0.016 0.089 -9999 0 -0.83 5 5
IGF1 pathway

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
NCK2 0 0 -9999 0 -10000 0 0
PTK2 0 0 -9999 0 -10000 0 0
CRKL 0.009 0.073 -9999 0 -0.38 16 16
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
IRS1/Crk -0.013 0.069 -9999 0 -0.39 16 16
IGF-1R heterotetramer/IGF1/PTP1B -0.015 0.081 -9999 0 -0.45 16 16
AKT1 0.029 0.064 -9999 0 -10000 0 0
BAD 0.035 0.061 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.073 -9999 0 -0.38 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.013 0.07 -9999 0 -0.39 16 16
RAF1 0.038 0.059 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.012 0.065 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.014 0.076 -9999 0 -0.42 16 16
PIK3CA 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.064 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.033 0.052 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.011 0.057 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.012 0.064 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.007 0.017 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.013 0.07 -9999 0 -0.39 16 16
Crk/p130 Cas/Paxillin -0.012 0.061 -9999 0 -10000 0 0
IGF1R 0.007 0.017 -9999 0 -10000 0 0
IGF1 -0.016 0.14 -9999 0 -0.74 17 17
IRS2/Crk -0.015 0.071 -9999 0 -0.4 3 3
PI3K -0.012 0.065 -9999 0 -10000 0 0
apoptosis 0.009 0.046 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.02 0.088 -9999 0 -0.46 16 16
RAF1/14-3-3 E 0.04 0.052 -9999 0 -10000 0 0
BAD/14-3-3 0.039 0.057 -9999 0 -10000 0 0
PRKCZ 0.029 0.064 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.009 0.047 -9999 0 -10000 0 0
PTPN1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.016 0.087 -9999 0 -0.49 16 16
BCAR1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.013 0.07 -9999 0 -0.39 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.013 0.069 -9999 0 -0.38 16 16
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0.009 0.073 -9999 0 -0.38 16 16
IRS1 0.002 0.079 -9999 0 -0.42 16 16
IRS2 0.007 0.081 -9999 0 -0.39 19 19
IGF-1R heterotetramer/IGF1 -0.02 0.1 -9999 0 -0.56 17 17
GRB2 0 0 -9999 0 -10000 0 0
PDPK1 -0.011 0.061 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKD1 0.007 0.12 -9999 0 -0.49 27 27
SHC1 0 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.046 0.12 -9999 0 -10000 0 0
TC10/GTP -0.045 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.047 0.18 -9999 0 -0.73 31 31
FOXO3 -0.004 0.014 -9999 0 -10000 0 0
AKT1 -0.021 0.081 -9999 0 -10000 0 0
INSR 0.011 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 0 -9999 0 -10000 0 0
SORBS1 -0.091 0.24 -9999 0 -0.74 60 60
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.031 0 -9999 0 -10000 0 0
CAV1 -0.1 0.2 -9999 0 -0.42 137 137
CBL/APS/CAP/Crk-II/C3G -0.049 0.13 -9999 0 -0.4 60 60
Insulin Receptor/Insulin/IRS1/NCK2 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.086 -9999 0 -10000 0 0
PARD6A 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.071 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -10000 0 0
Insulin Receptor 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0 0 -9999 0 -10000 0 0
PRKCI -0.006 0.021 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.087 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.021 0.081 -9999 0 -10000 0 0
PRKCZ -0.006 0.021 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.001 0.018 -9999 0 -0.39 1 1
F2RL2 -0.1 0.22 -9999 0 -0.58 88 88
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.053 0.14 -9999 0 -0.43 60 60
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D 0.023 0.02 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.007 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.022 0.02 -9999 0 -0.42 1 1
GRB2 0 0 -9999 0 -10000 0 0
EIF4EBP1 0.014 0.1 -9999 0 -10000 0 0
PTPRA 0.011 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.053 0.11 -9999 0 -0.41 3 3
ErbB2/ErbB3 signaling events

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
USP8 0.018 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.008 0.045 -9999 0 -10000 0 0
NFATC4 0.032 0.055 -9999 0 -10000 0 0
ERBB2IP 0.002 0.004 -9999 0 -10000 0 0
HSP90 (dimer) 0 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.011 0.06 -9999 0 -0.36 5 5
JUN 0.044 0.058 -9999 0 -0.49 1 1
HRAS 0 0 -9999 0 -10000 0 0
DOCK7 0.028 0.066 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.013 0.071 -9999 0 -0.42 14 14
AKT1 0.01 0.002 -9999 0 -10000 0 0
BAD 0.018 0.001 -9999 0 -10000 0 0
MAPK10 -0.009 0.046 -9999 0 -0.35 3 3
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.065 -9999 0 -0.39 4 4
RAF1 0.047 0.058 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.048 0.14 -9999 0 -0.44 53 53
STAT3 0 0 -9999 0 -10000 0 0
cell migration 0.04 0.045 -9999 0 -0.3 2 2
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.038 0.15 -9999 0 -0.56 8 8
FOS 0.009 0.2 -9999 0 -0.52 57 57
NRAS 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.06 -9999 0 -0.36 5 5
MAPK3 0.045 0.11 -9999 0 -0.47 5 5
MAPK1 0.045 0.11 -9999 0 -0.47 5 5
JAK2 0.028 0.066 -9999 0 -10000 0 0
NF2 -0.001 0.018 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.01 0.056 -9999 0 -0.33 14 14
NRG1 -0.012 0.12 -9999 0 -0.74 14 14
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.031 0.061 -9999 0 -0.31 5 5
MAPK9 -0.005 0.029 -9999 0 -10000 0 0
ERBB2 -0.002 0.027 -9999 0 -0.42 2 2
ERBB3 0.009 0.004 -9999 0 -10000 0 0
SHC1 0 0.001 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.003 0.008 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
RNF41 0.025 0.005 -9999 0 -10000 0 0
FRAP1 0.009 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.007 0.041 -9999 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.001 0.023 -9999 0 -0.35 2 2
CHRNA1 0.043 0.12 -9999 0 -0.63 6 6
myelination 0.036 0.053 -9999 0 -10000 0 0
PPP3CB 0.026 0.062 -9999 0 -10000 0 0
KRAS 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.008 0.047 -9999 0 -10000 0 0
NRG2 -0.077 0.23 -9999 0 -0.74 51 51
mol:GDP 0.014 0.06 -9999 0 -0.33 14 14
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 0.054 0.059 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 -0.01 0.057 -9999 0 -10000 0 0
MAP2K1 0.036 0.11 -9999 0 -0.48 5 5
heart morphogenesis -0.011 0.06 -9999 0 -0.36 5 5
RAS family/GDP -0.008 0.045 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PRKACA -0.001 0.005 -9999 0 -10000 0 0
CHRNE 0.02 0.017 -9999 0 -0.24 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.002 -9999 0 -10000 0 0
nervous system development -0.011 0.06 -9999 0 -0.36 5 5
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.005 0.048 -9999 0 -0.43 6 6
HDAC3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.049 0.16 -9999 0 -0.56 43 43
GATA1/HDAC5 -0.049 0.16 -9999 0 -0.56 43 43
GATA2/HDAC5 -0.059 0.17 -9999 0 -0.56 52 52
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.005 0.056 -9999 0 -0.61 4 4
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.079 0.23 -9999 0 -0.74 52 52
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.061 -9999 0 -0.56 6 6
Histones -0.001 0.014 -9999 0 -10000 0 0
ADRBK1 0 0 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0 0 -9999 0 -10000 0 0
HDAC6 0 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.005 0.058 -9999 0 -0.74 3 3
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
GATA1 -0.065 0.21 -9999 0 -0.74 43 43
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 -0.002 0.033 -9999 0 -0.74 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.022 -9999 0 -0.48 1 1
HDAC4/SRF -0.003 0.037 -9999 0 -0.48 3 3
HDAC4/ER alpha -0.025 0.12 -9999 0 -0.56 22 22
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.001 0.014 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.033 0.15 -9999 0 -0.74 22 22
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.015 0.1 -9999 0 -0.74 10 10
RAN 0 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.009 0.06 -9999 0 -0.4 11 11
GNG2 -0.008 0.074 -9999 0 -0.74 5 5
NCOR2 -0.002 0.033 -9999 0 -0.74 1 1
TUBB2A 0 0 -9999 0 -10000 0 0
HDAC11 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
ANKRA2 0 0 -9999 0 -10000 0 0
RFXANK 0 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.002 0.033 -10000 0 -0.74 1 1
EPHB2 -0.009 0.072 -10000 0 -0.57 8 8
EFNB1 0.018 0.028 -10000 0 -0.41 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.037 0.092 -10000 0 -0.53 1 1
Ephrin B2/EPHB1-2 -0.044 0.11 -10000 0 -0.53 2 2
neuron projection morphogenesis -0.036 0.088 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/Tiam1 -0.041 0.1 -10000 0 -0.49 2 2
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.069 -10000 0 -0.73 4 4
YES1 -0.007 0.087 -10000 0 -0.96 4 4
Ephrin B1/EPHB1-2/NCK2 -0.04 0.099 -10000 0 -0.57 1 1
PI3K -0.006 0.067 -10000 0 -0.74 4 4
mol:GDP -0.04 0.1 -10000 0 -0.48 2 2
ITGA2B -0.023 0.13 -10000 0 -0.74 15 15
endothelial cell proliferation -0.001 0.022 -10000 0 -0.48 1 1
FYN -0.008 0.087 -10000 0 -0.96 4 4
MAP3K7 -0.007 0.071 -10000 0 -0.78 4 4
FGR -0.019 0.099 -10000 0 -0.98 4 4
TIAM1 -0.002 0.033 -10000 0 -0.74 1 1
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.023 0.1 -10000 0 -0.55 7 7
LYN -0.008 0.088 -10000 0 -0.96 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.082 -10000 0 -0.9 4 4
Ephrin B1/EPHB1-2 -0.009 0.076 -10000 0 -0.84 4 4
SRC -0.008 0.086 -10000 0 -0.95 4 4
ITGB3 -0.012 0.094 -10000 0 -0.74 8 8
EPHB1 -0.07 0.19 -10000 0 -0.57 60 60
EPHB4 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.49 1 1
alphaIIb/beta3 Integrin -0.026 0.12 -10000 0 -0.56 23 23
BLK -0.014 0.095 -10000 0 -1 4 4
HCK -0.009 0.088 -10000 0 -0.95 4 4
regulation of stress fiber formation 0.04 0.098 0.57 1 -10000 0 1
MAPK8 0.021 0.065 -10000 0 -0.69 4 4
Ephrin B1/EPHB1-2/RGS3 -0.04 0.099 -10000 0 -0.57 1 1
endothelial cell migration -0.005 0.064 -10000 0 -0.62 5 5
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.003 0.078 -10000 0 -0.85 4 4
regulation of focal adhesion formation 0.04 0.098 0.57 1 -10000 0 1
chemotaxis 0.04 0.098 0.57 1 -10000 0 1
PIK3CA 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.037 0.09 -10000 0 -0.52 1 1
angiogenesis -0.009 0.075 -10000 0 -0.83 4 4
LCK -0.008 0.09 -10000 0 -0.98 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.046 0.019 -10000 0 -10000 0 0
NFATC2 0.002 0.069 -10000 0 -0.31 1 1
NFATC3 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.013 0.12 -10000 0 -0.51 19 19
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.035 0.1 -10000 0 -0.48 19 19
BCL2/BAX -0.001 0.019 -10000 0 -0.41 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.003 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.038 0.1 -10000 0 -0.51 17 17
Calcineurin A alpha-beta B1/BCL2 -0.001 0.026 -10000 0 -0.57 1 1
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.037 0.1 0.5 17 -10000 0 17
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 48 48
MAP3K8 0.006 0.048 -10000 0 -0.74 2 2
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.054 0.12 -10000 0 -0.45 13 13
CABIN1 -0.013 0.12 -10000 0 -0.52 19 19
CALM1 0.001 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.005 0.058 -10000 0 -0.74 3 3
mol:Ca2+ -0.001 0.007 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.036 -10000 0 -0.56 2 2
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.003 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.003 0.017 -10000 0 -10000 0 0
PRKCH 0 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.003 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.007 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.024 -10000 0 -10000 0 0
PRKCB -0.038 0.16 -10000 0 -0.74 25 25
PRKCE -0.002 0.033 -10000 0 -0.74 1 1
JNK2/NFAT4 0 0 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.003 -10000 0 -10000 0 0
PRKCA -0.003 0.047 -10000 0 -0.74 2 2
PRKCG -0.041 0.15 -10000 0 -0.57 35 35
PRKCQ -0.07 0.22 -10000 0 -0.74 46 46
FKBP38/BCL2 -0.001 0.019 -10000 0 -0.41 1 1
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.046 0.024 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.003 0.038 -10000 0 -0.49 3 3
NFATc/ERK1 0.049 0.018 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.034 0.1 -10000 0 -0.48 19 19
NR4A1 -0.052 0.25 -10000 0 -0.68 65 65
GSK3B 0.009 0.003 -10000 0 -10000 0 0
positive T cell selection 0 0 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.021 0.044 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.009 0.003 -10000 0 -10000 0 0
AKAP5 -0.003 0.047 -10000 0 -0.74 2 2
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.024 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.011 0.07 -9999 0 -0.45 12 12
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.06 -9999 0 -0.38 12 12
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.033 -9999 0 -0.74 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.005 0.03 -9999 0 -10000 0 0
YY1/LSF -0.001 0.013 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.009 0.053 -9999 0 -0.34 12 12
I kappa B alpha/HDAC1 -0.006 0.036 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.008 0.046 -9999 0 -0.3 12 12
HDAC1/Smad7 -0.001 0.022 -9999 0 -0.48 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.006 0.036 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.007 0.042 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.079 0.23 -9999 0 -0.74 52 52
GATA1 -0.065 0.21 -9999 0 -0.74 43 43
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.019 0.062 -9999 0 -0.45 1 1
RBBP7 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.007 0.041 -9999 0 -10000 0 0
KAT2B -0.002 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.006 0.033 -9999 0 -10000 0 0
YY1/HDAC2 -0.001 0.013 -9999 0 -10000 0 0
YY1/HDAC1 -0.001 0.013 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0 -9999 0 -10000 0 0
PPARG -0.052 0.13 -9999 0 -0.37 69 69
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.007 0.041 -9999 0 -0.43 1 1
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.021 -9999 0 -0.48 1 1
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.01 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.041 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.025 0.016 -9999 0 -0.34 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 -0.002 0.033 -9999 0 -0.74 1 1
NCOR2 -0.002 0.033 -9999 0 -0.74 1 1
MXD1 0 0 -9999 0 -10000 0 0
STAT3 0.022 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.022 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.041 -9999 0 -10000 0 0
histone deacetylation 0.041 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.032 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.052 0.14 -9999 0 -0.44 52 52
GATA1/HDAC1 -0.049 0.16 -9999 0 -0.56 43 43
GATA1/HDAC3 -0.044 0.13 -9999 0 -0.44 43 43
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.015 0.088 -9999 0 -0.55 13 13
SIN3/HDAC complex/Mad/Max 0 0 -9999 0 -10000 0 0
NuRD Complex 0 0.009 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.03 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.05 0.16 -9999 0 -0.56 44 44
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.019 0.12 -9999 0 -0.73 13 13
negative regulation of cell growth 0.041 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.01 0.063 -9999 0 -0.4 12 12
SIN3/HDAC complex/NCoR1 0 0 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 -0.002 0.033 -9999 0 -0.74 1 1
MBD2 0 0 -9999 0 -10000 0 0
Arf6 trafficking 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
SLC2A4 -0.006 0.067 -10000 0 -0.74 4 4
CLTC 0.027 0.009 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.023 0.008 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.014 -10000 0 -0.31 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.024 0.007 -10000 0 -10000 0 0
CPE 0.014 0.028 -10000 0 -0.42 2 2
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.007 -10000 0 -10000 0 0
CTNND1 0.027 0.014 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.006 -10000 0 -10000 0 0
TSHR 0.003 0.066 -10000 0 -0.35 16 16
INS 0.01 0.002 -10000 0 -10000 0 0
BIN1 -0.003 0.047 -10000 0 -0.74 2 2
mol:Choline -0.001 0.007 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.017 -10000 0 -0.35 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.014 -10000 0 -0.31 1 1
JUP 0.024 0.007 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.002 0.028 -10000 0 -0.44 2 2
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.024 0.007 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.01 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.04 0.12 -10000 0 -0.36 3 3
clathrin heavy chain/ACAP1 0.032 0.01 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.027 0.014 -10000 0 -10000 0 0
NME1 0.015 0.017 -10000 0 -0.35 1 1
clathrin coat assembly 0.027 0.009 -10000 0 -10000 0 0
IL2RA 0.022 0.026 -10000 0 -0.25 3 3
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.003 0.033 -10000 0 -0.36 4 4
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.01 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.028 0.007 -10000 0 -10000 0 0
SDC1 0.024 0.014 -10000 0 -0.25 1 1
ARF6/GDP -0.001 0.016 -10000 0 -0.35 1 1
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.01 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.007 -10000 0 -10000 0 0
endocytosis 0.002 0.028 0.44 2 -10000 0 2
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.087 0.19 -10000 0 -0.38 141 141
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.001 0.014 -10000 0 -0.31 1 1
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.065 0.18 -10000 0 -0.38 115 115
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.009 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.002 0.033 -9999 0 -0.74 1 1
ITGA4 -0.008 0.074 -9999 0 -0.74 5 5
alpha4/beta7 Integrin -0.007 0.061 -9999 0 -0.56 6 6
alpha4/beta1 Integrin -0.006 0.056 -9999 0 -0.56 5 5
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.042 -9999 0 -0.38 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.004 0.033 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.002 0.023 -9999 0 -0.49 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.013 0.045 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.038 -9999 0 -0.38 1 1
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.004 0.039 -9999 0 -0.38 1 1
AKT1 -0.004 0.034 -9999 0 -10000 0 0
MAP2K1 0.042 0.045 -9999 0 -10000 0 0
MAP3K11 0.033 0.045 -9999 0 -10000 0 0
IFNGR1 0.009 0.034 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.05 0.13 -9999 0 -0.48 37 37
Rap1/GTP -0.003 0.029 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.005 0.043 -9999 0 -0.4 5 5
CEBPB 0.041 0.13 -9999 0 -0.72 2 2
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.007 0.067 -9999 0 -1.2 1 1
STAT1 -0.004 0.039 -9999 0 -0.38 1 1
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0.002 0.076 -9999 0 -0.68 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.004 0.037 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.019 0.066 -9999 0 -0.41 2 2
mol:Ca2+ -0.005 0.041 -9999 0 -0.38 5 5
MAPK3 0.043 0.062 -9999 0 -10000 0 0
STAT1 (dimer) -0.017 0.059 -9999 0 -10000 0 0
MAPK1 0.043 0.062 -9999 0 -0.44 2 2
JAK2 0.01 0.005 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0.01 0.005 -9999 0 -10000 0 0
CAMK2D 0 0 -9999 0 -10000 0 0
DAPK1 0.02 0.18 -9999 0 -0.64 34 34
SMAD7 0.038 0.045 -9999 0 -0.33 1 1
CBL/CRKL/C3G -0.004 0.035 -9999 0 -10000 0 0
PI3K -0.004 0.037 -9999 0 -10000 0 0
IFNG 0.002 0.077 -9999 0 -0.68 6 6
apoptosis 0.018 0.13 -9999 0 -0.44 34 34
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.056 0.2 -9999 0 -0.74 37 37
CAMK2B -0.068 0.18 -9999 0 -0.57 58 58
FRAP1 0.044 0.038 -9999 0 -10000 0 0
PRKCD -0.004 0.034 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.013 0.045 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.065 0.038 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.004 0.037 -9999 0 -10000 0 0
SOCS1 -0.003 0.066 -9999 0 -1.5 1 1
mol:GDP -0.004 0.033 -9999 0 -10000 0 0
CASP1 0.037 0.047 -9999 0 -0.33 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.044 0.041 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.036 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.029 -9999 0 -10000 0 0
CBL 0.032 0.045 -9999 0 -0.38 1 1
MAP3K1 0.034 0.045 -9999 0 -0.4 1 1
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.013 0.045 -9999 0 -10000 0 0
PTPN11 0.025 0.046 -9999 0 -0.38 5 5
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.008 0.054 -10000 0 -0.38 10 10
cell-cell adhesion 0.032 0.079 0.46 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.007 0.044 -10000 0 -0.4 1 1
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.013 0.066 -10000 0 -0.35 18 18
Ephrin B1/EPHB1 -0.043 0.12 -10000 0 -0.35 60 60
HRAS/GDP -0.031 0.08 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.039 0.097 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.006 0.041 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.036 0.095 -10000 0 -0.4 1 1
endothelial cell migration -0.001 0.018 -10000 0 -0.4 1 1
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.005 0.052 -10000 0 -0.57 4 4
PAK1 -0.01 0.054 -10000 0 -10000 0 0
HRAS 0 0 -10000 0 -10000 0 0
RRAS -0.006 0.041 -10000 0 -10000 0 0
DNM1 -0.002 0.037 -10000 0 -0.57 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.035 0.09 -10000 0 -0.38 1 1
lamellipodium assembly -0.032 0.079 -10000 0 -0.46 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.018 0.047 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.009 0.073 -10000 0 -0.57 8 8
EPHB3 -0.021 0.11 -10000 0 -0.57 18 18
EPHB1 -0.07 0.19 -10000 0 -0.57 60 60
EPHB4 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.08 -10000 0 -0.43 1 1
Ephrin B/EPHB2 -0.007 0.045 -10000 0 -0.41 1 1
Ephrin B/EPHB3 -0.013 0.06 -10000 0 -0.41 1 1
JNK cascade -0.039 0.098 -10000 0 -0.57 1 1
Ephrin B/EPHB1 -0.037 0.097 -10000 0 -0.41 1 1
RAP1/GDP -0.018 0.069 -10000 0 -10000 0 0
EFNB2 -0.002 0.033 -10000 0 -0.74 1 1
EFNB3 -0.002 0.037 -10000 0 -0.57 2 2
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.044 0.11 -10000 0 -0.53 2 2
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.032 0.079 -10000 0 -0.46 1 1
Rap1/GTP -0.032 0.078 -10000 0 -0.47 1 1
axon guidance -0.008 0.054 -10000 0 -0.38 10 10
MAPK3 0.026 0.053 -10000 0 -10000 0 0
MAPK1 0.026 0.053 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.074 -10000 0 -0.39 1 1
actin cytoskeleton reorganization -0.027 0.066 -10000 0 -10000 0 0
CDC42/GDP -0.02 0.074 -10000 0 -0.39 1 1
PI3K -0.001 0.018 -10000 0 -0.41 1 1
EFNA5 -0.003 0.047 -10000 0 -0.74 2 2
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.48 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.003 0.024 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.031 0.076 -10000 0 -0.46 1 1
PTK2 0.01 0.026 -10000 0 -10000 0 0
MAP4K4 -0.039 0.098 -10000 0 -0.57 1 1
SRC 0 0 -10000 0 -10000 0 0
KALRN -0.006 0.067 -10000 0 -0.74 4 4
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.06 -10000 0 -10000 0 0
MAP2K1 0.019 0.055 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.043 0.11 -10000 0 -0.62 1 1
cell migration 0.027 0.056 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.006 0.041 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
TF 0.01 0.092 -10000 0 -10000 0 0
HRAS/GTP -0.035 0.085 -10000 0 -0.5 1 1
Ephrin B1/EPHB1-2 -0.044 0.11 -10000 0 -0.32 67 67
cell adhesion mediated by integrin -0.002 0.041 0.41 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.037 0.092 -10000 0 -0.54 1 1
RAC1-CDC42/GTP -0.039 0.086 -10000 0 -0.47 2 2
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.018 0.069 -10000 0 -10000 0 0
ruffle organization -0.032 0.078 -10000 0 -0.47 1 1
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.032 0.048 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.01 0.056 -10000 0 -10000 0 0
ROCK1 0.01 0.063 -10000 0 -0.31 18 18
RAS family/GDP -0.023 0.058 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.083 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src/Paxillin -0.018 0.049 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.007 0.071 -10000 0 -0.71 5 5
HRAS 0 0 -10000 0 -10000 0 0
EGFR -0.022 0.12 -10000 0 -0.63 17 17
AKT 0.032 0.023 -10000 0 -0.38 1 1
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.002 0.033 -10000 0 -0.74 1 1
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.004 0.054 -10000 0 -0.68 3 3
PIK3CA 0 0 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.066 0.21 -10000 0 -0.74 44 44
PIK3R3 0 0 -10000 0 -10000 0 0
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 0 0 -10000 0 -10000 0 0
RAS 0.016 0.034 -10000 0 -10000 0 0
ERBB2 -0.002 0.037 -10000 0 -0.57 2 2
proliferation/survival/translation -0.018 0.034 0.21 2 -10000 0 2
PI3K 0.014 0.051 -10000 0 -0.26 3 3
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.038 0.015 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.033 -10000 0 -0.74 1 1
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.028 0.28 1 -10000 0 1
DAPP1 0.009 0.12 -10000 0 -0.56 14 14
Src family/SYK family/BLNK-LAT/BTK-ITK 0.005 0.17 -10000 0 -0.65 22 22
mol:DAG 0.026 0.087 -10000 0 -0.28 22 22
HRAS 0.01 0.002 -10000 0 -10000 0 0
RAP1A 0 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.026 0.056 -10000 0 -0.32 7 7
PLCG2 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.03 0.25 1 -10000 0 1
ARF1/GTP -0.002 0.029 0.26 1 -10000 0 1
RHOA 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
RAP1A/GTP -0.002 0.029 -10000 0 -10000 0 0
ADAP1 -0.008 0.058 -10000 0 -10000 0 0
ARAP3 -0.002 0.03 0.25 1 -10000 0 1
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.011 0.088 -10000 0 -0.74 7 7
ARHGEF6 -0.027 0.14 -10000 0 -0.74 18 18
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0.01 0.002 -10000 0 -10000 0 0
FYN -0.002 0.033 -10000 0 -0.74 1 1
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.05 0.18 -10000 0 -0.74 33 33
mol:Ca2+ 0.023 0.047 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.002 0.033 -10000 0 -0.74 1 1
ZAP70 -0.012 0.094 -10000 0 -0.74 8 8
mol:IP3 0.026 0.064 -10000 0 -10000 0 0
LYN -0.003 0.047 -10000 0 -0.74 2 2
ARF1/GDP 0.026 0.056 -10000 0 -0.32 7 7
RhoA/GDP -0.006 0.035 0.26 1 -10000 0 1
PDK1/Src/Hsp90 0 0 -10000 0 -10000 0 0
BLNK -0.002 0.033 -10000 0 -0.74 1 1
actin cytoskeleton reorganization 0.045 0.066 -10000 0 -0.49 3 3
SRC 0 0 -10000 0 -10000 0 0
PLEKHA2 0.026 0.023 -10000 0 -0.48 1 1
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.033 -10000 0 -0.72 1 1
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.028 0.28 1 -10000 0 1
RhoA/GTP -0.002 0.028 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.032 0.11 -10000 0 -0.51 17 17
BLK -0.035 0.15 -10000 0 -0.66 26 26
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.002 0.028 -10000 0 -10000 0 0
HCK -0.008 0.074 -10000 0 -0.74 5 5
CYTH3 -0.002 0.028 -10000 0 -10000 0 0
CYTH2 -0.002 0.028 -10000 0 -10000 0 0
KRAS 0.01 0.002 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.001 0.016 -10000 0 -10000 0 0
SGK1 -0.001 0.017 -10000 0 -10000 0 0
INPP5D -0.002 0.033 -10000 0 -0.74 1 1
mol:GDP 0.022 0.058 -10000 0 -0.34 7 7
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.002 0.033 -10000 0 -0.74 1 1
ARF6/GDP -0.006 0.036 0.27 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 0.032 0.34 1 -10000 0 1
ARAP3/RAP1A/GTP -0.002 0.03 -10000 0 -10000 0 0
VAV1 -0.008 0.074 -10000 0 -0.74 5 5
mol:PI-3-4-P2 0.018 0.026 -10000 0 -0.56 1 1
RAS family/GTP/PI3K Class I -0.002 0.028 -10000 0 -10000 0 0
PLEKHA1 0.026 0.023 -10000 0 -0.48 1 1
Rac1/GDP 0.026 0.056 -10000 0 -0.32 7 7
LAT 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.019 0.1 -10000 0 -0.45 20 20
ITK -0.03 0.1 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.024 0.12 -10000 0 -0.4 22 22
LCK -0.002 0.033 -10000 0 -0.74 1 1
BTK -0.037 0.11 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.09 0.19 -9999 0 -0.6 11 11
RAD9A 0 0 -9999 0 -10000 0 0
AP1 -0.064 0.18 -9999 0 -0.56 56 56
IFNAR2 0.007 0.006 -9999 0 -10000 0 0
AKT1 -0.004 0.063 -9999 0 -0.3 10 10
ER alpha/Oestrogen -0.026 0.12 -9999 0 -0.57 22 22
NFX1/SIN3/HDAC complex 0.025 0.021 -9999 0 -10000 0 0
EGF -0.008 0.1 -9999 0 -0.69 10 10
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0.001 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.15 -9999 0 -0.64 7 7
SAP18 0.006 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.024 0.13 -9999 0 -0.58 26 26
WRN -0.002 0.033 -9999 0 -0.74 1 1
SP1 0.008 0.006 -9999 0 -10000 0 0
SP3 0.006 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.13 -9999 0 -0.64 5 5
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.092 0.2 -9999 0 -0.61 11 11
CCND1 -0.083 0.21 -9999 0 -1.2 7 7
MAX 0.006 0.005 -9999 0 -10000 0 0
RBBP7 0.006 0.005 -9999 0 -10000 0 0
RBBP4 0.006 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.006 0.005 -9999 0 -10000 0 0
Telomerase/911 0.016 0.032 -9999 0 -10000 0 0
CDKN1B 0.015 0.052 -9999 0 -0.46 4 4
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 0.006 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.006 0.005 -9999 0 -10000 0 0
JUN 0.006 0.005 -9999 0 -10000 0 0
E6 -0.003 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0.001 -9999 0 -10000 0 0
FOS -0.079 0.24 -9999 0 -0.74 56 56
IFN-gamma/IRF1 -0.006 0.056 -9999 0 -0.5 6 6
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.012 0.081 -9999 0 -0.57 10 10
Telomerase -0.027 0.053 -9999 0 -10000 0 0
IRF1 0.009 0.007 -9999 0 -10000 0 0
ESR1 -0.028 0.16 -9999 0 -0.74 22 22
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
HDAC1 0.006 0.005 -9999 0 -10000 0 0
HDAC2 0.007 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.022 0.005 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.006 0.005 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 0 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.14 -9999 0 -0.65 7 7
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.01 0.009 -9999 0 -10000 0 0
MAPK1 0.01 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.007 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.016 0.12 -9999 0 -0.64 17 17
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.027 0.12 -9999 0 -0.5 26 26
MYC 0.007 0.005 -9999 0 -10000 0 0
IL2 0 0.012 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
TGFB1 0.005 0.007 -9999 0 -10000 0 0
TRF2/BLM -0.008 0.054 -9999 0 -0.38 10 10
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.15 -9999 0 -0.64 7 7
SP1/HDAC2 0 0.002 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.13 -9999 0 -0.64 5 5
Smad3/Myc 0.011 0.014 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG 0 0.077 -9999 0 -0.68 6 6
Telomerase/PinX1 -0.1 0.13 -9999 0 -0.64 5 5
Telomerase/AKT1/mTOR/p70S6K -0.003 0.062 -9999 0 -10000 0 0
SIN3B 0.006 0.005 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.13 -9999 0 -0.64 5 5
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.001 0.024 -9999 0 -0.52 1 1
Telomerase/hnRNP C1/C2 -0.1 0.13 -9999 0 -0.64 5 5
E2F1 0.007 0.006 -9999 0 -10000 0 0
ZNFX1 0.006 0.005 -9999 0 -10000 0 0
PIF1 -0.055 0.17 -9999 0 -0.57 47 47
NCL 0 0 -9999 0 -10000 0 0
DKC1 0 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.018 0.073 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.06 -9999 0 -10000 0 0
HIF1A 0 0 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.011 0.046 -9999 0 -10000 0 0
PLCG1 0.018 0.074 -9999 0 -10000 0 0
NOS3 0.04 0.069 -9999 0 -0.58 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.04 0.067 -9999 0 -0.55 1 1
FLT1 0.026 0 -9999 0 -10000 0 0
PGF -0.029 0.13 -9999 0 -0.57 25 25
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.039 -9999 0 -0.43 4 4
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.044 0.065 -9999 0 -0.53 1 1
endothelial cell proliferation 0.018 0.094 -9999 0 -0.62 1 1
mol:Ca2+ 0.018 0.073 -9999 0 -10000 0 0
MAPK3 0.03 0.07 -9999 0 -10000 0 0
MAPK1 0.03 0.07 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.029 0.13 -9999 0 -0.57 25 25
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.21 0.33 -9999 0 -0.74 137 137
VEGFA homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.036 0.068 -9999 0 -10000 0 0
PI3K -0.014 0.061 -9999 0 -10000 0 0
PRKCA 0.023 0.074 -9999 0 -10000 0 0
PRKCB 0.003 0.12 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.017 0.075 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.073 -9999 0 -10000 0 0
RASA1 0.035 0 -9999 0 -10000 0 0
NRP2 -0.006 0.067 -9999 0 -0.74 4 4
VEGFR1 homodimer 0.026 0 -9999 0 -10000 0 0
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.066 0.19 -9999 0 -0.59 7 7
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.06 -9999 0 -10000 0 0
mol:L-citrulline 0.04 0.067 -9999 0 -0.55 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.013 0.056 -9999 0 -10000 0 0
PDPK1 -0.013 0.056 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.04 0.067 -9999 0 -0.55 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.004 0.043 -9999 0 -0.47 4 4
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
MAP2K3 0.027 0.024 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.034 0.022 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.009 0.081 -9999 0 -0.74 6 6
TXN 0.007 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GADD45B -0.023 0.13 -9999 0 -0.74 15 15
MAP3K1 0 0 -9999 0 -10000 0 0
MAP3K6 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
MAP3K4 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.005 -9999 0 -10000 0 0
TRAF6 0.007 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.068 0.18 -9999 0 -0.57 58 58
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.042 0.11 -9999 0 -0.35 58 58
MAPK11 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.037 0.1 -9999 0 -10000 0 0
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.014 0.019 -9999 0 -0.42 1 1
TAOK2 0.015 0 -9999 0 -10000 0 0
TAOK3 0.015 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAP3K10 -0.001 0.026 -9999 0 -0.57 1 1
MAP3K3 0 0 -9999 0 -10000 0 0
TRX/ASK1 0 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.018 0.087 -9999 0 -0.43 20 20
Circadian rhythm pathway

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
chromatin modification -0.001 0.012 -9999 0 -10000 0 0
CLOCK 0.013 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0 0 -9999 0 -10000 0 0
DEC1/BMAL1 -0.022 0.092 -9999 0 -0.41 26 26
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.038 0 -9999 0 -10000 0 0
ARNTL 0.013 0 -9999 0 -10000 0 0
TIMELESS 0.038 0 -9999 0 -10000 0 0
NPAS2 0.013 0 -9999 0 -10000 0 0
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 -0.001 0.026 -9999 0 -0.57 1 1
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 -0.005 0.058 -9999 0 -0.74 3 3
BMAL/CLOCK/NPAS2 0.035 0 -9999 0 -10000 0 0
BMAL1/CLOCK 0.037 0.037 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.012 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.012 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS -0.003 0.032 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.03 0.13 -9999 0 -0.57 26 26
Ceramide signaling pathway

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
SPHK2 0.017 0.037 -10000 0 -0.56 2 2
MAP4K4 0.032 0.057 -10000 0 -0.64 1 1
BAG4 -0.001 0.026 -10000 0 -0.57 1 1
PKC zeta/ceramide -0.002 0.018 0.17 2 -10000 0 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.081 -10000 0 -0.74 6 6
BAX 0.001 0.01 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.017 0.003 -10000 0 -10000 0 0
BAD -0.001 0.019 0.19 2 -10000 0 2
SMPD1 0.02 0.042 -10000 0 -0.23 12 12
RB1 -0.001 0.019 0.19 2 -10000 0 2
FADD/Caspase 8 0.04 0.054 -10000 0 -0.61 1 1
MAP2K4 0.005 0.018 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.005 0.018 -10000 0 -10000 0 0
EGF -0.014 0.098 -10000 0 -0.69 10 10
mol:ceramide -0.01 0.02 0.2 2 -10000 0 2
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.037 -10000 0 -0.56 2 2
ASAH1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.019 0.19 2 -10000 0 2
cell proliferation -0.012 0.06 -10000 0 -0.33 15 15
BID 0.024 0.039 -10000 0 -0.38 1 1
MAP3K1 -0.001 0.019 0.19 2 -10000 0 2
EIF2A 0.012 0.017 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.017 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.017 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.002 0.018 0.17 2 -10000 0 2
FADD 0.032 0.057 -10000 0 -0.64 1 1
KSR1 -0.001 0.019 0.19 2 -10000 0 2
MAPK8 0.009 0.017 0.18 2 -10000 0 2
PRKRA -0.001 0.019 0.19 2 -10000 0 2
PDGFA -0.003 0.047 -10000 0 -0.74 2 2
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.025 0.13 -10000 0 -0.73 17 17
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.01 0.02 0.2 2 -10000 0 2
CTSD 0 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.064 -10000 0 -0.35 15 15
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.037 -10000 0 -0.56 2 2
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.053 -10000 0 -0.68 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.077 -10000 0 -0.48 12 12
mol:Sphingosine-1-phosphate 0.017 0.037 -10000 0 -0.56 2 2
MAP2K1 0.012 0.017 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0.001 0.014 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -10000 0 -0.41 1 1
EIF2AK2 0.005 0.018 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.012 0.075 -10000 0 -0.48 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.027 -10000 0 -0.32 1 1
MAP2K2 0.012 0.017 -10000 0 -10000 0 0
SMPD3 0.017 0.064 -10000 0 -0.3 16 16
TNF -0.019 0.12 -10000 0 -0.73 13 13
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.005 0.039 0.23 11 -10000 0 11
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.001 0.014 0.14 2 -10000 0 2
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.006 0.054 -9999 0 -0.49 6 6
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.008 0.074 -9999 0 -0.74 5 5
alpha4/beta7 Integrin/MAdCAM1 -0.008 0.055 -9999 0 -0.43 6 6
EPO -0.007 0.063 -9999 0 -0.57 6 6
alpha4/beta7 Integrin -0.007 0.061 -9999 0 -0.56 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.056 -9999 0 -0.56 5 5
EPO/EPOR (dimer) -0.005 0.045 -9999 0 -0.41 6 6
lamellipodium assembly 0.001 0.005 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.006 0.039 -9999 0 -0.34 5 5
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.005 0.052 -9999 0 -0.57 4 4
cell adhesion -0.008 0.054 -9999 0 -0.43 6 6
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.02 0.074 -9999 0 -0.57 6 6
ITGB7 -0.002 0.033 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.01 0.077 -9999 0 -0.53 9 9
p130Cas/Crk/Dock1 -0.007 0.059 -9999 0 -0.72 2 2
VCAM1 -0.008 0.073 -9999 0 -0.66 6 6
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.043 -9999 0 -0.43 5 5
BCAR1 0.027 0.07 -9999 0 -0.53 6 6
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
Caspase 8 (4 units) -0.011 0.047 -9999 0 -10000 0 0
NEF -0.007 0.037 -9999 0 -10000 0 0
NFKBIA -0.001 0.012 -9999 0 -10000 0 0
BIRC3 0.03 0.087 -9999 0 -0.75 6 6
CYCS 0.033 0.064 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.024 0.13 -9999 0 -0.83 11 11
MAP2K7 0.034 0.05 -9999 0 -10000 0 0
protein ubiquitination 0.056 0.038 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.002 0.033 -9999 0 -0.74 1 1
BID 0.027 0.067 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.004 0.036 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
CFLAR 0 0 -9999 0 -10000 0 0
FADD 0 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.036 -9999 0 -10000 0 0
MAPK8 0.04 0.048 -9999 0 -10000 0 0
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.014 0.062 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.006 0.034 -9999 0 -10000 0 0
CHUK 0.057 0.04 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.018 -9999 0 -0.4 1 1
TCRz/NEF -0.027 0.12 -9999 0 -0.51 26 26
TNF -0.019 0.12 -9999 0 -0.73 13 13
FASLG -0.02 0.2 -9999 0 -0.82 26 26
NFKB1 -0.001 0.012 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.077 -9999 0 -0.48 12 12
CASP6 -0.006 0.028 -9999 0 -10000 0 0
CASP7 0.061 0.085 -9999 0 -0.6 6 6
RELA -0.001 0.012 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.061 0.085 -9999 0 -0.6 6 6
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -9999 0 -0.41 1 1
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.043 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.013 0.062 -9999 0 -0.49 6 6
BCL2 0.045 0.047 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.032 -9999 0 -0.62 1 1
PDGFB-D/PDGFRB/SLAP -0.031 0.13 -9999 0 -0.58 26 26
PDGFB-D/PDGFRB/APS/CBL -0.001 0.022 -9999 0 -0.48 1 1
AKT1 -0.005 0.04 -9999 0 -0.53 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.04 -9999 0 -0.66 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
FGR -0.04 0.15 -9999 0 -0.6 33 33
mol:Ca2+ 0.027 0.041 -9999 0 -0.7 1 1
MYC 0.044 0.051 -9999 0 -0.46 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.018 -9999 0 -0.39 1 1
LRP1/PDGFRB/PDGFB -0.001 0.022 -9999 0 -0.48 1 1
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.027 0.041 -9999 0 -0.71 1 1
PTEN -0.002 0.033 -9999 0 -0.74 1 1
GRB2 0 0 -9999 0 -10000 0 0
GRB7 -0.005 0.052 -9999 0 -0.57 4 4
PDGFB-D/PDGFRB/SHP2 -0.001 0.025 -9999 0 -0.56 1 1
PDGFB-D/PDGFRB/GRB10 -0.001 0.025 -9999 0 -0.56 1 1
cell cycle arrest -0.031 0.13 -9999 0 -0.58 26 26
HRAS 0 0 -9999 0 -10000 0 0
HIF1A 0.054 0.042 -9999 0 -0.46 1 1
GAB1 0.028 0.054 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.033 0.049 -9999 0 -0.66 1 1
PDGFB-D/PDGFRB 0.001 0.024 -9999 0 -0.49 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.025 -9999 0 -0.56 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.035 -9999 0 -0.63 1 1
positive regulation of MAPKKK cascade -0.001 0.025 -9999 0 -0.56 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.027 0.042 -9999 0 -0.72 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.005 0.045 -9999 0 -0.44 5 5
SHB 0 0 -9999 0 -10000 0 0
BLK -0.02 0.1 -9999 0 -0.59 15 15
PTPN2 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.025 -9999 0 -0.56 1 1
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.029 0.068 -9999 0 -0.57 2 2
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.003 0.044 -9999 0 -0.56 3 3
LCK -0.002 0.035 -9999 0 -0.55 2 2
PDGFRB 0.009 0.034 -9999 0 -0.75 1 1
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.006 0.065 -9999 0 -0.59 6 6
ABL1 0.024 0.052 -9999 0 -0.65 1 1
PDGFB-D/PDGFRB/CBL 0.026 0.059 -9999 0 -0.77 1 1
PTPN1 0.001 0.003 -9999 0 -10000 0 0
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 0 0 -9999 0 -10000 0 0
cell proliferation 0.043 0.048 -9999 0 -0.43 1 1
SLA -0.039 0.17 -9999 0 -0.74 26 26
actin cytoskeleton reorganization 0.002 0.02 -9999 0 -10000 0 0
SRC 0 0.022 -9999 0 -0.49 1 1
PI3K -0.005 0.044 -9999 0 -0.6 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.004 0.038 -9999 0 -0.48 1 1
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.031 0.041 -9999 0 -0.69 1 1
LYN -0.002 0.045 -9999 0 -0.56 3 3
LRP1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0 0 -9999 0 -10000 0 0
STAT5A 0 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.019 -9999 0 -10000 0 0
SPHK1 0.01 0.003 -9999 0 -10000 0 0
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.027 0.042 -9999 0 -0.72 1 1
PLCG1 0.027 0.043 -9999 0 -0.74 1 1
NHERF/PDGFRB -0.007 0.058 -9999 0 -0.56 4 4
YES1 0 0.022 -9999 0 -0.48 1 1
cell migration -0.007 0.058 -9999 0 -0.55 4 4
SHC/Grb2/SOS1 0 0.019 -9999 0 -10000 0 0
SLC9A3R2 -0.005 0.058 -9999 0 -0.74 3 3
SLC9A3R1 -0.005 0.052 -9999 0 -0.57 4 4
NHERF1-2/PDGFRB/PTEN -0.007 0.056 -9999 0 -0.49 5 5
FYN -0.001 0.034 -9999 0 -0.53 2 2
DOK1 0.029 0.021 -9999 0 -0.44 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.04 0.063 -9999 0 -0.66 1 1
PRKCD 0.029 0.021 -9999 0 -0.44 1 1
FER 0.029 0.021 -9999 0 -0.44 1 1
MAPKKK cascade -0.001 0.017 -9999 0 -10000 0 0
RASA1 0.029 0.021 -9999 0 -0.44 1 1
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk 0.001 0.02 -9999 0 -0.4 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.025 -9999 0 -0.56 1 1
chemotaxis 0.024 0.051 -9999 0 -0.63 1 1
STAT1-3-5/STAT1-3-5 -0.001 0.017 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.001 0.026 -9999 0 -0.57 1 1
PTPRJ -0.003 0.047 -9999 0 -0.74 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0 -9999 0 -10000 0 0
adherens junction organization 0.032 0.033 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.009 0.049 -9999 0 -10000 0 0
FMN1 0.012 0.1 -9999 0 -0.38 31 31
mol:IP3 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNND1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.038 0 -9999 0 -10000 0 0
VASP 0.039 0 -9999 0 -10000 0 0
ZYX 0.039 0 -9999 0 -10000 0 0
JUB 0.039 0 -9999 0 -10000 0 0
EGFR(dimer) -0.01 0.056 -9999 0 -0.38 6 6
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
FYN 0.042 0.036 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP -0.009 0.049 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.022 0.12 -9999 0 -0.63 17 17
CASR 0.036 0.039 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
actin cable formation 0.019 0.099 -9999 0 -0.36 31 31
apoptosis 0 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
mol:GDP -0.01 0.053 -9999 0 -10000 0 0
PIP5K1A 0.039 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.01 0.051 -9999 0 -0.34 6 6
homophilic cell adhesion 0.001 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.003 0.047 0.74 2 -10000 0 2
PI3K Class IB/PDE3B -0.003 0.047 -10000 0 -0.74 2 2
PDE3B -0.003 0.047 -10000 0 -0.74 2 2
PLK2 and PLK4 events

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
PLK2 -0.002 0.033 -9999 0 -0.74 1 1
PLK4 -0.001 0.026 -9999 0 -0.57 1 1
regulation of centriole replication 0.018 0.033 -9999 0 -0.48 2 2
EPO signaling pathway

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
BCL2L1 0.066 0.037 -10000 0 -10000 0 0
CRKL 0.039 0.038 -10000 0 -10000 0 0
mol:DAG -0.005 0.034 -10000 0 -0.39 2 2
HRAS -0.003 0.025 -10000 0 -10000 0 0
MAPK8 0.027 0.045 -10000 0 -0.44 2 2
RAP1A 0.039 0.038 -10000 0 -10000 0 0
GAB1 0.039 0.038 -10000 0 -10000 0 0
MAPK14 0.027 0.045 -10000 0 -0.44 2 2
EPO 0.004 0.063 -10000 0 -0.56 6 6
PLCG1 -0.005 0.034 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.006 0.047 -10000 0 -0.5 2 2
GAB1/SHC/GRB2/SOS1 -0.003 0.027 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.003 0.045 -10000 0 -0.4 6 6
IRS2 0.036 0.05 -10000 0 -10000 0 0
STAT1 0.051 0.042 -10000 0 -10000 0 0
STAT5B -0.005 0.034 -10000 0 -0.39 2 2
cell proliferation 0.034 0.043 -10000 0 -0.4 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.004 0.029 -10000 0 -10000 0 0
TEC 0.036 0.05 -10000 0 -10000 0 0
SOCS3 -0.003 0.047 -10000 0 -0.74 2 2
STAT1 (dimer) 0.051 0.041 -10000 0 -10000 0 0
JAK2 0.011 0.004 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.041 0.041 -10000 0 -0.37 2 2
EPO/EPOR -0.003 0.045 -10000 0 -0.4 6 6
LYN 0.008 0.048 -10000 0 -0.74 2 2
TEC/VAV2 0.04 0.067 -10000 0 -0.73 2 2
elevation of cytosolic calcium ion concentration 0.012 0.004 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.001 0.049 -10000 0 -0.49 2 2
mol:IP3 -0.005 0.034 -10000 0 -0.39 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.041 -10000 0 -10000 0 0
SH2B3 0.008 0.048 -10000 0 -0.74 2 2
NFKB1 0.027 0.045 -10000 0 -0.44 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.002 0.031 0.3 2 -10000 0 2
PTPN6 0.033 0.039 -10000 0 -0.37 2 2
TEC/VAV2/GRB2 -0.008 0.058 -10000 0 -0.7 2 2
EPOR 0.012 0.004 -10000 0 -10000 0 0
INPP5D -0.002 0.033 -10000 0 -0.74 1 1
mol:GDP -0.003 0.027 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.004 0.029 -10000 0 -10000 0 0
VAV2 0.036 0.055 -10000 0 -0.74 1 1
CBL 0.039 0.038 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.004 0.029 -10000 0 -10000 0 0
STAT5A -0.005 0.034 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.062 0.043 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.002 0.035 -10000 0 -0.56 2 2
PTPN11 0 0 -10000 0 -10000 0 0
BTK 0 0.13 -10000 0 -0.5 6 6
BCL2 0.065 0.04 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.001 0.022 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.033 0.032 0.22 1 -10000 0 1
YWHAZ 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.02 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP -0.002 0.037 -10000 0 -0.57 2 2
PRKCI 0 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0 0 -10000 0 -10000 0 0
GYS1 0.028 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.009 0.029 -10000 0 -10000 0 0
VAMP2 0 0 -10000 0 -10000 0 0
SLC2A4 0.034 0.035 0.23 1 -10000 0 1
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.022 0 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 48 48
LNPEP 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.006 0.035 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.047 -9999 0 -0.37 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
RhoA/GTP -0.007 0.035 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.007 0.04 -9999 0 -10000 0 0
GNAZ -0.009 0.081 -9999 0 -0.74 6 6
GNAI3 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
S1PR5 -0.01 0.076 -9999 0 -0.59 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.008 0.04 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.033 -9999 0 -0.74 1 1
FoxO family signaling

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
G6PC 0.024 0.033 -9999 0 -10000 0 0
PLK1 -0.089 0.21 -9999 0 -0.78 2 2
CDKN1B 0.051 0.085 -9999 0 -10000 0 0
FOXO3 -0.022 0.16 -9999 0 -0.63 3 3
KAT2B 0.007 0.037 -9999 0 -0.75 1 1
FOXO1/SIRT1 0.018 0.025 -9999 0 -10000 0 0
CAT -0.017 0.16 -9999 0 -1.4 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.009 0.016 -9999 0 -10000 0 0
FOXO1 0.027 0.02 -9999 0 -10000 0 0
MAPK10 0.022 0.057 -9999 0 -0.41 8 8
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.079 0.032 -9999 0 -10000 0 0
response to oxidative stress -0.003 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.062 0.099 -9999 0 -0.61 2 2
XPO1 0.01 0 -9999 0 -10000 0 0
EP300 0.006 0.006 -9999 0 -10000 0 0
BCL2L11 0.015 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.027 -9999 0 -10000 0 0
mol:GDP -0.003 0.02 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
GADD45A 0.046 0.073 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.053 0.03 -9999 0 -10000 0 0
MST1 0.007 0.029 -9999 0 -0.56 1 1
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.038 0.038 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.03 0.008 -9999 0 -10000 0 0
MAPK9 0.029 0.008 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
SIRT1 0.008 0.013 -9999 0 -10000 0 0
SOD2 0.054 0.096 -9999 0 -10000 0 0
RBL2 0.018 0.11 -9999 0 -10000 0 0
RAL/GDP 0.014 0.014 -9999 0 -10000 0 0
CHUK 0.008 0.015 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.017 0.017 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG -0.043 0.3 -9999 0 -1.5 20 20
SKP2 -0.004 0.045 -9999 0 -0.57 3 3
USP7 0.011 0 -9999 0 -10000 0 0
IKBKB 0.007 0.029 -9999 0 -0.56 1 1
CCNB1 -0.032 0.18 -9999 0 -0.78 2 2
FOXO1-3a-4/beta catenin -0.015 0.039 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.027 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.008 0.014 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.08 0.029 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.58 48 48
CDK2 0.006 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.052 -9999 0 -10000 0 0
CREBBP 0.006 0.006 -9999 0 -10000 0 0
FBXO32 -0.017 0.15 -9999 0 -0.66 2 2
BCL6 0.018 0.11 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.027 0 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.025 0.024 -9999 0 -10000 0 0
MAPK12 0.027 0.015 -9999 0 -0.3 1 1
CCND1 0.013 0.052 -9999 0 -0.44 6 6
p38 gamma/SNTA1 -0.001 0.013 -9999 0 -10000 0 0
MAP2K3 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.027 0.015 -9999 0 -0.3 1 1
MAP2K6 0.021 0.016 -9999 0 -0.34 1 1
MAPT 0.023 0.045 -9999 0 -0.37 6 6
MAPK13 0.02 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.006 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
ITGA4 -0.008 0.074 -10000 0 -0.74 5 5
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.061 -10000 0 -0.56 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.048 -10000 0 -0.48 5 5
alpha4/beta7 Integrin/Paxillin -0.005 0.048 -10000 0 -0.43 6 6
lamellipodium assembly 0.001 0.005 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
TLN1 0 0 -10000 0 -10000 0 0
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.037 -10000 0 -10000 0 0
cell adhesion -0.004 0.04 -10000 0 -0.4 5 5
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.043 -10000 0 -0.43 5 5
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.002 0.033 -10000 0 -0.74 1 1
ARF6/GDP 0.001 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.008 0.067 -10000 0 -0.54 6 6
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 -0.008 0.073 -10000 0 -0.66 6 6
alpha4/beta1 Integrin/Paxillin/Talin -0.004 0.041 -10000 0 -0.4 5 5
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.041 -10000 0 -0.4 5 5
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.04 0.4 5 -10000 0 5
CBL 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.004 0.041 -10000 0 -0.4 5 5
Rac1/GTP 0.001 0.006 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.008 0.064 -10000 0 -0.46 9 9
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.019 -10000 0 -0.42 1 1
GNB1/GNG2 -0.006 0.053 -10000 0 -0.48 6 6
GNB1 -0.002 0.033 -10000 0 -0.74 1 1
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.004 0.041 -10000 0 -0.45 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.01 0.11 4 -10000 0 4
GNAL -0.006 0.067 -10000 0 -0.74 4 4
GNG2 -0.008 0.074 -10000 0 -0.74 5 5
CRH -0.001 0.026 -10000 0 -0.57 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.007 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0 0 -9999 0 -9999 0 0
SMAD2 0.012 0 -9999 0 -9999 0 0
SMAD3 0.036 0 -9999 0 -9999 0 0
SMAD3/SMAD4 0 0 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
PPM1A 0 0 -9999 0 -9999 0 0
CALM1 0 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
MAP3K1 0 0 -9999 0 -9999 0 0
TRAP-1/SMAD4 0 0 -9999 0 -9999 0 0
MAPK3 0 0 -9999 0 -9999 0 0
MAPK1 0 0 -9999 0 -9999 0 0
NUP214 0 0 -9999 0 -9999 0 0
CTDSP1 0 0 -9999 0 -9999 0 0
CTDSP2 0 0 -9999 0 -9999 0 0
CTDSPL 0 0 -9999 0 -9999 0 0
KPNB1 0 0 -9999 0 -9999 0 0
TGFBRAP1 0 0 -9999 0 -9999 0 0
UBE2I 0 0 -9999 0 -9999 0 0
NUP153 0 0 -9999 0 -9999 0 0
KPNA2 0 0 -9999 0 -9999 0 0
PIAS4 0 0 -9999 0 -9999 0 0
Canonical NF-kappaB pathway

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
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.071 0.019 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.002 0.036 -9999 0 -0.56 2 2
NFKBIA 0.041 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
RIPK2 0 0 -9999 0 -10000 0 0
IKBKG -0.001 0.016 -9999 0 -10000 0 0
IKK complex/A20 -0.01 0.056 -9999 0 -10000 0 0
NEMO/A20/RIP2 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM -0.001 0.014 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.001 0.016 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.003 0.047 -9999 0 -0.74 2 2
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.015 0.088 -9999 0 -0.55 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.003 0.047 -9999 0 -0.74 2 2
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.019 0.12 -9999 0 -0.73 13 13
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex -0.001 0.017 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.027 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.037 0.003 -10000 0 -10000 0 0
regulation of axonogenesis -0.024 0.019 -10000 0 -10000 0 0
myoblast fusion 0.001 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.002 0.025 0.39 2 -10000 0 2
ARF1/GTP 0 0.002 -10000 0 -10000 0 0
mol:GM1 0.009 0.004 -10000 0 -10000 0 0
mol:Choline 0.023 0.028 -10000 0 -0.33 3 3
lamellipodium assembly -0.001 0.015 -10000 0 -10000 0 0
MAPK3 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.025 -10000 0 -0.39 2 2
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.013 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.012 -10000 0 -10000 0 0
ARF6 0.008 0.002 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 0.01 0.034 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.004 -10000 0 -10000 0 0
actin filament bundle formation 0.001 0.011 -10000 0 -10000 0 0
KALRN -0.003 0.04 -10000 0 -0.44 4 4
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.011 -10000 0 -10000 0 0
NME1 0.01 0.026 -10000 0 -0.57 1 1
Rac1/GDP -0.001 0.011 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.005 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.015 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development 0 0.005 -10000 0 -10000 0 0
ARF6/GTP 0 0.005 -10000 0 -10000 0 0
RhoA/GTP 0 0.002 -10000 0 -10000 0 0
mol:GDP -0.001 0.014 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.001 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.015 0.031 -10000 0 -0.38 3 3
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.015 -10000 0 -10000 0 0
ruffle organization 0.024 0.019 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.004 -10000 0 -10000 0 0
PIP5K1A -0.001 0.016 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.028 -10000 0 -0.33 3 3
Rac1/GTP -0.001 0.016 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 0.001 0.014 0.31 1 -10000 0 1
FRAP1 0.013 0.005 -10000 0 -10000 0 0
AKT1 0 0.011 0.23 1 -10000 0 1
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -10000 0 -10000 0 0
TSC2 0 0 -10000 0 -10000 0 0
RHEB/GDP 0 0 -10000 0 -10000 0 0
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.025 0.007 -10000 0 -10000 0 0
MAP3K5 0.009 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
apoptosis 0.009 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -10000 0 0
EIF4B 0.03 0.007 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.006 0.17 1 -10000 0 1
FKBP1A 0 0.001 -10000 0 -10000 0 0
RHEB/GTP 0 0 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -10000 0 0
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 0.001 0.011 0.25 1 -10000 0 1
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C 0 0.004 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.001 -10000 0 -10000 0 0
TSC1/TSC2 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 0.007 0 -10000 0 -10000 0 0
INS 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.033 -10000 0 -0.74 1 1
PDK2 0.001 0.011 0.25 1 -10000 0 1
EIF4EBP1 0.004 0.021 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PPP2R5D 0.019 0.005 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -10000 0 1
EEF2 0.015 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.003 0.014 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.02 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.033 0 -9999 0 -10000 0 0
CDKN1A 0.033 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
FOXO3 0.033 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0 0 -9999 0 -10000 0 0
AKT3 0.014 0.019 -9999 0 -0.42 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0 0 -9999 0 -10000 0 0
RAF1 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.033 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.033 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.021 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAPKAP1 0 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.03 0.025 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
AKT1S1 0.033 0 -9999 0 -10000 0 0
CASP9 0.033 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0 -9999 0 -10000 0 0
CHUK 0.033 0 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 0.027 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
MDM2 0.032 0.014 -9999 0 -10000 0 0
MAPKKK cascade 0 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0 0.011 -9999 0 -10000 0 0
TSC1/TSC2 0.038 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.01 -9999 0 -10000 0 0
glucose import 0.024 0.041 -9999 0 -0.43 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.028 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.024 0.041 -9999 0 -0.43 4 4
GSK3A 0.033 0 -9999 0 -10000 0 0
FOXO1 0.033 0 -9999 0 -10000 0 0
GSK3B 0.033 0 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.58 48 48
G1/S transition of mitotic cell cycle 0.038 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.029 0.038 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
KPNA1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
RHEB 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
ceramide signaling 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
MAP4K4 0.036 0.057 -9999 0 -0.53 1 1
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
BAD 0.027 0.021 -9999 0 -10000 0 0
NFKBIA 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.081 -9999 0 -0.74 6 6
BAX 0.027 0.021 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.015 -9999 0 -0.12 1 1
IKBKB 0.041 0.056 -9999 0 -0.49 1 1
MAP2K2 0.038 0.023 -9999 0 -10000 0 0
MAP2K1 0.038 0.023 -9999 0 -10000 0 0
SMPD1 0.017 0.015 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.042 0.055 -9999 0 -0.51 1 1
MAP2K4 0.033 0.021 -9999 0 -10000 0 0
protein ubiquitination 0.043 0.055 -9999 0 -0.5 1 1
EnzymeConsortium:2.7.1.37 0.042 0.025 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.033 0.022 -9999 0 -10000 0 0
CRADD 0.01 0.001 -9999 0 -10000 0 0
mol:ceramide 0.021 0.022 -9999 0 -0.16 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.01 0.001 -9999 0 -10000 0 0
MAP3K1 0.027 0.021 -9999 0 -10000 0 0
TRADD 0.01 0.001 -9999 0 -10000 0 0
RELA/p50 0 0 -9999 0 -10000 0 0
MAPK3 0.04 0.022 -9999 0 -10000 0 0
MAPK1 0.04 0.022 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.036 0.057 -9999 0 -0.53 1 1
KSR1 0.027 0.022 -9999 0 -10000 0 0
MAPK8 0.038 0.02 -9999 0 -10000 0 0
TRAF2 0 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.042 0.054 -9999 0 -0.49 1 1
TNF R/SODD -0.001 0.019 -9999 0 -0.41 1 1
TNF -0.01 0.12 -9999 0 -0.73 13 13
CYCS 0.028 0.02 -9999 0 -10000 0 0
IKBKG 0.042 0.054 -9999 0 -0.49 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.03 0.059 -9999 0 -0.56 1 1
RELA 0 0 -9999 0 -10000 0 0
RIPK1 0 0.001 -9999 0 -10000 0 0
AIFM1 0.028 0.02 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.013 0.077 -9999 0 -0.48 12 12
TNFRSF1A 0 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.023 0.015 -9999 0 -10000 0 0
NSMAF 0.036 0.056 -9999 0 -0.52 1 1
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.016 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.017 -9999 0 -10000 0 0
NFKBIA 0.025 0.018 -9999 0 -0.26 2 2
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.016 -9999 0 -0.34 1 1
ARRB2 0.015 0 -9999 0 -10000 0 0
REL 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.016 -9999 0 -0.34 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.016 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer -0.001 0.019 -9999 0 -0.41 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.019 0.02 -9999 0 -0.41 1 1
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.019 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.001 0.017 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.017 -9999 0 -10000 0 0
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK -0.002 0.033 -9999 0 -0.74 1 1
I kappa B alpha/PIK3R1 -0.001 0.015 -9999 0 -10000 0 0
cell death -0.001 0.016 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.016 -9999 0 -10000 0 0
LCK -0.002 0.033 -9999 0 -0.74 1 1
BCL3 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0 0 -9999 0 -10000 0 0
KLHL20 -0.004 0.031 -9999 0 -0.38 1 1
CYFIP2 -0.023 0.13 -9999 0 -0.74 15 15
Rac1/GDP 0.053 0.011 -9999 0 -10000 0 0
ENAH 0 0 -9999 0 -10000 0 0
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.034 -9999 0 -0.25 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.02 -9999 0 -0.43 1 1
RAPGEF1 0.048 0.002 -9999 0 -10000 0 0
CTNND1 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.042 0.005 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.001 0.025 -9999 0 -0.56 1 1
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.024 -9999 0 -0.38 2 2
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.002 0.033 -9999 0 -0.74 1 1
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0.052 0.011 -9999 0 -10000 0 0
actin cytoskeleton organization -0.003 0.022 -9999 0 -0.26 1 1
CDC42/GDP 0.052 0.011 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
ITGB7 -0.002 0.033 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.052 0.012 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.006 -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 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.004 0.031 -9999 0 -0.25 7 7
NME1 -0.001 0.026 -9999 0 -0.57 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
WASF2 -0.003 0.017 -9999 0 -0.14 1 1
Rap1/GTP 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.018 -9999 0 -10000 0 0
CCND1 -0.005 0.039 -9999 0 -0.32 7 7
VAV2 0.04 0.062 -9999 0 -0.74 3 3
RAP1/GDP 0 0.001 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.001 0.017 -9999 0 -10000 0 0
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.053 -9999 0 -0.49 3 3
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 -0.001 0.013 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.025 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.014 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0 0 -9999 0 -9999 0 0
JUP 0 0 -9999 0 -9999 0 0
CDH1 0 0 -9999 0 -9999 0 0
Arf1 pathway

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
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0 -9999 0 -10000 0 0
AP2 -0.001 0.019 -9999 0 -0.41 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.023 0.13 -9999 0 -0.74 15 15
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 -0.001 0.026 -9999 0 -0.57 1 1
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.022 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -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 -0.008 0.044 -9999 0 -0.26 15 15
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.015 0.084 -9999 0 -0.47 16 16
Alternative NF-kappaB 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
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 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 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.013 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.019 -9999 0 -0.41 1 1
RELB -0.001 0.026 -9999 0 -0.57 1 1
NFKB2 0 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.016 -9999 0 -0.35 1 1
regulation of B cell activation -0.001 0.016 -9999 0 -0.35 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 489 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V TCGA.O2.A52S
109_MAP3K5 0.047 0.047 0.047 -0.2
47_PPARGC1A 0 0 0 -0.74
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 -0.57 -0.57 0
105_BMP2 -0.74 0 0 0
131_RELN/VLDLR 0 0 0 -0.43
30_TGFB1/TGF beta receptor Type II 0.016 0.014 0.014 0.013
84_STAT5B -0.0053 0.038 0.038 -0.07
84_STAT5A -0.0053 0.038 0.038 -0.07
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/LUSC-TP/9830261/LUSC-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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