PARADIGM pathway analysis of mRNASeq expression and copy number data
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 59 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
Angiopoietin receptor Tie2-mediated signaling 239
Glypican 2 network 232
Class IB PI3K non-lipid kinase events 208
FOXM1 transcription factor network 200
Signaling events mediated by Stem cell factor receptor (c-Kit) 167
Signaling mediated by p38-alpha and p38-beta 156
Signaling events regulated by Ret tyrosine kinase 129
Aurora B signaling 121
Endothelins 114
Aurora C signaling 103
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 514 . 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 ( 514 ).

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
Angiopoietin receptor Tie2-mediated signaling 0.4650 239 21067 88 -0.94 0.2 1000 -1000 -0.05 -1000
Glypican 2 network 0.4514 232 929 4 0.094 0.16 1000 -1000 0.022 -1000
Class IB PI3K non-lipid kinase events 0.4047 208 624 3 -0.18 -1000 1000 -1000 -0.019 -1000
FOXM1 transcription factor network 0.3891 200 10249 51 -0.029 0.75 1000 -1000 -0.017 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3249 167 13102 78 -0.58 0.24 1000 -1000 -0.023 -1000
Signaling mediated by p38-alpha and p38-beta 0.3035 156 6871 44 -0.33 0.026 1000 -1000 -0.009 -1000
Signaling events regulated by Ret tyrosine kinase 0.2510 129 10648 82 -0.24 0.026 1000 -1000 -0.04 -1000
Aurora B signaling 0.2354 121 8140 67 -0.067 0.29 1000 -1000 -0.032 -1000
Endothelins 0.2218 114 11014 96 -0.39 0.062 1000 -1000 -0.018 -1000
Aurora C signaling 0.2004 103 725 7 0 0.22 1000 -1000 -0.006 -1000
Fc-epsilon receptor I signaling in mast cells 0.2004 103 10049 97 -0.21 0.028 1000 -1000 -0.04 -1000
Thromboxane A2 receptor signaling 0.1770 91 9630 105 -0.28 0.091 1000 -1000 -0.026 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1751 90 6178 68 -0.36 0.16 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 0.1595 82 10365 125 -0.16 0.095 1000 -1000 -0.045 -1000
TCGA08_retinoblastoma 0.1537 79 639 8 -0.027 0.13 1000 -1000 -0.002 -1000
Reelin signaling pathway 0.1440 74 4189 56 -0.14 0.05 1000 -1000 -0.018 -1000
Ephrin B reverse signaling 0.1420 73 3531 48 -0.21 0.061 1000 -1000 -0.028 -1000
IL4-mediated signaling events 0.1362 70 6436 91 -0.56 0.42 1000 -1000 -0.046 -1000
Arf6 signaling events 0.1245 64 3993 62 -0.28 0.061 1000 -1000 -0.033 -1000
Signaling events mediated by the Hedgehog family 0.1187 61 3221 52 -0.26 0.051 1000 -1000 -0.018 -1000
IL6-mediated signaling events 0.1187 61 4604 75 -0.18 0.063 1000 -1000 -0.025 -1000
PLK1 signaling events 0.1167 60 5117 85 -0.044 0.22 1000 -1000 -0.019 -1000
PDGFR-alpha signaling pathway 0.1148 59 2609 44 -0.26 0.037 1000 -1000 -0.021 -1000
Glypican 1 network 0.1109 57 2769 48 -0.24 0.051 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1089 56 4783 85 -0.19 0.026 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.1051 54 4565 84 -0.18 0.062 1000 -1000 -0.02 -1000
ErbB2/ErbB3 signaling events 0.1031 53 3480 65 -0.17 0.036 1000 -1000 -0.045 -1000
EGFR-dependent Endothelin signaling events 0.1031 53 1133 21 -0.07 0.036 1000 -1000 -0.029 -1000
FOXA2 and FOXA3 transcription factor networks 0.1012 52 2437 46 -0.34 0.11 1000 -1000 -0.014 -1000
Glucocorticoid receptor regulatory network 0.0973 50 5754 114 -0.39 0.058 1000 -1000 -0.041 -1000
HIF-1-alpha transcription factor network 0.0914 47 3626 76 -0.13 0.23 1000 -1000 -0.025 -1000
BMP receptor signaling 0.0875 45 3656 81 -0.3 0.072 1000 -1000 -0.022 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0875 45 5473 120 -0.29 0.18 1000 -1000 -0.037 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0837 43 1467 34 -0.038 0.026 1000 -1000 -0.023 -1000
S1P1 pathway 0.0837 43 1574 36 -0.31 0.025 1000 -1000 -0.021 -1000
Nongenotropic Androgen signaling 0.0817 42 2225 52 -0.2 0.11 1000 -1000 -0.018 -1000
TCGA08_p53 0.0798 41 289 7 -0.041 0.022 1000 -1000 -0.002 -1000
Calcium signaling in the CD4+ TCR pathway 0.0798 41 1284 31 -0.18 0.028 1000 -1000 -0.021 -1000
IL23-mediated signaling events 0.0778 40 2428 60 -0.19 0.064 1000 -1000 -0.002 -1000
Ras signaling in the CD4+ TCR pathway 0.0759 39 672 17 -0.088 0.029 1000 -1000 -0.006 -1000
Plasma membrane estrogen receptor signaling 0.0700 36 3136 86 -0.095 0.18 1000 -1000 -0.044 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0681 35 1934 54 -0.14 0.051 1000 -1000 -0.023 -1000
FAS signaling pathway (CD95) 0.0681 35 1682 47 -0.31 0.041 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 0.0642 33 231 7 -0.021 0.022 1000 -1000 0 -1000
amb2 Integrin signaling 0.0623 32 2656 82 -0.18 0.081 1000 -1000 -0.015 -1000
Wnt signaling 0.0603 31 217 7 0.002 0.071 1000 -1000 0.003 -1000
S1P3 pathway 0.0584 30 1293 42 -0.24 0.036 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 0.0564 29 1818 61 -0.1 0.1 1000 -1000 -0.022 -1000
TCR signaling in naïve CD8+ T cells 0.0564 29 2707 93 -0.042 0.038 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 0.0545 28 341 12 -0.062 0.004 1000 -1000 -0.014 -1000
Osteopontin-mediated events 0.0545 28 1097 38 -0.098 0.065 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0545 28 1506 52 -0.12 0.047 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.0545 28 1478 51 -0.1 0.1 1000 -1000 -0.02 -1000
ErbB4 signaling events 0.0525 27 1877 69 -0.13 0.073 1000 -1000 -0.021 -1000
Syndecan-1-mediated signaling events 0.0525 27 947 34 -0.16 0.06 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 0.0525 27 472 17 -0.081 0.043 1000 -1000 -0.025 -1000
LPA receptor mediated events 0.0525 27 2797 102 -0.097 0.06 1000 -1000 -0.048 -1000
Noncanonical Wnt signaling pathway 0.0506 26 685 26 -0.048 0.071 1000 -1000 -0.017 -1000
EPHB forward signaling 0.0506 26 2271 85 -0.046 0.054 1000 -1000 -0.041 -1000
Visual signal transduction: Rods 0.0486 25 1337 52 -0.05 0.11 1000 -1000 -0.013 -1000
Regulation of Androgen receptor activity 0.0486 25 1786 70 -0.16 0.19 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 0.0467 24 1837 76 -0.12 0.094 1000 -1000 -0.019 -1000
Aurora A signaling 0.0467 24 1457 60 -0.056 0.19 1000 -1000 -0.006 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0467 24 3083 125 -0.2 0.05 1000 -1000 -0.023 -1000
Syndecan-4-mediated signaling events 0.0447 23 1589 67 -0.16 0.14 1000 -1000 -0.027 -1000
Regulation of nuclear SMAD2/3 signaling 0.0428 22 3077 136 -0.15 0.18 1000 -1000 -0.03 -1000
IL12-mediated signaling events 0.0428 22 1948 87 -0.28 0.054 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 0.0428 22 890 39 -0.061 0.031 1000 -1000 -0.012 -1000
IL27-mediated signaling events 0.0428 22 1142 51 -0.22 0.066 1000 -1000 -0.037 -1000
TCGA08_rtk_signaling 0.0428 22 594 26 -0.074 0.032 1000 -1000 -0.018 -1000
BCR signaling pathway 0.0428 22 2218 99 -0.065 0.049 1000 -1000 -0.044 -1000
Syndecan-2-mediated signaling events 0.0409 21 1498 69 -0.083 0.047 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0389 20 662 33 -0.14 0.12 1000 -1000 -0.022 -1000
Coregulation of Androgen receptor activity 0.0370 19 1454 76 -0.1 0.12 1000 -1000 -0.007 -1000
Nectin adhesion pathway 0.0370 19 1239 63 -0.032 0.061 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0350 18 1058 58 -0.017 0.1 1000 -1000 -0.022 -1000
Effects of Botulinum toxin 0.0350 18 491 26 -0.015 0.055 1000 -1000 0 -1000
IGF1 pathway 0.0350 18 1055 57 -0.046 0.045 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0331 17 662 37 -0.069 0.063 1000 -1000 -0.017 -1000
Regulation of p38-alpha and p38-beta 0.0331 17 932 54 -0.2 0.058 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0331 17 1788 102 -0.093 0.19 1000 -1000 -0.021 -1000
Rapid glucocorticoid signaling 0.0331 17 340 20 -0.031 0.025 1000 -1000 -0.001 -1000
Signaling events mediated by HDAC Class II 0.0311 16 1213 75 -0.16 0.18 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 0.0311 16 716 43 -0.096 0.14 1000 -1000 -0.076 -1000
IL1-mediated signaling events 0.0292 15 967 62 -0.098 0.062 1000 -1000 -0.024 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0292 15 1176 74 -0.16 0.07 1000 -1000 -0.043 -1000
Insulin Pathway 0.0292 15 1119 74 -0.12 0.054 1000 -1000 -0.033 -1000
BARD1 signaling events 0.0272 14 843 57 -0.048 0.14 1000 -1000 -0.04 -1000
Visual signal transduction: Cones 0.0272 14 550 38 -0.05 0.048 1000 -1000 0 -1000
EPO signaling pathway 0.0272 14 783 55 -0.018 0.065 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 0.0272 14 580 40 -0.17 0.046 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 0.0272 14 213 15 -0.089 0.027 1000 -1000 -0.02 -1000
Signaling events mediated by PRL 0.0272 14 499 34 -0.037 0.094 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0253 13 927 68 -0.053 0.069 1000 -1000 -0.027 -1000
Ceramide signaling pathway 0.0253 13 1021 76 -0.07 0.069 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 0.0233 12 953 74 -0.041 0.052 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 0.0233 12 421 35 -0.029 0.051 1000 -1000 -0.014 -1000
IL2 signaling events mediated by PI3K 0.0233 12 714 58 -0.047 0.11 1000 -1000 -0.03 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0233 12 564 45 0 0.064 1000 -1000 -0.028 -1000
S1P5 pathway 0.0214 11 200 17 -0.002 0.026 1000 -1000 -0.004 -1000
ceramide signaling pathway 0.0214 11 566 49 0 0.045 1000 -1000 -0.02 -1000
IL2 signaling events mediated by STAT5 0.0214 11 263 22 -0.02 0.06 1000 -1000 -0.017 -1000
FoxO family signaling 0.0195 10 651 64 0.001 0.17 1000 -1000 -0.017 -1000
S1P4 pathway 0.0195 10 268 25 -0.005 0.042 1000 -1000 -0.013 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0175 9 782 83 -0.031 0.1 1000 -1000 -0.01 -1000
Paxillin-dependent events mediated by a4b1 0.0175 9 352 36 -0.069 0.044 1000 -1000 -0.027 -1000
Class I PI3K signaling events 0.0175 9 667 73 -0.044 0.045 1000 -1000 -0.019 -1000
E-cadherin signaling in keratinocytes 0.0175 9 420 43 -0.014 0.041 1000 -1000 -0.018 -1000
Hedgehog signaling events mediated by Gli proteins 0.0156 8 523 65 -0.059 0.058 1000 -1000 -0.03 -1000
TRAIL signaling pathway 0.0156 8 401 48 0 0.047 1000 -1000 -0.017 -1000
VEGFR1 specific signals 0.0156 8 457 56 -0.2 0.056 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0136 7 209 28 -0.005 0.048 1000 -1000 -0.007 -1000
mTOR signaling pathway 0.0136 7 412 53 -0.016 0.035 1000 -1000 -0.028 -1000
Class I PI3K signaling events mediated by Akt 0.0136 7 518 68 -0.056 0.046 1000 -1000 -0.024 -1000
PDGFR-beta signaling pathway 0.0136 7 732 97 -0.018 0.061 1000 -1000 -0.04 -1000
Canonical NF-kappaB pathway 0.0117 6 250 39 0 0.056 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 0.0117 6 34 5 0.015 0.03 1000 -1000 0.013 -1000
E-cadherin signaling in the nascent adherens junction 0.0117 6 460 76 -0.024 0.06 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 0.0097 5 161 32 -0.032 0.046 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class I 0.0097 5 546 104 -0.05 0.062 1000 -1000 -0.032 -1000
Arf6 trafficking events 0.0078 4 309 71 -0.11 0.047 1000 -1000 -0.029 -1000
p38 MAPK signaling pathway 0.0078 4 213 44 0 0.055 1000 -1000 -0.012 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0058 3 71 23 0.003 0.047 1000 -1000 -0.011 -1000
PLK2 and PLK4 events 0.0058 3 9 3 0.011 0.028 1000 -1000 -0.003 -1000
Arf6 downstream pathway 0.0039 2 126 43 -0.047 0.048 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0.0039 2 78 31 0 0.031 1000 -1000 -0.005 -1000
E-cadherin signaling events 0.0039 2 13 5 0.019 0.042 1000 -1000 0.014 -1000
Circadian rhythm pathway 0.0019 1 30 22 -0.007 0.052 1000 -1000 -0.013 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0019 1 33 27 0 0.061 1000 -1000 -0.025 -1000
Arf1 pathway 0.0019 1 90 54 -0.001 0.045 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.067 1000 -1000 0 -1000
Total NA 4904 285932 7203 -16 -990 131000 -131000 -2.8 -131000
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.67 0.42 -10000 0 -0.89 383 383
NCK1/PAK1/Dok-R -0.31 0.18 -10000 0 -0.41 378 378
NCK1/Dok-R -0.81 0.55 -10000 0 -1.1 383 383
PIK3CA 0.024 0.023 -10000 0 -0.46 1 1
mol:beta2-estradiol 0.16 0.11 0.23 337 -10000 0 337
RELA 0.026 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 0.2 0.14 0.29 345 -10000 0 345
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.75 0.51 -10000 0 -1 382 382
FN1 0.015 0.074 -10000 0 -0.46 12 12
PLD2 -0.86 0.57 -10000 0 -1.1 383 383
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 0.027 0.11 0.29 34 -0.46 17 51
ELK1 -0.75 0.49 -10000 0 -1 383 383
GRB7 0.02 0.044 -10000 0 -0.46 4 4
PAK1 0.026 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.8 0.54 -10000 0 -1.1 383 383
CDKN1A -0.46 0.26 -10000 0 -0.62 344 344
ITGA5 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.81 0.55 -10000 0 -1.1 383 383
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:NO -0.48 0.3 -10000 0 -0.64 382 382
PLG -0.85 0.57 -10000 0 -1.1 383 383
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.64 0.39 -10000 0 -0.84 382 382
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.031 -10000 0 -0.46 2 2
ANGPT2 -0.44 0.27 -10000 0 -0.66 261 261
BMX -0.88 0.59 -10000 0 -1.2 383 383
ANGPT1 -0.78 0.55 -10000 0 -1.2 336 336
tube development -0.52 0.3 -10000 0 -0.68 379 379
ANGPT4 -0.013 0.093 -10000 0 -0.46 20 20
response to hypoxia -0.05 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.88 0.61 -10000 0 -1.2 383 383
alpha5/beta1 Integrin 0.037 0.009 -10000 0 -10000 0 0
FGF2 -0.13 0.23 -10000 0 -0.46 163 163
STAT5A (dimer) -0.6 0.36 -10000 0 -0.78 375 375
mol:L-citrulline -0.48 0.3 -10000 0 -0.64 382 382
AGTR1 -0.27 0.23 0.29 1 -0.46 307 308
MAPK14 -0.85 0.56 -10000 0 -1.1 383 383
Tie2/SHP2 -0.5 0.53 -10000 0 -1.2 187 187
TEK -0.56 0.59 -10000 0 -1.3 188 188
RPS6KB1 -0.64 0.4 -10000 0 -0.85 383 383
Angiotensin II/AT1 -0.19 0.17 0.2 1 -0.33 307 308
Tie2/Ang1/GRB2 -0.88 0.61 -10000 0 -1.2 383 383
MAPK3 -0.77 0.5 -10000 0 -1 383 383
MAPK1 -0.78 0.5 -10000 0 -1 383 383
Tie2/Ang1/GRB7 -0.88 0.6 -10000 0 -1.2 383 383
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 -0.86 0.57 -10000 0 -1.1 383 383
PI3K -0.78 0.5 -10000 0 -1 383 383
FES -0.85 0.56 -10000 0 -1.1 383 383
Crk/Dok-R -0.81 0.55 -10000 0 -1.1 383 383
Tie2/Ang1/ABIN2 -0.88 0.61 -10000 0 -1.2 383 383
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.59 0.36 -10000 0 -0.78 383 383
STAT5A 0.025 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.63 0.4 -10000 0 -0.84 381 381
Tie2/Ang2 -0.73 0.46 -10000 0 -0.95 379 379
Tie2/Ang1 -0.94 0.66 -10000 0 -1.2 383 383
FOXO1 -0.59 0.37 -10000 0 -0.79 382 382
ELF1 -0.048 0.075 -10000 0 -0.5 6 6
ELF2 -0.85 0.58 -10000 0 -1.1 383 383
mol:Choline -0.8 0.53 -10000 0 -1.1 383 383
cell migration -0.18 0.1 -10000 0 -0.23 381 381
FYN -0.6 0.36 -10000 0 -0.78 379 379
DOK2 0.021 0.032 -10000 0 -0.46 2 2
negative regulation of cell cycle -0.42 0.24 -10000 0 -0.56 345 345
ETS1 -0.15 0.14 -10000 0 -0.25 320 320
PXN -0.52 0.32 -10000 0 -0.69 380 380
ITGB1 0.025 0.005 -10000 0 -10000 0 0
NOS3 -0.56 0.34 -10000 0 -0.74 382 382
RAC1 0.025 0.005 -10000 0 -10000 0 0
TNF -0.15 0.14 0.29 8 -0.25 316 324
MAPKKK cascade -0.8 0.53 -10000 0 -1.1 383 383
RASA1 0.021 0.048 -10000 0 -0.46 5 5
Tie2/Ang1/Shc -0.87 0.6 -10000 0 -1.2 383 383
NCK1 0.023 0.031 -10000 0 -0.46 2 2
vasculogenesis -0.43 0.26 -10000 0 -0.57 382 382
mol:Phosphatidic acid -0.8 0.53 -10000 0 -1.1 383 383
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.48 0.3 -10000 0 -0.64 382 382
Rac1/GTP -0.59 0.37 -10000 0 -0.79 383 383
MMP2 -0.86 0.57 -10000 0 -1.1 383 383
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.14 0.13 0.29 223 -9999 0 223
GPC2 0.094 0.12 0.29 132 -9999 0 132
GPC2/Midkine 0.16 0.13 0.26 287 -9999 0 287
neuron projection morphogenesis 0.16 0.13 0.26 287 -9999 0 287
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.17 0.24 0.46 208 -10000 0 208
PI3K Class IB/PDE3B -0.17 0.24 -10000 0 -0.46 208 208
PDE3B -0.18 0.24 -10000 0 -0.46 208 208
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 0.63 0.42 0.99 238 -0.82 3 241
PLK1 0.35 0.25 0.65 153 -0.58 1 154
BIRC5 0.38 0.25 0.62 205 -0.76 3 208
HSPA1B 0.64 0.44 1 232 -0.82 3 235
MAP2K1 0.18 0.13 0.32 202 -10000 0 202
BRCA2 0.63 0.43 0.99 236 -0.93 4 240
FOXM1 0.75 0.54 1.2 258 -0.94 3 261
XRCC1 0.63 0.43 1 237 -0.82 3 240
FOXM1B/p19 0.19 0.35 0.83 73 -0.81 4 77
Cyclin D1/CDK4 0.54 0.39 0.88 223 -0.75 4 227
CDC2 0.69 0.48 1.1 257 -0.85 3 260
TGFA 0.54 0.41 0.9 225 -0.71 4 229
SKP2 0.64 0.44 1 235 -0.82 3 238
CCNE1 0.17 0.15 0.33 224 -10000 0 224
CKS1B 0.68 0.45 1 254 -0.82 3 257
RB1 0.38 0.31 0.68 219 -0.76 1 220
FOXM1C/SP1 0.56 0.4 0.9 227 -0.94 3 230
AURKB 0.38 0.27 0.62 200 -0.67 8 208
CENPF 0.71 0.48 1.1 248 -0.82 3 251
CDK4 0.089 0.052 0.21 14 -10000 0 14
MYC 0.44 0.41 0.86 197 -0.86 3 200
CHEK2 0.18 0.13 0.33 190 -10000 0 190
ONECUT1 0.55 0.42 0.92 224 -0.78 3 227
CDKN2A -0.029 0.16 0.25 76 -0.23 102 178
LAMA4 0.62 0.44 0.99 238 -0.93 5 243
FOXM1B/HNF6 0.56 0.42 0.95 212 -0.87 3 215
FOS 0.4 0.64 1 196 -0.92 40 236
SP1 0.024 0.028 -10000 0 -0.2 4 4
CDC25B 0.64 0.44 1 238 -0.82 3 241
response to radiation 0.13 0.093 0.21 241 -10000 0 241
CENPB 0.64 0.44 1 247 -0.82 3 250
CENPA 0.71 0.48 1.1 253 -0.82 3 256
NEK2 0.74 0.49 1.1 264 -0.82 3 267
HIST1H2BA 0.63 0.43 1 235 -0.82 3 238
CCNA2 0.096 0.1 0.34 67 -10000 0 67
EP300 0.025 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.66 0.46 1.1 234 -0.9 3 237
CCNB2 0.7 0.48 1.1 251 -0.82 3 254
CCNB1 0.7 0.49 1.1 247 -0.85 3 250
ETV5 0.65 0.47 1 249 -1 5 254
ESR1 0.7 0.45 1.1 254 -0.82 2 256
CCND1 0.57 0.42 0.93 237 -0.76 4 241
GSK3A 0.15 0.1 0.27 144 -10000 0 144
Cyclin A-E1/CDK1-2 0.26 0.17 0.4 265 -10000 0 265
CDK2 0.063 0.033 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.17 0.12 0.26 272 -10000 0 272
FOXM1B/Cbp/p300 0.25 0.32 0.73 69 -0.8 4 73
GAS1 0.44 0.66 1 211 -0.91 53 264
MMP2 0.62 0.46 1 231 -0.92 11 242
RB1/FOXM1C 0.52 0.4 0.88 224 -0.78 4 228
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.21 0.22 -10000 0 -0.42 246 246
CRKL -0.23 0.24 -10000 0 -0.45 255 255
HRAS -0.19 0.2 -10000 0 -0.39 223 223
mol:PIP3 -0.18 0.23 0.28 2 -0.41 227 229
SPRED1 0.025 0.006 -10000 0 -10000 0 0
SPRED2 0.024 0.031 -10000 0 -0.46 2 2
GAB1 -0.24 0.25 -10000 0 -0.47 255 255
FOXO3 -0.19 0.22 0.33 1 -0.4 241 242
AKT1 -0.21 0.24 -10000 0 -0.43 245 245
BAD -0.19 0.22 -10000 0 -0.4 242 242
megakaryocyte differentiation -0.24 0.25 -10000 0 -0.47 257 257
GSK3B -0.19 0.22 0.34 1 -0.4 241 242
RAF1 -0.14 0.18 0.26 2 -0.32 219 221
SHC1 0.022 0.01 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.46 256 256
STAT1 -0.5 0.52 -10000 0 -0.99 256 256
HRAS/SPRED1 -0.14 0.18 -10000 0 -0.32 219 219
cell proliferation -0.23 0.25 -10000 0 -0.46 255 255
PIK3CA 0.022 0.023 -10000 0 -0.46 1 1
TEC 0.026 0.012 0.29 1 -10000 0 1
RPS6KB1 -0.23 0.26 -10000 0 -0.46 259 259
HRAS/SPRED2 -0.14 0.18 -10000 0 -0.32 218 218
LYN/TEC/p62DOK -0.2 0.25 -10000 0 -0.44 233 233
MAPK3 -0.1 0.13 0.25 1 -0.27 105 106
STAP1 -0.25 0.25 -10000 0 -0.48 260 260
GRAP2 -0.011 0.13 -10000 0 -0.46 37 37
JAK2 -0.43 0.46 -10000 0 -0.86 256 256
STAT1 (dimer) -0.49 0.51 -10000 0 -0.97 257 257
mol:Gleevec 0.007 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.25 -10000 0 -0.44 250 250
actin filament polymerization -0.23 0.24 -10000 0 -0.45 255 255
LYN 0.023 0.023 -10000 0 -0.46 1 1
STAP1/STAT5A (dimer) -0.34 0.34 -10000 0 -0.64 262 262
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
CBL/CRKL/GRB2 -0.2 0.23 -10000 0 -0.41 248 248
PI3K -0.2 0.25 -10000 0 -0.45 243 243
PTEN 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.57 0.61 -10000 0 -1.2 250 250
MAPK8 -0.24 0.25 -10000 0 -0.47 255 255
STAT3 (dimer) -0.23 0.24 0.27 1 -0.45 256 257
positive regulation of transcription -0.084 0.11 0.24 1 -0.23 93 94
mol:GDP -0.19 0.22 -10000 0 -0.4 225 225
PIK3C2B -0.23 0.24 -10000 0 -0.44 255 255
CBL/CRKL -0.21 0.23 -10000 0 -0.42 254 254
FER -0.24 0.25 -10000 0 -0.47 255 255
SH2B3 -0.24 0.25 -10000 0 -0.47 257 257
PDPK1 -0.17 0.22 0.29 4 -0.39 222 226
SNAI2 -0.24 0.25 -10000 0 -0.46 258 258
positive regulation of cell proliferation -0.39 0.4 -10000 0 -0.76 262 262
KITLG -0.1 0.2 -10000 0 -0.48 108 108
cell motility -0.39 0.4 -10000 0 -0.76 262 262
PTPN6 0.035 0.015 -10000 0 -10000 0 0
EPOR -0.14 0.23 -10000 0 -0.87 21 21
STAT5A (dimer) -0.33 0.34 -10000 0 -0.64 260 260
SOCS1 0.024 0.022 -10000 0 -0.46 1 1
cell migration 0.24 0.24 0.46 256 -10000 0 256
SOS1 0.026 0.004 -10000 0 -10000 0 0
EPO 0.009 0.062 0.28 21 -10000 0 21
VAV1 0.018 0.057 -10000 0 -0.46 7 7
GRB10 -0.24 0.25 -10000 0 -0.46 256 256
PTPN11 0.033 0.01 -10000 0 -10000 0 0
SCF/KIT -0.24 0.26 -10000 0 -0.47 271 271
GO:0007205 0.01 0.011 -10000 0 -10000 0 0
MAP2K1 -0.11 0.14 0.26 1 -0.26 211 212
CBL 0.025 0.006 -10000 0 -10000 0 0
KIT -0.58 0.61 -10000 0 -1.2 249 249
MAP2K2 -0.11 0.14 0.26 1 -0.26 206 207
SHC/Grb2/SOS1 -0.2 0.24 -10000 0 -0.44 222 222
STAT5A -0.34 0.36 -10000 0 -0.66 259 259
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.23 0.24 -10000 0 -0.45 257 257
SHC/GRAP2 0.013 0.077 -10000 0 -0.33 23 23
PTPRO -0.24 0.26 -10000 0 -0.48 257 257
SH2B2 -0.23 0.25 -10000 0 -0.46 255 255
DOK1 0.026 0.004 -10000 0 -10000 0 0
MATK -0.24 0.25 -10000 0 -0.47 256 256
CREBBP -0.033 0.076 -10000 0 -0.18 13 13
BCL2 -0.2 0.35 -10000 0 -1.2 47 47
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.33 0.45 0.42 1 -0.95 165 166
MKNK1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.11 0.18 -10000 0 -0.32 206 206
ATF2/c-Jun -0.1 0.16 -10000 0 -0.4 51 51
MAPK11 -0.098 0.18 -10000 0 -0.33 182 182
MITF -0.14 0.21 -10000 0 -0.38 202 202
MAPKAPK5 -0.14 0.21 -10000 0 -0.38 205 205
KRT8 -0.13 0.21 -10000 0 -0.38 201 201
MAPKAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.01 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.16 0.27 -10000 0 -0.46 207 207
CEBPB -0.13 0.2 -10000 0 -0.38 195 195
SLC9A1 -0.13 0.21 -10000 0 -0.38 200 200
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.13 0.21 -10000 0 -0.38 201 201
p38alpha-beta/MNK1 -0.12 0.23 -10000 0 -0.4 184 184
JUN -0.1 0.15 -10000 0 -0.4 47 47
PPARGC1A -0.28 0.3 -10000 0 -0.46 321 321
USF1 -0.13 0.2 0.33 1 -0.37 191 192
RAB5/GDP/GDI1 -0.098 0.16 -10000 0 -0.28 197 197
NOS2 -0.23 0.38 -10000 0 -0.92 97 97
DDIT3 -0.14 0.2 -10000 0 -0.38 205 205
RAB5A 0.026 0.005 -10000 0 -10000 0 0
HSPB1 -0.11 0.17 0.28 6 -0.32 197 203
p38alpha-beta/HBP1 -0.12 0.23 -10000 0 -0.4 185 185
CREB1 -0.14 0.22 -10000 0 -0.4 200 200
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.12 0.19 -10000 0 -0.36 177 177
RPS6KA4 -0.13 0.2 -10000 0 -0.38 198 198
PLA2G4A -0.12 0.19 0.28 1 -0.36 178 179
GDI1 -0.13 0.2 -10000 0 -0.38 200 200
TP53 -0.17 0.25 -10000 0 -0.47 191 191
RPS6KA5 -0.14 0.21 -10000 0 -0.38 199 199
ESR1 -0.063 0.22 0.29 1 -0.38 124 125
HBP1 0.026 0.005 -10000 0 -10000 0 0
MEF2C -0.15 0.22 -10000 0 -0.4 209 209
MEF2A -0.13 0.21 -10000 0 -0.38 195 195
EIF4EBP1 -0.14 0.22 -10000 0 -0.4 197 197
KRT19 -0.14 0.22 -10000 0 -0.39 200 200
ELK4 -0.13 0.2 0.33 1 -0.37 197 198
ATF6 -0.13 0.2 0.33 1 -0.37 191 192
ATF1 -0.14 0.22 -10000 0 -0.4 204 204
p38alpha-beta/MAPKAPK2 -0.12 0.21 -10000 0 -0.39 179 179
p38alpha-beta/MAPKAPK3 -0.12 0.23 -10000 0 -0.4 181 181
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.033 0.076 -10000 0 -0.43 12 12
Crk/p130 Cas/Paxillin -0.15 0.15 -10000 0 -0.3 222 222
JUN -0.11 0.14 0.2 1 -0.24 164 165
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.12 0.17 0.53 1 -0.27 269 270
RAP1A 0.026 0.002 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.17 0.53 1 -0.27 266 267
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.15 0.36 1 -0.26 263 264
RHOA 0.025 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.11 0.15 0.45 1 -0.24 269 270
GRB7 0.02 0.044 -10000 0 -0.46 4 4
RET51/GFRalpha1/GDNF -0.12 0.17 0.53 1 -0.27 259 260
MAPKKK cascade -0.12 0.15 0.35 1 -0.26 244 245
BCAR1 0.023 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.16 0.36 1 -0.26 268 269
lamellipodium assembly -0.14 0.14 -10000 0 -0.27 231 231
RET51/GFRalpha1/GDNF/SHC -0.1 0.16 0.49 1 -0.27 218 219
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.14 -10000 0 -0.26 214 214
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.15 0.36 1 -0.26 266 267
MAPK3 -0.12 0.14 0.31 12 -0.24 253 265
DOK1 0.026 0.004 -10000 0 -10000 0 0
DOK6 -0.046 0.17 -10000 0 -0.46 74 74
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.13 0.14 0.28 11 -0.33 74 85
DOK5 -0.015 0.13 0.29 1 -0.46 42 43
GFRA1 -0.24 0.24 0.29 1 -0.46 275 276
MAPK8 -0.12 0.14 0.2 2 -0.24 253 255
HRAS/GTP -0.13 0.18 0.45 1 -0.28 257 258
tube development -0.11 0.14 0.34 1 -0.24 260 261
MAPK1 -0.12 0.14 0.31 12 -0.24 255 267
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.12 0.19 1 -0.23 257 258
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.025 0.006 -10000 0 -10000 0 0
PDLIM7 0.026 0.013 0.29 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.19 0.51 1 -0.29 282 283
SHC1 0.022 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.12 0.17 0.53 1 -0.27 269 270
RET51/GFRalpha1/GDNF/Dok5 -0.14 0.19 0.53 1 -0.29 274 275
PRKCA 0.014 0.071 -10000 0 -0.46 11 11
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
CREB1 -0.12 0.14 0.31 1 -0.26 207 208
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.093 0.12 0.26 1 -0.23 209 210
RET51/GFRalpha1/GDNF/Grb7 -0.12 0.17 0.53 1 -0.27 262 263
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.019 0.11 0.29 22 -0.46 19 41
DOK4 0.023 0.008 -10000 0 -10000 0 0
JNK cascade -0.11 0.14 0.2 1 -0.42 28 29
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.15 0.36 1 -0.26 265 266
SHANK3 0.024 0.008 -10000 0 -10000 0 0
RASA1 0.021 0.048 -10000 0 -0.46 5 5
NCK1 0.023 0.031 -10000 0 -0.46 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.092 0.12 0.27 1 -0.23 208 209
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.13 0.27 1 -0.24 254 255
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.14 0.23 2 -0.24 253 255
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.14 0.35 1 -0.25 210 211
PI3K -0.2 0.22 0.37 1 -0.4 232 233
SOS1 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.14 0.35 1 -0.24 260 261
GRB10 0.024 0.031 -10000 0 -0.46 2 2
activation of MAPKK activity -0.11 0.13 0.24 1 -0.22 252 253
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.17 0.53 1 -0.27 268 269
GAB1 0.022 0.043 -10000 0 -0.46 4 4
IRS1 0.014 0.074 -10000 0 -0.46 12 12
IRS2 -0.054 0.18 -10000 0 -0.46 82 82
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.14 0.24 3 -0.25 211 214
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.18 0.53 1 -0.28 268 269
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
GDNF 0.022 0.025 0.29 4 -10000 0 4
RAC1 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.18 0.53 1 -0.28 271 272
Rac1/GTP -0.16 0.18 0.31 1 -0.33 218 219
RET9/GFRalpha1/GDNF -0.14 0.15 0.36 1 -0.28 267 268
GFRalpha1/GDNF -0.16 0.18 0.41 1 -0.33 267 268
Aurora B signaling

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
Condensin I complex 0.1 0.089 0.25 90 -0.26 1 91
STMN1 0.11 0.063 0.15 199 -10000 0 199
Aurora B/RasGAP/Survivin 0.24 0.15 0.34 314 -0.17 5 319
Chromosomal passenger complex/Cul3 protein complex 0.11 0.089 0.21 111 -0.25 3 114
BIRC5 0.19 0.13 0.3 309 -10000 0 309
DES -0.067 0.31 0.37 5 -0.57 68 73
Aurora C/Aurora B/INCENP 0.15 0.083 0.21 148 -0.23 2 150
Aurora B/TACC1 0.07 0.16 0.19 274 -0.24 83 357
Aurora B/PP2A 0.16 0.086 0.21 358 -10000 0 358
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.05 0.031 0.14 18 -10000 0 18
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.15 0.11 0.2 365 -10000 0 365
Cul3 protein complex 0.029 0.083 -10000 0 -0.29 31 31
KIF2C 0.15 0.096 0.23 284 -0.15 1 285
PEBP1 0.029 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.13 0.28 321 -10000 0 321
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.15 0.096 0.21 353 -0.27 5 358
SEPT1 0.026 0.013 0.29 1 -10000 0 1
SMC2 0.025 0.014 0.29 1 -10000 0 1
SMC4 0.025 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.12 0.16 0.3 22 -0.41 29 51
PSMA3 0.026 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.005 -10000 0 -10000 0 0
H3F3B 0.1 0.059 0.15 88 -10000 0 88
AURKB 0.22 0.12 0.29 369 -10000 0 369
AURKC 0.024 0.033 0.29 1 -0.46 2 3
CDCA8 0.11 0.12 0.3 148 -10000 0 148
cytokinesis 0.16 0.12 0.26 219 -0.34 1 220
Aurora B/Septin1 0.2 0.14 0.31 269 -0.3 2 271
AURKA 0.025 0.045 0.28 14 -10000 0 14
INCENP 0.033 0.007 -10000 0 -10000 0 0
KLHL13 -0.004 0.12 -10000 0 -0.46 32 32
BUB1 0.093 0.12 0.28 147 -10000 0 147
hSgo1/Aurora B/Survivin 0.29 0.18 0.4 337 -10000 0 337
EVI5 0.031 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.15 0.091 0.26 124 -0.29 1 125
SGOL1 0.13 0.13 0.29 204 -10000 0 204
CENPA 0.17 0.11 0.26 270 -0.21 1 271
NCAPG 0.1 0.12 0.29 152 -10000 0 152
Aurora B/HC8 Proteasome 0.16 0.085 0.21 363 -10000 0 363
NCAPD2 0.026 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.16 0.084 0.21 366 -10000 0 366
RHOA 0.025 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.12 0.29 153 -10000 0 153
NPM1 0.11 0.11 0.27 2 -0.44 8 10
RASA1 0.021 0.048 -10000 0 -0.46 5 5
KLHL9 0.024 0.022 -10000 0 -0.46 1 1
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.16 0.085 0.21 363 -10000 0 363
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin 0.17 0.1 0.27 163 -0.31 1 164
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
NSUN2 0.12 0.086 0.27 18 -0.28 2 20
MYLK 0.052 0.14 0.16 65 -0.24 73 138
KIF23 0.04 0.048 0.3 16 -10000 0 16
VIM 0.12 0.082 0.27 32 -0.27 2 34
RACGAP1 0.032 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.11 0.11 -10000 0 -0.57 5 5
Chromosomal passenger complex 0.18 0.11 0.25 313 -0.35 1 314
Chromosomal passenger complex/EVI5 0.29 0.17 0.4 323 -10000 0 323
TACC1 -0.056 0.18 -10000 0 -0.46 83 83
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.1 0.19 0.24 2 -0.33 167 169
PTK2B 0.021 0.032 -10000 0 -0.46 2 2
mol:Ca2+ -0.18 0.34 -10000 0 -0.82 95 95
EDN1 -0.072 0.16 -10000 0 -0.38 70 70
EDN3 0.021 0.19 0.29 88 -0.46 51 139
EDN2 0.044 0.073 0.29 38 -0.46 1 39
HRAS/GDP -0.21 0.23 -10000 0 -0.5 145 145
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.09 0.18 -10000 0 -0.44 81 81
ADCY4 -0.11 0.18 0.35 1 -0.36 127 128
ADCY5 -0.14 0.2 0.32 2 -0.38 171 173
ADCY6 -0.11 0.18 0.32 2 -0.36 125 127
ADCY7 -0.11 0.18 0.32 2 -0.36 125 127
ADCY1 -0.11 0.2 0.32 2 -0.38 128 130
ADCY2 -0.13 0.2 -10000 0 -0.37 157 157
ADCY3 -0.11 0.19 0.32 2 -0.37 125 127
ADCY8 -0.11 0.18 -10000 0 -0.36 121 121
ADCY9 -0.15 0.22 0.32 2 -0.39 183 185
arachidonic acid secretion -0.22 0.27 -10000 0 -0.52 193 193
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.19 -10000 0 -0.31 329 329
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
HRAS 0.024 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.078 0.18 0.34 2 -0.34 113 115
ETA receptor/Endothelin-1/Gs/GTP -0.1 0.2 0.31 2 -0.36 147 149
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.11 0.2 -10000 0 -0.5 63 63
EDNRB -0.28 0.23 -10000 0 -0.46 312 312
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.14 0.25 -10000 0 -0.54 114 114
CYSLTR1 -0.18 0.28 -10000 0 -0.61 134 134
SLC9A1 -0.058 0.12 -10000 0 -0.3 55 55
mol:GDP -0.22 0.25 -10000 0 -0.52 157 157
SLC9A3 -0.39 0.36 -10000 0 -0.69 223 223
RAF1 -0.24 0.27 -10000 0 -0.52 190 190
JUN -0.14 0.27 -10000 0 -0.72 67 67
JAK2 -0.11 0.19 0.24 2 -0.39 115 117
mol:IP3 -0.17 0.21 -10000 0 -0.47 123 123
ETA receptor/Endothelin-1 -0.11 0.22 0.4 2 -0.38 173 175
PLCB1 0.021 0.038 -10000 0 -0.46 3 3
PLCB2 0.018 0.026 -10000 0 -0.46 1 1
ETA receptor/Endothelin-3 -0.026 0.17 0.22 56 -0.34 78 134
FOS -0.32 0.39 -10000 0 -0.83 168 168
Gai/GDP -0.11 0.3 -10000 0 -0.79 75 75
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.23 0.25 -10000 0 -0.51 174 174
BCAR1 0.024 0.009 -10000 0 -10000 0 0
PRKCB1 -0.17 0.21 -10000 0 -0.46 126 126
GNAQ 0.015 0.035 -10000 0 -0.46 2 2
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
GNAL -0.031 0.16 -10000 0 -0.46 59 59
Gs family/GDP -0.22 0.23 -10000 0 -0.49 166 166
ETA receptor/Endothelin-1/Gq/GTP -0.099 0.19 -10000 0 -0.41 103 103
MAPK14 -0.18 0.19 0.22 2 -0.35 203 205
TRPC6 -0.19 0.37 -10000 0 -0.9 92 92
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.002 -10000 0 -10000 0 0
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.19 0.2 -10000 0 -0.37 205 205
ETB receptor/Endothelin-2 -0.18 0.18 0.22 10 -0.32 304 314
ETB receptor/Endothelin-3 -0.19 0.22 0.22 41 -0.35 311 352
ETB receptor/Endothelin-1 -0.24 0.2 -10000 0 -0.38 321 321
MAPK3 -0.32 0.37 -10000 0 -0.79 174 174
MAPK1 -0.32 0.38 -10000 0 -0.78 177 177
Rac1/GDP -0.2 0.23 -10000 0 -0.51 142 142
cAMP biosynthetic process -0.14 0.23 0.31 6 -0.44 145 151
MAPK8 -0.18 0.34 -10000 0 -0.75 104 104
SRC 0.025 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.16 0.16 -10000 0 -0.27 308 308
p130Cas/CRK/Src/PYK2 -0.22 0.28 -10000 0 -0.62 129 129
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.2 0.23 -10000 0 -0.5 142 142
COL1A2 -0.25 0.22 -10000 0 -0.55 140 140
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.014 0.12 0.22 15 -0.31 32 47
mol:DAG -0.17 0.21 -10000 0 -0.47 123 123
MAP2K2 -0.27 0.3 -10000 0 -0.62 183 183
MAP2K1 -0.27 0.3 -10000 0 -0.63 181 181
EDNRA -0.056 0.14 0.21 1 -0.3 73 74
positive regulation of muscle contraction -0.088 0.16 0.21 1 -0.37 85 86
Gq family/GDP -0.17 0.24 -10000 0 -0.5 130 130
HRAS/GTP -0.21 0.25 -10000 0 -0.5 164 164
PRKCH -0.17 0.21 -10000 0 -0.47 123 123
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.17 0.21 -10000 0 -0.47 120 120
PRKCB -0.19 0.22 -10000 0 -0.47 150 150
PRKCE -0.17 0.21 -10000 0 -0.46 129 129
PRKCD -0.17 0.21 -10000 0 -0.47 121 121
PRKCG -0.15 0.2 0.23 1 -0.46 118 119
regulation of vascular smooth muscle contraction -0.38 0.46 -10000 0 -0.98 168 168
PRKCQ -0.18 0.22 0.23 1 -0.46 146 147
PLA2G4A -0.24 0.3 -10000 0 -0.57 193 193
GNA14 -0.011 0.11 -10000 0 -0.46 29 29
GNA15 0.019 0.026 -10000 0 -0.46 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.007 0.08 -10000 0 -0.46 14 14
Rac1/GTP -0.078 0.18 0.34 2 -0.35 111 113
MMP1 0.062 0.15 0.31 62 -0.87 4 66
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.026 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.15 0.084 0.2 351 -0.23 2 353
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.025 0.015 -10000 0 -10000 0 0
AURKB 0.22 0.12 0.29 369 -10000 0 369
AURKC 0.024 0.033 0.29 1 -0.46 2 3
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.031 -10000 0 -0.46 2 2
LAT2 -0.13 0.16 -10000 0 -0.31 187 187
AP1 -0.18 0.21 -10000 0 -0.43 151 151
mol:PIP3 -0.15 0.21 0.34 7 -0.36 194 201
IKBKB -0.082 0.13 0.26 14 -0.26 97 111
AKT1 -0.077 0.19 0.3 56 -0.37 69 125
IKBKG -0.094 0.13 0.28 9 -0.26 109 118
MS4A2 -0.21 0.23 -10000 0 -0.45 237 237
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.022 0.023 -10000 0 -0.46 1 1
MAP3K1 -0.1 0.17 0.28 7 -0.36 87 94
mol:Ca2+ -0.12 0.16 0.31 7 -0.28 191 198
LYN 0.021 0.025 -10000 0 -0.47 1 1
CBLB -0.13 0.16 -10000 0 -0.31 189 189
SHC1 0.022 0.01 -10000 0 -10000 0 0
RasGAP/p62DOK -0.038 0.14 -10000 0 -0.26 137 137
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
PLD2 -0.11 0.21 0.32 44 -0.28 251 295
PTPN13 -0.19 0.2 -10000 0 -0.47 118 118
PTPN11 0.012 0.027 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.086 0.15 0.32 9 -0.31 73 82
SYK 0.021 0.039 -10000 0 -0.47 3 3
GRB2 0.024 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.17 0.19 -10000 0 -0.34 242 242
LAT -0.13 0.16 -10000 0 -0.31 189 189
PAK2 -0.11 0.18 0.25 17 -0.39 91 108
NFATC2 -0.13 0.21 -10000 0 -0.6 75 75
HRAS -0.13 0.19 0.25 5 -0.33 192 197
GAB2 0.026 0.004 -10000 0 -10000 0 0
PLA2G1B 0.004 0.14 -10000 0 -0.86 12 12
Fc epsilon R1 -0.16 0.2 -10000 0 -0.35 260 260
Antigen/IgE/Fc epsilon R1 -0.15 0.19 -10000 0 -0.31 260 260
mol:GDP -0.15 0.18 -10000 0 -0.35 193 193
JUN 0.024 0.031 -10000 0 -0.46 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.46 2 2
FOS -0.097 0.21 -10000 0 -0.46 128 128
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.14 0.17 -10000 0 -0.31 210 210
CHUK -0.091 0.13 0.35 8 -0.26 108 116
KLRG1 -0.12 0.14 -10000 0 -0.25 239 239
VAV1 -0.14 0.16 -10000 0 -0.31 192 192
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.13 0.16 -10000 0 -0.31 189 189
negative regulation of mast cell degranulation -0.11 0.15 -10000 0 -0.33 97 97
BTK -0.16 0.2 -10000 0 -0.45 110 110
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.16 0.2 -10000 0 -0.32 263 263
GAB2/PI3K/SHP2 -0.13 0.14 -10000 0 -0.32 132 132
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.13 0.17 -10000 0 -0.33 160 160
RAF1 0.008 0.15 -10000 0 -0.94 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.19 -10000 0 -0.3 262 262
FCER1G 0.028 0.023 0.3 1 -10000 0 1
FCER1A -0.13 0.22 -10000 0 -0.47 147 147
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.18 -10000 0 -0.29 258 258
MAPK3 0.004 0.14 -10000 0 -0.87 12 12
MAPK1 0.001 0.14 -10000 0 -0.88 12 12
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 -0.088 0.23 -10000 0 -0.62 66 66
DUSP1 -0.11 0.22 -10000 0 -0.46 138 138
NF-kappa-B/RelA -0.054 0.08 0.14 2 -0.16 84 86
actin cytoskeleton reorganization -0.14 0.18 -10000 0 -0.44 79 79
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.12 0.17 -10000 0 -0.39 92 92
FER -0.14 0.16 -10000 0 -0.31 194 194
RELA 0.026 0.003 -10000 0 -10000 0 0
ITK -0.055 0.1 -10000 0 -0.39 35 35
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG1 -0.15 0.19 0.26 1 -0.35 191 192
cytokine secretion -0.044 0.052 -10000 0 -0.15 10 10
SPHK1 -0.13 0.16 -10000 0 -0.31 188 188
PTK2 -0.15 0.19 -10000 0 -0.46 78 78
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.17 0.2 -10000 0 -0.35 245 245
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.15 0.21 0.34 7 -0.36 194 201
MAP2K2 0 0.14 -10000 0 -0.87 12 12
MAP2K1 0.002 0.14 -10000 0 -0.87 12 12
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.1 0.13 -10000 0 -0.31 99 99
MAP2K4 -0.093 0.33 -10000 0 -0.92 66 66
Fc epsilon R1/FcgammaRIIB -0.15 0.2 -10000 0 -0.32 263 263
mol:Choline -0.1 0.2 0.32 44 -0.28 251 295
SHC/Grb2/SOS1 -0.11 0.16 -10000 0 -0.3 175 175
FYN 0.026 0.004 -10000 0 -10000 0 0
DOK1 0.026 0.004 -10000 0 -10000 0 0
PXN -0.14 0.18 -10000 0 -0.43 77 77
HCLS1 -0.13 0.16 -10000 0 -0.31 188 188
PRKCB -0.13 0.17 0.3 8 -0.29 204 212
FCGR2B 0.012 0.068 -10000 0 -0.46 10 10
IGHE -0.003 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.11 0.15 -10000 0 -0.34 97 97
LCP2 0.02 0.048 -10000 0 -0.46 5 5
PLA2G4A -0.14 0.16 -10000 0 -0.31 199 199
RASA1 0.021 0.048 -10000 0 -0.46 5 5
mol:Phosphatidic acid -0.1 0.2 0.32 44 -0.28 251 295
IKK complex -0.057 0.11 0.3 15 -0.2 81 96
WIPF1 0.024 0.031 -10000 0 -0.46 2 2
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.023 0.022 -10000 0 -0.46 1 1
GNB1/GNG2 -0.095 0.093 -10000 0 -0.19 243 243
AKT1 -0.085 0.12 0.26 1 -0.23 49 50
EGF -0.07 0.19 -10000 0 -0.46 99 99
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.006 0.073 0.26 7 -0.24 7 14
mol:Ca2+ -0.14 0.17 0.28 1 -0.31 246 247
LYN -0.005 0.064 0.28 5 -0.21 1 6
RhoA/GTP -0.058 0.071 -10000 0 -0.13 228 228
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.16 0.19 0.28 1 -0.34 244 245
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
ARRB2 0.024 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.058 0.2 -10000 0 -0.54 60 60
G beta5/gamma2 -0.12 0.13 -10000 0 -0.25 241 241
PRKCH -0.17 0.2 -10000 0 -0.36 240 240
DNM1 0.025 0.006 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.014 0.022 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.017 0.13 -10000 0 -0.46 42 42
G12 family/GTP -0.14 0.16 -10000 0 -0.3 239 239
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
ADRBK2 0.022 0.038 -10000 0 -0.46 3 3
RhoA/GTP/ROCK1 0.033 0.008 -10000 0 -10000 0 0
mol:GDP 0.091 0.14 0.38 60 -10000 0 60
mol:NADP 0.025 0.013 0.29 1 -10000 0 1
RAB11A 0.025 0.006 -10000 0 -10000 0 0
PRKG1 -0.21 0.24 -10000 0 -0.46 239 239
mol:IP3 -0.18 0.21 0.3 1 -0.39 246 247
cell morphogenesis 0.032 0.008 -10000 0 -10000 0 0
PLCB2 -0.25 0.29 -10000 0 -0.53 246 246
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.008 0.068 0.31 5 -0.22 6 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.005 0.067 0.26 6 -0.26 4 10
RHOA 0.025 0.005 -10000 0 -10000 0 0
PTGIR 0.025 0.022 -10000 0 -0.46 1 1
PRKCB1 -0.18 0.21 -10000 0 -0.38 244 244
GNAQ 0.023 0.031 -10000 0 -0.46 2 2
mol:L-citrulline 0.025 0.013 0.29 1 -10000 0 1
TXA2/TXA2-R family -0.25 0.28 -10000 0 -0.53 244 244
LCK -0.005 0.072 0.26 7 -0.26 4 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.015 0.065 -10000 0 -0.21 31 31
TXA2-R family/G12 family/GDP/G beta/gamma -0.004 0.1 -10000 0 -0.41 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.017 0.063 -10000 0 -0.2 27 27
MAPK14 -0.1 0.13 0.23 1 -0.23 233 234
TGM2/GTP -0.2 0.23 0.37 1 -0.43 241 242
MAPK11 -0.1 0.12 0.23 1 -0.23 239 240
ARHGEF1 -0.081 0.099 0.28 1 -0.18 232 233
GNAI2 0.025 0.006 -10000 0 -10000 0 0
JNK cascade -0.18 0.21 0.3 1 -0.39 244 245
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.13 0.16 0.27 1 -0.28 243 244
cAMP biosynthetic process -0.17 0.19 0.29 1 -0.36 242 243
Gq family/GTP/EBP50 -0.013 0.088 -10000 0 -0.25 50 50
actin cytoskeleton reorganization 0.032 0.008 -10000 0 -10000 0 0
SRC -0.004 0.067 0.26 6 -0.26 1 7
GNB5 0.025 0.006 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.091 0.28 12 -0.23 16 28
VCAM1 -0.15 0.18 0.26 1 -0.33 244 245
TP beta/Gq family/GDP/G beta5/gamma2 -0.058 0.2 -10000 0 -0.54 60 60
platelet activation -0.14 0.17 0.28 1 -0.3 241 242
PGI2/IP 0.018 0.016 -10000 0 -0.33 1 1
PRKACA -0.003 0.066 -10000 0 -0.24 36 36
Gq family/GDP/G beta5/gamma2 -0.049 0.18 -10000 0 -0.48 57 57
TXA2/TP beta/beta Arrestin2 0.004 0.057 -10000 0 -0.34 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.058 -10000 0 -0.22 35 35
mol:DAG -0.2 0.24 -10000 0 -0.44 244 244
EGFR -0.013 0.13 -10000 0 -0.46 40 40
TXA2/TP alpha -0.23 0.26 -10000 0 -0.49 242 242
Gq family/GTP -0.025 0.096 -10000 0 -0.24 72 72
YES1 -0.003 0.067 0.26 7 -0.19 1 8
GNAI2/GTP -0.01 0.06 -10000 0 -0.2 38 38
PGD2/DP -0.011 0.096 -10000 0 -0.33 42 42
SLC9A3R1 0.025 0.006 -10000 0 -10000 0 0
FYN -0.006 0.068 0.27 6 -0.22 2 8
mol:NO 0.025 0.013 0.29 1 -10000 0 1
GNA15 0.023 0.023 -10000 0 -0.46 1 1
PGK/cGMP -0.12 0.16 -10000 0 -0.28 237 237
RhoA/GDP 0.026 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.018 0.091 -10000 0 -0.23 49 49
NOS3 0.026 0.013 0.29 1 -10000 0 1
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.17 0.2 0.29 1 -0.36 241 242
PRKCB -0.18 0.21 -10000 0 -0.39 244 244
PRKCE -0.16 0.2 0.32 2 -0.36 242 244
PRKCD -0.18 0.21 -10000 0 -0.39 243 243
PRKCG -0.17 0.21 -10000 0 -0.39 241 241
muscle contraction -0.23 0.26 0.34 1 -0.49 244 245
PRKCZ -0.16 0.19 0.28 1 -0.34 244 245
ARR3 0.021 0.013 0.29 1 -10000 0 1
TXA2/TP beta 0.012 0.069 -10000 0 -0.21 38 38
PRKCQ -0.17 0.21 0.32 2 -0.38 237 239
MAPKKK cascade -0.22 0.25 -10000 0 -0.47 243 243
SELE -0.17 0.2 0.26 1 -0.38 244 245
TP beta/GNAI2/GDP/G beta/gamma 0.017 0.093 -10000 0 -0.23 52 52
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 -0.003 0.11 -10000 0 -0.46 29 29
chemotaxis -0.28 0.32 -10000 0 -0.61 244 244
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.011 0.08 -10000 0 -0.46 14 14
Rac1/GTP 0.018 0.004 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.03 0.051 0.31 9 -0.26 4 13
NFATC2 -0.072 0.25 -10000 0 -0.53 91 91
NFATC3 -0.026 0.11 -10000 0 -0.27 69 69
CD40LG -0.29 0.42 -10000 0 -0.88 144 144
ITCH -0.14 0.12 -10000 0 -0.24 14 14
CBLB -0.14 0.12 -10000 0 -0.24 14 14
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.34 0.58 1 -0.8 86 87
JUNB 0.024 0.022 -10000 0 -0.46 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.17 0.14 -10000 0 -0.27 334 334
T cell anergy -0.25 0.19 -10000 0 -0.38 330 330
TLE4 -0.07 0.22 -10000 0 -0.58 61 61
Jun/NFAT1-c-4/p21SNFT -0.18 0.42 -10000 0 -0.84 123 123
AP-1/NFAT1-c-4 -0.29 0.51 -10000 0 -1 136 136
IKZF1 -0.062 0.21 -10000 0 -0.53 59 59
T-helper 2 cell differentiation -0.16 0.35 -10000 0 -0.78 92 92
AP-1/NFAT1 -0.1 0.23 -10000 0 -0.43 123 123
CALM1 -0.098 0.093 -10000 0 -0.18 14 14
EGR2 -0.28 0.55 -10000 0 -1.1 127 127
EGR3 -0.26 0.53 -10000 0 -1.1 132 132
NFAT1/FOXP3 -0.03 0.2 0.59 1 -0.44 62 63
EGR1 -0.042 0.17 -10000 0 -0.46 72 72
JUN 0.011 0.043 -10000 0 -0.46 2 2
EGR4 0.031 0.042 0.3 12 -10000 0 12
mol:Ca2+ -0.11 0.078 -10000 0 -0.16 342 342
GBP3 -0.057 0.2 -10000 0 -0.49 57 57
FOSL1 0.028 0.034 0.29 5 -0.46 1 6
NFAT1-c-4/MAF/IRF4 -0.21 0.45 -10000 0 -0.87 133 133
DGKA -0.048 0.17 -10000 0 -0.45 52 52
CREM 0.023 0.011 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.25 0.45 -10000 0 -0.91 137 137
CTLA4 -0.039 0.17 0.36 6 -0.41 54 60
NFAT1-c-4 (dimer)/EGR1 -0.21 0.46 -10000 0 -0.92 134 134
NFAT1-c-4 (dimer)/EGR4 -0.18 0.44 -10000 0 -0.85 132 132
FOS -0.11 0.21 -10000 0 -0.47 128 128
IFNG -0.1 0.26 -10000 0 -0.65 59 59
T cell activation -0.1 0.28 0.44 2 -0.65 71 73
MAF -0.002 0.11 -10000 0 -0.46 26 26
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.35 0.7 129 -10000 0 129
TNF -0.2 0.4 -10000 0 -0.82 132 132
FASLG -0.31 0.58 -10000 0 -1.2 137 137
TBX21 0.023 0.077 0.36 1 -0.46 11 12
BATF3 0.021 0.034 0.29 1 -0.46 2 3
PRKCQ -0.008 0.13 0.29 1 -0.46 37 38
PTPN1 -0.051 0.18 -10000 0 -0.45 53 53
NFAT1-c-4/ICER1 -0.18 0.42 -10000 0 -0.84 132 132
GATA3 -0.075 0.2 -10000 0 -0.46 105 105
T-helper 1 cell differentiation -0.098 0.25 -10000 0 -0.64 59 59
IL2RA -0.18 0.34 0.56 1 -0.75 96 97
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.049 0.17 -10000 0 -0.45 53 53
E2F1 0.04 0.055 0.29 23 -10000 0 23
PPARG -0.1 0.22 -10000 0 -0.46 135 135
SLC3A2 -0.05 0.17 -10000 0 -0.42 62 62
IRF4 -0.041 0.17 -10000 0 -0.46 69 69
PTGS2 -0.33 0.44 -10000 0 -0.87 165 165
CSF2 -0.27 0.41 -10000 0 -0.86 138 138
JunB/Fra1/NFAT1-c-4 -0.17 0.42 -10000 0 -0.82 128 128
IL4 -0.17 0.37 -10000 0 -0.83 90 90
IL5 -0.27 0.41 -10000 0 -0.86 139 139
IL2 -0.1 0.28 0.45 1 -0.66 70 71
IL3 -0.05 0.14 -10000 0 -0.81 12 12
RNF128 -0.36 0.27 -10000 0 -0.54 341 341
NFATC1 -0.16 0.35 -10000 0 -0.7 129 129
CDK4 0.12 0.24 0.56 81 -10000 0 81
PTPRK -0.052 0.18 -10000 0 -0.46 53 53
IL8 -0.27 0.41 -10000 0 -0.86 140 140
POU2F1 0.022 0.01 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.037 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.016 0.1 0.22 18 -0.32 36 54
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.057 0.16 -10000 0 -0.25 196 196
NGF (dimer)/p75(NTR)/BEX1 -0.075 0.2 -10000 0 -0.3 201 201
NT-4/5 (dimer)/p75(NTR) -0.16 0.22 -10000 0 -0.38 238 238
IKBKB 0.024 0.008 -10000 0 -10000 0 0
AKT1 -0.089 0.13 -10000 0 -0.25 180 180
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF 0.021 0.069 0.29 7 -0.46 8 15
MGDIs/NGR/p75(NTR)/LINGO1 -0.05 0.18 0.38 7 -0.28 179 186
FURIN 0.025 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.075 0.16 -10000 0 -0.29 186 186
LINGO1 0.058 0.087 0.29 62 -10000 0 62
Sortilin/TRAF6/NRIF 0.021 0.033 -10000 0 -0.23 6 6
proBDNF (dimer) 0.021 0.068 0.29 7 -0.46 8 15
NTRK1 0.021 0.054 0.29 7 -0.46 4 11
RTN4R 0.034 0.047 0.29 16 -10000 0 16
neuron apoptosis -0.099 0.16 -10000 0 -0.46 32 32
IRAK1 0.026 0.004 -10000 0 -10000 0 0
SHC1 -0.085 0.14 -10000 0 -0.29 155 155
ARHGDIA 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.051 0.049 -10000 0 -0.24 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.089 0.18 -10000 0 -0.28 218 218
MAGEH1 -0.017 0.14 -10000 0 -0.46 45 45
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.088 0.17 -10000 0 -0.27 222 222
Mammalian IAPs/DIABLO 0.052 0.063 -10000 0 -0.26 19 19
proNGF (dimer) 0.006 0.097 -10000 0 -0.46 21 21
MAGED1 0.025 0.022 -10000 0 -0.46 1 1
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.071 0.19 -10000 0 -0.46 99 99
ZNF274 0.025 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.073 0.14 -10000 0 -0.25 189 189
NGF 0.006 0.097 -10000 0 -0.46 21 21
cell cycle arrest -0.096 0.11 0.2 4 -0.22 193 197
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.073 0.13 -10000 0 -0.23 179 179
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.13 0.2 -10000 0 -0.32 236 236
NCSTN 0.022 0.01 -10000 0 -10000 0 0
mol:GTP -0.087 0.17 -10000 0 -0.29 198 198
PSENEN 0.025 0.006 -10000 0 -10000 0 0
mol:ceramide -0.092 0.14 0.18 4 -0.26 190 194
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.059 0.11 -10000 0 -0.38 12 12
p75(NTR)/beta APP -0.096 0.18 -10000 0 -0.33 181 181
BEX1 0.045 0.13 0.29 70 -0.46 18 88
mol:GDP -0.12 0.14 -10000 0 -0.29 194 194
NGF (dimer) 0.072 0.12 0.37 2 -0.25 37 39
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.034 0.17 0.37 7 -0.25 175 182
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
RAC1/GTP -0.069 0.14 -10000 0 -0.25 190 190
MYD88 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.087 0.17 -10000 0 -0.29 198 198
RHOB 0.025 0.022 -10000 0 -0.46 1 1
RHOA 0.025 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.043 0.037 0.22 20 -10000 0 20
NT3 (dimer) -0.009 0.13 0.29 3 -0.46 37 40
TP53 -0.088 0.12 -10000 0 -0.24 169 169
PRDM4 -0.094 0.14 0.18 4 -0.27 193 197
BDNF (dimer) 0.095 0.12 0.37 24 -0.25 27 51
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
SORT1 0.026 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.06 0.16 -10000 0 -0.25 196 196
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.066 0.16 -10000 0 -0.27 192 192
RHOC 0.026 0.002 -10000 0 -10000 0 0
XIAP 0.026 0.002 -10000 0 -10000 0 0
MAPK10 -0.12 0.17 0.23 2 -0.32 180 182
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.093 0.14 0.18 4 -0.27 190 194
APH1B 0.017 0.061 -10000 0 -0.46 8 8
APH1A 0.021 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.082 0.17 -10000 0 -0.29 193 193
PSEN1 0.026 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.12 0.2 0.22 2 -0.36 196 198
MAPK8 -0.1 0.15 0.24 3 -0.29 168 171
MAPK9 -0.1 0.15 0.24 3 -0.29 172 175
APAF1 0.026 0.002 -10000 0 -10000 0 0
NTF3 -0.009 0.13 0.29 3 -0.46 37 40
NTF4 -0.071 0.19 -10000 0 -0.46 99 99
NDN -0.01 0.13 -10000 0 -0.46 37 37
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.055 0.15 -10000 0 -0.24 191 191
p75 CTF/Sortilin/TRAF6/NRIF 0.058 0.036 -10000 0 -0.26 4 4
RhoA-B-C/GTP -0.087 0.17 -10000 0 -0.29 198 198
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.16 -10000 0 -0.25 183 183
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.058 0.16 -10000 0 -0.26 185 185
PRKACB 0.019 0.057 -10000 0 -0.46 7 7
proBDNF (dimer)/p75 ECD 0.031 0.057 0.22 7 -0.33 10 17
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.006 0.095 -10000 0 -0.46 20 20
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.14 0.15 -10000 0 -0.3 202 202
BAD -0.11 0.16 0.25 3 -0.31 171 174
RIPK2 0.024 0.008 -10000 0 -10000 0 0
NGFR -0.15 0.23 -10000 0 -0.46 182 182
CYCS -0.098 0.12 0.18 8 -0.25 185 193
ADAM17 0.021 0.043 -10000 0 -0.46 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.064 0.16 -10000 0 -0.27 180 180
BCL2L11 -0.11 0.16 0.25 3 -0.31 171 174
BDNF (dimer)/p75(NTR) -0.1 0.18 0.22 7 -0.34 186 193
PI3K -0.065 0.16 -10000 0 -0.27 181 181
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.066 0.16 -10000 0 -0.27 193 193
NDNL2 0.025 0.006 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.19 -10000 0 -0.34 194 194
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.064 0.16 -10000 0 -0.27 190 190
TRAF6 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
PLG 0.039 0.062 0.29 29 -10000 0 29
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.16 -10000 0 -0.29 195 195
SQSTM1 0.026 0.005 -10000 0 -10000 0 0
NGFRAP1 0.022 0.043 -10000 0 -0.46 4 4
CASP3 -0.11 0.15 0.24 3 -0.3 172 175
E2F1 0.037 0.055 0.29 23 -10000 0 23
CASP9 0.025 0.005 -10000 0 -10000 0 0
IKK complex -0.03 0.12 -10000 0 -0.35 21 21
NGF (dimer)/TRKA 0.017 0.08 0.22 7 -0.33 23 30
MMP7 0.06 0.14 0.29 100 -0.46 18 118
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.055 0.16 -10000 0 -0.25 189 189
MMP3 0.051 0.089 0.29 55 -0.46 2 57
APAF-1/Caspase 9 -0.1 0.099 -10000 0 -0.37 10 10
TCGA08_retinoblastoma

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
CDKN2B -0.024 0.14 -10000 0 -0.43 52 52
CDKN2C 0.003 0.04 -10000 0 -0.44 2 2
CDKN2A 0.13 0.13 0.29 192 -10000 0 192
CCND2 -0.02 0.091 0.19 52 -0.23 22 74
RB1 0.022 0.096 0.2 31 -0.2 51 82
CDK4 -0.021 0.097 0.2 52 -0.24 19 71
CDK6 -0.027 0.11 0.21 48 -0.22 44 92
G1/S progression -0.023 0.1 0.2 51 -0.25 23 74
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.015 0.22 1 -10000 0 1
VLDLR 0.023 0.031 -10000 0 -0.46 2 2
CRKL 0.025 0.006 -10000 0 -10000 0 0
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
ITGA3 0.02 0.048 -10000 0 -0.46 5 5
RELN/VLDLR/Fyn -0.065 0.16 0.21 4 -0.28 170 174
MAPK8IP1/MKK7/MAP3K11/JNK1 0.05 0.049 -10000 0 -0.24 6 6
AKT1 -0.062 0.11 0.17 3 -0.22 163 166
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
DAB1 0.035 0.055 0.29 22 -10000 0 22
RELN/LRP8/DAB1 -0.051 0.15 0.21 25 -0.26 174 199
LRPAP1/LRP8 0.038 0.016 0.22 3 -10000 0 3
RELN/LRP8/DAB1/Fyn -0.039 0.15 0.34 2 -0.24 171 173
DAB1/alpha3/beta1 Integrin -0.043 0.14 -10000 0 -0.24 160 160
long-term memory -0.089 0.18 0.34 4 -0.28 223 227
DAB1/LIS1 -0.037 0.15 -10000 0 -0.24 169 169
DAB1/CRLK/C3G -0.044 0.14 -10000 0 -0.23 167 167
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
DAB1/NCK2 -0.034 0.15 -10000 0 -0.24 169 169
ARHGEF2 0.02 0.011 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.074 0.19 0.29 1 -0.46 102 103
CDK5R1 0.025 0.014 0.29 1 -10000 0 1
RELN -0.14 0.23 0.29 5 -0.46 176 181
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
RELN/LRP8/Fyn -0.062 0.16 0.24 6 -0.28 171 177
GRIN2A/RELN/LRP8/DAB1/Fyn -0.089 0.19 0.37 1 -0.29 224 225
MAPK8 0.019 0.057 -10000 0 -0.46 7 7
RELN/VLDLR/DAB1 -0.054 0.15 0.21 21 -0.26 173 194
ITGB1 0.025 0.005 -10000 0 -10000 0 0
MAP1B -0.082 0.13 0.28 2 -0.26 177 179
RELN/LRP8 -0.064 0.16 0.24 5 -0.28 173 178
GRIN2B/RELN/LRP8/DAB1/Fyn -0.032 0.16 0.38 4 -0.25 169 173
PI3K 0.031 0.031 -10000 0 -0.33 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.032 0.038 -10000 0 -0.33 5 5
RAP1A -0.074 0.12 0.28 6 -0.23 59 65
PAFAH1B1 0.024 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.021 0.29 3 -10000 0 3
CRLK/C3G 0.036 0.011 -10000 0 -10000 0 0
GRIN2B 0.023 0.021 0.29 3 -10000 0 3
NCK2 0.026 0.003 -10000 0 -10000 0 0
neuron differentiation -0.029 0.1 0.24 2 -0.33 12 14
neuron adhesion -0.069 0.12 0.33 8 -0.4 4 12
LRP8 0.028 0.02 0.29 3 -10000 0 3
GSK3B -0.06 0.11 -10000 0 -0.21 161 161
RELN/VLDLR/DAB1/Fyn -0.043 0.15 0.35 1 -0.24 170 171
MAP3K11 0.026 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.061 0.12 0.18 4 -0.23 167 171
CDK5 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.13 0.2 0.67 2 -0.42 168 170
neuron migration -0.081 0.15 0.33 5 -0.29 155 160
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.03 0.1 0.24 2 -0.34 12 14
RELN/VLDLR -0.049 0.15 -10000 0 -0.26 170 170
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.018 0.057 -10000 0 -0.46 7 7
EPHB2 0.03 0.027 0.29 5 -10000 0 5
EFNB1 0.012 0.018 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.032 0.095 0.3 1 -0.23 52 53
Ephrin B2/EPHB1-2 0.016 0.098 0.2 5 -0.25 58 63
neuron projection morphogenesis 0.015 0.084 0.23 1 -0.22 52 53
Ephrin B1/EPHB1-2/Tiam1 0.024 0.098 0.32 1 -0.24 54 55
DNM1 0.026 0.007 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.15 0.25 0.25 2 -0.53 145 147
YES1 -0.21 0.35 -10000 0 -0.74 148 148
Ephrin B1/EPHB1-2/NCK2 0.027 0.093 0.32 1 -0.24 51 52
PI3K -0.13 0.26 -10000 0 -0.53 143 143
mol:GDP 0.023 0.096 0.31 1 -0.24 54 55
ITGA2B 0.061 0.092 0.29 70 -10000 0 70
endothelial cell proliferation 0.029 0.038 -10000 0 -0.28 7 7
FYN -0.2 0.35 -10000 0 -0.74 148 148
MAP3K7 -0.16 0.26 0.23 1 -0.56 146 147
FGR -0.2 0.34 -10000 0 -0.74 145 145
TIAM1 0.022 0.043 -10000 0 -0.46 4 4
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
RGS3 0.025 0.007 -10000 0 -10000 0 0
cell adhesion -0.13 0.26 0.27 7 -0.53 142 149
LYN -0.2 0.34 -10000 0 -0.74 148 148
Ephrin B1/EPHB1-2/Src Family Kinases -0.2 0.32 -10000 0 -0.68 149 149
Ephrin B1/EPHB1-2 -0.16 0.28 -10000 0 -0.61 142 142
SRC -0.2 0.34 -10000 0 -0.74 147 147
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
EPHB1 -0.022 0.15 -10000 0 -0.46 51 51
EPHB4 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.038 -10000 0 -0.28 7 7
alphaIIb/beta3 Integrin 0.023 0.13 0.22 61 -0.32 51 112
BLK -0.2 0.34 -10000 0 -0.74 145 145
HCK -0.2 0.34 -10000 0 -0.74 144 144
regulation of stress fiber formation -0.025 0.092 0.24 51 -0.31 1 52
MAPK8 -0.14 0.24 0.24 1 -0.51 145 146
Ephrin B1/EPHB1-2/RGS3 0.026 0.093 0.32 1 -0.24 51 52
endothelial cell migration -0.13 0.22 0.26 3 -0.47 144 147
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTPN13 -0.13 0.26 -10000 0 -0.57 134 134
regulation of focal adhesion formation -0.025 0.092 0.24 51 -0.31 1 52
chemotaxis -0.024 0.092 0.24 51 -0.31 1 52
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
Rac1/GTP 0.024 0.09 0.27 1 -0.23 52 53
angiogenesis -0.17 0.28 -10000 0 -0.6 144 144
LCK -0.2 0.34 -10000 0 -0.74 146 146
IL4-mediated signaling events

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
BCL2L1 -0.36 0.57 -10000 0 -1.1 131 131
STAT6 (cleaved dimer) -0.4 0.58 -10000 0 -1.2 148 148
IGHG1 -0.1 0.23 0.44 2 -0.47 36 38
IGHG3 -0.36 0.55 -10000 0 -1.1 146 146
AKT1 -0.18 0.32 -10000 0 -0.74 62 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.27 -10000 0 -0.71 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.33 -10000 0 -0.75 55 55
THY1 -0.37 0.57 -10000 0 -1.2 132 132
MYB 0.023 0.037 -10000 0 -0.46 3 3
HMGA1 0.032 0.04 0.29 12 -10000 0 12
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.39 -10000 0 -0.8 95 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.32 -10000 0 -0.75 53 53
SP1 0.03 0.007 -10000 0 -10000 0 0
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
SOCS5 0.026 0.038 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.39 0.58 -10000 0 -1.2 144 144
SOCS1 -0.23 0.37 -10000 0 -0.72 131 131
SOCS3 -0.2 0.37 -10000 0 -0.85 71 71
FCER2 -0.37 0.56 -10000 0 -1.1 141 141
PARP14 0.025 0.011 -10000 0 -10000 0 0
CCL17 -0.37 0.58 -10000 0 -1.2 132 132
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.26 -10000 0 -0.63 40 40
T cell proliferation -0.4 0.58 -10000 0 -1.2 147 147
IL4R/JAK1 -0.38 0.58 -10000 0 -1.2 134 134
EGR2 -0.47 0.68 -10000 0 -1.3 165 165
JAK2 -0.019 0.092 -10000 0 -0.49 11 11
JAK3 0.019 0.027 0.29 1 -10000 0 1
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
JAK1 0.001 0.056 -10000 0 -0.46 5 5
COL1A2 -0.082 0.21 -10000 0 -0.92 6 6
CCL26 -0.37 0.57 -10000 0 -1.2 130 130
IL4R -0.4 0.62 -10000 0 -1.2 132 132
PTPN6 0.025 0.028 -10000 0 -10000 0 0
IL13RA2 -0.37 0.58 -10000 0 -1.2 130 130
IL13RA1 -0.01 0.062 -10000 0 -10000 0 0
IRF4 -0.24 0.52 -10000 0 -1.2 98 98
ARG1 -0.066 0.19 -10000 0 -0.76 5 5
CBL -0.21 0.36 -10000 0 -0.75 95 95
GTF3A 0.031 0.017 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
IL13RA1/JAK2 -0.011 0.1 -10000 0 -0.35 11 11
IRF4/BCL6 -0.22 0.48 -10000 0 -1.1 97 97
CD40LG -0.028 0.14 -10000 0 -0.46 44 44
MAPK14 -0.21 0.37 -10000 0 -0.77 96 96
mitosis -0.16 0.31 -10000 0 -0.7 62 62
STAT6 -0.44 0.71 -10000 0 -1.4 137 137
SPI1 0.027 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.16 0.29 -10000 0 -0.68 59 59
STAT6 (dimer) -0.43 0.71 -10000 0 -1.4 137 137
STAT6 (dimer)/PARP14 -0.41 0.62 -10000 0 -1.2 140 140
mast cell activation 0.007 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.33 -10000 0 -0.74 64 64
FRAP1 -0.18 0.32 -10000 0 -0.75 62 62
LTA -0.37 0.57 -10000 0 -1.2 130 130
FES 0.025 0.005 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.42 0.67 1.3 137 -10000 0 137
CCL11 -0.41 0.6 -10000 0 -1.2 153 153
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.16 0.31 -10000 0 -0.73 53 53
IL2RG 0.017 0.05 0.3 1 -0.46 4 5
IL10 -0.35 0.58 0.82 1 -1.2 125 126
IRS1 0.014 0.074 -10000 0 -0.46 12 12
IRS2 -0.054 0.18 -10000 0 -0.46 82 82
IL4 -0.069 0.22 -10000 0 -1.1 11 11
IL5 -0.38 0.57 -10000 0 -1.2 133 133
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.28 0.48 -10000 0 -0.9 135 135
COL1A1 -0.12 0.3 -10000 0 -1 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.6 -10000 0 -1.2 131 131
IL2R gamma/JAK3 0.025 0.048 0.22 2 -0.3 5 7
TFF3 -0.38 0.64 0.73 1 -1.2 143 144
ALOX15 -0.41 0.63 -10000 0 -1.2 149 149
MYBL1 0.024 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.34 0.52 -10000 0 -0.98 150 150
SHC1 0.022 0.01 -10000 0 -10000 0 0
CEBPB 0.026 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.32 -10000 0 -0.7 70 70
mol:PI-3-4-5-P3 -0.18 0.32 -10000 0 -0.75 62 62
PI3K -0.19 0.34 -10000 0 -0.81 61 61
DOK2 0.021 0.032 -10000 0 -0.46 2 2
ETS1 0.015 0.062 -10000 0 -0.42 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.25 -10000 0 -0.6 35 35
ITGB3 -0.44 0.64 -10000 0 -1.3 154 154
PIGR -0.5 0.72 0.83 1 -1.3 184 185
IGHE 0.022 0.068 0.19 29 -0.18 1 30
MAPKKK cascade -0.098 0.24 -10000 0 -0.59 35 35
BCL6 0.022 0.032 -10000 0 -0.46 2 2
OPRM1 -0.37 0.57 -10000 0 -1.2 133 133
RETNLB -0.5 0.65 -10000 0 -1.2 189 189
SELP -0.56 0.76 0.82 1 -1.4 208 209
AICDA -0.36 0.55 -10000 0 -1.1 132 132
Arf6 signaling events

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
CENTA1/KIF3B 0.03 0.014 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.13 0.16 -10000 0 -0.85 9 9
EGFR -0.013 0.13 -10000 0 -0.46 40 40
EPHA2 0.025 0.005 -10000 0 -10000 0 0
USP6 0.024 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.022 -10000 0 -0.46 1 1
EGFR/EGFR/EGF/EGF -0.063 0.17 -10000 0 -0.35 129 129
ARRB2 0.008 0.003 -10000 0 -10000 0 0
mol:GTP 0.012 0.054 0.14 14 -0.18 13 27
ARRB1 -0.03 0.16 -10000 0 -0.46 58 58
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR 0.031 0.056 0.29 22 -10000 0 22
EGF -0.071 0.19 -10000 0 -0.46 99 99
somatostatin receptor activity 0 0 0.001 3 -0.001 194 197
ARAP2 0.01 0.085 -10000 0 -0.46 16 16
mol:GDP -0.19 0.15 0.19 2 -0.3 252 254
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 104 105
ITGA2B 0.061 0.091 0.29 70 -10000 0 70
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.037 -10000 0 -0.26 2 2
ADAP1 0.024 0.022 -10000 0 -0.46 1 1
KIF13B 0.023 0.009 -10000 0 -10000 0 0
HGF/MET -0.12 0.19 -10000 0 -0.35 201 201
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.17 0.11 0.23 2 -0.28 195 197
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.042 0.15 -10000 0 -0.3 130 130
ADRB2 -0.25 0.24 -10000 0 -0.46 287 287
receptor agonist activity 0 0 -10000 0 0 212 212
actin filament binding 0 0 0.001 3 0 248 251
SRC 0.025 0.006 -10000 0 -10000 0 0
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
GNAQ 0.022 0.031 -10000 0 -0.46 2 2
EFA6/PI-4-5-P2 -0.001 0 0.002 3 -0.001 119 122
ARF6/GDP -0.062 0.15 0.28 2 -0.49 42 44
ARF6/GDP/GULP/ACAP1 -0.19 0.16 -10000 0 -0.35 168 168
alphaIIb/beta3 Integrin/paxillin/GIT1 0.049 0.11 0.37 1 -0.25 48 49
ACAP1 0.023 0.033 0.29 1 -0.46 2 3
ACAP2 0.023 0.023 -10000 0 -0.46 1 1
LHCGR/beta Arrestin2 0.012 0.018 -10000 0 -10000 0 0
EFNA1 0.022 0.016 0.29 1 -10000 0 1
HGF -0.16 0.24 -10000 0 -0.46 191 191
CYTH3 0.006 0.001 -10000 0 -10000 0 0
CYTH2 0 0.13 -10000 0 -0.99 8 8
NCK1 0.023 0.031 -10000 0 -0.46 2 2
fibronectin binding 0 0 0 4 0 158 162
endosomal lumen acidification 0 0 0.001 6 0 116 122
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.01 0.13 -10000 0 -0.46 38 38
GNAQ/ARNO 0.011 0.12 -10000 0 -0.93 8 8
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 0 3 0 45 48
MET 0.003 0.1 -10000 0 -0.46 23 23
GNA14 -0.003 0.11 -10000 0 -0.46 29 29
GNA15 0.023 0.023 -10000 0 -0.46 1 1
GIT1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 3 -0.001 165 168
GNA11 0.011 0.08 -10000 0 -0.46 14 14
LHCGR -0.002 0.018 -10000 0 -10000 0 0
AGTR1 -0.28 0.23 0.29 1 -0.46 307 308
desensitization of G-protein coupled receptor protein signaling pathway 0.012 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO -0.042 0.15 -10000 0 -0.88 8 8
alphaIIb/beta3 Integrin 0.023 0.13 0.22 61 -0.32 51 112
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.008 0.15 0.37 1 -0.59 18 19
IHH 0.03 0.24 0.3 135 -0.48 71 206
SHH Np/Cholesterol/GAS1 -0.052 0.13 0.25 2 -0.27 117 119
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.051 0.13 0.27 117 -0.25 2 119
SMO/beta Arrestin2 0.003 0.16 -10000 0 -0.36 61 61
SMO -0.013 0.16 0.29 1 -0.37 64 65
AKT1 0.01 0.12 -10000 0 -0.43 17 17
ARRB2 0.024 0.007 -10000 0 -10000 0 0
BOC 0.025 0.025 0.29 1 -0.46 1 2
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
heart looping -0.006 0.16 0.28 1 -0.36 64 65
STIL 0.001 0.14 0.25 27 -0.4 23 50
DHH N/PTCH2 0.033 0.064 0.22 13 -0.33 12 25
DHH N/PTCH1 0.008 0.13 -10000 0 -0.28 68 68
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
DHH 0.016 0.068 -10000 0 -0.46 10 10
PTHLH -0.001 0.18 0.43 1 -0.57 18 19
determination of left/right symmetry -0.006 0.16 0.28 1 -0.36 64 65
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
skeletal system development 0 0.18 0.43 1 -0.56 18 19
IHH N/Hhip 0.012 0.18 0.23 3 -0.33 92 95
DHH N/Hhip 0.008 0.1 0.22 4 -0.34 40 44
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.006 0.16 0.28 1 -0.36 64 65
pancreas development -0.003 0.12 0.29 4 -0.46 31 35
HHAT 0.017 0.049 -10000 0 -0.46 5 5
PI3K 0.031 0.031 -10000 0 -0.33 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.076 0.2 -10000 0 -0.46 105 105
somite specification -0.006 0.16 0.28 1 -0.36 64 65
SHH Np/Cholesterol/PTCH1 -0.019 0.13 0.33 2 -0.36 35 37
SHH Np/Cholesterol/PTCH2 0.002 0.086 0.22 13 -0.25 43 56
SHH Np/Cholesterol/Megalin -0.14 0.15 0.25 1 -0.27 268 269
SHH -0.018 0.098 0.4 2 -0.33 42 44
catabolic process 0.001 0.13 -10000 0 -0.29 77 77
SMO/Vitamin D3 0.011 0.18 0.32 27 -0.34 63 90
SHH Np/Cholesterol/Hhip -0.016 0.1 0.2 6 -0.28 61 67
LRP2 -0.26 0.24 -10000 0 -0.46 297 297
receptor-mediated endocytosis -0.12 0.18 0.25 1 -0.45 72 73
SHH Np/Cholesterol/BOC -0.002 0.081 0.23 3 -0.26 41 44
SHH Np/Cholesterol/CDO -0.01 0.091 0.25 2 -0.26 54 56
mesenchymal cell differentiation 0.016 0.1 0.28 61 -0.2 6 67
mol:Vitamin D3 0.02 0.17 0.33 30 -0.38 29 59
IHH N/PTCH2 0.04 0.15 0.29 13 -0.29 68 81
CDON 0.012 0.08 -10000 0 -0.46 14 14
IHH N/PTCH1 0.028 0.16 0.27 1 -0.29 77 78
Megalin/LRPAP1 -0.18 0.18 -10000 0 -0.33 294 294
PTCH2 0.031 0.052 0.29 13 -0.46 2 15
SHH Np/Cholesterol -0.01 0.074 -10000 0 -0.25 42 42
PTCH1 0.001 0.13 -10000 0 -0.29 77 77
HHIP -0.003 0.12 0.29 4 -0.46 31 35
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.079 0.25 0.58 6 -0.65 24 30
CRP -0.062 0.26 0.64 10 -0.62 29 39
cell cycle arrest -0.1 0.27 0.57 6 -0.62 58 64
TIMP1 -0.065 0.22 0.54 5 -0.58 23 28
IL6ST -0.16 0.24 -10000 0 -0.46 199 199
Rac1/GDP -0.13 0.23 0.32 5 -0.46 122 127
AP1 -0.028 0.17 0.47 1 -0.53 15 16
GAB2 0.027 0.006 -10000 0 -10000 0 0
TNFSF11 -0.078 0.25 0.55 5 -0.59 37 42
HSP90B1 0.015 0.1 -10000 0 -0.72 5 5
GAB1 0.022 0.043 -10000 0 -0.46 4 4
MAPK14 -0.15 0.24 -10000 0 -0.54 101 101
AKT1 0.027 0.06 -10000 0 -0.42 4 4
FOXO1 0.029 0.055 -10000 0 -0.43 3 3
MAP2K6 -0.15 0.23 0.24 3 -0.48 125 128
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.11 0.22 0.4 6 -0.45 111 117
MITF -0.15 0.23 0.28 4 -0.47 126 130
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.008 -10000 0 -10000 0 0
A2M -0.014 0.22 -10000 0 -1.2 18 18
CEBPB 0.028 0.013 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.03 0.12 -10000 0 -0.45 16 16
STAT3 -0.11 0.28 0.59 5 -0.65 60 65
STAT1 0.006 0.071 -10000 0 -0.83 3 3
CEBPD -0.078 0.25 0.56 7 -0.64 29 36
PIK3CA 0.024 0.023 -10000 0 -0.46 1 1
PI3K 0.033 0.032 -10000 0 -0.33 3 3
JUN 0.024 0.031 -10000 0 -0.46 2 2
PIAS3/MITF -0.14 0.22 0.3 2 -0.45 122 124
MAPK11 -0.15 0.24 -10000 0 -0.53 103 103
STAT3 (dimer)/FOXO1 -0.078 0.23 0.52 6 -0.55 38 44
GRB2/SOS1/GAB family -0.11 0.22 -10000 0 -0.48 98 98
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.23 -10000 0 -0.48 127 127
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.015 0.071 -10000 0 -0.46 11 11
LBP -0.09 0.32 0.6 13 -0.83 48 61
PIK3R1 0.024 0.031 -10000 0 -0.46 2 2
JAK1 0.022 0.05 -10000 0 -0.46 5 5
MYC -0.077 0.28 0.59 8 -0.78 31 39
FGG -0.15 0.35 0.55 7 -0.89 69 76
macrophage differentiation -0.1 0.27 0.57 6 -0.62 58 64
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.14 0.22 -10000 0 -0.35 213 213
JUNB -0.081 0.24 0.53 6 -0.56 46 52
FOS -0.097 0.21 -10000 0 -0.46 128 128
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.24 0.31 4 -0.49 126 130
STAT1/PIAS1 -0.12 0.22 0.37 5 -0.45 109 114
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.058 -10000 0 -0.45 4 4
STAT3 (dimer) -0.11 0.28 0.59 5 -0.65 56 61
PRKCD -0.095 0.23 0.46 8 -0.49 80 88
IL6R -0.036 0.16 -10000 0 -0.46 61 61
SOCS3 -0.16 0.27 -10000 0 -0.68 74 74
gp130 (dimer)/JAK1/JAK1/LMO4 -0.081 0.17 -10000 0 -0.28 200 200
Rac1/GTP -0.13 0.23 0.33 4 -0.47 115 119
HCK 0.022 0.038 -10000 0 -0.46 3 3
MAPKKK cascade 0.003 0.11 0.37 1 -0.55 10 11
bone resorption -0.073 0.24 0.55 5 -0.56 37 42
IRF1 -0.089 0.24 0.59 5 -0.66 24 29
mol:GDP -0.14 0.23 0.3 4 -0.47 126 130
SOS1 0.027 0.006 -10000 0 -10000 0 0
VAV1 -0.15 0.23 0.3 4 -0.48 126 130
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.18 0.29 -10000 0 -0.63 115 115
PTPN11 0.005 0.082 -10000 0 -0.75 5 5
IL6/IL6RA -0.084 0.19 0.22 1 -0.38 138 139
gp130 (dimer)/TYK2/TYK2/LMO4 -0.075 0.16 -10000 0 -0.28 185 185
gp130 (dimer)/JAK2/JAK2/LMO4 -0.086 0.17 -10000 0 -0.28 203 203
IL6 -0.1 0.22 0.29 1 -0.46 135 136
PIAS3 0.025 0.005 -10000 0 -10000 0 0
PTPRE 0.007 0.064 -10000 0 -0.46 8 8
PIAS1 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.16 0.22 0.26 1 -0.37 207 208
LMO4 0.027 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.27 0.54 2 -0.59 77 79
MCL1 0.063 0.1 0.41 1 -0.5 1 2
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.044 0.055 0.12 13 -0.11 153 166
BUB1B 0.055 0.067 0.13 165 -0.14 13 178
PLK1 0.028 0.032 0.096 38 -0.097 6 44
PLK1S1 0.022 0.024 0.12 5 -0.16 2 7
KIF2A 0.022 0.029 0.17 3 -10000 0 3
regulation of mitotic centrosome separation 0.028 0.032 0.096 38 -0.1 5 43
GOLGA2 0.025 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.19 0.13 0.28 321 -10000 0 321
WEE1 0.023 0.07 -10000 0 -0.28 20 20
cytokinesis 0.085 0.086 0.17 132 -0.2 12 144
PP2A-alpha B56 0.086 0.1 -10000 0 -0.51 9 9
AURKA 0.025 0.034 0.13 21 -0.2 3 24
PICH/PLK1 0.053 0.069 0.21 63 -10000 0 63
CENPE 0.026 0.034 0.14 12 -10000 0 12
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.03 0.17 3 -10000 0 3
PPP2CA 0.026 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.007 -10000 0 -10000 0 0
TPX2 0.06 0.058 0.13 179 -0.22 1 180
PAK1 0.025 0.005 -10000 0 -10000 0 0
SPC24 0.17 0.13 0.29 286 -10000 0 286
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN 0.033 0.055 0.14 44 -0.23 9 53
GORASP1 0.026 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 8 -0.01 9 17
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.015 0.018 0.053 38 -0.052 4 42
G2 phase of mitotic cell cycle 0 0.004 0.014 19 -10000 0 19
STAG2 0.026 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.011 0.084 -10000 0 -0.49 13 13
spindle elongation 0.028 0.032 0.096 38 -0.1 5 43
ODF2 0.025 0.007 -10000 0 -10000 0 0
BUB1 0.069 0.11 -10000 0 -0.56 9 9
TPT1 0.011 0.052 0.12 2 -0.18 29 31
CDC25C 0.11 0.074 0.15 255 -0.25 10 265
CDC25B 0.026 0.009 -10000 0 -10000 0 0
SGOL1 0.044 0.055 0.11 153 -0.12 13 166
RHOA 0.025 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.054 0.06 0.2 49 -10000 0 49
CDC14B -0.001 0.026 -10000 0 -0.33 3 3
CDC20 0.22 0.12 0.29 365 -10000 0 365
PLK1/PBIP1 0.012 0.02 0.11 5 -10000 0 5
mitosis -0.001 0.004 0.023 5 -10000 0 5
FBXO5 0.022 0.031 0.14 11 -0.12 2 13
CDC2 0.002 0.003 0.011 59 -0.01 1 60
NDC80 0.096 0.12 0.29 136 -10000 0 136
metaphase plate congression 0.019 0.05 0.13 1 -0.22 18 19
ERCC6L 0.05 0.068 0.24 36 -10000 0 36
NLP/gamma Tubulin 0.015 0.026 0.074 13 -0.099 9 22
microtubule cytoskeleton organization 0.011 0.052 0.12 2 -0.18 29 31
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 6 -10000 0 6
PPP1R12A 0.027 0.003 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 0.15 0.098 0.23 304 -10000 0 304
GRASP65/GM130/RAB1/GTP/PLK1 0.057 0.03 -10000 0 -10000 0 0
RAB1A 0.026 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.02 0.026 0.088 35 -0.08 2 37
mitotic prometaphase 0.001 0.004 0.02 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.055 -10000 0 -0.34 4 4
microtubule-based process 0.15 0.095 0.22 319 -10000 0 319
Golgi organization 0.028 0.032 0.096 38 -0.1 5 43
Cohesin/SA2 0.039 0.027 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.038 0.009 -10000 0 -10000 0 0
KIF20A 0.19 0.13 0.29 321 -10000 0 321
APC/C/CDC20 0.16 0.092 0.22 364 -0.11 1 365
PPP2R1A 0.026 0.005 -10000 0 -10000 0 0
chromosome segregation 0.011 0.02 0.11 5 -10000 0 5
PRC1 0.031 0.039 0.29 11 -10000 0 11
ECT2 0.045 0.079 0.25 57 -10000 0 57
C13orf34 0.021 0.026 0.082 35 -0.083 3 38
NUDC 0.019 0.051 0.13 1 -0.22 18 19
regulation of attachment of spindle microtubules to kinetochore 0.055 0.066 0.13 165 -0.14 13 178
spindle assembly 0.022 0.027 0.09 22 -0.089 5 27
spindle stabilization 0.022 0.024 0.12 5 -0.16 2 7
APC/C/HCDH1 0.019 0.025 -10000 0 -0.28 3 3
MKLP2/PLK1 0.15 0.096 0.22 319 -10000 0 319
CCNB1 0.062 0.091 0.29 69 -10000 0 69
PPP1CB 0.026 0.005 -10000 0 -10000 0 0
BTRC 0.025 0.006 -10000 0 -10000 0 0
ROCK2 0.014 0.087 -10000 0 -0.35 23 23
TUBG1 0.011 0.047 -10000 0 -0.17 27 27
G2/M transition of mitotic cell cycle 0.024 0.041 0.23 3 -10000 0 3
MLF1IP 0.007 0.013 0.15 4 -10000 0 4
INCENP 0.026 0.005 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.067 0.18 -10000 0 -0.48 80 80
PDGF/PDGFRA/CRKL -0.035 0.13 -10000 0 -0.33 80 80
positive regulation of JUN kinase activity 0.01 0.096 -10000 0 -0.26 51 51
CRKL 0.025 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.038 0.13 -10000 0 -0.34 78 78
AP1 -0.26 0.4 0.32 1 -0.9 133 134
mol:IP3 -0.056 0.13 -10000 0 -0.36 72 72
PLCG1 -0.056 0.13 -10000 0 -0.36 72 72
PDGF/PDGFRA/alphaV Integrin -0.034 0.13 -10000 0 -0.33 79 79
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.13 -10000 0 -0.36 72 72
CAV3 0.018 0.005 -10000 0 -10000 0 0
CAV1 -0.2 0.24 -10000 0 -0.46 239 239
SHC/Grb2/SOS1 0.012 0.097 -10000 0 -0.26 51 51
PDGF/PDGFRA/Shf -0.034 0.13 -10000 0 -0.33 80 80
FOS -0.26 0.39 0.3 1 -0.89 133 134
JUN -0.038 0.038 -10000 0 -0.4 2 2
oligodendrocyte development -0.034 0.13 -10000 0 -0.33 79 79
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:DAG -0.056 0.13 -10000 0 -0.36 72 72
PDGF/PDGFRA -0.067 0.18 -10000 0 -0.48 80 80
actin cytoskeleton reorganization -0.033 0.13 -10000 0 -0.33 78 78
SRF 0.017 0.012 -10000 0 -10000 0 0
SHC1 0.022 0.01 -10000 0 -10000 0 0
PI3K -0.001 0.11 -10000 0 -0.28 63 63
PDGF/PDGFRA/Crk/C3G -0.005 0.12 -10000 0 -0.28 78 78
JAK1 -0.053 0.13 -10000 0 -0.34 81 81
ELK1/SRF -0.053 0.098 0.18 6 -0.28 66 72
SHB 0.025 0.005 -10000 0 -10000 0 0
SHF 0.025 0.006 -10000 0 -10000 0 0
CSNK2A1 0.037 0.022 -10000 0 -10000 0 0
GO:0007205 -0.066 0.14 -10000 0 -0.38 75 75
SOS1 0.026 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.01 0.096 -10000 0 -0.26 51 51
PDGF/PDGFRA/SHB -0.033 0.13 -10000 0 -0.33 78 78
PDGF/PDGFRA/Caveolin-1 -0.19 0.22 -10000 0 -0.39 260 260
ITGAV 0.026 0.004 -10000 0 -10000 0 0
ELK1 -0.074 0.12 -10000 0 -0.34 76 76
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PDGF/PDGFRA/Crk -0.034 0.13 -10000 0 -0.33 78 78
JAK-STAT cascade -0.053 0.13 -10000 0 -0.34 81 81
cell proliferation -0.034 0.13 -10000 0 -0.33 80 80
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.054 0.15 -10000 0 -0.28 149 149
fibroblast growth factor receptor signaling pathway -0.054 0.15 -10000 0 -0.28 149 149
LAMA1 0.047 0.12 0.29 62 -0.46 11 73
PRNP -0.028 0.15 -10000 0 -0.46 56 56
GPC1/SLIT2 -0.044 0.15 -10000 0 -0.33 110 110
SMAD2 -0.03 0.1 0.18 6 -0.25 82 88
GPC1/PrPc/Cu2+ -0.001 0.098 -10000 0 -0.28 56 56
GPC1/Laminin alpha1 0.05 0.082 0.22 60 -0.33 11 71
TDGF1 0.046 0.086 0.29 46 -0.46 3 49
CRIPTO/GPC1 0.051 0.06 0.22 46 -0.33 3 49
APP/GPC1 0.037 0.008 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.035 -10000 0 -0.28 3 3
FLT1 0.024 0.022 -10000 0 -0.46 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.12 -10000 0 -0.28 83 83
SERPINC1 0.021 0.02 0.29 2 -10000 0 2
FYN 0.019 0.035 -10000 0 -0.28 3 3
FGR 0.016 0.048 -10000 0 -0.28 9 9
positive regulation of MAPKKK cascade 0.028 0.084 0.3 11 -0.34 8 19
SLIT2 -0.081 0.2 -10000 0 -0.46 110 110
GPC1/NRG -0.11 0.18 -10000 0 -0.33 194 194
NRG1 -0.17 0.23 -10000 0 -0.46 196 196
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.048 0.021 -10000 0 -0.28 1 1
LYN 0.018 0.036 -10000 0 -0.28 3 3
mol:Spermine 0.006 0.001 -10000 0 -10000 0 0
cell growth -0.054 0.15 -10000 0 -0.28 149 149
BMP signaling pathway -0.026 0.004 -10000 0 -10000 0 0
SRC 0.019 0.036 -10000 0 -0.28 3 3
TGFBR1 0.025 0.007 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.24 0.24 -10000 0 -0.46 269 269
GPC1 0.026 0.004 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.026 0.004 -10000 0 -10000 0 0
BLK 0.015 0.047 0.19 6 -0.27 6 12
HCK 0.017 0.042 -10000 0 -0.28 6 6
FGF2 -0.13 0.23 -10000 0 -0.46 163 163
FGFR1 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer 0.024 0.022 -10000 0 -0.46 1 1
TGFBR2 -0.054 0.18 -10000 0 -0.46 83 83
cell death 0.037 0.008 -10000 0 -10000 0 0
ATIII/GPC1 0.031 0.019 0.22 2 -10000 0 2
PLA2G2A/GPC1 -0.16 0.18 -10000 0 -0.33 268 268
LCK 0.018 0.042 -10000 0 -0.28 6 6
neuron differentiation -0.11 0.18 -10000 0 -0.33 194 194
PrPc/Cu2+ -0.02 0.11 -10000 0 -0.33 56 56
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.054 0.18 -10000 0 -0.46 83 83
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.02 0.077 -10000 0 -0.33 23 23
CRKL -0.082 0.16 0.33 2 -0.46 46 48
mol:PIP3 -0.01 0.13 -10000 0 -0.82 12 12
AKT1 -0.01 0.12 0.4 2 -0.72 12 14
PTK2B 0.021 0.032 -10000 0 -0.46 2 2
RAPGEF1 -0.079 0.16 0.3 3 -0.44 45 48
RANBP10 0.023 0.009 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
HGF/MET/SHIP2 -0.087 0.17 -10000 0 -0.3 198 198
MAP3K5 -0.069 0.16 0.29 3 -0.46 45 48
HGF/MET/CIN85/CBL/ENDOPHILINS -0.071 0.17 -10000 0 -0.27 199 199
AP1 -0.065 0.14 -10000 0 -0.3 127 127
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.01 -10000 0 -10000 0 0
apoptosis -0.19 0.35 -10000 0 -0.74 139 139
STAT3 (dimer) -0.078 0.14 -10000 0 -0.25 168 168
GAB1/CRKL/SHP2/PI3K -0.05 0.16 0.28 1 -0.46 37 38
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
CBL/CRK -0.067 0.16 0.3 3 -0.46 41 44
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
ELK1 0 0.1 0.29 41 -10000 0 41
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.053 0.099 -10000 0 -0.25 52 52
PAK1 -0.009 0.12 0.38 6 -0.68 12 18
HGF/MET/RANBP10 -0.089 0.17 -10000 0 -0.29 201 201
HRAS -0.11 0.2 -10000 0 -0.59 46 46
DOCK1 -0.076 0.16 0.3 7 -0.48 40 47
GAB1 -0.085 0.17 -10000 0 -0.44 54 54
CRK -0.079 0.16 0.33 2 -0.46 45 47
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.17 0.25 -10000 0 -0.46 208 208
JUN 0.024 0.031 -10000 0 -0.46 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.073 0.11 -10000 0 -0.2 199 199
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
cell morphogenesis -0.078 0.17 0.33 9 -0.42 43 52
GRB2/SHC -0.038 0.1 -10000 0 -0.26 35 35
FOS -0.097 0.21 -10000 0 -0.46 128 128
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.001 0.1 0.29 41 -10000 0 41
HGF/MET/MUC20 -0.097 0.16 -10000 0 -0.29 201 201
cell migration -0.038 0.1 -10000 0 -0.26 35 35
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.017 0.077 -10000 0 -0.33 23 23
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.075 0.14 -10000 0 -0.25 177 177
MET/MUC20 0.003 0.072 -10000 0 -0.33 23 23
RAP1B -0.076 0.15 0.28 4 -0.44 41 45
RAP1A -0.077 0.14 0.28 3 -0.44 41 44
HGF/MET/RANBP9 -0.085 0.17 -10000 0 -0.3 192 192
RAF1 -0.1 0.19 -10000 0 -0.54 47 47
STAT3 -0.078 0.14 -10000 0 -0.26 167 167
cell proliferation -0.089 0.19 0.3 7 -0.35 148 155
RPS6KB1 -0.027 0.073 -10000 0 -0.35 16 16
MAPK3 -0.003 0.14 0.64 20 -10000 0 20
MAPK1 0.008 0.16 0.64 28 -10000 0 28
RANBP9 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.054 0.16 0.32 2 -0.45 43 45
SRC -0.074 0.12 -10000 0 -0.24 166 166
PI3K -0.044 0.11 -10000 0 -0.28 37 37
MET/Glomulin 0.005 0.066 -10000 0 -0.29 23 23
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K1 -0.098 0.18 -10000 0 -0.5 47 47
MET 0.003 0.1 -10000 0 -0.46 23 23
MAP4K1 -0.073 0.17 0.31 3 -0.48 46 49
PTK2 0.024 0.008 -10000 0 -10000 0 0
MAP2K2 -0.099 0.18 -10000 0 -0.51 45 45
BAD -0.009 0.12 0.4 5 -0.68 12 17
MAP2K4 -0.064 0.14 0.28 3 -0.42 43 46
SHP2/GRB2/SOS1/GAB1 -0.062 0.16 -10000 0 -0.45 45 45
INPPL1 0.026 0.004 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.025 0.022 -10000 0 -0.46 1 1
HGS -0.065 0.1 -10000 0 -0.19 183 183
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.16 0.24 -10000 0 -0.46 191 191
RASA1 0.021 0.048 -10000 0 -0.46 5 5
NCK1 0.023 0.031 -10000 0 -0.46 2 2
PTPRJ 0.026 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.052 0.12 -10000 0 -0.2 187 187
PDPK1 -0.012 0.12 -10000 0 -0.76 12 12
HGF/MET/SHIP -0.089 0.18 -10000 0 -0.3 198 198
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.02 0.079 -10000 0 -0.33 24 24
alphaV beta3 Integrin -0.087 0.18 0.21 1 -0.32 185 186
PTK2 -0.14 0.2 0.45 3 -0.47 100 103
IGF1R 0.017 0.064 -10000 0 -0.46 9 9
PI4KB 0.021 0.011 -10000 0 -10000 0 0
MFGE8 0.026 0.013 0.29 1 -10000 0 1
SRC 0.025 0.006 -10000 0 -10000 0 0
CDKN1B -0.091 0.2 -10000 0 -0.57 63 63
VEGFA 0.026 0.004 -10000 0 -10000 0 0
ILK -0.079 0.17 -10000 0 -0.53 55 55
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.075 0.16 -10000 0 -0.5 52 52
PTK2B -0.037 0.1 0.46 2 -0.28 61 63
alphaV/beta3 Integrin/JAM-A -0.079 0.17 -10000 0 -0.29 173 173
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.013 0.1 -10000 0 -0.28 51 51
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.039 0.097 -10000 0 -0.29 37 37
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.026 0.11 -10000 0 -0.37 23 23
alphaV/beta3 Integrin/Syndecan-1 0.014 0.1 0.21 2 -0.29 51 53
PI4KA 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.085 0.19 -10000 0 -0.3 198 198
PI4 Kinase 0.029 0.017 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
alphaV/beta3 Integrin/Osteopontin 0.035 0.12 0.38 1 -0.28 51 52
RPS6KB1 -0.12 0.15 0.34 2 -0.46 50 52
TLN1 0.025 0.006 -10000 0 -10000 0 0
MAPK3 -0.18 0.25 -10000 0 -0.49 171 171
GPR124 0.02 0.044 -10000 0 -0.46 4 4
MAPK1 -0.18 0.25 -10000 0 -0.49 173 173
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
alphaV/beta3 Integrin/Tumstatin -0.12 0.19 -10000 0 -0.31 233 233
cell adhesion 0.009 0.099 0.27 1 -0.28 48 49
ANGPTL3 0.022 0.013 0.29 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.071 -10000 0 -0.28 23 23
IGF-1R heterotetramer 0.017 0.064 -10000 0 -0.46 9 9
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 -0.054 0.18 -10000 0 -0.46 83 83
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
IGF1 0.009 0.1 0.29 5 -0.46 21 26
RAC1 0.025 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.011 0.1 0.21 1 -0.29 49 50
apoptosis 0.026 0.004 -10000 0 -10000 0 0
CD47 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.016 0.1 -10000 0 -0.28 49 49
VCL 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.11 0.19 -10000 0 -0.33 205 205
CSF1 0.015 0.074 -10000 0 -0.46 12 12
PIK3C2A -0.076 0.17 -10000 0 -0.52 52 52
PI4 Kinase/Pyk2 -0.08 0.15 -10000 0 -0.28 150 150
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.016 0.12 -10000 0 -0.29 63 63
FAK1/Vinculin -0.11 0.16 0.32 2 -0.38 91 93
alphaV beta3/Integrin/ppsTEM5 0.011 0.1 0.21 1 -0.29 49 50
RHOA 0.025 0.005 -10000 0 -10000 0 0
VTN -0.016 0.14 0.29 2 -0.46 43 45
BCAR1 0.023 0.009 -10000 0 -10000 0 0
FGF2 -0.13 0.23 -10000 0 -0.46 163 163
F11R -0.078 0.15 -10000 0 -0.33 128 128
alphaV/beta3 Integrin/Lactadherin 0.016 0.1 -10000 0 -0.28 50 50
alphaV/beta3 Integrin/TGFBR2 -0.034 0.17 -10000 0 -0.34 106 106
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.054 -10000 0 -0.26 12 12
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.016 0.092 0.2 2 -0.25 50 52
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.015 0.074 -10000 0 -0.46 12 12
alphaV/beta3 Integrin/Pyk2 0 0.11 -10000 0 -0.28 61 61
SDC1 0.021 0.048 -10000 0 -0.46 5 5
VAV3 -0.019 0.066 -10000 0 -0.26 26 26
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.014 0.074 -10000 0 -0.46 12 12
FAK1/Paxillin -0.11 0.17 0.42 3 -0.37 95 98
cell migration -0.1 0.14 0.28 3 -0.34 89 92
ITGAV 0.026 0.004 -10000 0 -10000 0 0
PI3K -0.054 0.16 -10000 0 -0.27 157 157
SPP1 0.062 0.091 0.29 70 -10000 0 70
KDR 0.003 0.1 -10000 0 -0.46 24 24
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.004 -10000 0 -10000 0 0
COL4A3 -0.18 0.24 -10000 0 -0.46 214 214
angiogenesis -0.17 0.26 -10000 0 -0.5 167 167
Rac1/GTP 0.015 0.064 -10000 0 -0.24 24 24
EDIL3 -0.16 0.24 -10000 0 -0.46 194 194
cell proliferation -0.034 0.17 -10000 0 -0.34 106 106
ErbB2/ErbB3 signaling events

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
USP8 -0.008 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.044 0.13 -10000 0 -0.28 41 41
NFATC4 -0.066 0.12 0.35 10 -0.23 40 50
ERBB2IP 0.025 0.023 -10000 0 -0.46 1 1
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.082 0.13 -10000 0 -0.25 172 172
JUN -0.024 0.08 0.28 3 -0.41 1 4
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK7 -0.089 0.12 0.36 2 -0.25 155 157
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.059 0.13 0.22 1 -0.26 138 139
AKT1 -0.001 0.01 -10000 0 -10000 0 0
BAD -0.007 0.007 -10000 0 -10000 0 0
MAPK10 -0.057 0.1 0.22 16 -0.23 52 68
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.087 0.14 -10000 0 -0.27 172 172
RAF1 -0.04 0.14 0.31 10 -0.29 39 49
ErbB2/ErbB3/neuregulin 2 -0.008 0.085 0.2 11 -0.28 34 45
STAT3 -0.015 0.19 -10000 0 -0.81 26 26
cell migration -0.047 0.11 0.26 19 -0.23 37 56
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.087 0.22 0.48 4 -0.49 62 66
FOS -0.11 0.24 0.36 10 -0.47 136 146
NRAS 0.024 0.037 -10000 0 -0.46 3 3
mol:Ca2+ -0.082 0.13 -10000 0 -0.25 172 172
MAPK3 -0.065 0.2 0.45 4 -0.54 31 35
MAPK1 -0.069 0.2 0.45 4 -0.57 28 32
JAK2 -0.091 0.12 0.36 2 -0.25 152 154
NF2 -0.002 0.048 -10000 0 -0.58 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.061 0.13 0.19 4 -0.25 136 140
NRG1 -0.17 0.23 -10000 0 -0.46 196 196
GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
MAPK8 -0.091 0.14 0.36 2 -0.27 168 170
MAPK9 -0.041 0.091 0.24 16 -0.22 5 21
ERBB2 -0.015 0.041 0.26 9 -0.33 1 10
ERBB3 0.017 0.057 -10000 0 -0.46 7 7
SHC1 0.022 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
apoptosis 0.006 0.011 -10000 0 -0.15 1 1
STAT3 (dimer) -0.014 0.18 -10000 0 -0.79 26 26
RNF41 -0.013 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.076 0.084 -10000 0 -0.19 153 153
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.035 0.2 9 -0.28 1 10
CHRNA1 -0.033 0.16 0.42 9 -0.38 22 31
myelination -0.05 0.14 0.31 28 -0.27 12 40
PPP3CB -0.082 0.11 0.43 1 -0.23 151 152
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.046 0.13 0.26 2 -0.23 124 126
NRG2 -0.006 0.12 0.29 2 -0.46 34 36
mol:GDP -0.062 0.13 0.19 4 -0.25 137 141
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K2 -0.042 0.13 0.3 13 -0.3 37 50
SRC 0.025 0.006 -10000 0 -10000 0 0
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.089 0.12 0.36 2 -0.25 155 157
MAP2K1 -0.091 0.21 0.43 3 -0.58 29 32
heart morphogenesis -0.082 0.13 -10000 0 -0.25 172 172
RAS family/GDP -0.039 0.14 0.28 1 -0.27 41 42
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.001 0.044 -10000 0 -0.68 2 2
CHRNE 0 0.022 0.1 1 -0.19 1 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.01 -10000 0 -10000 0 0
nervous system development -0.082 0.13 -10000 0 -0.25 172 172
CDC42 0.025 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.006 -9999 0 -10000 0 0
EGFR -0.013 0.13 -9999 0 -0.46 40 40
EGF/EGFR -0.047 0.15 -9999 0 -0.27 149 149
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.017 0.13 -9999 0 -0.26 105 105
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.015 0.071 -9999 0 -0.46 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.07 0.19 -9999 0 -0.46 99 99
EGF/EGFR dimer/SHC -0.039 0.14 -9999 0 -0.3 110 110
mol:GDP -0.02 0.13 -9999 0 -0.26 105 105
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.003 0.12 -9999 0 -0.46 30 30
GRB2/SOS1 0.036 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.028 0.12 -9999 0 -0.24 105 105
SHC1 0.022 0.01 -9999 0 -10000 0 0
HRAS/GDP -0.019 0.12 -9999 0 -0.25 105 105
FRAP1 -0.061 0.099 -9999 0 -0.25 105 105
EGF/EGFR dimer -0.062 0.17 -9999 0 -0.35 129 129
SOS1 0.026 0.004 -9999 0 -10000 0 0
GRB2 0.025 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.007 0.1 -9999 0 -0.34 40 40
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.028 0.23 0.55 7 -0.65 18 25
PCK1 -0.32 0.56 0.56 4 -1.1 164 168
HNF4A 0.004 0.28 0.76 15 -0.78 14 29
KCNJ11 -0.043 0.26 0.63 4 -0.73 19 23
AKT1 -0.009 0.16 0.43 6 -0.38 8 14
response to starvation 0.012 0.021 0.16 1 -10000 0 1
DLK1 -0.067 0.32 0.79 7 -0.86 41 48
NKX2-1 -0.34 0.59 0.61 7 -1.1 187 194
ACADM -0.037 0.25 0.57 6 -0.7 26 32
TAT -0.14 0.26 0.59 3 -0.61 70 73
CEBPB 0.026 0.011 -10000 0 -10000 0 0
CEBPA -0.042 0.17 -10000 0 -0.46 71 71
TTR -0.12 0.31 0.64 9 -0.66 68 77
PKLR 0.004 0.25 0.6 22 -0.65 15 37
APOA1 -0.009 0.31 0.78 13 -0.86 13 26
CPT1C -0.021 0.24 0.57 7 -0.66 17 24
ALAS1 -0.003 0.16 0.64 1 -0.72 2 3
TFRC -0.049 0.24 0.64 4 -0.62 19 23
FOXF1 0.095 0.12 0.25 159 -0.46 1 160
NF1 0.028 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.11 0.13 0.31 143 -10000 0 143
CPT1A -0.026 0.24 0.63 6 -0.69 15 21
HMGCS1 -0.022 0.24 0.57 9 -0.65 18 27
NR3C1 -0.15 0.24 -10000 0 -0.46 189 189
CPT1B -0.027 0.23 0.58 7 -0.68 15 22
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.025 -10000 0 -10000 0 0
GCK -0.023 0.26 0.63 11 -0.73 18 29
CREB1 -0.044 0.11 -10000 0 -0.21 137 137
IGFBP1 -0.073 0.21 0.52 7 -0.5 34 41
PDX1 0.035 0.2 0.6 10 -0.79 3 13
UCP2 -0.026 0.24 0.62 7 -0.69 15 22
ALDOB -0.043 0.26 0.6 5 -0.71 21 26
AFP -0.097 0.24 0.51 1 -0.58 62 63
BDH1 -0.012 0.24 0.59 8 -0.68 14 22
HADH -0.043 0.25 0.6 3 -0.7 20 23
F2 -0.015 0.3 0.82 12 -0.8 15 27
HNF1A 0.11 0.13 0.31 143 -10000 0 143
G6PC -0.05 0.16 0.51 1 -0.48 28 29
SLC2A2 0.029 0.2 0.68 7 -0.66 3 10
INS -0.023 0.025 0.28 1 -10000 0 1
FOXA1 -0.034 0.24 0.29 63 -0.4 132 195
FOXA3 -0.046 0.18 0.33 25 -0.36 64 89
FOXA2 -0.036 0.32 0.78 10 -0.74 26 36
ABCC8 -0.065 0.3 0.61 6 -0.84 34 40
ALB -0.1 0.25 0.51 1 -0.64 60 61
Glucocorticoid receptor regulatory network

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
PCK2 0.003 0.097 -10000 0 -0.43 2 2
SMARCC2 0.018 0.028 -10000 0 -0.13 4 4
SMARCC1 0.017 0.03 -10000 0 -0.13 2 2
TBX21 -0.009 0.16 -10000 0 -0.54 24 24
SUMO2 0.02 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.031 0.004 -10000 0 -10000 0 0
FKBP4 0.026 0.005 -10000 0 -10000 0 0
FKBP5 -0.063 0.19 -10000 0 -0.46 92 92
GR alpha/HSP90/FKBP51/HSP90 -0.074 0.21 0.31 19 -0.35 136 155
PRL 0.034 0.13 0.43 18 -0.59 1 19
cortisol/GR alpha (dimer)/TIF2 -0.011 0.25 0.47 55 -0.44 49 104
RELA -0.095 0.14 -10000 0 -0.25 160 160
FGG -0.037 0.26 0.43 44 -0.55 55 99
GR beta/TIF2 -0.071 0.2 0.31 19 -0.36 121 140
IFNG -0.032 0.21 0.42 5 -0.59 24 29
apoptosis -0.088 0.23 0.59 6 -0.56 52 58
CREB1 0.036 0.031 -10000 0 -10000 0 0
histone acetylation 0.017 0.17 0.42 30 -0.33 40 70
BGLAP 0.027 0.14 0.45 8 -0.42 6 14
GR/PKAc -0.022 0.16 0.3 19 -0.3 67 86
NF kappa B1 p50/RelA -0.18 0.26 -10000 0 -0.41 254 254
SMARCD1 0.017 0.031 -10000 0 -10000 0 0
MDM2 0.046 0.077 0.2 55 -10000 0 55
GATA3 -0.073 0.2 -10000 0 -0.46 105 105
AKT1 0.022 0.004 -10000 0 -10000 0 0
CSF2 0.01 0.12 0.39 1 -0.42 3 4
GSK3B 0.021 0.016 -10000 0 -10000 0 0
NR1I3 -0.05 0.21 0.64 5 -0.56 19 24
CSN2 -0.01 0.19 0.37 36 -0.4 33 69
BRG1/BAF155/BAF170/BAF60A 0.041 0.082 -10000 0 -0.26 25 25
NFATC1 0.015 0.074 -10000 0 -0.46 12 12
POU2F1 0.029 0.025 -10000 0 -10000 0 0
CDKN1A 0.009 0.12 -10000 0 -1.2 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.008 -10000 0 -10000 0 0
SFN 0.036 0.08 0.29 30 -0.46 5 35
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.057 0.2 0.3 19 -0.34 109 128
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.14 0.31 0.64 3 -0.75 85 88
JUN -0.001 0.17 0.38 14 -0.41 35 49
IL4 -0.006 0.13 0.37 1 -0.41 12 13
CDK5R1 0.024 0.015 0.29 1 -10000 0 1
PRKACA 0.025 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.079 0.12 -10000 0 -0.31 68 68
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.061 0.2 0.31 18 -0.34 117 135
cortisol/GR alpha (monomer) 0.02 0.3 0.55 69 -0.5 35 104
NCOA2 -0.017 0.14 -10000 0 -0.46 43 43
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.088 0.22 0.23 3 -0.45 130 133
AP-1/NFAT1-c-4 -0.051 0.26 0.46 8 -0.56 54 62
AFP -0.052 0.29 -10000 0 -1.2 25 25
SUV420H1 0.026 0.005 -10000 0 -10000 0 0
IRF1 0.015 0.15 0.42 18 -0.38 1 19
TP53 0.031 0.061 -10000 0 -0.73 3 3
PPP5C 0.026 0.004 -10000 0 -10000 0 0
KRT17 -0.05 0.29 0.5 13 -0.78 39 52
KRT14 -0.13 0.43 0.41 17 -1.1 76 93
TBP 0.033 0.016 -10000 0 -10000 0 0
CREBBP 0.037 0.13 0.32 60 -0.26 31 91
HDAC1 0.025 0.004 -10000 0 -10000 0 0
HDAC2 0.025 0.004 -10000 0 -10000 0 0
AP-1 -0.051 0.26 0.46 8 -0.56 54 62
MAPK14 0.022 0.014 -10000 0 -10000 0 0
MAPK10 -0.035 0.15 -10000 0 -0.46 58 58
MAPK11 0.02 0.016 -10000 0 -10000 0 0
KRT5 -0.11 0.4 0.5 16 -1 71 87
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.026 0.022 -10000 0 -0.46 1 1
STAT1 0.031 0.004 -10000 0 -10000 0 0
CGA 0.018 0.14 0.41 16 -0.4 10 26
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.084 0.2 0.35 25 -0.41 75 100
MAPK3 0.02 0.018 -10000 0 -10000 0 0
MAPK1 0.02 0.026 -10000 0 -0.46 1 1
ICAM1 -0.11 0.21 -10000 0 -0.49 75 75
NFKB1 -0.096 0.14 -10000 0 -0.23 231 231
MAPK8 0.01 0.17 0.42 15 -0.37 38 53
MAPK9 0.022 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.093 0.24 0.6 6 -0.59 53 59
BAX 0.013 0.065 -10000 0 -0.48 1 1
POMC -0.003 0.25 0.52 10 -0.85 19 29
EP300 0.036 0.12 0.32 58 -0.26 30 88
cortisol/GR alpha (dimer)/p53 0.013 0.25 0.49 58 -0.46 26 84
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.072 0.23 29 -10000 0 29
SGK1 -0.067 0.39 0.5 5 -1.2 48 53
IL13 -0.094 0.23 -10000 0 -0.65 37 37
IL6 -0.32 0.48 0.37 1 -0.98 159 160
PRKACG 0.018 0.014 0.29 1 -10000 0 1
IL5 -0.086 0.2 -10000 0 -0.57 36 36
IL2 -0.041 0.22 0.4 5 -0.55 39 44
CDK5 0.024 0.007 -10000 0 -10000 0 0
PRKACB 0.019 0.057 -10000 0 -0.46 7 7
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
IL8 -0.12 0.26 0.43 3 -0.58 73 76
CDK5R1/CDK5 0.033 0.019 0.22 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc -0.12 0.22 -10000 0 -0.37 169 169
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.024 0.24 0.47 62 -0.43 24 86
SMARCA4 0.017 0.028 -10000 0 -10000 0 0
chromatin remodeling -0.031 0.2 0.35 36 -0.45 45 81
NF kappa B1 p50/RelA/Cbp -0.13 0.27 0.38 23 -0.45 152 175
JUN (dimer) -0.001 0.17 0.38 14 -0.41 35 49
YWHAH 0.025 0.007 -10000 0 -10000 0 0
VIPR1 -0.17 0.37 0.68 1 -0.76 138 139
NR3C1 -0.048 0.26 0.39 43 -0.44 113 156
NR4A1 -0.009 0.14 -10000 0 -0.47 42 42
TIF2/SUV420H1 0.003 0.1 -10000 0 -0.33 43 43
MAPKKK cascade -0.088 0.23 0.59 6 -0.56 52 58
cortisol/GR alpha (dimer)/Src-1 0.023 0.26 0.49 66 -0.44 31 97
PBX1 0.023 0.058 -10000 0 -0.46 6 6
POU1F1 0.027 0.029 0.33 2 -10000 0 2
SELE -0.39 0.5 0.35 3 -0.94 216 219
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.032 0.2 0.35 36 -0.45 45 81
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.024 0.24 0.47 62 -0.43 24 86
mol:cortisol 0.058 0.14 0.3 78 -0.25 7 85
MMP1 0.001 0.19 0.39 10 -0.7 19 29
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.12 0.35 0.61 18 -0.72 37 55
HDAC7 0.027 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.12 0.33 0.7 14 -0.66 27 41
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 0.12 0.35 0.61 18 -0.72 38 56
AP1 -0.059 0.16 -10000 0 -0.34 129 129
ABCG2 0.088 0.39 0.61 18 -0.72 60 78
HIF1A 0.048 0.1 0.25 7 -0.2 11 18
TFF3 0.17 0.41 0.66 82 -0.73 43 125
GATA2 0.02 0.05 0.29 2 -0.47 4 6
AKT1 0.051 0.1 0.28 6 -0.21 4 10
response to hypoxia 0.031 0.1 0.21 19 -0.18 31 50
MCL1 0.075 0.33 0.62 7 -0.71 37 44
NDRG1 0.11 0.34 0.61 16 -0.72 34 50
SERPINE1 0.11 0.36 0.6 16 -0.74 41 57
FECH 0.12 0.35 0.61 18 -0.72 37 55
FURIN 0.12 0.35 0.61 17 -0.72 37 54
NCOA2 -0.015 0.14 -10000 0 -0.46 43 43
EP300 0.068 0.13 0.33 18 -0.28 11 29
HMOX1 0.11 0.35 0.61 19 -0.72 37 56
BHLHE40 0.12 0.35 0.61 17 -0.72 37 54
BHLHE41 0.098 0.38 0.62 14 -0.75 47 61
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.08 0.14 0.39 6 -0.37 2 8
ENG 0.077 0.12 0.36 6 -0.34 2 8
JUN 0.022 0.034 -10000 0 -0.46 2 2
RORA 0.085 0.38 0.61 18 -0.74 52 70
ABCB1 -0.13 0.33 -10000 0 -0.94 69 69
TFRC 0.12 0.34 0.61 18 -0.73 34 52
CXCR4 0.12 0.35 0.61 18 -0.72 37 55
TF 0.11 0.37 0.62 19 -0.77 40 59
CITED2 0.11 0.36 0.61 18 -0.75 41 59
HIF1A/ARNT 0.15 0.44 0.84 42 -0.82 33 75
LDHA -0.002 0.08 -10000 0 -0.53 7 7
ETS1 0.11 0.35 0.61 18 -0.73 40 58
PGK1 0.12 0.35 0.61 17 -0.72 37 54
NOS2 0.084 0.38 0.61 18 -0.72 53 71
ITGB2 0.12 0.35 0.62 18 -0.73 36 54
ALDOA 0.12 0.35 0.61 17 -0.72 37 54
Cbp/p300/CITED2 0.11 0.37 0.65 17 -0.8 37 54
FOS -0.099 0.21 -10000 0 -0.46 128 128
HK2 0.12 0.35 0.61 18 -0.72 38 56
SP1 0.011 0.053 -10000 0 -0.17 10 10
GCK 0.1 0.21 0.58 7 -0.88 7 14
HK1 0.12 0.35 0.61 18 -0.73 35 53
NPM1 0.12 0.35 0.61 17 -0.72 37 54
EGLN1 0.082 0.33 0.62 8 -0.72 37 45
CREB1 0.03 0.004 -10000 0 -10000 0 0
PGM1 0.12 0.35 0.61 18 -0.72 37 55
SMAD3 0.022 0.043 -10000 0 -0.46 4 4
EDN1 -0.02 0.32 -10000 0 -1.1 34 34
IGFBP1 0.13 0.35 0.64 20 -0.72 36 56
VEGFA 0.13 0.28 0.56 20 -0.58 25 45
HIF1A/JAB1 0.052 0.078 0.24 5 -0.17 1 6
CP 0.15 0.37 0.68 45 -0.72 37 82
CXCL12 0.029 0.41 0.61 17 -0.72 72 89
COPS5 0.026 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.034 -10000 0 -0.33 4 4
BNIP3 0.12 0.35 0.61 18 -0.72 36 54
EGLN3 0.12 0.35 0.62 18 -0.72 37 55
CA9 0.23 0.4 0.66 114 -0.7 34 148
TERT 0.17 0.37 0.67 60 -0.72 33 93
ENO1 0.12 0.35 0.61 18 -0.72 37 55
PFKL 0.12 0.35 0.61 18 -0.72 37 55
NCOA1 0.025 0.022 -10000 0 -0.46 1 1
ADM 0.12 0.35 0.61 18 -0.72 37 55
ARNT 0.041 0.087 0.27 3 -10000 0 3
HNF4A 0.041 0.09 0.29 38 -0.46 6 44
ADFP 0.088 0.34 0.57 23 -0.71 38 61
SLC2A1 0.14 0.29 0.59 20 -0.58 26 46
LEP 0.11 0.36 0.61 18 -0.75 41 59
HIF1A/ARNT/Cbp/p300 0.12 0.34 0.67 35 -0.67 28 63
EPO 0.11 0.3 0.64 17 -0.64 23 40
CREBBP 0.069 0.13 0.33 18 -0.33 13 31
HIF1A/ARNT/Cbp/p300/HDAC7 0.12 0.33 0.76 9 -0.66 25 34
PFKFB3 0.12 0.35 0.61 16 -0.75 36 52
NT5E 0.12 0.36 0.62 20 -0.7 42 62
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.011 0.15 0.35 2 -0.25 108 110
SMAD6-7/SMURF1 0.047 0.03 -10000 0 -0.28 3 3
NOG 0.049 0.082 0.29 49 -0.46 1 50
SMAD9 -0.066 0.2 -10000 0 -0.51 77 77
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD5 -0.022 0.1 0.23 1 -0.37 19 20
BMP7/USAG1 -0.1 0.19 0.22 20 -0.34 194 214
SMAD5/SKI -0.014 0.11 -10000 0 -0.39 19 19
SMAD1 0.013 0.062 0.25 2 -0.41 5 7
BMP2 -0.08 0.2 -10000 0 -0.46 110 110
SMAD1/SMAD1/SMAD4 0.022 0.062 -10000 0 -0.32 5 5
BMPR1A 0.025 0.006 -10000 0 -10000 0 0
BMPR1B 0.036 0.099 0.29 38 -0.46 10 48
BMPR1A-1B/BAMBI 0.046 0.087 0.21 41 -0.29 22 63
AHSG 0.023 0.022 0.29 3 -10000 0 3
CER1 0.022 0.027 0.29 5 -10000 0 5
BMP2-4/CER1 -0.036 0.15 0.24 6 -0.3 120 126
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.032 0.12 -10000 0 -0.37 30 30
BMP2-4 (homodimer) -0.057 0.17 0.22 5 -0.35 124 129
RGMB 0.025 0.022 -10000 0 -0.46 1 1
BMP6/BMPR2/BMPR1A-1B 0.047 0.099 -10000 0 -0.26 37 37
RGMA 0.007 0.092 -10000 0 -0.46 19 19
SMURF1 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.033 0.12 -10000 0 -0.35 28 28
BMP2-4/USAG1 -0.15 0.21 -10000 0 -0.34 256 256
SMAD6/SMURF1/SMAD5 -0.015 0.11 -10000 0 -0.4 18 18
SOSTDC1 -0.16 0.24 -10000 0 -0.46 193 193
BMP7/BMPR2/BMPR1A-1B 0.063 0.098 -10000 0 -0.26 25 25
SKI 0.025 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.003 0.12 -10000 0 -0.46 30 30
HFE2 0.022 0.025 0.29 4 -10000 0 4
ZFYVE16 0.025 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.032 0.15 0.21 7 -0.3 112 119
SMAD5/SMAD5/SMAD4 -0.013 0.11 -10000 0 -0.39 19 19
MAPK1 0.024 0.022 -10000 0 -0.46 1 1
TAK1/TAB family -0.017 0.11 -10000 0 -0.32 27 27
BMP7 (homodimer) 0.029 0.12 0.29 44 -0.46 19 63
NUP214 0.025 0.007 -10000 0 -10000 0 0
BMP6/FETUA 0.013 0.086 0.22 2 -0.33 29 31
SMAD1/SKI 0.021 0.071 -10000 0 -0.39 5 5
SMAD6 0.025 0.006 -10000 0 -10000 0 0
CTDSP2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.03 0.14 0.21 7 -0.29 110 117
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.032 0.16 0.29 1 -0.46 60 61
BMPR2 (homodimer) 0.026 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.042 0.07 0.22 37 -0.33 9 46
CHRDL1 -0.3 0.23 -10000 0 -0.46 338 338
ENDOFIN/SMAD1 0.021 0.07 -10000 0 -0.39 5 5
SMAD6-7/SMURF1/SMAD1 0.038 0.077 -10000 0 -0.36 5 5
SMAD6/SMURF1 0.026 0.004 -10000 0 -10000 0 0
BAMBI 0.016 0.086 0.29 7 -0.46 14 21
SMURF2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.24 0.2 -10000 0 -0.35 360 360
BMP2-4/GREM1 -0.07 0.19 -10000 0 -0.34 154 154
SMAD7 0.022 0.038 -10000 0 -0.46 3 3
SMAD8A/SMAD8A/SMAD4 -0.058 0.2 -10000 0 -0.48 82 82
SMAD1/SMAD6 0.019 0.073 -10000 0 -0.39 5 5
TAK1/SMAD6 0.038 0.008 -10000 0 -10000 0 0
BMP7 0.03 0.12 0.29 44 -0.46 19 63
BMP6 -0.003 0.12 -10000 0 -0.46 30 30
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.03 0.12 -10000 0 -0.36 32 32
PPM1A 0.026 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.022 0.07 -10000 0 -0.39 5 5
SMAD7/SMURF1 0.034 0.03 -10000 0 -0.33 3 3
CTDSPL 0.025 0.022 -10000 0 -0.46 1 1
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.002 -10000 0 -10000 0 0
CTDSP1 0.026 0.004 -10000 0 -10000 0 0
PPP1R15A 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.074 0.15 -10000 0 -0.38 67 67
CHRD 0.018 0.064 0.29 3 -0.46 8 11
BMPR2 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.039 0.12 -10000 0 -0.4 26 26
BMP4 0.004 0.11 0.29 6 -0.46 26 32
FST -0.07 0.19 0.29 2 -0.46 99 101
BMP2-4/NOG -0.023 0.16 0.22 43 -0.29 125 168
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.072 0.097 -10000 0 -0.25 25 25
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.032 0.09 -10000 0 -0.26 28 28
NT3 (dimer)/TRKC -0.074 0.19 0.22 1 -0.37 137 138
NT3 (dimer)/TRKB -0.25 0.21 -10000 0 -0.37 354 354
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.032 -10000 0 -0.22 3 3
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
BDNF 0.021 0.069 0.29 7 -0.46 8 15
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
NTRK1 0.021 0.054 0.29 7 -0.46 4 11
NTRK2 -0.24 0.24 -10000 0 -0.46 276 276
NTRK3 -0.091 0.21 -10000 0 -0.46 121 121
NT-4/5 (dimer)/TRKB -0.29 0.22 -10000 0 -0.4 376 376
neuron apoptosis 0.18 0.19 0.42 155 -10000 0 155
SHC 2-3/Grb2 -0.2 0.2 -10000 0 -0.46 155 155
SHC1 0.022 0.01 -10000 0 -10000 0 0
SHC2 -0.18 0.2 -10000 0 -0.46 153 153
SHC3 -0.2 0.23 -10000 0 -0.49 155 155
STAT3 (dimer) 0.027 0.032 -10000 0 -0.32 4 4
NT3 (dimer)/TRKA -0.082 0.17 0.21 4 -0.31 164 168
RIN/GDP -0.026 0.1 0.23 4 -0.24 33 37
GIPC1 0.025 0.007 -10000 0 -10000 0 0
KRAS 0.026 0.005 -10000 0 -10000 0 0
DNAJA3 -0.097 0.15 0.28 1 -0.3 153 154
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.01 0.063 -10000 0 -0.6 5 5
MAGED1 0.025 0.022 -10000 0 -0.46 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.071 0.19 -10000 0 -0.46 99 99
SHC/GRB2/SOS1 0.04 0.023 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.019 0.089 -10000 0 -0.3 31 31
TRKA/NEDD4-2 0.029 0.044 0.22 6 -0.33 5 11
ELMO1 0.02 0.053 -10000 0 -0.46 6 6
RhoG/GTP/ELMO1/DOCK1 0.027 0.049 -10000 0 -0.3 10 10
NGF 0.006 0.097 -10000 0 -0.46 21 21
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK1 0.02 0.048 -10000 0 -0.46 5 5
GAB2 0.026 0.004 -10000 0 -10000 0 0
RIT2 0.018 0.005 -10000 0 -10000 0 0
RIT1 0.02 0.011 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
DNM1 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.081 0.16 0.27 1 -0.29 153 154
mol:GDP -0.046 0.14 0.29 3 -0.34 40 43
NGF (dimer) 0.006 0.097 -10000 0 -0.46 21 21
RhoG/GDP 0.015 0.038 -10000 0 -0.33 6 6
RIT1/GDP -0.035 0.084 0.23 2 -0.23 32 34
TIAM1 0.022 0.043 -10000 0 -0.46 4 4
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
BDNF (dimer)/TRKB -0.14 0.16 -10000 0 -0.28 279 279
KIDINS220/CRKL/C3G 0.036 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.039 -10000 0 -0.33 5 5
FRS2 family/SHP2 0.051 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.038 -10000 0 -0.25 3 3
RIT1/GTP 0.015 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.009 0.13 0.29 3 -0.46 37 40
RAP1/GDP -0.025 0.084 -10000 0 -0.2 37 37
KIDINS220/CRKL 0.025 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.021 0.068 0.29 7 -0.46 8 15
ubiquitin-dependent protein catabolic process 0.027 0.075 0.21 5 -0.28 24 29
Schwann cell development -0.043 0.029 -10000 0 -10000 0 0
EHD4 0.025 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.06 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.017 0.047 -10000 0 -0.27 5 5
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.026 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.17 -10000 0 -0.29 312 312
ABL1 0.025 0.007 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.059 0.096 -10000 0 -0.32 27 27
STAT3 0.027 0.032 -10000 0 -0.32 4 4
axon guidance -0.17 0.16 -10000 0 -0.28 315 315
MAPK3 0.019 0.097 -10000 0 -0.27 30 30
MAPK1 0.018 0.098 -10000 0 -0.27 31 31
CDC42/GDP -0.024 0.1 0.23 3 -0.24 31 34
NTF3 -0.009 0.13 0.29 3 -0.46 37 40
NTF4 -0.071 0.19 -10000 0 -0.46 99 99
NGF (dimer)/TRKA/FAIM 0.028 0.073 -10000 0 -0.28 22 22
PI3K 0.031 0.031 -10000 0 -0.33 3 3
FRS3 0.026 0.004 -10000 0 -10000 0 0
FAIM 0.024 0.022 -10000 0 -0.46 1 1
GAB1 0.022 0.043 -10000 0 -0.46 4 4
RASGRF1 -0.089 0.15 0.18 9 -0.29 158 167
SOS1 0.026 0.004 -10000 0 -10000 0 0
MCF2L -0.077 0.15 -10000 0 -0.32 136 136
RGS19 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.096 0.36 1 -0.36 8 9
Rac1/GDP -0.025 0.1 0.24 4 -0.24 34 38
NGF (dimer)/TRKA/GRIT 0.016 0.069 0.19 7 -0.28 23 30
neuron projection morphogenesis -0.12 0.24 -10000 0 -0.77 35 35
NGF (dimer)/TRKA/NEDD4-2 0.027 0.075 0.21 5 -0.28 24 29
MAP2K1 0.032 0.092 0.38 9 -0.24 2 11
NGFR -0.15 0.23 -10000 0 -0.46 182 182
NGF (dimer)/TRKA/GIPC/GAIP 0.011 0.051 -10000 0 -0.23 16 16
RAS family/GTP/PI3K 0.017 0.034 -10000 0 -0.31 4 4
FRS2 family/SHP2/GRB2/SOS1 0.069 0.026 -10000 0 -10000 0 0
NRAS 0.023 0.037 -10000 0 -0.46 3 3
GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.008 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
MAPKKK cascade -0.057 0.15 -10000 0 -0.64 30 30
RASA1 0.021 0.048 -10000 0 -0.46 5 5
TRKA/c-Abl 0.029 0.042 0.22 7 -0.32 4 11
SQSTM1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.16 -10000 0 -0.26 263 263
NGF (dimer)/TRKA/p62/Atypical PKCs 0.043 0.071 -10000 0 -0.24 19 19
MATK 0.009 0.086 0.29 1 -0.46 16 17
NEDD4L 0.024 0.031 -10000 0 -0.46 2 2
RAS family/GDP -0.041 0.06 -10000 0 -0.18 38 38
NGF (dimer)/TRKA -0.1 0.15 0.29 1 -0.29 186 187
Rac1/GTP -0.081 0.11 -10000 0 -0.22 148 148
FRS2 family/SHP2/CRK family 0.069 0.026 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.013 0.12 0.34 61 -0.22 7 68
KIRREL -0.038 0.16 -10000 0 -0.46 63 63
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.013 0.12 0.22 7 -0.34 61 68
PLCG1 0.025 0.006 -10000 0 -10000 0 0
ARRB2 0.024 0.007 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.009 0.1 -10000 0 -0.25 63 63
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.012 0.087 -10000 0 -0.24 56 56
FYN 0.016 0.13 0.27 62 -0.24 60 122
mol:Ca2+ 0.009 0.1 0.26 1 -0.25 59 60
mol:DAG 0.01 0.1 0.27 1 -0.25 59 60
NPHS2 0.002 0.029 -10000 0 -10000 0 0
mol:IP3 0.01 0.1 0.27 1 -0.25 59 60
regulation of endocytosis 0.007 0.09 -10000 0 -0.23 59 59
Nephrin/NEPH1/podocin/Cholesterol 0 0.097 0.25 1 -0.25 61 62
establishment of cell polarity -0.013 0.12 0.22 7 -0.34 61 68
Nephrin/NEPH1/podocin/NCK1-2 0.02 0.1 0.27 1 -0.24 60 61
Nephrin/NEPH1/beta Arrestin2 0.009 0.092 -10000 0 -0.23 59 59
NPHS1 0.02 0.053 0.28 11 -10000 0 11
Nephrin/NEPH1/podocin 0.003 0.094 -10000 0 -0.24 60 60
TJP1 0.025 0.006 -10000 0 -10000 0 0
NCK1 0.023 0.031 -10000 0 -0.46 2 2
NCK2 0.026 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.01 0.1 0.27 1 -0.25 59 60
CD2AP 0.023 0.037 -10000 0 -0.46 3 3
Nephrin/NEPH1/podocin/GRB2 0.009 0.1 0.27 1 -0.25 60 61
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.15 0.28 57 -0.27 84 141
cytoskeleton organization -0.018 0.1 0.21 14 -0.27 56 70
Nephrin/NEPH1 -0.005 0.088 0.18 7 -0.23 61 68
Nephrin/NEPH1/ZO-1 0.002 0.1 0.23 1 -0.27 61 62
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.005 0.081 -10000 0 -0.34 24 24
PDGFRB 0.021 0.038 -10000 0 -0.47 3 3
SPHK1 -0.024 0.12 -10000 0 -0.78 11 11
mol:S1P -0.031 0.11 -10000 0 -0.69 11 11
S1P1/S1P/Gi -0.12 0.21 -10000 0 -0.4 162 162
GNAO1 -0.003 0.079 -10000 0 -0.47 13 13
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.19 -10000 0 -0.37 154 154
PLCG1 -0.12 0.19 -10000 0 -0.38 157 157
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.038 -10000 0 -0.47 3 3
GNAI2 0.01 0.024 -10000 0 -10000 0 0
GNAI3 0.011 0.023 -10000 0 -10000 0 0
GNAI1 -0.003 0.084 -10000 0 -0.47 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.06 -10000 0 -0.28 24 24
S1P1/S1P -0.047 0.11 -10000 0 -0.42 21 21
negative regulation of cAMP metabolic process -0.12 0.2 -10000 0 -0.39 162 162
MAPK3 -0.18 0.28 0.28 1 -0.54 171 172
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
KDR -0.008 0.1 -10000 0 -0.46 24 24
PLCB2 -0.039 0.1 0.25 1 -0.37 20 21
RAC1 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.038 0.096 -10000 0 -0.35 22 22
receptor internalization -0.045 0.1 -10000 0 -0.38 22 22
PTGS2 -0.31 0.45 -10000 0 -0.94 169 169
Rac1/GTP -0.039 0.097 -10000 0 -0.36 21 21
RHOA 0.025 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.019 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.12 0.2 -10000 0 -0.39 162 162
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.005 0.061 -10000 0 -0.47 7 7
MAPK1 -0.18 0.28 -10000 0 -0.56 170 170
S1P1/S1P/PDGFB-D/PDGFRB -0.045 0.12 0.29 1 -0.42 23 24
ABCC1 0.023 0.009 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0 0.11 -10000 0 -0.27 75 75
regulation of S phase of mitotic cell cycle -0.002 0.067 -10000 0 -0.23 39 39
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
HRAS 0.024 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.016 0.005 -10000 0 -10000 0 0
PELP1 0.023 0.008 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.049 0.088 0.22 5 -0.25 42 47
T-DHT/AR -0.018 0.1 -10000 0 -0.33 51 51
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 132 132
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.002 -10000 0 -10000 0 0
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
mol:GDP -0.034 0.11 -10000 0 -0.34 51 51
cell proliferation -0.11 0.19 0.27 4 -0.42 130 134
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
FOS -0.2 0.34 -10000 0 -0.76 134 134
mol:Ca2+ -0.009 0.022 -10000 0 -0.066 49 49
MAPK3 -0.083 0.15 0.27 4 -0.3 124 128
MAPK1 -0.065 0.14 0.22 1 -0.37 43 44
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.001 0.002 -10000 0 -0.004 132 132
cAMP biosynthetic process 0.001 0.017 -10000 0 -10000 0 0
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 132 132
HRAS/GTP -0.004 0.088 -10000 0 -0.24 44 44
actin cytoskeleton reorganization 0.032 0.026 -10000 0 -0.23 3 3
SRC 0.024 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 132 132
PI3K 0.029 0.027 -10000 0 -0.28 3 3
apoptosis 0.11 0.2 0.42 133 -0.28 1 134
T-DHT/AR/PELP1 -0.001 0.093 -10000 0 -0.28 49 49
HRAS/GDP -0.024 0.11 -10000 0 -0.33 50 50
CREB1 -0.12 0.21 0.29 1 -0.45 133 134
RAC1-CDC42/GTP 0.04 0.029 -10000 0 -0.23 3 3
AR -0.024 0.15 -10000 0 -0.46 51 51
GNB1 0.025 0.005 -10000 0 -10000 0 0
RAF1 -0.029 0.089 0.26 3 -0.25 42 45
RAC1-CDC42/GDP 0.005 0.11 -10000 0 -0.32 47 47
T-DHT/AR/PELP1/Src 0.013 0.087 -10000 0 -0.26 44 44
MAP2K2 -0.049 0.087 0.28 2 -0.25 41 43
T-DHT/AR/PELP1/Src/PI3K -0.002 0.067 -10000 0 -0.23 39 39
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
SHBG 0.024 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.038 0.14 -10000 0 -0.43 43 43
mol:T-DHT -0.001 0.001 0.002 2 -0.002 102 104
RAC1 0.025 0.005 -10000 0 -10000 0 0
GNRH1 0.004 0.015 -10000 0 -0.33 1 1
Gi family/GTP -0.02 0.081 -10000 0 -0.25 40 40
CDC42 0.025 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.063 0.072 0.15 200 -10000 0 200
TP53 0.008 0.045 -10000 0 -0.13 25 25
Senescence 0.009 0.046 -10000 0 -0.13 25 25
Apoptosis 0.009 0.046 -10000 0 -0.13 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.041 0.056 0.24 6 -0.18 8 14
MDM4 0.022 0.01 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.007 0.052 -10000 0 -0.29 11 11
NFATC2 -0.042 0.1 -10000 0 -0.29 73 73
NFATC3 -0.001 0.029 -10000 0 -0.12 2 2
CD40LG -0.15 0.22 -10000 0 -0.48 111 111
PTGS2 -0.18 0.26 -10000 0 -0.51 164 164
JUNB 0.024 0.022 -10000 0 -0.46 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.024 -10000 0 -10000 0 0
CALM1 0.015 0.022 -10000 0 -10000 0 0
JUN 0.013 0.038 -10000 0 -0.47 2 2
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.009 -10000 0 -10000 0 0
FOSL1 0.028 0.034 0.29 5 -0.46 1 6
CREM 0.024 0.009 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.039 0.13 0.29 1 -0.34 35 36
FOS -0.11 0.21 -10000 0 -0.47 128 128
IFNG -0.12 0.2 0.42 1 -0.45 92 93
AP-1/NFAT1-c-4 -0.13 0.24 0.48 1 -0.5 100 101
FASLG -0.12 0.19 0.42 1 -0.44 88 89
NFAT1-c-4/ICER1 -0.042 0.11 -10000 0 -0.26 80 80
IL2RA -0.13 0.2 -10000 0 -0.46 93 93
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.19 -10000 0 -0.45 92 92
JunB/Fra1/NFAT1-c-4 -0.03 0.12 -10000 0 -0.26 76 76
IL4 -0.13 0.19 -10000 0 -0.45 94 94
IL2 -0.01 0.18 -10000 0 -0.92 17 17
IL3 -0.012 0.12 -10000 0 -0.73 12 12
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
BATF3 0.021 0.034 0.29 1 -0.46 2 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.022 0.01 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.034 0.49 0.81 5 -1.1 55 60
IL23A -0.002 0.47 0.88 7 -1.1 42 49
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.44 0.66 2 -0.98 58 60
positive regulation of T cell mediated cytotoxicity -0.018 0.52 0.83 14 -1.1 59 73
ITGA3 -0.011 0.46 0.83 4 -1.1 41 45
IL17F 0.006 0.32 0.58 16 -0.64 59 75
IL12B 0.034 0.074 0.24 10 -10000 0 10
STAT1 (dimer) -0.028 0.48 0.76 4 -1.1 59 63
CD4 -0.009 0.45 0.8 5 -1 50 55
IL23 -0.006 0.45 0.79 6 -1.1 41 47
IL23R 0.056 0.14 0.57 3 -0.86 1 4
IL1B -0.015 0.49 0.87 6 -1.2 42 48
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.02 0.46 0.84 15 -0.98 49 64
TYK2 0.024 0.052 -10000 0 -10000 0 0
STAT4 0.015 0.071 -10000 0 -0.46 11 11
STAT3 0.025 0.006 -10000 0 -10000 0 0
IL18RAP 0.018 0.064 -10000 0 -0.46 9 9
IL12RB1 0.018 0.084 0.26 3 -0.49 8 11
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
IL12Rbeta1/TYK2 0.03 0.078 0.25 3 -0.37 7 10
IL23R/JAK2 0.064 0.18 0.55 4 -0.72 1 5
positive regulation of chronic inflammatory response -0.018 0.52 0.83 14 -1.1 59 73
natural killer cell activation -0.003 0.012 -10000 0 -0.048 4 4
JAK2 0.026 0.1 0.26 4 -0.48 11 15
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
NFKB1 0.027 0.023 -10000 0 -0.46 1 1
RELA 0.029 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0 0.43 0.79 6 -1 43 49
ALOX12B -0.003 0.44 0.81 8 -1.1 41 49
CXCL1 -0.04 0.52 0.8 12 -1.2 62 74
T cell proliferation -0.018 0.52 0.83 14 -1.1 59 73
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A 0.03 0.28 0.54 18 -0.54 38 56
PI3K -0.036 0.45 0.69 3 -1 59 62
IFNG 0.016 0.045 0.14 28 -0.11 3 31
STAT3 (dimer) -0.033 0.43 0.65 1 -0.95 59 60
IL18R1 0.019 0.061 -10000 0 -0.46 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 0.03 0.33 0.64 16 -0.67 43 59
IL18/IL18R 0.039 0.086 -10000 0 -0.33 22 22
macrophage activation 0.002 0.027 0.059 31 -0.044 36 67
TNF -0.007 0.48 0.83 10 -1.2 42 52
STAT3/STAT4 -0.036 0.46 0.68 1 -1 60 61
STAT4 (dimer) -0.033 0.48 0.76 4 -1.1 60 64
IL18 0.017 0.068 -10000 0 -0.46 10 10
IL19 0.044 0.47 0.84 17 -1 44 61
STAT5A (dimer) -0.033 0.48 0.75 4 -1.1 59 63
STAT1 0.026 0.003 -10000 0 -10000 0 0
SOCS3 0.011 0.082 -10000 0 -0.46 15 15
CXCL9 -0.035 0.5 0.81 8 -1.1 65 73
MPO -0.009 0.45 0.78 8 -0.95 58 66
positive regulation of humoral immune response -0.018 0.52 0.83 14 -1.1 59 73
IL23/IL23R/JAK2/TYK2 -0.033 0.57 0.83 14 -1.2 59 73
IL6 -0.19 0.64 0.86 5 -1.1 151 156
STAT5A 0.025 0.006 -10000 0 -10000 0 0
IL2 0.02 0.055 0.29 16 -10000 0 16
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.012 -10000 0 -0.048 4 4
CD3E -0.02 0.47 0.88 5 -1.1 48 53
keratinocyte proliferation -0.018 0.52 0.83 14 -1.1 59 73
NOS2 -0.11 0.57 0.83 5 -1.1 105 110
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.088 0.22 -10000 0 -0.39 137 137
MAP3K8 0.016 0.058 -10000 0 -0.46 7 7
FOS -0.061 0.17 -10000 0 -0.47 50 50
PRKCA 0.003 0.073 -10000 0 -0.46 11 11
PTPN7 0.01 0.035 0.26 2 -0.46 1 3
HRAS 0.024 0.006 -10000 0 -10000 0 0
PRKCB -0.042 0.15 -10000 0 -0.46 59 59
NRAS 0.023 0.037 -10000 0 -0.46 3 3
RAS family/GTP 0.029 0.039 -10000 0 -0.26 3 3
MAPK3 -0.031 0.15 -10000 0 -0.68 18 18
MAP2K1 -0.064 0.17 -10000 0 -0.43 77 77
ELK1 0.011 0.027 -10000 0 -10000 0 0
BRAF -0.051 0.15 -10000 0 -0.39 74 74
mol:GTP -0.001 0.002 -10000 0 -0.005 133 133
MAPK1 -0.036 0.15 -10000 0 -0.59 24 24
RAF1 -0.05 0.15 -10000 0 -0.4 73 73
KRAS 0.025 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.12 0.11 -10000 0 -0.22 29 29
ER alpha/Gai/GDP/Gbeta gamma 0.033 0.16 -10000 0 -0.46 28 28
AKT1 0.096 0.13 -10000 0 -0.71 8 8
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.1 0.14 -10000 0 -0.78 7 7
mol:Ca2+ -0.001 0.11 -10000 0 -0.34 35 35
IGF1R 0.017 0.064 -10000 0 -0.46 9 9
E2/ER alpha (dimer)/Striatin 0.11 0.11 0.2 290 -0.24 25 315
SHC1 0.022 0.01 -10000 0 -10000 0 0
apoptosis -0.095 0.13 0.68 8 -10000 0 8
RhoA/GTP 0.048 0.038 -10000 0 -0.22 4 4
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.076 0.14 0.3 3 -0.41 17 20
regulation of stress fiber formation -0.019 0.061 0.22 7 -0.22 10 17
E2/ERA-ERB (dimer) 0.13 0.084 0.2 307 -0.28 2 309
KRAS 0.026 0.005 -10000 0 -10000 0 0
G13/GTP 0.12 0.08 0.18 302 -0.24 2 304
pseudopodium formation 0.019 0.061 0.22 10 -0.22 7 17
E2/ER alpha (dimer)/PELP1 0.12 0.087 0.2 296 -0.28 2 298
GRB2 0.025 0.006 -10000 0 -10000 0 0
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
HRAS 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.066 0.14 0.28 4 -0.54 11 15
E2/ER beta (dimer) 0.019 0.003 -10000 0 -10000 0 0
mol:GDP 0.11 0.085 0.23 8 -0.28 2 10
mol:NADP 0.066 0.14 0.28 4 -0.54 11 15
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.004 0.11 -10000 0 -0.36 35 35
IGF-1R heterotetramer 0.017 0.064 -10000 0 -0.46 9 9
PLCB1 -0.002 0.12 -10000 0 -0.37 38 38
PLCB2 0.002 0.11 -10000 0 -0.35 38 38
IGF1 0.009 0.1 0.29 5 -0.46 21 26
mol:L-citrulline 0.066 0.14 0.28 4 -0.54 11 15
RHOA 0.025 0.005 -10000 0 -10000 0 0
Gai/GDP -0.038 0.22 -10000 0 -0.54 73 73
JNK cascade 0.019 0.003 -10000 0 -10000 0 0
BCAR1 0.023 0.009 -10000 0 -10000 0 0
ESR2 0.026 0.005 -10000 0 -10000 0 0
GNAQ 0.023 0.031 -10000 0 -0.46 2 2
ESR1 0.18 0.14 0.29 311 -0.46 2 313
Gq family/GDP/Gbeta gamma -0.057 0.24 -10000 0 -0.63 63 63
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.064 0.11 -10000 0 -0.57 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.06 0.14 0.32 2 -0.43 15 17
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
E2/ER alpha (dimer) 0.13 0.091 0.2 311 -0.33 2 313
STRN 0.004 0.1 -10000 0 -0.46 23 23
GNAL -0.031 0.16 -10000 0 -0.46 59 59
PELP1 0.024 0.007 -10000 0 -10000 0 0
MAPK11 0.011 0.005 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.002 -10000 0 -10000 0 0
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
HBEGF 0.033 0.16 0.32 9 -0.5 24 33
cAMP biosynthetic process 0.052 0.1 -10000 0 -0.2 61 61
SRC 0.035 0.15 0.3 2 -0.45 24 26
PI3K 0.031 0.031 -10000 0 -0.33 3 3
GNB1 0.025 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.1 0.1 -10000 0 -0.23 12 12
SOS1 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.025 0.085 -10000 0 -0.35 21 21
Gs family/GTP 0.069 0.12 -10000 0 -0.2 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.027 -10000 0 -0.26 3 3
vasodilation 0.066 0.13 0.28 4 -0.51 11 15
mol:DAG -0.004 0.11 -10000 0 -0.36 35 35
Gs family/GDP/Gbeta gamma 0.031 0.1 -10000 0 -0.24 34 34
MSN 0.02 0.064 0.23 10 -0.23 7 17
Gq family/GTP 0.007 0.12 -10000 0 -0.38 38 38
mol:PI-3-4-5-P3 0.1 0.13 -10000 0 -0.75 7 7
NRAS 0.023 0.037 -10000 0 -0.46 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.066 0.13 0.51 11 -0.28 4 15
GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.12 0.084 0.22 7 -0.35 1 8
NOS3 0.066 0.14 0.33 1 -0.57 11 12
GNA11 0.011 0.08 -10000 0 -0.46 14 14
MAPKKK cascade 0.077 0.15 -10000 0 -0.58 9 9
E2/ER alpha (dimer)/PELP1/Src 0.085 0.15 0.28 9 -0.43 17 26
ruffle organization 0.019 0.061 0.22 10 -0.22 7 17
ROCK2 0.028 0.071 0.24 12 -0.24 10 22
GNA14 -0.003 0.11 -10000 0 -0.46 29 29
GNA15 0.023 0.023 -10000 0 -0.46 1 1
GNA13 0.025 0.006 -10000 0 -10000 0 0
MMP9 0.046 0.15 0.33 12 -0.44 22 34
MMP2 0.037 0.14 0.29 5 -0.45 24 29
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.023 0.031 -10000 0 -0.46 2 2
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.064 0.16 0.24 5 -0.28 173 178
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.078 0.13 0.19 9 -0.25 172 181
IQGAP1/CaM 0.036 0.019 -10000 0 -0.33 1 1
DAB1 0.035 0.055 0.29 22 -10000 0 22
IQGAP1 0.025 0.022 -10000 0 -0.46 1 1
PLA2G7 0.025 0.025 0.29 1 -0.46 1 2
CALM1 0.025 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.038 0.016 0.22 3 -10000 0 3
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0.025 0.014 0.29 1 -10000 0 1
LIS1/Poliovirus Protein 3A 0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.051 0.082 0.29 53 -10000 0 53
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.062 0.16 0.22 21 -0.28 173 194
YWHAE 0.024 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.048 0.12 0.3 10 -0.26 8 18
MAP1B -0.001 0.042 -10000 0 -0.28 11 11
RAC1 0.011 0.009 -10000 0 -0.15 1 1
p35/CDK5 -0.068 0.12 0.24 1 -0.23 160 161
RELN -0.14 0.23 0.29 5 -0.46 176 181
PAFAH/LIS1 0.025 0.018 0.21 1 -0.28 1 2
LIS1/CLIP170 0.025 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.043 0.1 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.056 0.12 0.26 3 -0.22 163 166
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.06 0.11 0.3 5 -0.28 4 9
LIS1/IQGAP1 0.025 0.017 -10000 0 -0.28 1 1
RHOA 0.011 0.009 -10000 0 -0.15 1 1
PAFAH1B1 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.038 0.056 0.29 24 -10000 0 24
PAFAH1B2 0.022 0.038 -10000 0 -0.46 3 3
MAP1B/LIS1/Dynein heavy chain 0.016 0.039 -10000 0 -0.19 10 10
NDEL1/Katanin 60/Dynein heavy chain -0.041 0.12 0.3 9 -0.26 7 16
LRP8 0.028 0.02 0.29 3 -10000 0 3
NDEL1/Katanin 60 -0.05 0.12 0.3 10 -0.26 9 19
P39/CDK5 -0.059 0.13 0.34 4 -0.23 151 155
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.01 -10000 0 -10000 0 0
CDK5 -0.086 0.11 0.19 7 -0.24 167 174
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.008 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.049 0.14 0.36 1 -0.25 169 170
RELN/VLDLR -0.049 0.15 -10000 0 -0.26 170 170
CDC42 0.011 0.009 -10000 0 -0.15 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.039 0.19 17 -0.19 1 18
RFC1 0.002 0.041 0.19 19 -0.19 2 21
PRKDC 0.014 0.065 0.21 46 -10000 0 46
RIPK1 0.028 0.008 -10000 0 -10000 0 0
CASP7 -0.015 0.1 -10000 0 -0.61 13 13
FASLG/FAS/FADD/FAF1 0.031 0.081 0.2 57 -0.26 3 60
MAP2K4 -0.049 0.15 0.42 2 -0.29 99 101
mol:ceramide -0.021 0.092 -10000 0 -0.31 14 14
GSN 0 0.04 0.19 17 -0.22 3 20
FASLG/FAS/FADD/FAF1/Caspase 8 0.023 0.079 0.26 6 -0.29 3 9
FAS 0.007 0.049 -10000 0 -0.47 4 4
BID -0.016 0.019 0.25 2 -10000 0 2
MAP3K1 -0.023 0.12 0.29 4 -0.35 21 25
MAP3K7 0.021 0.013 -10000 0 -10000 0 0
RB1 0.001 0.041 0.19 18 -0.22 2 20
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.16 0.21 -10000 0 -0.34 273 273
ARHGDIB 0.002 0.046 0.2 21 -0.2 4 25
FADD 0.011 0.025 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.049 0.28 1 -0.19 17 18
NFKB1 -0.046 0.14 -10000 0 -0.55 23 23
MAPK8 -0.098 0.22 0.33 7 -0.44 139 146
DFFA 0.003 0.047 0.21 21 -0.19 2 23
DNA fragmentation during apoptosis -0.002 0.052 0.2 21 -10000 0 21
FAS/FADD/MET 0.011 0.077 -10000 0 -0.29 24 24
CFLAR/RIP1 0.041 0.013 -10000 0 -10000 0 0
FAIM3 0.021 0.038 -10000 0 -0.46 3 3
FAF1 0.01 0.028 -10000 0 -10000 0 0
PARP1 0.003 0.045 0.2 22 -0.19 3 25
DFFB 0.003 0.043 0.2 21 -0.19 2 23
CHUK -0.044 0.13 0.36 1 -0.5 22 23
FASLG 0.011 0.043 0.29 5 -0.46 1 6
FAS/FADD 0.014 0.047 -10000 0 -0.34 4 4
HGF -0.16 0.24 -10000 0 -0.46 191 191
LMNA 0.008 0.066 0.22 25 -10000 0 25
CASP6 0.002 0.045 0.21 19 -0.19 3 22
CASP10 0.001 0.075 -10000 0 -0.47 11 11
CASP3 0.006 0.047 0.23 20 -10000 0 20
PTPN13 -0.1 0.21 -10000 0 -0.46 134 134
CASP8 -0.017 0.028 0.33 3 -10000 0 3
IL6 -0.31 0.53 -10000 0 -1.1 152 152
MET 0.003 0.1 -10000 0 -0.46 23 23
ICAD/CAD 0.002 0.047 0.2 18 -10000 0 18
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.092 -10000 0 -0.31 14 14
activation of caspase activity by cytochrome c -0.016 0.019 0.25 2 -10000 0 2
PAK2 0.016 0.073 0.22 51 -0.19 3 54
BCL2 0.004 0.1 -10000 0 -0.46 23 23
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.004 0.089 0.19 2 -0.28 44 46
EFNA5 -0.017 0.14 -10000 0 -0.46 44 44
FYN -0.021 0.075 0.18 3 -0.26 44 47
neuron projection morphogenesis 0.004 0.089 0.19 2 -0.28 44 46
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.004 0.089 0.2 2 -0.28 44 46
EPHA5 0.022 0.018 0.29 2 -10000 0 2
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.005 0.092 -10000 0 -0.36 18 18
alphaM/beta2 Integrin/GPIbA 0.004 0.088 0.38 1 -0.32 19 20
alphaM/beta2 Integrin/proMMP-9 0.033 0.1 0.29 3 -0.35 12 15
PLAUR 0.027 0.017 0.29 2 -10000 0 2
HMGB1 0.005 0.038 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.012 0.079 -10000 0 -0.35 11 11
AGER 0.009 0.056 0.29 8 -0.5 1 9
RAP1A 0.026 0.002 -10000 0 -10000 0 0
SELPLG 0.026 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.005 0.14 0.33 2 -0.37 21 23
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.06 0.094 0.29 70 -0.46 1 71
CYR61 -0.004 0.12 -10000 0 -0.46 31 31
TLN1 0.025 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.12 0.21 1 -0.34 30 31
RHOA 0.025 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.13 0.22 -10000 0 -0.46 155 155
MYH2 -0.003 0.13 0.25 6 -0.43 22 28
MST1R 0.024 0.033 0.29 1 -0.46 2 3
leukocyte activation during inflammatory response -0.006 0.12 0.47 1 -0.28 64 65
APOB -0.035 0.16 0.29 1 -0.46 59 60
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.016 0.061 -10000 0 -0.46 8 8
JAM3 0.019 0.053 -10000 0 -0.46 6 6
GP1BA 0.017 0.058 0.29 1 -0.46 7 8
alphaM/beta2 Integrin/CTGF 0.003 0.098 -10000 0 -0.34 24 24
alphaM/beta2 Integrin -0.004 0.12 0.24 2 -0.42 22 24
JAM3 homodimer 0.019 0.053 -10000 0 -0.46 6 6
ICAM2 0.025 0.006 -10000 0 -10000 0 0
ICAM1 0.024 0.007 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.004 0.12 0.24 3 -0.41 23 26
cell adhesion 0.004 0.088 0.38 1 -0.32 19 20
NFKB1 -0.074 0.19 0.35 4 -0.37 131 135
THY1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.004 0.11 0.2 34 -0.28 59 93
alphaM/beta2 Integrin/LRP/tPA 0.004 0.11 -10000 0 -0.31 36 36
IL6 -0.18 0.33 0.38 3 -0.69 142 145
ITGB2 0.004 0.046 0.29 1 -0.49 1 2
elevation of cytosolic calcium ion concentration 0.021 0.078 -10000 0 -0.3 11 11
alphaM/beta2 Integrin/JAM2/JAM3 -0.057 0.16 -10000 0 -0.29 141 141
JAM2 -0.1 0.22 -10000 0 -0.46 136 136
alphaM/beta2 Integrin/ICAM1 0.037 0.091 -10000 0 -0.3 13 13
alphaM/beta2 Integrin/uPA/Plg 0.03 0.089 0.38 1 -0.3 12 13
RhoA/GTP -0.009 0.14 0.23 4 -0.39 36 40
positive regulation of phagocytosis -0.002 0.11 0.26 1 -0.37 21 22
Ron/MSP 0.047 0.051 0.22 32 -0.33 2 34
alphaM/beta2 Integrin/uPAR/uPA 0.023 0.079 -10000 0 -0.3 11 11
alphaM/beta2 Integrin/uPAR 0.013 0.08 -10000 0 -0.35 11 11
PLAU 0.025 0.006 -10000 0 -10000 0 0
PLAT -0.002 0.11 -10000 0 -0.46 26 26
actin filament polymerization -0.003 0.13 0.26 7 -0.41 24 31
MST1 0.041 0.064 0.29 31 -10000 0 31
alphaM/beta2 Integrin/lipoprotein(a) -0.003 0.13 0.5 1 -0.28 64 65
TNF -0.075 0.2 0.39 4 -0.37 119 123
RAP1B 0.026 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.011 0.078 -10000 0 -0.33 12 12
fibrinolysis 0.028 0.088 0.36 1 -0.3 12 13
HCK 0.022 0.038 -10000 0 -0.46 3 3
dendritic cell antigen processing and presentation -0.004 0.12 0.24 3 -0.41 23 26
VTN -0.016 0.14 0.29 2 -0.46 43 45
alphaM/beta2 Integrin/CYR61 -0.006 0.11 -10000 0 -0.34 40 40
LPA 0.042 0.069 0.29 36 -10000 0 36
LRP1 0.021 0.048 -10000 0 -0.46 5 5
cell migration 0.016 0.09 0.29 1 -0.34 17 18
FN1 0.015 0.074 -10000 0 -0.46 12 12
alphaM/beta2 Integrin/Thy1 0.011 0.08 -10000 0 -0.35 12 12
MPO 0.024 0.045 0.29 4 -0.46 3 7
KNG1 0.021 0.043 0.29 6 -0.46 2 8
RAP1/GDP 0.035 0.004 -10000 0 -10000 0 0
ROCK1 -0.006 0.14 0.24 7 -0.41 29 36
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.039 0.062 0.29 29 -10000 0 29
CTGF 0.012 0.08 -10000 0 -0.46 14 14
alphaM/beta2 Integrin/Hck 0.01 0.086 -10000 0 -0.36 13 13
ITGAM -0.006 0.084 -10000 0 -0.49 12 12
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.064 0.15 -10000 0 -0.28 148 148
HP 0.081 0.16 0.29 142 -0.46 16 158
leukocyte adhesion -0.076 0.18 -10000 0 -0.39 71 71
SELP -0.13 0.22 -10000 0 -0.46 155 155
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.019 0.093 0.19 19 -0.25 36 55
FZD6 0.021 0.038 -10000 0 -0.46 3 3
WNT6 0.071 0.099 0.29 86 -10000 0 86
WNT4 0.002 0.11 0.29 1 -0.46 25 26
FZD3 0.023 0.009 -10000 0 -10000 0 0
WNT5A 0.022 0.038 -10000 0 -0.46 3 3
WNT11 0.026 0.1 0.29 29 -0.46 15 44
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.038 -9999 0 -0.46 3 3
mol:S1P -0.006 0.013 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.032 0.1 -9999 0 -0.26 56 56
GNAO1 -0.001 0.082 -9999 0 -0.48 13 13
S1P/S1P3/G12/G13 0.028 0.038 -9999 0 -10000 0 0
AKT1 -0.015 0.12 -9999 0 -0.6 15 15
AKT3 -0.24 0.47 -9999 0 -1.1 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.037 -9999 0 -0.46 3 3
GNAI2 0.01 0.029 -9999 0 -10000 0 0
GNAI3 0.012 0.027 -9999 0 -10000 0 0
GNAI1 -0.002 0.086 -9999 0 -0.47 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.011 0.029 -9999 0 -10000 0 0
S1PR2 0.024 0.007 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.15 -9999 0 -0.31 114 114
MAPK3 -0.054 0.14 -9999 0 -0.3 102 102
MAPK1 -0.053 0.14 -9999 0 -0.3 103 103
JAK2 -0.06 0.15 -9999 0 -0.39 63 63
CXCR4 -0.058 0.14 -9999 0 -0.3 108 108
FLT1 0.009 0.039 -9999 0 -0.48 1 1
RhoA/GDP 0.019 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC -0.055 0.14 -9999 0 -0.3 105 105
S1P/S1P3/Gi -0.054 0.15 -9999 0 -0.31 114 114
RAC1 0.025 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.05 0.15 -9999 0 -0.29 113 113
VEGFA 0.01 0.032 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.028 0.11 -9999 0 -0.34 32 32
VEGFR1 homodimer/VEGFA homodimer 0.016 0.051 -9999 0 -0.36 1 1
RHOA 0.025 0.005 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.01 0.086 -9999 0 -0.27 45 45
GNAQ 0.023 0.031 -9999 0 -0.46 2 2
GNAZ 0.005 0.061 -9999 0 -0.46 7 7
G12/G13 0.036 0.011 -9999 0 -10000 0 0
GNA14 -0.003 0.11 -9999 0 -0.46 29 29
GNA15 0.023 0.023 -9999 0 -0.46 1 1
GNA12 0.025 0.006 -9999 0 -10000 0 0
GNA13 0.025 0.006 -9999 0 -10000 0 0
GNA11 0.011 0.08 -9999 0 -0.46 14 14
Rac1/GTP -0.051 0.14 -9999 0 -0.29 113 113
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.009 0.14 -10000 0 -0.43 43 43
HDAC1 0.025 0.009 -10000 0 -10000 0 0
AES 0.024 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.021 0.048 -10000 0 -0.46 5 5
LRP6/FZD1 0.035 0.029 -10000 0 -0.33 3 3
TLE1 0.025 0.007 -10000 0 -10000 0 0
AP1 -0.039 0.12 0.17 1 -0.26 104 105
NCSTN 0.022 0.01 -10000 0 -10000 0 0
ADAM10 0.017 0.061 -10000 0 -0.46 8 8
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.16 -10000 0 -0.64 23 23
NICD/RBPSUH 0.013 0.14 -10000 0 -0.42 43 43
WIF1 -0.1 0.23 0.29 23 -0.46 148 171
NOTCH1 -0.011 0.12 -10000 0 -0.45 33 33
PSENEN 0.025 0.006 -10000 0 -10000 0 0
KREMEN2 0.1 0.12 0.29 153 -10000 0 153
DKK1 0.026 0.16 0.29 67 -0.46 35 102
beta catenin/beta TrCP1 0.017 0.069 0.23 1 -0.3 5 6
APH1B 0.017 0.061 -10000 0 -0.46 8 8
APH1A 0.021 0.011 -10000 0 -10000 0 0
AXIN1 -0.015 0.12 -10000 0 -0.47 24 24
CtBP/CBP/TCF1/TLE1/AES 0.037 0.057 0.24 7 -10000 0 7
PSEN1 0.026 0.005 -10000 0 -10000 0 0
FOS -0.097 0.21 -10000 0 -0.46 128 128
JUN 0.024 0.031 -10000 0 -0.46 2 2
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.007 0.068 0.23 1 -0.29 8 9
MAPK3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.15 0.34 1 -0.26 82 83
HNF1A 0.1 0.12 0.29 143 -10000 0 143
CTBP1 0.025 0.006 -10000 0 -10000 0 0
MYC -0.017 0.21 -10000 0 -1.2 15 15
NKD1 0.053 0.088 0.29 58 -0.46 1 59
FZD1 0.023 0.038 -10000 0 -0.46 3 3
NOTCH1 precursor/Deltex homolog 1 0.011 0.14 -10000 0 -0.42 41 41
apoptosis -0.038 0.12 0.17 1 -0.26 104 105
Delta 1/NOTCHprecursor 0.009 0.15 -10000 0 -0.43 43 43
DLL1 0.019 0.057 -10000 0 -0.46 7 7
PPARD 0.019 0.049 -10000 0 -0.98 1 1
Gamma Secretase 0.051 0.049 -10000 0 -0.24 6 6
APC -0.013 0.12 -10000 0 -0.52 19 19
DVL1 -0.001 0.054 -10000 0 -0.3 10 10
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.091 0.13 0.37 19 -0.27 34 53
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
NLK 0.012 0.008 -10000 0 -10000 0 0
CCND1 -0.003 0.17 -10000 0 -1.1 11 11
WNT1 0.027 0.029 0.29 6 -10000 0 6
Axin1/APC/beta catenin 0.005 0.13 0.27 1 -0.42 26 27
DKK2 -0.053 0.18 0.29 2 -0.46 82 84
NOTCH1 precursor/DVL1 -0.022 0.14 -10000 0 -0.47 42 42
GSK3B 0.026 0.005 -10000 0 -10000 0 0
FRAT1 0.025 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.14 -10000 0 -0.42 41 41
PPP2R5D 0.001 0.036 0.26 1 -0.29 1 2
MAPK1 0.024 0.022 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 -0.023 0.16 -10000 0 -0.26 143 143
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.008 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.045 0.16 0.29 62 -0.42 26 88
FYN 0.007 0.18 0.34 12 -0.52 32 44
LAT/GRAP2/SLP76 0.009 0.16 0.29 8 -0.43 39 47
IKBKB 0.024 0.008 -10000 0 -10000 0 0
AKT1 0.004 0.14 0.3 12 -0.35 43 55
B2M 0.025 0.023 -10000 0 -0.46 1 1
IKBKG 0.005 0.045 0.13 10 -0.13 16 26
MAP3K8 0.019 0.057 -10000 0 -0.46 7 7
mol:Ca2+ -0.016 0.021 0.088 2 -0.069 48 50
integrin-mediated signaling pathway 0.027 0.03 -10000 0 -0.28 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.006 0.18 0.35 11 -0.47 50 61
TRPV6 -0.042 0.21 1.1 8 -0.46 61 69
CD28 0.011 0.086 -10000 0 -0.46 16 16
SHC1 0.026 0.18 0.3 63 -0.47 34 97
receptor internalization -0.004 0.17 0.29 4 -0.46 43 47
PRF1 -0.001 0.2 0.45 3 -0.76 22 25
KRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
COT/AKT1 0.014 0.12 0.29 11 -0.3 39 50
LAT 0.003 0.16 0.31 8 -0.5 32 40
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.018 0.077 0.3 4 -0.47 11 15
CD3E 0.016 0.074 0.32 1 -0.47 11 12
CD3G -0.005 0.12 -10000 0 -0.46 31 31
RASGRP2 0.001 0.037 0.083 1 -0.16 20 21
RASGRP1 -0.002 0.15 0.32 12 -0.41 39 51
HLA-A 0.028 0.018 0.29 2 -10000 0 2
RASSF5 0.018 0.044 -10000 0 -0.46 4 4
RAP1A/GTP/RAPL 0.028 0.03 -10000 0 -0.28 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.029 0.073 0.16 66 -0.13 28 94
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.057 -10000 0 -0.19 33 33
PRKCA 0.004 0.086 0.19 15 -0.24 28 43
GRAP2 -0.011 0.13 -10000 0 -0.46 37 37
mol:IP3 0.004 0.12 0.22 48 -0.35 31 79
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.007 0.13 0.28 4 -0.53 20 24
ORAI1 0.014 0.15 0.4 1 -0.97 8 9
CSK 0.005 0.16 0.33 5 -0.5 32 37
B7 family/CD28 0.019 0.17 0.38 4 -0.48 34 38
CHUK 0.025 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.003 0.18 0.37 3 -0.51 39 42
PTPN6 0.001 0.16 0.31 6 -0.5 32 38
VAV1 0.001 0.17 0.33 5 -0.5 35 40
Monovalent TCR/CD3 -0.006 0.099 0.22 2 -0.33 33 35
CBL 0.025 0.006 -10000 0 -10000 0 0
LCK 0.006 0.18 0.34 12 -0.53 32 44
PAG1 0.007 0.16 0.32 6 -0.49 32 38
RAP1A 0.026 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.18 0.31 6 -0.49 42 48
CD80 0.024 0.026 0.29 1 -0.47 1 2
CD86 0.015 0.071 -10000 0 -0.46 11 11
PDK1/CARD11/BCL10/MALT1 -0.007 0.072 -10000 0 -0.22 35 35
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.006 0.14 0.3 4 -0.4 35 39
CD8A 0.014 0.087 0.31 3 -0.46 15 18
CD8B 0.026 0.085 0.29 17 -0.47 10 27
PTPRC -0.012 0.12 -10000 0 -0.46 36 36
PDK1/PKC theta -0.004 0.16 0.33 13 -0.43 41 54
CSK/PAG1 0.011 0.16 0.31 10 -0.51 27 37
SOS1 0.026 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.024 0.22 2 -0.34 1 3
GRAP2/SLP76 0.008 0.18 0.32 6 -0.5 39 45
STIM1 0.009 0.07 1.2 1 -10000 0 1
RAS family/GTP 0.033 0.082 0.23 20 -0.17 20 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.006 0.18 0.29 4 -0.49 43 47
mol:DAG -0.018 0.095 0.12 7 -0.3 37 44
RAP1A/GDP 0.017 0.035 0.096 27 -0.063 16 43
PLCG1 0.025 0.006 -10000 0 -10000 0 0
CD247 0.021 0.033 -10000 0 -0.47 2 2
cytotoxic T cell degranulation 0.001 0.19 0.42 4 -0.73 22 26
RAP1A/GTP 0 0.014 -10000 0 -0.061 21 21
mol:PI-3-4-5-P3 0 0.16 0.34 11 -0.39 50 61
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.013 0.16 0.24 46 -0.43 34 80
NRAS 0.023 0.037 -10000 0 -0.46 3 3
ZAP70 0.028 0.057 0.29 10 -0.46 4 14
GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.001 0.15 0.32 2 -0.43 37 39
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.025 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.03 0.1 0.26 17 -0.39 21 38
CARD11 0.021 0.05 0.29 1 -0.46 5 6
PRKCB -0.009 0.11 0.19 13 -0.27 48 61
PRKCE 0.006 0.083 0.19 12 -0.24 27 39
PRKCQ -0.007 0.18 0.35 12 -0.46 48 60
LCP2 0.021 0.048 -10000 0 -0.46 5 5
BCL10 0.026 0.003 -10000 0 -10000 0 0
regulation of survival gene product expression 0.007 0.12 0.29 12 -0.32 38 50
IKK complex 0.014 0.064 0.2 23 -0.12 17 40
RAS family/GDP -0.001 0.011 -10000 0 -0.056 3 3
MAP3K14 0.01 0.092 0.25 10 -0.24 33 43
PDPK1 0.004 0.13 0.3 13 -0.34 40 53
TCR/CD3/MHC I/CD8/Fyn -0.009 0.2 0.36 3 -0.65 32 35
LPA4-mediated signaling events

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
ADCY4 -0.01 0.03 -10000 0 -0.28 6 6
ADCY5 -0.047 0.098 -10000 0 -0.28 73 73
ADCY6 -0.009 0.021 -10000 0 -0.28 3 3
ADCY7 -0.009 0.024 -10000 0 -0.28 4 4
ADCY1 -0.015 0.054 -10000 0 -0.28 19 19
ADCY2 -0.04 0.09 0.24 1 -0.28 62 63
ADCY3 -0.01 0.027 -10000 0 -0.28 5 5
ADCY8 -0.011 0.032 0.24 1 -0.28 6 7
PRKCE 0.004 0.026 -10000 0 -0.33 3 3
ADCY9 -0.062 0.11 -10000 0 -0.28 102 102
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.021 0.095 0.22 25 -0.23 31 56
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.018 0.086 -10000 0 -0.23 43 43
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.1 0.39 4 -0.33 3 7
alphaV/beta3 Integrin/Osteopontin/Src 0.065 0.062 0.22 68 -10000 0 68
AP1 -0.03 0.16 -10000 0 -0.44 29 29
ILK 0.005 0.091 0.39 2 -0.24 42 44
bone resorption -0.003 0.1 0.35 2 -0.42 7 9
PTK2B 0.021 0.032 -10000 0 -0.46 2 2
PYK2/p130Cas 0.042 0.11 0.3 1 -0.23 18 19
ITGAV 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.013 0.093 -10000 0 -0.35 30 30
alphaV/beta3 Integrin/Osteopontin 0.043 0.12 0.38 1 -0.27 51 52
MAP3K1 0.003 0.09 0.39 1 -0.25 48 49
JUN 0.024 0.031 -10000 0 -0.46 2 2
MAPK3 -0.004 0.082 0.32 2 -0.23 44 46
MAPK1 -0.003 0.082 0.32 2 -0.23 43 45
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 -0.008 0.087 0.39 1 -0.25 44 45
ITGB3 -0.021 0.15 0.29 2 -0.46 51 53
NFKBIA -0.005 0.08 0.38 1 -0.28 7 8
FOS -0.098 0.21 -10000 0 -0.46 128 128
CD44 0.01 0.085 -10000 0 -0.46 16 16
CHUK 0.025 0.006 -10000 0 -10000 0 0
PLAU -0.006 0.1 0.65 1 -0.45 4 5
NF kappa B1 p50/RelA 0.036 0.089 0.32 2 -0.41 1 3
BCAR1 0.023 0.009 -10000 0 -10000 0 0
RELA 0.026 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.004 0.11 0.22 2 -0.32 51 53
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.003 0.095 0.36 3 -0.25 50 53
VAV3 -0.014 0.099 0.35 3 -0.25 58 61
MAP3K14 0.006 0.091 0.32 2 -0.25 48 50
ROCK2 0.009 0.088 -10000 0 -0.46 17 17
SPP1 0.064 0.091 0.29 70 -10000 0 70
RAC1 0.025 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.093 0.31 3 -0.23 53 56
MMP2 -0.05 0.13 0.31 2 -0.4 31 33
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.066 1 1 -10000 0 1
VDR 0.017 0.064 -10000 0 -0.46 9 9
FAM120B 0.026 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.013 0.087 0.28 3 -0.31 11 14
RXRs/LXRs/DNA/Oxysterols 0.029 0.11 0.32 3 -0.42 12 15
MED1 0.024 0.007 -10000 0 -10000 0 0
mol:9cRA 0.004 0.012 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.062 0.12 -10000 0 -0.23 154 154
RXRs/NUR77 0.013 0.12 0.28 1 -0.27 64 65
RXRs/PPAR -0.058 0.13 -10000 0 -0.25 140 140
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.046 -10000 0 -0.33 9 9
RARs/VDR/DNA/Vit D3 0.044 0.058 -10000 0 -0.24 17 17
RARA 0.025 0.007 -10000 0 -10000 0 0
NCOA1 0.025 0.022 -10000 0 -0.46 1 1
VDR/VDR/DNA 0.017 0.064 -10000 0 -0.46 9 9
RARs/RARs/DNA/9cRA 0.037 0.046 -10000 0 -0.24 11 11
RARG 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.017 0.074 0.56 9 -10000 0 9
RARs/THRs/DNA/SMRT -0.06 0.12 -10000 0 -0.23 156 156
THRA 0.024 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0.046 -10000 0 -0.33 9 9
RXRs/PPAR/9cRA/PGJ2/DNA 0.026 0.092 0.31 1 -0.25 35 36
NR1H4 0.026 0.056 0.29 16 -0.46 2 18
RXRs/LXRs/DNA 0.047 0.1 0.35 1 -0.25 31 32
NR1H2 0.029 0.016 -10000 0 -10000 0 0
NR1H3 0.028 0.017 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.026 0.096 0.26 1 -0.26 39 40
NR4A1 -0.009 0.12 -10000 0 -0.46 36 36
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.015 0.083 0.23 6 -0.22 21 27
RXRG -0.012 0.13 0.29 4 -0.46 39 43
RXR alpha/CCPG 0.037 0.018 -10000 0 -10000 0 0
RXRA 0.027 0.017 -10000 0 -10000 0 0
RXRB 0.029 0.017 -10000 0 -10000 0 0
THRB -0.12 0.22 -10000 0 -0.46 151 151
PPARG -0.1 0.21 -10000 0 -0.46 135 135
PPARD 0.026 0.004 -10000 0 -10000 0 0
TNF 0.021 0.15 0.39 3 -0.99 7 10
mol:Oxysterols 0.004 0.01 -10000 0 -10000 0 0
cholesterol transport 0.029 0.11 0.32 3 -0.41 12 15
PPARA 0.024 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.015 0.071 -10000 0 -0.46 11 11
RXRs/NUR77/BCL2 -0.025 0.12 -10000 0 -0.29 71 71
SREBF1 0.023 0.097 0.4 1 -0.53 3 4
RXRs/RXRs/DNA/9cRA 0.026 0.092 0.31 1 -0.25 35 36
ABCA1 0.017 0.14 -10000 0 -0.82 10 10
RARs/THRs -0.032 0.15 -10000 0 -0.25 155 155
RXRs/FXR 0.032 0.097 0.32 1 -0.26 33 34
BCL2 0.003 0.1 -10000 0 -0.46 23 23
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.02 0.23 1 -10000 0 1
AES 0.025 0.019 0.2 2 -10000 0 2
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.03 -10000 0 -0.33 3 3
SMAD4 0.025 0.005 -10000 0 -10000 0 0
DKK2 -0.053 0.18 0.29 2 -0.46 82 84
TLE1 0.025 0.019 0.22 2 -10000 0 2
MACF1 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.044 0.099 0.27 17 -0.34 8 25
WIF1 -0.1 0.23 0.29 23 -0.46 148 171
beta catenin/RanBP3 0.016 0.1 0.41 23 -0.4 3 26
KREMEN2 0.1 0.12 0.29 153 -10000 0 153
DKK1 0.026 0.16 0.29 67 -0.46 35 102
beta catenin/beta TrCP1 0.053 0.096 0.28 14 -0.33 6 20
FZD1 0.023 0.038 -10000 0 -0.46 3 3
AXIN2 -0.017 0.18 0.6 8 -1.2 8 16
AXIN1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.11 -10000 0 -0.52 17 17
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.18 0.33 1 -0.58 30 31
Axin1/APC/GSK3 0.025 0.061 0.34 1 -0.35 3 4
Axin1/APC/GSK3/beta catenin/Macf1 0.03 0.068 0.26 3 -0.43 4 7
HNF1A 0.1 0.12 0.29 144 -10000 0 144
CTBP1 0.025 0.018 0.23 1 -10000 0 1
MYC 0.05 0.3 0.58 77 -1.2 13 90
RANBP3 0.024 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.15 0.22 12 -0.26 82 94
NKD1 0.053 0.088 0.29 58 -0.46 1 59
TCF4 0.021 0.051 0.21 2 -0.45 5 7
TCF3 0.025 0.021 0.23 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.062 0.035 -10000 0 -0.25 3 3
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.027 0.14 0.47 20 -0.46 10 30
LEF1 0.082 0.11 0.29 109 -10000 0 109
DVL1 0.034 0.063 -10000 0 -0.53 3 3
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.038 0.18 -10000 0 -0.56 33 33
DKK1/LRP6/Kremen 2 0.091 0.13 0.33 26 -0.27 34 60
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.026 0.019 0.23 1 -10000 0 1
NLK 0.024 0.011 -10000 0 -10000 0 0
CCND1 -0.013 0.18 0.59 11 -1.2 7 18
WNT1 0.027 0.029 0.29 6 -10000 0 6
GSK3A 0.026 0.004 -10000 0 -10000 0 0
GSK3B 0.026 0.005 -10000 0 -10000 0 0
FRAT1 0.025 0.006 -10000 0 -10000 0 0
PPP2R5D 0.019 0.052 0.27 1 -0.3 2 3
APC 0 0.043 0.18 17 -0.24 3 20
WNT1/LRP6/FZD1 0.061 0.091 0.21 125 -0.26 2 127
CREBBP 0.025 0.018 0.22 1 -10000 0 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.018 0.11 -10000 0 -0.36 15 15
epithelial cell differentiation -0.018 0.12 -10000 0 -0.41 13 13
ITCH 0.034 0.019 -10000 0 -10000 0 0
WWP1 0.002 0.072 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
EGFR -0.013 0.13 -10000 0 -0.46 40 40
PRL 0.039 0.063 0.29 30 -10000 0 30
neuron projection morphogenesis -0.044 0.15 0.35 10 -0.37 9 19
PTPRZ1 -0.13 0.22 0.29 3 -0.46 156 159
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.063 0.13 -10000 0 -0.33 36 36
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.1 0.14 -10000 0 -0.36 44 44
ADAM17 0.028 0.046 -10000 0 -0.44 4 4
ErbB4/ErbB4 -0.006 0.08 -10000 0 -0.37 7 7
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.037 0.12 -10000 0 -0.36 21 21
NCOR1 0.024 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.091 0.14 -10000 0 -0.34 45 45
GRIN2B -0.089 0.14 0.27 1 -0.34 39 40
ErbB4/ErbB2/betacellulin -0.002 0.096 -10000 0 -0.35 15 15
STAT1 0.026 0.003 -10000 0 -10000 0 0
HBEGF -0.017 0.14 -10000 0 -0.46 44 44
PRLR -0.007 0.12 -10000 0 -0.46 34 34
E4ICDs/ETO2 -0.026 0.12 -10000 0 -0.37 22 22
axon guidance 0.007 0.1 0.33 9 -0.37 1 10
NEDD4 -0.027 0.15 -10000 0 -0.45 56 56
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.1 0.22 26 -0.33 33 59
CBFA2T3 -0.033 0.15 -10000 0 -0.46 58 58
ErbB4/ErbB2/HBEGF -0.007 0.097 -10000 0 -0.35 12 12
MAPK3 -0.047 0.14 0.34 7 -0.32 36 43
STAT1 (dimer) 0.004 0.081 -10000 0 -0.33 7 7
MAPK1 -0.047 0.15 0.34 7 -0.32 37 44
JAK2 0.015 0.071 -10000 0 -0.46 11 11
ErbB4/ErbB2/neuregulin 1 beta -0.091 0.14 0.26 1 -0.34 44 45
NRG1 -0.12 0.17 -10000 0 -0.34 193 193
NRG3 -0.048 0.17 0.29 1 -0.46 73 74
NRG2 -0.006 0.12 0.29 2 -0.46 34 36
NRG4 0.03 0.035 0.29 9 -10000 0 9
heart development 0.007 0.1 0.33 9 -0.37 1 10
neural crest cell migration -0.09 0.14 0.26 1 -0.34 44 45
ERBB2 0.016 0.049 0.28 9 -0.31 5 14
WWOX/E4ICDs 0.006 0.076 -10000 0 -0.33 7 7
SHC1 0.022 0.01 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.001 0.11 -10000 0 -0.35 20 20
apoptosis 0.073 0.17 0.42 73 -10000 0 73
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.013 0.11 -10000 0 -0.4 16 16
ErbB4/ErbB2/epiregulin -0.036 0.13 0.28 1 -0.35 26 27
ErbB4/ErbB4/betacellulin/betacellulin -0.01 0.11 -10000 0 -0.37 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.002 0.14 -10000 0 -0.4 27 27
MDM2 -0.008 0.072 -10000 0 -0.33 7 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.089 0.13 -10000 0 -0.32 45 45
STAT5A 0.004 0.097 0.34 9 -0.35 1 10
ErbB4/EGFR/neuregulin 1 beta -0.11 0.16 -10000 0 -0.39 59 59
DLG4 0.025 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.03 0.017 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.003 0.073 -10000 0 -0.3 7 7
STAT5A (dimer) -0.005 0.14 -10000 0 -0.44 13 13
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.016 0.1 0.31 7 -0.33 2 9
LRIG1 0.023 0.031 -10000 0 -0.46 2 2
EREG -0.076 0.2 0.29 7 -0.46 108 115
BTC -0.003 0.11 -10000 0 -0.46 29 29
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.001 0.094 0.34 5 -0.37 1 6
ERBB4 -0.01 0.071 -10000 0 -0.37 7 7
STAT5B 0.025 0.006 -10000 0 -10000 0 0
YAP1 0.002 0.082 -10000 0 -0.46 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.016 0.077 0.32 3 -0.36 5 8
glial cell differentiation -0.003 0.072 0.3 7 -10000 0 7
WWOX 0.023 0.009 -10000 0 -10000 0 0
cell proliferation -0.089 0.17 0.32 5 -0.46 34 39
Syndecan-1-mediated signaling events

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
TGFB1 0.026 0.004 -10000 0 -10000 0 0
CCL5 0.023 0.048 0.29 3 -0.46 4 7
SDCBP 0.024 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.041 0.089 0.26 15 -0.32 5 20
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.043 0.088 0.25 8 -0.31 5 13
Syndecan-1/Syntenin 0.043 0.087 0.26 8 -0.31 5 13
MAPK3 0.036 0.08 0.24 8 -0.37 3 11
HGF/MET -0.12 0.19 -10000 0 -0.35 201 201
TGFB1/TGF beta receptor Type II 0.026 0.004 -10000 0 -10000 0 0
BSG 0.024 0.007 -10000 0 -10000 0 0
keratinocyte migration 0.043 0.087 0.25 8 -0.31 5 13
Syndecan-1/RANTES 0.047 0.097 0.27 13 -0.38 6 19
Syndecan-1/CD147 0.055 0.092 0.29 6 -0.39 3 9
Syndecan-1/Syntenin/PIP2 0.04 0.083 0.24 8 -0.3 5 13
LAMA5 0.024 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.039 0.082 0.24 8 -0.3 5 13
MMP7 0.06 0.14 0.29 100 -0.46 18 118
HGF -0.16 0.24 -10000 0 -0.46 191 191
Syndecan-1/CASK 0.026 0.083 0.23 6 -0.29 8 14
Syndecan-1/HGF/MET -0.045 0.16 0.31 3 -0.39 40 43
regulation of cell adhesion 0.026 0.076 0.25 3 -0.42 2 5
HPSE 0.015 0.072 0.29 1 -0.46 11 12
positive regulation of cell migration 0.041 0.089 0.26 15 -0.32 5 20
SDC1 0.041 0.087 0.27 12 -0.33 5 17
Syndecan-1/Collagen 0.041 0.089 0.26 15 -0.32 5 20
PPIB 0.026 0.013 0.29 1 -10000 0 1
MET 0.003 0.1 -10000 0 -0.46 23 23
PRKACA 0.025 0.006 -10000 0 -10000 0 0
MMP9 0.06 0.094 0.29 70 -0.46 1 71
MAPK1 0.035 0.08 0.24 5 -0.43 2 7
homophilic cell adhesion 0.042 0.09 0.26 16 -0.48 2 18
MMP1 0.048 0.092 0.29 51 -0.46 4 55
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.033 0.092 -10000 0 -0.27 37 37
MAP4K1 0.025 0.025 0.29 1 -0.46 1 2
MAP3K8 0.019 0.057 -10000 0 -0.46 7 7
PRKCB -0.031 0.16 -10000 0 -0.46 59 59
DBNL 0.026 0.005 -10000 0 -10000 0 0
CRKL 0.025 0.006 -10000 0 -10000 0 0
MAP3K1 -0.002 0.076 -10000 0 -0.24 33 33
JUN -0.08 0.24 -10000 0 -0.59 87 87
MAP3K7 -0.004 0.08 -10000 0 -0.25 34 34
GRAP2 -0.011 0.13 -10000 0 -0.46 37 37
CRK 0.024 0.007 -10000 0 -10000 0 0
MAP2K4 -0.005 0.089 -10000 0 -0.35 14 14
LAT 0.025 0.005 -10000 0 -10000 0 0
LCP2 0.021 0.048 -10000 0 -0.46 5 5
MAPK8 -0.081 0.25 -10000 0 -0.61 87 87
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.083 -10000 0 -0.26 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55 0.043 0.088 -10000 0 -0.26 34 34
LPA receptor mediated events

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
GNB1/GNG2 0.021 0.094 -10000 0 -0.27 45 45
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.093 0.32 5 -0.28 16 21
AP1 -0.031 0.15 0.19 1 -0.25 139 140
mol:PIP3 -0.014 0.092 -10000 0 -0.26 52 52
AKT1 0 0.08 0.3 3 -0.32 11 14
PTK2B -0.014 0.094 0.2 1 -0.29 34 35
RHOA 0.002 0.057 0.22 3 -0.29 11 14
PIK3CB 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.069 0.26 7 -0.25 15 22
MAGI3 0.023 0.037 -10000 0 -0.46 3 3
RELA 0.026 0.003 -10000 0 -10000 0 0
apoptosis 0.009 0.079 -10000 0 -0.28 28 28
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.084 0.13 0.24 2 -0.32 59 61
NF kappa B1 p50/RelA 0.017 0.093 -10000 0 -0.3 22 22
endothelial cell migration 0 0.088 -10000 0 -0.41 19 19
ADCY4 -0.016 0.1 -10000 0 -0.33 35 35
ADCY5 -0.042 0.13 -10000 0 -0.35 44 44
ADCY6 -0.015 0.098 -10000 0 -0.32 35 35
ADCY7 -0.014 0.098 -10000 0 -0.33 33 33
ADCY1 -0.021 0.11 -10000 0 -0.35 38 38
ADCY2 -0.038 0.14 -10000 0 -0.38 48 48
ADCY3 -0.017 0.1 -10000 0 -0.33 37 37
ADCY8 -0.016 0.093 -10000 0 -0.31 34 34
ADCY9 -0.051 0.12 -10000 0 -0.34 46 46
GSK3B -0.013 0.094 0.22 8 -0.29 31 39
arachidonic acid secretion -0.025 0.11 -10000 0 -0.33 46 46
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
TRIP6 0.018 0.026 -10000 0 -0.36 2 2
GNAO1 -0.003 0.08 -10000 0 -0.32 28 28
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA 0.003 0.09 0.3 5 -0.3 18 23
GAB1 0.022 0.043 -10000 0 -0.46 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.019 0.15 -10000 0 -0.81 16 16
JUN 0.024 0.031 -10000 0 -0.46 2 2
LPA/LPA2/NHERF2 0.033 0.018 -10000 0 -10000 0 0
TIAM1 0.004 0.17 -10000 0 -0.94 16 16
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 0.005 0.067 0.26 7 -0.25 16 23
PLCB3 0.019 0.034 0.19 18 -10000 0 18
FOS -0.097 0.21 -10000 0 -0.46 128 128
positive regulation of mitosis -0.025 0.11 -10000 0 -0.33 46 46
LPA/LPA1-2-3 0.049 0.1 0.21 14 -0.28 28 42
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.023 0.009 -10000 0 -10000 0 0
stress fiber formation 0.004 0.084 0.22 2 -0.33 16 18
GNAZ 0.001 0.073 -10000 0 -0.3 24 24
EGFR/PI3K-beta/Gab1 -0.003 0.1 -10000 0 -0.27 52 52
positive regulation of dendritic cell cytokine production 0.047 0.098 0.21 4 -0.28 28 32
LPA/LPA2/MAGI-3 0.032 0.029 -10000 0 -0.28 3 3
ARHGEF1 0.009 0.055 -10000 0 -0.24 16 16
GNAI2 0.004 0.06 -10000 0 -0.28 19 19
GNAI3 0.005 0.06 -10000 0 -0.29 19 19
GNAI1 -0.003 0.075 -10000 0 -0.28 32 32
LPA/LPA3 0.036 0.088 0.2 73 -0.27 18 91
LPA/LPA2 0.019 0.016 -10000 0 -0.11 6 6
LPA/LPA1 0.01 0.071 -10000 0 -0.34 19 19
HB-EGF/EGFR -0.008 0.12 0.21 3 -0.28 73 76
HBEGF 0.002 0.11 0.22 5 -0.32 41 46
mol:DAG 0.005 0.067 0.26 7 -0.25 16 23
cAMP biosynthetic process -0.035 0.11 0.2 5 -0.35 40 45
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
SRC 0.025 0.006 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
LYN 0.01 0.092 0.29 9 -0.3 18 27
GNAQ 0.016 0.058 0.21 3 -0.26 15 18
LPAR2 0.025 0.006 -10000 0 -10000 0 0
LPAR3 0.051 0.12 0.29 73 -0.46 13 86
LPAR1 0.012 0.083 -10000 0 -0.38 19 19
IL8 -0.042 0.17 0.31 4 -0.38 69 73
PTK2 0.007 0.072 0.2 6 -0.26 27 33
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.079 -10000 0 -0.28 28 28
EGFR -0.013 0.13 -10000 0 -0.46 40 40
PLCG1 0.007 0.07 0.18 7 -0.27 19 26
PLD2 0.007 0.075 0.24 2 -0.27 27 29
G12/G13 0.038 0.062 -10000 0 -0.27 17 17
PI3K-beta -0.005 0.079 -10000 0 -0.25 35 35
cell migration 0.016 0.061 -10000 0 -0.25 15 15
SLC9A3R2 0.025 0.006 -10000 0 -10000 0 0
PXN 0.004 0.085 0.22 2 -0.34 16 18
HRAS/GTP -0.026 0.11 -10000 0 -0.33 47 47
RAC1 0.025 0.005 -10000 0 -10000 0 0
MMP9 0.06 0.094 0.29 70 -0.46 1 71
PRKCE 0.023 0.037 -10000 0 -0.46 3 3
PRKCD 0 0.073 0.29 6 -0.3 7 13
Gi(beta/gamma) -0.017 0.1 -10000 0 -0.34 34 34
mol:LPA 0 0.019 -10000 0 -0.16 6 6
TRIP6/p130 Cas/FAK1/Paxillin 0.024 0.087 -10000 0 -0.34 14 14
MAPKKK cascade -0.025 0.11 -10000 0 -0.33 46 46
contractile ring contraction involved in cytokinesis 0.002 0.06 0.24 2 -0.27 13 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.003 0.083 0.21 3 -0.26 39 42
GNA15 0.018 0.057 0.21 3 -0.26 14 17
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
MAPT -0.086 0.13 0.24 2 -0.25 148 150
GNA11 0.01 0.075 0.21 2 -0.28 25 27
Rac1/GTP 0.019 0.16 -10000 0 -0.86 16 16
MMP2 0 0.088 -10000 0 -0.41 19 19
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.048 0.17 -10000 0 -0.46 76 76
GNB1/GNG2 0.024 0.12 -10000 0 -0.3 27 27
mol:DAG 0.007 0.1 0.26 4 -0.31 16 20
PLCG1 0.007 0.1 0.27 4 -0.32 16 20
YES1 0.007 0.089 0.22 6 -0.24 36 42
FZD3 0.023 0.009 -10000 0 -10000 0 0
FZD6 0.021 0.038 -10000 0 -0.46 3 3
G protein 0.027 0.12 0.27 3 -0.35 13 16
MAP3K7 -0.034 0.12 0.24 7 -0.33 27 34
mol:Ca2+ 0.008 0.099 0.26 4 -0.3 16 20
mol:IP3 0.007 0.1 0.26 4 -0.31 16 20
NLK -0.012 0.14 -10000 0 -0.77 16 16
GNB1 0.025 0.005 -10000 0 -10000 0 0
CAMK2A -0.03 0.13 0.26 7 -0.35 28 35
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.019 0.093 0.19 19 -0.25 36 55
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
GNAS 0.007 0.085 0.22 2 -0.24 34 36
GO:0007205 0.002 0.1 0.29 8 -0.32 16 24
WNT6 0.071 0.099 0.29 86 -10000 0 86
WNT4 0.002 0.11 0.29 1 -0.46 25 26
NFAT1/CK1 alpha -0.002 0.12 0.28 2 -0.42 12 14
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
WNT5A 0.022 0.038 -10000 0 -0.46 3 3
WNT11 0.026 0.1 0.29 29 -0.46 15 44
CDC42 0.006 0.084 0.24 4 -0.24 34 38
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.008 0.09 0.2 5 -0.28 44 49
cell-cell adhesion 0.042 0.072 0.22 67 -10000 0 67
Ephrin B/EPHB2/RasGAP 0.054 0.072 -10000 0 -0.24 23 23
ITSN1 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
SHC1 0.022 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.036 0.047 0.2 21 -0.36 3 24
Ephrin B1/EPHB1 0.002 0.095 -10000 0 -0.28 52 52
HRAS/GDP -0.018 0.099 -10000 0 -0.28 22 22
Ephrin B/EPHB1/GRB7 0.021 0.12 -10000 0 -0.25 69 69
Endophilin/SYNJ1 -0.013 0.054 0.21 2 -0.23 19 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.022 0.11 -10000 0 -0.25 65 65
endothelial cell migration 0.041 0.045 -10000 0 -0.24 10 10
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.02 0.044 -10000 0 -0.46 4 4
PAK1 -0.012 0.07 0.28 6 -0.26 20 26
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS -0.013 0.052 0.21 2 -0.23 18 20
DNM1 0.025 0.006 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.033 0.091 0.28 4 -0.24 65 69
lamellipodium assembly -0.042 0.072 -10000 0 -0.22 67 67
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.007 0.082 -10000 0 -0.23 47 47
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
EPHB2 0.028 0.026 0.29 5 -10000 0 5
EPHB3 0.032 0.066 0.29 21 -0.46 3 24
EPHB1 -0.024 0.15 -10000 0 -0.46 51 51
EPHB4 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.028 0.083 0.4 1 -0.31 20 21
Ephrin B/EPHB2 0.045 0.061 -10000 0 -0.24 18 18
Ephrin B/EPHB3 0.045 0.068 -10000 0 -0.26 16 16
JNK cascade -0.025 0.099 0.3 20 -0.24 53 73
Ephrin B/EPHB1 0.013 0.1 -10000 0 -0.25 66 66
RAP1/GDP -0.015 0.098 0.38 1 -0.28 22 23
EFNB2 0.018 0.057 -10000 0 -0.46 7 7
EFNB3 0.015 0.069 0.29 1 -0.46 10 11
EFNB1 0.025 0.022 -10000 0 -0.46 1 1
Ephrin B2/EPHB1-2 0.013 0.098 0.2 5 -0.25 58 63
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.026 0.002 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.1 0.25 1 -0.23 68 69
Rap1/GTP -0.01 0.088 -10000 0 -0.22 69 69
axon guidance 0.008 0.09 0.19 5 -0.28 44 49
MAPK3 -0.011 0.073 0.23 1 -0.29 5 6
MAPK1 -0.011 0.07 0.23 1 -0.33 3 4
Rac1/GDP -0.026 0.091 0.39 1 -0.29 21 22
actin cytoskeleton reorganization -0.046 0.065 -10000 0 -0.25 21 21
CDC42/GDP -0.023 0.094 0.39 1 -0.28 22 23
PI3K 0.045 0.047 -10000 0 -0.24 10 10
EFNA5 -0.017 0.14 -10000 0 -0.46 44 44
Ephrin B2/EPHB4 0.028 0.038 -10000 0 -0.28 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.058 -10000 0 -0.23 18 18
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.013 0.088 -10000 0 -0.23 69 69
PTK2 0.046 0.16 0.55 44 -10000 0 44
MAP4K4 -0.025 0.1 0.3 20 -0.25 53 73
SRC 0.025 0.006 -10000 0 -10000 0 0
KALRN 0.022 0.043 -10000 0 -0.46 4 4
Intersectin/N-WASP 0.037 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.1 0.34 18 -0.35 5 23
MAP2K1 -0.011 0.075 -10000 0 -0.3 6 6
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.03 0.1 -10000 0 -0.26 53 53
cell migration -0.002 0.11 0.31 5 -0.32 7 12
NRAS 0.023 0.037 -10000 0 -0.46 3 3
SYNJ1 -0.013 0.055 0.21 2 -0.23 19 21
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.027 0.072 0.2 3 -0.23 43 46
HRAS/GTP 0.008 0.099 0.23 1 -0.23 69 70
Ephrin B1/EPHB1-2 0.018 0.094 0.2 4 -0.25 52 56
cell adhesion mediated by integrin 0.003 0.057 0.24 16 -0.24 5 21
RAC1 0.025 0.005 -10000 0 -10000 0 0
mol:GTP 0.01 0.1 0.28 1 -0.24 70 71
RAC1-CDC42/GTP -0.041 0.075 -10000 0 -0.23 60 60
RASA1 0.021 0.048 -10000 0 -0.46 5 5
RAC1-CDC42/GDP -0.016 0.094 0.38 1 -0.28 20 21
ruffle organization -0.03 0.1 0.35 10 -0.4 3 13
NCK1 0.023 0.031 -10000 0 -0.46 2 2
receptor internalization -0.016 0.052 0.2 2 -0.22 18 20
Ephrin B/EPHB2/KALRN 0.054 0.073 -10000 0 -0.27 20 20
ROCK1 0.029 0.057 0.18 44 -0.33 3 47
RAS family/GDP -0.046 0.064 -10000 0 -0.26 20 20
Rac1/GTP -0.016 0.086 -10000 0 -0.23 66 66
Ephrin B/EPHB1/Src/Paxillin -0.01 0.089 0.19 1 -0.23 65 66
Visual signal transduction: Rods

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
mol:K + 0.025 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.019 0.024 0.2 9 -10000 0 9
Metarhodopsin II/Arrestin 0.031 0.028 0.19 14 -10000 0 14
PDE6G/GNAT1/GTP 0.027 0.062 0.2 17 -0.28 14 31
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.026 0.036 0.29 9 -10000 0 9
GRK1 0.02 0.022 0.29 3 -10000 0 3
CNG Channel -0.003 0.12 0.24 3 -0.25 80 83
mol:Na + 0.025 0.076 -10000 0 -0.23 30 30
mol:ADP 0.02 0.022 0.29 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.006 0.12 -10000 0 -0.28 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.034 0.083 -10000 0 -0.24 29 29
CNGB1 0.032 0.05 0.29 18 -10000 0 18
RDH5 0.023 0.037 -10000 0 -0.46 3 3
SAG 0.026 0.038 0.29 10 -10000 0 10
mol:Ca2+ -0.02 0.085 0.35 12 -10000 0 12
Na + (4 Units) 0.018 0.07 -10000 0 -0.22 28 28
RGS9 -0.05 0.18 -10000 0 -0.46 78 78
GNB1/GNGT1 0.092 0.085 0.22 159 -10000 0 159
GNAT1/GDP 0.004 0.11 -10000 0 -0.24 76 76
GUCY2D 0.024 0.022 0.29 3 -10000 0 3
GNGT1 0.11 0.12 0.29 168 -10000 0 168
GUCY2F 0.021 0.013 0.29 1 -10000 0 1
GNB5 0.025 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.003 0.096 0.21 7 -0.26 53 60
mol:11-cis-retinal 0.023 0.037 -10000 0 -0.46 3 3
mol:cGMP 0.046 0.031 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
Rhodopsin 0.033 0.035 0.22 5 -0.33 3 8
SLC24A1 0.025 0.006 -10000 0 -10000 0 0
CNGA1 -0.012 0.13 0.29 1 -0.46 40 41
Metarhodopsin II 0.026 0.022 0.18 8 -10000 0 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.056 0.035 -10000 0 -10000 0 0
RGS9BP 0.023 0.033 0.29 1 -0.46 2 3
Metarhodopsin II/Transducin 0.042 0.047 0.19 13 -10000 0 13
GCAP Family/Ca ++ 0.046 0.028 0.2 14 -10000 0 14
PDE6A/B 0.007 0.11 0.22 7 -0.33 44 51
mol:Pi -0.006 0.12 -10000 0 -0.28 77 77
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.088 0.078 0.36 6 -10000 0 6
PDE6B -0.017 0.14 -10000 0 -0.46 44 44
PDE6A 0.03 0.035 0.29 9 -10000 0 9
PDE6G 0.017 0.09 0.29 12 -0.46 14 26
RHO 0.023 0.027 0.29 5 -10000 0 5
PDE6 -0.011 0.16 -10000 0 -0.28 109 109
GUCA1A 0.03 0.046 0.29 15 -10000 0 15
GC2/GCAP Family 0.059 0.03 -10000 0 -10000 0 0
GUCA1C 0.018 0.004 -10000 0 -10000 0 0
GUCA1B 0.026 0.013 0.29 1 -10000 0 1
Regulation of Androgen receptor activity

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
HDAC1 0.012 0.003 -10000 0 -10000 0 0
SMARCC1 0.012 0.018 -10000 0 -10000 0 0
REL 0.011 0.08 -10000 0 -0.46 14 14
HDAC7 -0.011 0.095 0.23 3 -0.3 25 28
JUN 0.025 0.031 -10000 0 -0.46 2 2
EP300 0.025 0.007 -10000 0 -10000 0 0
KAT2B 0.005 0.097 -10000 0 -0.46 21 21
KAT5 0.026 0.003 -10000 0 -10000 0 0
MAPK14 0.013 0.034 0.24 4 -10000 0 4
FOXO1 0.024 0.022 -10000 0 -0.46 1 1
T-DHT/AR 0.011 0.11 -10000 0 -0.3 30 30
MAP2K6 0.027 0.046 0.29 13 -10000 0 13
BRM/BAF57 0.026 0.063 -10000 0 -0.32 15 15
MAP2K4 0.018 0.028 -10000 0 -0.45 1 1
SMARCA2 0.01 0.085 -10000 0 -0.46 16 16
PDE9A -0.004 0.11 -10000 0 -0.74 6 6
NCOA2 -0.017 0.14 -10000 0 -0.46 43 43
CEBPA -0.043 0.17 -10000 0 -0.46 71 71
EHMT2 0.026 0.004 -10000 0 -10000 0 0
cell proliferation 0.016 0.14 0.36 15 -0.39 11 26
NR0B1 0.031 0.054 0.29 21 -10000 0 21
EGR1 -0.043 0.17 -10000 0 -0.46 72 72
RXRs/9cRA 0.017 0.081 -10000 0 -0.25 37 37
AR/RACK1/Src 0.018 0.083 0.31 3 -0.28 6 9
AR/GR -0.097 0.15 0.2 3 -0.27 207 210
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
PKN1 0.025 0.006 -10000 0 -10000 0 0
RCHY1 0.026 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.001 -10000 0 -10000 0 0
MAPK8 0.003 0.041 -10000 0 -0.34 6 6
T-DHT/AR/TIF2/CARM1 0.001 0.11 -10000 0 -0.28 36 36
SRC -0.004 0.056 0.18 25 -0.26 5 30
NR3C1 -0.16 0.24 -10000 0 -0.46 189 189
KLK3 0.067 0.1 0.41 6 -0.47 3 9
APPBP2 0.02 0.018 -10000 0 -10000 0 0
TRIM24 0.026 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.005 0.076 0.26 5 -0.29 6 11
TMPRSS2 -0.097 0.32 -10000 0 -0.94 63 63
RXRG -0.014 0.13 0.29 4 -0.46 39 43
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.025 0.007 -10000 0 -10000 0 0
RXRB 0.026 0.004 -10000 0 -10000 0 0
CARM1 0.025 0.008 -10000 0 -10000 0 0
NR2C2 0.016 0.068 -10000 0 -0.46 10 10
KLK2 0.006 0.1 0.29 19 -0.37 8 27
AR -0.015 0.089 -10000 0 -0.26 53 53
SENP1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
MDM2 0.024 0.01 -10000 0 -10000 0 0
SRY -0.001 0.004 -10000 0 -0.026 13 13
GATA2 0.023 0.046 0.29 2 -0.46 4 6
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.19 0.13 0.29 317 -10000 0 317
T-DHT/AR/RACK1/Src 0.013 0.079 0.3 4 -0.28 6 10
positive regulation of transcription 0.023 0.046 0.29 2 -0.46 4 6
DNAJA1 0.02 0.018 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.005 -10000 0 -10000 0 0
NCOA1 0.029 0.027 -10000 0 -0.49 1 1
SPDEF 0.13 0.16 0.29 231 -0.46 14 245
T-DHT/AR/TIF2 -0.012 0.12 0.26 9 -0.33 31 40
T-DHT/AR/Hsp90 0.006 0.075 0.26 5 -0.29 6 11
GSK3B 0.025 0.007 -10000 0 -10000 0 0
NR2C1 0.026 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.012 0.04 0.18 2 -0.28 5 7
SIRT1 0.024 0.022 -10000 0 -0.46 1 1
ZMIZ2 0.023 0.01 -10000 0 -10000 0 0
POU2F1 0.014 0.042 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.008 0.081 0.31 7 -0.3 5 12
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.025 0.007 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.038 -10000 0 -0.46 3 3
Jak2/Leptin Receptor -0.04 0.16 -10000 0 -0.47 42 42
PTP1B/AKT1 -0.016 0.098 0.27 1 -0.32 25 26
FYN 0.026 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.028 0.1 0.3 1 -0.34 30 31
EGFR -0.023 0.13 -10000 0 -0.47 40 40
EGF/EGFR -0.064 0.16 0.25 1 -0.29 135 136
CSF1 0.015 0.074 -10000 0 -0.46 12 12
AKT1 0.025 0.006 -10000 0 -10000 0 0
INSR 0.025 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.023 0.13 0.25 18 -0.32 28 46
Insulin Receptor/Insulin -0.001 0.093 -10000 0 -0.34 13 13
HCK 0.022 0.038 -10000 0 -0.46 3 3
CRK 0.024 0.007 -10000 0 -10000 0 0
TYK2 -0.017 0.1 0.25 12 -0.34 23 35
EGF -0.075 0.19 -10000 0 -0.46 99 99
YES1 0.025 0.006 -10000 0 -10000 0 0
CAV1 -0.12 0.15 -10000 0 -0.36 108 108
TXN 0.023 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.013 0.12 -10000 0 -0.36 29 29
cell migration 0.028 0.1 0.34 30 -0.3 1 31
STAT3 0.025 0.006 -10000 0 -10000 0 0
PRLR -0.006 0.12 -10000 0 -0.46 34 34
ITGA2B 0.06 0.092 0.29 70 -10000 0 70
CSF1R 0.007 0.092 -10000 0 -0.46 19 19
Prolactin Receptor/Prolactin 0.023 0.1 0.22 6 -0.33 33 39
FGR 0.02 0.053 -10000 0 -0.46 6 6
PTP1B/p130 Cas -0.016 0.1 0.28 1 -0.34 25 26
Crk/p130 Cas -0.008 0.1 0.28 1 -0.34 22 23
DOK1 -0.021 0.1 0.36 1 -0.4 17 18
JAK2 -0.025 0.14 0.27 1 -0.47 30 31
Jak2/Leptin Receptor/Leptin -0.034 0.13 -10000 0 -0.36 44 44
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
PTPN1 -0.028 0.1 0.3 1 -0.34 30 31
LYN 0.023 0.023 -10000 0 -0.46 1 1
CDH2 0.094 0.12 0.29 133 -0.46 1 134
SRC -0.002 0.11 -10000 0 -0.53 18 18
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
CAT1/PTP1B -0.025 0.14 0.29 6 -0.4 30 36
CAPN1 0.025 0.006 -10000 0 -10000 0 0
CSK 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.006 0.089 -10000 0 -0.34 8 8
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.031 0.13 -10000 0 -0.35 44 44
negative regulation of transcription -0.024 0.14 0.27 1 -0.46 30 31
FCGR2A 0.022 0.01 -10000 0 -10000 0 0
FER 0.02 0.044 -10000 0 -0.47 4 4
alphaIIb/beta3 Integrin 0.021 0.13 0.22 61 -0.32 51 112
BLK 0.022 0.048 0.29 6 -0.46 3 9
Insulin Receptor/Insulin/Shc 0.035 0.023 -10000 0 -10000 0 0
RHOA 0.024 0.007 -10000 0 -10000 0 0
LEPR -0.036 0.16 -10000 0 -0.46 65 65
BCAR1 0.023 0.009 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.006 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.006 0.13 0.29 5 -0.45 20 25
PRL 0.035 0.066 0.29 30 -10000 0 30
SOCS3 -0.03 0.27 -10000 0 -1.2 24 24
SPRY2 0.014 0.065 -10000 0 -0.47 9 9
Insulin Receptor/Insulin/IRS1 0.035 0.053 -10000 0 -0.29 12 12
CSF1/CSF1R -0.023 0.13 -10000 0 -0.37 36 36
Ras protein signal transduction 0.024 0.12 0.58 21 -10000 0 21
IRS1 0.014 0.074 -10000 0 -0.46 12 12
INS 0.012 0.019 0.29 1 -10000 0 1
LEP -0.008 0.1 -10000 0 -0.46 25 25
STAT5B -0.028 0.13 0.3 1 -0.38 38 39
STAT5A -0.028 0.13 0.3 1 -0.38 38 39
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.02 0.1 -10000 0 -0.33 27 27
CSN2 0.009 0.079 -10000 0 -0.53 3 3
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
LAT 0.005 0.093 -10000 0 -0.51 13 13
YBX1 0.028 0.026 -10000 0 -0.37 2 2
LCK 0.023 0.038 -10000 0 -0.46 3 3
SHC1 0.022 0.01 -10000 0 -10000 0 0
NOX4 0.024 0.029 0.29 2 -0.47 1 3
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.002 0.041 -10000 0 -10000 0 0
BIRC5 0.19 0.13 0.29 309 -10000 0 309
NFKBIA -0.01 0.036 0.27 3 -10000 0 3
CPEB1 -0.054 0.18 -10000 0 -0.46 81 81
AKT1 -0.01 0.038 0.28 3 -10000 0 3
NDEL1 0.024 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.001 0.036 -10000 0 -10000 0 0
NDEL1/TACC3 0.02 0.059 0.26 8 -10000 0 8
GADD45A 0.026 0.003 -10000 0 -10000 0 0
GSK3B -0.006 0.029 -10000 0 -10000 0 0
PAK1/Aurora A -0.001 0.041 -10000 0 -10000 0 0
MDM2 0.026 0.003 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.075 0.082 0.28 31 -10000 0 31
TP53 0 0.048 -10000 0 -0.22 18 18
DLG7 -0.01 0.027 0.15 2 -10000 0 2
AURKAIP1 0.025 0.005 -10000 0 -10000 0 0
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.021 0.062 0.28 8 -10000 0 8
G2/M transition of mitotic cell cycle -0.001 0.036 -10000 0 -10000 0 0
AURKA -0.01 0.037 0.19 2 -10000 0 2
AURKB 0.11 0.066 0.17 236 -10000 0 236
CDC25B 0 0.027 -10000 0 -10000 0 0
G2/M transition checkpoint -0.01 0.025 -10000 0 -10000 0 0
mRNA polyadenylation -0.042 0.098 -10000 0 -0.26 77 77
Aurora A/CPEB -0.042 0.099 -10000 0 -0.26 77 77
Aurora A/TACC1/TRAP/chTOG -0.024 0.1 -10000 0 -0.25 69 69
BRCA1 0.025 0.006 -10000 0 -10000 0 0
centrosome duplication -0.001 0.041 -10000 0 -10000 0 0
regulation of centrosome cycle 0.019 0.057 0.26 8 -10000 0 8
spindle assembly -0.025 0.1 -10000 0 -0.25 69 69
TDRD7 0.024 0.023 -10000 0 -0.46 1 1
Aurora A/RasGAP/Survivin 0.12 0.088 0.26 25 -0.2 4 29
CENPA 0.11 0.071 0.18 238 -10000 0 238
Aurora A/PP2A -0.002 0.041 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.001 0.031 0.19 2 -10000 0 2
negative regulation of DNA binding -0.002 0.05 -10000 0 -0.22 18 18
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.035 0.012 -10000 0 -10000 0 0
RASA1 0.021 0.048 -10000 0 -0.46 5 5
Ajuba/Aurora A -0.01 0.025 -10000 0 -10000 0 0
mitotic prometaphase -0.019 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.037 0.19 2 -10000 0 2
TACC1 -0.056 0.18 -10000 0 -0.46 83 83
TACC3 0.039 0.061 0.29 28 -10000 0 28
Aurora A/Antizyme1 0.01 0.047 -10000 0 -10000 0 0
Aurora A/RasGAP -0.003 0.05 -10000 0 -0.3 5 5
OAZ1 0.024 0.007 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.005 0.028 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.075 0.082 0.28 31 -10000 0 31
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.044 0.064 0.24 14 -10000 0 14
PAK1 0.026 0.004 -10000 0 -10000 0 0
CKAP5 0.025 0.006 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0 0.11 0.22 2 -0.33 51 53
AKT1 -0.025 0.17 0.37 4 -0.56 33 37
PTK2B -0.042 0.16 -10000 0 -0.59 30 30
VEGFR2 homodimer/Frs2 -0.013 0.16 -10000 0 -0.48 44 44
CAV1 -0.2 0.24 -10000 0 -0.46 239 239
CALM1 0.025 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.005 0.15 -10000 0 -0.47 40 40
endothelial cell proliferation -0.036 0.17 0.35 8 -0.47 46 54
mol:Ca2+ -0.043 0.16 -10000 0 -0.6 30 30
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.017 0.15 -10000 0 -0.58 25 25
RP11-342D11.1 -0.051 0.16 -10000 0 -0.6 30 30
CDH5 0.017 0.057 -10000 0 -0.46 7 7
VEGFA homodimer 0.05 0.033 -10000 0 -0.26 1 1
SHC1 0.022 0.01 -10000 0 -10000 0 0
SHC2 0.022 0.047 0.29 2 -0.46 4 6
HRAS/GDP -0.019 0.14 -10000 0 -0.52 29 29
SH2D2A 0.027 0.039 0.29 10 -10000 0 10
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.005 0.16 -10000 0 -0.48 36 36
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.15 -10000 0 -0.46 40 40
VEGFR1 homodimer 0.024 0.022 -10000 0 -0.46 1 1
SHC/GRB2/SOS1 -0.007 0.17 -10000 0 -0.59 28 28
GRB10 -0.043 0.17 -10000 0 -0.62 30 30
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
PAK1 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.022 0.16 -10000 0 -0.61 25 25
HRAS 0.025 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.017 0.11 -10000 0 -0.39 30 30
HIF1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.015 0.15 -10000 0 -0.57 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.061 -10000 0 -0.46 8 8
Nck/Pak 0.035 0.025 -10000 0 -0.33 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.005 0.15 -10000 0 -0.46 41 41
mol:GDP -0.015 0.16 -10000 0 -0.56 29 29
mol:NADP -0.015 0.14 0.38 4 -0.42 35 39
eNOS/Hsp90 -0.005 0.13 0.37 4 -0.4 33 37
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.044 0.16 -10000 0 -0.61 30 30
HIF1A/ARNT 0.03 0.017 -10000 0 -10000 0 0
SHB 0.025 0.005 -10000 0 -10000 0 0
VEGFA 0.026 0.006 -10000 0 -10000 0 0
VEGFC 0.022 0.038 -10000 0 -0.46 3 3
FAK1/Vinculin -0.022 0.18 0.33 1 -0.62 31 32
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.01 0.18 -10000 0 -0.61 30 30
PTPN6 0.026 0.005 -10000 0 -10000 0 0
EPAS1 -0.013 0.15 -10000 0 -0.46 46 46
mol:L-citrulline -0.015 0.14 0.38 4 -0.42 35 39
ITGAV 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.018 0.14 -10000 0 -0.56 25 25
VEGFR2 homodimer/VEGFA homodimer -0.023 0.19 -10000 0 -0.66 30 30
VEGFR2/3 heterodimer -0.018 0.16 -10000 0 -0.47 50 50
VEGFB 0.026 0.005 -10000 0 -10000 0 0
MAPK11 -0.06 0.17 0.44 1 -0.6 35 36
VEGFR2 homodimer -0.031 0.17 -10000 0 -0.54 45 45
FLT1 0.024 0.022 -10000 0 -0.46 1 1
NEDD4 -0.028 0.15 -10000 0 -0.46 56 56
MAPK3 -0.059 0.16 0.35 5 -0.51 41 46
MAPK1 -0.061 0.16 0.35 5 -0.52 40 45
VEGFA145/NRP2 0.035 0.037 -10000 0 -0.33 5 5
VEGFR1/2 heterodimer -0.014 0.16 -10000 0 -0.48 44 44
KDR -0.031 0.17 -10000 0 -0.54 45 45
VEGFA165/NRP1/VEGFR2 homodimer -0.02 0.18 -10000 0 -0.62 30 30
SRC 0.025 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.062 0.17 0.39 4 -0.52 42 46
PI3K -0.029 0.17 -10000 0 -0.62 30 30
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.15 -10000 0 -0.46 41 41
FES -0.044 0.17 -10000 0 -0.62 30 30
GAB1 -0.013 0.18 -10000 0 -0.62 32 32
VEGFR2 homodimer/VEGFA homodimer/Src 0.004 0.15 -10000 0 -0.46 40 40
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.021 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.097 0.17 0.41 1 -0.41 70 71
VEGFR2 homodimer/VEGFA homodimer/Yes 0.005 0.15 -10000 0 -0.48 38 38
PI3K/GAB1 -0.009 0.16 -10000 0 -0.55 31 31
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.03 0.14 -10000 0 -0.55 25 25
PRKACA 0.025 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.005 0.16 -10000 0 -0.43 52 52
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 -0.044 0.17 -10000 0 -0.62 30 30
actin cytoskeleton reorganization 0 0.15 -10000 0 -0.46 40 40
PTK2 -0.039 0.18 0.39 1 -0.67 31 32
EDG1 -0.051 0.16 -10000 0 -0.6 30 30
mol:DAG -0.044 0.16 -10000 0 -0.61 30 30
CaM/Ca2+ -0.028 0.16 -10000 0 -0.57 30 30
MAP2K3 -0.062 0.15 -10000 0 -0.58 31 31
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.02 0.18 -10000 0 -0.65 30 30
PLCG1 -0.044 0.17 -10000 0 -0.62 30 30
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.016 0.15 -10000 0 -0.57 25 25
IQGAP1 0.025 0.022 -10000 0 -0.46 1 1
YES1 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.004 0.15 -10000 0 -0.46 41 41
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.005 0.15 -10000 0 -0.47 40 40
cell migration -0.017 0.16 0.28 1 -0.55 31 32
mol:PI-3-4-5-P3 -0.026 0.16 -10000 0 -0.56 31 31
FYN 0.026 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 -0.034 0.16 -10000 0 -0.57 30 30
mol:NO -0.015 0.14 0.38 4 -0.42 35 39
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.031 0.14 -10000 0 -0.52 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.028 0.18 -10000 0 -0.64 30 30
VHL 0.025 0.022 -10000 0 -0.46 1 1
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
NOS3 -0.02 0.15 0.38 4 -0.47 35 39
VEGFR2 homodimer/VEGFA homodimer/Sck 0.001 0.15 -10000 0 -0.45 44 44
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.062 0.15 -10000 0 -0.58 31 31
PRKCB -0.081 0.17 -10000 0 -0.55 42 42
VCL 0.025 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.17 -10000 0 -0.6 30 30
VEGFR1/2 heterodimer/VEGFA homodimer 0.003 0.15 -10000 0 -0.47 40 40
VEGFA165/NRP2 0.035 0.037 -10000 0 -0.33 5 5
MAPKKK cascade -0.001 0.16 0.34 1 -0.55 28 29
NRP2 0.021 0.048 -10000 0 -0.46 5 5
VEGFC homodimer 0.022 0.038 -10000 0 -0.46 3 3
NCK1 0.023 0.031 -10000 0 -0.46 2 2
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.021 0.18 0.35 2 -0.61 31 33
MAP3K13 -0.048 0.17 -10000 0 -0.6 32 32
PDPK1 -0.034 0.14 -10000 0 -0.53 30 30
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.022 0.094 -10000 0 -0.41 16 16
Syndecan-4/Syndesmos 0.059 0.11 0.39 3 -0.5 6 9
positive regulation of JNK cascade -0.02 0.16 0.38 3 -0.51 11 14
Syndecan-4/ADAM12 0.062 0.11 0.37 3 -0.5 6 9
CCL5 0.023 0.048 0.29 3 -0.46 4 7
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.024 0.007 -10000 0 -10000 0 0
ITGA5 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.008 -10000 0 -10000 0 0
PLG 0.033 0.066 0.29 29 -10000 0 29
ADAM12 0.029 0.031 0.29 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.015 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.075 0.13 0.41 10 -0.52 5 15
Syndecan-4/CXCL12/CXCR4 -0.02 0.16 0.39 3 -0.54 11 14
Syndecan-4/Laminin alpha3 0.05 0.12 0.39 3 -0.56 4 7
MDK 0.14 0.13 0.29 223 -10000 0 223
Syndecan-4/FZD7 0.039 0.13 0.35 2 -0.51 6 8
Syndecan-4/Midkine 0.13 0.14 0.41 21 -0.53 5 26
FZD7 -0.028 0.15 -10000 0 -0.46 56 56
Syndecan-4/FGFR1/FGF -0.008 0.14 0.44 1 -0.48 10 11
THBS1 -0.04 0.16 -10000 0 -0.46 68 68
integrin-mediated signaling pathway 0.053 0.11 0.35 2 -0.48 6 8
positive regulation of MAPKKK cascade -0.02 0.16 0.38 3 -0.51 11 14
Syndecan-4/TACI 0.058 0.11 0.42 4 -0.51 6 10
CXCR4 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0.009 0.053 0.19 10 -0.23 18 28
Syndecan-4/Dynamin 0.057 0.11 0.39 3 -0.48 6 9
Syndecan-4/TSP1 0.031 0.13 0.42 2 -0.47 12 14
Syndecan-4/GIPC 0.057 0.11 0.42 2 -0.48 6 8
Syndecan-4/RANTES 0.059 0.11 0.37 3 -0.5 6 9
ITGB1 0.025 0.005 -10000 0 -10000 0 0
LAMA1 0.047 0.12 0.29 62 -0.46 11 73
LAMA3 -0.001 0.11 -10000 0 -0.46 27 27
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.012 0.12 0.7 10 -0.44 11 21
Syndecan-4/alpha-Actinin 0.061 0.11 0.39 3 -0.51 6 9
TFPI -0.16 0.24 -10000 0 -0.46 198 198
F2 0.052 0.085 0.3 51 -10000 0 51
alpha5/beta1 Integrin 0.037 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.049 0.12 0.4 6 -0.52 5 11
ACTN1 0.026 0.005 -10000 0 -10000 0 0
TNC 0.012 0.081 0.29 1 -0.46 14 15
Syndecan-4/CXCL12 -0.021 0.16 0.39 3 -0.56 11 14
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
CXCL12 -0.16 0.24 -10000 0 -0.46 193 193
TNFRSF13B 0.025 0.03 0.29 6 -10000 0 6
FGF2 -0.13 0.23 -10000 0 -0.46 163 163
FGFR1 0.024 0.008 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.037 0.1 0.3 5 -0.5 6 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.074 -10000 0 -0.45 12 12
cell migration -0.019 0.011 -10000 0 -10000 0 0
PRKCD 0.02 0.019 -10000 0 -10000 0 0
vasculogenesis 0.031 0.13 0.41 2 -0.45 12 14
SDC4 0.046 0.099 0.32 7 -0.5 5 12
Syndecan-4/Tenascin C 0.054 0.11 0.35 2 -0.5 6 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.056 0.1 0.39 3 -0.53 5 8
MMP9 0.061 0.096 0.29 70 -0.47 1 71
Rac1/GTP 0.009 0.054 0.19 10 -0.23 18 28
cytoskeleton organization 0.058 0.11 0.39 3 -0.48 6 9
GIPC1 0.025 0.007 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.022 0.16 -10000 0 -0.48 16 16
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.011 0.026 -10000 0 -10000 0 0
HSPA8 0.026 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.13 0.11 0.27 4 -0.34 4 8
AKT1 0.015 0.035 -10000 0 -10000 0 0
GSC 0.095 0.14 0.49 2 -0.44 1 3
NKX2-5 0.048 0.088 0.28 57 -0.16 1 58
muscle cell differentiation -0.02 0.095 0.37 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.056 0.097 -10000 0 -0.34 4 4
SMAD4 0.014 0.049 -10000 0 -0.25 2 2
CBFB 0.023 0.009 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.033 0.053 0.22 11 -0.28 1 12
SMAD3/SMAD4/VDR 0.044 0.072 -10000 0 -0.26 11 11
MYC 0.017 0.076 -10000 0 -0.44 12 12
CDKN2B -0.13 0.39 -10000 0 -1.2 59 59
AP1 -0.03 0.13 -10000 0 -0.25 106 106
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.028 0.074 -10000 0 -0.43 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.014 0.11 0.24 1 -0.3 40 41
SP3 0.027 0.003 -10000 0 -10000 0 0
CREB1 0.026 0.003 -10000 0 -10000 0 0
FOXH1 0.066 0.095 0.3 67 -10000 0 67
SMAD3/SMAD4/GR -0.093 0.17 -10000 0 -0.3 185 185
GATA3 -0.073 0.2 -10000 0 -0.45 106 106
SKI/SIN3/HDAC complex/NCoR1 0.019 0.072 -10000 0 -0.45 8 8
MEF2C/TIF2 0.015 0.12 0.32 1 -0.44 18 19
endothelial cell migration 0.02 0.29 1.2 29 -10000 0 29
MAX 0.027 0.012 -10000 0 -10000 0 0
RBBP7 0.026 0.004 -10000 0 -10000 0 0
RBBP4 0.023 0.038 -10000 0 -0.46 3 3
RUNX2 0.022 0.043 -10000 0 -0.46 4 4
RUNX3 0.016 0.072 0.29 1 -0.46 11 12
RUNX1 0.022 0.043 -10000 0 -0.46 4 4
CTBP1 0.025 0.005 -10000 0 -10000 0 0
NR3C1 -0.15 0.24 -10000 0 -0.46 189 189
VDR 0.017 0.064 -10000 0 -0.46 9 9
CDKN1A -0.005 0.12 -10000 0 -1 5 5
KAT2B 0.002 0.098 -10000 0 -0.46 21 21
SMAD2/SMAD2/SMAD4/FOXH1 0.089 0.1 0.34 19 -0.23 2 21
DCP1A 0.025 0.005 -10000 0 -10000 0 0
SKI 0.026 0.005 -10000 0 -10000 0 0
SERPINE1 -0.021 0.29 -10000 0 -1.2 29 29
SMAD3/SMAD4/ATF2 0.024 0.074 -10000 0 -0.35 7 7
SMAD3/SMAD4/ATF3 -0.001 0.1 -10000 0 -0.31 39 39
SAP30 0.026 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.026 0.047 -10000 0 -10000 0 0
JUN -0.039 0.12 -10000 0 -0.26 69 69
SMAD3/SMAD4/IRF7 0.029 0.07 0.46 1 -0.29 4 5
TFE3 0.024 0.022 -10000 0 -10000 0 0
COL1A2 -0.001 0.039 -10000 0 -0.7 1 1
mesenchymal cell differentiation -0.024 0.073 0.33 7 -10000 0 7
DLX1 0.041 0.068 0.29 35 -10000 0 35
TCF3 0.024 0.007 -10000 0 -10000 0 0
FOS -0.096 0.22 -10000 0 -0.46 128 128
SMAD3/SMAD4/Max 0.03 0.068 -10000 0 -0.27 4 4
Cbp/p300/SNIP1 0.042 0.026 -10000 0 -10000 0 0
ZBTB17 0.03 0.02 -10000 0 -10000 0 0
LAMC1 0.004 0.048 -10000 0 -0.28 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.026 0.063 -10000 0 -0.28 3 3
IRF7 0.029 0.028 0.3 5 -10000 0 5
ESR1 0.18 0.14 0.29 311 -0.46 2 313
HNF4A 0.037 0.089 0.29 38 -0.46 6 44
MEF2C 0.031 0.12 0.35 6 -0.43 20 26
SMAD2-3/SMAD4 0.032 0.085 -10000 0 -0.3 5 5
Cbp/p300/Src-1 0.038 0.033 -10000 0 -0.27 1 1
IGHV3OR16-13 0.007 0.031 -10000 0 -0.33 3 3
TGIF2/HDAC complex 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.013 0.023 -10000 0 -10000 0 0
SKIL 0.022 0.031 -10000 0 -0.46 2 2
HDAC1 0.026 0.004 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.027 0.005 -10000 0 -10000 0 0
GCN5L2 -0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.03 0.07 -10000 0 -0.3 4 4
MSG1/HSC70 0.044 0.038 0.22 17 -0.33 1 18
SMAD2 0.023 0.042 -10000 0 -10000 0 0
SMAD3 0.004 0.059 -10000 0 -0.39 5 5
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.04 -10000 0 -0.24 4 4
SMAD2/SMAD2/SMAD4 -0.016 0.079 0.2 1 -0.29 27 28
NCOR1 0.024 0.008 -10000 0 -10000 0 0
NCOA2 -0.017 0.14 -10000 0 -0.46 43 43
NCOA1 0.025 0.022 -10000 0 -0.46 1 1
MYOD/E2A 0.037 0.034 0.22 16 -10000 0 16
SMAD2-3/SMAD4/SP1/MIZ-1 0.063 0.099 -10000 0 -0.32 4 4
IFNB1 0.003 0.054 0.3 5 -0.27 3 8
SMAD3/SMAD4/MEF2C 0.043 0.13 0.3 1 -0.44 18 19
CITED1 0.035 0.055 0.29 19 -0.46 1 20
SMAD2-3/SMAD4/ARC105 0.05 0.081 -10000 0 -0.28 4 4
RBL1 0.025 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.029 0.17 -10000 0 -0.5 54 54
RUNX1-3/PEBPB2 0.038 0.057 -10000 0 -0.28 14 14
SMAD7 -0.024 0.14 -10000 0 -0.52 14 14
MYC/MIZ-1 0.034 0.068 0.19 2 -0.3 11 13
SMAD3/SMAD4 -0.043 0.14 -10000 0 -0.46 34 34
IL10 -0.037 0.12 0.29 6 -0.27 84 90
PIASy/HDAC complex 0.024 0.017 -10000 0 -10000 0 0
PIAS3 0.022 0.012 -10000 0 -10000 0 0
CDK2 0.015 0.021 -10000 0 -10000 0 0
IL5 -0.048 0.12 -10000 0 -0.27 102 102
CDK4 0.014 0.023 -10000 0 -10000 0 0
PIAS4 0.024 0.017 -10000 0 -10000 0 0
ATF3 -0.013 0.12 -10000 0 -0.46 36 36
SMAD3/SMAD4/SP1 0.034 0.076 -10000 0 -0.3 6 6
FOXG1 0.16 0.14 0.29 279 -10000 0 279
FOXO3 0.001 0.036 -10000 0 -10000 0 0
FOXO1 0 0.04 -10000 0 -0.41 1 1
FOXO4 0 0.043 -10000 0 -0.37 2 2
heart looping 0.031 0.12 0.34 6 -0.43 20 26
CEBPB 0.017 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.036 0.076 0.25 1 -0.31 3 4
MYOD1 0.03 0.052 0.29 19 -10000 0 19
SMAD3/SMAD4/HNF4 0.033 0.086 0.24 1 -0.29 9 10
SMAD3/SMAD4/GATA3 -0.035 0.15 -10000 0 -0.3 107 107
SnoN/SIN3/HDAC complex/NCoR1 0.022 0.031 -10000 0 -0.46 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.081 -10000 0 -0.26 15 15
SMAD3/SMAD4/SP1-3 0.055 0.073 -10000 0 -0.33 3 3
MED15 0.025 0.006 -10000 0 -10000 0 0
SP1 0.023 0.024 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.11 0.12 0.37 31 -0.27 10 41
ITGB5 0.009 0.057 -10000 0 -0.33 2 2
TGIF/SIN3/HDAC complex/CtBP 0.025 0.052 -10000 0 -0.45 3 3
SMAD3/SMAD4/AR -0.006 0.12 -10000 0 -0.3 55 55
AR -0.023 0.15 -10000 0 -0.46 51 51
negative regulation of cell growth 0.004 0.08 -10000 0 -0.33 8 8
SMAD3/SMAD4/MYOD 0.029 0.073 0.26 1 -0.29 4 5
E2F5 0.024 0.008 -10000 0 -10000 0 0
E2F4 0.023 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.1 0.09 0.32 16 -10000 0 16
SMAD2-3/SMAD4/FOXO1-3a-4 -0.012 0.12 -10000 0 -0.35 52 52
TFDP1 0.025 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.015 0.14 -10000 0 -0.25 85 85
SMAD3/SMAD4/RUNX2 0.024 0.073 -10000 0 -0.34 7 7
TGIF2 0.025 0.005 -10000 0 -10000 0 0
TGIF1 0.025 0.006 -10000 0 -10000 0 0
ATF2 0.022 0.043 -10000 0 -0.46 4 4
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.009 0.099 0.35 5 -0.32 17 22
TBX21 -0.068 0.32 0.77 4 -1.1 25 29
B2M 0.024 0.025 -10000 0 -0.46 1 1
TYK2 0.013 0.037 0.24 1 -10000 0 1
IL12RB1 0.005 0.074 0.24 3 -0.49 8 11
GADD45B -0.06 0.29 0.65 4 -0.8 35 39
IL12RB2 0.008 0.077 0.28 5 -0.46 9 14
GADD45G -0.053 0.28 0.76 2 -0.82 26 28
natural killer cell activation 0 0.023 0.22 1 -10000 0 1
RELB 0.025 0.005 -10000 0 -10000 0 0
RELA 0.026 0.003 -10000 0 -10000 0 0
IL18 0.01 0.072 -10000 0 -0.47 10 10
IL2RA 0.018 0.063 0.29 2 -0.46 8 10
IFNG 0.039 0.061 0.29 28 -10000 0 28
STAT3 (dimer) -0.056 0.26 0.6 4 -0.61 55 59
HLA-DRB5 0.004 0.076 0.28 3 -0.46 11 14
FASLG -0.034 0.3 0.76 6 -0.77 38 44
NF kappa B2 p52/RelB -0.058 0.28 -10000 0 -0.73 45 45
CD4 0.011 0.038 -10000 0 -0.46 2 2
SOCS1 0.024 0.022 -10000 0 -0.46 1 1
EntrezGene:6955 -0.006 0.013 -10000 0 -10000 0 0
CD3D 0.003 0.078 0.28 4 -0.46 11 15
CD3E 0.003 0.075 0.29 1 -0.46 11 12
CD3G -0.018 0.12 -10000 0 -0.47 31 31
IL12Rbeta2/JAK2 0.011 0.09 0.28 5 -0.34 20 25
CCL3 -0.055 0.29 0.77 4 -0.85 27 31
CCL4 -0.058 0.3 0.77 4 -0.79 40 44
HLA-A 0.026 0.02 0.29 2 -10000 0 2
IL18/IL18R 0.036 0.1 -10000 0 -0.35 22 22
NOS2 -0.17 0.48 0.72 5 -1.1 96 101
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.097 0.35 5 -0.31 17 22
IL1R1 -0.068 0.31 0.73 4 -0.98 28 32
IL4 0 0.039 0.28 1 -0.24 1 2
JAK2 0.002 0.08 0.24 1 -0.47 11 12
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.036 0.2 0.27 1 -0.72 28 29
RAB7A -0.039 0.25 0.7 2 -0.72 23 25
lysosomal transport -0.035 0.24 0.69 2 -0.68 23 25
FOS -0.28 0.55 0.56 3 -1.1 141 144
STAT4 (dimer) -0.028 0.27 0.62 4 -0.68 40 44
STAT5A (dimer) -0.046 0.3 0.65 7 -0.72 46 53
GZMA -0.065 0.31 0.8 4 -0.83 45 49
GZMB -0.051 0.3 0.8 4 -0.96 22 26
HLX 0.022 0.01 -10000 0 -10000 0 0
LCK -0.064 0.3 0.73 4 -0.77 48 52
TCR/CD3/MHC II/CD4 -0.05 0.17 -10000 0 -0.31 96 96
IL2/IL2R 0.054 0.064 0.37 1 -0.28 11 12
MAPK14 -0.057 0.3 0.65 4 -0.8 36 40
CCR5 -0.061 0.31 0.65 4 -0.76 50 54
IL1B -0.004 0.099 0.24 1 -0.48 18 19
STAT6 0.004 0.1 0.49 4 -0.4 2 6
STAT4 0.015 0.071 -10000 0 -0.46 11 11
STAT3 0.025 0.006 -10000 0 -10000 0 0
STAT1 0.026 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
NFKB2 0.025 0.006 -10000 0 -10000 0 0
IL12B 0.012 0.04 0.28 2 -10000 0 2
CD8A 0.013 0.086 0.29 3 -0.46 15 18
CD8B 0.025 0.085 0.29 17 -0.46 10 27
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.009 0.099 0.32 17 -0.34 5 22
IL2RB 0.024 0.023 -10000 0 -0.46 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.26 0.61 4 -0.65 36 40
IL2RG 0.023 0.045 0.29 1 -0.46 4 5
IL12 0.021 0.066 0.25 7 -0.33 4 11
STAT5A 0.025 0.006 -10000 0 -10000 0 0
CD247 0.008 0.039 -10000 0 -0.47 2 2
IL2 0.028 0.048 0.29 16 -10000 0 16
SPHK2 0.026 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.066 0.27 9 -0.47 4 13
IL12/IL12R/TYK2/JAK2 -0.067 0.34 0.8 5 -0.84 47 52
MAP2K3 -0.066 0.3 0.65 4 -0.8 41 45
RIPK2 0.024 0.008 -10000 0 -10000 0 0
MAP2K6 -0.056 0.29 0.65 4 -0.78 38 42
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.071 -10000 0 -0.46 10 10
IL18RAP 0.011 0.068 -10000 0 -0.46 9 9
IL12Rbeta1/TYK2 0.015 0.068 0.26 3 -0.37 7 10
EOMES -0.025 0.2 -10000 0 -0.91 22 22
STAT1 (dimer) -0.029 0.26 0.62 8 -0.62 40 48
T cell proliferation -0.025 0.23 0.52 5 -0.52 51 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.065 -10000 0 -0.46 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.057 0.24 -10000 0 -0.58 53 53
ATF2 -0.054 0.28 0.61 4 -0.74 36 40
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.053 -10000 0 -0.46 6 6
ANTXR2 0 0.11 -10000 0 -0.46 26 26
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.015 -10000 0 -0.065 29 29
monocyte activation -0.061 0.18 -10000 0 -0.39 104 104
MAP2K2 -0.033 0.16 -10000 0 -0.58 40 40
MAP2K1 -0.006 0.015 0.13 1 -0.094 2 3
MAP2K7 -0.006 0.013 -10000 0 -0.094 2 2
MAP2K6 -0.004 0.021 0.18 3 -0.094 2 5
CYAA -0.02 0.058 -10000 0 -0.25 29 29
MAP2K4 -0.006 0.016 -10000 0 -0.14 3 3
IL1B -0.02 0.076 0.2 8 -0.22 44 52
Channel 0.014 0.072 -10000 0 -0.27 29 29
NLRP1 -0.02 0.058 -10000 0 -0.24 32 32
CALM1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.064 -10000 0 -0.45 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.015 0.065 29 -10000 0 29
MAPK3 -0.006 0.015 0.13 1 -0.094 2 3
MAPK1 -0.007 0.017 -10000 0 -0.14 3 3
PGR 0.001 0.058 0.14 3 -0.26 18 21
PA/Cellular Receptors 0.014 0.079 -10000 0 -0.3 29 29
apoptosis -0.005 0.015 -10000 0 -0.065 29 29
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.014 0.068 -10000 0 -0.25 29 29
macrophage activation -0.009 0.017 0.12 1 -0.23 1 2
TNF 0.031 0.08 0.29 23 -0.46 7 30
VCAM1 -0.061 0.18 -10000 0 -0.4 104 104
platelet activation 0 0.064 -10000 0 -0.45 9 9
MAPKKK cascade 0.002 0.024 0.1 8 -0.12 6 14
IL18 -0.02 0.066 0.11 1 -0.22 36 37
negative regulation of macrophage activation -0.005 0.015 -10000 0 -0.065 29 29
LEF -0.005 0.015 -10000 0 -0.065 29 29
CASP1 -0.014 0.05 -10000 0 -0.13 57 57
mol:cAMP 0 0.064 -10000 0 -0.45 9 9
necrosis -0.005 0.015 -10000 0 -0.065 29 29
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.015 0.068 -10000 0 -0.25 29 29
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.008 -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 0.066 0.15 0.49 22 -0.38 1 23
IL27/IL27R/JAK1 -0.033 0.2 0.8 1 -0.83 5 6
TBX21 -0.045 0.17 0.49 7 -0.48 13 20
IL12B 0.025 0.014 0.29 1 -10000 0 1
IL12A 0.006 0.038 0.17 10 -0.33 4 14
IL6ST -0.17 0.24 -10000 0 -0.46 199 199
IL27RA/JAK1 0.01 0.12 -10000 0 -1.1 4 4
IL27 0.024 0.029 0.31 3 -10000 0 3
TYK2 0.025 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.056 0.13 0.44 2 -10000 0 2
T-helper 2 cell differentiation 0.066 0.15 0.49 22 -0.38 1 23
T cell proliferation during immune response 0.066 0.15 0.49 22 -0.38 1 23
MAPKKK cascade -0.066 0.15 0.38 1 -0.49 22 23
STAT3 0.025 0.006 -10000 0 -10000 0 0
STAT2 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.006 -10000 0 -10000 0 0
IL12RB1 0.018 0.062 0.3 1 -0.46 8 9
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.039 0.17 0.5 9 -0.46 15 24
IL27/IL27R/JAK2/TYK2 -0.066 0.15 0.38 1 -0.5 22 23
positive regulation of T cell mediated cytotoxicity -0.066 0.15 0.38 1 -0.49 22 23
STAT1 (dimer) -0.016 0.25 0.53 51 -0.62 9 60
JAK2 0.015 0.072 -10000 0 -0.46 11 11
JAK1 0.023 0.048 -10000 0 -0.46 5 5
STAT2 (dimer) -0.058 0.15 0.35 1 -0.48 20 21
T cell proliferation -0.12 0.18 0.35 1 -0.46 68 69
IL12/IL12R/TYK2/JAK2 0.001 0.18 -10000 0 -0.72 25 25
IL17A -0.057 0.13 0.44 2 -10000 0 2
mast cell activation 0.066 0.15 0.49 22 -0.38 1 23
IFNG -0.003 0.037 0.12 13 -0.1 10 23
T cell differentiation -0.003 0.007 0.016 3 -0.019 30 33
STAT3 (dimer) -0.06 0.16 0.35 1 -0.48 21 22
STAT5A (dimer) -0.06 0.16 0.35 1 -0.49 20 21
STAT4 (dimer) -0.066 0.16 0.35 1 -0.48 27 28
STAT4 0.015 0.071 -10000 0 -0.46 11 11
T cell activation -0.008 0.013 0.12 4 -10000 0 4
IL27R/JAK2/TYK2 -0.068 0.17 -10000 0 -0.76 7 7
GATA3 -0.22 0.5 0.65 13 -1.2 105 118
IL18 0 0.047 -10000 0 -0.33 10 10
positive regulation of mast cell cytokine production -0.059 0.15 0.34 1 -0.47 21 22
IL27/EBI3 0.041 0.042 0.3 8 -10000 0 8
IL27RA -0.004 0.12 -10000 0 -1.1 4 4
IL6 -0.1 0.22 0.29 1 -0.46 135 136
STAT5A 0.025 0.006 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0 0.053 0.44 4 -10000 0 4
IL1B -0.005 0.062 -10000 0 -0.33 18 18
EBI3 0.029 0.036 0.31 7 -10000 0 7
TNF 0.008 0.049 0.14 23 -0.33 7 30
TCGA08_rtk_signaling

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
PDGFRA -0.051 0.18 -10000 0 -0.46 80 80
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.013 0.13 -10000 0 -0.46 40 40
AKT -0.032 0.14 0.29 2 -0.31 81 83
FOXO3 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.022 -10000 0 -0.46 1 1
AKT3 -0.074 0.19 -10000 0 -0.46 100 100
FOXO4 0.024 0.031 -10000 0 -0.46 2 2
MET 0.003 0.1 -10000 0 -0.46 23 23
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PIK3CB 0.025 0.005 -10000 0 -10000 0 0
NRAS 0.023 0.037 -10000 0 -0.46 3 3
PIK3CG -0.054 0.18 0.29 1 -0.46 83 84
PIK3R3 0.026 0.004 -10000 0 -10000 0 0
PIK3R2 0.025 0.006 -10000 0 -10000 0 0
NF1 0.025 0.007 -10000 0 -10000 0 0
RAS -0.012 0.084 0.19 2 -0.18 87 89
ERBB2 0.023 0.023 -10000 0 -0.46 1 1
proliferation/survival/translation -0.008 0.087 0.2 40 -0.27 5 45
PI3K -0.008 0.087 0.23 8 -0.25 29 37
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
KRAS 0.026 0.005 -10000 0 -10000 0 0
FOXO 0.032 0.06 0.26 3 -10000 0 3
AKT2 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.003 0.14 0.3 9 -0.38 29 38
IKBKB 0.011 0.093 0.28 11 -0.3 12 23
AKT1 0.006 0.11 0.27 30 -0.23 18 48
IKBKG 0.009 0.086 0.27 4 -0.3 11 15
CALM1 -0.013 0.12 0.26 3 -0.41 22 25
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
MAP3K1 -0.009 0.18 0.33 8 -0.5 40 48
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.12 0.26 1 -0.43 22 23
DOK1 0.026 0.004 -10000 0 -10000 0 0
AP-1 -0.017 0.097 0.28 6 -0.24 28 34
LYN 0.023 0.023 -10000 0 -0.46 1 1
BLNK 0.019 0.053 -10000 0 -0.46 6 6
SHC1 0.022 0.01 -10000 0 -10000 0 0
BCR complex 0.008 0.12 0.23 12 -0.36 42 54
CD22 -0.049 0.16 0.24 3 -0.5 41 44
CAMK2G -0.004 0.12 0.27 6 -0.38 20 26
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
SHC/GRB2/SOS1 0.005 0.075 -10000 0 -0.28 26 26
GO:0007205 -0.016 0.12 0.26 1 -0.43 23 24
SYK 0.022 0.038 -10000 0 -0.46 3 3
ELK1 -0.014 0.12 0.28 3 -0.42 22 25
NFATC1 -0.006 0.14 0.29 7 -0.42 32 39
B-cell antigen/BCR complex 0.008 0.12 0.23 12 -0.36 42 54
PAG1/CSK 0.032 0.031 -10000 0 -0.33 3 3
NFKBIB 0.02 0.048 0.16 8 -0.13 18 26
HRAS -0.007 0.12 0.26 5 -0.38 24 29
NFKBIA 0.02 0.047 0.16 8 -0.12 16 24
NF-kappa-B/RelA/I kappa B beta 0.024 0.042 0.16 9 -0.14 1 10
RasGAP/Csk 0.03 0.1 0.36 1 -0.27 42 43
mol:GDP -0.016 0.12 0.25 1 -0.41 24 25
PTEN 0.025 0.007 -10000 0 -10000 0 0
CD79B 0.016 0.069 0.29 1 -0.46 10 11
NF-kappa-B/RelA/I kappa B alpha 0.024 0.042 0.16 9 -0.15 1 10
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.009 0.18 0.33 5 -0.48 40 45
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.011 0.12 0.26 1 -0.43 23 24
CSK 0.025 0.005 -10000 0 -10000 0 0
FOS -0.065 0.15 0.3 5 -0.39 47 52
CHUK 0.003 0.1 0.27 4 -0.34 22 26
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.007 0.12 -10000 0 -0.38 22 22
PTPN6 -0.045 0.15 0.24 2 -0.53 31 33
RELA 0.026 0.003 -10000 0 -10000 0 0
BCL2A1 0.019 0.029 0.15 2 -10000 0 2
VAV2 -0.005 0.15 0.26 1 -0.51 28 29
ubiquitin-dependent protein catabolic process 0.022 0.047 0.16 9 -0.12 20 29
BTK -0.038 0.24 -10000 0 -0.95 31 31
CD19 -0.02 0.14 0.25 4 -0.47 29 33
MAP4K1 0.025 0.025 0.29 1 -0.46 1 2
CD72 0.027 0.021 0.29 3 -10000 0 3
PAG1 0.021 0.038 -10000 0 -0.46 3 3
MAPK14 -0.002 0.16 0.31 9 -0.44 35 44
SH3BP5 -0.007 0.12 -10000 0 -0.46 34 34
PIK3AP1 -0.011 0.13 0.28 1 -0.44 23 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.017 0.16 0.24 1 -0.5 36 37
RAF1 -0.006 0.11 0.3 5 -0.37 22 27
RasGAP/p62DOK/SHIP 0.028 0.11 0.33 1 -0.28 43 44
CD79A -0.004 0.13 0.29 12 -0.46 37 49
re-entry into mitotic cell cycle -0.017 0.096 0.29 5 -0.24 29 34
RASA1 0.021 0.048 -10000 0 -0.46 5 5
MAPK3 -0.003 0.098 0.28 6 -0.34 15 21
MAPK1 -0.005 0.096 0.28 5 -0.35 14 19
CD72/SHP1 -0.013 0.17 0.32 8 -0.51 29 37
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 -0.005 0.16 0.34 10 -0.43 39 49
actin cytoskeleton organization -0.001 0.14 0.35 6 -0.44 28 34
NF-kappa-B/RelA 0.049 0.08 0.29 9 -0.2 6 15
Calcineurin 0.007 0.11 -10000 0 -0.4 16 16
PI3K -0.033 0.12 -10000 0 -0.43 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.003 0.13 0.3 1 -0.43 24 25
SOS1 0.026 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.038 0.25 0.41 1 -0.69 55 56
DAPP1 -0.063 0.28 -10000 0 -0.78 55 55
cytokine secretion -0.004 0.14 0.27 9 -0.39 32 41
mol:DAG -0.011 0.12 0.26 1 -0.43 23 24
PLCG2 0.02 0.038 -10000 0 -0.46 3 3
MAP2K1 -0.005 0.1 0.29 5 -0.35 19 24
B-cell antigen/BCR complex/FcgammaRIIB 0.015 0.11 0.38 1 -0.32 38 39
mol:PI-3-4-5-P3 -0.02 0.095 0.2 4 -0.31 21 25
ETS1 -0.008 0.11 0.3 3 -0.4 15 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.038 0.1 0.36 1 -0.28 39 40
B-cell antigen/BCR complex/LYN -0.025 0.14 0.26 1 -0.4 47 48
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.025 0.006 -10000 0 -10000 0 0
RAC1 -0.003 0.15 0.34 5 -0.48 26 31
B-cell antigen/BCR complex/LYN/SYK -0.018 0.16 0.35 2 -0.51 28 30
CARD11 -0.015 0.13 0.26 6 -0.42 26 32
FCGR2B 0.012 0.068 -10000 0 -0.46 10 10
PPP3CA 0.023 0.038 -10000 0 -0.46 3 3
BCL10 0.026 0.003 -10000 0 -10000 0 0
IKK complex 0.019 0.057 0.18 23 -0.12 11 34
PTPRC -0.012 0.12 -10000 0 -0.46 36 36
PDPK1 -0.002 0.091 0.24 23 -0.21 21 44
PPP3CB 0.025 0.006 -10000 0 -10000 0 0
PPP3CC 0.02 0.038 -10000 0 -0.46 3 3
POU2F2 0.018 0.034 0.17 5 -10000 0 5
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.055 -10000 0 -0.27 17 17
EPHB2 0.028 0.026 0.29 5 -10000 0 5
Syndecan-2/TACI 0.018 0.046 0.2 6 -0.27 10 16
LAMA1 0.047 0.12 0.29 62 -0.46 11 73
Syndecan-2/alpha2 ITGB1 -0.018 0.13 -10000 0 -0.26 103 103
HRAS 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.002 0.039 -10000 0 -0.27 10 10
ITGA5 0.026 0.004 -10000 0 -10000 0 0
BAX -0.004 0.04 -10000 0 -10000 0 0
EPB41 0.025 0.022 -10000 0 -0.46 1 1
positive regulation of cell-cell adhesion 0.017 0.038 -10000 0 -0.25 10 10
LAMA3 -0.001 0.11 -10000 0 -0.46 27 27
EZR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.083 0.2 -10000 0 -0.46 113 113
Syndecan-2/MMP2 0.014 0.055 -10000 0 -0.31 13 13
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.029 0.14 -10000 0 -0.33 89 89
dendrite morphogenesis 0.021 0.049 0.26 5 -0.27 10 15
Syndecan-2/GM-CSF 0.016 0.042 -10000 0 -0.28 10 10
determination of left/right symmetry 0.003 0.046 -10000 0 -0.32 10 10
Syndecan-2/PKC delta 0.018 0.043 -10000 0 -0.27 10 10
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.014 0.064 0.19 42 -0.25 10 52
MAPK1 0.012 0.064 0.19 39 -0.25 11 50
Syndecan-2/RACK1 0.029 0.041 -10000 0 -0.24 10 10
NF1 0.025 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.003 0.046 -10000 0 -0.32 10 10
ITGA2 -0.063 0.19 -10000 0 -0.46 92 92
MAPK8 -0.001 0.047 -10000 0 -0.27 15 15
Syndecan-2/alpha2/beta1 Integrin 0.006 0.13 0.31 5 -0.24 94 99
Syndecan-2/Kininogen 0.017 0.045 0.23 6 -0.28 8 14
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC 0.022 0.06 0.18 38 -0.23 10 48
Syndecan-2/CASK/Protein 4.1 0.016 0.04 -10000 0 -0.25 11 11
extracellular matrix organization 0.018 0.043 -10000 0 -0.27 10 10
actin cytoskeleton reorganization 0.014 0.054 -10000 0 -0.27 17 17
Syndecan-2/Caveolin-2/Ras -0.025 0.12 -10000 0 -0.26 99 99
Syndecan-2/Laminin alpha3 0.003 0.079 -10000 0 -0.29 33 33
Syndecan-2/RasGAP 0.036 0.051 -10000 0 -0.23 15 15
alpha5/beta1 Integrin 0.037 0.009 -10000 0 -10000 0 0
PRKCD 0.025 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.049 0.26 5 -0.27 10 15
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.047 -10000 0 -0.22 15 15
RHOA 0.025 0.005 -10000 0 -10000 0 0
SDCBP 0.024 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.025 0.03 0.29 6 -10000 0 6
RASA1 0.021 0.048 -10000 0 -0.46 5 5
alpha2/beta1 Integrin -0.029 0.14 -10000 0 -0.33 89 89
Syndecan-2/Synbindin 0.018 0.04 -10000 0 -0.27 9 9
TGFB1 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.021 0.062 0.19 41 -0.25 10 51
FN1 0.015 0.074 -10000 0 -0.46 12 12
Syndecan-2/IL8 0.015 0.063 0.2 7 -0.28 20 27
SDC2 0.003 0.046 -10000 0 -0.32 10 10
KNG1 0.021 0.043 0.29 6 -0.46 2 8
Syndecan-2/Neurofibromin 0.018 0.042 -10000 0 -0.27 10 10
TRAPPC4 0.025 0.006 -10000 0 -10000 0 0
CSF2 0.022 0.006 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.018 0.043 -10000 0 -0.27 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.039 -10000 0 -0.25 10 10
Syndecan-2/Ezrin 0.031 0.042 -10000 0 -0.25 10 10
PRKACA 0.02 0.059 0.19 36 -0.25 9 45
angiogenesis 0.015 0.063 0.2 7 -0.27 20 27
MMP2 0.016 0.061 -10000 0 -0.46 8 8
IL8 0.019 0.078 0.29 7 -0.46 11 18
calcineurin-NFAT signaling pathway 0.018 0.046 0.2 6 -0.27 10 16
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.14 0.23 0.29 2 -0.46 176 178
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.013 0.29 1 -10000 0 1
TCEB1 0.024 0.008 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.061 0.26 1 -0.25 15 16
HIF1A 0.011 0.054 -10000 0 -0.26 15 15
COPS5 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.062 0.036 -10000 0 -0.24 1 1
FIH (dimer) 0.025 0.006 -10000 0 -10000 0 0
CDKN2A 0.12 0.13 0.29 192 -10000 0 192
ARNT/IPAS -0.07 0.16 0.22 2 -0.33 137 139
HIF1AN 0.025 0.006 -10000 0 -10000 0 0
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.016 0.05 -10000 0 -0.26 12 12
CUL2 0.025 0.005 -10000 0 -10000 0 0
OS9 0.026 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.02 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.061 -10000 0 -0.26 16 16
PHD1-3/OS9 0.054 0.036 -10000 0 -0.26 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.046 0.059 -10000 0 -0.24 12 12
VHL 0.025 0.022 -10000 0 -0.46 1 1
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.057 -10000 0 -0.25 12 12
EGLN3 0.028 0.036 0.29 6 -0.46 1 7
EGLN2 0.026 0.005 -10000 0 -10000 0 0
EGLN1 0.022 0.01 -10000 0 -10000 0 0
TP53 0.024 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.023 0.098 -10000 0 -0.52 15 15
ARNT 0.021 0.011 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.025 0.007 -10000 0 -10000 0 0
HIF1A/p19ARF 0.087 0.095 0.26 30 -0.22 14 44
Coregulation of Androgen receptor activity

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
NRIP1 0.023 0.043 -10000 0 -0.46 4 4
SVIL 0.017 0.068 -10000 0 -0.46 10 10
ZNF318 0.023 0.011 -10000 0 -10000 0 0
JMJD2C 0.009 0.025 0.12 24 -10000 0 24
T-DHT/AR/Ubc9 -0.004 0.11 -10000 0 -0.3 53 53
CARM1 0.024 0.007 -10000 0 -10000 0 0
PRDX1 0.026 0.004 -10000 0 -10000 0 0
PELP1 0.024 0.008 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.024 0.009 -10000 0 -10000 0 0
PTK2B 0.021 0.032 -10000 0 -0.46 2 2
MED1 0.023 0.01 -10000 0 -10000 0 0
MAK 0.035 0.057 0.29 24 -10000 0 24
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.016 0.071 -10000 0 -0.46 11 11
GSN 0.025 0.023 -10000 0 -0.46 1 1
NCOA2 -0.017 0.14 -10000 0 -0.46 43 43
NCOA6 0.026 0.006 -10000 0 -10000 0 0
DNA-PK 0.042 0.023 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.026 0.006 -10000 0 -10000 0 0
cell proliferation 0.015 0.064 0.24 23 -0.48 2 25
XRCC5 0.025 0.008 -10000 0 -10000 0 0
UBE3A 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.03 0.13 -10000 0 -0.29 93 93
FHL2 0.003 0.088 -10000 0 -0.92 3 3
RANBP9 0.027 0.006 -10000 0 -10000 0 0
JMJD1A -0.011 0.05 -10000 0 -0.13 71 71
CDK6 -0.004 0.12 -10000 0 -0.46 31 31
TGFB1I1 0.024 0.031 -10000 0 -0.46 2 2
T-DHT/AR/CyclinD1 -0.005 0.12 -10000 0 -0.3 60 60
XRCC6 0.023 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.002 0.14 -10000 0 -0.26 98 98
CTDSP1 0.026 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.009 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
TCF4 0.019 0.049 -10000 0 -0.46 5 5
CDKN2A 0.12 0.13 0.29 192 -10000 0 192
SRF 0.028 0.014 -10000 0 -0.18 1 1
NKX3-1 -0.049 0.19 -10000 0 -0.55 48 48
KLK3 -0.005 0.062 -10000 0 -10000 0 0
TMF1 0.025 0.006 -10000 0 -10000 0 0
HNRNPA1 0.024 0.008 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 0.009 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.003 0.11 -10000 0 -0.28 57 57
AR -0.03 0.16 -10000 0 -0.48 51 51
UBA3 0.026 0.006 -10000 0 -10000 0 0
PATZ1 0.023 0.01 -10000 0 -10000 0 0
PAWR 0.026 0.003 -10000 0 -10000 0 0
PRKDC 0.023 0.01 -10000 0 -10000 0 0
PA2G4 0.024 0.009 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.001 0.1 -10000 0 -0.26 56 56
RPS6KA3 0.02 0.057 -10000 0 -0.46 7 7
T-DHT/AR/ARA70 -0.003 0.11 -10000 0 -0.29 57 57
LATS2 0.021 0.038 -10000 0 -0.46 3 3
T-DHT/AR/PRX1 -0.002 0.1 -10000 0 -0.26 57 57
Cyclin D3/CDK11 p58 0.019 0.003 -10000 0 -10000 0 0
VAV3 0.012 0.085 -10000 0 -0.46 16 16
KLK2 0.005 0.088 0.29 24 -0.39 4 28
CASP8 0.026 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.012 0.13 -10000 0 -0.29 79 79
TMPRSS2 -0.1 0.3 -10000 0 -0.88 64 64
CCND1 0.021 0.048 -10000 0 -0.46 5 5
PIAS1 0.027 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.003 0.024 -10000 0 -0.066 53 53
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.026 0.01 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.02 0.13 -10000 0 -0.31 76 76
CMTM2 0.024 0.022 0.29 3 -10000 0 3
SNURF -0.015 0.13 -10000 0 -0.46 39 39
ZMIZ1 0.015 0.047 -10000 0 -0.48 2 2
CCND3 0.026 0.004 -10000 0 -10000 0 0
TGIF1 0.023 0.01 -10000 0 -10000 0 0
FKBP4 0.027 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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 0.023 0.038 -10000 0 -0.46 3 3
alphaV beta3 Integrin 0 0.11 0.22 2 -0.33 51 53
PTK2 -0.025 0.13 -10000 0 -0.43 35 35
positive regulation of JNK cascade 0.001 0.096 -10000 0 -0.3 32 32
CDC42/GDP 0.009 0.14 -10000 0 -0.41 36 36
Rac1/GDP 0.007 0.14 0.32 1 -0.41 37 38
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.026 0.002 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.006 0.12 -10000 0 -0.37 32 32
nectin-3/I-afadin 0.014 0.089 -10000 0 -0.33 31 31
RAPGEF1 -0.005 0.13 0.34 2 -0.46 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0.14 -10000 0 -0.5 33 33
PDGFB-D/PDGFRB 0.023 0.037 -10000 0 -0.46 3 3
TLN1 -0.032 0.095 -10000 0 -0.33 39 39
Rap1/GTP -0.004 0.095 -10000 0 -0.32 32 32
IQGAP1 0.025 0.022 -10000 0 -0.46 1 1
Rap1/GTP/I-afadin 0.049 0.011 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.014 0.089 -10000 0 -0.33 31 31
PVR 0.025 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.007 0.16 0.34 1 -0.5 37 38
MLLT4 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PI3K 0.045 0.085 -10000 0 -0.26 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.005 0.11 -10000 0 -0.33 37 37
PVRL1 0.025 0.006 -10000 0 -10000 0 0
PVRL3 -0.004 0.12 -10000 0 -0.46 31 31
PVRL2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
CDH1 0.019 0.044 -10000 0 -0.46 4 4
CLDN1 0.015 0.074 0.29 3 -0.46 11 14
JAM-A/CLDN1 0.024 0.088 -10000 0 -0.27 35 35
SRC -0.018 0.16 -10000 0 -0.55 36 36
ITGB3 -0.023 0.15 0.29 2 -0.46 51 53
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
FARP2 -0.002 0.16 -10000 0 -0.49 33 33
RAC1 0.025 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.029 0.08 -10000 0 -0.28 30 30
nectin-1/I-afadin 0.036 0.011 -10000 0 -10000 0 0
nectin-2/I-afadin 0.036 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.017 -10000 0 -0.28 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.028 0.081 -10000 0 -0.28 31 31
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.016 -10000 0 -0.28 1 1
F11R 0.019 0.038 -10000 0 -0.46 3 3
positive regulation of filopodium formation 0.001 0.096 -10000 0 -0.3 32 32
alphaV/beta3 Integrin/Talin -0.027 0.14 0.47 1 -0.31 81 82
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.01 -10000 0 -10000 0 0
PIP5K1C -0.031 0.1 -10000 0 -0.28 66 66
VAV2 -0.017 0.18 -10000 0 -0.52 42 42
RAP1/GDP 0.015 0.13 0.31 1 -0.39 33 34
ITGAV 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.029 0.08 -10000 0 -0.28 30 30
nectin-3(dimer)/I-afadin/I-afadin 0.014 0.089 -10000 0 -0.33 31 31
Rac1/GTP -0.002 0.14 -10000 0 -0.4 37 37
PTPRM -0.03 0.12 -10000 0 -0.3 69 69
E-cadherin/beta catenin/alpha catenin 0.061 0.042 -10000 0 -0.24 4 4
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.004 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR 0.017 0.064 -10000 0 -0.46 9 9
Cbp/p300/PCAF 0.034 0.066 -10000 0 -0.28 20 20
EP300 0.025 0.007 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.078 -10000 0 -0.29 18 18
KAT2B 0.005 0.097 -10000 0 -0.46 21 21
MAPK14 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.011 0.074 0.32 1 -0.29 14 15
RAR alpha/9cRA/Cyclin H 0.045 0.086 -10000 0 -0.3 16 16
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.006 0.095 -10000 0 -0.33 23 23
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.025 0.076 -10000 0 -0.33 14 14
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.046 -10000 0 -0.33 9 9
RXRs/RARs/NRIP1/9cRA 0.03 0.14 0.32 4 -0.49 21 25
NCOA2 -0.017 0.14 -10000 0 -0.46 43 43
NCOA3 0.025 0.007 -10000 0 -10000 0 0
NCOA1 0.025 0.022 -10000 0 -0.46 1 1
VDR/VDR/DNA 0.017 0.064 -10000 0 -0.46 9 9
RARG 0.026 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.01 -10000 0 -10000 0 0
MAPK3 0.025 0.007 -10000 0 -10000 0 0
MAPK1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 0.019 0.057 -10000 0 -0.46 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.046 0.12 0.3 1 -0.4 20 21
RARA 0.036 0.068 0.2 13 -0.27 10 23
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.11 -10000 0 -0.35 30 30
PRKCA 0.016 0.072 -10000 0 -0.46 11 11
RXRs/RARs/NRIP1/9cRA/HDAC1 0.037 0.15 0.32 2 -0.5 19 21
RXRG 0.03 0.12 0.24 28 -0.31 30 58
RXRA 0.03 0.064 0.21 10 -0.26 10 20
RXRB 0.051 0.079 0.24 12 -0.28 11 23
VDR/Vit D3/DNA 0.013 0.046 -10000 0 -0.33 9 9
RBP1 0.092 0.12 0.29 131 -0.46 1 132
CRBP1/9-cic-RA 0.064 0.08 0.2 131 -0.33 1 132
RARB 0.016 0.071 -10000 0 -0.46 11 11
PRKCG 0.1 0.12 0.29 152 -10000 0 152
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.13 0.28 1 -0.46 20 21
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.032 0.12 0.28 5 -0.39 21 26
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.11 0.24 10 -0.36 26 36
RXRs/RARs/NRIP1/9cRA/HDAC3 0.037 0.15 0.34 2 -0.5 20 22
positive regulation of DNA binding 0.031 0.076 -10000 0 -0.28 17 17
NRIP1 0.033 0.17 -10000 0 -0.88 8 8
RXRs/RARs 0.04 0.14 0.34 2 -0.44 25 27
RXRs/RXRs/DNA/9cRA 0.027 0.12 0.26 1 -0.39 20 21
PRKACA 0.025 0.006 -10000 0 -10000 0 0
CDK7 0.025 0.006 -10000 0 -10000 0 0
TFIIH 0.05 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.068 -10000 0 -0.29 6 6
CCNH 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.019 -10000 0 -10000 0 0
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.008 0.02 0.18 6 -10000 0 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.021 0.068 -10000 0 -0.33 18 18
STXBP1 0.007 0.092 -10000 0 -0.46 19 19
ACh/CHRNA1 0.036 0.07 0.21 56 -10000 0 56
RAB3GAP2/RIMS1/UNC13B 0.031 0.056 -10000 0 -0.28 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.094 -10000 0 -0.46 20 20
mol:ACh -0.003 0.035 0.087 22 -0.11 25 47
RAB3GAP2 0.022 0.01 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.01 0.077 -10000 0 -0.24 26 26
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.036 0.069 0.21 56 -10000 0 56
UNC13B 0.025 0.005 -10000 0 -10000 0 0
CHRNA1 0.055 0.083 0.29 57 -10000 0 57
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.012 0.096 0.24 4 -0.3 45 49
SNAP25 -0.007 0.058 0.1 4 -0.27 24 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.015 0.14 0.29 4 -0.46 45 49
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.012 0.06 0.2 2 -0.28 19 21
STX1A/SNAP25 fragment 1/VAMP2 0.01 0.077 -10000 0 -0.24 26 26
IGF1 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
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTK2 0.024 0.008 -10000 0 -10000 0 0
CRKL -0.004 0.071 0.16 1 -0.25 35 36
GRB2/SOS1/SHC 0.04 0.023 -10000 0 -10000 0 0
HRAS 0.025 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.005 0.074 -10000 0 -0.25 36 36
IGF-1R heterotetramer/IGF1/PTP1B 0.03 0.078 0.26 1 -0.28 25 26
AKT1 -0.012 0.081 0.22 2 -0.38 9 11
BAD -0.014 0.076 0.21 2 -0.36 9 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.004 0.071 0.16 1 -0.25 34 35
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.012 0.079 0.27 2 -0.25 37 39
RAF1 0 0.091 0.28 2 -0.38 14 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.037 0.081 -10000 0 -0.26 28 28
YWHAZ 0.024 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.013 0.083 0.18 5 -0.26 37 42
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
RPS6KB1 -0.014 0.077 0.22 2 -0.27 23 25
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.009 0.087 0.28 7 -0.32 10 17
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.036 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.011 0.06 -10000 0 -0.24 21 21
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.045 0.07 -10000 0 -0.23 21 21
IGF-1R heterotetramer 0.012 0.072 -10000 0 -0.49 9 9
IGF-1R heterotetramer/IGF1/IRS/Nck 0.027 0.083 -10000 0 -0.25 37 37
Crk/p130 Cas/Paxillin 0.031 0.079 -10000 0 -0.25 28 28
IGF1R 0.012 0.072 -10000 0 -0.49 9 9
IGF1 0.005 0.11 0.3 5 -0.48 21 26
IRS2/Crk -0.037 0.12 -10000 0 -0.26 105 105
PI3K 0.034 0.081 -10000 0 -0.28 24 24
apoptosis 0.011 0.073 0.33 7 -0.28 5 12
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
PRKCD -0.007 0.082 -10000 0 -0.32 28 28
RAF1/14-3-3 E 0.018 0.09 0.28 2 -0.34 13 15
BAD/14-3-3 -0.011 0.077 0.29 5 -0.35 7 12
PRKCZ -0.011 0.081 0.22 2 -0.38 9 11
Crk/p130 Cas/Paxillin/FAK1 0.016 0.067 -10000 0 -0.36 6 6
PTPN1 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.003 0.086 0.19 2 -0.32 30 32
BCAR1 0.023 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.036 0.072 0.26 1 -0.25 23 24
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
IRS1/NCK2 0.01 0.077 -10000 0 -0.25 37 37
GRB10 0.024 0.031 -10000 0 -0.46 2 2
PTPN11 -0.005 0.072 0.16 1 -0.25 37 38
IRS1 -0.005 0.078 -10000 0 -0.26 37 37
IRS2 -0.046 0.12 0.16 1 -0.27 106 107
IGF-1R heterotetramer/IGF1 0.014 0.098 0.22 5 -0.37 29 34
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.012 0.083 0.28 1 -0.29 23 24
YWHAE 0.024 0.007 -10000 0 -10000 0 0
PRKD1 -0.019 0.098 -10000 0 -0.33 31 31
SHC1 0.022 0.01 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.014 0.044 -10000 0 -0.32 8 8
CRKL 0.025 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DOCK1 0.02 0.048 -10000 0 -0.46 5 5
ITGA4 0.015 0.071 -10000 0 -0.46 11 11
alpha4/beta7 Integrin/MAdCAM1 0.063 0.07 -10000 0 -0.27 11 11
EPO 0.034 0.053 0.29 21 -10000 0 21
alpha4/beta7 Integrin 0.029 0.059 -10000 0 -0.36 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.052 -10000 0 -0.33 10 10
EPO/EPOR (dimer) 0.043 0.045 0.23 24 -10000 0 24
lamellipodium assembly 0.017 0.072 -10000 0 -0.4 8 8
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PI3K 0.031 0.031 -10000 0 -0.33 3 3
ARF6 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.018 0.064 0.22 2 -0.33 12 14
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
MADCAM1 0.044 0.072 0.29 40 -10000 0 40
cell adhesion 0.061 0.068 -10000 0 -0.27 11 11
CRKL/CBL 0.036 0.011 -10000 0 -10000 0 0
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC -0.033 0.12 -10000 0 -0.28 86 86
ITGB7 0.024 0.031 -10000 0 -0.46 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.017 0.14 -10000 0 -0.3 95 95
p130Cas/Crk/Dock1 -0.014 0.11 -10000 0 -0.24 80 80
VCAM1 -0.069 0.19 -10000 0 -0.46 99 99
RHOA 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.049 -10000 0 -0.26 10 10
BCAR1 -0.049 0.1 0.2 12 -0.26 85 97
EPOR 0.027 0.027 0.29 5 -10000 0 5
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.074 -10000 0 -0.42 8 8
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.042 0.29 13 -10000 0 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.023 0.023 -10000 0 -0.46 1 1
RAC1-CDC42/GTP/PAK family 0.009 0.03 -10000 0 -0.19 10 10
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
MAP3K12 0.025 0.022 -10000 0 -0.46 1 1
FGR 0.02 0.053 -10000 0 -0.46 6 6
p38 alpha/TAB1 -0.023 0.073 -10000 0 -0.3 22 22
PRKG1 -0.2 0.24 -10000 0 -0.46 239 239
DUSP8 0.021 0.043 -10000 0 -0.46 4 4
PGK/cGMP/p38 alpha -0.077 0.14 -10000 0 -0.32 54 54
apoptosis -0.022 0.07 -10000 0 -0.28 23 23
RAL/GTP 0.035 0.007 -10000 0 -10000 0 0
LYN 0.023 0.023 -10000 0 -0.46 1 1
DUSP1 -0.11 0.22 -10000 0 -0.46 138 138
PAK1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.025 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.058 0.024 -10000 0 -10000 0 0
TRAF6 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.009 -10000 0 -10000 0 0
MAPK11 0.026 0.1 0.27 8 -0.37 16 24
BLK 0.022 0.048 0.29 6 -0.46 3 9
HCK 0.022 0.038 -10000 0 -0.46 3 3
MAP2K3 0.024 0.007 -10000 0 -10000 0 0
DUSP16 0.025 0.022 -10000 0 -0.46 1 1
DUSP10 0.021 0.024 -10000 0 -0.46 1 1
TRAF6/MEKK3 0.031 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.1 0.24 9 -0.37 17 26
positive regulation of innate immune response 0.029 0.12 0.28 12 -0.44 16 28
LCK 0.023 0.038 -10000 0 -0.46 3 3
p38alpha-beta/MKP7 0.04 0.12 0.3 6 -0.44 15 21
p38alpha-beta/MKP5 0.03 0.11 0.32 6 -0.44 14 20
PGK/cGMP -0.15 0.17 -10000 0 -0.33 239 239
PAK2 0.024 0.008 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.016 0.15 0.31 4 -0.42 29 33
CDC42 0.025 0.005 -10000 0 -10000 0 0
RALB 0.026 0.003 -10000 0 -10000 0 0
RALA 0.026 0.004 -10000 0 -10000 0 0
PAK3 0.012 0.074 -10000 0 -0.46 12 12
Regulation of Telomerase

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
Telomerase catalytic core complex 0.13 0.16 0.48 4 -0.54 1 5
RAD9A 0.025 0.005 -10000 0 -10000 0 0
AP1 -0.047 0.16 -10000 0 -0.33 128 128
IFNAR2 0.034 0.025 -10000 0 -0.44 1 1
AKT1 0.073 0.052 0.23 17 -0.18 1 18
ER alpha/Oestrogen 0.13 0.092 0.2 311 -0.32 2 313
NFX1/SIN3/HDAC complex 0.03 0.063 0.19 1 -0.33 9 10
EGF -0.067 0.19 -10000 0 -0.45 99 99
SMG5 0.021 0.011 -10000 0 -10000 0 0
SMG6 0.024 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.053 0.023 -10000 0 -10000 0 0
TERT/c-Abl 0.12 0.14 -10000 0 -0.54 1 1
SAP18 0.027 0.007 -10000 0 -10000 0 0
MRN complex 0.045 0.024 -10000 0 -0.28 1 1
WT1 0.088 0.12 0.3 111 -0.45 3 114
WRN 0.023 0.009 -10000 0 -10000 0 0
SP1 0.039 0.018 -10000 0 -10000 0 0
SP3 0.03 0.007 -10000 0 -10000 0 0
TERF2IP 0.023 0.009 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.099 0.11 -10000 0 -0.48 1 1
Mad/Max 0.048 0.018 -10000 0 -10000 0 0
TERT 0.13 0.16 0.48 2 -0.55 1 3
CCND1 0.12 0.18 0.52 4 -0.92 6 10
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.024 0.038 -10000 0 -0.46 3 3
TERF2 0.021 0.011 -10000 0 -10000 0 0
PTGES3 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.006 -10000 0 -10000 0 0
Telomerase/911 0.061 0.054 0.27 4 -0.34 1 5
CDKN1B 0.012 0.1 -10000 0 -0.56 15 15
RAD1 0.025 0.005 -10000 0 -10000 0 0
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.025 0.007 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.033 0.015 -10000 0 -10000 0 0
UBE3A 0.029 0.008 -10000 0 -10000 0 0
JUN 0.028 0.031 -10000 0 -0.45 2 2
E6 0.004 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.027 0.014 -10000 0 -10000 0 0
FOS -0.093 0.21 -10000 0 -0.46 128 128
IFN-gamma/IRF1 0.052 0.073 0.23 28 -0.28 15 43
PARP2 0.026 0.005 -10000 0 -10000 0 0
BLM 0.027 0.021 0.29 3 -10000 0 3
Telomerase 0.071 0.093 0.27 5 -0.5 4 9
IRF1 0.027 0.035 -10000 0 -0.16 15 15
ESR1 0.19 0.14 0.29 311 -0.46 2 313
KU/TER 0.036 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.034 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.061 -10000 0 -0.3 9 9
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.034 0.062 -10000 0 -0.31 9 9
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.037 0.016 -10000 0 -10000 0 0
ATM 0.016 0.019 -10000 0 -10000 0 0
SMAD3 -0.003 0.03 -10000 0 -0.34 3 3
ABL1 0.025 0.007 -10000 0 -10000 0 0
MXD1 0.03 0.008 -10000 0 -10000 0 0
MRE11A 0.025 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.025 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.15 0.14 0.45 1 -0.5 1 2
NR2F2 0.004 0.039 -10000 0 -0.46 2 2
MAPK3 0.013 0.032 0.15 16 -10000 0 16
MAPK1 0.012 0.034 0.15 15 -0.32 1 16
TGFB1/TGF beta receptor Type II 0.022 0.01 -10000 0 -10000 0 0
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
HNRNPC 0.026 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.019 -10000 0 -10000 0 0
NBN 0.024 0.008 -10000 0 -10000 0 0
EGFR -0.01 0.13 -10000 0 -0.45 40 40
mol:Oestrogen 0.003 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.055 0.17 -10000 0 -0.34 129 129
MYC 0.015 0.075 -10000 0 -0.46 12 12
IL2 0.042 0.051 0.3 16 -10000 0 16
KU 0.036 0.01 -10000 0 -10000 0 0
RAD50 0.025 0.022 -10000 0 -0.46 1 1
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
TGFB1 0.022 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.034 0.019 0.21 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.13 0.14 -10000 0 -0.5 1 1
SP1/HDAC2 0.062 0.034 -10000 0 -10000 0 0
PINX1 0.023 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.095 0.11 -10000 0 -0.48 1 1
Smad3/Myc 0.001 0.055 -10000 0 -0.3 13 13
911 complex 0.049 0.016 -10000 0 -10000 0 0
IFNG 0.04 0.071 0.3 28 -0.17 15 43
Telomerase/PinX1 0.088 0.11 -10000 0 -0.48 1 1
Telomerase/AKT1/mTOR/p70S6K 0.085 0.087 0.29 12 -0.38 4 16
SIN3B 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.08 0.11 -10000 0 -0.48 1 1
response to DNA damage stimulus 0.005 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.058 0.035 -10000 0 -0.24 1 1
TRF2/WRN 0.031 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.098 0.11 -10000 0 -0.48 1 1
E2F1 0.046 0.056 0.29 23 -10000 0 23
ZNFX1 0.027 0.006 -10000 0 -10000 0 0
PIF1 0.12 0.13 0.29 188 -10000 0 188
NCL 0.026 0.004 -10000 0 -10000 0 0
DKC1 0.026 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.004 0.11 0.19 1 -0.26 76 77
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.023 0.16 9 -10000 0 9
GNB1/GNG2 0.016 0.073 0.2 1 -0.28 29 30
GNB1 0.025 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.015 0.085 -10000 0 -0.25 59 59
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 0.009 0.022 0.066 61 -10000 0 61
GNAL -0.031 0.16 -10000 0 -0.46 59 59
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
CRH 0.021 0.035 0.29 8 -10000 0 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.036 -10000 0 -0.3 7 7
MAPK11 0.006 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.045 0.073 -10000 0 -0.26 25 25
HDAC3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.034 0.008 -10000 0 -10000 0 0
GATA1/HDAC5 0.033 0.01 -10000 0 -10000 0 0
GATA2/HDAC5 0.034 0.036 0.22 2 -0.32 4 6
HDAC5/BCL6/BCoR 0.044 0.028 -10000 0 -0.28 2 2
HDAC9 0.025 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.075 0.16 -10000 0 -0.28 188 188
HDAC4/ANKRA2 0.037 0.01 -10000 0 -10000 0 0
HDAC5/YWHAB 0.035 0.012 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.005 -10000 0 -10000 0 0
GATA2 0.023 0.046 0.29 2 -0.46 4 6
HDAC4/RFXANK 0.038 0.022 0.22 6 -10000 0 6
BCOR 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.024 0.008 -10000 0 -10000 0 0
HDAC5 0.025 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.016 0.086 0.22 1 -0.33 29 30
Histones 0.02 0.039 -10000 0 -0.26 5 5
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
HDAC4 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.026 0.004 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.011 -10000 0 -10000 0 0
HDAC4/Ubc9 0.037 0.01 -10000 0 -10000 0 0
HDAC7 0.025 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.035 0.012 -10000 0 -10000 0 0
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
HDAC6 0.026 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.037 0.02 0.22 4 -10000 0 4
CAMK4 0.017 0.07 0.29 2 -0.46 10 12
Tubulin/HDAC6 0.049 0.027 -10000 0 -0.28 2 2
SUMO1 0.026 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.025 0.006 -10000 0 -10000 0 0
GATA1 0.021 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
NR3C1 -0.16 0.24 -10000 0 -0.46 189 189
SUMO1/HDAC4 0.03 0.044 -10000 0 -0.23 2 2
SRF 0.026 0.005 -10000 0 -10000 0 0
HDAC4/YWHAB 0.036 0.01 -10000 0 -10000 0 0
Tubulin 0.036 0.032 0.22 2 -0.33 3 5
HDAC4/14-3-3 E 0.036 0.012 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
RANGAP1 0.025 0.007 -10000 0 -10000 0 0
BCL6/BCoR 0.033 0.026 -10000 0 -0.33 2 2
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.013 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.048 -10000 0 -0.28 9 9
HDAC4/ER alpha 0.14 0.094 0.22 307 -0.32 2 309
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.02 0.039 -10000 0 -0.25 5 5
cell motility 0.049 0.027 -10000 0 -0.28 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.037 0.01 -10000 0 -10000 0 0
BCL6 0.022 0.031 -10000 0 -0.46 2 2
HDAC4/CaMK II delta B 0.026 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.037 0.01 -10000 0 -10000 0 0
ESR1 0.18 0.14 0.29 311 -0.46 2 313
HDAC6/HDAC11 0.036 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0.042 -10000 0 -0.23 1 1
NPC 0.016 0.002 -10000 0 -10000 0 0
MEF2C 0.002 0.1 -10000 0 -0.46 24 24
RAN 0.026 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.055 0.07 -10000 0 -0.24 23 23
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
NCOR2 0.026 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.041 0.29 2 -0.46 3 5
HDAC11 0.025 0.006 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RANBP2 0.026 0.003 -10000 0 -10000 0 0
ANKRA2 0.025 0.006 -10000 0 -10000 0 0
RFXANK 0.028 0.029 0.29 6 -10000 0 6
nuclear import -0.03 0.012 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.017 0.062 -10000 0 -0.57 4 4
oxygen homeostasis 0.009 0.015 -10000 0 -10000 0 0
TCEB2 0.026 0.013 0.29 1 -10000 0 1
TCEB1 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.076 0.12 0.35 5 -0.32 13 18
EPO 0.086 0.19 0.58 12 -0.54 7 19
FIH (dimer) 0.029 0.024 -10000 0 -10000 0 0
APEX1 0.03 0.03 -10000 0 -10000 0 0
SERPINE1 0.08 0.23 0.54 7 -0.56 25 32
FLT1 -0.007 0.18 -10000 0 -0.71 26 26
ADORA2A 0.11 0.2 0.48 23 -0.51 12 35
germ cell development 0.14 0.24 0.56 42 -0.58 10 52
SLC11A2 0.096 0.2 0.54 8 -0.52 13 21
BHLHE40 0.093 0.21 0.53 9 -0.53 13 22
HIF1AN 0.029 0.024 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.065 0.14 0.42 6 -0.38 11 17
ETS1 0.021 0.064 -10000 0 -0.43 8 8
CITED2 -0.024 0.24 -10000 0 -0.9 33 33
KDR -0.031 0.27 -10000 0 -1 31 31
PGK1 0.096 0.2 0.54 8 -0.52 13 21
SIRT1 0.025 0.022 -10000 0 -0.46 1 1
response to hypoxia 0.001 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.098 0.23 0.62 3 -0.6 13 16
EPAS1 0.045 0.12 0.28 24 -0.35 15 39
SP1 0.03 0.005 -10000 0 -10000 0 0
ABCG2 0.06 0.26 0.53 9 -0.53 48 57
EFNA1 0.067 0.18 0.6 2 -0.53 12 14
FXN 0.11 0.2 0.48 27 -0.5 13 40
POU5F1 0.14 0.24 0.57 41 -0.6 10 51
neuron apoptosis -0.096 0.22 0.58 13 -0.61 3 16
EP300 0.025 0.007 -10000 0 -10000 0 0
EGLN3 0.032 0.044 0.3 6 -0.46 1 7
EGLN2 0.029 0.025 -10000 0 -10000 0 0
EGLN1 0.025 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.025 0.21 1 -0.28 1 2
VHL 0.025 0.022 -10000 0 -0.46 1 1
ARNT 0.023 0.029 -10000 0 -10000 0 0
SLC2A1 0.12 0.21 0.48 33 -0.5 13 46
TWIST1 0.12 0.21 0.48 33 -0.51 14 47
ELK1 0.022 0.032 -10000 0 -0.13 3 3
HIF2A/ARNT/Cbp/p300 0.063 0.14 0.42 3 -0.37 12 15
VEGFA 0.094 0.2 0.53 8 -0.52 13 21
CREBBP 0.025 0.006 -10000 0 -10000 0 0
IL1-mediated 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
UBC13/UEV1A 0.058 0.079 0.22 82 -0.33 5 87
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.067 -10000 0 -0.25 23 23
IRAK/TOLLIP 0.036 0.045 0.2 4 -0.26 5 9
IKBKB 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.037 0.068 0.22 21 -0.36 10 31
IL1A 0.022 0.065 0.29 7 -0.46 7 14
IL1B -0.014 0.1 -10000 0 -0.41 30 30
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.051 -10000 0 -0.23 5 5
IL1R2 0.029 0.065 0.29 14 -0.46 5 19
IL1R1 0.018 0.061 -10000 0 -0.46 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.04 0.092 0.27 10 -0.31 9 19
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.018 0.057 -10000 0 -0.46 7 7
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.057 0.28 3 -10000 0 3
JUN 0 0.061 0.29 4 -0.24 7 11
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.1 -10000 0 -0.31 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88 0.048 0.071 -10000 0 -0.28 17 17
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.057 0.071 -10000 0 -0.27 17 17
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.098 -10000 0 -0.31 38 38
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MAPK8 0.004 0.063 0.31 4 -0.22 11 15
IRAK1 0.01 0.054 0.22 4 -0.28 5 9
IL1RN/IL1R1 0.029 0.058 0.22 2 -0.33 12 14
IRAK4 0.026 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.008 -10000 0 -10000 0 0
TRAF6 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.031 0.031 -10000 0 -0.33 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.08 -10000 0 -0.3 20 20
CHUK 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.098 -10000 0 -0.31 38 38
IL1 beta/IL1R2 0.015 0.12 0.22 9 -0.38 32 41
IRAK/TRAF6/TAK1/TAB1/TAB2 0.04 0.039 -10000 0 -0.23 5 5
NF kappa B1 p50/RelA 0.019 0.094 -10000 0 -0.47 9 9
IRAK3 -0.098 0.21 -10000 0 -0.46 129 129
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.029 0.1 -10000 0 -0.29 43 43
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.058 -10000 0 -0.26 17 17
IL1 alpha/IL1R1/IL1RAP 0.036 0.072 -10000 0 -0.31 17 17
RELA 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.005 -10000 0 -10000 0 0
MYD88 0.026 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.052 0.049 -10000 0 -0.24 5 5
IL1RAP 0.017 0.057 -10000 0 -0.46 7 7
UBE2N 0.026 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.086 -10000 0 -0.34 13 13
CASP1 0.003 0.1 -10000 0 -0.46 23 23
IL1RN/IL1R2 0.037 0.057 0.22 16 -0.33 8 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.022 0.098 -10000 0 -0.3 38 38
TMEM189-UBE2V1 0.058 0.11 0.29 83 -0.46 5 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.021 0.074 -10000 0 -0.34 13 13
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
IL1RN 0.022 0.046 0.29 2 -0.46 4 6
TRAF6/TAK1/TAB1/TAB2 0.06 0.058 -10000 0 -0.23 5 5
MAP2K6 0.012 0.063 0.3 4 -0.22 5 9
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.018 0.029 -10000 0 -0.24 5 5
epithelial cell differentiation 0.046 0.033 -10000 0 -0.24 4 4
CYFIP2 0.023 0.037 -10000 0 -0.46 3 3
ENAH -0.002 0.057 0.28 9 -10000 0 9
EGFR -0.013 0.13 -10000 0 -0.46 40 40
EPHA2 0.025 0.005 -10000 0 -10000 0 0
MYO6 -0.01 0.031 -10000 0 -0.23 5 5
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.048 0.026 -10000 0 -0.28 2 2
AQP5 0.07 0.093 0.3 1 -0.41 7 8
CTNND1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.024 -10000 0 -0.23 4 4
regulation of calcium-dependent cell-cell adhesion -0.015 0.046 0.17 5 -0.24 15 20
EGF -0.07 0.19 -10000 0 -0.46 99 99
NCKAP1 0.026 0.003 -10000 0 -10000 0 0
AQP3 -0.097 0.19 -10000 0 -0.43 122 122
cortical microtubule organization 0.046 0.033 -10000 0 -0.24 4 4
GO:0000145 -0.011 0.023 -10000 0 -0.22 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.051 0.035 -10000 0 -0.24 4 4
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.017 0.024 -10000 0 -0.22 6 6
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.037 -10000 0 -0.26 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.003 0.022 -10000 0 -10000 0 0
PVRL2 0.025 0.005 -10000 0 -10000 0 0
ZYX -0.009 0.029 -10000 0 -0.23 4 4
ARF6/GTP 0.053 0.039 -10000 0 -0.24 2 2
CDH1 0.019 0.044 -10000 0 -0.46 4 4
EGFR/EGFR/EGF/EGF -0.034 0.13 -10000 0 -0.24 130 130
RhoA/GDP 0.046 0.033 -10000 0 -0.23 4 4
actin cytoskeleton organization -0.011 0.027 -10000 0 -0.23 5 5
IGF-1R heterotetramer 0.017 0.064 -10000 0 -0.46 9 9
GIT1 0.025 0.006 -10000 0 -10000 0 0
IGF1R 0.017 0.064 -10000 0 -0.46 9 9
IGF1 0.009 0.1 0.29 5 -0.46 21 26
DIAPH1 0.036 0.1 -10000 0 -0.52 9 9
Wnt receptor signaling pathway -0.046 0.033 0.24 4 -10000 0 4
RHOA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.024 -10000 0 -0.22 6 6
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.012 0.028 -10000 0 -0.23 5 5
EFNA1 0.022 0.016 0.29 1 -10000 0 1
LPP -0.011 0.024 -10000 0 -0.22 3 3
Ephrin A1/EPHA2 0.033 0.034 -10000 0 -0.23 4 4
SEC6/SEC8 -0.016 0.016 -10000 0 -0.22 2 2
MGAT3 -0.015 0.047 0.18 5 -0.25 15 20
HGF/MET -0.069 0.14 -10000 0 -0.24 199 199
HGF -0.16 0.24 -10000 0 -0.46 191 191
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.018 0.029 -10000 0 -0.25 5 5
actin cable formation 0.055 0.1 0.33 27 -0.24 1 28
KIAA1543 -0.012 0.038 -10000 0 -0.25 9 9
KIFC3 -0.011 0.028 -10000 0 -0.23 4 4
NCK1 0.023 0.031 -10000 0 -0.46 2 2
EXOC3 0.025 0.007 -10000 0 -10000 0 0
ACTN1 -0.01 0.028 -10000 0 -0.23 4 4
NCK1/GIT1 0.034 0.026 -10000 0 -0.33 2 2
mol:GDP 0.046 0.033 -10000 0 -0.24 4 4
EXOC4 0.025 0.006 -10000 0 -10000 0 0
STX4 -0.009 0.03 -10000 0 -0.23 4 4
PIP5K1C -0.011 0.025 -10000 0 -0.23 4 4
LIMA1 0.025 0.022 -10000 0 -0.46 1 1
ABI1 0.025 0.006 -10000 0 -10000 0 0
ROCK1 0.026 0.089 0.33 15 -10000 0 15
adherens junction assembly -0.04 0.14 -10000 0 -0.56 27 27
IGF-1R heterotetramer/IGF1 0.026 0.072 -10000 0 -0.23 32 32
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.01 -10000 0 -10000 0 0
MET 0.003 0.1 -10000 0 -0.46 23 23
PLEKHA7 -0.012 0.04 -10000 0 -0.26 9 9
mol:GTP 0.046 0.036 -10000 0 -0.26 2 2
establishment of epithelial cell apical/basal polarity 0.003 0.07 0.36 8 -10000 0 8
cortical actin cytoskeleton stabilization 0.018 0.029 -10000 0 -0.24 5 5
regulation of cell-cell adhesion -0.011 0.027 -10000 0 -0.23 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.018 0.029 -10000 0 -0.25 5 5
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0 0.11 -10000 0 -0.24 76 76
TC10/GTP 0.005 0.097 -10000 0 -0.22 71 71
Insulin Receptor/Insulin/IRS1/Shp2 0.051 0.054 0.24 1 -0.26 12 13
HRAS 0.025 0.006 -10000 0 -10000 0 0
APS homodimer 0.039 0.059 0.29 27 -10000 0 27
GRB14 0.027 0.11 0.29 34 -0.46 17 51
FOXO3 -0.027 0.17 -10000 0 -0.54 48 48
AKT1 -0.001 0.087 0.27 12 -0.41 2 14
INSR 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.051 0.035 0.35 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.031 -10000 0 -0.46 2 2
SORBS1 -0.051 0.18 -10000 0 -0.46 79 79
CRK 0.024 0.007 -10000 0 -10000 0 0
PTPN1 0 0.028 -10000 0 -10000 0 0
CAV1 -0.12 0.13 0.18 1 -0.25 237 238
CBL/APS/CAP/Crk-II/C3G 0.023 0.12 -10000 0 -0.24 75 75
Insulin Receptor/Insulin/IRS1/NCK2 0.051 0.054 0.24 1 -0.26 12 13
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.049 -10000 0 -0.23 13 13
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.005 0.087 -10000 0 -0.33 22 22
RPS6KB1 -0.006 0.078 0.26 11 -0.38 2 13
PARD6A 0.023 0.009 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.028 -10000 0 -0.56 1 1
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.026 0.065 -10000 0 -0.38 2 2
HRAS/GTP -0.016 0.033 -10000 0 -0.22 9 9
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.052 -10000 0 -0.25 7 7
PRKCI 0.011 0.068 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.015 0.064 -10000 0 -0.25 21 21
SHC1 0.022 0.01 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.038 0.05 -10000 0 -0.41 4 4
PI3K 0.045 0.053 -10000 0 -0.24 13 13
NCK2 0.026 0.003 -10000 0 -10000 0 0
RHOQ 0.026 0.004 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.004 -10000 0 -10000 0 0
AKT2 -0.003 0.084 0.29 10 -0.41 2 12
PRKCZ 0.01 0.07 -10000 0 -0.36 1 1
SH2B2 0.039 0.06 0.29 27 -10000 0 27
SHC/SHIP 0.017 0.044 -10000 0 -0.24 12 12
F2RL2 0.019 0.079 0.29 8 -0.46 11 19
TRIP10 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.036 0.024 0.22 1 -10000 0 1
TC10/GTP/CIP4/Exocyst 0.032 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.054 0.037 -10000 0 -10000 0 0
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
RASA1 0.021 0.048 -10000 0 -0.46 5 5
NCK1 0.023 0.031 -10000 0 -0.46 2 2
CBL/APS/CAP/Crk-II 0.013 0.12 -10000 0 -0.25 75 75
TC10/GDP 0.019 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.046 0.037 -10000 0 -0.27 2 2
INPP5D -0.015 0.047 -10000 0 -0.26 15 15
SOS1 0.026 0.004 -10000 0 -10000 0 0
SGK1 -0.066 0.24 -10000 0 -0.78 51 51
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.014 0.074 -10000 0 -0.46 12 12
p62DOK/RasGAP 0.039 0.05 -10000 0 -0.41 4 4
INS 0.019 0.016 0.31 1 -10000 0 1
mol:PI-3-4-P2 -0.015 0.047 -10000 0 -0.26 15 15
GRB2 0.025 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.006 0.08 0.29 12 -0.36 2 14
PTPRA 0.027 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
TC10/GTP/CIP4 0.032 0.011 -10000 0 -10000 0 0
PDPK1 0.021 0.043 -10000 0 -0.46 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.04 -10000 0 -0.24 7 7
Insulin Receptor/Insulin/IRS1 0.036 0.05 0.22 1 -0.26 12 13
Insulin Receptor/Insulin/IRS3 0.034 0.017 0.25 1 -10000 0 1
Par3/Par6 0.047 0.051 -10000 0 -0.24 10 10
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.026 0.061 -10000 0 -0.33 14 14
ATM 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.025 0.005 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
ATR 0.025 0.005 -10000 0 -10000 0 0
UBE2L3 0.025 0.006 -10000 0 -10000 0 0
FANCD2 0.019 0.011 0.21 1 -10000 0 1
protein ubiquitination 0.1 0.092 -10000 0 -0.21 10 10
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.025 0.007 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.024 -10000 0 -0.28 1 1
MRE11A 0.025 0.005 -10000 0 -10000 0 0
DNA-PK 0.045 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.014 0.097 -10000 0 -0.44 16 16
FANCF 0.025 0.022 -10000 0 -0.46 1 1
BRCA1 0.025 0.006 -10000 0 -10000 0 0
CCNE1 0.14 0.13 0.29 224 -10000 0 224
CDK2/Cyclin E1 0.11 0.093 0.22 221 -10000 0 221
FANCG 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.061 -10000 0 -0.33 14 14
FANCE 0.026 0.004 -10000 0 -10000 0 0
FANCC 0.025 0.007 -10000 0 -10000 0 0
NBN 0.024 0.008 -10000 0 -10000 0 0
FANCA 0.03 0.045 0.29 14 -10000 0 14
DNA repair 0.02 0.076 0.26 4 -0.38 7 11
BRCA1/BARD1/ubiquitin 0.027 0.061 -10000 0 -0.33 14 14
BARD1/DNA-PK 0.049 0.056 -10000 0 -0.26 13 13
FANCL 0.026 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.061 0.33 14 -10000 0 14
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.058 -10000 0 -0.24 15 15
BRCA1/BACH1/BARD1/TopBP1 0.04 0.056 -10000 0 -0.28 14 14
BRCA1/BARD1/P53 0.05 0.056 -10000 0 -0.25 14 14
BARD1/CSTF1/BRCA1 0.039 0.056 -10000 0 -0.28 14 14
BRCA1/BACH1 0.025 0.006 -10000 0 -10000 0 0
BARD1 0.013 0.08 -10000 0 -0.46 14 14
PCNA 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.04 0.056 -10000 0 -0.28 14 14
BRCA1/BARD1/UbcH7 0.04 0.056 -10000 0 -0.28 14 14
BRCA1/BARD1/RAD51/PCNA 0.064 0.071 -10000 0 -0.24 14 14
BARD1/DNA-PK/P53 0.056 0.057 -10000 0 -0.24 13 13
BRCA1/BARD1/Ubiquitin 0.027 0.061 -10000 0 -0.33 14 14
BRCA1/BARD1/CTIP 0.031 0.05 -10000 0 -0.26 14 14
FA complex 0.024 0.037 0.19 2 -0.26 4 6
BARD1/EWS 0.026 0.061 -10000 0 -0.33 14 14
RBBP8 0.011 0.003 -10000 0 -10000 0 0
TP53 0.024 0.007 -10000 0 -10000 0 0
TOPBP1 0.026 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.048 0.056 0.25 14 -10000 0 14
BRCA1/BARD1 0.12 0.095 -10000 0 -0.21 10 10
CSTF1 0.025 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.01 0.057 -10000 0 -0.33 14 14
CDK2 0.026 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.05 0.078 0.29 48 -10000 0 48
RAD50 0.025 0.022 -10000 0 -0.46 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.061 -10000 0 -0.33 14 14
EWSR1 0.025 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.035 0.19 5 -0.24 5 10
RGS9BP 0.023 0.033 0.29 1 -0.46 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.02 0.022 0.29 3 -10000 0 3
mol:Na + 0.032 0.031 0.19 17 -10000 0 17
mol:ADP -0.008 0.023 0.27 1 -10000 0 1
GNAT2 0.026 0.021 0.29 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.006 0.12 -10000 0 -0.28 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.03 0.016 0.19 4 -10000 0 4
GRK7 0.023 0.018 0.29 2 -10000 0 2
CNGB3 0.029 0.049 0.29 17 -10000 0 17
Cone Metarhodopsin II/X-Arrestin 0.015 0.009 0.2 1 -10000 0 1
mol:Ca2+ 0.006 0.054 0.18 38 -10000 0 38
Cone PDE6 0.008 0.11 -10000 0 -0.25 76 76
Cone Metarhodopsin II 0.026 0.018 0.18 5 -10000 0 5
Na + (4 Units) 0.04 0.032 -10000 0 -10000 0 0
GNAT2/GDP 0.006 0.11 -10000 0 -0.24 77 77
GNB5 0.025 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.01 0.023 0.18 6 -10000 0 6
Cone Transducin 0.044 0.038 0.2 5 -0.26 5 10
SLC24A2 0.021 0.018 0.29 2 -10000 0 2
GNB3/GNGT2 0.034 0.041 0.22 4 -0.33 5 9
GNB3 0.027 0.032 0.29 4 -0.46 1 5
GNAT2/GTP 0.019 0.014 0.2 3 -10000 0 3
CNGA3 0.023 0.013 0.29 1 -10000 0 1
ARR3 0.021 0.013 0.29 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.032 0.032 0.19 17 -10000 0 17
mol:Pi -0.006 0.12 -10000 0 -0.28 77 77
Cone CNG Channel 0.048 0.032 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.021 0.018 0.29 2 -10000 0 2
RGS9 -0.05 0.18 -10000 0 -0.46 78 78
PDE6C 0.019 0.007 -10000 0 -10000 0 0
GNGT2 0.021 0.043 -10000 0 -0.46 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.013 0.29 1 -10000 0 1
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.034 0.09 -10000 0 -0.42 1 1
CRKL 0.021 0.06 0.24 5 -0.23 7 12
mol:DAG 0.027 0.057 0.27 3 -0.27 2 5
HRAS 0.027 0.09 0.29 19 -0.28 2 21
MAPK8 0.028 0.073 0.2 43 -0.27 7 50
RAP1A 0.022 0.061 0.24 5 -0.23 7 12
GAB1 0.02 0.065 0.24 5 -0.24 10 15
MAPK14 0.031 0.066 0.2 43 -0.26 1 44
EPO 0.035 0.056 0.29 21 -10000 0 21
PLCG1 0.027 0.058 0.27 3 -0.28 2 5
EPOR/TRPC2/IP3 Receptors 0.027 0.031 0.29 5 -10000 0 5
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.041 0.072 0.22 18 -0.29 14 32
GAB1/SHC/GRB2/SOS1 0.036 0.055 0.27 1 -0.29 2 3
EPO/EPOR (dimer) 0.043 0.048 0.23 22 -10000 0 22
IRS2 -0.018 0.11 0.26 4 -0.24 80 84
STAT1 0.028 0.071 0.36 1 -0.3 3 4
STAT5B 0.027 0.065 0.29 2 -0.28 4 6
cell proliferation 0.013 0.081 0.22 45 -0.26 7 52
GAB1/SHIP/PIK3R1/SHP2/SHC 0.025 0.058 -10000 0 -0.3 5 5
TEC 0.022 0.061 0.24 5 -0.23 7 12
SOCS3 0.011 0.082 -10000 0 -0.46 15 15
STAT1 (dimer) 0.028 0.071 0.35 1 -0.3 3 4
JAK2 0.016 0.07 -10000 0 -0.45 11 11
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
EPO/EPOR (dimer)/JAK2 0.065 0.07 0.34 3 -0.24 7 10
EPO/EPOR 0.043 0.048 0.23 22 -10000 0 22
LYN 0.021 0.025 -10000 0 -0.46 1 1
TEC/VAV2 0.034 0.059 0.26 4 -0.23 6 10
elevation of cytosolic calcium ion concentration 0.027 0.031 0.29 5 -10000 0 5
SHC1 0.022 0.01 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.049 0.31 2 -0.29 1 3
mol:IP3 0.027 0.057 0.27 3 -0.27 2 5
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.001 0.12 0.29 3 -0.24 79 82
SH2B3 0.025 0.033 -10000 0 -0.46 2 2
NFKB1 0.031 0.067 0.2 44 -0.24 2 46
EPO/EPOR (dimer)/JAK2/SOCS3 0.007 0.059 0.21 2 -0.21 24 26
PTPN6 0.022 0.059 0.24 3 -0.24 7 10
TEC/VAV2/GRB2 0.043 0.056 0.28 1 -0.29 1 2
EPOR 0.027 0.031 0.29 5 -10000 0 5
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
mol:GDP 0.035 0.055 0.27 1 -0.29 2 3
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG2 0.02 0.038 -10000 0 -0.46 3 3
CRKL/CBL/C3G 0.043 0.059 0.28 2 -0.29 1 3
VAV2 0.02 0.059 0.26 4 -0.23 6 10
CBL 0.021 0.06 0.26 4 -0.23 7 11
SHC/Grb2/SOS1 0.028 0.044 -10000 0 -0.25 2 2
STAT5A 0.027 0.065 0.35 1 -0.28 4 5
GRB2 0.025 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.038 0.086 0.35 1 -0.32 13 14
LYN/PLCgamma2 0.028 0.04 -10000 0 -0.42 3 3
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK 0.011 0.081 0.24 3 -0.26 23 26
BCL2 0.011 0.19 -10000 0 -0.78 25 25
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.007 -10000 0 -10000 0 0
HDAC4 0.026 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.038 0.33 1 -0.32 4 5
CDKN1A -0.01 0.037 -10000 0 -0.57 2 2
KAT2B 0.005 0.097 -10000 0 -0.46 21 21
BAX 0.026 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.022 -10000 0 -0.46 1 1
FOXO4 0.012 0.017 -10000 0 -0.26 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.025 0.007 -10000 0 -10000 0 0
TAT 0.022 0.019 0.29 2 -10000 0 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.01 0.071 0.4 1 -0.33 19 20
PPARGC1A -0.17 0.24 -10000 0 -0.46 207 207
FHL2 0.023 0.037 -10000 0 -0.46 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.034 0.023 0.29 1 -0.33 1 2
HIST2H4A -0.004 0.039 0.32 4 -0.33 1 5
SIRT1/FOXO3a 0.018 0.033 0.23 2 -0.22 4 6
SIRT1 0.023 0.03 0.42 1 -0.46 1 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.04 0.029 0.28 1 -0.28 1 2
SIRT1/Histone H1b 0.023 0.052 0.37 1 -0.22 9 10
apoptosis -0.045 0.025 0.28 1 -0.28 1 2
SIRT1/PGC1A -0.095 0.15 0.26 1 -0.28 201 202
p53/SIRT1 0.03 0.038 0.53 2 -0.33 1 3
SIRT1/FOXO4 0.017 0.047 0.29 1 -0.21 11 12
FOXO1/FHL2/SIRT1 0.043 0.033 0.26 1 -0.26 4 5
HIST1H1E 0.02 0.027 0.19 2 -10000 0 2
SIRT1/p300 0.034 0.023 0.29 1 -0.33 1 2
muscle cell differentiation -0.019 0.067 0.28 22 -0.25 3 25
TP53 0.024 0.026 0.34 3 -10000 0 3
KU70/SIRT1/BAX 0.046 0.025 0.28 1 -0.28 1 2
CREBBP 0.025 0.006 -10000 0 -10000 0 0
MEF2D 0.022 0.01 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.03 0.027 0.24 3 -0.34 1 4
ACSS2 -0.008 0.025 0.28 2 -0.33 1 3
SIRT1/PCAF/MYOD 0.019 0.067 0.25 3 -0.28 22 25
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.01 0.017 -10000 0 -0.28 2 2
SNTA1 0.025 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.01 0.019 -10000 0 -0.28 2 2
MAPK12 0.003 0.025 0.21 6 -10000 0 6
CCND1 0.007 0.044 -10000 0 -0.37 6 6
p38 gamma/SNTA1 0.027 0.036 0.26 4 -10000 0 4
MAP2K3 0.024 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint 0.004 0.028 0.21 8 -10000 0 8
MAP2K6 0.008 0.016 0.25 1 -10000 0 1
MAPT -0.089 0.15 0.22 6 -0.28 176 182
MAPK13 0.01 0.022 -10000 0 -0.33 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.013 0.004 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.14 0.13 0.29 224 -10000 0 224
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.007 0.092 -10000 0 -0.46 19 19
CDKN1A 0 0.063 -10000 0 -0.37 9 9
PRL-3/alpha Tubulin 0.035 0.015 0.22 1 -10000 0 1
mol:Ca2+ -0.037 0.091 0.26 2 -0.34 39 41
AGT -0.02 0.14 0.29 7 -0.46 47 54
CCNA2 -0.025 0.078 0.25 2 -10000 0 2
TUBA1B 0.026 0.003 -10000 0 -10000 0 0
EGR1 -0.034 0.12 -10000 0 -0.32 72 72
CDK2/Cyclin E1 0.094 0.11 0.3 13 -0.38 4 17
MAPK3 0.011 0.007 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.017 -10000 0 -0.33 1 1
PTP4A1 -0.034 0.082 -10000 0 -10000 0 0
PTP4A3 0.024 0.014 0.29 1 -10000 0 1
PTP4A2 0.026 0.004 -10000 0 -10000 0 0
ITGB1 0.011 0.007 0.15 1 -10000 0 1
SRC 0.025 0.006 -10000 0 -10000 0 0
RAC1 0 0.061 -10000 0 -0.38 8 8
Rab GGTase beta/Rab GGTase alpha 0.038 0.007 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.006 0.095 0.36 1 -10000 0 1
RABGGTA 0.026 0.004 -10000 0 -10000 0 0
BCAR1 -0.017 0.012 -10000 0 -0.2 1 1
RHOC 0.003 0.049 -10000 0 -0.36 4 4
RHOA -0.003 0.064 -10000 0 -0.34 12 12
cell motility 0.011 0.072 0.28 1 -0.38 6 7
PRL-1/alpha Tubulin -0.007 0.094 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.024 0.062 0.22 1 -0.33 14 15
ROCK1 0.012 0.069 0.28 1 -0.37 5 6
RABGGTB 0.026 0.002 -10000 0 -10000 0 0
CDK2 0.026 0.004 -10000 0 -10000 0 0
mitosis -0.034 0.081 -10000 0 -10000 0 0
ATF5 0.027 0.021 0.29 3 -10000 0 3
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.059 0.066 -10000 0 -0.23 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.025 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.043 0.054 0.28 2 -0.23 1 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.062 -10000 0 -0.29 16 16
antigen processing and presentation of peptide antigen via MHC class I -0.01 0.073 -10000 0 -0.24 20 20
CaM/Ca2+ 0.059 0.061 -10000 0 -0.22 15 15
RAP1A 0.026 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.026 0.053 -10000 0 -0.22 16 16
AKT1 0.009 0.078 0.28 13 -0.24 1 14
MAP2K1 -0.009 0.052 0.28 3 -0.22 7 10
MAP3K11 0.009 0.056 0.28 3 -0.22 16 19
IFNGR1 0.026 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.032 0.16 -10000 0 -0.37 83 83
Rap1/GTP 0.012 0.038 -10000 0 -0.19 14 14
CRKL/C3G 0.036 0.011 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.069 0.07 -10000 0 -0.24 16 16
CEBPB 0 0.14 0.4 1 -0.53 21 22
STAT3 0.025 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.046 0.16 -10000 0 -0.67 19 19
STAT1 0.008 0.055 0.28 3 -0.22 16 19
CALM1 0.025 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.037 0.063 0.29 28 -10000 0 28
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
STAT1 (dimer)/PIAS1 0.025 0.055 0.28 3 -0.22 15 18
CEBPB/PTGES2/Cbp/p300 0.018 0.089 -10000 0 -0.34 18 18
mol:Ca2+ 0.056 0.064 -10000 0 -0.23 16 16
MAPK3 -0.011 0.14 -10000 0 -0.61 23 23
STAT1 (dimer) -0.007 0.1 -10000 0 -0.33 19 19
MAPK1 -0.022 0.18 -10000 0 -0.66 31 31
JAK2 0.015 0.072 -10000 0 -0.46 11 11
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
JAK1 0.022 0.05 -10000 0 -0.46 5 5
CAMK2D 0.021 0.048 -10000 0 -0.46 5 5
DAPK1 0.006 0.1 0.35 1 -0.42 16 17
SMAD7 0.006 0.06 0.21 10 -0.21 7 17
CBL/CRKL/C3G 0.036 0.055 0.28 3 -0.22 7 10
PI3K 0.049 0.061 -10000 0 -0.22 15 15
IFNG 0.037 0.063 0.29 28 -10000 0 28
apoptosis 0.006 0.085 -10000 0 -0.37 11 11
CAMK2G 0.025 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.006 -10000 0 -10000 0 0
CAMK2A -0.053 0.18 -10000 0 -0.46 80 80
CAMK2B 0.038 0.087 0.29 36 -0.46 6 42
FRAP1 0.007 0.073 0.27 13 -0.22 2 15
PRKCD 0.007 0.079 0.29 13 -0.24 2 15
RAP1B 0.026 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.01 0.073 -10000 0 -0.24 20 20
PTPN2 0.026 0.005 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
IRF1 0 0.051 0.28 5 -0.32 1 6
STAT1 (dimer)/PIASy 0.022 0.055 0.27 3 -0.24 1 4
SOCS1 -0.013 0.2 -10000 0 -1 19 19
mol:GDP 0.033 0.052 0.26 3 -0.21 14 17
CASP1 0 0.076 0.21 10 -0.25 24 34
PTGES2 0.025 0.006 -10000 0 -10000 0 0
IRF9 0.015 0.043 0.22 2 -0.16 5 7
mol:PI-3-4-5-P3 0.035 0.053 -10000 0 -0.22 15 15
RAP1/GDP 0.033 0.045 -10000 0 -0.21 1 1
CBL 0.008 0.055 0.28 3 -0.22 15 18
MAP3K1 0.008 0.055 0.28 3 -0.22 15 18
PIAS1 0.025 0.006 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.01 0.073 -10000 0 -0.24 20 20
PTPN11 0.01 0.057 0.3 3 -0.23 16 19
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.009 0.026 -10000 0 -0.33 3 3
MAP4K4 0.004 0.067 0.2 2 -0.38 7 9
BAG4 0.02 0.044 -10000 0 -0.46 4 4
PKC zeta/ceramide -0.003 0.054 0.15 1 -0.2 17 18
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 0.006 0.095 -10000 0 -0.46 20 20
BAX -0.001 0.047 -10000 0 -0.33 8 8
RIPK1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.007 0.088 0.65 9 -10000 0 9
BAD -0.014 0.053 0.21 8 -0.19 18 26
SMPD1 0.011 0.06 0.19 9 -0.2 18 27
RB1 -0.017 0.046 0.17 2 -0.19 18 20
FADD/Caspase 8 0.007 0.079 0.26 2 -0.34 13 15
MAP2K4 -0.018 0.045 0.16 2 -0.19 17 19
NSMAF 0.024 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.054 0.2 10 -0.18 18 28
EGF -0.07 0.19 -10000 0 -0.46 99 99
mol:ceramide -0.016 0.048 0.14 3 -0.2 18 21
MADD 0.025 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.008 0.027 -10000 0 -0.33 3 3
ASAH1 0.023 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.046 0.17 2 -0.19 18 20
cell proliferation -0.001 0.07 0.2 2 -0.21 22 24
BID -0.018 0.17 -10000 0 -0.62 32 32
MAP3K1 -0.016 0.046 0.18 2 -0.19 18 20
EIF2A -0.006 0.064 0.19 30 -0.21 4 34
TRADD 0.023 0.009 -10000 0 -10000 0 0
CRADD 0.026 0.002 -10000 0 -10000 0 0
MAPK3 -0.013 0.054 0.2 9 -0.22 5 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.015 0.057 0.2 10 -0.2 8 18
Cathepsin D/ceramide -0.002 0.052 0.15 1 -0.19 18 19
FADD 0.005 0.068 0.2 5 -0.38 7 12
KSR1 -0.015 0.05 0.19 7 -0.19 18 25
MAPK8 -0.014 0.06 -10000 0 -0.28 9 9
PRKRA -0.015 0.048 0.18 6 -0.19 16 22
PDGFA 0.022 0.038 -10000 0 -0.46 3 3
TRAF2 0.025 0.007 -10000 0 -10000 0 0
IGF1 0.009 0.1 0.29 5 -0.46 21 26
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.015 0.048 0.14 3 -0.2 18 21
CTSD 0.025 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.036 0.018 -10000 0 -0.33 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.001 0.074 0.22 2 -0.22 22 24
PRKCD 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.008 0.027 -10000 0 -0.33 3 3
RelA/NF kappa B1 0.037 0.018 -10000 0 -0.33 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.011 0.065 0.17 2 -0.27 17 19
TNFR1A/BAG4/TNF-alpha 0.046 0.056 -10000 0 -0.28 8 8
mol:Sphingosine-1-phosphate 0.009 0.026 -10000 0 -0.33 3 3
MAP2K1 -0.015 0.052 0.19 11 -0.21 4 15
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.003 -10000 0 -10000 0 0
CYCS 0.003 0.05 0.16 19 -0.17 3 22
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
TNFR1A/BAG4 0.031 0.035 -10000 0 -0.33 4 4
EIF2AK2 -0.013 0.053 0.19 12 -0.18 14 26
TNF-alpha/TNFR1A/FAN 0.048 0.046 0.21 16 -0.28 4 20
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.017 0.068 -10000 0 -0.35 9 9
MAP2K2 -0.015 0.052 0.2 10 -0.19 11 21
SMPD3 -0.001 0.093 0.2 4 -0.27 45 49
TNF 0.031 0.08 0.29 23 -0.46 7 30
PKC zeta/PAR4 0.037 0.018 -10000 0 -0.33 1 1
mol:PHOSPHOCHOLINE 0.039 0.09 0.21 100 -0.18 2 102
NF kappa B1/RelA/I kappa B alpha 0.069 0.031 -10000 0 -0.24 2 2
AIFM1 0.002 0.05 0.17 6 -0.17 2 8
BCL2 0.003 0.1 -10000 0 -0.46 23 23
Caspase cascade in apoptosis

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
TOP1 0.015 0.099 -10000 0 -0.38 19 19
ACTA1 0.018 0.083 0.22 11 -0.36 7 18
NUMA1 0.014 0.1 0.22 1 -0.38 20 21
SPTAN1 0.007 0.078 0.22 3 -0.44 5 8
LIMK1 0.009 0.083 0.27 7 -0.4 6 13
BIRC3 0.006 0.095 -10000 0 -0.46 20 20
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.012 0.065 0.22 3 -0.33 15 18
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.002 -10000 0 -10000 0 0
PTK2 0.014 0.099 0.22 1 -0.38 19 20
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.078 0.22 3 -0.43 5 8
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.002 -10000 0 -10000 0 0
GSN 0.006 0.079 0.23 2 -0.44 5 7
MADD 0.025 0.006 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.56 25 25
BID 0.006 0.031 0.18 1 -0.22 6 7
MAP3K1 -0.001 0.1 -10000 0 -0.43 23 23
TRADD 0.023 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.007 0.085 0.31 5 -0.4 7 12
CASP9 0.025 0.005 -10000 0 -10000 0 0
DNA repair -0.021 0.051 0.28 4 -0.18 13 17
neuron apoptosis 0.012 0.11 -10000 0 -0.82 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.011 0.099 0.24 1 -0.4 15 16
APAF1 0.026 0.002 -10000 0 -10000 0 0
CASP6 -0.001 0.17 -10000 0 -0.87 17 17
TRAF2 0.025 0.007 -10000 0 -10000 0 0
ICAD/CAD 0.007 0.08 0.29 5 -0.43 5 10
CASP7 0.005 0.067 0.27 17 -0.24 9 26
KRT18 0.016 0.061 -10000 0 -0.64 3 3
apoptosis 0.011 0.12 0.39 18 -0.42 18 36
DFFA 0.008 0.081 0.26 6 -0.44 5 11
DFFB 0.007 0.08 0.22 4 -0.44 5 9
PARP1 0.021 0.051 0.18 13 -0.28 4 17
actin filament polymerization -0.009 0.083 0.38 5 -0.31 11 16
TNF 0.031 0.08 0.29 23 -0.46 7 30
CYCS 0.009 0.047 0.18 6 -0.2 10 16
SATB1 -0.041 0.18 0.34 2 -0.81 19 21
SLK 0.009 0.092 0.31 14 -0.34 9 23
p15 BID/BAX 0.021 0.046 -10000 0 -0.29 2 2
CASP2 0.008 0.063 0.22 6 -0.29 10 16
JNK cascade 0.001 0.1 0.43 23 -10000 0 23
CASP3 0.01 0.084 0.22 7 -0.33 11 18
LMNB2 -0.013 0.16 0.23 1 -0.47 42 43
RIPK1 0.025 0.005 -10000 0 -10000 0 0
CASP4 0.023 0.031 -10000 0 -0.46 2 2
Mammalian IAPs/DIABLO 0.052 0.064 -10000 0 -0.26 19 19
negative regulation of DNA binding 0.012 0.14 -10000 0 -0.56 25 25
stress fiber formation 0.009 0.092 0.31 14 -0.34 9 23
GZMB 0.015 0.057 0.16 32 -0.38 6 38
CASP1 -0.003 0.076 -10000 0 -0.33 23 23
LMNB1 0.007 0.13 0.25 2 -0.51 20 22
APP 0.011 0.12 -10000 0 -0.84 8 8
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.011 0.11 0.31 15 -0.41 20 35
LMNA 0.01 0.09 -10000 0 -0.37 17 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.009 0.065 -10000 0 -0.29 13 13
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.01 0.081 0.27 4 -0.44 5 9
APAF-1/Caspase 9 0.01 0.1 -10000 0 -0.63 11 11
nuclear fragmentation during apoptosis 0.014 0.1 0.22 1 -0.38 20 21
CFL2 0.009 0.084 0.31 11 -0.39 5 16
GAS2 -0.014 0.1 0.22 4 -0.28 39 43
positive regulation of apoptosis 0.002 0.14 0.23 2 -0.51 23 25
PRF1 0.024 0.043 0.29 3 -0.46 3 6
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.026 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.1 0.28 1 -0.34 10 11
Syndecan-3/Neurocan 0.021 0.063 0.28 2 -0.37 8 10
POMC 0.031 0.076 0.29 22 -0.46 6 28
EGFR -0.013 0.13 -10000 0 -0.46 40 40
Syndecan-3/EGFR 0.001 0.081 -10000 0 -0.37 9 9
AGRP 0.008 0.073 -10000 0 -0.46 12 12
NCSTN 0.022 0.01 -10000 0 -10000 0 0
PSENEN 0.025 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.017 0.061 -10000 0 -0.46 8 8
APH1A 0.021 0.011 -10000 0 -10000 0 0
NCAN 0.029 0.047 0.29 16 -10000 0 16
long-term memory 0.049 0.066 -10000 0 -0.34 9 9
Syndecan-3/IL8 0.015 0.072 0.28 1 -0.38 11 12
PSEN1 0.026 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.036 0.011 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
limb bud formation 0.002 0.052 -10000 0 -0.38 9 9
MC4R 0.04 0.069 0.29 36 -10000 0 36
SRC 0.025 0.006 -10000 0 -10000 0 0
PTN -0.029 0.15 0.29 1 -0.46 57 58
FGFR/FGF/Syndecan-3 0.002 0.053 -10000 0 -0.38 9 9
neuron projection morphogenesis -0.004 0.09 0.32 2 -0.34 8 10
Syndecan-3/AgRP 0.009 0.066 -10000 0 -0.37 10 10
Syndecan-3/AgRP/MC4R 0.045 0.087 0.3 4 -0.35 10 14
Fyn/Cortactin 0.037 0.009 -10000 0 -10000 0 0
SDC3 0.002 0.053 -10000 0 -0.39 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.015 0.071 0.28 1 -0.38 11 12
IL8 0.019 0.078 0.29 7 -0.46 11 18
Syndecan-3/Fyn/Cortactin 0.051 0.067 -10000 0 -0.35 9 9
Syndecan-3/CASK 0 0.052 -10000 0 -0.37 9 9
alpha-MSH/MC4R 0.048 0.072 0.22 51 -0.33 6 57
Gamma Secretase 0.051 0.049 -10000 0 -0.24 6 6
IL2 signaling events mediated by PI3K

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
BCL2L1 0.025 0.061 -10000 0 -0.43 1 1
UGCG -0.047 0.21 -10000 0 -0.62 57 57
AKT1/mTOR/p70S6K/Hsp90/TERT 0.059 0.13 0.31 4 -0.48 14 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.045 0.21 -10000 0 -0.6 58 58
mol:DAG 0.005 0.096 -10000 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.14 0.32 1 -0.4 29 30
FRAP1 0.027 0.16 0.35 1 -0.46 31 32
FOXO3 0.033 0.14 0.34 6 -0.46 19 25
AKT1 0.033 0.15 0.36 1 -0.49 20 21
GAB2 0.025 0.008 -10000 0 -10000 0 0
SMPD1 -0.003 0.13 -10000 0 -0.6 22 22
SGMS1 0.015 0.073 -10000 0 -0.61 6 6
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 0.002 0.023 -10000 0 -0.28 3 3
CALM1 0.025 0.005 -10000 0 -10000 0 0
cell proliferation 0.007 0.16 0.26 6 -0.42 38 44
EIF3A 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.032 0.033 -10000 0 -0.33 3 3
RPS6KB1 0.002 0.14 -10000 0 -0.79 15 15
mol:sphingomyelin 0.005 0.096 -10000 0 -0.82 6 6
natural killer cell activation 0 0.003 -10000 0 -0.02 1 1
JAK3 0.026 0.015 0.28 1 -10000 0 1
PIK3R1 0.023 0.032 -10000 0 -0.46 2 2
JAK1 0.022 0.048 -10000 0 -0.46 5 5
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
MYC 0.046 0.19 0.41 5 -0.87 15 20
MYB 0.021 0.11 -10000 0 -1.1 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.034 0.095 -10000 0 -0.45 8 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.13 -10000 0 -0.69 15 15
mol:PI-3-4-5-P3 0.036 0.095 -10000 0 -0.44 8 8
Rac1/GDP 0.016 0.025 -10000 0 -0.26 3 3
T cell proliferation 0.037 0.096 0.27 1 -0.43 8 9
SHC1 0.021 0.011 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.005 -10000 0 -0.066 3 3
PRKCZ 0.036 0.097 0.28 1 -0.44 8 9
NF kappa B1 p50/RelA 0.046 0.14 0.34 1 -0.42 25 26
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.021 0.05 -10000 0 -0.5 2 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.026 0.003 -10000 0 -10000 0 0
IL2RA 0.018 0.063 0.29 2 -0.46 8 10
IL2RB 0.024 0.023 -10000 0 -0.46 1 1
TERT 0.11 0.12 0.29 166 -10000 0 166
E2F1 0.028 0.073 -10000 0 -0.56 4 4
SOS1 0.025 0.008 -10000 0 -10000 0 0
RPS6 0.025 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 0.033 3 -10000 0 3
PTPN11 0.025 0.009 -10000 0 -10000 0 0
IL2RG 0.023 0.045 0.29 1 -0.46 4 5
actin cytoskeleton organization 0.037 0.096 0.27 1 -0.43 8 9
GRB2 0.024 0.01 -10000 0 -10000 0 0
IL2 0.028 0.049 0.29 16 -10000 0 16
PIK3CA 0.023 0.024 -10000 0 -0.46 1 1
Rac1/GTP 0.039 0.034 -10000 0 -0.24 3 3
LCK 0.023 0.038 -10000 0 -0.46 3 3
BCL2 0.006 0.21 -10000 0 -0.77 29 29
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.044 -10000 0 -0.46 4 4
Caspase 8 (4 units) 0.035 0.053 -10000 0 -0.65 1 1
NEF 0.002 0.028 -10000 0 -0.28 4 4
NFKBIA 0.022 0.025 -10000 0 -10000 0 0
BIRC3 0 0.1 -10000 0 -0.47 21 21
CYCS 0.031 0.072 0.25 3 -0.67 1 4
RIPK1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.022 0.034 -10000 0 -0.36 3 3
MAP2K7 0.011 0.18 0.3 2 -0.65 31 33
protein ubiquitination 0.012 0.081 0.28 6 -0.29 11 17
CRADD 0.026 0.002 -10000 0 -10000 0 0
DAXX 0.026 0.004 -10000 0 -10000 0 0
FAS 0.021 0.043 -10000 0 -0.46 4 4
BID 0.035 0.073 0.18 69 -0.29 6 75
NF-kappa-B/RelA/I kappa B alpha 0.043 0.064 -10000 0 -0.27 19 19
TRADD 0.023 0.009 -10000 0 -10000 0 0
MAP3K5 0.024 0.031 -10000 0 -0.46 2 2
CFLAR 0.026 0.003 -10000 0 -10000 0 0
FADD 0.025 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.064 -10000 0 -0.27 19 19
MAPK8 0.012 0.18 0.38 6 -0.59 32 38
APAF1 0.026 0.002 -10000 0 -10000 0 0
TRAF1 0.025 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.007 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.042 0.076 0.19 69 -0.3 6 75
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.005 0.093 -10000 0 -0.32 22 22
CHUK 0.013 0.082 0.29 6 -0.31 10 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.064 0.044 -10000 0 -0.24 6 6
TCRz/NEF 0.02 0.031 0.17 5 -0.31 3 8
TNF 0.031 0.08 0.29 23 -0.46 7 30
FASLG 0.015 0.042 0.28 5 -0.37 3 8
NFKB1 0.021 0.034 -10000 0 -0.25 3 3
TNFR1A/BAG4/TNF-alpha 0.046 0.056 -10000 0 -0.28 8 8
CASP6 0.048 0.11 -10000 0 -0.47 14 14
CASP7 0.028 0.13 0.48 4 -0.47 22 26
RELA 0.022 0.027 -10000 0 -10000 0 0
CASP2 0.025 0.005 -10000 0 -10000 0 0
CASP3 0.027 0.14 0.41 7 -0.47 22 29
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.031 0.035 -10000 0 -0.33 4 4
CASP8 0.026 0.003 -10000 0 -10000 0 0
CASP9 0.025 0.005 -10000 0 -10000 0 0
MAP3K14 0.01 0.085 -10000 0 -0.32 16 16
APAF-1/Caspase 9 0.028 0.087 -10000 0 -0.36 15 15
BCL2 0.004 0.17 0.38 4 -0.52 36 40
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.002 0.082 0.25 27 -10000 0 27
GNAI2 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.025 0.051 0.2 4 -0.28 12 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
RhoA/GTP 0.002 0.083 -10000 0 -0.26 27 27
negative regulation of cAMP metabolic process 0.001 0.077 -10000 0 -0.24 39 39
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
GNAI3 0.026 0.002 -10000 0 -10000 0 0
GNA12 0.025 0.006 -10000 0 -10000 0 0
S1PR5 0.014 0.081 0.29 4 -0.46 13 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.078 -10000 0 -0.25 39 39
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0 0.098 0.23 1 -0.34 26 27
BAG4 0.02 0.044 -10000 0 -0.46 4 4
BAD 0.005 0.043 0.18 7 -0.15 10 17
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 0.006 0.095 -10000 0 -0.46 20 20
BAX 0.004 0.044 0.2 6 -0.15 9 15
EnzymeConsortium:3.1.4.12 0.002 0.026 0.084 2 -0.087 19 21
IKBKB 0.015 0.11 0.29 12 -0.36 15 27
MAP2K2 0.004 0.044 0.22 8 -0.18 1 9
MAP2K1 0.004 0.044 0.23 7 -0.18 2 9
SMPD1 0.001 0.033 -10000 0 -0.14 12 12
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.008 0.1 0.26 2 -0.38 19 21
MAP2K4 0.004 0.036 0.21 1 -0.2 2 3
protein ubiquitination 0.007 0.1 0.29 5 -0.37 17 22
EnzymeConsortium:2.7.1.37 0.003 0.049 0.24 7 -0.19 2 9
response to UV 0 0.001 0.003 7 -0.002 1 8
RAF1 0.005 0.046 0.22 8 -0.18 3 11
CRADD 0.026 0.002 -10000 0 -10000 0 0
mol:ceramide 0.004 0.041 0.12 5 -0.14 19 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.008 -10000 0 -10000 0 0
MADD 0.025 0.006 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 2 -0.15 8 10
TRADD 0.023 0.009 -10000 0 -10000 0 0
RELA/p50 0.026 0.003 -10000 0 -10000 0 0
MAPK3 0.005 0.049 0.21 9 -0.18 4 13
MAPK1 0.003 0.053 0.21 9 -0.2 7 16
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD 0.004 0.097 0.25 2 -0.34 25 27
KSR1 0.005 0.042 0.18 5 -0.15 9 14
MAPK8 0.002 0.049 0.18 10 -0.19 7 17
TRAF2 0.025 0.007 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK 0.008 0.094 0.34 3 -0.38 14 17
TNF R/SODD 0.031 0.035 -10000 0 -0.33 4 4
TNF 0.031 0.08 0.29 23 -0.46 7 30
CYCS 0.01 0.047 0.15 13 -0.16 6 19
IKBKG 0.003 0.096 0.36 2 -0.37 18 20
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.097 -10000 0 -0.36 23 23
RELA 0.026 0.003 -10000 0 -10000 0 0
RIPK1 0.025 0.005 -10000 0 -10000 0 0
AIFM1 0.009 0.044 0.16 7 -0.16 5 12
TNF/TNF R/SODD 0.045 0.056 0.21 1 -0.28 8 9
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.019 0.086 -10000 0 -0.6 8 8
NSMAF 0.011 0.1 0.26 8 -0.33 23 31
response to hydrogen peroxide 0 0.001 0.003 7 -0.002 1 8
BCL2 0.003 0.1 -10000 0 -0.46 23 23
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.004 -10000 0 -10000 0 0
ELF1 0.02 0.068 -10000 0 -0.39 13 13
CCNA2 0.06 0.089 0.29 66 -10000 0 66
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
JAK3 0.026 0.013 0.29 1 -10000 0 1
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
JAK1 0.022 0.048 -10000 0 -0.46 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.086 -10000 0 -0.44 6 6
SHC1 0.022 0.01 -10000 0 -10000 0 0
SP1 0.013 0.08 -10000 0 -0.34 24 24
IL2RA 0.002 0.096 0.28 2 -0.53 14 16
IL2RB 0.024 0.023 -10000 0 -0.46 1 1
SOS1 0.026 0.004 -10000 0 -10000 0 0
IL2RG 0.023 0.045 0.29 1 -0.46 4 5
G1/S transition of mitotic cell cycle -0.02 0.19 0.3 5 -0.57 41 46
PTPN11 0.027 0.003 -10000 0 -10000 0 0
CCND2 -0.016 0.15 -10000 0 -0.7 23 23
LCK 0.023 0.038 -10000 0 -0.46 3 3
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL2 0.029 0.048 0.29 16 -10000 0 16
CDK6 -0.004 0.12 -10000 0 -0.46 31 31
CCND3 0.046 0.088 0.38 1 -0.45 3 4
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.013 0.069 -10000 0 -1.2 1 1
PLK1 0.2 0.19 0.59 18 -0.69 1 19
CDKN1B 0.12 0.16 0.43 4 -0.43 19 23
FOXO3 0.16 0.18 0.48 50 -0.53 7 57
KAT2B 0.032 0.099 -10000 0 -0.42 21 21
FOXO1/SIRT1 0.018 0.046 -10000 0 -0.28 3 3
CAT 0.15 0.2 0.57 7 -0.96 7 14
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.054 0.03 -10000 0 -10000 0 0
FOXO1 0.018 0.05 0.24 1 -0.32 2 3
MAPK10 0.004 0.087 0.24 9 -0.22 56 65
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.04 0.084 0.45 2 -0.43 5 7
response to oxidative stress 0.029 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.14 0.16 0.41 42 -0.54 7 49
XPO1 0.026 0.004 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
BCL2L11 0.055 0.076 -10000 0 -0.7 3 3
FOXO1/SKP2 0.029 0.048 -10000 0 -0.3 2 2
mol:GDP 0.029 0.026 -10000 0 -10000 0 0
RAN 0.027 0.004 -10000 0 -10000 0 0
GADD45A 0.12 0.12 0.41 5 -0.54 4 9
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.016 0.14 0.26 1 -0.51 27 28
MST1 0.067 0.07 0.32 31 -10000 0 31
CSNK1D 0.025 0.006 -10000 0 -10000 0 0
CSNK1E 0.025 0.007 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.017 0.11 -10000 0 -0.43 22 22
YWHAB 0.025 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.042 0.23 8 -0.23 7 15
MAPK9 0.032 0.034 0.24 10 -10000 0 10
YWHAG 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
YWHAZ 0.024 0.008 -10000 0 -10000 0 0
SIRT1 0.015 0.027 -10000 0 -0.46 1 1
SOD2 0.14 0.14 0.5 9 -0.46 4 13
RBL2 0.08 0.26 0.5 3 -0.68 34 37
RAL/GDP 0.055 0.022 -10000 0 -10000 0 0
CHUK 0.05 0.029 -10000 0 -10000 0 0
Ran/GTP 0.021 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.007 -10000 0 -10000 0 0
RAL/GTP 0.057 0.022 -10000 0 -10000 0 0
CSNK1G1 0.025 0.006 -10000 0 -10000 0 0
FASLG 0.052 0.12 -10000 0 -1.2 4 4
SKP2 0.025 0.006 -10000 0 -10000 0 0
USP7 0.026 0.006 -10000 0 -10000 0 0
IKBKB 0.047 0.029 -10000 0 -10000 0 0
CCNB1 0.17 0.18 0.53 44 -0.57 3 47
FOXO1-3a-4/beta catenin 0.13 0.13 0.42 10 -0.4 6 16
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.048 -10000 0 -0.3 2 2
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
SGK1 0.008 0.14 -10000 0 -0.43 47 47
CSNK1G3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.008 -10000 0 -10000 0 0
ZFAND5 0.038 0.076 0.42 2 -0.38 3 5
SFN 0.036 0.08 0.29 30 -0.46 5 35
CDK2 0.025 0.007 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.059 0.1 0.26 4 -0.38 13 17
CREBBP 0.024 0.008 -10000 0 -10000 0 0
FBXO32 0.17 0.21 0.59 30 -0.83 5 35
BCL6 0.14 0.16 0.48 3 -0.61 7 10
RALB 0.027 0.003 -10000 0 -10000 0 0
RALA 0.026 0.005 -10000 0 -10000 0 0
YWHAH 0.025 0.007 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
CDC42/GTP 0.002 0.085 -10000 0 -0.28 23 23
PLCG1 -0.005 0.072 -10000 0 -0.29 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.002 -10000 0 -10000 0 0
G12/G13 0.036 0.011 -10000 0 -10000 0 0
cell migration 0.002 0.083 -10000 0 -0.27 23 23
S1PR5 0.014 0.081 0.29 4 -0.46 13 17
S1PR4 0.021 0.045 0.29 1 -0.46 4 5
MAPK3 -0.005 0.074 -10000 0 -0.29 22 22
MAPK1 -0.003 0.071 -10000 0 -0.28 22 22
S1P/S1P5/Gi 0.001 0.078 -10000 0 -0.25 39 39
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
CDC42/GDP 0.019 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.025 0.051 0.2 4 -0.28 12 16
RHOA 0.013 0.035 0.18 13 -0.24 4 17
S1P/S1P4/Gi 0.003 0.077 -10000 0 -0.3 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
S1P/S1P4/G12/G13 0.042 0.032 0.2 1 -0.25 4 5
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.007 -10000 0 -10000 0 0
NFATC1 0.019 0.078 0.34 1 -0.39 4 5
NFATC2 -0.006 0.079 0.18 2 -0.24 25 27
NFATC3 0.016 0.018 -10000 0 -0.35 1 1
YWHAE 0.024 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.01 0.13 0.25 3 -0.37 33 36
Exportin 1/Ran/NUP214 0.048 0.016 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.007 0.11 0.27 1 -0.35 23 24
BCL2/BAX 0.02 0.077 -10000 0 -0.33 23 23
CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.011 -10000 0 -10000 0 0
CaM/Ca2+ 0.017 0.011 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.026 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D 0.001 0.11 0.22 1 -0.36 23 24
Calcineurin A alpha-beta B1/BCL2 0.003 0.1 -10000 0 -0.46 23 23
FKBP8 0.025 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.001 0.11 0.35 23 -0.22 1 24
KPNB1 0.025 0.006 -10000 0 -10000 0 0
KPNA2 0.025 0.006 -10000 0 -10000 0 0
XPO1 0.026 0.004 -10000 0 -10000 0 0
SFN 0.036 0.08 0.29 30 -0.46 5 35
MAP3K8 0.018 0.057 -10000 0 -0.46 7 7
NFAT4/CK1 alpha 0.022 0.025 -10000 0 -0.2 1 1
MEF2D/NFAT1/Cbp/p300 0.007 0.11 -10000 0 -0.28 41 41
CABIN1 -0.01 0.13 0.25 3 -0.37 33 36
CALM1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
CAMK4 0.017 0.07 0.29 2 -0.46 10 12
mol:Ca2+ -0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.025 0.006 -10000 0 -10000 0 0
YWHAH 0.025 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.031 0.041 -10000 0 -0.33 6 6
YWHAB 0.025 0.006 -10000 0 -10000 0 0
MAPK8 0.018 0.057 -10000 0 -0.46 7 7
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.017 0.088 0.28 1 -0.37 7 8
PRKCH 0.023 0.038 -10000 0 -0.46 3 3
CABIN1/Cbp/p300 0.031 0.021 -10000 0 -10000 0 0
CASP3 0.025 0.006 -10000 0 -10000 0 0
PIM1 0.026 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.007 -10000 0 -10000 0 0
apoptosis 0.012 0.032 -10000 0 -0.31 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.047 -10000 0 -0.33 4 4
PRKCB -0.031 0.16 -10000 0 -0.46 59 59
PRKCE 0.023 0.037 -10000 0 -0.46 3 3
JNK2/NFAT4 0.016 0.055 -10000 0 -0.32 1 1
BAD/BCL-XL 0.036 0.011 -10000 0 -10000 0 0
PRKCD 0.025 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.007 -10000 0 -10000 0 0
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
PRKCA 0.014 0.071 -10000 0 -0.46 11 11
PRKCG 0.1 0.12 0.29 152 -10000 0 152
PRKCQ -0.01 0.13 0.29 1 -0.46 37 38
FKBP38/BCL2 0.019 0.077 -10000 0 -0.33 23 23
EP300 0.022 0.014 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.028 0.082 0.33 1 -0.36 5 6
CaM/Ca2+/FKBP38 0.03 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSNK1A1 0.011 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.025 0.047 0.2 2 -0.28 10 12
NFATc/ERK1 0.032 0.077 0.33 1 -0.36 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.008 0.12 0.27 1 -0.35 29 30
NR4A1 0.001 0.16 0.26 6 -0.45 39 45
GSK3B 0.025 0.006 -10000 0 -10000 0 0
positive T cell selection 0.016 0.018 -10000 0 -0.34 1 1
NFAT1/CK1 alpha -0.002 0.06 0.15 1 -0.22 11 12
RCH1/ KPNB1 0.036 0.011 -10000 0 -10000 0 0
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
AKAP5 0.02 0.053 -10000 0 -0.46 6 6
MEF2D 0.019 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha 0.03 0.077 0.33 1 -0.37 4 5
CREBBP 0.022 0.014 -10000 0 -10000 0 0
BCL2 0.003 0.1 -10000 0 -0.46 23 23
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.013 -10000 0 -10000 0 0
DOCK1 0.02 0.048 -10000 0 -0.46 5 5
ITGA4 0.015 0.071 -10000 0 -0.46 11 11
RAC1 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.059 -10000 0 -0.36 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.041 0.049 -10000 0 -0.28 10 10
alpha4/beta7 Integrin/Paxillin 0.032 0.049 -10000 0 -0.28 11 11
lamellipodium assembly 0.003 0.087 -10000 0 -0.39 18 18
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PI3K 0.031 0.031 -10000 0 -0.33 3 3
ARF6 0.026 0.004 -10000 0 -10000 0 0
TLN1 0.025 0.006 -10000 0 -10000 0 0
PXN 0.011 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
ARF6/GTP 0.042 0.044 -10000 0 -0.23 10 10
cell adhesion 0.043 0.044 -10000 0 -0.24 9 9
CRKL/CBL 0.036 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.033 0.044 -10000 0 -0.26 10 10
ITGB1 0.025 0.005 -10000 0 -10000 0 0
ITGB7 0.024 0.031 -10000 0 -0.46 2 2
ARF6/GDP 0.023 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.006 0.12 -10000 0 -0.26 89 89
p130Cas/Crk/Dock1 0.041 0.038 -10000 0 -0.28 5 5
VCAM1 -0.069 0.19 -10000 0 -0.46 99 99
alpha4/beta1 Integrin/Paxillin/Talin 0.044 0.045 -10000 0 -0.24 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.046 -10000 0 -0.24 10 10
BCAR1 0.023 0.009 -10000 0 -10000 0 0
mol:GDP -0.042 0.046 0.24 10 -10000 0 10
CBL 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.044 0.045 -10000 0 -0.24 9 9
Rac1/GTP 0.002 0.095 -10000 0 -0.43 18 18
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.018 0.032 -10000 0 -0.23 3 3
DAPP1 0.02 0.093 0.29 8 -0.4 11 19
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.13 0.32 2 -0.5 17 19
mol:DAG 0.008 0.068 0.27 8 -0.24 6 14
HRAS 0.025 0.008 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
ARF5/GDP -0.004 0.1 0.21 1 -0.31 27 28
PLCG2 0.02 0.038 -10000 0 -0.46 3 3
PLCG1 0.025 0.006 -10000 0 -10000 0 0
ARF5 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.016 0.03 -10000 0 -0.23 3 3
ARF1/GTP -0.005 0.03 0.26 1 -0.22 2 3
RHOA 0.025 0.005 -10000 0 -10000 0 0
YES1 0.025 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.016 0.031 0.16 1 -0.23 3 4
ADAP1 -0.017 0.031 -10000 0 -0.23 4 4
ARAP3 -0.016 0.029 -10000 0 -0.23 3 3
INPPL1 0.026 0.004 -10000 0 -10000 0 0
PREX1 0.024 0.022 -10000 0 -0.46 1 1
ARHGEF6 -0.044 0.17 -10000 0 -0.46 73 73
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
ARF1 0.022 0.01 -10000 0 -10000 0 0
NRAS 0.024 0.038 -10000 0 -0.46 3 3
FYN 0.026 0.004 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
FGR 0.02 0.053 -10000 0 -0.46 6 6
mol:Ca2+ 0.01 0.053 0.22 18 -0.15 1 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.022 0.043 -10000 0 -0.46 4 4
ZAP70 0.027 0.057 0.29 10 -0.46 4 14
mol:IP3 0.009 0.065 0.25 19 -0.17 5 24
LYN 0.023 0.023 -10000 0 -0.46 1 1
ARF1/GDP -0.006 0.095 -10000 0 -0.33 21 21
RhoA/GDP 0.013 0.062 0.28 1 -0.29 4 5
PDK1/Src/Hsp90 0.045 0.034 -10000 0 -0.28 4 4
BLNK 0.019 0.053 -10000 0 -0.46 6 6
actin cytoskeleton reorganization -0.006 0.083 0.28 6 -0.3 12 18
SRC 0.025 0.006 -10000 0 -10000 0 0
PLEKHA2 -0.011 0.024 -10000 0 -0.28 4 4
RAC1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.01 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.018 0.033 -10000 0 -0.23 3 3
RhoA/GTP -0.017 0.03 -10000 0 -0.22 3 3
Src family/SYK family/BLNK-LAT 0.017 0.082 -10000 0 -0.46 8 8
BLK 0.022 0.048 0.29 6 -0.46 3 9
PDPK1 0.021 0.043 -10000 0 -0.46 4 4
CYTH1 -0.017 0.029 -10000 0 -0.23 3 3
HCK 0.022 0.038 -10000 0 -0.46 3 3
CYTH3 -0.017 0.03 -10000 0 -0.23 3 3
CYTH2 -0.017 0.03 -10000 0 -0.23 3 3
KRAS 0.026 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.026 0.13 -10000 0 -0.44 44 44
SGK1 -0.024 0.14 -10000 0 -0.48 44 44
INPP5D 0.02 0.053 -10000 0 -0.46 6 6
mol:GDP -0.017 0.1 0.2 3 -0.31 30 33
SOS1 0.026 0.004 -10000 0 -10000 0 0
SYK 0.022 0.038 -10000 0 -0.46 3 3
ARF6/GDP 0.001 0.057 0.27 1 -0.29 4 5
mol:PI-3-4-5-P3 -0.016 0.029 -10000 0 -0.23 3 3
ARAP3/RAP1A/GTP -0.016 0.031 0.16 1 -0.23 3 4
VAV1 0.018 0.057 -10000 0 -0.46 7 7
mol:PI-3-4-P2 0.008 0.037 -10000 0 -0.33 6 6
RAS family/GTP/PI3K Class I 0.038 0.033 -10000 0 -0.24 3 3
PLEKHA1 -0.012 0.024 -10000 0 -0.28 4 4
Rac1/GDP -0.004 0.1 0.21 2 -0.31 26 28
LAT 0.025 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.028 0.13 -10000 0 -0.33 70 70
ITK -0.027 0.052 -10000 0 -0.24 23 23
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.005 0.081 0.31 4 -0.31 8 12
LCK 0.023 0.038 -10000 0 -0.46 3 3
BTK -0.027 0.055 -10000 0 -0.24 24 24
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.011 0.058 0.21 2 -0.27 8 10
adherens junction organization -0.01 0.092 0.29 1 -0.34 25 26
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.08 0.22 1 -0.33 6 7
FMN1 -0.012 0.088 -10000 0 -0.31 21 21
mol:IP3 0.006 0.043 -10000 0 -0.24 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.085 -10000 0 -0.32 21 21
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.008 0.052 -10000 0 -0.26 4 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.12 -10000 0 -0.65 11 11
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0.07 -10000 0 -0.31 17 17
VASP 0.001 0.074 -10000 0 -0.31 16 16
ZYX -0.001 0.076 -10000 0 -0.31 19 19
JUB 0 0.08 -10000 0 -0.31 21 21
EGFR(dimer) -0.007 0.11 -10000 0 -0.34 27 27
E-cadherin/beta catenin-gamma catenin 0.041 0.039 -10000 0 -0.32 4 4
mol:PI-3-4-5-P3 0.022 0.063 -10000 0 -0.24 10 10
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PI3K 0.022 0.065 -10000 0 -0.24 10 10
FYN 0.011 0.051 0.21 2 -0.26 3 5
mol:Ca2+ 0.006 0.042 -10000 0 -0.24 4 4
JUP 0.025 0.022 -10000 0 -0.46 1 1
PIK3R1 0.024 0.031 -10000 0 -0.46 2 2
mol:DAG 0.006 0.043 -10000 0 -0.24 4 4
CDH1 0.02 0.044 -10000 0 -0.46 4 4
RhoA/GDP 0.01 0.082 0.22 1 -0.36 6 7
establishment of polarity of embryonic epithelium -0.001 0.076 -10000 0 -0.3 19 19
SRC 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
EGFR -0.013 0.13 -10000 0 -0.46 40 40
CASR 0.007 0.051 0.21 3 -0.32 1 4
RhoA/GTP 0.024 0.052 -10000 0 -0.22 4 4
AKT2 0.006 0.052 -10000 0 -0.26 5 5
actin cable formation -0.014 0.09 0.25 2 -0.32 20 22
apoptosis -0.014 0.07 0.26 11 -0.24 8 19
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
mol:GDP -0.006 0.077 -10000 0 -0.38 6 6
PIP5K1A -0.004 0.071 -10000 0 -0.31 17 17
PLCG1 0.006 0.044 -10000 0 -0.25 4 4
Rac1/GTP 0.002 0.1 -10000 0 -0.32 24 24
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.004 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.08 -10000 0 -0.28 30 30
forebrain development -0.013 0.15 -10000 0 -0.59 18 18
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
SMO/beta Arrestin2 0.031 0.034 -10000 0 -0.33 3 3
SMO 0.021 0.039 -10000 0 -0.46 3 3
ARRB2 0.024 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.004 0.11 -10000 0 -0.42 9 9
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.026 0.005 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.024 -10000 0 -10000 0 0
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
XPO1 0.024 0.014 -10000 0 -10000 0 0
GLI1/Su(fu) -0.007 0.14 -10000 0 -0.59 14 14
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.021 0.039 -10000 0 -0.46 3 3
MIM/GLI2A 0.01 0.077 -10000 0 -0.46 11 11
IFT88 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.004 -10000 0 -10000 0 0
GLI2 0.005 0.08 0.28 1 -0.38 11 12
GLI3 -0.006 0.11 -10000 0 -0.42 10 10
CSNK1D 0.025 0.006 -10000 0 -10000 0 0
CSNK1E 0.025 0.007 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.006 -10000 0 -10000 0 0
GNG2 -0.002 0.11 0.29 1 -0.46 29 30
Gi family/GTP 0.001 0.08 -10000 0 -0.27 34 34
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.025 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.005 0.095 -10000 0 -0.39 11 11
GLI2/Su(fu) 0.012 0.089 0.25 1 -0.36 17 18
FOXA2 -0.059 0.29 -10000 0 -0.87 53 53
neural tube patterning -0.013 0.15 -10000 0 -0.59 18 18
SPOP 0.025 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.036 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.007 -10000 0 -10000 0 0
CSNK1G3 0.026 0.004 -10000 0 -10000 0 0
MTSS1 0.01 0.077 -10000 0 -0.46 11 11
embryonic limb morphogenesis -0.013 0.15 -10000 0 -0.59 18 18
SUFU 0.018 0.018 -10000 0 -10000 0 0
LGALS3 0.023 0.037 -10000 0 -0.46 3 3
catabolic process 0.005 0.13 0.28 1 -0.41 20 21
GLI3A/CBP 0.015 0.075 -10000 0 -0.34 20 20
KIF3A 0.025 0.022 -10000 0 -0.46 1 1
GLI1 -0.014 0.15 -10000 0 -0.6 18 18
RAB23 0.025 0.022 -10000 0 -0.46 1 1
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
IFT172 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.044 -10000 0 -0.24 2 2
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
RBBP4 0.023 0.038 -10000 0 -0.46 3 3
CSNK1G1 0.025 0.006 -10000 0 -10000 0 0
PIAS1 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.017 0.088 0.26 1 -0.37 14 15
STK36 0.024 0.013 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.011 0.095 -10000 0 -0.36 22 22
PTCH1 -0.011 0.13 -10000 0 -0.61 12 12
MIM/GLI1 -0.011 0.17 -10000 0 -0.57 31 31
CREBBP 0.015 0.074 -10000 0 -0.34 20 20
Su(fu)/SIN3/HDAC complex 0.014 0.083 0.2 1 -0.42 12 13
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.009 0.082 -10000 0 -0.46 15 15
positive regulation of NF-kappaB transcription factor activity 0.014 0.078 -10000 0 -0.34 22 22
MAP2K4 0.008 0.057 -10000 0 -0.33 2 2
IKBKB 0.024 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.023 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.02 0.038 -10000 0 -0.46 3 3
SMPD1 0.005 0.032 -10000 0 -0.18 14 14
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.013 0.068 -10000 0 -0.46 10 10
TRAIL/TRAILR2 0.02 0.061 -10000 0 -0.33 14 14
TRAIL/TRAILR3 0.019 0.065 -10000 0 -0.33 16 16
TRAIL/TRAILR1 0.02 0.064 -10000 0 -0.33 15 15
TRAIL/TRAILR4 0.014 0.079 -10000 0 -0.34 22 22
TRAIL/TRAILR1/DAP3/GTP 0.024 0.052 -10000 0 -0.26 13 13
IKK complex 0.016 0.033 -10000 0 -10000 0 0
RIPK1 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.016 0.008 -10000 0 -10000 0 0
MAPK3 0 0.058 -10000 0 -0.33 15 15
MAP3K1 0.01 0.054 -10000 0 -0.23 18 18
TRAILR4 (trimer) 0.013 0.068 -10000 0 -0.46 10 10
TRADD 0.023 0.009 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.038 -10000 0 -0.46 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.049 -10000 0 -0.23 14 14
CFLAR 0.026 0.003 -10000 0 -10000 0 0
MAPK1 0 0.058 -10000 0 -0.33 15 15
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.061 -10000 0 -0.24 14 14
mol:ceramide 0.005 0.032 -10000 0 -0.18 14 14
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.009 0.063 -10000 0 -0.32 2 2
TRAF2 0.025 0.007 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.021 0.032 -10000 0 -0.46 2 2
CHUK 0.025 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.06 -10000 0 -0.28 15 15
DAP3 0.021 0.011 -10000 0 -10000 0 0
CASP10 0.008 0.082 0.23 8 -0.32 18 26
JNK cascade 0.014 0.078 -10000 0 -0.34 22 22
TRAIL (trimer) 0.009 0.082 -10000 0 -0.46 15 15
TNFRSF10C 0.021 0.032 -10000 0 -0.46 2 2
TRAIL/TRAILR1/DAP3/GTP/FADD 0.03 0.055 -10000 0 -0.24 13 13
TRAIL/TRAILR2/FADD 0.032 0.058 -10000 0 -0.28 14 14
cell death 0.005 0.032 -10000 0 -0.18 14 14
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.22 13 13
TRAILR2 (trimer) 0.023 0.009 -10000 0 -10000 0 0
CASP8 0.017 0.035 -10000 0 -0.51 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.047 0.06 -10000 0 -0.24 13 13
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.028 0.031 -10000 0 -0.63 1 1
VEGFR1 homodimer/NRP1 0.011 0.029 -10000 0 -0.63 1 1
mol:DAG 0.011 0.03 -10000 0 -0.58 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.029 -10000 0 -0.58 1 1
CaM/Ca2+ 0.025 0.029 -10000 0 -0.55 1 1
HIF1A 0.03 0.017 -10000 0 -0.33 1 1
GAB1 0.022 0.043 -10000 0 -0.46 4 4
AKT1 0.016 0.062 0.48 1 -0.46 3 4
PLCG1 0.011 0.03 -10000 0 -0.58 1 1
NOS3 0.021 0.051 0.44 2 -0.36 2 4
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:NO 0.028 0.066 0.44 5 -0.34 2 7
FLT1 0.014 0.033 -10000 0 -0.71 1 1
PGF 0.026 0.012 0.29 1 -10000 0 1
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.043 -10000 0 -0.31 6 6
CALM1 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
eNOS/Hsp90 0.037 0.058 0.4 1 -0.33 2 3
endothelial cell proliferation -0.013 0.084 0.34 3 -0.37 5 8
mol:Ca2+ 0.011 0.03 -10000 0 -0.57 1 1
MAPK3 -0.011 0.047 0.35 4 -0.25 8 12
MAPK1 -0.011 0.048 0.35 4 -0.36 1 5
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
PLGF homodimer 0.026 0.012 0.29 1 -10000 0 1
PRKACA 0.025 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.2 0.24 -10000 0 -0.46 239 239
VEGFA homodimer 0.026 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.028 0.031 -10000 0 -0.63 1 1
platelet activating factor biosynthetic process -0.013 0.046 0.33 4 -0.35 1 5
PI3K 0.048 0.039 -10000 0 -0.28 4 4
PRKCA -0.012 0.035 0.18 1 -0.26 8 9
PRKCB -0.033 0.079 0.18 1 -0.25 52 53
VEGFR1 homodimer/PLGF homodimer 0.029 0.032 -10000 0 -0.63 1 1
VEGFA 0.026 0.004 -10000 0 -10000 0 0
VEGFB 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.03 -10000 0 -0.58 1 1
RASA1 0.009 0.042 -10000 0 -0.31 6 6
NRP2 0.021 0.048 -10000 0 -0.46 5 5
VEGFR1 homodimer 0.014 0.033 -10000 0 -0.71 1 1
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.023 0.031 -10000 0 -0.46 2 2
eNOS/Caveolin-1 -0.068 0.13 0.45 1 -0.33 14 15
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.046 0.038 -10000 0 -0.28 4 4
mol:L-citrulline 0.028 0.066 0.44 5 -0.34 2 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.041 -10000 0 -0.32 4 4
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.039 0.032 -10000 0 -0.31 3 3
CD2AP 0.023 0.037 -10000 0 -0.46 3 3
PI3K/GAB1 0.056 0.046 -10000 0 -0.26 5 5
PDPK1 0.001 0.063 0.34 1 -0.42 3 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.041 0.032 -10000 0 -0.59 1 1
mol:NADP 0.028 0.066 0.44 5 -0.34 2 7
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.04 -10000 0 -0.32 4 4
VEGFR1 homodimer/NRP2 0.025 0.043 -10000 0 -0.33 6 6
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.026 0.004 -10000 0 -10000 0 0
SPHK1 0.025 0.006 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
mol:S1P 0.013 0.004 -10000 0 -10000 0 0
GNAO1 0.011 0.077 -10000 0 -0.46 13 13
mol:Sphinganine-1-P 0.012 0.012 0.27 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.048 0.039 -10000 0 -0.21 2 2
GNAI3 0.026 0.002 -10000 0 -10000 0 0
G12/G13 0.036 0.011 -10000 0 -10000 0 0
S1PR3 0.025 0.006 -10000 0 -10000 0 0
S1PR2 0.024 0.007 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.004 0.029 -10000 0 -0.22 5 5
S1PR5 0.014 0.081 0.29 4 -0.46 13 17
S1PR4 0.021 0.045 0.29 1 -0.46 4 5
GNAI1 0.011 0.082 -10000 0 -0.46 15 15
S1P/S1P5/G12 0.031 0.057 -10000 0 -0.23 16 16
S1P/S1P3/Gq -0.005 0.11 -10000 0 -0.28 57 57
S1P/S1P4/Gi 0.006 0.083 -10000 0 -0.3 25 25
GNAQ 0.023 0.031 -10000 0 -0.46 2 2
GNAZ 0.018 0.057 -10000 0 -0.46 7 7
GNA14 -0.003 0.11 -10000 0 -0.46 29 29
GNA15 0.023 0.023 -10000 0 -0.46 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.011 0.08 -10000 0 -0.46 14 14
ABCC1 0.025 0.005 -10000 0 -10000 0 0
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.013 0.043 -10000 0 -0.26 12 12
FRAP1 0.013 0.051 0.28 1 -0.37 4 5
AKT1 0.005 0.063 0.2 7 -0.26 10 17
INSR 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.012 0.2 1 -10000 0 1
mol:GTP 0.027 0.059 0.26 2 -0.31 2 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.031 -10000 0 -0.18 3 3
TSC2 0.025 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.012 0.038 -10000 0 -0.24 4 4
TSC1 0.024 0.023 -10000 0 -0.46 1 1
Insulin Receptor/IRS1 0.013 0.057 -10000 0 -0.26 19 19
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.039 -10000 0 -0.2 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.006 -10000 0 -10000 0 0
RPS6KB1 0.018 0.075 0.28 8 -0.31 7 15
MAP3K5 0.005 0.038 0.19 7 -0.25 7 14
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
apoptosis 0.005 0.038 0.19 7 -0.25 7 14
mol:LY294002 0 0 0.001 2 -0.001 19 21
EIF4B 0.018 0.072 0.26 10 -0.28 7 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.063 0.26 7 -0.25 6 13
eIF4E/eIF4G1/eIF4A1 0.014 0.027 -10000 0 -0.25 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.056 -10000 0 -0.26 16 16
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.05 0.22 12 -0.16 3 15
FKBP1A 0.026 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.03 0.052 0.21 1 -0.29 2 3
mol:Amino Acids 0 0 0.001 2 -0.001 19 21
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.006 0.063 0.17 6 -0.27 13 19
EIF4E 0.025 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.03 0.087 -10000 0 -0.54 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.078 -10000 0 -0.79 3 3
TSC1/TSC2 0.031 0.066 0.3 4 -0.33 2 6
tumor necrosis factor receptor activity 0 0 0.001 19 -0.001 2 21
RPS6 0.025 0.006 -10000 0 -10000 0 0
PPP5C 0.026 0.004 -10000 0 -10000 0 0
EIF4G1 0.024 0.008 -10000 0 -10000 0 0
IRS1 -0.002 0.057 -10000 0 -0.28 19 19
INS 0.017 0.013 0.29 1 -10000 0 1
PTEN 0.024 0.007 -10000 0 -10000 0 0
PDK2 -0.003 0.058 0.17 7 -0.24 11 18
EIF4EBP1 -0.016 0.21 -10000 0 -1 22 22
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
PPP2R5D 0.016 0.059 0.29 7 -0.34 4 11
peptide biosynthetic process -0.009 0.018 0.18 4 -10000 0 4
RHEB 0.025 0.005 -10000 0 -10000 0 0
EIF4A1 0.024 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 27 -0.003 2 29
EEF2 -0.009 0.018 0.18 4 -10000 0 4
eIF4E/4E-BP1 -0.004 0.2 -10000 0 -0.92 22 22
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0.018 -10000 0 -10000 0 0
CDKN1B 0.006 0.053 -10000 0 -0.29 5 5
CDKN1A 0.012 0.049 -10000 0 -0.31 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
FOXO3 0.012 0.039 -10000 0 -0.29 4 4
AKT1 0.012 0.029 -10000 0 -0.3 2 2
BAD 0.026 0.004 -10000 0 -10000 0 0
AKT3 -0.056 0.13 -10000 0 -0.31 103 103
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.044 -10000 0 -0.29 6 6
AKT1/ASK1 0.033 0.054 -10000 0 -0.29 5 5
BAD/YWHAZ 0.045 0.02 -10000 0 -10000 0 0
RICTOR 0.023 0.038 -10000 0 -0.46 3 3
RAF1 0.026 0.005 -10000 0 -10000 0 0
JNK cascade -0.03 0.05 0.28 5 -10000 0 5
TSC1 0.013 0.028 -10000 0 -0.28 1 1
YWHAZ 0.024 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.052 -10000 0 -0.29 4 4
EP300 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.013 0.042 -10000 0 -0.3 6 6
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.011 0.036 -10000 0 -0.29 4 4
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
TBC1D4 -0.004 0.048 -10000 0 -0.26 17 17
MAP3K5 0.024 0.031 -10000 0 -0.46 2 2
MAPKAP1 0.025 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.029 0.072 0.44 5 -0.22 3 8
YWHAH 0.025 0.007 -10000 0 -10000 0 0
AKT1S1 0.012 0.044 -10000 0 -0.29 6 6
CASP9 0.013 0.036 -10000 0 -0.29 3 3
YWHAB 0.025 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.07 0.33 2 -0.28 2 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.045 0.034 -10000 0 -0.28 4 4
YWHAE 0.024 0.007 -10000 0 -10000 0 0
SRC 0.025 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.016 0.055 0.25 3 -0.34 3 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.048 -10000 0 -0.27 12 12
CHUK 0.014 0.04 -10000 0 -0.29 3 3
BAD/BCL-XL 0.037 0.045 -10000 0 -0.28 1 1
mTORC2 0.029 0.024 -10000 0 -0.25 3 3
AKT2 0.01 0.028 -10000 0 -0.3 4 4
FOXO1-3a-4/14-3-3 family 0.035 0.084 0.25 9 -0.41 6 15
PDPK1 0.021 0.043 -10000 0 -0.46 4 4
MDM2 0.012 0.042 -10000 0 -0.29 5 5
MAPKKK cascade -0.037 0.051 0.28 4 -10000 0 4
MDM2/Cbp/p300 0.046 0.057 0.3 1 -0.28 1 2
TSC1/TSC2 0.011 0.033 0.28 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.055 0.29 1 -0.27 1 2
glucose import -0.046 0.1 0.21 3 -0.26 91 94
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.037 0.18 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.047 0.1 0.21 1 -0.26 91 92
GSK3A 0.012 0.044 -10000 0 -0.29 6 6
FOXO1 0.011 0.038 -10000 0 -0.29 5 5
GSK3B 0.011 0.044 -10000 0 -0.29 6 6
SFN 0.036 0.08 0.29 30 -0.46 5 35
G1/S transition of mitotic cell cycle 0.019 0.058 0.24 9 -0.29 2 11
p27Kip1/14-3-3 family 0.027 0.075 -10000 0 -0.62 4 4
PRKACA 0.025 0.006 -10000 0 -10000 0 0
KPNA1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
RHEB 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.026 0.076 0.28 6 -0.38 8 14
PDGFB-D/PDGFRB/SLAP 0.033 0.027 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/APS/CBL 0.055 0.044 0.22 1 -0.28 2 3
AKT1 0.023 0.097 0.33 27 -10000 0 27
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.034 0.087 0.31 3 -0.41 9 12
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
FGR -0.002 0.1 0.33 1 -0.48 16 17
mol:Ca2+ 0.024 0.094 0.3 5 -0.42 11 16
MYC 0.042 0.17 0.38 18 -0.76 14 32
SHC1 0.022 0.01 -10000 0 -10000 0 0
HRAS/GDP 0.029 0.045 -10000 0 -0.24 6 6
LRP1/PDGFRB/PDGFB 0.045 0.042 -10000 0 -0.28 7 7
GRB10 0.024 0.031 -10000 0 -0.46 2 2
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.024 0.095 0.3 5 -0.45 10 15
PTEN 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.02 0.044 -10000 0 -0.46 4 4
PDGFB-D/PDGFRB/SHP2 0.036 0.029 -10000 0 -0.33 3 3
PDGFB-D/PDGFRB/GRB10 0.034 0.038 -10000 0 -0.33 5 5
cell cycle arrest 0.033 0.027 -10000 0 -0.33 2 2
HRAS 0.025 0.006 -10000 0 -10000 0 0
HIF1A 0.018 0.091 0.31 28 -10000 0 28
GAB1 0.029 0.095 0.32 5 -0.4 11 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.031 0.095 0.31 14 -0.36 10 24
PDGFB-D/PDGFRB 0.047 0.028 -10000 0 -0.29 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.036 0.025 -10000 0 -0.33 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.068 0.24 1 -0.34 6 7
positive regulation of MAPKKK cascade 0.036 0.029 -10000 0 -0.33 3 3
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
mol:IP3 0.024 0.096 0.31 5 -0.45 10 15
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.03 0.045 -10000 0 -0.33 7 7
SHB 0.025 0.005 -10000 0 -10000 0 0
BLK -0.018 0.13 0.32 2 -0.42 37 39
PTPN2 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.036 0.029 -10000 0 -0.33 3 3
BCAR1 0.023 0.009 -10000 0 -10000 0 0
VAV2 0.03 0.11 0.33 6 -0.47 10 16
CBL 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.036 0.03 -10000 0 -0.33 3 3
LCK 0.004 0.084 0.33 1 -0.48 10 11
PDGFRB 0.023 0.038 -10000 0 -0.46 3 3
ACP1 0.025 0.005 -10000 0 -10000 0 0
HCK 0.009 0.074 0.33 1 -0.68 4 5
ABL1 0.025 0.091 0.27 11 -0.37 11 22
PDGFB-D/PDGFRB/CBL 0.027 0.1 0.32 4 -0.44 13 17
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.026 0.003 -10000 0 -10000 0 0
STAT3 0.025 0.006 -10000 0 -10000 0 0
STAT1 0.026 0.003 -10000 0 -10000 0 0
cell proliferation 0.043 0.16 0.36 21 -0.67 14 35
SLA 0.022 0.023 -10000 0 -0.46 1 1
actin cytoskeleton reorganization 0.035 0.06 0.34 8 -0.23 3 11
SRC 0.009 0.064 0.33 1 -0.81 2 3
PI3K -0.015 0.022 -10000 0 -0.22 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.045 -10000 0 -0.28 7 7
SH2B2 0.039 0.06 0.29 27 -10000 0 27
PLCgamma1/SPHK1 0.034 0.089 0.31 3 -0.42 9 12
LYN 0.01 0.047 0.33 1 -0.41 2 3
LRP1 0.021 0.048 -10000 0 -0.46 5 5
SOS1 0.026 0.004 -10000 0 -10000 0 0
STAT5B 0.025 0.006 -10000 0 -10000 0 0
STAT5A 0.025 0.006 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.061 0.043 -10000 0 -0.24 3 3
SPHK1 0.026 0.007 -10000 0 -10000 0 0
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.024 0.096 0.31 5 -0.45 10 15
PLCG1 0.024 0.098 0.31 5 -0.46 10 15
NHERF/PDGFRB 0.046 0.03 -10000 0 -0.28 3 3
YES1 0.002 0.082 -10000 0 -0.48 11 11
cell migration 0.046 0.03 -10000 0 -0.28 3 3
SHC/Grb2/SOS1 0.054 0.042 -10000 0 -0.24 1 1
SLC9A3R2 0.025 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.006 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.055 0.036 -10000 0 -0.25 3 3
FYN 0.01 0.058 0.33 1 -0.5 3 4
DOK1 0.021 0.041 0.18 27 -0.26 1 28
HRAS/GTP 0.019 0.004 -10000 0 -10000 0 0
PDGFB 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.14 0.36 5 -0.51 18 23
PRKCD 0.021 0.043 0.18 29 -0.26 1 30
FER 0.019 0.047 0.18 16 -0.26 4 20
MAPKKK cascade 0.035 0.099 0.41 13 -0.23 1 14
RASA1 0.018 0.052 0.18 21 -0.26 6 27
NCK1 0.023 0.031 -10000 0 -0.46 2 2
NCK2 0.026 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.033 0.035 -10000 0 -0.24 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.03 -10000 0 -0.33 3 3
chemotaxis 0.025 0.09 0.27 11 -0.36 11 22
STAT1-3-5/STAT1-3-5 0.055 0.03 -10000 0 -0.23 1 1
Bovine Papilomavirus E5/PDGFRB 0.017 0.027 -10000 0 -0.33 3 3
PTPRJ 0.026 0.005 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.094 0.26 5 -0.33 11 16
ERC1 0.026 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.027 -10000 0 -0.33 2 2
NFKBIA 0.009 0.015 -10000 0 -0.25 1 1
BIRC2 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.024 0.008 -10000 0 -10000 0 0
RIPK2 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.028 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.031 0.11 -10000 0 -0.33 28 28
NEMO/A20/RIP2 0.024 0.008 -10000 0 -10000 0 0
XPO1 0.026 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.017 0.11 0.27 2 -0.34 37 39
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.018 0.099 -10000 0 -0.32 29 29
BCL10/MALT1/TRAF6 0.049 0.015 -10000 0 -10000 0 0
NOD2 0.021 0.038 -10000 0 -0.46 3 3
NFKB1 0.026 0.022 -10000 0 -0.46 1 1
RELA 0.028 0.004 -10000 0 -10000 0 0
MALT1 0.025 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.037 0.01 -10000 0 -10000 0 0
ATM 0.025 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.041 0.056 0.22 23 -0.33 6 29
TRAF6 0.025 0.006 -10000 0 -10000 0 0
PRKCA 0.014 0.071 -10000 0 -0.46 11 11
CHUK 0.025 0.006 -10000 0 -10000 0 0
UBE2D3 0.025 0.005 -10000 0 -10000 0 0
TNF 0.031 0.08 0.29 23 -0.46 7 30
NF kappa B1 p50/RelA 0.056 0.021 -10000 0 -0.28 1 1
BCL10 0.026 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.015 -10000 0 -0.25 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.021 0.1 -10000 0 -0.33 30 30
CYLD 0.024 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.024 0.11 -10000 0 -0.33 29 29
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.025 0.005 -9999 0 -10000 0 0
ITGB7 0.024 0.031 -9999 0 -0.46 2 2
ITGA4 0.015 0.071 -9999 0 -0.46 11 11
alpha4/beta7 Integrin 0.029 0.059 -9999 0 -0.36 11 11
alpha4/beta1 Integrin 0.03 0.052 -9999 0 -0.33 10 10
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.011 0.096 -10000 0 -0.37 10 10
KLHL20 0 0.065 -10000 0 -0.21 25 25
CYFIP2 0.023 0.037 -10000 0 -0.46 3 3
Rac1/GDP 0.007 0.07 0.28 1 -0.27 6 7
ENAH -0.015 0.097 -10000 0 -0.36 13 13
AP1M1 0.025 0.006 -10000 0 -10000 0 0
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.026 0.002 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.031 -10000 0 -0.2 3 3
ABI1/Sra1/Nap1 -0.015 0.038 -10000 0 -0.14 28 28
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.052 0.045 -10000 0 -0.3 5 5
RAPGEF1 -0.005 0.079 0.23 1 -0.32 9 10
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.008 0.11 -10000 0 -0.28 59 59
CRK -0.003 0.083 -10000 0 -0.34 9 9
E-cadherin/gamma catenin/alpha catenin 0.042 0.041 -10000 0 -0.34 4 4
alphaE/beta7 Integrin 0.034 0.026 -10000 0 -0.33 2 2
IQGAP1 0.025 0.022 -10000 0 -0.46 1 1
NCKAP1 0.026 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.011 -10000 0 -10000 0 0
DLG1 -0.009 0.091 -10000 0 -0.35 11 11
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.018 -10000 0 -10000 0 0
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.028 -10000 0 -0.26 3 3
PI3K 0.006 0.027 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.03 0.042 -10000 0 -0.4 4 4
TIAM1 0.022 0.043 -10000 0 -0.46 4 4
E-cadherin(dimer)/Ca2+ 0.051 0.035 -10000 0 -0.24 4 4
AKT1 -0.007 0.023 -10000 0 -10000 0 0
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
CDH1 0.019 0.044 -10000 0 -0.46 4 4
RhoA/GDP 0.007 0.068 -10000 0 -0.26 6 6
actin cytoskeleton organization 0.002 0.05 0.17 2 -0.16 21 23
CDC42/GDP 0.009 0.07 0.28 1 -0.26 7 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.014 0.029 -10000 0 -0.28 4 4
ITGB7 0.024 0.031 -10000 0 -0.46 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.055 0.038 -10000 0 -0.26 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin 0.038 0.03 -10000 0 -0.24 4 4
mol:GDP -0.007 0.074 0.29 1 -0.31 7 8
CDC42/GTP/IQGAP1 0.033 0.016 -10000 0 -0.28 1 1
JUP 0.024 0.022 -10000 0 -0.46 1 1
p120 catenin/RhoA/GDP 0.015 0.071 -10000 0 -0.28 5 5
RAC1/GTP/IQGAP1 0.033 0.017 -10000 0 -0.28 1 1
PIP5K1C/AP1M1 0.035 0.012 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.006 0.041 0.14 3 -0.2 6 9
NME1 0.025 0.013 0.29 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.09 -10000 0 -0.36 11 11
regulation of cell-cell adhesion 0.012 0.025 -10000 0 -0.18 3 3
WASF2 0.003 0.027 -10000 0 -0.11 1 1
Rap1/GTP 0.024 0.041 -10000 0 -0.22 3 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.053 -10000 0 -0.33 5 5
CCND1 0.007 0.049 0.16 3 -0.24 6 9
VAV2 -0.024 0.16 -10000 0 -0.55 35 35
RAP1/GDP 0.023 0.059 -10000 0 -0.25 4 4
adherens junction assembly -0.006 0.088 -10000 0 -0.35 11 11
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.006 -10000 0 -10000 0 0
PIP5K1C 0.024 0.007 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.045 0.047 -10000 0 -0.32 5 5
E-cadherin/beta catenin 0.008 0.033 -10000 0 -0.31 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.011 0.096 -10000 0 -0.34 14 14
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
Rac1/GTP -0.016 0.091 -10000 0 -0.31 33 33
E-cadherin/beta catenin/alpha catenin 0.043 0.035 -10000 0 -0.28 4 4
ITGAE 0.024 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.008 0.11 -10000 0 -0.32 28 28
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.012 0.13 -10000 0 -0.37 28 28
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.006 -10000 0 -10000 0 0
STXBP4 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.027 0.14 0.31 2 -0.39 33 35
YWHAZ 0.024 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.005 -10000 0 -10000 0 0
YWHAQ 0.025 0.006 -10000 0 -10000 0 0
TBC1D4 0.001 0.058 -10000 0 -0.33 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.025 0.007 -10000 0 -10000 0 0
YWHAB 0.025 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.046 0.019 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
ASIP 0.025 0.03 0.29 6 -10000 0 6
PRKCI 0.024 0.008 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.026 0.004 -10000 0 -10000 0 0
GYS1 0.01 0.018 0.24 3 -10000 0 3
PRKCZ 0.024 0.022 -10000 0 -0.46 1 1
TRIP10 0.024 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.011 -10000 0 -10000 0 0
AS160/14-3-3 0.021 0.043 -10000 0 -0.25 3 3
VAMP2 0.024 0.008 -10000 0 -10000 0 0
SLC2A4 -0.032 0.15 0.32 2 -0.43 33 35
STX4 0.025 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.006 -10000 0 -10000 0 0
SFN 0.036 0.08 0.29 30 -0.46 5 35
LNPEP 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.056 0.065 -10000 0 -0.27 9 9
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.063 -10000 0 -0.27 12 12
SUMO1 0.026 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.005 -10000 0 -10000 0 0
FKBP3 0.026 0.004 -10000 0 -10000 0 0
Histones 0.061 0.041 -10000 0 -10000 0 0
YY1/LSF 0.005 0.084 -10000 0 -0.25 40 40
SMG5 0.021 0.011 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.024 0.034 -10000 0 -0.23 6 6
I kappa B alpha/HDAC1 0.034 0.036 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
RELA 0.025 0.039 0.28 1 -0.21 7 8
HDAC1/Smad7 0.047 0.03 -10000 0 -0.28 3 3
RANGAP1 0.025 0.007 -10000 0 -10000 0 0
HDAC3/TR2 0.035 0.038 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.034 0.043 -10000 0 -0.34 1 1
NF kappa B1 p50/RelA 0.025 0.069 0.24 1 -0.26 15 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.023 0.046 0.29 2 -0.46 4 6
GATA1 0.021 0.006 -10000 0 -10000 0 0
Mad/Max 0.037 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.024 0.074 -10000 0 -0.38 6 6
RBBP7 0.026 0.004 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.038 -10000 0 -0.46 3 3
MAX 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NFKBIA 0.02 0.026 -10000 0 -10000 0 0
KAT2B 0.005 0.097 -10000 0 -0.46 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.02 0.026 -10000 0 -10000 0 0
SIN3 complex 0.058 0.024 -10000 0 -10000 0 0
SMURF1 0.026 0.004 -10000 0 -10000 0 0
CHD3 0.024 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.024 0.008 -10000 0 -10000 0 0
YY1/HDAC3 0.011 0.069 -10000 0 -0.35 7 7
YY1/HDAC2 0.007 0.078 -10000 0 -0.24 37 37
YY1/HDAC1 0.01 0.076 -10000 0 -0.24 35 35
NuRD/MBD2 Complex (MeCP1) 0.034 0.043 -10000 0 -0.34 1 1
PPARG -0.05 0.14 -10000 0 -0.28 118 118
HDAC8/hEST1B 0.04 0.024 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.035 0.037 -10000 0 -10000 0 0
MBD3L2 0.025 0.048 0.29 16 -10000 0 16
ubiquitin-dependent protein catabolic process 0.046 0.03 -10000 0 -0.28 3 3
CREBBP 0.025 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.029 0.071 -10000 0 -0.38 5 5
HDAC1 0.026 0.004 -10000 0 -10000 0 0
HDAC3 0.021 0.026 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
YY1 0.007 0.052 -10000 0 -0.26 18 18
HDAC8 0.026 0.002 -10000 0 -10000 0 0
SMAD7 0.022 0.038 -10000 0 -0.46 3 3
NCOR2 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.004 -10000 0 -10000 0 0
STAT3 0.018 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.022 -10000 0 -0.46 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.081 -10000 0 -0.23 35 35
YY1/SAP30/HDAC1 0.025 0.074 -10000 0 -0.23 27 27
EP300 0.025 0.007 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.026 -10000 0 -10000 0 0
histone deacetylation 0.033 0.045 -10000 0 -0.29 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.031 -10000 0 -10000 0 0
nuclear export -0.039 0.023 -10000 0 -10000 0 0
PRKACA 0.025 0.006 -10000 0 -10000 0 0
GATAD2B 0.021 0.01 -10000 0 -10000 0 0
GATAD2A 0.025 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 0.032 0.046 0.28 1 -0.29 3 4
GATA1/HDAC1 0.034 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.03 0.038 -10000 0 -10000 0 0
CHD4 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.041 0.056 0.22 23 -0.33 6 29
SIN3/HDAC complex/Mad/Max 0.026 0.044 -10000 0 -0.57 1 1
NuRD Complex 0.031 0.067 -10000 0 -0.38 4 4
positive regulation of chromatin silencing 0.058 0.04 -10000 0 -10000 0 0
SIN3B 0.025 0.006 -10000 0 -10000 0 0
MTA2 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.025 0.005 -10000 0 -10000 0 0
XPO1 0.026 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.031 0.043 -10000 0 -0.24 2 2
HDAC complex 0.062 0.03 -10000 0 -0.26 3 3
GATA1/Fog1 0.031 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.05 0.013 -10000 0 -10000 0 0
TNF 0.031 0.08 0.29 23 -0.46 7 30
negative regulation of cell growth 0.024 0.05 -10000 0 -0.3 5 5
NuRD/MBD2/PRMT5 Complex 0.034 0.043 -10000 0 -0.34 1 1
Ran/GTP/Exportin 1 0.032 0.042 -10000 0 -0.23 1 1
NF kappa B/RelA/I kappa B alpha 0.017 0.057 -10000 0 -0.27 13 13
SIN3/HDAC complex/NCoR1 0.013 0.067 -10000 0 -0.37 9 9
TFCP2 0.021 0.048 -10000 0 -0.46 5 5
NR2C1 0.026 0.002 -10000 0 -10000 0 0
MBD3 0.024 0.007 -10000 0 -10000 0 0
MBD2 0.025 0.005 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.053 0.18 -10000 0 -0.46 81 81
CLTC 0.016 0.058 -10000 0 -0.43 7 7
calcium ion-dependent exocytosis 0.01 0.029 -10000 0 -0.29 2 2
Dynamin 2/GTP 0.023 0.009 -10000 0 -10000 0 0
EXOC4 0.025 0.006 -10000 0 -10000 0 0
CD59 0.01 0.037 -10000 0 -0.33 5 5
CPE -0.014 0.084 -10000 0 -0.28 46 46
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
membrane fusion 0.012 0.018 -10000 0 -10000 0 0
CTNND1 -0.006 0.028 0.18 11 -10000 0 11
DNM2 0.024 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.013 0.038 0.18 2 -0.4 2 4
TSHR 0.014 0.032 0.16 22 -10000 0 22
INS -0.007 0.1 -10000 0 -0.46 23 23
BIN1 0.024 0.031 -10000 0 -0.46 2 2
mol:Choline 0.012 0.018 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.009 -10000 0 -10000 0 0
JUP 0.011 0.03 -10000 0 -0.31 3 3
ASAP2/amphiphysin II 0.047 0.019 -10000 0 -0.26 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.038 -10000 0 -0.33 5 5
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.025 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.018 0.032 -10000 0 -0.31 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.034 0.046 0.34 3 -10000 0 3
positive regulation of phagocytosis 0.013 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.009 -10000 0 -10000 0 0
ACAP1 0.013 0.03 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.037 -10000 0 -0.32 5 5
clathrin heavy chain/ACAP1 0.017 0.049 -10000 0 -0.33 6 6
JIP4/KLC1 0.046 0.015 -10000 0 -10000 0 0
EXOC1 0.026 0.004 -10000 0 -10000 0 0
exocyst 0.018 0.032 -10000 0 -0.32 1 1
RALA/GTP 0.019 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.009 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 -0.007 0.026 0.18 9 -10000 0 9
NME1 0.013 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.016 0.062 0.26 1 -0.42 7 8
IL2RA 0.009 0.046 -10000 0 -0.33 5 5
VAMP3 0.013 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.095 -10000 0 -0.3 8 8
EXOC6 0.025 0.006 -10000 0 -10000 0 0
PLD1 0.01 0.018 -10000 0 -0.25 2 2
PLD2 0.012 0.006 -10000 0 -10000 0 0
EXOC5 0.025 0.022 -10000 0 -0.46 1 1
PIP5K1C 0.011 0.031 -10000 0 -0.49 1 1
SDC1 0.01 0.043 -10000 0 -0.36 5 5
ARF6/GDP 0.023 0.006 -10000 0 -10000 0 0
EXOC7 0.025 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.036 0.047 -10000 0 -0.35 3 3
mol:Phosphatidic acid 0.012 0.018 -10000 0 -10000 0 0
endocytosis -0.045 0.019 0.25 1 -10000 0 1
SCAMP2 0.025 0.005 -10000 0 -10000 0 0
ADRB2 -0.11 0.12 -10000 0 -0.4 17 17
EXOC3 0.025 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.01 -10000 0 -10000 0 0
KLC1 0.026 0.005 -10000 0 -10000 0 0
AVPR2 -0.034 0.12 0.24 4 -0.4 10 14
RALA 0.026 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.045 0.33 1 -0.33 3 4
p38 MAPK signaling 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
TRAF6/ASK1 0.016 0.025 -10000 0 -0.23 2 2
TRAF2/ASK1 0.031 0.023 -10000 0 -0.28 2 2
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 0 0.097 0.26 1 -0.38 19 20
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.005 0.09 0.32 2 -0.33 19 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.025 0.006 -10000 0 -10000 0 0
TXN 0.006 0.002 -10000 0 -10000 0 0
CALM1 0.025 0.005 -10000 0 -10000 0 0
GADD45A 0.026 0.003 -10000 0 -10000 0 0
GADD45B 0.023 0.023 -10000 0 -0.46 1 1
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
MAP3K6 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
MAP3K4 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.025 -10000 0 -0.33 2 2
TAK1/TAB family 0 0.021 -10000 0 -0.16 3 3
RAC1/OSM/MEKK3 0.046 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.018 0.083 -10000 0 -0.32 15 15
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.038 0.087 0.29 36 -0.46 6 42
CCM2 0.026 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.041 0.055 0.2 35 -0.28 6 41
MAPK11 0.024 0.008 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.052 0.057 0.2 34 -0.25 8 42
OSM/MEKK3 0.036 0.011 -10000 0 -10000 0 0
TAOK1 0.001 0.061 -10000 0 -0.32 18 18
TAOK2 0.013 0.004 -10000 0 -10000 0 0
TAOK3 0.013 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.024 0.031 -10000 0 -0.46 2 2
MAP3K10 0.025 0.006 -10000 0 -10000 0 0
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.015 0.034 -10000 0 -0.27 2 2
GADD45/MTK1/MTK1 0.055 0.022 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD2 0.003 0.045 0.25 4 -0.24 6 10
SMAD3 0.018 0.03 -10000 0 -0.24 2 2
SMAD3/SMAD4 0.022 0.091 -10000 0 -0.47 15 15
SMAD4/Ubc9/PIASy 0.047 0.019 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.05 -10000 0 -0.27 1 1
PPM1A 0.026 0.005 -10000 0 -10000 0 0
CALM1 0.025 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.016 0.044 0.22 3 -0.23 5 8
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.065 -10000 0 -0.33 16 16
MAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPK1 0.024 0.022 -10000 0 -0.46 1 1
NUP214 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.026 0.004 -10000 0 -10000 0 0
CTDSP2 0.026 0.002 -10000 0 -10000 0 0
CTDSPL 0.025 0.022 -10000 0 -0.46 1 1
KPNB1 0.025 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.011 0.085 -10000 0 -0.46 16 16
UBE2I 0.025 0.006 -10000 0 -10000 0 0
NUP153 0.025 0.022 -10000 0 -0.46 1 1
KPNA2 0.025 0.006 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.022 -10000 0 -0.46 1 1
PLK4 0.028 0.024 0.29 4 -10000 0 4
regulation of centriole replication 0.011 0.019 0.15 3 -0.33 1 4
Arf6 downstream 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
PLAUR 0.021 0.024 -10000 0 -10000 0 0
regulation of axonogenesis -0.007 0.023 0.23 3 -10000 0 3
myoblast fusion -0.023 0.027 -10000 0 -10000 0 0
mol:GTP 0.019 0.022 -10000 0 -0.15 7 7
regulation of calcium-dependent cell-cell adhesion -0.047 0.036 0.25 4 -10000 0 4
ARF1/GTP 0.028 0.024 -10000 0 -10000 0 0
mol:GM1 0.009 0.016 -10000 0 -10000 0 0
mol:Choline 0.007 0.02 -10000 0 -0.26 2 2
lamellipodium assembly 0.01 0.05 -10000 0 -0.36 7 7
MAPK3 0.022 0.018 0.19 2 -10000 0 2
ARF6/GTP/NME1/Tiam1 0.048 0.036 -10000 0 -0.25 4 4
ARF1 0.022 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.039 -10000 0 -0.23 4 4
ARF6 0.033 0.01 -10000 0 -10000 0 0
RAB11A 0.025 0.006 -10000 0 -10000 0 0
TIAM1 0.022 0.044 -10000 0 -0.46 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.024 0.19 2 -0.29 1 3
actin filament bundle formation -0.03 0.036 0.21 6 -10000 0 6
KALRN 0.011 0.027 -10000 0 -0.24 4 4
RAB11FIP3/RAB11A 0.036 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.037 -10000 0 -0.22 6 6
NME1 0.026 0.014 0.29 1 -10000 0 1
Rac1/GDP 0.031 0.038 -10000 0 -0.23 4 4
substrate adhesion-dependent cell spreading 0.019 0.022 -10000 0 -0.15 7 7
cortical actin cytoskeleton organization 0.01 0.05 -10000 0 -0.36 7 7
RAC1 0.025 0.005 -10000 0 -10000 0 0
liver development 0.019 0.022 -10000 0 -0.15 7 7
ARF6/GTP 0.019 0.022 -10000 0 -0.15 7 7
RhoA/GTP 0.033 0.021 -10000 0 -10000 0 0
mol:GDP 0.012 0.026 0.18 2 -0.21 4 6
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.021 -10000 0 -10000 0 0
RHOA 0.025 0.005 -10000 0 -10000 0 0
PLD1 0.015 0.026 -10000 0 -0.3 2 2
RAB11FIP3 0.025 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.01 0.05 -10000 0 -0.36 7 7
ruffle organization 0.007 0.023 -10000 0 -0.23 3 3
regulation of epithelial cell migration 0.019 0.022 -10000 0 -0.15 7 7
PLD2 0.018 0.014 -10000 0 -10000 0 0
PIP5K1A 0.007 0.023 -10000 0 -0.24 3 3
mol:Phosphatidic acid 0.007 0.02 -10000 0 -0.26 2 2
Rac1/GTP 0.01 0.05 -10000 0 -0.36 7 7
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 0.037 0.009 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.015 0.052 -10000 0 -0.28 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.041 -10000 0 -0.23 1 1
NFKBIA 0.014 0.028 -10000 0 -0.19 4 4
MAPK14 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.024 0.017 -10000 0 -0.28 1 1
ARRB2 0.012 0.004 -10000 0 -10000 0 0
REL 0.012 0.08 -10000 0 -0.46 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.023 0.017 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.024 0.017 -10000 0 -0.28 1 1
PIK3CA 0.023 0.023 -10000 0 -0.46 1 1
NF kappa B1 p50 dimer 0.018 0.02 0.25 1 -0.33 1 2
PIK3R1 0.023 0.031 -10000 0 -0.46 2 2
NFKB1 0.01 0.016 -10000 0 -0.33 1 1
RELA 0.026 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.036 -10000 0 -0.22 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.027 0.04 -10000 0 -10000 0 0
SRC 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.031 0.031 -10000 0 -0.33 3 3
NF kappa B1 p50/RelA 0.019 0.037 -10000 0 -0.22 4 4
IKBKB 0.024 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.022 0.038 -10000 0 -0.46 3 3
I kappa B alpha/PIK3R1 0.026 0.046 -10000 0 -0.22 3 3
cell death 0.026 0.039 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.015 0.052 -10000 0 -0.28 15 15
LCK 0.023 0.038 -10000 0 -0.46 3 3
BCL3 0.025 0.005 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.042 0.041 -9999 0 -0.34 4 4
E-cadherin/beta catenin 0.031 0.035 -9999 0 -0.33 4 4
CTNNB1 0.026 0.005 -9999 0 -10000 0 0
JUP 0.024 0.022 -9999 0 -0.46 1 1
CDH1 0.019 0.044 -9999 0 -0.46 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.045 0.021 -9999 0 -10000 0 0
CLOCK 0.025 0.037 -9999 0 -0.46 3 3
TIMELESS/CRY2 0.035 0.019 -9999 0 -10000 0 0
DEC1/BMAL1 0.03 0.019 -9999 0 -0.33 1 1
ATR 0.025 0.005 -9999 0 -10000 0 0
NR1D1 0.017 0.012 -9999 0 -10000 0 0
ARNTL 0.026 0.022 -9999 0 -0.46 1 1
TIMELESS 0.018 0.011 -9999 0 -10000 0 0
NPAS2 0.022 0.053 -9999 0 -0.46 6 6
CRY2 0.025 0.005 -9999 0 -10000 0 0
mol:CO -0.007 0 -9999 0 -10000 0 0
CHEK1 0.025 0.006 -9999 0 -10000 0 0
mol:HEME 0.007 0 -9999 0 -10000 0 0
PER1 0.015 0.064 -9999 0 -0.46 9 9
BMAL/CLOCK/NPAS2 0.052 0.047 -9999 0 -0.28 9 9
BMAL1/CLOCK 0.016 0.064 -9999 0 -0.46 1 1
S phase of mitotic cell cycle 0.045 0.021 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.046 0.022 -9999 0 -10000 0 0
mol:NADPH 0.007 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.028 0.039 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.017 0.005 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.004 0.013 -10000 0 -10000 0 0
MDM2/SUMO1 0.029 0.045 -10000 0 -0.18 11 11
HDAC4 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.004 0.012 -10000 0 -10000 0 0
SUMO1 0.026 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.014 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.008 0.003 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.03 0.044 -10000 0 -0.23 2 2
SUMO1/HDAC1 0.031 0.043 -10000 0 -0.24 2 2
RANGAP1 0.025 0.007 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.012 0.005 -10000 0 -10000 0 0
Ran/GTP 0.02 0.039 -10000 0 -0.17 9 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.003 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.043 0.2 7 -0.23 1 8
NPC 0.016 0.002 -10000 0 -10000 0 0
PIAS2 0.025 0.005 -10000 0 -10000 0 0
PIAS1 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 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 0.01 0.031 0.15 19 -10000 0 19
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.031 0.055 0.16 5 -0.22 2 7
AP2 0.035 0.013 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.012 -10000 0 -10000 0 0
CLTB 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.009 -10000 0 -10000 0 0
CD4 0.024 0.031 -10000 0 -0.46 2 2
CLTA 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.012 0.26 1 -10000 0 1
mol:PI-4-5-P2 0.005 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.017 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.01 0.2 1 -10000 0 1
mol:Choline 0.005 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.023 0.012 -10000 0 -10000 0 0
DDEF1 0.004 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.003 0.018 0.19 1 -0.11 2 3
AP2M1 0.024 0.008 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.008 -10000 0 -10000 0 0
Rac/GTP 0.022 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.029 0.019 0.19 1 -10000 0 1
ARFIP2 0.014 0.019 -10000 0 -10000 0 0
COPA 0.022 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.026 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.015 0.009 -10000 0 -10000 0 0
GGA3 0.025 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.047 -10000 0 -0.23 13 13
AP2A1 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.21 3 3
ARF1/GDP/Membrin 0.011 0.056 -10000 0 -0.23 23 23
Arfaptin 2/Rac/GDP 0.029 0.013 -10000 0 -10000 0 0
CYTH2 0.031 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.029 0.016 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.015 0.024 -10000 0 -0.19 2 2
PLD2 0.005 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.012 0.26 1 -10000 0 1
PIP5K1A 0.005 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.022 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.012 0.26 1 -10000 0 1
GOSR2 0.008 0.026 -10000 0 -0.31 3 3
USO1 0.007 0.03 -10000 0 -0.31 4 4
GBF1 0.007 0.029 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.029 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.028 -10000 0 -0.28 2 2
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 0.035 0.012 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
CHUK 0.025 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.067 0.028 -9999 0 -10000 0 0
NFKB1 0.024 0.022 -9999 0 -0.46 1 1
MAP3K14 0.025 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.036 0.019 -9999 0 -0.33 1 1
RELB 0.025 0.005 -9999 0 -10000 0 0
NFKB2 0.025 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.033 0.01 -9999 0 -10000 0 0
regulation of B cell activation 0.032 0.01 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 505 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.QS.A5YR TCGA.QS.A5YQ
109_MAP3K5 -0.15 0.027 0.027 -0.15
47_PPARGC1A -0.46 -0.46 -0.46 -0.46
105_BMP4 0.026 -0.46 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0 0.026 0.026
105_BMP2 0.026 -0.46 0.026 -0.46
131_RELN/VLDLR -0.26 -0.065 0.068 0.068
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.026 0.026
84_STAT5B -0.13 -0.19 0.019 -0.1
84_STAT5A -0.13 -0.19 0.019 -0.1
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/UCEC-TP/6044654/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/UCEC-TP/6154820/Gistic2_Analysis_6154889/all_data_by_genes.txt

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.

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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