PARADIGM pathway analysis of mRNASeq expression data
Brain Lower Grade Glioma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1T43RM6
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1T43RM6
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 65 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
IL23-mediated signaling events 93
Ephrin A reverse signaling 84
TCGA08_retinoblastoma 66
FOXM1 transcription factor network 65
IL12-mediated signaling events 63
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 59
Aurora B signaling 58
Effects of Botulinum toxin 56
TCR signaling in naïve CD8+ T cells 51
E-cadherin signaling events 49
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 365 . 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 ( 365 ).

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
IL23-mediated signaling events 0.2548 93 5599 60 -0.71 0.014 1000 -1000 -0.14 -1000
Ephrin A reverse signaling 0.2301 84 589 7 -0.13 0 1000 -1000 -0.025 -1000
TCGA08_retinoblastoma 0.1808 66 529 8 -0.1 0.073 1000 -1000 -0.02 -1000
FOXM1 transcription factor network 0.1781 65 3336 51 -0.4 0.025 1000 -1000 -0.17 -1000
IL12-mediated signaling events 0.1726 63 5543 87 -0.56 0.13 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1616 59 4033 68 -0.48 0.23 1000 -1000 -0.11 -1000
Aurora B signaling 0.1589 58 3922 67 -0.32 0.014 1000 -1000 -0.063 -1000
Effects of Botulinum toxin 0.1534 56 1480 26 -0.21 0.014 1000 -1000 -0.055 -1000
TCR signaling in naïve CD8+ T cells 0.1397 51 4782 93 -0.22 0.074 1000 -1000 -0.074 -1000
E-cadherin signaling events 0.1342 49 249 5 -0.13 0.014 1000 -1000 -0.042 -1000
Signaling events mediated by the Hedgehog family 0.1315 48 2516 52 -0.17 0.15 1000 -1000 -0.06 -1000
IL4-mediated signaling events 0.1315 48 4422 91 -0.6 0.43 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 0.1288 47 1621 34 -0.22 0.014 1000 -1000 -0.057 -1000
Thromboxane A2 receptor signaling 0.1205 44 4723 105 -0.23 0.064 1000 -1000 -0.053 -1000
Syndecan-4-mediated signaling events 0.1205 44 2988 67 -0.19 0.037 1000 -1000 -0.076 -1000
amb2 Integrin signaling 0.1041 38 3197 82 -0.22 0.014 1000 -1000 -0.07 -1000
Reelin signaling pathway 0.1041 38 2166 56 -0.29 0.014 1000 -1000 -0.07 -1000
a4b1 and a4b7 Integrin signaling 0.1014 37 189 5 -0.08 -0.041 1000 -1000 -0.036 -1000
Signaling events regulated by Ret tyrosine kinase 0.1014 37 3096 82 -0.18 0.014 1000 -1000 -0.08 -1000
Glypican 2 network 0.1014 37 151 4 -0.056 -0.014 1000 -1000 -0.033 -1000
Signaling mediated by p38-alpha and p38-beta 0.0986 36 1622 44 -0.15 0.014 1000 -1000 -0.058 -1000
Visual signal transduction: Cones 0.0959 35 1362 38 -0.16 0.016 1000 -1000 -0.056 -1000
Aurora C signaling 0.0959 35 247 7 -0.15 0 1000 -1000 -0.036 -1000
Endothelins 0.0959 35 3432 96 -0.18 0.016 1000 -1000 -0.072 -1000
Caspase cascade in apoptosis 0.0904 33 2475 74 -0.18 0.046 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.0904 33 1549 46 -0.27 0.017 1000 -1000 -0.052 -1000
EGFR-dependent Endothelin signaling events 0.0877 32 674 21 -0.11 0.014 1000 -1000 -0.06 -1000
Visual signal transduction: Rods 0.0877 32 1693 52 -0.2 0.014 1000 -1000 -0.074 -1000
Calcium signaling in the CD4+ TCR pathway 0.0849 31 972 31 -0.19 0.014 1000 -1000 -0.081 -1000
Ras signaling in the CD4+ TCR pathway 0.0849 31 527 17 -0.13 0.023 1000 -1000 -0.033 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0822 30 2594 85 -0.14 0.014 1000 -1000 -0.068 -1000
p75(NTR)-mediated signaling 0.0822 30 3833 125 -0.16 0.014 1000 -1000 -0.082 -1000
Glypican 1 network 0.0822 30 1470 48 -0.16 0.029 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.0822 30 1329 44 -0.16 0.027 1000 -1000 -0.066 -1000
Glucocorticoid receptor regulatory network 0.0795 29 3350 114 -0.43 0.24 1000 -1000 -0.065 -1000
Osteopontin-mediated events 0.0767 28 1090 38 -0.13 0.015 1000 -1000 -0.089 -1000
Arf6 signaling events 0.0767 28 1760 62 -0.2 0.014 1000 -1000 -0.057 -1000
BCR signaling pathway 0.0767 28 2811 99 -0.18 0.029 1000 -1000 -0.076 -1000
HIF-1-alpha transcription factor network 0.0740 27 2092 76 -0.18 0.087 1000 -1000 -0.11 -1000
TCGA08_p53 0.0740 27 194 7 -0.076 0.049 1000 -1000 -0.013 -1000
LPA receptor mediated events 0.0740 27 2766 102 -0.18 0.019 1000 -1000 -0.075 -1000
PLK1 signaling events 0.0712 26 2246 85 -0.17 0.038 1000 -1000 -0.045 -1000
IL1-mediated signaling events 0.0712 26 1647 62 -0.19 0.065 1000 -1000 -0.091 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0685 25 854 34 -0.067 0.014 1000 -1000 -0.054 -1000
Retinoic acid receptors-mediated signaling 0.0658 24 1411 58 -0.2 0.016 1000 -1000 -0.063 -1000
BMP receptor signaling 0.0630 23 1882 81 -0.18 0.049 1000 -1000 -0.079 -1000
Nongenotropic Androgen signaling 0.0630 23 1230 52 -0.099 0.03 1000 -1000 -0.057 -1000
PLK2 and PLK4 events 0.0603 22 68 3 -0.016 -0.005 1000 -1000 -0.014 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0603 22 836 37 -0.14 0.014 1000 -1000 -0.051 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0603 22 1151 52 -0.18 0.027 1000 -1000 -0.059 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0603 22 2017 88 -0.17 0.018 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 0.0575 21 1450 69 -0.16 0.034 1000 -1000 -0.046 -1000
Fc-epsilon receptor I signaling in mast cells 0.0575 21 2112 97 -0.19 0.04 1000 -1000 -0.074 -1000
Wnt signaling 0.0575 21 153 7 -0.041 -0.012 1000 -1000 -0.022 -1000
IL6-mediated signaling events 0.0575 21 1622 75 -0.16 0.063 1000 -1000 -0.095 -1000
Rapid glucocorticoid signaling 0.0575 21 425 20 -0.18 0.014 1000 -1000 -0.038 -1000
LPA4-mediated signaling events 0.0548 20 240 12 -0.056 0.014 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 0.0548 20 1551 76 -0.14 0.028 1000 -1000 -0.046 -1000
Ephrin B reverse signaling 0.0548 20 969 48 -0.12 0.089 1000 -1000 -0.06 -1000
IL2 signaling events mediated by STAT5 0.0548 20 459 22 -0.099 0.017 1000 -1000 -0.044 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0548 20 2514 120 -0.2 0.13 1000 -1000 -0.068 -1000
ErbB2/ErbB3 signaling events 0.0521 19 1283 65 -0.16 0.023 1000 -1000 -0.063 -1000
JNK signaling in the CD4+ TCR pathway 0.0521 19 323 17 -0.081 0.014 1000 -1000 -0.057 -1000
S1P5 pathway 0.0521 19 323 17 -0.12 0.053 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 0.0521 19 906 47 -0.15 0.016 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0493 18 2530 136 -0.23 0.22 1000 -1000 -0.066 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0493 18 1000 54 -0.16 0.029 1000 -1000 -0.084 -1000
Presenilin action in Notch and Wnt signaling 0.0493 18 1148 61 -0.27 0.032 1000 -1000 -0.072 -1000
IL27-mediated signaling events 0.0493 18 960 51 -0.17 0.017 1000 -1000 -0.08 -1000
E-cadherin signaling in the nascent adherens junction 0.0493 18 1422 76 -0.13 0.014 1000 -1000 -0.083 -1000
Cellular roles of Anthrax toxin 0.0466 17 679 39 -0.16 0.019 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 0.0466 17 600 35 -0.16 0.014 1000 -1000 -0.058 -1000
Noncanonical Wnt signaling pathway 0.0438 16 433 26 -0.12 0.014 1000 -1000 -0.054 -1000
Signaling events mediated by PTP1B 0.0438 16 1233 76 -0.15 0.021 1000 -1000 -0.077 -1000
Signaling events mediated by HDAC Class III 0.0438 16 652 40 -0.12 0.096 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0438 16 968 58 -0.097 0.032 1000 -1000 -0.076 -1000
Canonical Wnt signaling pathway 0.0438 16 865 51 -0.27 0.097 1000 -1000 -0.052 -1000
ErbB4 signaling events 0.0384 14 992 69 -0.15 0.041 1000 -1000 -0.081 -1000
Ceramide signaling pathway 0.0384 14 1082 76 -0.15 0.023 1000 -1000 -0.059 -1000
TRAIL signaling pathway 0.0384 14 674 48 -0.053 0.027 1000 -1000 -0.06 -1000
S1P1 pathway 0.0384 14 515 36 -0.1 0.014 1000 -1000 -0.052 -1000
TCGA08_rtk_signaling 0.0384 14 381 26 -0.14 0.029 1000 -1000 -0.017 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0384 14 1109 74 -0.16 0.068 1000 -1000 -0.087 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0384 14 1116 78 -0.062 0.039 1000 -1000 -0.064 -1000
Paxillin-dependent events mediated by a4b1 0.0356 13 489 36 -0.14 0.03 1000 -1000 -0.065 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0356 13 616 45 -0.15 0.029 1000 -1000 -0.078 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0329 12 355 28 -0.12 0.025 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0329 12 1051 83 -0.2 0.054 1000 -1000 -0.065 -1000
Integrins in angiogenesis 0.0329 12 1031 84 -0.095 0.014 1000 -1000 -0.088 -1000
EPHB forward signaling 0.0329 12 1096 85 -0.12 0.036 1000 -1000 -0.081 -1000
Aurora A signaling 0.0301 11 703 60 -0.13 0.032 1000 -1000 -0.06 -1000
Regulation of Telomerase 0.0301 11 1134 102 -0.13 0.046 1000 -1000 -0.1 -1000
E-cadherin signaling in keratinocytes 0.0301 11 483 43 -0.13 0.029 1000 -1000 -0.066 -1000
S1P4 pathway 0.0301 11 297 25 -0.12 0.028 1000 -1000 -0.046 -1000
BARD1 signaling events 0.0274 10 619 57 -0.052 0.03 1000 -1000 -0.055 -1000
Insulin-mediated glucose transport 0.0274 10 325 32 -0.11 0.034 1000 -1000 -0.059 -1000
Signaling mediated by p38-gamma and p38-delta 0.0274 10 161 15 -0.014 0.028 1000 -1000 -0.02 -1000
Regulation of p38-alpha and p38-beta 0.0274 10 560 54 -0.11 0.014 1000 -1000 -0.056 -1000
Plasma membrane estrogen receptor signaling 0.0274 10 929 86 -0.054 0.03 1000 -1000 -0.079 -1000
Regulation of Androgen receptor activity 0.0274 10 762 70 -0.13 0.03 1000 -1000 -0.062 -1000
Nectin adhesion pathway 0.0247 9 580 63 -0.13 0.045 1000 -1000 -0.066 -1000
ceramide signaling pathway 0.0247 9 454 49 -0.15 0.021 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0247 9 319 33 -0.1 0.041 1000 -1000 -0.054 -1000
Class I PI3K signaling events 0.0219 8 592 73 -0.095 0.029 1000 -1000 -0.062 -1000
p38 MAPK signaling pathway 0.0219 8 389 44 -0.074 0.019 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0192 7 274 39 -0.15 0.086 1000 -1000 -0.075 -1000
Circadian rhythm pathway 0.0192 7 157 22 -0.028 0.034 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 0.0192 7 234 31 -0.088 0.028 1000 -1000 -0.037 -1000
S1P3 pathway 0.0192 7 303 42 -0.043 0.028 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 0.0192 7 247 34 -0.059 0.021 1000 -1000 -0.034 -1000
EPO signaling pathway 0.0164 6 382 55 -0.11 0.055 1000 -1000 -0.081 -1000
IFN-gamma pathway 0.0164 6 473 68 -0.24 0.061 1000 -1000 -0.086 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0164 6 785 125 -0.075 0.076 1000 -1000 -0.085 -1000
VEGFR1 specific signals 0.0164 6 345 56 -0.088 0.041 1000 -1000 -0.063 -1000
Class IB PI3K non-lipid kinase events 0.0164 6 18 3 -0.004 0.004 1000 -1000 -0.013 -1000
Hedgehog signaling events mediated by Gli proteins 0.0137 5 335 65 -0.045 0.064 1000 -1000 -0.061 -1000
HIF-2-alpha transcription factor network 0.0137 5 221 43 -0.11 0.11 1000 -1000 -0.08 -1000
Signaling events mediated by HDAC Class I 0.0137 5 614 104 -0.15 0.059 1000 -1000 -0.059 -1000
Insulin Pathway 0.0137 5 392 74 -0.17 0.038 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class II 0.0110 4 351 75 -0.17 0.041 1000 -1000 -0.058 -1000
FoxO family signaling 0.0110 4 269 64 -0.11 0.13 1000 -1000 -0.054 -1000
PDGFR-beta signaling pathway 0.0110 4 473 97 -0.055 0.063 1000 -1000 -0.078 -1000
Class I PI3K signaling events mediated by Akt 0.0082 3 269 68 -0.11 0.054 1000 -1000 -0.051 -1000
Arf6 trafficking events 0.0082 3 258 71 -0.12 0.047 1000 -1000 -0.07 -1000
IGF1 pathway 0.0082 3 173 57 -0.049 0.054 1000 -1000 -0.086 -1000
Arf6 downstream pathway 0.0055 2 121 43 -0.026 0.027 1000 -1000 -0.038 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0027 1 37 23 -0.017 0.05 1000 -1000 -0.057 -1000
Alternative NF-kappaB pathway 0.0027 1 24 13 -0.006 0.014 1000 -1000 -0.063 -1000
mTOR signaling pathway 0.0000 0 49 53 -0.007 0.036 1000 -1000 -0.059 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 14 27 -0.005 0.036 1000 -1000 -0.055 -1000
Arf1 pathway 0.0000 0 19 54 -0.006 0.036 1000 -1000 -0.038 -1000
Total NA 2858 158786 7203 -20 5.6 131000 -131000 -8.1 -131000
IL23-mediated signaling events

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
CCL2 -0.62 0.56 -10000 0 -1.2 158 158
IL23A -0.62 0.56 -10000 0 -1.2 144 144
NF kappa B1 p50/RelA/I kappa B alpha -0.59 0.51 -10000 0 -1.1 152 152
positive regulation of T cell mediated cytotoxicity -0.65 0.62 -10000 0 -1.3 154 154
ITGA3 -0.56 0.52 -10000 0 -1.1 142 142
IL17F -0.36 0.33 -10000 0 -0.73 111 111
IL12B -0.023 0.062 -10000 0 -0.53 4 4
STAT1 (dimer) -0.62 0.59 -10000 0 -1.2 155 155
CD4 -0.55 0.51 -10000 0 -1.1 143 143
IL23 -0.6 0.53 -10000 0 -1.2 144 144
IL23R -0.084 0.084 -10000 0 -0.5 1 1
IL1B -0.66 0.61 -10000 0 -1.3 151 151
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.55 0.5 -10000 0 -1.1 142 142
TYK2 -0.001 0.018 -10000 0 -10000 0 0
STAT4 -0.17 0.26 -10000 0 -0.54 124 124
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.09 0.22 -10000 0 -0.54 69 69
IL12RB1 -0.05 0.16 -10000 0 -0.58 31 31
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
IL12Rbeta1/TYK2 -0.04 0.12 -10000 0 -0.43 31 31
IL23R/JAK2 -0.096 0.1 -10000 0 -0.49 1 1
positive regulation of chronic inflammatory response -0.65 0.62 -10000 0 -1.3 154 154
natural killer cell activation 0.008 0.007 0.046 1 -10000 0 1
JAK2 0.008 0.018 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.01 0.026 -10000 0 -0.49 1 1
RELA 0.011 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.57 0.49 -10000 0 -1.1 144 144
ALOX12B -0.62 0.56 -10000 0 -1.2 151 151
CXCL1 -0.61 0.55 -10000 0 -1.2 152 152
T cell proliferation -0.65 0.62 -10000 0 -1.3 154 154
NFKBIA 0.011 0.003 -10000 0 -10000 0 0
IL17A -0.27 0.26 -10000 0 -0.57 98 98
PI3K -0.61 0.52 -10000 0 -1.1 154 154
IFNG -0.024 0.032 -10000 0 -0.1 13 13
STAT3 (dimer) -0.57 0.48 -10000 0 -1.1 150 150
IL18R1 -0.049 0.18 -10000 0 -0.54 42 42
IL23/IL23R/JAK2/TYK2/SOCS3 -0.33 0.3 -10000 0 -0.66 112 112
IL18/IL18R -0.1 0.21 -10000 0 -0.39 112 112
macrophage activation -0.028 0.017 -10000 0 -0.044 136 136
TNF -0.65 0.6 -10000 0 -1.2 156 156
STAT3/STAT4 -0.67 0.53 -10000 0 -1.1 179 179
STAT4 (dimer) -0.69 0.6 -10000 0 -1.2 173 173
IL18 -0.031 0.15 -10000 0 -0.53 31 31
IL19 -0.55 0.5 -10000 0 -1.1 142 142
STAT5A (dimer) -0.62 0.59 -10000 0 -1.2 151 151
STAT1 -0.001 0.085 -10000 0 -0.48 11 11
SOCS3 -0.11 0.23 -10000 0 -0.52 85 85
CXCL9 -0.65 0.57 -10000 0 -1.2 160 160
MPO -0.64 0.57 -10000 0 -1.2 163 163
positive regulation of humoral immune response -0.65 0.62 -10000 0 -1.3 154 154
IL23/IL23R/JAK2/TYK2 -0.71 0.75 -10000 0 -1.4 154 154
IL6 -0.62 0.56 -10000 0 -1.2 157 157
STAT5A 0.001 0.09 -10000 0 -0.6 8 8
IL2 0.006 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.007 0.046 1 -10000 0 1
CD3E -0.63 0.56 -10000 0 -1.2 158 158
keratinocyte proliferation -0.65 0.62 -10000 0 -1.3 154 154
NOS2 -0.57 0.53 -10000 0 -1.2 130 130
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.13 0.22 -9999 0 -0.44 110 110
EFNA5 -0.081 0.21 -9999 0 -0.55 62 62
FYN -0.1 0.21 -9999 0 -0.4 110 110
neuron projection morphogenesis -0.13 0.22 -9999 0 -0.44 110 110
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.13 0.22 -9999 0 -0.44 110 110
EPHA5 -0.12 0.24 -9999 0 -0.55 87 87
TCGA08_retinoblastoma

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
CDKN2B -0.056 0.18 -10000 0 -0.55 45 45
CDKN2C -0.016 0.13 -10000 0 -0.44 29 29
CDKN2A -0.1 0.23 -10000 0 -0.55 74 74
CCND2 0.061 0.13 0.29 72 -0.14 2 74
RB1 -0.065 0.14 -10000 0 -0.31 72 72
CDK4 0.073 0.15 0.32 77 -10000 0 77
CDK6 0.064 0.15 0.32 72 -0.17 12 84
G1/S progression 0.053 0.15 0.31 74 -10000 0 74
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 -0.2 0.63 -9999 0 -1.2 82 82
PLK1 0 0.19 -9999 0 -0.56 25 25
BIRC5 -0.22 0.55 -9999 0 -1.5 54 54
HSPA1B -0.22 0.65 -9999 0 -1.2 90 90
MAP2K1 0.023 0.053 -9999 0 -0.53 1 1
BRCA2 -0.22 0.67 -9999 0 -1.2 94 94
FOXM1 -0.35 0.92 -9999 0 -1.8 88 88
XRCC1 -0.2 0.63 -9999 0 -1.2 82 82
FOXM1B/p19 -0.37 0.55 -9999 0 -1.3 91 91
Cyclin D1/CDK4 -0.19 0.59 -9999 0 -1.1 89 89
CDC2 -0.22 0.67 -9999 0 -1.3 88 88
TGFA -0.18 0.58 -9999 0 -1 91 91
SKP2 -0.2 0.64 -9999 0 -1.2 90 90
CCNE1 0.012 0.039 -9999 0 -0.5 2 2
CKS1B -0.2 0.63 -9999 0 -1.2 83 83
RB1 -0.17 0.29 -9999 0 -0.83 42 42
FOXM1C/SP1 -0.27 0.75 -9999 0 -1.5 89 89
AURKB -0.26 0.58 -9999 0 -1.2 91 91
CENPF -0.23 0.69 -9999 0 -1.3 86 86
CDK4 0.004 0.084 -9999 0 -0.48 10 10
MYC -0.16 0.57 -9999 0 -1 86 86
CHEK2 0.01 0.1 -9999 0 -0.55 10 10
ONECUT1 -0.21 0.62 -9999 0 -1.2 90 90
CDKN2A -0.11 0.24 -9999 0 -0.57 74 74
LAMA4 -0.2 0.63 -9999 0 -1.2 82 82
FOXM1B/HNF6 -0.29 0.76 -9999 0 -1.5 90 90
FOS -0.28 0.68 -9999 0 -1.2 113 113
SP1 0.015 0.004 -9999 0 -10000 0 0
CDC25B -0.2 0.63 -9999 0 -1.2 83 83
response to radiation 0.008 0.041 -9999 0 -10000 0 0
CENPB -0.2 0.63 -9999 0 -1.2 82 82
CENPA -0.24 0.69 -9999 0 -1.3 89 89
NEK2 -0.25 0.7 -9999 0 -1.3 96 96
HIST1H2BA -0.2 0.63 -9999 0 -1.2 84 84
CCNA2 -0.05 0.18 -9999 0 -0.55 43 43
EP300 0.007 0.064 -9999 0 -0.6 4 4
CCNB1/CDK1 -0.27 0.76 -9999 0 -1.5 86 86
CCNB2 -0.26 0.72 -9999 0 -1.4 93 93
CCNB1 -0.22 0.68 -9999 0 -1.3 84 84
ETV5 -0.22 0.64 -9999 0 -1.2 90 90
ESR1 -0.22 0.65 -9999 0 -1.2 93 93
CCND1 -0.2 0.6 -9999 0 -1.1 91 91
GSK3A 0.025 0.036 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.012 0.16 -9999 0 -0.4 46 46
CDK2 0.002 0.089 -9999 0 -0.55 9 9
G2/M transition of mitotic cell cycle 0.008 0.049 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.4 0.57 -9999 0 -1.3 90 90
GAS1 -0.2 0.64 -9999 0 -1.2 85 85
MMP2 -0.21 0.65 -9999 0 -1.2 85 85
RB1/FOXM1C -0.21 0.63 -9999 0 -1.2 90 90
CREBBP 0.014 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.13 0.17 -10000 0 -0.4 68 68
TBX21 -0.48 0.49 -10000 0 -1 130 130
B2M 0.01 0.046 -10000 0 -0.49 3 3
TYK2 0.001 0.018 -10000 0 -10000 0 0
IL12RB1 -0.048 0.16 -10000 0 -0.58 31 31
GADD45B -0.36 0.39 -10000 0 -0.83 110 110
IL12RB2 -0.14 0.24 -10000 0 -0.54 98 98
GADD45G -0.38 0.42 -10000 0 -0.89 107 107
natural killer cell activation -0.016 0.022 -10000 0 -10000 0 0
RELB 0.01 0.049 -10000 0 -0.52 3 3
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.035 0.16 -10000 0 -0.54 31 31
IL2RA -0.069 0.19 -10000 0 -0.51 55 55
IFNG -0.002 0.051 -10000 0 -0.48 4 4
STAT3 (dimer) -0.37 0.36 -10000 0 -0.74 143 143
HLA-DRB5 -0.13 0.24 -10000 0 -0.54 95 95
FASLG -0.46 0.46 -10000 0 -0.98 130 130
NF kappa B2 p52/RelB -0.46 0.43 -10000 0 -0.92 145 145
CD4 0.002 0.073 -10000 0 -0.52 7 7
SOCS1 -0.034 0.15 -10000 0 -0.51 34 34
EntrezGene:6955 -0.002 0.01 -10000 0 -10000 0 0
CD3D -0.12 0.23 -10000 0 -0.53 87 87
CD3E -0.14 0.25 -10000 0 -0.54 98 98
CD3G -0.026 0.13 -10000 0 -0.49 25 25
IL12Rbeta2/JAK2 -0.11 0.18 -10000 0 -0.4 98 98
CCL3 -0.56 0.57 -10000 0 -1.1 151 151
CCL4 -0.56 0.58 -10000 0 -1.2 146 146
HLA-A 0.007 0.058 -10000 0 -0.48 5 5
IL18/IL18R -0.1 0.23 -10000 0 -0.42 107 107
NOS2 -0.42 0.44 -10000 0 -0.98 108 108
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.16 -10000 0 -0.39 53 53
IL1R1 -0.46 0.47 -10000 0 -1 119 119
IL4 0.018 0.023 -10000 0 -10000 0 0
JAK2 0.001 0.018 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.26 -10000 0 -0.61 65 65
RAB7A -0.3 0.32 -10000 0 -0.74 77 77
lysosomal transport -0.28 0.3 -10000 0 -0.7 77 77
FOS -0.35 0.45 -10000 0 -1.1 80 80
STAT4 (dimer) -0.44 0.41 -10000 0 -0.86 143 143
STAT5A (dimer) -0.47 0.43 -10000 0 -0.92 149 149
GZMA -0.54 0.54 -10000 0 -1.1 145 145
GZMB -0.51 0.52 -10000 0 -1.1 132 132
HLX -0.004 0.097 -10000 0 -0.51 13 13
LCK -0.52 0.53 -10000 0 -1 158 158
TCR/CD3/MHC II/CD4 -0.17 0.26 -10000 0 -0.51 109 109
IL2/IL2R -0.12 0.2 -10000 0 -0.46 79 79
MAPK14 -0.37 0.4 -10000 0 -0.83 116 116
CCR5 -0.42 0.45 -10000 0 -0.95 113 113
IL1B -0.2 0.28 -10000 0 -0.57 128 128
STAT6 -0.11 0.11 -10000 0 -0.26 19 19
STAT4 -0.17 0.26 -10000 0 -0.54 124 124
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.001 0.085 -10000 0 -0.48 11 11
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
NFKB2 0.008 0.055 -10000 0 -0.51 4 4
IL12B -0.015 0.058 -10000 0 -0.52 4 4
CD8A -0.079 0.21 -10000 0 -0.55 61 61
CD8B -0.032 0.16 -10000 0 -0.56 29 29
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.13 0.17 0.39 68 -10000 0 68
IL2RB -0.099 0.22 -10000 0 -0.53 76 76
proteasomal ubiquitin-dependent protein catabolic process -0.4 0.36 -10000 0 -0.77 143 143
IL2RG -0.036 0.16 -10000 0 -0.51 35 35
IL12 -0.034 0.12 -10000 0 -0.45 24 24
STAT5A 0.001 0.09 -10000 0 -0.6 8 8
CD247 -0.021 0.13 -10000 0 -0.52 23 23
IL2 0 0.002 -10000 0 -10000 0 0
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.032 0.14 -10000 0 -0.61 20 20
IL12/IL12R/TYK2/JAK2 -0.53 0.57 -10000 0 -1.1 149 149
MAP2K3 -0.37 0.4 -10000 0 -0.82 122 122
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.37 0.4 -10000 0 -0.82 122 122
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.099 0.22 -10000 0 -0.54 74 74
IL18RAP -0.095 0.22 -10000 0 -0.55 69 69
IL12Rbeta1/TYK2 -0.037 0.12 -10000 0 -0.43 31 31
EOMES -0.016 0.19 -10000 0 -1.3 5 5
STAT1 (dimer) -0.36 0.35 -10000 0 -0.76 129 129
T cell proliferation -0.32 0.29 -10000 0 -0.62 134 134
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.054 0.18 -10000 0 -0.55 42 42
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.37 0.29 -10000 0 -0.69 138 138
ATF2 -0.34 0.36 -10000 0 -0.8 103 103
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.015 0.11 -10000 0 -0.58 10 10
NFATC2 -0.14 0.31 -10000 0 -0.68 72 72
NFATC3 -0.047 0.11 -10000 0 -0.31 7 7
CD40LG -0.38 0.49 -10000 0 -1 116 116
ITCH -0.035 0.13 -10000 0 -0.54 2 2
CBLB -0.037 0.13 -10000 0 -0.64 3 3
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.35 0.41 -10000 0 -0.94 89 89
JUNB -0.036 0.16 -10000 0 -0.51 35 35
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.088 0.13 -10000 0 -0.64 2 2
T cell anergy -0.11 0.21 -10000 0 -0.47 61 61
TLE4 -0.089 0.26 -10000 0 -0.66 44 44
Jun/NFAT1-c-4/p21SNFT -0.36 0.46 -10000 0 -0.99 100 100
AP-1/NFAT1-c-4 -0.46 0.59 -10000 0 -1.2 118 118
IKZF1 -0.1 0.28 -10000 0 -0.73 44 44
T-helper 2 cell differentiation -0.19 0.3 -10000 0 -0.75 53 53
AP-1/NFAT1 -0.17 0.26 -10000 0 -0.57 84 84
CALM1 -0.028 0.088 -10000 0 -0.76 1 1
EGR2 -0.3 0.54 -10000 0 -1 100 100
EGR3 -0.34 0.59 -10000 0 -1.2 92 92
NFAT1/FOXP3 -0.13 0.26 -10000 0 -0.64 58 58
EGR1 -0.11 0.23 -10000 0 -0.53 79 79
JUN -0.004 0.078 -10000 0 -0.51 8 8
EGR4 -0.21 0.28 -10000 0 -0.55 144 144
mol:Ca2+ -0.044 0.086 -10000 0 -0.3 1 1
GBP3 -0.17 0.36 -10000 0 -0.75 85 85
FOSL1 -0.096 0.22 -10000 0 -0.53 74 74
NFAT1-c-4/MAF/IRF4 -0.33 0.45 -10000 0 -0.97 96 96
DGKA -0.082 0.23 -10000 0 -0.6 43 43
CREM 0.011 0.041 -10000 0 -0.54 2 2
NFAT1-c-4/PPARG -0.34 0.46 -10000 0 -0.96 103 103
CTLA4 -0.13 0.31 -10000 0 -0.72 61 61
NFAT1-c-4 (dimer)/EGR1 -0.38 0.53 -10000 0 -1 117 117
NFAT1-c-4 (dimer)/EGR4 -0.44 0.49 -10000 0 -1 120 120
FOS -0.096 0.22 -10000 0 -0.56 66 66
IFNG -0.18 0.24 -10000 0 -0.75 35 35
T cell activation -0.17 0.28 -10000 0 -0.69 53 53
MAF 0.011 0.046 -10000 0 -0.6 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.23 0.41 0.87 76 -10000 0 76
TNF -0.48 0.51 -10000 0 -1 154 154
FASLG -0.35 0.56 -10000 0 -1.2 84 84
TBX21 -0.04 0.17 -10000 0 -0.53 37 37
BATF3 -0.037 0.16 -10000 0 -0.54 34 34
PRKCQ -0.007 0.11 -10000 0 -0.58 13 13
PTPN1 -0.082 0.23 -10000 0 -0.62 40 40
NFAT1-c-4/ICER1 -0.32 0.45 -10000 0 -0.96 100 100
GATA3 -0.1 0.22 -10000 0 -0.53 77 77
T-helper 1 cell differentiation -0.16 0.25 -10000 0 -0.73 35 35
IL2RA -0.32 0.35 -10000 0 -0.8 94 94
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.083 0.23 -10000 0 -0.64 37 37
E2F1 -0.004 0.1 -10000 0 -0.49 16 16
PPARG -0.013 0.12 -10000 0 -0.57 17 17
SLC3A2 -0.082 0.23 -10000 0 -0.64 36 36
IRF4 -0.048 0.18 -10000 0 -0.54 41 41
PTGS2 -0.41 0.53 -10000 0 -1.1 118 118
CSF2 -0.37 0.48 -10000 0 -1 110 110
JunB/Fra1/NFAT1-c-4 -0.38 0.46 -10000 0 -0.97 111 111
IL4 -0.19 0.31 -10000 0 -0.8 51 51
IL5 -0.37 0.48 -10000 0 -1 110 110
IL2 -0.17 0.29 -10000 0 -0.71 51 51
IL3 -0.066 0.076 -10000 0 -0.95 1 1
RNF128 -0.16 0.3 -10000 0 -0.57 124 124
NFATC1 -0.23 0.42 -10000 0 -0.88 76 76
CDK4 0.14 0.24 0.59 37 -0.49 1 38
PTPRK -0.086 0.24 -10000 0 -0.63 44 44
IL8 -0.44 0.53 -10000 0 -1.1 127 127
POU2F1 0.013 0.032 -10000 0 -0.6 1 1
Aurora B signaling

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
Condensin I complex -0.12 0.26 -9999 0 -0.59 71 71
STMN1 -0.098 0.2 -9999 0 -0.4 106 106
Aurora B/RasGAP/Survivin -0.17 0.28 -9999 0 -0.55 119 119
Chromosomal passenger complex/Cul3 protein complex -0.086 0.19 -9999 0 -0.39 87 87
BIRC5 -0.14 0.26 -9999 0 -0.57 95 95
DES -0.32 0.46 -9999 0 -0.95 112 112
Aurora C/Aurora B/INCENP -0.097 0.17 -9999 0 -0.33 118 118
Aurora B/TACC1 -0.091 0.16 -9999 0 -0.34 105 105
Aurora B/PP2A -0.11 0.19 -9999 0 -0.4 105 105
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.027 0.075 -9999 0 -0.17 66 66
mitotic metaphase/anaphase transition 0.001 0.006 -9999 0 -10000 0 0
NDC80 -0.19 0.32 -9999 0 -0.61 124 124
Cul3 protein complex -0.007 0.05 -9999 0 -0.36 7 7
KIF2C -0.12 0.27 -9999 0 -0.43 114 114
PEBP1 0.008 0.034 -9999 0 -0.62 1 1
KIF20A -0.17 0.27 -9999 0 -0.56 116 116
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.11 0.19 -9999 0 -0.4 105 105
SEPT1 0.009 0.052 -9999 0 -0.48 4 4
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 -0.009 0.1 -9999 0 -0.48 17 17
NSUN2/NPM1/Nucleolin -0.16 0.33 -9999 0 -0.84 66 66
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.072 0.15 -9999 0 -0.3 104 104
AURKB -0.15 0.27 -9999 0 -0.57 105 105
AURKC -0.019 0.13 -9999 0 -0.52 23 23
CDCA8 -0.047 0.17 -9999 0 -0.52 39 39
cytokinesis -0.26 0.41 -9999 0 -0.82 114 114
Aurora B/Septin1 -0.24 0.38 -9999 0 -0.77 113 113
AURKA -0.011 0.11 -9999 0 -0.49 18 18
INCENP 0.009 0.009 -9999 0 -10000 0 0
KLHL13 0.011 0.046 -9999 0 -0.6 2 2
BUB1 -0.11 0.24 -9999 0 -0.56 81 81
hSgo1/Aurora B/Survivin -0.22 0.35 -9999 0 -0.65 130 130
EVI5 0.013 0.003 -9999 0 -10000 0 0
RhoA/GTP -0.23 0.36 -9999 0 -0.73 110 110
SGOL1 -0.11 0.24 -9999 0 -0.55 83 83
CENPA -0.16 0.31 -9999 0 -0.56 115 115
NCAPG -0.12 0.24 -9999 0 -0.55 89 89
Aurora B/HC8 Proteasome -0.11 0.19 -9999 0 -0.4 105 105
NCAPD2 0.01 0.045 -9999 0 -0.48 3 3
Aurora B/PP1-gamma -0.11 0.19 -9999 0 -0.4 105 105
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH -0.061 0.19 -9999 0 -0.55 49 49
NPM1 -0.13 0.24 -9999 0 -0.62 66 66
RASA1 0.014 0 -9999 0 -10000 0 0
KLHL9 0.006 0.072 -9999 0 -0.6 5 5
mitotic prometaphase -0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.19 -9999 0 -0.4 105 105
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.26 0.4 -9999 0 -0.78 118 118
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.13 0.24 -9999 0 -0.62 66 66
MYLK -0.08 0.16 -9999 0 -0.3 112 112
KIF23 -0.11 0.23 -9999 0 -0.55 79 79
VIM -0.16 0.24 -9999 0 -0.44 143 143
RACGAP1 0.004 0.056 -9999 0 -0.52 4 4
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.13 0.24 -9999 0 -0.62 66 66
Chromosomal passenger complex -0.2 0.38 -9999 0 -0.68 118 118
Chromosomal passenger complex/EVI5 -0.17 0.3 -9999 0 -0.58 114 114
TACC1 0.014 0 -9999 0 -10000 0 0
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.06 0.15 -9999 0 -0.36 71 71
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.092 0.17 -9999 0 -0.4 84 84
STXBP1 -0.015 0.12 -9999 0 -0.49 21 21
ACh/CHRNA1 -0.13 0.17 -9999 0 -0.37 112 112
RAB3GAP2/RIMS1/UNC13B -0.076 0.14 -9999 0 -0.33 84 84
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.12 0.24 -9999 0 -0.55 84 84
mol:ACh -0.04 0.069 -9999 0 -0.14 120 120
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.14 0.21 -9999 0 -0.45 95 95
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.13 0.17 -9999 0 -0.37 112 112
UNC13B 0.012 0.032 -9999 0 -0.6 1 1
CHRNA1 -0.15 0.25 -9999 0 -0.53 111 111
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.16 0.21 -9999 0 -0.41 148 148
SNAP25 -0.075 0.13 -9999 0 -0.24 121 121
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.21 0.27 -9999 0 -0.53 148 148
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.057 0.16 -9999 0 -0.37 73 73
STX1A/SNAP25 fragment 1/VAMP2 -0.14 0.21 -9999 0 -0.45 95 95
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.14 0.19 -10000 0 -0.46 79 79
FYN -0.15 0.28 -10000 0 -0.55 97 97
LAT/GRAP2/SLP76 -0.17 0.23 -10000 0 -0.51 94 94
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.11 0.19 -10000 0 -0.4 87 87
B2M 0.008 0.046 -10000 0 -0.49 3 3
IKBKG -0.035 0.047 -10000 0 -0.15 19 19
MAP3K8 0 0.083 -10000 0 -0.49 10 10
mol:Ca2+ -0.028 0.043 -10000 0 -0.11 74 74
integrin-mediated signaling pathway -0.01 0.056 -10000 0 -0.32 11 11
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.16 0.27 -10000 0 -0.57 91 91
TRPV6 -0.12 0.24 -10000 0 -0.56 82 82
CD28 -0.078 0.21 -10000 0 -0.54 60 60
SHC1 -0.15 0.27 -10000 0 -0.55 92 92
receptor internalization -0.13 0.24 -10000 0 -0.52 83 83
PRF1 -0.18 0.37 -10000 0 -0.94 54 54
KRAS 0.013 0.026 -10000 0 -0.48 1 1
GRB2 0.014 0 -10000 0 -10000 0 0
COT/AKT1 -0.082 0.16 -10000 0 -0.34 72 72
LAT -0.17 0.27 -10000 0 -0.55 98 98
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.12 0.23 -10000 0 -0.53 87 87
CD3E -0.14 0.25 -10000 0 -0.55 98 98
CD3G -0.026 0.13 -10000 0 -0.49 25 25
RASGRP2 -0.007 0.025 -10000 0 -0.18 2 2
RASGRP1 -0.12 0.2 -10000 0 -0.4 91 91
HLA-A 0.005 0.059 -10000 0 -0.49 5 5
RASSF5 -0.002 0.095 -10000 0 -0.54 11 11
RAP1A/GTP/RAPL -0.01 0.056 -10000 0 -0.32 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.016 0.063 -10000 0 -0.11 40 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.065 0.082 -10000 0 -0.22 50 50
PRKCA -0.08 0.11 -10000 0 -0.26 72 72
GRAP2 -0.049 0.17 -10000 0 -0.52 43 43
mol:IP3 -0.1 0.2 0.21 45 -0.4 83 128
EntrezGene:6957 -0.002 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.22 -10000 0 -0.48 80 80
ORAI1 0.074 0.12 0.31 81 -10000 0 81
CSK -0.15 0.27 -10000 0 -0.56 93 93
B7 family/CD28 -0.22 0.28 -10000 0 -0.62 96 96
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.18 0.31 -10000 0 -0.61 99 99
PTPN6 -0.16 0.28 -10000 0 -0.56 98 98
VAV1 -0.16 0.29 -10000 0 -0.58 94 94
Monovalent TCR/CD3 -0.11 0.2 -10000 0 -0.37 122 122
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.17 0.3 -10000 0 -0.58 108 108
PAG1 -0.16 0.27 -10000 0 -0.56 92 92
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.3 -10000 0 -0.61 96 96
CD80 -0.053 0.18 -10000 0 -0.52 44 44
CD86 -0.026 0.14 -10000 0 -0.55 25 25
PDK1/CARD11/BCL10/MALT1 -0.079 0.1 -10000 0 -0.26 58 58
HRAS 0.013 0.026 -10000 0 -0.48 1 1
GO:0035030 -0.16 0.25 -10000 0 -0.52 92 92
CD8A -0.081 0.21 -10000 0 -0.55 61 61
CD8B -0.034 0.16 -10000 0 -0.57 29 29
PTPRC -0.045 0.17 -10000 0 -0.54 38 38
PDK1/PKC theta -0.13 0.24 -10000 0 -0.49 84 84
CSK/PAG1 -0.15 0.27 -10000 0 -0.56 85 85
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.006 0.058 -10000 0 -0.39 7 7
GRAP2/SLP76 -0.18 0.27 -10000 0 -0.57 96 96
STIM1 0.04 0.063 0.22 1 -10000 0 1
RAS family/GTP -0.023 0.085 -10000 0 -0.17 34 34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.26 -10000 0 -0.55 83 83
mol:DAG -0.11 0.16 -10000 0 -0.36 86 86
RAP1A/GDP -0.005 0.028 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.021 0.13 -10000 0 -0.52 23 23
cytotoxic T cell degranulation -0.16 0.34 -10000 0 -0.89 54 54
RAP1A/GTP -0.004 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.13 0.23 -10000 0 -0.47 90 90
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.25 0.23 39 -0.52 84 123
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.059 0.19 -10000 0 -0.53 49 49
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.17 0.23 -10000 0 -0.51 92 92
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.012 0.032 -10000 0 -0.6 1 1
CD8 heterodimer -0.082 0.2 -10000 0 -0.47 75 75
CARD11 -0.008 0.11 -10000 0 -0.58 14 14
PRKCB -0.1 0.12 -10000 0 -0.27 92 92
PRKCE -0.083 0.11 -10000 0 -0.26 74 74
PRKCQ -0.16 0.26 -10000 0 -0.55 89 89
LCP2 -0.004 0.094 -10000 0 -0.49 13 13
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.09 0.17 -10000 0 -0.34 87 87
IKK complex -0.011 0.062 -10000 0 -0.11 22 22
RAS family/GDP -0.007 0.01 -10000 0 -10000 0 0
MAP3K14 -0.055 0.13 -10000 0 -0.27 53 53
PDPK1 -0.1 0.18 -10000 0 -0.39 79 79
TCR/CD3/MHC I/CD8/Fyn -0.18 0.32 -10000 0 -0.62 99 99
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.09 0.15 -9999 0 -0.38 51 51
E-cadherin/beta catenin -0.1 0.17 -9999 0 -0.38 95 95
CTNNB1 0.014 0 -9999 0 -10000 0 0
JUP 0.001 0.086 -9999 0 -0.57 8 8
CDH1 -0.13 0.25 -9999 0 -0.54 95 95
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.095 0.29 -10000 0 -0.72 44 44
IHH -0.01 0.074 -10000 0 -0.47 4 4
SHH Np/Cholesterol/GAS1 -0.084 0.15 -10000 0 -0.32 96 96
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.084 0.15 0.32 96 -10000 0 96
SMO/beta Arrestin2 -0.035 0.18 -10000 0 -0.7 14 14
SMO -0.044 0.19 -10000 0 -0.63 21 21
AKT1 0.004 0.087 -10000 0 -0.32 6 6
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC 0.008 0.058 -10000 0 -0.54 4 4
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.043 0.19 -10000 0 -0.6 22 22
STIL -0.084 0.22 -10000 0 -0.55 47 47
DHH N/PTCH2 -0.056 0.14 -10000 0 -0.4 51 51
DHH N/PTCH1 -0.064 0.2 -10000 0 -0.56 27 27
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
DHH -0.042 0.17 -10000 0 -0.54 37 37
PTHLH -0.11 0.34 -10000 0 -0.93 43 43
determination of left/right symmetry -0.043 0.19 -10000 0 -0.6 22 22
PIK3R1 0.014 0 -10000 0 -10000 0 0
skeletal system development -0.1 0.34 -10000 0 -0.92 43 43
IHH N/Hhip -0.11 0.21 -10000 0 -0.44 102 102
DHH N/Hhip -0.14 0.2 -10000 0 -0.41 127 127
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.043 0.19 -10000 0 -0.6 22 22
pancreas development -0.14 0.25 -10000 0 -0.55 99 99
HHAT -0.007 0.11 -10000 0 -0.57 13 13
PI3K -0.001 0.023 -10000 0 -0.44 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.016 0.12 -10000 0 -0.49 22 22
somite specification -0.043 0.19 -10000 0 -0.6 22 22
SHH Np/Cholesterol/PTCH1 -0.087 0.22 -10000 0 -0.55 47 47
SHH Np/Cholesterol/PTCH2 -0.082 0.15 -10000 0 -0.32 93 93
SHH Np/Cholesterol/Megalin -0.17 0.2 -10000 0 -0.36 171 171
SHH -0.073 0.19 -10000 0 -0.42 80 80
catabolic process -0.044 0.19 -10000 0 -0.55 23 23
SMO/Vitamin D3 -0.079 0.22 -10000 0 -0.6 37 37
SHH Np/Cholesterol/Hhip -0.15 0.2 -10000 0 -0.36 151 151
LRP2 -0.17 0.27 -10000 0 -0.55 121 121
receptor-mediated endocytosis -0.17 0.22 -10000 0 -0.59 60 60
SHH Np/Cholesterol/BOC -0.072 0.14 -10000 0 -0.36 54 54
SHH Np/Cholesterol/CDO -0.086 0.16 -10000 0 -0.33 95 95
mesenchymal cell differentiation 0.15 0.2 0.36 151 -10000 0 151
mol:Vitamin D3 -0.085 0.22 -10000 0 -0.55 47 47
IHH N/PTCH2 -0.009 0.11 -10000 0 -0.44 19 19
CDON -0.018 0.13 -10000 0 -0.57 20 20
IHH N/PTCH1 -0.044 0.19 -10000 0 -0.56 23 23
Megalin/LRPAP1 -0.13 0.19 -10000 0 -0.39 121 121
PTCH2 -0.01 0.12 -10000 0 -0.58 15 15
SHH Np/Cholesterol -0.071 0.14 -10000 0 -0.33 80 80
PTCH1 -0.044 0.19 -10000 0 -0.56 23 23
HHIP -0.14 0.25 -10000 0 -0.55 99 99
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.39 0.44 -10000 0 -1.1 64 64
STAT6 (cleaved dimer) -0.47 0.44 -10000 0 -1 118 118
IGHG1 -0.16 0.22 -10000 0 -0.78 17 17
IGHG3 -0.38 0.42 -10000 0 -0.96 91 91
AKT1 -0.24 0.3 -10000 0 -0.76 52 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.78 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.27 -10000 0 -0.7 44 44
THY1 -0.4 0.47 -10000 0 -1.1 70 70
MYB -0.06 0.19 -10000 0 -0.54 48 48
HMGA1 0.011 0.041 -10000 0 -0.54 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.35 -10000 0 -0.77 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.27 -10000 0 -0.69 48 48
SP1 0.02 0.013 -10000 0 -10000 0 0
INPP5D 0.008 0.055 -10000 0 -0.51 4 4
SOCS5 0.027 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.46 -10000 0 -1 113 113
SOCS1 -0.3 0.33 -10000 0 -0.77 76 76
SOCS3 -0.36 0.42 -10000 0 -0.97 90 90
FCER2 -0.44 0.47 -10000 0 -1.1 84 84
PARP14 -0.002 0.086 -10000 0 -0.54 9 9
CCL17 -0.4 0.45 -10000 0 -1.1 79 79
GRB2 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.6 47 47
T cell proliferation -0.4 0.46 -10000 0 -1.1 79 79
IL4R/JAK1 -0.4 0.43 -10000 0 -1.1 68 68
EGR2 -0.5 0.54 -10000 0 -1.2 101 101
JAK2 -0.003 0.027 -10000 0 -10000 0 0
JAK3 -0.06 0.19 -10000 0 -0.53 49 49
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.005 0.012 -10000 0 -10000 0 0
COL1A2 -0.16 0.25 -10000 0 -0.75 32 32
CCL26 -0.4 0.45 -10000 0 -1.1 62 62
IL4R -0.42 0.46 -10000 0 -1.1 67 67
PTPN6 0.006 0.097 -10000 0 -0.52 12 12
IL13RA2 -0.6 0.59 -10000 0 -1.3 138 138
IL13RA1 -0.012 0.078 -10000 0 -0.63 5 5
IRF4 -0.18 0.35 -10000 0 -1.1 36 36
ARG1 -0.13 0.24 -10000 0 -0.86 22 22
CBL -0.3 0.33 -10000 0 -0.74 91 91
GTF3A 0.011 0.03 -10000 0 -10000 0 0
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
IL13RA1/JAK2 -0.012 0.066 -10000 0 -0.46 5 5
IRF4/BCL6 -0.16 0.32 -10000 0 -1 34 34
CD40LG -0.039 0.15 -10000 0 -0.49 36 36
MAPK14 -0.32 0.36 -10000 0 -0.8 95 95
mitosis -0.23 0.28 -10000 0 -0.71 52 52
STAT6 -0.44 0.51 -10000 0 -1.2 86 86
SPI1 -0.006 0.11 -10000 0 -0.52 15 15
RPS6KB1 -0.21 0.27 -10000 0 -0.69 49 49
STAT6 (dimer) -0.44 0.51 -10000 0 -1.2 86 86
STAT6 (dimer)/PARP14 -0.43 0.47 -10000 0 -1.1 90 90
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.32 -10000 0 -0.8 66 66
FRAP1 -0.24 0.3 -10000 0 -0.76 52 52
LTA -0.42 0.48 -10000 0 -1.1 78 78
FES 0.007 0.061 -10000 0 -0.5 5 5
T-helper 1 cell differentiation 0.43 0.49 1.1 86 -10000 0 86
CCL11 -0.38 0.42 -10000 0 -1.1 62 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.31 -10000 0 -0.8 55 55
IL2RG -0.037 0.16 -10000 0 -0.51 35 35
IL10 -0.49 0.56 -10000 0 -1.3 89 89
IRS1 0.014 0 -10000 0 -10000 0 0
IRS2 0.012 0.032 -10000 0 -0.6 1 1
IL4 -0.096 0.11 -10000 0 -10000 0 0
IL5 -0.39 0.44 -10000 0 -1.1 72 72
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.32 0.35 -10000 0 -0.83 72 72
COL1A1 -0.34 0.5 -10000 0 -1.1 83 83
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.44 -10000 0 -1.1 60 60
IL2R gamma/JAK3 -0.071 0.18 -10000 0 -0.43 72 72
TFF3 -0.41 0.45 -10000 0 -1.1 69 69
ALOX15 -0.4 0.44 -10000 0 -1.1 70 70
MYBL1 0.011 0.037 -10000 0 -0.48 2 2
T-helper 2 cell differentiation -0.35 0.38 -10000 0 -0.88 84 84
SHC1 0.009 0.052 -10000 0 -0.48 4 4
CEBPB -0.006 0.12 -10000 0 -0.57 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.26 -10000 0 -0.69 44 44
mol:PI-3-4-5-P3 -0.24 0.3 -10000 0 -0.76 52 52
PI3K -0.25 0.32 -10000 0 -0.82 52 52
DOK2 -0.071 0.2 -10000 0 -0.53 57 57
ETS1 0.02 0.054 -10000 0 -0.48 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.22 -10000 0 -0.58 44 44
ITGB3 -0.43 0.49 -10000 0 -1.2 82 82
PIGR -0.49 0.56 -10000 0 -1.3 94 94
IGHE 0.019 0.066 -10000 0 -0.26 11 11
MAPKKK cascade -0.17 0.22 -10000 0 -0.57 44 44
BCL6 0.016 0.006 -10000 0 -10000 0 0
OPRM1 -0.41 0.45 -10000 0 -1.1 74 74
RETNLB -0.4 0.44 -10000 0 -1.1 71 71
SELP -0.4 0.45 -10000 0 -1.1 74 74
AICDA -0.38 0.42 -10000 0 -1 68 68
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.078 -9999 0 -0.6 6 6
CCL5 -0.091 0.22 -9999 0 -0.53 70 70
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.18 -9999 0 -0.47 55 55
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.18 -9999 0 -0.44 57 57
Syndecan-1/Syntenin -0.12 0.18 -9999 0 -0.44 55 55
MAPK3 -0.094 0.16 -9999 0 -0.46 30 30
HGF/MET -0.16 0.22 -9999 0 -0.42 139 139
TGFB1/TGF beta receptor Type II 0.004 0.078 -9999 0 -0.6 6 6
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.12 0.18 -9999 0 -0.43 57 57
Syndecan-1/RANTES -0.17 0.22 -9999 0 -0.48 91 91
Syndecan-1/CD147 -0.11 0.17 -9999 0 -0.49 31 31
Syndecan-1/Syntenin/PIP2 -0.12 0.16 -9999 0 -0.42 55 55
LAMA5 0.011 0.041 -9999 0 -0.54 2 2
positive regulation of cell-cell adhesion -0.13 0.15 -9999 0 -0.42 55 55
MMP7 -0.15 0.25 -9999 0 -0.54 105 105
HGF -0.069 0.19 -9999 0 -0.5 59 59
Syndecan-1/CASK -0.13 0.17 -9999 0 -0.45 55 55
Syndecan-1/HGF/MET -0.22 0.24 -9999 0 -0.51 117 117
regulation of cell adhesion -0.084 0.16 -9999 0 -0.44 30 30
HPSE -0.057 0.19 -9999 0 -0.56 45 45
positive regulation of cell migration -0.13 0.18 -9999 0 -0.47 55 55
SDC1 -0.14 0.18 -9999 0 -0.47 55 55
Syndecan-1/Collagen -0.13 0.18 -9999 0 -0.47 55 55
PPIB 0.014 0 -9999 0 -10000 0 0
MET -0.14 0.25 -9999 0 -0.54 101 101
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.52 111 111
MAPK1 -0.094 0.16 -9999 0 -0.46 30 30
homophilic cell adhesion -0.13 0.18 -9999 0 -0.46 55 55
MMP1 -0.045 0.15 -9999 0 -0.48 39 39
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.01 0.037 -10000 0 -0.48 2 2
GNB1/GNG2 -0.083 0.081 -10000 0 -0.18 119 119
AKT1 -0.066 0.11 -10000 0 -0.21 77 77
EGF -0.044 0.17 -10000 0 -0.56 37 37
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR 0.015 0.072 -10000 0 -0.32 3 3
mol:Ca2+ -0.11 0.16 -10000 0 -0.3 121 121
LYN 0.013 0.078 -10000 0 -0.31 7 7
RhoA/GTP -0.054 0.053 -10000 0 -0.14 22 22
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.13 0.18 -10000 0 -0.35 119 119
GNG2 0.009 0.056 -10000 0 -0.6 3 3
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.011 0.095 -10000 0 -0.38 17 17
G beta5/gamma2 -0.1 0.1 -10000 0 -0.24 116 116
PRKCH -0.12 0.18 -10000 0 -0.34 113 113
DNM1 -0.12 0.24 -10000 0 -0.52 92 92
TXA2/TP beta/beta Arrestin3 -0.048 0.077 -10000 0 -0.25 26 26
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.045 0.16 -10000 0 -0.49 42 42
G12 family/GTP -0.13 0.13 -10000 0 -0.3 118 118
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.008 0.061 -10000 0 -0.57 4 4
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.064 0.11 0.3 25 -10000 0 25
mol:NADP 0.003 0.075 -10000 0 -0.53 7 7
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.048 0.18 -10000 0 -0.58 38 38
mol:IP3 -0.14 0.19 -10000 0 -0.37 121 121
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.19 0.25 -10000 0 -0.5 120 120
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.036 0.11 -10000 0 -0.34 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.093 -10000 0 -0.34 10 10
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.017 0.12 -10000 0 -0.52 21 21
PRKCB1 -0.14 0.19 -10000 0 -0.36 121 121
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.003 0.075 -10000 0 -0.53 7 7
TXA2/TXA2-R family -0.2 0.26 -10000 0 -0.52 122 122
LCK -0.029 0.12 -10000 0 -0.34 19 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.026 0.068 -10000 0 -0.35 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.023 0.05 -10000 0 -0.75 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.024 0.064 -10000 0 -0.35 4 4
MAPK14 -0.078 0.13 -10000 0 -0.23 117 117
TGM2/GTP -0.16 0.21 -10000 0 -0.42 122 122
MAPK11 -0.08 0.13 -10000 0 -0.23 118 118
ARHGEF1 -0.059 0.096 -10000 0 -0.18 72 72
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.14 0.2 -10000 0 -0.38 124 124
RAB11/GDP 0.015 0.001 -10000 0 -10000 0 0
ICAM1 -0.11 0.16 -10000 0 -0.29 123 123
cAMP biosynthetic process -0.14 0.18 -10000 0 -0.35 122 122
Gq family/GTP/EBP50 0.01 0.079 -10000 0 -0.29 18 18
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.016 0.07 -10000 0 -0.32 3 3
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.11 -10000 0 -0.3 19 19
VCAM1 -0.14 0.19 -10000 0 -0.37 121 121
TP beta/Gq family/GDP/G beta5/gamma2 0.011 0.095 -10000 0 -0.38 17 17
platelet activation -0.1 0.16 -10000 0 -0.3 118 118
PGI2/IP -0.018 0.089 -10000 0 -0.37 21 21
PRKACA -0.013 0.082 -10000 0 -0.3 14 14
Gq family/GDP/G beta5/gamma2 0.01 0.09 -10000 0 -0.35 17 17
TXA2/TP beta/beta Arrestin2 -0.075 0.15 -10000 0 -0.53 32 32
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.087 -10000 0 -0.3 17 17
mol:DAG -0.15 0.21 -10000 0 -0.41 118 118
EGFR -0.082 0.21 -10000 0 -0.55 62 62
TXA2/TP alpha -0.18 0.24 -10000 0 -0.48 122 122
Gq family/GTP -0.012 0.063 -10000 0 -0.23 23 23
YES1 0.015 0.073 -10000 0 -0.32 3 3
GNAI2/GTP -0.025 0.063 -10000 0 -0.35 4 4
PGD2/DP -0.038 0.12 -10000 0 -0.35 42 42
SLC9A3R1 0.011 0.046 -10000 0 -0.6 2 2
FYN 0.016 0.07 -10000 0 -0.32 3 3
mol:NO 0.003 0.075 -10000 0 -0.53 7 7
GNA15 -0.006 0.11 -10000 0 -0.56 13 13
PGK/cGMP -0.044 0.12 -10000 0 -0.35 45 45
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.024 0.073 -10000 0 -0.43 4 4
NOS3 0.003 0.075 -10000 0 -0.53 7 7
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.34 117 117
PRKCB -0.15 0.2 -10000 0 -0.38 126 126
PRKCE -0.12 0.18 -10000 0 -0.35 117 117
PRKCD -0.14 0.2 -10000 0 -0.39 118 118
PRKCG -0.18 0.22 -10000 0 -0.42 144 144
muscle contraction -0.18 0.24 -10000 0 -0.49 122 122
PRKCZ -0.13 0.18 -10000 0 -0.35 124 124
ARR3 0.001 0.026 -10000 0 -0.48 1 1
TXA2/TP beta -0.028 0.072 -10000 0 -0.37 5 5
PRKCQ -0.13 0.18 -10000 0 -0.35 121 121
MAPKKK cascade -0.17 0.23 -10000 0 -0.45 121 121
SELE -0.13 0.18 -10000 0 -0.34 138 138
TP beta/GNAI2/GDP/G beta/gamma -0.023 0.069 -10000 0 -0.38 4 4
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.006 0.11 -10000 0 -0.56 13 13
chemotaxis -0.23 0.3 -10000 0 -0.61 120 120
GNA12 0.012 0.032 -10000 0 -0.6 1 1
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.002 0.085 -10000 0 -0.6 7 7
Rac1/GTP 0.003 0.005 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.001 0.053 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.14 0.24 -9999 0 -0.55 76 76
positive regulation of JNK cascade -0.15 0.22 -9999 0 -0.51 81 81
Syndecan-4/ADAM12 -0.18 0.26 -9999 0 -0.52 114 114
CCL5 -0.091 0.22 -9999 0 -0.53 70 70
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.011 0.11 -9999 0 -0.49 18 18
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.003 0.025 -9999 0 -0.44 1 1
ADAM12 -0.074 0.2 -9999 0 -0.5 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.041 -9999 0 -0.18 1 1
Syndecan-4/Laminin alpha1 -0.17 0.27 -9999 0 -0.57 90 90
Syndecan-4/CXCL12/CXCR4 -0.14 0.25 -9999 0 -0.54 81 81
Syndecan-4/Laminin alpha3 -0.16 0.26 -9999 0 -0.57 85 85
MDK -0.039 0.16 -9999 0 -0.53 36 36
Syndecan-4/FZD7 -0.16 0.28 -9999 0 -0.6 86 86
Syndecan-4/Midkine -0.16 0.26 -9999 0 -0.55 93 93
FZD7 -0.045 0.18 -9999 0 -0.59 36 36
Syndecan-4/FGFR1/FGF -0.15 0.21 -9999 0 -0.5 79 79
THBS1 -0.085 0.21 -9999 0 -0.51 69 69
integrin-mediated signaling pathway -0.16 0.26 -9999 0 -0.55 95 95
positive regulation of MAPKKK cascade -0.15 0.22 -9999 0 -0.51 81 81
Syndecan-4/TACI -0.15 0.24 -9999 0 -0.55 80 80
CXCR4 -0.011 0.12 -9999 0 -0.55 16 16
cell adhesion 0.021 0.053 -9999 0 -0.26 9 9
Syndecan-4/Dynamin -0.14 0.24 -9999 0 -0.55 76 76
Syndecan-4/TSP1 -0.18 0.26 -9999 0 -0.53 108 108
Syndecan-4/GIPC -0.14 0.24 -9999 0 -0.55 76 76
Syndecan-4/RANTES -0.19 0.26 -9999 0 -0.55 99 99
ITGB1 0.011 0.037 -9999 0 -0.48 2 2
LAMA1 -0.054 0.19 -9999 0 -0.58 42 42
LAMA3 -0.031 0.16 -9999 0 -0.56 29 29
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.037 0.055 -9999 0 -0.54 1 1
Syndecan-4/alpha-Actinin -0.15 0.25 -9999 0 -0.54 91 91
TFPI -0.086 0.21 -9999 0 -0.53 68 68
F2 -0.005 0.052 -9999 0 -0.48 4 4
alpha5/beta1 Integrin -0.019 0.082 -9999 0 -0.36 19 19
positive regulation of cell adhesion -0.18 0.28 -9999 0 -0.58 95 95
ACTN1 -0.017 0.12 -9999 0 -0.49 23 23
TNC -0.056 0.18 -9999 0 -0.54 46 46
Syndecan-4/CXCL12 -0.14 0.24 -9999 0 -0.54 81 81
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 0.004 0.073 -9999 0 -0.52 7 7
TNFRSF13B -0.006 0.076 -9999 0 -0.48 9 9
FGF2 0.009 0.052 -9999 0 -0.56 3 3
FGFR1 0.012 0.032 -9999 0 -0.6 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.24 -9999 0 -0.55 76 76
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.002 0.088 -9999 0 -0.47 12 12
cell migration -0.006 0.018 -9999 0 -10000 0 0
PRKCD -0.01 0.13 -9999 0 -0.58 17 17
vasculogenesis -0.18 0.25 -9999 0 -0.51 109 109
SDC4 -0.15 0.25 -9999 0 -0.58 76 76
Syndecan-4/Tenascin C -0.17 0.27 -9999 0 -0.57 95 95
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.24 -9999 0 -0.55 76 76
MMP9 -0.15 0.25 -9999 0 -0.53 111 111
Rac1/GTP 0.021 0.054 -9999 0 -0.26 9 9
cytoskeleton organization -0.13 0.23 -9999 0 -0.52 76 76
GIPC1 0.014 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.18 0.26 -9999 0 -0.56 92 92
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.086 0.18 -9999 0 -0.45 63 63
alphaM/beta2 Integrin/GPIbA -0.077 0.17 -9999 0 -0.46 54 54
alphaM/beta2 Integrin/proMMP-9 -0.16 0.22 -9999 0 -0.41 136 136
PLAUR -0.023 0.13 -9999 0 -0.49 27 27
HMGB1 -0.001 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.066 0.16 -9999 0 -0.48 42 42
AGER -0.021 0.11 -9999 0 -0.61 12 12
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG -0.022 0.14 -9999 0 -0.59 22 22
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.18 -9999 0 -0.47 60 60
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.52 111 111
CYR61 -0.1 0.23 -9999 0 -0.55 75 75
TLN1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP -0.089 0.13 -9999 0 -0.43 31 31
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.025 0.13 -9999 0 -0.48 26 26
MYH2 -0.086 0.15 -9999 0 -0.4 41 41
MST1R 0.001 0.086 -9999 0 -0.57 8 8
leukocyte activation during inflammatory response -0.11 0.19 -9999 0 -0.4 86 86
APOB -0.073 0.2 -9999 0 -0.55 56 56
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.022 0.14 -9999 0 -0.53 24 24
JAM3 0.014 0 -9999 0 -10000 0 0
GP1BA -0.006 0.11 -9999 0 -0.58 12 12
alphaM/beta2 Integrin/CTGF -0.09 0.19 -9999 0 -0.45 64 64
alphaM/beta2 Integrin -0.097 0.17 -9999 0 -0.43 46 46
JAM3 homodimer 0.014 0 -9999 0 -10000 0 0
ICAM2 0.012 0.032 -9999 0 -0.6 1 1
ICAM1 -0.027 0.14 -9999 0 -0.5 29 29
phagocytosis triggered by activation of immune response cell surface activating receptor -0.096 0.16 -9999 0 -0.43 46 46
cell adhesion -0.077 0.17 -9999 0 -0.46 54 54
NFKB1 -0.16 0.27 -9999 0 -0.64 58 58
THY1 -0.003 0.1 -9999 0 -0.57 11 11
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.071 0.14 -9999 0 -0.33 80 80
alphaM/beta2 Integrin/LRP/tPA -0.083 0.17 -9999 0 -0.46 48 48
IL6 -0.21 0.34 -9999 0 -0.79 68 68
ITGB2 -0.048 0.16 -9999 0 -0.57 30 30
elevation of cytosolic calcium ion concentration -0.11 0.21 -9999 0 -0.47 75 75
alphaM/beta2 Integrin/JAM2/JAM3 -0.054 0.15 -9999 0 -0.44 41 41
JAM2 0.012 0.032 -9999 0 -0.6 1 1
alphaM/beta2 Integrin/ICAM1 -0.096 0.18 -9999 0 -0.51 39 39
alphaM/beta2 Integrin/uPA/Plg -0.098 0.19 -9999 0 -0.45 63 63
RhoA/GTP -0.088 0.16 -9999 0 -0.41 43 43
positive regulation of phagocytosis -0.1 0.19 -9999 0 -0.52 45 45
Ron/MSP -0.041 0.12 -9999 0 -0.4 38 38
alphaM/beta2 Integrin/uPAR/uPA -0.11 0.21 -9999 0 -0.52 61 61
alphaM/beta2 Integrin/uPAR -0.087 0.19 -9999 0 -0.48 59 59
PLAU -0.06 0.18 -9999 0 -0.51 52 52
PLAT -0.044 0.16 -9999 0 -0.48 43 43
actin filament polymerization -0.083 0.15 -9999 0 -0.38 41 41
MST1 -0.032 0.16 -9999 0 -0.55 30 30
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.19 -9999 0 -0.4 86 86
TNF -0.22 0.36 -9999 0 -0.78 85 85
RAP1B 0.013 0.026 -9999 0 -0.48 1 1
alphaM/beta2 Integrin/uPA -0.11 0.2 -9999 0 -0.44 82 82
fibrinolysis -0.098 0.18 -9999 0 -0.45 63 63
HCK -0.013 0.12 -9999 0 -0.53 18 18
dendritic cell antigen processing and presentation -0.096 0.16 -9999 0 -0.43 46 46
VTN -0.011 0.12 -9999 0 -0.55 16 16
alphaM/beta2 Integrin/CYR61 -0.13 0.22 -9999 0 -0.44 104 104
LPA -0.025 0.13 -9999 0 -0.48 26 26
LRP1 0.014 0 -9999 0 -10000 0 0
cell migration -0.16 0.22 -9999 0 -0.44 112 112
FN1 -0.002 0.088 -9999 0 -0.48 12 12
alphaM/beta2 Integrin/Thy1 -0.076 0.17 -9999 0 -0.48 51 51
MPO -0.13 0.24 -9999 0 -0.54 92 92
KNG1 -0.018 0.1 -9999 0 -0.48 17 17
RAP1/GDP -0.001 0.015 -9999 0 -0.28 1 1
ROCK1 -0.076 0.15 -9999 0 -0.4 37 37
ELA2 0 0 -9999 0 -10000 0 0
PLG 0.001 0.026 -9999 0 -0.48 1 1
CTGF -0.029 0.15 -9999 0 -0.53 29 29
alphaM/beta2 Integrin/Hck -0.08 0.21 -9999 0 -0.58 43 43
ITGAM -0.046 0.16 -9999 0 -0.6 27 27
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.092 0.21 -9999 0 -0.5 58 58
HP -0.1 0.22 -9999 0 -0.53 77 77
leukocyte adhesion -0.11 0.17 -9999 0 -0.56 35 35
SELP -0.025 0.13 -9999 0 -0.48 26 26
Reelin signaling pathway

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
CDK5R1/CDK5 -0.025 0.1 -9999 0 -0.43 21 21
VLDLR -0.002 0.099 -9999 0 -0.59 10 10
CRKL 0.014 0 -9999 0 -10000 0 0
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ITGA3 -0.008 0.1 -9999 0 -0.5 16 16
RELN/VLDLR/Fyn -0.094 0.15 -9999 0 -0.33 103 103
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.011 0.055 -9999 0 -10000 0 0
AKT1 -0.069 0.16 -9999 0 -0.49 21 21
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.091 0.23 -9999 0 -0.58 65 65
RELN/LRP8/DAB1 -0.13 0.18 -9999 0 -0.39 96 96
LRPAP1/LRP8 -0.001 0.023 -9999 0 -0.44 1 1
RELN/LRP8/DAB1/Fyn -0.12 0.17 -9999 0 -0.36 95 95
DAB1/alpha3/beta1 Integrin -0.12 0.17 -9999 0 -0.53 36 36
long-term memory -0.29 0.29 -9999 0 -0.65 118 118
DAB1/LIS1 -0.12 0.17 -9999 0 -0.54 27 27
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.52 27 27
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
DAB1/NCK2 -0.12 0.17 -9999 0 -0.54 27 27
ARHGEF2 0.012 0.032 -9999 0 -0.6 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.17 0.26 -9999 0 -0.55 118 118
CDK5R1 -0.021 0.14 -9999 0 -0.6 21 21
RELN -0.13 0.25 -9999 0 -0.54 96 96
PIK3R1 0.014 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.085 0.15 -9999 0 -0.32 96 96
GRIN2A/RELN/LRP8/DAB1/Fyn -0.21 0.24 -9999 0 -0.46 146 146
MAPK8 -0.003 0.1 -9999 0 -0.6 10 10
RELN/VLDLR/DAB1 -0.14 0.19 -9999 0 -0.36 145 145
ITGB1 0.011 0.037 -9999 0 -0.48 2 2
MAP1B -0.1 0.2 -9999 0 -0.37 101 101
RELN/LRP8 -0.085 0.15 -9999 0 -0.37 50 50
GRIN2B/RELN/LRP8/DAB1/Fyn -0.22 0.24 -9999 0 -0.45 147 147
PI3K -0.001 0.023 -9999 0 -0.44 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.017 0.078 -9999 0 -0.36 17 17
RAP1A -0.068 0.17 -9999 0 -0.48 27 27
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0.046 -9999 0 -0.6 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.18 0.27 -9999 0 -0.54 131 131
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.041 0.14 -9999 0 -0.44 21 21
neuron adhesion -0.061 0.18 -9999 0 -0.48 30 30
LRP8 0.012 0.032 -9999 0 -0.6 1 1
GSK3B -0.057 0.15 -9999 0 -0.47 20 20
RELN/VLDLR/DAB1/Fyn -0.13 0.18 -9999 0 -0.38 101 101
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.082 0.16 -9999 0 -0.31 102 102
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT 0.008 0.088 -9999 0 -0.55 8 8
neuron migration -0.066 0.19 -9999 0 -0.52 28 28
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.041 0.14 -9999 0 -0.45 21 21
RELN/VLDLR -0.084 0.14 -9999 0 -0.34 59 59
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0.037 -9999 0 -0.48 2 2
ITGB7 -0.041 0.17 -9999 0 -0.54 36 36
ITGA4 -0.048 0.18 -9999 0 -0.53 42 42
alpha4/beta7 Integrin -0.08 0.17 -9999 0 -0.44 67 67
alpha4/beta1 Integrin -0.045 0.13 -9999 0 -0.39 42 42
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.09 0.14 -9999 0 -0.43 35 35
JUN -0.08 0.2 -9999 0 -0.53 41 41
HRAS 0.013 0.026 -9999 0 -0.48 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.16 0.22 -9999 0 -0.45 96 96
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.011 0.041 -9999 0 -0.54 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.16 0.22 -9999 0 -0.46 95 95
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.092 0.17 -9999 0 -0.37 92 92
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.62 40 40
GRB7 -0.036 0.14 -9999 0 -0.48 34 34
RET51/GFRalpha1/GDNF -0.16 0.22 -9999 0 -0.45 95 95
MAPKKK cascade -0.12 0.18 -9999 0 -0.56 37 37
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.088 0.17 -9999 0 -0.41 63 63
lamellipodium assembly -0.084 0.13 -9999 0 -0.39 36 36
RET51/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.46 95 95
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
RET9/GFRalpha1/GDNF/SHC -0.09 0.18 -9999 0 -0.37 89 89
RET9/GFRalpha1/GDNF/Shank3 -0.092 0.17 -9999 0 -0.36 93 93
MAPK3 -0.11 0.21 -9999 0 -0.58 40 40
DOK1 0.012 0.032 -9999 0 -0.6 1 1
DOK6 -0.047 0.18 -9999 0 -0.58 38 38
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.1 0.22 -9999 0 -0.54 51 51
DOK5 0.004 0.078 -9999 0 -0.6 6 6
GFRA1 -0.069 0.2 -9999 0 -0.56 53 53
MAPK8 -0.087 0.2 -9999 0 -0.54 41 41
HRAS/GTP -0.14 0.21 -9999 0 -0.43 95 95
tube development -0.085 0.16 -9999 0 -0.38 64 64
MAPK1 -0.11 0.21 -9999 0 -0.58 40 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.04 0.15 -9999 0 -0.33 63 63
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.005 0.068 -9999 0 -0.48 7 7
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.26 -9999 0 -0.67 55 55
SHC1 0.009 0.052 -9999 0 -0.48 4 4
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.23 -9999 0 -0.47 101 101
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.46 100 100
PRKCA 0.012 0.032 -9999 0 -0.6 1 1
HRAS/GDP -0.001 0.018 -9999 0 -0.34 1 1
CREB1 -0.067 0.18 -9999 0 -0.4 64 64
PIK3R1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.042 0.15 -9999 0 -0.34 63 63
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.24 -9999 0 -0.49 97 97
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.24 -9999 0 -0.55 89 89
DOK4 -0.006 0.11 -9999 0 -0.6 12 12
JNK cascade -0.078 0.2 -9999 0 -0.51 41 41
RET9/GFRalpha1/GDNF/FRS2 -0.089 0.17 -9999 0 -0.37 89 89
SHANK3 0.006 0.066 -9999 0 -0.5 6 6
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.04 0.15 -9999 0 -0.33 63 63
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.092 0.2 -9999 0 -0.58 34 34
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.092 0.2 -9999 0 -0.51 45 45
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.095 0.21 -9999 0 -0.54 44 44
PI3K -0.088 0.23 -9999 0 -0.63 36 36
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.085 0.16 -9999 0 -0.38 64 64
GRB10 0.012 0.032 -9999 0 -0.6 1 1
activation of MAPKK activity -0.086 0.2 -9999 0 -0.48 56 56
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.46 95 95
GAB1 0.011 0.041 -9999 0 -0.54 2 2
IRS1 0.014 0 -9999 0 -10000 0 0
IRS2 0.012 0.032 -9999 0 -0.6 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.096 0.21 -9999 0 -0.63 34 34
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.46 95 95
GRB2 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.068 0.2 -9999 0 -0.58 50 50
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.45 95 95
Rac1/GTP -0.099 0.15 -9999 0 -0.47 36 36
RET9/GFRalpha1/GDNF -0.098 0.19 -9999 0 -0.41 88 88
GFRalpha1/GDNF -0.11 0.22 -9999 0 -0.47 88 88
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.039 0.16 -9999 0 -0.53 36 36
GPC2 -0.014 0.13 -9999 0 -0.58 17 17
GPC2/Midkine -0.056 0.15 -9999 0 -0.42 49 49
neuron projection morphogenesis -0.056 0.15 -9999 0 -0.41 49 49
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.38 -9999 0 -1.1 46 46
MKNK1 0.007 0.064 -9999 0 -0.6 4 4
MAPK14 -0.038 0.12 -9999 0 -0.35 7 7
ATF2/c-Jun -0.027 0.15 -9999 0 -0.61 13 13
MAPK11 -0.043 0.14 -9999 0 -0.51 9 9
MITF -0.039 0.16 -9999 0 -0.35 61 61
MAPKAPK5 -0.036 0.15 -9999 0 -0.35 57 57
KRT8 -0.1 0.22 -9999 0 -0.42 88 88
MAPKAPK3 0.011 0.046 -9999 0 -0.6 2 2
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.058 0.19 -9999 0 -0.44 59 59
CEBPB -0.051 0.19 -9999 0 -0.41 59 59
SLC9A1 -0.036 0.16 -9999 0 -0.35 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.043 0.18 -9999 0 -0.77 8 8
p38alpha-beta/MNK1 -0.037 0.16 -9999 0 -0.56 12 12
JUN -0.027 0.15 -9999 0 -0.6 13 13
PPARGC1A -0.057 0.19 -9999 0 -0.4 66 66
USF1 -0.036 0.15 -9999 0 -0.35 57 57
RAB5/GDP/GDI1 -0.05 0.095 -9999 0 -0.44 5 5
NOS2 -0.078 0.27 -9999 0 -1.1 18 18
DDIT3 -0.039 0.16 -9999 0 -0.35 57 57
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.036 0.15 -9999 0 -0.45 17 17
p38alpha-beta/HBP1 -0.033 0.16 -9999 0 -0.34 57 57
CREB1 -0.037 0.16 -9999 0 -0.37 58 58
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.026 0.14 -9999 0 -0.58 8 8
RPS6KA4 -0.036 0.15 -9999 0 -0.35 57 57
PLA2G4A -0.043 0.18 -9999 0 -0.61 17 17
GDI1 -0.036 0.15 -9999 0 -0.35 57 57
TP53 -0.058 0.2 -9999 0 -0.44 66 66
RPS6KA5 -0.044 0.17 -9999 0 -0.36 63 63
ESR1 -0.054 0.18 -9999 0 -0.39 64 64
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.044 0.16 -9999 0 -0.36 64 64
MEF2A -0.037 0.16 -9999 0 -0.36 57 57
EIF4EBP1 -0.041 0.17 -9999 0 -0.38 58 58
KRT19 -0.096 0.22 -9999 0 -0.41 91 91
ELK4 -0.037 0.16 -9999 0 -0.36 57 57
ATF6 -0.036 0.15 -9999 0 -0.35 57 57
ATF1 -0.037 0.16 -9999 0 -0.37 58 58
p38alpha-beta/MAPKAPK2 -0.033 0.16 -9999 0 -0.53 8 8
p38alpha-beta/MAPKAPK3 -0.035 0.16 -9999 0 -0.53 10 10
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.04 0.1 -9999 0 -0.29 50 50
RGS9BP -0.001 0.094 -9999 0 -0.59 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.011 0.032 -9999 0 -0.6 1 1
mol:Na + -0.1 0.15 -9999 0 -0.32 118 118
mol:ADP 0.016 0.044 -9999 0 -0.36 5 5
GNAT2 0.009 0.037 -9999 0 -0.48 2 2
RGS9-1/Gbeta5/R9AP -0.039 0.12 -9999 0 -0.39 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.012 0.061 -9999 0 -0.3 15 15
GRK7 0.006 0.052 -9999 0 -0.48 4 4
CNGB3 -0.014 0.1 -9999 0 -0.48 17 17
Cone Metarhodopsin II/X-Arrestin -0.001 0.018 -9999 0 -0.34 1 1
mol:Ca2+ -0.15 0.2 -9999 0 -0.34 171 171
Cone PDE6 -0.043 0.11 -9999 0 -0.35 32 32
Cone Metarhodopsin II -0.004 0.032 -9999 0 -0.27 5 5
Na + (4 Units) -0.16 0.19 -9999 0 -0.34 171 171
GNAT2/GDP -0.034 0.11 -9999 0 -0.35 32 32
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.004 0.061 -9999 0 -0.26 17 17
Cone Transducin -0.042 0.11 -9999 0 -0.31 50 50
SLC24A2 -0.12 0.24 -9999 0 -0.55 85 85
GNB3/GNGT2 -0.054 0.14 -9999 0 -0.4 49 49
GNB3 -0.035 0.16 -9999 0 -0.56 31 31
GNAT2/GTP -0.002 0.025 -9999 0 -0.34 2 2
CNGA3 -0.14 0.25 -9999 0 -0.53 103 103
ARR3 0.001 0.026 -9999 0 -0.48 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.16 -9999 0 -0.32 118 118
mol:Pi -0.039 0.12 -9999 0 -0.39 37 37
Cone CNG Channel -0.091 0.14 -9999 0 -0.34 48 48
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.12 0.24 -9999 0 -0.55 85 85
RGS9 -0.038 0.17 -9999 0 -0.58 32 32
PDE6C 0.003 0.037 -9999 0 -0.48 2 2
GNGT2 -0.014 0.12 -9999 0 -0.55 18 18
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.01 0.094 -9999 0 -0.48 14 14
Aurora C signaling

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
INCENP 0.014 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.1 0.16 -9999 0 -0.32 119 119
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.03 0.044 -9999 0 -10000 0 0
AURKB -0.15 0.26 -9999 0 -0.56 105 105
AURKC -0.019 0.13 -9999 0 -0.52 23 23
Endothelins

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
AKT1 -0.094 0.22 -10000 0 -0.56 39 39
PTK2B -0.01 0.11 -10000 0 -0.48 18 18
mol:Ca2+ -0.062 0.25 -10000 0 -0.83 22 22
EDN1 -0.085 0.19 -10000 0 -0.47 54 54
EDN3 -0.017 0.13 -10000 0 -0.59 19 19
EDN2 -0.009 0.08 -10000 0 -0.48 10 10
HRAS/GDP -0.091 0.21 -10000 0 -0.5 49 49
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.048 0.16 -10000 0 -0.44 30 30
ADCY4 -0.11 0.23 -10000 0 -0.51 67 67
ADCY5 -0.11 0.24 -10000 0 -0.56 62 62
ADCY6 -0.1 0.22 -10000 0 -0.52 59 59
ADCY7 -0.1 0.22 -10000 0 -0.51 62 62
ADCY1 -0.16 0.26 -10000 0 -0.53 88 88
ADCY2 -0.11 0.24 -10000 0 -0.54 65 65
ADCY3 -0.1 0.22 -10000 0 -0.51 62 62
ADCY8 -0.14 0.26 -10000 0 -0.54 82 82
ADCY9 -0.1 0.23 -10000 0 -0.52 61 61
arachidonic acid secretion -0.088 0.22 -10000 0 -0.52 48 48
ETB receptor/Endothelin-1/Gq/GTP -0.043 0.16 -10000 0 -0.41 39 39
GNAO1 0.004 0.078 -10000 0 -0.6 6 6
HRAS 0.012 0.026 -10000 0 -0.48 1 1
ETA receptor/Endothelin-1/G12/GTP -0.096 0.2 0.26 13 -0.54 38 51
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.23 0.24 13 -0.54 62 75
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.18 0.33 -10000 0 -0.63 107 107
EDNRB -0.046 0.18 -10000 0 -0.6 35 35
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.12 0.27 -10000 0 -0.68 48 48
CYSLTR1 -0.11 0.25 -10000 0 -0.65 43 43
SLC9A1 -0.066 0.1 -10000 0 -0.32 24 24
mol:GDP -0.1 0.23 -10000 0 -0.53 54 54
SLC9A3 -0.096 0.26 -10000 0 -0.65 54 54
RAF1 -0.1 0.22 -10000 0 -0.52 54 54
JUN -0.043 0.2 -10000 0 -0.72 12 12
JAK2 -0.094 0.22 -10000 0 -0.56 39 39
mol:IP3 -0.056 0.18 -10000 0 -0.5 31 31
ETA receptor/Endothelin-1 -0.13 0.25 0.3 13 -0.58 53 66
PLCB1 -0.008 0.11 -10000 0 -0.6 12 12
PLCB2 -0.015 0.12 -10000 0 -0.58 17 17
ETA receptor/Endothelin-3 -0.07 0.15 -10000 0 -0.48 37 37
FOS -0.13 0.32 -10000 0 -0.9 43 43
Gai/GDP 0 0.14 -10000 0 -1 6 6
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.26 -10000 0 -0.57 62 62
BCAR1 0.013 0.032 -10000 0 -0.6 1 1
PRKCB1 -0.055 0.17 -10000 0 -0.48 31 31
GNAQ 0.014 0.007 -10000 0 -10000 0 0
GNAZ 0.012 0.032 -10000 0 -0.6 1 1
GNAL -0.05 0.19 -10000 0 -0.6 38 38
Gs family/GDP -0.14 0.21 -10000 0 -0.5 72 72
ETA receptor/Endothelin-1/Gq/GTP -0.045 0.15 -10000 0 -0.41 28 28
MAPK14 -0.036 0.16 -10000 0 -0.48 26 26
TRPC6 -0.067 0.26 -10000 0 -0.89 22 22
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.004 0.1 -10000 0 -0.6 11 11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.046 0.17 -10000 0 -0.43 40 40
ETB receptor/Endothelin-2 -0.041 0.14 -10000 0 -0.42 44 44
ETB receptor/Endothelin-3 -0.048 0.17 -10000 0 -0.48 48 48
ETB receptor/Endothelin-1 -0.1 0.2 -10000 0 -0.46 69 69
MAPK3 -0.12 0.29 -10000 0 -0.77 48 48
MAPK1 -0.12 0.29 -10000 0 -0.79 45 45
Rac1/GDP -0.09 0.21 -10000 0 -0.52 43 43
cAMP biosynthetic process -0.12 0.24 -10000 0 -0.54 67 67
MAPK8 -0.058 0.22 -10000 0 -0.65 28 28
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.025 0.13 -10000 0 -0.38 27 27
p130Cas/CRK/Src/PYK2 -0.097 0.23 -10000 0 -0.58 43 43
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.09 0.21 -10000 0 -0.51 48 48
COL1A2 -0.14 0.29 -10000 0 -0.72 55 55
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.061 0.13 -10000 0 -0.42 30 30
mol:DAG -0.056 0.18 -10000 0 -0.5 31 31
MAP2K2 -0.11 0.25 -10000 0 -0.6 51 51
MAP2K1 -0.11 0.25 -10000 0 -0.61 50 50
EDNRA -0.063 0.16 -10000 0 -0.49 31 31
positive regulation of muscle contraction -0.072 0.19 -10000 0 -0.51 35 35
Gq family/GDP -0.11 0.2 -10000 0 -0.58 39 39
HRAS/GTP -0.098 0.22 -10000 0 -0.51 49 49
PRKCH -0.046 0.17 -10000 0 -0.53 24 24
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.047 0.18 -10000 0 -0.53 25 25
PRKCB -0.084 0.21 -10000 0 -0.5 47 47
PRKCE -0.051 0.18 -10000 0 -0.52 29 29
PRKCD -0.061 0.2 -10000 0 -0.6 30 30
PRKCG -0.15 0.24 -10000 0 -0.48 84 84
regulation of vascular smooth muscle contraction -0.15 0.37 -10000 0 -1.1 42 42
PRKCQ -0.056 0.19 -10000 0 -0.52 34 34
PLA2G4A -0.097 0.24 -10000 0 -0.58 48 48
GNA14 -0.007 0.11 -10000 0 -0.56 13 13
GNA15 -0.007 0.11 -10000 0 -0.57 13 13
GNA12 0.012 0.032 -10000 0 -0.6 1 1
GNA11 0.001 0.085 -10000 0 -0.6 7 7
Rac1/GTP -0.095 0.2 0.26 12 -0.53 38 50
MMP1 0.016 0.15 -10000 0 -0.41 21 21
Caspase cascade in apoptosis

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
TOP1 -0.046 0.15 -10000 0 -0.34 60 60
ACTA1 -0.069 0.19 -10000 0 -0.41 68 68
NUMA1 -0.046 0.15 -10000 0 -0.33 63 63
SPTAN1 -0.058 0.18 0.25 2 -0.4 65 67
LIMK1 -0.058 0.18 0.25 2 -0.4 65 67
BIRC3 -0.035 0.16 -10000 0 -0.55 32 32
BIRC2 0.014 0 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.086 0.2 -10000 0 -0.44 73 73
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.046 0.15 0.21 1 -0.33 65 66
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.057 0.18 0.25 2 -0.4 65 67
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.064 0.19 -10000 0 -0.41 63 63
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A -0.18 0.3 -10000 0 -0.65 94 94
BID -0.043 0.12 -10000 0 -0.24 76 76
MAP3K1 -0.014 0.069 -10000 0 -0.22 4 4
TRADD 0.011 0.041 -10000 0 -0.54 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.008 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.06 0.19 0.25 2 -0.41 66 68
CASP9 0.014 0 -10000 0 -10000 0 0
DNA repair 0.003 0.062 -10000 0 -0.2 13 13
neuron apoptosis 0.004 0.049 -10000 0 -0.43 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.05 0.18 -10000 0 -0.39 62 62
APAF1 0.014 0 -10000 0 -10000 0 0
CASP6 -0.028 0.12 -10000 0 -0.6 4 4
TRAF2 0.014 0 -10000 0 -10000 0 0
ICAD/CAD -0.049 0.18 0.25 1 -0.39 62 63
CASP7 0.019 0.078 0.27 27 -0.21 1 28
KRT18 -0.071 0.19 -10000 0 -0.63 35 35
apoptosis -0.069 0.18 -10000 0 -0.39 70 70
DFFA -0.058 0.18 0.25 2 -0.41 62 64
DFFB -0.058 0.18 0.25 2 -0.4 65 67
PARP1 -0.003 0.062 0.2 13 -10000 0 13
actin filament polymerization 0.046 0.17 0.37 62 -0.25 1 63
TNF -0.15 0.25 -10000 0 -0.54 109 109
CYCS -0.025 0.082 -10000 0 -0.21 27 27
SATB1 -0.023 0.12 -10000 0 -0.52 7 7
SLK -0.059 0.18 0.25 2 -0.4 65 67
p15 BID/BAX -0.031 0.1 -10000 0 -0.26 30 30
CASP2 -0.015 0.11 -10000 0 -0.34 12 12
JNK cascade 0.014 0.069 0.22 4 -10000 0 4
CASP3 -0.07 0.2 0.26 2 -0.43 68 70
LMNB2 -0.011 0.089 -10000 0 -0.36 7 7
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 -0.019 0.12 -10000 0 -0.49 24 24
Mammalian IAPs/DIABLO -0.025 0.082 -10000 0 -0.32 18 18
negative regulation of DNA binding -0.18 0.29 -10000 0 -0.64 94 94
stress fiber formation -0.058 0.18 0.25 2 -0.4 65 67
GZMB -0.11 0.23 -10000 0 -0.47 101 101
CASP1 -0.007 0.089 -10000 0 -0.29 30 30
LMNB1 -0.019 0.1 -10000 0 -0.39 11 11
APP 0.004 0.049 -10000 0 -0.43 1 1
TNFRSF1A 0.005 0.068 -10000 0 -0.52 6 6
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.073 -10000 0 -0.35 15 15
VIM -0.075 0.18 -10000 0 -0.39 71 71
LMNA -0.011 0.089 -10000 0 -0.35 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.025 0.11 -10000 0 -0.37 12 12
LRDD 0.008 0.061 -10000 0 -0.57 4 4
SREBF1 -0.068 0.19 0.24 1 -0.4 70 71
APAF-1/Caspase 9 -0.006 0.043 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.045 0.15 -10000 0 -0.33 63 63
CFL2 -0.048 0.18 0.25 1 -0.38 62 63
GAS2 -0.067 0.19 0.25 2 -0.41 69 71
positive regulation of apoptosis -0.012 0.093 -10000 0 -0.36 8 8
PRF1 -0.065 0.2 -10000 0 -0.54 52 52
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.17 0.39 -10000 0 -0.98 44 44
PCK1 -0.24 0.44 -10000 0 -1.1 61 61
HNF4A -0.2 0.43 -10000 0 -1.1 42 42
KCNJ11 -0.24 0.51 -10000 0 -1.2 61 61
AKT1 -0.074 0.17 -10000 0 -0.42 20 20
response to starvation -0.002 0.02 -10000 0 -10000 0 0
DLK1 -0.24 0.46 -10000 0 -1 66 66
NKX2-1 -0.067 0.21 -10000 0 -0.83 6 6
ACADM -0.17 0.39 -10000 0 -0.97 46 46
TAT -0.21 0.4 -10000 0 -0.97 56 56
CEBPB -0.009 0.12 -10000 0 -0.58 14 14
CEBPA -0.015 0.13 -10000 0 -0.56 19 19
TTR -0.15 0.28 -10000 0 -0.77 35 35
PKLR -0.19 0.4 -10000 0 -0.95 53 53
APOA1 -0.22 0.48 -10000 0 -1.3 43 43
CPT1C -0.17 0.39 -10000 0 -0.99 44 44
ALAS1 -0.063 0.21 0.48 1 -0.64 8 9
TFRC -0.17 0.32 -10000 0 -0.76 46 46
FOXF1 -0.005 0.09 -10000 0 -0.52 10 10
NF1 0.017 0.056 -10000 0 -0.6 3 3
HNF1A (dimer) 0.011 0.044 -10000 0 -0.66 1 1
CPT1A -0.17 0.39 -10000 0 -0.98 46 46
HMGCS1 -0.17 0.39 -10000 0 -0.96 47 47
NR3C1 -0.024 0.077 -10000 0 -0.3 1 1
CPT1B -0.19 0.41 -10000 0 -0.99 53 53
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.011 0.023 -10000 0 -10000 0 0
GCK -0.24 0.48 -10000 0 -1.1 70 70
CREB1 -0.004 0.056 -10000 0 -0.22 2 2
IGFBP1 -0.27 0.53 -10000 0 -1.3 68 68
PDX1 -0.073 0.21 -10000 0 -0.71 8 8
UCP2 -0.19 0.42 -10000 0 -1 54 54
ALDOB -0.19 0.44 -10000 0 -1.1 50 50
AFP -0.091 0.17 -10000 0 -0.54 26 26
BDH1 -0.21 0.45 -10000 0 -1.1 59 59
HADH -0.17 0.41 -10000 0 -0.99 48 48
F2 -0.2 0.42 -10000 0 -1.1 37 37
HNF1A 0.011 0.044 -10000 0 -0.66 1 1
G6PC -0.074 0.22 -10000 0 -0.8 19 19
SLC2A2 -0.088 0.23 -10000 0 -0.77 4 4
INS 0.016 0.094 0.24 9 -0.55 4 13
FOXA1 -0.051 0.16 -10000 0 -0.51 35 35
FOXA3 -0.13 0.24 -10000 0 -0.54 77 77
FOXA2 -0.21 0.47 -10000 0 -1.1 56 56
ABCC8 -0.26 0.53 -10000 0 -1.2 66 66
ALB -0.12 0.28 -10000 0 -0.92 30 30
EGFR-dependent Endothelin 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
HRAS 0.013 0.026 -9999 0 -0.48 1 1
EGFR -0.082 0.21 -9999 0 -0.55 62 62
EGF/EGFR -0.11 0.16 -9999 0 -0.37 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.075 0.14 -9999 0 -0.34 59 59
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.017 0.13 -9999 0 -0.53 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.044 0.17 -9999 0 -0.56 37 37
EGF/EGFR dimer/SHC -0.091 0.17 -9999 0 -0.37 91 91
mol:GDP -0.074 0.14 -9999 0 -0.34 59 59
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.039 0.16 -9999 0 -0.53 36 36
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.067 0.13 -9999 0 -0.5 12 12
SHC1 0.009 0.052 -9999 0 -0.48 4 4
HRAS/GDP -0.069 0.13 -9999 0 -0.51 12 12
FRAP1 -0.041 0.15 -9999 0 -0.33 59 59
EGF/EGFR dimer -0.11 0.19 -9999 0 -0.43 89 89
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.058 0.14 -9999 0 -0.39 54 54
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.022 0.086 -9999 0 -0.35 23 23
Metarhodopsin II/Arrestin -0.034 0.1 -9999 0 -0.32 39 39
PDE6G/GNAT1/GTP -0.052 0.12 -9999 0 -0.34 56 56
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.02 0.12 -9999 0 -0.49 23 23
GRK1 0.011 0.032 -9999 0 -0.6 1 1
CNG Channel -0.2 0.2 -9999 0 -0.56 63 63
mol:Na + -0.2 0.2 -9999 0 -0.5 75 75
mol:ADP 0.011 0.032 -9999 0 -0.6 1 1
RGS9-1/Gbeta5/R9AP -0.039 0.12 -9999 0 -0.39 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.2 0.2 -9999 0 -0.52 75 75
CNGB1 -0.2 0.27 -9999 0 -0.53 143 143
RDH5 -0.017 0.12 -9999 0 -0.48 23 23
SAG 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.21 -9999 0 -0.48 75 75
Na + (4 Units) -0.18 0.18 -9999 0 -0.47 75 75
RGS9 -0.038 0.17 -9999 0 -0.58 32 32
GNB1/GNGT1 -0.001 0.017 -9999 0 -0.33 1 1
GNAT1/GDP -0.048 0.11 -9999 0 -0.34 34 34
GUCY2D -0.002 0.072 -9999 0 -0.48 8 8
GNGT1 -0.001 0.025 -9999 0 -0.48 1 1
GUCY2F 0.004 0.051 -9999 0 -0.48 4 4
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.068 0.17 -9999 0 -0.36 61 61
mol:11-cis-retinal -0.017 0.12 -9999 0 -0.48 23 23
mol:cGMP -0.08 0.16 -9999 0 -0.39 45 45
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.06 0.14 -9999 0 -0.36 61 61
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.037 0.16 -9999 0 -0.56 32 32
Metarhodopsin II -0.031 0.09 -9999 0 -0.29 40 40
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.1 0.16 -9999 0 -0.39 66 66
RGS9BP -0.001 0.094 -9999 0 -0.59 9 9
Metarhodopsin II/Transducin -0.015 0.08 -9999 0 -0.3 15 15
GCAP Family/Ca ++ -0.1 0.16 -9999 0 -0.37 76 76
PDE6A/B -0.07 0.16 -9999 0 -0.41 62 62
mol:Pi -0.039 0.12 -9999 0 -0.39 37 37
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.017 0.068 -9999 0 -0.27 23 23
PDE6B -0.031 0.15 -9999 0 -0.54 30 30
PDE6A -0.043 0.17 -9999 0 -0.54 37 37
PDE6G -0.042 0.17 -9999 0 -0.57 35 35
RHO -0.046 0.17 -9999 0 -0.52 39 39
PDE6 -0.1 0.17 -9999 0 -0.6 22 22
GUCA1A -0.15 0.25 -9999 0 -0.54 106 106
GC2/GCAP Family -0.1 0.16 -9999 0 -0.38 64 64
GUCA1C -0.012 0.087 -9999 0 -0.48 12 12
GUCA1B -0.001 0.094 -9999 0 -0.59 9 9
Calcium signaling in the CD4+ TCR pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.095 -9999 0 -0.38 21 21
NFATC2 -0.046 0.14 -9999 0 -0.36 57 57
NFATC3 0.011 0.032 -9999 0 -0.39 1 1
CD40LG -0.15 0.29 -9999 0 -0.67 65 65
PTGS2 -0.19 0.33 -9999 0 -0.68 90 90
JUNB -0.036 0.16 -9999 0 -0.51 35 35
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.025 -9999 0 -0.46 1 1
CaM/Ca2+ -0.005 0.025 -9999 0 -0.46 1 1
CALM1 0.01 0.033 -9999 0 -0.61 1 1
JUN 0.001 0.075 -9999 0 -0.5 8 8
mol:Ca2+ -0.005 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.096 0.22 -9999 0 -0.53 74 74
CREM 0.011 0.041 -9999 0 -0.54 2 2
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -9999 0 -0.52 46 46
FOS -0.09 0.22 -9999 0 -0.55 66 66
IFNG -0.14 0.27 -9999 0 -0.62 56 56
AP-1/NFAT1-c-4 -0.17 0.32 -9999 0 -0.7 70 70
FASLG -0.15 0.29 -9999 0 -0.65 62 62
NFAT1-c-4/ICER1 -0.061 0.16 -9999 0 -0.44 30 30
IL2RA -0.17 0.3 -9999 0 -0.66 70 70
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.14 0.26 -9999 0 -0.61 56 56
JunB/Fra1/NFAT1-c-4 -0.14 0.2 -9999 0 -0.5 68 68
IL4 -0.14 0.26 -9999 0 -0.61 56 56
IL2 -0.008 0.015 -9999 0 -10000 0 0
IL3 -0.019 0.05 -9999 0 -0.88 1 1
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 -0.037 0.16 -9999 0 -0.54 34 34
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.032 -9999 0 -0.6 1 1
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.095 0.22 -9999 0 -0.46 81 81
MAP3K8 -0.001 0.083 -9999 0 -0.49 10 10
FOS -0.087 0.2 -9999 0 -0.5 58 58
PRKCA 0.011 0.033 -9999 0 -0.6 1 1
PTPN7 -0.13 0.24 -9999 0 -0.55 91 91
HRAS 0.013 0.026 -9999 0 -0.48 1 1
PRKCB -0.064 0.19 -9999 0 -0.52 53 53
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.023 0.023 -9999 0 -0.24 2 2
MAPK3 -0.071 0.18 -9999 0 -0.46 53 53
MAP2K1 -0.015 0.13 -9999 0 -0.49 16 16
ELK1 0.013 0.006 -9999 0 -10000 0 0
BRAF -0.055 0.14 -9999 0 -0.46 30 30
mol:GTP -0.001 0.002 -9999 0 -0.005 62 62
MAPK1 -0.071 0.18 -9999 0 -0.46 53 53
RAF1 -0.037 0.1 -9999 0 -0.47 15 15
KRAS 0.013 0.026 -9999 0 -0.48 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.17 -9999 0 -0.38 101 101
CRKL -0.041 0.12 -9999 0 -0.48 6 6
mol:PIP3 -0.019 0.007 -9999 0 -10000 0 0
AKT1 0.002 0.018 -9999 0 -0.33 1 1
PTK2B -0.01 0.11 -9999 0 -0.48 18 18
RAPGEF1 -0.031 0.12 -9999 0 -0.44 6 6
RANBP10 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
HGF/MET/SHIP2 -0.13 0.18 -9999 0 -0.35 139 139
MAP3K5 -0.035 0.14 -9999 0 -0.43 15 15
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.16 -9999 0 -0.38 70 70
AP1 -0.083 0.16 -9999 0 -0.4 66 66
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.009 0.052 -9999 0 -0.48 4 4
apoptosis -0.09 0.23 -9999 0 -0.77 35 35
STAT3 (dimer) -0.044 0.13 -9999 0 -0.4 9 9
GAB1/CRKL/SHP2/PI3K -0.054 0.091 -9999 0 -0.52 3 3
INPP5D 0.008 0.055 -9999 0 -0.51 4 4
CBL/CRK -0.031 0.12 -9999 0 -0.44 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
ELK1 -0.056 0.09 -9999 0 -0.2 101 101
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.044 0.067 -9999 0 -0.29 6 6
PAK1 -0.017 0.079 -9999 0 -0.31 4 4
HGF/MET/RANBP10 -0.13 0.18 -9999 0 -0.35 139 139
HRAS -0.097 0.23 -9999 0 -0.63 47 47
DOCK1 -0.033 0.12 -9999 0 -0.44 6 6
GAB1 -0.051 0.13 -9999 0 -0.3 50 50
CRK -0.041 0.12 -9999 0 -0.48 6 6
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.12 0.21 -9999 0 -0.58 54 54
JUN 0.003 0.075 -9999 0 -0.5 8 8
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.069 0.12 -9999 0 -0.28 70 70
PIK3R1 0.014 0 -9999 0 -10000 0 0
cell morphogenesis -0.014 0.13 -9999 0 -0.45 5 5
GRB2/SHC -0.047 0.12 -9999 0 -0.27 50 50
FOS -0.087 0.22 -9999 0 -0.55 66 66
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.056 0.09 -9999 0 -0.2 101 101
HGF/MET/MUC20 -0.14 0.19 -9999 0 -0.36 139 139
cell migration -0.046 0.11 -9999 0 -0.26 50 50
GRB2 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
MET/RANBP10 -0.1 0.17 -9999 0 -0.38 101 101
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.055 0.13 -9999 0 -0.34 22 22
MET/MUC20 -0.11 0.18 -9999 0 -0.39 101 101
RAP1B -0.022 0.11 -9999 0 -0.44 5 5
RAP1A -0.021 0.11 -9999 0 -0.44 5 5
HGF/MET/RANBP9 -0.13 0.18 -9999 0 -0.35 139 139
RAF1 -0.083 0.22 -9999 0 -0.58 47 47
STAT3 -0.044 0.13 -9999 0 -0.4 9 9
cell proliferation -0.055 0.17 -9999 0 -0.39 60 60
RPS6KB1 -0.018 0.047 -9999 0 -10000 0 0
MAPK3 -0.056 0.082 -9999 0 -0.21 2 2
MAPK1 -0.056 0.082 -9999 0 -0.2 45 45
RANBP9 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.021 0.14 -9999 0 -0.45 18 18
SRC -0.043 0.13 -9999 0 -0.4 9 9
PI3K -0.045 0.11 -9999 0 -0.36 6 6
MET/Glomulin -0.085 0.16 -9999 0 -0.34 101 101
SOS1 0.014 0 -9999 0 -10000 0 0
MAP2K1 -0.069 0.2 -9999 0 -0.54 46 46
MET -0.14 0.25 -9999 0 -0.54 101 101
MAP4K1 -0.043 0.14 -9999 0 -0.44 14 14
PTK2 0.014 0 -9999 0 -10000 0 0
MAP2K2 -0.069 0.2 -9999 0 -0.54 46 46
BAD 0.01 0.017 -9999 0 -0.31 1 1
MAP2K4 -0.025 0.13 -9999 0 -0.43 13 13
SHP2/GRB2/SOS1/GAB1 -0.083 0.13 -9999 0 -0.38 47 47
INPPL1 0.014 0 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
SH3KBP1 0.014 0 -9999 0 -10000 0 0
HGS -0.055 0.11 -9999 0 -0.26 62 62
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.069 0.19 -9999 0 -0.5 59 59
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
PTPRJ 0.013 0.026 -9999 0 -0.48 1 1
NCK/PLCgamma1 -0.044 0.11 -9999 0 -0.41 6 6
PDPK1 -0.008 0.02 -9999 0 -0.37 1 1
HGF/MET/SHIP -0.14 0.19 -9999 0 -0.36 140 140
p75(NTR)-mediated 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
Sortilin/TRAF6 -0.002 0.032 -10000 0 -0.44 2 2
Necdin/E2F1 -0.047 0.14 -10000 0 -0.42 41 41
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.076 0.13 -10000 0 -0.32 58 58
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.18 -10000 0 -0.37 109 109
NT-4/5 (dimer)/p75(NTR) -0.065 0.15 -10000 0 -0.39 61 61
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.044 0.15 -10000 0 -0.32 58 58
IKBKG 0.014 0 -10000 0 -10000 0 0
BDNF -0.087 0.21 -10000 0 -0.5 71 71
MGDIs/NGR/p75(NTR)/LINGO1 -0.087 0.18 -10000 0 -0.39 82 82
FURIN 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.1 0.17 -10000 0 -0.34 108 108
LINGO1 -0.02 0.14 -10000 0 -0.6 20 20
Sortilin/TRAF6/NRIF -0.001 0.018 -10000 0 -10000 0 0
proBDNF (dimer) -0.087 0.21 -10000 0 -0.5 71 71
NTRK1 -0.006 0.1 -10000 0 -0.52 14 14
RTN4R -0.028 0.15 -10000 0 -0.56 27 27
neuron apoptosis -0.063 0.17 -10000 0 -0.54 17 17
IRAK1 0.014 0 -10000 0 -10000 0 0
SHC1 -0.073 0.18 -10000 0 -0.35 100 100
ARHGDIA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.089 0.15 -10000 0 -0.35 65 65
MAGEH1 0.002 0.085 -10000 0 -0.6 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.17 -10000 0 -0.39 78 78
Mammalian IAPs/DIABLO -0.025 0.082 -10000 0 -0.32 18 18
proNGF (dimer) -0.072 0.2 -10000 0 -0.55 55 55
MAGED1 0.014 0 -10000 0 -10000 0 0
APP 0.014 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.09 -10000 0 -0.48 13 13
ZNF274 0.014 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.051 0.15 -10000 0 -0.33 57 57
NGF -0.072 0.2 -10000 0 -0.55 55 55
cell cycle arrest -0.072 0.14 -10000 0 -0.31 58 58
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.029 0.12 -10000 0 -0.4 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.055 0.12 -10000 0 -0.32 62 62
NCSTN 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.092 0.16 -10000 0 -0.34 98 98
PSENEN 0.014 0 -10000 0 -10000 0 0
mol:ceramide -0.056 0.16 -10000 0 -0.35 58 58
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.017 0.11 -10000 0 -0.4 11 11
p75(NTR)/beta APP -0.052 0.13 -10000 0 -0.38 50 50
BEX1 -0.015 0.13 -10000 0 -0.6 17 17
mol:GDP -0.08 0.17 -10000 0 -0.35 98 98
NGF (dimer) -0.13 0.17 -10000 0 -0.37 84 84
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.078 0.16 -10000 0 -0.41 51 51
PIK3R1 0.014 0 -10000 0 -10000 0 0
RAC1/GTP -0.079 0.14 -10000 0 -0.34 59 59
MYD88 0.008 0.061 -10000 0 -0.57 4 4
CHUK 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.092 0.16 -10000 0 -0.34 98 98
RHOB 0.009 0.052 -10000 0 -0.48 4 4
RHOA 0.014 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.015 0.071 -10000 0 -0.35 16 16
NT3 (dimer) -0.008 0.091 -10000 0 -0.48 13 13
TP53 -0.052 0.16 -10000 0 -0.51 20 20
PRDM4 -0.056 0.16 -10000 0 -0.35 58 58
BDNF (dimer) -0.16 0.19 -10000 0 -0.43 83 83
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
SORT1 0.012 0.032 -10000 0 -0.6 1 1
activation of caspase activity -0.075 0.13 -10000 0 -0.32 58 58
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.084 0.14 -10000 0 -0.36 59 59
RHOC 0.011 0.041 -10000 0 -0.54 2 2
XIAP 0.014 0 -10000 0 -10000 0 0
MAPK10 -0.045 0.16 -10000 0 -0.49 19 19
DIABLO 0.014 0 -10000 0 -10000 0 0
SMPD2 -0.056 0.16 -10000 0 -0.35 58 58
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.093 0.16 -10000 0 -0.34 99 99
PSEN1 0.014 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.064 0.15 -10000 0 -0.39 60 60
MAPK8 -0.048 0.16 -10000 0 -0.47 20 20
MAPK9 -0.042 0.16 -10000 0 -0.5 15 15
APAF1 0.014 0 -10000 0 -10000 0 0
NTF3 -0.008 0.091 -10000 0 -0.48 13 13
NTF4 -0.012 0.09 -10000 0 -0.48 13 13
NDN -0.031 0.16 -10000 0 -0.6 27 27
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.071 0.12 -10000 0 -0.48 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.006 0.051 -10000 0 -0.38 6 6
RhoA-B-C/GTP -0.092 0.16 -10000 0 -0.34 98 98
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.082 0.14 -10000 0 -0.52 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.09 0.15 -10000 0 -0.41 42 42
PRKACB 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.075 0.15 -10000 0 -0.37 74 74
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.55 32 32
BIRC2 0.014 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.087 0.15 0.21 3 -0.37 62 65
BAD -0.037 0.16 -10000 0 -0.46 18 18
RIPK2 0.014 0 -10000 0 -10000 0 0
NGFR -0.061 0.19 -10000 0 -0.54 50 50
CYCS -0.044 0.15 -10000 0 -0.32 58 58
ADAM17 0.006 0.072 -10000 0 -0.6 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.083 0.14 -10000 0 -0.36 58 58
BCL2L11 -0.037 0.16 -10000 0 -0.46 18 18
BDNF (dimer)/p75(NTR) -0.12 0.2 -10000 0 -0.41 107 107
PI3K -0.083 0.14 -10000 0 -0.35 58 58
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.083 0.14 -10000 0 -0.35 58 58
NDNL2 0.014 0 -10000 0 -10000 0 0
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.19 -10000 0 -0.41 98 98
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.083 0.14 -10000 0 -0.35 58 58
TRAF6 0.012 0.032 -10000 0 -0.6 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
PLG 0.001 0.026 -10000 0 -0.48 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.093 0.18 -10000 0 -0.46 42 42
SQSTM1 0.014 0 -10000 0 -10000 0 0
NGFRAP1 0.014 0 -10000 0 -10000 0 0
CASP3 -0.032 0.15 -10000 0 -0.42 18 18
E2F1 -0.008 0.1 -10000 0 -0.5 16 16
CASP9 0.014 0 -10000 0 -10000 0 0
IKK complex -0.063 0.12 -10000 0 -0.51 10 10
NGF (dimer)/TRKA -0.073 0.16 -10000 0 -0.41 66 66
MMP7 -0.15 0.25 -10000 0 -0.54 105 105
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.077 0.13 -10000 0 -0.53 8 8
MMP3 -0.032 0.14 -10000 0 -0.48 30 30
APAF-1/Caspase 9 -0.067 0.11 -10000 0 -0.43 12 12
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.047 -10000 0 -0.38 5 5
fibroblast growth factor receptor signaling pathway -0.005 0.047 -10000 0 -0.38 5 5
LAMA1 -0.054 0.19 -10000 0 -0.58 42 42
PRNP 0.012 0.032 -10000 0 -0.6 1 1
GPC1/SLIT2 -0.099 0.17 -10000 0 -0.38 94 94
SMAD2 0.029 0.049 -10000 0 -0.38 3 3
GPC1/PrPc/Cu2+ -0.003 0.028 -10000 0 -0.31 3 3
GPC1/Laminin alpha1 -0.05 0.14 -10000 0 -0.43 42 42
TDGF1 -0.084 0.22 -10000 0 -0.57 61 61
CRIPTO/GPC1 -0.071 0.16 -10000 0 -0.42 61 61
APP/GPC1 -0.002 0.025 -10000 0 -0.33 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.035 0.15 -10000 0 -0.36 61 61
FLT1 0.012 0.032 -10000 0 -0.6 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.05 -10000 0 -0.42 3 3
SERPINC1 0.007 0.052 -10000 0 -0.48 4 4
FYN -0.034 0.14 -10000 0 -0.35 61 61
FGR -0.035 0.15 -10000 0 -0.35 63 63
positive regulation of MAPKKK cascade -0.074 0.19 -10000 0 -0.47 51 51
SLIT2 -0.13 0.24 -10000 0 -0.54 92 92
GPC1/NRG -0.12 0.19 -10000 0 -0.4 111 111
NRG1 -0.16 0.26 -10000 0 -0.56 110 110
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.014 0.063 -10000 0 -0.29 17 17
LYN -0.039 0.15 -10000 0 -0.34 67 67
mol:Spermine 0.01 0.026 -10000 0 -0.34 2 2
cell growth -0.005 0.047 -10000 0 -0.38 5 5
BMP signaling pathway -0.011 0.036 0.48 2 -10000 0 2
SRC -0.034 0.14 -10000 0 -0.38 47 47
TGFBR1 0.011 0.041 -10000 0 -0.54 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.075 0.18 -10000 0 -0.49 59 59
GPC1 0.011 0.037 -10000 0 -0.48 2 2
TGFBR1 (dimer) 0.011 0.041 -10000 0 -0.54 2 2
VEGFA -0.006 0.098 -10000 0 -0.48 15 15
BLK -0.1 0.18 -10000 0 -0.42 59 59
HCK -0.05 0.17 -10000 0 -0.41 51 51
FGF2 0.009 0.052 -10000 0 -0.56 3 3
FGFR1 0.012 0.032 -10000 0 -0.6 1 1
VEGFR1 homodimer 0.012 0.032 -10000 0 -0.6 1 1
TGFBR2 0.007 0.061 -10000 0 -0.5 5 5
cell death -0.002 0.025 -10000 0 -0.33 2 2
ATIII/GPC1 -0.005 0.042 -10000 0 -0.33 6 6
PLA2G2A/GPC1 -0.057 0.13 -10000 0 -0.35 59 59
LCK -0.095 0.2 -10000 0 -0.44 70 70
neuron differentiation -0.12 0.19 -10000 0 -0.4 111 111
PrPc/Cu2+ -0.001 0.023 -10000 0 -0.45 1 1
APP 0.014 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.007 0.061 -10000 0 -0.5 5 5
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.063 0.2 -9999 0 -0.59 45 45
PDGF/PDGFRA/CRKL -0.05 0.14 -9999 0 -0.41 45 45
positive regulation of JUN kinase activity -0.039 0.1 -9999 0 -0.32 37 37
CRKL 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.057 0.14 -9999 0 -0.42 49 49
AP1 -0.16 0.31 -9999 0 -0.9 49 49
mol:IP3 -0.036 0.15 -9999 0 -0.43 45 45
PLCG1 -0.036 0.15 -9999 0 -0.43 45 45
PDGF/PDGFRA/alphaV Integrin -0.051 0.14 -9999 0 -0.42 45 45
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.036 0.15 -9999 0 -0.43 45 45
CAV3 0.001 0.057 -9999 0 -0.48 5 5
CAV1 -0.045 0.16 -9999 0 -0.49 43 43
SHC/Grb2/SOS1 -0.039 0.1 -9999 0 -0.32 37 37
PDGF/PDGFRA/Shf -0.054 0.15 -9999 0 -0.44 46 46
FOS -0.12 0.33 -9999 0 -0.88 49 49
JUN -0.02 0.062 -9999 0 -0.41 8 8
oligodendrocyte development -0.051 0.14 -9999 0 -0.42 45 45
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:DAG -0.036 0.15 -9999 0 -0.43 45 45
PDGF/PDGFRA -0.063 0.2 -9999 0 -0.59 45 45
actin cytoskeleton reorganization -0.05 0.14 -9999 0 -0.41 45 45
SRF 0.027 0.009 -9999 0 -10000 0 0
SHC1 0.009 0.052 -9999 0 -0.48 4 4
PI3K -0.043 0.12 -9999 0 -0.36 40 40
PDGF/PDGFRA/Crk/C3G -0.042 0.11 -9999 0 -0.35 39 39
JAK1 -0.03 0.14 -9999 0 -0.41 45 45
ELK1/SRF -0.001 0.11 -9999 0 -0.32 37 37
SHB 0.014 0 -9999 0 -10000 0 0
SHF 0.007 0.064 -9999 0 -0.6 4 4
CSNK2A1 0.013 0.022 -9999 0 -10000 0 0
GO:0007205 -0.037 0.15 -9999 0 -0.44 45 45
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.039 0.1 -9999 0 -0.32 37 37
PDGF/PDGFRA/SHB -0.05 0.14 -9999 0 -0.41 45 45
PDGF/PDGFRA/Caveolin-1 -0.09 0.18 -9999 0 -0.4 82 82
ITGAV 0.012 0.032 -9999 0 -0.6 1 1
ELK1 -0.028 0.14 -9999 0 -0.4 40 40
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
PDGF/PDGFRA/Crk -0.05 0.14 -9999 0 -0.41 45 45
JAK-STAT cascade -0.03 0.14 -9999 0 -0.41 45 45
cell proliferation -0.054 0.15 -9999 0 -0.44 46 46
Glucocorticoid receptor regulatory network

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
PCK2 0.018 0.11 -10000 0 -0.89 3 3
SMARCC2 0.015 0.01 -10000 0 -10000 0 0
SMARCC1 0.015 0.01 -10000 0 -10000 0 0
TBX21 -0.1 0.24 -10000 0 -0.71 40 40
SUMO2 0.013 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.002 0.1 -10000 0 -0.56 11 11
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 -0.1 0.23 -10000 0 -0.56 75 75
GR alpha/HSP90/FKBP51/HSP90 0.013 0.17 0.3 19 -0.33 33 52
PRL -0.049 0.095 -10000 0 -0.6 2 2
cortisol/GR alpha (dimer)/TIF2 0.18 0.25 0.51 82 -0.44 4 86
RELA -0.066 0.097 -10000 0 -0.28 8 8
FGG 0.17 0.16 0.46 40 -0.44 1 41
GR beta/TIF2 0.06 0.16 0.3 30 -0.4 28 58
IFNG -0.23 0.21 -10000 0 -0.63 40 40
apoptosis -0.002 0.19 0.6 15 -0.56 2 17
CREB1 0.013 0.023 -10000 0 -10000 0 0
histone acetylation -0.047 0.12 -10000 0 -0.37 26 26
BGLAP -0.051 0.13 -10000 0 -0.72 4 4
GR/PKAc 0.09 0.092 0.29 22 -10000 0 22
NF kappa B1 p50/RelA -0.12 0.18 -10000 0 -0.43 52 52
SMARCD1 0.015 0.01 -10000 0 -10000 0 0
MDM2 0.081 0.078 0.24 38 -10000 0 38
GATA3 -0.094 0.23 -10000 0 -0.53 77 77
AKT1 0.002 0.019 -10000 0 -10000 0 0
CSF2 -0.064 0.099 -10000 0 -10000 0 0
GSK3B 0.013 0.013 -10000 0 -10000 0 0
NR1I3 0.036 0.19 0.59 14 -0.72 2 16
CSN2 0.14 0.13 0.39 27 -10000 0 27
BRG1/BAF155/BAF170/BAF60A 0.039 0.034 -10000 0 -10000 0 0
NFATC1 -0.018 0.14 -10000 0 -0.57 21 21
POU2F1 0.013 0.033 -10000 0 -0.6 1 1
CDKN1A -0.073 0.33 -10000 0 -1.5 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.011 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.52 87 87
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.049 0.19 0.28 12 -0.41 26 38
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.037 0.3 0.57 14 -0.8 33 47
JUN -0.16 0.19 -10000 0 -0.5 50 50
IL4 -0.084 0.15 -10000 0 -0.54 19 19
CDK5R1 -0.022 0.14 -10000 0 -0.6 21 21
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.16 0.19 -10000 0 -0.47 72 72
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.023 0.16 0.29 19 -0.33 9 28
cortisol/GR alpha (monomer) 0.24 0.26 0.59 93 -10000 0 93
NCOA2 -0.035 0.17 -10000 0 -0.6 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.57 66 66
AP-1/NFAT1-c-4 -0.3 0.29 -10000 0 -0.67 96 96
AFP -0.12 0.18 -10000 0 -0.6 20 20
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.12 0.14 0.47 7 -0.5 2 9
TP53 -0.019 0.16 -10000 0 -0.54 26 26
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.43 0.48 -10000 0 -0.96 134 134
KRT14 -0.13 0.18 -10000 0 -0.54 33 33
TBP 0.022 0.022 -10000 0 -10000 0 0
CREBBP 0.031 0.059 -10000 0 -10000 0 0
HDAC1 0.006 0.047 -10000 0 -0.6 2 2
HDAC2 0.014 0 -10000 0 -10000 0 0
AP-1 -0.3 0.3 -10000 0 -0.67 96 96
MAPK14 0.013 0.011 -10000 0 -10000 0 0
MAPK10 0.006 0.065 -10000 0 -0.6 4 4
MAPK11 0.008 0.057 -10000 0 -0.6 3 3
KRT5 -0.38 0.42 -10000 0 -0.95 98 98
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.016 0.011 -10000 0 -10000 0 0
STAT1 0.002 0.1 -10000 0 -0.56 11 11
CGA -0.069 0.12 -10000 0 -0.48 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.082 0.11 0.34 18 -10000 0 18
MAPK3 0.013 0.012 -10000 0 -10000 0 0
MAPK1 0.013 0.011 -10000 0 -10000 0 0
ICAM1 -0.2 0.28 -10000 0 -0.72 56 56
NFKB1 -0.067 0.1 -10000 0 -0.39 4 4
MAPK8 -0.14 0.17 -10000 0 -0.42 64 64
MAPK9 0.013 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.005 0.2 0.61 15 -0.59 2 17
BAX -0.003 0.11 -10000 0 -0.49 2 2
POMC -0.13 0.22 -10000 0 -1.1 10 10
EP300 0.024 0.089 -10000 0 -0.6 4 4
cortisol/GR alpha (dimer)/p53 0.18 0.23 0.5 76 -0.53 2 78
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.068 0.22 19 -10000 0 19
SGK1 0.053 0.24 -10000 0 -1.4 9 9
IL13 -0.23 0.23 -10000 0 -0.66 44 44
IL6 -0.29 0.38 -10000 0 -0.85 95 95
PRKACG 0.005 0.045 -10000 0 -0.48 3 3
IL5 -0.2 0.19 -10000 0 -0.57 35 35
IL2 -0.23 0.21 -10000 0 -0.57 57 57
CDK5 0.014 0.006 -10000 0 -10000 0 0
PRKACB 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.33 0.41 -10000 0 -0.82 123 123
CDK5R1/CDK5 -0.02 0.1 -10000 0 -0.43 21 21
NF kappa B1 p50/RelA/PKAc -0.06 0.14 -10000 0 -0.4 11 11
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.48 89 -10000 0 89
SMARCA4 0.015 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.13 0.36 51 -0.34 2 53
NF kappa B1 p50/RelA/Cbp -0.059 0.16 -10000 0 -0.46 12 12
JUN (dimer) -0.16 0.19 -10000 0 -0.5 50 50
YWHAH -0.009 0.1 -10000 0 -0.48 17 17
VIPR1 -0.13 0.28 -10000 0 -0.74 56 56
NR3C1 0.14 0.14 0.42 48 -10000 0 48
NR4A1 -0.024 0.14 -10000 0 -0.49 31 31
TIF2/SUV420H1 -0.035 0.12 -10000 0 -0.44 29 29
MAPKKK cascade -0.002 0.19 0.6 15 -0.56 2 17
cortisol/GR alpha (dimer)/Src-1 0.22 0.22 0.51 93 -10000 0 93
PBX1 0.013 0.033 -10000 0 -0.6 1 1
POU1F1 0.004 0.027 -10000 0 -0.48 1 1
SELE -0.3 0.39 -10000 0 -0.84 100 100
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.13 0.36 51 -0.35 2 53
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.48 89 -10000 0 89
mol:cortisol 0.13 0.15 0.32 97 -10000 0 97
MMP1 -0.11 0.14 -10000 0 -0.53 21 21
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.039 0.17 -9999 0 -0.48 21 21
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.16 -9999 0 -0.49 16 16
alphaV/beta3 Integrin/Osteopontin/Src -0.069 0.15 -9999 0 -0.38 66 66
AP1 -0.082 0.23 -9999 0 -0.58 37 37
ILK -0.047 0.17 -9999 0 -0.49 22 22
bone resorption -0.08 0.24 -9999 0 -0.55 55 55
PTK2B -0.01 0.11 -9999 0 -0.48 18 18
PYK2/p130Cas -0.095 0.16 -9999 0 -0.51 33 33
ITGAV 0.015 0.032 -9999 0 -0.59 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.067 0.16 -9999 0 -0.42 59 59
alphaV/beta3 Integrin/Osteopontin -0.095 0.17 -9999 0 -0.4 71 71
MAP3K1 -0.05 0.17 -9999 0 -0.49 23 23
JUN 0.003 0.075 -9999 0 -0.5 8 8
MAPK3 -0.041 0.18 -9999 0 -0.5 22 22
MAPK1 -0.041 0.18 -9999 0 -0.5 22 22
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.013 0.026 -9999 0 -0.48 1 1
MAPK8 -0.047 0.18 -9999 0 -0.48 28 28
ITGB3 -0.051 0.18 -9999 0 -0.51 47 47
NFKBIA -0.032 0.18 -9999 0 -0.5 21 21
FOS -0.087 0.22 -9999 0 -0.55 66 66
CD44 -0.057 0.19 -9999 0 -0.55 46 46
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.074 0.28 -9999 0 -0.78 36 36
NF kappa B1 p50/RelA -0.077 0.13 -9999 0 -0.53 15 15
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.048 0.12 -9999 0 -0.36 48 48
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.062 0.2 -9999 0 -0.43 64 64
VAV3 -0.11 0.23 -9999 0 -0.57 49 49
MAP3K14 -0.05 0.18 -9999 0 -0.5 23 23
ROCK2 -0.011 0.12 -9999 0 -0.6 15 15
SPP1 -0.081 0.21 -9999 0 -0.54 65 65
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.19 -9999 0 -0.53 46 46
MMP2 -0.073 0.22 -9999 0 -0.52 45 45
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.018 0.076 -9999 0 -0.33 20 20
ARNO/beta Arrestin1-2 -0.019 0.074 -9999 0 -0.55 3 3
EGFR -0.082 0.21 -9999 0 -0.55 62 62
EPHA2 -0.018 0.12 -9999 0 -0.49 23 23
USP6 0.005 0.068 -9999 0 -0.48 7 7
IQSEC1 0.007 0.061 -9999 0 -0.5 5 5
EGFR/EGFR/EGF/EGF -0.11 0.19 -9999 0 -0.43 89 89
ARRB2 0.009 0.034 -9999 0 -0.19 10 10
mol:GTP 0.005 0.043 -9999 0 -0.16 14 14
ARRB1 0.002 0.085 -9999 0 -0.6 7 7
FBXO8 0.012 0.032 -9999 0 -0.6 1 1
TSHR -0.2 0.27 -9999 0 -0.54 143 143
EGF -0.044 0.17 -9999 0 -0.56 37 37
somatostatin receptor activity 0 0 -9999 0 -0.001 47 47
ARAP2 -0.008 0.11 -9999 0 -0.6 13 13
mol:GDP -0.068 0.12 -9999 0 -0.29 55 55
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 21 21
ITGA2B -0.043 0.17 -9999 0 -0.57 36 36
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.068 -9999 0 -0.41 3 3
ADAP1 -0.017 0.13 -9999 0 -0.55 20 20
KIF13B 0.014 0 -9999 0 -10000 0 0
HGF/MET -0.16 0.22 -9999 0 -0.42 139 139
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.059 0.12 -9999 0 -0.29 45 45
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.092 0.17 -9999 0 -0.37 91 91
ADRB2 -0.011 0.12 -9999 0 -0.6 15 15
receptor agonist activity 0 0 -9999 0 0 47 47
actin filament binding 0 0 -9999 0 -0.001 47 47
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.18 -9999 0 -0.51 47 47
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 35 35
ARF6/GDP -0.005 0.1 -9999 0 -0.41 11 11
ARF6/GDP/GULP/ACAP1 -0.11 0.17 -9999 0 -0.44 56 56
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.063 0.13 -9999 0 -0.36 37 37
ACAP1 -0.033 0.15 -9999 0 -0.49 34 34
ACAP2 0.012 0.032 -9999 0 -0.6 1 1
LHCGR/beta Arrestin2 0.003 0.048 -9999 0 -0.28 10 10
EFNA1 0.011 0.037 -9999 0 -0.48 2 2
HGF -0.07 0.19 -9999 0 -0.5 59 59
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
fibronectin binding 0 0 -9999 0 0 41 41
endosomal lumen acidification 0 0 -9999 0 0 51 51
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.052 0.19 -9999 0 -0.58 41 41
GNAQ/ARNO 0.014 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 21 21
MET -0.14 0.25 -9999 0 -0.54 101 101
GNA14 -0.006 0.11 -9999 0 -0.56 13 13
GNA15 -0.007 0.11 -9999 0 -0.56 13 13
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 39 39
GNA11 0.002 0.085 -9999 0 -0.6 7 7
LHCGR -0.005 0.08 -9999 0 -0.48 10 10
AGTR1 -0.036 0.16 -9999 0 -0.55 32 32
desensitization of G-protein coupled receptor protein signaling pathway 0.003 0.048 -9999 0 -0.28 10 10
IPCEF1/ARNO -0.054 0.14 -9999 0 -0.49 10 10
alphaIIb/beta3 Integrin -0.086 0.17 -9999 0 -0.4 78 78
BCR signaling 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
JUN -0.043 0.14 -10000 0 -0.37 40 40
IKBKB -0.014 0.078 -10000 0 -0.27 10 10
AKT1 -0.052 0.1 -10000 0 -0.25 36 36
IKBKG -0.012 0.083 -10000 0 -0.27 15 15
CALM1 -0.057 0.15 0.21 2 -0.4 42 44
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
MAP3K1 -0.069 0.19 -10000 0 -0.5 44 44
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.16 0.21 2 -0.42 42 44
DOK1 0.012 0.032 -10000 0 -0.6 1 1
AP-1 -0.035 0.099 -10000 0 -0.26 22 22
LYN 0.006 0.063 -10000 0 -0.48 6 6
BLNK -0.056 0.19 -10000 0 -0.58 43 43
SHC1 0.009 0.052 -10000 0 -0.48 4 4
BCR complex -0.086 0.18 -10000 0 -0.44 73 73
CD22 -0.18 0.22 -10000 0 -0.46 99 99
CAMK2G -0.046 0.14 -10000 0 -0.47 22 22
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.008 0.055 -10000 0 -0.51 4 4
SHC/GRB2/SOS1 -0.095 0.17 -10000 0 -0.55 31 31
GO:0007205 -0.069 0.16 0.21 2 -0.43 42 44
SYK -0.013 0.12 -10000 0 -0.56 17 17
ELK1 -0.057 0.15 0.21 2 -0.4 42 44
NFATC1 -0.069 0.18 -10000 0 -0.47 46 46
B-cell antigen/BCR complex -0.086 0.18 -10000 0 -0.44 73 73
PAG1/CSK -0.001 0.023 -10000 0 -0.44 1 1
NFKBIB 0.005 0.029 -10000 0 -10000 0 0
HRAS -0.052 0.16 -10000 0 -0.39 43 43
NFKBIA 0.006 0.028 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.012 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.14 0.19 -10000 0 -0.55 39 39
mol:GDP -0.063 0.15 0.22 2 -0.41 42 44
PTEN 0.014 0 -10000 0 -10000 0 0
CD79B -0.061 0.19 -10000 0 -0.54 50 50
NF-kappa-B/RelA/I kappa B alpha 0.012 0.024 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.093 0.19 -10000 0 -0.49 56 56
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.069 0.16 0.21 2 -0.44 42 44
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.093 0.18 -10000 0 -0.48 38 38
CHUK -0.012 0.083 -10000 0 -0.27 15 15
IBTK 0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.065 0.14 -10000 0 -0.51 24 24
PTPN6 -0.17 0.22 -10000 0 -0.53 69 69
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 -0.007 0.046 -10000 0 -0.1 26 26
VAV2 -0.12 0.19 -10000 0 -0.53 47 47
ubiquitin-dependent protein catabolic process 0.01 0.028 -10000 0 -10000 0 0
BTK -0.036 0.19 0.37 1 -1.1 10 11
CD19 -0.12 0.19 -10000 0 -0.52 51 51
MAP4K1 -0.025 0.15 -10000 0 -0.58 24 24
CD72 -0.008 0.1 -10000 0 -0.5 16 16
PAG1 0.012 0.032 -10000 0 -0.6 1 1
MAPK14 -0.051 0.16 -10000 0 -0.43 39 39
SH3BP5 0.011 0.046 -10000 0 -0.6 2 2
PIK3AP1 -0.069 0.18 0.24 2 -0.47 49 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.063 0.21 -10000 0 -0.56 39 39
RAF1 -0.041 0.15 -10000 0 -0.45 24 24
RasGAP/p62DOK/SHIP -0.13 0.19 -10000 0 -0.54 39 39
CD79A -0.039 0.16 -10000 0 -0.53 36 36
re-entry into mitotic cell cycle -0.035 0.099 -10000 0 -0.27 21 21
RASA1 0.014 0 -10000 0 -10000 0 0
MAPK3 -0.019 0.12 -10000 0 -0.4 18 18
MAPK1 -0.019 0.12 -10000 0 -0.4 18 18
CD72/SHP1 -0.14 0.22 -10000 0 -0.52 67 67
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
MAPK8 -0.058 0.17 -10000 0 -0.43 45 45
actin cytoskeleton organization -0.072 0.18 -10000 0 -0.47 43 43
NF-kappa-B/RelA 0.029 0.045 -10000 0 -10000 0 0
Calcineurin -0.059 0.12 -10000 0 -0.45 21 21
PI3K -0.14 0.18 -10000 0 -0.46 64 64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.083 0.17 0.24 2 -0.48 42 44
SOS1 0.014 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.28 -10000 0 -0.78 45 45
DAPP1 -0.14 0.29 -10000 0 -0.86 42 42
cytokine secretion -0.063 0.17 -10000 0 -0.43 46 46
mol:DAG -0.069 0.16 0.21 2 -0.44 42 44
PLCG2 0.002 0.082 -10000 0 -0.54 8 8
MAP2K1 -0.03 0.14 -10000 0 -0.44 19 19
B-cell antigen/BCR complex/FcgammaRIIB -0.16 0.22 -10000 0 -0.47 104 104
mol:PI-3-4-5-P3 -0.1 0.12 -10000 0 -0.33 58 58
ETS1 -0.037 0.13 -10000 0 -0.44 21 21
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.2 -10000 0 -0.42 81 81
B-cell antigen/BCR complex/LYN -0.11 0.19 -10000 0 -0.49 57 57
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.012 0.032 -10000 0 -0.6 1 1
RAC1 -0.077 0.19 -10000 0 -0.5 43 43
B-cell antigen/BCR complex/LYN/SYK -0.17 0.23 -10000 0 -0.57 69 69
CARD11 -0.068 0.18 -10000 0 -0.47 45 45
FCGR2B -0.15 0.25 -10000 0 -0.53 107 107
PPP3CA 0.011 0.037 -10000 0 -0.48 2 2
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.001 0.036 -10000 0 -0.12 1 1
PTPRC -0.043 0.17 -10000 0 -0.54 38 38
PDPK1 -0.053 0.097 -10000 0 -0.24 38 38
PPP3CB 0.01 0.045 -10000 0 -0.48 3 3
PPP3CC 0.014 0 -10000 0 -10000 0 0
POU2F2 0.012 0.024 -10000 0 -0.099 5 5
HIF-1-alpha transcription factor network

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
PKM2 -0.012 0.49 -9999 0 -1.1 33 33
HDAC7 0.017 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.34 -9999 0 -0.92 36 36
SMAD4 0.016 0.003 -9999 0 -10000 0 0
ID2 -0.012 0.49 -9999 0 -1.1 33 33
AP1 -0.06 0.18 -9999 0 -0.43 66 66
ABCG2 -0.013 0.49 -9999 0 -1.1 33 33
HIF1A 0.026 0.089 -9999 0 -0.55 1 1
TFF3 -0.048 0.5 -9999 0 -1.1 40 40
GATA2 -0.009 0.12 -9999 0 -0.56 15 15
AKT1 0.019 0.1 -9999 0 -10000 0 0
response to hypoxia 0.002 0.11 -9999 0 -0.24 11 11
MCL1 -0.012 0.49 -9999 0 -1.1 33 33
NDRG1 -0.016 0.49 -9999 0 -1.1 34 34
SERPINE1 -0.087 0.54 -9999 0 -1.1 49 49
FECH -0.012 0.49 -9999 0 -1.1 33 33
FURIN -0.012 0.49 -9999 0 -1.1 36 36
NCOA2 -0.033 0.17 -9999 0 -0.6 29 29
EP300 0.032 0.18 -9999 0 -0.36 23 23
HMOX1 -0.021 0.5 -9999 0 -1.2 37 37
BHLHE40 -0.02 0.5 -9999 0 -1.1 37 37
BHLHE41 -0.02 0.5 -9999 0 -1.1 39 39
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.014 0.061 -9999 0 -0.4 4 4
ENG 0.087 0.13 -9999 0 -0.52 5 5
JUN 0.003 0.076 -9999 0 -0.5 8 8
RORA -0.013 0.49 -9999 0 -1.1 33 33
ABCB1 -0.036 0.068 -9999 0 -0.6 1 1
TFRC -0.018 0.49 -9999 0 -1.1 34 34
CXCR4 -0.023 0.5 -9999 0 -1.2 36 36
TF -0.045 0.52 -9999 0 -1.2 40 40
CITED2 -0.013 0.49 -9999 0 -1.1 33 33
HIF1A/ARNT -0.18 0.51 -9999 0 -1.3 41 41
LDHA -0.032 0.099 -9999 0 -0.7 5 5
ETS1 -0.014 0.49 -9999 0 -1.1 34 34
PGK1 -0.012 0.49 -9999 0 -1.1 33 33
NOS2 -0.036 0.51 -9999 0 -1.2 37 37
ITGB2 -0.032 0.51 -9999 0 -1.1 41 41
ALDOA -0.012 0.49 -9999 0 -1.1 33 33
Cbp/p300/CITED2 -0.084 0.5 -9999 0 -1.2 37 37
FOS -0.087 0.22 -9999 0 -0.55 66 66
HK2 -0.024 0.51 -9999 0 -1.2 36 36
SP1 0.024 0.005 -9999 0 -10000 0 0
GCK -0.067 0.48 -9999 0 -1.3 38 38
HK1 -0.012 0.49 -9999 0 -1.1 33 33
NPM1 -0.012 0.49 -9999 0 -1.1 33 33
EGLN1 -0.012 0.49 -9999 0 -1.1 33 33
CREB1 0.022 0.004 -9999 0 -10000 0 0
PGM1 -0.012 0.49 -9999 0 -1.1 33 33
SMAD3 0.014 0.032 -9999 0 -0.6 1 1
EDN1 -0.053 0.34 -9999 0 -1 25 25
IGFBP1 -0.079 0.53 -9999 0 -1.1 47 47
VEGFA 0.02 0.41 -9999 0 -0.95 24 24
HIF1A/JAB1 -0.007 0.032 -9999 0 -0.4 1 1
CP -0.099 0.54 -9999 0 -1.1 51 51
CXCL12 -0.016 0.49 -9999 0 -1.1 34 34
COPS5 0.015 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.023 -9999 0 -0.43 1 1
BNIP3 -0.012 0.49 -9999 0 -1.1 32 32
EGLN3 -0.014 0.49 -9999 0 -1.2 33 33
CA9 -0.045 0.52 -9999 0 -1.2 40 40
TERT -0.08 0.51 -9999 0 -1.1 44 44
ENO1 -0.012 0.49 -9999 0 -1.1 33 33
PFKL -0.012 0.49 -9999 0 -1.1 33 33
NCOA1 0.015 0.001 -9999 0 -10000 0 0
ADM -0.048 0.52 -9999 0 -1.2 39 39
ARNT 0.016 0.089 -9999 0 -0.64 1 1
HNF4A -0.044 0.14 -9999 0 -0.48 31 31
ADFP -0.061 0.47 -9999 0 -1.1 40 40
SLC2A1 0.028 0.4 -9999 0 -0.88 22 22
LEP -0.049 0.48 -9999 0 -1.1 34 34
HIF1A/ARNT/Cbp/p300 -0.15 0.35 -9999 0 -0.94 39 39
EPO 0.022 0.37 -9999 0 -0.97 16 16
CREBBP 0.036 0.17 -9999 0 -0.34 20 20
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.35 -9999 0 -0.96 35 35
PFKFB3 -0.013 0.49 -9999 0 -1.1 33 33
NT5E -0.019 0.5 -9999 0 -1.1 38 38
TCGA08_p53

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
CDKN2A -0.076 0.18 -10000 0 -0.42 74 74
TP53 -0.035 0.093 0.19 2 -0.44 11 13
Senescence -0.035 0.093 0.19 2 -0.44 11 13
Apoptosis -0.035 0.093 0.19 2 -0.44 11 13
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.049 0.1 0.25 72 -0.25 2 74
MDM4 0.005 0.068 -10000 0 -0.48 7 7
LPA receptor mediated events

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 -0.05 0.11 -9999 0 -0.34 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.041 0.089 -9999 0 -0.4 9 9
AP1 -0.12 0.17 -9999 0 -0.44 47 47
mol:PIP3 -0.098 0.15 -9999 0 -0.47 33 33
AKT1 0.019 0.097 -9999 0 -0.34 7 7
PTK2B -0.019 0.11 -9999 0 -0.33 25 25
RHOA 0.006 0.066 -9999 0 -0.32 6 6
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.088 -9999 0 -0.35 7 7
MAGI3 0.002 0.085 -9999 0 -0.6 7 7
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.042 0.13 -9999 0 -0.35 40 40
HRAS/GDP -0.001 0.018 -9999 0 -0.34 1 1
positive regulation of microtubule depolymerization -0.008 0.11 -9999 0 -0.35 18 18
NF kappa B1 p50/RelA -0.069 0.13 -9999 0 -0.5 17 17
endothelial cell migration -0.05 0.18 -9999 0 -0.42 66 66
ADCY4 -0.022 0.15 -9999 0 -0.42 37 37
ADCY5 -0.026 0.16 -9999 0 -0.43 41 41
ADCY6 -0.019 0.15 -9999 0 -0.41 37 37
ADCY7 -0.019 0.15 -9999 0 -0.41 37 37
ADCY1 -0.048 0.17 -9999 0 -0.44 45 45
ADCY2 -0.026 0.16 -9999 0 -0.44 40 40
ADCY3 -0.019 0.15 -9999 0 -0.41 37 37
ADCY8 -0.044 0.19 -9999 0 -0.49 42 42
ADCY9 -0.02 0.15 -9999 0 -0.41 37 37
GSK3B -0.01 0.1 -9999 0 -0.34 18 18
arachidonic acid secretion -0.012 0.14 -9999 0 -0.38 37 37
GNG2 0.009 0.056 -9999 0 -0.6 3 3
TRIP6 0.006 0.068 -9999 0 -0.41 4 4
GNAO1 -0.036 0.14 -9999 0 -0.35 57 57
HRAS 0.013 0.026 -9999 0 -0.48 1 1
NFKBIA -0.011 0.12 -9999 0 -0.42 15 15
GAB1 0.011 0.041 -9999 0 -0.54 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.005 0.097 -9999 0 -1 3 3
JUN 0.003 0.075 -9999 0 -0.5 8 8
LPA/LPA2/NHERF2 -0.015 0.06 -9999 0 -0.31 13 13
TIAM1 -0.009 0.13 -9999 0 -1.3 3 3
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.004 0.089 -9999 0 -0.36 7 7
PLCB3 0.015 0.06 -9999 0 -0.33 5 5
FOS -0.087 0.22 -9999 0 -0.55 66 66
positive regulation of mitosis -0.012 0.14 -9999 0 -0.38 37 37
LPA/LPA1-2-3 -0.081 0.14 -9999 0 -0.38 45 45
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
stress fiber formation -0.022 0.12 -9999 0 -0.32 31 31
GNAZ -0.03 0.13 -9999 0 -0.33 53 53
EGFR/PI3K-beta/Gab1 -0.1 0.16 -9999 0 -0.49 33 33
positive regulation of dendritic cell cytokine production -0.081 0.14 -9999 0 -0.38 45 45
LPA/LPA2/MAGI-3 -0.021 0.078 -9999 0 -0.36 17 17
ARHGEF1 -0.01 0.12 -9999 0 -0.32 31 31
GNAI2 -0.029 0.13 -9999 0 -0.33 52 52
GNAI3 -0.029 0.13 -9999 0 -0.33 52 52
GNAI1 -0.041 0.15 -9999 0 -0.35 63 63
LPA/LPA3 -0.04 0.11 -9999 0 -0.36 36 36
LPA/LPA2 -0.018 0.07 -9999 0 -0.39 11 11
LPA/LPA1 -0.066 0.15 -9999 0 -0.36 66 66
HB-EGF/EGFR -0.14 0.21 -9999 0 -0.37 150 150
HBEGF -0.1 0.19 -9999 0 -0.38 113 113
mol:DAG 0.004 0.089 -9999 0 -0.36 7 7
cAMP biosynthetic process -0.024 0.16 -9999 0 -0.43 37 37
NFKB1 0.013 0.026 -9999 0 -0.48 1 1
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN -0.013 0.12 -9999 0 -0.42 16 16
GNAQ -0.011 0.085 -9999 0 -0.31 13 13
LPAR2 -0.003 0.095 -9999 0 -0.54 11 11
LPAR3 -0.042 0.14 -9999 0 -0.48 36 36
LPAR1 -0.061 0.19 -9999 0 -0.56 44 44
IL8 -0.18 0.23 -9999 0 -0.45 135 135
PTK2 -0.046 0.15 -9999 0 -0.36 43 43
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.042 0.13 -9999 0 -0.35 40 40
EGFR -0.082 0.21 -9999 0 -0.55 62 62
PLCG1 -0.011 0.091 -9999 0 -0.29 19 19
PLD2 -0.046 0.15 -9999 0 -0.36 43 43
G12/G13 -0.049 0.11 -9999 0 -0.35 31 31
PI3K-beta -0.038 0.085 -9999 0 -0.39 8 8
cell migration -0.027 0.056 -9999 0 -0.24 9 9
SLC9A3R2 0.011 0.037 -9999 0 -0.48 2 2
PXN -0.023 0.12 -9999 0 -0.34 29 29
HRAS/GTP -0.013 0.15 -9999 0 -0.39 37 37
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.52 111 111
PRKCE 0.002 0.079 -9999 0 -0.52 8 8
PRKCD -0.003 0.11 -9999 0 -0.4 13 13
Gi(beta/gamma) -0.015 0.14 -9999 0 -0.38 38 38
mol:LPA -0.006 0.041 -9999 0 -0.2 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.066 0.13 -9999 0 -0.43 21 21
MAPKKK cascade -0.012 0.14 -9999 0 -0.38 37 37
contractile ring contraction involved in cytokinesis 0.006 0.066 -9999 0 -0.32 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.021 0.098 -9999 0 -0.31 22 22
GNA15 -0.022 0.1 -9999 0 -0.31 24 24
GNA12 0.012 0.032 -9999 0 -0.6 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.008 0.11 -9999 0 -0.36 18 18
GNA11 -0.018 0.099 -9999 0 -0.33 20 20
Rac1/GTP -0.006 0.11 -9999 0 -1.1 3 3
MMP2 -0.05 0.18 -9999 0 -0.42 66 66
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.038 0.095 0.2 83 -10000 0 83
BUB1B -0.057 0.14 -10000 0 -0.3 89 89
PLK1 0 0.041 -10000 0 -0.13 18 18
PLK1S1 0.006 0.021 -10000 0 -10000 0 0
KIF2A 0.006 0.049 -10000 0 -0.32 4 4
regulation of mitotic centrosome separation 0 0.041 -10000 0 -0.12 18 18
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.13 0.23 -10000 0 -0.42 127 127
WEE1 -0.005 0.086 -10000 0 -0.35 14 14
cytokinesis -0.11 0.21 -10000 0 -0.43 95 95
PP2A-alpha B56 -0.065 0.23 -10000 0 -0.66 46 46
AURKA 0.002 0.039 -10000 0 -0.15 14 14
PICH/PLK1 -0.024 0.15 -10000 0 -0.43 34 34
CENPE -0.036 0.13 -10000 0 -0.32 57 57
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.006 0.049 -10000 0 -0.32 4 4
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 -0.02 0.082 -10000 0 -0.21 50 50
PAK1 -0.038 0.15 -10000 0 -0.49 38 38
SPC24 -0.12 0.24 -10000 0 -0.54 88 88
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN -0.033 0.1 -10000 0 -0.25 57 57
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.004 -10000 0 -0.013 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.021 -10000 0 -0.063 16 16
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.009 8 8
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.01 -10000 0 -10000 0 0
spindle elongation 0 0.041 -10000 0 -0.12 18 18
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.1 0.24 -10000 0 -0.73 46 46
TPT1 0.006 0.021 -10000 0 -10000 0 0
CDC25C -0.05 0.14 -10000 0 -0.34 55 55
CDC25B 0.014 0.003 -10000 0 -10000 0 0
SGOL1 -0.038 0.095 -10000 0 -0.2 83 83
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.024 0.08 -10000 0 -0.32 17 17
CDC14B 0.012 0.001 -10000 0 -10000 0 0
CDC20 -0.093 0.22 -10000 0 -0.54 70 70
PLK1/PBIP1 -0.05 0.12 -10000 0 -0.32 53 53
mitosis 0.001 0.004 0.021 8 -10000 0 8
FBXO5 0.005 0.044 -10000 0 -0.24 5 5
CDC2 0 0.004 -10000 0 -0.014 20 20
NDC80 -0.13 0.25 -10000 0 -0.55 94 94
metaphase plate congression 0.006 0.025 -10000 0 -0.14 1 1
ERCC6L -0.049 0.13 -10000 0 -0.43 32 32
NLP/gamma Tubulin 0.004 0.024 -10000 0 -0.1 1 1
microtubule cytoskeleton organization 0.006 0.021 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.002 0.01 3 -10000 0 3
PPP1R12A 0.014 0.001 -10000 0 -10000 0 0
interphase 0 0.002 0.01 3 -10000 0 3
PLK1/PRC1-2 -0.087 0.18 -10000 0 -0.34 116 116
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.021 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.033 -10000 0 -0.19 1 1
mitotic prometaphase -0.001 0.002 -10000 0 -0.01 13 13
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.06 -10000 0 -10000 0 0
microtubule-based process -0.092 0.17 -10000 0 -0.33 116 116
Golgi organization 0 0.041 -10000 0 -0.12 18 18
Cohesin/SA2 -0.011 0.027 -10000 0 -0.22 1 1
PPP1CB/MYPT1 0.004 0.009 -10000 0 -10000 0 0
KIF20A -0.17 0.27 -10000 0 -0.56 116 116
APC/C/CDC20 -0.051 0.14 -10000 0 -0.34 70 70
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.049 0.11 -10000 0 -0.32 53 53
PRC1 -0.002 0.088 -10000 0 -0.48 12 12
ECT2 0 0.07 -10000 0 -0.33 13 13
C13orf34 0.006 0.034 -10000 0 -0.19 1 1
NUDC 0.006 0.025 -10000 0 -0.14 1 1
regulation of attachment of spindle microtubules to kinetochore -0.057 0.14 -10000 0 -0.3 89 89
spindle assembly 0.003 0.033 -10000 0 -0.098 15 15
spindle stabilization 0.006 0.021 -10000 0 -10000 0 0
APC/C/HCDH1 0.02 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.092 0.17 -10000 0 -0.34 116 116
CCNB1 -0.012 0.11 -10000 0 -0.48 19 19
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 -0.006 0.094 -10000 0 -0.44 15 15
TUBG1 0.006 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.078 -10000 0 -0.32 17 17
MLF1IP -0.048 0.15 -10000 0 -0.4 53 53
INCENP 0.012 0.005 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.002 0.025 -10000 0 -0.33 2 2
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.013 0.026 -10000 0 -0.48 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.076 0.12 -10000 0 -0.43 19 19
IRAK/TOLLIP 0.031 0.02 -10000 0 -10000 0 0
IKBKB 0.014 0 -10000 0 -10000 0 0
IKBKG 0.014 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.17 0.22 -10000 0 -0.42 152 152
IL1A -0.1 0.23 -10000 0 -0.54 79 79
IL1B -0.13 0.22 -10000 0 -0.4 136 136
IRAK/TRAF6/p62/Atypical PKCs -0.012 0.054 -10000 0 -0.41 1 1
IL1R2 -0.12 0.24 -10000 0 -0.53 91 91
IL1R1 -0.022 0.13 -10000 0 -0.52 25 25
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.041 0.12 0.22 1 -0.42 14 15
TOLLIP 0.014 0 -10000 0 -10000 0 0
TICAM2 -0.002 0.097 -10000 0 -0.58 10 10
MAP3K3 0.014 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.065 0.032 -10000 0 -10000 0 0
JUN 0.034 0.072 -10000 0 -0.48 3 3
MAP3K7 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.13 0.17 -10000 0 -0.54 30 30
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.1 0.16 -10000 0 -0.38 60 60
PIK3R1 0.014 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.097 0.14 -10000 0 -0.5 16 16
IL1 beta fragment/IL1R1/IL1RAP -0.13 0.21 -10000 0 -0.42 84 84
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
MAPK8 0.032 0.062 -10000 0 -0.56 1 1
IRAK1 0.024 0.023 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.11 0.19 -10000 0 -0.4 103 103
IRAK4 0.013 0.026 -10000 0 -0.48 1 1
PRKCI 0.014 0 -10000 0 -10000 0 0
TRAF6 0.012 0.032 -10000 0 -0.6 1 1
PI3K -0.001 0.023 -10000 0 -0.44 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.06 0.14 -10000 0 -0.48 19 19
CHUK 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.13 0.21 -10000 0 -0.42 84 84
IL1 beta/IL1R2 -0.19 0.22 -10000 0 -0.38 196 196
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.49 30 30
IRAK3 0.006 0.069 -10000 0 -0.58 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.14 0.18 -10000 0 -0.54 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.04 0.12 -10000 0 -0.36 13 13
IL1 alpha/IL1R1/IL1RAP -0.12 0.17 -10000 0 -0.42 58 58
RELA 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.014 0 -10000 0 -10000 0 0
MYD88 0.008 0.061 -10000 0 -0.57 4 4
IRAK/TRAF6/MEKK3 0.038 0.026 -10000 0 -10000 0 0
IL1RAP -0.033 0.15 -10000 0 -0.51 33 33
UBE2N 0.014 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.11 0.15 -10000 0 -0.49 26 26
CASP1 -0.01 0.11 -10000 0 -0.53 16 16
IL1RN/IL1R2 -0.18 0.24 -10000 0 -0.46 143 143
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.12 0.2 -10000 0 -0.57 33 33
TMEM189-UBE2V1 0.005 0.037 -10000 0 -0.48 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.02 0.11 -10000 0 -0.37 13 13
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
IL1RN -0.11 0.23 -10000 0 -0.53 86 86
TRAF6/TAK1/TAB1/TAB2 -0.002 0.022 -10000 0 -0.3 1 1
MAP2K6 0.034 0.029 -10000 0 -0.29 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.067 0.16 0.4 60 -10000 0 60
KIRREL -0.039 0.17 -10000 0 -0.6 30 30
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.067 0.16 -10000 0 -0.41 60 60
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.049 0.11 -10000 0 -0.34 34 34
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.008 0.1 -10000 0 -0.29 32 32
FYN -0.028 0.11 -10000 0 -0.33 34 34
mol:Ca2+ -0.049 0.11 -10000 0 -0.34 34 34
mol:DAG -0.049 0.11 -10000 0 -0.34 34 34
NPHS2 -0.008 0.045 -10000 0 -0.54 2 2
mol:IP3 -0.049 0.11 -10000 0 -0.34 34 34
regulation of endocytosis -0.018 0.11 -10000 0 -0.3 34 34
Nephrin/NEPH1/podocin/Cholesterol -0.05 0.12 -10000 0 -0.3 57 57
establishment of cell polarity -0.067 0.16 -10000 0 -0.4 60 60
Nephrin/NEPH1/podocin/NCK1-2 -0.044 0.1 -10000 0 -0.42 8 8
Nephrin/NEPH1/beta Arrestin2 -0.017 0.11 -10000 0 -0.3 34 34
NPHS1 -0.038 0.15 -10000 0 -0.5 33 33
Nephrin/NEPH1/podocin -0.031 0.11 -10000 0 -0.33 34 34
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.012 0.032 -10000 0 -0.6 1 1
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.049 0.11 -10000 0 -0.34 34 34
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.049 0.11 -10000 0 -0.34 34 34
GRB2 0.014 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.047 0.14 -10000 0 -0.33 46 46
cytoskeleton organization -0.008 0.12 -10000 0 -0.34 32 32
Nephrin/NEPH1 -0.047 0.11 -10000 0 -0.29 60 60
Nephrin/NEPH1/ZO-1 -0.052 0.12 -10000 0 -0.37 33 33
Retinoic acid receptors-mediated 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
HDAC1 0.011 0.046 -10000 0 -0.6 2 2
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR -0.061 0.19 -10000 0 -0.53 50 50
Cbp/p300/PCAF -0.005 0.041 -10000 0 -0.36 4 4
EP300 0.007 0.064 -10000 0 -0.6 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.012 0.069 -10000 0 -0.44 4 4
KAT2B 0.013 0.026 -10000 0 -0.48 1 1
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.004 0.069 0.22 3 -0.3 3 6
RAR alpha/9cRA/Cyclin H -0.055 0.089 -10000 0 -0.92 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.01 0.061 -10000 0 -0.35 4 4
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.068 0.11 -10000 0 -0.54 10 10
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.053 0.14 -10000 0 -0.39 50 50
RXRs/RARs/NRIP1/9cRA -0.066 0.2 -10000 0 -0.45 65 65
NCOA2 -0.035 0.17 -10000 0 -0.6 29 29
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.061 0.19 -10000 0 -0.53 50 50
RARG 0.014 0.026 -10000 0 -0.48 1 1
RAR gamma1/9cRA -0.001 0.015 -10000 0 -0.28 1 1
MAPK3 0.015 0 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.002 0.1 -10000 0 -0.6 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.15 0.22 -10000 0 -0.55 71 71
RARA -0.056 0.12 -10000 0 -0.26 74 74
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.01 0.11 -10000 0 -0.4 15 15
PRKCA 0.016 0.032 -10000 0 -0.6 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.078 0.2 -10000 0 -0.46 65 65
RXRG -0.13 0.22 -10000 0 -0.45 90 90
RXRA -0.04 0.11 -10000 0 -0.22 74 74
RXRB -0.08 0.16 -10000 0 -0.35 65 65
VDR/Vit D3/DNA -0.053 0.14 -10000 0 -0.39 50 50
RBP1 -0.066 0.18 -10000 0 -0.49 58 58
CRBP1/9-cic-RA -0.056 0.13 -10000 0 -0.35 58 58
RARB 0.013 0.046 -10000 0 -0.6 2 2
PRKCG -0.2 0.27 -10000 0 -0.53 142 142
MNAT1 0.013 0.026 -10000 0 -0.48 1 1
RAR alpha/RXRs -0.07 0.21 -10000 0 -0.48 65 65
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.053 0.17 -10000 0 -0.38 65 65
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.1 -10000 0 -0.43 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.078 0.2 -10000 0 -0.46 65 65
positive regulation of DNA binding -0.052 0.084 -10000 0 -0.82 1 1
NRIP1 -0.069 0.18 -10000 0 -0.6 18 18
RXRs/RARs -0.085 0.2 -10000 0 -0.46 67 67
RXRs/RXRs/DNA/9cRA -0.13 0.2 -10000 0 -0.52 65 65
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH -0.001 0.014 -10000 0 -0.27 1 1
RAR alpha/9cRA -0.039 0.067 -10000 0 -0.8 1 1
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.014 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.061 0.13 -9999 0 -0.34 52 52
SMAD6-7/SMURF1 -0.004 0.036 -9999 0 -0.34 4 4
NOG -0.062 0.2 -9999 0 -0.59 46 46
SMAD9 -0.037 0.18 -9999 0 -0.59 30 30
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD5 -0.003 0.12 -9999 0 -0.47 13 13
BMP7/USAG1 -0.094 0.17 -9999 0 -0.38 91 91
SMAD5/SKI 0.005 0.12 -9999 0 -0.45 12 12
SMAD1 0.043 0.032 -9999 0 -0.32 1 1
BMP2 -0.079 0.22 -9999 0 -0.6 55 55
SMAD1/SMAD1/SMAD4 -0.004 0.026 -9999 0 -10000 0 0
BMPR1A 0.014 0 -9999 0 -10000 0 0
BMPR1B -0.026 0.15 -9999 0 -0.6 24 24
BMPR1A-1B/BAMBI -0.028 0.099 -9999 0 -0.37 28 28
AHSG -0.086 0.22 -9999 0 -0.55 64 64
CER1 -0.011 0.091 -9999 0 -0.48 13 13
BMP2-4/CER1 -0.08 0.19 -9999 0 -0.48 57 57
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.015 0.16 -9999 0 -0.47 27 27
BMP2-4 (homodimer) -0.082 0.2 -9999 0 -0.52 58 58
RGMB 0.002 0.082 -9999 0 -0.54 8 8
BMP6/BMPR2/BMPR1A-1B -0.031 0.098 -9999 0 -0.35 27 27
RGMA -0.002 0.099 -9999 0 -0.59 10 10
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.022 0.15 -9999 0 -0.46 27 27
BMP2-4/USAG1 -0.14 0.22 -9999 0 -0.49 82 82
SMAD6/SMURF1/SMAD5 0.005 0.12 -9999 0 -0.45 12 12
SOSTDC1 -0.11 0.23 -9999 0 -0.52 86 86
BMP7/BMPR2/BMPR1A-1B -0.027 0.089 -9999 0 -0.32 30 30
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.006 0.1 -9999 0 -0.52 14 14
HFE2 0.005 0.052 -9999 0 -0.48 4 4
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.072 0.17 -9999 0 -0.44 59 59
SMAD5/SMAD5/SMAD4 0.005 0.12 -9999 0 -0.45 12 12
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.048 0.11 -9999 0 -0.4 25 25
BMP7 (homodimer) 0.004 0.078 -9999 0 -0.6 6 6
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.082 0.17 -9999 0 -0.41 74 74
SMAD1/SKI 0.049 0.03 -9999 0 -10000 0 0
SMAD6 0.008 0.061 -9999 0 -0.57 4 4
CTDSP2 0.01 0.045 -9999 0 -0.48 3 3
BMP2-4/FETUA -0.13 0.22 -9999 0 -0.48 81 81
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.27 -9999 0 -0.55 120 120
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.004 0.035 -9999 0 -0.27 6 6
BMPR1A-1B (homodimer) -0.029 0.11 -9999 0 -0.44 24 24
CHRDL1 -0.074 0.21 -9999 0 -0.58 54 54
ENDOFIN/SMAD1 0.049 0.03 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.03 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI 0.007 0.064 -9999 0 -0.53 5 5
SMURF2 0.011 0.046 -9999 0 -0.6 2 2
BMP2-4/CHRDL1 -0.12 0.21 -9999 0 -0.44 97 97
BMP2-4/GREM1 -0.18 0.23 -9999 0 -0.46 117 117
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.027 0.17 -9999 0 -0.55 30 30
SMAD1/SMAD6 0.049 0.03 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.004 0.078 -9999 0 -0.6 6 6
BMP6 -0.006 0.1 -9999 0 -0.52 14 14
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.015 0.14 -9999 0 -0.41 27 27
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.047 0.039 -9999 0 -0.31 2 2
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.012 0.032 -9999 0 -0.6 1 1
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.006 0.063 -9999 0 -0.48 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.053 0.19 -9999 0 -0.49 39 39
CHRD 0.011 0.046 -9999 0 -0.6 2 2
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.16 -9999 0 -0.5 27 27
BMP4 -0.013 0.12 -9999 0 -0.6 16 16
FST -0.064 0.19 -9999 0 -0.54 52 52
BMP2-4/NOG -0.11 0.25 -9999 0 -0.59 66 66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.024 0.082 -9999 0 -0.3 30 30
Nongenotropic Androgen signaling

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
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.06 0.13 -10000 0 -0.33 56 56
regulation of S phase of mitotic cell cycle -0.017 0.1 -10000 0 -0.26 54 54
GNAO1 0.004 0.078 -10000 0 -0.6 6 6
HRAS 0.013 0.026 -10000 0 -0.48 1 1
SHBG/T-DHT -0.004 0.043 -10000 0 -0.36 5 5
PELP1 0.014 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.02 0.13 -10000 0 -0.38 17 17
T-DHT/AR -0.08 0.17 -10000 0 -0.42 70 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 60 60
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.004 0.1 -10000 0 -0.6 11 11
mol:GDP -0.076 0.16 -10000 0 -0.46 53 53
cell proliferation -0.031 0.18 -10000 0 -0.55 17 17
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
FOS -0.072 0.27 -10000 0 -0.78 40 40
mol:Ca2+ -0.011 0.02 -10000 0 -0.064 24 24
MAPK3 -0.024 0.15 -10000 0 -0.47 17 17
MAPK1 -0.01 0.089 -10000 0 -0.27 14 14
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 66 66
cAMP biosynthetic process 0.005 0.045 -10000 0 -0.33 5 5
GNG2 0.009 0.056 -10000 0 -0.6 3 3
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 66 66
HRAS/GTP -0.057 0.12 -10000 0 -0.31 55 55
actin cytoskeleton reorganization -0.001 0.015 -10000 0 -0.29 1 1
SRC 0.014 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 66 66
PI3K 0 0.02 -10000 0 -0.37 1 1
apoptosis 0.03 0.16 0.43 40 -10000 0 40
T-DHT/AR/PELP1 -0.067 0.14 -10000 0 -0.36 70 70
HRAS/GDP -0.071 0.16 -10000 0 -0.43 53 53
CREB1 -0.034 0.17 -10000 0 -0.46 40 40
RAC1-CDC42/GTP -0.001 0.015 -10000 0 -0.29 1 1
AR -0.099 0.23 -10000 0 -0.57 70 70
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.025 0.13 -10000 0 -0.35 17 17
RAC1-CDC42/GDP -0.065 0.14 -10000 0 -0.41 53 53
T-DHT/AR/PELP1/Src -0.059 0.13 -10000 0 -0.33 58 58
MAP2K2 -0.019 0.13 -10000 0 -0.36 17 17
T-DHT/AR/PELP1/Src/PI3K -0.018 0.11 -10000 0 -0.26 54 54
GNAZ 0.012 0.032 -10000 0 -0.6 1 1
SHBG 0.006 0.069 -10000 0 -0.58 5 5
Gi family/GNB1/GNG2/GDP 0.018 0.086 -10000 0 -0.47 7 7
mol:T-DHT 0 0.001 -10000 0 -0.003 21 21
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 0.003 0.06 -10000 0 -0.4 8 8
Gi family/GTP -0.013 0.085 -10000 0 -0.37 6 6
CDC42 0.014 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.016 0.12 -9999 0 -0.5 21 21
PLK4 -0.005 0.099 -9999 0 -0.5 14 14
regulation of centriole replication -0.011 0.12 -9999 0 -0.37 33 33
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.032 0.14 -9999 0 -0.38 45 45
CRKL 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.009 0.056 -9999 0 -0.6 3 3
ITGA4 -0.048 0.18 -9999 0 -0.53 42 42
alpha4/beta7 Integrin/MAdCAM1 -0.13 0.18 -9999 0 -0.41 79 79
EPO -0.01 0.1 -9999 0 -0.48 16 16
alpha4/beta7 Integrin -0.08 0.17 -9999 0 -0.44 67 67
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.045 0.13 -9999 0 -0.39 42 42
EPO/EPOR (dimer) -0.016 0.076 -9999 0 -0.35 17 17
lamellipodium assembly 0.009 0.023 -9999 0 -10000 0 0
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
PI3K -0.001 0.023 -9999 0 -0.44 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 0 0.09 -9999 0 -0.3 4 4
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
MADCAM1 -0.12 0.24 -9999 0 -0.54 87 87
cell adhesion -0.12 0.18 -9999 0 -0.4 79 79
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.011 0.037 -9999 0 -0.48 2 2
SRC -0.088 0.18 -9999 0 -0.35 88 88
ITGB7 -0.041 0.17 -9999 0 -0.54 36 36
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.13 0.18 -9999 0 -0.4 88 88
p130Cas/Crk/Dock1 -0.055 0.16 -9999 0 -0.51 11 11
VCAM1 -0.14 0.26 -9999 0 -0.57 97 97
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.033 0.093 -9999 0 -0.34 19 19
BCAR1 -0.075 0.17 -9999 0 -0.56 10 10
EPOR 0.011 0.037 -9999 0 -0.48 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.024 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.001 0.17 -9999 0 -1.3 6 6
VDR -0.061 0.19 -9999 0 -0.53 50 50
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.044 0.16 -9999 0 -0.47 19 19
RXRs/LXRs/DNA/Oxysterols -0.071 0.22 -9999 0 -0.46 64 64
MED1 0.014 0 -9999 0 -10000 0 0
mol:9cRA -0.008 0.024 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.027 0.056 -9999 0 -10000 0 0
RXRs/NUR77 -0.037 0.15 -9999 0 -0.35 55 55
RXRs/PPAR -0.016 0.12 -9999 0 -0.29 49 49
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.053 0.14 -9999 0 -0.39 50 50
RARs/VDR/DNA/Vit D3 -0.038 0.095 -9999 0 -0.32 23 23
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.061 0.19 -9999 0 -0.53 50 50
RARs/RARs/DNA/9cRA 0.017 0.032 -9999 0 -0.29 3 3
RARG 0.013 0.026 -9999 0 -0.48 1 1
RPS6KB1 0.02 0.066 -9999 0 -0.4 6 6
RARs/THRs/DNA/SMRT 0.027 0.056 -9999 0 -10000 0 0
THRA 0.011 0.046 -9999 0 -0.6 2 2
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.053 0.14 -9999 0 -0.39 50 50
RXRs/PPAR/9cRA/PGJ2/DNA -0.035 0.13 -9999 0 -0.35 44 44
NR1H4 -0.12 0.23 -9999 0 -0.52 91 91
RXRs/LXRs/DNA -0.022 0.14 -9999 0 -0.44 15 15
NR1H2 0.011 0.017 -9999 0 -10000 0 0
NR1H3 0.01 0.02 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.055 0.16 -9999 0 -0.36 65 65
NR4A1 -0.023 0.13 -9999 0 -0.5 26 26
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.064 0.14 -9999 0 -0.32 59 59
RXRG -0.065 0.2 -9999 0 -0.6 45 45
RXR alpha/CCPG 0.017 0.013 -9999 0 -10000 0 0
RXRA 0.011 0.016 -9999 0 -10000 0 0
RXRB 0.009 0.019 -9999 0 -10000 0 0
THRB -0.011 0.12 -9999 0 -0.53 17 17
PPARG -0.013 0.12 -9999 0 -0.57 17 17
PPARD 0.014 0 -9999 0 -10000 0 0
TNF -0.18 0.41 -9999 0 -1 57 57
mol:Oxysterols -0.006 0.021 -9999 0 -10000 0 0
cholesterol transport -0.07 0.22 -9999 0 -0.45 64 64
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.011 0.046 -9999 0 -0.6 2 2
RXRs/NUR77/BCL2 -0.024 0.12 -9999 0 -0.3 50 50
SREBF1 -0.074 0.27 -9999 0 -0.95 20 20
RXRs/RXRs/DNA/9cRA -0.035 0.14 -9999 0 -0.35 44 44
ABCA1 -0.072 0.26 -9999 0 -0.9 20 20
RARs/THRs -0.015 0.062 -9999 0 -10000 0 0
RXRs/FXR -0.091 0.19 -9999 0 -0.39 82 82
BCL2 0.006 0.072 -9999 0 -0.6 5 5
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.079 0.28 -10000 0 -0.91 26 26
NCK1/PAK1/Dok-R -0.094 0.13 -10000 0 -0.41 35 35
NCK1/Dok-R -0.11 0.31 -10000 0 -1.1 25 25
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
mol:beta2-estradiol 0.015 0.063 0.22 22 -10000 0 22
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.008 0.052 -10000 0 -0.48 4 4
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.016 0.077 0.25 11 -0.44 3 14
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.1 0.26 -10000 0 -1 25 25
FN1 -0.002 0.088 -10000 0 -0.48 12 12
PLD2 -0.078 0.31 -10000 0 -1.1 25 25
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.17 0.26 -10000 0 -0.53 123 123
ELK1 -0.055 0.28 -10000 0 -1 25 25
GRB7 -0.036 0.14 -10000 0 -0.48 34 34
PAK1 -0.038 0.15 -10000 0 -0.49 38 38
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.29 -10000 0 -1 29 29
CDKN1A -0.099 0.29 -10000 0 -0.69 53 53
ITGA5 -0.011 0.11 -10000 0 -0.49 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.11 0.31 -10000 0 -1.1 25 25
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO -0.052 0.22 -10000 0 -0.66 27 27
PLG -0.086 0.31 -10000 0 -1.2 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.07 0.26 -10000 0 -0.86 27 27
GRB2 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
ANGPT2 -0.1 0.27 -10000 0 -0.71 44 44
BMX -0.11 0.32 -10000 0 -1.2 25 25
ANGPT1 -0.13 0.35 -10000 0 -1.3 24 24
tube development -0.077 0.26 -10000 0 -0.66 42 42
ANGPT4 -0.047 0.18 -10000 0 -0.55 39 39
response to hypoxia -0.007 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.17 0.35 -10000 0 -1.2 27 27
alpha5/beta1 Integrin -0.019 0.082 -10000 0 -0.36 19 19
FGF2 0.01 0.052 -10000 0 -0.56 3 3
STAT5A (dimer) -0.1 0.31 -10000 0 -0.76 48 48
mol:L-citrulline -0.052 0.22 -10000 0 -0.66 27 27
AGTR1 -0.036 0.16 -10000 0 -0.55 32 32
MAPK14 -0.085 0.31 -10000 0 -1.1 25 25
Tie2/SHP2 -0.039 0.16 -10000 0 -1.1 6 6
TEK -0.019 0.19 -10000 0 -1.2 7 7
RPS6KB1 -0.066 0.27 -10000 0 -0.86 26 26
Angiotensin II/AT1 -0.026 0.12 -10000 0 -0.41 32 32
Tie2/Ang1/GRB2 -0.081 0.32 -10000 0 -1.2 25 25
MAPK3 -0.062 0.29 -10000 0 -1 25 25
MAPK1 -0.062 0.29 -10000 0 -1 25 25
Tie2/Ang1/GRB7 -0.11 0.33 -10000 0 -1.2 26 26
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
MAPK8 -0.086 0.32 -10000 0 -1.2 25 25
PI3K -0.089 0.31 -10000 0 -1 26 26
FES -0.085 0.31 -10000 0 -1.1 25 25
Crk/Dok-R -0.11 0.31 -10000 0 -1.1 25 25
Tie2/Ang1/ABIN2 -0.081 0.32 -10000 0 -1.2 25 25
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.069 0.26 -10000 0 -0.76 30 30
STAT5A 0 0.09 -10000 0 -0.6 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.066 0.27 -10000 0 -0.86 26 26
Tie2/Ang2 -0.12 0.34 -10000 0 -0.91 42 42
Tie2/Ang1 -0.094 0.34 -10000 0 -1.3 25 25
FOXO1 -0.075 0.27 -10000 0 -0.76 37 37
ELF1 0.018 0.037 -10000 0 -0.65 1 1
ELF2 -0.082 0.31 -10000 0 -1.1 25 25
mol:Choline -0.072 0.3 -10000 0 -1.1 25 25
cell migration -0.053 0.072 -10000 0 -0.24 29 29
FYN -0.09 0.29 -10000 0 -0.75 42 42
DOK2 -0.071 0.2 -10000 0 -0.53 57 57
negative regulation of cell cycle -0.086 0.26 -10000 0 -0.62 54 54
ETS1 -0.005 0.079 -10000 0 -0.5 4 4
PXN -0.045 0.23 -10000 0 -0.7 26 26
ITGB1 0.011 0.037 -10000 0 -0.48 2 2
NOS3 -0.062 0.25 -10000 0 -0.75 27 27
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.16 0.27 -10000 0 -0.56 109 109
MAPKKK cascade -0.072 0.3 -10000 0 -1.1 25 25
RASA1 0.014 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.086 0.33 -10000 0 -1.2 25 25
NCK1 0.012 0.032 -10000 0 -0.6 1 1
vasculogenesis -0.044 0.2 -10000 0 -0.58 27 27
mol:Phosphatidic acid -0.072 0.3 -10000 0 -1.1 25 25
mol:Angiotensin II -0.001 0.007 -10000 0 -10000 0 0
mol:NADP -0.052 0.22 -10000 0 -0.66 27 27
Rac1/GTP -0.11 0.22 -10000 0 -0.8 26 26
MMP2 -0.096 0.32 -10000 0 -1.1 25 25
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.002 0.09 -9999 0 -0.31 27 27
EPHB2 0.001 0.084 -9999 0 -0.52 9 9
Syndecan-2/TACI -0.011 0.084 -9999 0 -0.32 24 24
LAMA1 -0.054 0.19 -9999 0 -0.58 42 42
Syndecan-2/alpha2 ITGB1 -0.026 0.15 -9999 0 -0.37 39 39
HRAS 0.013 0.026 -9999 0 -0.48 1 1
Syndecan-2/CASK -0.014 0.068 -9999 0 -0.33 16 16
ITGA5 -0.011 0.11 -9999 0 -0.49 18 18
BAX 0.02 0.085 -9999 0 -10000 0 0
EPB41 0.009 0.052 -9999 0 -0.56 3 3
positive regulation of cell-cell adhesion -0.013 0.059 -9999 0 -0.29 16 16
LAMA3 -0.031 0.16 -9999 0 -0.56 29 29
EZR 0.004 0.078 -9999 0 -0.6 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.014 0.12 -9999 0 -0.49 20 20
Syndecan-2/MMP2 -0.011 0.11 -9999 0 -0.32 39 39
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.039 0.12 -9999 0 -0.38 37 37
dendrite morphogenesis 0.004 0.091 -9999 0 -0.34 23 23
Syndecan-2/GM-CSF -0.013 0.068 -9999 0 -0.33 16 16
determination of left/right symmetry 0.004 0.084 -9999 0 -0.38 16 16
Syndecan-2/PKC delta -0.006 0.12 -9999 0 -0.39 29 29
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.013 0.065 -9999 0 -0.29 16 16
MAPK1 0.013 0.065 -9999 0 -0.29 16 16
Syndecan-2/RACK1 -0.011 0.056 -9999 0 -0.3 8 8
NF1 0.009 0.056 -9999 0 -0.6 3 3
FGFR/FGF/Syndecan-2 0.004 0.084 -9999 0 -0.38 16 16
ITGA2 -0.039 0.16 -9999 0 -0.54 35 35
MAPK8 0.011 0.095 -9999 0 -0.33 26 26
Syndecan-2/alpha2/beta1 Integrin -0.039 0.16 -9999 0 -0.36 58 58
Syndecan-2/Kininogen -0.019 0.09 -9999 0 -0.3 33 33
ITGB1 0.011 0.037 -9999 0 -0.48 2 2
SRC 0.027 0.06 -9999 0 -0.28 8 8
Syndecan-2/CASK/Protein 4.1 -0.015 0.072 -9999 0 -0.32 17 17
extracellular matrix organization 0.005 0.086 -9999 0 -0.33 22 22
actin cytoskeleton reorganization 0.002 0.089 -9999 0 -0.31 27 27
Syndecan-2/Caveolin-2/Ras 0.004 0.094 -9999 0 -0.34 14 14
Syndecan-2/Laminin alpha3 -0.016 0.12 -9999 0 -0.35 42 42
Syndecan-2/RasGAP -0.011 0.052 -9999 0 -0.28 8 8
alpha5/beta1 Integrin -0.019 0.082 -9999 0 -0.36 19 19
PRKCD -0.015 0.13 -9999 0 -0.6 17 17
Syndecan-2 dimer 0.004 0.092 -9999 0 -0.34 23 23
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.034 0.058 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.006 0.076 -9999 0 -0.48 9 9
RASA1 0.014 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.039 0.12 -9999 0 -0.38 37 37
Syndecan-2/Synbindin 0.012 0.071 -9999 0 -0.32 16 16
TGFB1 0.004 0.078 -9999 0 -0.6 6 6
CASP3 0.004 0.11 -9999 0 -0.39 21 21
FN1 -0.002 0.088 -9999 0 -0.48 12 12
Syndecan-2/IL8 -0.096 0.17 -9999 0 -0.32 127 127
SDC2 0.004 0.084 -9999 0 -0.38 16 16
KNG1 -0.018 0.1 -9999 0 -0.48 17 17
Syndecan-2/Neurofibromin 0.009 0.082 -9999 0 -0.34 18 18
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 0.001 0.003 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.005 0.086 -9999 0 -0.33 22 22
Syndecan-2/Syntenin/PI-4-5-P2 -0.012 0.06 -9999 0 -0.29 16 16
Syndecan-2/Ezrin 0.015 0.092 -9999 0 -0.46 10 10
PRKACA 0.019 0.075 -9999 0 -0.34 11 11
angiogenesis -0.095 0.17 -9999 0 -0.32 127 127
MMP2 -0.022 0.14 -9999 0 -0.53 24 24
IL8 -0.16 0.26 -9999 0 -0.53 117 117
calcineurin-NFAT signaling pathway -0.011 0.084 -9999 0 -0.32 24 24
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.013 0.026 -9999 0 -0.48 1 1
LAT2 -0.051 0.17 -9999 0 -0.58 23 23
AP1 -0.099 0.17 -9999 0 -0.53 35 35
mol:PIP3 -0.065 0.2 -9999 0 -0.57 28 28
IKBKB -0.03 0.11 -9999 0 -0.3 22 22
AKT1 -0.035 0.14 -9999 0 -0.47 10 10
IKBKG -0.03 0.11 -9999 0 -0.28 28 28
MS4A2 -0.03 0.12 -9999 0 -0.48 24 24
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
MAP3K1 -0.015 0.15 -9999 0 -0.54 19 19
mol:Ca2+ -0.045 0.15 -9999 0 -0.41 28 28
LYN 0.005 0.065 -9999 0 -0.49 6 6
CBLB -0.037 0.14 -9999 0 -0.43 22 22
SHC1 0.009 0.052 -9999 0 -0.48 4 4
RasGAP/p62DOK -0.02 0.074 -9999 0 -0.33 12 12
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.055 -9999 0 -0.51 4 4
PLD2 -0.07 0.16 -9999 0 -0.36 50 50
PTPN13 -0.028 0.14 -9999 0 -0.56 13 13
PTPN11 0.011 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.003 0.12 -9999 0 -0.33 14 14
SYK -0.014 0.12 -9999 0 -0.57 17 17
GRB2 0.014 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.17 -9999 0 -0.59 27 27
LAT -0.056 0.15 -9999 0 -0.38 42 42
PAK2 -0.026 0.17 -9999 0 -0.6 21 21
NFATC2 -0.11 0.2 -9999 0 -0.57 48 48
HRAS -0.038 0.19 -9999 0 -0.66 22 22
GAB2 0.012 0.032 -9999 0 -0.6 1 1
PLA2G1B 0.04 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.18 -9999 0 -0.4 86 86
Antigen/IgE/Fc epsilon R1 -0.11 0.17 -9999 0 -0.39 73 73
mol:GDP -0.047 0.2 -9999 0 -0.68 24 24
JUN 0.003 0.075 -9999 0 -0.5 8 8
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
FOS -0.087 0.22 -9999 0 -0.55 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.062 0.13 -9999 0 -0.47 21 21
CHUK -0.03 0.11 -9999 0 -0.28 28 28
KLRG1 -0.041 0.13 -9999 0 -0.48 17 17
VAV1 -0.053 0.18 -9999 0 -0.55 29 29
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.036 0.13 -9999 0 -0.45 20 20
negative regulation of mast cell degranulation -0.033 0.14 -9999 0 -0.5 17 17
BTK -0.068 0.19 -9999 0 -0.73 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.19 -9999 0 -0.54 35 35
GAB2/PI3K/SHP2 -0.082 0.13 -9999 0 -0.46 17 17
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.053 0.15 -9999 0 -0.41 32 32
RAF1 0.029 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.22 -9999 0 -0.45 108 108
FCER1G -0.017 0.13 -9999 0 -0.57 19 19
FCER1A -0.14 0.25 -9999 0 -0.53 104 104
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.16 -9999 0 -0.37 65 65
MAPK3 0.039 0.023 -9999 0 -10000 0 0
MAPK1 0.039 0.023 -9999 0 -10000 0 0
NFKB1 0.013 0.026 -9999 0 -0.48 1 1
MAPK8 -0.003 0.11 -9999 0 -0.59 10 10
DUSP1 -0.022 0.14 -9999 0 -0.54 24 24
NF-kappa-B/RelA -0.033 0.05 -9999 0 -0.25 2 2
actin cytoskeleton reorganization -0.033 0.13 -9999 0 -0.44 20 20
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.068 0.16 -9999 0 -0.62 21 21
FER -0.054 0.16 -9999 0 -0.42 40 40
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.072 0.13 -9999 0 -0.36 47 47
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.045 0.2 -9999 0 -0.69 23 23
cytokine secretion -0.024 0.037 -9999 0 -10000 0 0
SPHK1 -0.056 0.16 -9999 0 -0.46 32 32
PTK2 -0.035 0.14 -9999 0 -0.47 19 19
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.18 -9999 0 -0.65 25 25
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.051 0.19 -9999 0 -0.54 27 27
MAP2K2 0.035 0.022 -9999 0 -10000 0 0
MAP2K1 0.034 0.026 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.046 0.12 -9999 0 -0.47 16 16
MAP2K4 0.02 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.19 0.23 -9999 0 -0.47 117 117
mol:Choline -0.069 0.16 -9999 0 -0.36 50 50
SHC/Grb2/SOS1 -0.057 0.11 -9999 0 -0.49 15 15
FYN 0.014 0 -9999 0 -10000 0 0
DOK1 0.012 0.032 -9999 0 -0.6 1 1
PXN -0.024 0.13 -9999 0 -0.5 13 13
HCLS1 -0.055 0.18 -9999 0 -0.57 26 26
PRKCB -0.054 0.14 -9999 0 -0.38 35 35
FCGR2B -0.15 0.25 -9999 0 -0.53 107 107
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.034 0.14 -9999 0 -0.51 17 17
LCP2 -0.004 0.094 -9999 0 -0.49 13 13
PLA2G4A -0.051 0.15 -9999 0 -0.43 35 35
RASA1 0.014 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.069 0.16 -9999 0 -0.36 50 50
IKK complex -0.009 0.086 -9999 0 -0.23 15 15
WIPF1 0.014 0 -9999 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.035 0.14 -9999 0 -0.42 21 21
FZD6 -0.012 0.11 -9999 0 -0.49 19 19
WNT6 -0.041 0.16 -9999 0 -0.53 37 37
WNT4 -0.04 0.16 -9999 0 -0.52 37 37
FZD3 0.009 0.056 -9999 0 -0.6 3 3
WNT5A -0.012 0.12 -9999 0 -0.57 16 16
WNT11 -0.016 0.13 -9999 0 -0.54 20 20
IL6-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
BCL2L1 -0.039 0.23 -10000 0 -0.76 8 8
CRP -0.047 0.23 -10000 0 -0.7 11 11
cell cycle arrest -0.06 0.26 -10000 0 -0.67 27 27
TIMP1 -0.081 0.27 -10000 0 -0.68 30 30
IL6ST -0.039 0.17 -10000 0 -0.6 31 31
Rac1/GDP -0.075 0.21 -10000 0 -0.54 35 35
AP1 -0.016 0.14 -10000 0 -0.49 11 11
GAB2 0.013 0.032 -10000 0 -0.6 1 1
TNFSF11 -0.049 0.24 -10000 0 -0.75 9 9
HSP90B1 0 0.17 -10000 0 -0.92 11 11
GAB1 0.012 0.041 -10000 0 -0.54 2 2
MAPK14 -0.11 0.24 -10000 0 -0.54 64 64
AKT1 0.058 0.034 -10000 0 -0.46 1 1
FOXO1 0.061 0.043 -10000 0 -0.43 1 1
MAP2K6 -0.093 0.22 -10000 0 -0.52 48 48
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.061 0.22 -10000 0 -0.55 33 33
MITF -0.074 0.2 -10000 0 -0.49 41 41
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.014 0 -10000 0 -10000 0 0
A2M 0.02 0.04 -10000 0 -10000 0 0
CEBPB 0 0.12 -10000 0 -0.57 14 14
GRB2/SOS1/GAB family/SHP2 0 0.084 -10000 0 -0.82 1 1
STAT3 -0.065 0.26 -10000 0 -0.71 27 27
STAT1 -0.008 0.034 -10000 0 -10000 0 0
CEBPD -0.081 0.33 -10000 0 -0.96 31 31
PIK3CA 0.014 0.032 -10000 0 -0.6 1 1
PI3K 0.023 0.024 -10000 0 -0.44 1 1
JUN 0.003 0.075 -10000 0 -0.5 8 8
PIAS3/MITF -0.063 0.18 -10000 0 -0.5 33 33
MAPK11 -0.11 0.25 -10000 0 -0.54 68 68
STAT3 (dimer)/FOXO1 0.011 0.21 -10000 0 -0.63 9 9
GRB2/SOS1/GAB family -0.079 0.14 -10000 0 -0.52 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.075 0.19 -10000 0 -0.52 33 33
GRB2 0.015 0.001 -10000 0 -10000 0 0
JAK2 0.014 0 -10000 0 -10000 0 0
LBP -0.036 0.23 -10000 0 -0.69 17 17
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.013 0.009 -10000 0 -10000 0 0
MYC -0.067 0.3 -10000 0 -0.98 22 22
FGG -0.047 0.23 -10000 0 -0.73 9 9
macrophage differentiation -0.06 0.26 -10000 0 -0.67 27 27
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.18 -10000 0 -0.54 33 33
JUNB -0.063 0.28 -10000 0 -0.81 23 23
FOS -0.087 0.22 -10000 0 -0.55 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.085 0.2 0.29 1 -0.47 51 52
STAT1/PIAS1 -0.061 0.19 0.29 1 -0.46 42 43
GRB2/SOS1/GAB family/SHP2/PI3K 0.044 0.037 -10000 0 -0.39 2 2
STAT3 (dimer) -0.063 0.26 -10000 0 -0.7 27 27
PRKCD -0.062 0.25 -10000 0 -0.65 32 32
IL6R -0.019 0.13 -10000 0 -0.57 20 20
SOCS3 -0.16 0.36 -10000 0 -1 41 41
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.11 -10000 0 -0.36 31 31
Rac1/GTP -0.076 0.21 -10000 0 -0.52 41 41
HCK -0.013 0.12 -10000 0 -0.53 18 18
MAPKKK cascade 0.023 0.073 -10000 0 -0.91 1 1
bone resorption -0.045 0.23 -10000 0 -0.69 10 10
IRF1 -0.046 0.24 -10000 0 -0.78 9 9
mol:GDP -0.087 0.21 -10000 0 -0.51 47 47
SOS1 0.015 0.001 -10000 0 -10000 0 0
VAV1 -0.089 0.22 -10000 0 -0.52 47 47
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.24 -10000 0 -0.58 50 50
PTPN11 -0.002 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.11 0.21 -10000 0 -0.42 109 109
gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.11 -10000 0 -0.36 31 31
gp130 (dimer)/JAK2/JAK2/LMO4 -0.009 0.11 -10000 0 -0.36 31 31
IL6 -0.13 0.24 -10000 0 -0.53 99 99
PIAS3 0.014 0 -10000 0 -10000 0 0
PTPRE 0.012 0.037 -10000 0 -0.61 1 1
PIAS1 0.007 0.064 -10000 0 -0.6 4 4
RAC1 0.015 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.075 0.17 0.27 1 -0.44 39 40
LMO4 0.014 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.21 0.35 1 -0.66 28 29
MCL1 0.063 0.031 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.035 0.1 -10000 0 -0.33 38 38
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.13 0.2 -10000 0 -0.4 127 127
GNB1/GNG2 -0.003 0.034 -10000 0 -0.37 3 3
GNB1 0.014 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.036 0.11 -10000 0 -0.35 38 38
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 0.027 0.088 38 -10000 0 38
GNAL -0.05 0.19 -10000 0 -0.6 38 38
GNG2 0.009 0.056 -10000 0 -0.6 3 3
CRH -0.18 0.27 -10000 0 -0.54 127 127
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.062 -10000 0 -0.37 10 10
MAPK11 0.006 0.034 -10000 0 -0.37 3 3
LPA4-mediated signaling 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
ADCY4 0.007 0.069 -9999 0 -0.31 16 16
ADCY5 0.002 0.091 -9999 0 -0.39 17 17
ADCY6 0.014 0.05 -9999 0 -0.32 8 8
ADCY7 0.014 0.05 -9999 0 -0.32 8 8
ADCY1 -0.056 0.15 -9999 0 -0.34 77 77
ADCY2 0.003 0.085 -9999 0 -0.37 17 17
ADCY3 0.014 0.05 -9999 0 -0.32 8 8
ADCY8 -0.035 0.14 -9999 0 -0.36 54 54
PRKCE 0.004 0.058 -9999 0 -0.38 8 8
ADCY9 0.012 0.06 -9999 0 -0.35 9 9
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.011 0.11 -9999 0 -0.36 18 18
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.004 -9999 0 -10000 0 0
SVIL -0.009 0.1 -9999 0 -0.49 16 16
ZNF318 0.019 0.018 -9999 0 -10000 0 0
JMJD2C -0.003 0.02 -9999 0 -0.076 24 24
T-DHT/AR/Ubc9 -0.063 0.16 -9999 0 -0.37 70 70
CARM1 0.014 0.001 -9999 0 -10000 0 0
PRDX1 -0.008 0.11 -9999 0 -0.6 13 13
PELP1 0.015 0.003 -9999 0 -10000 0 0
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.015 0.005 -9999 0 -10000 0 0
PTK2B -0.011 0.11 -9999 0 -0.48 18 18
MED1 0.015 0.005 -9999 0 -10000 0 0
MAK -0.037 0.16 -9999 0 -0.49 40 40
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 -0.004 0.1 -9999 0 -0.6 10 10
GSN 0.002 0.08 -9999 0 -0.57 7 7
NCOA2 -0.035 0.17 -9999 0 -0.6 29 29
NCOA6 0.013 0.004 -9999 0 -10000 0 0
DNA-PK 0.008 0.026 -9999 0 -10000 0 0
NCOA4 0.014 0.001 -9999 0 -10000 0 0
PIAS3 0.013 0.004 -9999 0 -10000 0 0
cell proliferation -0.041 0.1 -9999 0 -0.56 6 6
XRCC5 0.015 0.004 -9999 0 -10000 0 0
UBE3A 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.075 0.18 -9999 0 -0.39 77 77
FHL2 -0.043 0.21 -9999 0 -0.88 16 16
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.009 0.052 -9999 0 -0.11 72 72
CDK6 -0.036 0.16 -9999 0 -0.54 33 33
TGFB1I1 0.001 0.082 -9999 0 -0.54 8 8
T-DHT/AR/CyclinD1 -0.084 0.18 -9999 0 -0.4 83 83
XRCC6 0.015 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.071 0.18 -9999 0 -0.4 67 67
CTDSP1 0.013 0.004 -9999 0 -10000 0 0
CTDSP2 0.013 0.046 -9999 0 -0.48 3 3
BRCA1 0.011 0.037 -9999 0 -0.48 2 2
TCF4 0.015 0.033 -9999 0 -0.6 1 1
CDKN2A -0.1 0.24 -9999 0 -0.57 74 74
SRF 0.017 0.027 -9999 0 -10000 0 0
NKX3-1 -0.054 0.17 -9999 0 -0.98 7 7
KLK3 -0.019 0.12 -9999 0 -10000 0 0
TMF1 0.013 0.004 -9999 0 -10000 0 0
HNRNPA1 0.016 0.006 -9999 0 -10000 0 0
AOF2 -0.002 0.008 -9999 0 -10000 0 0
APPL1 0.028 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.074 0.17 -9999 0 -0.38 81 81
AR -0.11 0.24 -9999 0 -0.59 70 70
UBA3 0.013 0.004 -9999 0 -10000 0 0
PATZ1 0.016 0.006 -9999 0 -10000 0 0
PAWR -0.034 0.15 -9999 0 -0.52 32 32
PRKDC 0.015 0.004 -9999 0 -10000 0 0
PA2G4 0.016 0.007 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.057 0.15 -9999 0 -0.34 71 71
RPS6KA3 0.012 0.032 -9999 0 -0.6 1 1
T-DHT/AR/ARA70 -0.064 0.16 -9999 0 -0.37 70 70
LATS2 0.003 0.084 -9999 0 -0.52 9 9
T-DHT/AR/PRX1 -0.067 0.17 -9999 0 -0.37 77 77
Cyclin D3/CDK11 p58 0 0.018 -9999 0 -0.34 1 1
VAV3 -0.11 0.22 -9999 0 -0.51 84 84
KLK2 -0.063 0.12 -9999 0 -0.47 15 15
CASP8 -0.006 0.1 -9999 0 -0.49 15 15
T-DHT/AR/TIF2/CARM1 -0.077 0.18 -9999 0 -0.39 80 80
TMPRSS2 -0.14 0.31 -9999 0 -0.68 72 72
CCND1 -0.019 0.13 -9999 0 -0.53 22 22
PIAS1 0.005 0.065 -9999 0 -0.6 4 4
mol:T-DHT -0.011 0.031 -9999 0 -0.079 38 38
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.01 0.015 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.093 0.19 -9999 0 -0.39 94 94
CMTM2 -0.006 0.11 -9999 0 -0.56 13 13
SNURF -0.005 0.1 -9999 0 -0.6 11 11
ZMIZ1 0.006 0.026 -9999 0 -10000 0 0
CCND3 0.013 0.026 -9999 0 -0.48 1 1
TGIF1 -0.005 0.1 -9999 0 -0.53 14 14
FKBP4 0.013 0.004 -9999 0 -10000 0 0
Ephrin B reverse 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
EFNB2 0.003 0.077 -10000 0 -0.51 8 8
EPHB2 0.001 0.084 -10000 0 -0.52 9 9
EFNB1 -0.078 0.18 -10000 0 -0.38 93 93
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.087 0.15 -10000 0 -0.59 17 17
Ephrin B2/EPHB1-2 -0.035 0.12 -10000 0 -0.35 43 43
neuron projection morphogenesis -0.084 0.15 -10000 0 -0.56 17 17
Ephrin B1/EPHB1-2/Tiam1 -0.066 0.18 -10000 0 -0.4 56 56
DNM1 -0.12 0.24 -10000 0 -0.52 92 92
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.01 0.083 -10000 0 -0.74 4 4
YES1 -0.008 0.11 -10000 0 -1 4 4
Ephrin B1/EPHB1-2/NCK2 -0.066 0.18 -10000 0 -0.4 56 56
PI3K 0.012 0.083 -10000 0 -0.66 5 5
mol:GDP -0.088 0.17 -10000 0 -0.4 56 56
ITGA2B -0.043 0.17 -10000 0 -0.56 36 36
endothelial cell proliferation -0.007 0.045 -10000 0 -0.3 8 8
FYN -0.007 0.1 -10000 0 -0.96 4 4
MAP3K7 -0.007 0.083 -10000 0 -0.79 4 4
FGR -0.007 0.1 -10000 0 -0.96 4 4
TIAM1 0.012 0.032 -10000 0 -0.6 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
RGS3 0.01 0.045 -10000 0 -0.48 3 3
cell adhesion -0.035 0.15 -10000 0 -0.62 9 9
LYN -0.008 0.1 -10000 0 -0.96 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.097 -10000 0 -0.92 4 4
Ephrin B1/EPHB1-2 -0.013 0.09 -10000 0 -0.85 4 4
SRC -0.007 0.1 -10000 0 -0.96 4 4
ITGB3 -0.054 0.18 -10000 0 -0.51 47 47
EPHB1 -0.039 0.17 -10000 0 -0.6 31 31
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.004 0.046 -10000 0 -0.31 8 8
alphaIIb/beta3 Integrin -0.086 0.17 -10000 0 -0.4 78 78
BLK -0.023 0.11 -10000 0 -0.98 4 4
HCK -0.012 0.11 -10000 0 -1.1 4 4
regulation of stress fiber formation 0.087 0.17 0.39 56 -10000 0 56
MAPK8 0.009 0.098 -10000 0 -0.44 13 13
Ephrin B1/EPHB1-2/RGS3 -0.068 0.18 -10000 0 -0.4 56 56
endothelial cell migration -0.008 0.081 -10000 0 -0.55 6 6
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 0.003 0.082 -10000 0 -0.68 5 5
regulation of focal adhesion formation 0.087 0.17 0.39 56 -10000 0 56
chemotaxis 0.089 0.17 0.47 34 -10000 0 34
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
Rac1/GTP -0.086 0.15 -10000 0 -0.58 17 17
angiogenesis -0.013 0.089 -10000 0 -0.84 4 4
LCK -0.026 0.11 -10000 0 -0.99 4 4
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0.032 -9999 0 -0.6 1 1
ELF1 -0.021 0.1 -9999 0 -0.36 13 13
CCNA2 -0.051 0.18 -9999 0 -0.54 43 43
PIK3CA 0.013 0.032 -9999 0 -0.6 1 1
JAK3 -0.058 0.19 -9999 0 -0.53 49 49
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
JAK1 0.015 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.031 0.16 -9999 0 -0.43 23 23
SHC1 0.009 0.052 -9999 0 -0.48 4 4
SP1 0.015 0.048 -9999 0 -0.35 4 4
IL2RA -0.054 0.2 -9999 0 -0.5 56 56
IL2RB -0.099 0.22 -9999 0 -0.53 76 76
SOS1 0.015 0.001 -9999 0 -10000 0 0
IL2RG -0.036 0.16 -9999 0 -0.51 35 35
G1/S transition of mitotic cell cycle -0.04 0.2 -9999 0 -0.53 37 37
PTPN11 0.015 0.001 -9999 0 -10000 0 0
CCND2 0.017 0.1 -9999 0 -0.58 10 10
LCK -0.087 0.21 -9999 0 -0.53 68 68
GRB2 0.015 0.001 -9999 0 -10000 0 0
IL2 0.001 0.002 -9999 0 -10000 0 0
CDK6 -0.036 0.16 -9999 0 -0.54 33 33
CCND3 -0.017 0.14 -9999 0 -0.5 6 6
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.014 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.028 0.042 -10000 0 -0.51 1 1
NT3 (dimer)/TRKC -0.015 0.08 -10000 0 -0.4 14 14
NT3 (dimer)/TRKB -0.07 0.15 -10000 0 -0.36 71 71
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.034 -10000 0 -0.44 1 1
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.087 0.21 -10000 0 -0.5 71 71
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
DYNLT1 0.011 0.046 -10000 0 -0.6 2 2
NTRK1 -0.006 0.1 -10000 0 -0.52 14 14
NTRK2 -0.015 0.13 -10000 0 -0.6 17 17
NTRK3 0.009 0.056 -10000 0 -0.6 3 3
NT-4/5 (dimer)/TRKB -0.071 0.15 -10000 0 -0.38 57 57
neuron apoptosis 0.13 0.17 0.42 70 -10000 0 70
SHC 2-3/Grb2 -0.14 0.18 -10000 0 -0.46 70 70
SHC1 0.009 0.052 -10000 0 -0.48 4 4
SHC2 -0.07 0.11 -10000 0 -0.4 21 21
SHC3 -0.16 0.24 -10000 0 -0.56 78 78
STAT3 (dimer) 0.006 0.07 -10000 0 -0.35 9 9
NT3 (dimer)/TRKA -0.065 0.14 -10000 0 -0.34 69 69
RIN/GDP -0.035 0.11 -10000 0 -0.27 13 13
GIPC1 0.014 0 -10000 0 -10000 0 0
KRAS 0.013 0.026 -10000 0 -0.48 1 1
DNAJA3 -0.066 0.12 -10000 0 -0.35 30 30
RIN/GTP -0.16 0.2 -10000 0 -0.41 139 139
CCND1 -0.003 0.16 -10000 0 -0.58 22 22
MAGED1 0.014 0 -10000 0 -10000 0 0
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.09 -10000 0 -0.48 13 13
SHC/GRB2/SOS1 -0.003 0.028 -10000 0 -0.27 4 4
GRB2 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.12 0.19 -10000 0 -0.38 113 113
TRKA/NEDD4-2 -0.026 0.1 -10000 0 -0.39 25 25
ELMO1 -0.001 0.096 -10000 0 -0.6 9 9
RhoG/GTP/ELMO1/DOCK1 -0.012 0.067 -10000 0 -0.37 12 12
NGF -0.072 0.2 -10000 0 -0.55 55 55
HRAS 0.013 0.026 -10000 0 -0.48 1 1
DOCK1 0.009 0.056 -10000 0 -0.6 3 3
GAB2 0.012 0.032 -10000 0 -0.6 1 1
RIT2 -0.2 0.28 -10000 0 -0.56 139 139
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.011 0.041 -10000 0 -0.54 2 2
DNM1 -0.12 0.24 -10000 0 -0.52 92 92
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.072 0.12 -10000 0 -0.36 39 39
mol:GDP 0.045 0.069 -10000 0 -0.46 2 2
NGF (dimer) -0.072 0.2 -10000 0 -0.55 55 55
RhoG/GDP -0.011 0.069 -10000 0 -0.45 9 9
RIT1/GDP 0.041 0.05 -10000 0 -0.29 2 2
TIAM1 0.012 0.032 -10000 0 -0.6 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.077 0.14 -10000 0 -0.4 33 33
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.004 0.035 -10000 0 -0.33 4 4
FRS2 family/SHP2 -0.002 0.024 -10000 0 -0.32 2 2
SHC/GRB2/SOS1/GAB1 -0.004 0.039 -10000 0 -0.57 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.008 0.091 -10000 0 -0.48 13 13
RAP1/GDP -0.006 0.025 -10000 0 -0.24 2 2
KIDINS220/CRKL 0.014 0 -10000 0 -10000 0 0
BDNF (dimer) -0.087 0.21 -10000 0 -0.5 71 71
ubiquitin-dependent protein catabolic process -0.071 0.15 -10000 0 -0.36 72 72
Schwann cell development -0.02 0.027 -10000 0 -10000 0 0
EHD4 0.007 0.058 -10000 0 -0.48 5 5
FRS2 family/GRB2/SOS1 -0.002 0.021 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.02 -10000 0 -10000 0 0
RAP1B 0.013 0.026 -10000 0 -0.48 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.063 0.12 -10000 0 -0.48 13 13
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.023 0.044 -10000 0 -10000 0 0
STAT3 0.006 0.07 -10000 0 -0.34 9 9
axon guidance -0.061 0.12 -10000 0 -0.46 13 13
MAPK3 -0.08 0.19 -10000 0 -0.4 73 73
MAPK1 -0.08 0.19 -10000 0 -0.4 73 73
CDC42/GDP 0.041 0.05 -10000 0 -0.29 2 2
NTF3 -0.008 0.091 -10000 0 -0.48 13 13
NTF4 -0.012 0.09 -10000 0 -0.48 13 13
NGF (dimer)/TRKA/FAIM -0.062 0.14 -10000 0 -0.34 67 67
PI3K -0.001 0.023 -10000 0 -0.44 1 1
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.012 0.032 -10000 0 -0.6 1 1
GAB1 0.011 0.041 -10000 0 -0.54 2 2
RASGRF1 -0.11 0.16 -10000 0 -0.37 75 75
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L 0.012 0.075 -10000 0 -0.33 15 15
RGS19 0.013 0.026 -10000 0 -0.48 1 1
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.073 -10000 0 -10000 0 0
Rac1/GDP 0.041 0.05 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.063 0.14 -10000 0 -0.35 66 66
neuron projection morphogenesis -0.035 0.13 -10000 0 -0.47 6 6
NGF (dimer)/TRKA/NEDD4-2 -0.071 0.15 -10000 0 -0.36 72 72
MAP2K1 0.038 0.042 -10000 0 -0.53 1 1
NGFR -0.061 0.19 -10000 0 -0.54 50 50
NGF (dimer)/TRKA/GIPC/GAIP -0.057 0.14 -10000 0 -0.31 69 69
RAS family/GTP/PI3K 0.032 0.019 -10000 0 -0.26 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.019 -10000 0 -0.3 1 1
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
MAPKKK cascade -0.076 0.19 -10000 0 -0.6 39 39
RASA1 0.014 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.014 0.072 -10000 0 -0.37 14 14
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.067 0.13 -10000 0 -0.36 33 33
NGF (dimer)/TRKA/p62/Atypical PKCs -0.061 0.13 -10000 0 -0.35 46 46
MATK -0.087 0.22 -10000 0 -0.55 66 66
NEDD4L -0.004 0.098 -10000 0 -0.53 12 12
RAS family/GDP -0.005 0.023 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.072 0.12 -10000 0 -0.31 64 64
Rac1/GTP -0.063 0.095 -10000 0 -0.32 25 25
FRS2 family/SHP2/CRK family -0.001 0.019 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.018 0.006 -9999 0 -10000 0 0
RAS family/GTP -0.068 0.15 -9999 0 -0.51 19 19
NFATC4 -0.057 0.13 -9999 0 -0.37 23 23
ERBB2IP 0.014 0.032 -9999 0 -0.6 1 1
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.087 0.16 -9999 0 -0.48 19 19
JUN -0.021 0.1 -9999 0 -0.37 16 16
HRAS 0.012 0.026 -9999 0 -0.48 1 1
DOCK7 -0.082 0.16 -9999 0 -0.48 21 21
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.13 0.18 -9999 0 -0.38 96 96
AKT1 0.011 0.004 -9999 0 -10000 0 0
BAD 0.02 0.003 -9999 0 -10000 0 0
MAPK10 -0.048 0.077 -9999 0 -0.25 17 17
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.092 0.17 -9999 0 -0.52 19 19
RAF1 -0.059 0.15 -9999 0 -0.48 20 20
ErbB2/ErbB3/neuregulin 2 -0.046 0.12 -9999 0 -0.36 36 36
STAT3 0.004 0.005 -9999 0 -10000 0 0
cell migration -0.02 0.096 -9999 0 -0.25 15 15
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.26 -9999 0 -0.61 59 59
FOS -0.11 0.21 -9999 0 -0.46 66 66
NRAS 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.087 0.16 -9999 0 -0.48 19 19
MAPK3 -0.11 0.22 -9999 0 -0.5 57 57
MAPK1 -0.11 0.22 -9999 0 -0.5 57 57
JAK2 -0.076 0.15 -9999 0 -0.46 18 18
NF2 -0.003 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.089 0.18 -9999 0 -0.34 95 95
NRG1 -0.16 0.26 -9999 0 -0.56 110 110
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.075 0.15 -9999 0 -0.4 24 24
MAPK9 -0.046 0.073 -9999 0 -0.24 14 14
ERBB2 -0.006 0.046 -9999 0 -0.36 6 6
ERBB3 -0.063 0.2 -9999 0 -0.57 47 47
SHC1 0.008 0.052 -9999 0 -0.48 4 4
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.001 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.009 0.009 -9999 0 -10000 0 0
RNF41 0.023 0.009 -9999 0 -10000 0 0
FRAP1 0.009 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.072 0.1 -9999 0 -0.33 21 21
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.037 -9999 0 -0.29 6 6
CHRNA1 -0.13 0.25 -9999 0 -0.59 64 64
myelination -0.05 0.13 -9999 0 -0.35 23 23
PPP3CB -0.073 0.14 -9999 0 -0.42 19 19
KRAS 0.012 0.026 -9999 0 -0.48 1 1
RAC1-CDC42/GDP -0.062 0.16 -9999 0 -0.5 20 20
NRG2 0.012 0.032 -9999 0 -0.6 1 1
mol:GDP -0.088 0.18 -9999 0 -0.34 95 95
SOS1 0.014 0.001 -9999 0 -10000 0 0
MAP2K2 -0.057 0.15 -9999 0 -0.44 24 24
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.077 0.15 -9999 0 -0.46 18 18
MAP2K1 -0.12 0.21 -9999 0 -0.54 36 36
heart morphogenesis -0.087 0.16 -9999 0 -0.48 19 19
RAS family/GDP -0.065 0.15 -9999 0 -0.51 19 19
GRB2 0.014 0.001 -9999 0 -10000 0 0
PRKACA -0.006 0.009 -9999 0 -10000 0 0
CHRNE 0 0.048 -9999 0 -0.19 19 19
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.004 -9999 0 -10000 0 0
nervous system development -0.087 0.16 -9999 0 -0.48 19 19
CDC42 0.014 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.081 0.16 -9999 0 -0.39 60 60
MAP4K1 -0.025 0.15 -9999 0 -0.58 24 24
MAP3K8 0 0.083 -9999 0 -0.49 10 10
PRKCB -0.063 0.19 -9999 0 -0.52 53 53
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
MAP3K1 -0.007 0.11 -9999 0 -0.43 8 8
JUN -0.029 0.17 -9999 0 -0.59 24 24
MAP3K7 -0.006 0.11 -9999 0 -0.43 8 8
GRAP2 -0.049 0.17 -9999 0 -0.52 43 43
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0 0.11 -9999 0 -0.4 11 11
LAT -0.024 0.15 -9999 0 -0.6 23 23
LCP2 -0.004 0.094 -9999 0 -0.49 13 13
MAPK8 -0.033 0.17 -9999 0 -0.63 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.016 0.12 -9999 0 -0.46 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.075 0.15 -9999 0 -0.55 15 15
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.053 0.1 0.54 7 -10000 0 7
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.084 0.15 -10000 0 -0.34 90 90
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.078 -10000 0 -0.6 6 6
RhoA/GTP -0.054 0.11 -10000 0 -0.55 7 7
negative regulation of cAMP metabolic process -0.033 0.13 -10000 0 -0.29 55 55
GNAZ 0.012 0.032 -10000 0 -0.6 1 1
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.012 0.032 -10000 0 -0.6 1 1
S1PR5 -0.12 0.24 -10000 0 -0.55 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.034 0.14 -10000 0 -0.3 55 55
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.004 0.1 -10000 0 -0.6 11 11
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.057 0.25 5 -10000 0 5
RFC1 0.007 0.057 0.21 15 -10000 0 15
PRKDC 0.007 0.057 0.22 14 -10000 0 14
RIPK1 0.016 0.003 -10000 0 -10000 0 0
CASP7 -0.006 0.075 0.24 11 -0.31 6 17
FASLG/FAS/FADD/FAF1 -0.009 0.085 0.23 13 -0.31 10 23
MAP2K4 -0.005 0.12 -10000 0 -0.36 9 9
mol:ceramide -0.004 0.096 -10000 0 -0.39 7 7
GSN 0 0.071 0.25 4 -0.33 6 10
FASLG/FAS/FADD/FAF1/Caspase 8 -0.003 0.093 -10000 0 -0.34 10 10
FAS -0.009 0.1 -10000 0 -0.55 13 13
BID 0.003 0.084 0.3 11 -0.28 15 26
MAP3K1 0.008 0.091 0.21 9 -0.29 8 17
MAP3K7 0.012 0.004 -10000 0 -10000 0 0
RB1 0.006 0.06 0.22 14 -0.36 1 15
CFLAR 0.014 0.026 -10000 0 -0.47 1 1
HGF/MET -0.14 0.19 -10000 0 -0.36 141 141
ARHGDIB 0.004 0.065 0.22 14 -0.36 3 17
FADD 0.011 0.007 -10000 0 -10000 0 0
actin filament polymerization 0 0.07 0.33 6 -0.25 4 10
NFKB1 -0.04 0.067 -10000 0 -10000 0 0
MAPK8 -0.031 0.17 -10000 0 -0.42 41 41
DFFA 0.007 0.057 0.25 5 -10000 0 5
DNA fragmentation during apoptosis 0.007 0.057 0.25 5 -10000 0 5
FAS/FADD/MET -0.099 0.16 -10000 0 -0.34 108 108
CFLAR/RIP1 0.013 0.02 -10000 0 -0.32 1 1
FAIM3 -0.03 0.15 -10000 0 -0.53 30 30
FAF1 0.012 0.007 -10000 0 -10000 0 0
PARP1 0.006 0.059 0.25 5 -0.28 1 6
DFFB 0.007 0.057 0.25 5 -10000 0 5
CHUK -0.034 0.058 -10000 0 -10000 0 0
FASLG -0.031 0.13 -10000 0 -0.49 27 27
FAS/FADD 0.002 0.078 -10000 0 -0.4 13 13
HGF -0.069 0.19 -10000 0 -0.5 59 59
LMNA 0.004 0.06 0.23 5 -0.36 2 7
CASP6 0.005 0.063 0.25 5 -0.39 2 7
CASP10 0.011 0.007 -10000 0 -10000 0 0
CASP3 0.007 0.067 0.25 16 -10000 0 16
PTPN13 0.006 0.069 -10000 0 -0.58 5 5
CASP8 0.008 0.11 0.3 26 -0.33 15 41
IL6 -0.15 0.38 -10000 0 -1.3 31 31
MET -0.14 0.25 -10000 0 -0.54 101 101
ICAD/CAD 0.007 0.053 0.23 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.004 0.096 -10000 0 -0.4 7 7
activation of caspase activity by cytochrome c 0.003 0.084 0.3 11 -0.28 15 26
PAK2 0.007 0.057 0.25 5 -10000 0 5
BCL2 0.006 0.072 -10000 0 -0.6 5 5
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 0.007 0.066 -10000 0 -0.6 4 4
HSPA8 0.012 0.033 -10000 0 -0.6 1 1
SMAD3/SMAD4/ER alpha -0.028 0.11 0.22 3 -0.4 19 22
AKT1 0.009 0.023 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 48 48
NKX2-5 -0.087 0.2 -10000 0 -0.49 70 70
muscle cell differentiation 0.14 0.18 0.51 52 -10000 0 52
SMAD2-3/SMAD4/SP1 -0.006 0.11 -10000 0 -0.54 3 3
SMAD4 -0.016 0.065 -10000 0 -0.4 1 1
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.022 0.11 -10000 0 -0.37 21 21
SMAD3/SMAD4/VDR -0.034 0.12 -10000 0 -0.39 11 11
MYC -0.008 0.13 -10000 0 -0.57 17 17
CDKN2B -0.12 0.44 -10000 0 -1.4 38 38
AP1 -0.027 0.16 -10000 0 -0.62 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.044 0.057 -10000 0 -0.4 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.005 0.13 -10000 0 -0.38 20 20
SP3 0.016 0.006 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.017 0.1 -10000 0 -0.54 12 12
SMAD3/SMAD4/GR -0.01 0.061 -10000 0 -0.36 2 2
GATA3 -0.12 0.23 -10000 0 -0.56 77 77
SKI/SIN3/HDAC complex/NCoR1 0.046 0.031 -10000 0 -10000 0 0
MEF2C/TIF2 -0.077 0.18 -10000 0 -0.49 35 35
endothelial cell migration 0.22 0.49 1.4 53 -10000 0 53
MAX 0.023 0.019 -10000 0 -10000 0 0
RBBP7 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.002 -10000 0 -10000 0 0
RUNX2 -0.006 0.1 -10000 0 -0.52 14 14
RUNX3 -0.03 0.15 -10000 0 -0.54 29 29
RUNX1 -0.051 0.18 -10000 0 -0.53 44 44
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.023 0.019 -10000 0 -10000 0 0
VDR -0.061 0.19 -10000 0 -0.53 50 50
CDKN1A -0.056 0.3 -10000 0 -1.3 17 17
KAT2B 0.012 0.027 -10000 0 -0.48 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.027 0.12 -10000 0 -0.36 17 17
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.014 0.002 -10000 0 -10000 0 0
SERPINE1 -0.23 0.5 -10000 0 -1.4 53 53
SMAD3/SMAD4/ATF2 -0.028 0.084 -10000 0 -0.4 11 11
SMAD3/SMAD4/ATF3 -0.049 0.12 -10000 0 -0.38 33 33
SAP30 0.012 0.032 -10000 0 -0.6 1 1
Cbp/p300/PIAS3 0.013 0.06 -10000 0 -0.35 4 4
JUN -0.021 0.16 -10000 0 -0.61 12 12
SMAD3/SMAD4/IRF7 -0.036 0.097 -10000 0 -0.39 14 14
TFE3 0.008 0.029 -10000 0 -10000 0 0
COL1A2 -0.043 0.17 -10000 0 -0.47 39 39
mesenchymal cell differentiation 0.031 0.09 0.38 16 -10000 0 16
DLX1 -0.16 0.26 -10000 0 -0.54 113 113
TCF3 0.011 0.046 -10000 0 -0.6 2 2
FOS -0.085 0.22 -10000 0 -0.55 66 66
SMAD3/SMAD4/Max -0.01 0.061 -10000 0 -0.36 2 2
Cbp/p300/SNIP1 0.005 0.044 -10000 0 -0.36 4 4
ZBTB17 0.018 0.018 -10000 0 -10000 0 0
LAMC1 0.001 0.11 -10000 0 -0.48 12 12
TGIF2/HDAC complex/SMAD3/SMAD4 -0.023 0.078 -10000 0 -0.45 7 7
IRF7 -0.016 0.12 -10000 0 -0.51 21 21
ESR1 -0.015 0.13 -10000 0 -0.54 20 20
HNF4A -0.035 0.14 -10000 0 -0.48 31 31
MEF2C -0.058 0.17 -10000 0 -0.49 21 21
SMAD2-3/SMAD4 -0.034 0.073 -10000 0 -0.38 4 4
Cbp/p300/Src-1 0.009 0.049 -10000 0 -0.36 4 4
IGHV3OR16-13 -0.014 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.006 0.069 -10000 0 -0.58 5 5
CREBBP 0.014 0.012 -10000 0 -10000 0 0
SKIL 0.002 0.085 -10000 0 -0.6 7 7
HDAC1 0.011 0.046 -10000 0 -0.6 2 2
HDAC2 0.014 0.002 -10000 0 -10000 0 0
SNIP1 0.014 0.005 -10000 0 -10000 0 0
GCN5L2 -0.001 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.01 0.082 -10000 0 -0.38 4 4
MSG1/HSC70 -0.021 0.12 -10000 0 -0.37 38 38
SMAD2 -0.003 0.047 -10000 0 -10000 0 0
SMAD3 -0.006 0.06 -10000 0 -0.41 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.007 0.078 -10000 0 -0.4 3 3
SMAD2/SMAD2/SMAD4 -0.004 0.034 -10000 0 -10000 0 0
NCOR1 0.012 0.032 -10000 0 -0.6 1 1
NCOA2 -0.035 0.17 -10000 0 -0.6 29 29
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.13 0.19 -10000 0 -0.39 122 122
SMAD2-3/SMAD4/SP1/MIZ-1 0.004 0.11 -10000 0 -0.48 4 4
IFNB1 -0.01 0.098 -10000 0 -0.41 6 6
SMAD3/SMAD4/MEF2C -0.064 0.17 -10000 0 -0.47 24 24
CITED1 -0.04 0.16 -10000 0 -0.52 37 37
SMAD2-3/SMAD4/ARC105 -0.009 0.074 -10000 0 -0.47 1 1
RBL1 -0.011 0.12 -10000 0 -0.59 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.027 0.19 -10000 0 -0.54 39 39
RUNX1-3/PEBPB2 -0.062 0.14 -10000 0 -0.42 38 38
SMAD7 -0.009 0.14 -10000 0 -0.61 5 5
MYC/MIZ-1 -0.002 0.1 -10000 0 -0.42 15 15
SMAD3/SMAD4 -0.044 0.19 0.3 24 -0.42 46 70
IL10 -0.14 0.28 -10000 0 -0.62 79 79
PIASy/HDAC complex 0.016 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.007 -10000 0 -10000 0 0
CDK2 0.001 0.086 -10000 0 -0.53 9 9
IL5 -0.083 0.19 -10000 0 -0.5 34 34
CDK4 0.001 0.082 -10000 0 -0.48 10 10
PIAS4 0.016 0.013 -10000 0 -10000 0 0
ATF3 -0.036 0.16 -10000 0 -0.52 34 34
SMAD3/SMAD4/SP1 -0.008 0.1 -10000 0 -0.46 4 4
FOXG1 -0.011 0.12 -10000 0 -0.59 16 16
FOXO3 0.017 0.031 -10000 0 -10000 0 0
FOXO1 0.014 0.05 -10000 0 -0.42 3 3
FOXO4 0.016 0.041 -10000 0 -0.52 1 1
heart looping -0.058 0.16 -10000 0 -0.48 21 21
CEBPB -0.011 0.12 -10000 0 -0.58 14 14
SMAD3/SMAD4/DLX1 -0.12 0.17 -10000 0 -0.39 92 92
MYOD1 -0.17 0.26 -10000 0 -0.55 120 120
SMAD3/SMAD4/HNF4 -0.045 0.1 -10000 0 -0.35 21 21
SMAD3/SMAD4/GATA3 -0.12 0.19 -10000 0 -0.48 54 54
SnoN/SIN3/HDAC complex/NCoR1 0.002 0.084 -10000 0 -0.6 7 7
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.06 0.15 -10000 0 -0.44 31 31
SMAD3/SMAD4/SP1-3 0.01 0.097 -10000 0 -0.49 3 3
MED15 0.014 0 -10000 0 -10000 0 0
SP1 0.005 0.04 -10000 0 -10000 0 0
SIN3B 0.014 0.002 -10000 0 -10000 0 0
SIN3A 0.014 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.07 0.16 -10000 0 -0.4 26 26
ITGB5 0.021 0.11 -10000 0 -0.72 3 3
TGIF/SIN3/HDAC complex/CtBP 0.044 0.043 -10000 0 -0.45 1 1
SMAD3/SMAD4/AR -0.088 0.16 -10000 0 -0.4 65 65
AR -0.099 0.23 -10000 0 -0.57 70 70
negative regulation of cell growth -0.01 0.12 -10000 0 -0.44 14 14
SMAD3/SMAD4/MYOD -0.13 0.17 -10000 0 -0.42 76 76
E2F5 0.009 0.056 -10000 0 -0.6 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.009 0.098 -10000 0 -0.35 4 4
SMAD2-3/SMAD4/FOXO1-3a-4 -0.009 0.13 -10000 0 -0.37 29 29
TFDP1 0.014 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.026 0.16 -10000 0 -0.62 12 12
SMAD3/SMAD4/RUNX2 -0.031 0.09 -10000 0 -0.38 16 16
TGIF2 0.006 0.069 -10000 0 -0.58 5 5
TGIF1 -0.007 0.11 -10000 0 -0.53 14 14
ATF2 -0.003 0.1 -10000 0 -0.6 10 10
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR -0.002 0.099 -9999 0 -0.59 10 10
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.085 0.15 -9999 0 -0.37 50 50
CaM/Ca2+ -0.001 0.023 -9999 0 -0.45 1 1
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.048 0.14 -9999 0 -0.33 50 50
IQGAP1/CaM -0.007 0.052 -9999 0 -0.38 7 7
DAB1 -0.091 0.23 -9999 0 -0.58 65 65
IQGAP1 0.005 0.068 -9999 0 -0.52 6 6
PLA2G7 -0.033 0.16 -9999 0 -0.55 30 30
CALM1 0.012 0.032 -9999 0 -0.6 1 1
DYNLT1 0.011 0.046 -9999 0 -0.6 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.023 -9999 0 -0.44 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0.032 -9999 0 -0.6 1 1
CDK5R1 -0.021 0.14 -9999 0 -0.6 21 21
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.24 -9999 0 -0.57 73 73
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.21 -9999 0 -0.39 145 145
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.067 0.2 -9999 0 -0.6 26 26
MAP1B -0.001 0.017 -9999 0 -0.32 1 1
RAC1 -0.002 0.017 -9999 0 -10000 0 0
p35/CDK5 -0.044 0.16 -9999 0 -0.58 12 12
RELN -0.13 0.25 -9999 0 -0.54 96 96
PAFAH/LIS1 0 0.099 -9999 0 -0.36 18 18
LIS1/CLIP170 0.028 0.021 -9999 0 -0.36 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.079 0.13 -9999 0 -0.48 24 24
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.086 0.21 -9999 0 -0.7 24 24
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.08 0.21 -9999 0 -0.59 32 32
LIS1/IQGAP1 0.024 0.043 -9999 0 -0.36 2 2
RHOA -0.002 0.017 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0 -9999 0 -10000 0 0
PAFAH1B2 -0.01 0.12 -9999 0 -0.6 14 14
MAP1B/LIS1/Dynein heavy chain 0.027 0.011 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.099 0.16 -9999 0 -0.57 26 26
LRP8 0.012 0.032 -9999 0 -0.6 1 1
NDEL1/Katanin 60 -0.067 0.2 -9999 0 -0.6 26 26
P39/CDK5 -0.086 0.18 -9999 0 -0.54 23 23
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0 -9999 0 -10000 0 0
CDK5 -0.036 0.14 -9999 0 -0.3 50 50
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.016 -9999 0 -0.31 1 1
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.1 0.2 -9999 0 -0.37 101 101
RELN/VLDLR -0.084 0.14 -9999 0 -0.34 59 59
CDC42 -0.002 0.017 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.049 0.16 -10000 0 -0.72 15 15
HDAC1 0.009 0.046 -10000 0 -0.59 2 2
AES 0.014 0.004 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.004 0.076 -10000 0 -0.58 6 6
LRP6/FZD1 -0.005 0.039 -10000 0 -0.33 5 5
TLE1 0.014 0.004 -10000 0 -10000 0 0
AP1 -0.023 0.12 -10000 0 -0.3 44 44
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 -0.001 0.096 -10000 0 -0.6 9 9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.071 -10000 0 -10000 0 0
NICD/RBPSUH -0.022 0.12 -10000 0 -0.6 15 15
WIF1 -0.27 0.28 -10000 0 -0.54 189 189
NOTCH1 -0.026 0.13 -10000 0 -0.63 15 15
PSENEN 0.014 0 -10000 0 -10000 0 0
KREMEN2 -0.051 0.18 -10000 0 -0.52 45 45
DKK1 -0.12 0.23 -10000 0 -0.53 87 87
beta catenin/beta TrCP1 0.016 0.043 0.42 1 -10000 0 1
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 -0.002 0.045 0.21 2 -0.26 2 4
CtBP/CBP/TCF1/TLE1/AES 0.032 0.046 0.28 3 -0.27 2 5
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.087 0.22 -10000 0 -0.55 66 66
JUN 0.003 0.075 -10000 0 -0.5 8 8
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
CTNNB1 0.009 0.046 0.34 2 -10000 0 2
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 113 113
HNF1A 0.012 0.033 -10000 0 -0.6 1 1
CTBP1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.037 0.29 -10000 0 -1.4 15 15
NKD1 0 0.09 -10000 0 -0.56 9 9
FZD1 0.009 0.052 -10000 0 -0.48 4 4
NOTCH1 precursor/Deltex homolog 1 -0.027 0.13 -10000 0 -0.62 15 15
apoptosis -0.023 0.12 -10000 0 -0.3 44 44
Delta 1/NOTCHprecursor -0.047 0.16 -10000 0 -0.72 15 15
DLL1 -0.037 0.17 -10000 0 -0.6 30 30
PPARD 0.02 0.026 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.067 0.21 2 -0.5 3 5
DVL1 -0.021 0.025 -10000 0 -10000 0 0
CSNK2A1 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 119 119
LRP6 0.013 0.026 -10000 0 -0.48 1 1
CSNK1A1 0.014 0.003 -10000 0 -10000 0 0
NLK 0.016 0.016 -10000 0 -10000 0 0
CCND1 -0.026 0.24 -10000 0 -1.4 9 9
WNT1 -0.024 0.13 -10000 0 -0.48 26 26
Axin1/APC/beta catenin 0.016 0.063 0.34 2 -0.53 1 3
DKK2 -0.11 0.23 -10000 0 -0.54 80 80
NOTCH1 precursor/DVL1 -0.024 0.11 -10000 0 -0.57 15 15
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.009 0.049 -10000 0 -0.52 3 3
NOTCH/Deltex homolog 1 -0.029 0.13 -10000 0 -0.62 15 15
PPP2R5D -0.005 0.045 0.26 9 -10000 0 9
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.16 0.17 -10000 0 -0.38 99 99
RBPJ 0.014 0 -10000 0 -10000 0 0
CREBBP 0.017 0.005 -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 0.004 0.078 -10000 0 -0.6 6 6
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.011 0.11 0.43 7 -10000 0 7
IL27/IL27R/JAK1 -0.045 0.16 -10000 0 -0.55 8 8
TBX21 -0.067 0.22 -10000 0 -0.56 30 30
IL12B -0.001 0.051 -10000 0 -0.49 4 4
IL12A -0.012 0.1 -10000 0 -0.43 20 20
IL6ST -0.039 0.17 -10000 0 -0.61 31 31
IL27RA/JAK1 0.017 0.036 -10000 0 -10000 0 0
IL27 -0.016 0.11 -10000 0 -0.48 20 20
TYK2 0.014 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.055 0.12 -10000 0 -0.73 2 2
T-helper 2 cell differentiation 0.011 0.11 0.43 7 -10000 0 7
T cell proliferation during immune response 0.011 0.11 0.43 7 -10000 0 7
MAPKKK cascade -0.011 0.11 -10000 0 -0.43 7 7
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.011 0.037 -10000 0 -0.48 2 2
STAT1 -0.002 0.085 -10000 0 -0.48 11 11
IL12RB1 -0.034 0.16 -10000 0 -0.55 31 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.25 -10000 0 -0.54 48 48
IL27/IL27R/JAK2/TYK2 -0.011 0.11 -10000 0 -0.44 7 7
positive regulation of T cell mediated cytotoxicity -0.011 0.11 -10000 0 -0.43 7 7
STAT1 (dimer) -0.077 0.25 0.52 18 -0.66 14 32
JAK2 0.015 0.004 -10000 0 -10000 0 0
JAK1 0.013 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.004 0.11 -10000 0 -0.41 7 7
T cell proliferation -0.076 0.16 -10000 0 -0.5 13 13
IL12/IL12R/TYK2/JAK2 -0.007 0.095 -10000 0 -0.57 4 4
IL17A -0.055 0.12 -10000 0 -0.73 2 2
mast cell activation 0.011 0.11 0.43 7 -10000 0 7
IFNG 0 0.022 -10000 0 -0.089 4 4
T cell differentiation -0.004 0.005 -10000 0 -0.022 3 3
STAT3 (dimer) -0.003 0.1 -10000 0 -0.41 7 7
STAT5A (dimer) -0.01 0.12 -10000 0 -0.45 11 11
STAT4 (dimer) -0.098 0.17 -10000 0 -0.46 23 23
STAT4 -0.17 0.26 -10000 0 -0.54 124 124
T cell activation -0.009 0.007 0.061 2 -10000 0 2
IL27R/JAK2/TYK2 -0.018 0.097 -10000 0 -10000 0 0
GATA3 -0.14 0.39 -10000 0 -1.4 31 31
IL18 -0.021 0.11 -10000 0 -0.38 31 31
positive regulation of mast cell cytokine production -0.003 0.1 -10000 0 -0.4 7 7
IL27/EBI3 -0.023 0.13 -10000 0 -0.4 35 35
IL27RA 0.013 0.034 -10000 0 -10000 0 0
IL6 -0.13 0.24 -10000 0 -0.52 99 99
STAT5A 0.001 0.09 -10000 0 -0.6 8 8
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.001 0.02 -10000 0 -10000 0 0
IL1B -0.13 0.2 -10000 0 -0.39 128 128
EBI3 -0.016 0.13 -10000 0 -0.57 18 18
TNF -0.11 0.19 -10000 0 -0.39 109 109
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.042 0.17 -9999 0 -0.46 47 47
KLHL20 -0.028 0.058 -9999 0 -0.27 7 7
CYFIP2 0.008 0.055 -9999 0 -0.51 4 4
Rac1/GDP 0.003 0.12 -9999 0 -10000 0 0
ENAH -0.043 0.17 -9999 0 -0.46 47 47
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.013 0.026 -9999 0 -0.48 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.038 0.07 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.019 0.04 -9999 0 -0.18 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.1 0.16 -9999 0 -0.4 59 59
RAPGEF1 -0.02 0.15 -9999 0 -0.39 47 47
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.08 0.16 -9999 0 -0.48 47 47
CRK -0.031 0.16 -9999 0 -0.43 47 47
E-cadherin/gamma catenin/alpha catenin -0.09 0.15 -9999 0 -0.33 100 100
alphaE/beta7 Integrin -0.038 0.12 -9999 0 -0.39 36 36
IQGAP1 0.005 0.068 -9999 0 -0.52 6 6
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.022 -9999 0 -0.29 2 2
DLG1 -0.042 0.17 -9999 0 -0.46 47 47
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.05 -9999 0 -10000 0 0
MLLT4 0.012 0.032 -9999 0 -0.6 1 1
ARF6/GTP/NME1/Tiam1 0 0.018 -9999 0 -0.33 1 1
PI3K -0.035 0.064 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.11 0.18 -9999 0 -0.4 100 100
TIAM1 0.012 0.032 -9999 0 -0.6 1 1
E-cadherin(dimer)/Ca2+ -0.069 0.12 -9999 0 -0.31 47 47
AKT1 -0.02 0.036 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.13 0.25 -9999 0 -0.54 95 95
RhoA/GDP 0.003 0.12 -9999 0 -10000 0 0
actin cytoskeleton organization -0.021 0.043 -9999 0 -0.19 7 7
CDC42/GDP 0.003 0.12 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.037 0.11 -9999 0 -0.28 51 51
ITGB7 -0.041 0.17 -9999 0 -0.54 36 36
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.073 0.12 -9999 0 -0.32 47 47
E-cadherin/Ca2+/beta catenin/alpha catenin -0.071 0.12 -9999 0 -0.31 47 47
mol:GDP -0.008 0.13 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 -0.005 0.04 -9999 0 -0.31 6 6
JUP 0.001 0.086 -9999 0 -0.57 8 8
p120 catenin/RhoA/GDP -0.046 0.091 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.005 0.04 -9999 0 -0.31 6 6
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.008 0.065 -9999 0 -0.21 22 22
NME1 0.014 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.042 0.17 -9999 0 -0.46 47 47
regulation of cell-cell adhesion -0.034 0.062 -9999 0 -10000 0 0
WASF2 -0.009 0.021 -9999 0 -10000 0 0
Rap1/GTP -0.045 0.08 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.099 0.16 -9999 0 -0.39 63 63
CCND1 0.008 0.08 -9999 0 -0.26 22 22
VAV2 -0.025 0.16 -9999 0 -0.42 47 47
RAP1/GDP -0.043 0.085 -9999 0 -10000 0 0
adherens junction assembly -0.04 0.17 -9999 0 -0.45 47 47
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.061 0.17 -9999 0 -0.55 20 20
E-cadherin/beta catenin -0.073 0.14 -9999 0 -0.39 47 47
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.044 0.17 -9999 0 -0.46 47 47
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
Rac1/GTP -0.046 0.094 -9999 0 -0.46 7 7
E-cadherin/beta catenin/alpha catenin -0.083 0.14 -9999 0 -0.36 47 47
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.082 0.17 -9999 0 -0.5 47 47
Cellular roles of Anthrax toxin

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
ANTXR1 0.009 0.056 -10000 0 -0.6 3 3
ANTXR2 -0.001 0.089 -10000 0 -0.5 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.065 14 14
monocyte activation -0.16 0.26 -10000 0 -0.54 98 98
MAP2K2 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 -0.003 0.019 -10000 0 -0.32 1 1
MAP2K7 -0.002 0.01 -10000 0 -10000 0 0
MAP2K6 -0.003 0.02 -10000 0 -0.33 1 1
CYAA 0.006 0.055 -10000 0 -0.27 14 14
MAP2K4 -0.003 0.025 -10000 0 -0.32 2 2
IL1B -0.087 0.14 -10000 0 -0.28 128 128
Channel -0.011 0.055 -10000 0 -0.29 14 14
NLRP1 -0.004 0.023 -10000 0 -0.29 2 2
CALM1 0.012 0.032 -10000 0 -0.6 1 1
negative regulation of phagocytosis -0.004 0.032 -10000 0 -0.55 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.065 14 -10000 0 14
MAPK3 -0.002 0.01 -10000 0 -10000 0 0
MAPK1 -0.002 0.01 -10000 0 -10000 0 0
PGR -0.031 0.096 -10000 0 -0.33 33 33
PA/Cellular Receptors -0.012 0.061 -10000 0 -0.32 14 14
apoptosis -0.002 0.013 -10000 0 -0.065 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.007 0.054 -10000 0 -0.26 14 14
macrophage activation 0.019 0.012 -10000 0 -10000 0 0
TNF -0.15 0.25 -10000 0 -0.54 109 109
VCAM1 -0.16 0.27 -10000 0 -0.54 98 98
platelet activation -0.004 0.032 -10000 0 -0.55 1 1
MAPKKK cascade -0.014 0.019 0.17 2 -10000 0 2
IL18 -0.01 0.089 -10000 0 -0.29 31 31
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.065 14 14
LEF -0.002 0.013 -10000 0 -0.065 14 14
CASP1 -0.005 0.025 -10000 0 -0.26 2 2
mol:cAMP -0.004 0.032 -10000 0 -0.55 1 1
necrosis -0.002 0.013 -10000 0 -0.065 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.007 0.056 -10000 0 -0.27 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Syndecan-3-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
CTTN 0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.005 0.048 -9999 0 -0.84 1 1
Syndecan-3/Neurocan -0.02 0.084 -9999 0 -0.33 20 20
POMC -0.005 0.1 -9999 0 -0.53 13 13
EGFR -0.082 0.21 -9999 0 -0.55 62 62
Syndecan-3/EGFR -0.047 0.11 -9999 0 -0.32 35 35
AGRP 0.002 0.057 -9999 0 -0.48 5 5
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.014 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.024 0.15 -9999 0 -0.59 23 23
long-term memory -0.002 0.03 -9999 0 -0.56 1 1
Syndecan-3/IL8 -0.083 0.12 -9999 0 -0.31 46 46
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
limb bud formation -0.002 0.034 -9999 0 -0.63 1 1
MC4R -0.11 0.24 -9999 0 -0.56 78 78
SRC 0.014 0 -9999 0 -10000 0 0
PTN 0.007 0.061 -9999 0 -0.5 5 5
FGFR/FGF/Syndecan-3 -0.002 0.034 -9999 0 -0.64 1 1
neuron projection morphogenesis -0.02 0.082 -9999 0 -0.71 2 2
Syndecan-3/AgRP -0.005 0.042 -9999 0 -0.61 1 1
Syndecan-3/AgRP/MC4R -0.061 0.12 -9999 0 -0.3 53 53
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.002 0.035 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.082 0.12 -9999 0 -0.3 46 46
IL8 -0.16 0.26 -9999 0 -0.53 117 117
Syndecan-3/Fyn/Cortactin -0.002 0.031 -9999 0 -0.58 1 1
Syndecan-3/CASK -0.002 0.033 -9999 0 -0.61 1 1
alpha-MSH/MC4R -0.099 0.18 -9999 0 -0.41 87 87
Gamma Secretase 0 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.074 0.21 -9999 0 -0.56 56 56
GNB1/GNG2 -0.019 0.13 -9999 0 -0.42 18 18
mol:DAG -0.008 0.12 -9999 0 -0.47 8 8
PLCG1 -0.009 0.13 -9999 0 -0.49 8 8
YES1 -0.026 0.14 -9999 0 -0.44 19 19
FZD3 0.009 0.056 -9999 0 -0.6 3 3
FZD6 -0.012 0.11 -9999 0 -0.49 19 19
G protein -0.01 0.13 -9999 0 -0.49 8 8
MAP3K7 -0.11 0.16 -9999 0 -0.42 36 36
mol:Ca2+ -0.008 0.12 -9999 0 -0.45 8 8
mol:IP3 -0.008 0.12 -9999 0 -0.47 8 8
NLK -0.007 0.012 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.17 -9999 0 -0.46 36 36
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.035 0.14 -9999 0 -0.42 21 21
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.024 0.13 -9999 0 -0.41 18 18
GO:0007205 -0.008 0.12 -9999 0 -0.46 8 8
WNT6 -0.041 0.16 -9999 0 -0.53 37 37
WNT4 -0.04 0.16 -9999 0 -0.52 37 37
NFAT1/CK1 alpha -0.084 0.14 -9999 0 -0.47 27 27
GNG2 0.009 0.056 -9999 0 -0.6 3 3
WNT5A -0.012 0.12 -9999 0 -0.57 16 16
WNT11 -0.016 0.13 -9999 0 -0.54 20 20
CDC42 -0.017 0.13 -9999 0 -0.41 19 19
Signaling events mediated by PTP1B

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
PDGFRB 0.01 0.045 -10000 0 -0.48 3 3
Jak2/Leptin Receptor -0.01 0.11 0.2 16 -0.46 10 26
PTP1B/AKT1 -0.008 0.089 -10000 0 -0.36 7 7
FYN 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.017 0.098 -10000 0 -0.33 14 14
EGFR -0.083 0.22 -10000 0 -0.56 62 62
EGF/EGFR -0.094 0.17 -10000 0 -0.42 61 61
CSF1 -0.01 0.12 -10000 0 -0.6 14 14
AKT1 0.014 0.002 -10000 0 -10000 0 0
INSR 0.014 0.002 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.009 0.096 -10000 0 -0.39 8 8
Insulin Receptor/Insulin -0.027 0.063 -10000 0 -0.34 5 5
HCK -0.013 0.12 -10000 0 -0.53 18 18
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.008 0.093 -10000 0 -0.34 10 10
EGF -0.045 0.18 -10000 0 -0.56 37 37
YES1 0.011 0.046 -10000 0 -0.6 2 2
CAV1 -0.03 0.13 -10000 0 -0.39 23 23
TXN 0.011 0.027 -10000 0 -0.49 1 1
PTP1B/IRS1/GRB2 -0.004 0.087 -10000 0 -0.37 6 6
cell migration 0.017 0.098 0.33 14 -10000 0 14
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.018 0.14 -10000 0 -0.55 22 22
ITGA2B -0.043 0.17 -10000 0 -0.57 36 36
CSF1R -0.023 0.14 -10000 0 -0.57 23 23
Prolactin Receptor/Prolactin -0.017 0.1 -10000 0 -0.4 23 23
FGR 0.011 0.037 -10000 0 -0.48 2 2
PTP1B/p130 Cas -0.009 0.094 -10000 0 -0.33 12 12
Crk/p130 Cas -0.005 0.089 -10000 0 -0.36 7 7
DOK1 0 0.09 -10000 0 -0.36 8 8
JAK2 0 0.087 -10000 0 -0.35 9 9
Jak2/Leptin Receptor/Leptin -0.11 0.18 -10000 0 -0.45 68 68
PIK3R1 0.014 0 -10000 0 -10000 0 0
PTPN1 -0.017 0.099 -10000 0 -0.33 14 14
LYN 0.006 0.063 -10000 0 -0.48 6 6
CDH2 0.012 0.032 -10000 0 -0.6 1 1
SRC 0.011 0.039 -10000 0 -10000 0 0
ITGB3 -0.054 0.18 -10000 0 -0.51 47 47
CAT1/PTP1B -0.062 0.14 -10000 0 -0.39 32 32
CAPN1 0.015 0.002 -10000 0 -10000 0 0
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.021 0.059 -10000 0 -0.4 2 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.18 -10000 0 -0.45 70 70
negative regulation of transcription 0.001 0.087 -10000 0 -0.35 9 9
FCGR2A -0.035 0.16 -10000 0 -0.54 32 32
FER -0.023 0.15 -10000 0 -0.61 21 21
alphaIIb/beta3 Integrin -0.083 0.17 -10000 0 -0.4 78 78
BLK -0.095 0.21 -10000 0 -0.5 76 76
Insulin Receptor/Insulin/Shc -0.005 0.047 -10000 0 -0.31 8 8
RHOA 0.015 0.002 -10000 0 -10000 0 0
LEPR -0.001 0.097 -10000 0 -0.55 11 11
BCAR1 0.012 0.032 -10000 0 -0.6 1 1
p210 bcr-abl/Grb2 0.014 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.068 0.15 -10000 0 -0.42 35 35
PRL 0.002 0.025 -10000 0 -0.47 1 1
SOCS3 -0.15 0.38 -10000 0 -1.4 28 28
SPRY2 0.005 0.071 -10000 0 -0.5 7 7
Insulin Receptor/Insulin/IRS1 -0.001 0.037 -10000 0 -0.36 3 3
CSF1/CSF1R -0.035 0.15 -10000 0 -0.48 22 22
Ras protein signal transduction 0.021 0.03 -10000 0 -10000 0 0
IRS1 0.014 0 -10000 0 -10000 0 0
INS -0.006 0.06 -10000 0 -0.57 4 4
LEP -0.004 0.062 -10000 0 -0.48 6 6
STAT5B -0.004 0.088 -10000 0 -0.31 10 10
STAT5A -0.008 0.091 -10000 0 -0.31 12 12
GRB2 0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.098 -10000 0 -0.38 10 10
CSN2 0 0.041 -10000 0 -10000 0 0
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
LAT -0.046 0.16 -10000 0 -0.49 38 38
YBX1 0.021 0.032 -10000 0 -0.59 1 1
LCK -0.088 0.21 -10000 0 -0.53 68 68
SHC1 0.009 0.052 -10000 0 -0.48 4 4
NOX4 -0.066 0.19 -10000 0 -0.52 54 54
Signaling events mediated by HDAC Class III

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
EP300 0.007 0.064 -10000 0 -0.6 4 4
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.027 0.041 0.34 3 -10000 0 3
CDKN1A -0.059 0.18 -10000 0 -0.48 48 48
KAT2B 0.013 0.026 -10000 0 -0.48 1 1
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.005 0.048 0.46 4 -10000 0 4
FOXO1 0.009 0.052 -10000 0 -0.56 3 3
FOXO4 0.02 0.037 -10000 0 -0.3 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.069 0.2 -10000 0 -0.53 56 56
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.12 0.2 -10000 0 -0.39 120 120
PPARGC1A -0.017 0.13 -10000 0 -0.58 19 19
FHL2 -0.027 0.14 -10000 0 -0.52 28 28
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.014 0.037 -10000 0 -10000 0 0
HIST2H4A 0.027 0.042 -10000 0 -0.34 3 3
SIRT1/FOXO3a 0.015 0.044 0.29 4 -10000 0 4
SIRT1 0.017 0.047 0.2 14 -10000 0 14
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.012 0.042 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.003 0.068 -10000 0 -0.26 13 13
apoptosis -0.013 0.036 -10000 0 -10000 0 0
SIRT1/PGC1A -0.007 0.089 -10000 0 -0.36 19 19
p53/SIRT1 0.025 0.13 0.3 47 -0.42 11 58
SIRT1/FOXO4 0.012 0.05 -10000 0 -0.25 5 5
FOXO1/FHL2/SIRT1 -0.012 0.087 -10000 0 -0.27 30 30
HIST1H1E 0.009 0.067 -10000 0 -0.31 13 13
SIRT1/p300 0.009 0.06 -10000 0 -0.44 4 4
muscle cell differentiation 0.096 0.16 0.37 64 -10000 0 64
TP53 -0.002 0.12 -10000 0 -0.57 12 12
KU70/SIRT1/BAX 0.013 0.036 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.011 0.037 -10000 0 -0.48 2 2
HIV-1 Tat/SIRT1 -0.045 0.14 -10000 0 -0.37 56 56
ACSS2 0.03 0.025 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.096 0.16 -10000 0 -0.37 64 64
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.04 0.16 -10000 0 -0.52 10 10
UGCG -0.026 0.14 -10000 0 -0.66 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.038 0.16 -10000 0 -0.42 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.025 0.14 -10000 0 -0.65 16 16
mol:DAG -0.005 0.051 -10000 0 -0.97 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.07 0.12 -10000 0 -0.47 17 17
FRAP1 -0.028 0.18 -10000 0 -0.54 18 18
FOXO3 -0.021 0.17 -10000 0 -0.55 14 14
AKT1 -0.032 0.18 -10000 0 -0.48 28 28
GAB2 0.013 0.033 -10000 0 -0.61 1 1
SMPD1 0.004 0.036 -10000 0 -10000 0 0
SGMS1 0.002 0.05 -10000 0 -0.67 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.022 -10000 0 -0.39 1 1
CALM1 0.012 0.032 -10000 0 -0.6 1 1
cell proliferation -0.018 0.11 -10000 0 -0.3 33 33
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.023 0.026 -10000 0 -0.45 1 1
RPS6KB1 -0.003 0.063 -10000 0 -0.23 1 1
mol:sphingomyelin -0.005 0.051 -10000 0 -0.97 1 1
natural killer cell activation 0 0.002 -10000 0 -0.012 7 7
JAK3 -0.057 0.19 -10000 0 -0.53 49 49
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
MYC -0.04 0.24 -10000 0 -0.93 18 18
MYB -0.083 0.34 -10000 0 -1 34 34
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.041 0.17 -10000 0 -0.4 44 44
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.014 0.06 -10000 0 -0.28 1 1
mol:PI-3-4-5-P3 -0.039 0.17 -10000 0 -0.39 44 44
Rac1/GDP 0.028 0.021 -10000 0 -0.34 1 1
T cell proliferation -0.037 0.18 -10000 0 -0.48 27 27
SHC1 0.009 0.052 -10000 0 -0.48 4 4
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.02 -10000 0 -0.05 48 48
PRKCZ -0.04 0.18 -10000 0 -0.51 27 27
NF kappa B1 p50/RelA -0.064 0.12 -10000 0 -0.49 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.054 0.17 -10000 0 -0.42 46 46
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.069 0.19 -10000 0 -0.51 55 55
IL2RB -0.097 0.22 -10000 0 -0.53 76 76
TERT -0.079 0.2 -10000 0 -0.56 55 55
E2F1 -0.025 0.14 -10000 0 -0.42 34 34
SOS1 0.014 0.003 -10000 0 -10000 0 0
RPS6 0.013 0.026 -10000 0 -0.48 1 1
mol:cAMP 0 0.01 0.024 48 -10000 0 48
PTPN11 0.014 0.004 -10000 0 -10000 0 0
IL2RG -0.034 0.16 -10000 0 -0.51 35 35
actin cytoskeleton organization -0.037 0.18 -10000 0 -0.48 27 27
GRB2 0.014 0.003 -10000 0 -10000 0 0
IL2 0.003 0.004 -10000 0 -10000 0 0
PIK3CA 0.015 0.033 -10000 0 -0.61 1 1
Rac1/GTP 0.032 0.025 -10000 0 -0.33 1 1
LCK -0.085 0.21 -10000 0 -0.53 68 68
BCL2 -0.015 0.17 -10000 0 -0.62 13 13
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.05 -10000 0 -0.58 2 2
AES 0.01 0.022 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.002 0.04 -10000 0 -0.33 5 5
SMAD4 0.014 0 -10000 0 -10000 0 0
DKK2 -0.11 0.23 -10000 0 -0.54 80 80
TLE1 0.009 0.023 0.2 1 -10000 0 1
MACF1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.062 0.085 -10000 0 -10000 0 0
WIF1 -0.27 0.28 -10000 0 -0.54 189 189
beta catenin/RanBP3 0.019 0.11 0.4 23 -10000 0 23
KREMEN2 -0.051 0.18 -10000 0 -0.52 45 45
DKK1 -0.12 0.23 -10000 0 -0.53 87 87
beta catenin/beta TrCP1 0.067 0.08 -10000 0 -10000 0 0
FZD1 0.009 0.051 -10000 0 -0.48 4 4
AXIN2 -0.001 0.1 -10000 0 -0.84 3 3
AXIN1 0.015 0.001 -10000 0 -10000 0 0
RAN 0.014 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.025 0.036 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.051 0.3 2 -10000 0 2
Axin1/APC/GSK3 0.008 0.036 0.26 3 -10000 0 3
Axin1/APC/GSK3/beta catenin/Macf1 0.054 0.065 -10000 0 -10000 0 0
HNF1A 0.005 0.04 -10000 0 -0.61 1 1
CTBP1 0.007 0.025 -10000 0 -10000 0 0
MYC -0.05 0.3 -10000 0 -1.5 15 15
RANBP3 0.014 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 113 113
NKD1 0 0.09 -10000 0 -0.56 9 9
TCF4 0.005 0.038 -10000 0 -0.56 1 1
TCF3 0.004 0.046 -10000 0 -0.54 2 2
WNT1/LRP6/FZD1/Axin1 -0.018 0.069 -10000 0 -0.49 1 1
Ran/GTP 0.002 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.034 0.13 0.5 21 -10000 0 21
LEF1 0 0.061 -10000 0 -0.48 5 5
DVL1 0.06 0.046 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.086 0.08 -10000 0 -0.41 3 3
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 119 119
LRP6 0.013 0.026 -10000 0 -0.48 1 1
CSNK1A1 0.009 0.025 -10000 0 -10000 0 0
NLK 0.011 0.038 -10000 0 -0.5 2 2
CCND1 -0.038 0.25 -10000 0 -1.5 9 9
WNT1 -0.024 0.13 -10000 0 -0.48 26 26
GSK3A 0.015 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.049 -10000 0 -0.52 3 3
PPP2R5D 0.041 0.047 0.3 9 -10000 0 9
APC 0.021 0.075 -10000 0 -0.38 2 2
WNT1/LRP6/FZD1 0.097 0.1 0.24 79 -10000 0 79
CREBBP 0.007 0.024 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.018 0.068 -10000 0 -0.36 3 3
epithelial cell differentiation -0.041 0.085 -10000 0 -0.43 6 6
ITCH 0.019 0.013 -10000 0 -10000 0 0
WWP1 0.025 0.05 -10000 0 -10000 0 0
FYN 0.014 0 -10000 0 -10000 0 0
EGFR -0.082 0.21 -10000 0 -0.55 62 62
PRL 0 0.026 -10000 0 -0.48 1 1
neuron projection morphogenesis -0.027 0.14 -10000 0 -0.42 6 6
PTPRZ1 0.001 0.086 -10000 0 -0.57 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.085 0.12 -10000 0 -0.43 10 10
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.073 0.16 -10000 0 -0.34 81 81
ADAM17 0.01 0.072 -10000 0 -0.6 5 5
ErbB4/ErbB4 0.022 0.064 -10000 0 -0.42 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.004 0.12 -10000 0 -0.38 28 28
NCOR1 0.012 0.032 -10000 0 -0.6 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.061 0.15 -10000 0 -0.38 18 18
GRIN2B -0.15 0.21 -10000 0 -0.51 60 60
ErbB4/ErbB2/betacellulin -0.033 0.14 -10000 0 -0.42 17 17
STAT1 -0.001 0.085 -10000 0 -0.48 11 11
HBEGF 0.005 0.068 -10000 0 -0.48 7 7
PRLR -0.02 0.14 -10000 0 -0.55 22 22
E4ICDs/ETO2 0.019 0.068 -10000 0 -0.38 4 4
axon guidance -0.013 0.077 -10000 0 -10000 0 0
NEDD4 0.008 0.074 -10000 0 -0.51 7 7
Prolactin receptor/Prolactin receptor/Prolactin -0.025 0.098 -10000 0 -0.4 23 23
CBFA2T3 0.006 0.066 -10000 0 -0.55 5 5
ErbB4/ErbB2/HBEGF 0.022 0.078 -10000 0 -0.36 7 7
MAPK3 -0.036 0.14 -10000 0 -0.44 6 6
STAT1 (dimer) 0.015 0.074 -10000 0 -0.39 3 3
MAPK1 -0.036 0.14 -10000 0 -0.44 6 6
JAK2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.066 0.16 -10000 0 -0.39 22 22
NRG1 -0.11 0.2 -10000 0 -0.41 114 114
NRG3 -0.031 0.16 -10000 0 -0.6 27 27
NRG2 0.012 0.032 -10000 0 -0.6 1 1
NRG4 -0.049 0.17 -10000 0 -0.5 44 44
heart development -0.013 0.077 -10000 0 -10000 0 0
neural crest cell migration -0.065 0.16 -10000 0 -0.39 22 22
ERBB2 0.014 0.072 -10000 0 -0.37 12 12
WWOX/E4ICDs 0.023 0.054 -10000 0 -0.36 1 1
SHC1 0.009 0.052 -10000 0 -0.48 4 4
ErbB4/EGFR/neuregulin 4 -0.058 0.16 -10000 0 -0.48 25 25
apoptosis 0.041 0.12 0.42 28 -10000 0 28
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.022 0.059 -10000 0 -0.42 2 2
ErbB4/ErbB2/epiregulin 0.007 0.085 -10000 0 -0.38 8 8
ErbB4/ErbB4/betacellulin/betacellulin -0.041 0.14 -10000 0 -0.37 41 41
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.028 0.079 -10000 0 -0.47 4 4
MDM2 0.026 0.059 -10000 0 -0.36 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.092 0.14 -10000 0 -0.39 11 11
STAT5A -0.011 0.092 -10000 0 -0.44 6 6
ErbB4/EGFR/neuregulin 1 beta -0.11 0.2 -10000 0 -0.5 39 39
DLG4 0.006 0.063 -10000 0 -0.48 6 6
GRB2/SHC -0.004 0.035 -10000 0 -0.33 4 4
E4ICDs/TAB2/NCoR1 -0.013 0.044 -10000 0 -0.4 2 2
STAT5A (dimer) -0.043 0.09 -10000 0 -0.46 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.005 0.071 -10000 0 -10000 0 0
LRIG1 -0.004 0.1 -10000 0 -0.6 11 11
EREG -0.009 0.098 -10000 0 -0.48 15 15
BTC -0.088 0.22 -10000 0 -0.55 65 65
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.013 0.077 -10000 0 -10000 0 0
ERBB4 0.022 0.064 -10000 0 -0.42 1 1
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.033 0.13 -10000 0 -0.61 17 17
GRB2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.008 0.11 -10000 0 -0.39 13 13
glial cell differentiation 0.013 0.044 0.39 2 -10000 0 2
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.1 0.18 -10000 0 -0.51 30 30
Ceramide signaling pathway

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
SPHK2 -0.005 0.1 -10000 0 -0.34 30 30
MAP4K4 -0.021 0.12 -10000 0 -0.43 12 12
BAG4 -0.006 0.11 -10000 0 -0.6 12 12
PKC zeta/ceramide -0.01 0.069 0.16 3 -0.27 15 18
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.55 32 32
BAX 0.006 0.025 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.013 -10000 0 -10000 0 0
BAD 0.004 0.047 0.16 6 -10000 0 6
SMPD1 -0.024 0.087 -10000 0 -0.2 49 49
RB1 0.003 0.051 0.16 6 -0.41 1 7
FADD/Caspase 8 -0.012 0.12 -10000 0 -0.41 14 14
MAP2K4 0.009 0.051 -10000 0 -0.24 4 4
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.011 0.044 -10000 0 -10000 0 0
EGF -0.044 0.17 -10000 0 -0.56 37 37
mol:ceramide -0.006 0.05 0.14 28 -10000 0 28
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.005 0.1 -10000 0 -0.34 30 30
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.002 0.051 0.16 6 -0.41 1 7
cell proliferation 0.001 0.085 -10000 0 -0.4 9 9
BID -0.009 0.09 -10000 0 -0.36 9 9
MAP3K1 0.002 0.05 0.16 6 -0.25 2 8
EIF2A 0.014 0.058 -10000 0 -0.29 6 6
TRADD 0.011 0.041 -10000 0 -0.54 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.023 0.042 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.042 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.002 0.044 0.15 5 -10000 0 5
FADD -0.02 0.12 -10000 0 -0.45 11 11
KSR1 0.004 0.047 0.17 5 -10000 0 5
MAPK8 0 0.071 0.17 2 -0.24 18 20
PRKRA 0.004 0.047 0.16 6 -10000 0 6
PDGFA -0.027 0.14 -10000 0 -0.49 30 30
TRAF2 0.014 0 -10000 0 -10000 0 0
IGF1 -0.007 0.11 -10000 0 -0.55 14 14
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.05 0.14 28 -10000 0 28
CTSD 0.013 0.026 -10000 0 -0.48 1 1
regulation of nitric oxide biosynthetic process -0.001 0.017 -10000 0 -0.33 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.003 0.092 -10000 0 -0.44 9 9
PRKCD -0.015 0.13 -10000 0 -0.6 17 17
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.005 0.1 -10000 0 -0.34 30 30
RelA/NF kappa B1 -0.001 0.017 -10000 0 -0.33 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.033 0.15 -10000 0 -0.52 32 32
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.03 0.12 -10000 0 -0.48 11 11
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -10000 0 -0.34 120 120
mol:Sphingosine-1-phosphate -0.005 0.1 -10000 0 -0.34 30 30
MAP2K1 0.018 0.044 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS 0.008 0.039 0.19 4 -10000 0 4
TNFRSF1A 0.005 0.068 -10000 0 -0.52 6 6
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
TNFR1A/BAG4 -0.02 0.093 -10000 0 -0.44 17 17
EIF2AK2 0.006 0.061 -10000 0 -0.31 6 6
TNF-alpha/TNFR1A/FAN -0.099 0.15 -10000 0 -0.32 113 113
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.083 -10000 0 -0.34 6 6
MAP2K2 0.019 0.042 -10000 0 -10000 0 0
SMPD3 -0.046 0.13 -10000 0 -0.38 28 28
TNF -0.15 0.25 -10000 0 -0.54 109 109
PKC zeta/PAR4 -0.048 0.14 -10000 0 -0.4 44 44
mol:PHOSPHOCHOLINE 0.004 0.074 0.2 30 -10000 0 30
NF kappa B1/RelA/I kappa B alpha -0.033 0.097 -10000 0 -0.61 3 3
AIFM1 0.008 0.039 0.19 4 -10000 0 4
BCL2 0.006 0.072 -10000 0 -0.6 5 5
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.019 0.13 -10000 0 -0.54 22 22
positive regulation of NF-kappaB transcription factor activity -0.034 0.11 -10000 0 -0.37 34 34
MAP2K4 0.027 0.068 -10000 0 -0.34 2 2
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.012 0.032 -10000 0 -0.6 1 1
TNFRSF10A -0.029 0.15 -10000 0 -0.56 27 27
SMPD1 0.009 0.049 -10000 0 -0.22 11 11
IKBKG 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.003 0.092 -10000 0 -0.5 12 12
TRAIL/TRAILR2 -0.024 0.094 -10000 0 -0.38 23 23
TRAIL/TRAILR3 -0.048 0.13 -10000 0 -0.4 44 44
TRAIL/TRAILR1 -0.053 0.14 -10000 0 -0.41 47 47
TRAIL/TRAILR4 -0.035 0.11 -10000 0 -0.37 34 34
TRAIL/TRAILR1/DAP3/GTP -0.04 0.1 -10000 0 -0.31 47 47
IKK complex -0.012 0.031 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0 0.097 -10000 0 -0.38 22 22
MAP3K1 0.021 0.067 -10000 0 -0.28 1 1
TRAILR4 (trimer) -0.003 0.092 -10000 0 -0.5 12 12
TRADD 0.011 0.041 -10000 0 -0.54 2 2
TRAILR1 (trimer) -0.028 0.15 -10000 0 -0.56 27 27
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.086 -10000 0 -0.27 2 2
CFLAR 0.013 0.026 -10000 0 -0.48 1 1
MAPK1 0 0.097 -10000 0 -0.38 22 22
TRAIL/TRAILR1/FADD/TRADD/RIP -0.037 0.095 -10000 0 -0.31 31 31
mol:ceramide 0.009 0.049 -10000 0 -0.22 11 11
FADD 0.014 0 -10000 0 -10000 0 0
MAPK8 0.025 0.088 -10000 0 -0.37 7 7
TRAF2 0.014 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.023 0.14 -10000 0 -0.53 25 25
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.044 0.12 -10000 0 -0.34 47 47
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.023 0.089 0.28 1 -0.36 12 13
JNK cascade -0.034 0.11 -10000 0 -0.37 34 34
TRAIL (trimer) -0.019 0.13 -10000 0 -0.54 22 22
TNFRSF10C -0.023 0.14 -10000 0 -0.53 25 25
TRAIL/TRAILR1/DAP3/GTP/FADD -0.036 0.097 -10000 0 -0.32 30 30
TRAIL/TRAILR2/FADD -0.02 0.078 -10000 0 -0.32 23 23
cell death 0.009 0.049 -10000 0 -0.22 11 11
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.026 0.059 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.012 0.032 -10000 0 -0.6 1 1
CASP8 -0.004 0.058 -10000 0 -0.81 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.017 0.065 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.018 0.087 -9999 0 -0.38 19 19
PDGFRB 0.009 0.045 -9999 0 -0.49 3 3
SPHK1 -0.041 0.14 -9999 0 -0.79 12 12
mol:S1P -0.04 0.13 -9999 0 -0.66 13 13
S1P1/S1P/Gi -0.023 0.16 -9999 0 -0.38 46 46
GNAO1 0.002 0.079 -9999 0 -0.61 6 6
PDGFB-D/PDGFRB/PLCgamma1 -0.012 0.15 -9999 0 -0.54 11 11
PLCG1 -0.016 0.16 -9999 0 -0.55 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.045 -9999 0 -0.49 3 3
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 -0.006 0.11 -9999 0 -0.6 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.002 0.077 -9999 0 -0.32 19 19
S1P1/S1P -0.049 0.12 -9999 0 -0.48 19 19
negative regulation of cAMP metabolic process -0.022 0.16 -9999 0 -0.37 46 46
MAPK3 -0.041 0.22 -9999 0 -0.55 46 46
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.004 0.069 -9999 0 -0.52 6 6
PLCB2 -0.017 0.14 -9999 0 -0.48 20 20
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.041 0.097 -9999 0 -0.43 16 16
receptor internalization -0.047 0.11 -9999 0 -0.44 20 20
PTGS2 -0.1 0.36 -9999 0 -1 46 46
Rac1/GTP -0.041 0.097 -9999 0 -0.43 16 16
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA -0.007 0.098 -9999 0 -0.48 15 15
negative regulation of T cell proliferation -0.022 0.16 -9999 0 -0.37 46 46
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.033 -9999 0 -0.61 1 1
MAPK1 -0.041 0.22 -9999 0 -0.55 46 46
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.14 -9999 0 -0.51 16 16
ABCC1 0.011 0.037 -9999 0 -0.49 2 2
TCGA08_rtk_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
PDGFRA -0.059 0.2 -10000 0 -0.58 45 45
HRAS 0.013 0.026 -10000 0 -0.48 1 1
EGFR -0.082 0.21 -10000 0 -0.55 62 62
AKT 0.019 0.051 -10000 0 -0.38 4 4
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
FOXO1 0.009 0.052 -10000 0 -0.56 3 3
AKT3 0.006 0.072 -10000 0 -0.6 5 5
FOXO4 0.012 0.032 -10000 0 -0.6 1 1
MET -0.14 0.25 -10000 0 -0.54 101 101
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
PIK3CB 0.014 0 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
PIK3CG -0.061 0.19 -10000 0 -0.53 51 51
PIK3R3 0.013 0.026 -10000 0 -0.48 1 1
PIK3R2 0.014 0 -10000 0 -10000 0 0
NF1 0.009 0.056 -10000 0 -0.6 3 3
RAS -0.052 0.11 0.23 1 -0.29 36 37
ERBB2 0.005 0.068 -10000 0 -0.48 7 7
proliferation/survival/translation -0.008 0.054 0.22 8 -10000 0 8
PI3K -0.045 0.11 -10000 0 -0.26 50 50
PIK3R1 0.014 0 -10000 0 -10000 0 0
KRAS 0.013 0.026 -10000 0 -0.48 1 1
FOXO 0.029 0.03 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
PTEN 0.014 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.03 0.11 -10000 0 -0.26 54 54
epithelial cell differentiation -0.068 0.12 -10000 0 -0.3 47 47
CYFIP2 0.008 0.055 -10000 0 -0.51 4 4
ENAH 0.004 0.1 -10000 0 -0.37 1 1
EGFR -0.082 0.21 -10000 0 -0.55 62 62
EPHA2 -0.018 0.12 -10000 0 -0.49 23 23
MYO6 -0.033 0.13 -10000 0 -10000 0 0
CTNNB1 0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.003 0.031 -10000 0 -0.36 1 1
AQP5 -0.14 0.19 -10000 0 -0.52 54 54
CTNND1 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.032 0.12 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.036 0.13 -10000 0 -0.58 1 1
EGF -0.044 0.17 -10000 0 -0.56 37 37
NCKAP1 0.014 0 -10000 0 -10000 0 0
AQP3 -0.085 0.14 -10000 0 -0.53 19 19
cortical microtubule organization -0.068 0.12 -10000 0 -0.3 47 47
GO:0000145 -0.031 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.069 0.12 -10000 0 -0.31 47 47
MLLT4 0.012 0.032 -10000 0 -0.6 1 1
ARF6/GDP -0.061 0.096 -10000 0 -0.41 6 6
ARF6 0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.068 -10000 0 -0.41 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.032 0.12 -10000 0 -0.38 1 1
PVRL2 0.011 0.041 -10000 0 -0.54 2 2
ZYX -0.037 0.13 -10000 0 -10000 0 0
ARF6/GTP -0.016 0.061 -10000 0 -0.53 1 1
CDH1 -0.13 0.25 -10000 0 -0.54 95 95
EGFR/EGFR/EGF/EGF -0.13 0.16 -10000 0 -0.52 31 31
RhoA/GDP -0.063 0.11 -10000 0 -10000 0 0
actin cytoskeleton organization -0.028 0.12 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
IGF1R 0.014 0 -10000 0 -10000 0 0
IGF1 -0.007 0.11 -10000 0 -0.55 14 14
DIAPH1 0.001 0.04 -10000 0 -0.68 1 1
Wnt receptor signaling pathway 0.068 0.12 0.3 47 -10000 0 47
RHOA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.061 0.097 -10000 0 -0.41 6 6
CTNNA1 0.014 0 -10000 0 -10000 0 0
VCL -0.029 0.13 -10000 0 -10000 0 0
EFNA1 0.011 0.037 -10000 0 -0.48 2 2
LPP -0.045 0.14 -10000 0 -0.43 4 4
Ephrin A1/EPHA2 -0.073 0.11 -10000 0 -0.46 5 5
SEC6/SEC8 -0.055 0.097 -10000 0 -0.48 3 3
MGAT3 -0.037 0.13 -10000 0 -0.59 1 1
HGF/MET -0.16 0.17 -10000 0 -0.49 49 49
HGF -0.069 0.19 -10000 0 -0.5 59 59
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.03 0.11 -10000 0 -0.26 54 54
actin cable formation 0.016 0.1 -10000 0 -0.33 2 2
KIAA1543 -0.063 0.17 -10000 0 -0.54 17 17
KIFC3 -0.034 0.13 -10000 0 -0.59 1 1
NCK1 0.012 0.032 -10000 0 -0.6 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ACTN1 -0.048 0.14 -10000 0 -0.46 4 4
NCK1/GIT1 -0.001 0.023 -10000 0 -0.44 1 1
mol:GDP -0.068 0.12 -10000 0 -0.3 47 47
EXOC4 0.014 0 -10000 0 -10000 0 0
STX4 -0.033 0.13 -10000 0 -10000 0 0
PIP5K1C -0.033 0.13 -10000 0 -10000 0 0
LIMA1 0.002 0.085 -10000 0 -0.6 7 7
ABI1 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.006 0.11 -10000 0 -0.37 4 4
adherens junction assembly -0.043 0.16 -10000 0 -0.51 17 17
IGF-1R heterotetramer/IGF1 -0.069 0.12 -10000 0 -0.56 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.037 -10000 0 -0.4 3 3
MET -0.14 0.25 -10000 0 -0.54 101 101
PLEKHA7 -0.039 0.14 -10000 0 -0.57 3 3
mol:GTP -0.018 0.067 -10000 0 -0.4 3 3
establishment of epithelial cell apical/basal polarity -0.001 0.12 -10000 0 -0.45 3 3
cortical actin cytoskeleton stabilization -0.03 0.11 -10000 0 -0.26 54 54
regulation of cell-cell adhesion -0.028 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.03 0.11 -10000 0 -0.26 54 54
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.009 0.12 -10000 0 -0.4 13 13
CRKL 0.021 0.11 -10000 0 -0.42 13 13
HRAS 0.002 0.14 -10000 0 -0.45 13 13
mol:PIP3 0.003 0.099 -10000 0 -0.37 14 14
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.01 0.045 -10000 0 -0.48 3 3
GAB1 0.014 0.11 -10000 0 -0.44 14 14
FOXO3 0.026 0.097 -10000 0 -0.37 11 11
AKT1 0.019 0.1 -10000 0 -0.39 13 13
BAD 0.026 0.097 -10000 0 -0.37 11 11
megakaryocyte differentiation 0.003 0.13 -10000 0 -0.38 27 27
GSK3B 0.026 0.097 -10000 0 -0.37 11 11
RAF1 0.013 0.12 -10000 0 -0.37 11 11
SHC1 0.009 0.052 -10000 0 -0.48 4 4
STAT3 0.015 0.11 -10000 0 -0.41 14 14
STAT1 0.01 0.22 -10000 0 -0.92 16 16
HRAS/SPRED1 0.01 0.11 -10000 0 -0.38 10 10
cell proliferation 0.007 0.12 -10000 0 -0.4 22 22
PIK3CA 0.013 0.032 -10000 0 -0.6 1 1
TEC -0.004 0.1 -10000 0 -0.54 12 12
RPS6KB1 0.015 0.11 -10000 0 -0.36 21 21
HRAS/SPRED2 0.009 0.12 -10000 0 -0.38 12 12
LYN/TEC/p62DOK -0.035 0.11 -10000 0 -0.45 17 17
MAPK3 0.025 0.088 -10000 0 -0.27 6 6
STAP1 -0.003 0.13 -10000 0 -0.41 20 20
GRAP2 -0.049 0.17 -10000 0 -0.52 43 43
JAK2 -0.045 0.17 -10000 0 -0.79 14 14
STAT1 (dimer) 0.011 0.22 -10000 0 -0.9 16 16
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.056 0.12 -10000 0 -0.44 20 20
actin filament polymerization 0.008 0.12 -10000 0 -0.38 21 21
LYN 0.006 0.063 -10000 0 -0.48 6 6
STAP1/STAT5A (dimer) -0.004 0.17 -10000 0 -0.63 19 19
PIK3R1 0.014 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.032 0.097 -10000 0 -0.39 11 11
PI3K 0.024 0.1 -10000 0 -0.4 12 12
PTEN 0.014 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.002 0.26 -10000 0 -1.2 13 13
MAPK8 0.006 0.13 -10000 0 -0.41 22 22
STAT3 (dimer) 0.015 0.11 -10000 0 -0.41 14 14
positive regulation of transcription 0.026 0.076 -10000 0 -0.24 2 2
mol:GDP -0.062 0.12 -10000 0 -0.43 22 22
PIK3C2B 0.01 0.12 -10000 0 -0.4 17 17
CBL/CRKL 0.029 0.1 -10000 0 -0.39 13 13
FER -0.003 0.15 -10000 0 -0.44 28 28
SH2B3 0.014 0.11 -10000 0 -0.41 14 14
PDPK1 0.011 0.097 -10000 0 -0.36 13 13
SNAI2 -0.002 0.13 -10000 0 -0.4 23 23
positive regulation of cell proliferation 0.012 0.18 -10000 0 -0.72 16 16
KITLG 0 0.11 -10000 0 -0.6 11 11
cell motility 0.012 0.18 -10000 0 -0.72 16 16
PTPN6 -0.012 0.096 -10000 0 -0.53 12 12
EPOR 0.039 0.077 -10000 0 -10000 0 0
STAT5A (dimer) 0.007 0.16 -10000 0 -0.63 17 17
SOCS1 -0.034 0.15 -10000 0 -0.51 34 34
cell migration 0.036 0.16 0.37 47 -10000 0 47
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.008 0.1 -10000 0 -0.48 16 16
VAV1 -0.022 0.14 -10000 0 -0.56 23 23
GRB10 0.014 0.11 -10000 0 -0.4 15 15
PTPN11 0.012 0.005 -10000 0 -10000 0 0
SCF/KIT 0.007 0.11 0.23 5 -0.38 22 27
GO:0007205 -0.002 0.006 -10000 0 -10000 0 0
MAP2K1 0.021 0.096 -10000 0 -0.29 9 9
CBL 0.014 0 -10000 0 -10000 0 0
KIT 0 0.25 -10000 0 -1.3 12 12
MAP2K2 0.022 0.096 -10000 0 -0.29 10 10
SHC/Grb2/SOS1 -0.025 0.089 -10000 0 -0.4 13 13
STAT5A 0.006 0.17 -10000 0 -0.65 17 17
GRB2 0.014 0 -10000 0 -10000 0 0
response to radiation -0.001 0.13 -10000 0 -0.39 23 23
SHC/GRAP2 -0.047 0.13 -10000 0 -0.38 45 45
PTPRO 0.002 0.13 -10000 0 -0.39 27 27
SH2B2 0.007 0.12 -10000 0 -0.38 21 21
DOK1 0.012 0.032 -10000 0 -0.6 1 1
MATK -0.037 0.16 -10000 0 -0.37 47 47
CREBBP 0.039 0.012 -10000 0 -10000 0 0
BCL2 0.026 0.18 -10000 0 -1.4 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.014 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.016 -10000 0 -10000 0 0
DOCK1 0.009 0.056 -10000 0 -0.6 3 3
ITGA4 -0.048 0.18 -10000 0 -0.53 42 42
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.08 0.17 -10000 0 -0.44 67 67
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.037 0.1 -10000 0 -0.38 19 19
alpha4/beta7 Integrin/Paxillin -0.03 0.14 -10000 0 -0.37 44 44
lamellipodium assembly 0.003 0.041 -10000 0 -0.38 1 1
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
PI3K -0.001 0.023 -10000 0 -0.44 1 1
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.014 0 -10000 0 -10000 0 0
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.076 -10000 0 -0.42 2 2
cell adhesion -0.03 0.085 -10000 0 -0.31 19 19
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.1 -10000 0 -0.34 19 19
ITGB1 0.011 0.037 -10000 0 -0.48 2 2
ITGB7 -0.041 0.17 -10000 0 -0.54 36 36
ARF6/GDP 0.006 0.016 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.075 0.17 -10000 0 -0.32 88 88
p130Cas/Crk/Dock1 -0.004 0.038 -10000 0 -0.36 4 4
VCAM1 -0.14 0.26 -10000 0 -0.57 97 97
alpha4/beta1 Integrin/Paxillin/Talin 0.009 0.099 -10000 0 -0.32 19 19
alpha4/beta1 Integrin/Paxillin/GIT1 0.009 0.099 -10000 0 -0.46 2 2
BCAR1 0.012 0.032 -10000 0 -0.6 1 1
mol:GDP 0.03 0.085 0.45 2 -10000 0 2
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.009 0.099 -10000 0 -0.32 19 19
Rac1/GTP 0.003 0.044 -10000 0 -0.42 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.006 0.11 -9999 0 -0.6 12 12
Caspase 8 (4 units) -0.014 0.087 -9999 0 -0.36 14 14
NEF -0.005 0.032 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.003 0.17 -9999 0 -0.54 32 32
CYCS 0.022 0.088 -9999 0 -0.32 11 11
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.027 0.15 -9999 0 -0.6 23 23
MAP2K7 0.016 0.077 -9999 0 -0.33 1 1
protein ubiquitination 0.019 0.095 -9999 0 -0.4 6 6
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS -0.006 0.1 -9999 0 -0.55 13 13
BID 0.014 0.092 -9999 0 -0.33 14 14
NF-kappa-B/RelA/I kappa B alpha -0.023 0.076 -9999 0 -0.52 1 1
TRADD 0.011 0.041 -9999 0 -0.54 2 2
MAP3K5 0.009 0.056 -9999 0 -0.6 3 3
CFLAR 0.013 0.026 -9999 0 -0.48 1 1
FADD 0.014 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.023 0.077 -9999 0 -0.52 1 1
MAPK8 0.016 0.089 -9999 0 -0.55 1 1
APAF1 0.014 0 -9999 0 -10000 0 0
TRAF1 0.002 0.085 -9999 0 -0.6 7 7
TRAF2 0.014 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.095 -9999 0 -0.31 22 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.12 -9999 0 -0.53 7 7
CHUK 0.018 0.1 -9999 0 -0.44 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.021 0.074 -9999 0 -0.32 13 13
TCRz/NEF -0.041 0.13 -9999 0 -0.42 36 36
TNF -0.15 0.25 -9999 0 -0.54 109 109
FASLG -0.031 0.17 -9999 0 -0.54 34 34
NFKB1 0.007 0.042 -9999 0 -0.58 1 1
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -9999 0 -0.34 120 120
CASP6 -0.02 0.066 -9999 0 -0.52 2 2
CASP7 0.029 0.17 -9999 0 -0.52 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.029 0.16 -9999 0 -0.52 25 25
TNFRSF1A 0.005 0.068 -9999 0 -0.52 6 6
TNFR1A/BAG4 -0.02 0.093 -9999 0 -0.44 17 17
CASP8 -0.007 0.1 -9999 0 -0.49 15 15
CASP9 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.009 0.11 -9999 0 -0.48 7 7
APAF-1/Caspase 9 -0.041 0.11 -9999 0 -0.41 27 27
BCL2 0.019 0.091 -9999 0 -0.5 2 2
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.025 0.14 -9999 0 -0.54 26 26
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.007 0.066 -9999 0 -0.3 12 12
GNAO1 0.004 0.078 -9999 0 -0.6 6 6
mol:Sphinganine-1-P -0.004 0.1 -9999 0 -0.38 26 26
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.025 0.068 -9999 0 -0.44 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.023 -9999 0 -0.44 1 1
S1PR3 -0.044 0.17 -9999 0 -0.51 41 41
S1PR2 0.008 0.061 -9999 0 -0.57 4 4
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.051 -9999 0 -0.26 12 12
S1PR5 -0.12 0.24 -9999 0 -0.55 90 90
S1PR4 0 0.083 -9999 0 -0.49 10 10
GNAI1 -0.004 0.1 -9999 0 -0.6 11 11
S1P/S1P5/G12 -0.058 0.15 -9999 0 -0.34 56 56
S1P/S1P3/Gq -0.008 0.12 -9999 0 -0.45 12 12
S1P/S1P4/Gi 0.023 0.077 -9999 0 -0.38 7 7
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.012 0.032 -9999 0 -0.6 1 1
GNA14 -0.006 0.11 -9999 0 -0.56 13 13
GNA15 -0.006 0.11 -9999 0 -0.56 13 13
GNA12 0.012 0.032 -9999 0 -0.6 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.002 0.085 -9999 0 -0.6 7 7
ABCC1 0.011 0.037 -9999 0 -0.48 2 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0.026 -10000 0 -0.48 1 1
NFATC1 0.033 0.092 -10000 0 -0.44 2 2
NFATC2 0.009 0.078 -10000 0 -0.28 13 13
NFATC3 0.009 0.076 -10000 0 -0.41 10 10
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.064 0.16 -10000 0 -0.51 27 27
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.14 0.18 -10000 0 -0.48 57 57
BCL2/BAX -0.006 0.051 -10000 0 -0.44 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.024 -10000 0 -0.45 1 1
CaM/Ca2+ 0.01 0.024 -10000 0 -0.45 1 1
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.004 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.055 0.16 -10000 0 -0.48 28 28
Calcineurin A alpha-beta B1/BCL2 0.006 0.072 -10000 0 -0.6 5 5
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.054 0.15 0.48 28 -10000 0 28
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.013 0.026 -10000 0 -0.48 1 1
XPO1 0.014 0 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.52 87 87
MAP3K8 0 0.083 -10000 0 -0.5 10 10
NFAT4/CK1 alpha -0.011 0.048 -10000 0 -0.33 1 1
MEF2D/NFAT1/Cbp/p300 0.022 0.11 -10000 0 -0.46 8 8
CABIN1 -0.064 0.16 -10000 0 -0.51 27 27
CALM1 0.012 0.032 -10000 0 -0.6 1 1
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.011 0.037 -10000 0 -0.48 2 2
CAMK4 -0.17 0.27 -10000 0 -0.57 113 113
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH -0.009 0.1 -10000 0 -0.48 17 17
Calcineurin A alpha-beta B1/AKAP79/PKA -0.017 0.11 -10000 0 -0.34 37 37
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.1 -10000 0 -0.6 10 10
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.002 0.077 -10000 0 -0.48 9 9
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.04 0.099 -10000 0 -0.43 5 5
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.004 0.045 -10000 0 -0.44 4 4
CASP3 0.012 0.026 -10000 0 -0.48 1 1
PIM1 0.009 0.052 -10000 0 -0.48 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.003 -10000 0 -10000 0 0
apoptosis -0.002 0.022 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.076 -10000 0 -0.3 4 4
PRKCB -0.063 0.19 -10000 0 -0.52 53 53
PRKCE 0.002 0.08 -10000 0 -0.53 8 8
JNK2/NFAT4 0.017 0.07 -10000 0 -0.37 10 10
BAD/BCL-XL -0.001 0.017 -10000 0 -0.33 1 1
PRKCD -0.015 0.13 -10000 0 -0.6 17 17
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
PRKCA 0.012 0.032 -10000 0 -0.6 1 1
PRKCG -0.2 0.27 -10000 0 -0.54 142 142
PRKCQ -0.007 0.11 -10000 0 -0.58 13 13
FKBP38/BCL2 -0.006 0.051 -10000 0 -0.44 5 5
EP300 0.007 0.064 -10000 0 -0.6 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.099 -10000 0 -0.49 1 1
CaM/Ca2+/FKBP38 0.018 0.021 -10000 0 -0.37 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.02 0.021 -10000 0 -0.37 1 1
CaM/Ca2+/CAMK IV -0.097 0.18 -10000 0 -0.35 114 114
NFATc/ERK1 0.039 0.088 -10000 0 -0.49 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.14 0.18 -10000 0 -0.48 57 57
NR4A1 0.013 0.15 -10000 0 -0.45 29 29
GSK3B 0.014 0.004 -10000 0 -10000 0 0
positive T cell selection 0.009 0.076 -10000 0 -0.41 10 10
NFAT1/CK1 alpha -0.02 0.05 -10000 0 -0.39 2 2
RCH1/ KPNB1 -0.001 0.017 -10000 0 -0.33 1 1
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.004 -10000 0 -10000 0 0
AKAP5 -0.037 0.15 -10000 0 -0.49 37 37
MEF2D 0.012 0.037 -10000 0 -0.49 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.088 -10000 0 -0.49 1 1
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.006 0.072 -10000 0 -0.6 5 5
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.02 0.086 -9999 0 -0.38 19 19
alphaV beta3 Integrin -0.042 0.11 -9999 0 -0.4 15 15
PTK2 -0.012 0.15 -9999 0 -0.49 15 15
IGF1R 0.014 0 -9999 0 -10000 0 0
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.009 0.056 -9999 0 -0.6 3 3
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.03 0.095 -9999 0 -0.5 11 11
VEGFA -0.006 0.098 -9999 0 -0.48 15 15
ILK -0.03 0.095 -9999 0 -0.5 11 11
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0.007 0.097 -9999 0 -0.46 11 11
PTK2B -0.021 0.14 -9999 0 -0.5 14 14
alphaV/beta3 Integrin/JAM-A -0.016 0.14 -9999 0 -0.57 7 7
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.04 0.1 -9999 0 -0.32 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.011 0.056 -9999 0 -0.32 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.01 0.087 -9999 0 -0.37 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.062 0.14 -9999 0 -0.46 26 26
PI4KA 0.006 0.063 -9999 0 -0.48 6 6
IGF-1R heterotetramer/IGF1/IRS1 -0.045 0.11 -9999 0 -0.48 12 12
PI4 Kinase -0.005 0.042 -9999 0 -0.33 6 6
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
alphaV/beta3 Integrin/Osteopontin -0.095 0.17 -9999 0 -0.42 60 60
RPS6KB1 0.009 0.12 -9999 0 -0.45 12 12
TLN1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.001 0.14 -9999 0 -0.48 16 16
GPR124 0.01 0.045 -9999 0 -0.48 3 3
MAPK1 0.001 0.14 -9999 0 -0.48 16 16
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.077 0.15 -9999 0 -0.44 34 34
cell adhesion -0.035 0.089 -9999 0 -0.34 13 13
ANGPTL3 0.006 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.016 0.072 -9999 0 -0.45 4 4
IGF-1R heterotetramer 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.007 0.061 -9999 0 -0.5 5 5
ITGB3 -0.054 0.18 -9999 0 -0.51 47 47
IGF1 -0.007 0.11 -9999 0 -0.55 14 14
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.041 0.1 -9999 0 -0.38 14 14
apoptosis 0.012 0.032 -9999 0 -0.6 1 1
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.039 0.1 -9999 0 -0.36 13 13
VCL 0.005 0.071 -9999 0 -0.54 6 6
alphaV/beta3 Integrin/Del1 -0.087 0.17 -9999 0 -0.44 46 46
CSF1 -0.01 0.12 -9999 0 -0.6 14 14
PIK3C2A -0.032 0.1 -9999 0 -0.52 12 12
PI4 Kinase/Pyk2 -0.058 0.13 -9999 0 -0.44 23 23
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.12 -9999 0 -0.42 27 27
FAK1/Vinculin -0.003 0.13 -9999 0 -0.44 13 13
alphaV beta3/Integrin/ppsTEM5 -0.041 0.11 -9999 0 -0.38 14 14
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.011 0.12 -9999 0 -0.55 16 16
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
FGF2 0.009 0.052 -9999 0 -0.56 3 3
F11R 0.011 0.071 -9999 0 -0.36 13 13
alphaV/beta3 Integrin/Lactadherin -0.042 0.11 -9999 0 -0.36 16 16
alphaV/beta3 Integrin/TGFBR2 -0.043 0.11 -9999 0 -0.42 16 16
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.014 0.066 -9999 0 -0.32 16 16
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.035 0.092 -9999 0 -0.33 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.002 0.088 -9999 0 -0.48 12 12
alphaV/beta3 Integrin/Pyk2 -0.021 0.14 -9999 0 -0.5 14 14
SDC1 -0.027 0.14 -9999 0 -0.49 30 30
VAV3 -0.036 0.14 -9999 0 -0.36 26 26
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0 0.12 -9999 0 -0.39 13 13
cell migration 0.007 0.12 -9999 0 -0.44 8 8
ITGAV 0.012 0.032 -9999 0 -0.6 1 1
PI3K -0.045 0.1 -9999 0 -0.51 7 7
SPP1 -0.084 0.21 -9999 0 -0.54 65 65
KDR 0.005 0.068 -9999 0 -0.52 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0.032 -9999 0 -0.6 1 1
COL4A3 -0.053 0.18 -9999 0 -0.53 45 45
angiogenesis 0.003 0.14 -9999 0 -0.5 16 16
Rac1/GTP -0.06 0.11 -9999 0 -0.5 6 6
EDIL3 -0.069 0.21 -9999 0 -0.58 51 51
cell proliferation -0.043 0.11 -9999 0 -0.42 16 16
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.064 0.14 -10000 0 -0.35 67 67
cell-cell adhesion 0.036 0.1 0.49 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.02 0.083 -10000 0 -0.4 12 12
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
SHC1 0.009 0.052 -10000 0 -0.48 4 4
Ephrin B1/EPHB3 -0.004 0.033 -10000 0 -0.28 5 5
Ephrin B1/EPHB1 -0.034 0.11 -10000 0 -0.38 33 33
HRAS/GDP -0.032 0.098 -10000 0 -0.48 9 9
Ephrin B/EPHB1/GRB7 -0.06 0.14 -10000 0 -0.41 36 36
Endophilin/SYNJ1 0.018 0.09 -10000 0 -0.38 13 13
KRAS 0.013 0.026 -10000 0 -0.48 1 1
Ephrin B/EPHB1/Src -0.04 0.12 -10000 0 -0.58 8 8
endothelial cell migration -0.006 0.039 -10000 0 -0.3 3 3
GRB2 0.014 0 -10000 0 -10000 0 0
GRB7 -0.036 0.14 -10000 0 -0.48 34 34
PAK1 -0.005 0.13 -10000 0 -0.47 15 15
HRAS 0.013 0.026 -10000 0 -0.48 1 1
RRAS 0.019 0.092 -10000 0 -0.39 13 13
DNM1 -0.12 0.24 -10000 0 -0.52 92 92
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.001 0.12 -10000 0 -0.55 8 8
lamellipodium assembly -0.036 0.1 -10000 0 -0.49 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.11 -10000 0 -0.51 8 8
PIK3R1 0.014 0 -10000 0 -10000 0 0
EPHB2 0.001 0.084 -10000 0 -0.52 9 9
EPHB3 0.011 0.037 -10000 0 -0.48 2 2
EPHB1 -0.038 0.17 -10000 0 -0.6 31 31
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.094 -10000 0 -0.44 11 11
Ephrin B/EPHB2 -0.021 0.085 -10000 0 -0.41 12 12
Ephrin B/EPHB3 -0.016 0.068 -10000 0 -0.36 9 9
JNK cascade 0.004 0.12 -10000 0 -0.34 33 33
Ephrin B/EPHB1 -0.041 0.12 -10000 0 -0.37 36 36
RAP1/GDP -0.026 0.08 -10000 0 -0.42 7 7
EFNB2 0.003 0.077 -10000 0 -0.51 8 8
EFNB3 0 0.092 -10000 0 -0.58 9 9
EFNB1 0.01 0.045 -10000 0 -0.48 3 3
Ephrin B2/EPHB1-2 -0.041 0.12 -10000 0 -0.35 43 43
RAP1B 0.013 0.026 -10000 0 -0.48 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.037 0.11 -10000 0 -0.52 11 11
Rap1/GTP -0.036 0.1 -10000 0 -0.49 11 11
axon guidance -0.064 0.14 -10000 0 -0.35 67 67
MAPK3 0.022 0.1 -10000 0 -0.43 9 9
MAPK1 0.022 0.1 -10000 0 -0.43 9 9
Rac1/GDP 0.02 0.1 -10000 0 -0.41 10 10
actin cytoskeleton reorganization -0.027 0.08 -10000 0 -0.4 9 9
CDC42/GDP 0.02 0.1 -10000 0 -0.4 11 11
PI3K -0.006 0.039 -10000 0 -0.3 3 3
EFNA5 -0.081 0.21 -10000 0 -0.55 62 62
Ephrin B2/EPHB4 -0.007 0.045 -10000 0 -0.3 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.024 0.071 -10000 0 -0.41 5 5
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.1 -10000 0 -0.48 11 11
PTK2 0.009 0.027 -10000 0 -10000 0 0
MAP4K4 0.004 0.12 -10000 0 -0.35 33 33
SRC 0.014 0 -10000 0 -10000 0 0
KALRN 0.001 0.081 -10000 0 -0.48 10 10
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.12 -10000 0 -0.44 7 7
MAP2K1 0.015 0.11 -10000 0 -0.46 9 9
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.037 0.11 -10000 0 -0.37 33 33
cell migration 0.017 0.12 -10000 0 -0.52 8 8
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 0.018 0.091 -10000 0 -0.38 13 13
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.01 0.14 -10000 0 -0.58 8 8
HRAS/GTP -0.039 0.11 -10000 0 -0.53 11 11
Ephrin B1/EPHB1-2 -0.037 0.11 -10000 0 -0.36 38 38
cell adhesion mediated by integrin 0.009 0.067 0.32 11 -10000 0 11
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.042 0.12 -10000 0 -0.57 11 11
RAC1-CDC42/GTP -0.036 0.11 -10000 0 -0.5 12 12
RASA1 0.014 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.08 -10000 0 -0.41 8 8
ruffle organization 0.023 0.12 -10000 0 -0.49 11 11
NCK1 0.012 0.032 -10000 0 -0.6 1 1
receptor internalization -0.041 0.15 -10000 0 -0.59 11 11
Ephrin B/EPHB2/KALRN -0.026 0.09 -10000 0 -0.52 6 6
ROCK1 0.024 0.032 -10000 0 -0.24 5 5
RAS family/GDP -0.025 0.076 -10000 0 -0.43 6 6
Rac1/GTP -0.038 0.11 -10000 0 -0.52 11 11
Ephrin B/EPHB1/Src/Paxillin 0.004 0.11 -10000 0 -0.48 8 8
Aurora A signaling

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
Aurora A/GADD45A 0.007 0.089 -9999 0 -0.3 21 21
BIRC5 -0.13 0.25 -9999 0 -0.55 95 95
NFKBIA 0.031 0.045 -9999 0 -0.28 1 1
CPEB1 -0.001 0.096 -9999 0 -0.6 9 9
AKT1 0.031 0.045 -9999 0 -0.28 1 1
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.048 -9999 0 -0.34 3 3
NDEL1/TACC3 -0.009 0.081 -9999 0 -0.36 12 12
GADD45A -0.017 0.12 -9999 0 -0.49 23 23
GSK3B 0.018 0.014 -9999 0 -10000 0 0
PAK1/Aurora A -0.006 0.099 -9999 0 -0.3 12 12
MDM2 0.011 0.037 -9999 0 -0.48 2 2
JUB -0.016 0.13 -9999 0 -0.57 19 19
TPX2 -0.035 0.15 -9999 0 -0.38 54 54
TP53 0.02 0.064 -9999 0 -0.28 11 11
DLG7 0.02 0.045 -9999 0 -0.3 1 1
AURKAIP1 0.013 0.026 -9999 0 -0.48 1 1
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.007 0.087 -9999 0 -0.38 12 12
G2/M transition of mitotic cell cycle 0.003 0.047 -9999 0 -0.34 3 3
AURKA 0.025 0.057 -9999 0 -0.35 1 1
AURKB -0.079 0.13 -9999 0 -0.29 83 83
CDC25B 0.024 0.046 -9999 0 -0.28 1 1
G2/M transition checkpoint -0.012 0.075 -9999 0 -0.3 16 16
mRNA polyadenylation -0.004 0.066 -9999 0 -0.33 10 10
Aurora A/CPEB -0.004 0.067 -9999 0 -0.34 10 10
Aurora A/TACC1/TRAP/chTOG 0.011 0.046 -9999 0 -10000 0 0
BRCA1 0.011 0.037 -9999 0 -0.48 2 2
centrosome duplication -0.006 0.098 -9999 0 -0.3 12 12
regulation of centrosome cycle -0.017 0.075 -9999 0 -0.36 12 12
spindle assembly 0.003 0.041 -9999 0 -10000 0 0
TDRD7 0.011 0.046 -9999 0 -0.6 2 2
Aurora A/RasGAP/Survivin -0.069 0.12 -9999 0 -0.32 45 45
CENPA -0.052 0.12 -9999 0 -0.32 50 50
Aurora A/PP2A 0.026 0.043 -9999 0 -0.28 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.032 0.043 -9999 0 -0.27 1 1
negative regulation of DNA binding 0.02 0.064 -9999 0 -0.28 11 11
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.012 0.076 -9999 0 -0.3 16 16
mitotic prometaphase 0.021 0.038 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.057 -9999 0 -0.35 1 1
TACC1 0.014 0 -9999 0 -10000 0 0
TACC3 -0.016 0.12 -9999 0 -0.49 22 22
Aurora A/Antizyme1 0.009 0.043 -9999 0 -10000 0 0
Aurora A/RasGAP 0.026 0.043 -9999 0 -0.28 1 1
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.014 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.029 0.086 -9999 0 -0.36 3 3
Importin alpha/Importin beta/TPX2 -0.035 0.15 -9999 0 -0.38 54 54
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.011 0.13 -9999 0 -0.36 31 31
PAK1 -0.038 0.15 -9999 0 -0.49 38 38
CKAP5 0.014 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.38 -9999 0 -1.1 39 39
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.062 0.18 -9999 0 -0.43 66 66
IFNAR2 0.013 0.006 -9999 0 -10000 0 0
AKT1 0 0.051 -9999 0 -0.23 10 10
ER alpha/Oestrogen -0.013 0.094 -9999 0 -0.4 20 20
NFX1/SIN3/HDAC complex 0.041 0.029 -9999 0 -10000 0 0
EGF -0.045 0.17 -9999 0 -0.56 37 37
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.012 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.34 -9999 0 -1 39 39
SAP18 0.013 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.041 0.14 -9999 0 -0.48 35 35
WRN 0.009 0.056 -9999 0 -0.6 3 3
SP1 0.013 0.009 -9999 0 -10000 0 0
SP3 0.012 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.29 -9999 0 -0.91 39 39
Mad/Max 0.019 0.009 -9999 0 -10000 0 0
TERT -0.13 0.4 -9999 0 -1.2 39 39
CCND1 -0.11 0.36 -9999 0 -0.99 47 47
MAX 0.012 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.004 -9999 0 -10000 0 0
RBBP4 0.013 0.004 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.013 0.004 -9999 0 -10000 0 0
Telomerase/911 0.034 0.038 -9999 0 -10000 0 0
CDKN1B 0.014 0.068 -9999 0 -10000 0 0
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.011 0.032 -9999 0 -0.6 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.005 -9999 0 -10000 0 0
JUN 0.001 0.075 -9999 0 -0.5 8 8
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.007 -9999 0 -10000 0 0
FOS -0.089 0.22 -9999 0 -0.55 66 66
IFN-gamma/IRF1 -0.009 0.077 -9999 0 -0.33 15 15
PARP2 0.014 0 -9999 0 -10000 0 0
BLM -0.053 0.18 -9999 0 -0.53 45 45
Telomerase -0.035 0.1 -9999 0 -0.4 19 19
IRF1 -0.004 0.1 -9999 0 -0.47 16 16
ESR1 -0.017 0.13 -9999 0 -0.54 20 20
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0.022 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.03 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.046 0.031 -9999 0 -10000 0 0
HDAC1 0.01 0.046 -9999 0 -0.6 2 2
HDAC2 0.012 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.018 0.063 -9999 0 -0.43 7 7
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.012 0.006 -9999 0 -10000 0 0
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.13 0.32 -9999 0 -1 38 38
NR2F2 -0.011 0.12 -9999 0 -0.52 19 19
MAPK3 0.011 0.008 -9999 0 -10000 0 0
MAPK1 0.011 0.008 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.078 -9999 0 -0.6 6 6
NFKB1 0.013 0.026 -9999 0 -0.48 1 1
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.083 0.21 -9999 0 -0.55 62 62
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.092 0.2 -9999 0 -0.44 89 89
MYC -0.016 0.13 -9999 0 -0.59 17 17
IL2 -0.003 0.014 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.005 0.078 -9999 0 -0.6 6 6
TRF2/BLM -0.043 0.12 -9999 0 -0.35 45 45
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.1 0.35 -9999 0 -1 39 39
SP1/HDAC2 0.019 0.017 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.29 -9999 0 -0.91 39 39
Smad3/Myc 0.005 0.099 -9999 0 -0.38 21 21
911 complex 0 0 -9999 0 -10000 0 0
IFNG 0.002 0.051 -9999 0 -0.48 4 4
Telomerase/PinX1 -0.12 0.29 -9999 0 -0.92 38 38
Telomerase/AKT1/mTOR/p70S6K 0.01 0.073 -9999 0 -10000 0 0
SIN3B 0.013 0.004 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.12 0.29 -9999 0 -0.92 38 38
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.003 0.037 -9999 0 -0.4 3 3
Telomerase/hnRNP C1/C2 -0.12 0.29 -9999 0 -0.91 39 39
E2F1 -0.01 0.11 -9999 0 -0.5 16 16
ZNFX1 0.013 0.004 -9999 0 -10000 0 0
PIF1 -0.048 0.18 -9999 0 -0.54 41 41
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.016 0.071 -10000 0 -0.39 2 2
adherens junction organization -0.037 0.12 -10000 0 -0.38 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.022 0.12 -10000 0 -0.44 5 5
FMN1 -0.069 0.16 -10000 0 -0.5 21 21
mol:IP3 0.007 0.071 -10000 0 -0.4 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.021 0.12 -10000 0 -0.55 3 3
CTNNB1 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.08 -10000 0 -0.44 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.038 0.16 -10000 0 -0.41 48 48
CTNND1 0.014 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.11 -10000 0 -0.51 3 3
VASP -0.012 0.11 -10000 0 -0.52 3 3
ZYX -0.016 0.11 -10000 0 -0.52 3 3
JUB -0.027 0.13 -10000 0 -0.5 7 7
EGFR(dimer) -0.06 0.15 -10000 0 -0.43 17 17
E-cadherin/beta catenin-gamma catenin -0.088 0.15 -10000 0 -0.32 100 100
mol:PI-3-4-5-P3 -0.033 0.066 -10000 0 -0.41 3 3
PIK3CA 0.013 0.032 -10000 0 -0.6 1 1
PI3K -0.034 0.067 -10000 0 -0.42 3 3
FYN 0.016 0.07 -10000 0 -0.33 2 2
mol:Ca2+ 0.007 0.07 -10000 0 -0.39 2 2
JUP 0.003 0.086 -10000 0 -0.57 8 8
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
mol:DAG 0.007 0.071 -10000 0 -0.4 2 2
CDH1 -0.13 0.24 -10000 0 -0.54 95 95
RhoA/GDP -0.022 0.12 -10000 0 -0.44 5 5
establishment of polarity of embryonic epithelium -0.011 0.11 -10000 0 -0.51 3 3
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.082 0.21 -10000 0 -0.55 62 62
CASR 0.004 0.079 -10000 0 -0.37 2 2
RhoA/GTP -0.022 0.046 -10000 0 -0.36 2 2
AKT2 0.009 0.08 -10000 0 -0.44 2 2
actin cable formation -0.06 0.16 -10000 0 -0.48 21 21
apoptosis 0.029 0.059 0.37 3 -10000 0 3
CTNNA1 0.014 0.002 -10000 0 -10000 0 0
mol:GDP -0.032 0.13 -10000 0 -0.41 11 11
PIP5K1A -0.011 0.11 -10000 0 -0.52 3 3
PLCG1 0.007 0.072 -10000 0 -0.41 2 2
Rac1/GTP -0.079 0.12 -10000 0 -0.39 17 17
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.004 0.078 -9999 0 -0.6 6 6
CDC42/GTP -0.013 0.056 -9999 0 -0.4 4 4
PLCG1 0.028 0.068 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.023 -9999 0 -0.44 1 1
cell migration -0.013 0.055 -9999 0 -0.39 4 4
S1PR5 -0.12 0.24 -9999 0 -0.55 90 90
S1PR4 0 0.083 -9999 0 -0.49 10 10
MAPK3 0.028 0.068 -9999 0 -0.41 4 4
MAPK1 0.028 0.068 -9999 0 -0.41 4 4
S1P/S1P5/Gi -0.034 0.14 -9999 0 -0.3 55 55
GNAI1 -0.004 0.1 -9999 0 -0.6 11 11
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.084 0.15 -9999 0 -0.34 90 90
RHOA 0.026 0.047 -9999 0 -0.3 2 2
S1P/S1P4/Gi 0.021 0.072 -9999 0 -0.35 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.032 -9999 0 -0.6 1 1
S1P/S1P4/G12/G13 -0.008 0.045 -9999 0 -0.33 2 2
GNA12 0.012 0.032 -9999 0 -0.6 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.025 0.1 -10000 0 -0.43 21 21
ATM 0.014 0 -10000 0 -10000 0 0
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.017 0.054 -10000 0 -0.35 4 4
protein ubiquitination -0.025 0.092 -10000 0 -0.33 26 26
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.012 0.052 -10000 0 -0.42 3 3
FANCF 0.014 0 -10000 0 -10000 0 0
BRCA1 0.011 0.037 -10000 0 -0.48 2 2
CCNE1 0.011 0.037 -10000 0 -0.48 2 2
CDK2/Cyclin E1 -0.011 0.068 -10000 0 -0.4 10 10
FANCG 0.014 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.026 0.1 -10000 0 -0.44 22 22
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.011 0.041 -10000 0 -0.54 2 2
NBN 0.014 0 -10000 0 -10000 0 0
FANCA -0.021 0.13 -10000 0 -0.52 24 24
DNA repair 0.019 0.14 -10000 0 -0.5 12 12
BRCA1/BARD1/ubiquitin -0.026 0.1 -10000 0 -0.44 22 22
BARD1/DNA-PK -0.018 0.074 -10000 0 -0.32 19 19
FANCL 0.014 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.025 0.099 0.43 21 -10000 0 21
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.069 -10000 0 -0.36 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.022 0.088 -10000 0 -0.37 20 20
BRCA1/BARD1/P53 -0.03 0.1 -10000 0 -0.35 29 29
BARD1/CSTF1/BRCA1 -0.022 0.088 -10000 0 -0.36 22 22
BRCA1/BACH1 0.011 0.036 -10000 0 -0.48 2 2
BARD1 -0.021 0.14 -10000 0 -0.59 21 21
PCNA 0.013 0.026 -10000 0 -0.48 1 1
BRCA1/BARD1/UbcH5C -0.022 0.088 -10000 0 -0.37 20 20
BRCA1/BARD1/UbcH7 -0.022 0.088 -10000 0 -0.36 22 22
BRCA1/BARD1/RAD51/PCNA -0.052 0.13 -10000 0 -0.38 33 33
BARD1/DNA-PK/P53 -0.026 0.09 -10000 0 -0.32 28 28
BRCA1/BARD1/Ubiquitin -0.026 0.1 -10000 0 -0.44 22 22
BRCA1/BARD1/CTIP 0.012 0.095 -10000 0 -0.36 20 20
FA complex 0.03 0.054 -10000 0 -10000 0 0
BARD1/EWS -0.025 0.1 -10000 0 -0.43 21 21
RBBP8 0.022 0.032 -10000 0 -0.34 3 3
TP53 -0.006 0.11 -10000 0 -0.59 12 12
TOPBP1 0.014 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.03 0.1 0.35 29 -10000 0 29
BRCA1/BARD1 -0.026 0.094 -10000 0 -0.33 26 26
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.025 0.1 -10000 0 -0.44 21 21
CDK2 0.001 0.086 -10000 0 -0.54 9 9
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.05 0.17 -10000 0 -0.52 44 44
RAD50 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.026 0.1 -10000 0 -0.44 22 22
EWSR1 0.014 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.035 0.09 0.16 2 -0.38 11 13
CaM/Ca2+ -0.001 0.023 -10000 0 -0.45 1 1
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.025 0.13 0.24 40 -0.43 10 50
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.012 0.032 -10000 0 -0.6 1 1
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.009 0.1 -10000 0 -0.48 17 17
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.002 0.077 -10000 0 -0.48 9 9
ASIP -0.086 0.22 -10000 0 -0.55 64 64
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ -0.001 0.023 -10000 0 -0.45 1 1
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ -0.01 0.12 -10000 0 -0.56 15 15
TRIP10 0.005 0.071 -10000 0 -0.54 6 6
TC10/GTP/CIP4/Exocyst -0.005 0.042 -10000 0 -0.33 6 6
AS160/14-3-3 0.004 0.087 -10000 0 -0.36 4 4
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 0.024 0.14 0.27 20 -0.49 10 30
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.52 87 87
LNPEP -0.021 0.14 -10000 0 -0.6 21 21
YWHAE 0.014 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.006 0.094 -9999 0 -0.32 27 27
SNTA1 -0.014 0.12 -9999 0 -0.56 18 18
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.005 0.096 -9999 0 -0.32 28 28
MAPK12 0.028 0.037 -9999 0 -0.3 3 3
CCND1 0.007 0.073 -9999 0 -0.42 9 9
p38 gamma/SNTA1 0.018 0.076 -9999 0 -0.3 15 15
MAP2K3 0.011 0.037 -9999 0 -0.48 2 2
PKN1 0.014 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.028 0.036 -9999 0 -0.3 3 3
MAP2K6 0.022 0.035 -9999 0 -0.33 2 2
MAPT 0.009 0.09 -9999 0 -0.32 20 20
MAPK13 -0.006 0.11 -9999 0 -0.39 27 27
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.033 -9999 0 -0.22 7 7
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.012 0.032 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.011 0.037 -9999 0 -0.48 2 2
RAC1-CDC42/GTP/PAK family -0.032 0.1 -9999 0 -0.22 72 72
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0.046 -9999 0 -0.6 2 2
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
MAP3K12 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.037 -9999 0 -0.48 2 2
p38 alpha/TAB1 -0.024 0.057 -9999 0 -0.4 3 3
PRKG1 -0.048 0.18 -9999 0 -0.58 38 38
DUSP8 -0.001 0.091 -9999 0 -0.54 10 10
PGK/cGMP/p38 alpha -0.047 0.091 -9999 0 -0.31 25 25
apoptosis -0.023 0.054 -9999 0 -0.39 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.006 0.063 -9999 0 -0.48 6 6
DUSP1 -0.022 0.14 -9999 0 -0.54 24 24
PAK1 -0.038 0.15 -9999 0 -0.49 38 38
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.018 -9999 0 -10000 0 0
TRAF6 0.012 0.032 -9999 0 -0.6 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.001 0.097 -9999 0 -0.39 7 7
BLK -0.095 0.21 -9999 0 -0.5 76 76
HCK -0.013 0.12 -9999 0 -0.53 18 18
MAP2K3 0.011 0.037 -9999 0 -0.48 2 2
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 -0.009 0.11 -9999 0 -0.55 15 15
TRAF6/MEKK3 -0.001 0.018 -9999 0 -0.34 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.009 0.08 -9999 0 -0.39 4 4
positive regulation of innate immune response 0.004 0.11 -9999 0 -0.42 7 7
LCK -0.088 0.21 -9999 0 -0.53 68 68
p38alpha-beta/MKP7 0.011 0.1 -9999 0 -0.47 4 4
p38alpha-beta/MKP5 0.001 0.11 -9999 0 -0.44 7 7
PGK/cGMP -0.045 0.13 -9999 0 -0.43 38 38
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.005 0.12 -9999 0 -0.46 6 6
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.11 0.24 -9999 0 -0.56 80 80
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.026 0.082 -10000 0 -0.31 21 21
ER alpha/Gai/GDP/Gbeta gamma 0.021 0.1 -10000 0 -0.4 15 15
AKT1 0.012 0.13 -10000 0 -0.72 11 11
PIK3CA 0.012 0.032 -10000 0 -0.6 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.011 0.13 -10000 0 -0.73 11 11
mol:Ca2+ -0.005 0.14 -10000 0 -0.49 16 16
IGF1R 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.039 0.12 -10000 0 -0.36 40 40
SHC1 0.009 0.052 -10000 0 -0.48 4 4
apoptosis -0.013 0.13 0.69 11 -10000 0 11
RhoA/GTP -0.013 0.053 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.024 0.085 -10000 0 -0.4 15 15
regulation of stress fiber formation -0.011 0.11 0.39 10 -10000 0 10
E2/ERA-ERB (dimer) -0.029 0.097 -10000 0 -0.34 31 31
KRAS 0.013 0.026 -10000 0 -0.48 1 1
G13/GTP -0.016 0.068 -10000 0 -0.3 20 20
pseudopodium formation 0.011 0.11 -10000 0 -0.39 10 10
E2/ER alpha (dimer)/PELP1 -0.018 0.075 -10000 0 -0.33 20 20
GRB2 0.014 0 -10000 0 -10000 0 0
GNG2 0.009 0.056 -10000 0 -0.6 3 3
GNAO1 0.004 0.078 -10000 0 -0.6 6 6
HRAS 0.013 0.026 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.023 0.1 -10000 0 -0.45 11 11
E2/ER beta (dimer) -0.013 0.073 -10000 0 -0.4 12 12
mol:GDP -0.024 0.085 -10000 0 -0.37 18 18
mol:NADP 0.023 0.1 -10000 0 -0.45 11 11
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.006 0.14 -10000 0 -0.51 16 16
IGF-1R heterotetramer 0.014 0 -10000 0 -10000 0 0
PLCB1 -0.001 0.12 -10000 0 -0.47 12 12
PLCB2 -0.004 0.13 -10000 0 -0.55 13 13
IGF1 -0.007 0.11 -10000 0 -0.55 14 14
mol:L-citrulline 0.023 0.1 -10000 0 -0.45 11 11
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.019 0.1 -10000 0 -0.76 6 6
JNK cascade -0.013 0.072 -10000 0 -0.4 12 12
BCAR1 0.012 0.032 -10000 0 -0.6 1 1
ESR2 -0.004 0.1 -10000 0 -0.55 12 12
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.016 0.13 -10000 0 -0.54 20 20
Gq family/GDP/Gbeta gamma 0.013 0.11 -10000 0 -0.44 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.089 -10000 0 -0.42 15 15
GNAZ 0.012 0.032 -10000 0 -0.6 1 1
E2/ER alpha (dimer) -0.022 0.091 -10000 0 -0.4 20 20
STRN -0.021 0.14 -10000 0 -0.6 21 21
GNAL -0.05 0.19 -10000 0 -0.6 38 38
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.006 0.073 -10000 0 -0.34 15 15
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.004 0.1 -10000 0 -0.6 11 11
HBEGF -0.014 0.13 -10000 0 -0.48 9 9
cAMP biosynthetic process -0.054 0.12 -10000 0 -0.33 54 54
SRC 0.029 0.098 -10000 0 -0.38 15 15
PI3K -0.001 0.023 -10000 0 -0.44 1 1
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.023 0.075 -10000 0 -0.35 11 11
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.027 0.084 -10000 0 -0.47 5 5
Gs family/GTP -0.054 0.12 -10000 0 -0.33 53 53
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.018 -10000 0 -10000 0 0
vasodilation 0.023 0.1 -10000 0 -0.43 11 11
mol:DAG -0.006 0.14 -10000 0 -0.51 16 16
Gs family/GDP/Gbeta gamma -0.045 0.1 -10000 0 -0.38 18 18
MSN 0.01 0.11 -10000 0 -0.43 10 10
Gq family/GTP 0 0.1 -10000 0 -0.5 9 9
mol:PI-3-4-5-P3 0.012 0.13 -10000 0 -0.7 11 11
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.023 0.1 0.43 11 -10000 0 11
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.079 -10000 0 -0.34 18 18
NOS3 0.022 0.11 -10000 0 -0.48 11 11
GNA11 0.002 0.085 -10000 0 -0.6 7 7
MAPKKK cascade 0.016 0.14 -10000 0 -0.42 30 30
E2/ER alpha (dimer)/PELP1/Src -0.025 0.088 -10000 0 -0.42 15 15
ruffle organization 0.011 0.11 -10000 0 -0.39 10 10
ROCK2 0.025 0.09 -10000 0 -0.5 3 3
GNA14 -0.006 0.11 -10000 0 -0.56 13 13
GNA15 -0.006 0.11 -10000 0 -0.56 13 13
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.043 0.15 -10000 0 -0.47 13 13
MMP2 0.019 0.12 -10000 0 -0.48 8 8
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.034 -9999 0 -0.44 2 2
SMARCC1 0.009 0.013 -9999 0 -10000 0 0
REL -0.031 0.16 -9999 0 -0.57 29 29
HDAC7 0.021 0.1 -9999 0 -0.37 7 7
JUN 0.002 0.075 -9999 0 -0.5 8 8
EP300 0.007 0.064 -9999 0 -0.6 4 4
KAT2B 0.013 0.026 -9999 0 -0.48 1 1
KAT5 0.014 0 -9999 0 -10000 0 0
MAPK14 0.022 0.027 -9999 0 -0.43 1 1
FOXO1 0.009 0.052 -9999 0 -0.56 3 3
T-DHT/AR 0.017 0.11 -9999 0 -0.4 7 7
MAP2K6 0.012 0.033 -9999 0 -0.6 1 1
BRM/BAF57 0.004 0.025 -9999 0 -0.44 1 1
MAP2K4 0.011 0.037 -9999 0 -0.49 2 2
SMARCA2 0.012 0.032 -9999 0 -0.6 1 1
PDE9A -0.025 0.099 -9999 0 -0.9 2 2
NCOA2 -0.035 0.17 -9999 0 -0.6 29 29
CEBPA -0.015 0.13 -9999 0 -0.56 19 19
EHMT2 0.013 0.004 -9999 0 -10000 0 0
cell proliferation 0.028 0.13 -9999 0 -0.44 10 10
NR0B1 -0.084 0.22 -9999 0 -0.55 63 63
EGR1 -0.1 0.23 -9999 0 -0.53 79 79
RXRs/9cRA -0.035 0.11 -9999 0 -0.33 45 45
AR/RACK1/Src -0.012 0.079 -9999 0 -0.37 8 8
AR/GR -0.014 0.12 -9999 0 -0.37 16 16
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.014 0 -9999 0 -10000 0 0
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.009 0.081 -9999 0 -0.42 12 12
T-DHT/AR/TIF2/CARM1 -0.006 0.14 -9999 0 -0.51 19 19
SRC 0.028 0.066 -9999 0 -0.29 10 10
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.047 0.14 -9999 0 -0.46 18 18
APPBP2 0.014 0.005 -9999 0 -10000 0 0
TRIM24 0.012 0.026 -9999 0 -0.48 1 1
T-DHT/AR/TIP60 0.012 0.087 -9999 0 -0.37 11 11
TMPRSS2 -0.13 0.32 -9999 0 -1.1 32 32
RXRG -0.061 0.2 -9999 0 -0.6 45 45
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.001 -9999 0 -10000 0 0
RXRB 0.014 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.001 -9999 0 -10000 0 0
NR2C2 0.002 0.085 -9999 0 -0.6 7 7
KLK2 -0.011 0.15 -9999 0 -0.49 13 13
AR -0.022 0.13 -9999 0 -0.3 53 53
SENP1 0.014 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.013 0.037 -9999 0 -0.48 2 2
SRY -0.011 0.086 -9999 0 -0.48 12 12
GATA2 -0.01 0.12 -9999 0 -0.56 15 15
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.05 0.16 -9999 0 -0.49 41 41
T-DHT/AR/RACK1/Src 0.019 0.087 -9999 0 -0.38 8 8
positive regulation of transcription -0.01 0.12 -9999 0 -0.56 15 15
DNAJA1 0.014 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.024 -9999 0 -0.25 2 2
NCOA1 0.017 0.005 -9999 0 -10000 0 0
SPDEF -0.044 0.17 -9999 0 -0.53 39 39
T-DHT/AR/TIF2 0.011 0.13 -9999 0 -0.62 10 10
T-DHT/AR/Hsp90 0.012 0.087 -9999 0 -0.37 12 12
GSK3B 0.014 0.003 -9999 0 -10000 0 0
NR2C1 0.014 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.022 0.07 -9999 0 -0.32 12 12
SIRT1 0.014 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.005 -9999 0 -10000 0 0
POU2F1 0.023 0.036 -9999 0 -0.6 1 1
T-DHT/AR/DAX-1 -0.04 0.15 -9999 0 -0.39 34 34
CREBBP 0.014 0 -9999 0 -10000 0 0
SMARCE1 0.013 0.003 -9999 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.01 0.045 -9999 0 -0.48 3 3
alphaV beta3 Integrin -0.048 0.12 -9999 0 -0.36 48 48
PTK2 -0.034 0.12 -9999 0 -0.53 15 15
positive regulation of JNK cascade -0.011 0.053 -9999 0 -0.33 9 9
CDC42/GDP 0.043 0.085 -9999 0 -0.45 9 9
Rac1/GDP 0.045 0.085 -9999 0 -0.44 9 9
RAP1B 0.013 0.026 -9999 0 -0.48 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.013 0.066 -9999 0 -0.41 9 9
nectin-3/I-afadin -0.011 0.068 -9999 0 -0.44 9 9
RAPGEF1 0.037 0.095 -9999 0 -0.51 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.11 -9999 0 -0.59 9 9
PDGFB-D/PDGFRB 0.01 0.045 -9999 0 -0.48 3 3
TLN1 0.031 0.036 -9999 0 -0.35 1 1
Rap1/GTP -0.012 0.057 -9999 0 -0.35 9 9
IQGAP1 0.005 0.068 -9999 0 -0.52 6 6
Rap1/GTP/I-afadin -0.002 0.022 -9999 0 -0.29 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.011 0.068 -9999 0 -0.44 9 9
PVR 0.014 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0 -9999 0 -10000 0 0
mol:GDP 0.04 0.1 -9999 0 -0.56 9 9
MLLT4 0.012 0.032 -9999 0 -0.6 1 1
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
PI3K -0.01 0.056 -9999 0 -0.54 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.016 0.081 -9999 0 -0.44 13 13
positive regulation of lamellipodium assembly -0.011 0.056 -9999 0 -0.35 9 9
PVRL1 -0.006 0.11 -9999 0 -0.6 12 12
PVRL3 0.001 0.09 -9999 0 -0.6 8 8
PVRL2 0.011 0.041 -9999 0 -0.54 2 2
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.13 0.25 -9999 0 -0.54 95 95
CLDN1 -0.017 0.12 -9999 0 -0.52 21 21
JAM-A/CLDN1 -0.03 0.095 -9999 0 -0.36 20 20
SRC -0.024 0.11 -9999 0 -0.67 9 9
ITGB3 -0.054 0.18 -9999 0 -0.51 47 47
nectin-1(dimer)/I-afadin/I-afadin -0.016 0.081 -9999 0 -0.44 13 13
FARP2 0.034 0.1 -9999 0 -0.55 9 9
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.009 0.057 -9999 0 -0.36 9 9
nectin-1/I-afadin -0.016 0.081 -9999 0 -0.44 13 13
nectin-2/I-afadin -0.003 0.037 -9999 0 -0.4 3 3
RAC1/GTP/IQGAP1/filamentous actin -0.005 0.04 -9999 0 -0.31 6 6
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.021 0.092 -9999 0 -0.4 19 19
CDC42/GTP/IQGAP1/filamentous actin -0.005 0.04 -9999 0 -0.31 6 6
F11R 0 0.083 -9999 0 -0.49 10 10
positive regulation of filopodium formation -0.011 0.053 -9999 0 -0.33 9 9
alphaV/beta3 Integrin/Talin 0.01 0.1 -9999 0 -0.44 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.037 -9999 0 -0.4 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.037 -9999 0 -0.4 3 3
PIP5K1C 0.024 0.039 -9999 0 -0.38 1 1
VAV2 0.033 0.1 -9999 0 -0.56 9 9
RAP1/GDP -0.013 0.066 -9999 0 -0.41 9 9
ITGAV 0.012 0.032 -9999 0 -0.6 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.011 0.061 -9999 0 -0.36 11 11
nectin-3(dimer)/I-afadin/I-afadin -0.011 0.068 -9999 0 -0.44 9 9
Rac1/GTP -0.013 0.068 -9999 0 -0.42 9 9
PTPRM 0.015 0.042 -9999 0 -0.24 9 9
E-cadherin/beta catenin/alpha catenin -0.074 0.13 -9999 0 -0.61 6 6
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.014 0.12 -10000 0 -0.45 11 11
BAG4 -0.006 0.11 -10000 0 -0.6 12 12
BAD 0.009 0.044 -10000 0 -0.19 1 1
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.55 32 32
BAX 0.009 0.044 -10000 0 -0.19 1 1
EnzymeConsortium:3.1.4.12 -0.003 0.032 -10000 0 -0.099 11 11
IKBKB -0.005 0.11 -10000 0 -0.42 11 11
MAP2K2 0.019 0.048 -10000 0 -10000 0 0
MAP2K1 0.018 0.05 -10000 0 -0.3 1 1
SMPD1 0.004 0.032 -10000 0 -0.14 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.008 0.12 -10000 0 -0.42 12 12
MAP2K4 0.013 0.05 -10000 0 -0.29 1 1
protein ubiquitination -0.004 0.12 -10000 0 -0.42 11 11
EnzymeConsortium:2.7.1.37 0.02 0.055 -10000 0 -0.29 1 1
response to UV 0 0.001 -10000 0 -0.002 2 2
RAF1 0.014 0.047 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.001 0.045 -10000 0 -0.16 6 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.007 0.047 -10000 0 -0.2 3 3
TRADD 0.011 0.041 -10000 0 -0.54 2 2
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.021 0.049 -10000 0 -10000 0 0
MAPK1 0.021 0.049 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.013 0.12 -10000 0 -0.45 11 11
KSR1 0.008 0.046 -10000 0 -0.21 1 1
MAPK8 0.012 0.068 -10000 0 -0.28 11 11
TRAF2 0.014 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.005 0.11 -10000 0 -0.42 11 11
TNF R/SODD -0.019 0.094 -10000 0 -0.44 17 17
TNF -0.15 0.25 -10000 0 -0.54 109 109
CYCS 0.012 0.044 0.14 3 -0.19 1 4
IKBKG -0.005 0.11 -10000 0 -0.42 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.022 0.12 -10000 0 -0.48 11 11
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.012 0.044 0.14 3 -0.19 1 4
TNF/TNF R/SODD -0.11 0.17 -10000 0 -0.34 120 120
TNFRSF1A 0.005 0.068 -10000 0 -0.52 6 6
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.056 -10000 0 -0.72 1 1
NSMAF -0.013 0.12 -10000 0 -0.44 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 2 2
BCL2 0.006 0.072 -10000 0 -0.6 5 5
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.1 0.23 -9999 0 -0.56 72 72
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0 -9999 0 -10000 0 0
TCEB1 0.014 0 -9999 0 -10000 0 0
HIF1A/p53 0.022 0.058 -9999 0 -0.28 11 11
HIF1A 0.025 0.019 -9999 0 -10000 0 0
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.1 0.24 -9999 0 -0.57 74 74
ARNT/IPAS -0.081 0.16 -9999 0 -0.4 73 73
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.032 0.025 -9999 0 -0.3 1 1
CUL2 0.014 0 -9999 0 -10000 0 0
OS9 0.006 0.063 -9999 0 -0.48 6 6
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.032 0.019 -9999 0 -10000 0 0
PHD1-3/OS9 -0.008 0.048 -9999 0 -0.32 5 5
HIF1A/RACK1/Elongin B/Elongin C -0.001 0.01 -9999 0 -10000 0 0
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.032 0.019 -9999 0 -10000 0 0
EGLN3 0.006 0.072 -9999 0 -0.6 5 5
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 -0.006 0.11 -9999 0 -0.59 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.041 0.005 -9999 0 -10000 0 0
ARNT 0.013 0.026 -9999 0 -0.48 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.028 0.12 -9999 0 -0.28 59 59
Class I PI3K signaling events

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
ARF5/GTP -0.014 0.046 -9999 0 -10000 0 0
DAPP1 -0.03 0.14 -9999 0 -0.42 27 27
Src family/SYK family/BLNK-LAT/BTK-ITK -0.084 0.22 -9999 0 -0.57 41 41
mol:DAG -0.027 0.11 -9999 0 -0.29 20 20
HRAS 0.013 0.026 -9999 0 -0.48 1 1
RAP1A 0.014 0.003 -9999 0 -10000 0 0
ARF5/GDP 0.029 0.056 -9999 0 -0.29 4 4
PLCG2 0.002 0.082 -9999 0 -0.54 8 8
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.016 0.053 -9999 0 -10000 0 0
ARF1/GTP -0.013 0.043 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.011 0.046 -9999 0 -0.6 2 2
RAP1A/GTP -0.015 0.053 -9999 0 -10000 0 0
ADAP1 -0.028 0.081 -9999 0 -0.49 4 4
ARAP3 -0.016 0.053 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.002 0.085 -9999 0 -0.6 7 7
ARHGEF6 0.009 0.056 -9999 0 -0.6 3 3
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0.003 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.037 -9999 0 -0.48 2 2
mol:Ca2+ -0.004 0.058 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.012 0.032 -9999 0 -0.6 1 1
ZAP70 -0.059 0.19 -9999 0 -0.53 49 49
mol:IP3 -0.01 0.077 -9999 0 -0.21 7 7
LYN 0.006 0.063 -9999 0 -0.48 6 6
ARF1/GDP 0.029 0.056 -9999 0 -0.29 4 4
RhoA/GDP -0.015 0.044 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.019 -9999 0 -0.36 1 1
BLNK -0.056 0.19 -9999 0 -0.58 43 43
actin cytoskeleton reorganization 0.042 0.075 -9999 0 -0.39 3 3
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.029 0.034 -9999 0 -0.3 4 4
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0.003 0.009 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.014 0.046 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.049 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.079 0.2 -9999 0 -0.53 39 39
BLK -0.095 0.21 -9999 0 -0.5 76 76
PDPK1 0.012 0.032 -9999 0 -0.6 1 1
CYTH1 -0.014 0.049 -9999 0 -10000 0 0
HCK -0.013 0.12 -9999 0 -0.53 18 18
CYTH3 -0.014 0.049 -9999 0 -10000 0 0
CYTH2 -0.014 0.049 -9999 0 -10000 0 0
KRAS 0.013 0.026 -9999 0 -0.48 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.025 0.085 -9999 0 -0.45 9 9
SGK1 -0.02 0.08 -9999 0 -0.5 9 9
INPP5D 0.008 0.055 -9999 0 -0.51 4 4
mol:GDP 0.022 0.059 -9999 0 -0.31 4 4
SOS1 0.014 0 -9999 0 -10000 0 0
SYK -0.013 0.12 -9999 0 -0.56 17 17
ARF6/GDP -0.015 0.044 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.053 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.016 0.053 -9999 0 -10000 0 0
VAV1 -0.022 0.14 -9999 0 -0.56 23 23
mol:PI-3-4-P2 0.021 0.04 -9999 0 -0.36 4 4
RAS family/GTP/PI3K Class I 0.016 0.063 -9999 0 -10000 0 0
PLEKHA1 0.024 0.049 -9999 0 -0.28 9 9
Rac1/GDP 0.029 0.056 -9999 0 -0.29 4 4
LAT -0.024 0.15 -9999 0 -0.6 23 23
Rac1/GTP 0.024 0.085 -9999 0 -0.49 6 6
ITK -0.067 0.12 -9999 0 -0.42 18 18
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.044 0.14 -9999 0 -0.42 21 21
LCK -0.088 0.21 -9999 0 -0.53 68 68
BTK -0.025 0.07 -9999 0 -0.41 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.011 0.034 -10000 0 -0.31 4 4
TRAF2/ASK1 -0.003 0.034 -10000 0 -0.37 3 3
ATM 0.014 0 -10000 0 -10000 0 0
MAP2K3 0.018 0.053 -10000 0 -0.32 1 1
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.071 -10000 0 -0.45 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.037 0.16 -10000 0 -0.54 34 34
TXN 0.009 0.011 -10000 0 -0.2 1 1
CALM1 0.012 0.032 -10000 0 -0.6 1 1
GADD45A -0.017 0.12 -10000 0 -0.49 23 23
GADD45B -0.028 0.14 -10000 0 -0.52 29 29
MAP3K1 0.011 0.037 -10000 0 -0.48 2 2
MAP3K6 0.006 0.063 -10000 0 -0.48 6 6
MAP3K7 0.014 0 -10000 0 -10000 0 0
MAP3K4 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.009 0.058 -10000 0 -0.37 9 9
TAK1/TAB family 0.001 0.019 0.19 3 -0.18 1 4
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.024 -10000 0 -10000 0 0
TRAF6 0.008 0.02 -10000 0 -0.37 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.074 0.2 -10000 0 -0.54 58 58
CCM2 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.053 0.12 -10000 0 -0.33 58 58
MAPK11 0.009 0.056 -10000 0 -0.6 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.049 0.12 -10000 0 -0.31 58 58
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.024 0.12 -10000 0 -0.36 41 41
TAOK2 0.019 0 -10000 0 -10000 0 0
TAOK3 0.019 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.056 -10000 0 -0.6 3 3
MAP3K10 0.005 0.068 -10000 0 -0.48 7 7
MAP3K3 0.014 0 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.04 -10000 0 -0.42 3 3
GADD45/MTK1/MTK1 -0.059 0.13 -10000 0 -0.38 37 37
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.018 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.086 0.03 -9999 0 -10000 0 0
ERC1 0.013 0.026 -9999 0 -0.48 1 1
RIP2/NOD2 -0.018 0.081 -9999 0 -0.38 17 17
NFKBIA 0.05 0.014 -9999 0 -10000 0 0
BIRC2 0.014 0 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.006 0.031 -9999 0 -10000 0 0
IKK complex/A20 -0.067 0.1 -9999 0 -0.45 7 7
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.047 0.04 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.025 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.019 -9999 0 -0.36 1 1
NOD2 -0.012 0.12 -9999 0 -0.54 17 17
NFKB1 0.016 0.026 -9999 0 -0.47 1 1
RELA 0.018 0 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.12 0.18 -9999 0 -0.38 113 113
TRAF6 0.012 0.032 -9999 0 -0.6 1 1
PRKCA 0.012 0.032 -9999 0 -0.6 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.15 0.25 -9999 0 -0.54 109 109
NF kappa B1 p50/RelA -0.001 0.013 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.014 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.018 0 -9999 0 -10000 0 0
TNFRSF1A 0.005 0.068 -9999 0 -0.52 6 6
IKK complex 0.054 0.039 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.005 0.027 -9999 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.033 0.08 -10000 0 -0.54 4 4
CLOCK -0.028 0.16 -10000 0 -0.6 27 27
TIMELESS/CRY2 0.028 0.072 -10000 0 -10000 0 0
DEC1/BMAL1 0.008 0.06 -10000 0 -0.35 10 10
ATR 0.014 0 -10000 0 -10000 0 0
NR1D1 0.027 0.094 -10000 0 -0.93 2 2
ARNTL 0.013 0.05 -10000 0 -0.53 3 3
TIMELESS 0.026 0.075 -10000 0 -0.44 1 1
NPAS2 0.004 0.087 -10000 0 -0.57 8 8
CRY2 0.011 0.046 -10000 0 -0.6 2 2
mol:CO -0.012 0.016 0.074 12 -10000 0 12
CHEK1 0.009 0.052 -10000 0 -0.48 4 4
mol:HEME 0.012 0.016 -10000 0 -0.074 12 12
PER1 0.004 0.078 -10000 0 -0.6 6 6
BMAL/CLOCK/NPAS2 0.005 0.13 -10000 0 -0.39 33 33
BMAL1/CLOCK 0.012 0.14 -10000 0 -0.64 6 6
S phase of mitotic cell cycle 0.033 0.08 -10000 0 -0.54 4 4
TIMELESS/CHEK1/ATR 0.034 0.081 -10000 0 -0.54 4 4
mol:NADPH 0.012 0.016 -10000 0 -0.074 12 12
PER1/TIMELESS 0.024 0.08 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.001 0.067 -10000 0 -0.48 7 7
Atypical NF-kappaB pathway

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
BCL3/RelA -0.01 0.057 -9999 0 -0.33 11 11
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.1 -9999 0 -0.37 22 22
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.081 -9999 0 -0.4 2 2
NFKBIA -0.011 0.09 -9999 0 -0.23 42 42
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0.016 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL -0.032 0.16 -9999 0 -0.57 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.057 -9999 0 -0.54 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.016 -9999 0 -10000 0 0
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
NF kappa B1 p50 dimer 0.021 0.019 -9999 0 -0.33 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
NFKB1 0.024 0.019 -9999 0 -0.34 1 1
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.003 0.087 -9999 0 -0.44 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.079 -9999 0 -0.49 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.001 0.023 -9999 0 -0.44 1 1
NF kappa B1 p50/RelA -0.004 0.088 -9999 0 -0.45 1 1
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK -0.013 0.12 -9999 0 -0.56 17 17
I kappa B alpha/PIK3R1 -0.003 0.084 -9999 0 -0.55 1 1
cell death 0.017 0.077 -9999 0 -0.46 1 1
NF kappa B1 p105/c-Rel -0.001 0.1 -9999 0 -0.37 22 22
LCK -0.088 0.21 -9999 0 -0.53 68 68
BCL3 -0.001 0.085 -9999 0 -0.48 11 11
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.045 -9999 0 -0.48 3 3
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.023 0.07 -9999 0 -0.31 13 13
GNAO1 0.006 0.079 -9999 0 -0.61 6 6
S1P/S1P3/G12/G13 -0.004 0.098 -9999 0 -0.27 41 41
AKT1 0.024 0.045 -9999 0 -0.3 2 2
AKT3 0.019 0.17 -9999 0 -1.3 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.045 -9999 0 -0.48 3 3
GNAI2 0.016 0.002 -9999 0 -10000 0 0
GNAI3 0.016 0.002 -9999 0 -10000 0 0
GNAI1 -0.003 0.11 -9999 0 -0.61 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.043 0.16 -9999 0 -0.5 41 41
S1PR2 0.008 0.061 -9999 0 -0.57 4 4
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.1 -9999 0 -0.52 7 7
MAPK3 0.02 0.099 -9999 0 -0.49 7 7
MAPK1 0.02 0.099 -9999 0 -0.49 7 7
JAK2 0.018 0.1 -9999 0 -0.47 8 8
CXCR4 0.007 0.12 -9999 0 -0.45 10 10
FLT1 0.016 0.033 -9999 0 -0.62 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.02 0.099 -9999 0 -0.49 7 7
S1P/S1P3/Gi 0.012 0.1 -9999 0 -0.52 7 7
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.025 0.08 -9999 0 -0.47 7 7
VEGFA -0.003 0.099 -9999 0 -0.48 15 15
S1P/S1P2/Gi 0.028 0.074 -9999 0 -0.36 7 7
VEGFR1 homodimer/VEGFA homodimer 0.014 0.077 -9999 0 -0.34 16 16
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.01 0.11 -9999 0 -0.31 32 32
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.014 0.032 -9999 0 -0.6 1 1
G12/G13 -0.001 0.023 -9999 0 -0.44 1 1
GNA14 -0.006 0.11 -9999 0 -0.56 13 13
GNA15 -0.006 0.11 -9999 0 -0.56 13 13
GNA12 0.012 0.032 -9999 0 -0.6 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.002 0.085 -9999 0 -0.6 7 7
Rac1/GTP -0.025 0.08 -9999 0 -0.47 7 7
Signaling events mediated by PRL

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
CCNE1 0.011 0.037 -10000 0 -0.48 2 2
mol:Halofuginone 0.005 0.001 -10000 0 -10000 0 0
ITGA1 -0.012 0.12 -10000 0 -0.52 18 18
CDKN1A -0.024 0.12 -10000 0 -0.42 19 19
PRL-3/alpha Tubulin -0.004 0.035 -10000 0 -0.33 4 4
mol:Ca2+ -0.019 0.093 0.22 2 -0.43 17 19
AGT -0.014 0.13 -10000 0 -0.59 17 17
CCNA2 -0.05 0.15 -10000 0 -0.5 9 9
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 -0.059 0.16 -10000 0 -0.37 79 79
CDK2/Cyclin E1 -0.014 0.12 -10000 0 -0.39 22 22
MAPK3 0.021 0.037 -10000 0 -0.33 4 4
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.037 -10000 0 -0.33 4 4
PTP4A1 -0.026 0.13 -10000 0 -10000 0 0
PTP4A3 0.009 0.052 -10000 0 -0.48 4 4
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.019 0.046 -10000 0 -0.33 6 6
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.005 0.059 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.02 0.12 -10000 0 -10000 0 0
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.001 0.033 0.22 4 -0.45 1 5
RHOC 0.004 0.063 -10000 0 -0.39 1 1
RHOA 0.005 0.059 -10000 0 -10000 0 0
cell motility 0.008 0.063 -10000 0 -10000 0 0
PRL-1/alpha Tubulin -0.017 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.022 0.09 -10000 0 -0.38 21 21
ROCK1 0.008 0.064 -10000 0 -10000 0 0
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0.001 0.086 -10000 0 -0.54 9 9
mitosis -0.025 0.13 -10000 0 -10000 0 0
ATF5 0.009 0.052 -10000 0 -0.48 4 4
EPO signaling pathway

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
BCL2L1 0.06 0.093 -9999 0 -0.84 1 1
CRKL 0.033 0.075 -9999 0 -0.42 4 4
mol:DAG 0.04 0.072 -9999 0 -0.45 2 2
HRAS 0.054 0.08 -9999 0 -0.78 1 1
MAPK8 0.013 0.099 -9999 0 -0.41 12 12
RAP1A 0.033 0.075 -9999 0 -0.42 4 4
GAB1 0.032 0.083 -9999 0 -0.49 4 4
MAPK14 0.023 0.07 -9999 0 -0.37 2 2
EPO -0.007 0.1 -9999 0 -0.48 16 16
PLCG1 0.04 0.074 -9999 0 -0.46 2 2
EPOR/TRPC2/IP3 Receptors 0.013 0.038 -9999 0 -0.49 2 2
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.062 0.16 -9999 0 -0.4 40 40
GAB1/SHC/GRB2/SOS1 -0.016 0.067 -9999 0 -0.61 2 2
EPO/EPOR (dimer) 0.008 0.081 -9999 0 -0.35 17 17
IRS2 0.033 0.083 -9999 0 -0.49 4 4
STAT1 0.043 0.091 -9999 0 -0.48 4 4
STAT5B 0.045 0.077 -9999 0 -0.49 2 2
cell proliferation 0.022 0.093 -9999 0 -0.39 11 11
GAB1/SHIP/PIK3R1/SHP2/SHC -0.017 0.07 -9999 0 -0.66 2 2
TEC 0.024 0.099 -9999 0 -0.44 9 9
SOCS3 -0.11 0.23 -9999 0 -0.52 85 85
STAT1 (dimer) 0.043 0.09 -9999 0 -0.48 4 4
JAK2 0.015 0.007 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.039 0.083 -9999 0 -0.44 4 4
EPO/EPOR 0.008 0.081 -9999 0 -0.35 17 17
LYN 0.008 0.063 -9999 0 -0.48 6 6
TEC/VAV2 0.033 0.097 -9999 0 -0.42 9 9
elevation of cytosolic calcium ion concentration 0.013 0.038 -9999 0 -0.49 2 2
SHC1 0.009 0.052 -9999 0 -0.48 4 4
EPO/EPOR (dimer)/LYN 0.021 0.08 -9999 0 -0.34 8 8
mol:IP3 0.04 0.072 -9999 0 -0.45 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.042 0.086 -9999 0 -0.48 5 5
SH2B3 0.012 0.038 -9999 0 -0.49 2 2
NFKB1 0.022 0.071 -9999 0 -0.45 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.041 0.077 -9999 0 -0.26 7 7
PTPN6 0.026 0.079 -9999 0 -0.44 4 4
TEC/VAV2/GRB2 0.039 0.094 -9999 0 -0.42 8 8
EPOR 0.013 0.038 -9999 0 -0.49 2 2
INPP5D 0.008 0.055 -9999 0 -0.51 4 4
mol:GDP -0.016 0.068 -9999 0 -0.62 2 2
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG2 0.002 0.082 -9999 0 -0.54 8 8
CRKL/CBL/C3G 0.047 0.071 -9999 0 -0.38 4 4
VAV2 0.033 0.075 -9999 0 -0.42 4 4
CBL 0.033 0.075 -9999 0 -0.42 4 4
SHC/Grb2/SOS1 -0.016 0.064 -9999 0 -0.42 5 5
STAT5A 0.036 0.11 -9999 0 -0.53 7 7
GRB2 0.014 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.055 0.11 -9999 0 -0.53 7 7
LYN/PLCgamma2 0.008 0.086 -9999 0 -0.49 10 10
PTPN11 0.014 0 -9999 0 -10000 0 0
BTK 0.021 0.11 -9999 0 -0.48 11 11
BCL2 0.053 0.14 -9999 0 -0.96 5 5
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.034 0.028 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.045 0.09 -9999 0 -0.43 6 6
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.054 0.075 -9999 0 -0.32 13 13
CaM/Ca2+ -0.003 0.023 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.035 0.06 -9999 0 -0.37 1 1
AKT1 0.052 0.029 -9999 0 -10000 0 0
MAP2K1 0.049 0.035 -9999 0 -10000 0 0
MAP3K11 0.042 0.027 -9999 0 -10000 0 0
IFNGR1 0.016 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.2 -9999 0 -0.47 78 78
Rap1/GTP -0.002 0.014 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.001 0.024 -9999 0 -10000 0 0
CEBPB 0.061 0.1 -9999 0 -0.54 5 5
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.006 0.18 -9999 0 -1 9 9
STAT1 0.035 0.06 -9999 0 -0.33 3 3
CALM1 0.013 0.032 -9999 0 -0.6 1 1
IFN-gamma (dimer) 0.001 0.05 -9999 0 -0.47 4 4
PIK3CA 0.013 0.032 -9999 0 -0.6 1 1
STAT1 (dimer)/PIAS1 0.039 0.066 -9999 0 -0.34 1 1
CEBPB/PTGES2/Cbp/p300 -0.015 0.058 -9999 0 -0.36 5 5
mol:Ca2+ 0.018 0.029 -9999 0 -10000 0 0
MAPK3 0.056 0.043 -9999 0 -10000 0 0
STAT1 (dimer) -0.07 0.11 -9999 0 -0.46 13 13
MAPK1 0.056 0.043 -9999 0 -10000 0 0
JAK2 0.016 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.016 0.002 -9999 0 -10000 0 0
CAMK2D 0.013 0.032 -9999 0 -0.6 1 1
DAPK1 0.052 0.12 -9999 0 -0.63 11 11
SMAD7 0.006 0.064 -9999 0 -0.19 3 3
CBL/CRKL/C3G 0.037 0.031 -9999 0 -10000 0 0
PI3K -0.003 0.022 -9999 0 -10000 0 0
IFNG 0.001 0.05 -9999 0 -0.47 4 4
apoptosis 0.032 0.092 -9999 0 -0.45 11 11
CAMK2G 0.013 0.032 -9999 0 -0.6 1 1
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.28 -9999 0 -0.54 171 171
CAMK2B -0.074 0.2 -9999 0 -0.54 58 58
FRAP1 0.051 0.027 -9999 0 -10000 0 0
PRKCD 0.04 0.071 -9999 0 -10000 0 0
RAP1B 0.013 0.026 -9999 0 -0.48 1 1
negative regulation of cell growth -0.054 0.075 -9999 0 -0.32 13 13
PTPN2 0.014 0 -9999 0 -10000 0 0
EP300 0.008 0.064 -9999 0 -0.6 4 4
IRF1 0.034 0.14 -9999 0 -0.55 11 11
STAT1 (dimer)/PIASy 0.042 0.061 -9999 0 -10000 0 0
SOCS1 -0.053 0.21 -9999 0 -1.4 7 7
mol:GDP -0.001 0.015 -9999 0 -10000 0 0
CASP1 -0.001 0.084 -9999 0 -0.28 16 16
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.05 0.049 -9999 0 -0.24 4 4
mol:PI-3-4-5-P3 -0.003 0.021 -9999 0 -10000 0 0
RAP1/GDP -0.002 0.014 -9999 0 -10000 0 0
CBL 0.041 0.026 -9999 0 -10000 0 0
MAP3K1 0.041 0.032 -9999 0 -10000 0 0
PIAS1 0.007 0.064 -9999 0 -0.6 4 4
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.054 0.075 -9999 0 -0.32 13 13
PTPN11 0.034 0.027 -9999 0 -10000 0 0
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.048 0.12 -9999 0 -0.36 48 48
AKT1 0.075 0.08 -9999 0 -0.52 2 2
PTK2B -0.001 0.14 -9999 0 -0.49 16 16
VEGFR2 homodimer/Frs2 0.029 0.073 -9999 0 -0.6 3 3
CAV1 -0.045 0.16 -9999 0 -0.49 43 43
CALM1 0.012 0.032 -9999 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.018 0.08 -9999 0 -0.6 4 4
endothelial cell proliferation 0.062 0.1 -9999 0 -0.44 4 4
mol:Ca2+ 0.039 0.089 -9999 0 -0.54 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.019 0.083 -9999 0 -0.59 5 5
RP11-342D11.1 0.029 0.089 -9999 0 -0.55 4 4
CDH5 0.01 0.045 -9999 0 -0.48 3 3
VEGFA homodimer -0.011 0.049 -9999 0 -10000 0 0
SHC1 0.009 0.052 -9999 0 -0.48 4 4
SHC2 0.011 0.041 -9999 0 -0.54 2 2
HRAS/GDP -0.018 0.072 -9999 0 -0.49 5 5
SH2D2A -0.075 0.2 -9999 0 -0.53 59 59
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.021 0.072 -9999 0 -0.47 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.059 0.13 -9999 0 -0.59 9 9
VEGFR1 homodimer 0.012 0.032 -9999 0 -0.6 1 1
SHC/GRB2/SOS1 -0.019 0.078 -9999 0 -0.52 6 6
GRB10 0.038 0.095 -9999 0 -0.56 5 5
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PAK1 -0.038 0.15 -9999 0 -0.49 38 38
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.019 0.089 -9999 0 -0.65 5 5
HRAS 0.013 0.026 -9999 0 -0.48 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.08 -9999 0 -0.38 4 4
HIF1A 0.013 0.026 -9999 0 -0.48 1 1
FRS2 0.011 0.041 -9999 0 -0.54 2 2
oxygen and reactive oxygen species metabolic process -0.019 0.082 -9999 0 -0.58 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0 0.087 -9999 0 -0.52 10 10
Nck/Pak -0.037 0.11 -9999 0 -0.34 39 39
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.016 0.077 -9999 0 -0.6 4 4
mol:GDP -0.019 0.076 -9999 0 -0.5 6 6
mol:NADP 0.062 0.081 -9999 0 -0.42 4 4
eNOS/Hsp90 0.066 0.078 -9999 0 -0.4 4 4
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.039 0.09 -9999 0 -0.55 4 4
HIF1A/ARNT -0.002 0.025 -9999 0 -0.33 2 2
SHB 0.014 0 -9999 0 -10000 0 0
VEGFA -0.004 0.098 -9999 0 -0.48 15 15
VEGFC -0.002 0.091 -9999 0 -0.51 11 11
FAK1/Vinculin 0.034 0.12 -9999 0 -0.6 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.5 15 15
PTPN6 -0.004 0.098 -9999 0 -0.53 12 12
EPAS1 0.021 0.036 -9999 0 -0.34 2 2
mol:L-citrulline 0.062 0.081 -9999 0 -0.42 4 4
ITGAV 0.012 0.032 -9999 0 -0.6 1 1
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.016 0.074 -9999 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer -0.021 0.083 -9999 0 -0.6 4 4
VEGFR2/3 heterodimer 0.023 0.098 -9999 0 -0.61 6 6
VEGFB 0.014 0 -9999 0 -10000 0 0
MAPK11 0.039 0.095 -9999 0 -0.54 5 5
VEGFR2 homodimer 0.03 0.078 -9999 0 -0.54 6 6
FLT1 0.012 0.032 -9999 0 -0.6 1 1
NEDD4 0.006 0.073 -9999 0 -0.51 7 7
MAPK3 0.031 0.096 -9999 0 -0.49 4 4
MAPK1 0.031 0.096 -9999 0 -0.49 4 4
VEGFA145/NRP2 -0.02 0.085 -9999 0 -0.37 20 20
VEGFR1/2 heterodimer 0.03 0.071 -9999 0 -0.6 3 3
KDR 0.03 0.078 -9999 0 -0.54 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.033 0.097 -9999 0 -0.52 5 5
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.033 0.097 -9999 0 -0.48 5 5
PI3K 0.062 0.09 -9999 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.017 0.079 -9999 0 -0.6 4 4
FES 0.035 0.099 -9999 0 -0.61 4 4
GAB1 -0.016 0.077 -9999 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.016 0.077 -9999 0 -0.6 4 4
CTNNB1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.013 0.026 -9999 0 -0.48 1 1
eNOS/Caveolin-1 0.041 0.11 -9999 0 -0.49 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.018 0.08 -9999 0 -0.6 4 4
PI3K/GAB1 0.076 0.084 -9999 0 -0.48 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.036 0.091 -9999 0 -0.55 5 5
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.02 0.099 -9999 0 -0.64 6 6
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.039 0.091 -9999 0 -0.56 4 4
actin cytoskeleton reorganization -0.059 0.13 -9999 0 -0.59 9 9
PTK2 0.031 0.11 -9999 0 -0.6 4 4
EDG1 0.029 0.089 -9999 0 -0.55 4 4
mol:DAG 0.039 0.09 -9999 0 -0.55 4 4
CaM/Ca2+ -0.018 0.069 -9999 0 -0.5 4 4
MAP2K3 0.036 0.11 -9999 0 -0.55 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.038 0.097 -9999 0 -0.57 5 5
PLCG1 0.039 0.091 -9999 0 -0.56 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.015 0.072 -9999 0 -0.57 4 4
IQGAP1 0.005 0.068 -9999 0 -0.52 6 6
YES1 0.011 0.046 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.016 0.077 -9999 0 -0.6 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.025 0.093 -9999 0 -0.57 6 6
cell migration 0.057 0.12 -9999 0 -0.6 6 6
mol:PI-3-4-5-P3 0.061 0.085 -9999 0 -0.53 3 3
FYN 0.014 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.036 0.085 -9999 0 -0.51 4 4
mol:NO 0.062 0.081 -9999 0 -0.42 4 4
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.018 0.072 -9999 0 -0.49 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.097 -9999 0 -0.57 5 5
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.18 -9999 0 -0.51 47 47
NOS3 0.063 0.089 -9999 0 -0.48 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.018 0.083 -9999 0 -0.6 5 5
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.045 0.087 -9999 0 -0.51 4 4
PRKCB 0.007 0.14 -9999 0 -0.49 12 12
VCL 0.005 0.071 -9999 0 -0.54 6 6
VEGFA165/NRP1 0.029 0.09 -9999 0 -0.55 4 4
VEGFR1/2 heterodimer/VEGFA homodimer -0.017 0.079 -9999 0 -0.6 4 4
VEGFA165/NRP2 -0.02 0.085 -9999 0 -0.37 20 20
MAPKKK cascade 0.06 0.094 -9999 0 -0.53 4 4
NRP2 0.005 0.074 -9999 0 -0.56 6 6
VEGFC homodimer -0.002 0.091 -9999 0 -0.51 11 11
NCK1 0.012 0.032 -9999 0 -0.6 1 1
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.038 0.11 -9999 0 -0.56 4 4
MAP3K13 0.03 0.11 -9999 0 -0.55 5 5
PDPK1 0.066 0.08 -9999 0 -0.47 3 3
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.043 -9999 0 -0.73 1 1
VEGFR1 homodimer/NRP1 0.022 0.043 -9999 0 -0.74 1 1
mol:DAG -0.017 0.13 -9999 0 -0.66 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.012 0.06 -9999 0 -0.68 1 1
CaM/Ca2+ -0.01 0.12 -9999 0 -0.63 1 1
HIF1A 0.021 0.032 -9999 0 -0.4 2 2
GAB1 0.011 0.041 -9999 0 -0.54 2 2
AKT1 0.007 0.12 -9999 0 -0.57 2 2
PLCG1 -0.018 0.13 -9999 0 -0.67 1 1
NOS3 0.008 0.13 -9999 0 -0.48 3 3
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO 0.009 0.12 -9999 0 -0.46 3 3
FLT1 0.03 0.049 -9999 0 -0.57 2 2
PGF -0.088 0.22 -9999 0 -0.56 65 65
VEGFR1 homodimer/NRP2/VEGFR121 0.023 0.081 -9999 0 -0.58 2 2
CALM1 0.012 0.032 -9999 0 -0.6 1 1
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
eNOS/Hsp90 0.016 0.12 -9999 0 -0.49 2 2
endothelial cell proliferation -0.031 0.16 -9999 0 -0.51 15 15
mol:Ca2+ -0.017 0.13 -9999 0 -0.66 1 1
MAPK3 0.001 0.12 -9999 0 -0.58 1 1
MAPK1 0.001 0.12 -9999 0 -0.58 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
PLGF homodimer -0.088 0.22 -9999 0 -0.56 65 65
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.045 0.16 -9999 0 -0.49 43 43
VEGFA homodimer -0.006 0.098 -9999 0 -0.48 15 15
VEGFR1 homodimer/VEGFA homodimer 0.02 0.073 -9999 0 -0.73 1 1
platelet activating factor biosynthetic process 0.008 0.11 -9999 0 -0.55 1 1
PI3K -0.009 0.13 -9999 0 -0.62 2 2
PRKCA -0.008 0.12 -9999 0 -0.62 1 1
PRKCB -0.048 0.16 -9999 0 -0.55 13 13
VEGFR1 homodimer/PLGF homodimer -0.032 0.14 -9999 0 -0.37 42 42
VEGFA -0.006 0.098 -9999 0 -0.48 15 15
VEGFB 0.014 0 -9999 0 -10000 0 0
mol:IP3 -0.017 0.13 -9999 0 -0.66 1 1
RASA1 0.041 0.04 -9999 0 -0.67 1 1
NRP2 0.005 0.074 -9999 0 -0.56 6 6
VEGFR1 homodimer 0.03 0.049 -9999 0 -0.57 2 2
VEGFB homodimer 0.014 0 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
eNOS/Caveolin-1 -0.011 0.14 -9999 0 -0.48 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.049 0.11 -9999 0 -0.61 2 2
mol:L-citrulline 0.009 0.12 -9999 0 -0.46 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.036 0.063 -9999 0 -0.64 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.069 -9999 0 -0.68 1 1
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.1 -9999 0 -0.59 2 2
PDPK1 -0.001 0.12 -9999 0 -0.58 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.067 -9999 0 -0.68 1 1
mol:NADP 0.009 0.12 -9999 0 -0.46 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.011 0.053 -9999 0 -0.63 1 1
VEGFR1 homodimer/NRP2 0.027 0.063 -9999 0 -0.43 5 5
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.004 0.076 0.58 6 -10000 0 6
PI3K Class IB/PDE3B 0.004 0.076 -10000 0 -0.58 6 6
PDE3B 0.004 0.076 -10000 0 -0.58 6 6
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0.046 -9999 0 -0.6 2 2
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.01 0.058 -9999 0 -0.36 9 9
forebrain development -0.009 0.16 -9999 0 -0.45 31 31
GNAO1 0.004 0.079 -9999 0 -0.61 6 6
SMO/beta Arrestin2 0.014 0.062 -9999 0 -0.42 7 7
SMO 0.003 0.083 -9999 0 -0.59 7 7
ARRB2 0.014 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.04 0.07 -9999 0 -0.6 1 1
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.014 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.003 0.021 -9999 0 -0.32 1 1
GNAI1 -0.004 0.11 -9999 0 -0.6 11 11
XPO1 0.015 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.045 0.11 -9999 0 -0.56 9 9
SAP30 0.012 0.032 -9999 0 -0.6 1 1
mol:GDP 0.003 0.083 -9999 0 -0.59 7 7
MIM/GLI2A 0.011 0.054 -9999 0 -0.57 3 3
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0.002 -9999 0 -10000 0 0
GLI2 0.045 0.032 -9999 0 -10000 0 0
GLI3 0.034 0.073 -9999 0 -0.64 1 1
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.009 0.056 -9999 0 -0.6 3 3
Gi family/GTP 0.021 0.077 -9999 0 -0.35 7 7
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.053 0.054 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.055 0.048 -9999 0 -10000 0 0
FOXA2 -0.036 0.13 -9999 0 -1.2 2 2
neural tube patterning -0.009 0.16 -9999 0 -0.45 31 31
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.026 0.047 -9999 0 -0.32 4 4
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.011 0.054 -9999 0 -0.57 3 3
embryonic limb morphogenesis -0.009 0.16 -9999 0 -0.45 31 31
SUFU 0.026 0.033 -9999 0 -10000 0 0
LGALS3 -0.025 0.14 -9999 0 -0.48 29 29
catabolic process 0.064 0.065 -9999 0 -0.5 1 1
GLI3A/CBP -0.019 0.11 -9999 0 -0.35 25 25
KIF3A 0.012 0.032 -9999 0 -0.6 1 1
GLI1 -0.01 0.16 -9999 0 -0.46 31 31
RAB23 0.012 0.032 -9999 0 -0.6 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.009 0.056 -9999 0 -0.6 3 3
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.009 0.085 -9999 0 -0.45 3 3
GNAZ 0.013 0.032 -9999 0 -0.6 1 1
RBBP4 0.014 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0.026 -9999 0 -0.48 1 1
PIAS1 0.007 0.064 -9999 0 -0.6 4 4
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.049 0.03 -9999 0 -10000 0 0
STK36 0.015 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.027 0.078 -9999 0 -0.47 4 4
PTCH1 -0.011 0.2 -9999 0 -0.94 10 10
MIM/GLI1 -0.01 0.18 -9999 0 -0.56 17 17
CREBBP -0.019 0.11 -9999 0 -0.34 25 25
Su(fu)/SIN3/HDAC complex 0.051 0.027 -9999 0 -0.29 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.051 0.21 -10000 0 -1.1 12 12
oxygen homeostasis 0.008 0.017 -10000 0 -10000 0 0
TCEB2 0.014 0 -10000 0 -10000 0 0
TCEB1 0.014 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.003 0.045 -10000 0 -0.32 3 3
EPO 0.099 0.23 -10000 0 -0.72 10 10
FIH (dimer) 0.022 0.017 -10000 0 -10000 0 0
APEX1 0.021 0.017 -10000 0 -10000 0 0
SERPINE1 0.019 0.33 -10000 0 -0.77 16 16
FLT1 0.001 0.09 -10000 0 -1.6 1 1
ADORA2A 0.099 0.23 -10000 0 -0.72 9 9
germ cell development 0.09 0.24 -10000 0 -0.71 10 10
SLC11A2 0.1 0.23 -10000 0 -0.73 9 9
BHLHE40 0.092 0.25 -10000 0 -0.82 11 11
HIF1AN 0.022 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.022 0.086 -10000 0 -0.48 5 5
ETS1 0.025 0.058 -10000 0 -0.52 4 4
CITED2 0.002 0.041 -10000 0 -10000 0 0
KDR -0.006 0.11 -10000 0 -0.96 4 4
PGK1 0.1 0.23 -10000 0 -0.73 9 9
SIRT1 0.014 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.27 -10000 0 -0.88 10 10
EPAS1 0.073 0.11 -10000 0 -0.36 4 4
SP1 0.018 0.018 -10000 0 -10000 0 0
ABCG2 0.1 0.24 -10000 0 -0.77 9 9
EFNA1 0.1 0.23 -10000 0 -0.75 9 9
FXN 0.1 0.23 -10000 0 -0.7 10 10
POU5F1 0.089 0.25 -10000 0 -0.75 10 10
neuron apoptosis -0.11 0.26 0.84 10 -10000 0 10
EP300 0.007 0.064 -10000 0 -0.6 4 4
EGLN3 0.013 0.075 -10000 0 -0.61 5 5
EGLN2 0.022 0.017 -10000 0 -10000 0 0
EGLN1 0.022 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.019 0.033 -10000 0 -0.51 1 1
SLC2A1 0.1 0.23 -10000 0 -0.71 10 10
TWIST1 0.073 0.27 -10000 0 -0.73 18 18
ELK1 0.023 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.023 0.087 -10000 0 -0.46 7 7
VEGFA 0.094 0.25 -10000 0 -0.82 11 11
CREBBP 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.081 0.13 -10000 0 -0.36 51 51
Ran/GTP/Exportin 1/HDAC1 -0.001 0.02 -10000 0 -0.27 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.031 0.13 -10000 0 -0.32 49 49
SUMO1 0.014 0 -10000 0 -10000 0 0
ZFPM1 0.013 0.026 -10000 0 -0.48 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -10000 0 -10000 0 0
FKBP3 0.014 0 -10000 0 -10000 0 0
Histones -0.036 0.061 -10000 0 -0.4 1 1
YY1/LSF 0.03 0.035 -10000 0 -0.35 1 1
SMG5 0.014 0 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.037 0.12 -10000 0 -0.45 2 2
I kappa B alpha/HDAC1 -0.021 0.087 -10000 0 -0.31 4 4
SAP18 0.014 0 -10000 0 -10000 0 0
RELA -0.028 0.11 -10000 0 -0.26 51 51
HDAC1/Smad7 -0.002 0.027 -10000 0 -0.36 2 2
RANGAP1 0.014 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.019 0.085 -10000 0 -0.3 2 2
NuRD/MBD3 Complex 0.05 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.02 0.1 -10000 0 -0.35 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.01 0.12 -10000 0 -0.56 15 15
GATA1 0.003 0.057 -10000 0 -0.48 5 5
Mad/Max 0 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.025 -10000 0 -10000 0 0
RBBP7 0.014 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0.014 0 -10000 0 -10000 0 0
MAX 0.014 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
NFKBIA -0.03 0.095 -10000 0 -0.34 2 2
KAT2B 0.013 0.026 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.046 0.022 -10000 0 -10000 0 0
SIN3 complex -0.001 0.017 -10000 0 -0.32 1 1
SMURF1 0.014 0 -10000 0 -10000 0 0
CHD3 0.012 0.032 -10000 0 -0.6 1 1
SAP30 0.012 0.032 -10000 0 -0.6 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.012 0.032 -10000 0 -0.6 1 1
YY1/HDAC3 -0.005 0.084 -10000 0 -0.31 2 2
YY1/HDAC2 0.031 0.029 -10000 0 -10000 0 0
YY1/HDAC1 0.028 0.041 -10000 0 -0.35 2 2
NuRD/MBD2 Complex (MeCP1) 0.05 0.019 -10000 0 -10000 0 0
PPARG -0.085 0.13 -10000 0 -0.35 61 61
HDAC8/hEST1B -0.001 0.019 -10000 0 -0.36 1 1
UBE2I 0.014 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -10000 0 -10000 0 0
TNFRSF1A 0.005 0.068 -10000 0 -0.52 6 6
HDAC3/SMRT (N-CoR2) -0.019 0.085 -10000 0 -0.3 2 2
MBD3L2 0 0.001 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.027 -10000 0 -0.36 2 2
CREBBP 0.014 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.054 0.02 -10000 0 -10000 0 0
HDAC1 0.011 0.046 -10000 0 -0.6 2 2
HDAC3 -0.03 0.095 -10000 0 -0.34 2 2
HDAC2 0.014 0 -10000 0 -10000 0 0
YY1 0.029 0.035 -10000 0 -0.29 4 4
HDAC8 0.012 0.032 -10000 0 -0.6 1 1
SMAD7 0.014 0 -10000 0 -10000 0 0
NCOR2 0.014 0 -10000 0 -10000 0 0
MXD1 0.014 0 -10000 0 -10000 0 0
STAT3 0.024 0.039 -10000 0 -0.35 4 4
NFKB1 0.013 0.026 -10000 0 -0.48 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.014 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.034 0.041 -10000 0 -0.31 3 3
YY1/SAP30/HDAC1 0.034 0.041 -10000 0 -0.31 3 3
EP300 0.007 0.064 -10000 0 -0.6 4 4
STAT3 (dimer non-phopshorylated) 0.024 0.039 -10000 0 -0.35 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.094 -10000 0 -0.33 2 2
histone deacetylation 0.05 0.019 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.084 -10000 0 -0.36 2 2
nuclear export 0.001 0.019 0.36 1 -10000 0 1
PRKACA 0.014 0 -10000 0 -10000 0 0
GATAD2B 0.014 0 -10000 0 -10000 0 0
GATAD2A 0.014 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.032 0.11 -10000 0 -0.38 11 11
GATA1/HDAC1 -0.007 0.05 -10000 0 -0.36 7 7
GATA1/HDAC3 -0.031 0.086 -10000 0 -0.34 3 3
CHD4 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.12 0.18 -10000 0 -0.38 113 113
SIN3/HDAC complex/Mad/Max 0.05 0.019 -10000 0 -10000 0 0
NuRD Complex 0.059 0.02 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.036 0.06 -10000 0 -0.39 1 1
SIN3B 0.014 0 -10000 0 -10000 0 0
MTA2 0.014 0 -10000 0 -10000 0 0
SIN3A 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.031 0.024 -10000 0 -0.3 2 2
HDAC complex -0.002 0.024 -10000 0 -0.32 2 2
GATA1/Fog1 -0.005 0.042 -10000 0 -0.33 6 6
FKBP25/HDAC1/HDAC2 -0.002 0.027 -10000 0 -0.36 2 2
TNF -0.15 0.25 -10000 0 -0.54 109 109
negative regulation of cell growth 0.05 0.019 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0.019 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.039 0.14 -10000 0 -0.34 51 51
SIN3/HDAC complex/NCoR1 0.048 0.022 -10000 0 -10000 0 0
TFCP2 0.012 0.032 -10000 0 -0.6 1 1
NR2C1 0.014 0 -10000 0 -10000 0 0
MBD3 0.014 0 -10000 0 -10000 0 0
MBD2 0.014 0 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.012 0.059 -9999 0 -0.58 1 1
TC10/GTP -0.009 0.053 -9999 0 -0.56 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.029 -9999 0 -0.3 3 3
HRAS 0.013 0.026 -9999 0 -0.48 1 1
APS homodimer -0.001 0.094 -9999 0 -0.59 9 9
GRB14 -0.17 0.26 -9999 0 -0.53 123 123
FOXO3 -0.025 0.09 -9999 0 -0.57 9 9
AKT1 -0.035 0.13 -9999 0 -0.43 4 4
INSR 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.036 0.03 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.032 -9999 0 -0.6 1 1
SORBS1 0.007 0.064 -9999 0 -0.6 4 4
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.035 0.03 -9999 0 -10000 0 0
CAV1 -0.005 0.095 -9999 0 -0.38 6 6
CBL/APS/CAP/Crk-II/C3G -0.01 0.059 -9999 0 -0.62 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.029 -9999 0 -0.3 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.029 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.033 -9999 0 -10000 0 0
RPS6KB1 -0.024 0.12 -9999 0 -0.42 3 3
PARD6A 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.044 -9999 0 -0.83 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.061 0.09 -9999 0 -0.41 3 3
HRAS/GTP -0.007 0.038 -9999 0 -0.42 1 1
Insulin Receptor 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.005 0.035 -9999 0 -10000 0 0
PRKCI -0.022 0.054 -9999 0 -0.53 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.078 0.11 -9999 0 -0.47 4 4
SHC1 0.009 0.052 -9999 0 -0.48 4 4
negative regulation of MAPKKK cascade -0.002 0.041 -9999 0 -0.51 2 2
PI3K -0.003 0.029 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.018 -9999 0 -0.34 1 1
AKT2 -0.035 0.13 -9999 0 -0.43 4 4
PRKCZ -0.039 0.11 -9999 0 -0.58 13 13
SH2B2 -0.001 0.094 -9999 0 -0.59 9 9
SHC/SHIP 0.028 0.051 -9999 0 -0.39 2 2
F2RL2 -0.093 0.21 -9999 0 -0.5 76 76
TRIP10 0.005 0.071 -9999 0 -0.54 6 6
Insulin Receptor/Insulin/Shc -0.006 0.04 -9999 0 -0.28 7 7
TC10/GTP/CIP4/Exocyst -0.005 0.042 -9999 0 -0.33 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.005 0.035 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
CBL/APS/CAP/Crk-II -0.011 0.064 -9999 0 -0.35 11 11
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.007 0.043 -9999 0 -0.31 4 4
INPP5D 0.023 0.047 -9999 0 -0.35 4 4
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.027 0.14 -9999 0 -0.88 9 9
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
p62DOK/RasGAP -0.002 0.041 -9999 0 -0.71 1 1
INS -0.003 0.06 -9999 0 -0.57 4 4
mol:PI-3-4-P2 0.023 0.046 -9999 0 -0.35 4 4
GRB2 0.014 0 -9999 0 -10000 0 0
EIF4EBP1 -0.031 0.13 -9999 0 -0.43 10 10
PTPRA 0.016 0.003 -9999 0 -10000 0 0
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
TC10/GTP/CIP4 -0.005 0.042 -9999 0 -0.33 6 6
PDPK1 0.012 0.032 -9999 0 -0.6 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.03 -9999 0 -0.31 3 3
Insulin Receptor/Insulin/IRS3 -0.004 0.043 -9999 0 -0.41 4 4
Par3/Par6 -0.054 0.1 -9999 0 -0.32 18 18
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.003 0.029 -9999 0 -0.32 3 3
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.005 0.039 -9999 0 -0.33 5 5
GATA1/HDAC5 -0.005 0.039 -9999 0 -0.33 5 5
GATA2/HDAC5 -0.017 0.081 -9999 0 -0.4 15 15
HDAC5/BCL6/BCoR -0.001 0.014 -9999 0 -0.27 1 1
HDAC9 0.004 0.076 -9999 0 -0.53 7 7
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
GATA2 -0.01 0.12 -9999 0 -0.56 15 15
HDAC4/RFXANK -0.001 0.017 -9999 0 -0.33 1 1
BCOR 0.013 0.026 -9999 0 -0.48 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.004 0.039 -9999 0 -0.44 3 3
Histones 0.041 0.026 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.017 -9999 0 -0.33 1 1
CAMK4 -0.17 0.27 -9999 0 -0.57 113 113
Tubulin/HDAC6 -0.001 0.019 -9999 0 -0.36 1 1
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.003 0.057 -9999 0 -0.48 5 5
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.023 -9999 0 -0.44 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.017 -9999 0 -0.33 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.11 0.16 -9999 0 -0.34 113 113
HDAC4/ER alpha -0.021 0.089 -9999 0 -0.39 20 20
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.041 0.026 -9999 0 -10000 0 0
cell motility -0.001 0.019 -9999 0 -0.36 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.016 0.13 -9999 0 -0.54 20 20
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.005 0.095 -9999 0 -0.48 14 14
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.008 0.041 -9999 0 -10000 0 0
GNG2 0.009 0.056 -9999 0 -0.6 3 3
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.012 0.032 -9999 0 -0.6 1 1
HDAC11 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.013 0.026 -9999 0 -0.48 1 1
nuclear import -0.032 0 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC 0.011 0.17 -9999 0 -1.4 4 4
PLK1 0.057 0.2 -9999 0 -0.97 6 6
CDKN1B 0.1 0.11 -9999 0 -10000 0 0
FOXO3 0.071 0.14 -9999 0 -0.58 4 4
KAT2B 0.022 0.028 -9999 0 -0.46 1 1
FOXO1/SIRT1 -0.005 0.07 -9999 0 -0.41 4 4
CAT 0.075 0.13 -9999 0 -0.59 1 1
CTNNB1 0.014 0 -9999 0 -10000 0 0
AKT1 0.025 0.016 -9999 0 -10000 0 0
FOXO1 0.026 0.085 -9999 0 -0.35 10 10
MAPK10 0.037 0.04 -9999 0 -0.32 4 4
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.095 0.067 -9999 0 -10000 0 0
response to oxidative stress 0.011 0.019 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.018 0.12 -9999 0 -0.53 4 4
XPO1 0.015 0.001 -9999 0 -10000 0 0
EP300 0.009 0.065 -9999 0 -0.6 4 4
BCL2L11 0.033 0.08 -9999 0 -1.4 1 1
FOXO1/SKP2 0.022 0.097 -9999 0 -0.41 11 11
mol:GDP 0.011 0.019 -9999 0 -10000 0 0
RAN 0.016 0.001 -9999 0 -10000 0 0
GADD45A 0.082 0.14 -9999 0 -0.47 9 9
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.043 0.072 -9999 0 -10000 0 0
MST1 -0.023 0.16 -9999 0 -0.54 30 30
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.012 0.1 -9999 0 -0.51 1 1
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.032 0.059 -9999 0 -0.31 10 10
MAPK9 0.041 0.014 -9999 0 -10000 0 0
YWHAG 0.002 0.077 -9999 0 -0.48 9 9
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.009 0.011 -9999 0 -10000 0 0
SOD2 0.1 0.15 -9999 0 -0.68 2 2
RBL2 0.09 0.11 -9999 0 -10000 0 0
RAL/GDP 0.031 0.017 -9999 0 -10000 0 0
CHUK 0.023 0.013 -9999 0 -10000 0 0
Ran/GTP 0.014 0.005 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.038 0.018 -9999 0 -10000 0 0
CSNK1G1 0.013 0.026 -9999 0 -0.48 1 1
FASLG 0.003 0.1 -9999 0 -0.44 1 1
SKP2 0.002 0.084 -9999 0 -0.56 8 8
USP7 0.016 0.001 -9999 0 -10000 0 0
IKBKB 0.023 0.013 -9999 0 -10000 0 0
CCNB1 0.066 0.16 -9999 0 -0.7 3 3
FOXO1-3a-4/beta catenin 0.13 0.12 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.096 -9999 0 -0.41 11 11
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.007 0.099 -9999 0 -0.58 10 10
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.008 -9999 0 -10000 0 0
ZFAND5 0.097 0.061 -9999 0 -10000 0 0
SFN -0.11 0.23 -9999 0 -0.52 87 87
CDK2 0 0.086 -9999 0 -0.53 9 9
FOXO3A/14-3-3 0.025 0.092 -9999 0 -0.36 3 3
CREBBP 0.014 0.013 -9999 0 -10000 0 0
FBXO32 0.061 0.18 -9999 0 -1.1 4 4
BCL6 0.09 0.11 -9999 0 -10000 0 0
RALB 0.015 0.001 -9999 0 -10000 0 0
RALA 0.015 0.001 -9999 0 -10000 0 0
YWHAH -0.009 0.1 -9999 0 -0.48 17 17
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.014 0.076 -9999 0 -0.36 9 9
PDGFB-D/PDGFRB/SLAP -0.004 0.1 -9999 0 -0.4 21 21
PDGFB-D/PDGFRB/APS/CBL -0.01 0.065 -9999 0 -0.38 10 10
AKT1 0.059 0.037 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.01 0.085 -9999 0 -0.38 7 7
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
FGR 0.001 0.03 -9999 0 -10000 0 0
mol:Ca2+ 0.02 0.041 -9999 0 -10000 0 0
MYC 0.004 0.18 -9999 0 -0.82 15 15
SHC1 0.009 0.052 -9999 0 -0.48 4 4
HRAS/GDP 0.036 0.027 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.001 0.025 -9999 0 -10000 0 0
GRB10 0.012 0.032 -9999 0 -0.6 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0.02 0.041 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
GRB7 -0.036 0.14 -9999 0 -0.48 34 34
PDGFB-D/PDGFRB/SHP2 0.017 0.033 -9999 0 -0.33 3 3
PDGFB-D/PDGFRB/GRB10 0.015 0.04 -9999 0 -0.36 4 4
cell cycle arrest -0.005 0.099 -9999 0 -0.4 21 21
HRAS 0.013 0.026 -9999 0 -0.48 1 1
HIF1A 0.063 0.036 -9999 0 -10000 0 0
GAB1 0.008 0.071 -9999 0 -0.4 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.012 0.073 -9999 0 -0.39 2 2
PDGFB-D/PDGFRB 0.01 0.032 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.033 -9999 0 -0.33 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.024 0.086 -9999 0 -0.41 10 10
positive regulation of MAPKKK cascade 0.017 0.032 -9999 0 -0.33 3 3
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.042 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.014 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.019 0.11 -9999 0 -0.35 36 36
SHB 0.014 0 -9999 0 -10000 0 0
BLK -0.042 0.11 -9999 0 -0.54 13 13
PTPN2 0.014 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.033 -9999 0 -0.33 3 3
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
VAV2 0.01 0.085 -9999 0 -0.38 5 5
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.016 0.037 -9999 0 -0.33 4 4
LCK -0.055 0.15 -9999 0 -0.52 29 29
PDGFRB 0.01 0.045 -9999 0 -0.48 3 3
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.012 0.094 -9999 0 -0.59 8 8
ABL1 0.01 0.061 -9999 0 -0.34 2 2
PDGFB-D/PDGFRB/CBL 0.008 0.068 -9999 0 -0.41 1 1
PTPN1 0.014 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.001 0.085 -9999 0 -0.48 11 11
cell proliferation 0.008 0.16 -9999 0 -0.72 15 15
SLA -0.015 0.12 -9999 0 -0.55 19 19
actin cytoskeleton reorganization 0.048 0.036 -9999 0 -10000 0 0
SRC 0.002 0.028 -9999 0 -10000 0 0
PI3K -0.004 0.03 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.029 0.096 -9999 0 -0.3 38 38
SH2B2 -0.001 0.094 -9999 0 -0.59 9 9
PLCgamma1/SPHK1 0.01 0.087 -9999 0 -0.39 7 7
LYN 0 0.033 -9999 0 -10000 0 0
LRP1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.001 0.09 -9999 0 -0.6 8 8
NCK1-2/p130 Cas 0.004 0.034 -9999 0 -10000 0 0
SPHK1 -0.025 0.14 -9999 0 -0.54 26 26
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.02 0.042 -9999 0 -10000 0 0
PLCG1 0.02 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.004 0.042 -9999 0 -0.37 2 2
YES1 -0.001 0.051 -9999 0 -0.57 2 2
cell migration -0.005 0.042 -9999 0 -0.37 2 2
SHC/Grb2/SOS1 0.004 0.042 -9999 0 -0.44 2 2
SLC9A3R2 0.011 0.037 -9999 0 -0.48 2 2
SLC9A3R1 0.011 0.046 -9999 0 -0.6 2 2
NHERF1-2/PDGFRB/PTEN 0.007 0.042 -9999 0 -0.33 2 2
FYN 0.003 0.028 -9999 0 -10000 0 0
DOK1 0.032 0.032 -9999 0 -0.34 1 1
HRAS/GTP -0.001 0.018 -9999 0 -0.34 1 1
PDGFB 0.014 0 -9999 0 -10000 0 0
RAC1 0.015 0.11 -9999 0 -0.43 16 16
PRKCD 0.016 0.082 -9999 0 -0.33 17 17
FER 0.012 0.089 -9999 0 -0.33 21 21
MAPKKK cascade -0.004 0.037 -9999 0 -0.44 2 2
RASA1 0.033 0.026 -9999 0 -10000 0 0
NCK1 0.012 0.032 -9999 0 -0.6 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk 0.039 0.029 -9999 0 -0.3 1 1
PDGFB-D/PDGFRB/SHB 0.017 0.033 -9999 0 -0.33 3 3
chemotaxis 0.01 0.06 -9999 0 -0.33 2 2
STAT1-3-5/STAT1-3-5 -0.013 0.053 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.007 0.032 -9999 0 -0.35 3 3
PTPRJ 0.013 0.026 -9999 0 -0.48 1 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0.019 -10000 0 -0.34 1 1
BAD/BCL-XL/YWHAZ 0.035 0.014 -10000 0 -10000 0 0
CDKN1B 0.04 0.007 -10000 0 -10000 0 0
CDKN1A 0.005 0.093 -10000 0 -0.28 16 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
FOXO3 0.04 0.007 -10000 0 -10000 0 0
AKT1 0 0.006 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
AKT3 0.012 0.061 -10000 0 -0.46 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.018 -10000 0 -0.28 1 1
AKT1/ASK1 0.036 0.033 -10000 0 -0.32 3 3
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.014 0 -10000 0 -10000 0 0
RAF1 0.014 0 -10000 0 -10000 0 0
JNK cascade 0.003 0.028 0.31 3 -10000 0 3
TSC1 0.04 0.007 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.007 -10000 0 -10000 0 0
EP300 0.007 0.064 -10000 0 -0.6 4 4
mol:GDP 0.033 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.04 0.007 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.026 0.017 -10000 0 -0.3 1 1
MAP3K5 0.009 0.056 -10000 0 -0.6 3 3
MAPKAP1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.059 0.27 1 -10000 0 1
YWHAH -0.009 0.1 -10000 0 -0.48 17 17
AKT1S1 0.04 0.007 -10000 0 -10000 0 0
CASP9 0.04 0.007 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.047 0.007 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.019 -10000 0 -0.36 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
SRC 0.014 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.029 0.075 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.002 -10000 0 -10000 0 0
CHUK 0.04 0.007 -10000 0 -10000 0 0
BAD/BCL-XL 0.054 0.014 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.018 0.02 -10000 0 -0.36 1 1
FOXO1-3a-4/14-3-3 family 0.031 0.063 -10000 0 -0.29 1 1
PDPK1 0.012 0.032 -10000 0 -0.6 1 1
MDM2 0.039 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.007 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.049 0.039 -10000 0 -0.38 1 1
TSC1/TSC2 0.047 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.038 -10000 0 -0.36 1 1
glucose import -0.013 0.11 -10000 0 -0.28 53 53
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.013 0.11 -10000 0 -0.28 53 53
GSK3A 0.04 0.007 -10000 0 -10000 0 0
FOXO1 0.038 0.028 -10000 0 -0.28 2 2
GSK3B 0.04 0.007 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.52 87 87
G1/S transition of mitotic cell cycle 0.047 0.007 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.008 0.085 -10000 0 -0.37 4 4
PRKACA 0.014 0 -10000 0 -10000 0 0
KPNA1 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
YWHAG 0.002 0.077 -10000 0 -0.48 9 9
RHEB 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.066 0.2 -9999 0 -0.55 52 52
CLTC 0.031 0.015 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.016 0.046 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.014 0 -9999 0 -10000 0 0
CD59 0.026 0.021 -9999 0 -10000 0 0
CPE 0.009 0.066 -9999 0 -0.37 11 11
CTNNB1 0.014 0 -9999 0 -10000 0 0
membrane fusion 0.015 0.048 -9999 0 -10000 0 0
CTNND1 0.035 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -9999 0 -10000 0 0
TSHR -0.12 0.17 -9999 0 -0.33 143 143
INS 0.006 0.05 -9999 0 -0.52 3 3
BIN1 0.014 0 -9999 0 -10000 0 0
mol:Choline 0.015 0.048 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.02 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.021 0.04 -9999 0 -0.29 2 2
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 -0.024 0.093 -9999 0 -0.29 10 10
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 0.014 0 -9999 0 -10000 0 0
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.014 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.047 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.029 0.053 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -9999 0 -10000 0 0
ACAP1 0.013 0.042 -9999 0 -0.29 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 -0.02 0.085 -9999 0 -0.29 3 3
clathrin heavy chain/ACAP1 0.032 0.03 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.014 0 -9999 0 -10000 0 0
exocyst 0.047 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.035 0 -9999 0 -10000 0 0
NME1 0.021 0 -9999 0 -10000 0 0
clathrin coat assembly 0.031 0.015 -9999 0 -10000 0 0
IL2RA -0.001 0.063 -9999 0 -0.29 1 1
VAMP3 0.021 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.037 0.083 -9999 0 -0.35 4 4
EXOC6 0.014 0 -9999 0 -10000 0 0
PLD1 -0.021 0.072 -9999 0 -0.29 24 24
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.028 0.025 -9999 0 -10000 0 0
SDC1 0.014 0.045 -9999 0 -10000 0 0
ARF6/GDP 0.02 0 -9999 0 -10000 0 0
EXOC7 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.029 0.054 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.015 0.048 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.014 0 -9999 0 -10000 0 0
ADRB2 0.025 0.066 -9999 0 -0.33 4 4
EXOC3 0.014 0 -9999 0 -10000 0 0
ASAP2 0.014 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.028 0 -9999 0 -10000 0 0
KLC1 0.014 0 -9999 0 -10000 0 0
AVPR2 0.027 0.052 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.047 -9999 0 -10000 0 0
IGF1 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
NCK2 0.014 0 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
CRKL 0.019 0.053 -9999 0 -0.29 8 8
GRB2/SOS1/SHC -0.003 0.028 -9999 0 -0.27 4 4
HRAS 0.013 0.026 -9999 0 -0.48 1 1
IRS1/Crk 0.019 0.053 -9999 0 -0.3 8 8
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.058 -9999 0 -0.34 8 8
AKT1 0.039 0.051 -9999 0 -10000 0 0
BAD 0.045 0.049 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0.053 -9999 0 -0.29 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.019 0.053 -9999 0 -0.3 8 8
RAF1 0.049 0.049 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.027 0.051 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.01 0.058 -9999 0 -0.33 8 8
PIK3CA 0.012 0.032 -9999 0 -0.6 1 1
RPS6KB1 0.039 0.051 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.042 0.044 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.047 -9999 0 -0.35 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.011 0.054 -9999 0 -0.42 2 2
IGF-1R heterotetramer 0.012 0.013 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.019 0.054 -9999 0 -0.3 8 8
Crk/p130 Cas/Paxillin -0.009 0.043 -9999 0 -10000 0 0
IGF1R 0.012 0.013 -9999 0 -10000 0 0
IGF1 -0.007 0.11 -9999 0 -0.55 14 14
IRS2/Crk 0.026 0.056 -9999 0 -0.47 1 1
PI3K 0.026 0.053 -9999 0 -0.3 1 1
apoptosis -0.049 0.044 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.018 -9999 0 -0.34 1 1
PRKCD 0.018 0.11 -9999 0 -0.53 8 8
RAF1/14-3-3 E 0.054 0.044 -9999 0 -10000 0 0
BAD/14-3-3 0.051 0.046 -9999 0 -10000 0 0
PRKCZ 0.027 0.079 -9999 0 -0.43 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.007 0.034 -9999 0 -10000 0 0
PTPN1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.026 0.07 -9999 0 -0.4 8 8
BCAR1 0.012 0.032 -9999 0 -0.6 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.013 0.063 -9999 0 -0.33 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
IRS1/NCK2 0.019 0.053 -9999 0 -0.29 8 8
GRB10 0.012 0.032 -9999 0 -0.6 1 1
PTPN11 0.019 0.053 -9999 0 -0.29 8 8
IRS1 0.011 0.058 -9999 0 -0.33 8 8
IRS2 0.018 0.059 -9999 0 -0.32 9 9
IGF-1R heterotetramer/IGF1 0.004 0.081 -9999 0 -0.4 14 14
GRB2 0.014 0 -9999 0 -10000 0 0
PDPK1 0.032 0.053 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKD1 0.033 0.066 -9999 0 -0.37 8 8
SHC1 0.009 0.052 -9999 0 -0.48 4 4
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.013 0.13 -10000 0 -1.1 2 2
regulation of axonogenesis -0.005 0.069 -10000 0 -10000 0 0
myoblast fusion -0.003 0.062 0.41 2 -10000 0 2
mol:GTP -0.01 0.036 -10000 0 -0.23 2 2
regulation of calcium-dependent cell-cell adhesion -0.026 0.043 0.34 1 -10000 0 1
ARF1/GTP -0.006 0.023 -10000 0 -10000 0 0
mol:GM1 0.003 0.03 -10000 0 -10000 0 0
mol:Choline -0.006 0.1 -10000 0 -0.35 24 24
lamellipodium assembly -0.017 0.058 -10000 0 -0.45 2 2
MAPK3 0.016 0.057 -10000 0 -0.34 2 2
ARF6/GTP/NME1/Tiam1 0.027 0.044 -10000 0 -0.35 1 1
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP 0.003 0.063 -10000 0 -0.41 2 2
ARF1/GDP 0.013 0.058 -10000 0 -0.38 2 2
ARF6 0.007 0.021 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.013 0.033 -10000 0 -0.6 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.057 -10000 0 -0.34 2 2
actin filament bundle formation -0.012 0.057 0.37 2 -10000 0 2
KALRN -0.018 0.055 -10000 0 -0.32 2 2
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.012 0.057 -10000 0 -0.38 2 2
NME1 0.015 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.057 -10000 0 -0.38 2 2
substrate adhesion-dependent cell spreading -0.01 0.036 -10000 0 -0.23 2 2
cortical actin cytoskeleton organization -0.017 0.058 -10000 0 -0.45 2 2
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.01 0.036 -10000 0 -0.23 2 2
ARF6/GTP -0.01 0.036 -10000 0 -0.23 2 2
RhoA/GTP -0.006 0.023 -10000 0 -10000 0 0
mol:GDP -0.017 0.057 -10000 0 -0.42 2 2
ARF6/GTP/RAB11FIP3/RAB11A -0.004 0.018 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 -0.019 0.11 -10000 0 -0.38 30 30
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.017 0.058 -10000 0 -0.45 2 2
ruffle organization 0.005 0.069 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.036 -10000 0 -0.23 2 2
PLD2 0.015 0.03 -10000 0 -10000 0 0
PIP5K1A 0.005 0.069 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.006 0.1 -10000 0 -0.35 24 24
Rac1/GTP -0.017 0.058 -10000 0 -0.45 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD2 0.015 0.018 -9999 0 -0.25 1 1
SMAD3 0.043 0.023 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.01 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.014 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.012 0.032 -9999 0 -0.6 1 1
SMAD2/SMAD4 0.022 0.016 -9999 0 -10000 0 0
MAP3K1 0.011 0.037 -9999 0 -0.48 2 2
TRAP-1/SMAD4 -0.017 0.084 -9999 0 -0.44 14 14
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.01 0.045 -9999 0 -0.48 3 3
CTDSPL 0.012 0.032 -9999 0 -0.6 1 1
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.01 0.12 -9999 0 -0.6 14 14
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.013 0.026 -9999 0 -0.48 1 1
PIAS4 0.014 0 -9999 0 -10000 0 0
Alternative NF-kappaB 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
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.005 0.038 -9999 0 -0.46 1 1
NFKB1 0.013 0.026 -9999 0 -0.48 1 1
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.004 0.043 -9999 0 -0.47 3 3
RELB 0.01 0.049 -9999 0 -0.52 3 3
NFKB2 0.008 0.055 -9999 0 -0.51 4 4
NF kappa B2 p52/RelB -0.006 0.047 -9999 0 -0.36 6 6
regulation of B cell activation -0.006 0.047 -9999 0 -0.36 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -9999 0 -10000 0 0
MKNK1 0.007 0.064 -9999 0 -0.6 4 4
mol:PIP3 -0.001 0.015 -9999 0 -0.29 1 1
FRAP1 0.016 0.008 -9999 0 -10000 0 0
AKT1 0.03 0.019 -9999 0 -0.28 1 1
INSR 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.004 0.037 -9999 0 -0.35 4 4
mol:GTP -0.001 0.014 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.005 -9999 0 -10000 0 0
TSC2 0.014 0 -9999 0 -10000 0 0
RHEB/GDP -0.001 0.012 -9999 0 -10000 0 0
TSC1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.001 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.006 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EIF3A 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.013 -9999 0 -10000 0 0
MAP3K5 0.008 0.036 -9999 0 -0.39 3 3
PIK3R1 0.014 0 -9999 0 -10000 0 0
apoptosis 0.008 0.036 -9999 0 -0.39 3 3
mol:LY294002 0 0 -9999 0 -10000 0 0
EIF4B 0.036 0.012 -9999 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.012 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.002 0.019 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
PI3K 0.026 0.017 -9999 0 -0.3 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.01 -9999 0 -10000 0 0
FKBP1A 0.014 0 -9999 0 -10000 0 0
RHEB/GTP -0.001 0.012 -9999 0 -10000 0 0
mol:Amino Acids 0 0 -9999 0 -10000 0 0
FKBP12/Rapamycin 0.011 0.001 -9999 0 -10000 0 0
PDPK1 -0.002 0.021 -9999 0 -0.28 2 2
EIF4E 0.014 0 -9999 0 -10000 0 0
ASK1/PP5C 0.019 0.057 -9999 0 -0.61 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0 -9999 0 -10000 0 0
TSC1/TSC2 -0.001 0.014 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RPS6 0.013 0.026 -9999 0 -0.48 1 1
PPP5C 0.014 0 -9999 0 -10000 0 0
EIF4G1 0.014 0 -9999 0 -10000 0 0
IRS1 0.009 0.001 -9999 0 -10000 0 0
INS -0.006 0.06 -9999 0 -0.57 4 4
PTEN 0.014 0 -9999 0 -10000 0 0
PDK2 -0.001 0.014 -9999 0 -0.27 1 1
EIF4EBP1 -0.007 0.15 -9999 0 -1.1 6 6
PIK3CA 0.013 0.032 -9999 0 -0.6 1 1
PPP2R5D 0.023 0.007 -9999 0 -10000 0 0
peptide biosynthetic process 0.015 0.034 -9999 0 -0.31 4 4
RHEB 0.014 0 -9999 0 -10000 0 0
EIF4A1 0.014 0 -9999 0 -10000 0 0
mol:Rapamycin 0 0 -9999 0 -10000 0 0
EEF2 0.015 0.034 -9999 0 -0.31 4 4
eIF4E/4E-BP1 0.002 0.14 -9999 0 -1 6 6
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.011 0.046 -9999 0 -0.6 2 2
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.032 0.018 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.018 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.031 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.031 0.024 -9999 0 -0.3 2 2
RANGAP1 0.014 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.005 0.038 -9999 0 -0.32 4 4
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -10000 0 0
Ran/GTP 0.029 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.011 0.037 -9999 0 -0.48 2 2
UBE2I 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.014 0 -9999 0 -10000 0 0
PIAS1 0.007 0.064 -9999 0 -0.6 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.01 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.004 0.073 -9999 0 -0.52 7 7
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.011 0.019 -9999 0 -0.34 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0.013 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.012 -9999 0 -0.24 1 1
AP2M1 0.014 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.014 -9999 0 -0.23 1 1
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0.008 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.02 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.024 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.011 0.019 -9999 0 -0.34 1 1
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.019 -9999 0 -0.34 1 1
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.006 0.041 -9999 0 -0.3 7 7
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 365 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.TM.A7CF TCGA.TM.A7C5 TCGA.TM.A7C4 TCGA.TM.A7C3
109_MAP3K5 0.059 0.059 0.059 0.059
47_PPARGC1A 0.014 0.014 0.014 0.014
105_BMP4 0.014 0.014 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 0.014 0.014 0.014
131_RELN/VLDLR 0 -0.32 0 0
30_TGFB1/TGF beta receptor Type II 0.021 0.017 0.021 0.013
84_STAT5B -0.046 0.048 0.051 0.049
84_STAT5A -0.046 0.048 0.051 0.049
Methods & Data
Input

  • Expression Data Normalization = Tumor samples 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/LGG-TP/6044612/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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